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Publications

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Publications in peer reviewed journals

83 Publications found
  • Pangenomics reveals alternative environmental lifestyles among chlamydiae

    Köstlbacher S, Collingro A, Halter T, Schulz F, Jungbluth SP, Horn M
    2021 - Nature Commun, 12: 4021

    Abstract: 

    Chlamydiae are highly successful strictly intracellular bacteria associated with diverse eukaryotic hosts. Here we analysed metagenome-assembled genomes of the “Genomes from Earth’s Microbiomes” initiative from diverse environmental samples, which almost double the known phylogenetic diversity of the phylum and facilitate a highly resolved view at the chlamydial pangenome. Chlamydiae are defined by a relatively large core genome indicative of an intracellular lifestyle, and a highly dynamic accessory genome of environmental lineages. We observe chlamydial lineages that encode enzymes of the reductive tricarboxylic acid cycle and for light-driven ATP synthesis. We show a widespread potential for anaerobic energy generation through pyruvate fermentation or the arginine deiminase pathway, and we add lineages capable of molecular hydrogen production. Genome-informed analysis of environmental distribution revealed lineage-specific niches and a high abundance of chlamydiae in some habitats. Together, our data provide an extended perspective of the variability of chlamydial biology and the ecology of this phylum of intracellular microbes.

  • A critical perspective on interpreting amplicon sequencing data in soil ecological research

    Alteio LV, Séneca J, Canarini A, Angel R, Jansa J, Guseva K, Kaiser C, Richter A, Schmidt H
    2021 - Soil Biology and Biochemistry, 160: Article 108357

    Abstract: 

    Microbial community analysis via marker gene amplicon sequencing has become a routine method in the field of soil research. In this perspective, we discuss technical challenges and limitations of amplicon sequencing and present statistical and experimental approaches that can help addressing the spatio-temporal complexity of soil and the high diversity of organisms therein. We illustrate the impact of compositionality on the interpretation of relative abundance data and discuss effects of sample replication on the statistical power in soil community analysis. Additionally, we argue for the need of increased study reproducibility and data availability, as well as complementary techniques for generating deeper ecological insights into microbial roles and our understanding thereof in soil ecosystems. At this stage, we call upon researchers and specialized soil journals to consider the current state of data analysis, interpretation, and availability to improve the rigor of future studies.

  • Microbial activity responses to water stress in agricultural soils from simple and complex crop rotations

    Schnecker J, Meeden DB, Calderon F, Cavigelli M, Lehman RM, Tiemann LK, Grandy AS
    2021 - Soil, 547-561

    Abstract: 

    Increasing climatic pressures such as drought and flooding challenge agricultural systems and their management globally. How agricultural soils respond to soil water extremes will influence biogeochemical cycles of carbon and nitrogen in these systems. We investigated the response of soils from long-term agricultural field sites under varying crop rotational complexity to either drought or flooding stress. Focusing on these contrasting stressors separately, we investigated soil heterotrophic respiration during single and repeated stress cycles in soils from four different sites along a precipitation gradient (Colorado, MAP 421 mm; South Dakota, MAP 580 mm; Michigan, MAP 893 mm; Maryland, MAP 1192 mm); each site had two crop rotational complexity treatments. At the driest (Colorado) and wettest (Maryland) of these sites, we also analyzed microbial biomass, six potential enzyme activities, and N2O production during and after individual and repeated stress cycles. In general, we found site specific responses to soil water extremes, irrespective of crop rotational complexity and precipitation history. Drought usually caused more severe changes in respiration rates and potential enzyme activities than flooding. All soils returned to control levels for most measured parameters as soon as soils returned to control water levels following drought or flood stress, suggesting that the investigated soils were highly resilient to the applied stresses. The lack of sustained responses following the removal of the stressors may be because they are well in the range of natural in situ soil water fluctuations at the investigated sites. Without the inclusion of plants in our experiment, we found that irrespective of crop rotation complexity, soil and microbial properties in the investigated agricultural soils were more resistant to flooding but highly resilient to drought and flooding during single or repeated stress pulses.

  • Denitrification is the major nitrous acid production pathway in boreal agricultural soils

    Bhattarai HR, Wanek W, Siljanen H, Ronkainen J, Liimatainen M, Hu Y, Nykänen H, Biasi C, Maljanen M
    2021 - Communications Earth and Environment, 2: 54

    Abstract: 

    Nitrous acid (HONO) photolysis produces hydroxyl radicals—a key atmospheric oxidant. Soils are strong HONO emitters, yet HONO production pathways in soils and their relative contributions are poorly constrained. Here, we conduct 15N tracer experiments and isotope pool dilution assays on two types of agricultural soils in Finland to determine HONO emission fluxes and pathways. We show that microbial processes are more important than abiotic processes for HONO emissions. Microbial nitrate reduction (denitrification) considerably exceeded ammonium oxidation as a source of nitrite—a central nitrogen pool connected with HONO emissions. Denitrification contributed 97% and 62% of total HONO fluxes in low and high organic matter soil, respectively. Microbial ammonium oxidation only produced HONO in high organic matter soil (10%). Our findings indicate that microbial nitrate reduction is an important HONO production pathway in aerobic soils, suggesting that terrestrial ecosystems favouring it could be HONO emission hotspots, thereby influencing atmospheric chemistry.

  • Microbial responses to herbivory-induced vegetation changes in a high-Arctic peatland

    Bender KM, Svenning MM, Hu Y, Richter A, Schückel J, Liebner S, Tveit AT
    2021 - Polar Biology, 44: 899-911

    Abstract: 

    Herbivory by barnacle geese (Branta leucopsis) alters the vegetation cover and reduces ecosystem productivity in high-Arctic peatlands, limiting the carbon sink strength of these ecosystems. Here we investigate how herbivory-induced vegetation changes affect the activities of peat soil microbiota using metagenomics, metatranscriptomics and targeted metabolomics in a comparison of fenced exclosures and nearby grazed sites. Our results show that a different vegetation with a high proportion of vascular plants developed due to reduced herbivory, resulting in a larger and more diverse input of polysaccharides to the soil at exclosed study sites. This coincided with higher sugar and amino acid concentrations in the soil at this site as well as the establishment of a more abundant and active microbiota, including saprotrophic fungi with broad substrate ranges, like Helotiales (Ascomycota) and Agaricales (Basidiomycota). A detailed description of fungal transcriptional profiles revealed higher gene expression for cellulose, hemicellulose, pectin, lignin and chitin degradation at herbivory-exclosed sites. Furthermore, we observed an increase in the number of genes and transcripts for predatory eukaryotes such as Entomobryomorpha (Arthropoda). We conclude that in the absence of herbivory, the development of a vascular vegetation alters the soil polysaccharide composition and supports larger and more active populations of fungi and predatory eukaryotes.

  • Recovery of aboveground biomass, species richness and composition in tropical secondary forests in SW Costa Rica

    Oberleitner F, Egger C, Oberdorfer S, Dullinger S, Wanek W, Hietz P
    2021 - Forest Ecology and Management, 479: Article 118580

    Abstract: 

    Tropical secondary forests comprise about half of the world’s tropical forests and are important as carbon sinks and to conserve biodiversity. Their rate of recovery varies widely; however, particularly older secondary forests are difficult to date so that the recovery rate is uncertain. As a consequence, factors affecting recovery are difficult to analyse. We used aerial surveys going back to 1968 to date 12 secondary forests in the wet tropics of SW Costa Rica and evaluated the recovery of aboveground biomass, tree species richness and tree species composition in relation to nearby old-growth forests and previous land use. To confirm the validity of the space-for-time substitution, the plots were re-censused after four years. We found fast rates of aboveground biomass accumulation, especially in the first years of succession. After 20 years AGB had reached c. 164 Mg/ha equivalent to 52% of the biomass in old-growth forests in the region. Species richness increased at a slower pace and had reached c. 31% of old-growth forests after 20 years. Recovery rates differed substantially among forests, with biomass at least initially recovering faster in forests after clearcuts whereas species numbers increased faster in forests recovering from pastures. Biomass recovery was positively related to the forest cover in the vicinity and negatively to species richness, whereas species richness was related to soil parameters. The change during the four years between the censuses is broadly in line with the initial chronosequence. While the recovery of tropical secondary forests has been studied in many places, our study shows that various environmental parameters affect the speed of recovery, which is important to include in efforts to manage and restore tropical landscapes.

  • Permafrost causes unique fine-scale spatial variability across tundra soils

    Siewert MB., Lantuit H, Richter A, Hugelius G
    2021 - Global Biogeochemical Cycles, 35: e2020GB006659

    Abstract: 

    Spatial analysis in earth sciences is often based on the concept of spatial autocorrelation, expressed by W. Tobler as the first law of geography: “everything is related to everything else, but near things are more related than distant things." Here, we show that subsurface soil properties in permafrost tundra terrain exhibit tremendous spatial variability. We describe the subsurface variability of soil organic carbon (SOC) and ground ice content from the centimeter to the landscape scale in three typical tundra terrain types common across the Arctic region. At the soil pedon scale, that is, from centimeters to 1–2 m, variability is caused by cryoturbation and affected by tussocks, hummocks and nonsorted circles. At the terrain scale, from meters to tens of meters, variability is caused by different generations of ice‐wedges. Variability at the landscape scale, that is, ranging hundreds of meters, is associated with geomorphic disturbances and catenary shifts. The co‐occurrence and overlap of different processes and landforms creates a spatial structure unique to permafrost environments. The coefficient of variation of SOC at the pedon scale (21%–73%) exceeds that found at terrain (17%–66%) and even landscape scale (24%–67%). Such high values for spatial variation are otherwise found at regional to continental scale. Clearly, permafrost soils do not conform to Tobler's law, but are among the most variable soils on Earth. This needs to be accounted for in mapping and predictions of the permafrost carbon feedbacks through various ecosystem processes. We conclude that scale deserves special attention in permafrost regions.

  • Tree Species and Epiphyte Taxa Determine the “Metabolomic niche” of Canopy Suspended Soils in a Species-Rich Lowland Tropical Rainforest

    Gargallo-Garriga A, Sardans J, Alrefaei AF, Klem K, Fuchslueger L, Ramírez-Rojas I, Donald J, Leroy C, Van Langenhove L, Verbruggen E, Janssens IA, Urban O, Peñuelas J
    2021 - Metabolites, 11: Article 718

    Abstract: 

    Tropical forests are biodiversity hotspots, but it is not well understood how this diversity is structured and maintained. One hypothesis rests on the generation of a range of metabolic niches, with varied composition, supporting a high species diversity. Characterizing soil metabolomes can reveal fine-scale differences in composition and potentially help explain variation across these habitats. In particular, little is known about canopy soils, which are unique habitats that are likely to be sources of additional biodiversity and biogeochemical cycling in tropical forests. We studied the effects of diverse tree species and epiphytes on soil metabolomic profiles of forest floor and canopy suspended soils in a French Guianese rainforest. We found that the metabolomic profiles of canopy suspended soils were distinct from those of forest floor soils, differing between epiphyte-associated and non-epiphyte suspended soils, and the metabolomic profiles of suspended soils varied with host tree species, regardless of association with epiphyte. Thus, tree species is a key driver of rainforest suspended soil metabolomics. We found greater abundance of metabolites in suspended soils, particularly in groups associated with plants, such as phenolic compounds, and with metabolic pathways related to amino acids, nucleotides, and energy metabolism, due to the greater relative proportion of tree and epiphyte organic material derived from litter and root exudates, indicating a strong legacy of parent biological material. Our study provides evidence for the role of tree and epiphyte species in canopy soil metabolomic composition and in maintaining the high levels of soil metabolome diversity in this tropical rainforest. It is likely that a wide array of canopy microsite-level environmental conditions, which reflect interactions between trees and epiphytes, increase the microscale diversity in suspended soil metabolomes.

  • High-resolution topochemical analysis and thermochemical simulations of oxides and nitrides at grain boundaries and within the grains of a low alloy Mn-Cr hot-rolled steel sheet

    Praigad VG, Stöger-Pollach M, Schintlmeister A, Auinger M, Danninger H
    2021 - Journal of Alloys and Compounds, 876: in press

    Abstract: 

    The selective oxidation underneath the scale layer of an industrially hot rolled Fe-1.8Mn-0.8Cr steel at temperatures between 600 and 700 °C has been investigated. The spatial distribution and composition of formed precipitates has been studied by high-resolution topochemical analysis via TEM-EELS and NanoSIMS and revealed heterogeneities in chemical composition, especially along grain boundaries. It could be shown that grain boundary oxides are predominantly composed of aluminium, chromium or silicon oxides/nitrides, surrounded by manganese-rich oxides. Experimental results of phase stability have been compared to numerical simulations, considering the distribution of more than 40 potentially stable oxide-, nitride- and carbide phases, and differences are critically discussed.

  • Electrochemical enrichment of marine denitrifying bacteria to enhance nitrate metabolization in seawater

    De La Fuente MJ, de la Iglesia R, Farías L, Daims H, Lukumbuzya M, Vargas I
    2021 - J Environ Chem Eng, 9: 105604

    Abstract: 

    High concentrations of nitrate from industrial discharges to coastal marine environments are a matter of concern owing to their ecological consequences. In the last years, Bioelectrochemical Denitrification Systems (BEDS) have emerged as a promising nitrate removal technology. However, they still have limitations, such as the enrichment strategy for specific microbial communities in the electrodes under natural conditions. In this study, three-electrode electrochemical cells were used to test microbial enrichment from natural seawater by applying three reported potentials associated with the dissimilatory denitrification process (-130, -260, and -570 mV vs. Ag/AgCl). The microbial community analysis showed that by applying -260 mV (vs. Ag/AgCl) to the working electrode, it was possible to significantly enrich denitrifying microorganisms, specifically Marinobacter, in comparison with the control. Furthermore, -260 mV (vs. Ag/AgCl) led to a significantly higher nitrate removal than other conditions, which, combined with cyclic voltammetry analysis, suggested that the polarized electrodes worked as external electron donors for nitrate reduction. Hence, this work demonstrates for the first time that it is possible to enrich marine denitrifying microorganisms by applying an overpotential of -260 mV (vs. Ag/AgCl) without the need for a culture medium, the addition of an exogenous electron donor (i.e., organic matter) or a previously enriched inoculum.

  • Cyanate is a low abundance but actively cycled nitrogen compound in soil

    Mooshammer M, Wanek W, Jones SH, Richter A, Wagner M
    2021 - Communications Earth & Environment, 2: 161
    Cyanate soil

    Abstract: 

    Cyanate can serve as a nitrogen and/or carbon source for different microorganisms and as an energy source for autotrophic ammonia oxidizers. However, the extent of cyanate availability and utilisation in terrestrial ecosystems and its role in biogeochemical cycles is poorly known. Here we analyse cyanate concentrations in soils across a range of soil types, land management practices and climates. Soil cyanate concentrations were three orders of magnitude lower than ammonium or nitrate. We determined cyanate consumption in a grassland and rice paddy soil using stable isotope tracer experiments. We find that cyanate turnover was rapid and dominated by biotic processes. We estimated that in-situ cyanate production rates were similar to those associated with urea fertilizer decomposition, a major source of cyanate in the environment. We provide evidence that cyanate is actively turned over in soils and represents a small but continuous nitrogen/energy source for soil microbes.

  • Microplastics and nanoplastics barely enhance contaminant mobility in agricultural soils

    Stephanie Castan, Charlotte Henkel, Thorsten Hüffer, Thilo Hofmann
    2021 - Communications Earth & Environment, 193: 1-9

    Abstract: 

    Farmland soils are prone to contamination with micro- and nanoplastics through a variety of agricultural practices. Concerns are recurrently raised that micro- and nanoplastics act as vector for organic contaminants to deeper soil layers and endanger groundwater resources. Whether and to what extent micro- and nanoplastics facilitate the transport of organic contaminants in soil remains unclear. Here we calculated the ratio between transport and desorption time scales using two diffusion models for micro- and nanoplastics between 100 nm and 1 mm. To identify micro- and nanoplastics bound contaminant transport we evaluated diffusion and partitioning coefficients of prominent agrochemicals and additives and of frequently used polymers e.g., polyethylene and tire material. Our findings suggest that the desorption of most organic contaminants is too fast for micro- and nanoplastics to act as transport facilitators in soil. Contaminant transport enabled by microplastics was found to be relevant only for very hydrophobic contaminants (logKow >5) under preferential flow conditions. While micro- and nanoplastics might be a source of potentially harmful contaminants in farmland soils this study suggests that they do not considerably enhance contaminant mobility.

  • Methanol-based extraction protocol for insoluble and moderately water-soluble nanoparticles in plants to enable characterization by single particle ICP-MS

    Stephanie Laughton, Adam Laycock, Garret Bland, Frank von der Kammer, Thilo Hofmann, Elizabeth A. Casman, Gregory V. Lowry
    2021 - Analytical and Bioanalytical Chemistry, 413: 299–314

    Abstract: 

    The detection and characterization of soluble metal nanoparticles in plant tissues are an analytical challenge, though a scientific necessity for regulating nano-enabled agrichemicals. The efficacy of two extraction methods to prepare plant samples for analysis by single particle ICP-MS, an analytical method enabling both size determination and quantification of nanoparticles (NP), was assessed. A standard enzyme-based extraction was compared to a newly developed methanol-based approach. Au, CuO, and ZnO NPs were extracted from three different plant leaf materials (lettuce, corn, and kale) selected for their agricultural relevance and differing characteristics. The enzyme-based approach was found to be unsuitable because of changes in the recovered NP size distribution of CuO NP. The MeOH-based extraction allowed reproducible extraction of the particle size distribution (PSD) without major alteration caused by the extraction. The type of leaf tissue did not significantly affect the recovered PSD. Total metal losses during the extraction process were largely due to the filtration step prior to analysis by spICP-MS, though this did not significantly affect PSD recovery. The methanol extraction worked with the three different NPs and plants tested and is suitable for studying the fate of labile metal-based nano-enabled agrichemicals.

  • New guidance brings clarity to environmental hazard and behaviour testing of nanomaterials

    Elijah Joel Petersen, Greg Gerard Goss, Frank von der Kammer, Alan James Kennedy
    2021 - Nature Nanotechnology, 16: 482–483
  • Environmentally persistent free radicals are ubiquitous in wildfire charcoals and remain stable for years

    Gabriel Sigmund, Cristina Santín, Marc Pignitter, Nathalie Tepe, Stefan H. Doerr, Thilo Hofmann
    2021 - Communications Earth & Environment, 2: 68

    Abstract: 

    Globally landscape fires produce about 256 Tg of pyrogenic carbon or charcoal each year. The role of charcoal as a source of environmentally persistent free radicals, which are precursors of potentially harmful reactive oxygen species, is poorly constrained. Here, we analyse 60 charcoal samples collected from 10 wildfires, that include crown as well as surface fires in forest, shrubland and grassland spanning different boreal, temperate, subtropical and tropical climate. Using electron spin resonance spectroscopy, we measure high concentrations of environmentally persistent free radicals in charcoal samples, much higher than those found in soils. Concentrations increased with degree of carbonization and woody fuels favoured higher concentrations. Moreover, environmentally persistent free radicals remained stable for an unexpectedly long time of at least 5 years. We suggest that wildfire charcoal is an important global source of environmentally persistent free radicals, and therefore potentially of harmful reactive oxygen species.

  • PAHs sorption to biochar colloids changes their mobility over time

    Yang Wen, Qu Ting, Flury Markus, Zhang Xin, Gabriel Sigmund, Shang Jianying, Li Baoguo
    2021 - Journal of Hydrology, 603: 126839

    Abstract: 

    Biochar is an efficient sorbent for polycyclic aromatic hydrocarbons (PAHs). However, little is known about PAHs sorption kinetics and the effect on the mobility of biochar colloids in saturated porous media. In this study, naphthalene (NAP) and phenanthrene (PHE) were chosen as typical PAHs. In different stages, different sorption sites of PAHs on biochar played a distinct role in affecting the transport of biochar colloids in saturated porous media. The biochar colloids showed less negative surface charge as the contact time between biochar colloids and PAHs increased from 0.017 h to 96 h, which led to the mobility of biochar colloids decreasing over time. But after 168 h contact time, the surface charge of biochar colloids became more negative again, and the inhibition effect of PAHs on biochar colloid transport was weakened. This was related to the sorption kinetics of PAHs on biochar colloids: (1) PAHs sorption onto outer biochar surface; and (2) adsorbed PAHs diffusion into internal biochar pores. PAHs sorption onto the outer biochar surface shielded the negative surface charge and then decreased the mobility of biochar colloids, and then the adsorbed PAHs diffusion into internal biochar pores increased their mobility again. Our results suggested that porous colloids-facilitated PAHs transport in porous media might be highly related to interaction time between PAHs and porous colloids.

  • Functional traits of a rainforest vascular epiphyte community: trait covariation and indications for host specificity

    Wagner K, Wanek W, Zotz G
    2021 - Diversity, 13: 97

    Abstract: 

    Trait matching between interacting species may foster diversity. Thus, high epiphyte diversity in tropical forests may be partly due to the high diversity of trees and some degree of host specificity. However, possible trait matching between epiphyte and host is basically unexplored. Since the epiphytic habitat poses particular challenges to plants, their trait correlations should differ from terrestrial plants, but to what extent is unclear as epiphytes are underrepresented or missing in the large trait databases. We quantified 28 traits of 99 species of vascular epiphytes in a lowland forest in Panama that were related to plant size, leaf, stem, and root morphology; photosynthetic mode; and nutrient concentrations. We analyzed trait covariation, community weighted means, and functional diversity for assemblages on stems and in crowns of four tree species. We found intriguing differences between epiphytes and terrestrial plants regarding trait covariation in trait relations between plant maximal height, stem specific density, specific root length, and root tissue den-sity, i.e., stem and root economic spectra. Regarding host specificity, we found strong evidence for environmental filtering of epiphyte traits, but only in tree crowns. On stems, community weighted means differed in only one case, whereas > 2/3 of all traits differed in tree crowns. Although we were only partly able to interpret these differences in the light of tree trait differences, these findings mark an important step towards a functional understanding of epiphyte host specificity.

  • Reduced alpha diversity of the oral microbiome correlates with short progression-free survival in patients with relapsed/refractory multiple myeloma treated with ixazomib-based therapy (AGMT MM 1, phase II trial)

    Ludwig H, Hausmann B, Schreder M, Pönisch W, Zojer N, Knop S, Gunsilius E, Egle A, Petzer A, Einsele H, Hajek R, Weisel K, Krenosz KJ, Lang A, Lechner D, Greil R, Berry D
    2021 - eJHaem, 2: 102-106

    Abstract: 

    Alterations in the human microbiome have been linked to several malignant diseases. Here, we investigated the oral microbiome of 79 patients with relapsed/refractory multiple myeloma (MM) treated with ixazomib-thalidomide-dexamethasone. Increased alpha diversity (Shannon index) at the phylum level was associated with longer progression-free survival (PFS) (10.2 vs 8.5 months, P = .04), particularly in patients with very long (>75% quartile) PFS . Additionally, alpha diversity was lower in patients with progressive disease (P < .05). These findings suggest an interrelationship between the oral microbiome and outcome in patients with MM and encourage a novel direction for diagnostic and/or therapeutic strategies.

  • No effect of long-term soil warming on diffusive soil inorganic and organic nitrogen fluxes in a temperate forest soil

    Heinzle J, Wanek W, Tian Y, Kwatcho-Kengdo S, Borken W, Schindlbacher A, Inselsbacher E
    2021 - Soil Biology and Biochemistry, 158: Article 108261

    Abstract: 

    Climate warming affects nitrogen (N) cycling in forest soils, but implications for plant available N have remained unclear. We estimated in situ diffusive fluxes of amino acids and inorganic N in a temperate forest soil after 14 years of soil warming. Results from four sampling campaigns (n = 1152 microdialysis samples) during the growing season showed no effect of warming on diffusive N fluxes. Diffusive NH4+ fluxes increased from spring towards autumn while NO3 fluxes followed an opposite trend. Overall, the proportion of amino acids in the total diffusive N flux was low (13–30%) in this carbonate soil compared to other temperate and boreal forest soils.

  • Sensitivity and specificity of the antigen-based anterior nasal self-testing programme for detecting SARS-CoV-2 infection in schools, Austria, March 2021

    Willeit P, Bernar B, Zurl C, Al-Rawi M, Berghold A, Bernhard D, Borena W, Doppler C, Kerbl R, Köhler A, Krause R, Lamprecht B, Pröll J, Schmidt H, Steinmetz I, Evelyn S, Stoiber H, von Laer D, Zuber J, Müller T, Strenger V, Wagner M
    2021 - Eurosurveillance, 26: pii=2100797

    Abstract: 

    This study evaluates the performance of the antigen-based anterior nasal screening programme implemented in all Austrian schools to detect SARS-CoV-2 infections. We combined nationwide antigen-based screening data obtained in March 2021 from 5,370 schools (Grade 1–8) with an RT-qPCR-based prospective cohort study comprising a representative sample of 244 schools. Considering a range of assumptions, only a subset of infected individuals are detected with the programme (low to moderate sensitivity) and non-infected individuals mainly tested negative (very high specificity).

  • Microplastic extraction protocols can impact the polymer structure

    Patrizia Pfohl, Christian Roth, Lars Meyer, Ute Heinemeyer, Till Gruendling, Christiane Lang, Nikolaus Nestle, Thilo Hofmann, Wendel Wohlleben, Sarah Jessl
    2021 - Microplastics and Nanoplastics, 1: 8

    Abstract: 

    Although microplastics are ubiquitous in today’s natural environments, our understanding of the materials, quantities, and particle sizes involved remains limited. The recovery of microplastics from different types of environmental matrices requires standardized matrix digestion protocols that allow inter-laboratory comparisons and that have no effect on the polymers themselves. A number of commonly used digestion methods rely on oxidation with concentrated hydrogen peroxide solutions to remove organic matter from the matrix. However, this can alter the nature of polymers through hydrolysis and often does not lead to a complete matrix removal. We have therefore investigated the use of two altered matrix digestion protocols, an acidic (Fenton) protocol and a new alkaline (Basic Piranha) protocol, focusing mainly on the effect on biodegradable polymers (polylactide, polybutylene adipate terephthalate, polybutylene succinate) and polymers with known degradation pathways via hydrolysis (thermoplastic polyurethanes, polyamide). Comparing the initial surface textures, chemical compositions, and particle size distributions with those obtained after digestion revealed that the Fenton protocol left most of the polymers unchanged. The ferrous residue that remains following Fenton digestion had no effect on either the polymer composition or the particle size distribution, but could disturb further analytics (e.g. Raman microscopy due to auto-fluorescence). While increasing the chance of complete matrix removal, the more powerful Basic Piranha protocol is also more likely to affect the polymer properties: Polylactide polymers in particular showed signs of degradation under alkaline digestion (reduced polylactide content, holes in the polymer matrix), indicating the unsuitability of the Basic Piranha protocol in this specific case. Polyamide, however, remained stable during the Basic Piranha treatment, and the surface chemistry, the particle size as well as the molar mass distribution of the investigated thermoplastic polyurethanes were also not affected. Hence, this protocol offers a powerful alternative for microplastic analysis with focus on particle size in more complex environmental matrices (e.g. removal of cellulose in soil), while avoiding ferrous Fenton residue. Unexpectedly, also tire rubber, a frequent target analyte in microplastic monitoring, was found to be susceptible to artefact structures by both oxidation protocols. In summary, controls for the specific combination of polymer and sample preparation protocol are highly recommended to select the most fitting protocol. Here selected suitable combinations are reported.

  • Towards more Sustainable Peptide- based Antibiotics: Stable in Human Blood, Enzymatically Hydrolyzed in Wastewater?

    Michael Zumstein, Kathrin Fenner
    2021 - CHIMIA International Journal for Chemistry, 75: 267-271

    Abstract: 

    The emergence and spread of antibiotic resistance is a major societal challenge and new antibiotics are needed to successfully fight bacterial infections. Because the release of antibiotics into wastewater and downstream environments is expected to contribute to the problem of antibiotic resistance, it would be beneficial to consider the environmental fate of antibiotics in the development of novel antibiotics. In this article, we discuss the possibility of designing peptide-based antibiotics that are stable during treatment (e.g. in human blood), but rapidly inactivated through hydrolysis by peptidases after their secretion into wastewater. In the first part, we review studies on the biotransformation of peptide-based antibiotics during biological wastewater treatment and on the specificity of dissolved extracellular peptidases derived from wastewater. In the second part, we present first results of our endeavour to identify peptide bonds that are stable in human blood plasma and susceptible to hydrolysis by the industrially produced peptidase Subtilisin A.

  • Nano-scale imaging of dual stable isotope labeled oxaliplatin in human colon cancer cells reveals the nucleolus as a putative node for therapeutic effect

    Legin AA, Schintlmeister A, Sommerfeld NS, Eckhard M, Theiner S, Reipert S, Strohofer D, Jakupec MA, Galanski M, Wagner M, Keppler BK
    2021 - Nanoscale Advances, 3: 249-262

    Abstract: 

    Oxaliplatin shows a superior clinical activity in colorectal cancer compared to cisplatin. Nevertheless, the knowledge about its cellular distribution and the mechanisms responsible for the different range of oxaliplatin-responsive tumors is far from complete. In this study, we combined highly sensitive element specific and isotope selective imaging by nanometer-scale secondary ion mass spectrometry (NanoSIMS) with transmission electron microscopy to investigate the subcellular accumulation of oxaliplatin in three human colon cancer cell lines (SW480, HCT116 wt, HCT116 OxR). Oxaliplatin bearing dual stable isotope labeled moieties, i.e. 2H-labeled diaminocyclohexane (DACH) and 13C-labeled oxalate, were applied for comparative analysis of the subcellular distribution patterns of the central metal and the ligands. In all the investigated cell lines, oxaliplatin was found to have a pronounced tendency for cytoplasmic aggregation in single membrane bound organelles, presumably related to various stages of the endocytic pathway. Moreover, nuclear structures, heterochromatin and in particular nucleoli, were affected by platinum-drug exposure. In order to explore the consequences of oxaliplatin resistance, subcellular drug distribution patterns were investigated in a pair of isogenic malignant cell lines with distinct levels of drug sensitivity (HCT116 wt and HCT116 OxR, the latter with acquired resistance to oxaliplatin). The subcellular platinum distribution was found to be similar in both cell lines, with only slightly higher accumulation in the sensitive HCT116 wt cells which is inconsistent with the resistance factor of more than 20-fold. Instead, the isotopic analysis revealed a disproportionally high accumulation of the oxalate ligand in the resistant cell line.

  • The effect of salinity, light regime and food source on C and N uptake in a benthic foraminifera

    Lintner M, Lintner B, Wanek W, Keul N, Heinz P
    2021 - Biogeosciences, 18: 1395–1406

    Abstract: 

    Foraminifera are unicellular organisms that play an important role in marine organic matter cycles. Some species are able to isolate chloroplasts from their algal food source and incorporate them as kleptoplasts into their own metabolic pathways, a phenomenon known as kleptoplastidy. One species showing this ability is Elphidium excavatum, a common foraminifer in the Kiel Fjord, Germany. The Kiel Fjord is fed by several rivers and thus forms a habitat with strongly fluctuating salinity. Here, we tested the effects of the food source, salinity and light regime on the food uptake (via 15N and 13C algal uptake) in this kleptoplast-bearing foraminifer. In our study E. excavatum was cultured in the lab at three salinity levels (15, 20 and 25) and uptake of C and N from the food source Dunaliella tertiolecta (Chlorophyceae) and Leyanella arenaria (Bacillariophyceae) were measured over time (after 3, 5 and 7 d). The species was very well adapted to the current salinity of the sampling region, as both algal N and C uptake was highest at a salinity of 20. It seems that E. excavatum coped better with lower than with higher salinities. The amount of absorbed C from the green algae D. tertiolecta showed a tendency effect of salinity, peaking at a salinity of 20. Nitrogen uptake was also highest at a salinity of 20 and steadily increased with time. In contrast, C uptake from the diatom L. arenaria was highest at a salinity of 15 and decreased at higher salinities. We found no overall significant differences in C and N uptake from green algae vs. diatoms. Furthermore, the food uptake at a light–dark rhythm of 16:8h was compared to continuous darkness. Darkness had a negative influence on algal C and N uptake, and this effect increased with incubation time. Starving experiments showed a stimulation of food uptake after 7 d. In summary, it can be concluded that E. excavatum copes well with changes of salinity to a lower level. For changes in light regime, we showed that light reduction caused a decrease of C and N uptake by E. excavatum.

  • Editorial: Exchanges at the Root-Soil Interface: Resource Trading in the Rhizosphere That Drives Ecosystem Functioning

    Preece K, Canarin A, Verbruggen E, Fuchslueger L
    2021 - Frontiers in Forests and Global Change, 4: Article 747492
  • Leaf trait co-variation and trade-offs in gallery forest C3 and CAM epiphytes

    Oliveira RdP, Zotz G, Wanek W, Franco AC
    2021 - Biotropica, 3: 520–535

    Abstract: 

    Despite their unique adaptations to thrive in canopy environments without access to soil resources, epiphytes are underrepresented in studies of functional traits and of functional composition of tropical plant communities. We investigated functional traits of spermatophytic (seed‐bearing) C3 and CAM epiphyte communities in flooded and non‐flooded gallery forests in Central Brazil. The two forest types differ in floristic, structure, microclimate, and edaphic conditions. We studied plant size, leaf thickness, leaf dry matter content (LDMC), leaf water content, leaf area (LA), specific leaf area (SLA), leaf C, N, P, K, Mg, and Ca, and stable isotope ratios (δ13C and δ15N). Because photosynthetic pathway (C3 or CAM) is an important aspect of ecological differentiation for spermatophytic epiphytes, we expected that functional trait syndromes in a multivariate space would be more associated with photosynthetic pathway than forest type, and changes in abundance of C3 and CAM epiphytes would drive functional trait composition at the community level. C3 and CAM epiphytes segregated in the multivariate trait space; however, more complex functional typologies were also evident. Despite lower light levels, CAM epiphytes were more abundant in the flooded gallery forest. There, they accounted for 80% of all individuals, whereas C3 epiphytes dominated in the non‐flooded forest. These large differences in the proportion of CAM and C3 epiphytes strongly affected functional trait values at the community level, despite very little intraspecific variation in trait values between forest types for species that occurred in both forests.

  • Acidobacteria are active and abundant members of diverse atmospheric H2-oxidizing communities detected in temperate soils

    Giguere AT, Eichorst SA, Meier D, Herbold CW, Richter A, Greening C, Woebken D
    2021 - ISME J, 2: 363-376

    Abstract: 

    Significant rates of atmospheric H2 consumption have been observed in temperate soils due to the activity of high-affinity enzymes, such as the group 1h [NiFe]-hydrogenase. We designed broadly inclusive primers targeting the large subunit gene (hhyL) of group 1h [NiFe]-hydrogenases for long-read sequencing to explore its taxonomic distribution across soils. This approach revealed a diverse collection of microorganisms harboring hhyL, including previously unknown groups and taxonomically not assignable sequences. Acidobacterial group 1h [NiFe]-hydrogenases genes were abundant and expressed in temperate soils. To support the participation of acidobacteria in H2 consumption, we studied two representative mesophilic soil acidobacteria, which expressed group 1h [NiFe]-hydrogenases and consumed atmospheric H2 during carbon starvation. This is the first time mesophilic acidobacteria, which are abundant in ubiquitous temperate soils, have been shown to oxidize H2 down to below atmospheric concentrations. As this physiology allows bacteria to survive periods of carbon starvation, it could explain the success of soil acidobacteria. With our long-read sequencing approach of group 1h [NiFe]-hydrogenases genes, we show that the ability to oxidize atmospheric levels of His more widely distributed among soil bacteria than previously recognized and could represent a common mechanism enabling bacteria to persist during periods of carbon deprivation.

  • Spatiotemporal Dynamics of Maize (Zea mays L.) Root Growth and Its Potential Consequences for the Assembly of the Rhizosphere Microbiota

    Bonkowski M, Tarkka M, Razavi BS, Schmidt H, Blagodatskaya E, Koller R, Yu P, Knief C, Hochholdinger F, Vetterlein D
    2021 - Frontiers in microbiology, 12: Article 619499

    Abstract: 

    Numerous studies have shown that plants selectively recruit microbes from the soil to establish a complex, yet stable and quite predictable microbial community on their roots – their “microbiome” (Berg and Smalla, 2009Hartmann et al., 2009Weinert et al., 2010). Microbiome assembly is considered as a key process in the self-organization of root systems (Vetterlein et al., 2020). Better control of microbiome assembly would improve plant health and fitness by promoting beneficial microbial traits (Friesen et al., 2011Oyserman et al., 2018Wille et al., 2019). A fundamental question for understanding plant-microbe relationships is where a predictable microbiome is formed along the root axis and through which microbial dynamics the stable formation of a microbiome is challenged. Theoretically, community assembly begins with random, unregulated colonization of taxa from nearby sites (i.e., neutral processes), a process that continues throughout the lifetime of roots; while ordered dynamics (microbiome assembly) occur through selection (i.e., niche-based processes) when (i) exudates promote fast-growing copiotrophic taxa, (ii) root signals attract specific symbionts or pathogens, (iii) increased competition due to limited resource availability leads to species sorting, and (iv) predation selects for specific microbial traits among members of the microbiome (Vellend, 2010Hardoim et al., 2011Ho et al., 2017Kudjordjie et al., 2019Amacker et al., 2020Chen et al., 2020). These microbial assembly processes again are embedded in plant-driven spatiotemporal dynamics at small and large scales, caused by differences in the quality and quantity of rhizodeposition: (i) along the root axis, (ii) during diurnal cycles, (iii) on different root types, and (iv) during plant development. Emphasizing maize as a model species for which numerous data on dynamic root traits are available, this mini-review aims to give an integrative overview on the dynamic nature of root growth and its consequences for microbiome assembly based on theoretical considerations from microbial community ecology.

  • Bypass and hyperbole in soil science: A perspective from the next generation of soil scientists

    Portell X,  Sauzet O,  Balseiro-Romero M,  Benard P,  Cardinael R,  Couradeau E,  Danra DD,  Evans DL,  Fry EL, Hammer E,  Mamba D,  Merino-Martín L,  Mueller CW, Paradelo M, Rees F,  Rossi M, Schmidt H,  Schnee LS,  Védère C, Vidal A
    2021 - European Journal of Soil Science, 72: 31-34
  • Responses of grassland soil CO2 production and fluxes to drought are shifted in a warmer climate under elevated CO2

    Reinthaler D, Harris E, Richter A, Herndl M, Pötsch E, Wachter H, Bahn M
    2021 - Soil Biology and Biochemistry, 163: Article 108436

    Abstract: 

    As the climate warms, drought events are expected to increase in intensity and frequency, with consequences for the carbon cycleSoil respiration (Rs) accounts for the largest flux of CO2 from terrestrial ecosystems to the atmosphere. While the drought responses of Rs have been well studied, it is uncertain how they will be modified in a future world, when higher temperatures will occur in combination with elevated atmospheric CO2 concentrations. In a global change experiment in a managed temperate grassland, we studied drought and post-drought responses of Rs dynamics under current versus likely future conditions (+3°, +300 ppm CO2). Furthermore, to understand the soil CO2 production (Ps) and transport dynamics underlying Rs fluxes we continuously monitored in-situ soil CO2 concentrations across the soil profile. Our results show that Rs was higher and that drought-induced reductions in Rs were delayed under future compared to current conditions. Peak drought reductions and post-drought pulses of Rs were more pronounced in the future scenario. Annual Rs was reduced by drought only under current but not under future conditions. An in-depth analysis of soil CO2 gradients and fluxes across the soil profile showed that elevated CO2 stimulated Ps primarily in the main rooting horizon and that warming affected Ps also in deeper soil layers. We found that both in the current and the future scenario drought led to the strongest reductions of Ps in the most productive soil layers, which also exhibited the largest depletion of soil moisture. We conclude that a future warmer climate under elevated CO2 amplifies soil CO2 production and efflux and their peak drought and post-drought responses, but delays the onset of the drought responses and thereby eliminates the overall drought effect on annual soil CO2 emissions.

  • Sustained nitrogen loss in a symbiotic association of Comammox Nitrospira and Anammox bacteria

    Gottshall EY, Bryson SJ, Cogert KI, Landreau M, Sedlacek CJ, Stahl DA, Daims H, Winkler M
    2021 - Water Res, 202: 117426

    Abstract: 

    The discovery of anaerobic ammonia-oxidizing bacteria (Anammox) and, more recently, aerobic bacteria common in many natural and engineered systems that oxidize ammonia completely to nitrate (Comammox) have significantly altered our understanding of the global nitrogen cycle. A high affinity for ammonia (Km(app),NH3 ≈ 63nM) and oxygen place Comammox Nitrospira inopinata, the first described isolate, in the same trophic category as organisms such as some ammonia-oxidizing archaea. However, N. inopinata has a relatively low affinity for nitrite (Km,NO2 ≈ 449.2μM) suggesting it would be less competitive for nitrite than other nitrite-consuming aerobes and anaerobes. We examined the ecological relevance of the disparate substrate affinities by coupling it with the Anammox bacterium Candidatus Brocadia anammoxidans. Synthetic communities of the two were established in hydrogel granules in which Comammox grew in the aerobic outer layer to provide Anammox with nitrite in the inner anoxic core to form dinitrogen gas. This spatial organization was confirmed with FISH imaging, supporting a mutualistic or commensal relationship. The functional significance of interspecies spatial organization was informed by the hydrogel encapsulation format, broadening our limited understanding of the interplay between these two species. The resulting low nitrate formation and the competitiveness of Comammox over other aerobic ammonia- and nitrite-oxidizers sets this ecological cooperation apart and points to potential biotechnological applications. Since nitrate is an undesirable product of wastewater treatment effluents, the Comammox-Anammox symbiosis may be of economic and ecological importance to reduce nitrogen contamination of receiving waters.

  • Wildfire-Derived Pyrogenic Carbon Modulates Riverine Organic Matter and Biofilm Enzyme Activities in an In Situ Flume Experiment

    Lukas Thuile Bistarelli, Caroline Poyntner, Cristina Santín, Stefan Helmut Doerr, Matthew V. Talluto, Gabriel Singer, Gabriel Sigmund
    2021 - ACS EST Water, 1648–1656

    Abstract: 

    Wildfires produce large amounts of pyrogenic carbon (PyC), including charcoal, known for its chemical recalcitrance and sorption affinity for organic molecules. Wildfire-derived PyC can be transported to fluvial networks. Here it may alter the dissolved organic matter (DOM) concentration and composition as well as microbial biofilm functioning. Effects of PyC on carbon cycling in freshwater ecosystems remain poorly investigated. Employing in-stream flumes with a control versus treatment design (PyC pulse addition), we present evidence that field-aged PyC inputs to rivers can increase the dissolved organic carbon (DOC) concentration and alter the DOM composition. DOM fluorescence components were not affected by PyC. The in-stream DOM composition was altered due to leaching of pyrogenic DOM from PyC and possibly concurrent sorption of riverine DOM to PyC. Decreased DOM aromaticity indicated by a lower SUVA245 (−0.31 unit) and a higher pH (0.25 unit) was associated with changes in enzymatic activities in benthic biofilms, including a lower recalcitrance index (β-glucosidase/phenol oxidase), suggesting preferential usage of recalcitrant over readily available DOM by biofilms. The deposition of particulate PyC onto biofilms may further modulate the impacts of PyC due to direct contact with the biofilm matrix. This study highlights the importance of PyC for in-stream biogeochemical organic matter cycling in fire-affected watersheds. It was featured on the journal front cover.

  • Wood ash amended biochar for the removal of lead, copper, zinc and cadmium from aqueous solution

    Stuart Cairns, Sampriti Chaudhuri, Gabriel Sigmund, Iain Robertson, Natasha Hawkins, Tom Dunlop, Thilo Hofmann
    2021 - Environmental Technology & Innovation, 24: 1-11

    Abstract: 

    Heavy metals in motorway adjoined aqueous environments have increased at an alarming rate over recent years. This increase has been primarily attributed to anthropogenic activities such as the increase of motor vehicle use. Current remediation techniques, such as balancing ponds have the potential to leave toxic residue with the associated removal costs often proving prohibitive. In this study biochar and wood ash amended biochar were evaluated as remediators of inorganic vehicular pollutants found in motorway runoff, specifically Pb, Cu, Zn and Cd. Biochar from European larch (Larix decidua (L.) Karst.) was produced via fast pyrolysis-gasification (485–530 °C for 90 s) and amended with wood ash post pyrolysis. Pristine larch biochar (BC), larch biochar cold mixed with wood ash (WA) and larch biochar sintered with wood ash (WAS) were studied to evaluate metal immobilisation mechanisms and maximum removal capacities. This study demonstrates that the amendment of biochar with wood ash increases Pb, Cu, Zn, and Cd immobilisation by an order of magnitude compared to BC. The addition of wood ash increases pH whilst adding minerals causing precipitation. Precipitation and ion exchange dominate metal immobilisation and were not correlated to surface area. Sustainability of feedstock, low feedstock/production costs and maximum measured contaminant removal (61.5 mg/g, 38.9 mg/g, 12.1 mg/g and 10.2 mg/g for Pb, Cu, Zn and Cd respectively) indicate that wood ash amended biochar is a viable option to immobilise Pb, Cu, Zn and Cd from motorway runoff.

  • Prevalence of RT-qPCR-detected SARS-CoV-2 infection at schools: First results from the Austrian School-SARS-CoV-2 prospective cohort study

    Willeit P, Krause R, Lamprecht B, Berghold A, Hanson B, Stelzl E, Stoiber H, Zuber J, Heinen R, Köhler A, Bernhard D, Borena W, Doppler C, von Laer D, Schmidt H, Pröll J, Steinmetz I, Wagner M
    2021 - The Lancet Regional Health - Europe, 5:100086

    Abstract: 

    Background: The role of schools in the SARS-CoV-2 pandemic is much debated. We aimed to quantify reliably the prevalence of SARS-CoV-2 infections at schools detected with reverse-transcription polymerase-chain-reaction (RT-PCR). 

    Methods: This nationwide prospective cohort study monitors a representative sample of pupils (grade 1-8) and teachers at Austrian schools throughout the school year 2020/2021. We repeatedly test participants for SARS-CoV-2 infection using a gargling solution and RT-PCR. We herein report on the first two rounds of examinations. We used mixed-effect logistic regression to estimate odds ratios and robust 95% confidence intervals (95% CI). 

    Findings: We analysed data on 10734 participants from 245 schools (9465 pupils, 1269 teachers). Prevalence of SARS-CoV-2 infection increased from 0.39% at round 1 (95% CI 0.28-0·55%, 29 September-22 October 2020) to 1·42% at round 2 (95% CI 1·06-1·90%, 10-16 November). Odds ratios for SARS-CoV-2 infection were 2·29 (95% CI 1·26-4·17, P=0·007) in regions with >500 vs. ≤500 inhabitants/km2, 1·69 (95% CI 1·42-2·00, P<0·001) per two-fold higher regional 7-day incidence, and 2·71 (95% CI 1·68-4·39, P<0·001) in pupils at schools with high/very high vs. low/moderate social deprivation. Associations of community incidence and social deprivation persisted in a multivariable adjusted model. Prevalence did not differ by average number of pupils per class nor between age groups, sexes, pupils vs. teachers, or primary (grade 1-4) vs. secondary schools (grade 5-8).

    Interpretation: This monitoring study in Austrian schools revealed SARS-CoV-2 infection in 0·39%-1·42% of participants and identified associations of regional community incidence and social deprivation with higher prevalence. 

  • A critical evaluation of short columns for estimating the attachment efficiency of engineered nanomaterials in natural soils

    Knapp Karin Norrfors, Malfatti SE, Olga Borovinskaya, Frank von der Kammer, Thilo Hofmann, Geert Cornelis
    2021 - Environmental Science: Nano, in press

    Abstract: 

    Short, saturated packed columns are used frequently to estimate the attachment efficiency (α) of engineered nanomaterials (ENMs) in relatively homogeneous porous media, but a combined experimental and theoretical approach to obtain α-values for heterogeneous natural soils has not yet been agreed upon. Accurately determined α-values that can be used to study and predict ENM transport in natural soils should vary with ENM and soil properties, but not with experimental settings. We investigated the effect of experimental conditions, and used different methods to obtain soil parameters, essential to calculate α. We applied 150 different approaches onto 52 transport experiments using short columns with 5 different natural soils and 20 and 80 nm gold- or 27 nm silver sulphide ENMs. The choice of column end-filter material and pore size appeared critical to avoid overestimating α owing to filter – ENM interactions and/or incomplete saturation of the column. Using a low ionic strength (4.4 x 10-5 mol L-1) artificial rain water as an aqueous medium avoided ENM homo- or heteroaggregation in all soils, as confirmed by single-particle inductively coupled plasma - time of flight mass spectrometry. ENM breakthrough curves could be modelled using colloid filtration theory assuming irreversible attachment only. α-values calculated from this model, having the grain size represented by a single average size, accounting for dispersivity and effective porosity based on a prior inert tracer test, explained up to 42 % of the variance in α as revealed by partial least squares analysis. However, column length and dispersivity remained as important experimental parameters, which calls for further standardisation efforts of column tests with ENMs in natural soils, preferably cross-validated with batch tests.

  • Successional dynamics and alternative stable states in a saline activated sludge microbial community over 9 years.

    Wang Y, Ye J, Ju F, Liu L, Boyd JA, Deng Y, Parks DH, Jiang X, Yin X, Woodcroft BJ, Tyson GW, Hugenholtz P, Polz MF, Zhang T
    2021 - Microbiome, 1: 199

    Abstract: 

    Microbial communities in both natural and applied settings reliably carry out myriads of functions, yet how stable these taxonomically diverse assemblages can be and what causes them to transition between states remains poorly understood. We studied monthly activated sludge (AS) samples collected over 9 years from a full-scale wastewater treatment plant to answer how complex AS communities evolve in the long term and how the community functions change when there is a disturbance in operational parameters.
    Here, we show that a microbial community in activated sludge (AS) system fluctuated around a stable average for 3 years but was then abruptly pushed into an alternative stable state by a simple transient disturbance (bleaching). While the taxonomic composition rapidly turned into a new state following the disturbance, the metabolic profile of the community and system performance remained remarkably stable. A total of 920 metagenome-assembled genomes (MAGs), representing approximately 70% of the community in the studied AS ecosystem, were recovered from the 97 monthly AS metagenomes. Comparative genomic analysis revealed an increased ability to aggregate in the cohorts of MAGs with correlated dynamics that are dominant after the bleaching event. Fine-scale analysis of dynamics also revealed cohorts that dominated during different periods and showed successional dynamics on seasonal and longer time scales due to temperature fluctuation and gradual changes in mean residence time in the reactor, respectively.
    Our work highlights that communities can assume different stable states under highly similar environmental conditions and that a specific disturbance threshold may lead to a rapid shift in community composition. Video Abstract.

  • Novel Alcaligenes ammonioxydans sp. nov. from wastewater treatment sludge oxidizes ammonia to N2 with a previously unknown pathway.

    Wu MR, Hou TT, Liu Y, Miao LL, Ai GM, Ma L, Zhu HZ, Zhu YX, Gao XY, Herbold CW, Wagner M, Li DF, Liu ZP, Liu SJ
    2021 - Environ Microbiol, in press

    Abstract: 

    Heterotrophic nitrifiers are able to oxidize and remove ammonia from nitrogen-rich wastewaters but the genetic elements of heterotrophic ammonia oxidation are poorly understood. Here, we isolated and identified a novel heterotrophic nitrifier, Alcaligenes ammonioxydans sp. nov. strain HO-1, oxidizing ammonia to hydroxylamine and ending in the production of N gas. Genome analysis revealed that strain HO-1 encoded a complete denitrification pathway but lacks any genes coding for homologous to known ammonia monooxygenases or hydroxylamine oxidoreductases. Our results demonstrated strain HO-1 denitrified nitrite (not nitrate) to N and N O at anaerobic and aerobic conditions respectively. Further experiments demonstrated that inhibition of aerobic denitrification did not stop ammonia oxidation and N production. A gene cluster (dnfT1RT2ABCD) was cloned from strain HO-1 and enabled E. coli accumulated hydroxylamine. Sub-cloning showed that genetic cluster dnfAB or dnfABC already enabled E. coli cells to produce hydroxylamine and further to N from ( NH ) SO . Transcriptome analysis revealed these three genes dnfA, dnfB and dnfC were significantly upregulated in response to ammonia stimulation. Taken together, we concluded that strain HO-1 has a novel dnf genetic cluster for ammonia oxidation and this dnf genetic cluster encoded a previously unknown pathway of direct ammonia oxidation (Dirammox) to N .

  • Prokaryotic viruses impact functional microorganisms in nutrient removal and carbon cycle in wastewater treatment plants.

    Chen Y, Wang Y, Páez-Espino D, Polz MF, Zhang T
    2021 - Nat Commun, 1: 5398

    Abstract: 

    As one of the largest biotechnological applications, activated sludge (AS) systems in wastewater treatment plants (WWTPs) harbor enormous viruses, with 10-1,000-fold higher concentrations than in natural environments. However, the compositional variation and host-connections of AS viruses remain poorly explored. Here, we report a catalogue of ~50,000 prokaryotic viruses from six WWTPs, increasing the number of described viral species of AS by 23-fold, and showing the very high viral diversity which is largely unknown (98.4-99.6% of total viral contigs). Most viral genera are represented in more than one AS system with 53 identified across all. Viral infection widely spans 8 archaeal and 58 bacterial phyla, linking viruses with aerobic/anaerobic heterotrophs, and other functional microorganisms controlling nitrogen/phosphorous removal. Notably, Mycobacterium, notorious for causing AS foaming, is associated with 402 viral genera. Our findings expand the current AS virus catalogue and provide reference for the phage treatment to control undesired microorganisms in WWTPs.

  • Ecological memory of recurrent drought modifies soil processes via changes in soil microbial community

    Canarini A, Schmidt H, Fuchslueger L, Martin V, Herbold CW, Zezula D, Gündler P, Hasibeder R, Jecmenica M, Bahn M, Richter A
    2021 - Nature communications, 12: Article 5308

    Abstract: 

    Climate change is altering the frequency and severity of drought events. Recent evidence indicates that drought may produce legacy effects on soil microbial communities. However, it is unclear whether precedent drought events lead to ecological memory formation, i.e., the capacity of past events to influence current ecosystem response trajectories. Here, we utilize a long-term field experiment in a mountain grassland in central Austria with an experimental layout comparing 10 years of recurrent drought events to a single drought event and ambient conditions. We show that recurrent droughts increase the dissimilarity of microbial communities compared to control and single drought events, and enhance soil multifunctionality during drought (calculated via measurements of potential enzymatic activities, soil nutrients, microbial biomass stoichiometry and belowground net primary productivity). Our results indicate that soil microbial community composition changes in concert with its functioning, with consequences for soil processes. The formation of ecological memory in soil under recurrent drought may enhance the resilience of ecosystem functioning against future drought events.

  • Aberrant gut-microbiota-immune-brain axis development in premature neonates with brain damage.

    Seki D, Mayer M, Hausmann B, Pjevac P, Giordano V, Goeral K, Unterasinger L, Klebermaß-Schrehof K, De Paepe K, Van de Wiele T, Spittler A, Kasprian G, Warth B, Berger A, Berry D, Wisgrill L
    2021 - Cell Host Microbe, in press

    Abstract: 

    Premature infants are at substantial risk for suffering from perinatal white matter injury. Though the gut microbiota has been implicated in early-life development, a detailed understanding of the gut-microbiota-immune-brain axis in premature neonates is lacking. Here, we profiled the gut microbiota, immunological, and neurophysiological development of 60 extremely premature infants, which received standard hospital care including antibiotics and probiotics. We found that maturation of electrocortical activity is suppressed in infants with severe brain damage. This is accompanied by elevated γδ T cell levels and increased T cell secretion of vascular endothelial growth factor and reduced secretion of neuroprotectants. Notably, Klebsiella overgrowth in the gut is highly predictive for brain damage and is associated with a pro-inflammatory immunological tone. These results suggest that aberrant development of the gut-microbiota-immune-brain axis may drive or exacerbate brain injury in extremely premature neonates and represents a promising target for novel intervention strategies.

  • How can fertilization regimes and durations shape earthworm gut microbiota in a long-term field experiment?

    Bi Q-F, Jin B-J, Zhu D, Jiang Y-G, Zheng B-X, O’Connor P, Yang X-R, Richter A, Lin X-Y, Zhu Y-H 
    2021 - Ecotoxicology and Environmental Safety, 224: Article 112643

    Abstract: 

    The positive roles of earthworms on soil functionality has been extensively documented. The capacity of the earthworm gut microbiota on decomposition and nutrient cycling under long-term fertilization in field conditions has rarely been studied. Here, we report the structural, taxonomic, and functional responses of Eisenia foetida and Pheretima guillelmi gut microbiota to different fertilization regimes and durations using 16S rRNA gene-based Illumina sequencing and high-throughput quantitative PCR techniques. Our results revealed that the core gut microbiota, especially the fermentative bacteria were mainly sourced from the soil, but strongly stimulated with species-specificity, potential benefits for the host and soil health. The functional compositions of gut microbiota were altered by fertilization with fertilization duration being more influential than fertilization regimes. Moreover, the combination of organic and inorganic fertilization with the longer duration resulted in a higher richness and connectivity in the gut microbiota, and also their functional potential related to carbon (C), nitrogen, and phosphorus cycling, particularly the labile C decomposition, denitrification, and phosphate mobilization. We also found that long-term inorganic fertilization increased the abundance of pathogenic bacteria in the P. guillelmi gut. This study demonstrates that understanding earthworm gut microbiota can provide insights into how agricultural practices can potentially alte

  • Comparison of genovars and Chlamydia trachomatis infection loads in ocular samples from children in two distinct cohorts in Sudan and Morocco.

    Ghasemian E, Inic-Kanada A, Collingro A, Mejdoubi L, Alchalabi H, Keše D, Elshafie BE, Hammou J, Barisani-Asenbauer T
    2021 - PLoS Negl Trop Dis, 8: e0009655

    Abstract: 

    Trachoma is a blinding disease caused by repeated conjunctival infection with different Chlamydia trachomatis (Ct) genovars. Ct B genovars have been associated with more severe trachoma symptoms. Here, we investigated associations between Ct genovars and bacterial loads in ocular samples from two distinct geographical locations in Africa, which are currently unclear. We tested ocular swabs from 77 Moroccan children (28 with trachomatous inflammation-follicular (TF) and 49 healthy controls), and 96 Sudanese children (54 with TF and 42 healthy controls) with a Ct-specific real-time polymerase chain reaction (PCR) assay. To estimate bacterial loads, Ct-positive samples were further processed by multiplex real-time qPCR to amplify the chromosomal outer membrane complex B and plasmid open reading frame 2 of Ct. Genotyping was performed by PCR-based amplification of the outer membrane protein A gene (~1120 base pairs) of Ct and Sanger sequencing. Ct-positivities among the Moroccan and Sudanese patient groups were 60·7% and 31·5%, respectively. Significantly more Sudanese patients than Moroccan patients were genovar A-positive. In contrast, B genovars were significantly more prevalent in Moroccan patients than in Sudanese patients. Significantly higher Ct loads were found in samples positive for B genovars (598·596) than A genovar (51·005). Geographical differences contributed to the distributions of different ocular Ct genovars. B genovars may induce a higher bacterial load than A genovars in trachoma patients. Our findings emphasize the importance of conducting broader studies to elucidate if the noted difference in multiplication abilities are genovar and/or endemicity level dependent.

  • Shifts on the abundances of saprotrophic and ectomycorrhizal fungi at altered leaf litter inputs

    Marañon-Jimenez S, Radujkovic D, Verbruggen E, Grau O, Cuntz M, Peñuelas J, Richter A, Schrumpf M, Rebmann C
    2021 - Frontiers in Plant Science, 12: Article 682142

    Abstract: 

    Ectomycorrhizal (EcM) and saprotrophic fungi interact in the breakdown of organic matter, but the mechanisms underlying the EcM role on organic matter decomposition are not totally clear. We hypothesized that the ecological relations between EcM and saprotroph fungi are modulated by resources availability and accessibility, determining decomposition rates. We manipulated the amount of leaf litter inputs (No-Litter, Control Litter, Doubled Litter) on Trenched (root exclusion) and Non-Trenched plots (with roots) in a temperate deciduous forest of EcM-associated trees. Resultant shifts in soil fungal communities were determined by phospholipid fatty acids and DNA sequencing after 3 years, and CO2 fluxes were measured throughout this period. Different levels of leaf litter inputs generated a gradient of organic substrate availability and accessibility, altering the composition and ecological relations between EcM and saprotroph fungal communities. EcM fungi dominated at low levels of fresh organic substrates and lower organic matter quality, where short-distances exploration types seem to be better competitors, whereas saprotrophs and longer exploration types of EcM fungi tended to dominate at high levels of leaf litter inputs, where labile organic substrates were easily accessible. We were, however, not able to detect unequivocal signs of competition between these fungal groups for common resources. These results point to the relevance of substrate quality and availability as key factors determining the role of EcM and saprotroph fungi on litter and soil organic matter decay and represent a path forward on the capacity of organic matter decomposition of different exploration types of EcM fungi.

  • Ammonia-oxidizing archaea possess a wide range of cellular ammonia affinities.

    Jung MY, Sedlacek CJ, Kits KD, Mueller AJ, Rhee SK, Hink L, Nicol GW, Bayer B, Lehtovirta-Morley L, Wright C, De La Torre JR, Herbold CW, Pjevac P, Daims H, Wagner M
    2021 - ISME J, in press
    Kinetics of nitrifiers

    Abstract: 

    Nitrification, the oxidation of ammonia to nitrate, is an essential process in the biogeochemical nitrogen cycle. The first step of nitrification, ammonia oxidation, is performed by three, often co-occurring guilds of chemolithoautotrophs: ammonia-oxidizing bacteria (AOB), archaea (AOA), and complete ammonia oxidizers (comammox). Substrate kinetics are considered to be a major niche-differentiating factor between these guilds, but few AOA strains have been kinetically characterized. Here, the ammonia oxidation kinetic properties of 12 AOA representing all major cultivated phylogenetic lineages were determined using microrespirometry. Members of the genus Nitrosocosmicus have the lowest affinity for both ammonia and total ammonium of any characterized AOA, and these values are similar to previously determined ammonia and total ammonium affinities of AOB. This contrasts previous assumptions that all AOA possess much higher substrate affinities than their comammox or AOB counterparts. The substrate affinity of ammonia oxidizers correlated with their cell surface area to volume ratios. In addition, kinetic measurements across a range of pH values supports the hypothesis that-like for AOB-ammonia and not ammonium is the substrate for the ammonia monooxygenase enzyme of AOA and comammox. Together, these data will facilitate predictions and interpretation of ammonia oxidizer community structures and provide a robust basis for establishing testable hypotheses on competition between AOB, AOA, and comammox.

  • Evolutionarily recent dual obligatory symbiosis among adelgids indicates a transition between fungus- and insect-associated lifestyles

    Szabó G, Schulz F, Manzano-Marín A, Toenshoff ER, Horn M
    2021 - ISME J, in press

    Abstract: 

    Adelgids (Insecta: Hemiptera: Adelgidae) form a small group of insects but harbor a surprisingly diverse set of bacteriocyte-associated endosymbionts, which suggest multiple replacement and acquisition of symbionts over evolutionary time. Specific pairs of symbionts have been associated with adelgid lineages specialized on different secondary host conifers. Using a metagenomic approach, we investigated the symbiosis of the Adelges laricis/Adelges tardus species complex containing betaproteobacterial ("Candidatus Vallotia tarda") and gammaproteobacterial ("Candidatus Profftia tarda") symbionts. Genomic characteristics and metabolic pathway reconstructions revealed that Vallotia and Profftia are evolutionary young endosymbionts, which complement each other's role in essential amino acid production. Phylogenomic analyses and a high level of genomic synteny indicate an origin of the betaproteobacterial symbiont from endosymbionts of Rhizopus fungi. This evolutionary transition was accompanied with substantial loss of functions related to transcription regulation, secondary metabolite production, bacterial defense mechanisms, host infection, and manipulation. The transition from fungus to insect endosymbionts extends our current framework about evolutionary trajectories of host-associated microbes.

  • Microaerobic lifestyle at nanomolar O2 concentrations mediated by low-affinity terminal oxidases in abundant soil bacteria.

    Trojan D, Garcia-Robledo E, Meier DV, Hausmann B, Revsbech NP, Eichorst SA, Woebken D
    2021 - mSystems, e0025021

    Abstract: 

    High-affinity terminal oxidases (TOs) are believed to permit microbial respiration at low oxygen (O2) levels. Genes encoding such oxidases are widespread and their existence in microbial genomes are taken as an indicator for microaerobic respiration. We combined respiratory kinetics determined via highly sensitive optical trace O2 sensors, genomics and transcriptomics to test the hypothesis that high-affinity TOs are a prerequisite to respire micro- and nanooxic concentrations of O2 in environmentally relevant, model soil organisms – acidobacteria. Members of the Acidobacteria harbor branched respiratory chains terminating in low- (caa3-type cytochrome c oxidases) as well as high-affinity (cbb3-type cytochrome c oxidases and/or bd-type quinol oxidases) TOs, potentially enabling them to cope with varying O2 concentrations. The measured Km(app) values for O2 of selected strains ranged from 37–288 nmol O2 L-1, comparable to values previously assigned to low-affinity TOs. Surprisingly, we could not detect expression of the conventional high-affinity TO (cbb3-type) at micro- and nano-molar O2 concentrations, but of low-affinity TOs. To the best of our knowledge, this is the first observation of microaerobic respiration imparted by low-affinity TOs at O2 concentrations as low as 1 nanomolar. This challenges the standing hypothesis that a microaerobic lifestyle is exclusively imparted by the presence of high-affinity TOs. As low-affinity TOs are more efficient at generating ATP than high-affinity TOs, their utilization could provide a great benefit, even at low-nanomolar O2 levels. Our findings highlight energy conservation strategies that could promote the success of Acidobacteria in soil but might also be important for yet unrevealed microorganisms.

  • Recently photoassimilated carbon and fungal-delivered nitrogen are spatially correlated at the cellular scale in the ectomycorrhizal tissue of Fagus sylvatica.

    Mayerhofer W, Schintlmeister A, Dietrich M, Gorka S, Wiesenbauer J, Martin V, Gabriel R, Reipert S, Weidinger M, Clode P, Wagner M, Woebken D, Richter A, Kaiser C
    2021 - New Phytol, in press

    Abstract: 

    Ectomycorrhizal plants trade plant-assimilated carbon for soil nutrients with their fungal partners. The underlying mechanisms are, however, not fully understood. Here we investigated the exchange of carbon for nitrogen in the ectomycorrhizal symbiosis of Fagus Sylvatica across different spatial scales from the root-system to the cellular scale. We provided N-labelled Nitrogen to mycorrhizal hyphae associated with one half of the root system of young beech trees, while exposing plants to a CO2 atmosphere. We analysed the short-term distribution of C and N in the root system with isotope-ratio mass spectrometry, and at the cellular scale within a mycorrhizal root tip with nanoscale-secondary-ion mass spectrometry (NanoSIMS). At the root-system scale, plants did not allocate more C to root parts that received more N. NanoSIMS imaging, however, revealed a highly heterogenous, and spatially significantly correlated distribution of C and N at the cellular scale. Our results indicate that, on a coarse scale, plants are not allocating a larger proportion of photoassimilated C towards root parts associated with N-delivering ectomycorrhizal fungi. Within the ectomycorrhizal tissue, however, recently plant-assimilated C and fungal-delivered N were spatially strongly coupled. NanoSIMS visualisation provide first insights into regulation of ectomycorrhizal C and N exchange at the microscale.

  • Limitation of microbial processes at saturation-level salinities in a microbial mat covering a coastal saltflat

    Meier DV, Greve AJ, Chennu A, van Erk MR, Muthukrishnan T, Abed RMM, Woebken D, De Beer D
    2021 - Appl Environ Microbiol, in press

    Abstract: 

    Hypersaline microbial mats are dense microbial ecosystems capable of performing complete element cycling and are considered analogs of Early Earth and hypothetical extraterrestrial ecosystems. We studied the functionality and limits of key biogeochemical processes, such as photosynthesis, aerobic respiration, and sulfur cycling in salt crust-covered microbial mats from a tidal flat at the coast of Oman. We measured light, oxygen, and sulfide microprofiles as well as sulfate-reduction rates at salt saturation and in flood conditions and determined fine-scale stratification of pigments, biomass, and microbial taxa in the resident microbial community. The salt crust did not protect the mats against irradiation or evaporation. Although some oxygen production was measurable at salinity ≤ 30% (w/v) , at saturation-level salinity (40%), oxygenic photosynthesis was completely inhibited and only resumed two days after reducing the pore water salinity to 12%. Aerobic respiration and active sulfur cycling occurred at low rates under salt saturation and increased strongly upon salinity reduction. Apart from high relative abundances of photoheterotrophic , , and the mat contained a distinct layer harboring filamentous , which is unusual for such high salinities. Our results show that the diverse microbial community inhabiting this saltflat mat ultimately depends on periodic salt dilution to be self-sustaining and is rather adapted to merely survive salt saturation than to thrive under the salt crust. Due to their abilities to survive intense radiation and low water availability hypersaline microbial mats are often suggested to be analogs of potential extraterrestrial life. However, even on Earth the limitations imposed on microbial processes by saturation-level salinity have rarely been studied . While abundance and diversity of microbial life in salt-saturated environments is well documented, most of our knowledge on process limitations stems from culture-based studies, few studies, and theoretical calculations. Especially oxygenic photosynthesis has barely been explored beyond 5M NaCl (28% w/v). By applying a variety of biogeochemical and molecular methods we show that despite abundance of photoautotrophic microorganisms, oxygenic photosynthesis is inhibited in salt-crust covered microbial mats at saturation salinities, while rates of other energy generation processes are decreased several fold. Hence, the complete element cycling required for self-sustaining microbial communities only occurs at lower salt concentrations.

  • Mucosal Biofilms Are an Endoscopic Feature of Irritable Bowel Syndrome and Ulcerative Colitis.

    Baumgartner M, Lang M, Holley H, Crepaz D, Hausmann B, Pjevac P, Moser D, Haller F, Hof F, Beer A, Orgler E, Frick A, Khare V, Evstatiev R, Strohmaier S, Primas C, Dolak W, Köcher T, Kristaps K, Rath T, Neurath MF, Berry D, Makristathis A, Muttenthaler M, Gasche C
    2021 - Gastroenterology, in press

    Abstract: 

    Irritable bowel syndrome (IBS) and inflammatory bowel diseases result in a substantial reduction in quality of life and a considerable socioeconomic impact. In IBS, diagnosis and treatment options are limited, but evidence for involvement of the gut microbiome in disease pathophysiology is emerging. Here we analyzed the prevalence of endoscopically visible mucosal biofilms in gastrointestinal disease and associated changes in microbiome composition and metabolism.
    The presence of mucosal biofilms was assessed in 1426 patients at 2 European university-based endoscopy centers. One-hundred and seventeen patients were selected for in-depth molecular and microscopic analysis using 16S ribosomal RNA gene amplicon-sequencing of colonic biopsies and fecal samples, confocal microscopy with deep learning-based image analysis, scanning electron microscopy, metabolomics, and in vitro biofilm formation assays.
    Biofilms were present in 57% of patients with IBS and 34% of patients with ulcerative colitis compared with 6% of controls (P < .001). These yellow-green adherent layers of the ileum and right-sided colon were microscopically confirmed to be dense bacterial biofilms. 16S-sequencing links the presence of biofilms to a dysbiotic gut microbiome, including overgrowth of Escherichia coli and Ruminococcus gnavus. R gnavus isolates cultivated from patient biofilms also formed biofilms in vitro. Metabolomic analysis found an accumulation of bile acids within biofilms that correlated with fecal bile acid excretion, linking this phenotype with a mechanism of diarrhea.
    The presence of mucosal biofilms is an endoscopic feature in a subgroup of IBS and ulcerative colitis with disrupted bile acid metabolism and bacterial dysbiosis. They provide novel insight into the pathophysiology of IBS and ulcerative colitis, illustrating that biofilm can be seen as a tipping point in the development of dysbiosis and disease.

  • Degradation of host translational machinery drives tRNA acquisition in viruses.

    Yang JY, Fang W, Miranda-Sanchez F, Brown JM, Kauffman KM, Acevero CM, Bartel DP, Polz MF, Kelly L
    2021 - Cell Syst, in press

    Abstract: 

    Viruses are traditionally thought to be under selective pressure to maintain compact genomes and thus depend on host cell translational machinery for reproduction. However, some viruses encode abundant tRNA and other translation-related genes, potentially optimizing for codon usage differences between phage and host. Here, we systematically interrogate selective advantages that carrying 18 tRNAs may convey to a T4-like Vibriophage. Host DNA and RNA degrade upon infection, including host tRNAs, which are replaced by those of the phage. These tRNAs are expressed at levels slightly better adapted to phage codon usage, especially that of late genes. The phage is unlikely to randomly acquire as diverse an array of tRNAs as observed (p = 0.0017). Together, our results support that the main driver behind phage tRNA acquisition is pressure to sustain translation as host machinery degrades, a process resulting in a dynamically adapted codon usage strategy during the course of infection.

  • Genomic insights into diverse bacterial taxa that degrade extracellular DNA in marine sediments

    Wasmund K, Pelikan C, Schintlmeister A, Wagner M, Watzka M, Richter A, Bhatnagar A, Noel A, Hubert CRJ, Rattei T, Hofmann T, Hausmann B, Herbold CW, Loy A
    2021 - Nat Microbiol, 6: 885–898

    Abstract: 

    Extracellular DNA is a major macromolecule in global element cycles, and is a particularly crucial phosphorus, nitrogen and carbon source for microorganisms in the seafloor. Nevertheless, the identities, ecophysiology and genetic features of DNA-foraging microorganisms in marine sediments are largely unknown. Here, we combined microcosm experiments, DNA stable isotope probing (SIP), single-cell SIP using nano-scale secondary isotope mass spectrometry (NanoSIMS) and genome-centric metagenomics to study microbial catabolism of DNA and its subcomponents in marine sediments. 13C-DNA added to sediment microcosms was largely degraded within 10 d and mineralized to 13CO2. SIP probing of DNA revealed diverse ‘Candidatus Izemoplasma’, Lutibacter, Shewanella and Fusibacteraceae incorporated DNA-derived 13C-carbon. NanoSIMS confirmed incorporation of 13C into individual bacterial cells of Fusibacteraceae sorted from microcosms. Genomes of the 13C-labelled taxa all encoded enzymatic repertoires for catabolism of DNA or subcomponents of DNA. Comparative genomics indicated that diverse ‘Candidatus Izemoplasmatales’ (former Tenericutes) are exceptional because they encode multiple (up to five) predicted extracellular nucleases and are probably specialized DNA-degraders. Analyses of additional sediment metagenomes revealed extracellular nuclease genes are prevalent among Bacteroidota at diverse sites. Together, our results reveal the identities and functional properties of microorganisms that may contribute to the key ecosystem function of degrading and recycling DNA in the seabed.

  • An economical and flexible dual barcoding, two-step PCR approach for highly multiplexed amplicon sequencing

    Pjevac P, Hausmann B, Schwarz J, Kohl G, Herbold CW, Loy A, Berry D
    2021 - Front Microbiol, 12: 669776

    Abstract: 

    In microbiome research, phylogenetic and functional marker gene amplicon sequencing is the most commonly-used community profiling approach. Consequently, a plethora of protocols for the preparation and multiplexing of samples for amplicon sequencing have been developed. Here, we present two economical high-throughput gene amplification and sequencing workflows that are implemented as standard operating procedures at the Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna. These workflows are based on a previously-published two-step PCR approach, but have been updated to either increase the accuracy of results, or alternatively to achieve orders of magnitude higher numbers of samples to be multiplexed in a single sequencing run. The high-accuracy workflow relies on unique dual sample barcoding. It allows the same level of sample multiplexing as the previously-published two-step PCR approach, but effectively eliminates residual read missasignments between samples (crosstalk) which are inherent to single barcoding approaches. The high-multiplexing workflow is based on combinatorial dual sample barcoding, which theoretically allows for multiplexing up to 299,756 amplicon libraries of the same target gene in a single massively-parallelized amplicon sequencing run. Both workflows presented here are highly economical, easy to implement, and can, without significant modifications or cost, be applied to any target gene of interest.

  • Anaerobic Sulfur Oxidation Underlies Adaptation of a Chemosynthetic Symbiont to Oxic-Anoxic Interfaces.

    Paredes GF, Viehboeck T, Lee R, Palatinszky M, Mausz MA, Reipert S, Schintlmeister A, Maier A, Volland JM, Hirschfeld C, Wagner M, Berry D, Markert S, Bulgheresi S, König L
    2021 - mSystems, 3: e0118620

    Abstract: 

    Chemosynthetic symbioses occur worldwide in marine habitats, but comprehensive physiological studies of chemoautotrophic bacteria thriving on animals are scarce. Stilbonematinae are coated by thiotrophic . As these nematodes migrate through the redox zone, their ectosymbionts experience varying oxygen concentrations. However, nothing is known about how these variations affect their physiology. Here, by applying omics, Raman microspectroscopy, and stable isotope labeling, we investigated the effect of oxygen on " Thiosymbion oneisti." Unexpectedly, sulfur oxidation genes were upregulated in anoxic relative to oxic conditions, but carbon fixation genes and incorporation of C-labeled bicarbonate were not. Instead, several genes involved in carbon fixation were upregulated under oxic conditions, together with genes involved in organic carbon assimilation, polyhydroxyalkanoate (PHA) biosynthesis, nitrogen fixation, and urea utilization. Furthermore, in the presence of oxygen, stress-related genes were upregulated together with vitamin biosynthesis genes likely necessary to withstand oxidative stress, and the symbiont appeared to proliferate less. Based on its physiological response to oxygen, we propose that " T. oneisti" may exploit anaerobic sulfur oxidation coupled to denitrification to proliferate in anoxic sand. However, the ectosymbiont would still profit from the oxygen available in superficial sand, as the energy-efficient aerobic respiration would facilitate carbon and nitrogen assimilation. Chemoautotrophic endosymbionts are famous for exploiting sulfur oxidization to feed marine organisms with fixed carbon. However, the physiology of thiotrophic bacteria thriving on the surface of animals (ectosymbionts) is less understood. One longstanding hypothesis posits that attachment to animals that migrate between reduced and oxic environments would boost sulfur oxidation, as the ectosymbionts would alternatively access sulfide and oxygen, the most favorable electron acceptor. Here, we investigated the effect of oxygen on the physiology of " Thiosymbion oneisti," a gammaproteobacterium which lives attached to marine nematodes inhabiting shallow-water sand. Surprisingly, sulfur oxidation genes were upregulated under anoxic relative to oxic conditions. Furthermore, under anoxia, the ectosymbiont appeared to be less stressed and to proliferate more. We propose that animal-mediated access to oxygen, rather than enhancing sulfur oxidation, would facilitate assimilation of carbon and nitrogen by the ectosymbiont.

  • Prevotella diversity, niches and interactions with the human host.

    Tett A, Pasolli E, Masetti G, Ercolini D, Segata N
    2021 - Nat Rev Microbiol, in press

    Abstract: 

    The genus Prevotella includes more than 50 characterized species that occur in varied natural habitats, although most Prevotella spp. are associated with humans. In the human microbiome, Prevotella spp. are highly abundant in various body sites, where they are key players in the balance between health and disease. Host factors related to diet, lifestyle and geography are fundamental in affecting the diversity and prevalence of Prevotella species and strains in the human microbiome. These factors, along with the ecological relationship of Prevotella with other members of the microbiome, likely determine the extent of the contribution of Prevotella to human metabolism and health. Here we review the diversity, prevalence and potential connection of Prevotella spp. in the human host, highlighting how genomic methods and analysis have improved and should further help in framing their ecological role. We also provide suggestions for future research to improve understanding of the possible functions of Prevotella spp. and the effects of the Western lifestyle and diet on the host-Prevotella symbiotic relationship in the context of maintaining human health.

  • Functional iron-deficiency in women with allergic rhinitis is associated with symptoms after nasal provocation and lack of iron-sequestering microbes.

    Petje LM, Jensen SA, Szikora S, Sulzbacher M, Bartosik T, Pjevac P, Hausmann B, Hufnagl K, Untersmayr E, Fischer L, Vyskocil E, Eckl-Dorna J, Jensen-Jarolim E, Hofstetter G, Afify SM, Krenn CG, Roth GA, Rivelles E, Hann S, Roth-Walter F
    2021 - Allergy, in press
  • Novel taxa of Acidobacteriota implicated in seafloor sulfur cycling.

    Flieder M, Buongiorno J, Herbold CW, Hausmann B, Rattei T, Lloyd KG, Loy A, Wasmund K
    2021 - ISME J, in press

    Abstract: 

    Acidobacteriota are widespread and often abundant in marine sediments, yet their metabolic and ecological properties are poorly understood. Here, we examined metabolisms and distributions of Acidobacteriota in marine sediments of Svalbard by functional predictions from metagenome-assembled genomes (MAGs), amplicon sequencing of 16S rRNA and dissimilatory sulfite reductase (dsrB) genes and transcripts, and gene expression analyses of tetrathionate-amended microcosms. Acidobacteriota were the second most abundant dsrB-harboring (averaging 13%) phylum after Desulfobacterota in Svalbard sediments, and represented 4% of dsrB transcripts on average. Meta-analysis of dsrAB datasets also showed Acidobacteriota dsrAB sequences are prominent in marine sediments worldwide, averaging 15% of all sequences analysed, and represent most of the previously unclassified dsrAB in marine sediments. We propose two new Acidobacteriota genera, Candidatus Sulfomarinibacter (class Thermoanaerobaculia, "subdivision 23") and Ca. Polarisedimenticola ("subdivision 22"), with distinct genetic properties that may explain their distributions in biogeochemically distinct sediments. Ca. Sulfomarinibacter encode flexible respiratory routes, with potential for oxygen, nitrous oxide, metal-oxide, tetrathionate, sulfur and sulfite/sulfate respiration, and possibly sulfur disproportionation. Potential nutrients and energy include cellulose, proteins, cyanophycin, hydrogen, and acetate. A Ca. Polarisedimenticola MAG encodes various enzymes to degrade proteins, and to reduce oxygen, nitrate, sulfur/polysulfide and metal-oxides. 16S rRNA gene and transcript profiling of Svalbard sediments showed Ca. Sulfomarinibacter members were relatively abundant and transcriptionally active in sulfidic fjord sediments, while Ca. Polarisedimenticola members were more relatively abundant in metal-rich fjord sediments. Overall, we reveal various physiological features of uncultured marine Acidobacteriota that indicate fundamental roles in seafloor biogeochemical cycling.

  • Novel taxa of Acidobacteriota implicated in seafloor sulfur cycling.

    Flieder M, Buongiorno J, Herbold CW, Hausmann B, Rattei T, Lloyd KG, Loy A, Wasmund K
    2021 - ISME J, in press

    Abstract: 

    Acidobacteriota are widespread and often abundant in marine sediments, yet their metabolic and ecological properties are poorly understood. Here, we examined metabolisms and distributions of Acidobacteriota in marine sediments of Svalbard by functional predictions from metagenome-assembled genomes (MAGs), amplicon sequencing of 16S rRNA and dissimilatory sulfite reductase (dsrB) genes and transcripts, and gene expression analyses of tetrathionate-amended microcosms. Acidobacteriota were the second most abundant dsrB-harboring (averaging 13%) phylum after Desulfobacterota in Svalbard sediments, and represented 4% of dsrB transcripts on average. Meta-analysis of dsrAB datasets also showed Acidobacteriota dsrAB sequences are prominent in marine sediments worldwide, averaging 15% of all sequences analysed, and represent most of the previously unclassified dsrAB in marine sediments. We propose two new Acidobacteriota genera, Candidatus Sulfomarinibacter (class Thermoanaerobaculia, "subdivision 23") and Ca. Polarisedimenticola ("subdivision 22"), with distinct genetic properties that may explain their distributions in biogeochemically distinct sediments. Ca. Sulfomarinibacter encode flexible respiratory routes, with potential for oxygen, nitrous oxide, metal-oxide, tetrathionate, sulfur and sulfite/sulfate respiration, and possibly sulfur disproportionation. Potential nutrients and energy include cellulose, proteins, cyanophycin, hydrogen, and acetate. A Ca. Polarisedimenticola MAG encodes various enzymes to degrade proteins, and to reduce oxygen, nitrate, sulfur/polysulfide and metal-oxides. 16S rRNA gene and transcript profiling of Svalbard sediments showed Ca. Sulfomarinibacter members were relatively abundant and transcriptionally active in sulfidic fjord sediments, while Ca. Polarisedimenticola members were more relatively abundant in metal-rich fjord sediments. Overall, we reveal various physiological features of uncultured marine Acidobacteriota that indicate fundamental roles in seafloor biogeochemical cycling.

  • Tamock: simulation of habitat-specific benchmark data in metagenomics.

    Gerner SM, Graf AB, Rattei T
    2021 - BMC Bioinformatics, 1: 227

    Abstract: 

    Simulated metagenomic reads are widely used to benchmark software and workflows for metagenome interpretation. The results of metagenomic benchmarks depend on the assumptions about their underlying ecosystems. Conclusions from benchmark studies are therefore limited to the ecosystems they mimic. Ideally, simulations are therefore based on genomes, which resemble particular metagenomic communities realistically.
    We developed Tamock to facilitate the realistic simulation of metagenomic reads according to a metagenomic community, based on real sequence data. Benchmarks samples can be created from all genomes and taxonomic domains present in NCBI RefSeq. Tamock automatically determines taxonomic profiles from shotgun sequence data, selects reference genomes accordingly and uses them to simulate metagenomic reads. We present an example use case for Tamock by assessing assembly and binning method performance for selected microbiomes.
    Tamock facilitates automated simulation of habitat-specific benchmark metagenomic data based on real sequence data and is implemented as a user-friendly command-line application, providing extensive additional information along with the simulated benchmark data. Resulting benchmarks enable an assessment of computational methods, workflows, and parameters specifically for a metagenomic habitat or ecosystem of a metagenomic study.
    Source code, documentation and install instructions are freely available at GitHub ( https://github.com/gerners/tamock ).

  • ITN-VIROINF: Understanding (Harmful) Virus-Host Interactions by Linking Virology and Bioinformatics.

    Goettsch W, Beerenwinkel N, Deng L, Dölken L, Dutilh BE, Erhard F, Kaderali L, von Kleist M, Marquet R, Matthijnssens J, McCallin S, McMahon D, Rattei T, Van Rij RP, Robertson DL, Schwemmle M, Stern-Ginossar N, Marz M
    2021 - Viruses, 5: in press

    Abstract: 

    Many recent studies highlight the fundamental importance of viruses. Besides their important role as human and animal pathogens, their beneficial, commensal or harmful functions are poorly understood. By developing and applying tailored bioinformatical tools in important virological models, the Marie Skłodowska-Curie Initiative International Training Network VIROINF will provide a better understanding of viruses and the interaction with their hosts. This will open the door to validate methods of improving viral growth, morphogenesis and development, as well as to control strategies against unwanted microorganisms. The key feature of VIROINF is its interdisciplinary nature, which brings together virologists and bioinformaticians to achieve common goals.

  • Combined hormonal contraceptives are associated with minor changes in composition and diversity in gut microbiota of healthy women.

    Mihajlovic J, Leutner M, Hausmann B, Kohl G, Schwarz J, Röver H, Stimakovits N, Wolf P, Maruszczak K, Bastian M, Kautzky-Willer A, Berry D
    2021 - Environ Microbiol, 6: 3037-3047

    Abstract: 

    Recent human and animal studies have found associations between gut microbiota composition and serum levels of sex hormones, indicating that they could be an important factor in shaping the microbiota. However, little is known about the effect of regular hormonal fluctuations over the menstrual cycle or CHC-related changes of hormone levels on gut microbiota structure, diversity and dynamics. The aim of this study was to investigate the effect of CHCs on human gut microbiota composition. The effect of CHC pill intake on gut microbiota composition was studied in a group of seven healthy pre-menopausal women using the CHC pill, compared to the control group of nine age-matched healthy women that have not used hormonal contraceptives in the 6 months prior to the start of the study. By analysing the gut microbiota composition in both groups during one menstrual cycle, we found that CHC usage is associated with a minor decrease in gut microbiota diversity and differences in the abundance of several bacterial taxa. These results call for further investigation of the mechanisms underlying hormonal and hormonal contraceptive-related changes of the gut microbiota and the potential implications of these changes for women's health.

  • In vitro interactions of Alternaria mycotoxins, an emerging class of food contaminants, with the gut microbiota: a bidirectional relationship.

    Crudo F, Aichinger G, Mihajlovic J, Varga E, Dellafiora L, Warth B, Dall'Asta C, Berry D, Marko D
    2021 - Arch Toxicol, in press

    Abstract: 

    The human gut microbiota plays an important role in the maintenance of human health. Factors able to modify its composition might predispose the host to the development of pathologies. Among the various xenobiotics introduced through the diet, Alternaria mycotoxins are speculated to represent a threat for human health. However, limited data are currently available about the bidirectional relation between gut microbiota and Alternaria mycotoxins. In the present work, we investigated the in vitro effects of different concentrations of a complex extract of Alternaria mycotoxins (CE; containing eleven mycotoxins; e.g. 0.153 µM alternariol and 2.3 µM altersetin, at the maximum CE concentration tested) on human gut bacterial strains, as well as the ability of the latter to metabolize or adsorb these compounds. Results from the minimum inhibitory concentration assay showed the scarce ability of CE to inhibit the growth of the tested strains. However, the growth kinetics of most of the strains were negatively affected by exposure to the various CE concentrations, mainly at the highest dose (50 µg/mL). The CE was also found to antagonize the formation of biofilms, already at concentrations of 0.5 µg/mL. LC-MS/MS data analysis of the mycotoxin concentrations found in bacterial pellets and supernatants after 24 h incubation showed the ability of bacterial strains to adsorb some Alternaria mycotoxins, especially the key toxins alternariol, alternariol monomethyl ether, and altersetin. The tendency of these mycotoxins to accumulate within bacterial pellets, especially in those of Gram-negative strains, was found to be directly related to their lipophilicity.

  • Sulfoquinovose is a select nutrient of prominent bacteria and a source of hydrogen sulfide in the human gut.

    Hanson BT, Kits KD, Löffler J, Burrichter AG, Fiedler A, Denger K, Frommeyer B, Herbold CW, Rattei T, Karcher N, Segata N, Schleheck D, Loy A
    2021 - ISME J, In press

    Abstract: 

    Responses of the microbiota to diet are highly personalized but mechanistically not well understood because many metabolic capabilities and interactions of human gut microorganisms are unknown. Here we show that sulfoquinovose (SQ), a sulfonated monosaccharide omnipresent in green vegetables, is a selective yet relevant substrate for few but ubiquitous bacteria in the human gut. In human feces and in defined co-culture, Eubacterium rectale and Bilophila wadsworthia used recently identified pathways to cooperatively catabolize SQ with 2,3-dihydroxypropane-1-sulfonate as a transient intermediate to hydrogen sulfide (HS), a key intestinal metabolite with disparate effects on host health. SQ-degradation capability is encoded in almost half of E. rectale genomes but otherwise sparsely distributed among microbial species in the human intestine. However, re-analysis of fecal metatranscriptome datasets of four human cohorts showed that SQ degradation (mostly from E. rectale and Faecalibacterium prausnitzii) and HS production (mostly from B. wadsworthia) pathways were expressed abundantly across various health states, demonstrating that these microbial functions are core attributes of the human gut. The discovery of green-diet-derived SQ as an exclusive microbial nutrient and an additional source of HS in the human gut highlights the role of individual dietary compounds and organosulfur metabolism on microbial activity and has implications for precision editing of the gut microbiota by dietary and prebiotic interventions.

  • Sulfoquinovose is a select nutrient of prominent bacteria and a source of hydrogen sulfide in the human gut.

    Hanson BT, Dimitri Kits K, Löffler J, Burrichter AG, Fiedler A, Denger K, Frommeyer B, Herbold CW, Rattei T, Karcher N, Segata N, Schleheck D, Loy A
    2021 - ISME J, in press

    Abstract: 

    Responses of the microbiota to diet are highly personalized but mechanistically not well understood because many metabolic capabilities and interactions of human gut microorganisms are unknown. Here we show that sulfoquinovose (SQ), a sulfonated monosaccharide omnipresent in green vegetables, is a selective yet relevant substrate for few but ubiquitous bacteria in the human gut. In human feces and in defined co-culture, Eubacterium rectale and Bilophila wadsworthia used recently identified pathways to cooperatively catabolize SQ with 2,3-dihydroxypropane-1-sulfonate as a transient intermediate to hydrogen sulfide (HS), a key intestinal metabolite with disparate effects on host health. SQ-degradation capability is encoded in almost half of E. rectale genomes but otherwise sparsely distributed among microbial species in the human intestine. However, re-analysis of fecal metatranscriptome datasets of four human cohorts showed that SQ degradation (mostly from E. rectale and Faecalibacterium prausnitzii) and HS production (mostly from B. wadsworthia) pathways were expressed abundantly across various health states, demonstrating that these microbial functions are core attributes of the human gut. The discovery of green-diet-derived SQ as an exclusive microbial nutrient and an additional source of HS in the human gut highlights the role of individual dietary compounds and organosulfur metabolism on microbial activity and has implications for precision editing of the gut microbiota by dietary and prebiotic interventions.

  • Regulation of the Mitochondrion-Fatty Acid Axis for the Metabolic Reprogramming of Chlamydia trachomatis during Treatment with β-Lactam Antimicrobials.

    Shima K, Kaufhold I, Eder T, Käding N, Schmidt N, Ogunsulire IM, Deenen R, Köhrer K, Friedrich D, Isay SE, Grebien F, Klinger M, Richer BC, Günther UL, Deepe GS, Rattei T, Rupp J
    2021 - mBio, 2: in press

    Abstract: 

    Infection with the obligate intracellular bacterium is the most common bacterial sexually transmitted disease worldwide. Since no vaccine is available to date, antimicrobial therapy is the only alternative in infection. However, changes in chlamydial replicative activity and the occurrence of chlamydial persistence caused by diverse stimuli have been proven to impair treatment effectiveness. Here, we report the mechanism for regulating host signaling processes and mitochondrial function, which can be used for chlamydial metabolic reprogramming during treatment with β-lactam antimicrobials. Activation of signal transducer and activator of transcription 3 (STAT3) is a well-known host response in various bacterial and viral infections. In infection, inactivation of STAT3 by host protein tyrosine phosphatases increased mitochondrial respiration in both the absence and presence of β-lactam antimicrobials. However, during treatment with β-lactam antimicrobials, increased the production of citrate as well as the activity of host ATP-citrate lyase involved in fatty acid synthesis. Concomitantly, chlamydial metabolism switched from the tricarboxylic acid cycle to fatty acid synthesis. This metabolic switch was a unique response in treatment with β-lactam antimicrobials and was not observed in gamma interferon (IFN-γ)-induced persistent infection. Inhibition of fatty acid synthesis was able to attenuate β-lactam-induced chlamydial persistence. Our findings highlight the importance of the mitochondrion-fatty acid interplay for the metabolic reprogramming of during treatment with β-lactam antimicrobials. The mitochondrion generates most of the ATP in eukaryotic cells, and its activity is used for controlling the intracellular growth of Furthermore, mitochondrial activity is tightly connected to host fatty acid synthesis that is indispensable for chlamydial membrane biogenesis. Phospholipids, which are composed of fatty acids, are the central components of the bacterial membrane and play a crucial role in the protection against antimicrobials. Chlamydial persistence that is induced by various stimuli is clinically relevant. While one of the well-recognized inducers, β-lactam antimicrobials, has been used to characterize chlamydial persistence, little is known about the role of mitochondria in persistent infection. Here, we demonstrate how undergoes metabolic reprogramming to switch from the tricarboxylic acid cycle to fatty acid synthesis with promoted host mitochondrial activity in response to treatment with β-lactam antimicrobials.

  • Mosses reduce soil nitrogen availability in subarctic birch fores via effects oon soil thermal regime and sequestration of deposited nitrogen

    Koranda M, Michelsen A
    2021 - Journal of Ecology, 109: 1424-1438

    Abstract: 

    In high-latitude ecosystems bryophytes are important drivers of ecosystem functions. Alterations in abundance of mosses due to global change may thus strongly influence carbon (C) and nitrogen (N) cycling and hence cause feedback on climate. The effects of mosses on soil microbial activity are, however, still poorly understood. Our study aims at elucidating how and by which mechanisms bryophytes influence microbial decomposition processes of soil organic matter and thus soil nutrient availability.We present results from a field experiment in a subarctic birch forest in northern Sweden, where we partly removed the moss cover and replaced it with an artificial soil cover for simulating moss effects on soil temperature and moisture. We combined this with a fertilization experiment with 15N-labelled N for analysing the effects of moss N sequestration on soil processes.Our results demonstrate the capacity of mosses to reduce soil N availability and retard N cycling. The comparison with artificial soil cover plots suggests that the effect of mosses on N cycling is linked to the thermal insulation capacity of mosses causing low average soil temperature in summer and strongly reduced soil temperature fluctuations, the latter also leading to a decreased frequency of freeze-thaw events in autumn and spring. Our results also showed, however, that the negative temperature effect of mosses on soil microbial activity was in part compensated by stimulatory effects of the moss layer, possibly linked to leaching of labile substrates from the moss. Furthermore, our results revealed that bryophytes efficiently sequester added N from wet deposition and thus prevent effects of increased atmospheric N deposition on soil N availability and soil processes. Synthesis. Our study emphasizes the important role of mosses in carbon and nutrient cycling in high-latitude ecosystems and the potential strong impacts of reductions in moss abundance on microbial decomposition processes and nutrient availability in subarctic and boreal forests.

  • Learning From Limited Data: Towards Best Practice Techniques for Antimicrobial Resistance Prediction From Whole Genome Sequencing Data.

    Lüftinger L, Májek P, Beisken S, Rattei T, Posch AE
    2021 - Front Cell Infect Microbiol, 610348

    Abstract: 

    Antimicrobial resistance prediction from whole genome sequencing data (WGS) is an emerging application of machine learning, promising to improve antimicrobial resistance surveillance and outbreak monitoring. Despite significant reductions in sequencing cost, the availability and sampling diversity of WGS data with matched antimicrobial susceptibility testing (AST) profiles required for training of WGS-AST prediction models remains limited. Best practice machine learning techniques are required to ensure trained models generalize to independent data for optimal predictive performance. Limited data restricts the choice of machine learning training and evaluation methods and can result in overestimation of model performance. We demonstrate that the widely used random k-fold cross-validation method is ill-suited for application to small bacterial genomics datasets and offer an alternative cross-validation method based on genomic distance. We benchmarked three machine learning architectures previously applied to the WGS-AST problem on a set of 8,704 genome assemblies from five clinically relevant pathogens across 77 species-compound combinations collated from public databases. We show that individual models can be effectively ensembled to improve model performance. By combining models stacked generalization with cross-validation, a model ensembling technique suitable for small datasets, we improved average sensitivity and specificity of individual models by 1.77% and 3.20%, respectively. Furthermore, stacked models exhibited improved robustness and were thus less prone to outlier performance drops than individual component models. In this study, we highlight best practice techniques for antimicrobial resistance prediction from WGS data and introduce the combination of genome distance aware cross-validation and stacked generalization for robust and accurate WGS-AST.

  • Isolate-Based Surveillance of Bordetella pertussis, Austria, 2018-2020.

    Cabal A, Schmid D, Hell M, Chakeri A, Mustafa-Korninger E, Wojna A, Stöger A, Möst J, Leitner E, Hyden P, Rattei T, Habington A, Wiedermann U, Allerberger F, Ruppitsch W
    2021 - Emerg Infect Dis, 3: 862-871

    Abstract: 

    Pertussis is a vaccine-preventable disease, and its recent resurgence might be attributable to the emergence of strains that differ genetically from the vaccine strain. We describe a novel pertussis isolate-based surveillance system and a core genome multilocus sequence typing scheme to assess Bordetella pertussis genetic variability and investigate the increased incidence of pertussis in Austria. During 2018-2020, we obtained 123 B. pertussis isolates and typed them with the new scheme (2,983 targets and preliminary cluster threshold of <6 alleles). B. pertussis isolates in Austria differed genetically from the vaccine strain, both in their core genomes and in their vaccine antigen genes; 31.7% of the isolates were pertactin-deficient. We detected 8 clusters, 1 of them with pertactin-deficient isolates and possibly part of a local outbreak. National expansion of the isolate-based surveillance system is needed to implement pertussis-control strategies.

  • Conjugative plasmids interact with insertion sequences to shape the horizontal transfer of antimicrobial resistance genes.

    Che Y, Yang Y, Xu X, Břinda K, Polz MF, Hanage WP, Zhang T
    2021 - Proc Natl Acad Sci U S A, 6: in press

    Abstract: 

    It is well established that plasmids play an important role in the dissemination of antimicrobial resistance (AMR) genes; however, little is known about the role of the underlying interactions between different plasmid categories and other mobile genetic elements (MGEs) in shaping the promiscuous spread of AMR genes. Here, we developed a tool designed for plasmid classification, AMR gene annotation, and plasmid visualization and found that most plasmid-borne AMR genes, including those localized on class 1 integrons, are enriched in conjugative plasmids. Notably, we report the discovery and characterization of a massive insertion sequence (IS)-associated AMR gene transfer network (245 combinations covering 59 AMR gene subtypes and 53 ISs) linking conjugative plasmids and phylogenetically distant pathogens, suggesting a general evolutionary mechanism for the horizontal transfer of AMR genes mediated by the interaction between conjugative plasmids and ISs. Moreover, our experimental results confirmed the importance of the observed interactions in aiding the horizontal transfer and expanding the genetic range of AMR genes within complex microbial communities.

  • Survival strategies of ammonia-oxidizing archaea (AOA) in a full-scale WWTP treating mixed landfill leachate containing copper ions and operating at low-intensity of aeration.

    Yang Y, Herbold CW, Jung MY, Qin W, Cai M, Du H, Lin JG, Li X, Li M, Gu JD
    2021 - Water Res, 116798

    Abstract: 

    Recent studies indicate that ammonia-oxidizing archaea (AOA) may play an important role in nitrogen removal by wastewater treatment plants (WWTPs). However, our knowledge of the mechanisms employed by AOA for growth and survival in full-scale WWTPs is still limited. Here, metagenomic and metatranscriptomic analyses combined with a laboratory cultivation experiment revealed that three active AOAs (WS9, WS192, and WS208) belonging to family Nitrososphaeraceae were active in the deep oxidation ditch (DOD) of a full-scale WWTP treating landfill leachate, which is configured with three continuous aerobic-anoxic (OA) modules with low-intensity aeration (≤ 1.5 mg/L). AOA coexisted with AOB and complete ammonia oxidizers (Comammox), while the ammonia-oxidizing microbial (AOM) community was unexpectedly dominated by the novel AOA strain WS9. The low aeration, long retention time, and relatively high inputs of ammonium and copper might be responsible for the survival of AOA over AOB and Comammox, while the dominance of WS9, specifically may be enhanced by substrate preference and uniquely encoded retention strategies. The urease-negative WS9 is specifically adapted for ammonia acquisition as evidenced by the high expression of an ammonium transporter, whereas two metabolically versatile urease-positive AOA strains (WS192 and WS208) can likely supplement ammonia needs with urea. This study provides important information for the survival and application of the eutrophic Nitrososphaeraceae AOA and advances our understanding of archaea-dominated ammonia oxidation in a full-scale wastewater treatment system.

  • Distribution of Mixotrophy and Desiccation Survival Mechanisms across Microbial Genomes in an Arid Biological Soil Crust Community.

    Meier DV, Imminger S, Gillor O, Woebken D
    2021 - mSystems, 1: in press

    Abstract: 

    Desert surface soils devoid of plant cover are populated by a variety of microorganisms, many with yet unresolved physiologies and lifestyles. Nevertheless, a common feature vital for these microorganisms inhabiting arid soils is their ability to survive long drought periods and reactivate rapidly in rare incidents of rain. Chemolithotrophic processes such as oxidation of atmospheric hydrogen and carbon monoxide are suggested to be a widespread energy source to support dormancy and resuscitation in desert soil microorganisms. Here, we assessed the distribution of chemolithotrophic, phototrophic, and desiccation-related metabolic potential among microbial populations in arid biological soil crusts (BSCs) from the Negev Desert, Israel, via population-resolved metagenomic analysis. While the potential to utilize light and atmospheric hydrogen as additional energy sources was widespread, carbon monoxide oxidation was less common than expected. The ability to utilize continuously available energy sources might decrease the dependency of mixotrophic populations on organic storage compounds and carbon provided by the BSC-founding cyanobacteria. Several populations from five different phyla besides the cyanobacteria encoded CO fixation potential, indicating further potential independence from photoautotrophs. However, we also found population genomes with a strictly heterotrophic genetic repertoire. The highly abundant () genomes showed particular specialization for this extreme habitat, different from their closest cultured relatives. Besides the ability to use light and hydrogen as energy sources, they encoded extensive O stress protection and unique DNA repair potential. The uncovered differences in metabolic potential between individual, co-occurring microbial populations enable predictions of their ecological niches and generation of hypotheses on the dynamics and interactions among them. This study represents a comprehensive community-wide genome-centered metagenome analysis of biological soil crust (BSC) communities in arid environments, providing insights into the distribution of genes encoding different energy generation mechanisms, as well as survival strategies, among populations in an arid soil ecosystem. It reveals the metabolic potential of several uncultured and previously unsequenced microbial genera, families, and orders, as well as differences in the metabolic potential between the most abundant BSC populations and their cultured relatives, highlighting once more the danger of inferring function on the basis of taxonomy. Assigning functional potential to individual populations allows for the generation of hypotheses on trophic interactions and activity patterns in arid soil microbial communities and represents the basis for future resuscitation and activity studies of the system, e.g., involving metatranscriptomics.

  • Coastal Bacterial Community Response to Glacier Melting in the Western Antarctic Peninsula.

    Alcamán-Arias ME, Fuentes-Alburquenque S, Vergara-Barros P, Cifuentes-Anticevic J, Verdugo J, Polz M, Farías L, Pedrós-Alió C, Díez B
    2021 - Microorganisms, 1: in press

    Abstract: 

    Current warming in the Western Antarctic Peninsula (WAP) has multiple effects on the marine ecosystem, modifying the trophic web and the nutrient regime. In this study, the effect of decreased surface salinity on the marine microbial community as a consequence of freshening from nearby glaciers was investigated in Chile Bay, Greenwich Island, WAP. In the summer of 2016, samples were collected from glacier ice and transects along the bay for 16S rRNA gene sequencing, while in situ dilution experiments were conducted and analyzed using 16S rRNA gene sequencing and metatranscriptomic analysis. The results reveal that certain common seawater genera, such as , and HTCC2207, responded positively to decreased salinity in both the bay transect and experiments. The relative abundance of these bacteria slightly decreased, but their functional activity was maintained and increased the over time in the dilution experiments. However, while ice bacteria, such as and , tolerated the increased salinity after mixing with seawater, their gene expression decreased considerably. We suggest that these bacterial taxa could be defined as sentinels of freshening events in the Antarctic coastal system. Furthermore, these results suggest that a significant portion of the microbial community is resilient and can adapt to disturbances, such as freshening due to the warming effect of climate change in Antarctica.

  • Empirical support for the biogeochemical niche hypothesis in forest trees

    Sardans J, Vallicrosa H, Zuccarini P, Farré-Armengol G, Fernández-Martínez M, Guille P, Gargallo-Garriga A, Ciais P, Janssens IA, Obersteiner M, Richter A, Peñuelas J
    2021 - Nature Ecology & Evolution, 5: 184-194

    Abstract: 

    The possibility of using the elemental compositions of species as a tool to identify species/genotype niche remains to be tested at a global scale. We investigated relationships between the foliar elemental compositions (elementomes) of trees at a global scale with phylogeny, climate, N deposition and soil traits. We analysed foliar N, P, K, Ca, Mg and S concentrations in 23,962 trees of 227 species. Shared ancestry explained 60–94% of the total variance in foliar nutrient concentrations and ratios whereas current climate, atmospheric N deposition and soil type together explained 1–7%, consistent with the biogeochemical niche hypothesis which predicts that each species will have a specific need for and use of each bio-element. The remaining variance was explained by the avoidance of nutritional competition with other species and natural variability within species. The biogeochemical niche hypothesis is thus able to quantify species-specific tree niches and their shifts in response to environmental changes.

  • Transkingdom interactions between Lactobacilli and hepatic mitochondria attenuate western diet-induced diabetes.

    Rodrigues RR, Gurung M, Li Z, García-Jaramillo M, Greer R, Gaulke C, Bauchinger F, You H, Pederson JW, Vasquez-Perez S, White KD, Frink B, Philmus B, Jump DB, Trinchieri G, Berry D, Sharpton TJ, Dzutsev A, Morgun A, Shulzhenko N
    2021 - Nat Commun, 1: 101

    Abstract: 

    Western diet (WD) is one of the major culprits of metabolic disease including type 2 diabetes (T2D) with gut microbiota playing an important role in modulating effects of the diet. Herein, we use a data-driven approach (Transkingdom Network analysis) to model host-microbiome interactions under WD to infer which members of microbiota contribute to the altered host metabolism. Interrogation of this network pointed to taxa with potential beneficial or harmful effects on host's metabolism. We then validate the functional role of the predicted bacteria in regulating metabolism and show that they act via different host pathways. Our gene expression and electron microscopy studies show that two species from Lactobacillus genus act upon mitochondria in the liver leading to the improvement of lipid metabolism. Metabolomics analyses revealed that reduced glutathione may mediate these effects. Our study identifies potential probiotic strains for T2D and provides important insights into mechanisms of their action.

  • Dahlia variabilis cultivar 'Seattle' as a model plant for anthochlor biosynthesis.

    Walliser B, Lucaciu CR, Molitor C, Marinovic S, Nitarska DA, Aktaş D, Rattei T, Kampatsikas I, Stich K, Haselmair-Gosch C, Halbwirth H
    2021 - Plant Physiol Biochem, 193-201

    Abstract: 

    We investigated the bi-colored dahlia cultivar 'Seattle', which exhibits bright yellow petals with white tips, for its potential use as a model system for studies of the anthochlor biosynthesis. The yellow base contained high amounts of the 6'-deoxychalcones and the structurally related 4-deoxyaurones, as well as flavones. In contrast, only traces of anthochlors and flavones were detected in the white tips. No anthocyanins, flavonols, flavanones or dihydroflavonols were found in the petals. Gene expression studies indicated that the absence of anthocyanins in the petals is caused by a lack of flavanone 3-hydroxylase (FHT) expression, which is accompanied by a lack of expression of the bHLH transcription factor IVS. Expression of other genes involved in anthocyanidin biosynthesis such as dihydroflavonol 4-reductase (DFR) and anthocyanidin synthase (ANS) was not affected. The yellow and white petal parts showed significant differences in the expression of chalcone synthase 2 (CHS2), which is sufficient to explain the absence of yellow pigments in the white tips. Transcriptomes of both petal parts were de novo assembled and three candidate genes for chalcone reductase (CHR) were identified. None of them showed a significantly higher expression in the yellow base compared to the white tips. In summary, it was shown that the bicolouration is most likely caused by a bottleneck in chalcone formation in the white tip. The relative prevalence of flavones compared to the anthochlors in the white tips could be an indication for the presence of a so far unknown differentially expressed CHR.

  • Interaction with Ribosomal Proteins Accompanies Stress Induction of the Anticancer Metallodrug BOLD-100/KP1339 in the Endoplasmic Reticulum.

    Neuditschko B, Legin AA, Baier D, Schintlmeister A, Reipert S, Wagner M, Keppler BK, Berger W, Meier-Menches SM, Gerner C
    2021 - Angew Chem Int Ed Engl, 60: 5063-5068

    Abstract: 

    The ruthenium-based anticancer agent BOLD-100/KP1339 has shown promising results in several in vitro and in vivo tumour models as well as in early clinical trials. However, its mode of action remains to be fully elucidated. Recent evidence identified stress induction in the endoplasmic reticulum (ER) and concomitant down-modulation of HSPA5 (GRP78) as key drug effects. By exploiting the naturally formed adduct between BOLD-100 and human serum albumin as an immobilization strategy, we were able to perform target-profiling experiments that revealed the ribosomal proteins RPL10, RPL24, and the transcription factor GTF2I as potential interactors of this ruthenium(III) anticancer agent. Integrating these findings with proteomic profiling and transcriptomic experiments supported ribosomal disturbance and concomitant induction of ER stress. The formation of polyribosomes and ER swelling of treated cancer cells revealed by TEM validated this finding. Thus, the direct interaction of BOLD-100 with ribosomal proteins seems to accompany ER stress-induction and modulation of GRP78 in cancer cells.

  • Polyphenol Exposure, Metabolism, and Analysis: A Global Exposomics Perspective.

    Oesterle I, Braun D, Berry D, Wisgrill L, Rompel A, Warth B
    2021 - Annu Rev Food Sci Technol, 461-484

    Abstract: 

    Polyphenols are generally known for their health benefits and estimating actual exposure levels in health-related studies can be improved by human biomonitoring. Here, the application of newly available exposomic and metabolomic technology, notably high-resolution mass spectrometry, in the context of polyphenols and their biotransformation products, is reviewed. Comprehensive workflows for investigating these important bioactives in biological fluids or microbiome-related experiments are scarce. Consequently, this new era of nontargeted analysis and omic-scale exposure assessment offers a unique chance for better assessing exposure to, as well as metabolism of, polyphenols. In clinical and nutritional trials, polyphenols can be investigated simultaneously with the plethora of other chemicals to which we are exposed, i.e., the exposome, which may interact abundantly and modulate bioactivity. This research direction aims at ultimately eluting into atrue systems biology/toxicology evaluation of health effects associated with polyphenol exposure, especially during early life, to unravel their potential for preventing chronic diseases.

  • Rapid Responses of root traits and productivity to phosphorus and cation additions in a tropical lowland forest in Amazonia

    Lugli LF, Rosa JS, Andersen KM, Di Ponzio R, Almeida RV, Pires M, Cordeiro AL, Cunha HFV, Martins NP, Assis RL, Moraes ACM, Souza ST, Arag˜ao LEOC, Camargo JL, Fuchslueger L, Schaap KJ, Valverde-Barrantes OJ, Meir P, Quesada CA, Mercado LM, Hartley IP
    2021 - New Phytologist, 230: 116-128

    Abstract: 

    Soil nutrient availability can strongly affect root traits. In tropical forests, phosphorus (P) is often considered the main limiting nutrient for plants. However, support for the P paradigm is limited, and N and cations might also control tropical forests functioning. We used a large-scale experiment to determine how the factorial addition of nitrogen (N), P and cations affected root productivity and traits related to nutrient acquisition strategies (morphological traits, phosphatase activity, arbuscular mycorrhizal colonisation and nutrient contents) in a primary rainforest growing on low-fertility soils in Central Amazonia after 1 yr of fertilisation. Multiple root traits and productivity were affected. Phosphorus additions increased annual root productivity and root diameter, but decreased root phosphatase activity. Cation additions increased root productivity at certain times of year, also increasing root diameter and mycorrhizal colonisation. P and cation additions increased their element concentrations in root tissues. No responses were detected with N addition. Here we showed that rock-derived nutrients determined root functioning in low-fertility Amazonian soils, demonstrating not only the hypothesised importance of P, but also highlighting the role of cations. The changes in fine root traits and productivity indicated that even slow-growing tropical rainforests can respond rapidly to changes in resource availability.

  • Optofluidic Raman-activated cell sorting for targeted genome retrieval or cultivation of microbial cells with specific functions.

    Lee KS, Pereira FC, Palatinszky M, Behrendt L, Alcolombri U, Berry D, Wagner M, Stocker R
    2021 - Nat Protoc, 2: 634-676

    Abstract: 

    Stable isotope labeling of microbial taxa of interest and their sorting provide an efficient and direct way to answer the question "who does what?" in complex microbial communities when coupled with fluorescence in situ hybridization or downstream 'omics' analyses. We have developed a platform for automated Raman-based sorting in which optical tweezers and microfluidics are used to sort individual cells of interest from microbial communities on the basis of their Raman spectra. This sorting of cells and their downstream DNA analysis, such as by mini-metagenomics or single-cell genomics, or cultivation permits a direct link to be made between the metabolic roles and the genomes of microbial cells within complex microbial communities, as well as targeted isolation of novel microbes with a specific physiology of interest. We describe a protocol from sample preparation through Raman-activated live cell sorting. Subsequent cultivation of sorted cells is described, whereas downstream DNA analysis involves well-established approaches with abundant methods available in the literature. Compared with manual sorting, this technique provides a substantially higher throughput (up to 500 cells per h). Furthermore, the platform has very high sorting accuracy (98.3 ± 1.7%) and is fully automated, thus avoiding user biases that might accompany manual sorting. We anticipate that this protocol will empower in particular environmental and host-associated microbiome research with a versatile tool to elucidate the metabolic contributions of microbial taxa within their complex communities. After a 1-d preparation of cells, sorting takes on the order of 4 h, depending on the number of cells required.

  • Comparable canopy and soil free-living nitrogen fixation rates in a lowland tropical forest

    Van Langenhove L, Depaepe T, Verryckt LT, Fuchslueger L, Leroy JDC, Moorthy SMK, Gargallo-Garriga A, Ellwood MDF, Verbeeck H, Van Der Straeten D, Peñuelas J, Janssens IA
    2021 - Science of The Total Environment, 754: Article 142202

    Abstract: 

    Biological nitrogen fixation (BNF) is a fundamental part of nitrogen cycling in tropical forests, yet little is known about the contribution made by free-living nitrogen fixers inhabiting the often-extensive forest canopy. We used the acetylene reduction assay, calibrated with 15N2, to measure free-living BNF on forest canopy leaves, vascular epiphytes, bryophytes and canopy soil, as well as on the forest floor in leaf litter and soil. We used a combination of calculated and published component densities to upscale free-living BNF rates to the forest level. We found that bryophytes and leaves situated in the canopy in particular displayed high mass-based rates of free-living BNF. Additionally, we calculated that nearly 2 kg of nitrogen enters the forest ecosystem through free-living BNF every year, 40% of which was fixed by the various canopy components. Our results reveal that in the studied tropical lowland forest a large part of the nitrogen input through free-living BNF stems from the canopy, but also that the total nitrogen inputs by free-living BNF are lower than previously thought and comparable to the inputs of reactive nitrogen by atmospheric deposition.

  • Anaerobic bacterial degradation of protein and lipid macromolecules in subarctic marine sediment

    Pelikan C, Wasmund K, Glombitza C, Hausmann H, Herbold CW, Flieder M, Loy A
    2021 - ISME J, 15: 833-847

    Abstract: 

    Microorganisms in marine sediments play major roles in marine biogeochemical cycles by mineralizing substantial quantities of organic matter from decaying cells. Proteins and lipids are abundant components of necromass, yet the taxonomic identities of microorganisms that actively degrade them remain poorly resolved. Here, we revealed identities, trophic interactions and genomic features of bacteria that degraded 13C-labelled proteins and lipids in cold anoxic microcosms containing sulfidic subarctic marine sediment. Supplemented proteins and lipids were rapidly fermented to various volatile fatty acids within five days. DNA-stable isotope probing (SIP) suggested Psychrilyobacter atlanticus was an important primary degrader of proteins, and Psychromonas members were important primary degraders of both proteins and lipids. Closely related Psychromonas populations, as represented by distinct 16S rRNA gene variants, differentially utilized either proteins or lipids. DNA-SIP also showed 13C-labeling of various Deltaproteobacteria within ten days, indicating trophic transfer of carbon to putative sulfate-reducers. Metagenome-assembled genomes revealed the primary hydrolyzers encoded secreted peptidases or lipases, and enzymes for catabolism of protein or lipid degradation products. Psychromonas species are prevalent in diverse marine sediments, suggesting they are important players in organic carbon processing in situ. Together, this study provides new insights into the identities, functions and genomes of bacteria that actively degrade abundant necromass macromolecules in the seafloor.

  • Coevolving plasmids drive gene flow and genome plasticity in host-associated intracellular bacteria

    Köstlbacher S, Collingro A, Halter T, Domman D, Horn M
    2021 - Curr Biol, 2: 346-357.e3

    Abstract: 

    Plasmids are important in microbial evolution and adaptation to new environments. Yet, carrying a plasmid can be costly, and long-term association of plasmids with their hosts is poorly understood. Here, we provide evidence that the Chlamydiae, a phylum of strictly host-associated intracellular bacteria, have coevolved with their plasmids since their last common ancestor. Current chlamydial plasmids are amalgamations of at least one ancestral plasmid and a bacteriophage. We show that the majority of plasmid genes are also found on chromosomes of extant chlamydiae. The most conserved plasmid gene families are predominantly vertically inherited, while accessory plasmid gene families show significantly increased mobility. We reconstructed the evolutionary history of plasmid gene content of an entire bacterial phylum over a period of around one billion years. Frequent horizontal gene transfer and chromosomal integration events illustrate the pronounced impact of coevolution with these extrachromosomal elements on bacterial genome dynamics in host-dependent microbes.

  • Genomic and kinetic analysis of novel Nitrospinae enriched by cell sorting.

    Mueller AJ, Jung MY, Strachan CR, Herbold CW, Kirkegaard RH, Wagner M, Daims H
    2021 - ISME J, 15: 732–745

    Abstract: 

    Chemolithoautotrophic nitrite-oxidizing bacteria (NOB) are key players in global nitrogen and carbon cycling. Members of the phylum Nitrospinae are the most abundant, known NOB in the oceans. To date, only two closely affiliated Nitrospinae species have been isolated, which are only distantly related to the environmentally abundant uncultured Nitrospinae clades. Here, we applied live cell sorting, activity screening, and subcultivation on marine nitrite-oxidizing enrichments to obtain novel marine Nitrospinae. Two binary cultures were obtained, each containing one Nitrospinae strain and one alphaproteobacterial heterotroph. The Nitrospinae strains represent two new genera, and one strain is more closely related to environmentally abundant Nitrospinae than previously cultured NOB. With an apparent half-saturation constant of 8.7 ± 2.5 µM, this strain has the highest affinity for nitrite among characterized marine NOB, while the other strain (16.2 ± 1.6 µM) and Nitrospina gracilis (20.1 ± 2.1 µM) displayed slightly lower nitrite affinities. The new strains and N. gracilis share core metabolic pathways for nitrite oxidation and CO fixation but differ remarkably in their genomic repertoires of terminal oxidases, use of organic N sources, alternative energy metabolisms, osmotic stress and phage defense. The new strains, tentatively named "Candidatus Nitrohelix vancouverensis" and "Candidatus Nitronauta litoralis", shed light on the niche differentiation and potential ecological roles of Nitrospinae.

  • Flow-through stable isotope probing (Flow-SIP) minimizes cross-feeding in complex microbial communities.

    Mooshammer M, Kitzinger K, Schintlmeister A, Ahmerkamp S, Nielsen JL, Nielsen PH, Wagner M
    2021 - ISME J, 1: 348-353

    Abstract: 

    Stable isotope probing (SIP) is a key tool for identifying the microorganisms catalyzing the turnover of specific substrates in the environment and to quantify their relative contributions to biogeochemical processes. However, SIP-based studies are subject to the uncertainties posed by cross-feeding, where microorganisms release isotopically labeled products, which are then used by other microorganisms, instead of incorporating the added tracer directly. Here, we introduce a SIP approach that has the potential to strongly reduce cross-feeding in complex microbial communities. In this approach, the microbial cells are exposed on a membrane filter to a continuous flow of medium containing isotopically labeled substrate. Thereby, metabolites and degradation products are constantly removed, preventing consumption of these secondary substrates. A nanoSIMS-based proof-of-concept experiment using nitrifiers in activated sludge and C-bicarbonate as an activity tracer showed that Flow-SIP significantly reduces cross-feeding and thus allows distinguishing primary consumers from other members of microbial food webs.

Book chapters and other publications

3 Publications found
  • Natürliche Schwebstoffe in Flüssen: Zusammensetzung, Schlüsselkomponenten und Dynamiken

    Helene Walch, Frank von der Kammer, Thilo Hofmann
    2021 - Vom Wasser - das Journal, 51-53
  • Nanoparticle inventory in a sediment core from the Iron Gate I reservoir

    Jan Schüürman, Malfatti SE, Frank von der Kammer, Thilo Hofmann
    2021 - JDS4 Scientific Report, 501-510

    Abstract: 

    River sediments are a sink for natural and anthropogenic nanoparticles. Given their risk to harm ecosystems and humans the latter are among contaminants of emerging concern. Here we present multi-element single-particle data of a Danube sediment core, aiming to identify anthropogenic nanoparticles and elucidate their occurrence at different sediment depths. A fly ash dump near Kostolac, Serbia, on the right bank of the Danube River is a likely point source of anthropogenic fly ash particles. Kostolac fly ash particles are enriched in elements such as Cu, Ni, and V. The signatures of these elements within nanoparticles of the sediment core reveal four potential events of fly ash release into the Danube.

  • A genomic catalog of Earth's microbiomes

    Nayfach S, Roux S, Seshadri R, Udwary D, Varghese N, Schulz F, Wu D, Páez-Espino D, Chen IM, Huntemann M, Palaniappan K, Ladau J, Mukherjee S, Reddy TBK, Nielsen T, Kirton E, Faria JP, Edirisinghe JN, Henry CS, Jungbluth SP, Chivian D, Dehal P, Wood-Charlson EM, Arkin AP, Tringe SG, Visel A, IMG/M Data Consortium, Woyke T, Mouncey NJ, Ivanova NN, Kyrpides NC, Eloe-Fadrosh EA
    2021 - Nat Biotechnol, 39: 499-509

    Abstract: 

    The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering all of Earth's continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. The catalog expands the known phylogenetic diversity of bacteria and archaea by 44% and is broadly available for streamlined comparative analyses, interactive exploration, metabolic modeling and bulk download. We demonstrate the utility of this collection for understanding secondary-metabolite biosynthetic potential and for resolving thousands of new host linkages to uncultivated viruses. This resource underscores the value of genome-centric approaches for revealing genomic properties of uncultivated microorganisms that affect ecosystem processes.

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