Metamenu

Publications

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Publications in peer reviewed journals

70 Publications found
  • Negative priming of soil organic matter following long-term in situ warming of sub-arctic soils

    Verbrigghe N, Meeran K, Bahn M, Fuchslueger L, Janssens IA, Richter A, Sigurdsson BD, Soong JL, Vicca A
    2022 - Geoderma, 410: Article 115652

    Abstract: 

    Priming is the change of microbial soil organic matter (SOM) decomposition induced by a labile carbon (C) source. It is recognised as an important mechanism influencing soil C dynamics and C storage in terrestrial ecosystems. Microbial nitrogen (N) mining in SOM and preferential substrate utilisation, i.e., a shift in microbial carbon use from SOM to more labile energy sources, are possible, counteracting, mechanisms driving the priming effect. Climate warming and increased N availability might affect these mechanisms, and thus determine the direction and magnitude of the priming effect. Hence, these abiotic factors can indirectly affect soil C stocks, which makes their understanding crucial for predicting the soil C feedback in a warming world. We conducted a short-term incubation experiment (6 days) with soils from a subarctic grassland that had been subjected to long-term geothermal warming (>55 years) by 2-4°C above unwarmed soil. Soil samples were amended with 13C-labelled glucose and 15N-labelled NH4NO3. We found a significantly negative relationship between in situ warming and cumulative primed C, with negative priming in the warmed soils. The negative priming suggests that preferential substrate utilisation was a key mechanism in our experiment. Our results indicate that changes in SOM characteristics associated with the in situ warming gradient can play a major role in determining the rate and direction of the priming effect. Additionally, we found that neither microbial N limitation nor N addition affected the priming effect, providing evidence that in our experiment, N mining did not lead to positive priming.

  • Human follicular mites: Ectoparasites becoming symbionts

    Smith G, Manzano-Marín A, Reyes-Prieto M, Ribeiro Antunes CS, Ashworth V, Goselle ON, Jan AAA, Moya A, Latorre A, Perotti MA, Braig HR
    2022 - Mol Biol Evol, 39: msac125

    Abstract: 

    Most humans carry mites in the hair follicles of their skin for their entire lives. Follicular mites are the only metazoans that continuously live on humans. We propose that Demodex folliculorum (Acari) represents a transitional stage from a host-injuring obligate parasite to an obligate symbiont. Here, we describe the profound impact of this transition on the genome and physiology of the mite. Genome sequencing revealed that the permanent host association of D. folliculorum led to an extensive genome reduction through relaxed selection and genetic drift, resulting in the smallest number of protein-coding genes yet identified among panarthropods. Confocal microscopy revealed that this gene loss coincided with an extreme reduction in the number of cells. Single uninucleate muscle cells are sufficient to operate each of the three segments that form each walking leg. While it has been assumed that the reduction of the cell number in parasites starts early in development, we identified a greater total number of cells in the last developmental stage (nymph) than in the terminal adult stage, suggesting that reduction starts at the adult or ultimate stage of development. This is the first evolutionary step in an arthropod species adopting a reductive, parasitic, or endosymbiotic lifestyle. Somatic nuclei show under-replication at the diploid stage. Novel eye structures or photoreceptors as well as a unique human host melatonin-guided day/night rhythm are proposed for the first time. The loss of DNA repair genes coupled with extreme endogamy might have set this mite species on an evolutionary dead-end trajectory.

  • Omics research on abalone (Haliotis spp.): Current state and perspectives

    Nguyen TV, Alfaro AC, Mundy C, Petersen JM, Ragg NLC
    2022 - Aquaculture, 547: 737438

    Abstract: 

    The steady increase in abalone aquaculture production throughout the world has attracted growing interest in the application of new technologies, such as omics approaches for abalone research. Many omics techniques, such as genomics, transcriptomics, proteomics, and metabolomics are becoming established in abalone research and are beginning to reveal key molecules and pathways underlying many biological processes, and to identify associated candidate biomarkers of biological or environmental processes. In this contribution, we synthesize the published omics studies on abalone to highlight the current state of knowledge, open questions, and future directions. In addition, we outline the challenges and limitations of each omics field, some of which could be overcome by integrating multiple omics approaches – a future strategy with great potential for contributing to improve abalone production. Full text

  • Multi-strain probiotics show increased protection of intestinal epithelial cells against pathogens in rainbow trout (Oncorhynchus mykiss)

    Pillinger M, Weber B, Standen B, Schmid MC, Kesselring JC
    2022 - Aquaculture, 560: 738487

    Abstract: 

    The use of antibiotics to treat bacterial infections in aquaculture facilities adversely affects fish and environmental health, motivating the search for alternative products such as probiotics. The present study investigated the immune modulatory effects of inoculating the intestinal epithelial cells of rainbow trout (Oncorhynchus mykiss) with the probiotic bacteria Enterococcus faeciumPediococcus acidilacticiLactobacillus reuteri, and Bacillus subtilis alone (single-strains) or as mixtures, which either include or exclude B. subtilis (PWBsubtilis or PWOBsubtilis, respectively). To this end, isolated intestinal epithelial cells were either incubated without probiotics or with the single- or multi-strain probiotics and then challenged with common pathogens in aquaculture. The adhesion of probiotic and pathogenic bacteria to the intestinal cells was examined by flow cytometry and confocal microscopy and the relative expression of pro- and anti-inflammatory cytokine genes was assessed through quantitative real-time PCR. Although the highest inhibition of pathogen adhesion was observed for L. reuteri alone (88%), PWOBsubtilis and PWBsubtilis inhibited 77% and 71% of pathogen attachment, respectively. Single- and multi-strain probiotics were able to elicit an immune response by activation of both pro-inflammatory and anti-inflammatory cytokines production in rainbow trout intestinal epithelial cells. This expression was generally highest for multi-strain probiotics, particularly for PWBsubtilis. The tested probiotics present different modes of action, considering their inhibition capability and immunomodulatory effects. Hence the use of multi-strain products may promote a wider range of synergies on pathogens invasion and inhibition, and immunomodulatory effects that can represent an advantage to disease outbreaks prevention in rainbow trout production.

  • Identifying Functional Groups that Determine Rates of Micropollutant Biotransformations Performed by Wastewater Microbial Communities

    Stephanie L. Rich, Michael Zumstein, Damian E. Helbling
    2022 - Environmental Science & Technology, 56: 984–994

    Abstract: 

    The goal of this research was to identify functional groups that determine rates of micropollutant (MP) biotransformations performed by wastewater microbial communities. To meet this goal, we performed a series of incubation experiments seeded with four independent wastewater microbial communities and spiked them with a mixture of 40 structurally diverse MPs. We collected samples over time and used high-resolution mass spectrometry to estimate biotransformation rate constants for each MP in each experiment and to propose structures of 46 biotransformation products. We then developed random forest models to classify the biotransformation rate constants based on the presence of specific functional groups or observed biotransformations. We extracted classification importance metrics from each random forest model and compared them across wastewater microbial communities. Our analysis revealed 30 functional groups that we define as either biotransformation promoters, biotransformation inhibitors, structural features that can be biotransformed based on uncharacterized features of the wastewater microbial community, or structural features that are not rate-determining. Our experimental data and analysis provide novel insights into MP biotransformations that can be used to more accurately predict MP biotransformations or to inform the design of new chemical products that may be more readily biodegradable during wastewater treatment.

  • Crop rotational complexity affects plant-soil nitrogen cycling during water deficit

    Bowles TM, Jilling A, Morán-Rivera K, Schnecker J, Grandy AS
    2022 - Soil Biology and Biochemistry, 166: Article 108552

    Abstract: 

    One of the biggest environmental challenges facing agriculture is how to both supply and retain nitrogen (N), especially as precipitation becomes more variable with climate change. We used a greenhouse experiment to assess how contrasting histories of crop rotational complexity affect plant-soil-microbe interactions that govern N processes, including during water stress. With higher levels of carbon and N cycling hydrolytic enzymes, higher mineral-associated organic matter N concentrations, and an altered microbial community, soils from the most complex rotation enabled 80% more corn N uptake under two moisture regimes, compared to soil from monoculture corn. Higher levels of plant N likely drove the changes in corn leaf gas exchange, particularly increasing intrinsic water use efficiency by 9% in the most complex rotation. The water deficit increased the standing pool of nitrate 44-fold in soils with a history of complex crop rotations, compared to an 11-fold increase in soils from the corn monoculture. The implications of this difference must be considered in a whole cropping systems and field context. Cycling of 15N-labeled fresh clover residue into soil N pools did not depend on the water regime or rotation history, with 2-fold higher recovery in the mineral vs. particulate organic N pool. In contrast, the water deficit reduced recovery of clover 15N in corn shoots by 37%, showing greater impacts of water deficit on plant N uptake compared to organic N cycling in soil. This study provides direct experimental evidence that long-term crop rotational complexity influences microbial N cycling and availability with feedbacks to plant physiology. Collectively, these results could help explain general observations of higher yields in more complex crop rotations, including specifically during dry conditions.

  • Sulfur in lucinid bivalves inhibits intake rates of a molluscivore shorebird

    Tim Oortwijn, Jimmy de Fouw, Jillian Petersen, Jan A. van Gils
    2022 - Oecologia, in press

    Abstract: 

    A forager’s energy intake rate is usually constrained by a combination of handling time, encounter rate and digestion rate. On top of that, food intake may be constrained when a forager can only process a maximum amount of certain toxic compounds. The latter constraint is well described for herbivores with a limited tolerance to plant secondary metabolites. In sulfidic marine ecosystems, many animals host chemoautotrophic endosymbionts, which store sulfur compounds as an energy resource, potentially making their hosts toxic to predators. The red knot Calidris canutus canutus is a molluscivore shorebird that winters on the mudflats of Banc d’Arguin, where the most abundant bivalve prey Loripes orbiculatus hosts sulfide-oxidizing bacteria. In this system, we studied the potential effect of sulfur on the red knots’ intake rates, by offering Loripes with various sulfur content to captive birds. To manipulate toxicity, we starved Loripes for 10 days by removing them from their symbiont’s energy source sulfide. As predicted, we found lower sulfur concentrations in starved Loripes. We also included natural variation in sulfur concentrations by offering Loripes collected at two different locations. In both cases lower sulfur levels in Loripes resulted in higher consumption rates in red knots. Over time the red knots increased their intake rates on Loripes, showing their ability to adjust to a higher intake of sulfur.

  • Broad- and small-scale environmental gradients drive variation in chemical, but not morphological, leaf traits of vascular epiphytes

    Guzmán-Jacob V, Guerrero-Ramírez NR, Craven D, Brant PAterno G, Taylor A, Kromer T, Wanek W, Zotz G, Kreft H
    2022 - Functional Ecology, in press

    Abstract: 

    1. Variation in leaf functional traits along environmental gradients can reveal how vascular epiphytes respond to broad- and small-scale environmental gradients. Along elevational gradients, both temperature and precipitation likely play an important role as drivers of leaf trait variation, but these traits may also respond to small-scale changes in light, temperature and humidity along the vertical environmental gradient within forest canopies. However, the relative importance of broad- and small-scale environmental gradients as drivers of variation in leaf functional traits of vascular epiphytes is poorly understood.
    2. Here, we examined variation in morphological and chemical leaf traits of 102 vascular epiphyte species spanning two environmental gradients along Cofre de Perote mountain in Mexico: (i) a broad-scale environmental gradient approximated by elevation as well as by species' lower and upper elevational limits, and (ii) small-scale environmental gradients using the relative height of attachment of an epiphyte on a host tree as a proxy for variation in environmental conditions within the forest canopy. We also assessed whether variation in morphological and chemical leaf traits along these gradients was consistent across photosynthetic pathways (CAM and C3).
    3. Broad- and small-scale environmental gradients explained more variation in chemical traits (marginal R2: 11%–89%) than in morphological traits (marginal R2: 2%–31%). For example, leaf carbon isotope signatures (δ13C), which reflects water-use efficiency, varied systematically across both environmental gradients, suggesting a decrease in water-use efficiency with increasing lower and upper elevational limits and an increase in water-use efficiency with relative height of attachment. The influence of lower and upper elevational limits on trait variation differed between photosynthetic pathways, except for leaf dry matter content and leaf nitrogen-to-phosphorus ratio. Contrary to our expectations, broad- and small-scale environmental gradients explained minimal variation in morphological leaf traits, suggesting that environmental conditions do not constrain morphological leaf trait values of vascular epiphytes.
    4. Our findings suggest that assessing multiple drivers of leaf trait variation among photosynthetic pathways is key for disentangling the mechanisms underlying responses of vascular epiphytes to environmental conditions.

     

    Read the free Plain Language Summary for this article on the Journal blog.

     

    1. Variation in leaf functional traits along environmental gradients can reveal how vascular epiphytes respond to broad- and small-scale environmental gradients. Along elevational gradients, both temperature and precipitation likely play an important role as drivers of leaf trait variation, but these traits may also respond to small-scale changes in light, temperature and humidity along the vertical environmental gradient within forest canopies. However, the relative importance of broad- and small-scale environmental gradients as drivers of variation in leaf functional traits of vascular epiphytes is poorly understood.
    2. Here, we examined variation in morphological and chemical leaf traits of 102 vascular epiphyte species spanning two environmental gradients along Cofre de Perote mountain in Mexico: (i) a broad-scale environmental gradient approximated by elevation as well as by species' lower and upper elevational limits, and (ii) small-scale environmental gradients using the relative height of attachment of an epiphyte on a host tree as a proxy for variation in environmental conditions within the forest canopy. We also assessed whether variation in morphological and chemical leaf traits along these gradients was consistent across photosynthetic pathways (CAM and C3).
    3. Broad- and small-scale environmental gradients explained more variation in chemical traits (marginal R2: 11%–89%) than in morphological traits (marginal R2: 2%–31%). For example, leaf carbon isotope signatures (δ13C), which reflects water-use efficiency, varied systematically across both environmental gradients, suggesting a decrease in water-use efficiency with increasing lower and upper elevational limits and an increase in water-use efficiency with relative height of attachment. The influence of lower and upper elevational limits on trait variation differed between photosynthetic pathways, except for leaf dry matter content and leaf nitrogen-to-phosphorus ratio. Contrary to our expectations, broad- and small-scale environmental gradients explained minimal variation in morphological leaf traits, suggesting that environmental conditions do not constrain morphological leaf trait values of vascular epiphytes.
    4. Our findings suggest that assessing multiple drivers of leaf trait variation among photosynthetic pathways is key for disentangling the mechanisms underlying responses of vascular epiphytes to environmental conditions.

     

    Read the free Plain Language Summary for this article on the Journal blog.

  • Soil carbon loss in warmed subarctic grasslands is rapid and restricted to topsoil

    Verbrigghe N, Leblans NIW, Sigurdsson BD, Vicca S, Fang C, Fuchslueger L, Soong JL, Weedon JT, Poeplau C, Ariza-Carricondo C, Bahn M, Guenet B, Gundersen P, Gunnarsdóttir GE, Kätterer T, Liu Z, Maljanen M, Marañon-Jimenez S, Meeran K, Oddsdóttir ES, Ostonen I, Schiestl RH, Richter A, Sardans J, Sigurðsson P, Torn MS, Van Bodegom PM, Verbruggen E, Walker TWN, Wallander H, Janssens IA
    2022 - Biogeosciences, 19: 3381-3393

    Abstract: 

    Global warming may lead to carbon transfers from soils to the atmosphere, yet this positive feedback to the climate system remains highly uncertain, especially in subsoils (Ilyina and Friedlingstein2016Shi et al.2018). Using natural geothermal soil warming gradients of up to +6.4C in subarctic grasslands (Sigurdsson et al.2016), we show that soil organic carbon (SOC) stocks decline strongly and linearly with warming (−2.8 t ha−1C−1). Comparison of SOC stock changes following medium-term (5 and 10 years) and long-term (>50 years) warming revealed that all SOC stock reduction occurred within the first 5 years of warming, after which continued warming no longer reduced SOC stocks. This rapid equilibration of SOC observed in Andosol suggests a critical role for ecosystem adaptations to warming and could imply short-lived soil carbon–climate feedbacks. Our data further revealed that the soil C loss occurred in all aggregate size fractions and that SOC stock reduction was only visible in topsoil (0–10 cm). SOC stocks in subsoil (10–30 cm), where plant roots were absent, showed apparent conservation after >50 years of warming. The observed depth-dependent warming responses indicate that explicit vertical resolution is a prerequisite for global models to accurately project future SOC stocks for this soil type and should be investigated for soils with other mineralogies.

  • Nitrogen fixation by diverse diazotrophic communities can support population growth of arboreal ants

    Nepel M, Pfeifer J, Oberhauser FB, Richter A, Woebken D, Mayer VE
    2022 - BMC Biology, 20: 135

    Abstract: 

    Background: Symbiotic ant-plant associations, in which ants live on plants, feed on plant-provided food, and protect host trees against threats, are ubiquitous across the tropics, with the Azteca-Cecropia associations being amongst the most widespread interactions in the Neotropics. Upon colonization of Cecropia’s hollow internodes, Azteca queens form small patches with plant parenchyma, which are then used as waste piles when the colony grows. Patches—found in many ant-plant mutualisms—are present throughout the colony life cycle and may supplement larval food. Despite their initial nitrogen (N)-poor substrate, patches in Cecropia accommodate fungi, nematodes, and bacteria. In this study, we investigated the atmospheric N2 fixation as an N source in patches of early and established ant colonies. Results: Via 15N2 tracer assays, N2 fixation was frequently detected in all investigated patch types formed by three Azteca ant species. Quantified fixation rates were similar in early and established ant colonies and higher than in various tropical habitats. Based on amplicon sequencing, the identified microbial functional guild—the diazotrophs—harboring and transcribing the dinitrogenase reductase (nifH) gene was highly diverse and heterogeneous across Azteca colonies. The community composition differed between early and established ant colonies and partly between the ant species. Conclusions: Our data show that N2 fixation can result in reasonable amounts of N in ant colonies, which might not only enable bacterial, fungal, and nematode growth in the patch ecosystems but according to our calculations can even support the growth of ant populations. The diverse and heterogeneous diazotrophic community implies a functional redundancy, which could provide the ant-plant-patch system with a higher resilience towards changing environmental conditions. Hence, we propose that N2 fixation represents a previously unknown potential to overcome N limitations in arboreal ant colonies.

  • Geometry of the modelled freshwater/salt-water interface under variable-density-driven flow (Pétrola Lake, SE Spain)

    Sanz D, Valiente N, Dountcheva I, Muñoz-Martín A, Cassiraga E, Gómez-Alday JJ
    2022 - Hydrogeology Journal, 30: 975-988

    Abstract: 

    Pétrola Lake in southeast Spain is one of the most representative examples of hypersaline wetlands in southern Europe. The rich ecosystem and environmental importance of this lake are closely associated with the hydrogeological behaviour of the system. The wetland is fed by the underlying aquifer with relatively fresh groundwater—1 g L−1 of total dissolved solids (TDS)—with a centripetal direction towards the wetland. In addition, the high evaporation rates of the region promote an increase in the concentration of salts in the lake water, occasionally higher than 80 g L−1 TDS. The density difference between the superficial lake water and the regional groundwater can reach up to 0.25 g cm−3, causing gravitational instability and density-driven flow (DDF) under the lake bottom. The objective of this study was to gain an understanding of the geometry of the freshwater–saltwater interface by means of two-dimensional mathematical modelling and geophysical-resistivity-profile surveys. The magnitude and direction of mixed convective flows, generated by DDF, support the hypothesis that the autochthonous reactive organic matter produced in the lake by biomass can be transported effectively towards the freshwater–saltwater interface areas (e.g. springs in the lake edge), where previous research described biogeochemical processes of natural attenuation of nitrate pollution.

  • Plant-microbial linkages underpin carbon sequestration in contrasting mountain tundra vegetation types

    Gavazov K, Canarini A, Jassey VEJ, Mills R, Richter A, Sundqvist MK, Väisänen M, Walker TWN, Wardle DA, Dorrepaal E
    2022 - Soil Biology and Biochemistry, Article 108530

    Abstract: 

    Tundra ecosystems hold large stocks of soil organic matter (SOM), likely due to low temperatures limiting rates of microbial SOM decomposition more than those of SOM accumulation from plant primary productivity and microbial necromass inputs. Here we test the hypotheses that distinct tundra vegetation types and their carbon supply to characteristic rhizosphere microbes determine SOM cycling independent of temperature. In the subarctic Scandes, we used a three-way factorial design with paired heath and meadow vegetation at each of two elevations, and with each combination of vegetation type and elevation subjected during one growing season to either ambient light (i.e., ambient plant productivity), or 95% shading (i.e., reduced plant productivity). We assessed potential above- and belowground ecosystem linkages by uni- and multivariate analyses of variance, and structural equation modelling. We observed direct coupling between tundra vegetation type and microbial community composition and function, which underpinned the ecosystem's potential for SOM storage. Greater primary productivity at low elevation and ambient light supported higher microbial biomass and nitrogen immobilisation, with lower microbial mass-specific enzymatic activity and SOM humification. Congruently, larger SOM at lower elevation and in heath sustained fungal-dominated microbial communities, which were less substrate-limited, and invested less into enzymatic SOM mineralisation, owing to a greater carbon-use efficiency (CUE). Our results highlight the importance of tundra plant community characteristics (i.e., productivity and vegetation type), via their effects on soil microbial community size, structure and physiology, as essential drivers of SOM turnover. The here documented concerted patterns in above- and belowground ecosystem functioning is strongly supportive of using plant community characteristics as surrogates for assessing tundra carbon storage potential and its evolution under climate and vegetation changes.

  • Exploring Nanogeochemical Environments: New Insights from Single Particle ICP-TOFMS and AF4-ICPMS

    Manuel D. Montaño, Chad W. Cuss, Haley M. Holliday, Muhammad B. Javed, William Shotyk, Kathryn L. Sobocinski, Thilo Hofmann, Frank von der Kammer, James F. Ranville
    2022 - ACS Earth & Space Chemistry, 6: 943–952

    Abstract: 

    Nanogeochemistry is an emerging focus area recognizing the role of nanoparticles in Earth systems. Engineered nanotechnology has cultivated advanced analytical techniques that are also applicable to nanogeochemistry. Single particle inductively coupled plasma ICP-time-of-flight-mass spectrometry (ICP-TOF-MS) promises a significant step forward, as time-of-flight mass analyzers enable simultaneous quantification of the entire atomic mass spectrum (∼7–250 m/z+). To demonstrate the utility of this approach, samples were collected and analyzed from a large, boreal river, and its surrounding tributaries. These samples provided us with a diversity of particle compositions and morphologies, while their interconnected nature allowed for an examination of the various nanogeochemical processes present in this system. To further expand on this effort, we combined this high-throughput technique with AF4-ICPMS, focusing on major carriers of trace elements. Using spICP-TOF-MS, Al, Si, and Fe were grouped into classes having all combinations of one or more of these elements. Particle-by-particle ICP-TOF-MS analysis found chemically heterogeneous populations, indicating the predominance of diverse mineralogy or heteroaggregates. The importance of suspended Fe and Mn for the speciation of Pb was observed by single particle ICP-TOF-MS and complemented by AF4-ICPMS analysis of dissolved organic matter and nanoparticulate Fe/Mn. Our study exploits the combination of spICP-TOF-MS and AF4-ICP-MS for studying isotopic and elemental ratios (mineralogy) of individual nanoparticles, which opens the door to further explore the mechanisms of colloid facilitated transport of trace elements.

  • The breakthrough paradox - how focusing on one form of innovation jeopardizes the advancement of science

    Falkenberg F, Fochler M, Sigl L, Bürstmayr, Eichorst SA, Michel S, Oburger E, Staudinger C, Steiner B, Woebken D
    2022 - EMBO Reports, e54772

    Abstract: 

    Science is about venturing into the unknown to find unexpected insights and establish new knowledge. Increasingly, academic institutions and funding agencies such as the European Research Council (ERC) explicitly encourage and support scientists to foster risky and hopefully ground-breaking research. Such incentives are important and have been greatly appreciated by the scientific community. However, the success of the ERC has had its downsides, as other actors in the funding ecosystem have adopted the ERC’s focus on “breakthrough science” and respective notions of scientific excellence. We argue that these tendencies are concerning since disruptive breakthrough innovation is not the only form of innovation in research. While continuous, gradual innovation is often taken for granted, it could become endangered in a research and funding ecosystem that places ever higher value on breakthrough science. This is problematic since, paradoxically, breakthrough potential in science builds on gradual innovation. If the value of gradual innovation is not better recognized, the potential for breakthrough innovation may well be stifled.

  • Screening for genes involved in cellulase regulation by expression under the control of a novel constitutive promoter in Trichoderma reesei

    Beier S, Stiegler M, Hitzenhammer E, Schmoll M
    2022 - Current Research in Biotechnology, 4: 238-246

    Abstract: 

    The filamentous ascomycete Trichoderma reesei is a biotechnological workhorse used in the production of homologous and heterologous proteins for diverse applications including biofuel production, textile finishing and food additives. This fungus uses a complex adaptation machinery to regulate its cellulases in response to environmental conditions. Detailed understanding of this regulation allows for improvement of enzyme production using the strong enzyme gene promotors. Here, we selected six genes with characteristic transcript levels associated with cellulase production to be tested for their enzyme regulatory function. Machine learning for inference of a gene regulatory network (GRN) was applied to support the association of these genes with cellulase induction. Additionally, we screened available transcriptomic data for genes with strong constitutive transcript levels and selected the promoter of the gene cfe1, whose transcript levels were above those of tef1 and cDNA1 and near those of cbh1, for gene overexpression testing. Using this promoter, we explored the relevance to cellulose degradation efficiency of three transporters, two ferric reductases and one gene of unknown function, which were overexpressed in T. reesei grown on cellulose. This promoter enabled up to 400 fold overexpression and yielded transcript levels above those of tef1 or cDNA1. We provide evidence of effects of a ferric reductase, an ammonium permease and a gene of unknown function on the regulatory machinery of cellulase expression in T. reesei. In summary we identified the cfe1 promoter, a novel constitutive promoter with promising efficiency, as well as three genes relevant to cellulase regulation in T. reesei.

  • Vertical profiles of leaf photosynthesis and leaf traits and soil nutrients in two tropical rainforests in French Guiana before and after a 3-year nitrogen and phosphorus addition experiment

    Verryckt LT, Vicca S, Van Langenhove L, Stahl C, Asensio D, Urbina I, Ogaya R, Llusià J, Grau O, Peguero G, Gargallo-Garriga A, Courtois EA, Margalef O, Portillo-Estrada M, Ciais P, Obersteiner M, Fuchslueger L, Lugli LF, Fernandez-Garberi PR, Vallicrosa H, Verlinden M, Ranits C, Vermeir P, Coste S, Verbruggen E, Bréchet L, Sardans J, Chave J, Schiestl RH, Janssens IA
    2022 - Earth Syst. Sci. Data, 14: 5-8

    Abstract: 

    Terrestrial biosphere models typically use the biochemical model of Farquhar, von Caemmerer, and Berry (1980) to simulate photosynthesis, which requires accurate values of photosynthetic capacity of different biomes. However, data on tropical forests are sparse and highly variable due to the high species diversity, and it is still highly uncertain how these tropical forests respond to nutrient limitation in terms of C uptake. Tropical forests often grow on soils low in phosphorus (P) and are, in general, assumed to be P rather than nitrogen (N) limited. However, the relevance of P as a control of photosynthetic capacity is still debated. Here, we provide a comprehensive dataset of vertical profiles of photosynthetic capacity and important leaf traits, including leaf N and P concentrations, from two 3-year, large-scale nutrient addition experiments conducted in two tropical rainforests in French Guiana. These data present a unique source of information to further improve model representations of the roles of NP, and other leaf nutrients in photosynthesis in tropical forests. To further facilitate the use of our data in syntheses and model studies, we provide an elaborate list of ancillary data, including important soil properties and nutrients, along with the leaf data. As environmental drivers are key to improve our understanding of carbon (C) and nutrient cycle interactions, this comprehensive dataset will aid to further enhance our understanding of how nutrient availability interacts with C uptake in tropical forests. The data are available at https://doi.org/10.5281/zenodo.5638236 (Verryckt, 2021).

  • Global grassland diazotrophic communities are structured by combined abiotic, biotic, and spatial distance factors but resilient to fertilization

    Nepel M, Angel R, Borer ET, Frey B, MacDougall AS, McCulley RL, Risch AC, Schütz M, Seasbloom EW, Woebken D
    2022 - Front Microbiol, 13: 821030

    Abstract: 

    Grassland ecosystems cover around 37% of the ice-free land surface on Earth and have critical socioeconomic importance globally. As in many terrestrial ecosystems, biological dinitrogen (N2) fixation represents an essential natural source of nitrogen (N). The ability to fix atmospheric N2 is limited to diazotrophs, a diverse guild of bacteria and archaea. To elucidate the abiotic (climatic, edaphic), biotic (vegetation), and spatial factors that govern diazotrophic community composition in global grassland soils, amplicon sequencing of the dinitrogenase reductase gene—nifH—was performed on samples from a replicated standardized nutrient [N, phosphorus (P)] addition experiment in 23 grassland sites spanning four continents. Sites harbored distinct and diverse diazotrophic communities, with most of reads assigned to diazotrophic taxa within the Alphaproteobacteria (e.g., Rhizobiales), Cyanobacteria (e.g., Nostocales), and Deltaproteobacteria (e.g., Desulforomonadales) groups. Likely because of the wide range of climatic and edaphic conditions and spatial distance among sampling sites, only a few of the taxa were present at all sites. The best model describing the variation among soil diazotrophic communities at the OTU level combined climate seasonality (temperature in the wettest quarter and precipitation in the warmest quarter) with edaphic (C:N ratio, soil texture) and vegetation factors (various perennial plant covers). Additionally, spatial variables (geographic distance) correlated with diazotrophic community variation, suggesting an interplay of environmental variables and spatial distance. The diazotrophic communities appeared to be resilient to elevated nutrient levels, as 2–4 years of chronic N and P additions had little effect on the community composition. However, it remains to be seen, whether changes in the community composition occur after exposure to long-term, chronic fertilization regimes.

  • Targeting Gut Bacteria using Inulin-Conjugated Mesoporous Silica Nanoparticles

    von Baeckmann C, Riva A, Guggenberger P, Kählig H, Han SW, Inan D, Del Favero G, Berry D, Kleitz F
    2022 - Advanced Materials Interfaces, in press

    Abstract: 

    To facilitate the creation of novel nanocarrier systems targeting the intestinal microbiome, inulin-conjugated mesoporous silica nanoparticles (MSNs) are described herein for the first time. Surface functionalization is achieved on either hydrophilic or hydrophobic mesoporous nanoparticles using different conjugation methods. The targeting performance of the resulting materials is assessed and compared upon incubation with human stool. It appears that amide formation is the most favorable coupling method on hydrophilic MSNs to achieve the desired bioconjugate. Remarkably, high affinity of gut bacteria to the conjugated particles can be obtained, paving the way to novel targeted drug delivery systems.

  • How low can they go? Aerobic respiration by microorganisms under apparent anoxia

    Berg J, Ahmerkamp S, Pjevac P, Hausmann B, Milucka J, Kuypers MMM
    2022 - FEMS Microbiology Reviews, in press

    Abstract: 

    Oxygen (O2) is the ultimate oxidant on Earth and its respiration confers such an energetic advantage that microorganisms have evolved the capacity to scavenge O2 down to nanomolar concentrations. The respiration of O2 at extremely low levels is proving to be common to diverse microbial taxa, including organisms formerly considered strict anaerobes. Motivated by recent advances in O2 sensing and DNA/RNA sequencing technologies, we performed a systematic review of environmental metatranscriptomes revealing that microbial respiration of O2 at nanomolar concentrations is ubiquitous and drives microbial activity in seemingly anoxic aquatic habitats. These habitats were key to the early evolution of life and are projected to become more prevalent in the near future due to anthropogenic-driven environmental change. Here we summarize our current understanding of aerobic microbial respiration under apparent anoxia, including novel processes, their underlying biochemical pathways, the involved microorganisms, and their environmental importance and evolutionary origin.

  • Ecology and evolution of chlamydial symbionts of arthropods

    Halter T, Koestlbacher S, Collingro A, Sixt BS, Toenshoff ER, Hendrickx F, Kostanjšek R, Horn M
    2022 - ISME Commun., 2: 45

    Abstract: 

    The phylum Chlamydiae consists of obligate intracellular bacteria including major human pathogens and diverse environmental representatives. Here we investigated the Rhabdochlamydiaceae, which is predicted to be the largest and most diverse chlamydial family, with the few described members known to infect arthropod hosts. Using published 16S rRNA gene sequence data we identified at least 388 genus-level lineages containing about 14 051 putative species within this family. We show that rhabdochlamydiae are mainly found in freshwater and soil environments, suggesting the existence of diverse, yet unknown hosts. Next, we used a comprehensive genome dataset including metagenome assembled genomes classified as members of the family Rhabdochlamydiaceae, and we added novel complete genome sequences of Rhabdochlamydia porcellionis infecting the woodlouse Porcellio scaber, and of 'Candidatus R. oedothoracis' associated with the linyphiid dwarf spider Oedothorax gibbosus. Comparative analysis of basic genome features and gene content with reference genomes of well-studied chlamydial families with known host ranges, namely Parachlamydiaceae (protist hosts) and Chlamydiaceae (human and other vertebrate hosts) suggested distinct niches for members of the Rhabdochlamydiaceae. We propose that members of the family represent intermediate stages of adaptation of chlamydiae from protists to vertebrate hosts. Within the genus Rhabdochlamydia, pronounced genome size reduction could be observed (1.49-1.93 Mb). The abundance and genomic distribution of transposases suggests transposable element expansion and subsequent gene inactivation as a mechanism of genome streamlining during adaptation to new hosts. This type of genome reduction has never been described before for any member of the phylum Chlamydiae. This study provides new insights into the molecular ecology, genomic diversity, and evolution of representatives of one of the most divergent chlamydial families.

  • CT295 Is Chlamydia trachomatis’ phosphoglucomutase and a type 3 secretion substrate

    Triboulet A, N’Gadjaga MD, Niragire B, Köstlbacher S, Horn M, Aimanianda V, Subtil A
    2022 - Front Cell Infect Microbiol, 12: 866729

    Abstract: 

    The obligate intracellular bacteria Chlamydia trachomatis store glycogen in the lumen of the vacuoles in which they grow. Glycogen catabolism generates glucose-1-phosphate (Glc1P), while the bacteria can take up only glucose-6-phosphate (Glc6P). We tested whether the conversion of Glc1P into Glc6P could be catalyzed by a phosphoglucomutase (PGM) of host or bacterial origin. We found no evidence for the presence of the host PGM in the vacuole. Two C. trachomatis proteins, CT295 and CT815, are potential PGMs. By reconstituting the reaction using purified proteins, and by complementing PGM deficient fibroblasts, we demonstrated that only CT295 displayed robust PGM activity. Intriguingly, we showed that glycogen accumulation in the lumen of the vacuole of a subset of Chlamydia species (C. trachomatis, C. muridarum, C. suis) correlated with the presence, in CT295 orthologs, of a secretion signal recognized by the type three secretion (T3S) machinery of Shigella. C. caviae and C. pneumoniae do not accumulate glycogen, and their CT295 orthologs lack T3S signals. In conclusion, we established that the conversion of Glc1P into Glc6P was accomplished by a bacterial PGM, through the acquisition of a T3S signal in a “housekeeping” protein. Acquisition of this signal likely contributed to shaping glycogen metabolism within Chlamydiaceae.

  • Rapid analysis of gunshot residues with single-particle inductively coupled plasma time-of-flight mass spectrometry

    Robert Brünjes, Jan Schüürman, Frank von der Kammer, Thilo Hofmann
    2022 - Forensic Science International, 332: in press

    Abstract: 

    Gunshot residues (GSRs) from different types of ammunition have been characterized using a new method based on single-particle inductively coupled plasma time-of-flight mass spectrometry (sp-ICP-TOF-MS). This method can analyze thousands of particles per minute enabling rapid sample screening for GSR detection with minimal sample preparation. GSR particles are multi-elemental nanoparticles that are mainly defined by the elements lead, barium, and antimony. Sp-ICP-TOF-MS was also used to identify other elements contained in GSR particles while standard particle classification protocols do not consider the complexities of GSR compositions and can therefore miss out on valuable information. The proposed method can be used to support existing GSR detection methods, especially when lead-free, antimony-free, or tagged ammunition has been used; it also provides a possibility for multi-elemental fingerprinting of GSR particles.

  • Long-term warming reduced microbial biomass but increased recent plant-derived C in microbes of a subarctic grassland

    Verbrigghe N, Meeran K, Bahn M, Canarini A, Fransen E, Fuchslueger L, Ingrisch J, Janssens IA, Richter A, Sigurdsson BD, Soong JL, Vicca S
    2022 - Soil Biology and Biochemistry, 167: Article 108590

    Abstract: 

    Long-term soil warming and nitrogen (N) availability have been shown to affect microbial biomass and community composition. Altered assimilation patterns of recent plant-derived C and changes in soil C stocks following warming as well as increased N availability are critical in mediating the direction and magnitude of these community shifts. A 13C pulse labelling experiment was done on a warming gradient in an Icelandic grassland (Sigurdsson et al., 2016), to investigate the role of recent plant-derived C and warming on the microbial community structure and size. We observed an overall increase of microbial 13C (e.g., root-exudate) uptake, while warming led to significant microbial biomass loss in all microbial groups. The increase of microbial 13C uptake with warming differed between microbial groups: an increase was only observed in the general and Gram-positive bacterial phospholipid fatty acid (PLFA) markers and in the PLFA and neutral lipid fatty acid (NLFA) markers of arbuscular mycorrhizal fungi (AMF). Nitrogen addition of 50 kg ha−1 y−1 for two years had no effect on the microbial uptake, microbial biomass or community composition, indicating that microbes were not N limited, and no plant-mediated N addition effects occurred. Additionally, we show that both warming and soil C depletion were responsible for the microbial biomass loss. Soil warming caused stronger loss in microbial groups with higher 13C uptake. In our experiment, warming caused a general reduction of microbial biomass, despite a relative increase in microbial 13C uptake, and altered microbial community composition. The warming effects on microbial biomass and community composition were partly mediated through soil C depletion with warming and changes in recent plant-derived C uptake patterns of the microbial community.

  • Ligand-Induced U Mobilization from Chemogenic Uraninite and Biogenic Noncrystalline U(IV) under Anoxic Conditions

    Kyle J. Chardi, Anshuman Satpathy, Walter D. C. Schenkeveld*, Naresh Kumar, Vincent Noël, Stephan M. Kraemer, and Daniel E. Giammar
    2022 - Environmental Science and Technology, 56: 6369–6379

    Abstract: 

    Microbial reduction of soluble hexavalent uranium (U(VI)) to sparingly soluble tetravalent uranium (U(IV)) has been explored as an in situ strategy to immobilize U. Organic ligands might pose a potential hindrance to the success of such remediation efforts. In the current study, a set of structurally diverse organic ligands were shown to enhance the dissolution of crystalline uraninite (UO2) for a wide range of ligand concentrations under anoxic conditions at pH 7.0. Comparisons were made to ligand-induced U mobilization from noncrystalline U(IV). For both U phases, aqueous U concentrations remained low in the absence of organic ligands (<25 nM for UO2; 300 nM for noncrystalline U(IV)). The tested organic ligands (2,6-pyridinedicarboxylic acid (DPA), desferrioxamine B (DFOB), N,N′-di(2-hydroxybenzyl)ethylene-diamine-N,N′-diacetic acid (HBED), and citrate) enhanced U mobilization to varying extents. Over 45 days, the ligands mobilized only up to 0.3% of the 370 μM UO2, while a much larger extent of the 300 μM of biomass-bound noncrystalline U(IV) was mobilized (up to 57%) within only 2 days (>500 times more U mobilization). This work shows the potential of numerous organic ligands present in the environment to mobilize both recalcitrant and labile U forms under anoxic conditions to hazardous levels and, in doing so, undermine the stability of immobilized U(IV) sources.

  • Soil greenhouse gas fluxes in floodplain forests of the Danube National Park – Effects of flooding and soil microclimate

    Schindlbacher A, Heinzle J, Gollobich G, Wanek W, Michel K, Kitzler K
    2022 - Biogeochemistry, 159: 193-213

    Abstract: 

    The relevance of soil greenhouse gas (GHG) fluxes from temperate floodplain forests has yet remained elusive. We studied the soil methane (CH4), nitrous oxide (N2O) and carbon dioxide (CO2) dynamics at three forest sites along a flooding gradient in the Danube National Park (Austria) to estimate annual GHG budgets and to assess if and how seasonal flooding affects individual GHG fluxes. Soil surface GHG fluxes were determined along with GHG concentrations in soil air and pore-water at a non-flooded (NF), an infrequently-flooded (IF), and a frequently-flooded (FF) site. Both study years were characterized by dry summers, and only the FF site was flooded during the study period. Soils at all sites were annual CH4 sinks (NF: − 4.50 ± 0.85, IF: − 2.54 ± 0.57, FF: − 0.67 ± 1.06 kg CH4-C ha−1 year−1) and the sink strength correlated positively with soil moisture. Pulse-like CH4 emissions were not observed during or after flooding. Soil N2O fluxes showed large temporal and spatial variations, without any significant differences between sites (average NF: 6.5 ± 7.1, IF: 10.4 ± 14.3, FF: 9.4 ± 10.5 µg N2O-N m−2 h−1). Pulse N2O emissions (up to ~ 80 µg N2O-N m−2 h−1) occurred during freeze/thaw events, but not during or after flooding. Mean annual soil CO2 effluxes at NF and IF were 9.4 ± 1.1 and 9.4 ± 2.1 t C ha−1 year−1, respectively. Soil CO2 efflux was significantly higher at the FF site (18.54 ± 6.21 t C ha−1 year−1). High soil air CO2 concentrations (> 10%) in aerated deeper soil layers indicated a substantial contribution of the usually waterlogged sub-soils to the summertime soil CO2 efflux at the FF site. Overall, our results suggest that the studied temperate floodplain forest soils do not absorb/emit substantially more CH4 and N2O than soils of comparable upland forests, whereas low groundwater level can lead to periodically enhanced CO2 emissions from normally waterlogged soil layers.

  • Broad- and small-scale environmental gradients drive variation in chemical, but not morphological, leaf traits of vascular epiphytes

    Guzmán-Jacob V, Guerrero-Ramírez NR, Craven D, Paterno GB, Taylor A, Kromer T, Wanek W, Zotz G, Kreft H
    2022 - Functional Ecology, 36: 1858-1872

    Abstract: 

    1. Variation in leaf functional traits along environmental gradients can reveal how vascular epiphytes respond to broad- and small-scale environmental gradients. Along elevational gradients, both temperature and precipitation likely play an important role as drivers of leaf trait variation, but these traits may also respond to small-scale changes in light, temperature and humidity along the vertical environmental gradient within forest canopies. However, the relative importance of broad- and small-scale environmental gradients as drivers of variation in leaf functional traits of vascular epiphytes is poorly understood.
    2. Here, we examined variation in morphological and chemical leaf traits of 102 vascular epiphyte species spanning two environmental gradients along Cofre de Perote mountain in Mexico: (i) a broad-scale environmental gradient approximated by elevation as well as by species' lower and upper elevational limits, and (ii) small-scale environmental gradients using the relative height of attachment of an epiphyte on a host tree as a proxy for variation in environmental conditions within the forest canopy. We also assessed whether variation in morphological and chemical leaf traits along these gradients was consistent across photosynthetic pathways (CAM and C3).
    3. Broad- and small-scale environmental gradients explained more variation in chemical traits (marginal R2: 11%–89%) than in morphological traits (marginal R2: 2%–31%). For example, leaf carbon isotope signatures (δ13C), which reflects water-use efficiency, varied systematically across both environmental gradients, suggesting a decrease in water-use efficiency with increasing lower and upper elevational limits and an increase in water-use efficiency with relative height of attachment. The influence of lower and upper elevational limits on trait variation differed between photosynthetic pathways, except for leaf dry matter content and leaf nitrogen-to-phosphorus ratio. Contrary to our expectations, broad- and small-scale environmental gradients explained minimal variation in morphological leaf traits, suggesting that environmental conditions do not constrain morphological leaf trait values of vascular epiphytes.
    4. Our findings suggest that assessing multiple drivers of leaf trait variation among photosynthetic pathways is key for disentangling the mechanisms underlying responses of vascular epiphytes to environmental conditions.
  • Lignin Preservation and Microbial Carbohydrate Metabolism in Permafrost Soils

    Dao TT, Mikutta R, Sauheitl L, Gentsch N, Shibistova O, Wild B, Schnecker J, Barta J, Capek P, Gittel A, Lashchinskiy N, Urich T, Santruckova H, Richter A, Guggenberger G
    2022 - JGR Biogeosciences, 127: Article e2020JG00618

    Abstract: 

    Permafrost-affected soils in the northern circumpolar region store more than 1,000 Pg soil organic carbon (OC), and are strongly vulnerable to climatic warming. However, the extent to which changing soil environmental conditions with permafrost thaw affects different compounds of soil organic matter (OM) is poorly understood. Here, we assessed the fate of lignin and non-cellulosic carbohydrates in density fractionated soils (light fraction, LF vs. heavy fraction, HF) from three permafrost regions with decreasing continentality, expanding from east to west of northern Siberia (Cherskiy, Logata, Tazovskiy, respectively). In soils at the Tazovskiy site with thicker active layers, the LF showed smaller OC-normalized contents of lignin-derived phenols and plant-derived sugars and a decrease of these compounds with soil depth, while a constant or even increasing trend was observed in soils with shallower active layers (Cherskiy and Logata). Also in the HF, soils at the Tazovskiy site had smaller contents of OC-normalized lignin-derived phenols and plant-derived sugars along with more pronounced indicators of oxidative lignin decomposition and production of microbial-derived sugars. Active layer deepening, thus, likely favors the decomposition of lignin and plant-derived sugars, that is, lignocelluloses, by increasing water drainage and aeration. Our study suggests that climate-induced degradation of permafrost soils may promote carbon losses from lignin and associated polysaccharides by abolishing context-specific preservation mechanisms. However, relations of OC-based lignin-derived phenols and sugars in the HF with mineralogical properties suggest that future OM transformation and carbon losses will be modulated in addition by reactive soil minerals.

  • From diversity to complexity: Microbial networks in soils

    Guseva K, Darcy S, Simon E, Alteio LV, Montesinos-Navarro A, Kaiser C
    2022 - Soil Biology and Biochemistry, 169: Article 108604

    Abstract: 

    Network analysis has been used for many years in ecological research to analyze organismal associations, for example in food webs, plant-plant or plant-animal interactions. Although network analysis is widely applied in microbial ecology, only recently has it entered the realms of soil microbial ecology, shown by a rapid rise in studies applying co-occurrence analysis to soil microbial communities. While this application offers great potential for deeper insights into the ecological structure of soil microbial ecosystems, it also brings new challenges related to the specific characteristics of soil datasets and the type of ecological questions that can be addressed. In this Perspectives Paper we assess the challenges of applying network analysis to soil microbial ecology due to the small-scale heterogeneity of the soil environment and the nature of soil microbial datasets. We review the different approaches of network construction that are commonly applied to soil microbial datasets and discuss their features and limitations. Using a test dataset of microbial communities from two depths of a forest soil, we demonstrate how different experimental designs and network constructing algorithms affect the structure of the resulting networks, and how this in turn may influence ecological conclusions. We will also reveal how assumptions of the construction method, methods of preparing the dataset, and definitions of thresholds affect the network structure. Finally, we discuss the particular questions in soil microbial ecology that can be approached by analyzing and interpreting specific network properties. Targeting these network properties in a meaningful way will allow applying this technique not in merely descriptive, but in hypothesis-driven research. Analysing microbial networks in soils opens a window to a better understanding of the complexity of microbial communities. However, this approach is unfortunately often used to draw conclusions which are far beyond the scientific evidence it can provide, which has damaged its reputation for soil microbial analysis. In this Perspectives Paper, we would like to sharpen the view for the real potential of microbial co-occurrence analysis in soils, and at the same time raise awareness regarding its limitations and the many ways how it can be misused or misinterpreted.

  • Lowland plant arrival in alpine ecosystems facilitates a decrease in soil carbon content under experimental climate warming

    Walker TWN, Gavazov K, Guillaume T, Lambert T, Mariotte P, Routh D, Signarbieux C, Block S, Münkemüller T, Nomoto H, Crowther TW, Richter A, Buttler A, Alexander JM
    2022 - Elife, 11: Article e78555

    Abstract: 

    Climate warming is releasing carbon from soils around the world, constituting a positive climate feedback. Warming is also causing species to expand their ranges into new ecosystems. Yet, in most ecosystems, whether range expanding species will amplify or buffer expected soil carbon loss is unknown. Here, we used two whole-community transplant experiments and a follow-up glasshouse experiment to determine whether the establishment of herbaceous lowland plants in alpine ecosystems influences soil carbon content under warming. We found that warming (transplantation to low elevation) led to a negligible decrease in alpine soil carbon content, but its effects became significant and 52% ± 31% (mean ± 95% confidence intervals) larger after lowland plants were introduced at low density into the ecosystem. We present evidence that decreases in soil carbon content likely occurred via lowland plants increasing rates of root exudation, soil microbial respiration, and CO2 release under warming. Our findings suggest that warming-induced range expansions of herbaceous plants have the potential to alter climate feedbacks from this system, and that plant range expansions among herbaceous communities may be an overlooked mediator of warming effects on carbon dynamics.

  • Decay of similarity across tropical forest communities: integrating spatial distance with soil nutrients

    Peguero G, Ferrín M, Sardans J, Verbruggen E, Ramírez-Rojas I, Van Langenhove L, Verryckt LT, Murienne J, Iribar A, Zinger L, Grau O, Orivel J, Stahl C, Courtois EA, Asensio D, Gargallo-Garriga A, Llusià J, Margalef O, Ogaya R, Richter A, Janssens IA, Schiestl RH
    2022 - Ecology, 103: Article e03599

    Abstract: 

    Understanding the mechanisms that drive the change of biotic assemblages over space and time is the main quest of community ecology. Assessing the relative importance of dispersal and environmental species selection in a range of organismic sizes and motilities has been a fruitful strategy. A consensus for whether spatial and environmental distances operate similarly across spatial scales and taxa, however, has yet to emerge. We used censuses of four major groups of organisms (soil bacteria, fungi, ground insects, and trees) at two observation scales (1-m2 sampling point vs. 2,500-m2 plots) in a topographically standardized sampling design replicated in two tropical rainforests with contrasting relationships between spatial distance and nutrient availability. We modeled the decay of assemblage similarity for each taxon set and site to assess the relative contributions of spatial distance and nutrient availability distance. Then, we evaluated the potentially structuring effect of tree composition over all other taxa. The similarity of nutrient content in the litter and topsoil had a stronger and more consistent selective effect than did dispersal limitation, particularly for bacteria, fungi, and trees at the plot level. Ground insects, the only group assessed with the capacity of active dispersal, had the highest species turnover and the flattest nonsignificant distance−decay relationship, suggesting that neither dispersal limitation nor nutrient availability were fundamental drivers of their community assembly at this scale of analysis. Only the fungal communities at one of our study sites were clearly coordinated with tree composition. The spatial distance at the smallest scale was more important than nutrient selection for the bacteria, fungi, and insects. The lower initial similarity and the moderate variation in composition identified by these distance-decay models, however, suggested that the effects of stochastic sampling were important at this smaller spatial scale. Our results highlight the importance of nutrients as one of the main environmental drivers of rainforest communities irrespective of organismic or propagule size and how the overriding effect of the analytical scale influences the interpretation, leading to the perception of greater importance of dispersal limitation and ecological drift over selection associated with environmental niches at decreasing observation scales.

  • Growth of soil microbes is not limited by the availability of nitrogen and phosphorus in a Mediterranean oak-savanna

    Morris KA, Richter A, Migliavacca M, Schrumpf M
    2022 - Soil Biology and Biochemistry, 169: Article 108680

    Abstract: 

    The environmental conditions under which the availability of inorganic nutrients such as nitrogen (N) and phosphorus (P) influence soil microbial growth are poorly understood, especially with regards to how fertilization changes specific aspects of microbial growth such as carbon-use efficiency (CUE). Microbial CUE is the fraction of C converted into biomass out of all C taken in and plays a critical role in global C budgets. Using the 18O labeled water method we tested short vs. long-term effects of N and/or P fertilization on microbial growth, CUE, and C, N, and P-acquiring enzyme activities in two soils from an oak-savanna, which differ in their soil organic matter (SOM) content. We hypothesized that soils with more SOM (from under tree canopies) would have higher microbial growth rates than soils with less SOM (from open grassland), and that microbial growth and CUE would increase with fertilization. We further hypothesized that these increases would be associated with a decrease in enzyme activity and a shift towards older SOM substrates in the short-term, in contrast to substrates from recently fixed C resulting from increased plant productivity in the long-term. We found that nutrient additions did not affect microbial growth or CUE in the relatively high SOM habitat on either time scale. In contrast, the low SOM habitat had lower growth and CUE when single nutrients were added, with significantly reduced growth when P alone was added, but was unchanged when N and P were added together. Our results show that short-term, stoichiometric imbalances can reduce microbial growth and that microbial growth at this site is limited not by nutrients but by the amount of C available to soil microbes.

  • Dissolved organic matter characterization in soils and streams in a small coastal low-Arctic catchment

    Speetjens NJ, Tanski G, Martin V, Wagner J, Richter A, Hugelius G, Boucher C, Lodi R, Knoblauch C, Koch BP, Wünsch U, Lantuit H, Vonk JE
    2022 - Biogeosciences, 19: 3073-3097

    Abstract: 

    Ongoing climate warming in the western Canadian Arctic is leading to thawing of permafrost soils and subsequent mobilization of its organic matter pool. Part of this mobilized terrestrial organic matter enters the aquatic system as dissolved organic matter (DOM) and is laterally transported from land to sea. Mobilized organic matter is an important source of nutrients for ecosystems, as it is available for microbial breakdown, and thus a source of greenhouse gases. We are beginning to understand spatial controls on the release of DOM as well as the quantities and fate of this material in large Arctic rivers. Yet, these processes remain systematically understudied in small, high-Arctic watersheds, despite the fact that these watersheds experience the strongest warming rates in comparison. Here, we sampled soil (active layer and permafrost) and water (porewater and stream water) from a small ice wedge polygon (IWP) catchment along the Yukon coast, Canada, during the summer of 2018. We assessed the organic carbon (OC) quantity (using dissolved (DOC) and particulate OC (POC) concentrations and soil OC content), quality (δ13C DOC, optical properties and source apportionment) and bioavailability (incubations; optical indices such as slope ratio, Sr; and humification index, HIX) along with stream water properties (temperature, T; pH; electrical conductivity, EC; and water isotopes). We classify and compare different landscape units and their soil horizons that differ in microtopography and hydrological connectivity, giving rise to differences in drainage capacity. Our results show that porewater DOC concentrations and yield reflect drainage patterns and waterlogged conditions in the watershed. DOC yield (in mg DOC g−1 soil OC) generally increases with depth but shows a large variability near the transition zone (around the permafrost table). Active-layer porewater DOC generally is more labile than permafrost DOC, due to various reasons (heterogeneity, presence of a paleo-active-layer and sampling strategies). Despite these differences, the very long transport times of porewater DOC indicate that substantial processing occurs in soils prior to release into streams. Within the stream, DOC strongly dominates over POC, illustrated by  ratios around 50, yet storm events decrease that ratio to around 5. Source apportionment of stream DOC suggests a contribution of around 50 % from permafrost/deep-active-layer OC, which contrasts with patterns observed in large Arctic rivers (12 ± 8 %; Wild et al., 2019). Our 10 d monitoring period demonstrated temporal DOC patterns on multiple scales (i.e., diurnal patterns, storm events and longer-term trends), underlining the need for high-resolution long-term monitoring. First estimates of Black Creek annual DOC (8.2 ± 6.4 t DOC yr−1) and POC (0.21 ± 0.20 t yr−1) export allowed us to make a rough upscaling towards the entire Yukon Coastal Plain (34.51 ± 2.7 kt DOC yr−1 and 8.93 ± 8.5 kt POC yr−1). Rising Arctic temperatures, increases in runoff, soil organic matter (OM) leaching, permafrost thawing and primary production are likely to increase the net lateral OC flux. Consequently, altered lateral fluxes may have strong impacts on Arctic aquatic ecosystems and Arctic carbon cycling.

  • Stormwater management in urban areas using dry gallery infiltration systems

    Miguel Angel Marazuela, Alejandro García-Gil, Juan C. Santamarta, Samanta Gasco-Cavero, Noelia Cruz-Pérez, Thilo Hofmann
    2022 - Science of The Total Environment, 823: 153705

    Abstract: 

    The increase in the frequency of extreme precipitation events due to climate change, together with the continuous development of cities and surface sealing that hinder water infiltration into the subsoil, is accelerating the search for new facilities to manage stormwater. The Canary Islands (Spain) are taking advantage of the knowledge acquired in the construction of water mines to exploit a novel stormwater management facility, which we have defined as a dry gallery. Dry galleries are constituted by a vertical well connected to a horizontal gallery dug into highly permeable volcanic layers of the vadose zone, from where infiltration takes place. However, the lack of scientific knowledge about these facilities prevents them from being properly dimensioned and managed. In this work, we simulate for the first time the infiltration process and the wetting front propagation from dry galleries based on a 3D unsaturated flow model and provide some recommendations for the installation and sizing of these facilities. The fastest advance of the wetting front takes place during the earliest times of infiltration (<2 h), with plausible propagation velocities and infiltration rates higher than 1000 m∙d−1 and 2 m3∙s−1. As time progresses, the propagation velocity and infiltration rate decrease as a consequence of the hydraulic gradient attenuation between the gallery and the aquifer. Therefore, stormwater infiltration is a highly transient process in which a sizing underestimation of 100% may be committed if unsaturated conditions or geological configuration are neglected.

  • Interleukin-11 drives human and mouse alcohol-related liver disease

    Effenberger M, Widjaja AA, Grabherr F, Schaefer B, Grander C, Mayr L, Schwaerzler J, Enrich B, Moser P, Fink J, Pedrini A, Jaschke N, Kirchmair A, Pfister A, Hausmann B, Bale R, Putzer D, Zoller H, Schafer S, Pjevac P, Trajanoski Z, Oberhuber G, Adolph T Cook S, Tilg H
    2022 - BMJ, in press

    Abstract: 

    Objective Alcoholic hepatitis (AH) reflects acute exacerbation of alcoholic liver disease (ALD) and is a growing healthcare burden worldwide. Interleukin-11 (IL-11) is a profibrotic, proinflammatory cytokine with increasingly recognised toxicities in parenchymal and epithelial cells. We explored IL-11 serum levels and their prognostic value in patients suffering from AH and cirrhosis of various aetiology and experimental ALD.
    Design IL-11 serum concentration and tissue expression was determined in a cohort comprising 50 patients with AH, 110 patients with cirrhosis and 19 healthy volunteers. Findings were replicated in an independent patient cohort (n=186). Primary human hepatocytes exposed to ethanol were studied in vitro. Ethanol-fed wildtype mice were treated with a neutralising murine IL-11 receptor-antibody (anti-IL11RA) and examined for severity signs and markers of ALD.
    Results IL-11 serum concentration and hepatic expression increased with severity of liver disease, mostly pronounced in AH. In a multivariate Cox-regression, a serum level above 6.4 pg/mL was a model of end-stage liver disease independent risk factor for transplant-free survival in patients with compensated and decompensated cirrhosis. In mice, severity of alcohol-induced liver inflammation correlated with enhanced hepatic IL-11 and IL11RA expression. In vitro and in vivo, anti-IL11RA reduced pathogenic signalling pathways (extracellular signal-regulated kinases, c-Jun N-terminal kinase, NADPH oxidase 4) and protected hepatocytes and murine livers from ethanol-induced inflammation and injury.
    Conclusion Pathogenic IL-11 signalling in hepatocytes plays a crucial role in the pathogenesis of ALD and could serve as an independent prognostic factor for transplant-free survival. Blocking IL-11 signalling might be a therapeutic option in human ALD, particularly AH.
  • Elucidating the role of the gut microbiota in the physiological effects of dietary fiber

    Deehan EC, Zhang Z, Riva A, Armet AM, Perez-Muñoz ME, Nguyen NK, Krysa JA, Seethaler, B Zhao Y-Y, Cole J, Li F, Hausmann B, Spittler A, Nazare J-A, Delzenne NM, Curtis JM, Wismer WV, Proctor SD, Bakal JA, Bischoff SC, Knights D, Field CJ, Berry D, Prado CM, Walter J
    2022 - Microbiome, in press

    Abstract: 

    Dietary fiber is an integral part of a healthy diet, but questions remain about the mechanisms that underlie effects and the causal contributions of the gut microbiota. Here, we performed a 6-week exploratory trial in adults with excess weight (BMI: 25–35 kg/m2) to compare the effects of a high-dose (females: 25 g/day; males: 35 g/day) supplement of fermentable corn bran arabinoxylan (AX; n = 15) with that of microbiota-non-accessible microcrystalline cellulose (MCC; n = 16). Obesity-related surrogate endpoints and biomarkers of host-microbiome interactions implicated in the pathophysiology of obesity (trimethylamine N-oxide, gut hormones, cytokines, and measures of intestinal barrier integrity) were assessed. We then determined whether clinical outcomes could be predicted by fecal microbiota features or mechanistic biomarkers.

  • Towards Standardization for Determining Dissolution Kinetics of Nanomaterials in Natural Aquatic Environments: Continuous Flow Dissolution of Ag Nanoparticles

    Lucie Stetten, Aiga Mackevica, Nathalie Tepe, Thilo Hofmann, Frank von der Kammer
    2022 - Nanomaterials, 12: 519

    Abstract: 

    The dissolution of metal-based engineered nanomaterials (ENMs) in aquatic environments is an important mechanism governing the release of toxic dissolved metals. For the registration of ENMs at regulatory bodies such as REACH, their dissolution behavior must therefore be assessed using standardized experimental approaches. To date, there are no standardized procedures for dissolution testing of ENMs in environmentally relevant aquatic media, and the Organisation for Economic Co-operation and Development (OECD) strongly encourages their development into test guidelines. According to a survey of surface water hydrochemistry, we propose to use media with low concentrations of Ca2+ and Mg2+ for a better simulation of the ionic background of surface waters, at pH values representing acidic (5 < pH < 6) and near-neutral/alkaline (7 < pH < 8) waters. We evaluated a continuous flow setup adapted to expose small amounts of ENMs to aqueous media, to mimic ENMs in surface waters. For this purpose, silver nanoparticles (Ag NPs) were used as model for soluble metal-bearing ENMs. Ag NPs were deposited onto a 10 kg.mol−1 membrane through the injection of 500 µL of a 5 mg.L−1 or 20 mg.L−1 Ag NP dispersion, in order to expose only a few micrograms of Ag NPs to the aqueous media. The dissolution rate of Ag NPs in 10 mM NaNO3 was more than two times higher for ~2 µg compared with ~8 µg of Ag NPs deposited onto the membrane, emphasizing the importance of evaluating the dissolution of ENMs at low concentrations in order to keep a realistic scenario. Dissolution rates of Ag NPs in artificial waters (2 mM Ca(NO3)2, 0.5 mM MgSO4, 0–5 mM NaHCO3) were also determined, proving the feasibility of the test using environmentally relevant media. In view of the current lack of harmonized methods, this work encourages the standardization of continuous flow dissolution methods toward OECD guidelines focused on natural aquatic environments, for systematic comparisons of nanomaterials and adapted risk assessments.

  • Iron Nitride Nanoparticles for Enhanced Reductive Dechlorination of Trichloroethylene

    Miroslav Brumovský, Jana Oborná, Malfatti SE, Ondřej Malina, Josef Kašlík, Daniel Tunega, Miroslav Kolos, Thilo Hofmann, František Karlický, Jan Filip
    2022 - Environmental Science & Technology, 56: 4425-4436

    Abstract: 

    Nitriding has been used for decades to improve the corrosion resistance of iron and steel materials. Moreover, iron nitrides (FexN) have been shown to give an outstanding catalytic performance in a wide range of applications. We demonstrate that nitriding also substantially enhances the reactivity of zerovalent iron nanoparticles (nZVI) used for groundwater remediation, alongside reducing particle corrosion. Two different types of FexN nanoparticles were synthesized by passing gaseous NH3/N2 mixtures over pristine nZVI at elevated temperatures. The resulting particles were composed mostly of face-centered cubic (γ′-Fe4N) and hexagonal close-packed (ε-Fe2–3N) arrangements. Nitriding was found to increase the particles’ water contact angle and surface availability of iron in reduced forms. The two types of FexN nanoparticles showed a 20- and 5-fold increase in the trichloroethylene (TCE) dechlorination rate, compared to pristine nZVI, and about a 3-fold reduction in the hydrogen evolution rate. This was related to a low energy barrier of 27.0 kJ mol–1 for the first dechlorination step of TCE on the γ′-Fe4N(001) surface, as revealed by density functional theory calculations with an implicit solvation model. TCE dechlorination experiments with aged particles showed that the γ′-Fe4N nanoparticles retained high reactivity even after three months of aging. This combined theoretical-experimental study shows that FexN nanoparticles represent a new and potentially important tool for TCE dechlorination.

  • Demystifying mercury geochemistry in contaminated soil–groundwater systems with complementary mercury stable isotope, concentration, and speciation analyses

    David S. McLagan, Lorenz Schwab, Jan G. Wiederhold, Lu Chen, Jan Pietrucha, Stephan M. Kraemer, Harald Biester
    2022 - Environmental Science: Processes & Impacts, Advance Article

    Abstract: 

    Interpretation of mercury (Hg) geochemistry in environmental systems remains a challenge. This is largely associated with the inability to identify specific Hg transformation processes and species using established analytical methods in Hg geochemistry (total Hg and Hg speciation). In this study, we demonstrate the improved Hg geochemical interpretation, particularly related to process tracing, that can be achieved when Hg stable isotope analyses are complemented by a suite of more established methods and applied to both solid- (soil) and liquid-phases (groundwater) across two Hg2+-chloride (HgCl2) contaminated sites with distinct geological and physicochemical properties. This novel approach allowed us to identify processes such as Hg2+ (i.e., HgCl2) sorption to the solid-phase, Hg2+ speciation changes associated with changes in groundwater level and redox conditions (particularly in the upper aquifer and capillary fringe), Hg2+ reduction to Hg0, and dark abiotic redox equilibration between Hg0 and Hg(II). Hg stable isotope analyses play a critical role in our ability to distinguish, or trace, these in situ processes. While we caution against the non-critical use of Hg isotope data for source tracing in environmental systems, due to potentially variable source signatures and overprinting by transformation processes, our study demonstrates the benefits of combining multiple analytical approaches, including Hg isotope ratios as a process tracer, to obtain an improved picture of the enigmatic geochemical behavior and fate of Hg at contaminated legacy sites.

  • Isotopically characterised N2O reference materials for use as community standards

    Mohn J, Biasi C, Bodé S, Boeckx P, Brewer PJ, Eggleston S, Geilmann H, Guillevic M, Kaiser J, Kantnerová K, Moossen H, Muller J, Nakagawa M, Pearce R, von Rein I, Steger D, Toyoda S, Wanek W, Wexler SK, Yoshida N, Yu L
    2022 - Rapid Communications in Mass Spectrometry, 36: Article e9296

    Abstract: 

    Rationale

    Information on the isotopic composition of nitrous oxide (N2O) at natural abundance supports the identification of its source and sink processes. In recent years, a number of mass spectrometric and laser spectroscopic techniques have been developed and are increasingly used by the research community. Advances in this active research area, however, critically depend on the availability of suitable N2O isotope Reference Materials (RMs).

    Methods

    Within the project Metrology for Stable Isotope Reference Standards (SIRS), seven pure N2O isotope RMs have been developed and their 15N/14N, 18O/16O, 17O/16O ratios and 15N site preference (SP) have been analysed by specialised laboratories against isotope reference materials. A particular focus was on the 15N site-specific isotopic composition, as this measurand is both highly diagnostic for source appointment and challenging to analyse and link to existing scales.

    Results

    The established N2O isotope RMs offer a wide spread in delta (δ) values: δ15N: 0 to +104‰, δ18O: +39 to +155‰, and δ15NSP: −4 to +20‰. Conversion and uncertainty propagation of δ15N and δ18O to the Air-N2 and VSMOW scales, respectively, provides robust estimates for δ15N(N2O) and δ18O(N2O), with overall uncertainties of about 0.05‰ and 0.15‰, respectively. For δ15NSP, an offset of >1.5‰ compared with earlier calibration approaches was detected, which should be revisited in the future.

    Conclusions

    A set of seven N2O isotope RMs anchored to the international isotope-ratio scales was developed that will promote the implementation of the recommended two-point calibration approach. Particularly, the availability of δ17O data for N2O RMs is expected to improve data quality/correction algorithms with respect to δ15NSP and δ15N analysis by mass spectrometry. We anticipate that the N2O isotope RMs will enhance compatibility between laboratories and accelerate research progress in this emerging field.

  • Contrasting drivers of belowground nitrogen cycling in a montane grassland exposed to a multifactorial global change experiment with elevated CO, warming, and drought

    Maxwell TL, Canarini A, Bogdanovic I, Böckle T, Martin V, Noll L, Prommer J, Séneca J, Simon E, Piepho HP, Herndl M, Pötsch EM, Kaiser C, Richter A, Bahn M, Wanek W
    2022 - Global Change Biology, 28: 2425-2441

    Abstract: 

    Depolymerization of high-molecular weight organic nitrogen (N) represents the major bottleneck of soil N cycling and yet is poorly understood compared to the subsequent inorganic N processes. Given the importance of organic N cycling and the rise of global change, we investigated the responses of soil protein depolymerization and microbial amino acid consumption to increased temperature, elevated atmospheric CO2, and drought. The study was conducted in a global change facility in a managed montane grassland in Austria, where elevated CO2 (eCO2) and elevated temperature (eT) were stimulated for 4 years, and were combined with a drought event. Gross protein depolymerization and microbial amino acid consumption rates (alongside with gross organic N mineralization and nitrification) were measured using 15N isotope pool dilution techniques. Whereas eCO2 showed no individual effect, eT had distinct effects which were modulated by season, with a negative effect of eT on soil organic N process rates in spring, neutral effects in summer, and positive effects in fall. We attribute this to a combination of changes in substrate availability and seasonal temperature changes. Drought led to a doubling of organic N process rates, which returned to rates found under ambient conditions within 3 months after rewetting. Notably, we observed a shift in the control of soil protein depolymerization, from plant substrate controls under continuous environmental change drivers (eT and eCO2) to controls via microbial turnover and soil organic N availability under the pulse disturbance (drought). To the best of our knowledge, this is the first study which analyzed the individual versus combined effects of multiple global change factors and of seasonality on soil organic N processes and thereby strongly contributes to our understanding of terrestrial N cycling in a future world.

  • Stoichiometric regulation of priming effects and soil carbon balance by microbial life strategies

    Zhu Z, Fang Y, Liang Y, Li Y, Liu S, Li B, Gao W, Yuan H, Kuzyakov Y, Wu J, Richter A, Ge T
    2022 - Soil Biology and Biochemistry, 169: Article 108669

    Abstract: 

    Carbon and nutrient inputs are required to stimulate the formation and mineralization of soil organic carbon (SOC) through processes related to microbial growth and priming effects (PEs). PEs are thought to affect microbial life strategies, however, the mechanisms underlying their role in SOC formation and microbial dynamics remain largely unknown, particularly in paddy soils. Here, we examined the underlying strategies and response mechanisms of microorganisms in regulating PEs and C accumulation in flooded paddy soil. Levels and stoichiometric ratios of resources were evaluated over a 60-day incubation period. Low (equivalent to 50% soil microbial biomass C [MBC]) and high (500% MBC) doses of 13C-labeled glucose were added to the soil, along with mineral N, P, and S (NPS) fertilizers at five concentrations. Glucose mineralization increased linearly with NPS concentration under both low and high glucose inputs. However, glucose addition without nutrients induced the preferential microbial utilization of the readily available C, leading to negative PEs. Under high-glucose input, the intensity of negative PEs increased with increasing NPS addition (PE: from −460 to −710 mg C kg−1 soil). In contrast, under low-glucose inputs, the intensity of positive PEs increased with increasing NPS addition (PE: 60–100 mg C kg−1 soil). High-glucose input with NPS fertilization favored high-yield microbial strategists (Y-strategists), increasing glucose-derived SOC accumulation. This phenomenon was evidenced by the large quantities of 13C detected in microbial biomass and phospholipid fatty acids (PLFAs), increasing the soil net C balance (from 0.76 to 1.2 g C kg−1). In contrast, low levels of glucose and NPS fertilization shifted the microbial community composition toward dominance of resource-acquisition strategists (A-strategists), increasing SOC mineralization. This was evidenced by 13C incorporation into the PLFAs of gram-positive bacteria, increased activity of N- and P-hydrolases, and positive PEs for acquiring C and nutrients from soil organic matter. Consequently, the soil net C balance decreased from 0.31 to 0.01 g C kg−1 soil. In conclusion, high C input (i.e., 500% MBC), particularly alongside hig NPS addition, increases SOC content via negative priming and microbial-derived C accumulation due to the shift toward Y-strategist communities which efficiently utilize resources. This study highlights the importance of mineral fertilization management when incorporating organic supplements in paddy soils to stimulate microbial turnover and C sequestration.

  • Long-term soil warming alters fine root dynamics and morphology, and their ectomycorrhizal fungal community in a temperate forest soil

    Kwatcho Kengdo S, Peršoh D, Schindlbacher A, Heinzle J, Tian Y, Wanek W, Borken W
    2022 - Global Change Biology, in press

    Abstract: 

    Climate warming is predicted to affect temperate forests severely, but the response of fine roots, key to plant nutrition, water uptake, soil carbon, and nutrient cycling is unclear. Understanding how fine roots will respond to increasing temperature is a prerequisite for predicting the functioning of forests in a warmer climate. We studied the response of fine roots and their ectomycorrhizal (EcM) fungal and root-associated bacterial communities to soil warming by 4°C in a mixed spruce-beech forest in the Austrian Limestone Alps after 8 and 14 years of soil warming, respectively. Fine root biomass (FRB) and fine root production were 17% and 128% higher in the warmed plots, respectively, after 14 years. The increase in FRB (13%) was not significant after 8 years of treatment, whereas specific root length, specific root area, and root tip density were significantly higher in warmed plots at both sampling occasions. Soil warming did not affect EcM exploration types and diversity, but changed their community composition, with an increase in the relative abundance of Cenoccocum at 0–10 cm soil depth, a drought-stress-tolerant genus, and an increase in short- and long-distance exploration types like Sebacina and Boletus at 10–20 cm soil depth. Warming increased the root-associated bacterial diversity but did not affect their community composition. Soil warming did not affect nutrient concentrations of fine roots, though we found indications of limited soil phosphorus (P) and potassium (K) availability. Our findings suggest that, in the studied ecosystem, global warming could persistently increase soil carbon inputs due to accelerated fine root growth and turnover, and could simultaneously alter fine root morphology and EcM fungal community composition toward improved nutrient foraging.

  • Limnospira fusiformis harbors dinitrogenase reductase (nifH)-like genes, but does not show N2 fixation activity

    Schagerl M, Angel R, Donabaum U, Gschwandner AM, Woebken D
    2022 - Algal Research, 66: 102771

    Abstract: 

    East African soda lakes (EASLs), some of them world-renowned for their large flocks of flamingos, range amongst the most productive aquatic ecosystems worldwide. The non-heterocytous filamentous cyanobacterium Limnospira fusiformis (formerly Arthrospira fusiformis or Spirulina platensis), forming almost unialgal blooms, is supposed to be a key driver in those ecosystems and is gaining increasing attention because of its nutritional value. Compared to phosphorus and carbon availability, these lakes show reduced nitrogen supply. We studied the possibility of molecular nitrogen (N2) fixation in Limnospira, as contradictory statements have been published, and some closely related taxa were confirmed as N2 fixers (diazotrophs). We cultivated nine isolates originating from various EASLs under nitrate-rich and nitrate-depleted conditions. We detected dinitrogenase reductase (nifH)-like genes in all strains; however, the genes grouped within nifH cluster IV that mostly contains nitrogenases not functioning in N2 fixation. Accordingly, incubations with 15N2 gas did not support N2 fixation activity of the investigated strains. Under laboratory conditions, all strains faded during nitrate-depleted growth after approximately three weeks. Both phycocyanin and chlorophyll-a dropped to a threshold, and chlorophyll fluorescence indicated a severe problem with nitrogen supply. In summary, our data indicate that the investigated Limnospira fusiformis strains are not capable of N2 fixation.

     

  • Putting vascular epiphytes on the traits map

    Hietz P, Wagner K, Nunes Ramos F, Cabral J, Agudelo C, Benavides AM, Cach-Pérez MJ, Cardelús C, Chilpa Galván N, Costa L, de Paula Oliveira R, Einzmann H, Farias R, Guzmán JV, Kattge J, Kessler M, Kirby C, Kreft H, Kromer T, Males J, Monsalve Correa S, Moreno-Chacón M, Petter G, Reyes-Garcia C, Saldana A, Schellenberger Costa D, Taylor A, Velázquez Rosas N, Wanek W, Woods C, Zotz G
    2022 - Journal of Ecology, 110: 340-358

    Abstract: 

    1. Plant functional traits impact the fitness and environmental niche of plants. Major plant functional types have been characterized by their trait spectrum, and the environmental and phylogenetic imprints on traits have advanced several ecological fields. Yet, very few trait data on epiphytes, which represent almost 10% of vascular plants, are available.
    2. We collated 76,561 trait observations for 2,882 species of vascular epiphytes and compared these to non-epiphytic herbs and trees to test hypotheses related to how the epiphytic habit affects traits, and if epiphytes occupy a distinct region in the global trait space. We also compared variation in traits among major groups of epiphytes, and investigated the coordination of traits in epiphytes, ground-rooted herbs and trees.
    3. Epiphytes differ from ground-rooted plants mainly in traits related to water relations. Unexpectedly, we did not find lower leaf nutrient concentrations, except for nitrogen. Mean photosynthetic rates are much lower than in ground-rooted plants and lower than expected from the nitrogen concentrations. Trait syndromes clearly distinguish epiphytes from trees and from most non-epiphytic herbs.
    4. Among the three largest epiphytic taxa, orchids differ from bromeliads and ferns mainly by having smaller and more numerous stomata, while ferns differ from bromeliads by having thinner leaves, higher nutrient concentrations, and lower water content and water use efficiency.
    5. Trait networks differ among epiphytes, herbs and trees. While all have central nodes represented by SLA and mass-based photosynthesis, in epiphytes, traits related to plant water relations have stronger connections, and nutrients other than potassium have weaker connections to the remainder of the trait network. Whereas stem-specific density reflects mechanical support related to plant size in herbs and trees, in epiphytes it mostly reflects water storage and scales with leaf water content.
    6. Synthesis. Our findings advance our understanding of epiphyte ecology, but we note that currently mainly leaf traits are available. Important gaps are root, shoot and whole plant, demographic and gas exchange traits. We suggest how future research might use available data and fill data gaps.
    • We collated 76,561 trait observations for 2,882 species of vascular epiphytes and compared these to non-epiphytic herbs and trees to test hypotheses related to how the epiphytic habit affects traits, and if epiphytes occupy a distinct region in the global trait space. We also compared variation in traits among major groups of epiphytes, and investigated the coordination of traits in epiphytes, ground-rooted herbs and trees.
    • Epiphytes differ from ground-rooted plants mainly in traits related to water relations. Unexpectedly, we did not find lower leaf nutrient concentrations, except for nitrogen. Mean photosynthetic rates are much lower than in ground-rooted plants and lower than expected from the nitrogen concentrations. Trait syndromes clearly distinguish epiphytes from trees and from most non-epiphytic herbs.
    • Among the three largest epiphytic taxa, orchids differ from bromeliads and ferns mainly by having smaller and more numerous stomata, while ferns differ from bromeliads by having thinner leaves, higher nutrient concentrations, and lower water content and water use efficiency.
    • Trait networks differ among epiphytes, herbs and trees. While all have central nodes represented by SLA and mass-based photosynthesis, in epiphytes, traits related to plant water relations have stronger connections, and nutrients other than potassium have weaker connections to the remainder of the trait network. Whereas stem-specific density reflects mechanical support related to plant size in herbs and trees, in epiphytes it mostly reflects water storage and scales with leaf water content.
    • Synthesis. Our findings advance our understanding of epiphyte ecology, but we note that currently mainly leaf traits are available. Important gaps are root, shoot and whole plant, demographic and gas exchange traits. We suggest how future research might use available data and fill data gaps.
  • Litter diversity accelerates labile carbon but slows recalcitrant carbon decomposition

    Wang L, Zhou Y, Chen Y, Xu Z, Zhang J, Liu Y, Joly FX
    2022 - Soil Biology and Biochemistry, 168: Article 108632

    Abstract: 

    In biodiverse ecosystems, leaf litter of different plant species decomposes in mixtures, for which decomposition rates notoriously deviate from that expected from monospecific treatments. Despite important research efforts in past decades, these litter diversity effects remain difficult to predict. We hypothesized that this is due to a focus on bulk litter decomposition, while different carbon fractions constituting the litter may respond differently to litter diversity, thereby blurring the overall response. To test this hypothesis, we determined how the decomposition of (i) soluble compounds, (ii) cellulose, and (iii) lignin responded to litter mixing in a 3.5-year field experiment in an alpine forest. We found that the decomposition of soluble compounds and cellulose in mixtures was faster than expected from monospecific treatments, while that of lignin was slower. These deviations from expected decomposition rates of each litter carbon fraction were driven by different aspects of the litter functional diversity. This suggests that different mechanisms operating on distinct litter fractions lead to synergistic and antagonistic interactions that simultaneously affect bulk litter decomposition. Furthermore, the magnitude of these fraction-specific deviations from expected decomposition rates consistently decreased throughout decomposition. Considering the response of litter fractions and their temporality, rather than focusing on bulk litter thus seems critical to evaluate the response of decomposition to plant diversity and identify underlying mechanisms.

  • Freshwater suspended particulate matter—Key components and processes in floc formation and dynamics

    Helene Walch, Frank von der Kammer, Thilo Hofmann
    2022 - Water Research, 220: in press

    Abstract: 

    Freshwater suspended particulate matter (SPM) plays an important role in many biogeochemical cycles and serves multiple ecosystem functions. Most SPM is present as complex floc-like aggregate structures composed of various minerals and organic matter from the molecular to the organism level. Flocs provide habitat for microbes and feed for larger organisms. They constitute microbial bioreactors, with prominent roles in carbon and inorganic nutrient cycles, and transport nutrients as well as pollutants, affecting sediments, inundation zones, and the ocean. Composition, structure, size, and concentration of SPM flocs are subject to high spatiotemporal variability. Floc formation processes and compositional or morphological dynamics can be established around three functional components: phyllosilicates, iron oxides/(oxy)hydroxides (FeOx), and microbial extracellular polymeric substances (EPS). These components and their interactions increase heterogeneity in surface properties, enhancing flocculation. Phyllosilicates exhibit intrinsic heterogeneities in surface charge and hydrophobicity. They are preferential substrates for precipitation or attachment of reactive FeOx. FeOx form patchy coatings on minerals, especially on phyllosilicates, which increase surface charge heterogeneities. Both, phyllosilicates and FeOx strongly adsorb natural organic matter (NOM), preferentially certain EPS. EPS comprise various substances with heterogeneous properties that make them a sticky mixture, enhancing flocculation. Microbial metabolism, and thus EPS release, is supported by the high adsorption capacity and favorable nutrient composition of phyllosilicates, and FeOx supply essential Fe.

  • Trichoderma reesei

    Schmoll M
    2022 - Trends in microbiology, 30: 403-404

    Abstract: 

    The filamentous fungus Trichoderma reesei (teleomorph: Hypocrea jecorina) grows on rotting plant material in its natural habitat. It is among the most prolific producers of plant cell-wall-degrading enzymes and is frequently used in industry for production of those and other performance proteins. A complete telomere-to-telomere genome sequence is now available (34 Mb, 10 877 genes, 7 chromosomes). Sexual reproduction of the haploid T. reesei in the laboratory was achieved only about a decade ago and requires pheromones, but also other chemical signals. T. reesei is readily transformable, and a plethora of tools, including CRISPR/Cas, have been developed which facilitate functional genomics, genome-wide investigations, and live-cell imaging, and tools to investigate chemical communication. Studies focused on a detailed understanding of enzyme expression and its improvement revealed the interplay of numerous transcription factors, connections to signaling pathways, and a significant impact of light. Detailed understanding of the physiology of T. reesei will enable optimized enzyme expression and thereby support development of more sustainable, yet commercially viable, solutions for biofuel production, textile production and recycling, chemical conversions using enzymes, food processing, production of pharmaceuticals including antibodies, bioremediation, and agriculture.

  • Pharmaceutical pollution of the world’s rivers

    John L. Wilkinson, Alistair B. A. Boxall, Dana W. Kolpin, Kenneth M. Y. Leung, Racliffe W. S. Lai, Cristobal Galban-Malagon, Aiko D. Adell, Julie Mondon, Marc Metian, Robert A. Marchant, Alejandra Bouzas-Monroy, Aida Cuni-Sanchez, Anja Coors, Pedro Carriquiriborde, Macarena Rojo, Chris Gordon, Magdalena Cara, Monique Moermond, Thais Luarte, Vahagn Petrosyan, Yekaterina Perikhanyan, Clare S. Mahon, Christopher J. McGurk, Thilo Hofmann, Tapos Kormoker, Volga Iniguez, Jessica Guzman-Otazo, Jean L. Tavares, Francisco Gildasio De Figueiredo, Maria T. P. Razzolini, Victorien Dougnon, Gildas Gbaguidi, Oumar Traore, Jules M. Blais, Linda E. Kimpe, Michelle Wong, Donald Wong, Romaric Ntchantcho, Jaime Pizarro, Guang-Guo Ying, Chang-Er Chen, Martha Paez, Jina Martinez-Lara, Jean-Paul Otamonga, John Pote, Suspense A. Ifo, Penelope Wilson, Silvia Echeverria-Saenz, Nikolina Udikovic-Kolic, Milena Milakovic, Despo Fatta-Kassinos, Lida Ioannou-Ttofa, Vladimira Belusova, Jan Vymazal, Maria Cardenas-Bustamante, Bayable A. Kas
    2022 - PNAS, 119: e2113947119

    Abstract: 

    Environmental exposure to active pharmaceutical ingredients (APIs) can have negative effects on the health of ecosystems and humans. While numerous studies have monitored APIs in rivers, these employ different analytial methods, measure different APIs, and have ignored many of the countries of the world. This makes it difficult to quantify the scale of the problem from a global perspective. Furthermore, comparison of the existing data, generated for different studies/regions/continents, is challenging due to the vast differences between the analytical methodologies employed. Here, we present a global-scale study of API pollution in 258 of the world’s rivers, representing the environmental influence of 471.4 million people across 137 geographic regions. Samples were obtained from 1,052 locations in 104 countries (representing all continents and 36 countries not previously studied for API contamination) and analyzed for 61 APIs. Highest cumulative API concentrations were observed in sub-Saharan Africa, south Asia, and South America. The most contaminated sites were in low- to middle-income countries and were associated with areas with poor wastewater and waste management infrastructure and pharmaceutical manufacturing. The most frequently detected APIs were carbamazepine, metformin, and caffeine (a compound also arising from lifestyle use), which were detected at over half of the sites monitored. Concentrations of at least one API at 25.7% of the sampling sites were greater than concentrations considered safe for aquatic organisms, or which are of concern in terms of selection for antimicrobial resistance. Therefore, pharmaceutical pollution poses a global threat to environmental and human health, as well as to delivery of the United Nations Sustainable Development Goals.

  • Individual sweet taste perception influences salivary characteristics after orosensory stimulation with sucrose and non-caloric sweeteners

    Karl CM, Vidakovic A, Pjevac P, Hausmann B, Schleining G, Ley JP, Berry D, Hans J, WEndlin M, Koenig J, Somoza V, Lieder B
    2022 - Front Nutrition, 9: 831726

    Abstract: 

    Emerging evidence suggests a major role for salivary flow and the viscoelastic properties for taste perception and mouthfeel. Sweet-tasting compounds have also been proposed to have an effect on salivary characteristic. However, it is yet not clarified if perceived differences in the sensorial properties of structural diverse sweet tasting compounds contribute to salivary flow and viscoelasticity of saliva as part of mouthfeel and overall taste perception. Here we hypothesized that sensorially diverse sweeteners would affect salivary characteristics differently. Thus, we investigated the salivary flow, viscoelasticity of saliva, and selected influencing factors including the basal oral microbiome from 21 healthy test subjects after orosensory stimulation with sucrose, rebaudioside M (RebM), sucralose, and neohesperidin dihydrochalcone (NHDC) in a cross-over design. All test compounds enhanced the salivary flow by up to 1.51 ± 0.12 g/min for RebM, compared to 1.10 ± 0.09 g/min for water in the first minute after stimulation. The increase in the flow rate was correlated moderately to the individual perceived sweetness (r= 0.3, p< 0.01), but did not differ between the test compounds. The complex viscosity of the saliva was not affected by the test compounds, but analysis of covariance showed that the complex viscosity was associated (p< 0.05) with the concentration of mucin 5B (Muc5B). The oral microbiome showed a typical composition and diversity but was strongly individual-dependent (PERMANOVA: R²=0.76, p< 0.001), and was not associated with the changes in salivary characteristics. In conclusion, the present study indicates an impact of the individual sweetness impression on the flow rate without measurable changes in the complex viscosity of saliva, which may contribute to overall taste perception and mouthfeel of sweet tasting compounds.

  • Targeting Gut Bacteria Using Inulin-Conjugated Mesoporous Silica Nanoparticles

    von Baeckmann C, Riva A, Guggenberger P, Kählig H, Han SW, Inan D, Del Favero G, Berry D, Kleitz F
    2022 - Adv Mater Interfaces, 9: 202102558

    Abstract: 

    To facilitate the creation of novel nanocarrier systems targeting the intestinal microbiome, inulin-conjugated mesoporous silica nanoparticles (MSNs) are described herein for the first time. Surface functionalization is achieved on either hydrophilic or hydrophobic mesoporous nanoparticles using different conjugation methods. The targeting performance of the resulting materials is assessed and compared upon incubation with human stool. It appears that amide formation is the most favorable coupling method on hydrophilic MSNs to achieve the desired bioconjugate. Remarkably, high affinity of gut bacteria to the conjugated particles can be obtained, paving the way to novel targeted drug delivery systems.

  • Microbiome assembly in thawing permafrost and its feedbacks to climate

    Ernakovich JG, Barbato RA, Rich VI, Schädel C, Hewitt RE, Doherty SJ, Whalen ED, Abbott BW, Barta J, Biasi C, Chabot CL, Hultman J, Knoblauch C, Lau Vetter MCY, Leewis M-C, Liebner S, Mackelprang R, Onstott TC, Richter A, Schütte UME, Siljanen HMP, Taş N, Timling I, Vishnivetskaya TA, Waldrop MP, Winkel M
    2022 - Global Change Biology, in press

    Abstract: 

    The physical and chemical changes that accompany permafrost thaw directly influence the microbial communities that mediate the decomposition of formerly frozen organic matter, leading to uncertainty in permafrost–climate feedbacks. Although changes to microbial metabolism and community structure are documented following thaw, the generality of post-thaw assembly patterns across permafrost soils of the world remains uncertain, limiting our ability to predict biogeochemistry and microbial community responses to climate change. Based on our review of the Arctic microbiome, permafrost microbiology, and community ecology, we propose that Assembly Theory provides a framework to better understand thaw-mediated microbiome changes and the implications for community function and climate feedbacks. This framework posits that the prevalence of deterministic or stochastic processes indicates whether the community is well-suited to thrive in changing environmental conditions. We predict that on a short timescale and following high-disturbance thaw (e.g., thermokarst), stochasticity dominates post-thaw microbiome assembly, suggesting that functional predictions will be aided by detailed information about the microbiome. At a longer timescale and lower-intensity disturbance (e.g., active layer deepening), deterministic processes likely dominate, making environmental parameters sufficient for predicting function. We propose that the contribution of stochastic and deterministic processes to post-thaw microbiome assembly depends on the characteristics of the thaw disturbance, as well as characteristics of the microbial community, such as the ecological and phylogenetic breadth of functional guilds, their functional redundancy, and biotic interactions. These propagate across space and time, potentially providing a means for predicting the microbial forcing of greenhouse gas feedbacks to global climate change.

  • Bacterial growth in multicellular aggregates leads to the emergence of complex life cycles.

    Schwartzman JA, Ebrahimi A, Chadwick G, Sato Y, Roller BRK, Orphan VJ, Cordero OX
    2022 - Curr Biol, In press
    Picture credit to Julia Schwartzman, MIT

    Abstract: 

    Facultative multicellular behaviors expand the metabolic capacity and physiological resilience of bacteria. Despite their ubiquity in nature, we lack an understanding of how these behaviors emerge from cellular-scale phenomena. Here, we show how the coupling between growth and resource gradient formation leads to the emergence of multicellular lifecycles in a marine bacterium. Under otherwise carbon-limited growth conditions, Vibrio splendidus 12B01 forms clonal multicellular groups to collectively harvest carbon from soluble polymers of the brown-algal polysaccharide alginate. As they grow, groups phenotypically differentiate into two spatially distinct sub-populations: a static "shell" surrounding a motile, carbon-storing "core." Differentiation of these two sub-populations coincides with the formation of a gradient in nitrogen-source availability within clusters. Additionally, we find that populations of cells containing a high proportion of carbon-storing individuals propagate and form new clusters more readily on alginate than do populations with few carbon-storing cells. Together, these results suggest that local metabolic activity and differential partitioning of resources leads to the emergence of reproductive cycles in a facultatively multicellular bacterium.

  • Phage-host coevolution in natural populations.

    Piel D, Bruto M, Labreuche Y, Blanquart F, Goudenège D, Barcia-Cruz R, Chenivesse S, Le Panse S, James A, Dubert J, Petton B, Lieberman E, Wegner KM, Hussain FA, Kauffman KM, Polz MF, Bikard D, Gandon S, Rocha EPC, Le Roux F
    2022 - Nat Microbiol, 7: 1075-1086

    Abstract: 

    Coevolution between bacteriophages (phages) and their bacterial hosts occurs through changes in resistance and counter-resistance mechanisms. To assess phage-host evolution in wild populations, we isolated 195 Vibrio crassostreae strains and 243 vibriophages during a 5-month time series from an oyster farm and combined these isolates with existing V. crassostreae and phage isolates. Cross-infection studies of 81,926 host-phage pairs delineated a modular network where phages are best at infecting co-occurring hosts, indicating local adaptation. Successful propagation of phage is restricted by the ability to adsorb to closely related bacteria and further constrained by strain-specific defence systems. These defences are highly diverse and predominantly located on mobile genetic elements, and multiple defences are active within a single genome. We further show that epigenetic and genomic modifications enable phage to adapt to bacterial defences and alter host range. Our findings reveal that the evolution of bacterial defences and phage counter-defences is underpinned by frequent genetic exchanges with, and between, mobile genetic elements.

  • A nitrite-oxidising bacterium constitutively consumes atmospheric hydrogen

    Leung PM, Daebeler A, Chiri E, Hanchapola I, Gillett DL, Schittenhelm RB, Daims H, Greening C
    2022 - ISME J, in press

    Abstract: 

    Chemolithoautotrophic nitrite-oxidising bacteria (NOB) of the genus Nitrospira contribute to nitrification in diverse natural environments and engineered systems. Nitrospira are thought to be well-adapted to substrate limitation owing to their high affinity for nitrite and capacity to use alternative energy sources. Here, we demonstrate that the canonical nitrite oxidiser Nitrospira moscoviensis oxidises hydrogen (H2) below atmospheric levels using a high-affinity group 2a nickel-iron hydrogenase [Km(app) = 32 nM]. Atmospheric H2 oxidation occurred under both nitrite-replete and nitrite-deplete conditions, suggesting low-potential electrons derived from H2 oxidation promote nitrite-dependent growth and enable survival during nitrite limitation. Proteomic analyses confirmed the hydrogenase was abundant under both conditions and indicated extensive metabolic changes occur to reduce energy expenditure and growth under nitrite-deplete conditions. Thermodynamic modelling revealed that H2 oxidation theoretically generates higher power yield than nitrite oxidation at low substrate concentrations and significantly contributes to growth at elevated nitrite concentrations. Collectively, this study suggests atmospheric H2 oxidation enhances the growth and survival of NOB amid variability of nitrite supply, extends the phenomenon of atmospheric H2 oxidation to an eighth phylum (Nitrospirota), and reveals unexpected new links between the global hydrogen and nitrogen cycles. Long classified as obligate nitrite oxidisers, our findings suggest H2 may primarily support growth and survival of certain NOB in natural environments.

  • SRS-FISH: A high-throughput platform linking microbiome metabolism to identity at the single-cell level

    Gea X, Pereira FC, Mitteregger M, Berry D, Zhanga M, Hausmann B, Zhange J, Schintlmeister A, Wagner M, Cheng J-X
    2022 - Proc Natl Acad Sci U S A, 119: e2203519119
    Stimulated Raman Spectroscopy

    Abstract: 

    One of the biggest challenges in microbiome research in environmental and medicalsamples is to better understand functional properties of microbial community membersat a single-cell level. Single-cell isotope probing has become a key tool for this purpose,but the current detection methods for determination of isotope incorporation into singlecells do not allow high-throughput analyses. Here, we report on the development of animaging-based approach termed stimulated Raman scattering–two-photon fluorescencein situ hybridization (SRS-FISH) for high-throughput metabolism and identity analysesof microbial communities with single-cell resolution. SRS-FISH offers an imaging speedof 10 to 100 ms per cell, which is two to three orders of magnitude faster than achievableby state-of-the-art methods. Using this technique, we delineated metabolic responses of 30,000 individual cells to various mucosal sugars in the human gut microbiome viaincorporation of deuterium from heavy water as an activity marker. Application of SRS-FISH to investigate the utilization of host-derived nutrients by two major human gutmicrobiome taxa revealed that response to mucosal sugars tends to be dominated byBacteroidales, with an unexpected finding that Clostridia can outperform Bacteroidalesat foraging fucose. With high sensitivity and speed, SRS-FISH will enable researchers toprobe the fine-scale temporal, spatial, and individual activity patterns of microbial cellsin complex communities with unprecedented detail.

  • Elucidating the role of the gut microbiota in the physiological effects of dietary fiber.

    Deehan EC, Zhang Z, Riva A, Armet AM, Perez-Muñoz ME, Nguyen NK, Krysa JA, Seethaler B, Zhao YY, Cole J, Li F, Hausmann B, Spittler A, Nazare JA, Delzenne NM, Curtis JM, Wismer WV, Proctor SD, Bakal JA, Bischoff SC, Knights D, Field CJ, Berry D, Prado CM, Walter J
    2022 - Microbiome, 1: 77

    Abstract: 

    Dietary fiber is an integral part of a healthy diet, but questions remain about the mechanisms that underlie effects and the causal contributions of the gut microbiota. Here, we performed a 6-week exploratory trial in adults with excess weight (BMI: 25-35 kg/m) to compare the effects of a high-dose (females: 25 g/day; males: 35 g/day) supplement of fermentable corn bran arabinoxylan (AX; n = 15) with that of microbiota-non-accessible microcrystalline cellulose (MCC; n = 16). Obesity-related surrogate endpoints and biomarkers of host-microbiome interactions implicated in the pathophysiology of obesity (trimethylamine N-oxide, gut hormones, cytokines, and measures of intestinal barrier integrity) were assessed. We then determined whether clinical outcomes could be predicted by fecal microbiota features or mechanistic biomarkers.
    AX enhanced satiety after a meal and decreased homeostatic model assessment of insulin resistance (HOMA-IR), while MCC reduced tumor necrosis factor-α and fecal calprotectin. Machine learning models determined that effects on satiety could be predicted by fecal bacterial taxa that utilized AX, as identified by bioorthogonal non-canonical amino acid tagging. Reductions in HOMA-IR and calprotectin were associated with shifts in fecal bile acids, but correlations were negative, suggesting that the benefits of fiber may not be mediated by their effects on bile acid pools. Biomarkers of host-microbiome interactions often linked to bacterial metabolites derived from fiber fermentation (short-chain fatty acids) were not affected by AX supplementation when compared to non-accessible MCC.
    This study demonstrates the efficacy of purified dietary fibers when used as supplements and suggests that satietogenic effects of AX may be linked to bacterial taxa that ferment the fiber or utilize breakdown products. Other effects are likely microbiome independent. The findings provide a basis for fiber-type specific therapeutic applications and their personalization.
    Clinicaltrials.gov, NCT02322112 , registered on July 3, 2015. Video Abstract.

  • Differential Modulation of the European Sea Bass Gut Microbiota by Distinct Insect Meals.

    Rangel F, Enes P, Gasco L, Gai F, Hausmann B, Berry D, Oliva-Teles A, Serra CR, Pereira FC
    2022 - Front Microbiol, 831034

    Abstract: 

    The aquaculture industry is one of the fastest-growing sectors in animal food production. However, farming of carnivorous fish strongly relies on the use of wild fish-based meals, a practice that is environmentally and economically unsustainable. Insect-based diets constitute a strong candidate for fishmeal substitution, due to their high nutritional value and low environmental footprint. Nevertheless, data on the impact of insect meal (IM) on the gut microbiome of farmed fish are so far inconclusive, and very scarce in what concerns modulation of microbial-mediated functions. Here we use high-throughput 16S rRNA gene amplicon sequencing and quantitative PCR to evaluate the impact of different IMs on the composition and chitinolytic potential of the European sea bass gut digesta- and mucosa-associated communities. Our results show that insect-based diets of distinct origins differently impact the gut microbiota of the European sea bass (). We detected clear modulatory effects of IM on the gut microbiota, which were more pronounced in the digesta, where communities differed considerably among the diets tested. Major community shifts were associated with the use of black soldier fly larvae (, HM) and pupal exuviae (HEM) feeds and were characterized by an increase in the relative abundance of the Firmicutes families , , and and the Actinobacteria family , which all include taxa considered beneficial for fish health. Modulation of the digesta community by HEM was characterized by a sharp increase in and a decrease of several Gammaproteobacteria and Bacteroidota members. In turn, a mealworm larvae-based diet (, TM) had only a modest impact on microbiota composition. Further, using quantitative PCR, we demonstrate that shifts induced by HEM were accompanied by an increase in copy number of chitinase ChiA-encoding genes, predominantly originating from species with effective chitinolytic activity. Our study reveals an HEM-driven increase in chitin-degrading taxa and associated chitinolytic activity, uncovering potential benefits of adopting exuviae-supplemented diets, a waste product of insect rearing, as a functional ingredient.

  • Individuality of the Extremely Premature Infant Gut Microbiota Is Driven by Ecological Drift.

    Seki D, Schauberger C, Hausmann B, Berger A, Wisgrill L, Berry D
    2022 - mSystems, e0016322

    Abstract: 

    The initial contact between humans and their colonizing gut microbiota after birth is thought to have expansive and long-lasting consequences for physiology and health. Premature infants are at high risk of suffering from lifelong impairments, due in part to aberrant development of gut microbiota that can contribute to early-life infections and inflammation. Despite their importance to health, the ecological assembly and succession processes governing gut microbiome composition in premature infants remained incompletely understood. Here, we quantified these ecological processes in a spatiotemporally resolved 16S rRNA gene amplicon sequencing data set of 60 extremely premature neonates using an established mathematical framework. We found that gut colonization during the first months of life is predominantly stochastic, whereby interindividual diversification of microbiota is driven by ecological drift. Dispersal limitations are initially small but have increasing influence at later stages of succession. Furthermore, we find similar trends in a cohort of 32 healthy term-born infants. These results suggest that the uniqueness of individual gut microbiota of extremely premature infants is largely due to stochastic assembly. Our knowledge concerning the initial gut microbiome assembly in human neonates is limited, and scientific progression in this interdisciplinary field is hindered due to the individuality in composition of gut microbiota. Our study addresses the ecological processes that result in the observed individuality of microbes in the gastrointestinal tract between extremely premature and term-born infants. We find that initial assembly is mainly driven by neutral ecological processes. Interestingly, while this progression is predominantly random, limitations to the dispersal of microbiota between infants become increasingly important with age and are concomitant features of gut microbiome stability. This indicates that while we cannot predict gut microbiota assembly due to its random nature, we can expect the establishment of certain ecological features that are highly relevant for neonatal health.

  • Down-regulation of the bacterial protein biosynthesis machinery in response to weeks, years, and decades of soil warming

    Söllinger A, Séneca J, Dahl MB, Motleleng LL, Prommer J, Verbruggen E, Sigurdsson BD, Janssens I, Schiestl RH, Urich T, Richter A, Tveit AT
    2022 - Science Advances, 12: eabm3230

    Abstract: 

    How soil microorganisms respond to global warming is key to infer future soil-climate feedbacks, yet poorly understood. Here, we applied metatranscriptomics to investigate microbial physiological responses to medium-term (8 years) and long-term (>50 years) subarctic grassland soil warming of +6°C. Besides indications for a community-wide up-regulation of centralmetabolic pathways and cell replication, we observed a down-regulation of the bacterial protein biosynthesis machinery in the warmed soils, coinciding with a lower microbial biomass, RNA, and soil substrate content. We conclude that permanently accelerated reaction rates at higher temperatures and reduced substrate concentrations result in cellular reduction of ribosomes, the macromolecular complexes carrying out protein biosynthesis. Later efforts to test this, including a short-term warming experiment (6 weeks, +6°C), further supported our conclusion. Down-regulating the protein biosynthesis machinery liberates energy and matter, allowing soil bacteria to maintain high metabolic activities and cell division rates even after decades of warming.

  • Ecological Processes Shaping Microbiomes of Extremely Low Birthweight Infants.

    Zioutis C, Seki D, Bauchinger F, Herbold C, Berger A, Wisgrill L, Berry D
    2022 - Front Microbiol, 812136

    Abstract: 

    The human microbiome has been implicated in affecting health outcomes in premature infants, but the ecological processes governing early life microbiome assembly remain poorly understood. Here, we investigated microbial community assembly and dynamics in extremely low birth weight infants (ELBWI) over the first 2 weeks of life. We profiled the gut, oral cavity and skin microbiomes over time using 16S rRNA gene amplicon sequencing and evaluated the ecological forces shaping these microbiomes. Though microbiomes at all three body sites were characterized by compositional instability over time and had low body-site specificity (PERMANOVA, = 0.09, = 0.001), they could nonetheless be clustered into four discrete community states. Despite the volatility of these communities, deterministic assembly processes were detectable in this period of initial microbial colonization. To further explore these deterministic dynamics, we developed a probabilistic approach in which we modeled microbiome state transitions in each ELBWI as a Markov process, or a "memoryless" shift, from one community state to another. This analysis revealed that microbiomes from different body sites had distinctive dynamics as well as characteristic equilibrium frequencies. Time-resolved microbiome sampling of premature infants may help to refine and inform clinical practices. Additionally, this work provides an analysis framework for microbial community dynamics based on Markov modeling that can facilitate new insights, not only into neonatal microbiomes but also other human-associated or environmental microbiomes.

  • ‘Candidatus Phosphoribacter’, previously identified as Tetrasphaera, is the dominant polyphosphate accumulating lineage in wastewater treatment plants

    Singleton CM, Petriglieri F, Wasmund K, Nierychlo M, Kondrotaite Z, Petersen JF, Peces M, Dueholm MS, Wagner M, Nielsen PH
    2022 - ISME J, in press
    Phosphoribacter

    Abstract: 

    The bacterial genus Tetrasphaera encompasses abundant polyphosphate accumulating organisms (PAOs) that are responsible for enhanced biological phosphorus removal (EBPR) in wastewater treatment plants. Recent analyses of genomes from pure cultures revealed that 16S rRNA genes cannot resolve the lineage, and that Tetrasphaera spp. are from several different genera within the Dermatophilaceae. Here, we examine 14 recently recovered high-quality metagenome-assembled genomes from wastewater treatment plants containing full-length 16S rRNA genes identified as Tetrasphaera, 11 of which belong to the uncultured Tetrasphaera clade 3. We find that this clade represents two distinct genera, named here Ca. Phosphoribacter and Ca. Lutibacillus, and reveal that the widely used model organism Tetrasphaera elongata is less relevant for physiological predictions of this uncultured group. Ca. Phosphoribacter incorporates species diversity unresolved at the 16S rRNA gene level, with the two most abundant and often co-occurring species encoding identical V1-V3 16S rRNA gene amplicon sequence variants but different metabolic capabilities, and possibly, niches. Both Ca. P. hodrii and Ca. P. baldrii were visualised using fluorescence in situ hybridisation (FISH), and PAO capabilities were confirmed with FISH-Raman microspectroscopy and phosphate cycling experiments. Ca. Phosphoribacter represents the most abundant former Tetrasphaera lineage and PAO in EPBR systems in Denmark and globally. 

     

  • Persistence of the antagonistic effects of a natural mixture of Alternaria mycotoxins on the estrogen-like activity of human feces after anaerobic incubation.

    Crudo F, Aichinger G, Dellafiora L, Kiss E, Mihajlovic J, Del Favero G, Berry D, Dall'Asta C, Marko D
    2022 - Toxicol Lett, 88-99

    Abstract: 

    Several Alternaria mycotoxins are believed to act as endocrine disruptive chemicals (EDCs), since they are reported to bind estrogen receptors in several experimental models. After ingestion of contaminated food commodities, the mycotoxins reach the intestine, where they come into direct contact with food constituents as well as the gut microbiota. Thus, the aim of the present work was to evaluate the modulatory potential of a complex extract of cultured Alternaria fungi (CE; containing eleven chemically characterized compounds) on the estrogenic signaling cascade of mammalian cells before and after anaerobic incubation with fecal slurries, in order to simulate an in vivo-like condition in the gut. Assessing alkaline phosphatase expression in Ishikawa cells as a measure for estrogenicity, we found the CE to partially quench the intrinsic estrogenic properties of fecal slurries and fecal waters, even after 3 h of fecal incubation. Investigation of the mechanisms underlying the effects observed carried out through an in vitro/in silico approach revealed the ability of the extract to decrease the ERα/ERβ nuclear ratio, while a possible action of the mycotoxins as ER-antagonists was excluded. Our results suggest that Alternaria mycotoxins might act as EDCs in vivo, and warrant further investigation in animal models.

  • Plant phosphorus-use and -acquisition strategies in Amazonia

    Reichert T, Rammig A, Fuchslueger L, Lugli LF, Quesada CA, Fleischer K
    2022 - New Phytologist, 234: 1126-1143

    Abstract: 

    In the tropical rainforest of Amazonia, phosphorus (P) is one of the main nutrients controlling forest dynamics, but its effects on the future of the forest biomass carbon (C) storage under elevated atmospheric CO2 concentrations remain uncertain. Soils in vast areas of Amazonia are P-impoverished, and little is known about the variation or plasticity in plant P-use and -acquisition strategies across space and time, hampering the accuracy of projections in vegetation models. Here, we synthesize current knowledge of leaf P resorption, fine-root P foraging, arbuscular mycorrhizal symbioses, and root acid phosphatase and organic acid exudation and discuss how these strategies vary with soil P concentrations and in response to elevated atmospheric CO2. We identify knowledge gaps and suggest ways forward to fill those gaps. Additionally, we propose a conceptual framework for the variations in plant P-use and -acquisition strategies along soil P gradients of Amazonia. We suggest that in soils with intermediate to high P concentrations, at the plant community level, investments are primarily directed to P foraging strategies via roots and arbuscular mycorrhizas, whereas in soils with intermediate to low P concentrations, investments shift to prioritize leaf P resorption and mining strategies via phosphatases and organic acids.

  • Resolving the structure of phage-bacteria interactions in the context of natural diversity.

    Kauffman KM, Chang WK, Brown JM, Hussain FA, Yang J, Polz MF, Kelly L
    2022 - Nat Commun, 1: 372

    Abstract: 

    Microbial communities are shaped by viral predators. Yet, resolving which viruses (phages) and bacteria are interacting is a major challenge in the context of natural levels of microbial diversity. Thus, fundamental features of how phage-bacteria interactions are structured and evolve in the wild remain poorly resolved. Here we use large-scale isolation of environmental marine Vibrio bacteria and their phages to obtain estimates of strain-level phage predator loads, and use all-by-all host range assays to discover how phage and host genomic diversity shape interactions. We show that lytic interactions in environmental interaction networks (as observed in agar overlay) are sparse-with phage predator loads being low for most bacterial strains, and phages being host-strain-specific. Paradoxically, we also find that although overlap in killing is generally rare between tailed phages, recombination is common. Together, these results suggest that recombination during cryptic co-infections is an important mode of phage evolution in microbial communities. In the development of phages for bioengineering and therapeutics it is important to consider that nucleic acids of introduced phages may spread into local phage populations through recombination, and that the likelihood of transfer is not predictable based on lytic host range.

  • The life cycle-dependent transcriptional profile of the obligate intracellular amoeba symbiont Amoebophilus asiaticus.

    Selberherr E, Penz T, König L, Conrady B, Siegl A, Horn M, Schmitz-Esser S
    2022 - FEMS Microbiol Ecol, in press

    Abstract: 

    Free-living amoebae often harbor obligate intracellular bacterial symbionts. Amoebophilus (A.) asiaticus is a representative of a lineage of amoeba symbionts in the phylum Bacteroidota. Here, we analyze the transcriptome of A. asiaticus strain 5a2 at four time points during its infection cycle and replication within the Acanthamoeba host using RNA sequencing. Our results reveal a dynamic transcriptional landscape throughout different A. asiaticus life cycle stages. Many intracellular bacteria and pathogens utilize eukaryotic-like proteins (ELPs) for host cell interaction and the A. asiaticus 5a2 genome shows a particularly high abundance of ELPs. We show the expression of all genes encoding ELPs and found many ELPs to be differentially expressed. At the replicative stage of A. asiaticus, ankyrin repeat proteins and tetratricopeptide/Sel1-like repeat proteins were upregulated. At the later time points, high expression levels of a type 6 secretion system that likely prepares for a new infection cycle after lysing its host, were found. This study reveals comprehensive insights into the intracellular lifestyle of A. asiaticus and highlights candidate genes for host cell interaction. The results from this study have implications for other intracellular bacteria such as other amoeba-associated bacteria and the arthropod symbionts forming the sister lineage of A. asiaticus.

  • Genus-specific carbon fixation activity measurements reveal distinct responses to oxygen among hydrothermal vent Campylobacteria

    McNichol J, Dyksma S, Greuter L, Seewald JS, Sylva SP, Sievert SM
    2022 - Appl Environ Microbiol, 2: e0208321

    Abstract: 

    Molecular surveys of low temperature deep-sea hydrothermal vent fluids have shown that Campylobacteria (previously Epsilonproteobacteria) often dominate the microbial community and that three genera, ArcobacterSulfurimonas, and Sulfurovum, frequently coexist. In this study, we used replicated radiocarbon incubations of deep-sea hydrothermal fluids to investigate activity of each genus under three experimental conditions. To quantify genus-specific radiocarbon incorporation, we used newly designed oligonucleotide probes for ArcobacterSulfurimonas, and Sulfurovum to quantify their activity using catalyzed-reporter deposition fluorescence in situhybridization (CARD-FISH) combined with fluorescence-activated cell sorting. All three genera actively fixed CO2 in short-term (∼ 20 h) incubations, but responded differently to the additions of nitrate and oxygen. Oxygen additions had the largest effect on community composition, and caused a pronounced shift in community composition at the amplicon sequence variant (ASV) level after only 20 h of incubation. The effect of oxygen on carbon fixation rates appeared to depend on the initial starting community. The presented results support the hypothesis that these chemoautotrophic genera possess functionally redundant core metabolic capabilities, but also reveal finer-scale differences in growth likely reflecting adaptation of physiologically-distinct phylotypes to varying oxygen concentrations in situ. Overall, our study provides new insights into how oxygen controls community composition and total chemoautotrophic activity, and underscores how quickly deep-sea vent microbial communities respond to disturbances. IMPORTANCE Sulfidic environments worldwide are often dominated by sulfur-oxidizing, carbon-fixing Campylobacteria. Environmental factors associated with this group's dominance are now understood, but far less is known about the ecology and physiology of members of subgroups of chemoautotrophic Campylobacteria. In this study, we used a novel method to differentiate the genus-specific chemoautotrophic activity of three subtypes of Campylobacteria. In combination with evidence from microscopic counts, chemical consumption/production during incubations, and DNA-based measurements, our data show that oxygen concentration affects both community composition and chemoautotrophic function in situ. These results help us better understand factors controlling microbial diversity at deep-sea hydrothermal vents, and provide first-order insights into the ecophysiological differences between these distinct microbial taxa.

  • Lipid synthesis at the trophic base as the source for energy management to build complex structures.

    Schnorr SL, Berry D
    2022 - Curr Opin Biotechnol, 364-373

    Abstract: 

    The review explores the ecological basis for bacterial lipid metabolism in marine and terrestrial ecosystems. We discuss ecosystem stressors that provoked early organisms to modify their lipid membrane structures, and where these stressors are found across a variety of environments. A major role of lipid membranes is to manage cellular energy utility, including how energy is used for signal propagation. As different environments are imbued with properties that necessitate variation in energy regulation, bacterial lipid synthesis has undergone incalculable permutations of functional trial and error. This may hold clues for how biotechnology can improvise a short-hand version of the evolutionary gauntlet to stimulate latent functional competences for the synthesis of rare lipids. Reducing human reliance on marine resources and deriving solutions for production of essential nutrients is a pressing problem in sustainable agriculture and aquaculture, as well as timely considering the increasing fragility of human health in an aging population.

  • The role of coupled DNRA-Anammox during nitrate removal in a highly saline lake

    Valiente N, Jirsa F, Hein T, Wanek W, Prommer J, Bonin P, Gómez-Alday JJ
    2022 - Science of The Total Environment, 806: Article 150726

    Abstract: 

    Nitrate (NO3) removal from aquatic ecosystems involves several microbially mediated processes, including denitrification, dissimilatory nitrate reduction to ammonium (DNRA), and anaerobic ammonium oxidation (anammox), controlled by slight changes in environmental gradients. In addition, some of these processes (i.e. denitrification) may involve the production of undesirable compounds such as nitrous oxide (N2O), an important greenhouse gas. Saline lakes are prone to the accumulation of anthropogenic contaminants, making them highly vulnerable environments to NO3 pollution. The aim of this paper was to investigate the effect of light and oxygen on the different NO3 removal pathways under highly saline conditions. For this purpose, mesocosm experiments were performed using lacustrine, undisturbed, organic-rich sediments from the Pétrola Lake (Spain), a highly saline waterbody subject to anthropogenic NO3 pollution. The revised 15N-isotope pairing technique (15N-IPT) was used to determine NO3 sink processes. Our results demonstrate for the first time the coexistence of denitrification, DNRA, and anammox processes in a highly saline lake, and how their contribution was determined by environmental conditions (oxygen and light). DNRA, and especially denitrification to N2O, were the dominant nitrogen (N) removal pathways when oxygen and/or light were present (up to 82%). In contrast, anoxia and darkness promoted NO3 reduction by DNRA (52%), combined with N loss by anammox (28%). Our results highlight the role of coupled DNRA-anammox, which has not yet been investigated in lacustrine sediments. We conclude that anoxia and darkness favored DNRA and anammox processes over denitrification and therefore to restrict N2O emissions to the atmosphere.

  • 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
    2022 - ISME J, 1: 272-283
    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
    2022 - ISME J, 1: 247-256

    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.

Book chapters and other publications

1 Publication found
  • Editorial: Acidobacteriota-Towards unraveling the secrets of a widespread though enigmatic phylum

    Huber KJ, Pester M, Eichorst SA, Navarrete AA, Fösel BU
    2022 - Front Microbiol., 13: 960602
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