Publications

Physical disintegration of biochar has been postulated to determine the persistence and mobility in soil of this recalcitrant carbon pool. Therein, freeze–thaw cycling can induce substantial physical stress to biochars. We here investigated the physical disintegration and subsequent mobilisation of five different biochars under “realistic worst-case scenarios” in a laboratory soil column setup as well as in shaking and sonication batch experiments. The mobilization of carbon from biochar particles (0.25–1 mm) was investigated in the absence of clay at a pH of 6.3 with and without 80 freeze–thaw cycles. The small biochar particles used in this study did not strongly disintegrate after freeze–thaw cycling, possibly because of freezing point depression in biochar micropores. Our results in comparison with findings in literature suggest that freeze–thaw-induced physical disintegration of biochar is a process more pronounced for large biochar particles containing substantial meso- and macropores. Biochars with larger ash fractions disintegrated more, presumably because of the ash-associated formation of unstable cavities within the biochar. Physical stability of biochars produced from the same feedstock at different pyrolysis temperatures decreased with increasing aromaticity, which may be linked to a higher rigidity of more aromatic structures. Moisture content in the soil increased carbon mobilization from biochar more than physical stress such as freeze–thaw cycling. The physical disintegration of biochar and subsequent mobilization of micro-and nanosized carbon should thus be considered of minor relevance and is often not a driving factor for biochar stability in soil.

Soil organic nitrogen (N) cycling processes constitute a bottleneck of soil N cycling, yet little is known about how tree species composition may influence these rates, and even less under changes in soil water availability such as those that are being induced by climate change. In this study, we used a 12-year-old tree biodiversity experiment in southwestern France to assess the interactive effects of soil water availability (half of the blocks seasonally irrigated to double precipitation) and tree species composition (monocultural vs. mixed plots of coniferous Pinus pinaster, and of broadleaf Betula pendula). We measured gross protein depolymerisation rates using a novel high-throughput isotope pool dilution method, along with soil microbial biomass carbon and N to calculate microbial biomass-specific activities of soil organic N processes. Overall, high soil water availability led to a 42% increase in soil protein depolymerisation rates compared to the unirrigated plots, but we found no effect of species composition on these soil organic N cycling processes. When investigating the interactive effect of tree species mixing and soil water availability, the results suggest that mixing tree species had a negative effect on soil organic N cycling processes in the non-irrigated blocks subject to dry summers, but that this effect tended to become positive at higher soil water availability in irrigated plots. These results put forth that soil water availability could influence potential tree species mixing effects on soil organic N cycling processes in dry conditions.

Cable bacteria are centimeter-long filamentous bacteria that conduct electrons via internal wires, thus coupling sulfide oxidation in deeper, anoxic sediment with oxygen reduction in surface sediment. This activity induces geochemical changes in the sediment, and other bacterial groups appear to benefit from the electrical connection to oxygen. Here, we report that diverse bacteria swim in a tight flock around the anoxic part of oxygen-respiring cable bacteria and disperse immediately when the connection to oxygen is disrupted (by cutting the cable bacteria with a laser). Raman microscopy shows that flocking bacteria are more oxidized when closer to the cable bacteria, but physical contact seems to be rare and brief, which suggests potential transfer of electrons via unidentified soluble intermediates. Metagenomic analysis indicates that most of the flocking bacteria appear to be aerobes, including organotrophs, sulfide oxidizers, and possibly iron oxidizers, which might transfer electrons to cable bacteria for respiration. The association and close interaction with such diverse partners might explain how oxygen via cable bacteria can affect microbial communities and processes far into anoxic environments.

Microbial necromass comprises a large fraction of soil organic matter (SOM) due to the accumulation and stabilization of microbial residues from dead archaea, bacteria and fungi. Amino sugars, neutral sugars and uronic acids have been used as microbial necromass biomarkers to trace the origin and composition of microbial residues in the SOM pool. Due to the structural complexity of sugars, derivatization reactions and high-throughput analytical methods are required to separate and quantify these sugar-related compounds. Our aim was to develop a rapid and sensitive assay to measure amino sugar, neutral sugar and uronic acid compounds using pre-column 1-phenyl-3-methyl-5-pyrazolone (PMP) derivatization. PMP-derivatives were separated and quantified via reversed phase (RP) ultra-high-performance liquid chromatography (UPLC) coupled to high-resolution Orbitrap mass spectrometry (MS). The method was validated and applied on hydrolyzed peptidoglycans and the biomass of archaeal, bacterial, fungal and plant species, as well as with soils. This developed PMP method allowed the separation and quantification of 18 sugar-related compounds, including four amino sugars, three N-acetyl amino sugars, eight neutral sugars, and three uronic acids within 20 min. This PMP method showed a precision for isotope enrichment detection of 0.03–0.05 atom % 13C for D-glucose and D-glucosamine. This is the first time talosaminuronic acid (deriving from archaeal pseudopeptidoglycan) was identified and quantified using PMP derivatization. The application of this novel PMP method on pure hydrolyzed biomass and soils, showed the successful chromatographic and mass spectrometric separation and quantification of amino sugar, neutral sugar and uronic acid compounds. A multivariate analysis using these sugar-related PMP derivatives showed a clustering of the species according to their respective taxonomic group (archaea, gram-positive bacteria, gram-negative bacteria, fungi and plants). The modified PMP method can be applied to identify and quantify soil microbial necromass biomarkers, as well as their contribution to SOM. The sensitive isotope tracer detection allows tracing isotopically labeled materials into necromass biomarkers in SOM pools.

Summary

Extracellular enzymes (EE) play a vital role in soil nutrient cycling and thus affect terrestrial ecosystem functioning. Yet the drivers that regulate microbial activity, and therefore EE activity, remain under debate. In this study we investigate the temporal variation of soil EE in a tropical terra-firme forest. We found that EE activity peaked during the drier season in association with increased leaf litterfall, which was also reflected in negative relationships between EE activities and precipitation. Soil nutrients were weakly related to EE activities, although extractable N was related to EE activities in the top 5 cm of the soil. These results suggest that soil EE activity is synchronized with precipitation-driven substrate inputs and depends on the availability of N. Our results further indicate high investments in P acquisition, with a higher microbial N demand in the month before the onset of the drier season, shifting to higher P demand towards the end of the drier season. These seasonal fluctuations in the potential acquisition of essential resources imply dynamic shifts in microbial activity in coordination with climate seasonality and resource limitation of central-eastern Amazon forests.

Fine root litter represents an important carbon input to soils, but the effect of global warming on fine root turnover (FRT) is hardly explored in forest ecosystems. Understanding tree fine roots' response to warming is crucial for predicting soil carbon dynamics and the functioning of forests as a sink for atmospheric carbon dioxide (CO2). We studied fine root production (FRP) with ingrowth cores and used radiocarbon signatures of first-order, second- to third-order, and bulk fine roots to estimate fine root turnover times after 8 and 14 years of soil warming (+4 °C) in a temperate forest. Fine root turnover times of the individual root fractions were estimated with a one-pool model. Soil warming strongly increased fine root production by up to 128 % within one year, but after two years, the production was less pronounced (+35 %). The first-year production was likely very high due to the rapid exploitation of the root-free ingrowth cores. The radiocarbon signatures of fine roots were overall variable among treatments and plots. Soil warming tended to decrease fine root turnover times of all the measured root fractions after 8 and 14 years of warming, and there was a tendency for trees to use older carbon reserves for fine root production in warmed plots. Furthermore, soil warming increased fine root turnover from 50 to 106 g C m−2 yr−1 (based on two different approaches). Our findings suggest that future climate warming may increase carbon input into soils by enhancing fine root turnover. If this increase may partly offset carbon losses by increased mineralization of soil organic matter in temperate forest soils is still unclear and should guide future research.

Nitrite is an important precursor of many environmentally hazardous compounds (e.g., nitrate, nitrous oxide, and nitrous acid). However, its dynamics in the soil environment are not yet fully understood. The NtraceNitrite tool has been successful in analyzing 15N tracing data. Here, based on a 15N tracing experiment (under aerobic condition) where either the nitrite, the nitrate, or the ammonium pool was labelled, we developed an extended model (NO2Trace), which was featured by the addition of coupled nitrate reduction and nitrite re-oxidation and the separation of the nitrate pool in two sub-pools. With 5 additional parameters optimized, NO2Trace was able to achieve a superior fit to the data, as compared to the NtraceNitrite tool. The additional features might offer a suitable explanation for the isotopic composition of nitrate produced via nitrification in terrestrial ecosystems. Our results carry two important implications: (i) a key assumption of the classical isotope pool dilution technique (i.e., no reflux of tracer) for estimating gross nitrate fluxes is violated, leading to considerable underestimations (22–99% in the datasets tested); (ii) re-oxidation can dominate the consumption (∼75%) of nitrite derived from nitrate reduction, indicating the potential of this process as a target for nitrogen retention mechanism against gaseous nitrogen losses (through nitrite reduction). The additional features of the extended model show a tighter cycle between soil nitrite and nitrate than considered previously and provide a more comprehensive description of soil nitrite transformations. This study also highlights that more work is needed to develop methods capable of separating process- and pathways-specific nitrate and nitrite pools.

Phosphorus (P) is an essential and often limiting element that could play a crucial role in terrestrial ecosystem responses to climate warming. However, it has yet remained unclear how different P cycling processes are affected by warming. Here we investigate the response of soil P pools and P cycling processes in a mountain forest after 14 years of soil warming (+4 °C). Long-term warming decreased soil total P pools, likely due to higher outputs of P from soils by increasing net plant P uptake and downward transportation of colloidal and particulate P. Warming increased the sorption strength to more recalcitrant soil P fractions (absorbed to iron oxyhydroxides and clays), thereby further reducing bioavailable P in soil solution. As a response, soil microbes enhanced the production of acid phosphatase, though this was not sufficient to avoid decreases of soil bioavailable P and microbial biomass P (and biotic phosphate immobilization). This study therefore highlights how long-term soil warming triggers changes in biotic and abiotic soil P pools and processes, which can potentially aggravate the P constraints of the trees and soil microbes and thereby negatively affect the C sequestration potential of these forests.

Chronic rhinosinusitis (CRS) is an inflammatory disease phenotypically classified by the absence (CRSsNP) or presence of nasal polyps (CRSwNP). The latter may also be associated with asthma and hypersensitivity towards non-steroidal anti-inflammatory drugs (NSAID) as a triad termed NSAID-exacerbated respiratory disease (N-ERD). The role of the microbiome in these disease entities with regard to the underlying inflammatory process and disease burden is yet not fully understood. To address this question, we measured clinical parameters and collected nasal samples (nasal mucosal fluids and microbiome swabs) of patients suffering from CRSsNP (n=20), CRSwNP (n=20) or N-ERD (n=20) as well as from patients without CRS (=disease controls, n=20). Importantly, all subjects refrained from taking local or systemic corticosteroids or immunosuppressants for at least two weeks prior to sampling. The nasal microbiome was analyzed using 16S rRNA gene amplicon sequencing, and levels of 33 inflammatory cytokines were determined in nasal mucosal fluids using the MSD platform.

Patients suffering from N-ERD and CRSwNP showed significantly worse smell perception and significantly higher levels of type 2 associated cytokines IL-5, IL-9, Eotaxin and CCL17. Across all 4 patient groups, Corynebacteria and Staphylococci showed the highest relative abundances. Although no significant difference in alpha and beta diversity was observed between the control and the CRS groups, pairwise testing revealed a higher relative abundance of Staphylococci in the middle meatus in N-ERD patients as compared to CRSwNP (p<0.001), CRSsNP (p<0.01) and disease controls (p<0.05) and of Lawsonella in patients suffering from CRSwNP in middle meatus and anterior naris in comparison to CRSsNP (p<0.0001 for both locations) and disease controls (p<0.01 and p<0.0001). Furthermore, we observed a positive correlation of Staphylococci with IL-5 (Pearson r=0.548) and a negative correlation for Corynebacteria and Eotaxin-3 (r=-0.540). Thus, in patients refraining from oral and nasal corticosteroid therapy for at least two weeks known to alter microbiome composition, we did not observe differences in microbiome alpha or beta diversity between various CRS entities and disease controls. However, our data suggest a close association between increased bacterial colonization with Staphylococci and decreased colonization by Corynebacteria as well as increased type 2 inflammation and disease burden.

Aquifers providing drinking water are increasingly threatened by emerging contaminants due to wastewater inputs from multiple sources. These inputs have to be identified, differentiated, and characterized to allow an accurate risk assessment and thus ensure the safety of drinking water through appropriate management. We hypothesize, that in climates with seasonal temperature variations, the sweetener acesulfame potassium (ACE) provides new pathways to study wastewater inputs to aquifers. Specifically, this study investigates the temperature-driven seasonal oscillation of ACE to assess multiple sources of wastewater inputs at a riverbank filtration site. ACE concentrations in the river water varied from 0.2 to 1 μg L−1 in the cold season (T < 10 °C) to 0–0.1 μg L−1 in the warm season (T > 10 °C), due to temperature-dependent biodegradation during wastewater treatment. This oscillating signal could be traced throughout the aquifer over distances up to 3250 m from two different infiltration sources. A transient numerical model of groundwater flow and ACE transport was calibrated over hydraulic heads and ACE concentrations, allowing the accurate calculation of mixing ratios, travel times, and flow-path directions for each of the two infiltration sources. The calculated travel time from the distant infiltration source was of 67 days, while that from the near source was of 20 days. The difference in travel times leads to different potential degradation of contaminants flowing into the aquifer from the river, thus demonstrating the importance of individually assessing the locations of riverbank infiltration. The calibrated ACE transport model allowed calculating transient mixing ratios, which confirmed the impact of river stage and groundwater levels on the mixing ratio of the original groundwater and the bank filtrate. Therefore, continuous monitoring of ACE concentrations can help to optimize the management of the water works with the aim to avoid collection of water with very short travel times, which has important regulative aspects. Our findings demonstrate the suitability of ACE as a transient tracer for identifying multiple sources of wastewater, including riverbank filtration sites affected by wastewater treatment plant effluents. ACE seasonal oscillation tracking thus provides a new tool to be used in climates with pronounced seasonal temperature variations to assess the origins of contamination in aquifers, with time and cost advantages over multi-tracer approaches.

Microbial nitrogen use efficiency (NUE), which reflects the proportion of nitrogen (N) taken up to be allocated to microbial biomass and growth, is central to our understanding of soil N cycling. However, the factors influencing microbial NUE remain unclear. Here, we explored the effects of climate factors, soil properties, and microbial variables on microbial NUE based on a survey of soils from 11 locations along a forest transect in eastern China. We found microbial NUE decreased with the ratio of acid phosphatase (AP) activity versus microbial growth rate. This suggested that increased microbial phosphorus acquisition decreased microbial NUE due to increasing investment in AP. However, microbial NUE increased with soil organic carbon content, because soil organic carbon is the source of material and energy for microbial growth and metabolism. Soil pH and mean annual temperature indirectly affected microbial NUE through their effects on the ratio of AP activity relative to microbial growth rate and soil organic carbon content, respectively. Our results improve our understanding and prediction of microbial NUE on a large spatial scale and emphasize the importance of phosphorus in affecting microbial metabolic efficiency.

Electromicrobiology can be used to understand extracellular electron uptake in previously undescribed chemolithotrophs. Enrichment and characterization of the uncultivated electroautotroph "Candidatus Tenderia electrophaga" using electromicrobiology led to the designation of the order Tenderiales. Representative Tenderiales metagenome-assembled genomes (MAGs) have been identified in a number of environmental surveys, yet a comprehensive characterization of conserved genes for extracellular electron uptake has thus far not been conducted. Using comparative genomics, we identified conserved orthologous genes within the Tenderiales and nearest-neighbor orders important for extracellular electron uptake based on a previously proposed pathway from "Ca. Tenderia electrophaga." The Tenderiales contained a conserved cluster we designated uetABCDEFGHIJ, which encodes proteins containing features that would enable transport of extracellular electrons to cytoplasmic membrane-bound energy-transducing complexes such as two conserved cytochrome cbb3 oxidases. For example, UetJ is predicted to be an extracellular undecaheme c-type cytochrome that forms a heme wire. We also identified clusters of genes predicted to facilitate assembly and maturation of electron transport proteins, as well as cellular attachment to surfaces. Autotrophy among the Tenderiales is supported by the presence of carbon fixation and stress response pathways that could allow cellular growth by extracellular electron uptake. Key differences between the Tenderiales and other known neutrophilic iron oxidizers were revealed, including very few Cyc2 genes in the Tenderiales. Our results reveal a possible conserved pathway for extracellular electron uptake and suggest that the Tenderiales have an ecological role in coupling metal or mineral redox chemistry and the carbon cycle in marine and brackish sediments. IMPORTANCE Chemolithotrophic bacteria capable of extracellular electron uptake to drive energy metabolism and CO2 fixation are known as electroautotrophs. The recently described order Tenderiales contains the uncultivated electroautotroph "Ca. Tenderia electrophaga." The "Ca. Tenderia electrophaga" genome contains genes proposed to make up a previously undescribed extracellular electron uptake pathway. Here, we use comparative genomics to show that this pathway is well conserved among Tenderiales spp. recovered by metagenome-assembled genomes. This conservation extends to near neighbors of the Tenderiales but not to other well-studied chemolithotrophs, including iron and sulfur oxidizers, indicating that these genes may be useful markers of growth using insoluble extracellular electron donors. Our findings suggest that extracellular electron uptake and electroautotrophy may be pervasive among the Tenderiales, and the geographic locations from which metagenome-assembled genomes were recovered offer clues to their natural ecological niche.

Foraminifera are unicellular, marine organisms that occur worldwide. A very common species in the German Wadden Sea is Elphidium williamsoni. Some foraminifera (such as elphidia) are able to use kleptoplastidy, which allows them to incorporate chloroplasts from their algal food source into their own cell body. The experiments reported here are based on the fact that chlorophyll (a and c) can be detected in the intact cells with spectroscopic methods in the visible spectral range, which allows an indirect investigation of the presence of sequestered chloroplasts. Starving experiments of E. williamsoni in the light (24 h continuous) showed that the greatest decrease in chlorophyll content was recorded within the first 20–30 days. From day 60 on, chlorophyll was hardly detectable. Through subsequent feeding on a renewed algal food source a significant increase in the chlorophyll content in foraminifera was noticed. The degradation of chlorophyll in the dark (24 h continuous darkness) during the starving period was much more complex. Chlorophyll was still detected in the cells after 113 days of starving time. Therefore, we hypotheses that the effect of photoinhibition applies to chloroplasts in foraminifera under continuous illumination.

1. The circumboreal/circumpolar N2-fixing lichen Stereocaulon vesuvianum is among the most widespread and abundant fruticose species in montane Britain but has lost the capacity to fix N2 over large areas of the country.
2. To investigate whether loss of N2-fixation in S. vesuvianum is linked to increased N deposition, we examined thallus morphology, physiology and chemistry at twelve locations representing an N deposition gradient of 3–40 kg ha−1 year−1. Measurements were made in parallel on a non-N2-fixing reference species (Parmelia saxatilis). The presence or absence of cephalodia (N2-fixing nodules containing the cyanobacterium Stigonema sp) was recorded in over 500 herbarium specimens of S. vesuvianum dating back to 1820.
3. Cephalodium abundance in S. vesuvianum, and 15N concentration in S. vesuvianum and P. saxatilis, were strongly negatively correlated with N deposition and particularly with dry deposited N; cephalodia do not form at total N deposition rates ≥8–9 kg ha−1 year−1. Other morphological oddities in S. vesuvianum at N-polluted sites include increased apothecium (fungal reproductive structure) production and green algal biofilm development. Biofilm covered thalli without cephalodia lacked nitrogenase activity and cephalodia at sites where they rarely develop had nitrogenase activities typical for this species. The presence or absence of cephalodia in herbarium specimens of S. vesuvianum suggest that the present-day N-deposition linked gradient in N2-fixing capacity did not exist in the 19th century and largely developed between 1900–1940.
4. Synthesis. We provide clear evidence that N2-fixing capacity in S. vesuvianum has been lost in regions subjected to many decades of enhanced atmospheric N deposition. This loss is consistent with established models of diazotrophy, which identify supply of combined N as an inhibitor of N2-fixation. Progressive depletion of thallus 15N with increasing N deposition is in line with available data indicating that much atmospheric N pollution is 15N-depleted. Rates of nitrogenase activity in S. vesuvianum are low compared to other symbiotic systems and perhaps more likely supplanted by elevated N deposition. We suggest that other ecosystem compartments with low rates of fixation (e.g. soils) might also be susceptible to N pollution and merit investigation.

• The circumboreal/circumpolar N2-fixing lichen Stereocaulon vesuvianum is among the most widespread and abundant fruticose species in montane Britain but has lost the capacity to fix N2 over large areas of the country.
• To investigate whether loss of N2-fixation in S. vesuvianum is linked to increased N deposition, we examined thallus morphology, physiology and chemistry at twelve locations representing an N deposition gradient of 3–40 kg ha−1 year−1. Measurements were made in parallel on a non-N2-fixing reference species (Parmelia saxatilis). The presence or absence of cephalodia (N2-fixing nodules containing the cyanobacterium Stigonema sp) was recorded in over 500 herbarium specimens of S. vesuvianum dating back to 1820.
• Cephalodium abundance in S. vesuvianum, and 15N concentration in S. vesuvianum and P. saxatilis, were strongly negatively correlated with N deposition and particularly with dry deposited N; cephalodia do not form at total N deposition rates ≥8–9 kg ha−1 year−1. Other morphological oddities in S. vesuvianum at N-polluted sites include increased apothecium (fungal reproductive structure) production and green algal biofilm development. Biofilm covered thalli without cephalodia lacked nitrogenase activity and cephalodia at sites where they rarely develop had nitrogenase activities typical for this species. The presence or absence of cephalodia in herbarium specimens of S. vesuvianum suggest that the present-day N-deposition linked gradient in N2-fixing capacity did not exist in the 19th century and largely developed between 1900–1940.
• Synthesis. We provide clear evidence that N2-fixing capacity in S. vesuvianum has been lost in regions subjected to many decades of enhanced atmospheric N deposition. This loss is consistent with established models of diazotrophy, which identify supply of combined N as an inhibitor of N2-fixation. Progressive depletion of thallus 15N with increasing N deposition is in line with available data indicating that much atmospheric N pollution is 15N-depleted. Rates of nitrogenase activity in S. vesuvianum are low compared to other symbiotic systems and perhaps more likely supplanted by elevated N deposition. We suggest that other ecosystem compartments with low rates of fixation (e.g. soils) might also be susceptible to N pollution and merit investigation.

Nutrient pollution has increased plant litter nutrient concentrations in many ecosystems, which may profoundly impact litter decomposition and change the chemical composition of litter inputs to soils. Here, we report on a mesocosm experiment to study how variations in the nitrogen (N) and phosphorus (P) concentrations in Fagus sylvatica (European beech) litter from four sites differing in bedrock, atmospheric deposition, and climate affect lignin and carbohydrate loss rates and residual litter chemistry. We show with pyrolysis GC/MS and elemental analysis that nutrient concentrations had a strong influence on changes in litter chemistry during early decomposition (0–181 days), when greater lignin loss rates were associated with low P concentrations, whereas carbohydrate and bulk C loss were associated with high N concentrations. Nutrient concentrations, in contrast, did not influence changes in litter chemistry in the later decomposition stage (181–475 days), where the decomposition rates of lignin, carbohydrates, and bulk C all increased with litter N concentration and no differences in decomposition rates between major compound classes were detected. Our data indicate that these differences were related to the transition from increasing to constant or declining microbial biomass, and an associated decrease in microbial dependence on the mobilization of nutrients from the insoluble litter fraction.

Introduction: Organic phosphorus (Po) compounds constitute an important pool in soil P cycling, but their decomposition dynamics are poorly understood. Further, it has never been directly tested whether low molecular weight Po compounds are taken up by soil microbes in an intact form, which reduces the dependence of their P acquisition on extracellular phosphatases.

Methods: We investigated the short-term fate (24 h) of five 33P-labelled Po compounds (teichoic acids, phospholipids, DNA, RNA and soluble organophosphates) and 33P-labelled inorganic P (Pi) in two soils.

Results: We found indications that soil microbial breakdown of phosphodiesters was limited by the depolymerization step, and that direct microbial uptake of Po occurred to a substantial extent.

Discussion: We postulate a trade-off between direct Po uptake and complete extracellular Po mineralization. These findings have profound consequences for our understanding of microbial P cycling in soils.

The oscillating redox conditions that characterize coastal sandy sediments foster microbial communities capable of respiring oxygen and nitrate simultaneously, thereby increasing the potential for organic matter remineralization, nitrogen (N)-loss and emissions of the greenhouse gas nitrous oxide. It is unknown to what extent these conditions also lead to overlaps between dissimilatory nitrate and sulfate respiration. Here, we show that sulfate and nitrate respiration co-occur in the surface sediments of an intertidal sand flat. Furthermore, we found strong correlations between dissimilatory nitrite reduction to ammonium (DNRA) and sulfate reduction rates. Until now, the nitrogen and sulfur cycles were assumed to be mainly linked in marine sediments by the activity of nitrate-reducing sulfide oxidisers. However, transcriptomic analyses revealed that the functional marker gene for DNRA (nrfA) was more associated with microorganisms known to reduce sulfate rather than oxidise sulfide. Our results suggest that when nitrate is supplied to the sediment community upon tidal inundation, part of the sulfate reducing community may switch respiratory strategy to DNRA. Therefore increases in sulfate reduction rate in-situ may result in enhanced DNRA and reduced denitrification rates. Intriguingly, the shift from denitrification to DNRA did not influence the amount of N2O produced by the denitrifying community. Our results imply that microorganisms classically considered as sulfate reducers control the potential for DNRA within coastal sediments when redox conditions oscillate and therefore retain ammonium that would otherwise be removed by denitrification, exacerbating eutrophication.

Chemical pollution poses a threat to biodiversity on a global scale. This has been acknowledged in the Post-2020 Biological Diversity Framework which proposes to regulate the release of chemicals to the environment and names specific indicators focusing on pesticides, nutrients and plastic waste. We fully endorse the inclusion of these substances but argue that in order to protect biodiversity from hazardous chemicals, the scope of Target 7 should feature other groups of pollutants with potential to contribute to biodiversity loss. We propose the inclusion of non-agricultural biocides, per- and polyfluoroalkyl substances (PFASs), toxic metal(loid)s, and endocrine disrupting chemcials (EDCs). Furthermore, data on emerging pollutants (e.g., rare earth elements, industrial chemicals, liquid crystal monomers, pharmaceuticals, personal care products) need to be regularly scanned and these pollutants added to Target 7 in case of biodiversity risk. We suggest to amend Target 7 to postulate the aim for the overall reduction of chemical production and emissions, as well as the addition of the described substance groups of high concern to biodiversity for discussion and implementation in the Post-2020 Biodiversity Framework. We further elaborate on different strategies for the reduction of emissions of hazardous chemicals through chemical simplification and grouping, reduction of chemicals with non-essential use, and innovative synthesis strategies (“benign by design”). In this context the full life cycle of chemicals, i.e., production, use, end of life needs to be considered. Lastly, we propose to set up data inventories that transparently inform about production, transport and emissions of chemicals in cooperation with industry, that can serve as basis for indicators related to monitoring the effectiveness of the goals set under Target 7.

The filamentous fungus Trichoderma reesei is a prolific producer of plant cell wall degrading enzymes, which are regulated in response to diverse environmental signals for optimal adaptation, but also produces a wide array of secondary metabolites. Available carbon source and light are the strongest cues currently known to impact secreted enzyme levels and an interplay with regulation of secondary metabolism became increasingly obvious in recent years. While cellulase regulation is already known to be modulated by different mitogen activated protein kinase (MAPK) pathways, the relevance of the light signal, which is transmitted by this pathway in other fungi as well, is still unknown in T. reesei as are interconnections to secondary metabolism and chemical communication under mating conditions. Here we show that MAPkinases differentially influence cellulase regulation in light and darkness and that the Hog1 homologue TMK3, but not TMK1 or TMK2 are required for the chemotropic response to glucose in T. reesei. Additionally, MAPkinases regulate production of specific secondary metabolites including trichodimerol and bisorbibutenolid, a bioactive compound with cytostatic effect on cancer cells and deterrent effect on larvae, under conditions facilitating mating, which reflects a defect in chemical communication. Strains lacking either of the MAPkinases become female sterile, indicating the conservation of the role of MAPkinases in sexual fertility also in T. reesei. In summary, our findings substantiate the previously detected interconnection of cellulase regulation with regulation of secondary metabolism as well as the involvement of MAPkinases in light dependent gene regulation of cellulase and secondary metabolite genes in fungi.

Remediation of residually contaminated soils remains a widespread problem. Biochar can immobilize polycyclic aromatic hydrocarbons (PAH). However, studies on its ability to immobilize PAH and N, S, and O substituted PAH (hetero-PAH) in real soils, and benchmarking with commercial activated carbon are missing. Here, we compared the ability of pristine biochar (BC), steam-activated biochar (SABC), and commercial activated carbon (AC) to immobilize PAH and hetero-PAH. The three carbons were tested on soils from four different contaminated sites in Austria. Different amendment rates (w/w) of the carbons were investigated (BC: 1.0, 2.5, and 5%; SABC: 0.5, 1.0, and 2.0%; AC: 1%) in batch experiments to cover meaningful ranges in relation to their performance. SABC performed better than AC, removing at least 80% PAH with the lowest application rate of 0.5%, and achieving a complete removal at an application rate of 1.0%. BC performed slightly worse but still acceptable in residually contaminated soils (40 and 100% removal at 1 and 5% amendment, respectively). The ability of BC and SABC to immobilize PAH decreased as the PAH-molar volume increased. PAH with three or more rings were preferentially removed by AC compared to SABC or BC. This can be explained by the difference in pore size distribution of the carbons which could limit the accessibility of PAH and hetero-PAH to reach sorption sites for π- π electron donor-acceptor interactions, which drive PAH and hetero-PAH sorption to carbons. Column percolation tests confirmed the results obtained in batch tests, indicating, that decisions for soil remediation can be derived from simpler batch experiments. In soil samples with 1% BC, a reduction of over 90% in the total concentration of PAH in the leached water was observed. Overall, BC and SABC were demonstrated to be valid substitutes for AC for stabilizing residually contaminated soils.

The persistence of the artificial sweetener acesulfame potassium (ACE) during wastewater treatment and subsequently in the aquatic environment has made it a widely used tracer of wastewater inputs to both surface water and groundwater. However, the recently observed biodegradation of ACE during wastewater treatment has questioned the validity of this application. In this study, we assessed the use of ACE not only as a marker of wastewater, but also as a transient wastewater tracer that allows both the calculation of mixing ratios and travel times through the aquifer as well as the calibration of transient groundwater flow and mass transport models. Our analysis was based on data obtained in a nearly 8-year river water and groundwater sampling campaign along a confirmed wastewater-receiving riverbank filtration site located close to a drinking water supply system. We provide evidence that temperature controls ACE concentration and thus its seasonal oscillation. River water data showed that ACE loads decreased from 1.5–4 mg·s−1 in the cold season (December to June; T<10 °C) to 0–0.5 mg·s−1 in the warm season (July to November; T>10 °C). This seasonal variability of >600% was detectable in the aquifer and preserved >3 km, with ACE concentrations oscillating between <LOQ in the warm season up to 1 μg·L−1 in the cold season. The large seasonal variation in ACE concentrations during wastewater treatment, compared to the other sweeteners (sucralose, cyclamate, and saccharin) and chloride enables its use as a transient tracer of wastewater inflows and riverbank filtration. In addition, the arrival time of the ACE concentration peak can be used to estimate groundwater flow velocity and mixing ratios, thereby demonstrating its potential in the calibration of groundwater numerical models.

Increasing global temperatures have been reported to accelerate soil carbon (C) cycling, but also to promote nitrogen (N) and phosphorus (P) dynamics in terrestrial ecosystems. However, warming can differentially affect ecosystem C, N and P dynamics, potentially intensifying elemental imbalances between soil resources, plants and soil microorganisms. Here, we investigated the effect of long-term soil warming on microbial resource limitation, based on measurements of microbial growth (18O incorporation into DNA) and respiration after C, N and P amendments. Soil samples were taken from two soil depths (0–10, 10–20 cm) in control and warmed (>14 years warming, +4°C) plots in the Achenkirch soil warming experiment. Soils were amended with combinations of glucose-C, inorganic/organic N and inorganic/organic P in a full factorial design, followed by incubation at their respective mean field temperatures for 24 h. Soil microbes were generally C-limited, exhibiting 1.8-fold to 8.8-fold increases in microbial growth upon C addition. Warming consistently caused soil microorganisms to shift from being predominately C limited to become C-P co-limited. This P limitation possibly was due to increased abiotic P immobilization in warmed soils. Microbes further showed stronger growth stimulation under combined glucose and inorganic nutrient amendments compared to organic nutrient additions. This may be related to a prolonged lag phase in organic N (glucosamine) mineralization and utilization compared to glucose. Soil respiration strongly positively responded to all kinds of glucose-C amendments, while responses of microbial growth were less pronounced in many of these treatments. This highlights that respiration–though easy and cheap to measure—is not a good substitute of growth when assessing microbial element limitation. Overall, we demonstrate a significant shift in microbial element limitation in warmed soils, from C to C-P co-limitation, with strong repercussions on the linkage between soil C, N and P cycles under long-term warming.

Global warming is considered to impact the fluxes of methane (CH4) and nitrous oxide (N2O) between forest soils and the atmosphere, but it is unclear whether the responses change over time. In this study the response of soil CH4 and N2O fluxes to field soil warming (+4 °C) were determined during years 2–5 and 14–16 in a soil warming experiment in a temperate forest. In the second and sixteenth year of soil warming, temperature sensitivities of CH4 and N2O fluxes were assessed in-situ by gradually rising field soil temperatures to ∼10 °C above ambient within a short period of three to four days. Production of dinitrogen (N2) was measured ex-situ in the sixteenth year of warming. Soil warming significantly reduced CH4 uptake (-19.5%) and increased N2O emissions (+41.6%) during the first years of warming, whereas no warming effects on soil CH4 and N2O fluxes were observed during the later years. Dinitrogen production was up to ten times higher than N2O production, though the high spatiotemporal variability masked any significant effects of soil warming on soil N2 fluxes. Temperature sensitivities (Q10) for CH4 uptake and N2O emissions were 2.07 and 4.06, respectively, in the second year of warming and 1.52 and 1.79, respectively, in the sixteenth year of soil warming. The diminishing warming response of the soil N2O fluxes likely were caused by longer-term changes in soil N availability and/or simultaneous acclimation of the soil microbial community to soil warming. Soil moisture was largely unaffected by soil warming, and soil temperature alone was only a weak predictor of soil CH4 fluxes. Methane fluxes therefore can be expected to be generally less affected than N2O fluxes. Overall, our results suggest that soil warming has only limited and transient effects on soil CH4 and N2O fluxes in this type of temperate forest.

Tire wear particle (TWP)-derived compounds may be of high concern to consumers when released in the root zone of edible plants. We exposed lettuce plants to the TWP-derived compounds diphenylguanidine (DPG), hexamethoxymethylmelamine (HMMM), benzothiazole (BTZ), N-phenyl-N′-(1,3-dimethylbutyl)-p-phenylenediamine (6PPD), and its quinone transformation product (6PPD-q) at concentrations of 1 mg L–1 in hydroponic solutions over 14 days to analyze if they are taken up and metabolized by the plants. Assuming that TWP may be a long-term source of TWP-derived compounds to plants, we further investigated the effect of leaching from TWP on the concentration of leachate compounds in lettuce leaves by adding constantly leaching TWP to the hydroponic solutions. Concentrations in leaves, roots, and nutrient solution were quantified by triple quadrupole mass spectrometry, and metabolites in the leaves were identified by Orbitrap high resolution mass spectrometry. This study demonstrates that TWP-derived compounds are readily taken up by lettuce with measured maximum leaf concentrations between ∼0.75 (6PPD) and 20 μg g–1 (HMMM). Although these compounds were metabolized in the plant, we identified several transformation products, most of which proved to be more stable in the lettuce leaves than the parent compounds. Furthermore, continuous leaching from TWP led to a resupply and replenishment of the metabolized compounds in the lettuce leaves. The stability of metabolized TWP-derived compounds with largely unknown toxicities is particularly concerning and is an important new aspect for the impact assessment of TWP in the environment.

The role of the gut microbiome in developing Inflammatory Bowel Disease (IBD) in humans and dogs has received attention in recent years. Evidence suggests that IBD is associated with alterations in gut microbial composition, but further research is needed in veterinary medicine. The impact of IBD treatment on the gut microbiome needs to be better understood, especially in a breed-specific form of IBD in Yorkshire Terriers known as Yorkshire Terrier Enteropathy (YTE). This study aimed to investigate the difference in gut microbiome composition between YTE dogs during disease and remission and healthy Yorkshire Terriers. Our results showed a significant increase in specific taxa such as Clostridium sensu stricto 1, Escherichia-Shigella, and Streptococcus, and a decrease in Bacteroides, Prevotella, Alloprevotella, and Phascolarctobacterium in YTE dogs compared to healthy controls. No significant difference was found between the microbiome of dogs in remission and those with active disease, suggesting that the gut microbiome is affected beyond clinical recovery.

is a semi-wild cactus cultivated for its fruit. However, the cladodes are often discarded, wasting the potentially useful mucilage in them. The mucilage is composed primarily of heteropolysaccharides, characterized by their molar mass distribution, monosaccharide composition, structural features (by vibrational spectroscopy, FT IR, and atomic force microscopy, AFM), and fermentability by known saccharolytic commensal members of the gut microbiota. After fractionation with ion exchange chromatography, four polysaccharides were found: one neutral (composed mainly of galactose, arabinose, and xylose) and three acidic, with a galacturonic acid content from 10 to 35%. Their average molar masses ranged from 1.8 × 10 to 2.8 × 10 g·mol. Distinct structural features such as galactan, arabinan, xylan, and galacturonan motifs were present in the FT IR spectra. The intra- and intermolecular interactions of the polysaccharides, and their effect on the aggregation behavior, were shown by AFM. The composition and structural features of these polysaccharides were reflected in their prebiotic potential. and were not able to utilize them, whereas members of showed utilization capacity. The obtained data suggest a high economic potential for this species, with potential uses such as animal feed in arid areas, precise prebiotic, and symbiotic formulations, or as the carbon skeleton source in a green refinery. Our methodology can be used to evaluate the saccharides as the phenotype of interest, helping to guide the breeding strategy.

Marine and freshwater sponges harbor diverse communities of bacteria with vast potential to produce secondary metabolites that may play an important role in protecting the host from predators and infections. In this work, we initially used cultivation and metagenomics to investigate the microbial community of the freshwater sponge Spongilla lacustris collected in an Austrian lake. Representatives of 41 bacterial genera were isolated from the sponge sample and classified according to their 16S rRNA gene sequences. The genomes of 33 representative isolates and the 20 recovered metagenome-assembled genomes (MAGs) contained in total 306 secondary metabolite biosynthesis gene clusters (BGCs). Comparative 16S rRNA gene and genome analyses showed very little taxon overlap between the recovered isolates and the sponge community as revealed by cultivation-independent methods. Both culture-independent and -dependent analyses suggested high biosynthetic potential of the S. lacustris microbiome, which was confirmed experimentally even at the subspecies level for two isolates. To our knowledge, this is the most thorough description of the secondary metabolite production potential of a freshwater sponge microbiome to date. A large body of research is dedicated to marine sponges, filter-feeding animals harboring rich bacterial microbiomes believed to play an important role in protecting the host from predators and infections. Freshwater sponges have received so far much less attention with respect to their microbiomes, members of which may produce bioactive secondary metabolites with potential to be developed into drugs to treat a variety of diseases. In this work, we investigated the potential of bacteria associated with the freshwater sponge to biosynthesize diverse secondary metabolites. Using culture-dependent and -independent methods, we discovered over 300 biosynthetic gene clusters in sponge-associated bacteria and proved production of several compounds by selected isolates using genome mining. Our results illustrate the importance of a complex approach when dealing with microbiomes of multicellular organisms that may contain producers of medically important secondary metabolites.

Infectious disease is widely considered to be a major driver of evolution. A preponderance of signatures of balancing selection at blood group-related genes is thought to be driven by inherent trade-offs in susceptibility to disease. B4galnt2 is subject to long-term balancing selection in house mice, where two divergent allele classes direct alternative tissue-specific expression of a glycosyltransferase in the intestine versus blood vessels. The blood vessel allele class leads to prolonged bleeding times similar to von Willebrand disease in humans, yet has been maintained for millions of years. Based on in vivo functional studies in inbred lab strains, it is hypothesized that the cost of prolonged bleeding times may be offset by an evolutionary trade-off involving susceptibility to a yet unknown pathogen(s). To identify candidate pathogens for which resistance could be mediated by B4galnt2 genotype, we here employed a novel "pathometagenomic" approach in a wild mouse population, which combines bacterial 16S rRNA gene-based community profiling with histopathology of gut tissue. Through subsequent isolation, genome sequencing and controlled experiments in lab mice, we show that the presence of the blood vessel allele is associated with resistance to a newly identified subspecies of Morganella morganii, a clinically important opportunistic pathogen. Given the increasing importance of zoonotic events, the approach outlined here may find useful application in the detection of emerging diseases in wild animal populations.

Simultaneous identification and metabolic analysis of microbes with single-cell resolution and high throughput are necessary to answer the question of "who eats what, when, and where" in complex microbial communities. Here, we present a mid-infrared photothermal-fluorescence in situ hybridization (MIP-FISH) platform that enables direct bridging of genotype and phenotype. Through multiple improvements of MIP imaging, the sensitive detection of isotopically labeled compounds incorporated into proteins of individual bacterial cells became possible, while simultaneous detection of FISH labeling with rRNA-targeted probes enabled the identification of the analyzed cells. In proof-of-concept experiments, we showed that the clear spectral red shift in the protein amide I region due to incorporation of C atoms originating from C-labeled glucose can be exploited by MIP-FISH to discriminate and identify C-labeled bacterial cells within a complex human gut microbiome sample. The presented methods open new opportunities for single-cell structure-function analyses for microbiology.

Nitrite-oxidizing bacteria (NOB) catalyse the second nitrification step and are the main biological source of nitrate. The most diverse and widespread NOB genus is Nitrospira, which also contains complete ammonia oxidizers (comammox) that oxidize ammonia to nitrate. To date, little is known about the occurrence and biology of comammox and canonical nitrite oxidizing Nitrospira in extremely alkaline environments. Here, we studied the seasonal distribution and diversity, and the effect of short-term pH changes on comammox and canonical Nitrospira in sediments of two saline, highly alkaline lakes. We identified diverse canonical and comammox Nitrospira clade A-like phylotypes as the only detectable NOB during more than a year, suggesting their major importance for nitrification in these habitats. Gross nitrification rates measured in microcosm incubations were highest at pH 10 and considerably faster than reported for other natural, aquatic environments. Nitrification could be attributed to canonical and comammox Nitrospira and to Nitrososphaerales ammonia-oxidizing archaea. Furthermore, our data suggested that comammox Nitrospira contributed to ammonia oxidation at an extremely alkaline pH of 11. These results identify saline, highly alkaline lake sediments as environments of uniquely strong nitrification with novel comammox Nitrospira as key microbial players.

The activities of different microbes in the cow rumen have been shown to modulate the host's ability to utilize plant biomass, while the host-rumen interface has received little attention. As datasets collected worldwide have pointed to Campylobacteraceae as particularly abundant members of the rumen epithelial microbiome, we targeted this group in a subset of seven cows with meta- and isolate genome analysis. We show that the dominant Campylobacteraceae lineage has recently speciated into two populations that were structured by genome-wide selective sweeps followed by population-specific gene import and recombination. These processes led to differences in gene expression and enzyme domain composition that correspond to the ability to utilize acetate, the main carbon source for the host, at the cost of inhibition by propionate. This trade-off in competitive ability further manifests itself in differential dynamics of the two populations in vivo. By exploring population-level adaptations that otherwise remain cryptic in culture-independent analyses, our results highlight how recent evolutionary dynamics can shape key functional roles in the rumen microbiome.

Chlamydiae is a bacterial phylum composed of obligate animal and protist endosymbionts. However, other members of the Planctomycetes-Verrucomicrobia-Chlamydiae superphylum are primarily free living. How Chlamydiae transitioned to an endosymbiotic lifestyle is still largely unresolved. Here we reconstructed Planctomycetes-Verrucomicrobia-Chlamydiae species relationships and modelled superphylum genome evolution. Gene content reconstruction from 11,996 gene families suggests a motile and facultatively anaerobic last common Chlamydiae ancestor that had already gained characteristic endosymbiont genes. Counter to expectations for genome streamlining in strict endosymbionts, we detected substantial gene gain within Chlamydiae. We found that divergence in energy metabolism and aerobiosis observed in extant lineages emerged later during chlamydial evolution. In particular, metabolic and aerobic genes characteristic of the more metabolically versatile protist-infecting chlamydiae were gained, such as respiratory chain complexes. Our results show that metabolic complexity can increase during endosymbiont evolution, adding an additional perspective for understanding symbiont evolutionary trajectories across the tree of life.

The incidence of nephrolithiasis is rising worldwide. Although it is a multifactorial disease, lifestyle plays a major role in its etiology. Another considerable factor could be an aberrant microbiome. In our observational single-center study, we aimed to investigate the composition of bacteria in kidney stones and urine focusing on patients with features of metabolic syndrome. Catheterized urine and kidney stones were collected prospectively from 100 consecutive patients undergoing endoscopic nephrolithotomy between 2020 and 2021 at our clinic. Microbiome composition was analyzed via 16S rRNA gene amplicon sequencing. Detection of bacteria was successful in 24% of the analyzed kidney stones. These patients had a prolonged length of stay compared to patients without verifiable bacteria in their stones (2.9 vs 1.5 days). Patients with features of metabolic syndrome were characterized by kidney stones colonized with classical gastrointestinal bacteria and displayed a significant enrichment of Enterococcaceae and Enterobacteriaceae. Stones of patients without features of metabolic syndrome characterized by Ureaplasma and Staphylococcaceae. Patients with bacteria in their kidney stones exhibit a longer length of stay, possibly due to more complex care. Patients presenting with features of metabolic syndrome displayed a distinct stone microbiome compared to metabolically fit patients. Understanding the role of bacteria in stone formation could enable targeted therapy, prevention of post-operative complications and new therapeutic strategies.