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12. Biogeographical drivers of supraglacial microbial communities

Author

Mourot, Rey, primary, Trivedi, Christopher B., additional, Keuschnig, Christoph, additional, Winkel, Matthias, additional, Bradley, James A., additional, Larose, Catherine, additional, Luks, Bartlomiej, additional, Feord, Helen, additional, Anesio, Alexandre M., additional, Tranter, Martyn, additional, and Benning, Liane G., additional

Published
2023
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14. Active and dormant microorganisms on glacier surfaces

Author

Bradley, James A., primary, Trivedi, Christopher B., additional, Winkel, Matthias, additional, Mourot, Rey, additional, Lutz, Stefanie, additional, Larose, Catherine, additional, Keuschnig, Christoph, additional, Doting, Eva, additional, Halbach, Laura, additional, Zervas, Athanasios, additional, Anesio, Alexandre M., additional, and Benning, Liane G., additional

Published
2022
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16. Reduced methane emissions in former permafrost soils driven by vegetation and microbial changes following drainage

Author

Keuschnig, Christoph, Larose, Catherine, Rudner, Mario, Pesqueda, Argus, Doleac, Stéphane, Elberling, Bo, Björk, Robert G., Klemedtsson, Leif, Björkman, Mats P., Keuschnig, Christoph, Larose, Catherine, Rudner, Mario, Pesqueda, Argus, Doleac, Stéphane, Elberling, Bo, Björk, Robert G., Klemedtsson, Leif, and Björkman, Mats P.

Abstract

In Arctic regions, thawing permafrost soils are projected to release 50 to 250 Gt of carbon by 2100. This data is mostly derived from carbon-rich wetlands, although 71% of this carbon pool is stored in faster-thawing mineral soils, where ecosystems close to the outer boundaries of permafrost regions are especially vulnerable. Although extensive data exists from currently thawing sites and short-term thawing experiments, investigations of the long-term changes following final thaw and co-occurring drainage are scarce. Here we show ecosystem changes at two comparable tussock tundra sites with distinct permafrost thaw histories, representing 15 and 25 years of natural drainage, that resulted in a 10-fold decrease in CH4 emissions (3.2 ± 2.2 vs. 0.3 ± 0.4 mg C-CH4 m−2 day−1), while CO2 emissions were comparable. These data extend the time perspective from earlier studies based on short-term experimental drainage. The overall microbial community structures did not differ significantly between sites, although the drier top soils at the most advanced site led to a loss of methanogens and their syntrophic partners in surface layers while the abundance of methanotrophs remained unchanged. The resulting deeper aeration zones likely increased CH4 oxidation due to the longer residence time of CH4 in the oxidation zone, while the observed loss of aerenchyma plants reduced CH4 diffusion from deeper soil layers directly to the atmosphere. Our findings highlight the importance of including hydrological, vegetation and microbial specific responses when studying long-term effects of climate change on CH4 emissions and underscores the need for data from different soil types and thaw histories.

Published
2022

17. Active and dormant microorganisms on glacier surfaces.

Author

Bradley, James A., Trivedi, Christopher B., Winkel, Matthias, Mourot, Rey, Lutz, Stefanie, Larose, Catherine, Keuschnig, Christoph, Doting, Eva, Halbach, Laura, Zervas, Athanasios, Anesio, Alexandre M., and Benning, Liane G.

Subjects
GLACIERS, POLAR climate, ICE sheets, BIOGEOCHEMICAL cycles, BIOTIC communities, ECOLOGICAL models
Abstract

Glacier and ice sheet surfaces host diverse communities of microorganisms whose activity (or inactivity) influences biogeochemical cycles and ice melting. Supraglacial microbes endure various environmental extremes including resource scarcity, frequent temperature fluctuations above and below the freezing point of water, and high UV irradiance during summer followed by months of total darkness during winter. One strategy that enables microbial life to persist through environmental extremes is dormancy, which despite being prevalent among microbial communities in natural settings, has not been directly measured and quantified in glacier surface ecosystems. Here, we use a combination of metabarcoding and metatranscriptomic analyses, as well as cell‐specific activity (BONCAT) incubations to assess the diversity and activity of microbial communities from glacial surfaces in Iceland and Greenland. We also present a new ecological model for glacier microorganisms and simulate physiological state‐changes in the glacial microbial community under idealized (i) freezing, (ii) thawing, and (iii) freeze–thaw conditions. We show that a high proportion (>50%) of bacterial cells are translationally active in‐situ on snow and ice surfaces, with Actinomycetota, Pseudomonadota, and Planctomycetota dominating the total and active community compositions, and that glacier microorganisms, even when frozen, could resume translational activity within 24 h after thawing. Our data suggest that glacial microorganisms respond rapidly to dynamic and changing conditions typical of their natural environment. We deduce that the biology and biogeochemistry of glacier surfaces are shaped by processes occurring over short (i.e., daily) timescales, and thus are susceptible to change following the expected alterations to the melt‐regime of glaciers driven by climate change. A better understanding of the activity of microorganisms on glacier surfaces is critical in addressing the growing concern of climate change in Polar regions, as well as for their use as analogues to life in potentially habitable icy worlds. [ABSTRACT FROM AUTHOR]

Published
2023
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18. DNA/RNA Preservation in Glacial Snow and Ice Samples

Author

Trivedi, Christopher B., primary, Keuschnig, Christoph, additional, Larose, Catherine, additional, Rissi, Daniel Vasconcelos, additional, Mourot, Rey, additional, Bradley, James A., additional, Winkel, Matthias, additional, and Benning, Liane G., additional

Published
2022
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23. Long‐term warming effects on the microbiome and nifH gene abundance of a common moss species in sub‐Arctic tundra.

Author

Klarenberg, Ingeborg J., Keuschnig, Christoph, Russi Colmenares, Ana J., Warshan, Denis, Jungblut, Anne D., Jónsdóttir, Ingibjörg S., and Vilhelmsson, Oddur

Subjects
*PLANT biomass, *SHRUBS, *BACTERIAL communities, *BACTERIAL diversity, *CLIMATE change, *CARBON fixation, *TUNDRAS, *NITROGEN fixation
Abstract

Summary: Bacterial communities form the basis of biogeochemical processes and determine plant growth and health. Mosses harbour diverse bacterial communities that are involved in nitrogen fixation and carbon cycling. Global climate change is causing changes in aboveground plant biomass and shifting species composition in the Arctic, but little is known about the response of moss microbiomes in these environments.Here, we studied the total and potentially active bacterial communities associated with Racomitrium lanuginosum in response to a 20‐yr in situ warming in an Icelandic heathland. We evaluated the effect of warming and warming‐induced shrub expansion on the moss bacterial community composition and diversity, and nifH gene abundance.Warming changed both the total and the potentially active bacterial community structure, while litter abundance only affected the total bacterial community structure. The abundance of nifH genes was negatively affected by litter abundance. We also found shifts in the potentially nitrogen‐fixing community, with Nostoc decreasing and noncyanobacterial diazotrophs increasing in relative abundance.Our data suggest that the moss microbial community and potentially nitrogen fixing taxa will be sensitive to future warming, partly via changes in litter and shrub abundance. [ABSTRACT FROM AUTHOR]

Published
2022
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26. Long-term warming effects on the microbiome and nitrogen fixation associated with the moss Racomitrium lanuginosum in a subarctic alpine heathland

Author

Klarenberg, Ingeborg J., Keuschnig, Christoph, Colmenares, Ana J. Russi, Jungblut, Anne D., Jónsdóttir, Ingibjörg S., and Vilhelmsson, Oddur

Abstract

Bacterial communities form the basis of biogeochemical processes and determine plant growth and health. Mosses, an abundant plant group in many Arctic ecosystems, harbour diverse bacterial communities that are for instance involved in nitrogen fixation. Global climate change is causing changes in aboveground plant biomass and shifting species composition in the Arctic, but little is known about the response of the moss microbiome. Here, we study the bacterial community associated with the moss Racomitrium lanuginosum , a common species in the Arctic, in a 20-year in situ warming experiment in an Icelandic heathland. We evaluate changes in bacterial community composition and diversity. Further, we assess the consequences of warming for nifH gene copy numbers and nitrogen fixation rates. Our findings indicate an increase in the relative abundance of Proteobacteria and a decrease in the relative abundance of Cyanobacteria and Acidobacteria with warming. The nifH gene copy number decreases, while the rate of nitrogen fixation is not affected. This contradiction could be explained by a shift in the nitrogen fixing bacterial community. Although climate warming might not change the contribution of R. lanuginosum to nitrogen input in nitrogen-limited ecosystems, the microbial community resilience and the nitrogen fixing taxa may shift.

Published
2019
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28. Fungal and bacterial involvement in nitrogen cycling and N2O production in soil

Author

Keuschnig , Christoph, Ampère, École Centrale de Lyon ( ECL ), Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Institut National des Sciences Appliquées de Lyon ( INSA Lyon ), Université de Lyon-Institut National des Sciences Appliquées ( INSA ) -Institut National des Sciences Appliquées ( INSA ) -Centre National de la Recherche Scientifique ( CNRS ), Université de Lyon, Pascal Simonet, Catherine Larose, Ampère (AMPERE), École Centrale de Lyon (ECL), Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Ampère, Département Bioingénierie (BioIng), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-École Centrale de Lyon (ECL), and STAR, ABES

Subjects
[SPI.OTHER]Engineering Sciences [physics]/Other, Champignons, Bacteria, Sol, [ SPI.OTHER ] Engineering Sciences [physics]/Other, [SPI.OTHER] Engineering Sciences [physics]/Other, Monoxyde d’azote, Nitous oxide, Fungi, Protoxyde d’azote, Nitric oxide, Nitrogen cycle, Greenhouse gas, Soil, Cycle de l'azote, Bactéries, Gaz à effet de serre
Abstract

The main objective of this thesis is to determine the role of microbial communities in N2O emissions from soil, and more specifically to define to what extent fungi are involved. Therefore, their community structure at the micro scale, their behavior in reducing nitrogen and producing N2O, and their impact on nitrogen cycling communities as decomposers in soil were investigated. Analysis of soil fractions of unmanaged, pristine Rothamsted Park Grass soil showed that fungal communities change within isolated fractions in contrast to bacterial communities. Also, nitrifying, denitrifying and N2O reducing potentials were detected in all fractions and found to be linked to carbon and nitrogen chemistry. Pure culture experiments on 24 fungal strains quantifying NO and N2O production from nitrite showed that Fusarium species are true N2O producers among fungi. Monitoring NO revealed that nitrite medium is unstable under anoxic conditions and produces NO abiotically, which implies that low N2O producing strains are actually detoxifying this NO rather than respiring it, as previously assumed. The lack of a nirK - p450nor in most fungi supported this hypothesis. Interspecies relationships between fungi and bacteria were studied following community development after organic matter addition. Different organic amendments triggered distinct responses of a soil community with respect to bacterial and fungal activity. Functional signatures identified in this study corroborated our hypothesis that fungi are involved in N2O production by influencing a N-cycling bacterial community via carbohydrate degradation processes. The results from this thesis provide a basis for exploring interspecies relationships in nitrogen cycling processes in soil and mark a step towards integrating all members of the community in soil ecosystem research., L'objectif principal de cette thèse est de déterminer le rôle des communautés microbiennes dans les émissions de N2O du sol, et plus précisément de définir dans quelle mesure les champignons sont impliqués. Par conséquent, leur structure communautaire à l'échelle micro, leur comportement dans la réduction de l'azote et la production de N2O, et leur interaction avec les communautés microbiennes impliquées dans le cycle de l'azote en tant que décomposeurs de matière organique dans le sol ont été étudiés. L'analyse des fractions de sol du parc Rothamsted a montré que les communautés fongiques changent au sein de fractions isolées, contrairement aux communautés bactériennes. De plus, des potentiels de nitrification, de dénitrification et de réduction de N2O ont été détectés dans toutes les fractions et se sont révélés liés à la chimie du carbone et de l'azote. Des expériences quantifiant la production de NO et N2O à partir de nitrite sur 24 souches de champignons de culture pure ont montré que les espèces de Fusarium sont de véritables producteurs de N2O parmi les champignons. Le suivit de NO a révélé que le milieu de nitrite est instable dans des conditions anoxiques et produit du NO abiotiquement, ce qui implique que des souches produisant du N2O à de faibles taux détoxifient ce NO plutôt que de le respirer, comme précédemment supposé. L’absence d’un nirK - p450nor dans la plupart des champignons a étayé cette hypothèse. Les relations interspécifiques entre champignons et bactéries ont été étudiées après l'addition de matière organique. Différentes modifications organiques ont déclenché des réponses distinctes en termes d’activité bactérienne et fongique sein d'une même communauté de sol. Les signatures fonctionnelles identifiées dans cette étude corroborent notre hypothèse selon laquelle les champignons sont impliqués dans la production de N2O en influençant les bactéries impliquées dans le cycle N par des processus de dégradation de glucides. Les résultats de cette thèse fournissent une base pour explorer les relations interspécifiques dans le cycle biogéochimique de l’azote dans le sol et marque une étape vers l'intégration de tous les membres de la communauté dans la recherche sur les écosystèmes du sol.

Published
2016

29. NO and N2O transformations of diverse fungi in hypoxia: evidence for anaerobic respiration only in Fusarium strains.

Author

Keuschnig, Christoph, Gorfer, Markus, Li, Guofen, Mania, Daniel, Frostegård, Åsa, Bakken, Lars, and Larose, Catherine

Subjects
*NITRATE reductase, *FUSARIUM, *FUSARIUM solani, *FUSARIUM oxysporum, *RESPIRATION, *RHIZOCTONIA solani, *DENITRIFYING bacteria
Abstract

Summary: Fungal denitrification is claimed to produce non‐negligible amounts of N2O in soils, but few tested species have shown significant activity. We hypothesized that denitrifying fungi would be found among those with assimilatory nitrate reductase, and tested 20 such batch cultures for their respiratory metabolism, including two positive controls, Fusarium oxysporum and Fusarium lichenicola, throughout the transition from oxic to anoxic conditions in media supplemented with NO2−. Enzymatic reduction of NO2− (NIR) and NO (NOR) was assessed by correcting measured NO‐ and N2O‐kinetics for abiotic NO‐ and N2O‐production (sterile controls). Significant anaerobic respiration was only confirmed for the positive controls and for two of three Fusarium solani cultures. The NO kinetics in six cultures showed NIR but not NOR activity, observed through the accumulation of NO. Others had NOR but not NIR activity, thus reducing abiotically produced NO to N2O. The presence of candidate genes (nirK and p450nor) was confirmed in the positive controls, but not in some of the NO or N2O accumulating cultures. Based on our results, we conclude that only the Fusarium cultures were able to sustain anaerobic respiration and produced low amounts of N2O as a response to an abiotic NO production from the medium. [ABSTRACT FROM AUTHOR]

Published
2020
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30. Effective NO reduction mechanisms in fungi might not be coupled to denitrification

Author

Keuschnig, Christoph, Frostegard, Asa, Bakken, Lars, Larose, Catherine, Simonet, Pascal, Ampère, Département Bioingénierie (BioIng), Ampère (AMPERE), École Centrale de Lyon (ECL), Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-École Centrale de Lyon (ECL), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Dept. of Chemistry Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), and Larose, Catherine

Subjects
[SDE] Environmental Sciences, [SPI]Engineering Sciences [physics], [SPI] Engineering Sciences [physics], [SDE]Environmental Sciences, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2015

31. Dissimilatory nitrogen reduction by soil fungal community members and their possible contribution to N2O production in soi

Author

Keuschnig, Christoph, Larose, Catherine, Simonet, Pascal, Ampère, Département Bioingénierie (BioIng), Ampère (AMPERE), École Centrale de Lyon (ECL), Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-École Centrale de Lyon (ECL), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Larose, Catherine

Subjects
[SDE] Environmental Sciences, [SPI]Engineering Sciences [physics], [SPI] Engineering Sciences [physics], [SDE]Environmental Sciences, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2015

33. Comparison of microbial communities colonizing different microhabitats in Rothamsted Park Grass Soil - An attempt to localize denitrifying hot-spots in the soil matrix

Author

Keuschnig, Christoph, Simonet, Pascal, Larose, Catherine, Ampère, Département Bioingénierie (BioIng), Ampère (AMPERE), École Centrale de Lyon (ECL), Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-École Centrale de Lyon (ECL), and Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
[SPI]Engineering Sciences [physics], [SDE]Environmental Sciences, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2014

34. Microscale localization of denitrifying communities in the soil matrix

Author

Keuschnig, Christoph, Simonet, Pascal, Larose, Catherine, Ampère, Département Bioingénierie (BioIng), Ampère (AMPERE), École Centrale de Lyon (ECL), Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-École Centrale de Lyon (ECL), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Larose, Catherine

Subjects
[SDE] Environmental Sciences, [SPI]Engineering Sciences [physics], [SPI] Engineering Sciences [physics], [SDE]Environmental Sciences, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2014

35. Nitrite production by controlled nitrification of liquid pig manure

Author

Keuschnig, Christoph

Subjects
Nitrite, Nitrification, selective inhibition, acidified nitrite, AOB, NOB, Schwein, Nitrifikation, Gülle, Phytopathogene Pilze, Nitrit, Nitrifizierung, selektive Inhibierung, saures Nitrit, AOB, NOB, Inhibition
Abstract

Christoph Keuschnig Zsfassung in dt. Sprache Wien, Univ. für Bodenkultur, Masterarb., 2013

Published
2013

37. NO and N 2 O transformations of diverse fungi in hypoxia: evidence for anaerobic respiration only in Fusarium strains.

Author

Keuschnig C, Gorfer M, Li G, Mania D, Frostegård Å, Bakken L, and Larose C

Subjects
Anaerobiosis, Fusarium genetics, Genes, Fungal, Fusarium metabolism, Nitrogen Oxides metabolism
Abstract

Fungal denitrification is claimed to produce non-negligible amounts of N 2 O in soils, but few tested species have shown significant activity. We hypothesized that denitrifying fungi would be found among those with assimilatory nitrate reductase, and tested 20 such batch cultures for their respiratory metabolism, including two positive controls, Fusarium oxysporum and Fusarium lichenicola, throughout the transition from oxic to anoxic conditions in media supplemented with NO 2 - . Enzymatic reduction of NO 2 - (NIR) and NO (NOR) was assessed by correcting measured NO- and N 2 O-kinetics for abiotic NO- and N 2 O-production (sterile controls). Significant anaerobic respiration was only confirmed for the positive controls and for two of three Fusarium solani cultures. The NO kinetics in six cultures showed NIR but not NOR activity, observed through the accumulation of NO. Others had NOR but not NIR activity, thus reducing abiotically produced NO to N 2 O. The presence of candidate genes (nirK and p450nor) was confirmed in the positive controls, but not in some of the NO or N 2 O accumulating cultures. Based on our results, we conclude that only the Fusarium cultures were able to sustain anaerobic respiration and produced low amounts of N 2 O as a response to an abiotic NO production from the medium., (© 2020 Society for Applied Microbiology and John Wiley & Sons Ltd.)

Published
2020
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