Publications

Publications in peer reviewed journals

9 Publications found
  • Synergistic effects of diffusion and microbial physiology reproduce the Birch effect in a micro-scale model

    Evans S, Dieckmann U, Franklin O, Kaiser C
    2016 - Soil Biology and Biochemistry, 93: 28-37

    Abstract: 

    Large rainfall events following drought cause pulses of CO2 flux that are higher than models predict. This phenomenon, named the “Birch effect” after its discoverer, has been observed for decades, and will influence carbon-climate feedbacks as drying–rewetting (DRW) cycles become more common under intensified climates. Yet, the many interacting factors that determine how soil DRW cycles affect C balance have been difficult to separate empirically. Here we use a spatially explicit biogeochemical–microbial model to examine the mechanisms underlying CO2 dynamics under DRW. We independently model physiological activity and diffusion based on how they vary with (constant) moisture levels in nature, and subject the model to DRW to test the importance of different mechanisms in models with one or two microbial functional groups (cheaters and producers). Our model reproduces respiration patterns similar to empirical observations of the Birch effect when we include mechanisms that link water content to microbial growth and to diffusion rate, whereas inclusion of either mechanism alone produces significantly lower pulses upon rewetting. Diffusion limitation under drought increases substrate availability under rewetting, a process mediated by biogeochemical hotspots and continued enzyme activity under drought. At the same time, high microbial growth under rewetting is needed to replenish enzyme pools and to sustain the biomass required to generate respiration pulses under repeated DRW. Inclusion of cheaters in the model dampens the size of the rewetting pulse and the cumulative amount of CO2release, as cheaters outcompete producers and reduce overall biomass. Our results provide several novel hypotheses regarding the microbial, biogeochemical, and spatial processes that mediate the Birch effect, which will contribute to a better mechanistic understanding of this important deviation from model predictions.

    Keywords

    • Dry/wet cycles
    • Birch effect
    • Microbial communities
    • Spatial dynamics
    • Individual-based model
    • Carbon cycling
    • Rainfall timing
  • Mycorrhizas across scales: a journey between genomics, global patterns of biodiversity and biogeochemistry

    Chagnon P, Rineau F, Kaiser C
    2016 - New Phytologist, 209: 913-916

    Abstract: 

    Mycorrhizal fungi are found in almost all ecosystems of the planet.
    They interact with a majority of plant species, and it seems that
    every single aspect of the life history of a plant individual is affected
    by the presence of mycorrhizal fungal symbion ts in its roots (van der
    Heijden et al., 2015). Mycorrhizal fungi are also known to affect
    plant population-level and community-level dynamics. Yet, classic
    800-page plant ecology textbooks typically devote only one to two
    pages to mycorrhizal symbioses. Is it time to put mycorrhizal
    ecologists on the editorial boards of these textbooks? Meetings like
    the International Conference on Mycorrhizas (ICOM) tend to
    suggest that this might not be a bad idea.
    On August 37, 2015, mycorrhizal researchers from around the
    world shared their thoughts and empirical results on these globally
    widespread symbioses at a comfortable elevation of 2135 m in
    Flagstaff, Arizona, surrounded by beautiful landscapes, like
    widespread Ponderosa Pine forests, the San Francisco Peaks area,
    and the impressive Grand Canyon. New Phytologist was present
    as a sponsor, continuing its ongoing support of mycorrhizal
    research (Selosse & Martin, 2013; Dickie et al., 2015). Through
    talks and posters, mycorrhizal researchers literally took us on a
    journey across all scales of observation of this symbiosis: from the
    intracellular environment to global patterns of mycorrhizal
    fungal diversity and biogeochemical cycles (Fig. 1).

    Mycorrhizal fungi are found in almost all ecosystems of the planet.

    They interact with a majority of plant species, and it seems that
    every single aspect of the life history of a plant individual is affected
    by the presence of mycorrhizal fungal symbion ts in its roots (van der
    Heijden et al., 2015). Mycorrhizal fungi are also known to affect
    plant population-level and community-level dynamics. Yet, classic
    800-page plant ecology textbooks typically devote only one to two
    pages to mycorrhizal symbioses. Is it time to put mycorrhizal
    ecologists on the editorial boards of these textbooks? Meetings like
    the International Conference on Mycorrhizas (ICOM) tend to
    suggest that this might not be a bad idea.
    On August 37, 2015, mycorrhizal researchers from around the
    world shared their thoughts and empirical results on these globally
    widespread symbioses at a comfortable elevation of 2135 m in
    Flagstaff, Arizona, surrounded by beautiful landscapes, like
    widespread Ponderosa Pine forests, the San Francisco Peaks area,
    and the impressive Grand Canyon. New Phytologist was present
    as a sponsor, continuing its ongoing support of mycorrhizal
    research (Selosse & Martin, 2013; Dickie et al., 2015). Through
    talks and posters, mycorrhizal researchers literally took us on a
    journey across all scales of observation of this symbiosis: from the
    intracellular environment to global patterns of mycorrhizal
    fungal diversity and biogeochemical cycles (Fig. 1).
  • Social dynamics within decomposer communities lead to nitrogen retention and organic matter build-up in soils

    Kaiser C, Franklin O, Richter A, Dieckmann U
    2015 - Nature Communication, 6: 8960

    Abstract: 

    The chemical structure of organic matter has been shown to be only marginally important for its decomposability by microorganisms. The question of why organic matter does accumulate in the face of powerful microbial degraders is thus key for understanding terrestrial carbon and nitrogen cycling. Here we demonstrate, based on an individual-based microbial community model, that social dynamics among microbes producing extracellular enzymes (‘decomposers’) and microbes exploiting the catalytic activities of others (‘cheaters’) regulate organic matter turnover. We show that the presence of cheaters increases nitrogen retention and organic matter build-up by downregulating the ratio of extracellular enzymes to total microbial biomass, allowing nitrogen-rich microbial necromass to accumulate. Moreover, increasing catalytic efficiencies of enzymes are outbalanced by a strong negative feedback on enzyme producers, leading to less enzymes being produced at the community level. Our results thus reveal a possible control mechanism that may buffer soil CO2 emissions in a future climate.

  • Exploring the transfer of recent plant photosynthates to soil microbes: mycorrhizal pathway vs direct root exudation

    Kaiser C, Kilburn MR, Clode PL, Fuchslueger L, Koranda M, Cliff JB, Solaiman ZM, Murphy DV
    2015 - New Phytologist, 205: 1537-1551

    Abstract: 

    Plants rapidly release photoassimilated carbon (C) to the soil via direct root exudation and associated mycorrhizal fungi, with both pathways promoting plant nutrient availability. This study aimed to explore these pathways from the root's vascular bundle to soil microbial communities. Using nanoscale secondary ion mass spectrometry (NanoSIMS) imaging and (13) C-phospho- and neutral lipid fatty acids, we traced in-situ flows of recently photoassimilated C of (13) CO2 -exposed wheat (Triticum aestivum) through arbuscular mycorrhiza (AM) into root- and hyphae-associated soil microbial communities. Intraradical hyphae of AM fungi were significantly (13) C-enriched compared to other root-cortex areas after 8 h of labelling. Immature fine root areas close to the root tip, where AM features were absent, showed signs of passive C loss and co-location of photoassimilates with nitrogen taken up from the soil solution. A significant and exclusively fresh proportion of (13) C-photosynthates was delivered through the AM pathway and was utilised by different microbial groups compared to C directly released by roots. Our results indicate that a major release of recent photosynthates into soil leave plant roots via AM intraradical hyphae already upstream of passive root exudations. AM fungi may act as a rapid hub for translocating fresh plant C to soil microbes. © 2014 The Authors New Phytologist © 2014 New Phytologist Trust.

  • Site- and horizon-specific patterns of microbial community structure and enzyme activities in permafrost-affected soils of Greenland

    Gittel A, Barta J, Kohoutová I, Schnecker J, Wild B, Capek P, Kaiser C, Torsvik VL, Richter A, Schleper C, Urich T
    2014 - Frontiers in microbiology, 14

    Abstract: 

    Permafrost-affected soils in the Northern latitudes store huge amounts of organic carbon (OC) that is prone to microbial degradation and subsequent release of greenhouse gasses to the atmosphere. In Greenland, the consequences of permafrost thaw have only recently been addressed, and predictions on its impact on the carbon budget are thus still highly uncertain. However, the fate of OC is not only determined by abiotic factors, but closely tied to microbial activity. We investigated eight soil profiles in northeast Greenland comprising two sites with typical tundra vegetation and one wet fen site. We assessed microbial community structure and diversity (SSU rRNA gene tag sequencing, quantification of bacteria, archaea and fungi), and measured hydrolytic and oxidative enzyme activities. Sampling site and thus abiotic factors had a significant impact on microbial community structure, diversity and activity, the wet fen site exhibiting higher potential enzyme activities and presumably being a hot spot for anaerobic degradation processes such as fermentation and methanogenesis. Lowest fungal to bacterial ratios were found in topsoils that had been relocated by cryoturbation ("buried topsoils"), resulting from a decrease in fungal abundance compared to recent ("unburied") topsoils. Actinobacteria (in particular Intrasporangiaceae) accounted for a major fraction of the microbial community in buried topsoils, but were only of minor abundance in all other soil horizons. It was indicated that the distribution pattern of Actinobacteria and a variety of other bacterial classes was related to the activity of phenol oxidases and peroxidases supporting the hypothesis that bacteria might resume the role of fungi in oxidative enzyme production and degradation of phenolic and other complex substrates in these soils. Our study sheds light on the highly diverse, but poorly-studied communities in permafrost-affected soils in Greenland and their role in OC degradation.

  • Microbial community dynamics alleviate stoichiometric constraints during litter decay

    Kaiser C, Franklin O, Dieckmann U, Richter A
    2014 - Ecology Letters, 17: 680-690

    Abstract: 

    Under the current paradigm, organic matter decomposition and nutrient cycling rates are a function of the imbalance between substrate and microbial biomass stoichiometry. Challenging this view, we demonstrate that in an individual-based model, microbial community dynamics alter relative C and N limitation during litter decomposition, leading to a system behaviour not predictable from stoichiometric theory alone. Rather, the dynamics of interacting functional groups lead to an adaptation at the community level, which accelerates nitrogen recycling in litter with high initial C : N ratios and thus alleviates microbial N limitation. This mechanism allows microbial decomposers to overcome large imbalances between resource and biomass stoichiometry without the need to decrease carbon use efficiency (CUE), which is in contrast to predictions of traditional stoichiometric mass balance equations. We conclude that identifying and implementing microbial community-driven mechanisms in biogeochemical models are necessary for accurately predicting terrestrial C fluxes in response to changing environmental conditions. © 2014 The Authors. Ecology Letters published by John Wiley & Sons Ltd and CNRS.

  • Fungal and bacterial utilization of organic substrates depends on substrate complexity and N availability

    Koranda M, Kaiser C, Fuchslueger L, Kitzler B, Sessitsch A, Zechmeister-Boltenstern S, Richter A
    2014 - FEMS Microbiology Ecology, 87: 142-152

    Abstract: 

    There is growing evidence of a direct relationship between microbial community composition and function, which implies that distinct microbial communities vary in their functional properties. The aim of this study was to determine whether differences in initial substrate utilization between distinct microbial communities are due to the activities of certain microbial groups. We performed a short-term experiment with beech forest soils characterized by three different microbial communities (winter and summer community, and a community from a tree-girdling plot). We incubated these soils with different (13) C-labelled substrates with or without inorganic N addition and analyzed microbial substrate utilization by (13) C-phospholipid fatty acid (PLFA) analysis. Our results revealed that the fate of labile C (glucose) was similar in the three microbial communities, despite differences in absolute substrate incorporation between the summer and winter community. The active microbial community involved in degradation of complex C substrates (cellulose, plant cell walls), however, differed between girdling and control plots and was strongly affected by inorganic N addition. Enhanced N availability strongly increased fungal degradation of cellulose and plant cell walls. Our results indicate that fungi, at least in the presence of a high N supply, are the main decomposers of polymeric C substrates. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  • Nitrogen dynamics in Turbic Cryosols from Siberia and Greenland.

    Wild B, Schnecker J, Barta J, Capek P, Guggenberger G, Hofhansl F, Kaiser C, Lashchinsky N, Mikutta R, Mooshammer M, Santruckova H, Shibistova O, Urich T, Zimov SA, Richter A
    2013 - Soil Biology and Biochemistry, 67: 85-93

    Abstract: 

    Turbic Cryosols (permafrost soils characterized by cryoturbation, i.e., by mixing of soil layers due to freezing and thawing) are widespread across the Arctic, and contain large amounts of poorly decomposed organic material buried in the subsoil. This cryoturbated organic matter exhibits retarded decomposition compared to organic material in the topsoil. Since soil organic matter (SOM) decomposition is known to be tightly linked to N availability, we investigated N transformation rates in different soil horizons of three tundra sites in north-eastern Siberia and Greenland. We measured gross rates of protein depolymerization, N mineralization (ammonification) and nitrification, as well as microbial uptake of amino acids and NH4 + using an array of 15N pool dilution approaches. We found that all sites and horizons were characterized by low N availability, as indicated by low N mineralization compared to protein depolymerization rates (with gross N mineralization accounting on average for 14% of gross protein depolymerization). The proportion of organic N mineralized was significantly higher at the Greenland than at the Siberian sites, suggesting differences in N limitation. The proportion of organic N mineralized, however, did not differ significantly between soil horizons, pointing to a similar N demand of the microbial community of each horizon. In contrast, absolute N transformation rates were significantly lower in cryoturbated than in organic horizons, with cryoturbated horizons reaching not more than 32% of the transformation rates in organic horizons. Our results thus indicate a deceleration of the entire N cycle in cryoturbated soil horizons, especially strongly reduced rates of protein depolymerization (16% of organic horizons) which is considered the rate-limiting step in soil N cycling.

  • Seasonal variation in functional properties of microbial communities in beech forest soil

    Koranda M, Kaiser C, Fuchslueger L, Kitzler B, Sessitsch A, Zechmeister-Boltenstern S, Richter A
    2013 - Soil Biology and Biochemistry, 60: 95-104

    Abstract: 

    Substrate quality and the availability of nutrients are major factors controlling microbial decomposition processes in soils. Seasonal alteration in resource availability, which is driven by plants via belowground C allocation, nutrient uptake and litter fall, also exerts effects on soil microbial community composition. Here we investigate if seasonal and experimentally induced changes in microbial community composition lead to alterations in functional properties of microbial communities and thus microbial processes. Beech forest soils characterized by three distinct microbial communities (winter and summer community, and summer community from a tree girdling plot, in which belowground carbon allocation was interrupted) were incubated with different 13C-labeled substrates with or without inorganic N supply and analyzed for substrate use and various microbial processes. Our results clearly demonstrate that the three investigated microbial communities differed in their functional response to addition of various substrates. The winter communities revealed a higher capacity for degradation of complex C substrates (cellulose, plant cell walls) than the summer communities, indicated by enhanced cellulase activities and reduced mineralization of soil organic matter. In contrast, utilization of labile C sources (glucose) was lower in winter than in summer, demonstrating that summer and winter community were adapted to the availability of different substrates. The saprotrophic community established in girdled plots exhibited a significantly higher utilization of complex C substrates than the more plant root associated community in control plots if additional nitrogen was provided. In this study we were able to demonstrate experimentally that variation in resource availability as well as seasonality in temperate forest soils cause a seasonal variation in functional properties of soil microorganisms, which is due to shifts in community structure and physiological adaptations of microbial communities to altered resource supply.

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