Publications in peer reviewed journals

23 Publications found
  • Quantifying microbial growth and carbon use efficiency in dry soil environments via 18O water vapor equilibration

    Canarini A, Wanek W, Watzka M, Sandén T, Spiegel H, Šantrůček J, Schnecker J
    2020 - Global Change Biology, 9: 5333-5341


    Soil microbial physiology controls large fluxes of C to the atmosphere, thus, improving our ability to accurately quantify microbial physiology in soil is essential. However, current methods to determine microbial C metabolism require liquid water addition, which makes it practically impossible to measure microbial physiology in dry soil samples without stimulating microbial growth and respiration (namely, the “Birch effect”). We developed a new method based on in vivo 18O‐water vapor equilibration to minimize soil rewetting effects. This method allows the isotopic labeling of soil water without direct liquid water addition. This was compared to the main current method (direct 18O‐liquid water addition) in moist and air‐dry soils. We determined the time kinetics and calculated the average 18O enrichment of soil water over incubation time, which is necessary to calculate microbial growth from 18O incorporation in genomic DNA. We tested isotopic equilibration patterns in three natural and six artificially constructed soils covering a wide range of soil texture and soil organic matter content. We then measured microbial growth, respiration and carbon use efficiency (CUE) in three natural soils (either air‐dry or moist). The proposed 18O‐vapor equilibration method provided similar results as the current method of liquid 18O‐water addition when used for moist soils. However, when applied to air‐dry soils the liquid 18O‐water addition method overestimated growth by up to 250%, respiration by up to 500%, and underestimated CUE by up to 40%. We finally describe the new insights into biogeochemical cycling of C that the new method can help uncover, and we consider a range of questions regarding microbial physiology and its response to global change that can now be addressed.

  • Successional habitat filtering of rainforest trees is explained by potential growth more than by functional traits

    Kleinschmidt S,  Wanek W, Kreinecker F,  Hackl D, Jenking D,  Weissenhofer A, Hietz P
    2020 - Functional Ecology, 34: 1438-1447



    • Species along successional gradients differ in functional traits, which may function as environmental filters and also explain differences in growth rates. Alternatively, species might be filtered by growth rates and these are explained by differences in other traits. We explored the relationships between leaf and wood traits, growth and successional habitat, and asked if growth is related to habitat because both are driven by a similar set of traits or if growth is the main trait explaining habitat and relationships with other traits are indirect.
    • Tropical trees are often classified as second‐growth (SG) or old‐growth (OG) specialists, and generalists. Since succession is a continuous process and lumping species into three groups may not do justice to gradual differences, we tested if a continuous variable based on relative tree abundance in OG and SG forests might be a better predictor than classifying trees' habitat preferences into categories.
    • We measured the height growth of 47 trees species planted in a reforestation trial in Costa Rica and evaluated size‐standardized potential growth during the first years when there was little shading among trees. Growth and habitat were related to wood density (WD), theoretical hydraulic conductivity (Kh), specific leaf area (SLA), leaf dry matter content (LDMC) and leaf nitrogen content (N).
    • Potential growth rates and Kh were significantly correlated with habitat measured on a continuous scale, while growth and LDMC differed among the three groups of habitat specialization. Growth was also correlated with WD and Kh.
    • Habitat specialization was correlated with the first principal component of the functional traits space. However, structural equation models suggest that the relationship with leaf and wood traits is mostly indirect and potential growth is the most important trait directly related to environmental filtering along a successional gradient. In our dataset, classifiying the successional status of species using the proportion of records from OG forests explains traits about as well as a classification into three groups, but provides more information about the species' position along the successional gradient.
    • Species along successional gradients differ in functional traits, which may function as environmental filters and also explain differences in growth rates. Alternatively, species might be filtered by growth rates and these are explained by differences in other traits. We explored the relationships between leaf and wood traits, growth and successional habitat, and asked if growth is related to habitat because both are driven by a similar set of traits or if growth is the main trait explaining habitat and relationships with other traits are indirect.
    • Tropical trees are often classified as second‐growth (SG) or old‐growth (OG) specialists, and generalists. Since succession is a continuous process and lumping species into three groups may not do justice to gradual differences, we tested if a continuous variable based on relative tree abundance in OG and SG forests might be a better predictor than classifying trees' habitat preferences into categories.
    • We measured the height growth of 47 trees species planted in a reforestation trial in Costa Rica and evaluated size‐standardized potential growth during the first years when there was little shading among trees. Growth and habitat were related to wood density (WD), theoretical hydraulic conductivity (Kh), specific leaf area (SLA), leaf dry matter content (LDMC) and leaf nitrogen content (N).
    • Potential growth rates and Kh were significantly correlated with habitat measured on a continuous scale, while growth and LDMC differed among the three groups of habitat specialization. Growth was also correlated with WD and Kh.
    • Habitat specialization was correlated with the first principal component of the functional traits space. However, structural equation models suggest that the relationship with leaf and wood traits is mostly indirect and potential growth is the most important trait directly related to environmental filtering along a successional gradient. In our dataset, classifiying the successional status of species using the proportion of records from OG forests explains traits about as well as a classification into three groups, but provides more information about the species' position along the successional gradient.
  • Increased microbial growth, biomass, and turnover drive soil organic carbon accumulation at higher plant diversity

    Prommer J, Walker TWN, Wanek W, Braun J, Zezula D, Hu Y, Hofhansl F, Richter A
    2020 - Global Change Biology, 2: 669-681


    Species‐rich plant communities have been shown to be more productive and to exhibit increased long‐term soil organic carbon (SOC) storage. Soil microorganisms are central to the conversion of plant organic matter into SOC, yet the relationship between plant diversity, soil microbial growth, turnover as well as carbon use efficiency (CUE) and SOC accumulation is unknown. As heterotrophic soil microbes are primarily carbon limited, it is important to understand how they respond to increased plant‐derived carbon inputs at higher plant species richness (PSR). We used the long‐term grassland biodiversity experiment in Jena, Germany, to examine how microbial physiology responds to changes in plant diversity and how this affects SOC content. The Jena Experiment considers different numbers of species (1–60), functional groups (1–4) as well as functional identity (small herbs, tall herbs, grasses, and legumes). We found that PSR accelerated microbial growth and turnover and increased microbial biomass and necromass. PSR also accelerated microbial respiration, but this effect was less strong than for microbial growth. In contrast, PSR did not affect microbial CUE or biomass‐specific respiration. Structural equation models revealed that PSR had direct positive effects on root biomass, and thereby on microbial growth and microbial biomass carbon. Finally, PSR increased SOC content via its positive influence on microbial biomass carbon. We suggest that PSR favors faster rates of microbial growth and turnover, likely due to greater plant productivity, resulting in higher amounts of microbial biomass and necromass that translate into the observed increase in SOC. We thus identify the microbial mechanism linking species‐rich plant communities to a carbon cycle process of importance to Earth's climate system.

  • Lability classification of soil organic matter in the northern permafrost region

    Kuhry P, Barta J, Blok D, Elberling B, Faucherre S, Hugelius G, Jørgensen C J, Richter A, Santruckova H, Weiss N
    2020 - Biogeosciences, 17: 361-379


    The large stocks of soil organic carbon (SOC) in soils and deposits of the northern permafrost region are sensitive to global warming and permafrost thawing. The potential release of this carbon (C) as greenhouse gases to the atmosphere does not only depend on the total quantity of soil organic matter (SOM) affected by warming and thawing, but it also depends on its lability (i.e., the rate at which it will decay). In this study we develop a simple and robust classification scheme of SOM lability for the main types of soils and deposits in the northern permafrost region. The classification is based on widely available soil geochemical parameters and landscape unit classes, which makes it useful for upscaling to the entire northern permafrost region. We have analyzed the relationship between C content and C-CO2 production rates of soil samples in two different types of laboratory incubation experiments. In one experiment, ca. 240 soil samples from four study areas were incubated using the same protocol (at 5 C, aerobically) over a period of 1 year. Here we present C release rates measured on day 343 of incubation. These long-term results are compared to those obtained from short-term incubations of ca. 1000 samples (at 12 C, aerobically) from an additional three study areas. In these experiments, C-CO2 production rates were measured over the first 4 d of incubation. We have focused our analyses on the relationship between C-CO2 production per gram dry weight per day (µgC-CO2 gdw−1 d−1) and C content (%C of dry weight) in the samples, but we show that relationships are consistent when using C ∕ N ratios or different production units such as µgC per gram soil C per day (µgC-CO2 gC−1 d−1) or per cm3 of soil per day (µgC-CO2 cm−3 d−1). C content of the samples is positively correlated to C-CO2 production rates but explains less than 50 % of the observed variability when the full datasets are considered. A partitioning of the data into landscape units greatly reduces variance and provides consistent results between incubation experiments. These results indicate that relative SOM lability decreases in the order of Late Holocene eolian deposits to alluvial deposits and mineral soils (including peaty wetlands) to Pleistocene yedoma deposits to C-enriched pockets in cryoturbated soils to peat deposits. Thus, three of the most important SOC storage classes in the northern permafrost region (yedoma, cryoturbated soils and peatlands) show low relative SOM lability. Previous research has suggested that SOM in these pools is relatively undecomposed, and the reasons for the observed low rates of decomposition in our experiments need urgent attention if we want to better constrain the magnitude of the thawing permafrost carbon feedback on global warming.

  • Persistence of soil organic carbon caused by functional complexity

    Lehmann J, Hansel CM, Kaiser C, Kleber M, Maher K, Manzoni S, Nunan N, Reichstein M, Schimel J, Torn MS, Wieder WR, Kögl-Knabner I
    2020 - Nature Geoscience, 13: 529-534


    Soil organic carbon management has the potential to aid climate change mitigation through drawdown of atmospheric carbon dioxide. To be effective, such management must account for processes influencing carbon storage and re-emission at different space and time scales. Achieving this requires a conceptual advance in our understanding to link carbon dynamics from the scales at which processes occur to the scales at which decisions are made. Here, we propose that soil carbon persistence can be understood through the lens of decomposers as a result of functional complexity derived from the interplay between spatial and temporal variation of molecular diversity and composition. For example, co-location alone can determine whether a molecule is decomposed, with rapid changes in moisture leading to transport of organic matter and constraining the fitness of the microbial community, while greater molecular diversity may increase the metabolic demand of, and thus potentially limit, decomposition. This conceptual shift accounts for emergent behaviour of the microbial community and would enable soil carbon changes to be predicted without invoking recalcitrant carbon forms that have not been observed experimentally. Functional complexity as a driver of soil carbon persistence suggests soil management should be based on constant care rather than one-time action to lock away carbon in soils.

  • C:N:P stoichiometry regulates soil organic carbon mineralization and concomitant shifts in microbial community composition in paddy soil

    Wei X, Zhu Z, Liu Y, Luo Y, Deng Y, Xu X, Liu S, Richter A, Shibistova O, Guggenberger G, Wu J, Ge T
    2020 - Biology and Fertility of Soils, 56: 1093-1107


    Stoichiometric control of input substrate (glucose) and native soil organic C (SOC) mineralization was assessed by performing a manipulation experiment based on N or P fertilization in paddy soil. Glucose mineralization increased with nutrient addition up to 11.6% with combined N and P application compared with that without nutrient addition. During 100 days of incubation, approximately 4.5% of SOC was mineralized and was stimulated by glucose addition. Glucose and SOC mineralization increased exponentially with dissolved organic C (DOC):NH4+-N, DOC:Olsen P, and microbial biomass (MB)C:MBN ratios. The relative abundances of Clostridia and β-Proteobacteria (r-strategists) were increased with combined C and NP application at the beginning of the experiment, while the relative abundances of Acidobacteria (K-strategists) were enhanced with the exhaustion of available resource at the end of incubation. The bacteria abundance and diversity were negatively related to the DOC:NH4+-N and DOC:Olsen P, which had direct positive effects (+ 0.63) on SOC mineralization. Combined glucose and NP application decreased the network density of the bacterial community. Moreover, P addition significantly decreased the negative associations among bacterial taxa, which suggested that microbial competition for nutrients was alleviated. The relative abundances of keystone species showed significant positive correlations with SOC mineralization in the soils without P application, revealing that microbes increased their activity for mining of limited nutrients from soil organic matter. Hence, bacteria shifted their community composition and their interactions to acquire necessary elements by increasing SOC mineralization to maintain the microbial biomass C:N:P stoichiometric balance in response to changes in resource stoichiometry.

  • Denitrification Is the Main Nitrous Oxide Source Process in Grassland Soils According to Quasi-Continuous Isotopocule Analysis and Biogeochemical Modeling

    Ibraim E, Denk T, Wolf B, Barthel M, Gasche R,  Wanek W,  Zhang S, Kiese R, Butterbach-Bahl K, Eggleston S, Emmenegger L, Six J, Mohn J
    2020 - Global Biogeochemical Cycles, 34: 1-19


    Isotopic composition of soil‐emitted nitrous oxide (N2O), especially the intramolecular distribution of 15N in N2O known as site preference (SP), can be used to track the two major N2O emitting soil‐processes nitrification and denitrification. Online analysis of SP in ambient air has been achieved recently, yet those approaches only allowed addressing large areas (footprints) on the basis of strong changes in surface atmospheric N2O concentrations. Here, we combined laser spectroscopy with automated static flux chambers to measure, for the first time, SP of low N2O fluxes with high sensitivity and temporal resolution and to explore its spatial variability. The measurements were then used to test the N2O isotope module SIMONE in combination with the biogeochemical model LandscapeDNDC to identify N2O source processes. End‐member mixing analysis of the data revealed denitrification as the predominant N2O source. This finding was independent of the soil water content close to the soil surface, suggesting that N2O production in the subsoil under high water‐filled pore space conditions outweighed the potential production of N2O by nitrification closer to the surface. Applying the SIMONE‐LandscapeDNDC model framework to our field site showed that the modeled SP was on average 4.2‰ lower than the observed values. This indicates that the model parameterization reflects the dominant N2O production pathways but overestimates the contribution of denitrification by 6%. Applying the stable isotope‐based model framework at other sites and comparing with other models will help identifying model shortcomings and improve our capability to support N2O mitigation from agricultural ecosystems.

  • Microbial carbon limitation: The need for integrating microorganisms into our understanding of ecosystem carbon cycling

    Soong JL, Fuchslueger L, Marañon‐Jimenez S, Torn MS, Janssens IA, Peñuelas J, Richter A
    2020 - Global Change Biology, 4: 1953-1961


    Numerous studies have demonstrated that fertilization with nutrients such as nitrogen, phosphorus, and potassium increases plant productivity in both natural and managed ecosystems, demonstrating that primary productivity is nutrient limited in most terrestrial ecosystems. In contrast, it has been demonstrated that heterotrophic microbial communities in soil are primarily limited by organic carbon or energy. While this concept of contrasting limitations, that is, microbial carbon and plant nutrient limitation, is based on strong evidence that we review in this paper, it is often ignored in discussions of ecosystem response to global environment changes. The plant‐centric perspective has equated plant nutrient limitations with those of whole ecosystems, thereby ignoring the important role of the heterotrophs responsible for soil decomposition in driving ecosystem carbon storage. To truly integrate carbon and nutrient cycles in ecosystem science, we must account for the fact that while plant productivity may be nutrient limited, the secondary productivity by heterotrophic communities is inherently carbon limited. Ecosystem carbon cycling integrates the independent physiological responses of its individual components, as well as tightly coupled exchanges between autotrophs and heterotrophs. To the extent that the interacting autotrophic and heterotrophic processes are controlled by organisms that are limited by nutrient versus carbon accessibility, respectively, we propose that ecosystems by definition cannot be ‘limited’ by nutrients or carbon alone. Here, we outline how models aimed at predicting non‐steady state ecosystem responses over time can benefit from dissecting ecosystems into the organismal components and their inherent limitations to better represent plant–microbe interactions in coupled carbon and nutrient models.

  • Direct measurement of the in situ decomposition of microbial-derived soil organic matter

    Hu Y, Zheng Q, Noll L, zhang S, Wanek W
    2020 - Soil Biology and Biochemistry, 141: Article 107660


    Soil organic matter (SOM) is the dominant reservoir of terrestrial organic carbon and nitrogen, and microbial necromass represents a primary input to it. However, knowledge of stabilization mechanisms and direct measurements of the decomposition of microbial-derived SOM are lacking. Here we report a novel 15N isotope pool dilution approach using labeled amino sugars and muropeptides as tracers to quantify the decomposition of proteins and microbial cell walls, which allows to estimate in situ decomposition rates of microbial-derived SOM. Our results demonstrate that microbial cell walls are as recalcitrant as soil protein, exhibiting comparable turnover times across various ecosystems. The bacterial peptidoglycan in soils was primarily decomposed to muropeptides which can be directly utilized by microbes without being further depolymerized to free amino compounds. Moreover, bacterial peptidoglycan decomposition was correlated with soil microbial biomass while fungal chitin and soil protein decomposition were correlated with high soil pH and fine soil texture. This approach thereby provides new insights into the decomposition pathways and stabilization mechanisms of microbial-derived SOM constituents pertaining to SOM persistence.

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

    Portell X, Sauzet O, Balseiro‐Romero M, Benard P, Cardinael R, Couradeau E, Danra DD, Evans DL, Fry EL, Hammer EC, Mamba D, Merino‐Martín L, Mueller CW, Paradelo M, Rees F, Rossi LMW, Schmidt H, Schnee LS, Védère C, Vidal A
    2020 - European Journal of Soil Science, in press
  • Regulation of nitrogen fixation from free-living organisms in soil and leaf litter of two tropical forests of the Guiana shield

    Van Langenhove L, Depaepe T, Vicca S, Van den Berge J, Stahl C, Courtois E, Weedon J, Urbina I, Grau O, Asensio D, Peñuelas J, Boeckx P, Richter A, Van Der Straeten D, Janssens IA
    2020 - Plant and soil, 450: 93-110


    Background and aims

    Biological fixation of atmospheric nitrogen (N2) is the main pathway for introducing N into unmanaged ecosystems. While recent estimates suggest that free-living N fixation (FLNF) accounts for the majority of N fixed in mature tropical forests, the controls governing this process are not completely understood. The aim of this study was to quantify FLNF rates and determine its drivers in two tropical pristine forests of French Guiana.


    We used the acetylene reduction assay to measure FLNF rates at two sites, in two seasons and along three topographical positions, and used regression analyses to identify which edaphic explanatory variables, including carbon (C), nitrogen (N), phosphorus (P) and molybdenum (Mo) content, pH, water and available N and P, explained most of the variation in FLNF rates.


    Overall, FLNF rates were lower than measured in tropical systems elsewhere. In soils seasonal variability was small and FLNF rates differed among topographies at only one site. Water, P and pH explained 24% of the variation. In leaf litter, FLNF rates differed seasonally, without site or topographical differences. Water, C, N and P explained 46% of the observed variation. We found no regulatory role of Mo at our sites.


    Rates of FLNF were low in primary rainforest on poor soils on the Guiana shield. Water was the most important rate-regulating factor and FLNF increased with increasing P, but decreased with increasing N. Our results support the general assumption that N fixation in tropical lowland forests is limited by P availability.

  • Numerical modelling of the effect of intermittent upwelling events on plankton blooms

    Guseva K,  Feudel U
    2020 - Journal of the Royal Society, 17: Article 20190889


    In the marine environment, biological processes are strongly affected by oceanic currents, particularly by eddies (vortices) formed by the hydrodynamic flow field. Employing a kinematic flow field coupled to a population dynamical model for plankton growth, we study the impact of an intermittent upwelling of nutrients on triggering harmful algal blooms (HABs). Though it is widely believed that additional nutrients boost the formation of HABs or algal blooms in general, we show that the response of the plankton to nutrient plumes depends crucially on the mesoscale hydrodynamic flow structure. In general, nutrients can either be quickly washed out from the observation area, or can be captured by the vortices in the flow. The occurrence of either scenario depends on the relation between the time scales of the vortex formation and nutrient upwelling as well as the time instants at which upwelling pulses occur and how long they last. We show that these two scenarios result in very different responses in plankton dynamics which makes it very difficult to predict whether nutrient upwelling will lead to a HAB or not. This may in part explain why observational data are sometimes inconclusive in establishing a connection between upwelling events and plankton blooms.

  • Salinity-dependent algae uptake and subsequent carbon and nitrogen metabolisms of two intertidal foraminifera (Ammonia tepida and Haynesina germanica)

    Lintner M,  Biedrawa B,  Wukovits J,  Wanek W, Heinz P
    2020 - Biogeosciences, 17: 3723-3732


    Benthic foraminifera are abundant marine protists which play an important role in the transfer of energy in the form of organic matter and nutrients to higher trophic levels. Due to their aquatic lifestyle, factors such as water temperature, salinity and pH are key drivers controlling biomass turnover through foraminifera. In this study the influence of salinity on the feeding activity of foraminifera was tested. Two species, Ammonia tepida and Haynesina germanica, were collected from a mudflat in northern Germany (Friedrichskoog) and cultured in the laboratory at 20 C and a light–dark cycle of 16:08 h. A lyophilized algal powder from Dunaliella tertiolecta, which was isotopically enriched with 13C and 15N, was used as a food source. The feeding experiments were carried out at salinity levels of 11, 24 and 37 practical salinity units (PSU) and were terminated after 1, 5 and 14 d. The quantification of isotope incorporation was carried out by isotope ratio mass spectrometry. Ammonia tepida exhibited a 10-fold higher food uptake compared to H. germanica. Furthermore, in A. tepida the food uptake increased with increasing salinity but not in H. germanica. Over time (from 1–5 to 14 d) food C retention increased relative to food N in A. tepida while the opposite was observed for H. germanica. This shows that if the salinity in the German Wadden Sea increases, A. tepida is predicted to exhibit a higher C and N uptake and turnover than H. germanica, with accompanying changes in C and N cycling through the foraminiferal community. The results of this study show how complex and differently food C and N processing of foraminiferal species respond to time and to environmental conditions such as salinity.

  • A systemic overreaction to years versus decades of warming in a subarctic grassland ecosystem

    Walker TWN, Janssens IA, Weedon JT, Sigurdsson BD, Richter A, Peñuelas J, Leblans NI Bahn M, Bartrons M, De Jonge C, Fuchslueger L, Gargallo-Garriga A, Gunnarsdóttir GE, Marañon-Jimenez S, Oddsdóttir ES, Ostonen I, Poeplau C, Prommer J, Radujković D, Sardans J, Sigurðsson P, Soong JL, Vicca S, Wallander H, Ilieva-Makulec K, Verbruggen E
    2020 - Nature Ecology & Evolution, 4: 101-108


    Temperature governs most biotic processes, yet we know little about how warming affects whole ecosystems. Here we examined the responses of 128 components of a subarctic grassland to either 5–8 or >50 years of soil warming. Warming of >50 years drove the ecosystem to a new steady state possessing a distinct biotic composition and reduced species richness, biomass and soil organic matter. However, the warmed state was preceded by an overreaction to warming, which was related to organism physiology and was evident after 5–8 years. Ignoring this overreaction yielded errors of >100% for 83 variables when predicting their responses to a realistic warming scenario of 1 °C over 50 years, although some, including soil carbon content, remained stable after 5–8 years. This study challenges long-term ecosystem predictions made from short-term observations, and provides a framework for characterization of ecosystem responses to sustained climate change.

  • Assessing microbial residues in soil as a potential carbon sink and moderator of carbon use efficiency

    Geyer K, Schnecker J, Grand AS, Richter A, Frey S
    2020 - Biogeochemistry, 151: 237-249


    A longstanding assumption of glucose tracing experiments is that all glucose is microbially utilized during short incubations of ≤2 days to become microbial biomass or carbon dioxide. Carbon use efficiency (CUE) estimates have consequently ignored the formation of residues (non-living microbial products) although such materials could represent an important sink of glucose that is prone to stabilization as soil organic matter. We examined the dynamics of microbial residue formation from a short tracer experiment with frequent samplings over 72 h, and conducted a meta-analysis of previously published glucose tracing studies to assess the generality of these experimental results. Both our experiment and meta-analysis indicated 30–34% of amended glucose-C (13C or 14C) was in the form of residues within the first 6 h of substrate addition. We expand the conventional efficiency calculation to include residues in both the numerator and denominator of efficiency, thereby deriving a novel metric of the potential persistence of glucose-C in soil as living microbial biomass plus residues (‘carbon stabilization efficiency’). This new metric indicates nearly 40% of amended glucose-C persists in soil 180 days after amendment, the majority as non-biomass residues. Starting microbial biomass and clay content emerge as critical factors that positively promote such long term stabilization of labile C. Rapid residue production supports the conclusion that non-growth maintenance activity can illicit high demands for C in soil, perhaps equaling that directed towards growth, and that residues may have an underestimated role in the cycling and sequestration potential of C in soil.

  • Climatic and edaphic controls over tropical forest diversity and vegetation carbon storage

    Hofhansl F, Chacón-Madrigal E, Fuchslueger L, Jenking D, Morera-Beita A, Plutzar C, Silla F, Andersen KM, Buchs DM, Dullinger S, Fiedler K, Franklin O, Hietz P, Huber W, Quesada CA, Rammig A, Schrodt F, Vincent AG, Weissenhofer A, Wanek W
    2020 - Scientific Reports, 10: Article 5066


    Tropical rainforests harbor exceptionally high biodiversity and store large amounts of carbon in vegetation biomass. However, regional variation in plant species richness and vegetation carbon stock can be substantial, and may be related to the heterogeneity of topoedaphic properties. Therefore, aboveground vegetation carbon storage typically differs between geographic forest regions in association with the locally dominant plant functional group. A better understanding of the underlying factors controlling tropical forest diversity and vegetation carbon storage could be critical for predicting tropical carbon sink strength in response to projected climate change. Based on regionally replicated 1-ha forest inventory plots established in a region of high geomorphological heterogeneity we investigated how climatic and edaphic factors affect tropical forest diversity and vegetation carbon storage. Plant species richness (of all living stems >10 cm in diameter) ranged from 69 to 127 ha−1 and vegetation carbon storage ranged from 114 to 200 t ha−1. While plant species richness was controlled by climate and soil water availability, vegetation carbon storage was strongly related to wood density and soil phosphorus availability. Results suggest that local heterogeneity in resource availability and plant functional composition should be considered to improve projections of tropical forest ecosystem functioning under future scenarios.

  • Carbon loss from northern circumpolar permafrost soils amplified by rhizosphere priming

    Keuper F, Wild B, Kummu M, Beer C, Blume-Werry G, Fontaine S, Gavazov K, Gentsch N, Guggenberger G, Hugelius G, Jalava M, Koven C, Krab EJ, Kuhry P, Monteux S, Richter A, Shahzad T, Weedon J, Dorrepaal E
    2020 - Nature Geoscience, 13: 560-565


    As global temperatures continue to rise, a key uncertainty of climate projections is the microbial decomposition of vast organic carbon stocks in thawing permafrost soils. Decomposition rates can accelerate up to fourfold in the presence of plant roots, and this mechanism—termed the rhizosphere priming effect—may be especially relevant to thawing permafrost soils as rising temperatures also stimulate plant productivity in the Arctic. However, priming is currently not explicitly included in any model projections of future carbon losses from the permafrost area. Here, we combine high-resolution spatial and depth-resolved datasets of key plant and permafrost properties with empirical relationships of priming effects from living plants on microbial respiration. We show that rhizosphere priming amplifies overall soil respiration in permafrost-affected ecosystems by ~12%, which translates to a priming-induced absolute loss of ~40 Pg soil carbon from the northern permafrost area by 2100. Our findings highlight the need to include fine-scale ecological interactions in order to accurately predict large-scale greenhouse gas emissions, and suggest even tighter restrictions on the estimated 200 Pg anthropogenic carbon emission budget to keep global warming below 1.5 °C.

  • Microbial growth and carbon use efficiency show seasonal responses in a multifactorial climate change experiment

    Simon E, Canarini A, Martin V, Séneca J, Böckle T, Reinthaler D, Pötsch E M, Piepho H-P, Bahn M, Wanek W, Richter A
    2020 - Communications Biology, 3: article 584


    Microbial growth and carbon use efficiency (CUE) are central to the global carbon cycle, as microbial remains form soil organic matter. We investigated how future global changes may affect soil microbial growth, respiration, and CUE. We aimed to elucidate the soil microbial response to multiple climate change drivers across the growing season and whether effects of multiple global change drivers on soil microbial physiology are additive or interactive. We measured soil microbial growth, CUE, and respiration at three time points in a field experiment combining three levels of temperature and atmospheric CO2, and a summer drought. Here we show that climate change-driven effects on soil microbial physiology are interactive and season-specific, while the coupled response of growth and respiration lead to stable microbial CUE (average CUE = 0.39). These results suggest that future research should focus on microbial growth across different seasons to understand and predict effects of global changes on soil carbon dynamics.

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

    Eichorst S, Giguere A, Meier D, Herbold C, Richter A, Greening C, Woebken D
    2020 - ISME Journal, in press


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

  • Cutting out the middle clam: lucinid endosymbiotic bacteria are also associated with seagrass roots worldwide

    Martin BC, Middleton JA, Fraser MW, Marshall IPG, Scholz VV, Hausl B, Schmidt H
    2020 - The ISME Journal, 14: 2901-2905


    Seagrasses and lucinid bivalves inhabit highly reduced sediments with elevated sulphide concentrations. Lucinids house symbiotic bacteria (Ca. Thiodiazotropha) capable of oxidising sediment sulphide, and their presence in sediments has been proposed to promote seagrass growth by decreasing otherwise phytotoxic sulphide levels. However, vast and productive seagrass meadows are present in ecosystems where lucinids do not occur. Hence, we hypothesised that seagrasses themselves host these sulphur-oxidising Ca. Thiodiazotropha that could aid their survival when lucinids are absent. We analysed newly generated and publicly available 16S rRNA gene sequences from seagrass roots and sediments across 14 seagrass species and 10 countries and found that persistent and colonising seagrasses across the world harbour sulphur-oxidising Ca. Thiodiazotropha, regardless of the presence of lucinids. We used fluorescence in situ hybridisation to visually confirm the presence of Ca. Thiodiazotropha on roots of Halophila ovalis, a colonising seagrass species with wide geographical, water depth range, and sedimentary sulphide concentrations. We provide the first evidence that Ca. Thiodiazotropha are commonly present on seagrass roots, providing another mechanism for seagrasses to alleviate sulphide stress globally.

  • Nitrogen Isotope Fractionation During Archaeal Ammonia Oxidation: Coupled Estimates From Measurements of Residual Ammonium and Accumulated Nitrite

    Mooshammer M, Alves RJE, Bayer B, Melcher M, Stieglmeier M, Jochum L, Rittmann SK-MR, Watzka M, Schleper C, Herndl G, Wanek W
    2020 - Frontiers in microbiology, 11: Article 1710


    The naturally occurring nitrogen (N) isotopes, 15N and 14N, exhibit different reaction rates during many microbial N transformation processes, which results in N isotope fractionation. Such isotope effects are critical parameters for interpreting natural stable isotope abundances as proxies for biological process rates in the environment across scales. The kinetic isotope effect of ammonia oxidation (AO) to nitrite (NO2), performed by ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), is generally ascribed to the enzyme ammonia monooxygenase (AMO), which catalyzes the first step in this process. However, the kinetic isotope effect of AMO, or εAMO, has been typically determined based on isotope kinetics during product formation (cumulative product, NO2) alone, which may have overestimated εAMO due to possible accumulation of chemical intermediates and alternative sinks of ammonia/ammonium (NH3/NH4+). Here, we analyzed 15N isotope fractionation during archaeal ammonia oxidation based on both isotopic changes in residual substrate (RS, NH4+) and cumulative product (CP, NO2) pools in pure cultures of the soil strain Nitrososphaera viennensis EN76 and in highly enriched cultures of the marine strain Nitrosopumilus adriaticus NF5, under non-limiting substrate conditions. We obtained εAMO values of 31.9–33.1‰ for both strains based on RS (δ15NH4+) and showed that estimates based on CP (δ15NO2) give larger isotope fractionation factors by 6–8‰. Complementary analyses showed that, at the end of the growth period, microbial biomass was 15N-enriched (10.1‰), whereas nitrous oxide (N2O) was highly 15N depleted (−38.1‰) relative to the initial substrate. Although we did not determine the isotope effect of NH4+ assimilation (biomass formation) and N2O production by AOA, our results nevertheless show that the discrepancy between εAMO estimates based on RS and CP might have derived from the incorporation of 15N-enriched residual NH4+ after AMO reaction into microbial biomass and that N2O production did not affect isotope fractionation estimates significantly.

  • Composition and activity of nitrifier communities in soil are unresponsive to elevated temperature and CO2, but strongly affected by drought

    Séneca J, Pjevac P, Canarini A, Herbold CW, Zioutis C, Dietrich M, Simon E, Prommer J, Bahn M, Pötsch EM, Wagner M, Wanek W, Richter A
    2020 - The ISME Journal, 14: 3038-3053


    Nitrification is a fundamental process in terrestrial nitrogen cycling. However, detailed information on how climate change affects the structure of nitrifier communities is lacking, specifically from experiments in which multiple climate change factors are manipulated simultaneously. Consequently, our ability to predict how soil nitrogen (N) cycling will change in a future climate is limited. We conducted a field experiment in a managed grassland and simultaneously tested the effects of elevated atmospheric CO2, temperature, and drought on the abundance of active ammonia-oxidizing bacteria (AOB) and archaea (AOA), comammox (CMX) Nitrospira, and nitrite-oxidizing bacteria (NOB), and on gross mineralization and nitrification rates. We found that N transformation processes, as well as gene and transcript abundances, and nitrifier community composition were remarkably resistant to individual and interactive effects of elevated CO2 and temperature. During drought however, process rates were increased or at least maintained. At the same time, the abundance of active AOB increased probably due to higher NH4+ availability. Both, AOA and comammox Nitrospira decreased in response to drought and the active community composition of AOA and NOB was also significantly affected. In summary, our findings suggest that warming and elevated CO2 have only minor effects on nitrifier communities and soil biogeochemical variables in managed grasslands, whereas drought favors AOB and increases nitrification rates. This highlights the overriding importance of drought as a global change driver impacting on soil microbial community structure and its consequences for N cycling.

  • The ecology of heterogeneity: soil bacterial communities and C dynamics

    Nunan N, Schmidt H, Raynaud X
    2020 - Phil. Trans. R. Soc. B, 1798: 11


    Heterogeneity is a fundamental property of soil that is often overlooked in microbial ecology. Although it is generally accepted that the heterogeneity of soil underpins the emergence and maintenance of microbial diversity, the profound and far-reaching consequences that heterogeneity can have on many aspects of microbial ecology and activity have yet to be fully apprehended and have not been fully integrated into our understanding of microbial functioning. In this contribution we first discuss how the heterogeneity of the soil microbial environment, and the consequent uncertainty associated with acquiring resources, may have affected how microbial metabolism, motility and interactions evolved and, ultimately, the overall microbial activity that is represented in ecosystem models, such as heterotrophic decomposition or respiration. We then present an analysis of predicted metabolic pathways for soil bacteria, obtained from the MetaCyc pathway/genome database collection ( The analysis suggests that while there is a relationship between phylogenic affiliation and the catabolic range of soil bacterial taxa, there does not appear to be a trade-off between the 16S rRNA gene copy number, taken as a proxy of potential growth rate, of bacterial strains and the range of substrates that can be used. Finally, we present a simple, spatially explicit model that can be used to understand how the interactions between decomposers and environmental heterogeneity affect the bacterial decomposition of organic matter, suggesting that environmental heterogeneity might have important consequences on the variability of this process.

Book chapters and other publications

No matching database entries were found.