Publications

Publications in peer reviewed journals

52 Publications found
  • Rhizospheric microbial community of Caesalpinia spinosa (Mol.) Kuntze in conserved and deforested zones of the Atiquipa fog forest in Peru

    Cordero I, Ruiz-Diez B, Balaguer L, Richter A, Pueyo JJ, Rincon A
    2017 - Applied Soil Ecology, 114: 132-141

    Abstract: 

    Caesalpinia spinosa, tara, is the predominant fog catcher tree in the fog forest of Atiquipa, a biodiversity hotspot ecosystem within the coastal Peruvian desert highly threatened by intense land use over time. We investigated the impact of deforestation, as well as potential effects of the tree age (juveniles vs adults) and the type of tree (recruited vs planted), on the rhizospheric microbial communities of tara growing in contrasting landscapes (conserved vs deforested) of the Atiquipa forest.

    We used a phospholipid fatty acids analysis approach to study the microbial community associated with tara. Additionally, we isolated and sought for native rhizospheric bacteria with plant growth promoting (PGPR) traits to be used as potential inoculants for restoration projects.

    Deforestation profoundly altered the chemical and biological fertility of soils. All rhizospheric microorganisms were clearly reduced in abundance by deforestation, while the age or the type of trees had no effects. Both, deforestation and tree age influenced the assemblage of microbial communities, which tightly correlated with soil pH and organic matter among other soil properties. Adult trees harboured similar microbial communities in conserved and deforested soils being potential reservoirs of native microorganisms in the degraded areas. Some selected bacterial strains showed high plant growth promoting abilities, and PGPR traits were related with the isolation source of bacteria. The knowledge about key factors structuring the rhizospheric microbiota of tara and the identification of high-performing PGPR strains, provide a solid framework to formulate inocula for their use in restoration programmes in the Atiquipa fog forest.

  • Microbial utilization of mineral-associated nitrogen in soils

    Turner S, Meyer-Stüve S, Schippers A, Guggenberger G, Schaarschmidt F, Wild B, Richter A, Dohrmann R, Mikutta R
    2017 - Soil Biology and Biochemistry, 104: 185-196

    Abstract: 

    In soils, a large portion of organic nitrogen (ON) is associated with minerals and thus, possibly stabilized against biological decay. We therefore tested if mineral-associated N is an important N source for soil microorganisms, and which soil parameters control its bioavailability. Microcosm experiments with mineral-associated organic matter, obtained as heavy fraction (HF) via density fractionation, and bulk soil from mineral topsoil of the Franz Josef chronosequence were conducted for 125 days. We examined the effects of O2 status, soil age (differences in mineralogical properties), as well as cellulose and phosphate additions on the turnover of mineral-associated N. Using a combination of activity measurements and quantitative PCR, microbial N transformation rates and abundances of N-related functional genes (amoAnarGchiA) were determined. Similar or higher values for microbial N cycling rates and N-related functional abundances in the HF compared to bulk soil indicated that mineral-associated N provides an important bioavailable N source for soil microorganism. The turnover of mineral-associated N was mainly controlled by the O2 status. Besides, soil mineralogical properties significantly affected microbial N cycling and related gene abundances with the effect depending on the N substrate type (ON, NH4+ or NO3). In contrast, cellulose or phosphate addition hardly enhanced microbial utilization of mineral-associated N. The results of our microcosm study indicate that mineral-associated N is highly bioavailable in mineral topsoils, but effects of the mineral phase differ between N cycling processes.

  • Optimal metabolic regulation along resource stoichiometry gradients

    Manzoni S, Capek P, Mooshammer M, Lindahl BD, Richter A, Santruckova H
    2017 - Ecology Letters, 20: 1182-1191

    Abstract: 

    Most heterotrophic organisms feed on substrates that are poor in nutrients compared to their
    demand, leading to elemental imbalances that may constrain their growth and function. Flexible
    carbon (C)-use efficiency (CUE, C used for growth over C taken up) can represent a strategy to
    reduce elemental imbalances. Here, we argue that metabolic regulation has evolved to maximise
    the organism growth rate along gradients of nutrient availability and translated this assumption
    into an optimality model that links CUE to substrate and organism stoichiometry. The optimal
    CUE is predicted to decrease with increasing substrate C-to-nutrient ratio, and increase with
    nutrient amendment. These predictions are generally confirmed by empirical evidence from a new
    database of c. 2200 CUE estimates, lending support to the hypothesis that CUE is optimised
    across levels of organisation (microorganisms and animals), in aquatic and terrestrial systems, and
    when considering nitrogen or phosphorus as limiting nutrients.

  • Decoupling of microbial carbon, nitrogen, and phosphorus cycling in response to extreme temperature events

    Mooshammer M, Hofhansl F, Frank AH, Wanek W, Hämmerle I, Leitner S, Schnecker J, Wild B, Watzka M, Keiblinger KM, Zechmeister­‐Boltenstern S, Richter A
    2017 - Science Advances, 3: 13

    Abstract: 

    Predicted changes in the intensity and frequency of climate extremes urge a better mechanistic understanding of the
    stress response of microbially mediated carbon (C) and nutrient cycling processes. We analyzed the resistance and
    resilience of microbial C, nitrogen (N), and phosphorus (P) cycling processes and microbial community composition
    in decomposing plant litter to transient, but severe, temperature disturbances, namely, freeze-thaw and heat. Disturbances
    led temporarily to a more rapid cycling of C and N but caused a down-regulation of P cycling. In contrast to the
    fast recovery of the initially stimulated C and N processes, we found a slow recovery of P mineralization rates, which
    was not accompanied by significant changes in community composition. The functional and structural responses to
    the two distinct temperature disturbances were markedly similar, suggesting that direct negative physical effects and
    costs associated with the stress response were comparable. Moreover, the stress response of extracellular enzyme
    activities, but not that of intracellular microbial processes (for example, respiration or N mineralization), was
    dependent on the nutrient content of the resource through its effect on microbial physiology and community
    composition. Our laboratory study provides novel insights into the mechanisms of microbial functional stress responses
    that can serve as a basis for field studies and, in particular, illustrates the need for a closer integration of
    microbial C-N-P interactions into climate extremes research.

  • Global patterns of phosphatase activity in natural soils

    Margalef O, Sardans J, Fernández-Martínez M, Molowny-Horas R, Janssens IA, Ciais P, Richter A, Obersteiner M, Asenio D, Peñuelas J
    2017 - Scientific Reports, 7: 13

    Abstract: 

    Soil phosphatase levels strongly control the biotic pathways of phosphorus (P), an essential element for
    life, which is often limiting in terrestrial ecosystems. We investigated the influence of climatic and soil
    traits on phosphatase activity in terrestrial systems using metadata analysis from published studies.
    This is the first analysis of global measurements of phosphatase in natural soils. Our results suggest
    that organic P (Porg), rather than available P, is the most important P fraction in predicting phosphatase
    activity. Structural equation modeling using soil total nitrogen (TN), mean annual precipitation, mean
    annual temperature, thermal amplitude and total soil carbon as most available predictor variables
    explained up to 50% of the spatial variance in phosphatase activity. In this analysis, Porg could not be
    tested and among the rest of available variables, TN was the most important factor explaining the
    observed spatial gradients in phosphatase activity. On the other hand, phosphatase activity was also
    found to be associated with climatic conditions and soil type across different biomes worldwide. The
    close association among different predictors like Porg, TN and precipitation suggest that P recycling is
    driven by a broad scale pattern of ecosystem productivity capacity.

  • Geothermal ecosystems as natural climate change experiments: The ForHot research site in Iceland as a case study

    Sigurdsson BD, Leblans NIW, Dauwe S, Guðmundsdóttir E, Gundersen P, Gunnarsdóttir GE, Holmstrup M, Ilieva-Makulec K, Kätterer T, Marteinsdóttir B, Maljanen M, Oddsdóttir ES, Ostonen I, Peñuelas J, Poeplau C, Richter A, Sigurðsson P, Van Bodegom P, Wallander H, Weedon J, Janssens I
    2016 - Icelandic Agricultural Sciences (IAS), 29: 53-71

    Abstract: 

    This article describes how natural geothermal soil temperature gradients in Iceland have been used to study terrestrial ecosystem responses to soil warming. The experimental approach was evaluated at three study sites in southern Iceland; one grassland site that has been warm for at least 50 years (GO), and another comparable grassland site (GN) and a Sitka spruce plantation (FN) site that have both been warmed since an earthquake took place in 2008. Within each site type, five ca. 50 m long transects, with six permanent study plots each, were established across the soil warming gradients, spanning from unwarmed control conditions to gradually warmer soils. It was attempted to select the plots so the annual warming levels would be ca. +1, +3, +5, +10 and +20 °C within each transect. Results of continuous measurements of soil temperature (Ts) from 2013-2015 revealed that the soil warming was relatively constant and followed the seasonal Ts cycle of the unwarmed control plots. Volumetric water content in the top 5 cm of soil was repeatedly surveyed during 2013-2016. The grassland soils were wetter than the FN soils, but they had sometimes some significant warming-induced drying in the surface layer of the warmest plots, in contrast to FN. Soil chemistry did not show any indications that geothermal water had reached the root zone, but soil pH did increase somewhat with warming, which was probably linked to vegetation changes. As expected, the potential decomposition rate of organic matter increased significantly with warming. It was concluded that the natural geothermal gradients at the ForHot sites in Iceland offered realistic conditions for studying terrestrial ecosystem responses to warming with minimal artefacts. 

  • Drought history affects grassland plant and microbial carbon turnover during and after a subsequent drought event

    Fuchslueger L, Bahn M, Hasibeder R, Kienzl S, Fritz K, Schmitt M, Watzka M, Richter A
    2016 - Journal of Ecology, 104: 1453-1465

    Abstract: 

    Summary

    1. Drought periods are projected to become more severe and more frequent in many European regions. While effects of single strong droughts on plant and microbial carbon (C) dynamics have been studied in some detail, impacts of recurrent drought events are still little understood.
    2. We tested whether the legacy of extreme experimental drought affects responses of plant and microbial C and nitrogen (N) turnover to further drought and rewetting. In a mountain grassland, we conducted a 13C pulse-chase experiment during a naturally occurring drought and rewetting event in plots previously exposed to experimental droughts and in ambient controls (AC). After labelling, we traced 13C below-ground allocation and incorporation into soil microbes using phospholipid fatty acid biomarkers.
    3. Drought history (DH) had no effects on the standing shoot and fine root plant biomass. However, plants with experimental DH displayed decreased shoot N concentrations and increased fine root N concentrations relative to those in AC. During the natural drought, plants with DH assimilated and allocated less 13C below-ground; moreover, fine root respiration was reduced and not fuelled by fresh C compared to plants in AC.
    4. Regardless of DH, microbial biomass remained stable during natural drought and rewetting. Although microbial communities initially differed in their composition between soils with and without DH, they responded to the natural drought and rewetting in a similar way: gram-positive bacteria increased, while fungal and gram-negative bacteria remained stable. In soils with DH, a strongly reduced uptake of recent plant-derived 13C in microbial biomarkers was observed during the natural drought, pointing to a smaller fraction of active microbes or to a microbial community that is less dependent on plant C.
    5. Synthesis. Drought history can induce changes in above- vs. below-ground plant N concentrations and affect the response of plant C turnover to further droughts and rewetting by decreasing plant C uptake and below-ground allocation. DH does not affect the responses of the microbial community to further droughts and rewetting, but alters microbial functioning, particularly the turnover of recent plant-derived carbon, during and after further drought periods.
  • Exploring the metabolic potential of microbial communities in ultra-basic, reducing springs at The Cedars, CA, USA: Experimental evidence of microbial methanogenesis and heterotrophic acetogenesis

    Kohl L, Cumming E, Cox A, Rietze A, Morrissey L, Lang SQ, Richter A, Suzuki S, Nealson KH, Morrill PL
    2016 - Journal of Geophysical Research Biogeosciences, 4: 1203-1220

    Abstract: 

    Present-day serpentinization generates groundwaters with conditions (pH > 11, Eh < −550 mV) favorable for the microbial and abiotic production of organic compounds from inorganic precursors. Elevated concentrations of methane, C2-C6 alkanes, acetate, and formate have been detected at these sites, but the microbial or abiotic origin of these compounds remains unclear. While geochemical data indicate that methane at most sites of present-day serpentinization is abiogenic, the stable carbon, hydrogen, and clumped isotope data as well as the hydrocarbon gas composition from The Cedars, CA, USA, are consistent with a microbial origin for methane. However, there is no direct evidence of methanogenesis at this site of serpentinization. We report on laboratory experiments in which the microbial communities in fluids and sediments from The Cedars were incubated with 13C labeled substrates. Increasing methane concentrations and the incorporation of 13C into methane in live experiments, but not in killed controls, demonstrated that methanogens converted methanol, formate, acetate (methyl group), and bicarbonate to methane. The apparent fractionation between methane and potential substrates (α13CCH4-CO2(g) = 1.059 to 1.105, α13CCH4-acetate = 1.042 to 1.119) indicated that methanogenesis was dominated by the carbonate reduction pathway. Increasing concentrations of volatile organic acid anions indicated microbial acetogenesis. α13CCO2(g)-acetate values (0.999 to 1.000), however, were inconsistent with autotrophic acetogenesis, thus suggesting that acetate was produced through fermentation. This is the first study to show direct evidence of microbial methanogenesis and acetogenesis by the native microbial community at a site of present-day serpentinization.

  • Environmental and landscape controls of soil organic carbon storage in continuous permafrost terrain of the Taymyr Peninsula (N Siberia, Russia)

    Palmtag J, Ramage J, Hugelius G, Gentsch N, Lashchinskiy N, Richter A, Kuhry P
    2016 - European Journal of Soil Science, 67: 478-491

    Abstract: 

    Summary


    This research examined soil organic carbon (SOC), total nitrogen (TN) and aboveground phytomass carbon (PhC) stocks in two areas of the Taymyr Peninsula, northern Siberia. We combined field sampling, chemical and 14C radiocarbon dating analyses with land cover classifications for landscape-level assessments. The estimated mean for the 0–100-cm depth SOC stocks was 14.8 and 20.8 kg C m−2 in Ary-Mas and Logata, respectively. The corresponding values for TN were 1.0 and 1.3 kg N m−2. On average, about 2% only (range 0–12%) of the total ecosystem C is stored in PhC. In both study areas about 34% of the SOC at 0–100 cm is stored in cryoturbated pockets, which have formed since at least the early Holocene. The larger carbon/nitrogen (C/N) ratio of this cryoturbated material indicates that it consists of relatively undecomposed soil organic matter (SOM). There are substantial differences in SOC stocks and SOM properties within and between the two study areas, which emphasizes the need to consider both geomorphology and soil texture in the assessment of landscape-level and regional SOC stocks.


    Highlights

    • This research addresses landscape-scale and regional variation in SOC stocks.
    • Landform and soil texture are taken into account in the analysis.
    • The contribution of phytomass to total ecosystem C stored is limited.
    • Large SOC stocks are susceptible to decomposition following permafrost thaw.

  • Soil microbial carbon use efficiency and biomass turnover in a long-term fertilization experiment in a temperate grassland

    Spohn M, Pötsch EM, Eichhorst SA, Woebken D, Wanek W, Richter A
    2016 - Soil Biology and Biochemistry, 97: 168-175

    Abstract: 

    Soil microbial carbon use efficiency (CUE), defined as the ratio of organic C allocated to growth over organic C taken up, strongly affects soil carbon (C) cycling. Despite the importance of the microbial CUE for the terrestrial C cycle, very little is known about how it is affected by nutrient availability. Therefore, we studied microbial CUE and microbial biomass turnover time in soils of a long-term fertilization experiment in a temperate grassland comprising five treatments (control, PK, NK, NP, NPK). Microbial CUE and the turnover of microbial biomass were determined using a novel substrate-independent method based on incorporation of 18O from labeled water into microbial DNA. Microbial respiration was 28–37% smaller in all three N treatments (NK, NP, and NPK) compared to the control, whereas the PK treatment did not affect microbial respiration. N-fertilization decreased microbial C uptake, while the microbial growth rate was not affected. Microbial CUE ranged between 0.31 and 0.45, and was 1.3- to 1.4-fold higher in the N-fertilized soils than in the control. The turnover time ranged between 80 and 113 days and was not significantly affected by fertilization. Net primary production (NPP) and the abundance of legumes differed strongly across the treatments, and the fungal:bacterial ratio was very low in all treatments. Structural equation modeling revealed that microbial CUE was exclusively controlled by N fertilization and that neither the abundance of legumes (as a proxy for the quality of the organic matter inputs) nor NPP (as a proxy for C inputs) had an effect on microbial CUE. Our results show that N fertilization did not only decrease microbial respiration, but also microbial C uptake, indicating that less C was intracellularly processed in the N fertilized soils. The reason for reduced C uptake and increased CUE in the N-fertilization treatments is likely an inhibition of oxidative enzymes involved in the degradation of aromatic compounds by N in combination with a reduced energy requirement for microbial N acquisition in the fertilized soils. In conclusion, the study shows that N availability can control soil C cycling by affecting microbial CUE, while plant community-mediated changes in organic matter inputs and P and K availability played no important role for C partitioning of the microbial community in this temperate grassland.

  • Microbial carbon use efficiency and biomass turnover times depending on soil depth - Implications for carbon cycling.

    Spohn M, Klaus K, Wanek W, Richter A
    2016 - Soil Biology and Biochemistry, 96: 74-81

    Abstract: 

    Processing of organic carbon (C) by soil microorganisms is a key process of terrestrial C cycling. For this reason we studied (i) microbial carbon use efficiency (CUE) defined as C allocated to growth over organic C taken up by the microbial community, and (ii) the turnover time of microbial biomass in a pasture and in two forest soils. We hypothesized that microbial CUE decreases in mineral soils with depth from the topsoil to the subsoil, while the turnover time of the microbial biomass increases due to energetic constrains. We determined microbial CUE and turnover of microbial biomass C using a novel substrate-independent method based on incorporation of 18O from labeled water into microbial DNA with concurrent measurements of basal respiration. Microorganisms showed decreasing C uptake rates with decreasing C contents in the deeper soil layers. In the forest soils, no adaptation of microbial CUE with soil depth took place, i.e., microbes in the forest topsoil used C at the same efficiency as microbes in the subsoil. However, in the pasture soil, microbial CUE decreased in the lower soil layers compared to the topsoil, indicating that microorganisms in the deeper soil layers allocated relatively more C to respiration. In the organic soil layer, microorganisms respired more per unit microbial biomass C than in the subsoil, but had a similar CUE despite the high C-to-nitrogen and C-to-phosphorus ratios of the litter layers. The turnover time of microbial biomass increased with soil depth in the two forest soils. Thus, in the forest soils, a lower microbial C uptake rate in the deeper soil layers was partially compensated by a longer turnover time of microbial biomass C. In conclusion, our findings emphasize that in addition to microbial CUE, the turnover time of the microbial biomass strongly affects soil C cycling.

    Keywords

    • Soil microbial carbon use efficiency
    • Growth efficiency
    • Organic matter decomposition;
    • Microbial metabolism
    • Stoichiometry
    • Microbial biomass carbon turnover
  • Stress-induced changes in carbon allocation among metabolite pools influence isotope-based predictions of water use efficiency in Phaseolus vulgaris

    Lockhart R, Wild B, Richter A, Simonin K, Merchant A
    2016 - Functional Plant Biology, 1149-1158

    Abstract: 

    Understanding how major food crops respond to environmental stress will expand our capacity to improve food production with growing populations and a changing climate. This study uses chemical and physiological adaptations to heat, water deficit and elevated light stresses in Phaseolus vulgaris L. to identify changes in carbon (C) allocation that, combined with post-photosynthetic fractionation of C isotopes, influences water use efficiency (WUE) predictions. The chemical stress response was explored through changes in C allocation to the carbohydrate and cyclitol pools using GC–triple quadrupole MS. Carbon allocation to the sucrose pool fluctuated significantly among treatments, and the putative osmolytes and osmoprotectants (myo-inositol and D-ononitol) accumulated under stress. Significant osmotic adjustment (P < 0.05), quantified via pressure–volume curve analysis, was detected between control and stress treatments, although this was not attributable to active accumulation of the metabolites. Compound-specific 13C isotope abundance was measured using liquid chromatography isotope ratio MS to predict intrinsic WUE. In contrast to other metabolites measured, the δ13C of the sucrose pool fluctuated according to treatment and was proportional to predicted values based upon modelled Δ13C from gas exchange data. The results suggest that the accuracy and precision of predicting WUE may be enhanced by compound-specific analysis of Δ13C and that changes in the allocation of C among metabolite pools may influence WUE predictions based upon analysis of total soluble C. Overall, the plants appeared to use a range of mechanisms to cope with adverse conditions that could be utilised to improve plant breeding and management strategies.

  • Carbon isotope composition of carbohydrates and polyols in leaf and phloem sap of Phaseolus vulgaris L. influences predictions of plant water use efficiency

    Smith M, Wild B, Richter A, Simonin K, Merchant A
    2016 - Plant and Cell Physiology, 57: 1756-1766

    Abstract: 

    The use of carbon isotope abundance (δ13C) to assess plant carbon acquisition and water use has significant potential for use in crop management and plant improvement programs. Utilising Phaseolus vulgaris L. as a model system, this study demonstrates the occurrence and sensitivity of carbon isotope fractionation during the onset of abiotic stresses between leaf and phloem carbon pools. In addition to gas exchange data; compound-specific measures of carbon isotope abundance and concentrations of soluble components of phloem sap were compared to major carbohydrate and sugar alcohol pools in leaf tissue. Differences in both δ13C and concentration of metabolites were found in leaf and phloem tissues, the magnitude of which responded to changing environmental conditions. These changes have inplications for the modelling of leaf level gas exchange based upon δ13C natural abundance. While estimates of δ13C of low molecular weight carbohydrates and polyols increased the precision of predictions of water use efficiency compared to those based on bulk soluble carbon. The use of this technique requires consideration of the dynamics of the δ13C pool under investigation. Understanding the dynamics of changes in δ13C during movement and incorporation into heterotrophic tissues is vital for the continued development of tools that provide information on plant physiological performance relating to water use.

  • Plant-derived compounds stimulate the decomposition of organic matter in arctic permafrost soils

    Wild B, Gentsch N, Capek P, Diakova K, Alves RJ, Barta J, Gittel A, Hugelius G, Knoltsch A, Kuhry P, Lashchinskiy N, Mikutta R, Palmtag J, Schleper C, Schnecker J, Shibistova O, Takriti M, Torsvik VL, Urich T, Watzka M, Santruckova H, Guggenberger G, Richter A
    2016 - Scientific Reports, 6: 11

    Abstract: 

    Arctic ecosystems are warming rapidly, which is expected to promote soil organic matter (SOM) decomposition. In addition to the direct warming effect, decomposition can also be indirectly stimulated via increased plant productivity and plant-soil C allocation, and this so called “priming effect” might significantly alter the ecosystem C balance. In this study, we provide first mechanistic insights into the susceptibility of SOM decomposition in arctic permafrost soils to priming. By comparing 119 soils from four locations across the Siberian Arctic that cover all horizons of active layer and upper permafrost, we found that an increased availability of plant-derived organic C particularly stimulated decomposition in subsoil horizons where most of the arctic soil carbon is located. Considering the 1,035 Pg of arctic soil carbon, such an additional stimulation of decomposition beyond the direct temperature effect can accelerate net ecosystem C losses, and amplify the positive feedback to global warming.

  • Microbes as engines of ecosystem function: when does community structure enhance predictions of ecosystem processes?

    Graham EB, Knelman JE, Schindlbacher A, Siciliano S, Breulmann M, Yannarell A, Beman JM, Abell G, Philippot L, Prosser J, Foulquier A, Yuste JC, Glanville HC, Jones DL, Angel R, Salminen J, Newton RJ, Bürgmann H, Ingram LJ, Hamer U, Siljanen HM, Peltoniemi K, Potthast K, Bañeras L, Hartmann M, Banerjee S, Yu RQ, Nogaro G, Richter A, Koranda M, Castle SC, Goberna M, Song B, Chatterjee A, Nunes OC, Lopes AR, Cao Y, Kaisermann A, Hallin S, Strickland MS, Garcia-Pausas J, Barba J, Kang H, Isobe K, Papaspyrou S, Pastorelli R, Lagomarsino A, Lindström ES, Basiliko N, Nemergut DR
    2016 - Frontiers in microbiology, 7: 214

    Abstract: 

    Microorganisms are vital in mediating the earth's biogeochemical cycles; yet, despite our rapidly increasing ability to explore complex environmental microbial communities, the relationship between microbial community structure and ecosystem processes remains poorly understood. Here, we address a fundamental and unanswered question in microbial ecology: 'When do we need to understand microbial community structure to accurately predict function?' We present a statistical analysis investigating the value of environmental data and microbial community structure independently and in combination for explaining rates of carbon and nitrogen cycling processes within 82 global datasets. Environmental variables were the strongest predictors of process rates but left 44% of variation unexplained on average, suggesting the potential for microbial data to increase model accuracy. Although only 29% of our datasets were significantly improved by adding information on microbial community structure, we observed improvement in models of processes mediated by narrow phylogenetic guilds via functional gene data, and conversely, improvement in models of facultative microbial processes via community diversity metrics. Our results also suggest that microbial diversity can strengthen predictions of respiration rates beyond microbial biomass parameters, as 53% of models were improved by incorporating both sets of predictors compared to 35% by microbial biomass alone. Our analysis represents the first comprehensive analysis of research examining links between microbial communitystructure and ecosystem function. Taken together, our results indicate that a greater understanding of microbial communities informed by ecological principles may enhance our ability to predict ecosystem process rates relative to assessments based on environmental variables and microbial physiology.

  • Storage and transformation of organic matter fractions in cryoturbated permafrost soils across the Siberian Arctic

    Gentsch N, Mikutta R, Alves RJE, Barta J, Capek P, Gittel A, Hugelius G, Kuhry P, Lashchinskiy N, Palmtag J, Richter A, Santrukova H, Schnecker J, Shibistova O, Urich T, Wild B, Guggenberger G
    2015 - Biogeosciences, 12: 4525-4542

    Abstract: 

    In permafrost soils, the temperature regime and the resulting cryogenic processes are important determinants of the storage of organic carbon (OC) and its small-scale spatial variability. For cryoturbated soils, there is a lack of research assessing pedon-scale heterogeneity in OC stocks and the transformation of functionally different organic matter (OM) fractions, such as particulate and mineral-associated OM. Therefore, pedons of 28 Turbels were sampled in 5m wide soil trenches across the Siberian Arctic to calculate OC and total nitrogen (TN) stocks based on digital profile mapping. Density fractionation of soil samples was performed to distinguish between particulate OM (light fraction, LF, < 1.6 g cm(-3)), mineral associated OM (heavy fraction, HF, > 1.6 g cm(-3)), and a mobilizable dissolved pool (mobilizable fraction, MoF). Across all investigated soil profiles, the total OC storage was 20.2 +/- 8.0 kgm(-2) (mean +/- SD) to 100 cm soil depth. Fifty-four percent of this OC was located in the horizons of the active layer (annual summer thawing layer), showing evidence of cryoturbation, and another 35% was present in the upper permafrost. The HF-OC dominated the overall OC stocks (55 %), followed by LF-OC (19% in mineral and 13% in organic horizons). During fractionation, approximately 13% of the OC was released as MoF, which likely represents a readily bioavailable OM pool. Cryogenic activity in combination with cold and wet conditions was the principle mechanism through which large OC stocks were sequestered in the subsoil (16.4 +/- 8.1 kgm(-2); all mineral B, C, and permafrost horizons). Approximately 22% of the subsoil OC stock can be attributed to LF material subducted by cryoturbation, whereas migration of soluble OM along freezing gradients appeared to be the principle source of the dominant HF (63 %) in the subsoil. Despite the unfavourable abiotic conditions, low C/N ratios and high delta C-13 values indicated substantial microbial OM transformation in the subsoil, but this was not reflected in altered LF and HF pool sizes. Partial least-squares regression analyses suggest that OC accumulates in the HF fraction due to co-precipitation with multivalent cations (Al, Fe) and association with poorly crystalline iron oxides and clay minerals. Our data show that, across all permafrost pedons, the mineral-associated OM represents the dominant OM fraction, suggesting that the HF-OC is the OM pool in permafrost soils on which changing soil conditions will have the largest impact.

  • The application of ecological stoichiometry to plant-microbial-soil organic matter transformations

    Zechmeister-Boltenstern S, Keiblinger KM, Mooshammer M, Peñuelas J, Richter A, Sardans J, Wanek W
    2015 - Ecological Monographs, 85: 135-155

    Abstract: 

    Elemental stoichiometry constitutes an inherent link between biogeochemistry and the structure and processes within food webs, and thus is at the core of ecosystem functioning. Stoichiometry allows for spanning different levels of biological organization, from cellular metabolism to ecosystem structure and nutrient cycling, and is therefore particularly useful for establishing links between different ecosystem compartments. We review elemental carbon : nitrogen : phosphorus (C:N:P) ratios in terrestrial ecosystems (from vegetation, leaf litter, woody debris, and dead roots, to soil microbes and organic matter). While the stoichiometry of the plant, litter, and soil compartments of ecosystems is well understood, heterotrophic microbial communities, which dominate the soil food web and drive nutrient cycling, have received increasing interest in recent years. This review highlights the effects of resource stoichiometry on soil microorganisms and decomposition, specifically on the structure and function of heterotrophic microbial communities and suggests several general patterns. First, latitudinal gradients of soil and litter stoichiometry are reflected in microbial community structure and function. Second, resource stoichiometry may cause changes in microbial interactions and community dynamics that lead to feedbacks in nutrient availability. Third, global change alters the C:N, C:P, and N:P ratios of primary producers, with repercussions for microbial decomposer communities and critical ecosystem services such as soil fertility. We argue that ecological stoichiometry provides a framework to analyze and predict such global change effects at various scales.

  • 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.

  • Microbial nitrogen dynamics in organic and mineral soil horizons along a latitudinal transect in western Siberia

    Wild B, Schnecker J, Knoltsch A, Takriti M, Mooshammer M, Gentsch N, Mikutta R, Eloy Alves RJ, Gittel A, Lashchinskiy N, Richter A
    2015 - Global Biogeochemical Cycles, 29: 567-582

    Abstract: 

    Soil N availability is constrained by the breakdown of N-containing polymers such as proteins to oligopeptides and amino acids that can be taken up by plants and microorganisms. Excess N is released from microbial cells as ammonium (N mineralization), which in turn can serve as substrate for nitrification. According to stoichiometric theory, N mineralization and nitrification are expected to increase in relation to protein depolymerization with decreasing N limitation, and thus from higher to lower latitudes and from topsoils to subsoils. To test these hypotheses, we compared gross rates of protein depolymerization, N mineralization and nitrification (determined using N-15 pool dilution assays) in organic topsoil, mineral topsoil, and mineral subsoil of seven ecosystems along a latitudinal transect in western Siberia, from tundra (67 degrees N) to steppe (54 degrees N). The investigated ecosystems differed strongly in N transformation rates, with highest protein depolymerization and N mineralization rates in middle and southern taiga. All N transformation rates decreased with soil depth following the decrease in organic matter content. Related to protein depolymerization, N mineralization and nitrification were significantly higher in mineral than in organic horizons, supporting a decrease in microbial N limitation with depth. In contrast, we did not find indications for a decrease in microbial N limitation from arctic to temperate ecosystems along the transect. Our findings thus challenge the perception of ubiquitous N limitation at high latitudes, but suggest a transition from N to C limitation of microorganisms with soil depth, even in high-latitude systems such as tundra and boreal forest.

  • Storage, landscape distribution, and burial history of soil organic matter in contrasting areas of continuous permafrost

    Palmtag J, Hugelius G, Lashchinskiy N, Tamstorf MP, Richter A, Elberling B, Kuhry P
    2015 - Arctic Antarctic and Alpine Research, 47: 71-88

    Abstract: 

    This study describes and compares soil organic matter (SOM) quantity and characteristics in two areas of continuous permafrost, a mountainous region in NE Greenland (Zackenberg study site) and a lowland region in NE Siberia (Cherskiy and Shalaurovo study sites). Our assessments are based on stratified-random landscape-level inventories of soil profiles down to 1 m depth, with physico-chemical, elemental, and radiocarbon-dating analyses. The estimated mean soil organic carbon (SOC) storage in the upper meter of soils in the NE Greenland site is 8.3 +/- 1.8 kg C m(-2) compared to 20.3 +/- 2.2 kg C m(-2) and 30.0 +/- 2.0 kg C m(-2) in the NE Siberian sites (95% confidence intervals). The lower SOC storage in the High Arctic site in NE Greenland can be largely explained by the fact that 59% of the study area is located at higher elevation with mostly barren ground and thus very low SOC contents. In addition, SOC-rich fens and bogs occupy a much smaller proportion of the landscape in NE Greenland (similar to 3%) than in NE Siberia (similar to 20%). The contribution of deeper buried C-enriched material in the mineral soil horizons to the total SOC storage is lower in the NE Greenland site (similar to 13%) compared to the NE Siberian sites (similar to 24%-30%). Buried SOM seems generally more decomposed in NE Greenland than in NE Siberia, which we relate to different burial mechanisms prevailing in these regions.

  • The effect of warming on the vulnerability of subducted organic carbon in arctic soils

    Capek P, Diakova K, Dickopp JE, Barta J, Wild B, Schnecker J, Alves RJE, Aiglsdorfer S, Guggenberger G, Gentsch N, Hugelius G, Kuhry P, Lashchinsky N, Gittel A, Schleper C, Mikutta R, Palmtag J, Shibistova O, Urich T, Richter A, Santruckova H
    2015 - Soil Biology and Biochemistry, 90: 19-29

    Abstract: 

    Arctic permafrost soils contain large stocks of organic carbon (OC). Extensive cryogenic processes in these soils cause subduction of a significant part of OC-rich topsoil down into mineral soil through the process of cryoturbation. Currently, one-fourth of total permafrost OC is stored in subducted organic horizons. Predicted climate change is believed to reduce the amount of OC in permafrost soils as rising temperatures will increase decomposition of OC by soil microorganisms. To estimate the sensitivity of OC decomposition to soil temperature and oxygen levels we performed a 4-month incubation experiment in which we manipulated temperature (4-20 degrees C) and oxygen level of topsoil organic, subducted organic and mineral soil horizons. Carbon loss (C-LOSS) was monitored and its potential biotic and abiotic drivers, including concentrations of available nutrients, microbial activity, biomass and stoichiometry, and extracellular oxidative and hydrolytic enzyme pools, were measured. We found that independently of the incubation temperature, C-LOSS from subducted organic and mineral soil horizons was one to two orders of magnitude lower than in the organic topsoil horizon, both under aerobic and anaerobic conditions. This corresponds to the microbial biomass being lower by one to two orders of magnitude. We argue that enzymatic degradation of autochthonous subducted OC does not provide sufficient amounts of carbon and nutrients to sustain greater microbial biomass. The resident microbial biomass relies on allochthonous fluxes of nutrients, enzymes and carbon from the OC-rich topsoil. This results in a "negative priming effect", which protects autochthonous subducted OC from decomposition at present. The vulnerability of subducted organic carbon in cryoturbated arctic soils under future climate conditions will largely depend on the amount of allochthonous carbon and nutrient fluxes from the topsoil. (C) 2015 Elsevier Ltd. All rights reserved.

  • Properties and bioavailability of particulate and mineral-associated organic matter in Arctic permafrost soils, Lower Kolyma Region, Russia

    Gentsch N, Mikutta R, Shibistova O, Wild B, Schnecker J, Richter A, Urich T, Gittel A, Santruckova H, Barta J, Lashchinskiy N, Mueller CW, Fuß R, Guggenberger G
    2015 - European Journal of Soil Science, 66: 722-734

    Abstract: 

    Permafrost degradation may cause strong feedbacks of arctic ecosystems to global warming, but this will depend on if, and to what extent, organic matter (OM) is protected against biodegradation by mechanisms other than freezing and anoxia. Here, we report on the amount, chemical composition and bioavailability of particulate (POM) and mineral-associated OM (MOM) in permafrost soils of the East Siberian Arctic. The average total organic carbon (OC) stock across all soils was 24.0 +/- 6.7 kg m(-2) within 100 cm soil depth. Density fractionation (density cut-off 1.6 g cm(-3)) revealed that 54 +/- 16% of the total soil OC and 64 +/- 18% of OC in subsoil horizons was bound to minerals. As well as sorption of OM to clay-sized minerals (R-2 = 0.80; P < 0.01), co-precipitation of OM with hydrolyzable metals may also transfer carbon into the mineral-bound fraction. Carbon:nitrogen ratios, stable carbon and nitrogen isotopes, C-13-NMR and X-ray photoelectron spectroscopy showed that OM is transformed in permafrost soils, which is a prerequisite for the formation of mineral-organic associations. Mineral-associated OM in deeper soil was enriched in C-13 and N-15, and had narrow C:N and large alkyl C:(O-/N-alkyl C) ratios, indicating an advanced stage of decomposition. Despite being up to several thousands of years old, when incubated under favourable conditions (60% water-holding capacity, 15 degrees C, adequate nutrients, 90 days), only 1.5-5% of the mineral-associated OC was released as CO2. In the topsoils, POM had the largest mineralization but was even less bioavailable than the MOM in subsoil horizons. Our results suggest that the formation of mineral-organic associations acts as an important additional factor in the stabilization of OM in permafrost soils. Although the majority of MOM was not prone to decomposition under favourable conditions, mineral-organic associations host a readily accessible carbon fraction, which may actively participate in ecosystem carbon exchange.

  • Non-structural carbohydrates in woody plants compared among laboratories

    Quentin AG, Pinkard EA, Ryan MG, Tissue DT, Baggett LS, Adams HD, Maillard P, Marchand J, Landhäusser SM, Lacointe A, Gibon Y, Anderegg WR, Asao S, Atkin OK, Bonhomme M, Claye C, Chow PS, Clément-Vidal A, Davies ND, Dickman LT, Dumbur R, Ellsworth DS, Falk K, Galiano L, Grünzweig JM, Hartmann H, Hoch G, Jones JE, Koike T, Kuhlmann I, Lloret F, Maestro M, Mansfield SD, Martínez-Vilalta J, Maucourt M, McDowell NG, Moing A, Muller B, Nebauer SG, Niinemets U, Palacio S, Piper F, Raveh E, Richter A, Rolland G, Rosas T, Saint Joanis B, Sala A, Smith RA, Sterck F, Stinziano JR, Tobias M, Unda F, Watanabe M, Way DA, Weerasinghe LK, Wild B, Wiley E, Woodruff DR
    2015 - Tree Physiology, 35: 1146-1165

    Abstract: 

    Non-structural carbohydrates (NSC) in plant tissue are frequently quantified to make inferences about plant responses to environmental conditions. Laboratories publishing estimates of NSC of woody plants use many different methods to evaluate NSC. We asked whether NSC estimates in the recent literature could be quantitatively compared among studies. We also asked whether any differences among laboratories were related to the extraction and quantification methods used to determine starch and sugar concentrations. These questions were addressed by sending sub-samples collected from five woody plant tissues, which varied in NSC content and chemical composition, to 29 laboratories. Each laboratory analyzed the samples with their laboratory-specific protocols, based on recent publications, to determine concentrations of soluble sugars, starch and their sum, total NSC. Laboratory estimates differed substantially for all samples. For example, estimates for Eucalyptus globulus leaves (EGL) varied from 23 to 116 (mean = 56) mg g(-1) for soluble sugars, 6-533 (mean = 94) mg g(-1) for starch and 53-649 (mean = 153) mg g(-1) for total NSC. Mixed model analysis of variance showed that much of the variability among laboratories was unrelated to the categories we used for extraction and quantification methods (method category R(2) = 0.05-0.12 for soluble sugars, 0.10-0.33 for starch and 0.01-0.09 for total NSC). For EGL, the difference between the highest and lowest least squares means for categories in the mixed model analysis was 33 mg g(-1) for total NSC, compared with the range of laboratory estimates of 596 mg g(-1). Laboratories were reasonably consistent in their ranks of estimates among tissues for starch (r = 0.41-0.91), but less so for total NSC (r = 0.45-0.84) and soluble sugars (r = 0.11-0.83). Our results show that NSC estimates for woody plant tissues cannot be compared among laboratories. The relative changes in NSC between treatments measured within a laboratory may be comparable within and between laboratories, especially for starch. To obtain comparable NSC estimates, we suggest that users can either adopt the reference method given in this publication, or report estimates for a portion of samples using the reference method, and report estimates for a standard reference material. Researchers interested in NSC estimates should work to identify and adopt standard methods. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  • Microbial community composition shapes enzyme patterns in topsoil and subsoil horizons along a latitudinal transect in Western Siberia

    Schnecker J, Wild B, Takriti M, Eloy Alves RJ, Gentsch N, Gittel A, Hofer A, Klaus K, Knoltsch A, Lashchinskiy N, Mikutta R, Richter A
    2015 - Soil Biology and Biochemistry, 83: 106-115

    Abstract: 

    Soil horizons below 30 cm depth contain about 60% of the organic carbon stored in soils. Although insight into the physical and chemical stabilization of soil organic matter (SOM) and into microbial community composition in these horizons is being gained, information on microbial functions of subsoil microbial communities and on associated microbially-mediated processes remains sparse. To identify possible controls on enzyme patterns, we correlated enzyme patterns with biotic and abiotic soil parameters, as well as with microbial community composition, estimated using phospholipid fatty acid profiles. Enzyme patterns (i.e. distance-matrixes calculated from these enzyme activities) were calculated from the activities of six extracellular enzymes (cellobiohydrolase, leucine-amino-peptidase, N-acetylglucosaminidase, chitotriosidase, phosphatase and phenoloxidase), which had been measured in soil samples from organic topsoil horizons, mineral topsoil horizons, and mineral subsoil horizons from seven ecosystems along a 1500 km latitudinal transect in Western Siberia. We found that hydrolytic enzyme activities decreased rapidly with depth, whereas oxidative enzyme activities in mineral horizons were as high as, or higher than in organic topsoil horizons. Enzyme patterns varied more strongly between ecosystems in mineral subsoil horizons than in organic topsoils. The enzyme patterns in topsoil horizons were correlated with SOM content (i.e., C and N content) and microbial community composition. In contrast, the enzyme patterns in mineral subsoil horizons were related to water content, soil pH and microbial community composition. The lack of correlation between enzyme patterns and SOM quantity in the mineral subsoils suggests that SOM chemistry, spatial separation or physical stabilization of SOM rather than SOM content might determine substrate availability for enzymatic breakdown. The correlation of microbial community composition and enzyme patterns in all horizons, suggests that microbial community composition shapes enzyme patterns and might act as a modifier for the usual dependency of decomposition rates on SOM content or C/N ratios.

  • Metatranscriptomic census of active protists in soils

    Geisen S, Tveit AT, Clark IM, Richter A, Svenning MM, Bonkowski M, Urich T
    2015 - The ISME Journal, 9: 2178-2190

    Abstract: 

    The high numbers and diversity of protists in soil systems have long been presumed, but their true diversity and community composition have remained largely concealed. Traditional cultivation-based methods miss a majority of taxa, whereas molecular barcoding approaches employing PCR introduce significant biases in reported community composition of soil protists. Here, we applied a metatranscriptomic approach to assess the protist community in 12 mineral and organic soil samples from different vegetation types and climatic zones using small subunit ribosomal RNA transcripts as marker. We detected a broad diversity of soil protists spanning across all known eukaryotic supergroups and revealed a strikingly different community composition than shown before. Protist communities differed strongly between sites, with Rhizaria and Amoebozoa dominating in forest and grassland soils, while Alveolata were most abundant in peat soils. The Amoebozoa were comprised of Tubulinea, followed with decreasing abundance by Discosea, Variosea and Mycetozoa. Transcripts of Oomycetes, Apicomplexa and Ichthyosporea suggest soil as reservoir of parasitic protist taxa. Further, Foraminifera and Choanoflagellida were ubiquitously detected, showing that these typically marine and freshwater protists are autochthonous members of the soil microbiota. To the best of our knowledge, this metatranscriptomic study provides the most comprehensive picture of active protist communities in soils to date, which is essential to target the ecological roles of protists in the complex soil system.

  • Convergence of soil nitrogen isotopes across global climate gradients

    Craine JM, Elmore AJ, Wang L, Augusto L, Baisden WT, Brookshire EN, Cramer MD, Hasselquist NJ, Hobbie EA, Kahmen A; Koba K, Kranabetter JM, Mack MC, Marin-Spiotta E, Mayor JR, McLauchlan KK, Michelsen A, Nardoto GB, Oliveira RS, Perakis SS, Peri PL, Quesada CA, Richter A, Schipper LA, Stevenson BA, Turner BL, Viani RA, Wanek W, Zeller B
    2015 - Scientific Reports, 5: 8

    Abstract: 

    Quantifying global patterns of terrestrial nitrogen (N) cycling is central to predicting future patterns of primary productivity, carbon sequestration, nutrient fluxes to aquatic systems, and climate forcing. With limited direct measures of soil N cycling at the global scale, syntheses of the (15)N:(14)N ratio of soil organic matter across climate gradients provide key insights into understanding global patterns of N cycling. In synthesizing data from over 6000 soil samples, we show strong global relationships among soil N isotopes, mean annual temperature (MAT), mean annual precipitation (MAP), and the concentrations of organic carbon and clay in soil. In both hot ecosystems and dry ecosystems, soil organic matter was more enriched in (15)N than in corresponding cold ecosystems or wet ecosystems. Below a MAT of 9.8°C, soil δ(15)N was invariant with MAT. At the global scale, soil organic C concentrations also declined with increasing MAT and decreasing MAP. After standardizing for variation among mineral soils in soil C and clay concentrations, soil δ(15)N showed no consistent trends across global climate and latitudinal gradients. Our analyses could place new constraints on interpretations of patterns of ecosystem N cycling and global budgets of gaseous N loss.

  • A pan-Arctic synthesis of CH4 and CO2 production from anoxic soil incubations

    Treat C, Natali S, Ernakovich J, Iversen CM, Lupascu M, McGuire AD, Norby RJ, Roy Chowdhury T, Richter A, Santruckova H, Schädel C, Schuur EA, Sloan VL, Turetsky MR, Waldrop MP
    2015 - Global Change Biology, 21: 2787-2803

    Abstract: 

    Permafrost thaw can alter the soil environment through changes in soil moisture, frequently resulting in soil saturation, a shift to anaerobic decomposition, and changes in the plant community. These changes, along with thawing of previously frozen organic material, can alter the form and magnitude of greenhouse gas production from permafrost ecosystems. We synthesized existing methane (CH4 ) and carbon dioxide (CO2 ) production measurements from anaerobic incubations of boreal and tundra soils from the geographic permafrost region to evaluate large-scale controls of anaerobic CO2 and CH4 production and compare the relative importance of landscape-level factors (e.g., vegetation type and landscape position), soil properties (e.g., pH, depth, and soil type), and soil environmental conditions (e.g., temperature and relative water table position). We found fivefold higher maximum CH4 production per gram soil carbon from organic soils than mineral soils. Maximum CH4 production from soils in the active layer (ground that thaws and refreezes annually) was nearly four times that of permafrost per gram soil carbon, and CH4 production per gram soil carbon was two times greater from sites without permafrost than sites with permafrost. Maximum CH4 and median anaerobic CO2 production decreased with depth, while CO2 :CH4 production increased with depth. Maximum CH4 production was highest in soils with herbaceous vegetation and soils that were either consistently or periodically inundated. This synthesis identifies the need to consider biome, landscape position, and vascular/moss vegetation types when modeling CH4 production in permafrost ecosystems and suggests the need for longer-term anaerobic incubations to fully capture CH4 dynamics. Our results demonstrate that as climate warms in arctic and boreal regions, rates of anaerobic CO2 and CH4 production will increase, not only as a result of increased temperature, but also from shifts in vegetation and increased ground saturation that will accompany permafrost thaw. © 2015 John Wiley & Sons Ltd.

  • Summer drought alters carbon allocation to roots and root respiration in mountain grassland

    Hasibeder R, Fuchslueger L, Richter A, Bahn M
    2015 - New Phytologist, 3: 1117-1127

    Abstract: 

    Drought affects the carbon (C) source and sink activities of plant organs, with potential consequences for belowground C allocation, a key process of the terrestrial C cycle. The responses of belowground C allocation dynamics to drought are so far poorly understood. We combined experimental rain exclusion with (13)C pulse labelling in a mountain meadow to analyse the effects of summer drought on the dynamics of belowground allocation of recently assimilated C and how it is partitioned among different carbohydrate pools and root respiration. Severe soil moisture deficit decreased the ecosystem C uptake and the amounts and velocity of C allocated from shoots to roots. However, the proportion of recently assimilated C translocated belowground remained unaffected by drought. Reduced root respiration, reflecting reduced C demand under drought, was increasingly sustained by C reserves, whilst recent assimilates were preferentially allocated to root storage and an enlarged pool of osmotically active compounds. Our results indicate that under drought conditions the usage of recent photosynthates is shifted from metabolic activity to osmotic adjustment and storage compounds. © 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.

  • Effects of drought on nitrogen turnover and abundances of ammonia-oxidizers in mountain grassland

    Fuchslueger L, Kastl EM, Bauer F, Kienzl S, Hasibeder R, Ladreiter-Knauss T, Schmitt M, Bahn M, Schloter M, Richter A, Szukics UFM
    2014 - Biogeosciences, 11: 6003-6015

    Abstract: 

    Future climate scenarios suggest an increased frequency of summer drought periods in the European Alpine Region. Drought can affect soil nitrogen (N) cycling, by altering N transformation rates, as well as the abundances of ammonia-oxidizing bacteria and archaea. However, the extent to which drought affects N cycling under in situ conditions is still controversial. The goal of this study was to analyse effects of drought on soil N turnover and ammonia-oxidizer abundances in soil without drought history. To this end we conducted rain-exclusion experiments at two differently managed mountain grassland sites, an annually mown and occasionally fertilized meadow and an abandoned grassland. Soils were sampled before, during and after drought and were analysed for potential gross rates of N mineralization, microbial uptake of inorganic N, nitrification, and the abundances of bacterial and archaeal ammonia-oxidizers based on gene copy numbers of the amoA gene (AOB and AOA, respectively). Drought induced different responses at the two studied sites. At the managed meadow drought increased NH4+ immobilization rates and NH4+ concentrations in the soil water solution, but led to a reduction of AOA abundance compared to controls. At the abandoned site gross nitrification and NO3- immobilization rates decreased during drought, while AOB and AOA abundances remained stable. Rewetting had only minor, short-term effects on the parameters that had been affected by drought. Seven weeks after the end of drought no differences to control plots could be detected. Thus, our findings demonstrated that in mountain grasslands drought had distinct transient effects on soil nitrogen cycling and ammonia-oxidizers, which could have been related to a niche differentiation of AOB and AOA with increasing NH4+ levels. However, the effect strength of drought was modulated by grassland management.

  • Nutrient limitation of alpine plants: Implications from leaf N : P stoichiometry and leaf delta N-15

    Xu X, Wanek W, Zhou C, Richter A, Song M, Cao G, Ouyang H, Kuzyakov Y
    2014 - Journal of Plant Nutrition and Soil Science, 177: 178-387

    Abstract: 

    Nitrogen (N) deposition can affect grassland ecosystems by altering biomass production, plant species composition and abundance. Therefore, a better understanding of the response of dominant plant species to N input is a prerequisite for accurate prediction of future changes and interactions within plant communities. We evaluated the response of seven dominant plant species on the Tibetan Plateau to N input at two levels: individual species and plant functional group. This was achieved by assessing leaf N : P stoichiometry, leaf delta N-15 and biomass production for the plant functional groups. Seven dominant plant species-three legumes, two forbs, one grass, one sedge-were analyzed for N, P, and delta N-15 2 years after fertilization with one of the three N forms: NO3-, NH4+, or NH4NO3 at four application rates (0, 7.5, 30, and 150 kg N ha(-1) y(-1)). On the basis of biomass production and leaf N : P ratios, we concluded that grasses were limited by available N or co-limited by available P. Unlike for grasses, leaf N : P and biomass production were not suitable indicators of N limitation for legumes and forbs in alpine meadows. The poor performance of legumes under high N fertilization was mainly due to strong competition with grasses. The total above-ground biomass was not increased by N fertilization. However, species composition shifted to more productive grasses. A significant negative correlation between leaf N : P and leaf delta N-15 indicated that the two forbs Gentiana straminea and Saussurea superba switched from N deficiency to P limitation (e. g., N excess) due to N fertilization. These findings imply that alpine meadows will be more dominated by grasses under increased atmospheric N deposition.

  • 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.

  • Growth of nitrite-oxidizing bacteria by aerobic hydrogen oxidation

    Koch H, Galushko A, Albertsen M, Schintlmeister A, Gruber-Dorninger C, Lücker S, Pelletier E, Le Paslier D, Spieck E, Richter A, Nielsen PH, Wagner M, Daims H
    2014 - Science, 345: 1052-1054

    Abstract: 

    The bacterial oxidation of nitrite to nitrate is a key process of the biogeochemical nitrogen cycle. Nitrite-oxidizing bacteria are considered a highly specialized functional group, which depends on the supply of nitrite from other microorganisms and whose distribution strictly correlates with nitrification in the environment and in wastewater treatment plants. On the basis of genomics, physiological experiments, and single-cell analyses, we show that Nitrospira moscoviensis, which represents a widely distributed lineage of nitrite-oxidizing bacteria, has the genetic inventory to utilize hydrogen (H2) as an alternative energy source for aerobic respiration and grows on H2 without nitrite. CO2 fixation occurred with H2 as the sole electron donor. Our results demonstrate a chemolithoautotrophic lifestyle of nitrite-oxidizing bacteria outside the nitrogen cycle, suggesting greater ecological flexibility than previously assumed. Copyright © 2014, American Association for the Advancement of Science.

  • Input of easily available organic C and N stimulates microbial decomposition of soil organic matter in arctic permafrost soil

    Wild B, Schnecker J, Knoltsch A, Takriti M, Mooshammer M, Gentsch N, Mikutta R, Alves ERJ Gittel A, Lashchinskiy N, Richter A
    2014 - Soil Biology and Biochemistry, 75: 143-151

    Abstract: 

    Rising temperatures in the Arctic can affect soil organic matter (SOM) decomposition directly and indirectly, by increasing plant primary production and thus the allocation of plant-derived organic compounds into the soil. Such compounds, for example root exudates or decaying fine roots, are easily available for microorganisms, and can alter the decomposition of older SUM ("priming effect"). We here report on a SUM priming experiment in the active layer of a permafrost soil from the central Siberian Arctic, comparing responses of organic topsoil, mineral subsoil, and cryoturbated subsoil material (i.e., poorly decomposed topsoil material subducted into the subsoil by freeze-thaw processes) to additions of C-13-labeled glucose, cellulose, a mixture of amino acids, and protein (added at levels corresponding to approximately 1% of soil organic carbon). SUM decomposition in the topsoil was barely affected by higher availability of organic compounds, whereas SUM decomposition in both subsoil horizons responded strongly. In the mineral subsoil, SUM decomposition increased by a factor of two to three after any substrate addition (glucose, cellulose, amino acids, protein), suggesting that the microbial decomposer community was limited in energy to break down more complex components of SOM. In the cryoturbated horizon, SUM decomposition increased by a factor of two after addition of amino acids or protein, but was not significantly affected by glucose or cellulose, indicating nitrogen rather than energy limitation. Since the stimulation of SUM decomposition in cryoturbated material was not connected to microbial growth or to a change in microbial community composition, the additional nitrogen was likely invested in the production of extracellular enzymes required for SUM decomposition. Our findings provide a first mechanistic understanding of priming in permafrost soils and suggest that an increase in the availability of organic carbon or nitrogen, e.g., by increased plant productivity, can change the decomposition of SUM stored in deeper layers of permafrost soils, with possible repercussions on the global climate. (C) 2014 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/3.0/).

  • Adjustment of microbial nitrogen use efficiency to carbon:nitrogen imbalances regulates soil nitrogen cycling

    Mooshammer M, Wanek W, Hämmerle I, Fuchslueger L, Hofhansl F, Knoltsch A, Schnecker J, Takriti M, Watzka M, Wild B, Keiblinger KM, Zechmeister-Boltenstern S, Richter A
    2014 - Nature Communications, 5: 3694

    Abstract: 

    Microbial nitrogen use efficiency (NUE) describes the partitioning of organic N taken up between growth and the release of inorganic N to the environment (that is, N mineralization), and is thus central to our understanding of N cycling. Here we report empirical evidence that microbial decomposer communities in soil and plant litter regulate their NUE. We find that microbes retain most immobilized organic N (high NUE), when they are N limited, resulting in low N mineralization. However, when the metabolic control of microbial decomposers switches from N to C limitation, they release an increasing fraction of organic N as ammonium (low NUE). We conclude that the regulation of NUE is an essential strategy of microbial communities to cope with resource imbalances, independent of the regulation of microbial carbon use efficiency, with significant effects on terrestrial N cycling.

  • Effects of soil organic matter properties and microbial community composition on enzyme activities in cryoturbated arctic soils

    Schnecker J, Wild B, Hofhansl F, Alves ERJ, Barta J, Capek P, Fuchslueger L, Gentsch N, Gittel A, Guggenberger G, Hofer A, Kienzl S, Knoltsch A, Lashchinskiy N, Mikutta R, Santruckova H, Shibistova O, Takriti M, Urich T, Weltin G, Richter A
    2014 - PLoS One, 9: e94076

    Abstract: 

    Enzyme-mediated decomposition of soil organic matter (SOM) is controlled, amongst other factors, by organic matter properties and by the microbial decomposer community present. Since microbial community composition and SOM properties are often interrelated and both change with soil depth, the drivers of enzymatic decomposition are hard to dissect. We investigated soils from three regions in the Siberian Arctic, where carbon rich topsoil material has been incorporated into the subsoil (cryoturbation). We took advantage of this subduction to test if SOM properties shape microbial community composition, and to identify controls of both on enzyme activities. We found that microbial community composition (estimated by phospholipid fatty acid analysis), was similar in cryoturbated material and in surrounding subsoil, although carbon and nitrogen contents were similar in cryoturbated material and topsoils. This suggests that the microbial community in cryoturbated material was not well adapted to SOM properties. We also measured three potential enzyme activities (cellobiohydrolase, leucine-amino-peptidase and phenoloxidase) and used structural equation models (SEMs) to identify direct and indirect drivers of the three enzyme activities. The models included microbial community composition, carbon and nitrogen contents, clay content, water content, and pH. Models for regular horizons, excluding cryoturbated material, showed that all enzyme activities were mainly controlled by carbon or nitrogen. Microbial community composition had no effect. In contrast, models for cryoturbated material showed that enzyme activities were also related to microbial community composition. The additional control of microbial community composition could have restrained enzyme activities and furthermore decomposition in general. The functional decoupling of SOM properties and microbial community composition might thus be one of the reasons for low decomposition rates and the persistence of 400 Gt carbon stored in cryoturbated material.

  • 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.

  • Stoichiometric imbalances between terrestrial decomposer communities and their resources: mechanisms and implications of microbial adaptations to their resources

    Mooshammer M, Wanek W, Zechmeister-Boltenstern S, Richter A
    2014 - Frontiers in microbiology, 5: 1-10

    Abstract: 

    Terrestrial microbial decomposer communities thrive on a wide range of organic matter types that rarely ever meet their elemental demands. In this review we synthesize the current state-of-the-art of microbial adaptations to resource stoichiometry, in order to gain a deeper understanding of the interactions between heterotrophic microbial communities and their chemical environment. The stoichiometric imbalance between microbial communities and their organic substrates generally decreases from wood to leaf litter and further to topsoil and subsoil organic matter. Microbial communities can respond to these imbalances in four ways: first, they adapt their biomass composition toward their resource in a non-homeostatic behavior. Such changes are, however, only moderate, and occur mainly because of changes in microbial community structure and less so due to cellular storage of elements in excess. Second, microbial communities can mobilize resources that meet their elemental demand by producing specific extracellular enzymes, which, in turn, is restricted by the C and N requirement for enzyme production itself. Third, microbes can regulate their element use efficiencies (ratio of element invested in growth over total element uptake), such that they release elements in excess depending on their demand (e.g., respiration and N mineralization). Fourth, diazotrophic bacteria and saprotrophic fungi may trigger the input of external N and P to decomposer communities. Theoretical considerations show that adjustments in element use efficiencies may be the most important mechanism by which microbes regulate their biomass stoichiometry. This review summarizes different views on how microbes cope with imbalanced supply of C, N and P, thereby providing a framework for integrating and linking microbial adaptation to resource imbalances to ecosystem scale fluxes across scales and ecosystems.

  • Aerobic nitrous oxide production through N-nitrosating hybrid formation in ammonia-oxidizing archaea

    Stieglmeier M, Mooshammer M, Kitzler B, Wanek W, Zechmeister-Boltenstern S, Richter A, Schleper C
    2014 - ISME Journal, 8: 1135-1146

    Abstract: 

    Soil emissions are largely responsible for the increase of the potent greenhouse gas nitrous oxide (N2O) in the atmosphere and are generally attributed to the activity of nitrifying and denitrifying bacteria. However, the contribution of the recently discovered ammonia-oxidizing archaea (AOA) to N2O production from soil is unclear as is the mechanism by which they produce it. Here we investigate the potential of Nitrososphaera viennensis, the first pure culture of AOA from soil, to produce N2O and compare its activity with that of a marine AOA and an ammonia-oxidizing bacterium (AOB) from soil. N. viennensis produced N2O at a maximum yield of 0.09% N2O per molecule of nitrite under oxic growth conditions. N2O production rates of 4.6±0.6 amol N2O cell(-1) h(-1) and nitrification rates of 2.6±0.5 fmol NO2(-) cell(-1) h(-1) were in the same range as those of the AOB Nitrosospira multiformis and the marine AOA Nitrosopumilus maritimus grown under comparable conditions. In contrast to AOB, however, N2O production of the two archaeal strains did not increase when the oxygen concentration was reduced, suggesting that they are not capable of denitrification. In (15)N-labeling experiments we provide evidence that both ammonium and nitrite contribute equally via hybrid N2O formation to the N2O produced by N. viennensis under all conditions tested. Our results suggest that archaea may contribute to N2O production in terrestrial ecosystems, however, they are not capable of nitrifier-denitrification and thus do not produce increasing amounts of the greenhouse gas when oxygen becomes limiting.

  • Distinct microbial communities associated with buried soils in the Siberian tundra

    Gittel A, Barta J, Kohoutovác I, Mikutta R, Owens S, Gilbert J, Schnecker J, Wild B, Hannisdal B, Maerz J, Lashchinskiyk N, Capek P, Santruckova H, Gentsch N, Shibistova O, Guggenberger G, Richter A, Torsvik V, Schleper C, Urich T
    2014 - ISME Journal, 8: 841-853

    Abstract: 

    Cryoturbation, the burial of topsoil material into deeper soil horizons by repeated freeze-thaw events, is an important storage mechanism for soil organic matter (SOM) in permafrost-affected soils. Besides abiotic conditions, microbial community structure and the accessibility of SOM to the decomposer community are hypothesized to control SOM decomposition and thus have a crucial role in SOM accumulation in buried soils. We surveyed the microbial community structure in cryoturbated soils from nine soil profiles in the northeastern Siberian tundra using high-throughput sequencing and quantification of bacterial, archaeal and fungal marker genes. We found that bacterial abundances in buried topsoils were as high as in unburied topsoils. In contrast, fungal abundances decreased with depth and were significantly lower in buried than in unburied topsoils resulting in remarkably low fungal to bacterial ratios in buried topsoils. Fungal community profiling revealed an associated decrease in presumably ectomycorrhizal (ECM) fungi. The abiotic conditions (low to subzero temperatures, anoxia) and the reduced abundance of fungi likely provide a niche for bacterial, facultative anaerobic decomposers of SOM such as members of the Actinobacteria, which were found in significantly higher relative abundances in buried than in unburied topsoils. Our study expands the knowledge on the microbial community structure in soils of Northern latitude permafrost regions, and attributes the delayed decomposition of SOM in buried soils to specific microbial taxa, and particularly to a decrease in abundance and activity of ECM fungi, and to the extent to which bacterial decomposers are able to act as their functional substitutes.

  • Experimental drought reduces the transfer of recently fixed plant carbon to soil microbes and alters the bacterial community composition in a mountain meadow

    Fuchslueger L, Bahn M, Fritz K, Hasibeder R, Richter A
    2014 - New Phytologist, 201: 916-927

    Abstract: 

    Drought affects plants and soil microorganisms, but it is still not clear how it alters the carbon (C) transfer at the plant-microbial interface. Here, we tested direct and indirect effects of drought on soil microbes and microbial turnover of recent plant-derived C in a mountain meadow. Microbial community composition was assessed using phospholipid fatty acids (PLFAs); the allocation of recent plant-derived C to microbial groups was analysed by pulse-labelling of canopy sections with (13) CO2 and the subsequent tracing of the label into microbial PLFAs. Microbial biomass was significantly higher in plots exposed to a severe experimental drought. In addition, drought induced a shift of the microbial community composition, mainly driven by an increase of Gram-positive bacteria. Drought reduced belowground C allocation, but not the transfer of recently plant-assimilated C to fungi, and in particular reduced tracer uptake by bacteria. This was accompanied by an increase of (13) C in the extractable organic C pool during drought, which was even more pronounced after plots were mown. We conclude that drought weakened the link between plant and bacterial, but not fungal, C turnover, and facilitated the growth of potentially slow-growing, drought-adapted soil microbes, such as Gram-positive bacteria. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

  • NxrB encoding the beta subunit of nitrite oxidoreductase as functional and phylogenetic marker for nitrite-oxidizing Nitrospira

    Pester M, Maixner F, Berry D, Rattei T, Koch H, Lücker S, Nowka B, Richter A, Spieck E, Lebedeva E, Loy A, Wagner M, Daims H
    2014 - Environmental Microbiology, 16: 3055-3071

    Abstract: 

    Nitrospira are the most widespread and diverse known nitrite-oxidizing bacteria and key nitrifiers in natural and engineered ecosystems. Nevertheless, their ecophysiology and environmental distribution are understudied because of the recalcitrance of Nitrospira to cultivation and the lack of a molecular functional marker, which would allow the detection of Nitrospira in the environment. Here we introduce nxrB, the gene encoding subunit beta of nitrite oxidoreductase, as a functional and phylogenetic marker for Nitrospira. Phylogenetic trees based on nxrB of Nitrospira were largely congruent to 16S ribosomal RNA-based phylogenies. By using new nxrB-selective polymerase chain reaction primers, we obtained almost full-length nxrB sequences from Nitrospira cultures, two activated sludge samples, and several geographically and climatically distinct soils. Amplicon pyrosequencing of nxrB fragments from 16 soils revealed a previously unrecognized diversity of terrestrial Nitrospira with 1801 detected species-level operational taxonomic units (OTUs) (using an inferred species threshold of 95% nxrB identity). Richness estimates ranged from 10 to 946 coexisting Nitrospira species per soil. Comparison with an archaeal amoA dataset obtained from the same soils [Environ. Microbiol. 14: 525-539 (2012)] uncovered that ammonia-oxidizing archaea and Nitrospira communities were highly correlated across the soil samples, possibly indicating shared habitat preferences or specific biological interactions among members of these nitrifier groups. © 2013 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

  • Soil warming alters microbial substrate use in alpine soils

    Streit K, Hagedorn F, Hiltbrunner D, Portmann M, Saurer M, Buchmann N, Wild B, Richter A, Wipf S, Siegwolf R
    2014 - Global Change Biology, 20: 1327-1338

    Abstract: 

    Will warming lead to an increased use of older soil organic carbon (SOC) by microbial communities, thereby inducing C losses from C-rich alpine soils? We studied soil microbial community composition, activity, and substrate use after 3 and 4 years of soil warming (+4 °C, 2007-2010) at the alpine treeline in Switzerland. The warming experiment was nested in a free air CO2 enrichment experiment using depleted (13)CO2 (δ(13)C = -30‰, 2001-2009). We traced this depleted (13)C label in phospholipid fatty acids (PLFA) of the organic layer (0-5 cm soil depth) and in C mineralized from root-free soils to distinguish substrate ages used by soil microorganisms: fixed before 2001 ('old'), from 2001 to 2009 ('new') or in 2010 ('recent'). Warming induced a sustained stimulation of soil respiration (+38%) without decline in mineralizable SOC. PLFA concentrations did not reveal changes in microbial community composition due to soil warming, but soil microbial metabolic activity was stimulated (+66%). Warming decreased the amount of new and recent C in the fungal biomarker 18:2ω6,9 and the amount of new C mineralized from root-free soils, implying a shift in microbial substrate use toward a greater use of old SOC. This shift in substrate use could indicate an imbalance between C inputs and outputs, which could eventually decrease SOC storage in this alpine ecosystem. © 2013 John Wiley & Sons Ltd.

  • 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.

  • Microbial N immobilization is of great importance in acidified mountain spruce forest soils

    Tahovska K, Kana J, Barta J, Oulehle F, Richter A, Santruckova H
    2013 - Soil Biology and Biochemistry, 59: 58-71

    Abstract: 

    he prevailing N saturation paradigm still considers microbial N immobilization as a less important process of ecosystem N retention. On the contrary, we hypothesize that it can even be a primary process affecting N leaching from N saturated soils. We studied N transformations in soils of acidified near-natural and primeval forests in the Bohemian Forest (watersheds of Plegne and Certovo Lakes, Czech Republic) and Pop Ivan Massif (Ukraine). Organic soils were sampled from similar conditions (1100-1500 m a.s.I., precipitation 1400-1800 mm, acidic bedrock, forest dominated by Picea abies) and had similar chemical properties (pH(KCI) 2.5-3.2, BS similar to 45%, Al-ex similar to 40 meq kg(-1)). However, the Ukrainian soil had lower soil C/N ratio (24 vs. 30) and C availability (water soluble C and C/N ratio of 65 vs. similar to 114-163 mu mol g(-1) and 6 vs. 21-24, respectively) than the other soils. We ran laboratory experiments in which mixtures of different N sources (N-NH4, N-NO3 and glycine) were added to the soil with only one source N-15-labelled. We followed N-15 partitioning within soil N pools and analysed the composition of the microbial community (16SrDNA-DGGE fingerprint of bacteria, ergosterol analyses, qPCR of fungal 18S rDNA gene). The microbial N pool was always three to five times higher than the total soluble N pool. We found rapid (15 min) and simultaneous immobilization of all added N forms into the microbial biomass with clear preferences for organic N over inorganic sources. The total N flux to the microbial pool always exceeded N flux into mineral N pools. The pattern of N transformation in the C limited soil was different from the other soils. The microbial pool and N flux into it were smaller compared to the mineral N pools and fluxes. The contribution of N-NO3 to microbial immobilization was negligible, while nitrification was almost equal to N mineralization. Total N flux through soluble N pools was greater than total N flux to insoluble pools (residual and microbial N); this was accompanied by lower microbial N uptake efficiency and shorter residence time of N in microbial pool than in soils with higher C availability. The composition of bacterial community was related to DOC content and C and N in microbial biomass. In soils with higher fungal abundance, more glycine was immobilized regardless of soil C availability, but with higher deamination (similar to 50 vs. 20%) and subsequent release of N-NH4 back to the soil. Our study emphasized the role of microbial N immobilization in preventing N-NO3 loss from N saturated ecosystems as a function of C availability. Nitrification was favoured when enough N-NH4 was available in the C limited soil. The discharged N-NO3 was not immobilized by the microbes and could be, if not immobilized by plants, leached out. C limitation plays an important role in the susceptibility of ecosystems to N leaching and could partially explain the observed differences in some Nsaturated ecosystems. (C) 2013 Elsevier Ltd. All rights reserved.

  • Linking microbial community structure and allocation of plant-derived carbon in an organic agricultural soil using (CO2)-C-13 pulse-chase labelling combined with C-13-PLFA profiling

    Tavi NM, Martikainen PJ, Lokko K, Kontro M, Wild B, Richter A, Biasi C
    2013 - Soil Biology and Biochemistry, 58: 207-2015

    Abstract: 

    We conducted a (CO2)-C-13 pulse-chase labelling experiment in a drained boreal organic (peat) soil cultivated with perennial crop, reed canary grass (RCG; Phalaris arundinacea) to study the flow of carbon from plants to soil microbes. Both limed and unlimed soils were studied, since liming is a common agricultural practice for acidic organic soils. Soil samples taken within three months after the labelling and three times in the following year were used for the delta C-13 analysis of microbial phospholipid fatty acids (PLFAs), root sugars and root lipids. We estimated the contribution of carbon from root exudates to microbial PLFA synthesis. The flow of carbon from plants to microbes was fast as the label allocation in PLFAs had a peak 1-3 days after labelling. The results showed that fungi were important in the incorporation of fresh, plant-derived carbon, including root sugars. None of the main microbial PLFA biomarker groups (fungi, Gram-positive bacteria, Gram-negative bacteria, arbuscular mycorrhizal fungi) was completely lacking label over the measurement period. One year after the labelling, when the labelled carbon was widely distributed into plant biomass and soil, bacterial biomarkers increased their share of the label allocation. Liming had a minor effect on the label allocation rate into PLFAs. The mixing model approach used to calculate the root exudate contribution to microbial biomass resulted in a highly conservative estimate of utilization of this important C-source (0-6.5%, with highest incorporation into fungi). In summary, the results of this study provide new information about the role of various microbial groups in the turnover of plant-derived, fresh carbon in boreal organic soil. (C) 2012 Elsevier 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.

  • Metabolic features of Protochlamydia amoebophila elementary bodies--a link between activity and infectivity in Chlamydiae

    Sixt BS, Siegl A, Mueller C, Watzka M, Wultsch A, Tziotis D, Montanaro J, Richter A, Schmitt-Kopplin P, Horn M
    2013 - PLoS Pathogens, 9: in press

    Abstract: 

    The Chlamydiae are a highly successful group of obligate intracellular bacteria, whose members are remarkably diverse, ranging from major pathogens of humans and animals to symbionts of ubiquitous protozoa. While their infective developmental stage, the elementary body (EB), has long been accepted to be completely metabolically inert, it has recently been shown to sustain some activities, including uptake of amino acids and protein biosynthesis. In the current study, we performed an in-depth characterization of the metabolic capabilities of EBs of the amoeba symbiont Protochlamydia amoebophila. A combined metabolomics approach, including fluorescence microscopy-based assays, isotope-ratio mass spectrometry (IRMS), ion cyclotron resonance Fourier transform mass spectrometry (ICR/FT-MS), and ultra-performance liquid chromatography mass spectrometry (UPLC-MS) was conducted, with a particular focus on the central carbon metabolism. In addition, the effect of nutrient deprivation on chlamydial infectivity was analyzed. Our investigations revealed that host-free P. amoebophila EBs maintain respiratory activity and metabolize D-glucose, including substrate uptake as well as host-free synthesis of labeled metabolites and release of labeled CO2 from 13C-labeled D-glucose. The pentose phosphate pathway was identified as major route of D-glucose catabolism and host-independent activity of the tricarboxylic acid (TCA) cycle was observed. Our data strongly suggest anabolic reactions in P. amoebophila EBs and demonstrate that under the applied conditions D-glucose availability is essential to sustain metabolic activity. Replacement of this substrate by L-glucose, a non-metabolizable sugar, led to a rapid decline in the number of infectious particles. Likewise, infectivity of Chlamydia trachomatis, a major human pathogen, also declined more rapidly in the absence of nutrients. Collectively, these findings demonstrate that D-glucose is utilized by P. amoebophila EBs and provide evidence that metabolic activity in the extracellular stage of chlamydiae is of major biological relevance as it is a critical factor affecting maintenance of infectivity.

  • 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.

  • Carbon use efficiency of microbial communities: stoichiometry, methodology and modelling

    Sinsabaugh RL, Manzoni S, Moorhead DL, Richter A
    2013 - Ecology Letters, 16: 930-939

    Abstract: 

    Carbon use efficiency (CUE) is a fundamental parameter for ecological models based on the physiology of microorganisms. CUE determines energy and material flows to higher trophic levels, conversion of plant-produced carbon into microbial products and rates of ecosystem carbon storage. Thermodynamic calculations support a maximum CUE value of ~ 0.60 (CUE max). Kinetic and stoichiometric constraints on microbial growth suggest that CUE in multi-resource limited natural systems should approach ~ 0.3 (CUE max /2). However, the mean CUE values reported for aquatic and terrestrial ecosystems differ by twofold (~ 0.26 vs. ~ 0.55) because the methods used to estimate CUE in aquatic and terrestrial systems generally differ and soil estimates are less likely to capture the full maintenance costs of community metabolism given the difficulty of measurements in water-limited environments. Moreover, many simulation models lack adequate representation of energy spilling pathways and stoichiometric constraints on metabolism, which can also lead to overestimates of CUE. We recommend that broad-scale models use a CUE value of 0.30, unless there is evidence for lower values as a result of pervasive nutrient limitations. Ecosystem models operating at finer scales should consider resource composition, stoichiometric constraints and biomass composition, as well as environmental drivers, to predict the CUE of microbial communities. © 2013 John Wiley & Sons Ltd/CNRS.

  • Host-compound foraging by intestinal microbiota revealed by single-cell stable isotope probing

    Berry D, Stecher B, Schintlmeister A, Reichert J, Brugiroux S, Wild B, Wanek W, Richter A, Rauch I, Decker T, Loy A, Wagner M
    2013 - Proceedings of the National Academy of Sciences of the United States of America (PNAS), 110: 4720-4725

    Abstract: 

    The animal and human intestinal mucosa secretes an assortment of compounds to establish a physical barrier between the host tissue and intestinal contents, a separation that is vital for health. Some pathogenic microorganisms as well as members of the commensal intestinal microbiota have been shown to be able to break down these secreted compounds. Our understanding of host-compound degradation by the commensal microbiota has been limited to knowledge about simplified model systems because of the difficulty in studying the complex intestinal ecosystem in vivo. In this study, we introduce an approach that overcomes previous technical limitations and allows us to observe which microbial cells in the intestine use host-derived compounds. We added stable isotope-labeled threonine i.v. to mice and combined fluorescence in situ hybridization with high-resolution secondary ion mass spectrometry imaging to characterize utilization of host proteins by individual bacterial cells. We show that two bacterial species, Bacteroides acidifaciens and Akkermansia muciniphila, are important host-protein foragers in vivo. Using gnotobiotic mice we show that microbiota composition determines the magnitude and pattern of foraging by these organisms, demonstrating that a complex microbiota is necessary in order for this niche to be fully exploited. These results underscore the importance of in vivo studies of intestinal microbiota, and the approach presented in this study will be a powerful tool to address many other key questions in animal and human microbiome research.

  • Nitrification rates in Arctic soils are associated with functionally distinct populations of ammonia-­‐oxidizing archaea

    Alves, RJE, Wanek W, Zappe A, Richter A, Svenning MM, Schleper C, Urich T
    2013 - The ISME Journal: multidisciplinary journal of microbial ecology, 7: 1620-1631

    Abstract: 

    The functioning of Arctic soil ecosystems is crucially important for global climate, and basic knowledge regarding their biogeochemical processes is lacking. Nitrogen (N) is the major limiting nutrient in these environments, and its availability is strongly dependent on nitrification. However, microbial communities driving this process remain largely uncharacterized in Arctic soils, namely those catalyzing the rate-limiting step of ammonia (NH3) oxidation. Eleven Arctic soils were analyzed through a polyphasic approach, integrating determination of gross nitrification rates, qualitative and quantitative marker gene analyses of ammonia-oxidizing archaea (AOA) and bacteria (AOB) and enrichment of AOA in laboratory cultures. AOA were the only NH3 oxidizers detected in five out of 11 soils and outnumbered AOB in four of the remaining six soils. The AOA identified showed great phylogenetic diversity and a multifactorial association with the soil properties, reflecting an overall distribution associated with tundra type and with several physico-chemical parameters combined. Remarkably, the different gross nitrification rates between soils were associated with five distinct AOA clades, representing the great majority of known AOA diversity in soils, which suggests differences in their nitrifying potential. This was supported by selective enrichment of two of these clades in cultures with different NH3 oxidation rates. In addition, the enrichments provided the first direct evidence for NH3 oxidation by an AOA from an uncharacterized Thaumarchaeota-AOA lineage. Our results indicate that AOA are functionally heterogeneous and that the selection of distinct AOA populations by the environment can be a determinant for nitrification activity and N availability in soils.

  • Responses of belowground carbon allocation dynamics to extended shading in mountain grassland

    Bahn M, Lattanzi FA, Hasibeder R, Wild B, Koranda M, Danese V, Brüggemann N, Schmitt M, Siegwolf R, Richter A
    2013 - New Phytologist, 198: 116-126

    Abstract: 

    Carbon (C) allocation strongly influences plant and soil processes. Short-term C allocation dynamics in ecosystems and their responses to environmental changes are still poorly understood. Using in situ (13) CO(2) pulse labeling, we studied the effects of 1 wk of shading on the transfer of recent photoassimilates between sugars and starch of above- and belowground plant organs and to soil microbial communities of a mountain meadow. C allocation to roots and microbial communities was rapid. Shading strongly reduced sucrose and starch concentrations in shoots, but not roots, and affected tracer dynamics in sucrose and starch of shoots, but not roots: recent C was slowly incorporated into root starch irrespective of the shading treatment. Shading reduced leaf respiration more strongly than root respiration. It caused no reduction in the amount of (13) C incorporated into fungi and Gram-negative bacteria, but increased its residence time. These findings suggest that, under interrupted C supply, belowground C allocation (as reflected by the amount of tracer allocated to root starch, soil microbial communities and belowground respiration) was maintained at the expense of aboveground C status, and that C source strength may affect the turnover of recent plant-derived C in soil microbial communities. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

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