Publications in peer reviewed journals

31 Publications found
  • Editorial: Rhizosphere Functioning and Structural Development as Complex Interplay Between Plants, Microorganisms and Soil Minerals

    Mueller CW, Carminati A, Kaiser C, Subke JA, Gutjahr C
    2019 - Frontiers in Environmental Science, 7: Article 130
  • Growth explains microbial carbon use efficiency across soils differing in land use and geology

    Zheng Q, Hu Y, zhang S, Noll L, Boeckle T, Richter A, Wanek W
    2019 - Soil Biology and Biochemistry, 128: 45-55


    The ratio of carbon (C) that is invested into microbial growth to organic C taken up is known as microbial carbon use efficiency (CUE), which is influenced by environmental factors such as soil temperature and soil moisture. How microbes will physiologically react to short-term environmental changes is not well understood, primarily due to methodological restrictions. Here we report on two independent laboratory experiments to explore short-term temperature and soil moisture effects on soil microbial physiology(i.e. respiration, growth, CUE, and microbial biomass turnover): (i) a temperature experiment with 1-day pre-incubation at 5, 15 and 25 °C at 60% water holding capacity (WHC), and (ii) a soil moisture/oxygen (O2) experiment with 7-day pre-incubation at 20 °C at 30%, 60% WHC (both at 21% O2) and 90% WHC at 1% O2. Experiments were conducted with soils from arable, pasture and forest sites derived from both silicate and limestone bedrocks. We found that microbial CUE responded heterogeneously though overall positively to short-term temperature changes, and decreased significantly under high moisture level (90% WHC)/suboxic conditions due to strong decreases in microbial growth. Microbial biomass turnover time decreased dramatically with increasing temperature, and increased significantly at high moisture level (90% WHC)/suboxic conditions. Our findings reveal that the responses of microbial CUE and microbial biomass turnover to short-term temperature and moisture/O2 changes depended mainly on microbial growth responses and less on respiration responses to the environmental cues, which were consistent across soils differing in land use and geology.

  • A novel isotope pool dilution approach to quantify gross rates of key abiotic and biological processes in the soil phosphorus cycle

    Wanek W, Zezula D, Wasner D, Mooshammer M, Prommer J
    2019 - Biogeosciences, 16: 3047-3068


    Efforts to understand and model the current and future behavior of the global phosphorus (P) cycle are limited by the availability of global data on rates of soil P processes, as well as their environmental controls. Here, we present a novel isotope pool dilution approach using 33Plabeling of live and sterile soils, which allows for high-quality data on gross fluxes of soil inorganic P (Pi) sorption and desorption, as well as of gross fluxes of organic P mineralization and microbial Pi uptake to be obtained. At the same time, net immobilization of 33Pi by soil microbes and abiotic sorption can be easily derived and partitioned. Compared with other approaches, we used short incubation times (up to 48 h), avoiding tracer remineralization, which was confirmed by the separation of organic P and Pi using isobutanol fractionation. This approach is also suitable for strongly weathered and P-impoverished soils, as the sensitivity is increased by the extraction of exchangeable bioavailable Pi(Olsen Pi; 0.5 M NaHCO3) followed by Pi measurement using the malachite green assay. Biotic processes were corrected for desorption/sorption processes using adequate sterile abiotic controls that exhibited negligible microbial and extracellular phosphatase activities. Gross rates were calculated using analytical solutions of tracer kinetics, which also allowed for the study of gross soil P dynamics under non-steady-state conditions. Finally, we present major environmental controls of gross P-cycle processes that were measured for three P-poor tropical forest and three P-rich temperate grassland soils.

  • Environmental effects on soil microbial nitrogen use efficiency are controlled by allocation of organic nitrogen to microbial growth and regulate gross N mineralization

    zhang S, Zheng Q, Noll L, Hu Y, Wanek W
    2019 - Soil Biology and Biochemistry, 135: 304-315


    Microbial nitrogen use efficiency (NUE) is the efficiency by which microbes allocate organic N acquired to biomass formation relative to the N in excess of microbial demand released through N mineralization. Microbial NUE thus is critical to estimate the capacity of soil microbes to retain N in soils and thereby affects inorganic N availability to plants and ecosystem N losses. However, how soil temperature and soil moisture/O2 affect microbial NUE to date is not clear. Therefore, two independent incubation experiments were conducted with soils from three land uses (cropland, grassland and forest) on two bedrocks (silicate and limestone). Soils were exposed to 5, 15 and 25 °C overnight at 60% water holding capacity (WHC) or acclimated to 30 and 60% WHC at 21% O2 and to 90% WHC at 1% O2 over one week at 20 °C. Microbial NUE was measured as microbial growth over microbial organic N uptake (the sum of growth N demand and gross N mineralization). Microbial NUE responded positively to temperature increases with Q10 values ranging from 1.30 ± 0.11 to 2.48 ± 0.67. This was due to exponentially increasing microbial growth rates with incubation temperature while gross N mineralization rates were relatively insensitive to temperature increases (Q10 values 0.66 ± 0.30 to 1.63 ± 0.15). Under oxic conditions (21% O2), microbial NUE as well as gross N mineralization were not stimulated by the increase in soil moisture from 30 to 60% WHC. Under suboxic conditions (90% WHC and 1% O2), microbial NUE markedly declined as microbial growth rates were strongly negatively affected due to increasing microbial energy limitation. In contrast, gross N mineralization rates increased strongly as organic N uptake became in excess of microbial growth N demand. Therefore, in the moisture/O2 experiment microbial NUE was mainly regulated by the shift in O2 status (to suboxic conditions) and less affected by increasing water availability per se. These temperature and moisture/O2 effects on microbial organic N metabolism were consistent across the soils differing in bedrock and land use. Overall it has been demonstrated that microbial NUE was controlled by microbial growth, and that NUE controlled gross N mineralization as an overflow metabolism when energy (C) became limiting or N in excess in soils. This study thereby greatly contributes to the understanding of short-term environmental responses of microbial community N metabolism and the regulation of microbial organic-inorganic N transformations in soils.

  • Resistant Soil Microbial Communities Show Signs of Increasing Phosphorus Limitation in Two Temperate Forests After Long-Term Nitrogen Addition

    Forstner SJ, Wechselberger V, Stecher S, Müller S, Keiblinger KM, Wanek W, Schleppi P, Gundersen P, Tatzber M, Gerzabek MH, Zechmeister­‐Boltenstern S
    2019 - Frontiers in Forests and Global Change, 2: Article 73


    Forest soils harbor diverse microbial communities responsible for the cycling of elements including carbon (C), nitrogen (N), and phosphorus (P). Conversely, anthropogenic N deposition can negatively feed back on soil microbes and reduce soil organic matter (SOM) decomposition. Mechanistically, this can include reductions of decomposer biomass, especially fungi, and decreases in activities of lignin-modifying enzyme (LMEs). Moreover, N inputs can lower resource C:N and thus decrease the C:N imbalance between microbial decomposers and their resources. As a result, microbially-mediated decomposition might slow down, resulting in larger SOM pools with consequences for ecosystem nutrition and climate regulation. Here, we studied the long-term impact of experimental N addition on soil microbes and microbially-mediated decomposition in two coniferous forests in Switzerland and Denmark. We measured microbial biomass C and N, phospholipid fatty acid (PLFA) biomarkers and potential enzyme activities related to C, N, and P acquisition along the topsoil profile (0–30 cm). In particular, we investigated shifts in microbial C:N homeostasis and relative C:N:P limitation. Contrary to prevailing theory, microbial biomass and community composition were remarkably resistant against two decades of 750 and 1,280 kg ha−1 of cumulative N inputs at the Swiss and Danish site, respectively. While N reduced fungal-specific PLFAs and lowered fungi-to-bacteria (F:B) ratios in some (mainly organic) horizons where soil organic carbon (SOC) has accumulated, it increased F:B ratios in other (mainly mineral) horizons where SOC has declined. We did not find a consistent reduction of LME activities in response to N. Rather, relationships between LME activities and SOC concentrations were largely unaffected by N addition. This questions prevalent theories of lignin decomposition and SOC storage under elevated N inputs. By using C:N stoichiometry, we further show that microbial communities responded in part non-homeostatically to decreasing resource C:N, in addition to a likely increase in their carbon use efficiency and a decrease in nitrogen use efficiency. While the expected increased allocation to C- and decreased allocation to N-acquiring enzymes was not found, microbial investment in P acquisition (acid phosphatase activity) increased in the nutrient-poor Podzol (but not in the nutrient-rich Gleysol). Enzyme vector analysis showed decreasing C but increasing P limitation of soil microbial communities at both sites. We conclude that simulated N deposition led to physiological adaptations of soil microbial communities across the topsoil profile in two independent experiments, with long-term implications for tree nutrition and SOC sequestration. However, we expect that microbial adaptations are not endless and may reach a tipping point when ecosystems experience nitrogen saturation.

  • How to disentangle microbially functional complexity: an insight from the network analysis of C, N, P and S cycling genes

    Zheng BX, Zhao Y, Bi QF, Zhou GW, Wang HJ, Hao XL, Ding K
    2019 - Science Bulletin, 64: 1129-1131


    A complete ecosystem is also a complex network in which mul-tifarious species interact with each other to achieve system-levelfunctions, such as nutrient biogeochemistry[1]. Microbial commu-nity is commonly considered as the primary driving force ofecosystem nutrient mobilization and metabolism, especially car-bon (C), nitrogen (N), phosphorus (P), sulfur (S) and methane cou-pling process[2]. The rise of metagenomics and high-throughputarray (e.g. PhyloChip, GeoChip, etc.) technologies enable acquiringthe detailed information on microbial community functional geneabundance and diversity[3,4]; however, there has been far lessattention focusing on the direct and indirect interactions betweennutrient cycling genes coexisting in environmental samples. Docu-menting these interactions between functional genes acrossdiverse microbial communities may help to clarify the functionalroles and even environmental niches in different contexts[5]. Withthe increasing accumulation of functional gene data from modernhigh-throughput technologies, we are facing the challenge of thoseinteraction explorations, and to extend analyses beyond sole abun-dance and diversity comparisons.

  • Wide-spread limitation of soil organic nitrogen transformations by substrate availability and not by extracellular enzyme content

    Noll L, zhang S, Zheng Q, Hu Y, Wanek W
    2019 - Soil Biology and Biochemistry, 133: 37-49


    Proteins constitute the single largest soil organic nitrogen (SON) reservoir and its decomposition drives terrestrial N availability. Protein cleavage by extracellular enzymes is the rate limiting step in the soil organic N cycle and can be controlled by extracellular enzyme production or protein availability/stabilization in soil. Both controls can be affected by geology and land use, as well as be vulnerable to changes in soil temperature and moisture/O2. To explore major controls of soil gross protein depolymerization we sampled six soils from two soil parent materials (calcareous and silicate), where each soil type included three land uses (cropland, pasture and forest). Soil samples were subjected to three temperature treatments (5, 15, 25 °C at 60% water-holding capacity (WHC) and aerobic conditions) or three soil moisture/O2 treatments (30 and 60% WHC at 21% O2, 90% WHC at 1% O2, at 20 °C) in short-term experiments. Samples were incubated for one day in the temperature experiment and for one week in the moisture/O2experiment. Gross protein depolymerization rates were measured by a novel 15N isotope pool dilution approach. The low temperature sensitivity of gross protein depolymerization, the lack of relationship with protease activity and strong effects of soil texture and pHdemonstrate that this process is constrained by organo-mineral associations and not by soil enzyme content. This also became apparent from the inverse effects in calcareous and silicate soils caused by water saturation/O2 limitation. We highlight that the specific soil mineralogy influenced the response of gross depolymerization rates to water saturation/O2 limitation, causing (I) increasing gross depolymerization rates due to release of adsorbed proteins by reductive dissolution of Fe- and Mn-oxyhydroxides in calcareous soils and (II) decreasing gross depolymerization rates due to mobilization of coagulating and toxic Al3+compounds in silicate soils.

  • Characterization of a thaumarchaeal symbiont that drives incomplete nitrification in the tropical sponge Ianthella basta

    Moeller FU, Webster NS, Herbold CW, Behmann F, Domman D, Albertsen M, Mooshammer M, Market S, Turaev D, Becher D, Rattei T, Schweder T, Richter A, Watzka M, Nielsen PH, Wagner M
    2019 - Environmental Microbiology, 21: 3831-3854


    Marine sponges represent one of the few eukaryotic
    groups that frequently harbour symbiotic members of
    the Thaumarchaeota, which are important chemoautotrophic
    ammonia-oxidizers in many environments.
    However, in most studies, direct demonstration of
    ammonia-oxidation by these archaea within sponges
    is lacking, and little is known about sponge-specific
    adaptations of ammonia-oxidizing archaea (AOA). Here,
    we characterized the thaumarchaeal symbiont of the
    marine sponge Ianthella basta using metaproteogenomics,
    fluorescence in situ hybridization, qPCR
    and isotope-based functional assays. ‘Candidatus
    Nitrosospongia ianthellae’ is only distantly related
    to cultured AOA. It is an abundant symbiont that is
    solely responsible for nitrite formation from ammonia
    in I. basta that surprisingly does not harbour nitriteoxidizing
    microbes. Furthermore, this AOA is equipped
    with an expanded set of extracellular subtilisin-like proteases,
    a metalloprotease unique among archaea, as
    well as a putative branched-chain amino acid ABC
    transporter. This repertoire is strongly indicative of a
    mixotrophic lifestyle and is (with slight variations) also
    found in other sponge-associated, but not in free-living
    AOA. We predict that this feature as well as an expanded
    and unique set of secreted serpins (protease inhibitors),
    a unique array of eukaryotic-like proteins, and a DNAphosporothioation
    system, represent important adaptations
    of AOA to life within these ancient filter-feeding

  • Novel high-throughput approach to determine key processes of soil organic nitrogen cycling: Gross protein depolymerization and microbial amino acid uptake

    Noll L, zhang S, Wanek W
    2019 - Soil Biology and Biochemistry, 130: 73-81


    Proteins comprise the largest soil N reservoir but cannot be taken up directly by microorganisms and plants due to size constraints and stabilization of proteins in organo-mineral associations. Therefore the cleavage of this high molecular weight organic N to smaller soluble compounds as amino acids is a key step in the terrestrial N cycle. In the last years two isotope pool dilution approaches have been successfully established to measure gross rates of protein depolymerization and microbial amino acid uptake in soils. However, both require laborious sample preparation and analyses, which limits sample throughput. Therefore, we here present a novel isotope pool dilution approach based on the addition of 15N-labeled amino acids to soils and subsequent concentration and 15N analysis by the oxidation of α-amino groups to NO2 and further reduction to N2O, followed by purge-and-trap isotope ratio mass spectrometry (PT-IRMS). We applied this method in mesocosm experiments with forest and meadow soils as well as with a cropland soil amended with either organic C (cellulose) or organic N (bovine serum albumin). To measure direct organic N mineralization to NH4+, the latter was captured in acid traps and analyzed by an elemental analyzer coupled to an isotope ratio mass spectrometer (EA-IRMS). Our results demonstrate that the proposed method provides fast and precise measurements of at%15N even at low amino acid concentrations, allows high sample throughput and enables parallel estimations of instantaneous organic N mineralization rates.

  • Substrate quality and concentration control decomposition and microbial strategies in a model soil system

    Schnecker J, Bowles T, Hobbie EA, Smith RG, Grandy AS
    2019 - Biogeochemistry, 144: 47-59


    Soil carbon models typically scale decomposition linearly with soil carbon (C) concentration, but this linear relationship has not been experimentally verified. Here we investigated the underlying biogeochemical mechanisms controlling the relationships between soil C concentration and decomposition rates. We incubated a soil/sand mixture with increasing amounts of finely ground plant residue in the laboratory at constant temperature and moisture for 63 days. The plant residues were rye (Secale cereale, C/N ratio of 23) and wheat straw (Triticum spp., C/N ratio of 109) at seven soil C concentrations ranging from 0.38 to 2.99%. We measured soil respiration, dissolved organic carbon (DOC) concentrations, microbial biomass, and potential enzyme activities over the course of the incubation. Rye, which had higher N and DOC contents, lost 6 to 8 times more C as CO2 compared to wheat residue. Under rye and wheat amendment, absolute C losses as CO2 (calculated per g dry soil) increased linearly with C concentration while relative C losses as CO2 (expressed as percent of initial C) increased with C concentration following a quadratic function. In low C concentration treatments (0.38–0.79% OC), DOC decreased gradually from day 3 to day 63, microbial C increased towards the end in the rye treatment or decreased only slightly with straw amendment, and microbes invested in general enzymes such as proteases and oxidative enzymes. At increasing C levels, enzyme activity shifted to degrading cellulose after 15 days and degrading microbial necromass (e.g. chitin) after 63 days. At the highest C concentrations (2.99% OC), microbial biomass peaked early in the incubation and remained high in the rye treatment and decreased only slightly in the wheat treatment. While wheat lost C as CO2 constantly at all C concentrations, respiration dynamics in the rye treatment strongly depended on C concentration. Our results indicate that litter quality and C concentration regulate enzyme activities, DOC concentrations, and microbial respiration. The potential for non-linear relationships between soil C concentration and decomposition may need to be considered in soil C models and soil C sequestration management approaches.

  • Variation in rhizosphere priming and microbial growth and carbon use efficiency caused by wheat genotypes and temperatures

    Yin L, Corneo PE, Richter A, Wang P, Cheng W, Dijkstra FA
    2019 - Soil Biology and Biochemistry, 134: 54-61


    Living roots can influence microbial decomposition of soil organic matter, which has been referred to as the rhizosphere priming effect (RPE). Both microbial carbon efficiency (CUE) and microbial growth and turnover rates are associated with microbial decomposition and respiration of soil-derived C, but their linkage to the RPE remains poorly understood. Here we used a natural 13C tracer method to determine the RPE in soils planted with two wheat genotypes (249 or IAW2013) grown at high (30/24 °C during day/night) and low temperature (25/17 °C during day/night). We also determined microbial CUE, growth and biomassturnover rate using a substrate-independent H218O labeling method. The RPE varied from −2 to +455%, with significant effects of genotype, sampling date and their interaction with temperature. Compared to the unplanted control, microbial biomass C and growth/turnover rate were both enhanced in planted pots, with an average increase of 17% and 70%, respectively. Microbial CUE was lowest in pots planted with IAW2013 at low temperature, but there were no significant main effects of planting and temperature. Microbial biomass growth/turnover rate together with CUE accounted for 83% of the variation in soil-derived CO2, with a relatively larger contribution of microbial biomass growth/turnover rate (52%) than CUE (31%). Furthermore, using linear regression, we demonstrated that the RPE was significantly positively related to microbial biomass growth/turnover rate. No net soil organic C (SOC) loss or gain was detected, indicating that any increase in SOC due to increased microbial growth/turnover was counteracted by C loss caused by a higher RPE during the relatively short time of planting. These findings suggest that microbial biomass turnover associated with growth could control the loss of SOC with planting. We highlight the importance of plant-induced changes in microbial CUE and biomass growth/turnover for long-term soil C dynamics.

  • Beta diversity and oligarchic dominance in the tropical forests of Southern Costa Rica

    Morera-Beita A, Sánchez D, Wanek W, Hofhansl F, Huber W, Chacón-Madrigal E, Montero-Munoz JL, Silla F
    2019 - Biotropica, 51: 117-128


    Recent studies have reported a consistent pattern of strong dominance of a small subset of tree species in neotropical forests. These species have been called “hyperdominant” at large geographical scales and “oligarchs” at regional‐landscape scales when being abundant and frequent. Forest community assembly is shaped by environmental factors and stochastic processes, but so far the contribution of oligarchic species to the variation of community composition (i.e., beta diversity) remains poorly known. To that end, we established 20.1‐ha plots, that is, five sites with four forest types (ridge, slope and ravine primary forest, and secondary forest) per site, in humid lowland tropical forests of southwestern Costa Rica to (a) investigate how community composition responds to differences in topography, successional stage, and distance among plots for different groups of species (all, oligarch, common and rare/very rare species) and (b) identify oligarch species characterizing changes in community composition among forest types. From a total of 485 species of trees, lianas and palms recorded in this study only 27 species (i.e., 6%) were nominated as oligarch species. Oligarch species accounted for 37% of all recorded individuals and were present in at least half of the plots. Plant community composition significantly differed among forest types, thus contributing to beta diversity at the landscape scale. Oligarch species was the component best explained by geographical and topographic variables, allowing a confident characterization of the beta diversity among tropical lowland forest stands.

  • Life at 0 °C: the biology of the alpine snowbed plant Soldanella pus

    Körner C, Riedl S, Keplinger T, Richter A, Wiesenbauer J, Schweingruber F, Hiltbrunner E
    2019 - Alpine Botany, 129: 63-80


    All plant species reach a low temperature range limit when either low temperature extremes exceed their freezing tolerance
    or when their metabolism becomes too restricted. In this study, we explore the ultimate thermal limit of plant tissue formation
    exemplified by a plant species that seemingly grows through snow. By a combination of studies in alpine snowbeds and
    under controlled environmental conditions, we demonstrate and quantify that the clonal herb Soldanella pusilla (Primulaceae)
    does indeed grow its entire flowering shoot at 0 °C. We show that plants resume growth under 2–3 m of snow in mid-winter,
    following an internal clock, with the remaining period under snow until snow melt (mostly in July) sufficient to produce a
    flowering shoot that is ready for pollination. When snow pack gets thin, the flowering shoot intercepts and re-radiates longwave
    solar radiation, so that snow and ice gently melt around the fragile shoot and the flowers emerge without any mechanical
    interaction. We evidence bud preformation in the previous season and enormous non-structural carbohydrate reserves
    in tissues (mainly below ground) in the form of soluble sugars (largely stachyose) that would support basic metabolism for
    more than 2 entire years under snow. However, cell-wall formation at 0 °C appears to lack unknown strengthening factors,
    including lignification (assessed by confocal Raman spectroscopy imaging) that require between a few hours or a day of
    warmth after snow melt to complete tissue strengthening. Complemented with a suite of anatomical data, the work opens a
    window towards understanding low temperature limits of plant growth in general, with potential relevance for winter crops
    and trees at the natural climatic treeline.

  • Nitrogen and phosphorus constrain the CO2 fertilization of global plant biomass

    Terrer C, Jackson RB, Prentice IC, Keenan TF, Kaiser C, Vicca S, Fisher JB, Reich PB, Stocker BD, Hungate BA, Peñuelas J, McCallum I, Soudzilovskaia NA, Cernusak LA, Talhelm AF, Van Sundert K, Piao S, Newton PCD, Hoveden MJ, Blumenthal DM, Liu YY, Müller C, Winter K, Field CB, Viechtbauer W, Van Lissa CJ, Hoosbeek MR, Watanabe M, Kolke T, Leshyk VO, Polley HW, Franklin O
    2019 - Nature Climate Change, 9: 684-689


    Elevated CO2 (eCO2) experiments provide critical information
    to quantify the effects of rising CO2 on vegetation1–6.
    Many eCO2 experiments suggest that nutrient limitations
    modulate the local magnitude of the eCO2 effect on plant
    biomass1,3,5, but the global extent of these limitations has
    not been empirically quantified, complicating projections of
    the capacity of plants to take up CO2
    7,8. Here, we present a
    data-driven global quantification of the eCO2 effect on biomass
    based on 138 eCO2 experiments. The strength of CO2
    fertilization is primarily driven by nitrogen (N) in ~65% of
    global vegetation and by phosphorus (P) in ~25% of global
    vegetation, with N- or P-limitation modulated by mycorrhizal
    association. Our approach suggests that CO2 levels expected
    by 2100 can potentially enhance plant biomass by 12 ± 3%
    above current values, equivalent to 59 ± 13 PgC. The globalscale
    response to eCO2 we derive from experiments is similar
    to past changes in greenness9 and biomass10 with rising CO2,
    suggesting that CO2 will continue to stimulate plant biomass
    in the future despite the constraining effect of soil nutrients.
    Our research reconciles conflicting evidence on CO2 fertilization
    across scales and provides an empirical estimate of
    the biomass sensitivity to eCO2 that may help to constrain
    climate projections.

  • Combination of techniques to quantify the distribution of bacteria in their soil microhabitats at different spatial scales

    Juyal A, Otten W, Falconer R, Hapca S, Schmidt H, Baveye PC, Eickhorst T
    2019 - Geoderma, 334: 165-174


    To address a number of issues of great societal concern at the moment, like the sequestration of carbon, information is direly needed about interactions between soil architecture and microbial dynamics. Unfortunately, soils are extremely complex, heterogeneous systems comprising highly variable and dynamic micro-habitats that have significant impacts on the growth and activity of inhabiting microbiota. Data remain scarce on the influence of soil physical parameters characterizing the pore space on the distribution and diversity of bacteria. In this context, the objective of the research described in this article was to develop a method where X-ray microtomography, to characterize the soil architecture, is combined with fluorescence microscopy to visualize and quantify bacterial distributions in resin-impregnated soil sections. The influence of pore geometry (at a resolution of 13.4 μm) on the distribution of Pseudomonas fluorescens was analysed at macro- (5.2 mm × 5.2 mm), meso- (1 mm × 1 mm) and microscales (0.2 mm × 0.2 mm) based on an experimental setup simulating different soil architectures. The cell density of P. fluorescenswas 5.59 x 107(SE 2.6 x 106) cells g−1 soil in 1–2 mm and 5.84 x 107(SE 2.4 x 106) cells g−1 in 2–4 mm size aggregates soil. Solid-pore interfaces influenced bacterial distribution at micro- and macroscale, whereas the effect of soil porosity on bacterial distribution varied according to three observation scales in different soil architectures. The influence of soil porosity on the distribution of bacteria in different soil architectures was observed mainly at the macroscale, relative to micro- and mesoscales. Experimental data suggest that the effect of pore geometry on the distribution of bacteria varied with the spatial scale, thus highlighting the need to consider an “appropriate spatial scale” to understand the factors that regulate the distribution of microbial communities in soils. The results obtained to date also indicate that the proposed method is a significant step towards a full mechanistic understanding of microbial dynamics in structured soils.

  • Soil multifunctionality is affected by the soil environment and by microbial community composition and diversity

    Zheng Q, Hu Y, zhang S, Noll L, Böckle T, Dietrich M, Herbold CW, Eichhorst SA, Woebken D, Richter A, Wanek W
    2019 - Soil Biology and Biochemistry, 136: Article 107521


    Microorganisms are critical in mediating carbon (C) and nitrogen (N) cycling processes in soils. Yet, it has long been debated whether the processes underlying biogeochemical cycles are affected by the composition and diversity of the soil microbial community or not. The composition and diversity of soil microbial communities can be influenced by various environmental factors, which in turn are known to impact biogeochemical processes. The objectives of this study were to test effects of multiple edaphic drivers individually and represented as the multivariate soil environment interacting with microbial community composition and diversity, and concomitantly on multiple soil functions (i.e. soil enzyme activities, soil C and N processes). We employed high-throughput sequencing (Illumina MiSeq) to analyze bacterial/archaeal and fungal community composition by targeting the 16S rRNA gene and the ITS1 region of soils collected from three land uses (cropland, grassland and forest) deriving from two bedrock forms (silicate and limestone). Based on this data set we explored single and combined effects of edaphic variables on soil microbial community structure and diversity, as well as on soil enzyme activities and several soil C and N processes. We found that both bacterial/archaeal and fungal communities were shaped by the same edaphic factors, with most single edaphic variables and the combined soil environment representation exerting stronger effects on bacterial/archaeal communities than on fungal communities, as demonstrated by (partial) Mantel tests. We also found similar edaphic controls on the bacterial/archaeal/fungal richness and diversity. Soil C processes were only directly affected by the soil environment but not affected by microbial community composition. In contrast, soil N processes were significantly related to bacterial/archaeal community composition and bacterial/archaeal/fungal richness/diversity but not directly affected by the soil environment. This indicates direct control of the soil environment on soil C processes and indirect control of the soil environment on soil N processes by structuring the microbial communities. The study further highlights the importance of edaphic drivers and microbial communities (i.e. composition and diversity) on important soil C and N processes.

  • Microbial carbon and nitrogen cycling responses to drought and temperature in differently managed mountain grasslands

    Fuchslueger L, Wild B, Mooshammer M, Takriti M, Kienzl S, Knoltsch A, Hofhansl F, Bahn M, Richter A
    2019 - Soil Biology and Biochemistry, 135: 144-153


    Grassland management can modify soil microbial carbon (C) and nitrogen (N) cycling, affecting the resistance to extreme weather events, which are predicted to increase in frequency and magnitude in the near future. However, effects of grassland management on microbial C and N cycling and their responses to extreme weather events, such as droughts and heatwaves, have rarely been tested in a combined approach. We therefore investigated whether grassland management affects microbial C and N cycling responses to drought and temperature manipulation. We collected soils from in situdrought experiments conducted in an extensively managed and an abandoned mountain grassland and incubated them at two temperature levels. We measured microbial respiration and substrate incorporation, as well as gross rates of organic and inorganic N cycling to estimate microbial C and N use efficiencies (CUE and NUE). The managed grassland was characterized by lower microbial biomass, lower fungi to bacteria ratio, and higher microbial CUE, but only slightly different microbial NUE. At both sites drought induced a shift in microbial community composition driven by an increase in Gram-positive bacterial abundance. Drought significantly reduced C substrate respiration and incorporation by microbes at both sites, while microbial CUE remained constant. In contrast, drought increased gross rates of N mineralization at both sites, whereas gross amino acid uptake rates only marginally changed. We observed a significant direct, as well as interactive effect between land management and drought on microbial NUE. Increased temperatures significantly stimulated microbial respiration and reduced microbial CUE independent of drought or land management. Although microbial N processing rates showed no clear response, microbial NUE significantly decreased at higher temperatures. In summary in our study, microbial CUE, in particular respiration, is more responsive to temperature changes. Although N processing rates were stronger responding to drought than to temperature microbial NUE was affected by both drought and temperature increase. We conclude that direct effects of drought and heatwaves can induce different responses in soil microbial C and N cycling similarly in the studied land management systems.

  • Coupled carbon and nitrogen losses in response to seven years of chronic warming in subarctic soils

    Marañon-Jimenez S, Peñuelas J, Richter A, Sigurdsson BD, Fuchslueger L, Leblans NIW, Janssens IA
    2019 - Soil Biology and Biochemistry, 134: 152-161


    Increasing temperatures may alter the stoichiometric demands of soil microbes and impair their capacity to stabilize carbon (C) and retain nitrogen (N), with critical consequences for the soil C and N storage at high latitude soils. Geothermally active areas in Iceland provided wide, continuous and stable gradients of soil temperatures to test this hypothesis. In order to characterize the stoichiometric demands of microbes from these subarctic soils, we incubated soils from ambient temperatures after the factorial addition of C, N and P substrates separately and in combination. In a second experiment, soils that had been exposed to different in situ warming intensities (+0, +0.5, +1.8, +3.4, +8.7, +15.9 °C above ambient) for seven years were incubated after the combined addition of C, N and P to evaluate the capacity of soil microbes to store and immobilize C and N at the different warming scenarios. The seven years of chronic soil warming triggered large and proportional soil C and N losses (4.1 ± 0.5% °C−1 of the stocks in unwarmed soils) from the upper 10 cm of soil, with a predominant depletion of the physically accessible organic substrates that were weakly sorbed in soil minerals up to 8.7 °C warming. Soil microbes met the increasing respiratory demands under conditions of low C accessibility at the expenses of a reduction of the standing biomass in warmer soils. This together with the strict microbial C:N stoichiometric demands also constrained their capacity of N retention, and increased the vulnerability of soil to N losses. Our findings suggest a strong control of microbial physiology and C:N stoichiometric needs on the retention of soil N and on the resilience of soil C stocks from high-latitudes to warming, particularly during periods of vegetation dormancy and low C inputs.

  • A Bioinformatics Guide to Plant Microbiome Analysis

    Lucaciu R, Pelikan C, Gerner SM, Zioutis C, Köstlbacher S, Marx H, Herbold CW, Schmidt H, Rattei T
    2019 - Frontiers in Plant Science, 10: Article 1313


    Recent evidence for intimate relationship of plants with their microbiota shows that plants host individual and diverse microbial communities that are essential for their survival. Understanding their relatedness using genome-based and high-throughput techniques remains a hot topic in microbiome research. Molecular analysis of the plant holobiont necessitates the application of specific sampling and preparatory steps that also consider sources of unwanted information, such as soil, co-amplified plant organelles, human DNA, and other contaminations. Here, we review state-of-the-art and present practical guidelines regarding experimental and computational aspects to be considered in molecular plant–microbiome studies. We discuss sequencing and “omics” techniques with a focus on the requirements needed to adapt these methods to individual research approaches. The choice of primers and sequence databases is of utmost importance for amplicon sequencing, while the assembly and binning of shotgun metagenomic sequences is crucial to obtain quality data. We discuss specific bioinformatic workflows to overcome the limitation of genome database resources and for covering large eukaryotic genomes such as fungi. In transcriptomics, it is necessary to account for the separation of host mRNA or dual-RNAseq data. Metaproteomics approaches provide a snapshot of the protein abundances within a plant tissue which requires the knowledge of complete and well-annotated plant genomes, as well as microbial genomes. Metabolomics offers a powerful tool to detect and quantify small molecules and molecular changes at the plant– bacteria interface if the necessary requirements with regard to (secondary) metabolite databases are considered. We highlight data integration and complementarity which should help to widen our understanding of the interactions among individual players of the plant holobiont in the future.

  • The Forest Observation System, building a global reference dataset for remote sensing of forest biomass

    Schepaschenko D, et al, Wanek W, Zo-Bi IC
    2019 - Scientific Data, 6: Article 198


    Forest biomass is an essential indicator for monitoring the Earth's ecosystems and climate. It is a critical input to greenhouse gas accounting, estimation of carbon losses and forest degradation, assessment of renewable energy potential, and for developing climate change mitigation policies such as REDD+, among others. Wall-to-wall mapping of aboveground biomass (AGB) is now possible with satellite remote sensing (RS). However, RS methods require extant, up-to-date, reliable, representative and comparable in situ data for calibration and validation. Here, we present the Forest Observation System (FOS) initiative, an international cooperation to establish and maintain a global in situ forest biomass database. AGB and canopy height estimates with their associated uncertainties are derived at a 0.25 ha scale from field measurements made in permanent research plots across the world's forests. All plot estimates are geolocated and have a size that allows for direct comparison with many RS measurements. The FOS offers the potential to improve the accuracy of RS-based biomass products while developing new synergies between the RS and ground-based ecosystem research communities.

  • Plant roots increase both decomposition and stable organic matter formation in boreal forest soil

    Adamczyk B, Sietiö OM, Straková P, Prommer J, Wild B, Hagner M, Pihlatie M, Fritze H, Richter A, Heinonsalo J
    2019 - Nature Communications, 10: Article 3982
  • Nutrient scarcity strengthens soil fauna control over leaf litter decomposition in tropical rainforests

    Peguero G, Sardans J, Asensio D, Fernández-Martínez M, Gargallo-Garriga A, Grau O, Llusià J, Margalef O, Márquez L, Ogaya R, Urbina I, Courtois EA, Stah C, Van Langenhove L, Verryckt LT, Richter A, anssens IA, Peñuelas J
    2019 - Proceedings of the Royal Society B: Biological Sciences, 286: Article 20191300


    Soil fauna is a key control of the decomposition rate of leaf litter, yet its
    interactions with litter quality and the soil environment remain elusive. We
    conducted a litter decomposition experiment across different topographic
    levels within the landscape replicated in two rainforest sites providing natural
    gradients in soil fertility to test the hypothesis that low nutrient availability in
    litter and soil increases the strength of fauna control over litter decomposition.
    We crossed these data with a large dataset of 44 variables characterizing
    the biotic and abiotic microenvironment of each sampling point and found
    that microbe-driven carbon (C) and nitrogen (N) losses from leaf litter were
    10.1 and 17.9% lower, respectively, in the nutrient-poorest site, but this
    among-site difference was equalized when meso- and macrofauna had
    access to the litterbags. Further, on average, soil fauna enhanced the rate of
    litter decomposition by 22.6%, and this contribution consistently increased
    as nutrient availability in the microenvironment declined. Our results indicate
    that nutrient scarcity increases the importance of soil fauna on C and N
    cycling in tropical rainforests. Further, soil fauna is able to equalize differences
    in microbial decomposition potential, thus buffering to a remarkable extent
    nutrient shortages at an ecosystem level.

  • Carbon isotopic tracing of sugars throughout whole-trees exposed to climate warming

    Furze M., Drake JE, Wiesenbauer J, Richter A, Pendall E
    2019 - Plant Cell and Environment, 42: 3253-3263


    Trees allocate C from sources to sinks by way of a series of processes involving carbohydrate transport and utilization. Yet these dynamics are not well characterized in trees, and it is unclear how these dynamics will respond to a warmer world. Here, we conducted a warming and pulse‐chase experiment on Eucalyptus parramattensis growing in a whole‐tree chamber system to test whether warming impacts carbon allocation by increasing the speed of carbohydrate dynamics. We pulse‐labelled large (6‐m tall) trees with 13C‐CO2 to follow recently fixed C through different organs by using compound‐specific isotope analysis of sugars. We then compared concentrations and mean residence times of individual sugars between ambient and warmed (+3°C) treatments. Trees dynamically allocated 13C‐labelled sugars throughout the aboveground‐belowground continuum. We did not, however, find a significant treatment effect on C dynamics, as sugar concentrations and mean residence times were not altered by warming. From the canopy to the root system, 13C enrichment of sugars decreased, and mean residence times increased, reflecting dilution and mixing of recent photoassimilates with older reserves along the transport pathway. Our results suggest that a locally endemic eucalypt was seemingly able to adjust its physiology to warming representative of future temperature predictions for Australia.

  • Low yield and abiotic origin of NO formed by the complete nitrifier Nitrospira inopinata

    Kits KD, Jung MY, Vierheilig J, Pjevac P, Sedlacek CJ, Liu S, Herbold C, Stein LY, Richter A, Wissel H, Brüggemann N, Wagner M, Daims H
    2019 - Nature Communications, 10: Article 1836


    Nitrous oxide (NO) and nitric oxide (NO) are atmospheric trace gases that contribute to climate change and affect stratospheric and ground-level ozone concentrations. Ammonia oxidizing bacteria (AOB) and archaea (AOA) are key players in the nitrogen cycle and major producers of NO and NO globally. However, nothing is known about NO and NO production by the recently discovered and widely distributed complete ammonia oxidizers (comammox). Here, we show that the comammox bacterium Nitrospira inopinata is sensitive to inhibition by an NO scavenger, cannot denitrify to NO, and emits NO at levels that are comparable to AOA but much lower than AOB. Furthermore, we demonstrate that NO formed by N. inopinata formed under varying oxygen regimes originates from abiotic conversion of hydroxylamine. Our findings indicate that comammox microbes may produce less NO during nitrification than AOB.

  • Molecular Mechanisms of Tungsten Toxicity Differ for Glycine max Depending on Nitrogen Regime

    Preiner J, Wienkoop S, Weckwerth W, Oburger E
    2019 - Frontiers in Plant Science, 10: Article 367


    Tungsten (W) finds increasing application in military, aviation and household appliance industry, opening new paths into the environment. Since W shares certain chemical properties with the essential plant micronutrient molybdenum (Mo), it is proposed to inhibit enzymatic activity of molybdoenzymes [e.g., nitrate reductase (NR)] by replacing the Mo-ion bound to the co-factor. Recent studies suggest that W, much like other heavy metals, also exerts toxicity on its own. To create a comprehensive picture of tungsten stress, this study investigated the effects of W on growth and metabolism of soybean (Glycine max), depending on plant nitrogen regime [nitrate fed (N fed) vs. symbiotic N2 fixation (N fix)] by combining plant physiological data (biomass production, starch and nutrient content, N2 fixation, nitrate reductase activity) with root and nodule proteome data. Irrespective of N regime, NR activity and total N decreased with increasing W concentrations. Nodulation and therefore also N2 fixation strongly declined at high W concentrations, particularly in N fix plants. However, N2 fixation rate (g N fixed g−1 nodule dwt) remained unaffected by increasing W concentrations. Proteomic analysis revealed a strong decline in leghemoglobin and nitrogenase precursor levels (NifD), as well as an increase in abundance of proteins involved in secondary metabolism in N fix nodules. Taken together this indicates that, in contrast to the reported direct inhibition of NR, N2 fixation appears to be indirectly inhibited by a decrease in nitrogenase synthesis due to W induced changes in nodule oxygen levels of N fix plants. Besides N metabolism, plants exhibited a strong reduction of shoot (both N regimes) and root (N fed only) biomass, an imbalance in nutrient levels and a failure of carbon metabolic pathways accompanied by an accumulation of starch at high tungsten concentrations, independent of N-regime. Proteomic data (available via ProteomeXchange with identifier PXD010877) demonstrated that the response to high W concentrations was independent of nodule functionality and dominated by several peroxidases and other general stress related proteins. Based on an evaluation of several W responsive proteotypic peptides, we identified a set of protein markers of W stress and possible targets for improved stress tolerance.

  • Widespread soil bacterium that oxidizes atmospheric methane

    Tveit AT, Hestnes AG, Robinson SL, Schintlmeister A, Dedysh SN, Jehmlich N, von Bergen M, Herbold CW, Wagner M, Richter A, Svenning MM
    2019 - Proceedings of the National Academy of Sciences of the United States of America (PNAS), 17: 8515-8524


    The global atmospheric level of methane (CH), the second most important greenhouse gas, is currently increasing by ∼10 million tons per year. Microbial oxidation in unsaturated soils is the only known biological process that removes CH from the atmosphere, but so far, bacteria that can grow on atmospheric CH have eluded all cultivation efforts. In this study, we have isolated a pure culture of a bacterium, strain MG08 that grows on air at atmospheric concentrations of CH [1.86 parts per million volume (p.p.m.v.)]. This organism, named , is globally distributed in soils and closely related to uncultured members of the upland soil cluster α. CH oxidation experiments and C-single cell isotope analyses demonstrated that it oxidizes atmospheric CH aerobically and assimilates carbon from both CH and CO Its estimated specific affinity for CH (a) is the highest for any cultivated methanotroph. However, growth on ambient air was also confirmed for and , close relatives with a lower specific affinity for CH, suggesting that the ability to utilize atmospheric CH for growth is more widespread than previously believed. The closed genome of MG08 encodes a single particulate methane monooxygenase, the serine cycle for assimilation of carbon from CH and CO, and CO fixation via the recently postulated reductive glycine pathway. It also fixes dinitrogen and expresses the genes for a high-affinity hydrogenase and carbon monoxide dehydrogenase, suggesting that atmospheric CH oxidizers harvest additional energy from oxidation of the atmospheric trace gases carbon monoxide (0.2 p.p.m.v.) and hydrogen (0.5 p.p.m.v.).

  • Vertical Redistribution of Soil Organic Carbon Pools After Twenty Years of Nitrogen Addition in Two Temperate Coniferous Forests

    Forstner, SJ, Wechselberger V, Müller S, Keiblinger KM, Díaz-Pinés E, Wanek W, Scheppi P, Hagedorn F, Gundersen P, Tatzber M, Gerzabek MH, Zechmeister-Boltenstern S
    2019 - Ecosystems, 22: 379-400


    Nitrogen (N) inputs from atmospheric deposition can increase soil organic carbon (SOC) storage in temperate and boreal forests, thereby mitigating the adverse effects of anthropogenic CO2 emissions on global climate. However, direct evidence of N-induced SOC sequestration from low-dose, long-term N addition experiments (that is, addition of < 50 kg N ha−1 y−1 for > 10 years) is scarce worldwide and virtually absent for European temperate forests. Here, we examine how tree growth, fine roots, physicochemical soil properties as well as pools of SOC and soil total N responded to 20 years of regular, low-dose N addition in two European coniferous forests in Switzerland and Denmark. At the Swiss site, the addition of 22 kg N ha−1 y−1 (or 1.3 times throughfall deposition) stimulated tree growth, but decreased soil pH and exchangeable calcium. At the Danish site, the addition of 35 kg N ha−1 y−1 (1.5 times throughfall deposition) impaired tree growth, increased fine root biomass and led to an accumulation of N in several belowground pools. At both sites, elevated N inputs increased SOC pools in the moderately decomposed organic horizons, but decreased them in the mineral topsoil. Hence, long-term N addition led to a vertical redistribution of SOC pools, whereas overall SOC storage within 30 cm depth was unaffected. Our results imply that an N-induced shift of SOC from older, mineral-associated pools to younger, unprotected pools might foster the vulnerability of SOC in temperate coniferous forest soils.

  • Root exudation of primary metabolites: mechanisms and their roles in plant responses to environmental stimuli

    2019 - Frontiers in Plant Science, 10: Article 157


    Root exudation is an important process determining plant interactions with the soil environment. Many studies have linked this process to soil nutrient mobilization. Yet, it remains unresolved how exudation is controlled and how exactly and under what circumstances plants benefit from exudation. The majority of root exudates include primary metabolites (sugars, amino acids and organic acids) believed to be passively lost from the root and used by rhizosphere-dwelling microbes. In this review, we synthetize recent advances in ecology and plant biology to explain and propose mechanisms by which root exudation of primary metabolites is controlled, and what role their exudation plays in plant nutrient acquisition strategies. Specifically, we propose a novel conceptual framework for root exudates. This framework is built upon two main concepts: (i) root exudation of primary metabolites is driven by diffusion, with plants and microbes both modulating concentration gradients and therefore diffusion rates to soil depending on their nutritional status; (ii) exuded metabolite concentrations can be sensed at the root tip and signals are translated to modify root architecture. The flux of primary metabolites through root exudation is mostly located at the root tip, where the lack of cell differentiation favors diffusion of metabolites to the soil. We show examples of how the root tip senses concentration changes of exuded metabolites and translate that into signals to modify root growth. Plants can modify the concentration of metabolites either by controlling source/sink processes or by expressing and regulating efflux carriers, therefore challenging the idea of root exudation as a purely unregulated passive process. Through root exudate flux, plants can locally enhance concentrations of many common metabolites which can serve as sensors and integrators of the plant nutritional status and of the nutrient availability in the surrounding environment. Plant-associated micro-organisms also constitute a strong sink for plant carbon thereby increasing concentration gradients of metabolites and affecting root exudation. Understanding the mechanisms of, and the effects that, environmental stimuli have on the magnitude and type of root exudation will ultimately improve our knowledge of processes determining soil CO2 emissions, ecosystem functioning and how to improve the sustainability of agricultural production.

  • Rapid transfer of plant photosynthates to soil bacteria via ectomycorrhizal hyphae and its interaction with nitrogen availability

    Gorka S, Dietrich M, Mayerhofer W, Gabriel R, Wiesenbauer J, Martin V, Zheng Q, Imai B, Prommer J, Weidinger M, Schweiger P, Eichorst SA, Wagner M, Richter A, Schintlmeister A, Woebken D, Kaiser C
    2019 - Frontiers Microbioly, 10: Article 168


    Plant roots release recent photosynthates into the rhizosphere, accelerating decomposition of organic matter by saprotrophic soil microbes (’rhizosphere priming effect’) which consequently increases nutrient availability for plants. However, about 90% of all higher plant species are mycorrhizal, transferring a significant fraction of their photosynthates directly to their fungal partners. Whether mycorrhizal fungi pass on plant-derived carbon (C) to bacteria in root-distant soil areas, i.e. incite a ‘hyphosphere priming effect’, is not known. Experimental evidence for C transfer from mycorrhizal hyphae to soil bacteria is limited, especially for ectomycorrhizal systems. As ectomycorrhizal fungi possess enzymatic capabilities to degrade organic matter themselves, it remains unclear whether they cooperate with soil bacteria by providing photosynthates, or compete for available nutrients.

    To investigate a possible C transfer from ectomycorrhizal hyphae to soil bacteria, and its response to changing nutrient availability, we planted young beech trees (Fagus sylvatica) into ‘split-root’ boxes, dividing their root systems into two disconnected soil compartments. Each of these compartments was separated from a litter compartment by a mesh penetrable for fungal hyphae, but not for roots. Plants were exposed to a 13C-CO2–labeled atmosphere, while 15N-labeled ammonium and amino acids were added to one side of the split-root system.

    We found a rapid transfer of recent photosynthates via ectomycorrhizal hyphae to bacteria in root-distant soil areas. Fungal and bacterial phospholipid fatty acid (PLFA) biomarkers were significantly enriched in hyphae-exclusive compartments 24 h after 13C-CO2–labeling. Isotope imaging with nanometer-scale secondary ion mass spectrometry (NanoSIMS) allowed for the first time in situ visualization of plant-derived C and N taken up by extraradical fungal hyphae, and in microbial cells thriving on hyphal surfaces. When N was added to the litter compartments, bacterial biomass and the amount of incorporated 13C strongly declined. Interestingly, this effect was also observed in adjacent soil compartments where added N was only available for bacteria through hyphal transport, indicating that ectomycorrhizal fungi were acting on soil bacteria. Together, our results demonstrate that (i) ectomycorrhizal hyphae rapidly transfer plant-derived C to bacterial communities in root-distant areas, and (ii) this transfer promptly responds to changing soil nutrient conditions.

  • Increased risk of phosphorus and metal leaching from paddy soils after excessive manure application: Insights from a mesocosm study

    Liu XP, Bi QF, Qiu LL, Li KJ, Yang XR, Lin XY
    2019 - Science of The Total Environment, 666: 778-785


    Livestock manure has gradually become an alternative fertilizer for maintaining soil fertility, whereas excessive application of manure leads to the release of phosphorus (P) and toxic metals that may cause complex environmental risks. To investigate the accumulation and migration of P within soil profiles, a mesocosm experiment was conducted to analyze the content and leaching of soil P, metals, and dissolved organic carbon after different fertilization treatments, including control (no fertilizer, CK), chemical fertilizer (CF), chemical fertilizer combined low (CF + LPM) and high (CF + HPM) rate of manure application. Results showed that a high rate of manure application significantly enhanced the accumulation of total soil P (by ~14%) and P availability (easily-available P, by ~24%; Olsen-P, by ~20%) in topsoil, and also increased the content of easily-available organic P (EA-Po) in both topsoil and subsoil compared to the CK treatment. The migration of dissolved inorganic and organic P (DIP and DOP) in leachate within soil profiles was strengthened by manure application. Moreover, significant positive correlations between P, metals, and dissolved organic carbon (DOC) in leachate indicated that downward co-migration occurred within the soil profiles, and also suggested that excessive manure application can intensify the risk of P loss by increasing the migration of manure-derived DOC. Overall, our findings provide insights into P accumulation and migration within soil profiles after excessive manure application, which is useful for predicting the potential risk of P and metal leaching from paddy soils.

  • Cyanate and urea are substrates for nitrification by Thaumarchaeota in the marine environment

    Kitzinger K, Padilla CC, Marchant HK, Hach PF, Herbold CW, Kidane AT, Könneke M, Littmann S, Mooshammer M, Niggemann J, Petriv S, Richter A, Stewart FJ, Wagner M, Kuypers MMM, Bristow LA
    2019 - Nature Microbiology, 4: 234-243


    Ammonia-oxidizing archaea of the phylum Thaumarchaeota are among the most abundant marine microorganisms1. These organisms thrive in the oceans despite ammonium being present at low nanomolar concentrations2,3. Some Thaumarchaeota isolates have been shown to utilize urea and cyanate as energy and N sources through intracellular conversion to ammonium4,5,6. Yet, it is unclear whether patterns observed in culture extend to marine Thaumarchaeota, and whether Thaumarchaeota in the ocean directly utilize urea and cyanate or rely on co-occurring microorganisms to break these substrates down to ammonium. Urea utilization has been reported for marine ammonia-oxidizing communities7,8,9,10, but no evidence of cyanate utilization exists for marine ammonia oxidizers. Here, we demonstrate that in the Gulf of Mexico, Thaumarchaeota use urea and cyanate both directly and indirectly as energy and N sources. We observed substantial and linear rates of nitrite production from urea and cyanate additions, which often persisted even when ammonium was added to micromolar concentrations. Furthermore, single-cell analysis revealed that the Thaumarchaeota incorporated ammonium-, urea- and cyanate-derived N at significantly higher rates than most other microorganisms. Yet, no cyanases were detected in thaumarchaeal genomic data from the Gulf of Mexico. Therefore, we tested cyanate utilization in Nitrosopumilus maritimus, which also lacks a canonical cyanase, and showed that cyanate was oxidized to nitrite. Our findings demonstrate that marine Thaumarchaeota can use urea and cyanate as both an energy and N source. On the basis of these results, we hypothesize that urea and cyanate are substrates for ammonia-oxidizing Thaumarchaeota throughout the ocean.

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