TY - JOUR AB - Understanding the impact of agricultural land use on the soil prokaryotic communities in connected downslope sites is crucial for developing sustainable strategies to preserve ecosystem properties and mitigate agriculture’s environmental impacts. In this study, we investigated topsoil samples collected at three time points in 2022 (March, June, and November) from two adjacent catenas, reaching from hillslope to floodplain. The catenas differed in land use (extensive grassland vs. extensive cropland) at the top and middle parts, while the floodplain remained an extensive grassland due to legal restrictions. Using quantitative real-time PCRs and metabarcoding, we assessed prokaryotic abundance and prokaryotic community composition. Results show higher bacterial abundance in the cropland-influenced floodplain part across all time points compared to the grassland-influenced floodplain part. Temporal dynamics revealed a progressive decrease in the shared prokaryotic communities of the floodplain parts, peaking at the summer sampling time point, indicating a significant influence of the respective management type of the agricultural sites over the bacterial and archaeal communities of the floodplain parts. Differential abundance analyses identified several nitrifying taxa as more abundant in the cropland-influenced floodplain. Upstream land use also influenced the prokaryotic network of the cropland-floodplain, with some cropland taxa becoming keystone taxa and altering network morphology, an effect not observed in the grassland-influenced floodplain. These findings suggest that upstream agricultural land use practices have exerted a long-term influence on the floodplain prokaryotic communities over the past three decades. Moreover, there is evidence suggesting that these prokaryotic communities may undergo a potential reset during winter, which requires further investigation. AU - Martinez-Cuesta, R. AU - Holmer, A.* AU - Buegger, F. AU - Dannenmann, M.* AU - Schloter, M. AU - Schulz, S. C1 - 72063 C2 - 56361 CY - One New York Plaza, Suite 4600, New York, Ny, United States TI - Land use drives prokaryotic community composition of directly adjacent grasslands. JO - Biol. Fertil. Soils PB - Springer PY - 2024 SN - 0178-2762 ER - TY - JOUR AB - Essential soil functions such as plant productivity, C storage, nutrient cycling and the storage and purification of water all depend on soil biological processes. Given this insight, it is remarkable that in modeling of these soil functions, the various biological actors usually do not play an explicit role. In this review and perspective paper we analyze the state of the art in modeling these soil functions and how biological processes could more adequately be accounted for. We do this for six different biologically driven processes clusters that are key for understanding soil functions, namely i) turnover of soil organic matter, ii) N cycling, iii) P dynamics, iv) biodegradation of contaminants v) plant disease control and vi) soil structure formation. A major conclusion is that the development of models to predict changes in soil functions at the scale of soil profiles (i.e. pedons) should be better rooted in the underlying biological processes that are known to a large extent. This is prerequisite to arrive at the predictive models that we urgently need under current conditions of Global Change. AU - Vogel, H.J.* AU - Amelung, W.* AU - Baum, C.* AU - Bonkowski, M.* AU - Blagodatsky, S.* AU - Grosch, R.* AU - Herbst, M.* AU - Kiese, R.* AU - Koch, S.* AU - Kuhwald, M.* AU - König, S.* AU - Leinweber, P.* AU - Lennartz, B.* AU - Müller, C.W.* AU - Pagel, H.* AU - Rillig, M.C.* AU - Rüschhoff, J.* AU - Russell, D.* AU - Schnepf, A.* AU - Schulz, S. AU - Siebers, N.* AU - Vetterlein, D.* AU - Wachendorf, C.* AU - Weller, U.* AU - Wollschläger, U.* C1 - 70273 C2 - 55480 CY - One New York Plaza, Suite 4600, New York, Ny, United States SP - 263–306 TI - How to adequately represent biological processes in modeling multifunctionality of arable soils. JO - Biol. Fertil. Soils VL - 60 PB - Springer PY - 2024 SN - 0178-2762 ER - TY - JOUR AB - One of the most prominent changes in the rhizospheric soil structure is associated with the formation of a strongly bound soil layer in the surroundings of the root, which is named rhizosheath. In this study, we investigated how root hair elongation, a ubiquitous root morphological trait, affect the stability of rhizosheath aggregates. Using 13CO2 pulse labeling, we tracked the fate of root-derived 13C inputted into the rhizosheath of two Zea mays L. genotypes with contrasting root hair elongation: a mutant with root hair defective elongation (rth3) and a corresponding wild type (WT). In addition, we also investigated the differences between two 13CO2 labeling approaches (single vs. multiple pulse labeling) in the distribution of 13C in the rhizosheath aggregates. We were able to demonstrate that the rhizosheath aggregate stability and the resulting aggregate size distribution follows the same mechanisms irrespective of the root hair elongation. This result reinforces the assumption that other soil properties are more decisive for the soil structure formation in the rhizosheath in comparison to root hair elongation. The majority of recently deposited root-derived C (57%) was found in the macroaggregates. Increasing the number of pulses (multiple pulse labeling approach) resulted in a higher 13C enrichment of the rhizosheath aggregates fractions in comparison to the application of a single pulse. While both labeling approaches resulted in a similar distribution of 13C in the rhizosheath aggregates, the higher enrichment given by multiple pulse labeling allowed the separation of significant differences between the genotypes in plant C allocation in the rhizosheath. AU - Teixeira, P.P.C.* AU - Trautmann, S.* AU - Buegger, F. AU - Felde, V.J.M.N.L.* AU - Pausch, J.* AU - Müller, C.W.* AU - Kögel-Knabner, I.* C1 - 67552 C2 - 53590 CY - One New York Plaza, Suite 4600, New York, Ny, United States SP - 351–361 TI - Role of root hair elongation in rhizosheath aggregation and in the carbon flow into the soil. JO - Biol. Fertil. Soils VL - 59 IS - 3 PB - Springer PY - 2023 SN - 0178-2762 ER - TY - JOUR AB - The above article’s initial published version contained an error regarding the co-author Vincent J. M. N. L. Felde’s affiliation. Instead of “Institute of Soil Science and Soil Conservation, Justus Liebig University Giessen, Giessen, Germany”, the right affiliation should have been “Institute of Soil Science, Leibniz University of Hannover, Germany”. The original article has been corrected. AU - Teixeira, P.P.C.* AU - Trautmann, S.* AU - Buegger, F. AU - Felde, V.J.M.N.L.* AU - Pausch, J.* AU - Müller, C.W.* AU - Kögel-Knabner, I.* C1 - 68143 C2 - 53874 CY - One New York Plaza, Suite 4600, New York, Ny, United States TI - Correction to: Role of root hair elongation in rhizosheath aggregation and in the carbon flow into the soil (Biology and Fertility of Soils, (2023), 59, 3, (351-361), 10.1007/s00374-023-01708-6). JO - Biol. Fertil. Soils VL - 59 IS - 4 PB - Springer PY - 2023 SN - 0178-2762 ER - TY - JOUR AB - The GHG (CO2, CH4, N2O) emission potential along a chronosequence of former agricultural soils abandoned for 9 to 32 years were compared to an actively managed (on-going) agricultural soil (reference). The soils were incubated in mesocosms with and without manure amendment, and microbial functional groups involved in nitrous oxide emission were quantitatively assessed. Carbon dioxide emission significantly increased after agriculture abandonment (< 24 years) consistent with higher decomposition rate, but total emission decreased in the long term (> 29 years). With the cessation of agriculture, the abandoned sites generally became a net methane sink. Notably, total nitrous oxide emission showed a significant monotonic decrease over years of abandonment in response to manure amendment, possibly reflecting an altered capacity for (de)nitrification as indicated in the response of the (de)nitrifier abundance. Overall, our findings suggest that the GHG legacy of agriculture diminishes over time (> 29 years), with lowered GHG emissions and global warming potential (GWP) after abandonment of agriculture. AU - El-Hawwary, A.* AU - Brenzinger, K.* AU - Lee, H.J.* AU - Veraart, A.J.* AU - Morriën, E.* AU - Schloter, M. AU - van der Putten, W.H.* AU - Bodelier, P.L.E.* AU - Ho, A.D.* C1 - 64951 C2 - 52586 SP - 579–591 TI - Greenhouse gas (CO2, CH4, and N2O) emissions after abandonment of agriculture. JO - Biol. Fertil. Soils VL - 58 PY - 2022 SN - 0178-2762 ER - TY - JOUR AB - In previous two-tier experiments designed to test agronomical (treated wastewater) and worst-case scenario (wastewater spiked with a mixture of 14 pharmaceuticals and personal care products (PPCPs) at 10 and 100 μg/L), 14 different wastewater-borne PPCPs accumulated in soil, lettuce roots, and leaves leading to a significant ecotoxicological impact on soil and root-associated bacteria. Here, we assessed the effects of wastewater irrigation on the arbuscular mycorrhizal fungal (AMF) colonization, diversity, and composition in lettuce roots. Neither the wastewater nor the concentration of spiked PPCPs had an impact on the colonization, alpha-diversity indices (Chao1, PD whole tree, Simpson reciprocal, and Shannon), and composition of root-associated AMF communities. Taxonomical analysis of the fungi revealed the presence of 14 major phylotypes, 13 of which belonged to the Glomeromycota division. As for the alpha and beta diversity indices, none of the phylotypes was affected by either the wastewater or the PPCPs. This indicates that under both agronomical and worst-case scenario, the irrigation of lettuce with wastewater had no effect on the root-associated AMF community. AU - Gallego, S.* AU - Bigott, Y. AU - Mounier, A.* AU - Spor, A.* AU - Schröder, P. AU - Martin-Laurent, F.* C1 - 64834 C2 - 52513 SP - 607–611 TI - Impact of repeated irrigation of lettuce cultures with municipal wastewater on the diversity and composition of root-associated arbuscular mycorrhizal fungi. JO - Biol. Fertil. Soils VL - 58 PY - 2022 SN - 0178-2762 ER - TY - JOUR AB - Plant residues with larger carbon (C) to nitrogen (N) ratios can stimulate microbial growth and thereby protect soil nutrients from leaching. In poorly fertilized soil, excessive immobilization may limit nutrient availability and thus plant growth. Little is known about the impact of a shallow straw incorporation on soil microbial regulation of top-dressing fertilizer nutrients and spring crop establishment. We aimed to evaluate if wheat straw in combination with mineral fertilizer has more positive effects on plant performance than mineral fertilization alone and if this relates to changes of the extractable C:N:P ratio and microbial activity close to the roots. In order to conduct small-scale sampling with minimal disturbance during growth of spring barley (Hordeum vulgare L.), we developed rhizotrons with resealable ports. Rhizotrons were filled with loamy-sandy soil and fertilized with an equivalent of 150 kg N and 80 kg P ha−1. Half of the rhizotrons received the top dressing together with 4500 kg wheat straw-C ha−1. Throughout a 90-day greenhouse experiment, we analyzed soil C:N:P dynamics, and carbon dioxide (CO2) and nitrous oxide (N2O) emission, together with microbial biomass, selected bacterial genes (abundance), and transcripts (activity) in bulk and root-affected soil at multiple times. We focused on nitrifiers and denitrifiers and linked our data to barley growth. Interactions between straw and roots caused shifts towards larger C:P and C:N ratios in root-affected soil. These shifts were associated with increased 16S rRNA transcripts and denitrifier activities. Straw increased microbial biomass by 124% in the topsoil and at the same time increased root biomass by 125% and number of tillers by 80%. We concluded that microbial activation at the root-straw interface may positively feed back on soil nutrient regulation and plant performance. Further research has to evaluate if plant roots actively prime mining of previously immobilized nutrients in the straw detritusphere or if effects of pathogen suppression and growth promotion are dominating. AU - Reichel, R.* AU - Kamau, C.W. AU - Kumar, A.* AU - Li, Z.* AU - Radl, V. AU - Temperton, V.M.* AU - Schloter, M. AU - Brüggemann, N.* C1 - 64392 C2 - 52217 CY - One New York Plaza, Suite 4600, New York, Ny, United States SP - 375–388 TI - Spring barley performance benefits from simultaneous shallow straw incorporation and top dressing as revealed by rhizotrons with resealable sampling ports. JO - Biol. Fertil. Soils VL - 58 PB - Springer PY - 2022 SN - 0178-2762 ER - TY - JOUR AB - A 2-year outdoor mesocosm experiment was carried out to determine the effects of high C amendments (HCAs; wheat straw and sawdust) compared to a control with no addition of HCAs (no-HCA) and 2 different crop rotation systems (spring barley/winter barley and faba bean/winter barley) on soil bacterial communities using a molecular barcoding approach. Samples were analyzed after pre-crop harvest (T1) and harvest of winter barley (T2). Our data demonstrate a clear drop in bacterial diversity after winter barley harvest in the no-HCA and wheat straw treatment compared to the pre-crops. Sawdust application had a stabilizing effect on bacterial diversity compared to the pre-crops and induced an increase in carbon (C) stocks in soil which were however negatively correlated with yields. Main responders in the no-HCA and wheat straw treatment compared to the pre-crops were bacteria of the phyla Actinobacteria and Bacteroidetes which were enriched and bacteria belonging to Firmicutes, Gemmatimonadetes, Proteobacteria, and Gemmatimonadaceae which were depleted. Overall differences between wheat straw–amended and no-HCA control samples were small and included single ASVs from various phyla. In sawdust-amended samples, only a shift of some Proteobacteria families was observed compared to the no-HCA control. Overall, pre-crop plant species had small influence on the observed response pattern of the soil microbiome towards the amendments and was only visible for wheat straw. AU - Kamau, C.W. AU - van Duijnen, R.* AU - Schmid, C. AU - Balazs, H.-E. AU - Roy, J.* AU - Rillig, M.* AU - Schröder, P. AU - Radl, V. AU - Temperton, V.M.* AU - Schloter, M. C1 - 60800 C2 - 49589 CY - One New York Plaza, Suite 4600, New York, Ny, United States SP - 305-317 TI - Impact of high carbon amendments and pre-crops on soil bacterial communities. JO - Biol. Fertil. Soils VL - 57 IS - 2 PB - Springer PY - 2021 SN - 0178-2762 ER - TY - JOUR AB - Soil P pools are strongly driven by microbial activities, and vice versa, P pools shape bacterial communities and their functional potential. Biological soil crusts (biocrusts) represent a microbial hotspot for nutrient turnover. We compared biocrusts and bulk soil samples from different temperate beech (Fagus sylvaticaL.) forests representing a gradient in soil texture, nutrient concentrations, and pH values at biocrust peak biomass. We measured the total and plant-available P and N concentrations and assessed the bacterial potential to mineralize (phoD,phnX), solubilize (gcd), and take up P (pstSandpitA) and mineralize (chiA,apr) and fix N (nifH) by quantifying the respective marker genes (qPCR). We found an increase of absolute and relative bacterial abundance involved in P turnover in biocrusts, but the strategy to acquire P differed between the regions as bacteria harboring the starvation-inducedpstSgene were most abundant where labile P was lowest. In contrast, the region with lowest total P concentrations has a higher potential to utilize more stable phosphonates. N mineralization was strongly correlated to P turnover at regions with increased labile N and P concentrations. Interestingly, the potential to fix N was highest in the bulk soil where total P concentrations were highest. Even though the correlation of N and P turnover is strongest if their ratio is low, the acquisition strategy strongly depends on soil properties. AU - Kurth, J. AU - Albrecht, M.* AU - Karsten, U.* AU - Gläser, K.* AU - Schloter, M. AU - Schulz, S. C1 - 60317 C2 - 49259 CY - One New York Plaza, Suite 4600, New York, Ny, United States SP - 179-192 TI - Correlation of the abundance of bacteria catalyzing phosphorus and nitrogen turnover in biological soil crusts of temperate forests of Germany. JO - Biol. Fertil. Soils VL - 57 IS - 2 PB - Springer PY - 2020 SN - 0178-2762 ER - TY - JOUR AB - Short-lived pulses of soil nitrous oxide (N2O) emissions during freeze-thaw periods can dominate annual cumulative N2O fluxes from temperate managed and natural soils. However, the effects of freeze thaw cycles (FTCs) on dinitrogen (N-2) emissions, i.e., the dominant terminal product of the denitrification process, and ratios of N-2/N2O emissions have remained largely unknown because methodological difficulties were so far hampering detailed studies. Here, we quantified both N-2 and N2O emissions of montane grassland soils exposed to three subsequent FTCs under two different soil moisture levels (40 and 80% WFPS) and under manure addition at 80% WFPS. In addition, we also quantified abundance and expression of functional genes involved in nitrification and denitrification to better understand microbial drivers of gaseous N losses. Our study shows that each freeze thaw cycle was associated with pulse emissions of both N2O and N-2, with soil N-2 emissions exceeding N2O emissions by a factor of 5-30. Increasing soil moisture from 40 to 80% WFPS and addition of cow slurry increased the cumulative FTC N-2 emissions by 102% and 77%, respectively. For N2O, increasing soil moisture from 40 to 80% WFPS and addition of slurry increased the cumulative emissions by 147% and 42%, respectively. Denitrification gene cnorB and nosZ clade I transcript levels showed high explanatory power for N2O and N-2 emissions, thereby reflecting both N gas flux dynamics due to FTC and effects of different water availability and fertilizer addition. In agreement with several other studies for various ecosystems, we show here for mountainous grassland soils that pulse emissions of N2O were observed during freeze-thaw. More importantly, this study shows that the freeze-thaw N-2 pulse emissions strongly exceeded those of N2O in magnitude, which indicates that N-2 emissions during FTCs could represent an important N loss pathway within the grassland N mass balances. However, their actual significance needs to be assessed under field conditions using intact plant-soil systems. AU - Wu, X.* AU - Chen, Z.* AU - Kiese, R.* AU - Fu, J.* AU - Gschwendtner, S. AU - Schloter, M. AU - Liu, C.* AU - Butterbach-Bahl, K.* AU - Wolf, B.* AU - Dannenmann, M.* C1 - 59234 C2 - 48705 CY - One New York Plaza, Suite 4600, New York, Ny, United States SP - 959–972 TI - Dinitrogen (N2) pulse emissions during freeze-thaw cycles from montane grassland soil. JO - Biol. Fertil. Soils VL - 56 PB - Springer PY - 2020 SN - 0178-2762 ER - TY - JOUR AU - Nannipieri, P.* AU - Penton, C.R.* AU - Purahong, W.* AU - Schloter, M. AU - van Elsas, J.D.* C1 - 57324 C2 - 47694 CY - 233 Spring St, New York, Ny 10013 Usa SP - 765-766 TI - Recommendations for soil microbiome analyses. JO - Biol. Fertil. Soils VL - 55 IS - 8 PB - Springer PY - 2019 SN - 0178-2762 ER - TY - JOUR AB - Our understanding of the interactions between minerals, organic matter, and microorganisms at so-called biogeochemical interfaces in soil is still hampered by the inherent complexity of these systems. Artificial soil maturation experiments can help to bridge a gap in complexity between simple abiotic sorption experiments and larger-scale field experiments. By controlling other soil-forming factors, the effect of a particular variable can be identified in a simplified system. Here, we review the findings of a series of artificial soil incubation experiments with the aim of revealing general trends and conclusions. The artificial soils were designed to determine the effect of mineral composition and charcoal presence on the development of abiotic and biotic soil properties during maturation. In particular, the development of soil aggregates, organic matter (OM) composition and turnover, sorption properties, and the establishment of microbial community composition and function were considered. The main objectives of the research were to determine (1) how surface properties and sorption of chemicals modify biogeochemical interfaces; (2) how much time is required to form aggregates from mixtures of pure minerals, OM, and a microbial inoculum; and (3) how the presence of different mineral and charcoal surfaces affects aggregation, OM turnover, and the development of microbial community composition. AU - Pronk, G.J.* AU - Heister, K.* AU - Vogel, C.* AU - Babin, D.* AU - Bachmann, J.* AU - Ding, G.C.* AU - Ditterich, F.* AU - Gerzabek, M.H.* AU - Giebler, J.* AU - Hemkemeyer, M.* AU - Kandeler, E.* AU - Kunhi Mouvenchery, Y.* AU - Miltner, A.* AU - Poll, C.* AU - Schaumann, G.E.* AU - Smalla, K.* AU - Steinbach, A.* AU - Tanuwidjaja, I. AU - Tebbe, C.C.* AU - Wick, L.Y.* AU - Woche, S.K.* AU - Totsche, K.U.* AU - Schloter, M. AU - Kögel-Knabner, I.* C1 - 50062 C2 - 42058 CY - New York SP - 9-22 TI - Interaction of minerals, organic matter, and microorganisms during biogeochemical interface formation as shown by a series of artificial soil experiments. JO - Biol. Fertil. Soils VL - 53 IS - 1 PB - Springer PY - 2017 SN - 0178-2762 ER - TY - JOUR AB - The living soil is instrumental to key life support functions (LSF) that safeguard life on Earth. The soil microbiome has a main role as a driver of these LSF. Current global developments, like anthropogenic threats to soil (e.g., via intensive agriculture) and climate change, pose a burden on soil functioning. Therefore, it is important to dispose of robust indicators that report on the nature of deleterious changes and thus soil quality. There has been a long debate on the best selection of biological indicators (bioindicators) that report on soil quality. Such indicators should ideally describe organisms with key functions in the system, or with key regulatory/connecting roles (so-called keystone species). However, in the light of the huge functional redundancy in most soil microbiomes, finding specific keystone markers is not a trivial task. The current rapid development of molecular (DNA-based) methods that facilitate deciphering microbiomes with respect to key functions will enable the development of improved criteria by which molecular information can be tuned to yield molecular markers of soil LSF. This review critically examines the current state-of-the-art in molecular marker development and recommends avenues to come to improved future marker systems. AU - Schloter, M. AU - Nannipieri, P.* AU - Sørensen, S.J.* AU - van Elsas, J.D.* C1 - 52232 C2 - 43807 CY - New York TI - Microbial indicators for soil quality. JO - Biol. Fertil. Soils VL - 54 IS - 1 PB - Springer PY - 2017 SN - 0178-2762 ER - TY - JOUR AB - The use of cultivation independent methods has revolutionized soil biology in the last decades. Most popular approaches are based on directly extracted DNA from soil and subsequent analysis of PCR-amplified marker genes by next-generation sequencing. While these high-throughput methods offer novel possibilities over cultivation-based approaches, several key points need to be considered to minimize potential biases during library preparation and downstream bioinformatic analysis. This opinion paper highlights crucial steps that should be considered for accurate analysis and data interpretation. AU - Schöler, A. AU - Jacquiod, S.* AU - Vestergaard, G. AU - Schulz, S. AU - Schloter, M. C1 - 51146 C2 - 43481 CY - New York SP - 485–489 TI - Analysis of soil microbial communities based on amplicon sequencing of marker genes. JO - Biol. Fertil. Soils VL - 53 IS - 5 PB - Springer PY - 2017 SN - 0178-2762 ER - TY - JOUR AB - In this study, we investigated how co-occurrence patters of ammonia and nitrite oxidizers, which drive autotrophic nitrification, are influenced by tree species composition as well as soil pH in different forest soils. We expected that a decline of ammonia oxidizers in coniferous forests, as a result of excreted nitrification inhibitors and at acidic sites with low availability of ammonia, would reduce the abundance of nitrite-oxidizing bacteria (NOB). To detect shifts in co-occurrence patterns, the abundance of key players was measured at 50 forest plots with coniferous respectively deciduous vegetation and different soil pH levels in the region Schwäbische Alb (Germany). We found ammonia-oxidizing archaea (AOA) and Nitrospira-like NOB (NS) to be dominating in numbers over their counterparts across all forest types. AOA co-occurred mostly with NS, while bacterial ammonia oxidizers (AOB) were correlated with Nitrobacter-like NOB (NB). Co-occurrence patterns changed from tight significant relationships of all ammonia and nitrite oxidizers in deciduous forests to a significant relationship of AOB and NB in coniferous forests, where AOA abundance was reduced. Surprisingly, no co-occurrence structures between ammonia and nitrite oxidizers could be determined at acidic sites, although abundances were correlated to the respective nitrogen pools. This raises the question whether interactions with heterotrophic nitrifiers may occur, which needs to be addressed in future studies. AU - Stempfhuber, B. AU - Richter-Heitmann, T.* AU - Bienek, L. AU - Schöning, I.* AU - Schrumpf, M.* AU - Friedrich, M.* AU - Schulz, S. AU - Schloter, M. C1 - 51381 C2 - 43044 CY - New York SP - 691–700 TI - Soil pH and plant diversity drive co-occurrence patterns of ammonia and nitrite oxidizer in soils from forest ecosystems. JO - Biol. Fertil. Soils VL - 53 IS - 6 PB - Springer PY - 2017 SN - 0178-2762 ER - TY - JOUR AU - Vestergaard, G. AU - Schulz, S. AU - Schöler, A. AU - Schloter, M. C1 - 51420 C2 - 43117 CY - New York SP - 479-484 TI - Making big data smart-how to use metagenomics to understand soil quality. JO - Biol. Fertil. Soils VL - 53 IS - 5 PB - Springer PY - 2017 SN - 0178-2762 ER - TY - JOUR AB - The topography significantly affects microclimatic conditions and the physical properties of soil along and between slopes of different orientations in desert ecosystems. The goal of the present study was to determine the relationship between slope orientation and bacterial, as well as fungal, community composition both in bulk soil and soil particle-size fractions at different time points throughout the seasons (very dry autumn and moister winter). The soil bacterial and fungal community composition was assessed by 16S ribosomal RNA (rRNA) gene respectively ITS fingerprinting after PCR amplification of extracted DNA from soil. Our results indicate that bacterial community composition was mainly affected by the different sampling time points, whereas fungal community composition was affected by both slope orientation and sampling time point. Soil fractionation revealed that these differences are mainly due to shifts of fungal communities in the clay fractions. AU - Ehrlich, R.* AU - Schulz, S. AU - Schloter, M. AU - Steinberger, Y.* C1 - 43297 C2 - 36364 CY - New York SP - 507-510 TI - Effect of slope orientation on microbial community composition in different particle size fractions from soils obtained from desert ecosystems. JO - Biol. Fertil. Soils VL - 51 IS - 4 PB - Springer PY - 2015 SN - 0178-2762 ER - TY - JOUR AB - Exploitative fast-growing plants have higher demands for nutrients compared to conservative slow-growing plants. We presume that these differences in nutrient uptake highly influence the microbial performance mainly in the rhizosphere of nutrient-poor soils. In order to investigate the influence of plants with contrasting exploitation types on microbial communities at the root-soil interface, we performed a greenhouse experiment in a N-poor, sandy soil using the fast-growing plant Dactylis glomerata and the conservative, slow-growing plant Festuca rubra. We applied four different amounts of the inorganic fertilizer ammonium nitrate (0, 50, 100, and 200 kg NH4NO3 ha-1). After 6 weeks, the abundance of nitrifiers and denitrifiers was investigated in the root-rhizosphere complex (RRC) based on the quantification of the marker genes amoA, nirK, nirS, and nosZ. Furthermore, soil chemical properties and the plant biomass were determined. Independent from the investigated plant species, fertilizer applications up to 100 kg ha-1 resulted in a clear depletion of ammonium and nitrate in the RRC, with ammonium and nitrate concentrations <1 mg kg-1 dry weight (dw). Only the highest fertilizer rate increased both ammonium and nitrate concentrations in the RRC of both plants reaching concentrations of 9.5 mg kg-1 dw for ammonium and 92.5 mg kg-1 dw for nitrate. The abundance of bacterial ammonia oxidizers (AOB) followed this trend (increase in abundance in response to the highest fertilizer rate), and copy numbers up to 3.2 × 107 copies g-1 dw were measured in the RRC of treatments with F. rubra where 200 kg N ha-1 was applied. As the archaeal ammonia oxidizers (AOA) did respond neither to plant species nor to the fertilizer application, the AOA/AOB ratio decreased from 10 in the non-fertilized treatments to 2 in treatments with 200 kg N ha-1. Also the abundance of microbes involved in denitrification strongly increased in response to higher fertilization rates in the RRC of both plant species, although higher gene copy numbers were detected in the rhizosphere of D. glomerata mainly for nitrous oxide reducers (up to 2.7 × 108 copies g-1 dw). Surprisingly, the highest fertilization rates resulted in a 50 % decrease in abundance of microbes involved in nitrite as well as nitrous oxide reduction. AU - Kastl, E.-M. AU - Schloter-Hai, B. AU - Buegger, F. AU - Schloter, M. C1 - 32062 C2 - 34939 SP - 57-64 TI - Impact of fertilization on the abundance of nitrifiers and denitrifiers at the root-soil interface of plants with different uptake strategies for nitrogen. JO - Biol. Fertil. Soils VL - 51 IS - 1 PY - 2015 SN - 0178-2762 ER - TY - JOUR AB - A long-term field experiment was run for 12 years to evaluate the impact of minimum tillage (MT) compared to conventional mouldboard ploughing (CT) on soil chemical, physical and microbial properties in a shallow Cambisol formed over fluvioglacial deposits of Drava river in Slovenia. Significant differences between MT and CT were found in vertical distribution of soil organic C (SOC) and nutrients (total N and plant available potassium); under MT, concentrations decreased from the soil surface to the lower layers, as opposed to CT which maintained rather uniform distribution down to the ploughing depth. MT in comparison with CT also increased the proportion of water-stable 2–4-mm-sized aggregates (80.9 and 61.3 %, respectively), water holding capacity (24.8 and 22.2 %, respectively) and plant available water (13.4 and 10.3 %, respectively) in the upper 0–10-cm soil layer. Bulk density, porosity, the proportion of water-stable 1–2-mm-sized aggregates and infiltration rate showed no significant differences between the tillage treatments. SOC content in the upper 0–10-cm soil layer was not significantly different between MT and CT (1.60 ± 0.07 and 1.45 ± 0.05 %, respectively), as well as the overall stock in the investigated soil profile (0–60 cm) remained unaffected (57.4 ± 0.8 and 59.1 ± 2.2 t ha−1, respectively). Microbial biomass, estimated by the total soil DNA, was higher in MT than CT in the 0–10-cm layer. Furthermore, a positive linear dependence of microbial biomass on SOC content was observed. Fingerprinting of bacterial, fungal and archaeal communities indicated that microbial community composition changed by long-term MT, whereas changes in microbial diversity were not detected for any domain. The most pronounced shifts in the composition were found for bacterial communities in the 10–20-cm layer, while the composition of fungal communities slightly changed in the upper 0–10 cm of MT soil. The composition of archaeal communities was not affected by the tillage or by the soil depth. Our results indicate that MT generates modest changes in soil structure and soil water retention properties and could support measures against erosion, drought and nutrient leaching. Considering increased microbial biomass in the topsoil of MT and shifts in microbial diversity, the impacts of MT on soil microbiome are also evident and need to be further investigated to identify the affected functional traits. AU - Kaurin, A.* AU - Mihelic, R.* AU - Kastelec, D.* AU - Schloter, M. AU - Suhaldoc, M.* AU - Grčman, H.* C1 - 46917 C2 - 39032 SP - 923-933 TI - Consequences of minimum soil tillage on abiotic soil properties and composition of microbial communities in a shallow Cambisol originated from fluvioglacial deposits. JO - Biol. Fertil. Soils VL - 51 IS - 8 PY - 2015 SN - 0178-2762 ER - TY - JOUR AB - © 2015 Springer-Verlag Berlin Heidelberg The spatial heterogeneity of nutrient turnover in subsoils has been rarely studied in the past, although drilosphere and rhizosphere are found to be important microbial hotspots in this oligotrophic environment. In this study, we measured different potential enzyme activities in different soil compartments of subsoil and topsoil. It could be shown that the activities of hydrolases, which cleave readily available organic substrates, are significantly higher in samples from the drilosphere and rhizosphere both in topsoil and subsoil. In bulk soil, hydrolase activities decrease with depth. In contrast, oxidative enzymes, which are involved in the decay of recalcitrant organic material, are released from the microbial community especially in the bulk fraction of subsoil. This emphasizes the importance of subsoil for nutrient acquisition and gives evidence for a distinct spatial separation of microbes with diverging lifestyles. AU - Uksa, M. AU - Schloter, M. AU - Kautz, T.* AU - Athmann, M.* AU - Köpke, U.* AU - Fischer, D. C1 - 43285 C2 - 36622 CY - New York SP - 517-521 TI - Spatial variability of hydrolytic and oxidative potential enzyme activities in different subsoil compartments. JO - Biol. Fertil. Soils VL - 51 IS - 4 PB - Springer PY - 2015 SN - 0178-2762 ER - TY - JOUR AB - The interaction between minerals and organic matter (OM) is a key to the turnover of OM in soils. In particular, clay minerals, iron oxides and charcoal are considered as important constituents affecting the sequestration of carbon (C) and nitrogen (N). Here, we incubated pre-produced artificial soils (842 days) and a natural soil (Ap, Luvisol) with 13C- and 15N-labelled plant litter over 63 days to follow OM turnover and the formation of organo-mineral associations regarding different compositions (montmorillonite (MT), illite (IL), montmorillonite + charcoal (MT+CH), illite + ferrihydrite (IL+FH)). The microbial biomass, salt extractable organic C, the isotopic C and N composition in the bulk soil and the soil fractions (combined density and particle size fractionation) were determined. By comparison of the artificial soils with the natural soil, we were able to show that the produced soil-like systems have OM dynamics comparable to the natural soil. We found out that the decomposition of the added plant litter was affected by the type of clay mineral that formed the artificial soils, as the soil MT exhibited a slower mineralisation compared to IL, which was in line with a lower microbial biomass. Although a high specific surface area (SSA) provides a high sequestration capacity for C and N, smaller amounts were sequestered in the MT soil with a higher SSA compared to the soil IL. We suppose that a more intensive decomposition is associated with a higher microbial biomass and thus leads to higher amounts of microbial products sequestered in the clay-sized fraction. Charcoal and ferrihydrite had no additional effect in this experiment. AU - Vogel, C.* AU - Heister, K.* AU - Buegger, F. AU - Tanuwidjaja, I. AU - Haug, S.* AU - Schloter, M. AU - Kögel-Knabner, I.* C1 - 43283 C2 - 36337 CY - New York SP - 427-442 TI - Clay mineral composition modifies decomposition and sequestration of organic carbon and nitrogen in fine soil fractions. JO - Biol. Fertil. Soils VL - 51 IS - 4 PB - Springer PY - 2015 SN - 0178-2762 ER - TY - JOUR AB - Microcosm experiments were designed to investigate the effects of the widely used antibiotic ciprofloxacin (CIP) on soil microbial communities by using four different concentrations (0, 1, 5, and 50 mg kg-1 of soil) and five sampling times (1, 3, 9, 22, and 40 days). Untreated controls only received water. The addition of CIP significantly decreased microbial biomass (p < 0.05) but did not affect soil respiration at high doses. Potential nitrification rates were stimulated at low CIP concentrations (1 mg kg-1) and inhibited at high CIP concentrations (50 mg kg-1) after 9 days of incubation. The nitrate and ammonium contents of soil were not altered after CIP addition at any time. The structure of soil microbial communities was assessed by phospholipid fatty acid (PLFA) analysis. The addition of CIP decreased the ratio of bacteria to fungi and increased the ratio of Gram-positive to Gram-negative bacteria. Principal component analysis of the PLFA data clearly distinguished among the different CIP concentrations. Redundancy analysis indicated that the CIP concentration and incubation time explained 33.5 % of the total variance in the PLFA data. These results confirmed that a single addition of CIP can influence structure and function of microbial communities in soil. AU - Cui, H. AU - Wang, S.-P.* AU - Fu, J.* AU - Zhou, Z.-Q.* AU - Zhang, N.* AU - Guo, L.* C1 - 30925 C2 - 34014 CY - New York SP - 939-947 TI - Influence of ciprofloxacin on microbial community structure and function in soils. JO - Biol. Fertil. Soils VL - 50 IS - 6 PB - Springer PY - 2014 SN - 0178-2762 ER - TY - JOUR AB - In this study, we assessed the abundance and diversity of bacterial communities by 16S rRNA gene-based qPCR and T-RFLP across different soil depths of three sites located on the Tibetan Plateau which are affected by discontinuous permafrost or characterized as seasonally frozen ground. Our data indicates that bacterial community structure was significantly influenced by soil depth mainly at the site affected by seasonal freezing and thawing. In contrast at sites affected by permafrost, diversity pattern of bacterial communities in the top soil and deeper soil layers changed to a far lower extend. This might be related to the fact that the investigated sites were not waterlogged at the permafrost layer, thus no processes that shifts towards bacterial communities, which require anoxic environments, could be expected. Overall, at all sites, labile and stable C as well as N pools act as main drivers for bacterial communities. AU - Ollivier, J. AU - Yang, S.* AU - Dörfer, C.* AU - Welzl, G. AU - Kühn, P.* AU - Scholten, T.* AU - Wagner, D.E.* AU - Schloter, M. C1 - 27915 C2 - 32856 CY - New York SP - 555-559 TI - Bacterial community structure in soils of the Tibetan Plateau affected by discontinuous permafrost or seasonal freezing. JO - Biol. Fertil. Soils VL - 50 IS - 3 PB - Springer PY - 2014 SN - 0178-2762 ER - TY - JOUR AB - The role of subsoils and their microbial communities for the nutrient supply for plants is to a large extent unknown, especially in comparison to well investigated topsoil layers. Therefore, in this study, the influence of three different plant species with different rooting systems and different N uptake strategies on ammonium and nitrate levels and microbial communities involved in ammonia oxidation and denitrification was investigated in different soil horizons. Overall, our results show a higher genetic potential for both processes in topsoils than in subsoils independent of the present plant. Although we found accumulation of N in top and subsoils in plots with legumes, we could not observe an impact of the higher nitrate content on the genetic potential of denitrification and ammonia oxidation. However, differences in the ratios of ammonia oxidizing archaea to bacteria and also between denitrifying bacteria harboring genes for copper- (nirK) or cytochrome- (nirS) dependent nitrite reductase in top and subsoil samples reveal different ecophysiologies of microbes involved in N turnover in top and subsoil habitats. AU - Fischer, D. AU - Uksa, M.* AU - Tischler, W. AU - Kautz, T.* AU - Köpke, U.* AU - Schloter, M. C1 - 27911 C2 - 32854 SP - 1243-1246 TI - Abundance of ammonia oxidizing microbes and denitrifiers in different soil horizons of an agricultural soil in relation to the cultivated crops. JO - Biol. Fertil. Soils VL - 49 IS - 8 PB - Springer PY - 2013 SN - 0178-2762 ER - TY - JOUR AB - Many studies have shown effects of plants species on fungal communities, but these are often confounded with soil effects. Thus, the specific role of plant species in structuring rhizospheric and soil fungal communities is poorly described. Our study used microcosms in which plants were grown under artificial conditions to bridge this gap. Two perennial grasses dominating subalpine grasslands, Festuca paniculata and Dactylis glomerata, were grown at two levels of fertilization on standard soil. Fungal communities were determined by 454 pyrosequencing of the internal transcribed spacer 1 region. Among the fungal communities characterized by the primers used, original communities were associated to each plant species and also diverged between rhizosphere and bulk soils within each plant species, though there were no significant fertilization effects. Differences regarded global composition of the fungal communities and abundant molecular operational taxonomic units (MOTUs). Both plant species and location effects were reflected more in the abundance than in the composition of MOTUs. The observed differences in fungal communities coincide with differing strategies of plant root growth, with D. glomerata having greater root mass, length, and area than F. paniculata. Our study, by dissociating soil effects from plant effects, demonstrated that plant species exert a key control on soil fungi. We suggest that such effects may be linked to inter-specific differences in root traits and their consequences on nitrogen uptake. AU - Mouhamadou, B.* AU - Puissant, J.* AU - Personeni, E.* AU - Desclos-Theveniau, M.* AU - Kastl, E.-M. AU - Schloter, M. AU - Zinger, L.* AU - Roy, J.* AU - Geremia, R.A.* AU - Lavorel, S.* C1 - 26186 C2 - 32112 SP - 1131-1139 TI - Effects of two grass species on the composition of soil fungal communities. JO - Biol. Fertil. Soils VL - 49 IS - 8 PB - Springer PY - 2013 SN - 0178-2762 ER - TY - JOUR AB - In the present study, the temporal and spatial variation of the abundance of the alkane monooxygenase gene alkB and 16S rRNA genes in different soil compartments was analysed in the presence or absence of 2-methyl- 4-chlorophenoxyacetic acid (MCPA) after the addition of pea litter to soil in a microcosm study. Samples were analysed shortly after litter addition (T0) and 1 week (T1), 3 weeks (T3) and 6 weeks (T6) after the addition of litter. In addition also, the quantity and quality of litter-derived alkanes was analysed and measured. The results revealed a fast and complete degradation of MCPA in all compartments throughout the experiment. Nevertheless, significant changes in the distribution patterns of short- andmiddle-chained alkanes suggest an interaction of MCPA and alkane degradation. alkB gene copy numbers were highly influenced by the time point of analysis and by the investigated soil compartment. Overall, an increase in alkB gene copy numbers from T0 to T3 was visible in the upper soil compartments whereas a decrease compared to T0 was measured in the deeper soil compartments. MCPA addition resulted in an increase of alkB abundance at T6. Gene copy numbers of 16S rRNA were not influenced by sampling time and soil compartment. In contrast to the control treatments, a slight increase in 16S rRNA gene copy numbers was visible at T1 and T3 compared to T0 in all soil compartments. AU - Schulz, S.* AU - Yukunkina, T.* AU - Pagel, H.* AU - Wick, L.Y.* AU - Poll, C.* AU - Streck,T.* AU - Kanddeler, E.* AU - Schloter, M. C1 - 10861 C2 - 30382 SP - 933-940 TI - The influence of the herbicide 2-methyl-4-chlorophenoxyacetic acid (MCPA) on the mineralization of litter-derived alkanes and the abundance of the alkane monooxygenase gene (alkB) in the detritusphere of Pisum sativum (L.). JO - Biol. Fertil. Soils VL - 48 IS - 8 PB - Springer PY - 2012 SN - 0178-2762 ER - TY - JOUR AB - In the last years, archaea have been identified as key players in global N cycling, especially in nitrification. Ammonia-oxidizing archaea (AOA) are postulated tobelong to the new phylum Thaumarchaeota for which the lipid crenarchaeol should be specific. The ratios between two independent markers for AOA, the ammonia monooxygenase gene and crenarchaeol have been studied in different aerated soils, but so far not in flooded soils. This study investigated ammonia-oxidizing archaea in four paddy soils and a tidal wetland. Ratios were significantly higher in the paddy soils compared to the tidal wetland and in general higher as in upland soils, leading to the assumption that archaeal ammonia oxidizers different from crenarchaeol-containing Thaumarchaeota may play an important role in paddy soils. AU - Bannert, A.* AU - Mueller-Niggemann, C.* AU - Kleineidam, K. AU - Wissing, L.* AU - Cao, Z.-H.* AU - Schwark, L.* AU - Schloter, M. C1 - 6546 C2 - 28858 SP - 839-843 TI - Comparison of lipid biomarker and gene abundance characterizing the archaeal ammonia-oxidizing community in flooded soils. JO - Biol. Fertil. Soils VL - 47 IS - 7 PB - Springer PY - 2011 SN - 0178-2762 ER - TY - JOUR AB - Difloxacin (DIF) belongs to the fluoroquinolones, a frequently detected group of antibiotics in the environment. It is excreted in pig manure to a large extent and may consequently reach soils in potentially effective concentrations via manuring. The aim of this study was to assess the effects of DIF-spiked manure on microbial communities and selected functions in soils in a microcosm experiment up to 1 month after application. To test a dose dependency of the effects, three different concentrations of DIF (1, 10 and 100 mg/kg of soil) were used. Microcosms with application of pure manure, as well as untreated microcosms served as control. The addition of pure manure resulted in an increase of microbial biomass and soil respiration as well as a reduced bacteria/fungi ratio. Due to the fast and strong immobilisation of DIF, effects of the antbiotic compound were only visible up to 8 days after application (microbial biomass; respiration; potential denitrification; ratio of bacteria/fungi). As expected these short-term effects resulted in reduced potential denitrification rates as well as a reduced bacteria/fungal ratio in the treatments were DIF has been applied. Surprisingly, microbial biomass values as well as respiration rates were increased by DIF application. Other parameters like nitrate and ammonium content in soil were not influenced by DIF application at any time point. Long-term effects (32 days after application) were only visible for the potential nitrification rates. For those parameters that were influenced by the DIF application a clear dose dependency could not be described. AU - Kotzerke, A.* AU - Hammesfahr, U.* AU - Kleineidam, K. AU - Lamshöft, M.* AU - Thiele-Bruhn, S.* AU - Schloter, M. AU - Wilke, B.M.* C1 - 4788 C2 - 28407 CY - New York SP - 177-186 TI - Influence of difloxacin-contaminated manure on microbial community. JO - Biol. Fertil. Soils VL - 47 IS - 2 PB - Springer PY - 2011 SN - 0178-2762 ER - TY - JOUR AB - Ethyl tert-butyl ether (ETBE) and tert-amyl methyl ether (TAME) are synthetic compounds that are used as gasoline additives in order to reduce emissions from vehicles. In the present study, effects of these compounds were investigated on the dynamics of inorganic N in soil. Therefore, soil samples with different water contents were contaminated with ETBE and TAME, respectively. It could be shown that in the presence of TAME and ETBE, NH (4) (+) -N accumulated; moreover, ETBE addition to soil resulted in increased NO (2) (-) -N concentrations. These results indicated for the first time that ETBE and TAME can affect nitrification in soil. Thus, their impact on soil ecology should be investigated more intensively. AU - Bartling, J.* AU - Schloter, M. AU - Wilke, B.M.* C1 - 196 C2 - 27063 SP - 299-302 TI - Ethyl tert-butyl ether (ETBE) and tert-amyl methyl ether (TAME) can affect distribution pattern of inorganic N in soil. JO - Biol. Fertil. Soils VL - 46 IS - 3 PB - Springer PY - 2010 SN - 0178-2762 ER - TY - JOUR AB - In terrestrial ecosystems, the majority of soil N is present in organic macromolecules like proteins, nucleic acids and chitin. Because these compounds cannot be assimilated by plants, plant growth is often N-limited. Therefore, the hydrolysis of proteins and chitin is particularly important in making N available for plants. In this study, we investigated the influence of different potato cultivars and different plant developmental stages on the abundance of genes encoding for alkaline and neutral metalloproteases (apr, npr) as well as bacterial chitinases (chiA) in the rhizosphere using quantitative real-time PCR in a greenhouse trial and a field study. It could be clearly demonstrated that abundance pattern was mainly affected by the plant vegetation stage, whilst the used plant genotype had only a minor influence on the development of the two functional populations. AU - Gschwendtner, S. AU - Reichmann, M.* AU - Müller, M.* AU - Radl, V. AU - Munch, J.-C. AU - Schloter, M. C1 - 771 C2 - 27236 SP - 649-652 TI - Abundance of bacterial genes encoding for proteases and chitinases in the rhizosphere of three different potato cultivars. JO - Biol. Fertil. Soils VL - 46 IS - 6 PB - Springer PY - 2010 SN - 0178-2762 ER - TY - JOUR AB - The antibiotic sulfadiazine (SDZ) can affect denitrifying bacteria in soil. However, effects on denitrifiers in the gut of earthworms have not been described so far. Therefore, the influence of SDZcontaminated manure applied to soil on denitrifiers in the gut of the earthworm Eisenia fetida was assessed by quantitative PCR targeting genes coding for nirK- and nirS- type nitrite reductases of denitrifiers. Gut contents of Eisenia fetida contained 2.5 x 106 and 5.1 x 105 gene copies of nirK and nirS, respectively, after two weeks in soils amended with manure only. Copy numbers of nirK and nirS in gut contents from manure treatments with SDZ were up to 10 times less. Overall, the data indicate a negative impact of SDZ on denitrifiers in the gut of earthworms. AU - Kotzerke, A.* AU - Klemer, S.* AU - Kleineidam, K. AU - Horn, M.A.* AU - Drake, H.L.* AU - Schloter, M. AU - Wilke, B.-M.* C1 - 413 C2 - 27104 SP - 415-418 TI - Manure contaminated with the antibiotic sulfadiazine impairs the abundance of nirK- and nirS-type denitrifiers in the gut of the earthworm Eisenia fetida. JO - Biol. Fertil. Soils VL - 46 IS - 4 PB - Springer PY - 2010 SN - 0178-2762 ER - TY - JOUR AB - Due to disruption of soil aggregates and cell lysis and the subsequent release of organic C and N, increased microbial N transformation processes can be observed after freeze-thaw cycles. In a microcosm study, we investigated the influence of plant residues with different C/N ratios (lucerne-clover-grass-mix and wheat straw) on N transformations and the abundance pattern of the corresponding functional genes in an arable soil after freezing and thawing. Unfrozen soil samples, continuously incubated at 10°C, served as control. Concentration of soil NH4+, NO3−, and water-extractable organic C (WEOC) as well as genes involved in nitrification and denitrification, quantified by real-time PCR, were determined before freezing and 1, 3, and 7 days after thawing. The amounts of inorganic N and WEOC as well as the investigated gene abundance pattern did hardly differ between control samples and samples subjected to freezing and thawing that have been amended with straw. In contrast, clear alterations of the measured parameters and abundances were observed after freezing and thawing in samples being amended with the lucerne-clover-grass-mix compared to the control samples. AU - Su, M. AU - Kleineidam, K. AU - Schloter, M. C1 - 2220 C2 - 27170 SP - 537-541 TI - Influence of different litter quality on the abundance of genes involved in nitrification and denitrification after freezing and thawing of an arable soil. JO - Biol. Fertil. Soils VL - 46 IS - 5 PB - Springer PY - 2010 SN - 0178-2762 ER - TY - JOUR AB - The diversity of soil proteolytic community encoding for subtilisin (sub) was investigated at a cultivated field site with four different soil types and at three different depths in April, July, and October. A terminal restriction fragment length polymorphism (T-RFLP) analysis of subtilisin gene (sub) was applied to study dynamic of the sub gene pool. The aim of the present study was to relate differences in sub community structure to the vertical, site, and seasonal variations naturally occurring at the field site under investigation. A significant spatial variability in the community structure of sub-containing bacteria was observed. The richness of sub proteolytic bacterial population decreased with increasing soil depth, revealing the highest values in upper layers. A similar trend was observed among the different sites; the highest diversity was noticed at the site with the highest silt and nutrient content. The reasons behind the observed patterns in the community structure might be varying water amount and spatial isolation along the soil profile as well as variability of the quantity and quality of available substrates among different depths and different sites. AU - Fuka, M.M. AU - Engel, M. AU - Haesler, F. AU - Welzl, G. AU - Munch, J.-C. AU - Schloter, M. C1 - 3380 C2 - 25823 SP - 185-191 TI - Diversity of proteolytic community encoding for subtilisin in an arable field: Spatial and temporal variability. JO - Biol. Fertil. Soils VL - 45 IS - 2 PB - Springer PY - 2008 SN - 0178-2762 ER - TY - JOUR AB - In this study, the role of compost amendments for the biocontrol of Pythium ultimum was evaluated in bioassays with cucumber (Cucumis sativa L. variety “Chinesische Schlangen”). The addition of compost to the peat-based growing substrates resulted in a significant reduction of disease symptoms of cucumber plants in the presence of P. ultimum compared to pure substrate. Microbial community composition of compost-amended substrates and with different levels of P. ultimum inoculum (0, 5‰) was analyzed by polymerase-chain-reaction-based techniques. To detect and compare dominant bacterial and fungal representatives of suppressive substrate mixes with different pathogen inoculum, 16S and 18S rRNA clone libraries were established. Phylogenetic analysis of the 16S rRNA clones revealed Actinobacteria and ?-Proteobacteria to be the prominent classes in the presence of P. ultimum, which are not part of the dominant microflora in the mixes without the pathogen. 18S rRNA sequences for the Pythium-inoculated compost supplemented samples were dominated by Chytridiomycota and Sordariomycetes, whereas in uncontaminated soil–compost mixes, a large part of the sequences were related to Homobasidiomycetes. Thus, it is assumed that the presence of P. ultimum induces distinct shifts in microbial communities favoring to groups known to comprise potential biocontrol agents. AU - Hagn, A. AU - Engel, M. AU - Kleikamp, B.* AU - Munch, J.-C. AU - Schloter, M. AU - Bruns, C.* C1 - 4159 C2 - 25107 SP - 481-490 TI - Microbial community shifts in Pythium ultimum -inoculated suppressive substrates. JO - Biol. Fertil. Soils VL - 44 IS - 3 PB - Springer PY - 2008 SN - 0178-2762 ER - TY - JOUR AB - The changes in size, activity and structure of soil microbial community caused by N fertilization were studied in a laboratory incubation experiment. The rates of N fertiliser applied (KNO3) were 0 (control), 100 and 2,000 ?g N g-1 soil. Despite no extra C sources added, a high percentage of N was immobilized. Whereas no significant increase of microbial C was revealed during incubation period, microbial growth kinetics as determined by the substrate-induced growth-response method demonstrated a significant decrease in the specific growth rate of microbial community in soil treated with 2,000 ?g N g-1 soil. Additionally, a shift in microbial community structure resulting in an increase in fungal biomarkers, mainly in the treatment with 2,000 ?g N g-1 soil was visible. AU - Yevdokimov., I.* AU - Gattinger, A.* AU - Buegger, F. AU - Munch, J.-C. AU - Schloter, M. C1 - 1385 C2 - 25553 SP - 1103-1106 TI - Changes in microbial community structure in soil as a result of different amounts of nitrogen fertilization. JO - Biol. Fertil. Soils VL - 44 IS - 8 PB - Springer PY - 2008 SN - 0178-2762 ER - TY - JOUR AB - To improve our knowledge about the effect of soil structure on potential nitrification (PN) rates in different soil aggregate fractions, we adapted and validated the standard method based on International Organization of Standardization (ISO) 15685 to small sample volumes. This assay was used to determine the distribution of PN in soil aggregates obtained from three different sites (natural grassland, agricultural land and forest). Overall, the external surface layers of the aggregates showed higher PN rates than the interior fractions of the aggregates. These differences were more clear in clayey than in sandy soils. AU - Hoffmann, H.* AU - Schloter, M. AU - Wilke, B.-M.* C1 - 2703 C2 - 24815 SP - 411-413 TI - Microscale-scale measurement of potential nitrification rates of soil aggregates. JO - Biol. Fertil. Soils VL - 44 IS - 2 PB - Springer PY - 2007 SN - 0178-2762 ER - TY - JOUR AB - The turnover of N derived from rhizodeposition of faba bean (Vicia faba L.), pea (Pisum sativum L.) and white lupin (Lupinus albus L.) and the effects of the rhizodeposition on the subsequent C and N turnover of its crop residues were investigated in an incubation experiment (168 days, 15 °C). A sandy loam soil for the experiment was either stored at 6 °C or planted with the respective grain legume in pots. Legumes were in situ 15N stem labelled during growth and visible roots were removed at maturity. The remaining plant-derived N in soil was defined as N rhizodeposition. In the experiment the turnover of C and N was compared in soils with and without previous growth of three legumes and with and without incorporation of crop residues. After 168 days, 21% (lupin), 26% (faba bean) and 27% (pea) of rhizodeposition N was mineralised in the treatments without crop residues. A smaller amount of 15–17% was present as microbial biomass and between 30 and 55% of mineralised rhizodeposition N was present as microbial residue pool, which consists of microbial exoenzymes, mucous substances and dead microbial biomass. The effect of rhizodeposition on the C and N turnover of crop residues was inconsistent. Rhizodeposition increased the crop residue C mineralisation only in the lupin treatment; a similar pattern was found for microbial C, whereas the microbial N was increased by rhizodeposition in all treatments. The recovery of residual 15N in the microbial and mineral N pool was similar between the treatments containing only labelled crop residues and labelled crop residues + labelled rhizodeposits. This indicates a similar decomposability of both rhizodeposition N and crop residue N and may be attributable to an immobilisation of both N sources (rhizodeposits and crop residues) as microbial residues and a subsequent remineralisation mainly from this pool. AU - Mayer, J.* AU - Buegger, F. AU - Jensen, E.S.* AU - Schloter, M. AU - Hess J.* C1 - 1243 C2 - 21689 SP - 153-164 TI - Turnover of grain legume N rhizodeposits and effect of rhizodeposition on the turnover of crop residues. JO - Biol. Fertil. Soils VL - 39 IS - 3 PB - Springer PY - 2004 SN - 0178-2762 ER - TY - JOUR AB - Fungal communities and their dynamics were investigated in relation to season, soil type and farming management practice. The research was done using soils from high- (H) and low-yield areas (L) of a field site cultivated with winter wheat under two different farming management systems (precision farming, P; conventional farming, C) over the vegetation period. Fungal diversity was analysed by cultivation-independent methods [direct extraction of DNA from soil followed by PCR amplification of a subunit of the 18S rDNA and fingerprinting (DGGE)] as well as cultivation-dependent techniques (isolation of pure cultures). The comparisons of the PCR amplicons by DGGE patterns showed no differences between the different sampling sites and no influence of the farming management systems. Only small differences were observed over the vegetation period. For cultivation purposes active hyphae were isolated using a soil-washing technique. The resulting isolates were subcultured and grouped by their morphology and genotype. In contrast to the cultivation independent approaches, clear site-specific and seasonal effects on the fungal community structure could be observed. However, minor effects of the different farming management techniques applied were visible for active populations. These results clearly indicate that the potential fungal community (including spores), investigated by the cultivation-independent approach, is almost entirely uninfluenced by the investigated factors, whereas active populations show a clear response to environmental changes. The most abundant group consisting of Trichoderma species was investigated in more detail using strain-specific genotype based fingerprinting techniques as well as a screening for potential biocontrol activity against the wheat pathogen Fusarium graminearum. The genotypic distribution as well as the potential biocontrol activity revealed clear site-specific patterns. AU - Hagn, A. AU - Pritsch, K. AU - Schloter, M. AU - Munch, J.-C. C1 - 22317 C2 - 21136 SP - 236-244 TI - Fungal diversity in agricultural soil under different farming management systems, with special reference to biocontrol strains of Trichoderma spp. JO - Biol. Fertil. Soils VL - 38 IS - 4 PY - 2003 SN - 0178-2762 ER - TY - JOUR AU - Lucas Garcia, J.A.* AU - Schloter, M. AU - Durkaya, T. AU - Hartmann, A. AU - Gutiérrez Manero, F.J.* C1 - 22278 C2 - 21053 SP - 381-385 TI - Colonization of pepper roots by a plant growth promoting Pseudomonas fluorescens strain. JO - Biol. Fertil. Soils VL - 37 PB - Springer PY - 2003 SN - 0178-2762 ER - TY - JOUR AB - This review discusses the analysis of whole-community phospholipid fatty acid (PLFA) profiles and the composition of lipopolysaccharides in order to assess the microbial biomass and the community structure in soils. For the determination of soil microbial biomass a good correlation was obtained between the total amount of PLFAs and the microbial biomass measured with methods commonly used for determinations such as total adenylate content and substrate-induced respiration. Generally, after the application of multivariate statistical analyses, whole-community fatty acid profiles indicate which communities are similar or different. However, in most cases, the organisms accounting for similarity or difference cannot be determined, and therefore artefacts could not be excluded. The fatty acids used to determine the biomass vary from those which determine the community structure. Specific attention has to be paid when choosing extraction methods in order to avoid the liberation of fatty acids from non-living organic material and deposits, and to exclude the non-target selection of lipids from living organisms, as well. By excluding the fatty acids which were presumed to be common and widespread prior to multivariate statistical analysis, estimates were improved considerably. Results from principal component analysis showed that determining the levels of fatty acids present in both low and high concentrations is essential in order to correctly identify microorganisms and accurately classify them into taxonomically defined groups. The PLFA technique has been used to elucidate different strategies employed by microorganisms to adapt to changed environmental conditions under wide ranges of soil types, management practices, climatic origins and different perturbations. It has been proposed that the classification of PLFAs into a number of chemically different subgroups should simplify the evaluating procedure and improve the assessment of soil microbial communities, since then only the subgroups assumed to be involved in key processes would be investigated. AU - Zelles, L. C1 - 20852 C2 - 18906 SP - 111-129 TI - Fatty acid patterns of phospholipids and lipopolysaccarides in the characterisation of microbial communities in soil : a review. JO - Biol. Fertil. Soils VL - 29 IS - 2 PY - 1999 SN - 0178-2762 ER - TY - JOUR AB - Three soil types - Calcaric Phaeozem, Eutric Cambisol and Dystric Lithosol - in large container pots were experimentally contaminated with heavy metals at four different levels (light pollution: 300 ppm Zn, 100 ppm Cu, 50 ppm Ni, 50 ppm V and 3 ppm Cd: medium pollution: twofold concentrations; heavy pollution: threefold concentrations: uncontaminated control). We investigated the prognostic potential of 16 soil microbial properties (microbial biomass, respiration, N mineralization, 13 soil enzymes involved in cycling of C, N, P and S) with regard to their ability to differentiate the four contamination levels. Microbial biomass and enzyme activities decreased with increasing heavy metal pollution, but the amount of decrease differed among the enzymes. Enzymes involved in the C-cycling were least affected, whereas various enzyme activities related to the cycling of N, P and S showed a considerable decrease in activity. In particular, arylsulfatase and phosphatase activities were dramatically affected. Their activity decreased to a level of a few percent of their activities in the corresponding unpolluted controls. The data suggest that aside front the loss of rare biochemical capabilities - such as the growth of organisms at the expense of aromatics (Reber 1992) - heavy metal contaminated soils lose very common biochemical propertities which are necessary for the functioning of the ecosystem. Cluster analysis as well as discriminant analysis underline the similarity of the enzyme activity pattern among the controls and among the polluted soils. The trend toward a significant functional diversity loss becomes obvious already at the lowest pollution level. This implies that concentrations of heavy metals in soils near the current EC limits will most probably lead to a considerable reduction in decomposition and nutrient cycling rates. We conclude that heavy metal pollution severely decreases the functional diversity of the soil microbial community and impairs specific pathways of nutrient cycling. AU - Kandeler, E.* AU - Kampichler, C. AU - Horak, O.* C1 - 53848 C2 - 0 SP - 299-306 TI - Influence of heavy metals on the functional diversity of soil microbial communities. JO - Biol. Fertil. Soils VL - 23 IS - 3 PY - 1996 SN - 0178-2762 ER - TY - JOUR AB - Heat output can be used as an indicator of microbial activity and is usually measured in a microcalorimeter with closed ampoules. In long-term experiments particularly, interpretation of the data is hindered by the changing environment in the closed ampoules because of O2 consumption and CO2 enrichment. We used a combination of a flow-microcalorimeter and a gas chromatograph to measure the heat flux and CO2 and N2O production rates under controlled conditions. Simultaneous detection of the heat output and CO2 emission allowed calculation of the calorimetric: CO2 (Cal/CO2) ratio. A mean ratio of-435 kJ mol-1 CO2 was detected in six different soils amended with glucose and incubated under aerobic conditions. This ratio indicated that CO2 was the end-product of catabolism. In wet 10-12 mm soil aggregates of a gleyic vertisol amended with glucose, values of-285 kJ mol-1 CO2 under an aerobic and-141 kJ mol-1 CO2 under a N2 atmosphere was determined. These findings indicated that fermentative metabolism occurred. The Cal/CO2 ratio was not affected when enough NOinf3 sup-was available and denitrification processes (N2O production) were possible. © 1995 Springer-Verlag. AU - Albers, B.P. AU - Beese, F. AU - Hartmann, A. C1 - 23186 C2 - 31479 SP - 203-208 TI - Flow-microcalorimetry measurements of aerobic and anaerobic soil microbial activity. JO - Biol. Fertil. Soils VL - 10 IS - 2-3 PB - Springer PY - 1995 SN - 0178-2762 ER - TY - JOUR AB - Sublethal effects of terbuthylazine and carbofuran on the growth and reproduction of Eisenia andrei were investigated over a period of three generations. Reproduction was assessed by measuring the coccon production of worms treated chronically with pesticides. Inhibition of cocoon production was found in the parental generation. Hatchlings were raised from cocoons to provide the F1 generation. During raising a more rapid growth of juveniles treated with terbuthylazine was observed, compared with the growth of untreated worms. The increase in vitality was also found in cocoon production. Groups treated with terbuthylazine produced more cocoons than controls. The F2 generation was raised from hatchlings of the F1 generation, and here, also the terbuthylazine treatments increased earthworm growth, but not cocoon production. Exposure to carbofuran decreased cocoon production in all generations. Growth of the F1 generation was not influenced by low concentrations of carbofuran. AU - Brunninger, B.M. AU - Beese, F. AU - Viswanathan, R. C1 - 20622 C2 - 13835 SP - 83-88 TI - Terbuthylazine and Carbofuran Effects on Growth and Reproduction within three Generations of Eisenia foetida SAV. (Oligachaeta). JO - Biol. Fertil. Soils VL - 18 IS - 2 PY - 1994 SN - 0178-2762 ER - TY - JOUR AB - The presence of tryptophan in soil and auxin production by indigenous soil microbes are considered to be important natural plant growth-promoting factors. In order to elucidate the natural regulation of microbial auxin synthesis, we treated different soils by an air drying/rewetting cycle and measured pool sizes of auxins, auxin precursors, and degradation products of tryptophan together with a range of respiration parameters. Potential (tryptophan addition) microbial production of indole-3-acetic acid (auxin) was predominant in the equilibrated fresh soils. Auxin production depended on the soil nutrient content, and the size and metabolic status of the microbial biomass. Immediately after rewetting, potential auxin production was low, whereas potential indole-3-ethanol and anthranilic acid production as well as basal respiration were transitionally enhanced. This was concurrent with proliferation of r-strategist microbes. After the respiration flush, the natural tryptophan contents increased, indicating cell lysis, probably caused by a rise in protozoan grazing on the r-strategists. Auxin production was high in fresh and in re-equilibrating rewetted soils, probably due to nutritional limitations under stationary conditions. Hence, this high production was attributed to the K-strategist component of the soil microflora. The differences observed in the recovery of auxin production between the different rewetted soils suggest that original activities can become re-established rapidly when the indigenous microbial community is pre-adapted to the stress. We propose that the release of tryptophan, microbial auxin, and the shift towards indole-3-ethanol production function as stimulants for root development induced by environmental fluctuations. © 1994 Springer-Verlag. AU - Lebuhn, M. AU - Heilmann, B. AU - Hartmann, A. C1 - 23188 C2 - 31487 SP - 302-310 TI - Effects of drying/rewetting stress on microbial auxin production and L-tryptophan catabolism in soils. JO - Biol. Fertil. Soils VL - 18 IS - 4 PB - Springer PY - 1994 SN - 0178-2762 ER - TY - JOUR AB - Seasonal effects of liming, irrigation, and acid precipitation on microbial biomass N and some physicochemical properties of different topsoil horizons in a spruce forest (Picea abies L.) were measured throughout one growing season. The highest biomass N was recorded in autumn and spring in the upper soil horizons, while the lowest values were obtained in summer and in deeper horizons. The clearest differences between the different soil treatments were apparent in autumn and in the upper horizons. Liming increased the microbial biomass N from 1.7% of the total N content to 6.8% (Olf1 layer) and from 1% to 2% of the total N content in the Of2 layer. The main inorganic-N fraction in the deeper horizons was NOinf3 sup-. An increase in cation exchange capacity was observed down to the Oh layer, while soil pH was only slightly higher in the Olf1 and Of2 layers after liming. The effects of irrigation were less marked. The microbial biomass N increased from 1.7% of total N to 4.8% in the Olf1 layer and from 1% to 2% of total N in the Of2 layer. In the Olf1 layer an increase in C mineralization was observed. Acid precipitation decreased the microbial biomass N in the upper horizons from 4.8% of total N to 1.8% in the Olf1 layer and from 2% to 0.5% in the Of2 layer. No significant changes in soil pH were observed, but the decrease in cation exchange capacity may result in a decrease in the proton buffering capacity in the near future. AU - von Lützow, M. AU - Zelles, L. AU - Scheunert, I. AU - Ottow, J.C.G.* C1 - 40517 C2 - 38794 SP - 130-134 TI - Seasonal effects of liming, irrigation, and acid precipitation on microbial biomass N in a spruce (Picea abies L.) forest soil. JO - Biol. Fertil. Soils VL - 13 IS - 3 PY - 1992 SN - 0178-2762 ER - TY - JOUR AB - The use of lime increased heat output and decreased the C:N ratio (global indicators of biological activity) in the organic horizons of a spruce forest (Picea abies L.) soil. These changes were still present after 18 years. During the same period, the muramic acid content increased slightly, while the concentration of both ergosterol and glucosamine decreases. The ratios of ergosterol or glucosamine to muramic acid decreased significantly after 3 years in the plots that had been irrigated and limed, and after 8 years in the limed non-irrigated plots. AU - Zelles, L. AU - Stepper, K.* AU - Zsolnay, A. C1 - 42595 C2 - 40235 SP - 78-82 TI - The effect of lime on microbial activity in spruce (Picea abies L.) forests. JO - Biol. Fertil. Soils VL - 9 IS - 1 PY - 1990 SN - 0178-2762 ER - TY - JOUR AB - The optimal release and quantitative estimation of muramic acid and glucosamine were studied simultaneously in soil samples. The effect of hydrolysis conditions, HCl concentration, hydrolysis time, the ratio of soil dry weight to acid, and the recovery of reference substances were investigated. Derivatization of the fluorogenic reagent o-phthalaldehyde, in the presence of 2-mercaptoethanol with the residue of a soil hydrolysate, was achieved by optimizing the relative amounts of o-phthalaldehyde to hydrolysate in the reaction mixture, the pH of both, and the incubation period. A linear relationship was found between the fluorescence response and the concentration of the test substances. The muramic acid, as well as the glucosamine (o-phthalaldehyde) derivatives gave single peaks, and complete separation from interfering substances at the picomol level was achieved in a short time (3 h preparation and 30 min for chromatography) by using high-performance liquid chromatography. AU - Zelles, L. C1 - 42156 C2 - 36132 SP - 125-130 TI - The simultaneous determination of muramic acid and glucosamine in soil by high-performance liquid chromatography with precolumn fluorescence derivatization. JO - Biol. Fertil. Soils VL - 6 IS - 2 PY - 1988 SN - 0178-2762 ER - TY - JOUR AB - The stimulative effect of lime on the bioactivity of various soil horizons was demonstrated by the ATP test, and respiration and microcalorimetric measurements, but not by FDA hydrolysis or the iron reduction test. The latter showed clear inhibition. When the natural structure of layers was saved while sampling, a smaller stimulation of bioactivity was observed than in the case of mixing natural layers. No stimulation was recorded when the lime layer was removed. AU - Zelles, L. AU - Scheunert, I. AU - Kreutzer, K.* C1 - 41180 C2 - 36609 SP - 211-216 TI - Bioactivity in limed soil of a spruce forest. JO - Biol. Fertil. Soils VL - 3 IS - 4 PY - 1987 SN - 0178-2762 ER - TY - JOUR AB - The effects of irrigation, acid precipitation and liming on the bioactivity in a spruce forest soil were measured with different tests. Except for the iron reduction test and the FDA hydrolysis, the highest activities were measured in the upper horizons and mostly decreased gradually in the deeper ones. The determination of heat output and respiration without additional energy supply and ATP measurement gave similar results: acid precipitation inhibits the bioactivity in O1 and Of1, layers; lime stimulated it mostly in Of2 horizons. Except for the results of ATP measurement, in Of2 horizons the influence of lime exceeded that of acid irrigation. The results obtained from respiration and microcalorimetric measurements after the introduction of an energy supply were similar: Humidity, derived either from acid precipitation or from irrigation, stimulated the activity as well as lime, clearly in Of2, to a smaller extent also in deeper horizons. The bioactivity in Oft increased significantly in the plots in the order: control, plot with acid irrigation, plot with normal irrigation, limed plot, limed plot with acid irrigation, and limed plot with normal irrigation. The difference between irrigated and acid-irrigated plots is due to the inhibitive effects of protons and SO4 2-. The FDA hydrolysis test showed a clear stimulative effect of humidity in Of horizons of non-limed plots. With the iron reduction test, stimulation in acid-irrigated and inhibition in limed samples was demonstrated. The maximum bioactivity measured with this method was localized in deeper horizons. AU - Zelles, L. AU - Scheunert, I. AU - Kreutzer, K.* C1 - 41883 C2 - 36237 SP - 137-143 TI - Effect of artificial irrigation, acid precipitation and liming on the microbial activity in soil of a spruce forest. JO - Biol. Fertil. Soils VL - 4 IS - 3 PY - 1987 SN - 0178-2762 ER -