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Acidobacteria occur in a large variety of ecosystems worldwide and are particularly abundant and highly diverse in soils. In spite of their diversity, only few species have been characterized to date which makes Acidobacteria one of the most poorly understood phyla among the domain Bacteria. We used a culture-independent niche modeling approach to elucidate ecological adaptations and their evolution for 4,154 operational taxonomic units (OTUs) of Acidobacteria across 150 different, comprehensively characterized grassland soils in Germany. Using the relative abundances of their 16S rRNA gene transcripts, the responses of active OTUs along gradients of 41 environmental variables were modeled using hierarchical logistic regression (HOF), which allowed to determine values for optimum activity for each variable (niche optima). By linking 16S rRNA transcripts to the phylogeny of full 16S rRNA gene sequences, we could trace the evolution of the different ecological adaptations during the diversification of Acidobacteria. This approach revealed a pronounced ecological diversification even among acidobacterial sister clades. Although the evolution of habitat adaptation was mainly cladogenic, it was disrupted by recurrent events of convergent evolution that resulted in frequent habitat switching within individual clades. Our findings indicate that the high diversity of soil acidobacterial communities is largely sustained by differential habitat adaptation even at the level of closely related species. A comparison of niche optima of individual OTUs with the phenotypic properties of their cultivated representatives showed that our niche modeling approach (1) correctly predicts those physiological properties that have been determined for cultivated species of Acidobacteria but (2) also provides ample information on ecological adaptations that cannot be inferred from standard taxonomic descriptions of bacterial isolates. These novel information on specific adaptations of not-yet-cultivated Acidobacteria can therefore guide future cultivation trials and likely will increase their cultivation success. [ABSTRACT FROM AUTHOR]

Evidence from experimental and established grasslands indicates that plant biodiversity can modify the water cycle. One suspected mechanism behind this is a higher infiltration capacity (νB) and hydraulic conductivity (K) of the soil on species‐rich grasslands. However, in established and agriculturally managed grasslands, biodiversity effects cannot be studied independent of land‐use effects. Therefore, we investigated in established grassland systems how land‐use intensity and associated biodiversity of plants and soil animals affect νB and K at and close to saturation. On 50 grassland plots along a land‐use intensity gradient in the Biodiversity Exploratory Schwäbische Alb, Germany, we measured νB with a hood infiltrometer at several matrix potentials and calculated the saturated and unsaturated K. We statistically analysed the relationship between νB or K and land‐use information (e.g., fertilising intensity), abiotic (e.g., soil texture) and biotic data (e.g., plant species richness, earthworm abundance). Land‐use intensity decreased and plant species richness increased νB and K, while the direction of the effects of soil animals was inconsistent. The effect of land‐use intensity on νB and K was mainly attributable to its negative effect on plant species richness. Our results demonstrate that plant species richness was a better predictor of νB and K at and close to saturation than land‐use intensity or soil physical properties in the established grassland systems of the Schwäbische Alb. [ABSTRACT FROM AUTHOR]

Aims: An essential task of agricultural systems is to improve internal phosphorus (P) recycling. Cover crops and tillage reduction can increase sustainability, but it is not known whether stimulation of the soil microbial community can increase the availability of soil organic P pools. Methods: In a field experiment in southwest Germany, the effects of a winter cover crop mixture (vs. bare fallow) and no-till (vs. non-inversion tillage) on microbial P-cycling were assessed with soybean as the main crop. Microbial biomass, phospholipid fatty acids (PLFAs), P cycling enzymes, and carbon-substrate use capacity were linked for the first time with the lability of organic P pools measured by enzyme addition assays (using phosphodiesterase, non-phytase-phosphomonoesterase and fungal phytase). Results: Microbial phosphorus, phosphatase, and fatty acids increased under cover crops, indicating an enhanced potential for organic P cycling. Enzyme-stable organic P shifted towards enzyme-labile organic P pools. Effects of no-till were weaker, and a synergy with cover crops was not evident. Conclusions: In this experiment, cover crops were able to increase the microbially mediated internal P cycling in a non-P-limited, temperate agroecosystems. [ABSTRACT FROM AUTHOR]

Aerated topsoils are important sinks for atmospheric methane (CH4) via oxidation by CH4‐oxidizing bacteria (MOB). However, intensified management of grasslands and forests may reduce the CH4 sink capacity of soils. We investigated the influence of grassland land‐use intensity (150 sites) and forest management type (149 sites) on potential atmospheric CH4 oxidation rates (PMORs) and the abundance and diversity of MOB (with qPCR) in topsoils of three temperate regions in Germany. PMORs measurements in microcosms under defined conditions yielded approximately twice as much CH4 oxidation in forest than in grassland soils. High land‐use intensity of grasslands had a negative effect on PMORs (−40%) in almost all regions and fertilization was the predominant factor of grassland land‐use intensity leading to PMOR reduction by 20%. In contrast, forest management did not affect PMORs in forest soils. Upland soil cluster (USC)‐α was the dominant group of MOBs in the forests. In contrast, USC‐γ was absent in more than half of the forest soils but present in almost all grassland soils. USC‐α abundance had a direct positive effect on PMOR in forest, while in grasslands USC‐α and USC‐γ abundance affected PMOR positively with a more pronounced contribution of USC‐γ than USC‐α. Soil bulk density negatively influenced PMOR in both forests and grasslands. We further found that the response of the PMORs to pH, soil texture, soil water holding capacity and organic carbon and nitrogen content differ between temperate forest and grassland soils. pH had no direct effects on PMOR, but indirect ones via the MOB abundances, showing a negative effect on USC‐α, and a positive on USC‐γ abundance. We conclude that reduction in grassland land‐use intensity and afforestation has the potential to increase the CH4 sink function of soils and that different parameters determine the microbial methane sink in forest and grassland soils. [ABSTRACT FROM AUTHOR]

This paper aims to reconstruct Middle Bronze Age (MBA; 1600–1250 BCE) land use practices in the northwestern Alpine foreland (SW Germany, Hegau). We used a multi-proxy approach including the analysis of biogeochemical proxies from colluvial deposits and buried topsoils in the surroundings of the well-documented settlement site of Anselfingen and off-site pollen data from two peat bogs. This approach allowed for in-depth insights into the MBA subsistence economy and shows that the MBA in the northwestern Alpine foreland was a period of establishing settlements with sophisticated land management and land use practices. The reconstruction of phases of colluvial deposition was based on ages from optically stimulated luminescence (OSL) and radiocarbon (AMS 14 C) dating from multi-layered colluvial deposits and supports the local archaeological record with the first phase of major colluvial deposition occurring during the MBA followed by phases of colluvial deposition during the Iron Age, the Medieval period and modern times. The on-site deposition of charred archaeobotanical remains and animal bones from archaeological features, as well as polycyclic aromatic hydrocarbons (PAHs), charcoal spectra, phytoliths, soil microstructure, urease enzymatic activity, microbial biomass carbon (C mic) and heavy metal contents from colluvial deposits, were used as proxies for on-site and near-site land use practices. The charcoal spectra indicate MBA forest management which favored the dominance of Quercus in the woodland vegetation in the surrounding area north of the settlement site. Increased levels of 5 β stanols (up to 40 %) and the occurrence of pig bones (up to 14 %) support the presence of a forest pasture mainly used for pig farming. In the surrounding area south of the settlement, an arable field with a buried MBA plow horizon (2Apb) could be verified by soil micromorphological investigations and high concentrations of grass phytoliths from leaves and stems. Agricultural practices (e.g., plowing) focussed on five staple crops (Hordeum distichon/vulgare , Triticum dicoccum , Triticum monococcum, Triticum spelta , Triticum aestivum/turgidum), while the presence of stilted pantries as storage facilities and of heat stones indicate post-harvest processing of cereal crops and other agrarian products within the settlement. In the area surrounding the settlement, increased levels of urease activity, compared to microbial biomass carbon (up to 2.1 µ g N µ g C mic-1), and input of herbivorous and omnivorous animal faeces indicate livestock husbandry on fallow land. The PAH suites and their spatial distribution support the use of fire for various purposes, e.g., for opening and maintaining the landscape, for domestic burning and for technical applications. The off-site palynological data support the observed change in on-site and near-site vegetation as well as the occurrence of related land use practices. During the Early and Middle Bronze Age, fire played a major role in shaping the landscape (peak of micro-charcoal during the MBA), and anthropogenic activities promoted Quercus -dominated forest ecosystems at the expense of natural beech forests. This indicates a broader regional human influence in the northwestern Alpine foreland at low- and mid-altitude inland sites during the Middle Bronze Age. [ABSTRACT FROM AUTHOR]

Summary: Soils provide a heterogeneous environment varying in space and time; consequently, the biodiversity of soil microorganisms also differs spatially and temporally. For soil microbes tightly associated with plant roots, such as arbuscular mycorrhizal fungi (AMF), the diversity of plant partners and seasonal variability in trophic exchanges between the symbionts introduce additional heterogeneity. To clarify the impact of such heterogeneity, we investigated spatiotemporal variation in AMF diversity on a plot scale (10 × 10 m) in a grassland managed at low intensity in southwest Germany. AMF diversity was determined using 18S rDNA pyrosequencing analysis of 360 soil samples taken at six time points within a year. We observed high AMF alpha‐ and beta‐diversity across the plot and at all investigated time points. Relationships were detected between spatiotemporal variation in AMF OTU richness and plant species richness, root biomass, minimal changes in soil texture and pH. The plot was characterized by high AMF turnover rates with a positive spatiotemporal relationship for AMF beta‐diversity. However, environmental variables explained only ≈20% of the variation in AMF communities. This indicates that the observed spatiotemporal richness and community variability of AMF was largely independent of the abiotic environment, but related to plant properties and the cooccurring microbiome. [ABSTRACT FROM AUTHOR]

Soil protists are increasingly appreciated as essential components of soil foodwebs; however, there is a dearth of information on the factors structuring their communities. Here we investigate the importance of different biotic and abiotic factors as key drivers of spatial and seasonal distribution of protistan communities. We conducted an intensive survey of a 10 m2 grassland plot in Germany, focusing on a major group of protists, the Cercozoa. From 177 soil samples, collected from April to November, we obtained 694 Operational Taxonomy Units representing >6 million Illumina reads. All major cercozoan taxonomic and functional groups were present, dominated by the small flagellates of the Glissomonadida. We found evidence of environmental selection structuring the cercozoan communities both spatially and seasonally. Spatial analyses indicated that communities were correlated within a range of 3.5 m. Seasonal variations in the abundance of bacterivores and bacteria, followed by that of omnivores suggested a dynamic prey-predator succession. The most influential edaphic properties were moisture and clay content, which differentially affected each functional group. Our study is based on an intense sampling of protists at a small scale, thus providing a detailed description of the biodiversity of different taxa/functional groups and the ecological processes involved in shaping their distribution. [ABSTRACT FROM AUTHOR]

The influence of elevated atmospheric CO2 concentrations ([CO2]) on the decomposition of spring wheat (Triticum aestivum L. cv. Triso) residues remaining in the soil after harvest was simulated in a microcosm incubation experiment in the lab. Undisturbed soil cores with and without visible wheat residues were taken in the third year after establishment from a Mini-free-air carbon dioxide enrichment (FACE) system, in which we used 13C-depleted CO2 to determine the contribution of plant-derived carbon to overall carbon mineralization. The Mini-FACE system is located on a Gleyic Cambisol near Hohenheim (Baden-Württemberg, Germany). Carbon dioxide production and leaching of nitrogen and inorganic and organic carbon were measured during 191 days of incubation. Rates of CO2 production were generally highest in all treatments during the first two weeks of the incubation and this was followed by a steady decrease until day 58. After this day mineralization rates declined only weakly until the end of the incubation. Cumulative carbon mineralization was similar in the two treatments without visible wheat residues, but significantly lower in the elevated (−19.0%) versus ambient [CO2] treatment with visible plant residues (significant [CO2]×residue interaction; F 1,13 =7.17; P =0.019). This result demonstrated reduced decomposition of wheat residues grown under elevated [CO2]. The contribution of plant-derived carbon to soil respiration was highest in the beginning, followed by a steady decrease until the end of the incubation. Irrespective of incubation time, the amount of mineralized, plant-derived carbon was higher in the treatment with visible wheat residues. Leaching of inorganic carbon (DIC) tended to be affected by [CO2] (F 6,8 =4.50; P =0.057), with more DIC leached in the elevated [CO2] treatment without (+47.2%) and with visible plant residues (+29.5%) than in the respective ambient CO2 treatments. The amount of carbon potentially sequestered as DIC in the wheat cropping system was small compared to the effects of elevated [CO2] on the amounts and decomposition of plant residues. Increased input of plant residues and reduced decomposition of plant-derived carbon are discussed as possible mechanisms for enhanced carbon sequestration under elevated atmospheric CO2 concentration. [Copyright &y& Elsevier]

Contrasting environmental conditions in topsoil and subsoil determine both abundance and function of soil microbial communities, affecting carbon (C) dynamics throughout the entire soil profile. Although the response of soil microorganisms to single factors such as substrate availability or micro-climatic conditions has been frequently studied, fewer studies have focused on complex interactions between substrate availability and environmental conditions. To address this, we employed vertical soil translocations between topsoil and subsoil horizons of an acid and sandy Dystric Cambisol under European beech forest in Lower Saxony, Germany, to investigate the impact of changing habitat conditions on microbial decomposer communities. To follow microbial substrate utilization at different soil depths, we created hot spots of fresh organic matter (OM) by adding 13C-labelled root litter. Soil samples were taken every three months over an experimental period of twelve months (June 2014 to June 2015). Generally, microbial biomass was strongly controlled by C availability throughout the profile. The importance of root litter as a microbial C source increased from topsoil to subsoil, but changes in available C sources affected fungi and bacteria differently. Fungi preferentially used root litter-derived C throughout the entire soil profile, demonstrating that limited access to preferred substrates, rather than micro-climatic conditions, was the main driver of decreasing fungal abundance with soil depth. In contrast, bacteria intensified utilization of root-derived C only in the absence of alternative C sources in the subsoil and were more strongly affected by spatial separation from C sources. Low soil moisture in combination with the highly sandy subsoil environment limited bacterial access to their substrates and, consequently, bacterial growth. In conclusion, fungal C utilization relies mainly on the quantity of recent plant-derived substrates, whereas bacterial access to substrates is additionally controlled by environmental conditions. This study indicates that limited microbial access to their heterogeneously distributed substrates may be an important factor for C accumulation and stabilization in subsoils. • Micro-climatic conditions inhibit bacterial carbon utilization in subsoil. • Substrate limitation is the main driver of low fungal abundance in subsoil. • Altered carbon sources with soil depth affect the microbial community structure. [ABSTRACT FROM AUTHOR]

Temporal dynamics create unique and often ephemeral conditions that can influence soil microbial biogeography at different spatial scales. This study investigated the relation between decimeter to meter spatial variability of soil microbial community structure, plant diversity, and soil properties at six dates from April through November. We also explored the robustness of these interactions over time. An historically unfertilized, unplowed grassland in southwest Germany was selected to characterize how seasonal variability in the composition of plant communities and substrate quality changed the biogeography of soil microorganisms at the plot scale (10 m × 10 m). Microbial community spatial structure was positively correlated with the local environment, i.e. physical and chemical soil properties, in spring and autumn, while the density and diversity of plants had an additional effect in the summer period. Spatial relationships among plant and microbial communities were detected only in the early summer and autumn periods when aboveground biomass increase was most rapid and its influence on soil microbial communities was greatest due to increased demand by plants for nutrients. Individual properties exhibited varying degrees of spatial structure over the season. Differential responses of Gram positive and Gram negative bacterial communities to seasonal shifts in soil nutrients were detected. We concluded that spatial distribution patterns of soil microorganisms change over a season and that chemical soil properties are more important controlling factors than plant density and diversity. Finer spatial resolution, such as the mm to cm scale, as well as taxonomic resolution of microbial groups, could help determine the importance of plant species density, composition, and growth stage in shaping microbial community composition and spatial patterns. [ABSTRACT FROM AUTHOR]

In this study, drivers for ammonia-oxidation and the related microbial communities (ammonia-oxidizing bacteria and archaea) were investigated in grassland soils on the local as well as on the regional scale focusing on the role of land-use intensity (LUI). To this end, 150 sites from three distinct regions across Germany were selected, covering the whole range of LUI levels (from natural grasslands up to intensive managed meadows). Furthermore, the role of contrasting soil types was analyzed in one of the regions (high vs low organic matter content) for ammonia-oxidation. We revealed a significant increase in potential nitrification rates and abundance of ammonia-oxidizing microbes at two sites on the local level from extensively to intensively managed sites, which indicates that the response pattern of ammonia-oxidizing microbes in grassland soils is likely triggered to a large extent by LUI. However at a third site, where two different soil types were investigated, no correlation between LUI and potential nitrification rates was observed, and only a site-specific effect was apparent. At this site, on the one hand the specific soil type (Histosol) and the related continuous nutrient mobilization from the former peat matrix, as well as the high groundwater level, which could induce a high abundance of methane- oxidizing microbes in the top soil, may be of greater importance as a driver for potential nitrification rates and abundance of ammonia- oxidizing microbes than LUI. On the other hand, the mineral soils of this site were characterized by extreme water shortage, which may also explain the lack of potential nitrification and the abundance of ammonia-oxidizing bacteria and archaea. Thus any extrapolation of local data to regional predictions must be made with care, as factors other than LUI may be of importance if the nitrification potential of a soil is to be described. [ABSTRACT FROM AUTHOR]

The adsorption of bacteria and fungi on clay-sized minerals, which are the most active inorganic colloidal components in soils, is an important pre-requisite for the survival and function of soil microorganisms in ecosystems. Exposing mineral containers (illite/goethite/quartz plus labelled Dactylis glomerta and Lolium perenne roots) in grassland soils (five sites of low and five of high land use intensity) of the "Schwäbische Alb" (South-West Germany) provided novel insights into the microbial colonization of mineral surfaces. The concept of the mineralosphere as a specific ecological habitat was verified by group specific C enrichment of soil microorganisms over a time period of 31 months. The colonizing microbial groups associated with the pristine mineral surfaces differed from the surrounding soil in their functional traits: for example, pristine mineral surfaces were fast colonized by fungi. After 31 months, fungal biomass contained up to 75% C derived from the added root litter source. It can be assumed that fungal growth strategies gave these microorganisms a competitive advantage over bacteria, which relied mainly on passive transport processes during colonization of the pristine surfaces. Since bacterial and fungal growth rates were variable during the succession of microorganisms in the mineralosphere, we concluded that differences in life strategies (copio- versus oligotrophic microorganisms) were also an important criterion for the early colonization. The production of extracellular enzymes by mineral-associated microorganisms and their stabilization onto mineral surfaces were found to be an important pre-requisite for microbial decomposition of the added carbon source in the mineralosphere. Nevertheless, the local environment of the mineralosphere was less important than expected: the choice of the food source (either added root material or carbon sources derived from organic matter of the surrounding soil) was only important under low land use intensity, as fungi with their hyphal growth could re-allocate nutrients within their mycelium and depend to lower extent on external input of C and nutrients than bacteria. In conclusion, pristine minerals developed over a period of 31 months into specific mineralospheres colonized by a microbial community which differed from the surrounding soil. [ABSTRACT FROM AUTHOR]