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The plant root defines the interface between a multicellular eukaryote and soil, one of the richest microbial ecosystems on Earth (1). Notably, soil bacteria are able to multiply inside roots as benign endophytes and modulate plant growth and development (2), with implications ranging from enhanced crop productivity (3) to phytoremediation (4). Endophytic colonization represents an apparent paradox of plant innate immunity because plant cells can detect an array of microbe-associated molecular patterns (also known as MAMPs) to initiate immune responses to terminate microbial multiplication (5). Several studies attempted to describe the structure of bacterial root endophytes (6); however, different sampling protocols and low-resolution profiling methods make it difficult to infer general principles. Here we describe methodology to characterize and compare soil- and root-inhabiting bacterial communities, which reveals not only a function for metabolically active plant cells but also for inert cell-wall features in the selection of soil bacteria for host colonization. We show that the roots of Arabidopsis thaliana, grown in different natural soils under controlled environmental conditions, are preferentially colonized by Proteobacteria, Bacteroidetes and Actinobacteria, and each bacterial phylum is represented by a dominating class or family. Soil type defines the composition of root-inhabiting bacterial communities and host genotype determines their ribotype profiles to a limited extent. The identification of soil-type-specific members within the root-inhabiting assemblies supports our conclusion that these represent soil-derived root endophytes. Surprisingly, plant cell-wall features of other tested plant species seem to provide a sufficient cue for the assembly of approximately 40% of the Arabidopsis bacterial root-inhabiting microbiota, with a bias for Betaproteobacteria. Thus, this root sub-community may not be Arabidopsis-specific but saprophytic bacteria that would naturally be found on any plant root or plant debris in the tested soils. By contrast, colonization of Arabidopsis roots by members of the Actinobacteria depends on other cues from metabolically active host cells., We have grown Arabidopsis ecotypes Shakdara (Sha) and Landsberg erecta (Ler) in natural soils of contrasting geochemistry, designated Cologne (clay- and silt-rich) or Golm (sand-rich) soil, under controlled environmental conditions [...]

Land plants associate with a root microbiota distinct from the complex microbial community present in surrounding soil. The microbiota colonizing the rhizosphere (immediately surrounding the root) and the endophytic compartment (within the root) contribute to plant growth, productivity, carbon sequestration and phytoremediation (1-3). Colonization of the root occurs despite a sophisticated plant immune system (4,5), suggesting finely tuned discrimination of mutualists and commensals from pathogens. Genetic principles governing the derivation of host-specific endophyte communities from soil communities are poorly understood. Here we report the pyrosequencing of the bacterial 16S ribosomal RNA gene of more than 600 Arabidopsis thaliana plants to test the hypotheses that the root rhizosphere and endophytic compartment microbiota of plants grown under controlled conditions in natural soils are sufficiently dependent on the host to remain consistent across different soil types and developmental stages, and sufficiently dependent on host genotype to vary between inbred Arabidopsis accessions. We describe different bacterial communities in two geochemically distinct bulk soils and in rhizosphere and endophytic compartments prepared from roots grown in these soils. The communities in each compartment are strongly influenced by soil type. Endophytic compartments from both soils feature overlapping, low-complexity communities that are markedly enriched in Actinobacteria and specific families from other phyla, notably Proteobacteria. Some bacteria vary quantitatively between plants of different developmental stage and genotype. Our rigorous definition of an endophytic compartment microbiome should facilitate controlled dissection of plant-microbe interactions derived from complex soil communities., Roots influence the rhizosphere by altering soil pH, soil structure, oxygen availability, antimicrobial concentration, and quorum-sensing mimicry, and by providing an energy source of dead root material and carbon-rich exudates [...]

The plant root defines the interface between a multicellular eukaryote and soil, one of the richest microbial ecosystems on Earth (1). Notably, soil bacteria are able to multiply inside roots [...]

Land plants associate with a root microbiota distinct from the complex microbial community present in surrounding soil. The microbiota colonizing the rhizosphere (immediately surrounding the root) and the endophytic compartment [...]

For over a half a century, researchers have been aware of the fact that the physical and chemical characteristics of microenvironments in soils strongly influence the activity, growth and metabolism of microorganisms. However, many aspects of the effect of soil physical characteristics, such as the pore geometry, remain poorly understood. Therefore, the objective of the present research was to determine the influence of soil pore characteristics on the spread of bacteria, observed at the scale relevant to microbes. Pseudomonas fluorescens was introduced in columns filled with 1–2 mm soil aggregates, packed at different bulk densities. Soil microcosms were scanned at 10.87 μm voxel resolution using X‐ray computed tomography (CT) to characterize the geometry of pores. Thin sections were prepared to determine the spread and colonization of bacteria. The results showed that average bacterial cell density was 174 cells mm−2 in soil with bulk density of 1.3 g cm−3 and 99 cells mm−2 in soil with bulk density of 1.5 g cm−3. Soil porosity and solid‐pore interfaces influence the spread of bacteria and their colonization of the pore space at lower bulk density, resulting in relatively higher bacterial densities in larger pore spaces. The study also demonstrates that thin sectioning of resin‐impregnated soil samples can be combined with X‐ray CT to visualize bacterial colonization of a 3D pore volume. This research therefore represents a significant step towards understanding how environmental change and soil management impact bacterial diversity in soils. Highlights: We used a quantitative approach to study bacterial spread in soil at scales relevant to microbes.The rate of pseudomonas spread decreased with increased bulk density of soil.Soil porosity and soil‐pore interface influence Pseudomonas in lower bulk density soil.Soil structure with different pore characteristics effects spread and activity of bacteria in soil. [ABSTRACT FROM AUTHOR]

As Bacillus thuringiensis (Bt) are entomopathogenic bacteria for use as biological insecticide and serve as a main source for genetically modified crops, it is imperative to investigate fate of Bt-toxins (Cry-proteins) released in soil. Four differently textured paddy soils, i.e. sandy loam, loam, silt loam and silty clay, were selected to investigate production and release of Cry-proteins by two Bt-strains (subspecies thuringiensis and kurstaki) and by transgenic Bt-rice (cultivar TT51-1). After amended with Cry-proteins, soil can adsorb proteins while sorption rate was variable among different paddy soils, with the highest amount of Cry-proteins in the silty clay soil. During the period of incubation with Bt-strains, the silty clay soil showed significant accumulation of Cry-proteins. Additionally, level of Cry-protein production was different between two Bt-strains. Inactivation of indigenous microorganisms in the soil samples led to slightly higher production of Cry-proteins by Bt-strains in all four soil types. Cry-proteins were released via root exudates of transgenic Bt-rice in sterile hydroponic culture and in non-sterile soils throughout the growth of plants. Protein release significantly varied among different paddy soils, up to 34.9 ng Cry-proteins g−1 soil in clayey soil. It indicates differently textured paddy soils reflect variable sorption, persistence, and accumulation of Cry-proteins. [ABSTRACT FROM AUTHOR]

The flux of methane, a potent greenhouse gas, from the seabed is largely controlled by anaerobic oxidation of methane (AOM) coupled to sulfate reduction (S-AOM) in the sulfate methane transition (SMT). S-AOM is estimated to oxidize 90% of the methane produced in marine sediments and is mediated by a consortium of anaerobic methanotrophic archaea (ANME) and sulfate reducing bacteria. An additional methane sink, i.e., iron oxide coupled AOM (Fe-AOM), has been suggested to be active in the methanic zone of marine sediments. Geochemical signatures below the SMT such as high dissolved iron, low to undetectable sulfate and high methane concentrations, together with the presence of iron oxides are taken as prerequisites for this process. So far, Fe-AOM has neither been proven in marine sediments nor have the governing key microorganisms been identified. Here, using a multidisciplinary approach, we show that Fe-AOM occurs in iron oxide-rich methanic sediments of the Helgoland Mud Area (North Sea). When sulfate reduction was inhibited, different iron oxides facilitated AOM in long-term sediment slurry incubations but manganese oxide did not. Especially magnetite triggered substantial Fe-AOM activity and caused an enrichment of ANME-2a archaea. Methane oxidation rates of 0.095 ± 0.03 nmol cm -3 d -1 attributable to Fe-AOM were obtained in short-term radiotracer experiments. The decoupling of AOM from sulfate reduction in the methanic zone further corroborated that AOM was iron oxide-driven below the SMT. Thus, our findings prove that Fe-AOM occurs in methanic marine sediments containing mineral-bound ferric iron and is a previously overlooked but likely important component in the global methane budget. This process has the potential to sustain microbial life in the deep biosphere., (Copyright © 2020 Aromokeye, Kulkarni, Elvert, Wegener, Henkel, Coffinet, Eickhorst, Oni, Richter-Heitmann, Schnakenberg, Taubner, Wunder, Yin, Zhu, Hinrichs, Kasten and Friedrich.)