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X-ray computed tomography (CT) scanning is used to study the physical characteristics of soil and sediment cores, allowing scientists to analyze stratigraphy without destroying core integrity. Microbiologists often work with geologists to understand the microbial properties in such cores; however, we do not know whether CT scanning alters microbial DNA such that DNA sequencing, a common method of community characterization, changes as a result of X-ray exposure. Our objective was to determine whether CT scanning affects the estimates of the composition of microbial communities that exist in cores. Sediment cores were extracted from a salt marsh and then submitted for CT scanning. We observed a minimal effect of CT scanning on microbial community composition in the sediment cores either when the cores were examined shortly after recovery from the field or after the cores had been stored for several weeks. In contrast, properties such as sediment layer and marsh location did affect microbial community structure. While we observed that CT scanning did not alter microbial community composition as a whole, we identified a few amplicon sequence variants (13 out of 7,037) that showed differential abundance patterns between scanned and unscanned samples among paired sample sets. Our overall conclusion is that the CT-scanning conditions typically used to obtain images for geological core characterization do not significantly alter microbial community structure. We stress that minimizing core exposure to X-rays is important if cores are to be studied for biological properties. Future investigations might consider variables, such as the length and energy of radiation exposure, the volume of the core, or the degree, to which microbial communities are stressed as important factors in assessing the impact of X-rays on microbes in geological cores. [ABSTRACT FROM AUTHOR]

Microorganisms residing on root surfaces play a central role in plant development and performance and may promote growth in agricultural settings. Studies have started to uncover the environmental parameters and host interactions governing their assembly. However, soil microbial communities are extremely diverse and heterogeneous, showing strong variations over short spatial scales. Here, we quantify the relative effect of meter-scale variation in soil bacterial community composition among adjacent field microsites, to better understand how microbial communities vary by host plant genotype as well as soil microsite heterogeneity. We used bacterial 16S rDNA amplicon sequencing to compare rhizosphere communities from four Brassica rapa cultivars grown in three contiguous field plots (blocks) and evaluated the relative contribution of resident soil communities and host genotypes in determining rhizosphere community structure. We characterize concomitant meter-scale variation in bacterial community structure among soils and rhizospheres and show that this block-scale variability surpasses the influence of host genotype in shaping rhizosphere communities. We identified biomarker amplicon sequence variants (ASVs) associated with bulk soil and rhizosphere habitats, each block, and three of four cultivars. Numbers and percent abundances of block-specific biomarkers in rhizosphere communities far surpassed those from bulk soils. These results highlight the importance of fine-scale variation in the pool of colonizing microorganisms during rhizosphere assembly and demonstrate that microsite variation may constitute a confounding effect while testing biotic and abiotic factors governing rhizosphere community structure. [ABSTRACT FROM AUTHOR]

Summary: Anaerobic methanotrophic archaea (ANME) consume methane in marine sediments, limiting its release to the water column, but their responses to changes in methane and sulfate supplies remain poorly constrained. To address how methane exposure may affect microbial communities and methane‐ and sulfur‐cycling gene abundances in Arctic marine sediments, we collected sediments from offshore Svalbard that represent geochemical horizons where anaerobic methanotrophy is expected to be active, previously active, and long‐inactive based on reaction‐transport biogeochemical modelling of porewater sulfate profiles. Sediment slurries were incubated at in situ temperature and pressure with different added methane concentrations. Sediments from an active area of seepage began to reduce sulfate in a methane‐dependent manner within months, preceding increased relative abundances of anaerobic methanotrophs ANME‐1 within communities. In previously active and long‐inactive sediments, sulfur‐cycling Deltaproteobacteria became more dominant after 30 days, though these communities showed no evidence of methanotrophy after nearly 8 months of enrichment. Overall, enrichment conditions, but not methane, broadly altered microbial community structure across different enrichment times and sediment types. These results suggest that active ANME populations may require years to develop, and consequently microbial community composition may affect methanotrophic responses to potential large‐scale seafloor methane releases in ways that provide insight for future modelling studies. [ABSTRACT FROM AUTHOR]

Submarine mud volcanoes (MVs) along continental margins emit mud breccia and globally significant amounts of hydrocarbon-rich fluids from the subsurface, and host distinct chemosynthetic communities of microbes and macrofauna. Venere MV lies at 1,600 m water depth in the Ionian Sea offshore Italy and is located in a forearc basin of the Calabrian accretionary prism. Porewaters of recently extruded mud breccia flowing from its west summit are considerably fresher than seawater (10 PSU), high in Li+ and B (up to 300 and 8,000 μM, respectively), and strongly depleted in K+ (<1 mM) at depths as shallow as 20 cm below seafloor. These properties document upward transport of fluids sourced from >3 km below seafloor. 16S rRNA gene and metagenomic sequencing were used to characterize microbial community composition and gene content within deep-sourced mud breccia flow deposits as they become exposed to seawater along a downslope transect of Venere MV. Summit samples showed consistency in microbial community composition. However, beta-diversity increased markedly in communities from downslope cores, which were dominated by methyl- and methanotrophic genera of Gammaproteobacteria. Methane, sulfate, and chloride concentrations were minor but significant contributors to variation in community composition. Metagenomic analyses revealed differences in relative abundances of predicted protein categories between Venere MV and other subsurface microbial communities, characterizing MVs as windows into distinct deep biosphere habitats. [ABSTRACT FROM AUTHOR]