Kathleen Beilsmith

Leptothrix mechoopdaensis BB-3 and BB-4 are metal-oxidizing, sheathed, filamentous bacteria that were isolated from a woodland iron seep near Centerville, Chico, CA, USA. Here, we report a closed circular genome sequence for each strain, assembled from reads sequenced on an Oxford Nanopore FLO-MIN114 flow cell.

Coastal soils are dynamic systems where unique microbial niches are shaped by the intensity and duration of flooding between the terrestrial and aquatic boundaries of the terrestrial-aquatic interface (TAI). We aimed to understand the soil microbial community (16S rRNA gene) along the TAIs of a freshwater versus estuarine region and how it relates to organic matter (OM, via Fourier Transform Ion Cyclotron Resonance Mass Spectrometry). We studied the TAI gradients along a transect from upland (forested), transition (stressed forest), to wetland at three sites in each of the Lake Erie (freshwater) and Chesapeake Bay (estuarine) regions. Microbial communities differed significantly by region, transect position, and site. Contrary to expectations, given their dynamic hydrologies, transitions represented midpoints in microbial richness and diversity. We identified a core microbiome conserved across all transect positions within a region, highlighting potential microbial functions most resilient to environmental change. Indicator taxa unique to each transect position defined specific niches shaped by soil biogeochemistry. Co-expression networks of feature-level β-nearest-taxon indices revealed positive relationships in bacterial and OM feature contributions to community assembly. Our study provides critical insights into microbial communities at the forefront of hydrological changes in coastal areas that connect the land to lakes and oceans and remain vulnerable to changing weather patterns.

A high-fat, low-fibre Western-style diet (WD) induces microbiome dysbiosis characterized by reduced taxonomic diversity and metabolic breadth^1,2, which in turn increases risk for a wide array of metabolic^3,4,5, immune⁶ and systemic pathologies. Recent work has established that WD can impair microbiome resilience to acute perturbations such as antibiotic treatment^7,8, although little is known about the mechanism of impairment and the specific consequences for the host of prolonged post-antibiotic dysbiosis. Here we characterize the trajectory by which the gut microbiome recovers its taxonomic and functional profile after antibiotic treatment in mice on regular chow (RC) or WD, and find that only mice on RC undergo a rapid successional process of recovery. Metabolic modelling indicates that a RC diet promotes the development of syntrophic cross-feeding interactions, whereas in mice on WD, a dominant taxon monopolizes readily available resources without releasing syntrophic byproducts. Intervention experiments reveal that an appropriate dietary resource environment is both necessary and sufficient for rapid and robust microbiome recovery, whereas microbial transplant is neither. Furthermore, prolonged post-antibiotic dysbiosis in mice on WD renders them susceptible to infection by the intestinal pathogen Salmonella enterica serovar Typhimurium. Our data challenge widespread enthusiasm for faecal microbiota transplant (FMT) as a strategy to address dysbiosis, and demonstrate that specific dietary interventions are, at a minimum, an essential prerequisite for effective FMT, and may afford a safer, more natural and less invasive alternative.

DNA/RNA-stable isotope probing (SIP) is a powerful tool to link in situ microbial activity to sequencing data. Every SIP dataset captures distinct information about microbial community metabolism, process rates, and population dynamics, offering valuable insights for a wide range of research questions. Data reuse maximizes the information derived from the labor and resource-intensive SIP approaches. Yet, a review of publicly available SIP sequencing metadata showed that critical information necessary for reproducibility and reuse was often missing. Here, we outline the Minimum Information for any Stable Isotope Probing Sequence (MISIP) according to the Minimum Information for any (x) Sequence (MIxS) framework and include examples of MISIP reporting for common SIP experiments. Our objectives are to expand the capacity of MIxS to accommodate SIP-specific metadata and guide SIP users in metadata collection when planning and reporting an experiment. The MISIP standard requires 5 metadata fields—isotope, isotopolog, isotopolog label, labeling approach, and gradient position—and recommends several fields that represent best practices in acquiring and reporting SIP sequencing data (e.g., gradient density and nucleic acid amount). The standard is intended to be used in concert with other MIxS checklists to comprehensively describe the origin of sequence data, such as for marker genes (MISIP-MIMARKS) or metagenomes (MISIP-MIMS), in combination with metadata required by an environmental extension (e.g., soil). The adoption of the proposed data standard will improve the reuse of any sequence derived from a SIP experiment and, by extension, deepen understanding of in situ biogeochemical processes and microbial ecology.

DNA/RNA-stable isotope probing (SIP) is a powerful tool to link in situ microbial activity to sequencing data. Every SIP dataset captures distinct information about microbial community metabolism, kinetics, and population dynamics, offering novel insights according to diverse research questions. Data re-use maximizes the information available from the time and resource intensive SIP experimental approach. Yet, a review of publicly available SIP sequencing metadata reveals that critical information necessary for reproducibility and reuse is often missing. Here, we outline the Minimum Information for any Stable Isotope Probing Sequence (MISIP) according to the Minimum Information for any (x) Sequence (MIxS) data standard framework and include examples of MISIP reporting for common SIP approaches. Our objectives are to expand the capacity of MIxS to accommodate SIP-specific metadata and guide SIP users in metadata collection when planning and reporting an experiment. The MISIP standard requires five metadata fields: isotope, isotopolog, isotopolog label and approach, and gradient position, and recommends several fields that represent best practices in acquiring and reporting SIP sequencing data ( ex. gradient density and nucleic acid amount). The standard is intended to be used in concert with other MIxS checklists to comprehensively describe the origin of sequence data, such as for marker genes (MISIP-MIMARKS) or metagenomes (MISIP-MIMS), in combination with metadata required by an environmental extension ( e.g. , soil). The adoption of the proposed data standard will assure the reproducibility and reuse of any sequence derived from a SIP experiment and, by extension, deepen understanding of in situ biogeochemical processes and microbial ecology.

Research can be more transparent and collaborative by using Findable, Accessible, Interoperable, and Reusable (FAIR) principles to publish Earth and environmental science data. Reporting formats—instructions, templates, and tools for consistently formatting data within a discipline—can help make data more accessible and reusable. However, the immense diversity of data types across Earth science disciplines makes development and adoption challenging. Here, we describe 11 community reporting formats for a diverse set of Earth science (meta)data including cross-domain metadata (dataset metadata, location metadata, sample metadata), file-formatting guidelines (file-level metadata, CSV files, terrestrial model data archiving), and domain-specific reporting formats for some biological, geochemical, and hydrological data (amplicon abundance tables, leaf-level gas exchange, soil respiration, water and sediment chemistry, sensor-based hydrologic measurements). More broadly, we provide guidelines that communities can use to create new (meta)data formats that integrate with their scientific workflows. Such reporting formats have the potential to accelerate scientific discovery and predictions by making it easier for data contributors to provide (meta)data that are more interoperable and reusable.

Developing synthetic microbial communities that can increase plant yield or deter pathogens requires basic research on several fronts, including the efficiency with which microbes colonize plant tissues, how plant genes shape the microbiome, and the microbe-microbe interactions involved in community assembly. Findings on each of these fronts depend upon the spatial and temporal scales at which plant microbiomes are surveyed.

Interactions between bacteria are thought to play an important role in the assembly of plant microbial communities (1), yet the extent of temporal variation in these interactions is unclear. We inferred interactions from sequence-based counts of bacteria in a series of Arabidopsis thaliana tissue samples spanning major developmental transitions in the plant life cycle (2). Bacterial interactions were transient, even among variants found together at consecutive developmental stages. The overwhelming majority of these interactions were positive, indicating that competition for the plant niche might be a less important driver of bacterial abundances than cooperation or common responses to host and environmental factors. Over time, interaction networks diverged from an initial scale-free structure and became increasingly modular. In all networks, we found evidence of a hierarchical structure in which hub bacteria bridged network modules. However, the identities of bacteria in these influential roles also varied during plant growth.