J. F. Banfield

Characterization of sediment and granite hosted deep underground research laboratories reveals diverse microbiome functions, limited temporal variation and substantial genomic conservation

The paper characterizes microbiomes in underground research labs, finding genomic conservation and similar functional profiles despite environmental differences.

Model cyanobacterial consortia reveal a consistent core microbiome independent of inoculation source or cyanobacterial host species

The paper models cyanobacterial consortia to identify a consistent core microbiome across different hosts and inoculation sources.

Asgard archaea modulate potential methanogenesis substrates in wetland soil

The paper reconstructs genomes of soil-associated Asgard archaea and uses metatranscriptomics to show their role in carbon compound metabolism relevant to methane production in wetlands.

Methanotrophic Methanoperedens archaea host diverse and interacting extrachromosomal elements

The paper identifies and characterizes diverse extrachromosomal elements in Methanoperedens archaea, including mini-Borgs and viruses, and shows their genetic exchange and potential impact on archaeal activity.

Extensive and diverse lanthanide-dependent metabolism in the ocean

The paper identifies widespread lanthanide-dependent enzymes in ocean metagenomes, showing their role in carbon metabolism and biogeochemical cycles.

Genomic analysis of cultivated infant microbiomes identifies Bifidobacterium 2'-fucosyllactose utilization can be facilitated by co-existing species

The paper shows that Bifidobacterium breve can utilize 2'-fucosyllactose with help from co-existing species like Ruminococcus gnavus in infant microbiomes.

Vitamin interdependencies predicted by metagenomics-informed network analyses validated in microbial community microcosms

The paper predicts vitamin interdependencies in microbial communities using metagenomics-informed network analysis and validates these predictions in microcosms.

Fine scale sampling reveals spatial heterogeneity of rhizosphere microbiome in young Brachypodium plants

The paper examines spatial microbial heterogeneity in Brachypodium roots using EcoFABs, revealing distinct microbial communities at root tips and bases with different functional gene profiles.

Host translation machinery is not a barrier to phages that infect both CPR and non-CPR bacteria

The paper identifies phages capable of infecting both CPR and non-CPR bacteria, revealing their ability to use alternative genetic codes and expand host range.

Autotrophic biofilms sustained by deeply-sourced groundwater host diverse CPR bacteria implicated in sulfur and hydrogen metabolism

The paper identifies CPR bacteria in sulfide-rich biofilms, linking them to sulfur and hydrogen metabolism through genomic and spectroscopic analyses.

A subset of viruses thrives following microbial resuscitation during rewetting of a seasonally dry California grassland soil

The paper investigates virus-host dynamics in soil following rewetting, finding that a subset of viruses thrive and drive microbial lysis, contributing to CO2 efflux.

Quantitative stable-isotope probing (qSIP) with metagenomics links microbial physiology and activity to soil moisture in Mediterranean-climate grassland ecosystems

This study uses qSIP with metagenomics to link microbial activity and physiology to soil moisture in Mediterranean grasslands, finding that precipitation levels influence microbial growth and phage dynamics.

Candidatus Nealsonbacteria (OD1) are biomass recycling ectosymbionts of methanogenic archaea in a stable benzene-degrading enrichment culture

The paper identifies Ca. Nealsonbacteria DGGOD1a as a biomass recycling ectosymbiont of methanogenic archaea in a benzene-degrading consortium.

Do lanthanide-dependent microbial metabolisms drive the release of REEs from weathered granites?

This study identifies microbial gene clusters involved in lanthanide metabolism in weathered granites, highlighting their role in phosphate mineral dissolution and soil formation.

A widespread group of large plasmids in methanotrophic Methanoperedens archaea

This paper identifies large plasmids in Methanoperedens archaea that are essential for their physiology and may be used to study and manipulate methane oxidation.

Using strain-resolved analysis to identify contamination in metagenomics data

This study identifies contamination in metagenomics data using strain-resolved analysis, finding that contamination is more common in low-biomass samples and adjacent extraction plate positions.

Stop codon recoding is widespread in diverse phage lineages and has the potential to regulate translation of late stage and lytic genes

The paper surveys stop codon recoding in bacteriophages, finding it widespread and suggesting it regulates gene expression and lysis timing.

Borgs are giant extrachromosomal elements with the potential to augment methane oxidation

The paper identifies Borgs, large extrachromosomal elements in Methanoperedens archaea, which enhance methane oxidation capacity and may influence greenhouse gas emissions.

Genetic and behavioral adaptation of Candida parapsilosis to the microbiome of hospitalized infants revealed by in situ genomics, transcriptomics and proteomics

This study identifies genetic and behavioral adaptations of C. parapsilosis in the gut microbiome of hospitalized infants using in situ genomics, transcriptomics, and proteomics.

Meanders as a scaling motif for understanding of floodplain soil microbiome and biogeochemical potential at the watershed scale

The paper investigates microbial metabolic potential in floodplain soils along a river corridor, finding that meander-bound regions predict biogeochemical capacities at the watershed scale.

Syntrophic H2 production enhances the performance of primarily acetate-supplemented reactors treating sulphate contaminated solutions

This study shows that adding a small amount of fermentable substrate to acetate-supplemented sulfate-reducing bioreactors improves performance through syntrophic H2 production.

A widely distributed genus of soil Acidobacteria genomically enriched in biosynthetic gene clusters

The paper expands genomic sampling of Ca. Angelobacter, showing they are common in soil communities and enriched in biosynthetic gene clusters for specialized metabolites.

Soils and sediments host novel archaea with divergent monooxygenases implicated in ammonia oxidation

The paper identifies novel archaea in soils and sediments with divergent CuMMO enzymes, suggesting they contribute to nitrogen cycling through ammonia oxidation.

Thiocyanate and organic carbon inputs drive convergent selection for specific autotrophic Afipia and Thiobacillus strains within complex microbiomes

The paper shows that thiocyanate and organic carbon inputs select for specific autotrophic Afipia and Thiobacillus strains in microbiomes, with molasses removal favoring a dominant Afipia variant.

Patterns of gene content and co-occurrence constrain the evolutionary path toward animal association in CPR bacteria

This study examines gene content and co-occurrence patterns in CPR bacteria to understand their evolutionary transitions between environmental and animal-associated habitats.

Infant gut strain persistence is associated with maternal origin, phylogeny, and functional potential including surface adhesion and iron acquisition

The paper investigates factors influencing gut microbiome strain persistence in infants, finding maternal origin and specific genetic functions are associated with strain survival.

Wide distribution of alternatively coded Lak megaphages in animal microbiomes

The paper identifies a wide distribution of alternatively coded Lak phages in animal microbiomes, including new genomes and associations with specific animal types.

Structural coordination between active sites of a Cas6-reverse transcriptase-Cas1--Cas2 CRISPR integrase complex

The paper determines the cryo-EM structure of a Cas6-RT-Cas1-Cas2 complex and shows bidirectional and unidirectional crosstalk between its active sites.

Stable isotope informed genome-resolved metagenomics uncovers potential trophic interactions in rhizosphere soil

This study uses stable isotope-informed genome-resolved metagenomics to trace carbon flow in rhizosphere soil and identify microbial interactions with plants and phages.

Targeted Genome Editing of Bacteria Within Microbial Communities

This paper develops a method to edit specific bacteria within microbial communities using ET-Seq and DART systems, enabling genetic manipulation in complex environments.