T. Woyke

Time-series metagenomics reveals changing protistan ecology of a temperate dimictic lake

The paper analyzes time-series metagenomic data from Lake Mendota to study changes in protistan ecology, revealing shifts in community structure linked to invasive species and environmental factors.

Local adaptation to mercury contamination by nitrogen-fixing rhizobia is driven by horizontal gene transfer, copy number, and enhanced gene expression

This study identifies that horizontal gene transfer, copy number, and enhanced expression of the Mer operon confer mercury tolerance in rhizobia, with implications for plant-metal interactions.

Differential expression of core metabolic functions in Candidatus Altiarchaeum inhabiting distinct subsurface ecosystems

This study compares the metatranscriptomes of two Candidatus Altiarchaeum populations in different subsurface ecosystems, identifying gene expression differences related to metabolism and defense mechanisms.

Genetic and functional diversity help explain pathogenic, weakly pathogenic, and commensal lifestyles in the genus Xanthomonas

This study examines the genetic and functional diversity of Xanthomonas strains to understand their pathogenic, weakly pathogenic, and commensal lifestyles through genomic analysis and phylogenetic relationships.

Physiological adaptation of sulfate reducing bacteria in syntrophic partnership with anaerobic methanotrophic archaea

This study examines the metabolic adaptations of sulfate-reducing bacteria in syntrophic partnerships with methanotrophic archaea, revealing unique evolutionary changes in protein pathways.

A centimeter-long bacterium with DNA compartmentalized in membrane-bound organelles

The paper characterizes Ca. Thiomargarita magnifica, a centimeter-long bacterium with DNA compartmentalized in membrane-bound organelles, revealing unique biology and challenging traditional bacterial cell concepts.

Comparative genomics reveals electron transfer and syntrophic mechanisms differentiating methanotrophic and methanogenic archaea

The paper compares genomes of methanotrophic and methanogenic archaea to identify differences in electron transfer and metabolic pathways.

Repeated losses and gains of bacterial symbionts in gutless marine annelids over 150 million years

This study investigates the evolutionary dynamics of bacterial symbionts in gutless marine annelids over 150 million years, showing host-driven stability and convergent gains of symbionts.

DNA methylation in Ensifer species during free-living growth and during nitrogen-fixing symbiosis with Medicago spp.

The paper identifies DNA methylation patterns in Ensifer species during free-living growth and symbiosis, showing changes in GANTC motif methylation linked to cell cycle and differentiation.

Recoding enhances the metabolic capabilities of two novel methylotrophic Asgardarchaeota lineages

This study identifies two new Asgardarchaeota lineages with methylotrophic metabolism enhanced by genetic code expansions, including selenocysteine and pyrrolysine recoding.

A Catalog of the Diversity and Ubiquity of Metabolic Organelles in Bacteria

The paper catalogs the diversity and ubiquity of bacterial microcompartments (BMCs) using genome-resolved metagenomics, finding a twenty-fold increase in identifiable BMC loci and doubling the number of distinct BMC types since 2014.

A genomic perspective on genome size distribution across Earth's microbiomes reveals a tendency to gene loss

The paper analyzes genome size distribution across Earth's microbiomes and finds that environmental microorganisms have smaller genomes than lab-cultivated ones, with ecological and phylogenetic factors influencing genome size.

Methylotrophy, alkane-degradation, and pigment production as defining features of the globally distributed yet-uncultured phylum Binatota

This study analyzes genomes from the uncultured bacterial phylum Binatota, revealing their methylotrophic, alkane-degrading, and pigment-producing capabilities, along with ecological preferences.

Genome-informed microscopy reveals infections of uncultivated carbon-fixing archaea by lytic viruses in Earth's crust

The paper uses genome-informed microscopy to show lytic viruses infect uncultivated carbon-fixing archaea in Earth's crust, challenging previous assumptions about viral lifestyles in subsurface ecosystems.

Ancestral absence of electron transport chains in Patescibacteria and DPANN

The paper investigates Patescibacteria and DPANN, finding they lack electron transport chains and rely on fermentation, suggesting ancestral adaptations to symbiotic lifestyles.

Advantages and limits of metagenomic assembly and binning of a giant virus

This study evaluates genome-resolved metagenomics for recovering giant virus genomes, showing success at high spike-in levels but highlighting the underdetection of most giant viruses.

Niche differentiation is spatially and temporally regulated in the rhizosphere

This study identifies four microbial guilds in the rhizosphere and detritusphere of Avena fatua, showing niche differentiation drives carbohydrate depolymerization and soil carbon cycling.

Cryptic inoviruses are pervasive in bacteria and archaea across Earth's biomes

The paper identifies 10,295 inovirus-like genomes across diverse ecosystems, revealing their widespread presence and complex interactions with bacterial and archaeal hosts.

Lipid analysis of CO2-rich subsurface aquifers suggests an autotrophy-based deep biosphere with lysolipids enriched in CPR bacteria

The paper analyzes lipid composition in CO2-rich subsurface aquifers to infer microbial carbon cycling and lipid sources, finding CPR bacteria may rely on lysolipids from other community members.

Hydrogenotrophic methanogenesis in archaeal phylum Verstraetearchaeota reveals the shared ancestry of all methanogens

The paper discovers a hydrogenotrophic methanogenesis pathway in Verstraetearchaeota and the Wood-Ljungdahl pathway in Desulfurococcales, suggesting an ancient origin of hydrogenotrophic methanogenesis and a later adaptation to methylotrophic methanogenesis.

Hydrogen-based metabolism - An ancestral trait in lineages sibling to the Cyanobacteria

This paper predicts the metabolisms of Margulisbacteria and Saganbacteria using genomic data and compares them to their phylogenetic neighbors, supporting the hypothesis that their ancestor used hydrogen metabolism and fermentation.

Archaeal, bacterial, and eukaryal microbial community structure of sediment and seawater in a coastal region near Puerto Nuevo, Baja California

The paper characterizes microbial communities in sediment and seawater near Puerto Nuevo, finding greater diversity in sediment and distinct phyla in each environment.

Contrasting patterns of genome-level diversity across distinct co-occurring bacterial populations

The paper examines genetic and ecological differentiation in freshwater bacterial populations using single-cell genomes and metagenomic data, finding ecologically distinct populations within some lineages but not others.

Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples

This paper introduces a microfluidic-based mini-metagenomic method to extract novel microbial genomes from complex environmental samples, revealing 29 new genomes with diverse metabolic pathways and SNP distributions.