Advantages and Limits of Metagenomic Assembly and Binning of a Giant Virus
Giant viruses have large genomes, often within the size range of cellular organisms. This distinguishes them from most other viruses and demands additional effort for the successful recovery of their genomes from environmental sequence data. Here, we tested the performance of genome-resolved metagenomics on a recently isolated giant virus, Fadolivirus, by spiking it into an… [Read More]
Giant virus diversity and host interactions through global metagenomics
Our current knowledge about nucleocytoplasmic large DNA viruses (NCLDVs) is largely derived from viral isolates that are co-cultivated with protists and algae. Here we reconstructed 2,074 NCLDV genomes from sampling sites across the globe by building on the rapidly increasing amount of publicly available metagenome data. This led to an 11-fold increase in phylogenetic diversity… [Read More]
A dynamic microbial sulfur cycle in a serpentinizing continental ophiolite
Serpentinization is the hydration and oxidation of ultramafic rock, which occurs as oceanic lithosphere is emplaced onto continental margins (ophiolites), and along the seafloor as faulting exposes this mantle-derived material to circulating hydrothermal fluids. This process leads to distinctive fluid chemistries as molecular hydrogen (H2 ) and hydroxyl ions (OH(-) ) are produced and reduced… [Read More]
Abundant nitrite-oxidizing metalloenzymes in the mesopelagic zone of the tropical Pacific Ocean
Numerous biogeochemical reactions occur within the oceans’ major oxygen minimum zones, but less attention has been paid to the open ocean extremities of these zones. Here we report measurements on oxygen minimum zone waters from the Eastern to the Central Tropical North Pacific, which we analysed using metaproteomic techniques to discern the microbial functions present… [Read More]
Medium-Chain Fatty Acid Synthesis by “Candidatus Weimeria bifida” gen. nov., sp. nov., and “Candidatus Pseudoramibacter fermentans” sp. nov.
Chain elongation is emerging as a bioprocess to produce valuable medium-chain fatty acids (MCFA; 6 to 8 carbons in length) from organic waste streams by harnessing the metabolism of anaerobic microbiomes. Although our understanding of chain elongation physiology is still evolving, the reverse beta-oxidation pathway has been identified as a key metabolic function to elongate… [Read More]
Impacts of directed evolution and soil management legacy on the maize rhizobiome
Domestication and agricultural intensification dramatically altered maize and its cultivation environment. Changes in maize genetics (G) and environmental (E) conditions increased productivity under high-syntheticinput conditions. However, novel selective pressures on the rhizobiome may have incurred undesirable tradeoffs in organic agroecosystems, where plants obtain nutrients via microbially mediated processes including mineralization of organic matter. Using twelve… [Read More]
Temperature and Nutrient Levels Correspond with Lineage-Specific Microdiversification in the Ubiquitous and Abundant Freshwater Genus Limnohabitans
Most freshwater bacterial communities are characterized by a few dominant taxa that are often ubiquitous across freshwater biomes worldwide. Our understanding of the genomic diversity within these taxonomic groups is limited to a subset of taxa. Here, we investigated the genomic diversity that enables Limnohabitans, a freshwater genus key in funneling carbon from primary producers… [Read More]
Depth-Differentiation and Seasonality of Planktonic Microbial Assemblages in the Monterey Bay Upwelling System
Coastal upwelling regions are hotspots of biological productivity, supporting diverse communities of microbial life and metabolisms. Monterey Bay (MB), a coastal ocean embayment in central California, experiences seasonal upwelling of cold, nutrient-rich waters that sustain episodes of high phytoplankton production in surface waters. While productivity in surface waters is intimately linked to metabolisms of diverse… [Read More]
A Glycan Array-Based Assay for the Identification and Characterization of Plant Glycosyltransferases
Growing plants with modified cell wall compositions is a promising strategy to improve resistance to pathogens, increase biomass digestibility, and tune other important properties. In order to alter biomass architecture, a detailed knowledge of cell wall structure and biosynthesis is a prerequisite. We report here a glycan array-based assay for the high-throughput identification and characterization… [Read More]