A5067109718- Earthquake Detection and Analysis
- Superconducting Materials and Applications
- Methane Hydrates and Related Phenomena
- Microbial Community Ecology and Physiology
- Astrophysics and Cosmic Phenomena
- Genomics and Phylogenetic Studies
- Gut microbiota and health
- Bacteriophages and microbial interactions
- Ionosphere and magnetosphere dynamics
- Geophysics and Gravity Measurements
- Atmospheric and Environmental Gas Dynamics
- Peatlands and Wetlands Ecology
- Environmental DNA in Biodiversity Studies
- Microbial Fuel Cells and Bioremediation
- Protist diversity and phylogeny
- Diet and metabolism studies
- Biofuel production and bioconversion
- Probiotics and Fermented Foods
- Anaerobic Digestion and Biogas Production
- Metabolomics and Mass Spectrometry Studies
- Hydrocarbon exploration and reservoir analysis
- Coastal wetland ecosystem dynamics
- Solar and Space Plasma Dynamics
- Wastewater Treatment and Nitrogen Removal
- Seismic Waves and Analysis
Colorado State University
2015-2025
The Ohio State University
2014-2024
Color (United States)
2024
Syracuse University
2024
UK Health Security Agency
2024
The University of Queensland
2024
Washington University in St. Louis
2024
Agency for Science, Technology and Research
2024
University of Birmingham
2024
University of Freiburg
2024
Abstract Microbial and viral communities transform the chemistry of Earth's ecosystems, yet specific reactions catalyzed by these biological engines are hard to decode due absence a scalable, metabolically resolved, annotation software. Here, we present DRAM (Distilled Refined Annotation Metabolism), framework translate deluge microbiome-based genomic information into catalog microbial traits. To demonstrate applicability across diverse genomes, evaluated performance on defined, in silico...
Bacterial PERegrinations Many branches of the bacterial domain life are only known from sequences that turn up in metagenomic analyses and still named by acronym—for example, phylum-level groups BD1-5, OP11, OD1, PERs. The parent organisms probably widespread, but they have not been cultured, very little is about their metabolisms or contributions functions natural environment. Wrighton et al. (p. 1661 ) pumped acetate into an aquifer Colorado to prompt naturally occurring bacteria action...
Abstract Background Sediments are massive reservoirs of carbon compounds and host a large fraction microbial life. Microorganisms within terrestrial aquifer sediments control buried organic turnover, degrade contaminants, impact drinking water quality. Recent 16S rRNA gene profiling indicates that members the bacterial phylum Chloroflexi common in sediment. Only role class Dehalococcoidia, which halogenated solvents, is well understood. Genomic sampling available for only six approximate 30...
This paper presents standards and best practices for reporting genome sequences of uncultivated viruses. We present an extension the Minimum Information about any (x) Sequence (MIxS) standard virus genomes. Uncultivated Virus Genome (MIUViG) were developed within Genomic Standards Consortium framework include origin, quality, annotation, taxonomic classification, biogeographic distribution in silico host prediction. Community-wide adoption MIUViG standards, which complement a Single...
Bacteriophages typically have small genomes
Cyanobacteria were responsible for the oxygenation of ancient atmosphere; however, evolution this phylum is enigmatic, as relatives have not been characterized. Here we use whole genome reconstruction human fecal and subsurface aquifer metagenomic samples to obtain complete genomes members a new candidate sibling Cyanobacteria, which propose designation ‘Melainabacteria’. Metabolic analysis suggests that ancestors both lineages non-photosynthetic, anaerobic, motile, obligately fermentative....
Bacteria from phyla lacking cultivated representatives are widespread in natural systems and some have very small genomes. Here we test the hypothesis that these cells thus might be enriched by filtration for coupled genomic ultrastructural characterization. Metagenomic analysis of groundwater passed through a ~0.2-μm filter reveals wide diversity bacteria WWE3, OP11 OD1 candidate phyla. Cryogenic transmission electron microscopy demonstrates that, despite morphological variation,...
This work is part of a 10-year project to examine thawing permafrost peatlands and the first virome-particle-based approach characterize viruses in these systems. method yielded >2-fold-more viral populations (vOTUs) per gigabase metagenome than vOTUs derived from bulk-soil metagenomes same site (J. B. Emerson, S. Roux, J. R. Brum, Bolduc, et al., Nat Microbiol 3:870–880, 2018, https://doi.org/10.1038/s41564-018-0190-y ). We compared ecology recovered along thaw gradient found (i) habitat...
ABSTRACT Cultivation-independent surveys of microbial diversity have revealed many bacterial phyla that lack cultured representatives. These lineages, referred to as candidate phyla, been detected across environments. Here, we deeply sequenced communities from acetate-stimulated aquifer sediment recover the complete and essentially genomes single representatives SR1, WWE3, TM7, OD1. All four these are very small, 0.7 1.2 Mbp, large inventories novel proteins. Additionally, all identifiable...
Abstract Bacteriophages from the Inoviridae family (inoviruses) are characterized by their unique morphology, genome content and infection cycle. One of most striking features inoviruses is ability to establish a chronic whereby viral resides within cell in either an exclusively episomal state or integrated into host chromosome virions continuously released without killing host. To date, relatively small number inovirus isolates have been extensively studied, for biotechnological...
Abstract The current paradigm, widely incorporated in soil biogeochemical models, is that microbial methanogenesis can only occur anoxic habitats. In contrast, here we show clear geochemical and biological evidence for methane production well-oxygenated soils of a freshwater wetland. A comparison oxic to reveal up ten times greater nine more activity oxygenated soils. Metagenomic metatranscriptomic sequencing recover the first near-complete genomes novel methanogen species, acetoclastic from...
Hydraulic fracturing is the industry standard for extracting hydrocarbons from shale formations. Attention has been paid to economic benefits and environmental impacts of this process, yet biogeochemical changes induced in deep subsurface are poorly understood. Recent single-gene investigations revealed that halotolerant microbial communities were enriched after hydraulic fracturing. Here, reconstruction 31 unique genomes coupled metabolite data Marcellus Utica shales many persisting...
Microorganisms in the subsurface represent a substantial but poorly understood component of Earth's biosphere. Subsurface environments are complex and difficult to characterize; thus, their microbiota have remained as 'dark matter' carbon other biogeochemical cycles. Here we deeply sequence two sediment-hosted microbial communities from an aquifer adjacent Colorado River, CO, USA. No single organism represents more than ~1% either community. Remarkably, many bacteria archaea these novel at...
The first cultivated representative of the enigmatic phylum Saccharibacteria (formerly TM7) was isolated from humans and revealed an ultra-small cell size (200–300 nm), a reduced genome with limited biosynthetic capabilities, unique parasitic lifestyle. TM7x only member candidate phyla radiation (CPR), estimated to encompass 26% domain Bacteria. Here we report on divergent genomes major lineages across in mammals, as well ancient dental calculus. These are present at high prevalence within...
Abstract Microbial breakdown of organic matter is one the most important processes on Earth, yet controls decomposition are poorly understood. Here we track 36 terrestrial human cadavers in three locations and show that a phylogenetically distinct, interdomain microbial network assembles during despite selection effects location, climate season. We generated metagenome-assembled genome library from cadaver-associated soils integrated it with metabolomics data to identify links between...
Despite their importance in iron redox cycles and bioenergy production, the underlying physiological, genetic, biochemical mechanisms of extracellular electron transfer by Gram-positive bacteria remain insufficiently understood. In this work, we investigated respiration Thermincola potens strain JR, a isolate obtained from anode surface microbial fuel cell, using insoluble acceptors. We found no evidence that soluble redox-active components were secreted into surrounding medium on basis...
In microbial ecology, a fundamental question relates to how community diversity and composition change in response perturbation. Most studies have had limited ability deeply sample structure (e.g. Sanger-sequenced 16S rRNA libraries), or taxonomic resolution based on hypervariable region sequencing). Here, we combine the higher of near-full-length gene amplicons with economics sensitivity short-read sequencing assay abundance identity organisms that represent as little 0.01% sediment...
Abstract Because of their agricultural value, there is a great body research dedicated to understanding the microorganisms responsible for rumen carbon degradation. However, we lack holistic view microbial food web processing in this ecosystem. Here, sampled rumen-fistulated moose, allowing access communities actively degrading woody plant biomass real time. We resolved 1,193 viral contigs and 77 unique, near-complete metagenome-assembled genomes, many which lacked previous metabolic...