A5016018436- Microbial Community Ecology and Physiology
- Genomics and Phylogenetic Studies
- Protist diversity and phylogeny
- Marine and coastal ecosystems
- Bacteriophages and microbial interactions
- Methane Hydrates and Related Phenomena
- Marine Biology and Ecology Research
- Environmental DNA in Biodiversity Studies
- Gut microbiota and health
- Soil and Water Nutrient Dynamics
- Microbial Fuel Cells and Bioremediation
- Aquatic Ecosystems and Phytoplankton Dynamics
- Wastewater Treatment and Nitrogen Removal
- Single-cell and spatial transcriptomics
- Groundwater and Isotope Geochemistry
- Antibiotic Resistance in Bacteria
- Photoreceptor and optogenetics research
- Microbial Natural Products and Biosynthesis
- Hydrocarbon exploration and reservoir analysis
- Plant Virus Research Studies
- Microbial Metabolic Engineering and Bioproduction
- Marine Bivalve and Aquaculture Studies
- Pharmaceutical and Antibiotic Environmental Impacts
- Coastal wetland ecosystem dynamics
- Biocrusts and Microbial Ecology
Bigelow Laboratory for Ocean Sciences
2016-2025
Wellcome Centre for Mitochondrial Research
2018
University of Newcastle Australia
2018
Newcastle University
2018
University of Georgia
2003-2006
Savannah River National Laboratory
2003-2006
University of South Carolina
2005
Lund University
1999-2003
Genome sequencing enhances our understanding of the biological world by providing blueprints for evolutionary and functional diversity that shapes biosphere. However, microbial genomes are currently available limited phylogenetic breadth, owing to historical inability cultivate most microorganisms in laboratory. We apply single-cell genomics target sequence 201 uncultivated archaeal bacterial cells from nine diverse habitats belonging 29 major mostly uncharted branches tree life, so-called...
We present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of Minimum Information about Any (x) Sequence (MIxS). The a Single Amplified Genome (MISAG) Metagenome-Assembled (MIMAG), including, but not limited to, assembly quality, estimates completeness contamination. These can be used in combination with other GSC checklists, including (MIGS), Metagenomic (MIMS), Marker Gene (MIMARKS). Community-wide...
Recent advances in single-cell genomics provide an alternative to largely gene-centric metagenomics studies, enabling whole-genome sequencing of uncultivated bacteria. However, assembly projects are challenging due (i) the highly nonuniform read coverage and (ii) a greatly elevated number chimeric reads pairs. While recently developed assemblers have addressed former challenge, methods for assembling remain poorly explored. We present algorithms identifying edges resolving complex bulges de...
Recent studies suggest that unidentified prokaryotes fix inorganic carbon at globally significant rates in the immense dark ocean. Using single-cell sorting and whole-genome amplification of from two subtropical gyres, we obtained genomic DNA 738 cells representing most cosmopolitan lineages. Multiple Deltaproteobacteria cluster SAR324, Gammaproteobacteria clusters ARCTIC96BD-19 Agg47, some Oceanospirillales lower mesopelagic contained ribulose-1,5-bisphosphate carboxylase-oxygenase sulfur...
Cyanobacterial Diversity What does it mean to be a global species? The marine cyanobacterium Prochlorococcus is ubiquitous and, arguably, the most abundant and productive of all living organisms. Although our eyes seas look uniform, bacterium ocean's bulk plethora microhabitats, by large-scale single-cell genomic analysis uncultured cells, Kashtan et al. (p. 416 ; see Perspective Bowler Scanlan ) reveal that has diversified match. This “species” constitutes mass subpopulations—each with...
Planktonic bacteria dominate surface ocean biomass and influence global biogeochemical processes, but remain poorly characterized owing to difficulties in cultivation. Using large-scale single cell genomics, we obtained insight into the genome content biogeography of many bacterial lineages inhabiting ocean. We found that, compared with existing cultures, natural bacterioplankton have smaller genomes, fewer gene duplications, are depleted guanine cytosine, noncoding nucleotides, genes...
The difficulty associated with the cultivation of most microorganisms and complexity natural microbial assemblages, such as marine plankton or human microbiome, hinder genome reconstruction representative taxa using metagenomic approaches. Here we used an alternative, single cell sequencing approach to obtain high-quality assemblies two uncultured, numerically significant microorganisms. We employed fluorescence-activated sorting multiple displacement amplification hundreds micrograms...
Marine protist cells from the wild environment contain DNA several viruses and bacteria, but apparently lack plastids.
We describe the microbiota of two hypersaline saltern ponds, one intermediate salinity (19%) and a NaCl saturated crystallizer pond (37%) using pyrosequencing. The analyses these metagenomes (nearly 784 Mb) reaffirmed vast dominance Haloquadratum walsbyi but also revealed novel, abundant previously unsuspected microbial groups. for first time, group low GC Actinobacteria, related to freshwater in salinities. Metagenomic assembly three new microbes: low-GC euryarchaeon with lowest content...
Carbon fixation by chemoautotrophic microorganisms in the dark ocean has a major impact on global carbon cycling and ecological relationships ocean's interior, but relevant taxa energy sources remain enigmatic. We show evidence that nitrite-oxidizing bacteria affiliated with Nitrospinae phylum are important chemoautotrophy. Single-cell genomics community metagenomics revealed most abundant globally distributed ocean. Metaproteomics metatranscriptomics analyses suggest nitrite oxidation is...
Microbial hydrolysis of polysaccharides is critical to ecosystem functioning and great interest in diverse biotechnological applications, such as biofuel production bioremediation. Here we demonstrate the use a new, efficient approach recover genomes active polysaccharide degraders from natural, complex microbial assemblages, using combination fluorescently labeled substrates, fluorescence-activated cell sorting, single genomics. We employed this analyze freshwater coastal bacterioplankton...
Viruses modulate microbial communities and alter ecosystem functions. However, due to cultivation bottlenecks, specific virus–host interaction dynamics remain cryptic. In this study, we examined 127 single-cell amplified genomes (SAGs) from uncultivated SUP05 bacteria isolated a model marine oxygen minimum zone (OMZ) identify 69 viral contigs representing five new genera within dsDNA Caudovirales ssDNA Microviridae. Infection frequencies suggest that ∼1/3 of is viral-infected, with higher...
Abstract Viral infections dynamically alter the composition and metabolic potential of marine microbial communities evolutionary trajectories host populations with resulting feedback on biogeochemical cycles. It is quite possible that all in ocean are impacted by viral infections. Our knowledge virus–host relationships, however, has been limited to a minute fraction cultivated groups. Here, we utilized single-cell sequencing obtain genomic blueprints viruses inside or attached individual...
High-throughput RNA sequencing offers broad opportunities to explore the Earth virome. Mining 5,150 diverse metatranscriptomes uncovered >2.5 million virus contigs. Analysis of >330,000 RNA-dependent polymerases (RdRPs) shows that this expansion corresponds a 5-fold increase known diversity. Gene content analysis revealed multiple protein domains previously not found in viruses and implicated virus-host interactions. Extended RdRP phylogeny supports monophyly five established phyla reveals...
Abstract Microbial single-cell genomics can be used to provide insights into the metabolic potential, interactions, and evolution of uncultured microorganisms. Here we present WGA-X, a method based on multiple displacement amplification DNA that utilizes thermostable mutant phi29 polymerase. WGA-X enhances genome recovery from individual microbial cells viral particles while maintaining ease use scalability. The greatest improvements are observed when amplifying high G+C content templates,...
Abstract A unique collection of oceanic samples was gathered by the Tara Oceans expeditions (2009–2013), targeting plankton organisms ranging from viruses to metazoans, and providing rich environmental context measurements. Thanks recent advances in field genomics, extensive sequencing has been performed for a deep genomic analysis this huge samples. strategy based on different approaches, such as metabarcoding, metagenomics, single-cell genomics metatranscriptomics, chosen size-fractionated...
ABSTRACT Deep-ocean regions beyond the reach of sunlight contain an estimated 615 Pg dissolved organic matter (DOM), much which persists for thousands years. It is thought that bacteria oxidize DOM until it too dilute or refractory to support microbial activity. We analyzed five single-amplified genomes (SAGs) from abundant SAR202 clade dark-ocean bacterioplankton and found they encode multiple families paralogous enzymes involved in carbon catabolism, including several oxidative we...