A5020220914- Genomics and Phylogenetic Studies
- Microbial Community Ecology and Physiology
- Bacteriophages and microbial interactions
- Photosynthetic Processes and Mechanisms
- Algal biology and biofuel production
- Evolution and Genetic Dynamics
- Methane Hydrates and Related Phenomena
- Microbial bioremediation and biosurfactants
- Atmospheric and Environmental Gas Dynamics
- Bacterial Genetics and Biotechnology
- Marine Bivalve and Aquaculture Studies
- Marine and fisheries research
- CRISPR and Genetic Engineering
- Healthcare and Venom Research
- Escherichia coli research studies
- Bee Products Chemical Analysis
- Antibiotic Resistance in Bacteria
- Metal Extraction and Bioleaching
- Hydrocarbon exploration and reservoir analysis
- Gene expression and cancer classification
- RNA and protein synthesis mechanisms
- Marine Biology and Ecology Research
- Enzyme Production and Characterization
- Probiotics and Fermented Foods
- Coastal wetland ecosystem dynamics
Marine Biological Laboratory
2020-2025
University of California, Santa Barbara
2015-2021
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Abstract In the evolutionary arms race between microbes, their parasites, and neighbours, capacity for rapid protein diversification is a potent weapon. Diversity-generating retroelements (DGRs) use mutagenic reverse transcription retrohoming to generate myriad variants of target gene. Originally discovered in pathogens, these have been identified bacteria viruses, but never archaea. Here we report discovery intact DGRs two distinct intraterrestrial archaeal systems: novel virus that appears...
Abstract Changes in the sequence of an organism’s genome, i.e., mutations, are raw material evolution. The frequency and location mutations can be constrained by specific molecular mechanisms, such as diversity-generating retroelements (DGRs). DGRs have been characterized from cultivated bacteria bacteriophages, perform error-prone reverse transcription leading to being introduced target genes. DGR loci were also identified several metagenomes, but ecological roles evolutionary drivers these...
CPR bacteria are generally predicted to be symbionts due their extensive biosynthetic deficits. Although monophyletic, they not monolithic in terms of lifestyles. The organism described here appears have evolved an unusual metabolic platform reliant on glucose or pentose sugars. Its biology centered around bacterial host-derived compounds and/or cell detritus. Amino acids likely provide building blocks for nucleic acids, peptidoglycan, and protein synthesis. We resolved repeat region that...
Diversity-generating retroelements (DGRs) are used by bacteria, archaea, and viruses as a targeted mutagenesis tool. Through error-prone reverse transcription, DGRs introduce random mutations at specific genomic loci, enabling rapid evolution of these genes. However, the function benefits DGR-diversified proteins in cellular hosts remain elusive. We find that 82% from one major monophyletic lineages DGR transcriptases encoded multicellular which often have two or more loci their genomes....
Abstract Many natural resources are managed without essential, biologically relevant data. Fisheries particularly susceptible to this reality and, thus, vulnerable environmental changes and disturbances, with both human livelihoods the health of ecological systems at stake. Here, we explore how Pacific Northwest Crab Research Group (PCRG) employs a collaborative, stakeholder-driven approach generate information needed inform data-poor, co-managed fishery, using example Dungeness crab...
The marine subsurface is a reservoir of the greenhouse gas methane. While microorganisms living in water column and seafloor ecosystems are known to be major sink limiting net methane transport from atmosphere, few studies have assessed flow methane-derived carbon through benthic mat communities that line on continental shelf where emitted. We analyzed abundance isotope composition fatty acids microbial mats grown shallow Coal Oil Point seep field off Santa Barbara, CA, mixture CO2. further...
Industrial-scale dumping of organic waste to the deep ocean was once common practice, leaving a legacy chemical pollution for which paucity information exists. Using nested approach with autonomous and remotely operated underwater vehicles, dumpsite offshore California surveyed sampled. Discarded containers littered site structured suboxic benthic environment. Dichlorodiphenyltrichloroethane (DDT) reportedly dumped in area, sediment analysis revealed substantial variability concentrations...
Abstract Background Cyanobacteria maintain extensive repertoires of regulatory genes that are vital for adaptation to environmental stress. Some cyanobacterial genomes have been noted encode diversity-generating retroelements (DGRs), which promote protein hypervariation through localized retrohoming and codon rewriting in target genes. Past research has shown DGRs mainly diversify proteins involved cell-cell attachment or viral-host within viral, bacterial, archaeal lineages. However, these...
Diversity-generating retroelements (DGRs) provide organisms with a unique means for adaptation to dynamic environment through massive protein sequence variation. The potential scope of this variation exceeds that the vertebrate adaptive immune system. DGRs were known exist only in viruses and bacteria until their recent discovery archaea belonging 'microbial dark matter', specifically closely related Nanoarchaeota. However, Nanoarchaeota DGR variable proteins unassignable folds apparently...
Abstract Changes in the sequence of an organism’s genome, i.e. mutations, are raw material evolution 1 . The frequency and location mutations can be constrained by specific molecular mechanisms, such as Diversity-generating retroelements (DGRs) 2–4 DGRs introduce target genes, were characterized from several cultivated bacteria bacteriophages 2 Whilst a larger diversity DGR loci has been identified genomic data environmental samples, metagenomes, ecological role these their associated...
Marine benthic environments may be shaped by anthropogenic and other localized events, leading to changes in microbial community composition evident decades after a disturbance. sediments particular harbor exceptional taxonomic diversity can shed light on distinctive evolutionary strategies. Genetic code expansion is strategy that increases the structural functional of proteins cells, repurposing stop codons encode non-canonical amino acids: pyrrolysine (Pyl) selenocysteine (Sec). Here, we...
The exchange of antibiotic production and resistance genes between microorganisms can lead to the emergence new pathogens. In this study, short-read mapping metagenomic samples taken over time from illeal pouch a patient with ulcerative colitis Bacteroides fragilis metagenome-assembled genome revealed two distinct genomic arrangements novel conjugative transposon, CTn214, that encodes tetracycline resistance. autonomous amplification plasmid-like circular form CTn214 includes tetQ...
Fatty acids produced by H2-metabolizing bacteria are sometimes observed to be more D-depleted than those of photoautotrophic organisms, a trait that has been suggested as diagnostic for chemoautotrophic bacteria. The biochemical reasons such depletion not known, but often assumed involve the strong D-depletion H2. Here we cultivated bacterium Cupriavidus necator H16 (formerly Ralstonia eutropha H16) under aerobic, H2-consuming, conditions and measured isotopic compositions its fatty acids....
Abstract The Candidate Phyla Radiation (CPR) comprises a large monophyletic group of bacterial lineages known almost exclusively based on genomes obtained using cultivation-independent methods. Within the CPR, Gracilibacteria (BD1-5) are particularly poorly understood due to undersampling and inherent fragmented nature available genomes. Here, we report first closed, curated genome from an enrichment experiment inoculated Gulf Mexico designed investigate hydrocarbon degradation....
Salt marshes are known for their significant carbon storage capacity, and sulfur cycling is closely linked with the ecosystem-scale in these ecosystems. Sulfate reducers key decomposition of organic matter, oxidizers remove toxic sulfide, supporting productivity marsh plants. To date, complexity coastal environments, heterogeneity rhizosphere, high microbial diversity, uncultured majority hindered our understanding genomic diversity sulfur-cycling microbes salt marshes. Here, we use...
Aqueous-soluble hydrocarbons dissolve into the ocean interior and structure deep-sea microbial populations influenced by natural oil seeps spills. n-Pentane is a seawater-soluble, volatile compound abundant in petroleum products reservoirs will partially partition to deep-water column following release from seafloor. In this study, we explore ecology niche partitioning of two free-living Cycloclasticus strains recovered seawater incubations with n-pentane using distinguish them as an open...
Abstract Filamentous cyanobacteria of the Nostocaceae family are able to differentiate into multicellular forms adapt environmental stresses, and members can establish symbiosis with various embryophytes. Representative laboratory strains typically grown under continuous light maintain stable metabolic conditions, however, this departure from a natural diel cycle result in extended stress. Early genomic examination Nostoc punctiforme suggests genetic potential for circadian clock, but we...
Abstract Marine benthic environments may be shaped by anthropogenic and other localized events, leading to changes in microbial community composition evident decades after a disturbance. sediments particular harbor exceptional taxonomic diversity can shed light on distinctive evolutionary strategies. Genetic code expansion increase the structural functional of proteins cells, repurposing stop codons encode noncanonical amino acids: pyrrolysine (Pyl) selenocysteine (Sec). Here, we show that...