A5036168880- Microbial Community Ecology and Physiology
- Genomics and Phylogenetic Studies
- Methane Hydrates and Related Phenomena
- Environmental DNA in Biodiversity Studies
- Protist diversity and phylogeny
- Bacteriophages and microbial interactions
- Hydrocarbon exploration and reservoir analysis
- Genetic diversity and population structure
- Genetics, Bioinformatics, and Biomedical Research
- Gut microbiota and health
- Molecular Biology Techniques and Applications
- Metal Extraction and Bioleaching
- Drilling and Well Engineering
- Offshore Engineering and Technologies
- Geochemistry and Elemental Analysis
- Machine Learning in Bioinformatics
- Algal biology and biofuel production
- Metabolomics and Mass Spectrometry Studies
- Marine and coastal ecosystems
- Computational and Text Analysis Methods
- Biomedical and Engineering Education
- Cancer Genomics and Diagnostics
- Scientific Computing and Data Management
- Probiotics and Fermented Foods
- Advanced biosensing and bioanalysis techniques
University of Southern California
2016-2025
Southern California Earthquake Center
2025
Alfred Mann Foundation
2023
Bioscience (China)
2023
University of California, Los Angeles
2020
Southern California University for Professional Studies
2014-2017
Laboratoire d'Océanographie Microbienne
2016
Abstract Microorganisms play a crucial role in mediating global biogeochemical cycles the marine environment. By reconstructing genomes of environmental organisms through metagenomics, researchers are able to study metabolic potential Bacteria and Archaea that resistant isolation laboratory. Utilizing large metagenomic dataset generated from 234 samples collected during Tara Oceans circumnavigation expedition, we were assemble 102 billion paired-end reads into 562 million contigs, which turn...
Aerobic anoxygenic phototrophs (AAnPs) are common in marine environments and associated with photoheterotrophic activity. To date, AAnPs that possess the potential for carbon fixation have not been identified surface ocean. Using Tara Oceans metagenomic dataset, we draft genomes of nine bacteria genomic phototrophy, via Calvin-Benson-Bassham cycle, oxidation sulfite thiosulfate. Forming a monophyletic clade within Alphaproteobacteria lacking cultured representatives, organisms compose minor...
Metagenomics has become an integral part of defining microbial diversity in various environments. Many ecosystems have characteristically low biomass and few cultured representatives. Linking potential metabolisms to phylogeny environmental microorganisms is important for interpreting community functions the impacts these communities on geochemical cycles. However, with metagenomic studies there computational hurdle 'binning' contigs into phylogenetically related units or putative genomes....
The rock-hosted subseafloor crustal aquifer harbors a reservoir of microbial life that may influence global marine biogeochemical cycles. Here we utilized metagenomic libraries fluid samples from North Pond, located on the flanks Mid-Atlantic Ridge, site with cold, oxic circulation within upper basement to query diversity. Twenty-one were collected during 2-year period examine potential metabolism and community dynamics. We observed minor changes in geochemical signatures over 2 years, yet...
Abstract The rock-hosted, oceanic crustal aquifer is one of the largest ecosystems on Earth, yet little known about its indigenous microorganisms. Here we provide first phylogenetic and functional description an active microbial community residing in cold oxic aquifer. Using subseafloor observatories, recovered fluids found that geochemical composition similar to bottom seawater, as are cell abundances. However, based relative abundances potential key bacterial groups, fluid heterogeneous...
Abstract Despite their discovery over 25 years ago, the Marine Group II Euryarchaea (MGII) remain a difficult group of organisms to study, lacking cultured isolates and genome references. The MGII have been identified in marine samples from around world, evidence supports photoheterotrophic lifestyle combining phototrophy via proteorhodopsins with remineralization high molecular weight organic matter. Divided between two clades, distinct ecological patterns that are not understood based on...
Single-celled eukaryotes play ecologically significant roles in the marine environment, yet fundamental questions about their biodiversity, ecological function, and interactions remain. Environmental sequencing enables researchers to document naturally occurring protistan communities, without culturing bias, metagenomic metatranscriptomic approaches cannot separate individual species from communities. To more completely capture genomic content of mixed populations, we can create bins...
The Tara Oceans Expedition has provided large, publicly-accessible microbial metagenomic datasets from a circumnavigation of the globe. Utilizing several size fractions samples originating in Mediterranean Sea, we have used current assembly and binning techniques to reconstruct 290 putative draft metagenome-assembled bacterial archaeal genomes, with an estimated completion ≥50%, additional 2,786 bins, 0-50%. We submitted our results, including initial taxonomic phylogenetic assignments, for...
Abstract It is now widely accepted that siderophores play a role in marine iron biogeochemical cycling. However, the mechanisms by which affect availability of from specific sources and resulting significance these processes on cycling as whole have remained largely untested. In this study, we develop model system for testing effects siderophore production bioavailability using copiotroph Alteromonas macleodii ATCC 27126. Through generation knockout cell line ΔasbB::kmr, lacks biosynthetic...
The remineralization of organic material via heterotrophy in the marine environment is performed by a diverse and varied group microorganisms that can specialize type degraded niche they occupy. Dadabacteria are cosmopolitan belong to candidate phylum for which there has not been comprehensive assessment available genomic data date. Here in, we assess functional potential pelagic comparison members originate from terrestrial, hydrothermal, subsurface environments. Our analysis reveals have...
Summary Thaumarchaea , which represent as much 20% of prokaryotic biomass in the open ocean, have been linked to environmentally relevant biogeochemical processes, such ammonia oxidation (nitrification) and inorganic carbon fixation. We used culture‐independent methods study this group because current cultivation limitations proved a hindrance studying these organisms. From metagenomic data set obtained from surface waters Gulf Maine, we identified 36 111 sequence reads (containing 30 Mbp)...
The formation and maintenance of deep-sea ferromanganese/polymetallic nodules still remains a mystery 140 years after their discovery. wealth rare metals concentrated in these has spurred global interest exploring the mining potential resources. prevailing theory abiotic been called into question role microbial metabolisms nodule development is now an area active research. To understand community structure microbes associated with surrounding sediment, we performed targeted sequencing V4...
Background Advances in sequencing, assembly, and assortment of contigs into species-specific bins has enabled the reconstruction genomes from metagenomic data (MAGs). Though a powerful technique, it is difficult to determine whether assembly binning techniques are accurate when applied environmental metagenomes due lack complete reference genome sequences against which check resulting MAGs. Methods We compared MAGs derived an enrichment culture containing ~20 organisms 10 isolated culture....
Abstract Metagenomics is a powerful method for interpreting the ecological roles and physiological capabilities of mixed microbial communities. Yet, many tools processing metagenomic data are not designed to consider eukaryotes, nor they built an increasing amount sequence data. EukHeist automated pipeline retrieve eukaryotic prokaryotic metagenome assembled genomes (MAGs) from large-scale datasets. We developed workflow specifically process large amounts both and/or metatranscriptomic in...
ABSTRACT The South Pacific Gyre (SPG) possesses the lowest rates of sedimentation, surface chlorophyll concentration, and primary productivity in global oceans. As a direct result, deep-sea sediments are thin contain small amounts labile organic carbon. It was recently shown that entire SPG sediment column is oxygenated may be representative up to third marine environment. To understand microbial processes contribute removal matter at water-sediment interface, sample collected subjected...
Abstract The oceanic crustal aquifer is one of the largest habitable volumes on Earth, and it harbors a reservoir microbial life that influences global-scale biogeochemical cycles. Here, we use time series metagenomic metatranscriptomic data from low-temperature, ridge flank environment representative majority global hydrothermal fluid circulation in ocean to reconstruct metabolic potential, transcript abundance, community dynamics. We also present metagenome-assembled genomes recently...
ABSTRACT Though archaea are ubiquitous in the oceans, at times present quantities equal to bacteria, general, underreported when compared with and little is known about archaeal connectivity ocean. Here, we first time series data of size‐fractionated temporal resolution days across a depth transect oligotrophic Atlantic Ocean. Archaeal communities were variable from day day, both regards community composition relative abundance. In context total prokaryotic community, found that water...
Microbial ecology within oligotrophic marine sediment is poorly understood, yet critical for understanding geochemical cycles. Here, 16S rRNA sequences from RNA and DNA inform the structure of active total microbial communities in on western flank Mid-Atlantic Ridge. Sequences identified as Bacillariophyta chloroplast were detected DNA, but undetectable RNA, suggesting preservation 5.6-million-year-old sediment. Statistical analysis revealed that RNA-based populations correlated...
The Gulf of Maine is an important biological province the Northwest Atlantic with high productivity year round. From environmental Sanger-based metagenome, sampled in summer and winter, we were able to assemble explore partial genomes uncultured members class Flavobacteria. Each represents organisms that compose less than 1% total microbial metagenome.Four assembled varying degrees estimated completeness (37%-84% complete) analyzed from a perspective gathering information regarding niche...
As the importance of microbiome research continues to become more prevalent and essential understanding a wide variety ecosystems (e.g. marine, built, host associated, etc.), there is need for researchers be able perform highly reproducible quality analysis microbial genomes. MetaSanity incorporates analyses from 11 existing widely used genome evaluation annotation suites into single, distributable workflow, thereby decreasing workload microbiologists by allowing flexible, expansive data...
The cold, oxic subseafloor is an understudied habitat that difficult to access, yet important global biogeochemical cycles and starkly different compared microbial habitats on the surface of Earth. Our understanding evolution population dynamics largely molded by studies microbes living in can host 10 1,000 times more biomass than frequently observed subsurface.
Abstract Gene prediction and annotation for eukaryotic genomes is challenging with large data demands complex computational requirements. For most eukaryotes, are recovered from specific target taxa. However, it now feasible to reconstruct or sequence hundreds of metagenome-assembled (MAGs) single-amplified directly the environment. To meet this forth-coming wave genome generation, we introduce EukMetaSanity, which combines state-of-the-art tools into three pipelines that have been...
Hypersaline systems near salt saturation levels represent an extreme environment, in which organisms grow and survive the limits of life. One abundant members microbial communities hypersaline is square archaeon, Haloquadratum walsbyi. Utilizing a short-read metagenome from Lake Tyrrell, ecosystem Victoria, Australia, we performed comparative genomic analysis H. walsbyi to better understand extent variation between strains/subspecies. Results revealed that previously isolated...
A wealth of viral data sits untapped in publicly available metagenomic sets when it might be extracted to create a usable index for the virological research community. We hypothesized that work this complexity and scale could done hackathon setting. Ten teams comprised over 40 participants from six countries, assembled crowd-sourced set analysis processing pipelines complex biological three-day event on San Diego State University campus starting 9 January 2019. Prior hackathon, 141,676...
Heterotrophic microbes play an important role in the Earth System as key drivers of major biogeochemical cycles. Specifically, consumption rate organic matter is set by interaction between diverse microbial communities and chemical physical environment which they reside. Modeling these dynamics requires reducing complexity linking directly with functions. Microbial metabolic functional guilds provide one approach for incorporating functions into models. However, we lack a way to identify...