A5081165829- Microbial Community Ecology and Physiology
- Marine and coastal ecosystems
- Protist diversity and phylogeny
- Environmental DNA in Biodiversity Studies
- Genomics and Phylogenetic Studies
- Methane Hydrates and Related Phenomena
- Marine Biology and Ecology Research
- Marine Toxins and Detection Methods
- Underwater Vehicles and Communication Systems
- Identification and Quantification in Food
- Advanced Chemical Sensor Technologies
- Aquatic Ecosystems and Phytoplankton Dynamics
- Aquaculture disease management and microbiota
- Marine Sponges and Natural Products
- Wastewater Treatment and Nitrogen Removal
- Microbial bioremediation and biosurfactants
- Marine Ecology and Invasive Species
- Marine animal studies overview
- Scientific Computing and Data Management
- Coral and Marine Ecosystems Studies
- Underwater Acoustics Research
- Photoreceptor and optogenetics research
- Metabolomics and Mass Spectrometry Studies
- Oceanographic and Atmospheric Processes
- Astrophysics and Star Formation Studies
Monterey Bay Aquarium Research Institute
2013-2024
Netherlands Institute for Radio Astronomy
2024
Oceanography Society
2017
San Diego State University
2006
University of Hawaiʻi at Mānoa
2006
University of Hawaii System
2006
Massachusetts Institute of Technology
2006
Pacific University
2004
Joint Genome Institute
2004
Stanford University
2004
Microbial life predominates in the ocean, yet little is known about its genomic variability, especially along depth continuum. We report here analyses of planktonic microbial communities North Pacific Subtropical Gyre, from ocean's surface to near-sea floor depths. Sequence variation community genes reflected vertical zonation taxonomic groups, functional gene repertoires, and metabolic potential. The distributional patterns suggested depth-variable trends carbon energy metabolism,...
Microbial methane consumption in anoxic sediments significantly impacts the global environment by reducing flux of greenhouse gases from ocean to atmosphere. Despite its significance, biological mechanisms controlling anaerobic oxidation are not well characterized. One current model suggests that relatives methane-producing Archaea developed capacity reverse methanogenesis and thereby consume produce cellular carbon energy. We report here a test "reverse-methanogenesis" hypothesis genomic...
Newly described phylogenetic lineages within the domain Archaea have recently been found to be significant components of marine picoplankton assemblages. To better understand ecology these microorganisms, we investigated relative abundance, distribution, and composition in Santa Barbara Channel. Significant amounts archaeal rRNA rDNA (genes coding for rRNA) were detected all samples analyzed. The abundance as measured by quantitative oligonucleotide hybridization experiments was low surface...
Marine Crenarchaeota represent an abundant component of oceanic microbiota with potential to significantly influence biogeochemical cycling in marine ecosystems. Prior studies using specific archaeal lipid biomarkers and isotopic analyses indicated that planktonic have the capacity for autotrophic growth, more recent cultivation support ammonia-based chemolithoautotrophic energy metabolism. We report here analysis fosmid sequences derived from uncultivated crenarchaeote, Cenarchaeum...
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...
Summary The recent isolation of the ammonia‐oxidizing crenarchaeon Nitrosopumilus maritimus has expanded known phylogenetic distribution nitrifying phenotypes beyond domain Bacteria . To further characterize nitrification in marine environment and explore potential crenarchaeal contribution to this process, we quantified putative genes phylotypes picoplankton genomic libraries environmental DNA samples from coastal open ocean habitats. Betaproteobacteria ammonia monooxygenase subunit A (...
ABSTRACT A previous report of high levels members the domain Archaea in Antarctic coastal waters prompted us to investigate ecology planktonic prokaryotes. rRNA hybridization techniques and denaturing gradient gel electrophoresis (DGGE) analysis bacterial V3 region were used study variation picoplankton assemblages. In Anvers Island nearshore during late winter early spring, amounts archaeal ranged from 17.1 3.6% total 1996 16.0 1.0% 1995. Offshore Palmer Basin, throughout water column...
Crenarchaeota are ubiquitous and abundant microbial constituents of soils, sediments, lakes, ocean waters. To further describe the cosmopolitan nonthermophilic Crenarchaeota, we analyzed genome sequence one representative, uncultivated sponge symbiont Cenarchaeum symbiosum. C. symbiosum genotypes coinhabiting same host partitioned into two dominant populations, corresponding to previously described a- b-type ribosomal RNA variants. Although they were syntenic, overlapping ribotype genomes...
Aerobic, anoxygenic, phototrophic bacteria containing bacteriochlorophyll a (Bchla) require oxygen for both growth and Bchla synthesis1,2,3,4,5,6. Recent reports suggest that these are widely distributed in marine plankton, they may account up to 5% of surface ocean photosynthetic electron transport7 11% the total microbial community8. Known planktonic anoxygenic phototrophs belong only few restricted groups within Proteobacteria α-subclass. Here we report genomic analyses gene content...
Phylogenetic and stable-isotope analyses implicated two methanogen-like archaeal groups, ANME-1 ANME-2, as key participants in the process of anaerobic methane oxidation. Although nothing is known about oxidation at molecular level, evolutionary relationship between methane-oxidizing archaea (MOA) methanogenic raises possibility that MOA have co-opted elements pathway, reversing many its steps to oxidize anaerobically. In order explore this hypothesis, existence genomic conservation methyl...
ABSTRACT Fluorescent in situ hybridization (FISH) using rRNA-specific oligonucleotide probes has emerged as a popular technique for identifying individual microbial cells. In natural samples, however, the signal derived from fluor-labeled often is undetectable above background fluorescence many To circumvent this difficulty, we applied fluorochrome-labeled polyribonucleotide to identify and enumerate marine planktonic archaea bacteria. The approach greatly enhanced sensitivity applicability...
Polyribonucleotide probes targeting planktonic archaeal (Group I and II) bacterial rRNA revealed that Archaea comprised a significant fraction of total prokaryote cell abundance in the marine waters west Antarctic Peninsula. Determinations Bacteria abundances were made during two research cruises to Palmer Long‐Term Ecological Research region austral winter summer 1999. During summer, surface water Group (GI) generally low, averaging 4.7 x 10 3 cells ml −1 accounting for 1% picoplankton...
We compared the detection of bacteria and archaea in coastal North Sea at Monterey Bay, Calif., after fluorescence situ hybridization (FISH) either with rRNA-targeted oligonucleotide probes monolabeled cyanin dye Cy3 (oligoFISH) or fluorescein-labeled polyribonucleotide (polyFISH). During an annual cycle German Bight surface waters, percentages visualized by polyFISH (annual mean, 77% total counts) were significantly higher than those detected oligoFISH (53%). The fraction declined during...
Divers inspecting the subsurface instrument package during pre-deployment testing.
Environmental DNA (eDNA) can be used to identify macroorganisms and describe biodiversity, thus has promise supplement biological monitoring in marine ecosystems. Despite this promise, scaling sample acquisition the size temporal scales needed for effective would require prohibitively large investments time human resources. To improve upon these problems, here we test efficacy of an autonomous eDNA sampling system compare results obtained traditional methods. The instrument consisted Sample...
ABSTRACT Molecular phylogenetic surveys have recently revealed an ecologically widespread crenarchaeal group that inhabits cold and temperate terrestrial marine environments. To date these organisms resisted isolation in pure culture, so their phenotypic genotypic characteristics remain largely unknown. characterize archaea, to extend methodological approaches for characterizing uncultivated microorganisms, we initiated genomic analyses of the nonthermophilic crenarchaeote Cenarchaeum...
The Environmental Sample Processor (ESP) is a device that allows for the underwater, autonomous application of DNA and protein probe array technologies as means to remotely identify quantify, in situ, marine microorganisms substances they produce. Here, we added functionality ESP through development incorporation module capable solid-phase nucleic acid extraction quantitative PCR (qPCR). Samples collected by instrument were homogenized chaotropic buffer compatible with direct detection...
The sequestration of carbon in the deep ocean relies on export sinking particulate organic matter (POM) originating surface waters and its attenuation by organisms that reprocess repackage it. Despite decades research, predicting variability POM to remains difficult as there is still a gap knowledge which how control or influence export. Here, we used DNA metabarcoding 16S 18S rRNA genes investigate community particulates collected over 9-months (November 2016–July 2017) at Station M,...
Abstract Environmental DNA (eDNA) is increasingly used for monitoring marine organisms; however, offshore sampling and time lag from to results remain problematic. In order overcome these challenges a robotic sampler, 2nd generation Sample Processor (ESP), was tested autonomous analysis of eDNA four commercial fish species in 4.5 million liter mesocosm. The ESP enabled situ analysis, consisting water collection, filtration, extraction qPCR which allowed real-time remote reporting archival...
A team of coordinated robots autonomously observed and sampled open-ocean microbial communities in a Lagrangian mode.
Abstract Environmental DNA (eDNA) is an emerging and powerful method for use in marine research, conservation, management, yet time‐ resource‐intensive protocols limit the scale of implementation. Long‐range autonomous underwater vehicles equipped with environmental sample processors (LRAUV‐ESPs) provide a new means scaling up eDNA collection processing. Here, we used metabarcoding four marker genes (mitochondrial 12S rRNA, bacterial archaeal 16S nuclear 18S mitochondrial COI), which...
Summary Proteorhodopsins (PRs), bacterial photoactive proton pumps, were originally detected in the uncultured marine γ‐proteobacterial SAR86 group. PRs are now known to occur both γ and α proteobacterial lineages. Recent environmental shotgun sequence analysis Sargasso Sea has added yet more diversity, a potentially broader taxonomic distribution, PR family. Much remains be learned, however, about within‐taxon variability organismal distribution of different types. We report here genomic...