A5032498927- Microbial Community Ecology and Physiology
- Gut microbiota and health
- Clostridium difficile and Clostridium perfringens research
- Genomics and Phylogenetic Studies
- Microscopic Colitis
- Polar Research and Ecology
- Wastewater Treatment and Nitrogen Removal
- Methane Hydrates and Related Phenomena
- Indoor Air Quality and Microbial Exposure
- Probiotics and Fermented Foods
- Environmental DNA in Biodiversity Studies
- Coral and Marine Ecosystems Studies
- Aquaculture disease management and microbiota
- Legume Nitrogen Fixing Symbiosis
- Soil Carbon and Nitrogen Dynamics
- Geology and Paleoclimatology Research
- Water Treatment and Disinfection
- Marine Sponges and Natural Products
- Gastrointestinal motility and disorders
- Gene expression and cancer classification
- Marine Biology and Ecology Research
- Marine and coastal ecosystems
- Microbial bioremediation and biosurfactants
- Geochemistry and Geologic Mapping
- Atmospheric and Environmental Gas Dynamics
University of California, San Francisco
2019-2022
Symbiom (Czechia)
2021
Lawrence Berkeley National Laboratory
2009-2018
NASA Earth Science
2014
Energy Biosciences Institute
2014
Chinese Research Academy of Environmental Sciences
2010
Tongji University
2010
University of California, Berkeley
2006-2010
State Key Laboratory of Pollution Control and Resource Reuse
2010
Rockford University
2003
A common plant pathogen induces the growth of disease-suppressive microbes in local soil communities.
The biological effects and expected fate of the vast amount oil in Gulf Mexico from Deepwater Horizon blowout are unknown owing to depth magnitude this event. Here, we report that dispersed hydrocarbon plume stimulated deep-sea indigenous γ-Proteobacteria closely related known petroleum degraders. Hydrocarbon-degrading genes coincided with concentration various contaminants. Changes composition distance source incubation experiments environmental isolates demonstrated faster-than-expected...
Microbiologists conducting surveys of bacterial and archaeal diversity often require comparative alignments thousands 16S rRNA genes collected from a sample. The computational resources bioinformatics expertise required to construct such an alignment has inhibited high-throughput analysis. It was hypothesized that online tool could be developed efficiently align via the NAST (Nearest Alignment Space Termination) algorithm for creating multiple sequence (MSA). implemented with web-interface...
Considering the importance of its potential implications for human health, agricultural productivity, and ecosystem stability, surprisingly little is known regarding composition or dynamics atmosphere's microbial inhabitants. Using a custom high-density DNA microarray, we detected monitored bacterial populations in two U.S. cities over 17 weeks. These urban aerosols contained at least 1,800 diverse types, richness approaching that some soil communities. We also reveal consistent presence...
Intestinal microbiome constitutes a symbiotic ecosystem that is essential for health, and changes in its composition/function cause various illnesses. Biochemical milieu shapes the structure function of microbiome. Recently, we found marked differences abundance numerous bacterial taxa between ESRD healthy individuals. Influx urea uric acid dietary restriction fruits vegetables to prevent hyperkalemia alter patients' intestinal milieu. We hypothesized relative abundances bacteria possessing...
The Deepwater Horizon oil spill produced large subsurface plumes of dispersed and gas in the Gulf Mexico that stimulated growth psychrophilic, hydrocarbon degrading bacteria. We tracked succession plume bacteria before, during after 83-day to determine microbial response biodegradation potential throughout incident. Dominant shifted substantially over time were dependent on relative quantities different fractions. Unmitigated flow from wellhead early resulted highest proportions n-alkanes...
The phylogenetic composition of bacterial communities in the rhizosphere three potato cultivars grown at two distant field sites was analysed. Ribosomal gene fragments amplified from total community DNA were hybridized to PhyloChips. A 2432 operational taxonomic units (OTUs) detected by PhyloChips, which 65% found all both sites. From OTUs, 9% revealed a cultivar-dependent abundance one or other site and 4% Differential on mainly observed for OTUs belonging Pseudomonadales, Actinomycetales...
Current knowledge of the microbial communities within biological wastewater treatment reactors is incomplete due to limitations traditional culture-based techniques and despite emergence recently applied molecular techniques. Here we demonstrate application high-density microarrays targeting universal 16S rRNA genes evaluate community composition in five China United States. Results suggest a surprisingly consistent structure among all reactors. All investigated contained core bacterial...
Coastal salt marshes are highly sensitive wetland ecosystems that can sustain long-term impacts from anthropogenic events such as oil spills. In this study, we examined the microbial communities of a Gulf Mexico coastal marsh during and after influx petroleum hydrocarbons following Deepwater Horizon spill. Total hydrocarbon concentrations in sediments were highest June July 2010 decreased September 2010. Coupled PhyloChip GeoChip microarray analyses demonstrated community structure function...
The microbial community structure of bacteria, archaea and fungi is described in an Australian native grassland soil after more than 5 years exposure to different atmospheric CO2 concentrations ([CO2]) (ambient, +550 ppm) temperatures + 2°C) under plant functional types (C3 C4 grasses) at two depths (0-5 cm 5-10 cm). Archaeal diversity was influenced by elevated [CO2], while warming archaeal 16S rRNA gene copy numbers increased for Themeda triandra decreased the C3 (P < 0.05). Fungal...
ABSTRACT Oil reservoirs are major sites of methane production and carbon turnover, processes with significant impacts on energy resources global biogeochemical cycles. We applied a cultivation-independent genomic approach to define microbial community membership predict roles for specific organisms in transformations Alaska North Slope oil fields. Produced water samples were collected from six locations between 1,128 m (24 27°C) 2,743 (80 83°C) below the surface. Microbial complexity...
Natural scrublands in semi-arid deserts are increasingly being converted into fields. This results losses of characteristic flora and fauna, may also affect microbial diversity. In the present study, long-term effect (50 years) such a transition on soil bacterial communities was explored at two sites typical deserts. Comparisons were made between samples from alfalfa fields adjacent by complementary methods based 16S rRNA gene fragments amplified total community DNA. Denaturing gradient gel...
ABSTRACT N 2 fixation by diazotrophic bacteria associated with the roots of smooth cordgrass, Spartina alterniflora , is an important source new nitrogen in many salt marsh ecosystems. However, diversity and phylogenetic affiliations these rhizosphere diazotrophs are unknown. Denaturing gradient gel electrophoresis (DGGE) PCR-amplified nifH sequence segments was used previous studies to examine stability dynamics diazotroph assemblages North Inlet marsh, near Georgetown, S.C. In this study,...
Microbial sulfate reduction is a primary cause of oil reservoir souring. Here we show that amendment with chlorate or perchlorate [collectively (per)chlorate] potentially resolves this issue. Triplicate packed columns inoculated marine sediment were flushed coastal water amended yeast extract and one nitrate, chlorate, perchlorate. Results showed although sulfide production was dramatically reduced by all treatments, effluent observed in the nitrate (10 mM) treatment after an initial...
Emerging trials suggest fecal microbiota transplantation (FMT) is a promising treatment for ulcerative colitis; however, there paucity of data in Crohn disease (CD).The objectives this article are to determine whether single-dose FMT improves clinical and endoscopic outcomes CD patients identify meaningful changes the microbiome response FMT.We performed prospective, open-label, single-center study. Ten underwent were evaluated (defined as decrease Harvey-Bradshaw Index score ≥3 at one month...