A5054609598- Microbial Community Ecology and Physiology
- Genomics and Phylogenetic Studies
- Microbial Metabolism and Applications
- Gut microbiota and health
- Microplastics and Plastic Pollution
- Chromium effects and bioremediation
- Microbial Metabolic Engineering and Bioproduction
- Calcium Carbonate Crystallization and Inhibition
- Soil Carbon and Nitrogen Dynamics
- Bacterial biofilms and quorum sensing
- Microbial Fuel Cells and Bioremediation
- Wastewater Treatment and Nitrogen Removal
- Evolution and Genetic Dynamics
- Vibrio bacteria research studies
- Biofuel production and bioconversion
- Mine drainage and remediation techniques
- Bacterial Genetics and Biotechnology
- Pharmaceutical and Antibiotic Environmental Impacts
- Anaerobic Digestion and Biogas Production
- Environmental Toxicology and Ecotoxicology
- Microbial bioremediation and biosurfactants
- Escherichia coli research studies
- Metal Extraction and Bioleaching
- Physiological and biochemical adaptations
- Metabolomics and Mass Spectrometry Studies
University of Oklahoma
2016-2025
Texas A&M University
2024
Micro-organisms play critical roles in many important biogeochemical processes the Earth's biosphere. However, understanding and characterizing functional capacity of microbial communities are still difficult due to extremely diverse often uncultivable nature most micro-organisms. In this study, we developed a new gene array, GeoChip 4, for analysing diversity, composition, structure, metabolic potential/activity dynamics communities. 4 contained approximately 82 000 probes covering 141 995...
Significance Networks are fundamental units for studying complex systems, but reconstructing networks from large-scale experimental data is very challenging in systems biology and microbial ecology, primarily due to the difficulty unraveling direct indirect interactions. By tackling several mathematical challenges, this study provides a conceptual framework disentangling relationships association networks. The application of iDIRECT (Inference Direct Indirect Relationships with Effective...
Polyethylene (PE) is the most widely produced synthetic polymer and abundant plastic waste worldwide due to its recalcitrance biodegradation low recycle rate. Microbial degradation of PE has been reported, but underlying mechanisms are poorly understood. Here, we isolated a Rhodococcus strain A34 from 609 day enriched cultures derived naturally weathered identified potential key enzymes. After 30 days incubation with A34, 1% weight loss was achieved. Decreased molecular weight, appearance...
Abstract Soil microbial respiration is an important source of uncertainty in projecting future climate and carbon (C) cycle feedbacks. However, its feedbacks to warming underlying mechanisms are still poorly understood. Here we show that the temperature sensitivity soil ( Q 10 ) a temperate grassland ecosystem persistently decreases by 12.0 ± 3.7% across 7 years warming. Also, shifts communities play critical roles regulating thermal adaptation respiration. Incorporating functional gene...
The rapid development of metagenomic technologies, including microarrays, over the past decade has greatly expanded our understanding complex microbial systems. However, because ever-expanding number novel sequences discovered each year, developing a microarray that is representative real communities, specific and sensitive, provides quantitative information remains challenge. newly developed GeoChip 5.0 most comprehensive available to date for examining functional capabilities communities...
BRI1-like receptor kinase (BRL1) was identified as an extragenic suppressor of a weak bri1 allele, bri1-5, in activation-tagging genetic screen for novel brassinosteroid (BR) signal transduction regulators. BRL1 encodes leucine-rich repeat receptor-like protein (LRR-RLK). Sequence alignment revealed that is closely related to BRI1, which involved BR perception. Overexpression cDNA, driven by constitutive CaMV 35S promoter, recapitulates the bri1-5 suppression phenotypes, and partially...
Soil microbial communities play critical roles in ecosystem functioning and are likely altered by climate warming. However, so far, little is known about effects of warming on functional gene expressions. Here, we applied array (GeoChip 3.0) to analyze cDNA reversely transcribed from total RNA assess expressed genes active soil after nine years experimental a tallgrass prairie. Our results showed that significantly the community wide Specifically, for degrading more recalcitrant carbon were...
Bacterial predation is an important selective force in microbial community structure and dynamics. However, only a limited number of predatory bacteria have been reported, their strategies evolutionary adaptations remain elusive. We recently isolated novel group bacterial predators, Bradymonabacteria, representative the order Bradymonadales δ-Proteobacteria. Compared with those other predators (e.g., Myxococcales Bdellovibrionales), living are still largely unknown.
ABSTRACT Uncultivated but abundant soil microorganisms have untapped potential for producing broad ranges of natural products, as well bioremediation. However, cultivating while maintaining a microorganism diversity to enable phenotyping and functional analysis diverse individual isolates possible remains challenging. In this study, we developed tested the ability several culture media formulations that contain defined metabolites or extracts maintain during culture. We also assessed their...
Summary To understand how sulphate‐reducing bacteria respond to oxidative stresses, the responses of Desulfovibrio vulgaris Hildenborough H 2 O ‐induced stresses were investigated with transcriptomic, proteomic and genetic approaches. induced chemical species (e.g. polysulfide, ROS) redox potential shift increased expressions genes involved in detoxification, thioredoxin‐dependent reduction system, protein DNA repair, decreased those sulfate reduction, lactate oxidation synthesis. A gene...
Complex interactions exist among microorganisms in a community to carry out ecological processes and adapt changing environments. Here, we constructed quad-culture consisting of cellulolytic bacterium (Ruminiclostridium cellulolyticum), hydrogenotrophic methanogen (Methanospirillum hungatei), an acetoclastic (Methanosaeta concilii), sulfate-reducing (Desulfovibrio vulgaris). The four the cooperated via cross-feeding produce methane using cellulose as only carbon source electron donor....
ABSTRACT The response of Desulfovibrio vulgaris Hildenborough to salt adaptation (long-term NaCl exposure) was examined by performing physiological, global transcriptional, and metabolite analyses. Salt reflected increased expression genes involved in amino acid biosynthesis transport, electron transfer, hydrogen oxidation, general stress responses (e.g., heat shock proteins, phage oxidative proteins). carbon metabolism, cell growth, structures decreased. Transcriptome profiles D. were...
Thermophilic anaerobic noncellulolytic Thermoanaerobacter species are of great biotechnological importance in cellulosic ethanol production due to their ability produce high yields by simultaneous fermentation hexose and pentose. Understanding the genome structure these is critical improving implementing bacteria for possible use consolidated bioprocessing schemes (CBP) production. Here we describe a comparative analysis two ethanologenic bacteria, sp. X514 pseudethanolicus 39E. Compared...
Thermoanaerobic bacteria are of interest in cellulosic-biofuel production, due to their simultaneous pentose and hexose utilization (co-utilization) thermophilic nature. In this study, we experimentally reconstructed the structure dynamics first genome-wide carbon network thermoanaerobes. The uncovers numerous novel pathways identifies previously unrecognized but crucial pathway interactions associated key junctions. First, glucose, xylose, fructose, cellobiose catabolism each featured...
ABSTRACT Crp/Fnr-type global transcriptional regulators regulate various metabolic pathways in bacteria and typically function response to environmental changes. However, little is known about the of four annotated Crp/Fnr homologs (DVU0379, DVU2097, DVU2547, DVU3111) Desulfovibrio vulgaris Hildenborough. A systematic study using bioinformatic, transcriptomic, genetic, physiological approaches was conducted characterize their roles stress responses. Similar growth phenotypes were observed...