A5011788533- Microbial Community Ecology and Physiology
- Genomics and Phylogenetic Studies
- Soil Carbon and Nitrogen Dynamics
- Gut microbiota and health
- Microbial Fuel Cells and Bioremediation
- Wastewater Treatment and Nitrogen Removal
- Gene expression and cancer classification
- Chromium effects and bioremediation
- Polar Research and Ecology
- Atmospheric and Environmental Gas Dynamics
- Radioactive element chemistry and processing
- Microbial bioremediation and biosurfactants
- Bioinformatics and Genomic Networks
- Mycorrhizal Fungi and Plant Interactions
- Peatlands and Wetlands Ecology
- Environmental DNA in Biodiversity Studies
- Mine drainage and remediation techniques
- Methane Hydrates and Related Phenomena
- Microbial Metabolic Engineering and Bioproduction
- Metal Extraction and Bioleaching
- Molecular Biology Techniques and Applications
- Climate change and permafrost
- Biofuel production and bioconversion
- Evolution and Genetic Dynamics
- Anaerobic Digestion and Biogas Production
University of Oklahoma
2016-2025
Fuzhou University
2025
Lawrence Berkeley National Laboratory
2016-2025
Shanghai Institute of Technology
2025
Tsinghua University
2015-2024
State Key Joint Laboratory of Environment Simulation and Pollution Control
2015-2024
Beijing Normal University
2024
Royal Netherlands Institute for Sea Research
2022
Applied BioPhysics (United States)
2022
University of Freiburg
2022
A simple, rapid method for bacterial lysis and direct extraction of DNA from soils with minimal shearing was developed to address the risk chimera formation small template during subsequent PCR. The based on a high-salt buffer (1.5 M NaCl) extended heating (2 3 h) soil suspension in presence sodium dodecyl sulfate (SDS), hexadecyltrimethylammonium bromide, proteinase K. required 6 h tested eight differing organic carbon, clay content, pH, including ones which is difficult. fragment size...
Understanding the interaction among different species within a community and their responses to environmental changes is central goal in ecology. However, defining network structure microbial very challenging due extremely high diversity as-yet uncultivated status. Although recent advance of metagenomic technologies, such as throughout sequencing functional gene arrays, provide revolutionary tools for analyzing structure, it still difficult examine interactions based on high-throughput...
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...
Abstract While interactions between roots and microorganisms have been intensively studied, we know little about among root‐associated microbes. We used random matrix theory‐based network analysis of 16S rRNA genes to identify bacterial networks associated with wild oat ( Avena fatua ) over two seasons in greenhouse microcosms. Rhizosphere were substantially more complex than those surrounding soils, indicating the rhizosphere has a greater potential for niche‐sharing. Network complexity...
Biodiversity and its responses to environmental changes are central issues in ecology for society. Almost all microbial biodiversity research focuses on "species" richness abundance but not their interactions. Although a network approach is powerful describing ecological interactions among species, defining the structure community great challenge. Also, although stimulating effects of elevated CO(2) (eCO(2)) plant growth primary productivity well established, influences belowground...
Understanding the interactions among different species and their responses to environmental changes, such as elevated atmospheric concentrations of CO(2), is a central goal in ecology but poorly understood microbial ecology. Here we describe novel random matrix theory (RMT)-based conceptual framework discern phylogenetic molecular ecological networks using metagenomic sequencing data 16S rRNA genes from grassland soil communities, which were sampled long-term free-air CO(2) enrichment...
Abstract Unraveling the drivers controlling community assembly is a central issue in ecology. Although it generally accepted that selection, dispersal, diversification and drift are major processes, defining their relative importance very challenging. Here, we present framework to quantitatively infer mechanisms by phylogenetic bin-based null model analysis (iCAMP). iCAMP shows high accuracy (0.93–0.99), precision (0.80–0.94), sensitivity (0.82–0.94), specificity (0.95–0.98) on simulated...
Understanding the community assembly mechanisms controlling biodiversity patterns is a central issue in ecology. Although it generally accepted that both deterministic and stochastic processes play important roles assembly, quantifying their relative importance challenging. Here we propose general mathematical framework to quantify ecological stochasticity under different situations which factors drive communities more similar or dissimilar than null expectation. An index, normalized ratio...
ABSTRACT Genomic information has already been applied to prokaryotic species definition and classification. However, the contribution of genome sequence genus delimitation less studied. To gain insights into for prokaryotes, we attempted reveal genus-level genomic differences in current classification system delineate boundary a on basis information. The average nucleotide identity between two genomes can be used delineation, but it is not suitable demarcation. We percentage conserved...
Significance The study of ecological succession remains at the core ecology. Understanding trajectories and mechanisms controlling is crucial to predicting responses ecosystems environmental change projecting their future states. By definition, deterministic expected under homogeneous abiotic biotic starting conditions. This study, however, shows that groundwater microbial communities in response nutrient amendment primarily stochastic, but drivers biodiversity are dynamic rather than...
To begin defining the key determinants that drive microbial community structure in soil, we examined 29 soil samples from four geographically distinct locations taken surface, vadose zone, and saturated subsurface using a small-subunit rRNA-based cloning approach. While communities low-carbon, saturated, soils showed dominance, low-carbon surface remarkably uniform distributions, all species were equally abundant. Two diversity indices, reciprocal of Simpson's index (1/D) log series index,...
Abstract Climate warming is increasingly leading to marked changes in plant and animal biodiversity, but it remains unclear how temperatures affect microbial particularly terrestrial soils. Here we show that, accordance with metabolic theory of ecology, taxonomic phylogenetic diversity soil bacteria, fungi nitrogen fixers are all better predicted by variation environmental temperature than pH. However, the rates turnover across global gradients substantially lower those recorded for trees...
Abstract The Deepwater Horizon oil spill in the Gulf of Mexico resulted a deep-sea hydrocarbon plume that caused shift indigenous microbial community composition with unknown ecological consequences. Early history, bloom uncultured, thus uncharacterized, members Oceanospirillales was previously detected, but their role disposition unknown. Here our aim to determine functional and other active using deep sequencing DNA RNA, as well single-cell genomics. Shotgun metagenomic metatranscriptomic...
ABSTRACT Shewanella oneidensis MR-1 is a gram-negative facultative anaerobe capable of utilizing broad range electron acceptors, including several solid substrates. S. can reduce Mn(IV) and Fe(III) oxides produce current in microbial fuel cells. The mechanisms that are employed by to execute these processes have not yet been fully elucidated. Several different deletion mutants were generated tested for production metal oxide reduction. results showed few key cytochromes play role all the but...
ABSTRACT Genetic heterogeneity of denitrifying bacteria in sediment samples from Puget Sound and two sites on the Washington continental margin was studied by PCR approaches amplifying nirK nirS genes. These structurally different but functionally equivalent single-copy genes coding for nitrite reductases, a key enzyme denitrification process, were used as molecular marker bacteria. sequences could be amplified both sampling sites, whereas detected only margin. To assess underlying nir gene...
Recent studies have demonstrated the ability for polystyrene (PS) degradation within gut of mealworms (Tenebrio molitor). To determine whether plastics may be broadly susceptible to biodegradation mealworms, we evaluated fate polyethylene (PE) and mixtures (PE + PS). We find that PE biodegrades at comparable rates PS. Mass balances indicate conversion up 49.0 ± 1.4% ingested into a putative gas fraction (CO2). The molecular weights (Mn) egested polymer residues decreased by 40.1 8.5% in...
ABSTRACT To evaluate PCR-generated artifacts (i.e., chimeras, mutations, and heteroduplexes) with the 16S ribosomal DNA (rDNA)-based cloning approach, a model community of four species was constructed from alpha, beta, gamma subdivisions division Proteobacteria as well gram-positive bacterium, all which could be distinguished by Hha I restriction digestion patterns. The overall PCR were significantly different among three Taq polymerases examined: 20% for Z- , highest processitivity; 15% LA-...