A5082911363- Microbial Community Ecology and Physiology
- Soil Carbon and Nitrogen Dynamics
- Gut microbiota and health
- Polar Research and Ecology
- Climate change and permafrost
- Genomics and Phylogenetic Studies
- Legume Nitrogen Fixing Symbiosis
- Mycorrhizal Fungi and Plant Interactions
- Bacteriophages and microbial interactions
- Peatlands and Wetlands Ecology
- Cryospheric studies and observations
- Plant-Microbe Interactions and Immunity
- Bioenergy crop production and management
- Analytical Chemistry and Sensors
- Biofuel production and bioconversion
- Conducting polymers and applications
- Plant and Fungal Interactions Research
- Molecular Sensors and Ion Detection
- Electrochemical sensors and biosensors
- Plant Parasitism and Resistance
- Electrochemical Analysis and Applications
- Microbial Metabolic Engineering and Bioproduction
- Soil and Water Nutrient Dynamics
- Species Distribution and Climate Change
- Protist diversity and phylogeny
University of Oklahoma
2016-2025
University of California, Berkeley
2019-2025
University of Hawaii System
2025
Pacific Biosciences (United States)
2025
University of Hawaiʻi at Mānoa
2025
Hebei Agricultural University
2023
Zhejiang University of Science and Technology
2023
Northeastern University
2019-2021
University of Jinan
2020
Central South University
2020
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...
Microbes play key roles in various biogeochemical processes, including carbon (C) and nitrogen (N) cycling. However, changes of microbial community at the functional gene level by livestock grazing, which is a global land-use activity, remain unclear. Here we use array, GeoChip 4.0, to examine effects free grazing on an experimental site Tibet, region known be very sensitive anthropogenic perturbation warming. Our results showed that changed structure, addition aboveground vegetation soil...
Summary Despite the important roles of soil microbes, especially most diverse rare taxa in maintaining community diversity and multifunctionality, how different climate regimes alter stability functions microbial biosphere remains unknown. We reciprocally transplanted field soils across a latitudinal gradient to simulate change sampled annually after harvesting maize over following 6 years (from 2005 2011). By sequencing 16S ribosomal RNA gene amplicons, we found that changing significantly...
Abstract Soil organic matter (SOM) stocks contain nearly three times as much carbon (C) the atmosphere and changes in soil C may have a major impact on future atmospheric dioxide concentrations climate. Over past two decades, research has been devoted to examining influence of warming SOM decomposition topsoil. Most SOM, however, is old stored subsoil. The fate subsoil under remains highly uncertain. Here, by combining long-term field experiment meta-analysis study, we showed that...
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...
Soil microbial inoculants are expected to boost crop productivity under climate change and soil degradation. However, the efficiency of native vs commercialized in soils with different fertility impacts on resident communities remain unclear. We investigated differential plant growth responses synthetic community (SynCom) commercial growth-promoting rhizobacteria (PGPR). quantified colonization dynamic niche structure emphasize home-field advantages for inoculants. A SynCom 21 bacterial...
Arbuscular mycorrhizal fungi (AMF) transport substantial plant carbon (C) that serves as a substrate for soil organisms, precursor of organic matter (SOM), and driver microbial dynamics. Using two-chamber microcosms where an air gap isolated AMF from roots, we
Plants release a wealth of metabolites into the rhizosphere that can shape composition and activity microbial communities in response to environmental stress. The connection between rhizodeposition microbiome succession has been suggested, particularly under stress conditions, yet definitive evidence is scarce. In this study, we investigated relationship chemistry, dynamics, abiotic bioenergy crop switchgrass grown marginal soil nutrient-limited, moisture-limited, nitrogen (N)-replete,...
Soil microbial communities are extremely complex, being composed of thousands low-abundance species (<0.1% total). How such complex respond to natural or human-induced fluctuations, including major perturbations as global climate change, remains poorly understood, severely limiting our predictive ability for soil ecosystem functioning and resilience. In this study, we compared 12 whole-community shotgun metagenomic data sets from a grassland in the Midwestern United States, half representing...
Abstract Understanding the response of permafrost microbial communities to climate warming is crucial for evaluating ecosystem feedbacks global change. This study investigated soil bacterial and archaeal by Illumina MiSeq sequencing 16S r RNA gene amplicons across a thaw gradient at different depths in Alaska with progression over three decades. Over 4.6 million passing sequences were obtained from total 97 samples, corresponding 61 known classes 470 genera. Soil depth associated...
Abstract Background It is well-known that global warming has effects on high-latitude tundra underlain with permafrost. This leads to a severe concern decomposition of soil organic carbon (SOC) previously stored in this region, which accounts for about 50% the world’s SOC storage, will cause positive feedback accelerates climate warming. We have shown short-term (1.5 years) stimulates rapid, microbe-mediated without affecting composition microbial community (based depth 42684 sequence reads...
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...
Abstract Quantifying soil organic carbon ( SOC ) decomposition under warming is critical to predict carbon–climate feedbacks. According the substrate regulating principle, would decrease as labile declines field warming, but observations of do not always support this prediction. This discrepancy could result from varying changes in components and microbial communities warming. study aimed determine with different turnover times after subjected long‐term and/or root exclusion limit C input,...
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...
Despite their widespread distribution and ecological importance, protists remain one of the least understood components soil rhizosphere microbiome. Knowledge roles that play in stimulating organic matter decomposition shaping microbiome dynamics continues to grow, but there remains a need understand extent which biological environmental factors mediate protist community assembly dynamics. We hypothesize communities are filtered by influence plants on physicochemical environment, resulting...
Abstract Background Anthropogenic activities have increased the inputs of atmospheric reactive nitrogen (N) into terrestrial ecosystems, affecting soil carbon stability and microbial communities. Previous studies primarily examined effects deposition on taxonomy, enzymatic activities, functional processes. Here, we various traits communities how these are interrelated in a Mediterranean-type grassland administrated with 14 years 7 g m −2 year −1 N amendment, based estimated areas within...
Soils near living and decomposing roots form distinct niches that promote microorganisms with distinctive environmental preferences interactions. Yet few studies have assessed the community-level cooccurrence of bacteria fungi in these soil as plant grow senesce.
Viruses shape microbial communities, food web dynamics, and carbon nutrient cycling in diverse ecosystems. However, little is known about the patterns drivers of viral community composition, particularly soil, precluding a predictive understanding impacts on terrestrial habitats. To investigate soil assembly processes, here we analyzed 43 viromes from rainfall manipulation experiment Mediterranean grassland California. We identified 5,315 populations (viral operational taxonomic units...