A5023442989- Microbial Community Ecology and Physiology
- Genomics and Phylogenetic Studies
- Soil Carbon and Nitrogen Dynamics
- Environmental DNA in Biodiversity Studies
- Gut microbiota and health
- Mycorrhizal Fungi and Plant Interactions
- Legume Nitrogen Fixing Symbiosis
- Wastewater Treatment and Nitrogen Removal
- Isotope Analysis in Ecology
- Actinomycetales infections and treatment
- Evolution and Genetic Dynamics
- Bacteriophages and microbial interactions
- Plant-Microbe Interactions and Immunity
- Protist diversity and phylogeny
- Plant Disease Resistance and Genetics
- Nematode management and characterization studies
- Metabolomics and Mass Spectrometry Studies
- Mycobacterium research and diagnosis
- Microbial Metabolic Engineering and Bioproduction
- Microbial Natural Products and Biosynthesis
- Marine Biology and Ecology Research
- Marine and coastal ecosystems
- Paleontology and Stratigraphy of Fossils
- Forest Ecology and Biodiversity Studies
- Biocrusts and Microbial Ecology
Cornell University
2016-2025
Oakland University
2023
Purdue University West Lafayette
2023
Technical University of Munich
2023
Pacific Northwest National Laboratory
2020
Argonne National Laboratory
2020
New York State College of Agriculture & Life Sciences
2020
Ithaca College
2020
Butler University
2015
Marine Biological Laboratory
2010-2014
Abstract The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology evolution environmental host-associated microbiomes. Here we applied this approach to >10,000 collected diverse habitats covering all Earth’s continents oceans, including human animal hosts, engineered environments, natural agricultural soils, capture extant microbial, metabolic functional potential. This comprehensive catalog includes 52,515 metagenome-assembled...
Despite increasing popularity and improvements in terminal restriction fragment length polymorphism (T-RFLP) other microbial community fingerprinting techniques, there are still numerous obstacles that hamper the analysis of these datasets. Many steps required to process raw data into a format ready for interpretation. These can be time-intensive, error-prone, introduce unwanted variability analysis. Accordingly, we developed T-REX, free, online software processing T-RFLP data. Analysis...
The nifH gene is the most widely sequenced marker used to identify nitrogen-fixing Bacteria and Archaea. Numerous PCR primers have been designed amplify nifH, but a comprehensive evaluation of has not performed. We performed an in silico analysis specificity coverage 51 universal 35 group-specific by using aligned database 23,847 sequences. found that there are 15 target 90% or more nitrogen fixers, also 23 less than 50% we evaluated vary their phylogenetic bias ability recover sequences...
We describe a nitrogenase gene sequence database that facilitates analysis of the evolution and ecology nitrogen-fixing organisms. The contains 32 954 aligned nifH sequences linked to phylogenetic trees associated metadata. includes 185 multigene entries including full-length nifH, nifD, nifK 16S ribosomal RNA (rRNA) sequences. Evolutionary analyses enabled by support an ancient horizontal transfer genes between Archaea Bacteria provide evidence has different history from nifDK enzyme core....
Calcium (Ca) can contribute to soil organic carbon (SOC) persistence by mediating physico-chemical interactions between compounds and minerals. Yet, Ca is also crucial for microbial adhesion, potentially affecting colonization of plant mineral surfaces. The importance as a mediator microbe-mineral-organic matter resulting SOC transformation has been largely overlooked. We incubated 44Ca labeled soils with 13C15N leaf litter study how affects formation associated matter. Here we show that...
Soil microbiomes are sensitive to current and previous soil conditions, bacterial 'bioindicators' of biological, physical, chemical properties have considerable potential for health assessment. However, the lack ecological or physiological information most microorganisms limits our ability interpret associations bioindicators and, thus, their utility guiding management. We identified tillage intensity twelve used rate using a 16S rRNA gene-based survey farmland across North America. then...
Summary Soil microbial communities are integrally involved in biogeochemical cycles and their activities crucial to the productivity of terrestrial ecosystems. Despite importance soil microorganisms, little is known about distribution microorganisms or manner which community structure responds changes land management. We investigated over two years a series replicated plots, that included, cultivated fields, fields abandoned from cultivation with no history cultivation. Microbial was...
Within the last several years, molecular techniques have uncovered numerous 16S rRNA gene (rDNA) sequences which represent a unique and globally distributed lineage of kingdom Crenarchaeota that is phylogenetically distinct from currently characterized crenarchaeotal species. rDNA members this novel group been recovered low- to moderate-temperature environments (-1.5 32 degreesC), in contrast high-temperature (temperature, >80 degreesC) required for growth recognized We determined diversity...
ABSTRACT Members of the Planctomycetes , which were once thought to occur primarily in aquatic environments, have been discovered soils on five continents, revealing that these Bacteria are a widespread and numerically abundant component microbial communities soil. We examined diversity soil samples obtained from experimental plots at an agricultural site order assess extent soil, determine whether management effects such as past land cover compost addition affected composition community,...
Summary The global diversity of nitrogen‐fixing microorganisms was assessed through construction and analysis an aligned database 16 989 nifH sequences. We conclude that the diazotrophs is still poorly described many organisms remain to be discovered. Our analyses indicate not distributed evenly across phylogenetic groups or environments some most diverse assemblages characterized. majority OTUs were rare, falling in long tail frequency distribution. dominant fell into either Cyanobacteria α...
Biological nitrogen fixation is a fundamental component of the cycle and dominant natural process through which fixed made available to biosphere. While has been studied extensively with limited set cultivated isolates, examinations nifH gene diversity in systems reveal existence wide range noncultivated diazotrophs. These diazotrophs remain uncharacterized, as do their contributions systems. We have employed novel 15N2-DNA stable isotope probing (5N2-DNA-SIP) method identify free-living...
We explored microbial contributions to decomposition using a sophisticated approach DNA Stable Isotope Probing (SIP). Our experiment evaluated the dynamics and ecological characteristics of functionally defined groups that metabolize labile structural C in soils. added soil complex amendment representing plant derived organic matter substituted with either 13C-xylose or 13C-cellulose represent pools from abundant components biomass. found evidence for 13C-incorporation into 49 63 operational...