A5090803123- Microbial Community Ecology and Physiology
- Gut microbiota and health
- Soil Carbon and Nitrogen Dynamics
- Genomics and Phylogenetic Studies
- Polar Research and Ecology
- Environmental DNA in Biodiversity Studies
- Peatlands and Wetlands Ecology
- Mycorrhizal Fungi and Plant Interactions
- Indoor Air Quality and Microbial Exposure
- Protist diversity and phylogeny
- Soil and Water Nutrient Dynamics
- Plant Pathogens and Fungal Diseases
- Geology and Paleoclimatology Research
- Legume Nitrogen Fixing Symbiosis
- Insect symbiosis and bacterial influences
- Species Distribution and Climate Change
- Air Quality and Health Impacts
- Forest Ecology and Biodiversity Studies
- Lichen and fungal ecology
- Ecology and Vegetation Dynamics Studies
- Probiotics and Fermented Foods
- Plant-Microbe Interactions and Immunity
- Atmospheric and Environmental Gas Dynamics
- Atmospheric chemistry and aerosols
- Plant and animal studies
University of Colorado Boulder
2016-2025
Cooperative Institute for Research in Environmental Sciences
2016-2025
University of Colorado System
2010-2023
University of Colorado Colorado Springs
2023
University of Waikato
2020
University of Tennessee at Knoxville
2019
John Wiley & Sons (United States)
2018
Jonah’s Just Begun
2016-2018
Wellcome Centre for Mitochondrial Research
2018
University of Newcastle Australia
2018
The ongoing revolution in high-throughput sequencing continues to democratize the ability of small groups investigators map microbial component biosphere. In particular, coevolution new platforms and software tools allows data acquisition analysis on an unprecedented scale. Here we report next stage this coevolutionary arms race, using Illumina GAIIx platform sequence a diverse array 25 environmental samples three known “mock communities” at depth averaging 3.1 million reads per sample. We...
DNA sequencing continues to decrease in cost with the Illumina HiSeq2000 generating up 600 Gb of paired-end 100 base reads a ten-day run. Here we present protocol for community amplicon on and MiSeq platforms, apply that sequence 24 microbial communities from host-associated free-living environments. A critical question as more platforms become available is whether biological conclusions derived one platform are consistent what would be different platform. We show developed these instruments...
For centuries, biologists have studied patterns of plant and animal diversity at continental scales. Until recently, similar studies were impossible for microorganisms, arguably the most diverse abundant group organisms on Earth. Here, we present a continental-scale description soil bacterial communities environmental factors influencing their biodiversity. We collected 98 samples from across North South America used ribosomal DNA-fingerprinting method to compare community composition...
Although researchers have begun cataloging the incredible diversity of bacteria found in soil, we are largely unable to interpret this information an ecological context, including which groups most abundant different soils and why. With study, examined how abundances major soil bacterial phyla correspond biotic abiotic characteristics environment determine if they can be divided into ecologically meaningful categories. To do this, collected 71 unique samples from a wide range ecosystems...
Upon delivery, the neonate is exposed for first time to a wide array of microbes from variety sources, including maternal bacteria. Although prior studies have suggested that delivery mode shapes microbiota's establishment and, subsequently, its role in child health, most researchers focused on specific bacterial taxa or single body habitat, gut. Thus, initiation stage human microbiome development remains obscure. The goal present study was obtain community-wide perspective influence and...
ABSTRACT Soils harbor enormously diverse bacterial populations, and soil communities can vary greatly in composition across space. However, our understanding of the specific changes community structure that occur larger spatial scales is limited because most previous work has focused on either surveying a relatively small number soils detail or analyzing with techniques provide little about phylogenetic communities. Here we used bar-coded pyrosequencing technique to characterize 88 from...
Growing on You The human gut and skin harbor diverse microbial communities that are known to vary strikingly among individuals. Here, Costello et al. (p. 1694 , published online 5 November) analyzed diversity several distinct body habitats (including the gut, mouth, inside ears nose, skin) of same person at different times. They found habitat had more influence community composition than temporal differences variation people. Some locations, such as index finger, back knee, sole foot,...
We present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of Minimum Information about Any (x) Sequence (MIxS). The a Single Amplified Genome (MISAG) Metagenome-Assembled (MIMAG), including, but not limited to, assembly quality, estimates completeness contamination. These can be used in combination with other GSC checklists, including (MIGS), Metagenomic (MIMS), Marker Gene (MIMARKS). Community-wide...
The immense diversity of soil bacterial communities has stymied efforts to characterize individual taxa and document their global distributions. We analyzed soils from 237 locations across six continents found that only 2% phylotypes (~500 phylotypes) consistently accounted for almost half the worldwide. Despite overwhelming communities, relatively few are abundant in globally. clustered these dominant into ecological groups build first atlas taxa. Our study narrows down number a "most...
Abstract Terrestrial ecosystems are receiving elevated inputs of nitrogen (N) from anthropogenic sources and understanding how these increases in N availability affect soil microbial communities is critical for predicting the associated effects on belowground ecosystems. We used a suite approaches to analyze structure functional characteristics replicated plots two long-term fertilization experiments located contrasting systems. Pyrosequencing-based analyses 16S rRNA genes revealed no...
ABSTRACT Here we describe a quantitative PCR-based approach to estimating the relative abundances of major taxonomic groups bacteria and fungi in soil. Primers were thoroughly tested for specificity, method was applied three distinct soils. The technique provides rapid robust index microbial community structure.
For centuries ecologists have studied how the diversity and functional traits of plant animal communities vary across biomes. In contrast, we only just begun exploring similar questions for soil microbial despite microbes being dominant engines biogeochemical cycles a major pool living biomass in terrestrial ecosystems. We used metagenomic sequencing to compare composition attributes 16 collected from cold deserts, hot forests, grasslands, tundra. Those found plant-free desert soils...
Significance Human activities have resulted in large increases the availability of nutrients terrestrial ecosystems worldwide. Although plant community responses to elevated been well studied, soil microbial remain poorly understood, despite their critical importance ecosystem functioning. Using DNA-sequencing approaches, we assessed response communities experimentally added nitrogen and phosphorus at 25 grassland sites across globe. Our results demonstrate that composition these shifts...
Abstract Ecosystems worldwide are receiving increasing amounts of reactive nitrogen ( N ) via anthropogenic activities with the added having potentially important impacts on microbially mediated belowground carbon dynamics. However, a comprehensive understanding how elevated availability affects soil microbial processes and community dynamics remains incomplete. The mechanisms responsible for observed responses poorly resolved we do not know if communities respond in similar manner across...
Abstract Background Understanding the normal temporal variation in human microbiome is critical to developing treatments for putative microbiome-related afflictions such as obesity, Crohn's disease, inflammatory bowel disease and malnutrition. Sequencing computational technologies, however, have been a limiting factor performing dense time series analysis of microbiome. Here, we present largest microbiota date, covering two individuals at four body sites over 396 timepoints. Results We find...