A5039540408- Microbial Community Ecology and Physiology
- Genomics and Phylogenetic Studies
- Wastewater Treatment and Nitrogen Removal
- Microbial Fuel Cells and Bioremediation
- Marine and coastal ecosystems
- Bacteriophages and microbial interactions
- Environmental DNA in Biodiversity Studies
- Gut microbiota and health
- Protist diversity and phylogeny
- Aquatic Ecosystems and Phytoplankton Dynamics
- Microbial Metabolic Engineering and Bioproduction
- Phosphorus and nutrient management
- Mercury impact and mitigation studies
- Soil and Water Nutrient Dynamics
- Plant Virus Research Studies
- Chromium effects and bioremediation
- Pharmaceutical and Antibiotic Environmental Impacts
- Evolution and Genetic Dynamics
- Constructed Wetlands for Wastewater Treatment
- Methane Hydrates and Related Phenomena
- Advanced biosensing and bioanalysis techniques
- Pancreatic and Hepatic Oncology Research
- Isotope Analysis in Ecology
- Photoreceptor and optogenetics research
- Aquatic Invertebrate Ecology and Behavior
University of Wisconsin–Madison
2016-2025
St. Vincent Hospital
2022-2023
Madison Group (United States)
2022
Great Lakes Bioenergy Research Center
2021
Wellcome Centre for Mitochondrial Research
2018
University of Newcastle Australia
2018
Newcastle University
2018
Ursinus College
2018
Universitat de Miguel Hernández d'Elx
2011
Oregon State University
2007
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...
Abstract Microbial communities mediating anaerobic ammonium oxidation (anammox) represent one of the most energy-efficient environmental biotechnologies for nitrogen removal from wastewater. However, little is known about functional role heterotrophic bacteria play in anammox granules. Here, we use genome-centric metagenomics to recover 17 draft genomes and a laboratory-scale bioreactor. We combine metabolic network reconstruction with metatranscriptomics examine gene expression identify...
Abstract The ability to predict microbial community dynamics lags behind the quantity of data available in these systems. Most predictive models use only environmental parameters, although a long history ecological literature suggests that complexity should also be an informative parameter. Thus, we hypothesize incorporating information about community’s might improve power models. Here, present new metric, called ‘cohesion,’ quantifies degree connectivity community. We analyze six long-term...
We describe the microbiota of two hypersaline saltern ponds, one intermediate salinity (19%) and a NaCl saturated crystallizer pond (37%) using pyrosequencing. The analyses these metagenomes (nearly 784 Mb) reaffirmed vast dominance Haloquadratum walsbyi but also revealed novel, abundant previously unsuspected microbial groups. for first time, group low GC Actinobacteria, related to freshwater in salinities. Metagenomic assembly three new microbes: low-GC euryarchaeon with lowest content...
Abstract Our current knowledge about nucleocytoplasmic large DNA viruses (NCLDVs) is largely derived from viral isolates that are co-cultivated with protists and algae. Here we reconstructed 2,074 NCLDV genomes sampling sites across the globe by building on rapidly increasing amount of publicly available metagenome data. This led to an 11-fold increase in phylogenetic diversity a parallel 10-fold expansion functional diversity. Analysis 58,023 major capsid proteins giant using metagenomic...
Summary The influence of biotic interactions on microbial community assembly is intensely debated. We hypothesized that keystone taxa, which through strong interactions, are important for regulating composition. While highly connected microbes have been identified, evidence these taxa act as keystones lacking, because status requires whole‐community dynamics. address this gap, showing small subsets (generally 1%–5% richness) can be optimal predictors compositional change. In three long‐term...
Abstract Multiple models describe the formation and evolution of distinct microbial phylogenetic groups. These evolutionary make different predictions regarding how adaptive alleles spread through populations genetic diversity is maintained. Processes predicted by competing models, for example, genome-wide selective sweeps vs gene-specific sweeps, could be captured in natural using time-series metagenomics if approach were applied over a sufficiently long time frame. Direct observations...
Abstract Disturbances act as powerful structuring forces on ecosystems. To ask whether environmental microbial communities have capacity to recover after a large disturbance event, we conducted whole-ecosystem manipulation, during which imposed an intense freshwater by artificially mixing temperate lake peak summer thermal stratification. We employed sensors and water chemistry analyses evaluate the physical chemical responses of lake, bar-coded 16S ribosomal RNA gene pyrosequencing...
Abstract Viruses represent the most abundant life forms on planet. Recent experimental and computational improvements have led to a dramatic increase in number of viral genome sequences identified primarily from metagenomic samples. As result expanding catalog sequences, there exists need for comprehensive platform integrating all these with associated metadata analytical tools. Here we present IMG/VR (https://img.jgi.doe.gov/vr/), largest publicly available database 3908 isolate reference...
High-throughput RNA sequencing offers broad opportunities to explore the Earth virome. Mining 5,150 diverse metatranscriptomes uncovered >2.5 million virus contigs. Analysis of >330,000 RNA-dependent polymerases (RdRPs) shows that this expansion corresponds a 5-fold increase known diversity. Gene content analysis revealed multiple protein domains previously not found in viruses and implicated virus-host interactions. Extended RdRP phylogeny supports monophyly five established phyla reveals...
Despite advances in sequencing, lack of standardization makes comparisons across studies challenging and hampers insights into the structure function microbial communities multiple habitats on a planetary scale. Here we present multi-omics analysis diverse set 880 community samples collected for Earth Microbiome Project. We include amplicon (16S, 18S, ITS) shotgun metagenomic sequence data, untargeted metabolomics data (liquid chromatography-tandem mass spectrometry gas chromatography...
Lake Tanganyika (LT) is the largest tropical freshwater lake, and body of anoxic on Earth's surface. LT's mixed oxygenated surface waters float atop a permanently layer host rich animal biodiversity. However, little known about microorganisms inhabiting 1470 meter deep water column their contributions to nutrient cycling, which affect ecosystem-level function productivity. Here, we applied genome-resolved metagenomics environmental analyses link specific taxa key biogeochemical processes...
Metagenomes encode an enormous diversity of proteins, reflecting a multiplicity functions and activities
An aggressive start-up strategy was used to initiate codigestion in two anaerobic, continuously mixed bench-top reactors at mesophilic (37°C) and thermophilic (55°C) conditions. The digesters were inoculated with anaerobic sewage sludge cattle manure fed a mixture of simulated municipal solid waste biosolids proportions that reflect U.S. production rates. design organic loading rate 3.1 kg volatile solids/m3/day the retention time 20 days. Ribosomal RNA-targeted oligonucleotide probes...
We investigated the fine-scale population structure of "Candidatus Accumulibacter" lineage in enhanced biological phosphorus removal (EBPR) systems using polyphosphate kinase 1 gene (ppk1) as a genetic marker. retrieved fragments 16S rRNA and ppk1 genes from one laboratory-scale several full-scale EBPR systems. Phylogenies reconstructed were largely congruent, with granting higher phylogenetic resolution clearer tree topology thus serving better marker than for revealing within lineage....
River water is a small percentage of the total freshwater on Earth but represents an essential resource for mankind. Microbes in rivers perform ecosystem roles including mineralization significant quantities organic matter originating from terrestrial habitats. The Amazon river particular famous its size and importance mobilization both carbon out enormous basin. Here we present first metagenomic study microbiota this river. It presents many features common with other metagenome available...
Summary The capability of ‘ Candidatus Accumulibacter’ to use nitrate as an electron acceptor for phosphorus uptake was investigated using two activated sludge communities. communities were enriched in Accumulibacter clade IA and IIA, respectively. By performing a series batch experiments, we found that able couple reduction with uptake, but IIA could not. These results agree previously proposed hypothesis different populations have capabilities, they will help understand the ecological...