Spatial and temporal metagenomics of river compartments reveals viral community dynamics in an urban impacted stream

Autor: Josué Rodríguez-Ramos, Angela Oliverio, Mikayla A. Borton, Robert Danczak, Birgit M. Mueller, Hanna Schulz, Jared Ellenbogen, Rory M. Flynn, Rebecca A. Daly, LeAundra Schopflin, Michael Shaffer, Amy Goldman, Joerg Lewandowski, James C. Stegen, Kelly C. Wrighton

Publikováno v: Frontiers in Microbiomes, Vol 2 (2023)

Although river ecosystems constitute a small fraction of Earth’s total area, they are critical modulators of microbially and virally orchestrated global biogeochemical cycles. However, most studies either use data that is not spatially resolved or

Externí odkaz: https://doaj.org/article/5dcc07c18d5e4384a59d8a1508855007

Microbial Genome-Resolved Metaproteomic Analyses Frame Intertwined Carbon and Nitrogen Cycles in River Hyporheic Sediments

Autor: Kelly C. Wrighton, Samuel O. Purvine, David W. Hoyt, Mikayla A. Borton, Rebecca A. Daly, Michael Shaffer, Elizabeth K. Eder, Mary S. Lipton, Carrie D. Nicora, Josué Rodríguez-Ramos, Bridget B. McGivern, Garrett J. Smith, Lindsey M. Solden, James C. Stegen

Background:Rivers serve as a nexus for nutrient transfer between terrestrial and marine ecosystems and as such, have a significant impact on global carbon and nitrogen cycles. In river ecosystems, the sediments found within the hyporheic zone are mic

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::8e60806c26dad40137898809af292d97
https://doi.org/10.21203/rs.3.rs-746574/v1

DRAM for distilling microbial metabolism to automate the curation of microbiome function

Autor: Kelly C. Wrighton, Benjamin Bolduc, Rebecca A. Daly, Simon Roux, Michael Shaffer, Pengfei Liu, M. Consuelo Gazitúa, Garrett J. Smith, Sabina Leanti La Rosa, Josué Rodríguez-Ramos, Matthew B. Sullivan, Bridget B. McGivern, Ahmed A. Zayed, Phillip B. Pope, Lindsey M. Solden, Adrienne B. Narrowe, Mikayla A. Borton, Dean R. Vik

Publikováno v: Nucleic acids research, vol 48, iss 16
Nucleic Acids Research

Microbial and viral communities transform the chemistry of Earth’s ecosystems, yet the specific reactions catalyzed by these biological engines are hard to decode due to the absence of a scalable, metabolically resolved, annotation software. Here,

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::bc4907e1772814d679349d51c606fa1c
https://doi.org/10.1101/2020.06.29.177501

Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils

Autor: Benjamin Bolduc, Gareth Trubl, Natalie Solonenko, Simon Roux, Virginia I. Rich, Yueh-Fen Li, Matthew B. Sullivan, Josué Rodríguez-Ramos, Emiley A. Eloe-Fadrosh

Publikováno v: PeerJ
Trubl, Gareth; Roux, Simon; Solonenko, Natalie; Li, Yueh-Fen; Bolduc, Benjamin; Rodríguez-Ramos, Josué; et al.(2019). Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils. Lawrence Berkeley National Laboratory: Retrieved from: http://www.escholarship.org/uc/item/09w470qn
PeerJ, Vol 7, p e7265 (2019)
PeerJ, vol 7, iss 7

Soils impact global carbon cycling and their resident microbes are critical to their biogeochemical processing and ecosystem outputs. Based on studies in marine systems, viruses infecting soil microbes likely modulate host activities via mortality, h

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::129f7ec59e5d3a69bc2da18f51a460fd