Water Microbiome

Created September 2015, updated September 2016.

Seawater

Structure and function of the global ocean microbiome – Shinichi Sunagawa, Luis Pedro Coelho, Samuel Chaffron, et al. – Science – 2015

We analyzed 7.2 terabases of metagenomic data from 243 Tara Oceans samples from 68 locations in epipelagic and mesopelagic waters across the globe to generate an ocean microbial reference gene catalog with >40 million nonredundant, mostly novel sequences from viruses, prokaryotes, and picoeukaryotes.

The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific – Douglas B Rusch, Aaron L Halpern, Granger Sutton, et al. – PLOS Biology – 2007

We report here a metagenomic study of the marine planktonic microbiota in which surface (mostly marine) water samples were analyzed as part of the Sorcerer II Global Ocean Sampling expedition. These samples, collected across a several-thousand km transect from the North Atlantic through the Panama Canal and ending in the South Pacific yielded an extensive dataset consisting of 7.7 million sequencing reads (6.3 billion bp).

River and lake water

Multidrug resistance phenotypes are widespread over different bacterial taxonomic groups thriving in surface water – Carlos Narciso-da-Rocha – Science of the Total Environment – May 2016

Seasonal changes in microbial community composition in river water studied using 454-pyrosequencing – Marija Kaevska – SpringerPlus – April 2016

Review: The ecology and biogeochemistry of stream biofilms – Tom J. Battin – Nature Reviews Microbiology – March 2016

Metagenomic and metatranscriptomic inventories of the lower Amazon River, May 2011 – Brandon M. Satinsky, Caroline S. Fortunato, Mary Doherty, et al. – Microbiome – 2015

A quantitative inventory of genes and transcripts benchmarked with internal standards was obtained at five stations in the lower Amazon River during May 2011. At each station, metagenomes and metatranscriptomes were obtained in duplicate for two microbial size fractions (free-living, 0.2 to 2.0 μm; particle-associated, 2.0 to 297 μm) using 150 × 150 paired-end Illumina sequencing. Forty eight sample datasets were obtained, averaging 15 × 10 6 potential protein-encoding reads each (730 × 10 6 total).

The Amazon continuum dataset: quantitative metagenomic and metatranscriptomic inventories of the Amazon River plume, June 2010 – Brandon M Satinsky, Brian L Zielinski, Mary Doherty, Christa B Smith, Shalabh Sharma, John H Paul, Byron C Crump and Mary Ann Moran – Microbiome – 2014

We inventoried genes and transcripts at six stations in the Amazon River plume during June 2010. At each station, internal standard-spiked metagenomes, non-selective metatranscriptomes, and poly(A)-selective metatranscriptomes were obtained in duplicate for two discrete size fractions (0.2 to 2.0 μm and 2.0 to 156 μm) using 150 × 150 paired-end Illumina sequencing.

Changes in bacterial and eukaryotic communities during sewage decomposition in Mississippi river water – Asja Korajkic, Laura Wegener Parfrey, Brian R. McMinn, Yoshiki Vazquez Baeza, Will VanTeuren, Rob Knight, Orin C. Shanks – Water Research – 2015

We investigated decay of sewage in upper Mississippi River using Illumina sequencing of 16S and 18S rRNA gene hypervariable regions and qPCR for human-associated and general fecal Bacteroidales indicators.

Human and Environmental Impacts on River Sediment Microbial Communities – Sean M. Gibbons, Edwin Jones, Angelita Bearquiver, Frederick Blackwolf, Wayne Roundstone, Nicole Scott, Jeff Hooker, Robert Madsen, Maureen L. Coleman, Jack A. Gilbert – PLOS ONE – 2014

Here we present a spatiotemporal study of sediments in the Tongue River (Montana, USA), comprising six sites along 134 km of river sampled in both spring and fall for two years. Sequencing of 16S rRNA amplicons and shotgun metagenomes revealed that these sediments are the richest (~65,000 microbial ‘species’ identified) and most novel (93% of OTUs do not match known microbial diversity) ecosystems analyzed by the Earth Microbiome Project to date, and display more functional diversity than was detected in a recent review of global soil metagenomes.

Linking community tolerance and structure with low metallic contamination: A field study on 13 biofilms sampled across the Seine river basin – Lise C. Fechner, Catherine Gourlay-Francé, Marie-Hélène Tusseau-Vuillemin – Water Research – 2014

The study was designed as an attempt to link biofilm metal tolerance and metallic contamination in a field survey covering 13 different sampling sites in the Seine river basin (north of France) with low contamination levels.

Drinking water

Elucidation of Taste- and Odor-Producing Bacteria and Toxigenic Cyanobacteria in a Midwestern Drinking Water Supply Reservoir by Shotgun Metagenomic Analysis – Timothy G. Otten – Applied and Environmental Microbiology – September 2016

Emerging investigators series: microbial communities in full-scale drinking water distribution systems – a meta-analysis – Quyen M. Bautista-de los Santos – Environmental Science: Water Research & Technology – March 2016

Metagenomic Evidence for the Presence of Comammox Nitrospira-Like Bacteria in a Drinking Water System – Ameet J. Pinto – mSphere – December 2015

Bacterial Community Structure in the Drinking Water Microbiome Is Governed by Filtration Processes – Ameet J. Pinto – Environmental Science & Technology – July 2012