Created September 2015, updated February 2018. Not meant to be comprehensive, but hopefully a nice start to find more papers.

Seawater

Organic matter processing by microbial communities throughout the Atlantic water column as revealed by metaproteomics – Kristin Bergauer – PNAS – January 2018

Influence of Darkness and Aging on Marine and Freshwater Biofilm Microbial Communities Using Microcosm Experiments – Niyati Hede – Microbial Ecology – January 2018

Microbial Community Structure of Sea Spray Aerosols at Three California Beaches –
Katherine Graham – FEMS Microbial Ecology – January 2018

Metagenomes from deep Baltic Sea sediments reveal how past and present environmental conditions determine microbial community composition – Ian P.G.Marshall – Marine Genomics – August 2017

A Pelagic Microbiome (Viruses to Protists) from a Small Cup of Seawater – Flavia Flaviani – Viruses – March 2017

Microbiome and bacterioplankton rRNA gene sequence data collected from Gulf of Mexico seawater samples, Cruises DP01 and DP02 from May 2015 – August 2015 – Cole Easson – NSU works (dataset) – February 2017

Enhanced CO2 concentrations change the structure of Antarctic marine microbial communities – Andrew T. Davidson – Marine Ecology Progress Series – June 2016

Enhanced salinities, as a proxy of seawater desalination discharges, impact coastal microbial communities of the eastern Mediterranean Sea – Natalia Belkin – Environmental Microbiology – August 2015

Differential Decay of Wastewater Bacteria and Change of Microbial Communities in Beach Sand and Seawater Microcosms – Qian Zhang – Environmental Science & Technology – June 2015

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

Review: Using dispersants after oil spills: impacts on the composition and activity of microbial communities – Sara Kleindienst – Nature Reviews Microbiology – May 2015

Temporal Stability of the Microbial Community in Sewage-Polluted Seawater Exposed to Natural Sunlight Cycles and Marine Microbiota – Lauren M. Sassoubre – Applied and Environmental Microbiology – March 2015

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

River and lake water

Shift in the microbial community composition of surface water and sediment along an urban river – Lan Wang – Science of the Total Environment – February 2018

Microbial communities and their predicted metabolic functions in a desiccating acid salt lake – Elena Zaikova – Extremophiles – January 2018

Nutrient dynamics and stream order influence microbial community patterns along a 2914 km transect of the Mississippi River – Michael W Henson – bioRxiv – December 2017

Untreated urban waste contaminates Indian river sediments with resistance genes to last resort antibiotics – Nachiket P. Marathe – November 2017

Potential Activity of Subglacial Microbiota Transported to Anoxic River Delta Sediments – Karen A. Cameron – Microbial Ecology – July 2017

Water metagenomic analysis reveals low bacterial diversity and the presence of antimicrobial residues and resistance genes in a river containing wastewater from backyard aquacultures in the Mekong Delta, Vietnam – Tatsuya Nakayama – Environmental Pollution – March 2017

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

The Source of the River as a Nursery for Microbial Diversity – Luiz Felipe Valter de Oliveira – PLOS ONE – March 2015

Changes in bacterial and eukaryotic communities during sewage decomposition in Mississippi river water – Asja Korajkic – Water Research – February 2015

 

The Amazon continuum dataset: quantitative metagenomic and metatranscriptomic inventories of the Amazon River plume, June 2010 – Brandon M Satinsky, – Microbiome – May 2014

Human and Environmental Impacts on River Sediment Microbial Communities – Sean M. Gibbons – PLOS ONE – 2014

Linking community tolerance and structure with low metallic contamination: A field study on 13 biofilms sampled across the Seine river basin – Lise C. Fechner – Water Research – 2014

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