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Title: Human and Environmental Impacts on River Sediment Microbial Communities

Journal Article · · PLoS ONE
 [1];  [2];  [2];  [2];  [2];  [3];  [2];  [2];  [4];  [5]
  1. Univ. of Chicago, IL (United States); Argonne National Lab. (ANL), Argonne, IL (United States); Chief Dull Knife College, Lame Deer, MT (United States)
  2. Chief Dull Knife College, Lame Deer, MT (United States)
  3. Argonne National Lab. (ANL), Argonne, IL (United States)
  4. Univ. of Chicago, IL (United States)
  5. Univ. of Chicago, IL (United States); Argonne National Lab. (ANL), Argonne, IL (United States)
+ Show Author Affiliations

Sediment microbial communities are responsible for a majority of the metabolic activity in river and stream ecosystems. Understanding the dynamics in community structure and function across freshwater environments will help us to predict how these ecosystems will change in response to human land-use practices. 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. Community structure and functional potential have been significantly altered by anthropogenic drivers, including increased pathogenicity and antibiotic metabolism markers near towns and metabolic signatures of coal and coalbed methane extraction byproducts. The core (OTUs shared across all samples) and the overall microbial community exhibited highly similar structure, and phylogeny was weakly coupled with functional potential. Together, these results suggest that microbial community structure is shaped by environmental drivers and niche filtering, though stochastic assembly processes likely play a role as well. These results indicate that sediment microbial communities are highly complex and sensitive to changes in land use practices.

Research Organization:
Argonne National Laboratory (ANL), Argonne, IL (United States)
Sponsoring Organization:
USDOE; National Science Foundation (NSF); USEPA; USNRC
Grant/Contract Number:
AC02-06CH11357; NRC-27-10-1124
OSTI ID:
1392593
Journal Information:
PLoS ONE, Vol. 9, Issue 5; ISSN 1932-6203
Publisher:
Public Library of ScienceCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 96 works
Citation information provided by
Web of Science

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Verrucomicrobia are prevalent in north-temperate freshwater lakes and display class-level preferences between lake habitats journal March 2018
Bacterial community structure is indicative of chemical inputs in the Upper Mississippi River journal October 2014
metaxa 2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data journal March 2015
Geochemical and Microbial Community Attributes in Relation to Hyporheic Zone Geological Facies journal September 2017
Integrated biogeography of planktonic and sedimentary bacterial communities in the Yangtze River journal January 2018
Antibiotic distribution, risk assessment, and microbial diversity in river water and sediment in Hong Kong journal March 2018
Metagenome Sequences of Sediment from a Recovering Industrialized Appalachian River in West Virginia journal May 2018
Modelling of zero-inflation improves inference of metagenomic gene count data journal November 2018
The Earth Microbiome project: successes and aspirations journal August 2014
World’s Largest Mass Bathing Event Influences the Bacterial Communities of Godavari, a Holy River of India journal March 2018
The presence of plasmids in Aeromonas hydrophila and its relationship with antimicrobial and heavy metal-resistance profiles journal January 2018
Sediment bacterial communities in a eutrophic lake influenced by multiple inflow-rivers journal July 2017
Species abundance information improves sequence taxonomy classification accuracy text January 2019
Species abundance information improves sequence taxonomy classification accuracy journal October 2019
Ecological determinants of health: food and environment on human health journal November 2015
Microbial community composition and diversity in Caspian Sea sediments journal December 2014
Spatial-Temporal Changes of Bacterioplankton Community along an Exhorheic River journal March 2016
Taxonomic and Functional Metagenomic Profile of Sediment From a Commercial Catfish Pond in Mississippi journal November 2018

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