Human and environmental impacts on river sediment microbial communities.
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.
Graduate Program in Biophysical Sciences, University of Chicago, Chicago, Illinois, United States of America; Institute for Genomics and Systems Biology, Argonne National Laboratory, Lemont, Illinois, United States of America; Biology Department, Chief Dull Knife College, Lame Deer, Montana, United States of America.
Sean M
SM
Gibbons
Biology Department, Chief Dull Knife College, Lame Deer, Montana, United States of America.
Edwin
E
Jones
Biology Department, Chief Dull Knife College, Lame Deer, Montana, United States of America.
Angelita
A
Bearquiver
Biology Department, Chief Dull Knife College, Lame Deer, Montana, United States of America.
Frederick
F
Blackwolf
Biology Department, Chief Dull Knife College, Lame Deer, Montana, United States of America.
Wayne
W
Roundstone
Institute for Genomics and Systems Biology, Argonne National Laboratory, Lemont, Illinois, United States of America.
Nicole
N
Scott
Biology Department, Chief Dull Knife College, Lame Deer, Montana, United States of America.
Jeff
J
Hooker
Biology Department, Chief Dull Knife College, Lame Deer, Montana, United States of America.
Robert
R
Madsen
Graduate Program in Biophysical Sciences, University of Chicago, Chicago, Illinois, United States of America; Department of the Geophysical Sciences, University of Chicago, Chicago, Illinois, United States of America.
Maureen L
ML
Coleman
Graduate Program in Biophysical Sciences, University of Chicago, Chicago, Illinois, United States of America; Institute for Genomics and Systems Biology, Argonne National Laboratory, Lemont, Illinois, United States of America; Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America.
Jack A
JA
Gilbert
D044822:Biodiversity; D019015:Geologic Sediments / Q000382:microbiology*; D006801:Humans; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D045483:Rivers
D012336:RNA, Ribosomal, 16S