title: Functional metagenomic profiling of nine biomes.
abstract: Microbial activities shape the biogeochemistry of the planet and macroorganism health. Determining the metabolic processes performed by microbes is important both for understanding and for manipulating ecosystems (for example, disruption of key processes that lead to disease, conservation of environmental services, and so on). Describing microbial function is hampered by the inability to culture most microbes and by high levels of genomic plasticity. Metagenomic approaches analyse microbial communities to determine the metabolic processes that are important for growth and survival in any given environment. Here we conduct a metagenomic comparison of almost 15 million sequences from 45 distinct microbiomes and, for the first time, 42 distinct viromes and show that there are strongly discriminatory metabolic profiles across environments. Most of the functional diversity was maintained in all of the communities, but the relative occurrence of metabolisms varied, and the differences between metagenomes predicted the biogeochemical conditions of each environment. The magnitude of the microbial metabolic capabilities encoded by the viromes was extensive, suggesting that they serve as a repository for storing and sharing genes among their microbial hosts and influence global evolutionary and metabolic processes.
authors.affiliation: Department of Biology, San Diego State University, San Diego, California 92182, USA. elizabeth_dinsdale@hotmail.com
authors.forename: Elizabeth A
authors.initials: EA
authors.lastname: Dinsdale
authors.forename: Robert A
authors.initials: RA
authors.lastname: Edwards
authors.forename: Dana
authors.initials: D
authors.lastname: Hall
authors.forename: Florent
authors.initials: F
authors.lastname: Angly
authors.forename: Mya
authors.initials: M
authors.lastname: Breitbart
authors.forename: Jennifer M
authors.initials: JM
authors.lastname: Brulc
authors.forename: Mike
authors.initials: M
authors.lastname: Furlan
authors.forename: Christelle
authors.initials: C
authors.lastname: Desnues
authors.forename: Matthew
authors.initials: M
authors.lastname: Haynes
authors.forename: Linlin
authors.initials: L
authors.lastname: Li
authors.forename: Lauren
authors.initials: L
authors.lastname: McDaniel
authors.forename: Mary Ann
authors.initials: MA
authors.lastname: Moran
authors.forename: Karen E
authors.initials: KE
authors.lastname: Nelson
authors.forename: Christina
authors.initials: C
authors.lastname: Nilsson
authors.forename: Robert
authors.initials: R
authors.lastname: Olson
authors.forename: John
authors.initials: J
authors.lastname: Paul
authors.forename: Beltran Rodriguez
authors.initials: BR
authors.lastname: Brito
authors.forename: Yijun
authors.initials: Y
authors.lastname: Ruan
authors.forename: Brandon K
authors.initials: BK
authors.lastname: Swan
authors.forename: Rick
authors.initials: R
authors.lastname: Stevens
authors.forename: David L
authors.initials: DL
authors.lastname: Valentine
authors.forename: Rebecca Vega
authors.initials: RV
authors.lastname: Thurber
authors.forename: Linda
authors.initials: L
authors.lastname: Wegley
authors.forename: Bryan A
authors.initials: BA
authors.lastname: White
authors.forename: Forest
authors.initials: F
authors.lastname: Rohwer
mesh_terms: D000818:Animals; D037421:Anthozoa / Q000502:physiology; D001105:Archaea / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism; D001419:Bacteria / Q000235:genetics* / Q000302:isolation & purification / Q000378:metabolism*; D002633:Chemotaxis / Q000235:genetics; D019295:Computational Biology; D009033:Culicidae / Q000502:physiology; D017753:Ecosystem; D005399:Fishes / Q000502:physiology; D005618:Fresh Water; D020869:Gene Expression Profiling; D020745:Genome, Archaeal; D016680:Genome, Bacterial; D016679:Genome, Viral; D023281:Genomics; D008829:Microbiology; D012623:Seawater; D014780:Viruses / Q000235:genetics* / Q000302:isolation & purification / Q000378:metabolism*