title: Metagenomic and small-subunit rRNA analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soil.
abstract: Recent studies have highlighted the surprising richness of soil bacterial communities; however, bacteria are not the only microorganisms found in soil. To our knowledge, no study has compared the diversities of the four major microbial taxa, i.e., bacteria, archaea, fungi, and viruses, from an individual soil sample. We used metagenomic and small-subunit RNA-based sequence analysis techniques to compare the estimated richness and evenness of these groups in prairie, desert, and rainforest soils. By grouping sequences at the 97% sequence similarity level (an operational taxonomic unit [OTU]), we found that the archaeal and fungal communities were consistently less even than the bacterial communities. Although total richness levels are difficult to estimate with a high degree of certainty, the estimated number of unique archaeal or fungal OTUs appears to rival or exceed the number of unique bacterial OTUs in each of the collected soils. In this first study to comprehensively survey viral communities using a metagenomic approach, we found that soil viruses are taxonomically diverse and distinct from the communities of viruses found in other environments that have been surveyed using a similar approach. Within each of the four microbial groups, we observed minimal taxonomic overlap between sites, suggesting that soil archaea, bacteria, fungi, and viruses are globally as well as locally diverse.
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado 80309-0216, USA. Noah.Fierer@colorado.edu
authors.forename: Noah
authors.initials: N
authors.lastname: Fierer
authors.forename: Mya
authors.initials: M
authors.lastname: Breitbart
authors.forename: James
authors.initials: J
authors.lastname: Nulton
authors.forename: Peter
authors.initials: P
authors.lastname: Salamon
authors.forename: Catherine
authors.initials: C
authors.lastname: Lozupone
authors.forename: Ryan
authors.initials: R
authors.lastname: Jones
authors.forename: Michael
authors.initials: M
authors.lastname: Robeson
authors.forename: Robert A
authors.initials: RA
authors.lastname: Edwards
authors.forename: Ben
authors.initials: B
authors.lastname: Felts
authors.forename: Steve
authors.initials: S
authors.lastname: Rayhawk
authors.forename: Rob
authors.initials: R
authors.lastname: Knight
authors.forename: Forest
authors.initials: F
authors.lastname: Rohwer
authors.forename: Robert B
authors.initials: RB
authors.lastname: Jackson
mesh_terms: D001105:Archaea / Q000145:classification* / Q000235:genetics; D001419:Bacteria / Q000145:classification* / Q000235:genetics / Q000254:growth & development; D004247:DNA / Q000302:isolation & purification; D004275:DNA, Ribosomal / Q000032:analysis / Q000235:genetics; D014644:Genetic Variation; D016678:Genome; D012329:RNA, Bacterial / Q000235:genetics; D012335:RNA, Ribosomal / Q000032:analysis* / Q000235:genetics; D012988:Soil Microbiology; D014780:Viruses / Q000145:classification* / Q000235:genetics