Comparison of bacterial communities from lava cave microbial mats to overlying surface soils from Lava Beds National Monument, USA

Subsurface habitats harbor novel diversity that has received little attention until recently. Accessible subsurface habitats include lava caves around the world that often support extensive microbial mats on ceilings and walls in a range of colors. Little is known about lava cave microbial diversity...

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Bibliographic Details
Published in:	PloS one Vol. 12; no. 2; p. e0169339
Main Authors:	Lavoie, Kathleen H, Winter, Ara S, Read, Kaitlyn J H, Hughes, Evan M, Spilde, Michael N, Northup, Diana E
Format:	Journal Article
Language:	English
Published:	United States Public Library of Science 15-02-2017 Public Library of Science (PLoS)
Subjects:	Actinobacteria Astrobiology Bacteria Bacteria - genetics Biodiversity Biology Biology and Life Sciences Caves Caves - microbiology Ceilings Communities Diversity indices DNA sequencing DNA, Bacterial - genetics DNA, Bacterial - metabolism DNA, Ribosomal - genetics DNA, Ribosomal - metabolism Earth Sciences Ecology and Environmental Sciences Entrances Habitats Islands Lava Mats Microbial activity Microbial colonies Microbial Consortia - physiology Microbial mats Microorganisms Morphology National parks Natural products Nitrogen Physical Sciences Proteobacteria Research and Analysis Methods RNA, Ribosomal, 16S - genetics RNA, Ribosomal, 16S - metabolism rRNA 16S Soil investigations Soil Microbiology Soil microorganisms Soil surfaces Soils Species diversity Species richness Studies Taxonomy United States United States
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Summary:	Subsurface habitats harbor novel diversity that has received little attention until recently. Accessible subsurface habitats include lava caves around the world that often support extensive microbial mats on ceilings and walls in a range of colors. Little is known about lava cave microbial diversity and how these subsurface mats differ from microbial communities in overlying surface soils. To investigate these differences, we analyzed bacterial 16S rDNA from 454 pyrosequencing from three colors of microbial mats (tan, white, and yellow) from seven lava caves in Lava Beds National Monument, CA, USA, and compared them with surface soil overlying each cave. The same phyla were represented in both surface soils and cave microbial mats, but the overlap in shared OTUs (operational taxonomic unit) was only 11.2%. Number of entrances per cave and temperature contributed to observed differences in diversity. In terms of species richness, diversity by mat color differed, but not significantly. Actinobacteria dominated in all cave samples, with 39% from caves and 21% from surface soils. Proteobacteria made up 30% of phyla from caves and 36% from surface soil. Other major phyla in caves were Nitrospirae (7%) followed by minor phyla (7%), compared to surface soils with Bacteroidetes (8%) and minor phyla (8%). Many of the most abundant sequences could not be identified to genus, indicating a high degree of novelty. Surface soil samples had more OTUs and greater diversity indices than cave samples. Although surface soil microbes immigrate into underlying caves, the environment selects for microbes able to live in the cave habitats, resulting in very different cave microbial communities. This study is the first comprehensive comparison of bacterial communities in lava caves with the overlying soil community.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Competing Interests: The authors have declared that no competing interests exist. Conceptualization: DEN.Data curation: DEN.Formal analysis: ASW KJHR KHL DEN.Funding acquisition: DEN.Investigation: KJHR EMH MNS DEN.Methodology: DEN KJHR ASW.Project administration: DEN.Resources: KJHR DEN.Software: ASW.Supervision: DEN.Validation: DEN ASW KHL.Visualization: KHL DEN ASW.Writing – original draft: KHL DEN ASW.Writing – review & editing: KHL DEN ASW.
ISSN:	1932-6203 1932-6203
DOI:	10.1371/journal.pone.0169339