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Microorganisms 2015, 3(2), 113-136; doi:10.3390/microorganisms3020113

High Throughput Sequencing to Detect Differences in Methanotrophic Methylococcaceae and Methylocystaceae in Surface Peat, Forest Soil, and Sphagnum Moss in Cranesville Swamp Preserve, West Virginia, USA

Department of Natural Sciences and Mathematics, West Liberty University, 208 University Drive, CUB#139, West Liberty, WV 26074, USA
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Author to whom correspondence should be addressed.
Academic Editors: Marina G. Kalyuzhnaya and Ludmila Chistoserdova
Received: 25 January 2015 / Revised: 23 February 2015 / Accepted: 26 March 2015 / Published: 2 April 2015
(This article belongs to the Special Issue Microbial C1 Metabolism)
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Abstract

Northern temperate forest soils and Sphagnum-dominated peatlands are a major source and sink of methane. In these ecosystems, methane is mainly oxidized by aerobic methanotrophic bacteria, which are typically found in aerated forest soils, surface peat, and Sphagnum moss. We contrasted methanotrophic bacterial diversity and abundances from the (i) organic horizon of forest soil; (ii) surface peat; and (iii) submerged Sphagnum moss from Cranesville Swamp Preserve, West Virginia, using multiplex sequencing of bacterial 16S rRNA (V3 region) gene amplicons. From ~1 million reads, >50,000 unique OTUs (Operational Taxonomic Units), 29 and 34 unique sequences were detected in the Methylococcaceae and Methylocystaceae, respectively, and 24 potential methanotrophs in the Beijerinckiaceae were also identified. Methylacidiphilum-like methanotrophs were not detected. Proteobacterial methanotrophic bacteria constitute <2% of microbiota in these environments, with the Methylocystaceae one to two orders of magnitude more abundant than the Methylococcaceae in all environments sampled. The Methylococcaceae are also less diverse in forest soil compared to the other two habitats. Nonmetric multidimensional scaling analyses indicated that the majority of methanotrophs from the Methylococcaceae and Methylocystaceae tend to occur in one habitat only (peat or Sphagnum moss) or co-occurred in both Sphagnum moss and peat. This study provides insights into the structure of methanotrophic communities in relationship to habitat type, and suggests that peat and Sphagnum moss can influence methanotroph community structure and biogeography. View Full-Text
Keywords: Methanotrophic bacteria; high throughput sequencing; Illumina® MiSeq; multiplex sequencing; microbial ecology; upland forest soils; peatlands; surface peat; Sphagnum moss; Methylococcaceae; Methylocystaceae; Evenness; Shannon-Weiner Index; Nonmetric multidimensional scaling; biogeography Methanotrophic bacteria; high throughput sequencing; Illumina® MiSeq; multiplex sequencing; microbial ecology; upland forest soils; peatlands; surface peat; Sphagnum moss; Methylococcaceae; Methylocystaceae; Evenness; Shannon-Weiner Index; Nonmetric multidimensional scaling; biogeography
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Lau, E.; IV, E.J.N.; Dillard, Z.W.; Dague, R.D.; Semple, A.L.; Wentzell, W.L. High Throughput Sequencing to Detect Differences in Methanotrophic Methylococcaceae and Methylocystaceae in Surface Peat, Forest Soil, and Sphagnum Moss in Cranesville Swamp Preserve, West Virginia, USA. Microorganisms 2015, 3, 113-136.

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