title: Tropical soil bacterial communities in Malaysia: pH dominates in the equatorial tropics too.
abstract: The dominant factors controlling soil bacterial community variation within the tropics are poorly known. We sampled soils across a range of land use types--primary (unlogged) and logged forests and crop and pasture lands in Malaysia. PCR-amplified soil DNA for the bacterial 16S rRNA gene targeting the V1-V3 region was pyrosequenced using the 454 Roche machine. We found that land use in itself has a weak but significant effect on the bacterial community composition. However, bacterial community composition and diversity was strongly correlated with soil properties, especially soil pH, total carbon, and C/N ratio. Soil pH was the best predictor of bacterial community composition and diversity across the various land use types, with the highest diversity close to neutral pH values. In addition, variation in phylogenetic structure of dominant lineages (Alphaproteobacteria, Beta/Gammaproteobacteria, Acidobacteria, and Actinobacteria) is also significantly correlated with soil pH. Together, these results confirm the importance of soil pH in structuring soil bacterial communities in Southeast Asia. Our results also suggest that unlike the general diversity pattern found for larger organisms, primary tropical forest is no richer in operational taxonomic units of soil bacteria than logged forest, and agricultural land (crop and pasture) is actually richer than primary forest, partly due to selection of more fertile soils that have higher pH for agriculture and the effects of soil liming raising pH.
authors.affiliation: Department of Biological Sciences, Seoul National University, Gwanak, Seoul, 151, Republic of Korea.
authors.forename: Binu M
authors.initials: BM
authors.lastname: Tripathi
authors.forename: Mincheol
authors.initials: M
authors.lastname: Kim
authors.forename: Dharmesh
authors.initials: D
authors.lastname: Singh
authors.forename: Larisa
authors.initials: L
authors.lastname: Lee-Cruz
authors.forename: Ang
authors.initials: A
authors.lastname: Lai-Hoe
authors.forename: A N
authors.initials: AN
authors.lastname: Ainuddin
authors.forename: Rusea
authors.initials: R
authors.lastname: Go
authors.forename: Raha Abdul
authors.initials: RA
authors.lastname: Rahim
authors.forename: M H A
authors.initials: MH
authors.lastname: Husni
authors.forename: Jongsik
authors.initials: J
authors.lastname: Chun
authors.forename: Jonathan M
authors.initials: JM
authors.lastname: Adams
mesh_terms: D039903:Actinobacteria / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D000383:Agriculture; D044822:Biodiversity; D002244:Carbon / Q000032:analysis; D004269:DNA, Bacterial / Q000032:analysis; D004275:DNA, Ribosomal / Q000032:analysis; D016468:Forestry; D020459:Genes, rRNA; D006090:Gram-Negative Bacteria / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D006863:Hydrogen-Ion Concentration; D008296:Malaysia; D008969:Molecular Sequence Data; D009584:Nitrogen / Q000032:analysis; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S; D017422:Sequence Analysis, DNA / Q000379:methods; D012987:Soil / Q000032:analysis* / Q000737:chemistry; D012988:Soil Microbiology; D014329:Tropical Climate
chemical_list: D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S; D012987:Soil; D002244:Carbon; D009584:Nitrogen