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The impact of tropical forest logging and oil palm agriculture on the soil microbiome. / Tripathi, B. M.; Edwards, D. P.; Mendes, L. W.; Kim, M.; Dong, K.; Kim, H.; Adams, J. M.

In: Molecular Ecology, Vol. 25, No. 10, 2016, p. 2244-2257.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Harvard

Tripathi, BM, Edwards, DP, Mendes, LW, Kim, M, Dong, K, Kim, H & Adams, JM 2016, 'The impact of tropical forest logging and oil palm agriculture on the soil microbiome' Molecular Ecology, vol. 25, no. 10, pp. 2244-2257. https://doi.org/10.1111/mec.13620

APA

Tripathi, B. M., Edwards, D. P., Mendes, L. W., Kim, M., Dong, K., Kim, H., & Adams, J. M. (2016). The impact of tropical forest logging and oil palm agriculture on the soil microbiome. Molecular Ecology, 25(10), 2244-2257. https://doi.org/10.1111/mec.13620

Vancouver

Tripathi BM, Edwards DP, Mendes LW, Kim M, Dong K, Kim H et al. The impact of tropical forest logging and oil palm agriculture on the soil microbiome. Molecular Ecology. 2016;25(10):2244-2257. https://doi.org/10.1111/mec.13620

Author

Tripathi, B. M. ; Edwards, D. P. ; Mendes, L. W. ; Kim, M. ; Dong, K. ; Kim, H. ; Adams, J. M. / The impact of tropical forest logging and oil palm agriculture on the soil microbiome. In: Molecular Ecology. 2016 ; Vol. 25, No. 10. pp. 2244-2257.

BibTeX

@article{ff437cd1673641d88a6645efe817dbd7,
title = "The impact of tropical forest logging and oil palm agriculture on the soil microbiome",
abstract = "Selective logging and forest conversion to oil palm agriculture are rapidly altering tropical forests. However, functional responses of the soil microbiome to these land-use changes are poorly understood. Using 16S rRNA gene and shotgun metagenomic sequencing, we compared composition and functional attributes of soil biota between unlogged, once-logged and twice-logged rainforest, and areas converted to oil palm plantations in Sabah, Borneo. Although there was no significant effect of logging history, we found a significant difference between the taxonomic and functional composition of both primary and logged forests and oil palm. Oil palm had greater abundances of genes associated with DNA, RNA, protein metabolism and other core metabolic functions, but conversely, lower abundance of genes associated with secondary metabolism and cell-cell interactions, indicating less importance of antagonism or mutualism in the more oligotrophic oil palm environment. Overall, these results show a striking difference in taxonomic composition and functional gene diversity of soil microorganisms between oil palm and forest, but no significant difference between primary forest and forest areas with differing logging history. This reinforces the view that logged forest retains most features and functions of the original soil community. However, networks based on strong correlations between taxonomy and functions showed that network complexity is unexpectedly increased due to both logging and oil palm agriculture, which suggests a pervasive effect of both land-use changes on the interaction of soil microbes.",
keywords = "international",
author = "Tripathi, {B. M.} and Edwards, {D. P.} and Mendes, {L. W.} and M. Kim and K. Dong and H. Kim and Adams, {J. M.}",
note = "6132, ME; Data Archiving: data archived at MG-Rast and at Dryad Tripathi, Binu M. Edwards, David P. Mendes, Lucas William Kim, Mincheol Dong, Ke Kim, Hyoki Adams, Jonathan M. 1365-294x <Go to ISI>://WOS:000377024200011",
year = "2016",
doi = "10.1111/mec.13620",
language = "English",
volume = "25",
pages = "2244--2257",
journal = "Molecular Ecology",
issn = "0962-1083",
publisher = "Wiley-Blackwell",
number = "10",

}

RIS

TY - JOUR

T1 - The impact of tropical forest logging and oil palm agriculture on the soil microbiome

AU - Tripathi, B. M.

AU - Edwards, D. P.

AU - Mendes, L. W.

AU - Kim, M.

AU - Dong, K.

AU - Kim, H.

AU - Adams, J. M.

N1 - 6132, ME; Data Archiving: data archived at MG-Rast and at Dryad Tripathi, Binu M. Edwards, David P. Mendes, Lucas William Kim, Mincheol Dong, Ke Kim, Hyoki Adams, Jonathan M. 1365-294x <Go to ISI>://WOS:000377024200011

PY - 2016

Y1 - 2016

N2 - Selective logging and forest conversion to oil palm agriculture are rapidly altering tropical forests. However, functional responses of the soil microbiome to these land-use changes are poorly understood. Using 16S rRNA gene and shotgun metagenomic sequencing, we compared composition and functional attributes of soil biota between unlogged, once-logged and twice-logged rainforest, and areas converted to oil palm plantations in Sabah, Borneo. Although there was no significant effect of logging history, we found a significant difference between the taxonomic and functional composition of both primary and logged forests and oil palm. Oil palm had greater abundances of genes associated with DNA, RNA, protein metabolism and other core metabolic functions, but conversely, lower abundance of genes associated with secondary metabolism and cell-cell interactions, indicating less importance of antagonism or mutualism in the more oligotrophic oil palm environment. Overall, these results show a striking difference in taxonomic composition and functional gene diversity of soil microorganisms between oil palm and forest, but no significant difference between primary forest and forest areas with differing logging history. This reinforces the view that logged forest retains most features and functions of the original soil community. However, networks based on strong correlations between taxonomy and functions showed that network complexity is unexpectedly increased due to both logging and oil palm agriculture, which suggests a pervasive effect of both land-use changes on the interaction of soil microbes.

AB - Selective logging and forest conversion to oil palm agriculture are rapidly altering tropical forests. However, functional responses of the soil microbiome to these land-use changes are poorly understood. Using 16S rRNA gene and shotgun metagenomic sequencing, we compared composition and functional attributes of soil biota between unlogged, once-logged and twice-logged rainforest, and areas converted to oil palm plantations in Sabah, Borneo. Although there was no significant effect of logging history, we found a significant difference between the taxonomic and functional composition of both primary and logged forests and oil palm. Oil palm had greater abundances of genes associated with DNA, RNA, protein metabolism and other core metabolic functions, but conversely, lower abundance of genes associated with secondary metabolism and cell-cell interactions, indicating less importance of antagonism or mutualism in the more oligotrophic oil palm environment. Overall, these results show a striking difference in taxonomic composition and functional gene diversity of soil microorganisms between oil palm and forest, but no significant difference between primary forest and forest areas with differing logging history. This reinforces the view that logged forest retains most features and functions of the original soil community. However, networks based on strong correlations between taxonomy and functions showed that network complexity is unexpectedly increased due to both logging and oil palm agriculture, which suggests a pervasive effect of both land-use changes on the interaction of soil microbes.

KW - international

UR - http://metagenomics.anl.gov/metagenomics.cgi?page=MetagenomeProject&project=10865

UR - http://dx.doi.org/10.5061/dryad.17n4d

U2 - 10.1111/mec.13620

DO - 10.1111/mec.13620

M3 - Article

VL - 25

SP - 2244

EP - 2257

JO - Molecular Ecology

JF - Molecular Ecology

SN - 0962-1083

IS - 10

ER -

ID: 2221382