Changes of Soil Bacterial Diversity as a Consequence of Agricultural Land Use in a Semi-Arid Ecosystem

Ding, Guo-Chun; Piceno, Yvette M.; Heuer, Holger; Weinert, Nicole; Dohrmann, Anja B.; Carrillo, Angel; Andersen, Gary L.; Castellanos, Thelma; Tebbe, Christoph C.; Smalla, Kornelia

doi:10.1371/journal.pone.0059497

Changes of Soil Bacterial Diversity as a Consequence of Agricultural Land Use in a Semi-Arid Ecosystem

Journal Article · Wed Mar 20 00:00:00 EDT 2013 · PLoS ONE

DOI:https://doi.org/10.1371/journal.pone.0059497· OSTI ID:1627594

Ding, Guo-Chun ^[1]; Piceno, Yvette M. ^[2]; Heuer, Holger ^[3]; Weinert, Nicole ^[3]; Dohrmann, Anja B. ^[4]; Carrillo, Angel ^[5]; Andersen, Gary L. ^[2]; Castellanos, Thelma ^[5]; Tebbe, Christoph C. ^[4]; Smalla, Kornelia ^[3]

Federal Research Centre for Cultivated Plants (JKI), Braunschweig (Germany); DOE/OSTI
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Federal Research Centre for Cultivated Plants (JKI), Braunschweig (Germany)
Johann Heinrich von Thunen-Institut (TI), Braunschweig (Germany)
Centro de Investigaciones biologicas del Noroeste, S.C. La Paz (Mexico)

Natural scrublands in semi-arid deserts are increasingly being converted into fields. This results in losses of characteristic flora and fauna, and may also affect microbial diversity. In the present study, the long-term effect (50 years) of such a transition on soil bacterial communities was explored at two sites typical of semi-arid deserts. Comparisons were made between soil samples from alfalfa fields and the adjacent scrublands by two complementary methods based on 16S rRNA gene fragments amplified from total community DNA. Denaturing gradient gel electrophoresis (DGGE) analyses revealed significant effects of the transition on community composition of Bacteria, Actinobacteria, Alpha- and Betaproteobacteria at both sites. PhyloChip hybridization analysis uncovered that the transition negatively affected taxa such as Acidobacteria, Chloroflexi, Acidimicrobiales, Rubrobacterales, Deltaproteobacteria and Clostridia, while Alpha-, Beta- and Gammaproteobacteria, Bacteroidetes and Actinobacteria increased in abundance. Redundancy analysis suggested that the community composition of phyla responding to agricultural use (except for Spirochaetes) correlated with soil parameters that were significantly different between the agricultural and scrubland soil. The arable soils were lower in organic matter and phosphate concentration, and higher in salinity. The variation in the bacterial community composition was higher in soils from scrubland than from agriculture, as revealed by DGGE and PhyloChip analyses, suggesting reduced beta diversity due to agricultural practices. The long-term use for agriculture resulted in profound changes in the bacterial community and physicochemical characteristics of former scrublands, which may irreversibly affect the natural soil ecosystem.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: Concejo Nacional de Ciencia Y Tecnologia (CONACYT); German Federal Ministry for Education and Research; USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1627594

Journal Information:: PLoS ONE, Journal Name: PLoS ONE Journal Issue: 3 Vol. 8; ISSN 1932-6203

Publisher:: Public Library of ScienceCopyright Statement

Country of Publication:: United States

Language:: English

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Oasis desert farming selects environment-specific date palm root endophytic communities and cultivable bacteria that promote resistance to drought: Oasis palm endophytes promote drought resistance Cherif, Hanene; Marasco, Ramona; Rolli, Eleonora Environmental Microbiology Reports, Vol. 7, Issue 4 https://doi.org/10.1111/1758-2229.12304	journal	July 2015
The microbially mediated soil organic carbon loss under degenerative succession in an alpine meadow Zhang, Yuguang; Liu, Xiao; Cong, Jing Molecular Ecology, Vol. 26, Issue 14 https://doi.org/10.1111/mec.14148	journal	May 2017
Microbial Ecology Dynamics during Rye and Wheat Sourdough Preparation Ercolini, Danilo; Pontonio, Erica; De Filippis, Francesca Applied and Environmental Microbiology, Vol. 79, Issue 24 https://doi.org/10.1128/aem.02955-13	journal	October 2013
Plant Community and Nitrogen Deposition as Drivers of Alpha and Beta Diversities of Prokaryotes in Reconstructed Oil Sand Soils and Natural Boreal Forest Soils Masse, Jacynthe; Prescott, Cindy E.; Renaut, Sébastien Applied and Environmental Microbiology, Vol. 83, Issue 9 https://doi.org/10.1128/aem.03319-16	journal	February 2017
A 16S rDNA PCR-based theoretical to actual delta approach on culturable mock communities revealed severe losses of diversity information dos Santos, Hellen Ribeiro Martins; Argolo, Caio Suzart; Argôlo-Filho, Ronaldo Costa BMC Microbiology, Vol. 19, Issue 1 https://doi.org/10.1186/s12866-019-1446-2	journal	April 2019
Differences in Bacterial Diversity, Composition and Function due to Long-Term Agriculture in Soils in the Eastern Free State of South Africa Dube, Joel P.; Valverde, Angel; Steyn, Joachim M. Diversity, Vol. 11, Issue 4 https://doi.org/10.3390/d11040061	journal	April 2019
Impact of Land Use on Bacterial Diversity and Community Structure in Temperate Pine and Indigenous Forest Soils Amoo, Adenike Eunice; Babalola, Olubukola Oluranti Diversity, Vol. 11, Issue 11 https://doi.org/10.3390/d11110217	journal	November 2019
Bacterial Community Changes Associated with Land Use Type in the Forest Montane Region of Northeast China Wu, Shi-Jun; Deng, Jiao-Jiao; Yin, You Forests, Vol. 11, Issue 1 https://doi.org/10.3390/f11010040	journal	December 2019

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