Intensive tropical land use massively shifts soil fungal communities

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Abstract

Soil fungi are key players in nutrient cycles as decomposers, mutualists and pathogens, but the impact of tropical rain forest transformation into rubber or oil palm plantations on fungal community structures and their ecological functions are unknown. We hypothesized that increasing land use intensity and habitat loss due to the replacement of the hyperdiverse forest flora by nonendemic cash crops drives a drastic loss of diversity of soil fungal taxa and impairs the ecological soil functions. Unexpectedly, rain forest conversion was not associated with strong diversity loss but with massive shifts in soil fungal community composition. Fungal communities clustered according to land use system and loss of plant species. Network analysis revealed characteristic fungal genera significantly associated with different land use systems. Shifts in soil fungal community structure were particularly distinct among different trophic groups, with substantial decreases in symbiotrophic fungi and increases in saprotrophic and pathotrophic fungi in oil palm and rubber plantations in comparison with rain forests. In conclusion, conversion of rain forests and current land use systems restructure soil fungal communities towards enhanced pathogen pressure and, thus, threaten ecosystem health functions.

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Tropical forests were the primary sources of new agricultural land in the 1980s and 1990s.

H K Gibbs, A S Ruesch, F Achard … (2010)

Global demand for agricultural products such as food, feed, and fuel is now a major driver of cropland and pasture expansion across much of the developing world. Whether these new agricultural lands replace forests, degraded forests, or grasslands greatly influences the environmental consequences of expansion. Although the general pattern is known, there still is no definitive quantification of these land-cover changes. Here we analyze the rich, pan-tropical database of classified Landsat scenes created by the Food and Agricultural Organization of the United Nations to examine pathways of agricultural expansion across the major tropical forest regions in the 1980s and 1990s and use this information to highlight the future land conversions that probably will be needed to meet mounting demand for agricultural products. Across the tropics, we find that between 1980 and 2000 more than 55% of new agricultural land came at the expense of intact forests, and another 28% came from disturbed forests. This study underscores the potential consequences of unabated agricultural expansion for forest conservation and carbon emissions.

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Roots shaping their microbiome: global hotspots for microbial activity.

Barbara Reinhold-Hurek, Wiebke Bünger, Claudia Burbano … (2015)

Land plants interact with microbes primarily at roots. Despite the importance of root microbial communities for health and nutrient uptake, the current understanding of the complex plant-microbe interactions in the rhizosphere is still in its infancy. Roots provide different microhabitats at the soil-root interface: rhizosphere soil, rhizoplane, and endorhizosphere. We discuss technical aspects of their differentiation that are relevant for the functional analysis of their different microbiomes, and we assess PCR (polymerase chain reaction)-based methods to analyze plant-associated bacterial communities. Development of novel primers will allow a less biased and more quantitative view of these global hotspots of microbial activity. Based on comparison of microbiome data for the different root-soil compartments and on knowledge of bacterial functions, a three-step enrichment model for shifts in community structure from bulk soil toward roots is presented. To unravel how plants shape their microbiome, a major research field is likely to be the coupling of reductionist and molecular ecological approaches, particularly for specific plant genotypes and mutants, to clarify causal relationships in complex root communities.

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Back to Basics – The Influence of DNA Extraction and Primer Choice on Phylogenetic Analysis of Activated Sludge Communities

Mads Albertsen, Søren Karst, Anja S. Ziegler … (2015)

DNA extraction and primer choice have a large effect on the observed community structure in all microbial amplicon sequencing analyses. Although the biases are well known, no comprehensive analysis has been conducted in activated sludge communities. In this study we systematically explored the impact of a number of parameters on the observed microbial community: bead beating intensity, primer choice, extracellular DNA removal, and various PCR settings. In total, 176 samples were subjected to 16S rRNA amplicon sequencing, and selected samples were investigated through metagenomics and metatranscriptomics. Quantitative fluorescence in situ hybridization was used as a DNA extraction-independent method for qualitative comparison. In general, an effect on the observed community was found on all parameters tested, although bead beating and primer choice had the largest effect. The effect of bead beating intensity correlated with cell-wall strength as seen by a large increase in DNA from Gram-positive bacteria (up to 400%). However, significant differences were present at lower phylogenetic levels within the same phylum, suggesting that additional factors are at play. The best primer set based on in silico analysis was found to underestimate a number of important bacterial groups. For 16S rRNA gene analysis in activated sludge we recommend using the FastDNA SPIN Kit for Soil with four times the normal bead beating and V1-3 primers.

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Author and article information

Contributors

Nicole Brinkmann: nbrinkm3@gwdg.de

Journal

Journal ID (nlm-ta): Sci Rep

Journal ID (iso-abbrev): Sci Rep

Title: Scientific Reports

Publisher: Nature Publishing Group UK (London )

ISSN (Electronic): 2045-2322

Publication date (Electronic): 4 March 2019

Publication date PMC-release: 4 March 2019

Publication date Collection: 2019

Volume: 9

Electronic Location Identifier: 3403

Affiliations

[1 ]ISNI 0000 0001 2364 4210, GRID grid.7450.6, Forest Botany and Tree Physiology, , University of Goettingen, ; Göttingen, Germany

[2 ]ISNI 0000 0001 2364 4210, GRID grid.7450.6, Genomic and Applied Microbiology and Göttingen Genomics Laboratory, , University of Goettingen, ; Göttingen, Germany

[3 ]GRID grid.444111.5, Department of Agrotechnology, Faculty of Agriculture, , Tadulako University, ; Palu, Indonesia

[4 ]GRID grid.443495.b, Department of Forestry, , University of Jambi, ; Jambi, Indonesia

[5 ]Department of Silviculture, Faculty of Forestry, Bogor Agriculture University, Bogor, Indonesia

[6 ]ISNI 0000 0001 2364 4210, GRID grid.7450.6, Department of Agricultural Economics and Rural Development, , University of Goettingen, ; Göttingen, Germany

Author information

Dominik Schneider http://orcid.org/0000-0002-1134-5026

Nur Edy http://orcid.org/0000-0001-9013-5141

Rolf Daniel http://orcid.org/0000-0002-8646-7925

Andrea Polle http://orcid.org/0000-0001-8697-6394

Article

Publisher ID: 39829

DOI: 10.1038/s41598-019-39829-4

PMC ID: 6399230

PubMed ID: 30833601

SO-VID: a90667e4-633b-4b9f-ad58-8ec3d0140ce4

License:

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

History

Date received : 26 August 2018

Date accepted : 30 January 2019

Funding

Funded by: FundRef https://doi.org/10.13039/501100001659, Deutsche Forschungsgemeinschaft (German Research Foundation);

Award ID: CRC990-B07

Award Recipient : Nicole Brinkmann Dominik Schneider Josephine Sahner Johannes Ballauff Nur Edy Henry Barus Bambang Irawan Sri Wilarso Budi Matin Qaim Rolf Daniel Andrea Polle

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Intensive tropical land use massively shifts soil fungal communities

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Abiotic gradients in fragmented landscapes

Most cited references 82

Tropical forests were the primary sources of new agricultural land in the 1980s and 1990s.

Roots shaping their microbiome: global hotspots for microbial activity.

Back to Basics – The Influence of DNA Extraction and Primer Choice on Phylogenetic Analysis of Activated Sludge Communities

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Cited by 42

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