New Biological Insights Into How Deforestation in Amazonia Affects Soil Microbial Communities Using Metagenomics and Metagenome-Assembled Genomes

Kroeger, Marie E.; Delmont, Tom O.; Eren, A. Murat; Meyer, Kyle; Guo, Jiarong; Khan, Kiran Yasmin; Rodrigues, Jorge L. Mazza; Bohannan, Brendan J. M.; Tringe, Susannah G.; Borges, Clóvis Daniel; Tiedje, James M.; Tsai, Siu Mui; Nüsslein, Klaus

doi:10.3389/fmicb.2018.01635

Cited by 67 publications

(64 citation statements)

References 83 publications

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“…Ecosystem functioning depends to a large extent on the functional diversity and activity of the belowground microbial system [5,6]. In addition, microorganisms play a key role in decomposing soil organic matter and mineralizing nutrients in soil [7]. It has been shown that rainforest conversion to plantations has negative effects on the biodiversity of fungi [8,9], protists [10], vertebrates [11], insects and plants [12][13][14], archaea [15], but not on bacterial diversity which increased [15,16].…”

Section: Introductionmentioning

confidence: 99%

Unravelling the effects of tropical land use conversion on the soil microbiome

Hölscher

Schneider

Meryandini

et al. 2020

Environmental Microbiome

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Background: The consequences of deforestation and agricultural treatments are complex and affect all trophic levels. Changes of microbial community structure and composition associated with rainforest conversion to managed systems such as rubber and oil palm plantations have been shown by 16S rRNA gene analysis previously, but functional profile shifts have been rarely addressed. In this study, we analysed the effects of rainforest conversion to different converted land use systems, including agroforestry ("jungle rubber") and monoculture plantations comprising rubber and oil palm, on soilborne microbial communities by metagenomic shotgun sequencing in Sumatra, Indonesia.Results: The diversity of bacteria and archaea decreased whereas diversity of fungi increased in the converted land use systems. The soil microbiome was dominated by bacteria followed by fungi. We detected negative effects of land use conversion on the abundance of Proteobacteria (especially on Rhizobiales and Burkholderiales) and positive effects on the abundance of Acidobacteria and Actinobacteria. These abundance changes were mainly driven by pH, C:N ratio, and Fe, C and N content. With increasing land use intensity, the functional diversity decreased for bacteria, archaea and fungi. Gene abundances of specific metabolisms such as nitrogen metabolism and carbon fixation were affected by land use management practices. The abundance of genes related to denitrification and nitrogen fixation increased in plantations while abundance of genes involved in nitrification and methane oxidation showed no significant difference. Linking taxonomic and functional assignment per read indicated that nitrogen metabolism-related genes were mostly assigned to members of the Rhizobiales and Burkholderiales. Abundances of carbon fixation genes increased also with increasing land use intensity. Motility-and interaction-related genes, especially genes involved in flagellar assembly and chemotaxis genes, decreased towards managed land use systems. This indicated a shift in mobility and interspecific interactions in bacterial communities within these soils. Conclusions: Rainforest conversion to managed land use systems drastically affects structure and functional potential of soil microbial communities. The decrease in motility-and interaction-related functions from rainforest to converted land use systems indicated not only a shift in nutrient cycling but also in community dynamics. Fertilizer application and correspondingly higher availability of nutrients in intensively managed plantations lead to an environment in which interspecific interactions are not favoured compared to rainforest soils. We could directly link effects of land management, microbial community structure and functional potential for several metabolic processes. As our study is the first study of this size and detail on soil microbial communities in tropical systems, we provide a basis for further analyses.

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Section: Introductionmentioning

confidence: 99%

Unravelling the effects of tropical land use conversion on the soil microbiome

Hölscher

Schneider

Meryandini

et al. 2020

Environmental Microbiome

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“…The comparative data in Fig 6 cluster genes by the sequences of the 16S rRNA gene identified in this study. This analysis was carried out as a survey of biotechnological potential [18,19] mainly related to biodegradation in the storage tanks of water contaminated with agrochemicals, which are considered a significant environmental liability.…”

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

“…Thus, the composition and relative abundance of soil microbiomes in the Amazon were correlated with different types of land use, such as deforestation, which leads to carbon cycle disturbances and, consequently, climate change [18]. Therefore, microbiomes, which play key roles in biogeochemical cycles, are affected by anthropogenic action, particularly by the use of xenobiotic compounds, leading to changes in sustainability and environmental quality [18,19]. High-density DNA microarray and 16S rDNA amplicon next-generation sequencing were used to study the impact of the insecticide chlorpyrifos, the herbicide isoproturon and the fungicide tebuconazole on the soil bacterial community, and significant differences have been found in field experiments but not in soil microcosms exposed to these pesticides [20].…”

Section: Introductionmentioning

confidence: 99%

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Population structure determined by comparative amplicon gene sequencing in biofilm and planktonic bacterial communities from pesticide-contaminated water

Lima

Moreira

Costa

et al. 2019

Preprint

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“…Also, belowground biodiversity loss is very likely to have negative effects both on the environment and on the sustainability of agricultural production as microbial functions will be altered (Tardy et al, 2014). Recently, metagenomic approaches have investigated the impact on the composition and structure of soil microbiome of converting semi-deciduous Amazonian rainforest and natural grasslands to arable soils (Mendes et al, 2015;Castañeda and Barbosa, 2017;Goss-Souza et al, 2017;Kroeger et al, 2018). These studies found that arable soils were similar or more diverse than the original ecosystem and that functional redundancy overcomes the ecosystem transformation.…”

Section: Discussionmentioning

confidence: 99%

Soil microbial diversity drops with land‐use change in a high mountain temperate forest: a metagenomics survey

Muñoz-Arenas

Fusaro

Hernández‐Guzmán

et al. 2020

Environ Microbiol Rep

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Summary Land‐use change has been identified as the most severe threat to biodiversity. Soils are important biodiversity reservoirs, but to what extent conversion of high‐altitude temperate forest to arable land affects taxonomic and functional soil biodiversity is still largely unknown. Shotgun metagenomics was used to determine the taxonomic and functional diversity of bacteria, archaea and DNA virus in terms of effective number of species in high‐altitude temperate oak and pine‐oak forest and arable soils from Mexico. Generally, the soil ecosystem maintained its microbial species richness notwithstanding land‐use change. Archaea diversity was not affected by land‐use change, but the bacterial diversity decreased with 45–55% when the oak forest was converted to arable land and 65–75% when the pine‐oak forest was. Loss in bacterial diversity as a result of land‐use change was positively correlated (R2 = 0.41) with the 10–25% loss in functional diversity. The archaeal communities were evener than the bacterial ones, which might explain their different response to land‐use change. We expected a decrease in DNA viral communities as the bacterial diversity decreased, i.e. their potential hosts. However, a higher viral diversity was found in the arable than in the forest soils. It was found that converting high altitude oak and pine‐oak forests to arable land more than halved the bacterial diversity, but did not affect the archaeal and even increased the viral diversity.

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New Biological Insights Into How Deforestation in Amazonia Affects Soil Microbial Communities Using Metagenomics and Metagenome-Assembled Genomes

Cited by 67 publications

References 83 publications

Unravelling the effects of tropical land use conversion on the soil microbiome

Unravelling the effects of tropical land use conversion on the soil microbiome

Population structure determined by comparative amplicon gene sequencing in biofilm and planktonic bacterial communities from pesticide-contaminated water

Soil microbial diversity drops with land‐use change in a high mountain temperate forest: a metagenomics survey

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