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

Abstract

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.

Impacts of Intensive Land use on Soil Biodiversity and Ecosystem Functions in Central China

“…In our study, citrus planting caused a decline in soil pH, resulting in decreases in soil bacterial diversity. Soil pH has been widely accepted as the most important factor that affects soil bacterial/fungal community composition (Lauber et al The conversion of natural vegetation land to citrus orchards altered the soil microbial community composition, which is in agreement with the results in previous studies (37). Proteobacteria (Alphaproteobacteria and Deltaproteobacteria) and Acidobacteria (Subgroup_6 and Subgroup_4) were negatively influenced by the conversion, which might be due to the decline in soil pH and SOC.…”

“…Conversion from natural to agricultural ecosystems has been considered as the most important driving force to regulate soil microbial communities (37). In this study, citrus planting was found to reduce soil bacterial and fungal diversity in a time dependent manner.…”

“…For example, citrus planting mainly affected ecological cluster #1 and #2, while had little effect on cluster #0, which was dominant in natural vegetation land. Soil Rhizobiales were mainly distributed in ecological cluster #0, due to the higher plant diversity on natural vegetation land than on agricultural land (37). Similarly, higher abundance of soil Rhizobiales was observed in the forest sites (49).…”

“…In this study, citrus planting was found to reduce soil bacterial and fungal diversity in a time dependent manner. Similarly, Berkelmann et al (2020) found that the conversion from rainforest to rubber and oil palm plantation resulted in a decline in bacterial diversity. These negative effects of the conversion of natural vegetation land to agricultural land on soil bacterial diversity may be ascribed to the homogenization of soil bacteria (38).…”

“…Considering the sharp loss of plant diversity in the agricultural ecosystem, the reduction of soil bacterial communities might be ascribed to the decreases in plant-related microbial groups, such as mycorrhizal fungi and rhizosphere microbes (41). For example, Rhizobiales are highly related to the diversity of aboveground plants, and thus a decrease in plant diversity would lead to corresponding decreases in Rhizobiales (37,42).…”