How Rainforest Conversion to Agricultural Systems in Sumatra (Indonesia) Affects Active Soil Bacterial Communities

Abstract

Palm oil production in Indonesia increased constantly over the last decades, which led to massive deforestation, especially on Sumatra island. The ongoing conversion of rainforest to agricultural systems results in high biodiversity loss. Here, we present the first RNA-based study on the effects of rainforest transformation to rubber and oil palm plantations in Indonesia for the active soil bacterial communities. For this purpose, bacterial communities of three different converted systems (jungle rubber, rubber plantation, and oil palm plantation) were studied in two landscapes with rainforest as reference by RT-PCR amplicon-based analysis of 16S rRNA gene transcripts. Active soil bacterial communities were dominated by Frankiales (Actinobacteria), subgroup 2 of the Acidobacteria and Alphaproteobacteria (mainly Rhizobiales and Rhodospirillales). Community composition differed significantly between the converted land use systems and rainforest reference sites. Alphaproteobacteria decreased significantly in oil palm samples compared to rainforest samples. In contrast, relative abundances of taxa within the Acidobacteria increased. Most important abiotic drivers for shaping soil bacterial communities were pH, calcium concentration, base saturation and C:N ratio. Indicator species analysis showed distinct association patterns for the analyzed land use systems. Nitrogen-fixing taxa including members of Rhizobiales and Rhodospirillales were associated with rainforest soils while nitrifiers and heat-resistant taxa including members of Actinobacteria were associated with oil palm soils. Predicted metabolic profiles revealed that the relative abundances of genes associated with fixation of nitrogen significantly decreased in plantation soils. Furthermore, predicted gene abundances regarding motility, competition or gene transfer ability indicated rainforest conversion-induced changes as well.

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

“…The soil microbial community composition changed in the converted land use systems compared to rainforest with similar trends as in previous studies targeting these sampling sites [9,15,16]. Proteobacteria were negatively and Acidobacteria positively affected by rainforest conversion.…”

“…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]. Additionally, the microbial community composition was severely affected by these conversion processes with a high impact on Proteobacteria which showed an abundance decrease and Actinobacteria, which showed an abundance increase with increasing land use intensity [15,16].…”

“…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]. Additionally, the microbial community composition was severely affected by these conversion processes with a high impact on Proteobacteria which showed an abundance decrease and Actinobacteria, which showed an abundance increase with increasing land use intensity [15,16]. Furthermore, negative effects on aboveground and belowground carbon stocks, CO 2 fluxes and leaching in these converted land use systems were shown before [17][18][19][20][21].…”

“…This is cost-efficient, taxonomically accurate and relatively fast but functional profiles can only be predicted based on taxonomic information using bioinformatic tools such as Tax4Fun2 [25], Piphillin [26] and PiCrust [15,[27][28][29][30][31]. Prediction-based analysis of microbiome functions provides first insights into environmental microbial processes such as nutrient cycling and emission of climate gases influenced by agricultural management [16]. While these studies provided a first impression of the functional potential, direct sequencing of metagenomic DNA and identification of functional genes is needed to verify prediction-based findings [32].…”

“…We linked functional results with their corresponding taxonomic background. Based on our previous studies analysing the 16S rRNA marker gene sequences in the same sampling sites and studies on similar systems in Southeast Asia [9,10,15,16,18,33], we formulated three hypotheses. We assume that diversity will decrease for soilborne archaea, Eukaryotes and increase for bacteria with increasing land use intensity (H1).…”