High-throughput sequencing characterization of land use impact on archaeal community: Amazon native forest and oil palm plantation

Soil management practices and land-use have direct impact on the physicochemical and biological properties of soil thus influencing soil microbial communities. This study characterized and compared soil archaeal communities of the Amazon forest (NF – native forest) and an oil palm-cultivated adjacent area (CA – cultivated area) by high-throughput sequencing of the 16S ribosomal RNA gene. Mothur was used for bioinformatics analysis and SILVA database (release 119) for taxonomic classification. The existing diversity of both samples was covered by number of sequences obtained, especially for CA. NF had a greater diversity (richness and abundance), with higher number of observed OTUs than for CA. The predominant phylum in both areas was the Euryachaeota, followed by Thaumarchaeota; sequences belonging to other phyla were not found. However, the NF archaeal community showed more than twice the number of Thaumarchaeota OTUs than CA. Within the phylum Euryarchaeota the predominant classes identified were Halobacteria, Methanomicrobia and Thermoplasmata, in that order; the latter two being significantly more abundant in the CA. In the phylum Thaumarchaeota, South African Gold Mine Gp 1, Terrestrial Group and Soil Crenarcheotic Group were the main classes identified, the latter two being significantly more abundant in NF. We also found more rare archaeal genera in NF than in CA. Examples of such genera are Methanimicrococcus, Methanospirillum, Methanoregula and Methanoculleus. This work showed that there is a decrease in archaeal community diversity in soils of the Amazon native forest when the land is used for agricultural purposes such as for oil palm farming.