Distinctive Bacteria Consortium of Rhizosphere and Surface Soil from Semi-Organic Potato Cultivation in Magelang, Indonesia

Abstract

Potato cultivation in the middle land is an alternative solution to avoid pathogens. Although it reduces potato quantity and requires more chemical fertilizers to increase production that potentially damages the environment. Therefore, this study aims to characterize contaminations and indigenous microbes from semi-organic potato cultivation centers in Central Java. Soil samples from the semi-organic potato cultivation center of Kledung, Central, were analyzed for metal contamination using the atomic absorption spectrophotometry method and metagenomic soil bacterial diversity profiles. Specifically targeted genes of distinct regions 16SV3-V5. OTUs were identified using Uparse v7.0.1001, while Beta diversity analysis used UniFrac. All these indices in our samples were calculated with QIIME (Version 1.7.0) and displayed with R software (Version 2.15.3). The results showed that semi-organic cultivations had been polluted with Pb > Cd > Cr > As, and carbamate residue was detected in the rhizosphere and surface soil. Manure and compost application alongside NPK fertilizer increases N input, decreasing surface soil bacteria. The surface soil (with a depth of ≤ 5 cm) has a lower index of species richness, diversity, and relative abundance than the rhizosphere layer (depth > 5 cm). Firmicutes, Proteobacteria, and Actinobacterium dominate soil-level bacteria. In comparison, the rhizosphere soil has a higher bacteria diversity dominated by N-tethering rhizobia from the phylum Proteobacteria. The potato root attracts rhizobacteria consortium that support plant growth. A further study should be conducted to describe how the bacterial consortium formed, rhizobia migration from surface to rhizosphere soil, and its interaction with the potato plants. HIGHLIGHTS Semi-organic potato cultivation in Kledung, Temanggung, Indonesia, is contaminated with heavy metals, especially Pb, which is the highest pollutant, and the carbamate residue Excessive nitrogen (N) input from organic and chemical fertilizers reduces the diversity of soil surface bacteria Then manure application as organic fertilizer introduces pathogenic bacteria such as Eschericia-Shigella, Faecalibaculum, Fusobacteria, Bacilli, and Enterococcus The rhizosphere soil is dominated by N-fixating rhizobia from Proteobacteria, including Pseudoxanthomonas Mexicana, Lysobacteria , Devosia riboflavina, Aminobacter sp., Bosea sp., Allorhizobium, Neorhizobium, Pararhizobium, and Rhizobium GRAPHICAL ABSTRACT