Diversity and structure of bacterial communities in saline and non-saline rice fields in Cilacap Regency, Indonesia

Abstract Increased concerns for sustainable agriculture have led to increased use of beneficial rhizobacteria as biofertilizers. Soil bacteria play a significant role in the nutrient cycle of soil, but their presence can be affected by abiotic stress, such as salinity. This study aimed to compare the chemical characteristics of slightly saline and non-saline rice soil and examine the bacterial community structure in both rhizosphere and bulk soil. We utilized 16SrRNA gene sequencing and performed arithmetic means clustering, a type of hierarchical clustering, on the samples collected from the rice fields of Cimrutu and Rawaapu Village in Cilacap Regency, Indonesia. Although the nutrient content was similar in both soils, there was a noticeable difference in their electrical conductivity (EC) despite the two locations being less than 4 km apart. The EC value in the Cimrutu soil suggests that it is non-saline, while the Rawaapu soil exhibits a low salinity level. The study found that Proteobacteria was the most prevalent phylum in saline rhizospheric soil. In contrast, Firmicutes was the most abundant group in saline bulk soil and non-saline rhizospheric and bulk soil. Additionally, Halothiobacillus, Thioalkalispira-Slvurivermis, and Acidothermus genera dominated the saline rhizospheric soil, suggesting that halotolerant microbes play a significant role as plant growth-promoting rhizobacteria in saline soil. The study provides valuable insights into cultured or uncultured bacterial populations and structure in saline and non-saline soil to develop future strategies related to salinity by introducing beneficial microbes.