Effect of water management on microbial diversity and composition in an Italian rice field system

Abstract

Traditional rice cultivation consumes up to 2500 L of water per kg yield and new strategies such as the ‘Alternate Wetting and Drying’ (AWD) might be promising water-saving alternatives. However, they might have large impacts on the soil microbiology. In this study, we compared the bacterial and archaeal communities in experimental field plots, cultivated under continuously flooding (CF) and AWD management, by high-throughput sequencing of the 16S rRNA gene. We analysed alpha and beta diversity in bulk soil and on plant roots, in plots cultivated with two different rice cultivars. The strongest difference was found between soil and root communities. Beside others, the anaerobic methanotroph Methanoperedens was abundant in soil, however, we detected a considerable number of ANME-2a-2b on plant roots. Furthermore, root communities were significantly affected by the water management: Differential abundance analysis revealed the enrichment of aerobic and potentially plant-growth-promoting bacteria under AWD treatment, such as Sphingomonadaceae and Rhizobiaceae (both Alphaproteobacteria), and Bacteroidetes families. Microorganisms with an overall anaerobic lifestyle, such as various Delta- and Epsilonproteobacteria, and Firmicutes were depleted. Our study indicates that the bulk soil communities seem overall well adapted and more resistant to changes in the water treatment, whereas the root microbiota seems more vulnerable.

The diversity of rhizospheric bacterial communities associated with Trichoderma-treated rice fields

“…1). Generally, the mentioned major bacterial phyla had also been reported as the common taxa in the soil microbiome of rice fields of previous studies that involved different places and crop managements (Huang et al 2020;Hester et al 2022). Compared to the previous studies, most of the differences in bacterial communities occurred in the taxa with low abundance.…”

“…Proteobacteria play important roles in the degradation of soil inorganic materials, nitrogen fixation, degradation of organic matters and sulphur reduction (Mhete et al 2020). Acidobacteria and Actinobacteria were found to be involved in nutrient cycle and plant growth promotion (Hester et al 2022). Chloroflexi was reported able to ferment carbohydrates and degrade complex organic compounds (Speirs et al 2019).…”

“…This indicated that the majority of the soil microbiome variation between the control and treatment plots was attributed to presence of distinctive taxa at low abundance, rather than the taxa abundance. We postulated that these differences might be caused by different water management or cultivation systems practised (Doni et al 2022;Hester et al 2022).…”

“…2020; Hester et al . 2022). Compared to the previous studies, most of the differences in bacterial communities occurred in the taxa with low abundance.…”

“…Acidobacteria and Actinobacteria were found to be involved in nutrient cycle and plant growth promotion (Hester et al . 2022). Chloroflexi was reported able to ferment carbohydrates and degrade complex organic compounds (Speirs et al .…”