Physicochemical properties of acid sulphate soil profoundly influence the composition of rhizobacterial community of rice (Oryza sativa L.)

The soils of kari lands of Kuttanad, the ‘Rice bowl’ of Kerala, India are characterized as acid sulphate as they comprise of pyrite deposits. Productivity in these soils is at stake due to several constraints like high acidity and salinity, metal toxicity, nutrient unavailability, redox fluctuations, besides seasonal flooding. Sustainable management of acid sulphate soil is a critical priority to improve the rice output from these areas. Such soils would harbor unique innate microbial communities with definite abilities which could be exploited further for their sustainable amelioration. Development of inoculant technology with soil and crop specific beneficial microbial agents is expected to boost the production potential of kari soils. However, the soil parameters would impose a great influence on the rhizobacterial community development in these geologically distinct soils. We studied the rhizobacterial communities (at the family level), associated with rice grown in five acid sulphate (Purakkad, Vaikom, Ambalappuzha, Thakazhi and Kallara) as well as one non-acid sulphate (Muhamma) soil series of geographically unique Kuttanad region. We also examined the effects of soil physicochemical attributes on shaping the rhizosphere bacterial community assemblage. The soil physicochemical attributes were analyzed using standard procedures and correlations existing amongst them were also determined. A metagenomic approach was adopted to study the rhizobacterial communities (family level) and were correlated with soil parameters using canonical correspondence analysis (CCA). Compared to other acid sulphate regions, Thakazhi and Kallara soils indicated higher electrical conductivity, available nitrogen, potassium, organic carbon, aluminium as well as iron and lowest pH and available phosphorus. Intense significant relationships were exhibited amongst the acid sulphate properties and soil nutrient contents. The taxa summary after the Illumina MiSeq sequencing revealed the abundant rhizobacterial families in the soil samples as Anaerolineaceae, Ktedonobacteriaceae, Acidothermaceae, Acidimicrobiaceae, Clostridiaceae, Nocardioidaceae, Xanthobacteraceae, Methanobacteriaceae, Sphingomonadaceae and Peptostreptococcaceae. Acidothermaceae (14%) and Acidimicrobiaceae (12%) were found abundant exclusively in highly acid sulphate soil samples. Moreover, only a few shared taxa were observed between the soil samples, which denoted the uniqueness of each sample in terms of rhizobacterial communities. The shared taxa between highly acidic sampling areas include members of Acidothermaceae, Ktedonobacteraceae, Acidimicrobiaceae, Micrococcaceae, Stellaceae and Anaerolineaceae. CCA showed that pH, EC and Al content were the soil properties governing the bacterial assembly in the rhizosphere of actively tillering rice grown in acid sulphate soil followed by P and K. The data generated in the present study are considered to be of use in developing consortia of kari soil specific rice rhizosphere microbial agents which could be used as inoculants in future.