Microbiome Characterization of Rhizobacteria under different agricultural practices of Thung Kula Rong Hai, and their abilities in promoting growth, salt tolerance and aromatic compound of KDML 105 aromatic rice

Abstract

Khao Dawk Mali 105 (KDML105) is a premium aromatic rice variety and is widely grown in salt-affected inland areas of Thung Kula Rong Hai (TKR), northeast Thailand. Due to its unique aroma, KDML105 from the TKR area is registered as one of the geographical indications (GI) products. However, excessive salinity and low nutrient status have been identified as significant constraints for KDML105 aromatic rice production in the TKR region. Furthermore, recently, climate change and high agrochemical inputs has magnified the severity of salinity stress and negatively affects yield and the level of main aroma compound (2-acetyl-1-pyrroline: 2AP) in KDML105 rice. Therefore, in the first experiment, the influence of organic and conventional rice farming (ORF and CRF, respectively) in TKR farmers’ paddy fields on soil properties and their relationship with 2AP in KDML105 rice grains was investigated. The results indicated that, the ORF system had a strong positive effect on major soil quality indicators and the 2AP content in the rice grains. The soil organic matter (SOM) was approximately twice as much in the ORF than in the CRF system, thus leading to much higher total nitrogen (TN), humic acid (HA) and microbial populations in the ORF system. The higher SOM in the ORF system not only enhanced the soil quality indicators but also contributed to approximately 3.5 times higher 2AP than in the CRF system. Principle component analysis indicated a close correlation among SOM, TN, HA, and microbial population under the ORF system; these variables exhibited strong correlations with the 2AP contents in KDML105 rice grains. Agricultural practice might also influence microbial diversity and abundance, therefore, in the second experiment, metagenomic analysis of 16S rRNA gene of soil rhizosphere bacteria were performed using 16S rRNA gene next generation sequences. The results indicated that the phylum Proteobacteria was the most relative abundance both in the ORF and CRF accounting for around 30%, and similar proportion of other phyla was also observed. However, the phylum Planctomycetes values of the ORF system were significantly higher than those obtained from the CRF system. The species richness indices showed that the ORF system had the highest species diversity values. The ORF system provided significantly higher species richness than the CRF system (P < 0.0001). Surprisingly, the Pearson correlation matrix revealed that the species richness not only had a significant positive correlation with major soil properties (SOM, r = 0.82***; HA, r = 0.59**; and TN, r = 0.76***), but also with the 2AP concentration in rice grains (r = 0.93**).