Microbial Diversity of Rhizosphere Soils of Sugarcane Fields under Waterlogged Conditions

This study compared the soil microbial community in both plant and ratoon crop under waterlogging and control conditions and their relationship with plant attributes. It also looked at the impact of waterlogging stress on the physicochemical characteristics of the rhizosphere soil in a sugarcane growing plots. Waterlogging is one of the major abiotic stresses adversely affects crop growth, development, and yield contributing attributes. The microbial community, such as fungi and bacteria in the rhizosphere, has special importance to crop productivity. Sugarcane cultivars were grown for two cycles, plant and ratoon crops in the sub-tropical region of India at Kharika block research farm of ICAR-Indian Institute of Sugarcane Research, Lucknow under control and waterlogged conditions. For microbial diversity, microbial DNA was isolated, and high throughput gene sequencing of 16SRNA was performed using four soil samples of different sugarcane fields viz., waterlogged ratoon crop (S1), waterlogged plant crop (S2), control plant crop (S3) and ratoon crop (S4), along with soil composition. A heat map indicating the abundance of each category in every sample was generated at different classification levels, with each square representing the degree of abundance. Clustering was performed using the ward clustering algorithm, and the measurement tool used was Euclidean distance. Results obtained indicated lower soil pH, organic matter, and available nitrogen, but higher potassium, phosphorus, and EC values in waterlogged soil as compared to the control plot. Plant attributes of sugarcane genotypes determined indicated higher cane height and root weight, while leaf parameters decreased due to waterlogging. Raw reads of microbial populations of rhizosphere soils of control and waterlogged plots with plant and ratoon crops were sequenced based on 16S rRNA (V3-V4 regions) genes and deposited in NCBI metagenome (Bethesda, MD, USA) under SRA module. A total of 153066 OTUs were identified, with 91% classified under Kingdom Bacteria in waterlogged ratoon crop (S1) and 92% in waterlogged plant crop (S2), 94% in control plant crop (S3) and 94% in ratoon crop (S4) and 6 – 9 % from all samples were assigned to unknown species. Taxonomic analysis revealed that the bacterial community structure of the sugarcane rhizosphere soils predominantly consisted of the phyla Proteobacteria (24-61%), Actinobacteria (2-27%), Gemmatimonadetes (2-5%), Chloroflexi (7-16%), Cyanobacteria (2-3%), and Acidobacteria (7-8%), Planctomyces (4-11%), Bacteriodetes (1-10%) and Firmicutes (3-58%) in control and waterlogged plots. In the waterlogged rhizosphere, Proteobacteria (24-28%), Actinobacteria (22-27%), Chloroflexi (7-16%), Acidobacteria (7-8%), Planctomyces (4-11%), and Gemmatimonadetes (2-5%) were the dominant phyla. The alpha diversity of the bacteria community significantly increased due to waterlogging. A significant positive relation was observed among microbial communities viz., Acidobacteria, Cyanobacteria, Chloroflexi, Planctomycetes, Proteobacteria, Actinobacteria, and Gemmatimonadetes with plant height, root weight and cane length. Waterlogged ratoon (S1) showed a higher abundance of genus Planctomyces, Bacillus, Gemmata, Streptomyces, Rhodoplanes, Balneimonas, Nitrospira, S2 with Anaeromyxobacter, Kaistobacter, Anaerolinea, S3 having Paenibacillus, Acinetobacter, Brevibacillu and S4 with Chloronema genus. This study reveals that the sugarcane rhizosphere has a rich pool of bacterial communities even under waterlogging stress, and which may help to improve waterlogging tolerance in sugarcane. Ratoon crop field under waterlogged and control conditions showed a higher Simpson index with greater evenness in species diversity as compared to the plant crop field. These data underpin future improvement of the waterlogging tolerance of sugarcane via the soil microbial community.