Microbiome analysis of rhizospheres of plant and winter-initiated ratoon crops of sugarcane grown in sub-tropical India: utility to improve ratoon crop productivity

Abstract

One plant and one to two ratoon crops are the predominant patterns of sugarcane cultivation in sub-tropical part of India. Despite high agricultural inputs, yield of ratoon crop gets dwindled in the subsequent years. The microbial community, particularly bacteria and fungi, in the rhizosphere and their interaction with the root system, in general influences plant productivity. For the present study, an early maturing sugarcane variety (CoLk 94184), was used to establish plant and winter-initiated ratoon crops in 2016-2018. Soils pertaining to both plant and ratoon rhizospheres were subjected to biochemical analysis, microbial DNA isolation and high-throughput sequencing of 16S rRNA genes to assess the microbial diversity and associated characteristics impacting cane yield. Although alpha diversity of bacterial community was observed high in the soils of both plant and ratoon crops, the species richness/diversity was more in plant crop. Bacterial community structure in the rhizosphere of plant crop was predominantly consisted of phyla Actinobacteria (35.68%), Gemmatimonadetes (29.26%), Chloroflexi (26.73%) and Proteobacteria (16.68%), while ratoon rhizosphere revealed dominance of Acidobacteria (20.77%) and Bacteroidetes (10.7%). Though studies revealed the presence of rich bacterial community in the rhizospheres of both plant and ratoon crops of sugarcane, dominance of Acidobacteria and meager proportion of Actinobacteria and Proteobacteria in ratoon crop possibly limited its productivity. Along with high total phenols (7.27 mg/g dry wt), ratoon crop depicted less active root system as revealed by scanning electron microscopy. Dominance of thermophilic bacterial phyla Chloroflexi and Gemmatimonadetes which was observed in sugarcane rhizosphere supports better crop growth in drought. However, management of soil microbial community is required to improve the ratoon crop productivity.

Keywords: 16S rRNA sequencing; Metagenome; Plant crop; Ratoon crop; Rhizosphere soil; Sugarcane.

Fig. 1

Operational taxonomic units (OTUs) of microbial communities found in rhizosphere soil of plant and ratoon crops of sugarcane. a Venn diagram indicating number of specific and shared OTUs between plant and ratoon crops b Taxonomical classification of some major OTUs observed in rhizospheres of plant and ratoon crops of sugarcane

Fig. 2

Heat map of bacterial diversity classification depicting microbial abundance at phylum level in rhizosphere soil samples of plant and ratoon crops of sugarcane

Fig. 3

Class level distribution of bacterial communities in rhizosphere soil samples of plant and ratoon crops of sugarcane

Fig. 4

Measuring species richness and diversity through Alpha diversity using a Chao1, b Shannon for richness and c Simpson index representing evenness at species level in rhizosphere soil samples of plant and ratoon crops of sugarcane

Fig. 5

Heat map representing the core microbiome at Order level in rhizosphere soil samples of plant and ratoon crops of sugarcane. X-axis represented the detection threshold (Relative abundance) range and Y-axis showed level of prevalence. Prevalence levels are depicted by colored bar

Fig. 6

Scanning electron microscopic analysis (magnification levels from left to right, × 50, × 250, × 500) depicting magnitude of root hairs on the root surface of plant (top) and ratoon (bottom) crops of sugarcane Bars indicate 1, 300 and 100 µm from left to right