High-Throughput Sequencing-Based Analysis of Rhizosphere and Diazotrophic Bacterial Diversity Among Wild Progenitor and Closely Related Species of Sugarcane (Saccharum spp. Inter-Specific Hybrids)

Abstract

Considering the significant role of genetic background in plant-microbe interactions and that most crop rhizospheric microbial research was focused on cultivars, understanding the diversity of root-associated microbiomes in wild progenitors and closely related crossable species may help to breed better cultivars. This study is aimed to fill a critical knowledge gap on rhizosphere and diazotroph bacterial diversity in the wild progenitors of sugarcane, the essential sugar and the second largest bioenergy crop globally. Using a high-throughput sequencing (HTS) platform, we studied the rhizosphere and diazotroph bacterial community of Saccharum officinarum L. cv. Badila (BRS), Saccharum barberi (S. barberi) Jesw. cv Pansahi (PRS), Saccharum robustum [S. robustum; (RRS), Saccharum spontaneum (S. spontaneum); SRS], and Saccharum sinense (S. sinense) Roxb. cv Uba (URS) by sequencing their 16S rRNA and nifH genes. HTS results revealed that a total of 6,202 bacteria-specific operational taxonomic units (OTUs) were identified, that were distributed as 107 bacterial groups. Out of that, 31 rhizobacterial families are commonly spread in all five species. With respect to nifH gene, S. barberi and S. spontaneum recorded the highest and lowest number of OTUs, respectively. These results were validated by quantitative PCR analysis of both genes. A total of 1,099 OTUs were identified for diazotrophs with a core microbiome of 9 families distributed among all the sugarcane species. The core microbiomes were spread across 20 genera. The increased microbial diversity in the rhizosphere was mainly due to soil physiochemical properties. Most of the genera of rhizobacteria and diazotrophs showed a positive correlation, and few genera negatively correlated with the soil properties. The results showed that sizeable rhizospheric diversity exists across progenitors and close relatives. Still, incidentally, the rhizosphere microbial abundance of progenitors of modern sugarcane was at the lower end of the spectrum, indicating the prospect of Saccharum species introgression breeding may further improve nutrient use and disease and stress tolerance of commercial sugarcane. The considerable variation for rhizosphere microbiome seen in Saccharum species also provides a knowledge base and an experimental system for studying the evolution of rhizobacteria-host plant association during crop domestication.

Microbiome differences in sugarcane and metabolically engineered oilcane accessions and their implications for bioenergy production

“…Previous studies have characterized the microbiomes of non-modified sugarcane [24,31,[34][35][36][37][38]. Consistent with previous observations in non-modified sugarcane [24,31], plant compartments had the greatest effect on the variation of microbiomes in oilcane (Additional file 6: Table S1).…”

Physiological and molecular insights into the resilience of biological nitrogen fixation to applied nitrogen in Saccharum spontaneum, wild progenitor of sugarcane

“…This result has considerable practical significance in that the native N fixing property of S. spontaneum could be introgressed into commercial sugarcane breeding population, similar to disease resistance, abiotic stress tolerance, vigour, ratooning, stalk population traits previously introduced (Lakshmanan et al, 2022). There are very few reports on BNF in S. spontaneum (Dong et al, 2018;Malviya et al, 2022), and extensive screening of geographically diverse accessions for BNF has not been reported. The data presented here forms the first evidence that high-BNF S. spontaneum with desirable agronomic attributes could be a potentially valuable genetic source for sugarcane BNF improvement through breeding.…”

“…The reasons for the conflicting results are unclear, but strong host genotype specificity and soil environmental sensitivity of diazotrophs are now well-recognised (Imran et al, 2021). Considering the remarkable variation for host genotypic compatibility of diazotrophs (Malviya et al, 2022) and the inherent narrow genetic base of current commercial sugarcane varieties in general (Hemaprabha et al, 2022), we studied the abundance and diversity of rhizosphere diazotrophs in sugarcane ancestral species and found large rhizospheric microbial diversity in the analysed species (Malviya et al, 2022). Of the five wild Saccharum species analysed, Saccharum spontaneum is the most crossable, highly genetically diverse and ubiquitous in distribution.…”

Microbiome Analysis of Sugarcane Juices and Biofilms from Louisiana Raw Sugar Factories

“…Lactobacillales , which are the most abundant bacteria in isolation-based studies ( 11 – 14 ), were similarly the most abundant in the 16S V4 data set in this study. However, Lactobacillales do not appear as an abundant taxon in amplicon-sequencing results of the sugarcane rhizosphere ( 19 – 21 ), which suggests that they may become enriched during the delay between harvesting and milling. Our finding that Weissella or Lactobacillus were more abundant than Leuconostoc in certain samples, such as MJ-Fact1-Oct and Biofilm1-Fact3-Dec support recent commentary that these bacteria may play a larger role in EPS production than previously thought ( 12 ).…”

“…Amplicon-based sequencing has wide-ranging applications in the food industry, from plant-microbiome interactions, animal health, food safety, and production of fermented foods ( 18 ). While a few studies have applied amplicon sequencing to sugarcanes in fields ( 19 – 21 ), bioethanol refineries ( 22 ), and more recently filter mud and bagasse ( 23 ), this study profiled the microbes present in crusher juices, mixed juices, and biofilm samples from raw sugar factories, to focus on the microbes which are most closely involved in postharvest deterioration of sugarcane juice. Additionally, the NCBI RefSeq database ( 24 ) was leveraged to estimate the likelihood for the identified bacterial taxa to contribute to dextran and levan EPS production.…”