Abstract
BackgroundSeeds of plants are a confirmation of their next generation and come associated with a unique microbia community. Vertical transmission of this microbiota signifies the importance of these organisms for a healthy seedling and thus a healthier next generation for both symbionts. Seed endophytic bacterial community composition is guided by plant genotype and many environmental factors. In north-east India, within a narrow geographical region, several indigenous rice genotypes are cultivated across broad agroecosystems having standing water in fields ranging from 0-2 m during their peak growth stage. Here we tried to trap the effect of rice genotypes and agroecosystems where they are cultivated on the rice seed microbiota. We used culturable and metagenomics approaches to explore the seed endophytic bacterial diversity of seven rice genotypes (8 replicate hills) grown across three agroecosystems.ResultsFrom seven growth media, 16 different species of culturable EB were isolated. A predictive metabolic pathway analysis of the EB showed the presence of many plant growth promoting traits such as siroheme synthesis, nitrate reduction, phosphate acquisition, etc. Vitamin B12 biosynthesis restricted to bacteria and archaea; pathways were also detected in the EB of two landraces. Analysis of 522,134 filtered metagenomic sequencing reads obtained from seed samples (n=56) gave 4061 OTUs. Alpha diversity indices showed significant differences in observed OTU richness (P≤0.05) across genotypes. Significant differences were also found between the individual hills of a rice genotype. PCoA analysis exhibited three separate clusters and revealed the clusters separated based on genotype, while agroecosystem showed a minimal effect on the variation of seed microbiota (adonis, R2=0.07, P=0.024). Interestingly, animal gut resident bacteria such as Bifidobacterium, Faecalibacterium, Lactobacillus, etc. were found in abundance as members of the seed microbiota.ConclusionOverall, our study demonstrates, indigenous rice genotypes of north-east India have a unique blend of endophytic bacteria in their mature seeds. While there are notable variations among plants of the same genotype, we found similarities among genotypes cultivated in completely different environmental conditions. The beta diversity variations across the seven rice genotypes were significantly shaped by their genotype rather than their agroecosystems.
Highlights
Seeds of plants are a confirmation of their generation and come associated with a unique microbia community
The population of endophytic bacteria (EB) from hill landraces Idaw, Fazai, and Taiklwangh ranged from 3.00-7.16 cfu/g dry seeds (DS) in different media, except on pikovskaya’s agar (PKA) no colony was detected from Idaw
Upon identifying the EB based on their 16S rRNA gene sequences, we found that the genus Pantoea is consistent in the three agroecosystems as well as the six rice genotypes beyond the borders of geography, genotype and growth conditions
Summary
Seeds of plants are a confirmation of their generation and come associated with a unique microbia community. Hardoim et al [7] reported that in the absence of soil or any other environmental microflora, endophytes in seeds shape the plant microflora This seed endophytic community is comprised of many bacterial species, and they display multiple functionalities [7,8,9]. Several studies have reported the population and community composition of endophytic bacteria (EB) in rice plants of different genotypes adapted to distinct environments. Among such studies, Hardoim et al [11] found that roots or shoots of nine different rice cultivars grown under similar substrate conditions had a specific fraction of bacterial communities common to all
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