Seed interior microbiome of rice genotypes indigenous to three agroecosystems of Indo-Burma biodiversity hotspot

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.

Soil microbial diversity impacts plant microbiota more than herbivory

“…The fact that seeds were not surface-sterilized might be a caveat of our study, potentially influencing the structure of plant microbiome differently for each species. However, previous studies show that even surface-sterilized seeds show differences in their endophytic microbiome according to the plant genotype (Walitang et al , 2018; Raj et al , 2019; Liu et al , 2020), and our results show a major effect driven by soil microbial community composition, thus we are confident that our results were not biased by not surface-sterilizing seeds.…”

Analogous wheat root rhizosphere microbial successions in field and greenhouse trials in the presence of biocontrol agents Paenibacillus peoriae SP9 and Streptomyces fulvissimus FU14

“…Taking into account the network analyses it was noticed that some of the most connected genera in roots were acquired from the initial seeds, reinforcing the influence of some taxa, for example Streptococcus , Propionibacterium , and Enhydrobacter , for the overall plant microbiome. These endophytic genera, frequently described as protective for the plant, are capable of producing multiple enzymes, resist plant pathogens, and are highly adaptable to the unique seed environment (Vorobjeva, ; Mitter et al , ; Raj et al , ; Xie et al , ), being inherited in wheat seeds. Hence it is suggested some genetic determinants (OTUs) are transmitted vertically and complemented by OTUs obtained from the rhizosphere soils at multiple stages of plant development.…”

Diversity and Taxonomic Distribution of Endophytic Bacterial Community in the Rice Plant and Its Prospective

“…Many researchers isolated Bacillus , Pantoea , Methylobacterium and Sphingomonas genera, they are in high abundance with diverse species from the seed [ 23 , 24 ], root [ 25 , 26 ], and leaf part [ 27 , 28 ] of the rice plant ( Supplementary Materials Data 1, Figure S1 ). Most species of Rhizobium , Azospirillum , Burkholderia, and Herbaspirillum were isolated from root tissues with distinct species [ 29 , 30 , 31 , 32 ], and Xanthomonas , Flavobacterium , and Knoellia genera were isolated from seeds ( Supplementary Materials Data 1, Figure S1 ) [ 33 , 34 ]. These endophytes genera also have been identified after isolation from different plants, such as ben tree, ( Moringa peregrina ) [ 35 ], maize ( Zea mays ) [ 36 , 37 ], Datura metel (local name Devil’s Trumpet) [ 38 ], Kudouzi ( Sophora alopecuroides ) [ 39 ], Scots pine ( Pinus sylvestris ) [ 40 ], strawberry ( Fragaria ananassa ) [ 41 , 42 ], wheat ( Triticum aestivum L.) [ 43 ], rose gum ( Eucalyptus grandis ) [ 44 ], sugarcane ( Saccharum officinarum ) [ 45 ], grapevine ( Vitis vinifera ) [ 46 , 47 ], poplar ( Populus deltoides ) [ 48 ], pepper ( Capsicum annuum ) [ 49 ], Huang-Qin ( Scutellaria baicalensis Georgi) [ 50 ], cotton ( Gossypium hirsutum ) [ 51 ], potato ( Solanum tuberosum ) [ 52 ], cucumber ( Cucumis sativus ) [ 53 ], tobacco ( Nicotiana tabacum L.) [ 54 ], peanut ( Echinopsis chamaecereus “Lutea”) [ 55 ], tulasi ( Ocimum sanctum ) [ 56 ], and pea ( Pisum sativum ...…”