Taxonomic structure and functional association of foxtail millet root microbiome

Abstract

The root microbes play pivotal roles in plant productivity, nutrient uptakes, and disease resistance. The root microbial community structure has been extensively investigated by 16S/18S/ITS amplicons and metagenomic sequencing in crops and model plants. However, the functional associations between root microbes and host plant growth are poorly understood. This work investigates the root bacterial community of foxtail millet (Setaria italica) and its potential effects on host plant productivity. We determined the bacterial composition of 2882 samples from foxtail millet rhizoplane, rhizosphere and corresponding bulk soils from 2 well-separated geographic locations by 16S rRNA gene amplicon sequencing. We identified 16 109 operational taxonomic units (OTUs), and defined 187 OTUs as shared rhizoplane core OTUs. The β-diversity analysis revealed that microhabitat was the major factor shaping foxtail millet root bacterial community, followed by geographic locations. Large-scale association analysis identified the potential beneficial bacteria correlated with plant high productivity. Besides, the functional prediction revealed specific pathways enriched in foxtail millet rhizoplane bacterial community. We systematically described the root bacterial community structure of foxtail millet and found its core rhizoplane bacterial members. Our results demonstrated that host plants enrich specific bacteria and functions in the rhizoplane. The potentially beneficial bacteria may serve as a valuable knowledge foundation for bio-fertilizer development in agriculture.

Composition and function of rhizosphere microbiome of Panax notoginseng with discrepant yields

“…The above taxa were also negatively correlated with P. notoginseng yields in our study. Variovorax was positively correlated with the Solanum tuberosum L. common scab severity level and was supposedly responsible for inducing common scab by stimulating thaxtomin production [43]. Moreover, the high abundances of Variovorax were shown in soils with low P. notoginseng yields in our study.…”

“…Moreover, these functional traits contained bacterial secretion system, ABC transporters, metabolism of xenobiotics by cytochrome P450 and drug metabolism-cytochrome P450 which were negatively associated with P. notoginseng yields. ABC transporters and bacterial secretion system were enriched in soils of potato with high scab severity level [43], and those functional traits mediated the communication between microorganisms and environments or other organisms [53][54][55].Thaxtomins are highly phytotoxic cyclic dipeptides produced by plant-pathogenic members of the genus Streptomyces [56]. Thaxtomins have the basic structure L-4-nitrotryptophyl-L-phenylalanyl [57], and the biosynthetic pathway of Thaxtomin A (ThxA) involves nitric oxide synthase and cytochrome P450 [58][59][60].…”

The Distribution of Tryptophan-Dependent Indole-3-Acetic Acid Synthesis Pathways in Bacteria Unraveled by Large-Scale Genomic Analysis

“…We retrieved 7282 complete and draft genomes of microbes across 5 phyla from NCBI, comprising 114 Acidobacteria, 923 Actinobacteria, 281 Bacteroidetes, 1705 Firmicutes and 4259 Proteobacteria, mostly prevailing in soil and root environment [21]. We surveyed the four major Trp-dependent IAA synthesis pathways in these genomes.…”

“…Foxtail millet seeds were sowed in the field in Yangling (Shanxi, China). For each cultivar, the root samples from three individuals were harvested during the ripening stage and separated into rhizosphere and rhizoplane samples using an established protocol as our previous study [21]. All the samples were placed in 15ml clean microcentrifuge tubes and transferred back to the lab under -20℃.…”

Root-associated microbiomes of Gymnadenia conopsea under the combined effect of plant geographical location and developmental stage

“…To enhance plant growth and health, it is essential to investigate the community structure of microorganisms within the plant and their function. So far, most research work has made on certain model and crop plant species, such as Arabidopsis [6,7], rice [8], maize [9], millet [10], populus [11], and citrus [12], the results revealed clear taxonomically structured microbiome and the factors that determine assembly of the microbiome. This work may enable new plant management approaches and provide novel tools to improve the robustness of crop plant performance.…”