Rhizosphere Bacteria Exhibit Narrower Environmental Adaptation in Proso Millet Than in Foxtail Millet and Sorghum in Agricultural Fields

It is of great ecological significance to understand how the assembly processes of soil microbe communities respond to environmental change. However, the assembly processes of the rhizosphere bacterial communities in three minor grain crops (i.e., foxtail millet, proso millet, and sorghum) across agro-ecosystems are rarely investigated. Here, we investigated the environmental thresholds and phylogenetic signals for ecological preferences of rhizosphere bacterial communities of three minor grain crop taxa across complex environmental gradients to reflect their environmental adaptation. Additionally, we reported environmental factors affecting their community assembly processes based on a large-scale soil survey in agricultural fields across northern China using high-throughput sequencing.. The results demonstrated a narrower range of environmental thresholds and weaker phylogenetic signals for the ecological traits of rhizosphere bacteria in proso millet than in foxtail millet and sorghum fields, while proso millet rhizosphere community was the most phylogenetically clustered. The null model analysis indicated that homogeneous selection belonging to deterministic processes governed the sorghum rhizosphere community, whereas dispersal limitation belonging to stochastic processes was the critical assembly process in the foxtail and proso millet. Mean annual temperature was the decisive factor for adjusting the balance between stochasticity and determinism of the foxtail millet, proso millet, and sorghum rhizosphere communities. A higher temperature resulted in stochasticity in the proso millet and sorghum communities. For the foxtail millet community, the deterministic assembly increased with an increase in temperature. These results contribute to the understanding of root-associated bacterial community assembly processes in agro-ecosystems on a large scale.

The nutrient-improvement bacteria selected by Agave lechuguilla T. and their role in the rhizosphere community

Agave lechuguilla has one of the widest distributions among other agaves species in the Chihuahuan desert. Their capacity to grow in poorly developed soils and harsh conditions has been related to its association with plant growth-promoting rhizobacteria. In this work, we explored how soil properties and plant growth stage influence the composition of the rhizobacterial communities, their interactions, and the enzymatic activity and abundance of nitrogen-fixing bacteria and organic phosphorus mineralizing bacteria in two subregions of the Chihuahuan desert. We found that mature plants of lechuguilla stimulated the activity and abundance of nutrient-improvement rhizobacteria, and these soil samples had a higher content of total organic carbon, ammonium (NH4), and nitrite + nitrate (NO2+NO3). Nutrient availability seems to be an essential driver of the bacterial community's structure since the genera with more connections (hubs) were those with known mechanisms related to the availability of nutrients, such as env OPS17 (Bacteroidetes), Gemmatimonadaceae Uncultured, S0134 terrestrial group, BD211 terrestrial group (Gemmatimonadetes), Chthoniobacteracea, and Candidatus Udaeobacter (Verrucomicrobia). This work shows that the late growth stages of lechuguilla recruit beneficial bacteria that favor its establishment and tolerance to harsh conditions of the arid lands.

Does plant diversity determine the diversity of the rhizosphere microbial community?

The rhizosphere community represents an “ecological interface” between plant and soil, providing the plant with a number of advantages. Close connection and mutual influence in this communication allow to talk about the self-adjusting “plant-rhizosphere community” system, which should be be studied in connection. Diversity estimation is one of the ways of describing both bacterial and plant communities. Based on the literature, there are two assumptions of how the diversity of plant communities related to the diversity of bacterial communities: 1) an increase in the species richness of plants leads to an increase in the number of available micro-niches, and increasing of microbial diversity, 2) an increase in the species richness of plants is accompanied by the predominant development of bacteria from highly productive specific taxa and decreasing in the diversity of microorganisms. E xperimental studies show controversial results. We analyzed field sites (rye crop field and two fallow sites), using DNA isolation of both the plant root mass (followed by sequencing of the ITS1 region) and rhizosphere microorganisms (followed by sequencing of the 16s rDNA V4 region). This allowed us to 1) accurately determine the abundance and taxonomic position of plant communities; 2) extract information about both plant and microbial communities from the same sample. There was no correlation between alpha-diversity indices of plants and rhizosphere communities. Alpha-diversity connection should be explored in similar plant communities, such as synusia. We hypothesize, that the significant differences in plant abundances lead to significant changes in exudation profiles, and the loss of diversity connection. T he beta-diversity between rhizosphere communities and plant communities is highly correlated, in particular in terms of the abundance of taxa. This can be explained by a potential correlation (as reported in the literature) or by the presence of statistical artifacts. p { margin-bottom: 0.1in; direction: ltr; color: #000000; line-height: 115%; text-align: left; orphans: 2; widows: 2; background: transparent }p.western { font-family: "Liberation Serif", serif; font-size: 12pt; so-language: en-US }p.cjk { font-family: "Noto Serif CJK SC"; font-size: 12pt; so-language: zh-CN }p.ctl { font-family: "Lohit Devanagari"; font-size: 12pt; so-language: hi-IN }a:link { color: #000080; text-decoration: underline

Does plant diversity determine the diversity of the rhizosphere microbial community?

The rhizosphere community represents an “ecological interface” between plant and soil, providing the plant with a number of advantages. Close connection and mutual influence in this communication allow to talk about the self-adjusting “plant-rhizosphere community” system, which should be be studied in connection. Diversity estimation is one of the ways of describing both bacterial and plant communities. Based on the literature, there are two assumptions of how the diversity of plant communities related to the diversity of bacterial communities: 1) an increase in the species richness of plants leads to an increase in the number of available micro-niches, and increasing of microbial diversity, 2) an increase in the species richness of plants is accompanied by the predominant development of bacteria from highly productive specific taxa and decreasing in the diversity of microorganisms. E xperimental studies show controversial results. We analyzed field sites (rye crop field and two fallow sites), using DNA isolation of both the plant root mass (followed by sequencing of the ITS1 region) and rhizosphere microorganisms (followed by sequencing of the 16s rDNA V4 region). This allowed us to 1) accurately determine the abundance and taxonomic position of plant communities; 2) extract information about both plant and microbial communities from the same sample. There was no correlation between alpha-diversity indices of plants and rhizosphere communities. Alpha-diversity connection should be explored in similar plant communities, such as synusia. We hypothesize, that the significant differences in plant abundances lead to significant changes in exudation profiles, and the loss of diversity connection. T he beta-diversity between rhizosphere communities and plant communities is highly correlated, in particular in terms of the abundance of taxa. This can be explained by a potential correlation (as reported in the literature) or by the presence of statistical artifacts. p { margin-bottom: 0.1in; direction: ltr; color: #000000; line-height: 115%; text-align: left; orphans: 2; widows: 2; background: transparent }p.western { font-family: "Liberation Serif", serif; font-size: 12pt; so-language: en-US }p.cjk { font-family: "Noto Serif CJK SC"; font-size: 12pt; so-language: zh-CN }p.ctl { font-family: "Lohit Devanagari"; font-size: 12pt; so-language: hi-IN }a:link { color: #000080; text-decoration: underline

Soil Microsite Outweighs Cultivar Genotype Contribution to Brassica Rhizobacterial Community Structure

Microorganisms residing on root surfaces play a central role in plant development and performance and may promote growth in agricultural settings. Studies have started to uncover the environmental parameters and host interactions governing their assembly. However, soil microbial communities are extremely diverse and heterogeneous, showing strong variations over short spatial scales. Here, we quantify the relative effect of meter-scale variation in soil bacterial community composition among adjacent field microsites, to better understand how microbial communities vary by host plant genotype as well as soil microsite heterogeneity. We used bacterial 16S rDNA amplicon sequencing to compare rhizosphere communities from four Brassica rapa cultivars grown in three contiguous field plots (blocks) and evaluated the relative contribution of resident soil communities and host genotypes in determining rhizosphere community structure. We characterize concomitant meter-scale variation in bacterial community structure among soils and rhizospheres and show that this block-scale variability surpasses the influence of host genotype in shaping rhizosphere communities. We identified biomarker amplicon sequence variants (ASVs) associated with bulk soil and rhizosphere habitats, each block, and three of four cultivars. Numbers and percent abundances of block-specific biomarkers in rhizosphere communities far surpassed those from bulk soils. These results highlight the importance of fine-scale variation in the pool of colonizing microorganisms during rhizosphere assembly and demonstrate that microsite variation may constitute a confounding effect while testing biotic and abiotic factors governing rhizosphere community structure.

Interactive Effects of Scion and Rootstock Genotypes on the Root Microbiome of Grapevines (Vitis spp. L.)

Diversity and community structure of soil microorganisms are increasingly recognized as important contributors to sustainable agriculture and plant health. In viticulture, grapevine scion cultivars are grafted onto rootstocks to reduce the incidence of the grapevine pest phylloxera. However, it is unknown to what extent this practice influences root-associated microbial communities. A field survey of bacteria in soil surrounding the roots (rhizosphere) of 4 cultivars × 4 rootstock combinations was conducted to determine whether rootstock and cultivar genotypes are important drivers of rhizosphere community diversity and composition. Differences in α-diversity was highly dependent on rootstock–cultivar combinations, while bacterial community structure primarily clustered according to cultivar differences, followed by differences in rootstocks. Twenty-four bacterial indicator genera were significantly more abundant in one or more cultivars, while only thirteen were found to be specifically associated with one or more rootstock genotypes, but there was little overlap between cultivar and rootstock indicator genera. Bacterial diversity in grafted grapevines was affected by both cultivar and rootstock identity, but this effect was dependent on which diversity measure was being examined (i.e., α- or β-diversity) and specific rootstock–cultivar combinations. These findings could have functional implications, for instance, if specific combinations varied in their ability to attract beneficial microbial taxa which can control pathogens and/or assist plant performance.

Do Phaseolus vulgaris Development Stages Influence the Total Rhizospheric Bacterial and the Phytate Utilising Community?

Background: The occupation of soil by plants is known to induce changes in the soil chemical and physical properties by shoot decomposition and root growth and secretion. Methods: In this study we investigate the degree to which the total and the phytate mineralising rhizospheric communities bacteria are affected by the growth of six Recombinant Inbred Lines (RILs) of common bean (Phaseolus vulgaris). The six RILs tested were contrasted on adaptation to P (phosphorus)-deficiency from sensitive to tolerant. Rhizosphere samples were taken three times during the plant developmental stage and the changes in the density and the phytase activity of those communities relative to the P content were studied. Bacterial community was followed by culturing and measuring total community DNA of soil to allow a cultivation- independent analysis, by amplification of the 16S rRNA gene using real time PCR. Result: Our results showed that successional moves in the rhizosphere bacterial density as plant mature confirmed that plants select their own rhizosphere community. Moves of the bacterial community in the rhizosphere were more pronounced in mature common bean and phytase enzymatic activity confirmed the ability of this plant to mobilise a functional bacterial community when the bean needs high quantities of phosphorus. This study demonstrates that common bean selects a microbial community and its density change in response to plant growth.

Sorghum Root Flavonoid Chemistry, Cultivar, and Frost Stress Effects on Rhizosphere Bacteria and Fungi

Biotic stresses, including fungal infections, result in increased production of flavonoid compounds, including 3-deoxyanthocyanidins (3-DAs), in the leaf tissues of Sorghum bicolor. Our objectives were to determine whether sorghum genotypic variation influenced root flavonoid and 3-DA concentrations and rhizosphere microbial communities and to identify how these relationships were affected by abiotic stress. We evaluated root chemicals and rhizosphere microbiomes of five near-isogenic lines of sorghum before and after a late-season frost. Roots were analyzed for total flavonoids, total phenolics, 3-DA concentrations, and antioxidant activity. Amplicon sequencing of 16S ribosomal RNA genes and internal transcribed spacer regions was performed on rhizosphere soils. Concentrations of luteolinidin (a 3-DA) and total flavonoids differed between several lines before frost; however, these relationships changed after frost. Luteolinidin increased in three lines after frost, whereas total flavonoids decreased in all the lines after frost. Lines that differed in luteolinidin and total flavonoid concentrations before frost were different from those after frost. Rhizosphere community compositions also differed before and after frost but only fungal community compositions differed among sorghum lines. Bacterial community compositions were highly correlated with total flavonoid and luteolinidin concentrations. Furthermore, a greater number of bacterial taxa were correlated with total flavonoids and luteolinidin compared with fungal taxa. Collectively, this study provides evidence that plant genotypic variation influences root flavonoids and rhizosphere community composition and that these relationships are affected by frost. Plant–microbe interactions and secondary metabolite production may be important components to include for selective breeding of sorghum for frost stress tolerance.

Predominance of soil vs root effect in rhizosphere microbiota reassembly

ABSTRACT Rhizosphere community assembly is simultaneously affected by both plants and bulk soils and is vital for plant health. However, it is still unclear how and to what extent disease-suppressive rhizosphere microbiota can be constructed from bulk soil, and the underlying agents involved in the process that render the rhizosphere suppressive against pathogenic microbes remain elusive. In this study, the evolutionary processes of the rhizosphere microbiome were explored based on transplanting plants previously growing in distinct disease-incidence soils to one disease-suppressive soil. Our results showed that distinct rhizoplane bacterial communities were assembled on account of the original bulk soil communities with different disease incidences. Furthermore, the bacterial communities in the transplanted rhizosphere were noticeably influenced by the second disease-suppressive microbial pool, rather than that of original formed rhizoplane microbiota and homogenous nontransplanted rhizosphere microbiome, contributing to a significant decrease in the pathogen population. In addition, Spearman's correlations between relative abundances of bacterial taxa and the abundance of Ralstonia solanacearum indicated Anoxybacillus, Flavobacterium, Permianibacter and Pseudomonas were predicted to be associated with disease-suppressive function formation. Altogether, our results showed that bulk soil played an important role in the process of assembling and reassembling the rhizosphere microbiome of plants.