Tapping into the maize root microbiome to identify bacteria that promote growth under chilling conditions

Background When maize (Zea mays L.) is grown in the Northern hemisphere, its development is heavily arrested by chilling temperatures, especially at the juvenile phase. As some endophytes are beneficial for plants under stress conditions, we analyzed the impact of chilling temperatures on the root microbiome and examined whether microbiome-based analysis might help to identify bacterial strains that could promote growth under these temperatures. Results We investigated how the maize root microbiome composition changed by means of 16S rRNA gene amplicon sequencing when maize was grown at chilling temperatures in comparison to ambient temperatures by repeatedly cultivating maize in field soil. We identified 12 abundant and enriched bacterial families that colonize maize roots, consisting of bacteria recruited from the soil, whereas seed-derived endophytes were lowly represented. Chilling temperatures modified the root microbiome composition only slightly, but significantly. An enrichment of several chilling-responsive families was detected, of which the Comamonadaceae and the Pseudomonadaceae were the most abundant in the root endosphere of maize grown under chilling conditions, whereas only three were strongly depleted, among which the Streptomycetaceae. Additionally, a collection of bacterial strains isolated from maize roots was established and a selection was screened for growth-promoting effects on juvenile maize grown under chilling temperatures. Two promising strains that promoted maize growth under chilling conditions were identified that belonged to the root endophytic bacterial families, from which the relative abundance remained unchanged by variations in the growth temperature. Conclusions Our analyses indicate that chilling temperatures affect the bacterial community composition within the maize root endosphere. We further identified two bacterial strains that boost maize growth under chilling conditions. Their identity revealed that analyzing the chilling-responsive families did not help for their identification. As both strains belong to root endosphere enriched families, visualizing and comparing the bacterial diversity in these communities might still help to identify new PGPR strains. Additionally, a strain does not necessarely need to belong to a high abundant family in the root endosphere to provoke a growth-promoting effect in chilling conditions

Daring to be differential : metabarcoding analysis of soil and plant-related microbial communities using amplicon sequence variants and operational taxonomical units

Background: Microorganisms are not only indispensable to ecosystem functioning, they are also keystones for emerging technologies. In the last 15 years, the number of studies on environmental microbial communities has increased exponentially due to advances in sequencing technologies, but the large amount of data generated remains difficult to analyze and interpret. Recently, metabarcoding analysis has shifted from clustering reads using Operational Taxonomical Units (OTUs) to Amplicon Sequence Variants (ASVs). Differences between these methods can seriously affect the biological interpretation of metabarcoding data, especially in ecosystems with high microbial diversity, as the methods are benchmarked based on low diversity datasets. Results: In this work we have thoroughly examined the differences in community diversity, structure, and complexity between the OTU and ASV methods. We have examined culture-based mock and simulated datasets as well as soil- and plant-associated bacterial and fungal environmental communities. Four key findings were revealed. First, analysis of microbial datasets at family level guaranteed both consistency and adequate coverage when using either method. Second, the performance of both methods used are related to community diversity and sample sequencing depth. Third, differences in the method used affected sample diversity and number of detected differentially abundant families upon treatment; this may lead researchers to draw different biological conclusions. Fourth, the observed differences can mostly be attributed to low abundant (relative abundance < 0.1%) families, thus extra care is recommended when studying rare species using metabarcoding. The ASV method used outperformed the adopted OTU method concerning community diversity, especially for fungus-related sequences, but only when the sequencing depth was sufficient to capture the community complexity. Conclusions: Investigation of metabarcoding data should be done with care. Correct biological interpretation depends on several factors, including in-depth sequencing of the samples, choice of the most appropriate filtering strategy for the specific research goal, and use of family level for data clustering

Plant growth promotion driven by a novel Caulobacter strain

Soil microbial communities hold great potential for sustainable and ecologically compatible agriculture. Although numerous plant-beneficial bacterial strains from a wide range of taxonomic groups have been reported, very little evidence is available on the plant-beneficial role of bacteria from the genus Caulobacter. Here, the mode of action of a Caulobacter strain, designated RHG1, which had originally been identified through a microbial screen for plant growth-promoting (PGP) bacteria in maize (Zea mays) is investigated in Arabidopsis thaliana. RHG1 colonized both roots and shoots of Arabidopsis, promoted lateral root formation in the root, and increased leaf number and leaf size in the shoot. The genome of RHG1 was sequenced and was utilized to look for PGP factors. Our data revealed that the bacterial production of nitric oxide, auxins, cytokinins, or 1-aminocyclopropane-1-carboxylate deaminase as PGP factors could be excluded. However, the analysis of brassinosteroid mutants suggests that an unknown PGP mechanism is involved that impinges directly or indirectly on the pathway of this growth hormone

Streptomyces as a plant's best friend?

Here we discuss the advantages of the majority of this versatile and diverse group of microorganisms for plant health and growth as demonstrated by their contribution to disease-suppressive soils, their antifungal and antibacterial activities, their ability to produce volatile compounds and their capacity to enhance plant biomass. Although much is still to be discovered about the colonization strategies and molecular interactions between plant roots and these microorganisms, they are destined to become important players in the field of plant growth-promoting rhizobacteria for agriculture.Streptomyces strains have a great potential for plant growth promotion or protection, but fundamental insights into the action mechanisms are urgently required.Streptomyces strains have a great potential for plant growth promotion or protection, but fundamental insights into the action mechanisms are urgently required

Stenotrophomonas sp. SRS1 promotes growth of Arabidopsis and tomato plants under salt stress conditions

Aims Plant Growth-Promoting Rhizobacteria (PGPR) support plant growth by alleviating plant stresses, among which those triggered by saline soils. We isolated Stenotrophomonas sp. SRS1 from salt-resistant Carex distans (distant sedge) roots to understand how this growth promotion was enabled and whether an active contribution of the bacteria and/or plant was required. Methods Various growth assays were used to analyze the effect of bacterial inoculation on Arabidopsis thaliana and Solanum lycopersicum (cherry tomato MicroTom) growth. Furthermore, droplet microfluidics, bacterial genome mining, and bacterial and plant gene expression analysis combined with plant mutant analysis were used for in-depth analysis. Results SRS1 application enhanced plant growth in both saline and nonsaline environments. The fresh weight of SRS1-inoculated plants was higher than that of noninoculated plants, whereas the fresh weight ratio between SRS1-inoculated and noninoculated plants differed whether the plants were grown on agar plates, white sand or in soil. We demonstrated that the strain grew well in high salt-containing media and that, besides plant-growth-promotion-related genes, the bacterium contained various active stress genes. Interestingly, inoculation with the strain increased the induction of plant genes related to abscisic acid and auxin signaling pathways under saline conditions. Conclusions SRS1 inoculation promoted the growth of Arabidopsis and MicroTom tomato under saline and nonsaline conditions, also when the plants were grown in white sand and potting soil. Overall, genetic traits related to stress alleviation, derived from both the bacteria and the plants, play a crucial role in the impact of this novel PGPR strain on plant performance

Digging into the lettuce cold-specific root microbiome in search of chilling stress tolerance-conferring plant growth-promoting bacteria

Growth of lettuce (Lactuca sativa) is severely hampered by low temperatures, even when cultivated under greenhouse conditions. Root-associated bacteria might promote plant growth under stressful conditions. Therefore, we analyzed the effect of low temperatures on the lettuce root-associated microbiome to evaluate whether microbiome-based selection aids in identiying bacteria that stimulate plant growth in the cold. 16S ribosomal RNA gene amplicon sequencing was used to examine the compositional differences in the lettuce root-associated microbiome when grown under low- and control-temperature conditions. Chilling temperatures significantly altered the lettuce root endosphere composition, whereas their effects were less severe in the rhizosphere and absent in the bulk soil. Several cold-enriched families were found in both the rhizosphere and the root endosphere, nine of which were Oxalobacteraceae, Pseudomonadaceae, Flavobacteriaceae, Microscillaceae, Sphingobacteriaceae, Comamonadaceae, Devosiaceae, Methylophilaceae and env.OPS_17. Concurrently, a collection of lettuce root-colonizing bacteria was established and, based on correlation with these families, representative isolates were screened. None of the lettuce root isolates showed growth-promoting effects but three growth-promoting Flavobacterium strains from an available collection of grass root-colonizing bacteria were identified. Amplicon sequence variant (ASV) annotation of the lettuce and grass strains revealed that strains matching cold-enriched or highly abundant ASVs in at least one soil promoted growth in the cold. Overall, our data demonstrate that microbiome analyses, combined with high-throughput bacterial isolations might be a helpful tool to isolate effective cold growth-promoting strains

Tapping into the maize root microbiome to identify bacteria that promote growth under chilling conditions

BACKGROUND: When maize (Zea mays L.) is grown in the Northern hemisphere, its development is heavily arrested by chilling temperatures, especially at the juvenile phase. As some endophytes are beneficial for plants under stress conditions, we analyzed the impact of chilling temperatures on the root microbiome and examined whether microbiome-based analysis might help to identify bacterial strains that could promote growth under these temperatures. RESULTS: We investigated how the maize root microbiome composition changed by means of 16S rRNA gene amplicon sequencing when maize was grown at chilling temperatures in comparison to ambient temperatures by repeatedly cultivating maize in field soil. We identified 12 abundant and enriched bacterial families that colonize maize roots, consisting of bacteria recruited from the soil, whereas seed-derived endophytes were lowly represented. Chilling temperatures modified the root microbiome composition only slightly, but significantly. An enrichment of several chilling-responsive families was detected, of which the Comamonadaceae and the Pseudomonadaceae were the most abundant in the root endosphere of maize grown under chilling conditions, whereas only three were strongly depleted, among which the Streptomycetaceae. Additionally, a collection of bacterial strains isolated from maize roots was established and a selection was screened for growth-promoting effects on juvenile maize grown under chilling temperatures. Two promising strains that promoted maize growth under chilling conditions were identified that belonged to the root endophytic bacterial families, from which the relative abundance remained unchanged by variations in the growth temperature. CONCLUSIONS: Our analyses indicate that chilling temperatures affect the bacterial community composition within the maize root endosphere. We further identified two bacterial strains that boost maize growth under chilling conditions. Their identity revealed that analyzing the chilling-responsive families did not help for their identification. As both strains belong to root endosphere enriched families, visualizing and comparing the bacterial diversity in these communities might still help to identify new PGPR strains. Additionally, a strain does not necessarely need to belong to a high abundant family in the root endosphere to provoke a growth-promoting effect in chilling conditions. Video abstract.status: publishe

Interactions between soil compositions and the wheat root microbiome under drought stress : from an in silico to in planta perspective

As wheat (Triticum aestivum) is an important staple food across the world, preservation of stable yields and increased productivity are major objectives in breeding programs. Drought is a global concern because its adverse impact is expected to be amplified in the future due to the current climate change. Here, we analyzed the effects of edaphic, environmental, and host factors on the wheat root microbiomes collected in soils from six regions in Belgium. Amplicon sequencing analysis of unplanted soil and wheat root endosphere samples indicated that the microbial community variations can be significantly explained by soil pH, microbial biomass, wheat genotype, and soil sodium and iron levels. Under drought stress, the biodiversity in the soil decreased significantly, but increased in the root endosphere community, where specific soil parameters seemingly determine the enrichment of bacterial groups. Indeed, we identified a cluster of drought-enriched bacteria that significantly correlated with soils compositions. Interestingly, integration of a functional analysis further revealed a strong correlation between the same cluster of bacteria and β-glucosidase and osmoprotectant proteins, two functions known to be involved in coping with drought stress. By means of this in silico analysis, we identified amplicon sequence variants (ASVs) that could potentially protect the plant from drought stress and validated them in planta. Yet, ASVs based on 16S rRNA sequencing data did not completely distinguish individual isolates because of their intrinsic short sequences. Our findings support the efforts to maintain stable crop yields under drought conditions through implementation of root microbiome analyses

Flemish soils contain rhizobia partners for Northwestern Europe‐adapted soybean cultivars

In Europe, soybean (Glycine max) used for food and feed has to be imported, causing negative socioeconomic and environmental impacts. To increase the local production, breeding generated varieties that grow in colder climates, but the yield using the commercial inoculants is not satisfactory in Belgium because of variable nodulation efficiencies. To look for indigenous nodulating strains possibly adapted to the local environment, we initiated a nodulation trap by growing early-maturing cultivars under natural and greenhouse conditions in 107 garden soils in Flanders. Nodules occurred in 18 and 21 soils in the garden and greenhouse experiments respectively. By combining 16S rRNA PCR on single isolates with HiSeq 16S metabarcoding on nodules, we found a large bacterial richness and diversity from different soils. Furthermore, using Oxford Nanopore Technologies sequencing of DNA from one nodule, we retrieved the entire genome of a Bradyrhizobium species, not previously isolated, but profusely present in that nodule. These data highlight the need of combining diverse identification techniques to capture the true nodule rhizobial community. Eight selected rhizobial isolates were subdivided by whole-genome analysis in three genera containing six genetically distinct species that, except for two, aligned with known type strains and were all able to nodulate soybean in the laboratory