Root Microbiota Research Articles

Taxonomic and functional assembly cues enrich the endophytic tobacco microbiota across epiphytic compartments.

The plant microbiome plays a critical role in plant growth, development, and health, with endophytes being recognized as essential members due to their close interactions with host plants. However, knowledge gaps remain in understanding the mechanisms driving the colonization and establishment of endophytic communities. To address this issue, we investigated the microbiota of tobacco roots and leaves, including both epiphytic and endophytic microorganisms. We found that Actinobacteria and Alphaproteobacteria were significantly enriched in the root endosphere. Additionally, we identified higher abundances of functional traits involved in antibiotic synthesis, plant cell wall degradation, iron metabolism, secretion systems, and nicotine degradation enzymes in the endosphere. We further studied metagenome-assembled genomes from the rhizosphere and root endosphere, revealing a greater diversity of secondary metabolites in bacteria within the root endosphere. Together, this study provides insights into the taxonomic and functional assembly cues that may contribute to shaping the endophytic plant microbiota.IMPORTANCEThe presence of diverse microorganisms within plant tissues under natural conditions is a well-established fact. However, due to the plant immune system's barrier and the unique microhabitat of the plant interior, it remains unclear what specific characteristics bacteria require to successfully colonize and thrive in the plant endosphere. Recognizing the significance of unraveling these functional features, our study focused on investigating the enriched traits in the endophytic microbiota compared to the epiphytes. Through our research, we have successfully identified the taxonomic and functional assembly cues that drive the enrichment of the endophytic microbiota across the epiphytic compartments. These findings shed new light on the intricate mechanisms of endophyte colonization, thereby deepening our understanding of plant-microbe interactions and paving the way for further advancements in microbiome manipulation.

Analysis of the endophytic microbiota of roots and culms of two commercial sugarcane cultivars inoculated with a synthetic microbial community

The adoption of bioinputs in agriculture has aroused great interest in recent years and, in this scenario, the inoculation of crops with synthetic microbial communities (SynComs) has shown to be promising. In sugarcane crop, inoculation with nitrogen-fixing bacteria (NFB) in consortium with arbuscular mycorrhizal fungi (AMF) has shown positive results on plant development and nutrition. However, considering that the microbiota plays a fundamental role in the growth and health of the host plant, especially the endophytes, which are closely associated, few studies have explored the effects of SynCom inoculation on the endophytic microbiota of sugarcane. This study aimed to evaluate the impact of SynCom inoculation on the structure of the endophytic microbiota of sugarcane. The results of the analyses revealed that the microbiota diversity remained unchanged due to the inoculation treatment, while differences in microbial communities were found between the two evaluated commercial cultivars, RB867515 and RB92579, and between the two plant organs, roots and culms, under field conditions at the end of the first crop growth cycle (~360 days). Furthermore, microbes specifically detected in roots or culms present potential valuable applications in sugarcane cultivation in the future. Altogether, our data support that the inoculated microorganisms exerted their beneficial effects during the initial stages of plant development, which opens up space for new research with SynComs in these primordial stages of cane cropping.

Attribution of dispersal limitation can better explain the assembly patterns of plant microbiota.

Disentangling community assembly processes is crucial for fully understanding the function of microbiota in agricultural ecosystems. However, numerous plant microbiome surveys have gradually revealed that stochastic processes dominate the assembly of the endophytic root microbiota in conflict with strong host filtering effects, which is an important issue. Resolving such conflicts or inconsistencies will not only help accurately predict the composition and structure of the root endophytic microbiota and its driving mechanisms, but also provide important guidance on the correlation between the relative importance of deterministic and stochastic processes in the assembly of the root endophytic microbiota, and crop productivity and nutritional quality. Here, we propose that the inappropriate division of dispersal limitation may be the main reason for such inconsistency, which can be resolved after the proportion of dispersal limitation is incorporated into the deterministic processes. The rationality of this adjustment under the framework of the formation of a holobiont between the microbiome and the plant host is herein explained, and a potential theoretical framework for dynamic assembly patterns of endophytic microbiota along the soil-plant continuum is proposed. Considering that the assembly of root endophytic microbiota is complicated, we suggest caution and level-by-level verification from deterministic processes to neutral components to stochastic processes when deciding on the attribution of dispersal limitation in the future to promote the expansion and application of microbiome engineering in sustainable agricultural development based on community assembly patterns.

The mycoparasite Pythium oligandrum induces legume pathogen resistance and shapes rhizosphere microbiota without impacting mutualistic interactions.

Pythium oligandrum is a soil-borne oomycete associated with rhizosphere and root tissues. Its ability to enhance plant growth, stimulate plant immunity and parasitize fungal and oomycete preys has led to the development of agricultural biocontrol products. Meanwhile, the effect of P. oligandrum on mutualistic interactions and more generally on root microbial communities has not been investigated. Here, we developed a biological system comprising P. oligandrum interacting with two legume plants, Medicago truncatula and Pisum sativum. P. oligandrum activity was investigated at the transcriptomics level through an RNAseq approach, metabolomics and finally metagenomics to investigate the impact of P. oligandrum on root microbiota. We found that P. oligandrum promotes plant growth in these two species and protects them against infection by the oomycete Aphanomyces euteiches, a devastating legume root pathogen. In addition, P. oligandrum up-regulated more than 1000 genes in M. truncatula roots including genes involved in plant defense and notably in the biosynthesis of antimicrobial compounds and validated the enhanced production of M. truncatula phytoalexins, medicarpin and formononetin. Despite this activation of plant immunity, we found that root colonization by P. oligandrum did not impaired symbiotic interactions, promoting the formation of large and multilobed symbiotic nodules with Ensifer meliloti and did not negatively affect the formation of arbuscular mycorrhizal symbiosis. Finally, metagenomic analyses showed the oomycete modifies the composition of fungal and bacterial communities. Together, our results provide novel insights regarding the involvement of P. oligandrum in the functioning of plant root microbiota.

Root microbiota confers rice resistance to aluminium toxicity and phosphorus deficiency in acidic soils.

Aluminium (Al) toxicity impedes crop growth in acidic soils and is considered the second largest abiotic stress after drought for crops worldwide. Despite remarkable progress in understanding Al resistance in plants, it is still unknown whether and how the soil microbiota confers Al resistance to crops. Here we found that a synthetic community composed of highly Al-resistant bacterial strains isolated from the rice rhizosphere increased rice yield by 26.36% in acidic fields. The synthetic community harvested rhizodeposited carbon for successful proliferation and mitigated soil acidification and Al toxicity through extracellular protonation. The functional coordination between plants and microbes offers a promising way to increase the usage of legacy phosphorus in topsoil. These findings highlight the potential of microbial tools for advancing sustainable agriculture in acidic soils.

ER body-resident myrosinases and tryptophan specialized metabolism modulate root microbiota assembly.

Endoplasmic reticulum (ER) bodies are ER-derived structures that contain a large amount of PYK10 myrosinase, which hydrolyzes tryptophan (Trp)-derived indole glucosinolates (IGs). Given the well-described role of IGs in root-microbe interactions, we hypothesized that ERbodies in roots are important for interaction with soil-borne microbes at the root-soil interface. We used mutants impaired in ER bodies (nai1), ER body-resident myrosinases (pyk10bglu21), IG biosynthesis (myb34/51/122), and Trp specialized metabolism (cyp79b2b3) to profile their root microbiota community in natural soil, evaluate the impact of axenically collected root exudates on soil or synthetic microbial communities, and test their response to fungal endophytes in a mono-association setup. Tested mutants exhibited altered bacterial and fungal communities in rhizoplane and endosphere, respectively. Natural soils and bacterial synthetic communities treated with mutant root exudates exhibited distinctive microbial profiles from those treated with wild-type (WT) exudates. Most tested endophytes severely restricted the growth of cyp79b2b3, a part of which also impaired the growth of pyk10bglu21. Our results suggest that root ER bodies and their resident myrosinases modulate the profile of root-secreted metabolites and thereby influence root-microbiota interactions.

A virus induces alterations in root morphology while exerting minimal effects on the rhizosphere and endosphere microorganisms in rice.

The highly destructive southern rice black-streaked dwarf virus (SRBSDV) causes significant losses in rice production. To understand its impact on rice root, we studied fibrous root development and root microbiota variation (rhizosphere and endosphere) after SRBSDV infection. SRBSDV infection reduced the number and length of fibrous roots in rice. Interestingly, the rhizosphere had higher bacterial diversity and abundance at the initial (0 days) and 30-day postinfection stages, while 30-day-old roots showed increased diversity and abundance. However, there were no significant differences in microbiota diversity between infected and noninfected rice plants. The major rhizosphere microbiota included Proteobacteria, Bacteroidota, Acidobacteriota, and Planctomycetota, comprising about 80% of the community. The endosphere was dominated by Proteobacteria and Cyanobacteria, constituting over 90%, with Bacteroidota as the next most prominent group. Further, we identified differentially expressed genes related to plant-pathogen interactions, plant hormone signal, and ABC transporters, potentially affecting root morphology. Notably, specific bacteria (e.g. Inquilinus and Actinoplanes) showed correlations with these pathways. In conclusion, SRBSDV primarily influences root growth through host metabolism, rather than exerting direct effects on the root microbiota. These insights into the interactions among the pathogen, rice plant, and associated microbiota could have implications for managing SRBSDV's detrimental effects on rice production.

Collaborative impact of bacterial exometabolites governing root microbiota formation

The majority of the root microbiota formation derives from soil-dwelling microorganisms. The limited extent of thorough investigation leads to a dearth of knowledge concerning the intricate mechanisms of microbe-microbe interaction implicated in the establishment of root microbiota. Therefore, the taxonomic signatures in bacterial inhibition profiles were determined by in vitro testing of 39,204 binary interbacterial interactions. However, findings from genetic and metabolomic studies elucidated that co-functioning of the antimicrobial 2,4-d iacetylphloroglucinol (DAPG) and the iron chelator pyoverdine as exometabolites has significantly contributed to the potent inhibitory activities of the highly antagonistic Pseudomonas brassicacearum R401. Microbiota restoration with a core of Arabidopsis thaliana root commensals showed that these exometabolites possess a root niche-specific function in establishing root competence and inducing anticipated changes in root surroundings. Both biosynthetic operons are abundant in roots in natural habitats, indicating that these exometabolites co-functioning is an adaptive feature that helps Pseudomonad dominate the root microbiota.

Biochar contributes to resistance against root rot disease by stimulating soil polyphenol oxidase

Biochar has been considered an effective approach as soil amendment for decreasing incidences of disease and regulating microbial populations in continuous-cropping soil. Although researches have extensively focused on changes of soil microbes and unbalance of nutrition in continuous-cropping soil, the relationship between soil properties and pathogens by biochar application remains poorly understood. In this study, we applied ITS ribosomal RNA gene profiling to analyze tobacco root microbiota of biochar and non-biochar treatment in a 3-year continuous-cropping tobacco field, comparing firstly planting tobacco as control. We found that biochar application decreased the relative abundance of the soil fungal pathogens (Ceratobasidium and Monosporascus), which are the prime pathogens of tobacco root rot in continuous-cropping soil. Using RDA, co-occurrence and PLS-PM approaches, we provided evidence that there was a negative correlation between fungal genera (especially for Ceratobasidium and Monosporascus) and soil polyphenol oxidase (PPO) activity (R2incidence rate = − 0.930, R2disease index = − 0.905, both p < 0.001). The PPO was up-regulated by different biochar treatment intensities. Together, we demonstrated that biochar in continuous-cropping soil regulated the soil PPO activity to suppress pathogens, and further decrease incidence of root rot. Notably, biochar application forward continuous cropping was more effective for the continuous-cropping soil improvement than the other treatments. The data should help in appropriate timing of biochar application for alleviating continuous-cropping obstacle.Graphical abstract

Root microbiota alters response to root rot in Rhododendron delavayi Franch.

Root microbiota have a significant effect on plant health. However, the role of root microbiota in the resistance of Rhododendron against root rot is not known. In this study, we employed amplicon 16S and ITS sequencing to investigate the bacterial and fungal communities associated with four distinct niches (bulk soil, rhizosphere, rhizoplane, and endosphere) of both healthy and diseased Rhododendron plants in the Baili Rhododendron nature reserve in China. The amplicon data analysis identified 182 bacterial genera and 141 fungal genera that were impacted by root rot across all niches. Specifically, the rhizoplane appeared to exert a selective gating effect, resulting in a reduction in the complexity of bacterial communities, but not fungal communities, in wild Rhododendron delavayi Franch roots. Nevertheless, the stress induced by root rot led to alterations in the root microbiota and compromised the gating function of the rhizoplane, thereby significantly increasing the complexity of the bacterial community within the plant root. In the root tissue following root rot outbreak, the relative abundance of the pathogenic species Pezicula brunnea and Diaporthe helianthi was enriched by as much as 6.13% and 1.71%, respectively. These findings provide novel insights into the contribution of enrichment of root-associated microbiota to wild plant hosts under the disease stress of root rot. The root rot-causing pathogenic fungi may interact with beneficial bacteria and induce plants to send out "cry for help" signals, which may encourage the specific assembly of microbiota. In the Rhododendron delavayi Franch root microbiota, we found 23 potentially beneficial microbes. Notably, certain beneficial bacteria, such as Sporolactobacillus and Stenotrophomonas, were found to accumulate in the rhizoplane and endosphere under root rot disease stress. Overall, our results lend support to our hypothesis that Rhododendron recruits protective microbes as a strategy to suppress root rot outbreaks. Future endeavors in isolating beneficial microbes capable of mitigating root rot have the potential to enhance plant resilience against root diseases.

Cadmium alters the rhizosphere bacterial community structure in blueberry roots and increases the content of lipids in the soil

Vaccinium spp. Is a small berry that grows in acidic environments. Relying on the exchange of nutrients and defense against adverse environments through the root system microbiota, bacteria play an important role. As a widely distributed pollutant, the mobility and bioavailability of Cd are enhanced in acidic environments, which can affect the community composition of blueberry root microbiota and alter the composition of soil metabolites. Therefore, studying the changes in the bacterial microbiota of blueberry roots and soil metabolomics under Cd stress can provide a foundation for the development of blueberry microbial fertilizers and the management of soil Cd pollution. In this study, 16 S rDNA sequencing and untargeted metabolomics were used to analyze the rhizosphere, root surface and root endophytic bacterial diversity as well as soil metabolites of Vaccinium spp. Under cadmium (Cd) contamination. The results indicate that the addition of cadmium (Cd) significantly reduces the α-diversity of the rhizosphere, rhizoplane, and endophytic bacteria in blueberries and has a significant impact on the dominant bacterial species. With the application of Cd, the relative abundance of the dominant taxa such as Diplorickettsiaceae_unclassified, Legionella, Streptomyces and Rhodanobacter decreased significantly at the genus level and turned into general or rare bacterial taxa. Meanwhile, the relative abundance of LWQ8_unclassified, WPS-2_unclassified, Acetobacteraceae_unclassified, Acidibacter, Acidiphilium and Granulicella with extreme tolerances increased significantly and gradually became the dominant taxa. Of the 364 metabolites in the soil, 31 varied significantly as the structure of the rhizosphere bacterial community changed. Among them, the lipids and lipid-like molecules clade showed the greatest variation in species and a significant increase in content. It was also associated with changes in bacterial taxa such as Tundrisphaera, Spirochaetaceae_unclassified, Dyella and CHAB_XI_27_unclassified.

Research Progress in Crop Root Biology and Nitrogen Uptake and Use, with Emphasis on Cereal Crops

The biological characteristics of crop roots are closely related to the efficient utilization of nitrogen and have become a research hotspot in agricultural cultivation and breeding in recent years. The root system and root microbiota play a crucial role in both the basic and the plastic growth and development of plants in response to external environmental changes. Nitrogen is an indispensable nutrient element for crop growth, and the efficient utilization of nitrogen is the key to achieving the high yield and quality of crops and establishing environmentally friendly agricultural production. The nitrogen absorbed and utilized by rice mainly enters the aboveground part of the plant through the root system from within the soil. This process is explored from the perspective of root biology (root morphology, physiological and biochemical characteristics, root growth and development process and regulation, rhizosphere microorganisms, and their symbiotic systems), which is in line with the directions of “less investment, increased production, environmental protection, and sustainable development” in China. Based on the research status in this field at present, this article explored the interaction mechanism between crop root biology and nitrogen absorption and utilization, and looks forward to the future research directions for root biology. This study provides a theoretical basis for reducing nitrogen fertilizer application, optimizing nitrogen-efficient cultivation management techniques, and selecting nitrogen-efficient varieties.

Integrated microbiology and metabolomics analysis reveal patterns and mechanisms of improvement the Achnatherum inebrians adaptability to N addition by endophytic fungus Epichloë gansuensis

Frequent anthropogenic activities have led to a rapid increase in atmospheric reactive N inputs in terrestrial ecosystems, negatively affecting plant and microbial communities. Endophytic fungi are important symbiotic microbes that are beneficial for improving host environmental adaptability. However, it remains poorly understood how endophytic fungi affect bacterial communities and related root metabolites contribute to improved plant adaptability to elevated N inputs. Here, we used 16 S rRNA gene sequencing and GC-MS platform to investigate the effects of Epichloë gansuensis infection on Achnatherum inebrians response to N addition. The results showed E. gansuensis infected (E+) A. inebrians exhibited more biomass and less phosphorus (P) limitation than E. gansuensis uninfected (E-) A. inebrians under N enrichment conditions. Analysis of the bacterial community indicated that rhizosphere and endophyte bacterial community compositions and structures presented significant differences between E+ and E- plants. N addition enhanced the proportion of Proteobacteria, Firmicutes, Nitrospirae, and putative plant growth promoting rhizobacteria (PGPR) (e.g. Bacillus and Lysobacter) in the E+ plant, facilitating the uptake of rhizosphere nutrients. Network analysis showed that E. gansuensis-infection enhanced the complexity and intraspecific cooperation of bacterial community under N addition conditions. Moreover, metabolomics analysis indicated that the compositions of root exudates of E- plant were more susceptible to N addition than those of E+ plant. Correlation analysis showed that root microbiota were also closely related to the accumulation of root metabolites. Our findings provide a significant understanding of the symbiotic relationship between host and endophytic fungi in the N enrichment environment.

Schizotrophic Sclerotinia sclerotiorum-Mediated Root and Rhizosphere Microbiome Alterations Activate Growth and Disease Resistance in Wheat.

Sclerotinia sclerotiorum, a widespread pathogen of dicotyledons, can grow endophytically in wheat, providing protection against Fusarium head blight and stripe rust and enhancing wheat yield. In this study, we found that wheat seed treatment with strain DT-8, infected with S. sclerotiorum hypovirulence-associated DNA virus 1 (SsHADV-1) and used as a "plant vaccine" for brassica protection, could significantly increase the diversity of the fungal and bacterial community in rhizosphere soil, while the diversity of the fungal community was obviously decreased in the wheat root. Interestingly, the relative abundance of potential plant growth-promoting rhizobacteria (PGPR) and biocontrol agents increased significantly in the DT-8-treated wheat rhizosphere soil. These data might be responsible for wheat growth promotion and disease resistance. These results may provide novel insights for understanding the interaction between the schizotrophic microorganism and the microbiota of plant roots and rhizosphere, screening and utilizing beneficial microorganisms, and further reducing chemical pesticide utilization and increasing crop productivity. IMPORTANCE Fungal pathogens are seriously threatening food security and natural ecosystems; efficient and environmentally friendly control methods are essential to increase world crop production. S. sclerotiorum, a widespread pathogen of dicotyledons, can grow endophytically in wheat, providing protection against Fusarium head blight and stripe rust and enhancing wheat yield. In this study, we discovered that S. sclerotiorum treatment increased the diversity of the soil fungal and bacterial community in rhizosphere soil, while the diversity of the fungal community was obviously decreased in the wheat root. More importantly, the relative abundance of potential PGPR and bio-control agents increased significantly in the S. sclerotiorum-treated wheat rhizosphere soil. The importance of this work is that schizotrophic S. sclerotiorum promotes wheat growth and enhances resistance against fungal diseases via changes in the structure of the root and rhizosphere microbiome.

Crop rotation significantly influences the composition of soil, rhizosphere, and root microbiota in canola (Brassica napus L.)

BackgroundCrop rotation is an agronomic practice that is known to enhance productivity and yield, and decrease pest and disease pressure. Economic and other factors have increased the frequency of certain crops, including canola, with unknown effects on the below ground microbial communities that impact plant health and performance. This study investigated the effect of 12 years of crop rotation including canola-wheat; canola-pea-barley; and unrotated canola across three geographic sites in Western Canada with diverse soil types and environmental conditions. To provide data on mature, established crop rotation strategies, root exudate profiles, soil nutrient fluxes, and bacterial and fungal microbial community profiles were determined at the flowering stage in the final two (canola) years of the 12-year rotations.ResultsAfter 12 years of rotation, nutrient fluxes were affected in the soil in an inconsistent manner, with K, NO3, Mg, Ca, P, and Fe fluxes variably impacted by rotation depending on the year and site of sampling. As expected, rotation positively influenced yield and oil content, and decreased disease pressure from Leptosphaeria and Alternaria. In two of the three sites, root exudate profiles were significantly influenced by crop rotation. Bacterial soil, root, and rhizosphere communities were less impacted by crop rotation than the fungal communities. Fungal sequences that were associated with specific rotation strategies were identified in the bulk soil, and included known fungal pathogens in the canola-only strategy. Two closely related fungal sequences identified as Olpidium brassicae were extremely abundant at all sites in both years. One of these sequences was observed uniquely at a single site and was significantly associated with monocropped canola; moreover, its abundance correlated negatively with yield in both years.ConclusionsLong-term canola monoculture affected root exudate profiles and soil nutrient fluxes differently in the three geographic locations. Bacterial communities were less impacted by rotation compared to the fungal communities, which consistently exhibited changes in composition in all ecological niches at all sites, in both years. Fungal sequences identified as O. brassicae were highly abundant at all sites, one of which was strongly associated with canola monoculture. Soil management decisions should include consideration of the effects on the microbial ecosystems associated with the plants in order to inform best management practices.

Effect of rhizosphere microorganisms on aflatoxin contamination of maize

The continued large consumption of maize makes it one of the most important food crops worldwide. However, the yield and quality of maize are greatly affected by global warming, and mycotoxin pollution keeps increasing. The effect of environmental factors, especially rhizosphere microorganisms, on mycotoxin pollution of maize is not completely clear, so we carried out relevant studies. In this study, we found that microbial communities inhabiting the maize rhizosphere, which consists of soil particles firmly attached to roots, as well as the soil, have a significant influence on the aflatoxin pollution of maize. The ecoregion and soil properties also had considerable effects on the microbial structure and diversity. The bacterial communities from the rhizosphere soil were profiled using a high-throughput next-generation sequencing method. The ecoregion and soil properties had considerable effects on the microbial structure and diversity. A comparison of the aflatoxin high concentration group with the low concentration group found that bacteria of the phylum Gemmatimonadetes and order Burkholderiales were significantly more abundant in the high concentration samples. Furthermore, these bacteria were significantly correlated with aflatoxin contamination and could aggravate its contamination of maize. The results of these analyses showed that seeding location could cause significant shifts in the root microbiota of maize, and the bacteria enriched in high aflatoxin contamination area soils should attract special concern. These findings will support strategies for improving maize yield and aflatoxin contamination control.

Genome Sequence of the Streptomyces Strain AgN23 Revealed Expansion and Acquisition of Gene Repertoires Potentially Involved in Biocontrol Activity and Rhizosphere Colonization

Streptomycetes are gram-positive actinobacteria largely represented in the plant root microbiota. The genetic determinants involved in the adaption of Streptomyces in the rhizosphere environment are mostly unknown but can rely on the ability to release phytohormones, degrade plant cell-wall polysaccharides, and produce specialized metabolites notably involved in microbial competition. Here, we sequenced the genome of the rhizospheric and plant defense-stimulating strain Streptomyces sp. AgN23. We found that it belongs to the soil- and plant root-dwelling S. violaceusniger clade. The genome annotation of AgN23 revealed the genetic potential of the bacterium to degrade the plant cell wall with a large repertoire of carbohydrate degrading enzymes, to synthesize auxin, a major regulator of plant development, and to produce antimicrobials (rustmicin, mediomycin, niphimycin, nigericin) and plant bioactive compounds (nigericin, echosides, elaiophylin) through a set of biosynthetic gene clusters. We also found that these genomic features are well conserved among members of the S. violaceusniger clade. In addition, AgN23 displays original events of biosynthetic gene cluster acquisitions and losses, which may account for its interaction with plants. Taken together, our work supports the hypothesis that evolution of a large set of conserved hydrolytic enzymes directed against plant polymers and specialized metabolite repertoires can mediate the adaptation of S. violaceusniger strains to the rhizospheric ecological niches. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Genetic determinants of switchgrass-root-associated microbiota in field sites spanning its natural range

A fundamental goal in plant microbiome research is to determine the relative impacts of host and environmental effects on root microbiota composition, particularly how host genotype impacts bacterial community composition. Most studies characterizing the effect of plant genotype on root microbiota undersample host genetic diversity and grow plants outside of their native ranges, making the associations between host and microbes difficult to interpret. Here, we characterized the root microbiota of a large diversity panel of switchgrass, a North American native C4 bioenergy crop, in three field locations spanning its native range. Our data, composed of 1,961 samples, suggest that field location is the primary determinant of microbiome composition; however, substantial heritable variation is widespread across bacterial taxa, especially those in the Sphingomonadaceae family. Despite diverse compositions, relatively few highly prevalent taxa make up the majority of the switchgrass root microbiota, a large fraction of which is shared across sites. Local genotypes preferentially recruit/filter for local microbes, supporting the idea of affinity between local plants and their microbiota. Using genome-wide association, we identified loci impacting the abundance of >400 microbial strains and found an enrichment of genes involved in immune responses, signaling pathways, and secondary metabolism. We found loci associated with over half of the core microbiota (i.e., microbes in >80% of samples), regardless of field location. Finally, we show a genetic relationship between a basal plant immunity pathway and relative abundances of root microbiota. This study brings us closer to harnessing and manipulating beneficial microbial associations via host genetics.

The Genetic Architecture of Adaptation to Leaf and Root Bacterial Microbiota inArabidopsis thaliana

Understanding the role of the host genome in modulating microbiota variation is a need to shed light on the holobiont theory and overcome the current limits on the description of host-microbiota interactions at the genomic and molecular levels. However, the host genetic architecture structuring microbiota is only partly described in plants. In addition, most association genetic studies on microbiota are often carried out outside the native habitats where the host evolves and the identification of signatures of local adaptation on the candidate genes has been overlooked. To fill these gaps and dissect the genetic architecture driving adaptive plant-microbiota interactions, we adopted a genome-environment association (GEA) analysis on 141 whole-genome sequenced natural populations of Arabidopsis thaliana characterized in situ for their leaf and root bacterial communities in fall and spring, and a large range of nonmicrobial ecological factors (i.e., climate, soil, and plant communities). A much higher fraction of among-population microbiota variance was explained by the host genetics than by nonmicrobial ecological factors. Importantly, the relative importance of host genetics and nonmicrobial ecological factors in explaining the presence of particular operational taxonomic units (OTUs) differs between bacterial families and genera. In addition, the polygenic architecture of adaptation to bacterial communities was highly flexible between plant compartments and seasons. Relatedly, signatures of local adaptation were stronger on quantitative trait loci (QTLs) of the root microbiota in spring. Finally, plant immunity appears as a major source of adaptive genetic variation structuring bacterial assemblages in A. thaliana.

Bacterial diversity and function shift of strawberry root in different cultivation substrates

With the increasing use of soilless cultivation, artificial substrates are becoming more common, which inevitably leads to changes in the crop root environment. However, the impact of artificial substrate application on crop root microflora remains incompletely investigated. This study collected strawberry root samples from two artificial substrates and one greenhouse soil and used. 16S rRNA amplicon sequencing method to analyze the changes in the bacterial communities surrounding strawberry roots in different cultivation substrates. The corresponding root microbiota was predicted by PICRUSt. The results demonstrated that the α and β diversity of bacterial microbiota in samples from artificial substrates and greenhouse soil were significantly different. Almost all bacteria detected in root samples from greenhouse soils were also found in root samples from artificial substrates. The abundance of the genera Cellvibrio and Streptomyces in root samples from greenhouse soil were significantly higher than those of artificial substrate 1 and substrate 2. Bacteria found in substrate 1 including Acidocella, Vibrio and other 8 genera were significantly enriched compared to greenhouse soil; Bacteria identified in substrate 2 including Asticcacaulis, Bordetella, and other 13 genera were significantly higher than those in greenhouse soil. According to PICRUSt prediction, there were 34 pathways in substrate 1 and 47 pathways in substrate 2, including pathways related to cellular processes, environmental information processing, genetic information processing, human diseases, metabolism, and organismal systems in root microbiota from different substrates might significantly shifted. Among these pathways, those related to plant growth promotion, such as flavonoids and flavanols synthesis, were significantly up-regulated and pathways regarding antimicrobial compound synthesis including clavulanic acid, stilbenoid, and macrolides were significantly down-regulated in root microbiota from artificial substrates. This work provides basic information on root bacterial diversity of strawberries grown in different substrates and help to explore beneficial root microorganisms for sustainable strawberry production.