Root-associated Bacterial Communities Research Articles

Assembly of root-associated bacterial community and soil health in cadmium-contaminated soil affected by nano/bulk-biochar compost associations

Biochar (BC) has been proven effective in promoting the production of safety food in cadmium (Cd)-polluted soil and the impact can be further enhanced through interaction with compost (CM). However, there existed unclear impacts of biochar with varying particle sizes in conjunction with compost on microbiome composition, rhizosphere functions, and soil health. Hence, in this study, two bulk-biochar derived from wood chips and pig manure were fabricated into nano-biochar using a ball-milling method. Subsequently, in a field experiment, the root-associated bacterial community and microbial functions of lettuce were evaluated in respond to Cd-contaminated soil remediated with nano/bulk-BCCM. The results showed that compared to bulk-BCCM, nano-BCCM significantly reduced the Cd concentration in the edible part of lettuce and the available Cd in the soil. Both nano-BCCM and bulk-BCCM strongly influenced the composition of bacterial communities in the four root-associated niches, and enhanced rhizosphere functions involved in nitrogen, phosphorus, and carbon cycling, as well as the relative abundance and biodiversity of keystone modules in rhizosphere soil. Furthermore, soil quality index analysis indicated that nano-BCCM exhibited greater potential than bulk-BCCM in maintaining soil health. The data revealed that nano-BCCM could regulate the Cd concentration in lettuce shoot by promoting microbial biodiversity of keystone modules in soil-root continuum and rhizosphere bacterial functions. These findings suggest that nano-biochar compost associations can be a superior strategy for enhancing microbial functions, maintaining soil health, and ensuring crop production safety in the Cd-contaminated soil compared to the mix of bulk-biochar and compost.

Preceding crop rotation systems shape the selection process of wheat root-associated bacterial communities

Wheat-maize (WM) and wheat-soybean (WS) double-cropping rotation systems are predominant in the North China Plain, with implications for national agricultural output and sustainability. As rotation systems exert legacy effects on soil health and crop productivity, the role of crop rotation in shaping the root-associated microbiome of the succeeding crops has emerged as a pivotal aspect of crop management research. Here, the effects of the preceding two cycles of WM and WS rotations on the recruitment and filtering of wheat root-associated bacterial communities across wheat developmental stages were investigated. Our results revealed that bacterial community diversity and composition were primarily influenced by compartment and developmental stage, while the preceding rotation systems had a slight but significant effect on wheat root-associated bacterial communities. The co-occurrence networks under WM were more complex in the wheat rhizosphere and rhizoplane, with the OTUs related to cellulolysis showing greater connectivity. The co-occurrence networks under WS were simple but stable in the rhizosphere and complex in the rhizoplane and endosphere, with the OTUs related to ureolysis and nitrogen fixation showing greater connectivity. While both stochastic and deterministic processes contributed to the assembly of wheat root-associated bacterial communities, the contributions of deterministic processes under WS were 19.4–38.5% higher than those under the WM rotation across the root-associated compartments, indicating the substantial impact of a soybean legacy effect on wheat root selection of microbes. Plant growth-promoting rhizobacteria with the potential to fix nitrogen, produce indole-3-acetic acid, and inhibit diseases such as Betaproteobacteriales, Azospirillales and Dyella sp., were identified within the OTUs that were consistently enriched across all the wheat root-associated compartments and developmental stages, which were also important predictors of wheat yield. This study elucidates the role of crop rotation in modulating the dynamics of crop root-associated bacterial communities, and underscores the potential of targeted microbiome manipulation for optimizing wheat production and enhancing soil health.

CeO2 nanoparticle dose and exposure modulate soybean development and plant-mediated responses in root-associated bacterial communities

Agricultural soils are increasingly undergoing inadvertent and purposeful exposures to engineered CeO2 nanoparticles (NPs), which can impact crops and root-associated microbial communities. However, interactions between NP concentration and exposure duration on plant-mediated responses of root-associated bacterial communities are not well understood. Soybeans seedlings were grown in soil with uncoated NPs added at concentrations of 0, 1 or 100 mg kg−1. Total soil exposure durations were either 190 days, starting 106 days before planting or 84 days with NP amendments coinciding with planting. We assessed plant development, bacterial diversity, differential abundance and inferred functional changes across rhizosphere, rhizoplane, and root tissue compartments. Plant non-monotonic dose responses were mirrored in bacterial communities. Most notably, effects were magnified in the rhizoplane under low-dose, short-exposures. Enriched metabolic pathways were primarily related to biosynthesis and degradation/utilization/assimilation, rather than responses to metals or oxidative stress. Our results indicate that plant-mediated bacterial responses were greater than direct NP impacts. Also, we identify needs for modeling non-monotonic legume stress responses that account for coinfection with mutualistic and parasitic bacteroids. Our findings provide new insights regarding effects of applications of soil amendments such as biosolids containing NPs or nano-enabled formulations used in cultivation of legumes and other crops.

Soil depths and microhabitats shape soil and root-associated bacterial and archaeal communities more than crop rotation in wheat

The plethora of microorganisms inhabiting the immediate vicinity of healthy root systems plays a pivotal role in facilitating optimal nutrient and water acquisition by plants. In this study, we investigated the soil microbial communities associated with wheat roots within distinct microhabitats, root-affected soil (RA), rhizosphere (RH), and rhizoplane (RP). These microhabitats were explored at five soil depths, and our investigation focused on wheat cultivated in a monoculture (WM) and wheat crop rotation (WR). Overall, there were significant differences in microbiota composition between WM and WR, although no difference in bacterial diversity was observed. Differentially abundant taxa between WM and WR were observed in all three microhabitats, emphasizing important insights on the localization of commonly associated bacteria to wheat roots. Comparing the microhabitats, RP exhibited the most dissimilar microbial composition between WM and WR. Taxa that were differentially abundant between WM and WR were observed in the three microhabitats. The high relative abundance of taxa belonging to the phylum Proteobacteria in the rhizoplane, such as Devosia, Pseudomonas, Shinella, and Sphingomonas, along with other genera, such as Pedobacter (Bacteroidota), Agromyces and Streptomyces (Actinobacteriota) highlight the recruitment of potentially beneficial bacterial taxa to the vicinity of the roots. Interestingly, these taxa were observed along the entire length of wheat roots, even at depths of up to 120 cm. The presence of specific taxa associated with wheat roots at all soil depths may be beneficial for coping with nutrient and water shortages, particularly under upcoming climate scenarios, where water may be a limiting factor for plant growth. This study provides valuable insights for designing management strategies to promote a diverse and healthy microbial community in wheat cropping systems, considering soil depth and microhabitats as key factors. Although, at this time, we cannot link specific bacterial taxa to yield reductions commonly observed in monocultural fields, we propose that some genera may enhance plant nutrient or water acquisition in rotation compared with monoculture. Advanced technologies, including functional analyses and culturomics, may further enhance our understanding of the ecological roles played by these microbes and their potential applications in sustainable agriculture.

Bacterially enhanced plant-growing media for controlled environment agriculture.

Microbe-plant interactions in the root zone not only shape crop performance in soil but also in hydroponic cultivation systems. The biological and physicochemical properties of the plant-growing medium determine the root-associated microbial community and influence bacterial inoculation effectiveness, which affects plant growth. This study investigated the combined impact of plant-growing media composition and bacterial community inoculation on the root-associated bacterial community of hydroponically grown lettuce (Lactuca sativa L.). Ten plant-growing media were composed of varying raw materials, including black peat, white peat, coir pith, wood fibre, composted bark, green waste compost, perlite and sand. In addition, five different bacterial community inocula (BCI S1-5) were collected from the roots of lettuce obtained at different farms. After inoculation and cultivation inside a vertical farm, lettuce root-associated bacterial community structures, diversity and compositions were determined by evaluating 16S rRNA gene sequences. The study revealed distinct bacterial community structures among experimental replicates, highlighting the influence of raw material variations on root-associated bacterial communities, even at the batch level. However, bacterial community inoculation allowed modulation of the root-associated bacterial communities independently from the plant-growing medium composition. Bacterial diversity was identified as a key determinant of plant growth performance with green waste compost introducing Bacilli and Actinobacteria, and bacterial community inoculum S3 introducing Pseudomonas, which positively correlated with plant growth. These findings challenge the prevailing notion of hydroponic cultivation systems as sterile environments and highlight the significance of proper plant-growing media raw material selection and bacterial community inoculation in shaping root-associated microbiomes that provide stability through microbial diversity. This study supports the concept of creating bacterially enhanced plant-growing media to promote plant growth in controlled environment agriculture.

Root-associated bacterial communities and root metabolite composition are linked to nitrogen use efficiency in sorghum.

The development of cereal crops with high nitrogen use efficiency (NUE) is a priority for worldwide agriculture. In addition to conventional plant breeding and genetic engineering, the use of the plant microbiome offers another approach to improving crop NUE. To gain insight into the bacterial communities associated with sorghum lines that differ in NUE, a field experiment was designed comparing 24 diverse Sorghum bicolor lines under sufficient and deficient nitrogen (N). Amplicon sequencing and untargeted gas chromatography-mass spectrometry were used to characterize the bacterial communities and the root metabolome associated with sorghum genotypes varying in sensitivity to low N. We demonstrated that N stress and sorghum type (energy, sweet, and grain sorghum) significantly impacted the root-associated bacterial communities and root metabolite composition of sorghum. We found a positive correlation between sorghum NUE and bacterial richness and diversity in the rhizosphere. The greater alpha diversity in high NUE lines was associated with the decreased abundance of a dominant bacterial taxon, Pseudomonas. Multiple strong correlations were detected between root metabolites and rhizosphere bacterial communities in response to low N stress. This indicates that the shift in the sorghum microbiome due to low N is associated with the root metabolites of the host plant. Taken together, our findings suggest that host genetic regulation of root metabolites plays a role in defining the root-associated microbiome of sorghum genotypes differing in NUE and tolerance to low N stress.IMPORTANCEThe development of crops that are more nitrogen use-efficient (NUE) is critical for the future of the enhanced sustainability of agriculture worldwide. This objective has been pursued mainly through plant breeding and plant molecular engineering, but these approaches have had only limited success. Therefore, a different strategy that leverages soil microbes needs to be fully explored because it is known that soil microbes improve plant growth through multiple mechanisms. To design approaches that use the soil microbiome to increase NUE, it will first be essential to understand the relationship among soil microbes, root metabolites, and crop productivity. Using this approach, we demonstrated that certain key metabolites and specific microbes are associated with high and low sorghum NUE in a field study. This important information provides a new path forward for developing crop genotypes that have increased NUE through the positive contribution of soil microbes.

Can Phytoremediation-Induced Changes in the Microbiome Improve Saline/Sodic Soil and Plant Health?

Increasing soil salinity and/or sodicity is an expanding problem in the Northern Great Plains (NGP) of North America. This study investigated the impact of phytoremediation on the soil microbiome and if changes, in turn, had positive or negative effects on plant establishment. Amplicon sequencing and gas chromatograph/mass spectrometer analysis compared root metabolites and microbial composition of bulk vs. rhizosphere soils between two soil types (productive and saline/sodic). Beta-diversity analysis indicated that bacterial and fungal communities from both the bulk and rhizosphere soils from each soil type clustered separately, indicating dissimilar microbial composition. Plant species also influenced both root-associated bacterial and fungal communities with separate clustering of operational taxonomic units (OTUs) identified. Canonical correlation analysis (CCA) found a clear association between specific soil characteristics and soil types. Bacterial and fungal OTUs from productive soil were correlated with greater %Ca Sat, %H Sat, and potassium (ppm), especially for OTUs differentially enriched in productive soil. Both bacterial and fungal OTUs from saline/sodic soil are associated with increased Ca (ppm), soil pH, %Na Sat and CEC. Metabolite analysis showed that kochia (Bassia scoparia) roots from the saline/sodic soil had a 4.4-fold decrease in pantothenate accumulation (p = 0.004). Moreover, two endophytic bacterial isolates, a Bacillus spp. and a previously uncultured halophile, isolated from creeping foxtail (Alopecurus arundinaceus) grown in saline/sodic soil and used as buckwheat (Fagopyrum esculentum) seed inoculants, significantly increased seed germination by >30% and vigor index by 0.2 under osmotic stress (0.2 M NaCl) (p < 0.05). This study revealed the importance of soil, root-associated, and endophytic microbiomes. Using native microbes as seed inoculants may help in establishment and growth of species used for phytoremediation of saline/sodic soil.

Root-associated bacteria strengthen their community stability against disturbance of antibiotics on structure and functions

Antibiotics affect bacterial community structure and functions in soil. However, the response and adaptation of root-associated bacterial communities to antibiotic stress remains poorly understood. Here, rhizobox experiments were conducted with maize (Zea mays L.) upon exposure to antibiotics ciprofloxacin or tetracycline. High-throughput sequencing analysis of bacterial community and quantitative PCR analysis of nitrogen cycling genes show that ciprofloxacin and tetracycline significantly shift bacterial community structure in bulk soil, whereas plant host may mitigate the disturbances of antibiotics on bacterial communities in root-associated niches (i.e., rhizosphere and rhizoplane) through the community stabilization. Deterministic assembly, microbial interaction, and keystone species (e.g., Rhizobium and Massilia) of root-associated bacterial communities benefit the community stability compared with those in bulk soil. Meanwhile, the rhizosphere increases antibiotic dissipation, potentially reducing the impacts of antibiotics on root-associated bacterial communities. Furthermore, rhizospheric effects deriving from root exudates alleviate the impacts of antibiotics on the nitrogen cycle (i.e., nitrification, organic nitrogen conversion and denitrification) as confirmed by functional gene quantification, which is largely attributed to the bacterial community stability in rhizosphere. The present study enhances the understanding on the response and adaptation of root-associated bacterial community to antibiotic pollution.

Assembly processes and ecological dynamics of root-associated bacterial communities during phytoremediation of vanadium-titanium mine tailings using Millettia pinnata

The vanadium-titanium magnetite (V–Ti) mine tailings are a reservoir of heavy metals, posing a grave peril to the adjacent soil environment. Millettia pinnata has emerged as a proficient pioneer tree species for the purpose of phytoremediation of V–Ti tailings. In the course of phytoremediation, the soil microbiota play an indispensable role within the rhizosphere ecosystem. The aim of this study was to dissect the underlying mechanisms governing the assembly processes of the bacterial community. The βNTI and RCbray analyses revealed that while the overall community assembly manifested deterministic attributes, rare taxa were chiefly impacted by stochastic processes (73.7%), inclusive of dispersal limitation and undominated mechanisms. In contrast, the abundant subcommunity was primarily subject to deterministic forces (84.3%), notably heterogeneous selection. Mantel test, regression analysis and ecological niche analysis showed that soil nitrogen availability emerged as a pivotal driver of the microbial assembly processes, exerting substantial influence on both rare (Mantel's r = 0.6817, p = 0.0001) and abundant taxa (Mantel's r = 0.5103, p = 0.0001) by amplifying their diversity and community turnover, constricting habitat niche breadth and overlap, and fostering the proliferation of ecological specialists. However, the heavy metal content was not found to wield significant influence in shaping the structure and assembly of the rhizosphere community (p > 0.05). The present results affirm the proposition that rare taxa are important in upholding ecological stability and providing essential microbial ecosystem services, while abundant taxa serve to fortify the entirety of the community. These insights advance our understanding of the community dynamics pertaining to the rhizosphere community associated with M. pinnata, holding paramount theoretical implications for the endeavour of plant-assisted ecological restoration in polluted tailings sites.

α-Tomatine gradient across artificial roots recreates the recruitment of tomato root-associated Sphingobium.

α-Tomatine is a major saponin that accumulates in tomatoes (Solanum lycopersicum). We previously reported that α-tomatine secreted from tomato roots modulates root-associated bacterial communities, particularly by enriching the abundance of Sphingobium belonging to the family Sphingomonadaceae. To further characterize the α-tomatine-mediated interactions between tomato plants and soil bacterial microbiota, we first cultivated tomato plants in pots containing different microbial inoculants originating from three field soils. Four bacterial genera, namely, Sphingobium, Bradyrhizobium, Cupriavidus, and Rhizobacter, were found to be commonly enriched in tomato root-associated bacterial communities. We constructed a pseudo-rhizosphere system using a mullite ceramic tube as an artificial root to investigate the influence of α-tomatine in modifying bacterial communities. The addition of α-tomatine from the artificial root resulted in the formation of a concentration gradient of α-tomatine that mimicked the tomato rhizosphere, and distinctive bacterial communities were observed in the soil close to the artificial root. Sphingobium was enriched according to the α-tomatine concentration gradient, whereas Bradyrhizobium, Cupriavidus, and Rhizobacter were not enriched in α-tomatine-treated soil. The tomato root-associated bacterial communities were similar to the soil bacterial communities in the vicinity of artificial root-secreting exudates; however, hierarchical cluster analysis revealed a distinction between root-associated and pseudo-rhizosphere bacterial communities. These results suggest that the pseudo-rhizosphere device at least partially creates a rhizosphere environment in which α-tomatine enhances the abundance of Sphingobium in the vicinity of the root. Enrichment of Sphingobium in the tomato rhizosphere was also apparent in publicly available microbiota data, further supporting the tight association between tomato roots and Sphingobium mediated by α-tomatine.

Root-associated microbial community and diversity in napiergrass across radiocesium-contaminated lands after the Fukushima-Daiichi nuclear disaster in Japan

The microbiome derived from soil associated with plant roots help in plant growth and stress resistance. It exhibits potential benefits for soil remediation and restoration of radioactive-cesium (137Cs)-contaminated soils. However, there is still limited information about the community and diversity of root-associated microbiome in 137Cs-contaminated soil after the Fukushima-Daiichi Nuclear Power Plant (FDNPP) disaster. To address this, a comparative analysis of communities and diversity of root-associated microbiomes was conducted in two field types after the FDNPP disaster. In 2013, we investigated the community and diversity of indigenous root-associated microbiome of napiergrass (Pennisetum purpureum) grown in both grassland and paddy fields of 137Cs-contaminated land-use type within a 30-km radius around the FDNPP. Results showed that the root-associated bacterial communities in napiergrass belonged to 32 phyla, 75 classes, 174 orders, 284 families, and 521 genera, whereas the root-associated fungal communities belonged to 5 phyla, 11 classes, 31 orders, 59 families, and 64 genera. The most frequently observed phylum in both grassland and paddy field was Proteobacteria (47.4% and 55.9%, respectively), followed by Actinobacteriota (23.8% and 27.9%, respectively) and Bacteroidota (10.1% and 11.3%, respectively). The dominant fungal phylum observed in both grassland and paddy field was Basidiomycota (75.9% and 94.2%, respectively), followed by Ascomycota (24.0% and 5.8%, respectively). Land-use type significantly affected the bacterial and fungal communities that colonize the roots of napiergrass. Several 137Cs-tolerant bacterial and fungal taxa were also identified, which may be potentially applied for the phytoremediation of 137Cs-contaminated areas around FDNPP. These findings contribute to a better understanding of the distribution of microbial communities in 137Cs-contaminated lands and their long-term ecosystem benefits for phytoremediation efforts.

The root of influence: root-associated bacterial communities alter resource allocation in seagrass seedlings

IntroductionSeagrass roots harbour diverse assemblages of microorganisms that likely benefit the growth and survival of meadows. Yet, restoration efforts rarely consider their effect on developing seagrass seedlings. Sediment origin should determine the types of rhizosphere and root-colonising (rhizoplane) microorganisms and thus the performance of seedlings during restoration, particularly for slow growing climax species like Posidonia. Recent Posidonia restoration attempts in South Australia used commercially sourced 'play pit sand' for seedling propagation and planting, but have been impacted by high mortality. More natural substrates like seagrass meadow sediment have not been previously investigated for suitability over conventional substrates with regard to seedling growth and survival.MethodsTo assess the relevance of seagrass associated microorganisms in the growth of Posidonia angustifolia seedlings, we investigated the bacterial communities from tank-raised seedlings propagated in autoclave treated and untreated 'play pit sand' and meadow mix (comprising a 1:3 ratio of natural meadow sediment and beach sand) over a 12-week period. Autoclave treatment was adopted in order to diminish the bacterial load prior to planting and thus inform their contribution (if any) on early seedling growth. Samples for bacterial community analysis and seedling growth measurements (numbers and total length of roots/leaves, root diameter, seedling weight, starch reserves) were taken at 4 and 12 weeks. Bacterial assemblages were surveyed from DNA extracts from bulk and rhizosphere sediments and root tissues, as well as from swabs of P. angustifolia fruit, established meadow sediment and water samples prior to seedling propagation, by constructing Illumina 16S rRNA gene libraries.ResultsWhile most growth measurements did not vary significantly between sediment type or treatment, proportional growth of roots versus leaves (as expressed as a pseudo root:shoot ratio) was significantly related to treatment, sediment type and seed length. Seedlings from meadow mix invested more in leaves, regardless of treatment, when compared to play sand. Autoclave treatment increased investment in roots for play sand but increased the investment in leaves for meadow mix. Bacterial communities differed significantly between sediments and between sample types (bulk, rhizosphere and roots), with the roots from meadow mix seedlings containing an increased abundance of various potentially beneficial bacterial taxa.DiscussionWhile such changes appear to affect the early development of seedlings, bacterial community dynamics are also likely coupled to changes in nutrient availability. Further research is thus required to disentangle host seedling growth-nutrient-bacterial community dynamics with the view to identifying microbes that may support the growth and vigour of seedlings under different nutrient conditions as part of future restoration efforts.

Potential role of root-associated bacterial communities in adjustments of desert plant physiology to osmotic stress

Plants possess the ability to adapt to osmotic stress by adjusting their physiology and morphology and by cooperating with their root-associated (rhizosphere and endosphere) microbial communities. However, the coordination of host self-regulation with root-associated microorganisms at the community level, especially for desert plants, remains unclear. This study investigated the morphophysiological responses of seedlings from the desert plant Alhagi sparsifolia Shap to osmotic stress, as well as the relationships between these adaptations and their root-associated bacterial communities. The results indicated that osmotic stress contributed to a reduction in height and increased levels of reactive oxygen species (ROS) and malondialdehyde (MDA). In response, A. sparsifolia exhibited a series of morphophysiological adjustments, including increased ratio of root to shoot biomass (R/S) and the number of root tip, enhanced vitality, high levels of peroxidase (POD), ascorbate peroxidase (APX), and glutathione (GSH), as well as osmolytes (proline, soluble protein, and soluble sugar) and modification in phytohormones (abscisic acid (ABA) and jasmonic acid (JA)). Additionally, osmotic stress resulted in alterations in the compositions and co-occurrence patterns of root-associated bacterial communities, but not α-diversity (Chao1). Specifically, the rhizosphere Actinobacteria phylum was significantly increased by osmotic stress. These shifts in root-associated bacterial communities were significantly correlated with the host's adaptation to osmotic stress. Overall, the findings revealed that osmotic stress, in addition to its impacts on plant physiology, resulted in a restructuring of root-associated microbial communities and suggested that the concomitant adjustment in plant microbiota may potentially contribute to the survival of desert plants under extreme environmental stress.

The Influence of the Genotype and Planting Density on the Structure and Composition of Root and Rhizosphere Microbial Communities in Maize.

Maize has the largest cultivation area of any crop in the world and plays an important role in ensuring food security. High-density planting is essential for maintaining high maize yields in modern intensive agriculture. Nonetheless, how high-density planting and the tolerance of individual genotypes to such planting shape the root-associated microbiome of maize is still unknown. In this study, we analyzed the root and rhizosphere bacterial communities of two maize accessions with contrasting shoot architectures grown under high- and low-density planting conditions. Our results suggested that maize hosted specific, distinct bacterial communities in the root endocompartment and that the maize genotype had a significant effect on the selection of specific microbes from the rhizosphere. High-density planting also had significant effects on root-associated bacterial communities. Specifically, genotype and high-density planting coordinated to shape the structure, composition, and function of root and rhizosphere bacterial communities. Taken together, our results provide insights into how aboveground plant architecture and density may alter the belowground bacterial community in root-associated compartments of maize.

Assembly, diversity and coexistence of bacteria communities in various rhizocompartment niches in Sorghum Cultivars

Root-associated microbial communities play a vital role in plant health, but the assembly processes in sorghum and associated soil factors remain unclear. We conducted 16S rDNA sequencing on bulk soils and rhizocompartments (rhizosphere, rhizoplane, and endosphere) of three sorghum cultivars. Physicochemical properties were measured in bulk and rhizosphere soils. Alpha-diversity decreased from bulk soil to endosphere, and beta-diversity showed compartmental separation. Relative abundances of 16 dominant genera varied among compartments and cultivars. Dispersal limitation increased from (17.0%) to endosphere (35.8%), with homogenous selection dominating rhizocompartment assembly (51.1%–83.0%). Certain soil factors mediated community assembly and shaped phylogenetic structures. Rhizosphere displayed the most complex network, followed by bulk soil, rhizoplane, and endosphere. Differentially abundant taxa were more important in maintaining network stability and connectivity in the endosphere (47.0%–68.4%) compared to the other rhizocompartments. This study provides insights into the factors influencing the assembly of root-associated bacterial communities in sorghum, highlighting the roles of compartment niches, sorghum cultivars, and soil properties. These findings contribute to our understanding of plant-microbe interactions and have implications for agricultural management and ecological restoration efforts. Furthermore, the identification of key soil factors that mediate community assembly processes and shape phylogenetic structures offers potential targets for manipulating microbial communities in agricultural systems, leading to improved plant health and productivity.

Nodulation number tempers the relative importance of stochastic processes in the assembly of soybean root-associated communities

Identifying the ecological forces that structure root-associated microbial communities is an essential step toward more sustainable agriculture. Legumes are widely utilized as model plants to study selective forces and their functioning in plant-microbial interactions owing to their ability to establish mutualism with rhizobia. Root nodules act as symbiotic organs to optimize the cost-benefit balance in this mutualistic relationship by modulating the number of nodules. However, it is not known whether the number of nodules is related to the structure of root-associated bacterial communities. Here, the root-associated bacterial communities of soybean grown in native soil by means of soybean cultivars with super- or normal nodulation were investigated across four developmental stages. We compared ecological processes between communities and found decreased relative importance of neutral processes for super-nodulating soybean, although the overall structures resembled those of normal-nodulating soybean. We identified the generalist core bacterial populations in each root-associated compartment, that are shared across root-associated niches, and persist through developmental stages. Within core bacterial species, the relative abundances of bacterial species in the rhizosphere microbiome were linked to host-plant functional traits and can be used to predict these traits from microbes using machine learning algorithms. These findings broaden the comprehensive understanding of the ecological forces and associations of microbiotas in various root-associated compartments and provide novel insights to integrate beneficial plant microbiomes into agricultural production to enhance plant performance.

Home-field advantage affects the local adaptive interaction between Andropogon gerardii ecotypes and root-associated bacterial communities.

Due to climate change, drought frequencies and severities are predicted to increase across the United States. Plant responses and adaptation to stresses depend on plant genetic and environmental factors. Understanding the effect of those factors on plant performance is required to predict species' responses to environmental change. We used reciprocal gardens planted with distinct regional ecotypes of the perennial grass Andropogon gerardii adapted to dry, mesic, and wet environments to characterize their rhizosphere communities using 16S rRNA metabarcode sequencing. Even though the local microbial pool was the main driver of these rhizosphere communities, the significant plant ecotypic effect highlighted active microbial recruitment in the rhizosphere, driven by ecotype or plant genetic background. Our data also suggest that ecotypes planted at their homesites were more successful in recruiting rhizosphere community members that were unique to the location. The link between the plants' homesite and the specific local microbes supported the "home field advantage" hypothesis. The unique homesite microbes may represent microbial specialists that are linked to plant stress responses. Furthermore, our data support ecotypic variation in the recruitment of congeneric but distinct bacterial variants, highlighting the nuanced plant ecotype effects on rhizosphere microbiome recruitment. These results improve our understanding of the complex plant host-soil microbe interactions and should facilitate further studies focused on exploring the functional potential of recruited microbes. Our study has the potential to aid in predicting grassland ecosystem responses to climate change and impact restoration management practices to promote grassland sustainability. IMPORTANCE In this study, we used reciprocal gardens located across a steep precipitation gradient to characterize rhizosphere communities of distinct dry, mesic, and wet regional ecotypes of the perennial grass Andropogon gerardii. We used 16S rRNA amplicon sequencing and focused oligotyping analysis and showed that even though location was the main driver of the microbial communities, ecotypes could potentially recruit distinct bacterial populations. We showed that different A. gerardii ecotypes were more successful in overall community recruitment and recruitment of microbes unique to the "home" environment, when growing at their "home site." We found evidence for "home-field advantage" interactions between the host and host-root-associated bacterial communities, and the capability of ecotypes to recruit specialized microbes that were potentially linked to plant stress responses. Our study aids in a better understanding of the factors that affect plant adaptation, improve management strategies, and predict grassland function under the changing climate.

Sugarcane mosaic virus reduced bacterial diversity and network complexity in the maize root endosphere.

Sugarcane mosaic virus (SCMV) causes mosaic disease in crops such as maize and sugarcane by its vector-an aphid-and is transmitted top-down into the root system. However, understanding of the effects of the aphid-borne virus on root-associated microbes after plant invasion remains limited. The current project investigated maize root-associated (rhizosphere and endosphere) bacterial communities, potential interspecies interaction, and assembly processes in response to SCMV invasion based on 16S rRNA gene amplicon sequencing. SCMV was detected in the roots 9 days after inoculation, and leaf mosaic and chlorosis appeared. The SCMV invasion markedly reduced the α-diversity of endosphere bacteria compared with uninoculated controls (Mock). The connectivity and complexity of the bacterial co-occurrence network in the root endosphere decreased after SCMV invasion, implying that the plant virus may alter root endophyte-microbial interactions. Moreover, a signature that deviates more from stochastic processes was observed in virus-infected plants. Unexpectedly, the rhizosphere bacterial communities were rarely affected by the viral invasion. This study lays the foundation for elucidating the fate of the microbial component of the plant holobiont following aphid-borne virus exposure. IMPORTANCE Biotic (e.g., soil-borne viruses) stress can alter root-associated bacterial communities, essential in maintaining host plant growth and health. However, the regulation of root-associated microorganisms by plant viruses from shoots is still largely unknown. Our results show that plant virus invasion leads to reduced and simpler inter-microbial communication in the maize endosphere. In addition, stochastic processes act on bacterial community assembly in both rhizosphere and endosphere, and bacterial communities in virus-invaded plant endosphere tend to shift toward deterministic processes. Our study highlights the negative effects of plant viruses on root endophytes from the microbial ecology perspective, which may be microbially mediated mechanisms of plant diseases.

Water pH, not soil pH, alters bacterial community structural pattern and nitrogen cycling pathways in date palm (Phoenix dactylifera L.) roots and bulk soil under freshwater irrigation regime

Date palms are widely cultivated in arid agroecosystems, where knowledge of irrigation water effect on their soil and root-associated bacterial communities is limited. Using 16S rDNA metabarcoding, we studied soil and root-associated bacterial communities of date palms growing in United Arab Emirates. Overall, 12.18% of bacterial operational taxonomic units (OTUs) were unique to roots, whereas 41.55% were specific to soil. The bacterial diversity was lower in root and community patterns were distinct between compartments, wherein irrigation water pH was a key structuring factor in both compartments, while salinity (electrical conductivity) was important only in the soil. Co-occurrence network analysis revealed a decrease in complexity in the soil–root continuum, and specific taxa/modules also varied with water pH. We observed a higher abundance of endophyte–saprotroph (Bacillus, Streptomyces and Dongia) dual-role OTUs in both compartments, possibly involved in nutrient mobilisation and plant growth. Based on PICRUSt and trait-based analyses, we showed that these OTUs are putatively involved in the nitrogen cycle (nitrification, denitrification, and assimilatory nitrate reduction). Taken together, we suggest that irrigation water pH, not soil pH, transiently affects belowground bacterial communities and selects bacteria in specific pH ranges, which may be important for nutrient cycling (i.e. nitrogen cycle) in arid agroecosystems.

Resilience of barley (Hordeum vulgare) plants upon exposure to tramadol: Implication for the root-associated bacterial community and the antioxidative plant defence system

Insufficiently treated reclaimed water can act as a source of contamination by introducing recalcitrant contaminants (e.g., pharmaceutical compounds) to various water bodies and/or agricultural soils after irrigation. Tramadol (TRD) is one of these pharmaceuticals that can be detected in influents and effluents of wastewater treatment plants, at discharge points as well as in surface waters in Europe. While the uptake of TRD by plants through irrigation water has been shown, plant responses towards this compound are still unclear. Therefore, this study aims to evaluate the effects of TRD on selected plant enzymes as well as on the root bacterial community structure. A hydroponic experiment was conducted to test the effects of TRD (100 μg L−1 TRD) on barley plants, at two harvesting time points after treatment. Accumulation of TRD in root tissues over time was observed reaching concentrations of 111.74 and 138.39 μg g−1 in total root FW after 12 and 24 days of exposure, respectively. Furthermore, noticeable inductions in guaiacol peroxidase (5.47-fold), catalase (1.83-fold) and glutathione S-transferase (3.23- and 2.09-fold) were recorded in roots of TRD-treated plants compared to controls after 24 days. A significant alteration in the beta diversity of root-associated bacteria due to TRD treatment was observed. Three amplicon sequence variants assigned to Hydrogenophaga, U. Xanthobacteraceae and Pseudacidovorax were differentially abundant in TRD-treated compared to control plants at both harvesting time points. This study reveals the resilience of plants through the induction of the antioxidative system and changes in the root-associated bacterial community to cope with the TRD metabolization/detoxification process.