Root-associated Microbial Communities Research Articles

Comparing root-associated microbial communities in Tamarix ramosissima across three Xinjiang basins, China

Analyzing the root-associated microbial communities in desert plants during different seasons may provide a valuable understanding of how desert plants adapt to climate change in harsh environments. Hence, we selected root-associated microbial communities (bacteria and fungi) of Tamarix ramosissima from three regions (Cele, CL; Turpan, TLF; Mosuowan, MSW), focusing on three compartments: root endosphere (RE), rhizosphere soil (RS), and bulk soil (BS). Results indicated that the relative abundance of Actinobacteriota, Proteobacteria, and Ascomycota of root bacteria and fungi taxa was higher the in three compartments (RE, RS, and BS). In the CL region, there was a decline in the relative abundance of Proteobacteria within the RE followed by RS and BS during the autumn. During both summer and autumn, the relative abundance of Ascomycota declined with increasing sampling distance (from the TLF to the MSW to the CL) in the BS. Furthermore, in spring, the bacterial (BS) and fungal (BS) Chao1 and ACE index decreased in TLF compared to the MSW region. However, MSW had a higher bacterial Chao1 and Shannon index of the RE (in summer) and RS (in autumn) than the CL area. Overall, in spring, summer, and autumn, root-associated bacterial and fungal communities across various regions (CL, TLF, and MSW) were more responsive to climate and soil factors than plant nutrients. This research provides compelling theoretical evidence advocating for the restoration of degraded vegetation within arid environments, underscoring the critical significance of judicious plant management practices in these regions.

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.

The Contributions of Sub-Communities to the Assembly Process and Ecological Mechanisms of Bacterial Communities along the Cotton Soil–Root Continuum Niche Gradient

Soil microbes are crucial in shaping the root-associated microbial communities. In this study, we analyzed the effect of the soil–root niche gradient on the diversity, composition, and assembly of the bacterial community and co-occurrence network of two cotton varieties. The results revealed that the bacterial communities in cotton soil–root compartment niches exhibited a skewed species abundance distribution, dominated by abundant taxa showing a strong spatial specificity. The assembly processes of the rhizosphere bacterial communities were mainly driven by stochastic processes, dominated by the enrichment pattern and supplemented by the depletion pattern to recruit bacteria from the bulk soil, resulting in a more stable bacterial community. The assembly processes of the endosphere bacterial communities were determined by processes dominated by the depletion pattern and supplemented by the enrichment pattern to recruit species from the rhizosphere, resulting in a decrease in the stability and complexity of the community co-occurrence network. The compartment niche shaped the diversity of the bacterial communities, and the cotton variety genotype was an important source of diversity in bacterial communities within the compartment niche. We suggest that the moderate taxa contribute to significantly more changes in the diversity of the bacterial community than the rare and abundant taxa during the succession of bacterial communities in the cotton root–soil continuum.

Plants attacked above-ground by leaf-mining flies change below-ground microbiota to enhance plant defense

Abstract Root-associated microbiomes play a crucial role in plant responses to biotic and abiotic stresses. Plants can recruit beneficial microbes to increase their stress-relieving ability. Above-ground insect herbivory is among the most detrimental stresses for plants, especially to crop production. However, few studies have explored how root-associated microbiomes respond to herbivores and influence plant-defense functions under herbivory stress. We investigate the changes and functional role of root-associated microbial communities under herbivory stress using leafminer (Liriomyza trifolii) and cowpea (Vigna unguiculata) as a focal system. We did this by using a combination of 16S ribosomal RNA gene profiling and metagenomic sequencing to test for differences in co-occurrence networks and functions between cowpea plants infested and noninfested with leafminers. The results demonstrated that leafminer infestation caused a shift in the rhizosphere microbiome, which was characterized by a significant variation in microbiome community structure and composition, the selection of hub microbes involved in nitrogen (N) metabolism, and functional enrichment related to N metabolism. Notably, nitrogen-fixing bacteria Bradyrhizobium species were actively recruited and selected to be hubs in the rhizosphere. Inoculation with Bradyrhizobium enhanced cowpea performance under leafminer stress and increased protease inhibitor levels to decrease leafminer fitness. Overall, our study characterized the changes of root-associated microbiota between leafminer-infested and noninfested cowpea plants and revealed the mechanisms underlying the rhizosphere microbiome shift that enhance plant performance and defense against herbivory. Our findings provide further support for the notion that plants recruit rhizosphere microbes to counteract aboveground insect herbivores.

Interplay of biotic and abiotic factors shapes tree seedling growth and root-associated microbial communities

Root-associated microbes can alleviate plant abiotic stresses, thus potentially supporting adaptation to a changing climate or to novel environments during range expansion. While climate change is extending plant species fundamental niches northward, the distribution and colonization of mutualists (e.g., arbuscular mycorrhizal fungi) and pathogens may constrain plant growth and regeneration. Yet, the degree to which biotic and abiotic factors impact plant performance and associated microbial communities at the edge of their distribution remains unclear. Here, we use root microscopy, coupled with amplicon sequencing, to study bacterial, fungal, and mycorrhizal root-associated microbial communities from sugar maple seedlings distributed across two temperate-to-boreal elevational gradients in southern Québec, Canada. Our findings demonstrate that soil pH, soil Ca, and distance to sugar maple trees are key drivers of root-associated microbial communities, overshadowing the influence of elevation. Interestingly, changes in root fungal community composition mediate an indirect effect of soil pH on seedling growth, a pattern consistent at both sites. Overall, our findings highlight a complex role of biotic and abiotic factors in shaping tree-microbe interactions, which are in turn correlated with seedling growth. These findings have important ramifications for tree range expansion in response to shifting climatic niches.

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 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.

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.

Association between host nitrogen absorption and root-associated microbial community in field-grown wheat.

Plant roots and rhizosphere soils assemble diverse microbial communities, and these root-associated microbiomes profoundly influence host development. Modern wheat has given rise to numerous cultivars for its wide range of ecological adaptations and commercial uses. Variations in nitrogen uptake by different wheat cultivars are widely observed in production practices. However, little is known about the composition and structure of the root-associated microbiota in different wheat cultivars, and it is not sure whether root-associated microbial communities are relevant in host nitrogen absorption. Therefore, there is an urgent need for systematic assessment of root-associated microbial communities and their association with host nitrogen absorption in field-grown wheat. Here, we investigated the root-associated microbial community composition, structure, and keystone taxa in wheat cultivars with different nitrogen absorption characteristics at different stages and their relationships with edaphic variables and host nitrogen uptake. Our results indicated that cultivar nitrogen absorption characteristics strongly interacted with bacterial and archaeal communities in the roots and edaphic physicochemical factors. The impact of host cultivar identity, developmental stage, and spatial niche on bacterial and archaeal community structure and network complexity increased progressively from rhizosphere soils to roots. The root microbial community had a significant direct effect on plant nitrogen absorption, while plant nitrogen absorption and soil temperature also significantly influenced root microbial community structure. The cultivar with higher nitrogen absorption at the jointing stage tended to cooperate with root microbial community to facilitate their own nitrogen absorption. Our work provides important information for further wheat microbiome manipulation to influence host nitrogen absorption. KEY POINTS: • Wheat cultivar and developmental stage affected microbiome structure and network. • The root microbial community strongly interacted with plant nitrogen absorption. • High nitrogen absorption cultivar tended to cooperate with root microbiome.

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.

Impact of conservation tillage on wheat performance and its microbiome.

Winter wheat is an important cereal consumed worldwide. However, current management practices involving chemical fertilizers, irrigation, and intensive tillage may have negative impacts on the environment. Conservation agriculture is often presented as a sustainable alternative to maintain wheat production, favoring the beneficial microbiome. Here, we evaluated the impact of different water regimes (rainfed and irrigated), fertilization levels (half and full fertilization), and tillage practices (occasional tillage and no-tillage) on wheat performance, microbial activity, and rhizosphere- and root-associated microbial communities of four winter wheat genotypes (Antequera, Allez-y, Apache, and Cellule) grown in a field experiment. Wheat performance (i.e., yield, plant nitrogen concentrations, and total nitrogen uptake) was mainly affected by irrigation, fertilization, and genotype, whereas microbial activity (i.e., protease and alkaline phosphatase activities) was affected by irrigation. Amplicon sequencing data revealed that habitat (rhizosphere vs. root) was the main factor shaping microbial communities and confirmed that the selection of endophytic microbial communities takes place thanks to specific plant-microbiome interactions. Among the experimental factors applied, the interaction of irrigation and tillage influenced rhizosphere- and root-associated microbiomes. The findings presented in this work make it possible to link agricultural practices to microbial communities, paving the way for better monitoring of these microorganisms in the context of agroecosystem sustainability.

Exposure to three herbicide mixtures influenced maize root-associated microbial community structure, function and the network complexity

Herbicide mixtures are a new and effective agricultural strategy for managing suppress weed resistance and have been widely used in controlling weeding growth in maize fields. However, the potential ecotoxicological impact of these mixtures on the microbial community structure and function within various root-associated niches, remains inadequately understood. Here, the effects of nicosulfuron, mesotrione and atrazine on soil enzyme activity and microbial community structure and function were investigated when applied alone and in combination. The findings indicated that herbicide mixtures exhibit a prolonged half-life compared to single herbicides. Ecological niches are the major factor influencing the structure and functions of the microbial community, with the rhizosphere exhibiting a more intensive response to herbicide stress. Herbicides significantly inhibited the activities of soil functional enzymes, including dehydrogenase, urease and sucrose in the short-term. Single herbicide did not drastically influence the alpha or beta diversity of the soil bacterial community, but herbicide mixtures significantly increased the richness of the fungal community. Meanwhile, the key functional microbial populations, such as Pseudomonas and Enterobacteriaceae, were significantly altered by herbicide stress. Both individual and combined use of the three herbicides reduced the complexity and stability of the bacterial network but increased the interspecific cooperations of fungal community in the rhizosphere. Moreover, by quantification of residual herbicide concentrations in the soil, we showed that the degradation period of the herbicide mixture was longer than that of single herbicides. Herbicide mixtures increased the contents of NO3−-N and NH4+-N in the soil in the short-term. Overall, our study provided a comprehensive insight into the response of maize root-associated microbial communities to herbicide mixtures and facilitated the assessment of the ecological risks posed by herbicide mixtures to the agricultural environment from an agricultural sustainability perspective.

Communication between Plants and Rhizosphere Microbiome: Exploring the Root Microbiome for Sustainable Agriculture.

Plant roots host numerous microorganisms around and inside their roots, forming a community known as the root microbiome. An increasing bulk of research is underlining the influences root-associated microbial communities can have on plant health and development. However, knowledge on how plant roots and their associated microbes interact to bring about crop growth and yield is limited. Here, we presented (i) the communication strategies between plant roots and root-associated microbes and (ii) the applications of plant root-associated microbes in enhancing plant growth and yield. This review has been divided into three main sections: communications between root microbiome and plant root; the mechanism employed by root-associated microbes; and the chemical communication mechanisms between plants and microbes and their application in plant growth and yield. Understanding how plant root and root-associated microbes communicate is vital in designing ecofriendly strategies for targeted disease suppression and improved plant growth that will help in sustainable agriculture. Ensuring that plants become healthy and productive entails keeping plants under surveillance around the roots to recognize disease-causing microbes and similarly exploit the services of beneficial microorganisms in nutrient acquisition, stress mitigation, and growth promotion.

The Application of Sulfur Influences Microbiome of Soybean Rhizosphere and Nutrient-Mobilizing Bacteria in Andosol.

This study aimed to determine the effect of sulfur (S) application on a root-associated microbial community resulting in a rhizosphere microbiome with better nutrient mobilizing capacity. Soybean plants were cultivated with or without S application, the organic acids secreted from the roots were compared. High-throughput sequencing of 16S rRNA was used to analyze the effect of S on microbial community structure of the soybean rhizosphere. Several plant growth-promoting bacteria (PGPB) isolated from the rhizosphere were identified that can be harnessed for crop productivity. The amount of malic acid secreted from the soybean roots was significantly induced by S application. According to the microbiota analysis, the relative abundance of Polaromonas, identified to have positive association with malic acid, and arylsulfatase-producing Pseudomonas, were increased in S-applied soil. Burkholderia sp. JSA5, obtained from S-applied soil, showed multiple nutrient-mobilizing traits among the isolates. In this study, S application affected the soybean rhizosphere bacterial community structure, suggesting the contribution of changing plant conditions such as in the increase in organic acid secretion. Not only the shift of the microbiota but also isolated strains from S-fertilized soil showed PGPB activity, as well as isolated bacteria that have the potential to be harnessed for crop productivity.

Diversity and assembly of root-associated microbiomes of rubber trees.

Understanding the diversity and assembly of the microbiomes of plant roots is crucial to manipulate them for sustainable ecosystem functioning. However, there are few reports about microbial communities at a continuous fine-scale of roots for rubber trees. We investigate the structure, diversity, and assembly of bacterial and fungal communities for the soil (non-rhizosphere), rhizosphere, and rhizoplane as well as root endosphere of rubber trees using the amplicon sequencing of 16S ribosomal ribonucleic acid (rRNA) and Internally Transcribed Spacer (ITS) genes. We show that 18.69% of bacterial and 20.20% of fungal operational taxonomic units (OTUs) in the rhizoplane derived from the endosphere and 20.64% of bacterial and 20.60% of fungal OTUs from the soil. This suggests that the rhizoplane microbial community was a mixed community of soil and endosphere microbial communities and that microorganisms can disperse bidirectionally across different compartments of the plant root. On the other hand, in the absence of an enrichment or depletion of core bacterial and fungal OTUs in the rhizosphere, little differences in microbial composition as well as a more shared microbial network structure between the soil and the rhizosphere support the theory that the rhizosphere microbial community is a subset of the soil community. A large number of functional genes (such as nitrogen fixation and nitrite reduction) and more enriched core OTUs as well as a less stable but more complex network structure were observed in the rhizoplane of rubber tree roots. This demonstrated that the rhizoplane is the most active root compartment and a hotspot for plant-soil-environment interactions. In addition, bacterial and fungal communities in the rhizoplane were more stochastic compared to the rhizosphere and soil. Our study expands our understanding of root-associated microbial community structure and function, which may provide the scientific basis for sustainable agriculture through biological process management.

Construction of hybrid constructed wetlands for phosphorus chemical industry tailwater treatment in the middle Yangtze river basin: Responses of plant growth and root-associated microbial communities

Constructed wetlands are commonly utilized to treat industrial wastewater due to their effectiveness, affordability, and environmental benefits. Many phosphorus chemical enterprises in the middle Yangtze River basin are facing high pollution load challenges and efforts are needed to improve removal efficiency of pollutants. This work was the first to use constructed wetlands for phosphorus chemical industry tailwater (PCITW) treatment. The new hybrid constructed wetlands (CWs) proposed were the aeration horizontal subsurface flow constructed wetland (AHSCW) and the integrated vertical flow constructed wetland (IVCW), which were constructed on a pilot scale. Here, the effectiveness of pollutant removal along hybrid CWs, wetland plant growth, and root-associated microbial community responses to the PCITW were investigated. The results showed that there was spatial variation in removal of carbon, nitrogen, and phosphorus in the hybrid CWs, and that the AHSCW and the IVCW played synergistic roles in the removal of pollutants. Compared with influent, the toxic effect of effluent to embryos of a rare minnow (Gobiocypris rarus) was alleviated. Exposure to the effluent resulted in no malformation or death for embryos. Plants and microorganisms in the wetland system of the phosphate chemical tailwater were then compared with the control system of municipal tailwater. Plants in the former system had lower root density, and higher average root diameter, root shoot ratio, specific root length, and specific surface area. Plant roots also had decreased NH4+ uptake ability but increased Ca2+ uptake to adapt to the high load and complex pollution stress. Unlike the control system, stochastic mechanisms had a more important role than deterministic processes in shaping the microbial community assembly associated with the PCITW. Meanwhile, analysis of microbial network-level topological characteristics demonstrated substantial reduction in network interactions complexity and microbiome stability in the treatment system. Findings from this study suggest wetlands will be helpful for efficient purification of phosphorus chemical industry wastewater in the Yangtze River basin.

Co-occurrence network analysis unveils the actual differential impact on the olive root microbiota by two Verticillium wilt biocontrol rhizobacteria

BackgroundVerticillium wilt of olive (VWO), caused by Verticillium dahliae Kleb, is one of the most threatening diseases affecting olive cultivation. An integrated disease management strategy is recommended for the effective control of VWO. Within this framework, the use of biological control agents (BCAs) is a sustainable and environmentally friendly approach. No studies are available on the impact that the introduction of BCAs has on the resident microbiota of olive roots. Pseudomonas simiae PICF7 and Paenibacillus polymyxa PIC73 are two BCAs effective against VWO. We examined the effects of the introduction of these BCAs on the structure, composition and co-occurrence networks of the olive (cv. Picual) root-associated microbial communities. The consequences of the subsequent inoculation with V. dahliae on BCA-treated plants were also assessed.ResultsInoculation with any of the BCAs did not produce significant changes in the structure or the taxonomic composition of the ‘Picual’ root-associated microbiota. However, significant and distinctive alterations were observed in the topologies of the co-occurrence networks. The introduction of PIC73 provoked a diminution of positive interactions within the ‘Picual’ microbial community; instead, PICF7 inoculation increased the microbiota’s compartmentalization. Upon pathogen inoculation, the network of PIC73-treated plants decreased the number of interactions and showed a switch of keystone species, including taxa belonging to minor abundant phyla (Chloroflexi and Planctomycetes). Conversely, the inoculation of V. dahliae in PICF7-treated plants significantly increased the complexity of the network and the number of links among their modules, suggestive of a more stable network. No changes in their keystone taxa were detected.ConclusionThe absence of significant modifications on the structure and composition of the ‘Picual’ belowground microbiota due to the introduction of the tested BCAs underlines the low/null environmental impact of these rhizobacteria. These findings may have important practical consequences regarding future field applications of these BCAs. Furthermore, each BCA altered the interactions among the components of the olive belowground microbiota in idiosyncratic ways (i.e. PIC73 strongly modified the number of positive relations in the ‘Picual’ microbiota whereas PICF7 mostly affected the network stability). These modifications may provide clues on the biocontrol strategies used by these BCAs.

Seed treatment with plant-defense elicitors decreases the abundance of ammonia oxidizers associated with winter wheat roots

Priming with elicitors, including phytohormones, is known to induce physiological changes in plants that affect resource allocation and nutrient uptake strategies. However, effects of these changes on belowground microbial communities, particularly those involved in nitrogen (N) transformations, remain poorly characterized. Here, we tested the hypothesis that treating seeds with elicitors would affect N-transforming communities associated to roots and rhizosphere, influencing soil N availability and thus plant performance. We measured the effects of treating winter wheat seeds with cis-jasmone, methyl jasmonate or methyl salicylate on plant traits and on the genetic potential for ammonia oxidation by ammonia-oxidizing bacteria (AOB) and archaea (AOA), the initial inorganic N transformation process resulting in N loss. Elicitors reduced the genetic potential for ammonia oxidation by AOB in root-associated microbial communities and increased traits reflecting N uptake in winter wheat. Proposed mechanisms include increased exploitative competition for ammonium, limiting substrate availability for microorganisms, and induced biological nitrification inhibition capacity actively suppressing ammonia oxidizers. There were minor effects on the composition of the AOB and AOA communities, but an indicator species analysis showed that several AOB and a few AOA genotypes were indicative of elicitor treatments. Seed treatment with elicitors may represent an overlooked strategy to minimize nitrification to mitigate N losses from arable soils.

Association of soil fungal community composition with incidence of Fusarium wilt of banana in Malaysia

ABSTRACT Banana (Musa spp.), an important food crop in many parts of the world, is threatened by a deadly wilt disease caused by Fusarium oxysporum f. sp. cubense Tropical Race 4 (TR4). Increasing evidence indicates that plant actively recruits beneficial microbes in the rhizosphere to suppress soil-borne pathogens. Hence, studies on the composition and diversity of the root-associated microbial communities are important for banana health. Research on beneficial microbial communities has focused on bacteria, although fungi can also influence soil-borne disease. Here, high-throughput sequencing targeting the fungal internal transcribed spacer (ITS) was employed to systematically characterize the difference in the soil fungal community associated with Fusarium wilt (FW) of banana. The community structure of fungi in the healthy and TR4-infected rhizospheres was significantly different compared with that of bulk soil within the same farm. The rhizosphere soils of infected plants exhibited higher richness and diversity compared with healthy plants, with significant abundance of Fusarium genus at 14%. In the healthy rhizosphere soil, Penicillium spp. were more abundant at 7% and positively correlated with magnesium. This study produced a detailed description of fungal community structure in healthy and TR4-infected banana soils in Malaysia and identified candidate biomarker taxa that may be associated with FW disease promotion and suppression. The findings also expand the global inventory of fungal communities associated with the components of asymptomatic and symptomatic banana plants infected by TR4.