Research priorities for harnessing plant microbiomes in sustainable agriculture

Changes in Endophyte Communities across the Different Plant Compartments in Response to the Rice Blast Infection

The rice blast disease, caused by the fungal pathogen, Magnaporthe oryzae (syn. Pyricularia oryzae), poses a significant threat to the global rice production. Understanding how this disease impacts the plant's microbial communities is crucial for gaining insights into hostpathogen interactions. In this study, we investigated the changes in communities of bacterial and fungal endophytes inhabiting different compartments in healthy and diseased plants. We found that both alpha and beta diversities of endophytic communities do not change significantly by the pathogen infection. Rather, the type of plant compartment appeared to be the main driver of endophytic community structures. Although the overall structure seemed to be consistent between healthy and diseased plants, our analysis of differentially abundant taxa revealed the specific bacterial and fungal operational taxonomic units that exhibited enrichment in the root and leaf compartments of infected plants. These findings suggest that endophyte communities are robust to the changes at the early stage of pathogen infection, and that some of endophytes enriched in infected plants might have roles in the defense against the pathogen.

Factors affecting the production of sugarcane yield and sucrose accumulation: suggested potential biological solutions

Environmental stresses are the main constraints on agricultural productivity and food security worldwide. This issue is worsened by abrupt and severe changes in global climate. The formation of sugarcane yield and the accumulation of sucrose are significantly influenced by biotic and abiotic stresses. Understanding the biochemical, physiological, and environmental phenomena associated with these stresses is essential to increase crop production. This review explores the effect of environmental factors on sucrose content and sugarcane yield and highlights the negative effects of insufficient water supply, temperature fluctuations, insect pests, and diseases. This article also explains the mechanism of reactive oxygen species (ROS), the role of different metabolites under environmental stresses, and highlights the function of environmental stress-related resistance genes in sugarcane. This review further discusses sugarcane crop improvement approaches, with a focus on endophytic mechanism and consortium endophyte application in sugarcane plants. Endophytes are vital in plant defense; they produce bioactive molecules that act as biocontrol agents to enhance plant immune systems and modify environmental responses through interaction with plants. This review provides an overview of internal mechanisms to enhance sugarcane plant growth and environmental resistance and offers new ideas for improving sugarcane plant fitness and crop productivity.

A synthetic microbial community used as a bioinoculant can overcome rice production constraints in acid soils

A customised synthetic microbial community (SynCom) composed of carefully selected rhizosphere-competent bacterial strains improved rice growth, yield and resistance to soil acidity and Al toxicity.

Soil prokaryotic and fungal biome structures associated with crop disease status across the Japan Archipelago

Archaea, bacteria, and fungi in the soil are increasingly recognized as determinants of agricultural productivity and sustainability. A crucial step for exploring soil microbiomes with important ecosystem functions is to perform statistical analyses on the potential relationship between microbiome structure and functions based on comparisons of hundreds or thousands of environmental samples collected across broad geographic ranges. In this study, we integrated agricultural field metadata with microbial community analyses by targeting 2,903 bulk soil samples collected along a latitudinal gradient from cool-temperate to subtropical regions in Japan (26.1-42.8 °N). The data involving 632 archaeal, 26,868 bacterial, and 4,889 fungal operational taxonomic units detected across the fields of 19 crop plant species allowed us to conduct statistical analyses (permutational analyses of variance, generalized linear mixed models, randomization analyses, and network analyses) on the relationship among edaphic factors, microbiome compositions, and crop disease prevalence. We then examined whether the diverse microbes form species sets varying in potential ecological impacts on crop plants. A network analysis suggested that the observed prokaryotes and fungi were classified into several species sets (network modules), which differed substantially in association with crop disease prevalence. Within the network of microbe-to-microbe coexistence, ecologically diverse microbes, such as an ammonium-oxidizing archaeon, an antibiotics-producing bacterium, and a potentially mycoparasitic fungus, were inferred to play key roles in shifts between crop-disease-promotive and crop-disease-suppressive states of soil microbiomes. The bird's-eye view of soil microbiome structure will provide a basis for designing and managing agroecosystems with high disease-suppressive functions.IMPORTANCEUnderstanding how microbiome structure and functions are organized in soil ecosystems is one of the major challenges in both basic ecology and applied microbiology. Given the ongoing worldwide degradation of agroecosystems, building frameworks for exploring structural diversity and functional profiles of soil microbiomes is an essential task. Our study provides an overview of cropland microbiome states in light of potential crop-disease-suppressive functions. The large data set allowed us to explore highly functional species sets that may be stably managed in agroecosystems. Furthermore, an analysis of network architecture highlighted species that are potentially used to cause shifts from disease-prevalent states of agroecosystems to disease-suppressive states. By extending the approach of comparative analyses toward broader geographic ranges and diverse agricultural practices, agroecosystem with maximized biological functions will be further explored.

Understanding and exploring the diversity of soil microorganisms in tea (Camellia sinensis) gardens: toward sustainable tea production

Leaves of Camellia sinensis plants are used to produce tea, one of the most consumed beverages worldwide, containing a wide variety of bioactive compounds that help to promote human health. Tea cultivation is economically important, and its sustainable production can have significant consequences in providing agricultural opportunities and lowering extreme poverty. Soil parameters are well known to affect the quality of the resultant leaves and consequently, the understanding of the diversity and functions of soil microorganisms in tea gardens will provide insight to harnessing soil microbial communities to improve tea yield and quality. Current analyses indicate that tea garden soils possess a rich composition of diverse microorganisms (bacteria and fungi) of which the bacterial Proteobacteria, Actinobacteria, Acidobacteria, Firmicutes and Chloroflexi and fungal Ascomycota, Basidiomycota, Glomeromycota are the prominent groups. When optimized, these microbes' function in keeping garden soil ecosystems balanced by acting on nutrient cycling processes, biofertilizers, biocontrol of pests and pathogens, and bioremediation of persistent organic chemicals. Here, we summarize research on the activities of (tea garden) soil microorganisms as biofertilizers, biological control agents and as bioremediators to improve soil health and consequently, tea yield and quality, focusing mainly on bacterial and fungal members. Recent advances in molecular techniques that characterize the diverse microorganisms in tea gardens are examined. In terms of viruses there is a paucity of information regarding any beneficial functions of soil viruses in tea gardens, although in some instances insect pathogenic viruses have been used to control tea pests. The potential of soil microorganisms is reported here, as well as recent techniques used to study microbial diversity and their genetic manipulation, aimed at improving the yield and quality of tea plants for sustainable production.

Root microbiota analysis of Oryza rufipogon and Oryza sativa reveals an orientation selection during the domestication process

The root-associated microbiota has a close relation to the life activities of plants, and its composition is affected by the rhizospheric environment and plant genotypes. Rice (Oryza sativa) was domesticated from the ancestor species Oryza rufipogon. Many important agricultural traits and adversity resistance of rice have changed during a long time of natural domestication and artificial selection. However, the influence of rice genotypes on root microbiota in important agricultural traits remains to be explained. In this study, we performed 16S rRNA and internal transcribed spacer (ITS) gene amplicon sequencing to generate bacterial and fungal community profiles of O. rufipogon and O. sativa, both of which were planted in a farm in Guangzhou and had reached the reproductive stage. We compared their root microbiota in detail by alpha diversity, beta diversity, different species, core microbiota, and correlation analyses. We found that the relative abundance of bacteria was significantly higher in the cultivated rice than in the common wild rice, while the relative abundance of fungi was the opposite. Significant differences in agricultural traits between O. rufipogon and O. sativa showed a high correlation with core microorganisms in the two Oryza species, which only existed in either or had obviously different abundance in both two species, indicating that rice genotype/phenotype had a strong influence on recruiting specific microorganisms. Our study provides a theoretical basis for the in-depth understanding of rice root microbiota and the improvement of rice breeding from the perspective of the interaction between root microorganisms and plants.IMPORTANCEPlant root microorganisms play a vital role not only in plant growth and development but also in responding the biotic and abiotic stresses. Oryza sativa is domesticated from Oryza rufipogon which has many excellent agricultural traits especially containing resistance to biotic and abiotic stresses. To improve the yield and resistance of cultivated rice, it is particularly important to deeply research on differences between O. sativa and O. rufipogon and find beneficial microorganisms to remodel the root microbiome of O. sativa.

Arbuscular Mycorrhizal Fungi and Rhizobium Improve Nutrient Uptake and Microbial Diversity Relative to Dryland Site-Specific Soil Conditions

Arbuscular mycorrhizal fungi (AMF) and rhizobium play a significant role in plant symbiosis. However, their influence on the rhizosphere soil microbiome associated with nutrient acquisition and soil health is not well defined in the drylands of Montana (MT), USA. This study investigated the effect of microbial inoculants as seed treatment on pea yield, nutrient uptake, potential microbial functions, and rhizosphere soil microbial communities using high-throughput sequencing of 16S and ITS rRNA genes. The experiment was conducted under two contrasting dryland conditions with four treatments: control, single inoculation with AMF or Rhizobium, and dual inoculations of AMF and Rhizobium (AMF+Rhizobium). Our findings revealed that microbial inoculation efficacy was site-specific. AMF+Rhizobium synergistically increased grain yield at Sidney dryland field site (DFS) 2, while at Froid site, DFS 1, AMF improved plant resilience to acidic soil but contributed a marginal yield under non-nutrient limiting conditions. Across dryland sites, the plants' microbial dependency on AMF+Rhizobium (12%) was higher than single inoculations of AMF (8%) or Rhizobium (4%) alone. Variations in microbial community structure and composition indicate a site-specific response to AMF and AMF+Rhizobium inoculants. Overall, site-specific factors significantly influenced plant nutrient uptake, microbial community dynamics, and functional potential. It underscores the need for tailored management strategies that consider site-specific characteristics to optimize benefits from microbial inoculation.

Environmental drivers and cryptic biodiversity hotspots define endophytes in Earth's largest terrestrial biome

Understanding how symbiotic associations differ across environmental gradients is key to predicting the fate of symbioses as environments change, and it is vital for detecting global reservoirs of symbiont biodiversity in a changing world.1,2,3 However, sampling of symbiotic partners at the full-biome scale is difficult and rare. As Earth's largest terrestrial biome, boreal forests influence carbon dynamics and climate regulation at a planetary scale. Plants and lichens in this biome host the highest known phylogenetic diversity of fungal endophytes, which occur within healthy photosynthetic tissues and can influence hosts' resilience to stress.4,5 We examined how communities of endophytes are structured across the climate gradient of the boreal biome, focusing on the dominant plant and lichen species occurring across the entire south-to-north span of the boreal zone in eastern North America. Although often invoked for understanding the distribution of biodiversity, neither a latitudinal gradient nor mid-domain effect5,6,7 can explain variation in endophyte diversity at this trans-biome scale. Instead, analyses considering shifts in forest characteristics, Picea biomass and age, and nutrients in host tissues from 46° to 58° N reveal strong and distinctive signatures of climate in defining endophyte assemblages in each host lineage. Host breadth of endophytes varies with climate factors, and biodiversity hotspots can be identified at plant-community transitions across the boreal zone at a global scale. Placed against a backdrop of global circumboreal sampling,4 our study reveals the sensitivity of endophytic fungi, their reservoirs of biodiversity, and their important symbiotic associations, to climate.

Unraveling plant-microbe interactions: can integrated omics approaches offer concrete answers?

Advances in high throughput omics techniques provide avenues to decipher plant microbiomes. However, there is limited information on how integrated informatics can help provide deeper insights into plant-microbe interactions in a concerted way. Integrating multi-omics datasets can transform our understanding of the plant microbiome from unspecified genetic influences on interacting species to specific gene-by-gene interactions. Here, we highlight recent progress and emerging strategies in crop microbiome omics research and review key aspects of how the integration of host and microbial omics-based datasets can be used to provide a comprehensive outline of complex crop-microbe interactions. We describe how these technological advances have helped unravel crucial plant and microbial genes and pathways that control beneficial, pathogenic, and commensal plant-microbe interactions. We identify crucial knowledge gaps and synthesize current limitations in our understanding of crop microbiome omics approaches. We highlight recent studies in which multi-omics-based approaches have led to improved models of crop microbial community structure and function. Finally, we recommend holistic approaches in integrating host and microbial omics datasets to achieve precision and efficiency in data analysis, which is crucial for biotic and abiotic stress control and in understanding the contribution of the microbiota in shaping plant fitness.

Manipulation of the seagrass-associated microbiome reduces disease severity

Host-associated microbes influence host health and function and can be a first line of defence against infections. While research increasingly shows that terrestrial plant microbiomes contribute to bacterial, fungal, and oomycete disease resistance, no comparable experimental work has investigated marine plant microbiomes or more diverse disease agents. We test the hypothesis that the eelgrass (Zostera marina) leaf microbiome increases resistance to seagrass wasting disease. From field eelgrass with paired diseased and asymptomatic tissue, 16S rRNA gene amplicon sequencing revealed that bacterial composition and richness varied markedly between diseased and asymptomatic tissue in one of the two years. This suggests that the influence of disease on eelgrass microbial communities may vary with environmental conditions. We next experimentally reduced the eelgrass microbiome with antibiotics and bleach, then inoculated plants with Labyrinthula zosterae, the causative agent of wasting disease. We detected significantly higher disease severity in eelgrass with a native microbiome than an experimentally reduced microbiome. Our results over multiple experiments do not support a protective role of the eelgrass microbiome against L. zosterae. Further studies of these marine host-microbe-pathogen relationships may continue to show new relationships between plant microbiomes and diseases.

Influence of cultivation duration on microbial taxa aggregation in Panax ginseng soils across ecological niches

Introduction

Microbial communities are crucial for plant health and productivity. However, the influence of cultivation age on the ecological processes in assembling plant microbiomes at various ecological niches remains unclear.

Methods

We selected 12 samples from ginseng farmlands with different cultivation years (N4: 4 years old, N6: 6 years old). We used soil physicochemical properties, enzyme activities, and high-throughput sequencing (16S rDNA and ITS) to examine the rhizoplane (RP), rhizosphere (RS), and bulk soil (BS).

Results

Our results indicated that cultivation years significantly affect the soil microbiome's diversity and community composition across different ecological niches. The BS microbiome experienced the largest effect, while the RS experienced the smallest. N6 showed a greater impact than N4. This effect was more pronounced on the fungal communities than the bacterial communities of various ecological niches and can be closely related to the soil's physicochemical properties. In N4 soils, we observed an upward trend in both the number of ASVs (amplicon sequence variations) and the diversity of soil microbial taxa across various ecological niches. In N4RP, the bacteria Sphingomonas, known for degrading toxic soil compounds, was present. All ecological niches in N4 showed significant enrichment of Tetracladium fungi, positively associated with crop yield (N4RP at 6.41%, N4RS at 11.31%, and N4BS at 3.45%). In N6 soils, we noted a stark decline in fungal diversity within the BS, with a 57.5% reduction in ASVs. Moreover, Sphingomonas was abundantly present in N6RS and N6BS soils. The relative abundance of the pathogen-inhibiting fungus Exophiala in N6RP and N6RS reached 34.18% and 13.71%, respectively, marking increases of 4.9-fold and 7.7-fold. Additionally, another pathogeninhibiting fungus, Humicola, showed significant enrichment in N6BS, with a 7.5-fold increase. The phenolic acid-producing fungus Pseudogymnoascus in N6RP, N6RS, and N6BS showed increases of 2.41-fold, 2.55-fold, and 4.32-fold, respectively. We hypothesize that functional genes related to the metabolism of terpenoids and polyketides, as well as signaling molecules and interactions, regulate soil microbial taxa in ginseng from different cultivation years.

Discussion

In conclusion, our study enhances understanding of plant-microbe interactions and aids the sustainable development of medicinal plants, particularly by addressing ginseng succession disorder.

B. subtilis CNBG-PGPR-1 induces methionine to regulate ethylene pathway and ROS scavenging for improving salt tolerance of tomato

Soil salinity severely threatens plant growth and crop yields. The utilization of PGPR is an effective strategy for enhancing plant salt tolerance, but the mechanisms involved in this process have rarely been reported. In this study, we investigated the effects of Bacillus subtilis CNBG-PGPR-1 on improving plant salt tolerance and elucidated the molecular pathways involved. The results showed that CNBG-PGPR-1 significantly improved the cellular homeostasis and photosynthetic efficiency of leaves and reduced ion toxicity and osmotic stress caused by salt in tomato. Transcriptome analysis uncovered that CNBG-PGPR-1 enhanced plant salt tolerance through the activation of complex molecular pathways, with plant hormone signal transduction playing an important role. Comparative analysis and pharmacological experiments confirmed that the ethylene pathway was closely related to the beneficial effect of CNBG-PGPR-1 on improving plant salt tolerance. Furthermore, we found that methionine, a precursor of ethylene synthesis, significantly accumulated in response to CNBG-PGPR-1 in tomato. Exogenous L-methionine largely mimicked the beneficial effects of CNBG-PGPR-1 and activated the expression of ethylene pathway-related genes, indicating CNBG-PGPR-1 induces methionine accumulation to regulate the ethylene pathway in tomato. Finally, CNBG-PGPR-1 reduced salt-induced ROS by activating ROS scavenger-encoding genes, mainly involved in GSH metabolism and POD-related genes, which were also closely linked to methionine metabolism. Overall, our studies demonstrate that CNBG-PGPR-1-induced methionine is a key regulator in enhancing plant salt tolerance through the ethylene pathway and ROS scavenging, providing a novel understanding of the mechanism by which beneficial microbes improve plant salt tolerance.

Conspecific versus heterospecific transmission shapes host specialization of the phyllosphere microbiome

In disease ecology, pathogen transmission among conspecific versus heterospecific hosts is known to shape pathogen specialization and virulence, but we do not yet know if similar effects occur at the microbiome level. We tested this idea by experimentally passaging leaf-associated microbiomes either within conspecific or across heterospecific plant hosts. Although conspecific transmission results in persistent host-filtering effects and more within-microbiome network connections, heterospecific transmission results in weaker host-filtering effects but higher levels of interconnectivity. When transplanted onto novel plants, heterospecific lines are less differentiated by host species than conspecific lines, suggesting a shift toward microbiome generalism. Finally, conspecific lines from tomato exhibit a competitive advantage on tomato hosts against those passaged on bean or pepper, suggesting microbiome-level host specialization. Overall, we find that transmission mode and previous host history shape microbiome diversity, with repeated conspecific transmission driving microbiome specialization and repeated heterospecific transmission promoting microbiome generalism.

Variety-driven rhizosphere microbiome bestows differential salt tolerance to alfalfa for coping with salinity stress

Soil salinization is a global environmental issue and a significant abiotic stress that threatens crop production. Root-associated rhizosphere microbiota play a pivotal role in enhancing plant tolerance to abiotic stresses. However, limited information is available concerning the specific variations in rhizosphere microbiota driven by different plant genotypes (varieties) in response to varying levels of salinity stress. In this study, we compared the growth performance of three alfalfa varieties with varying salt tolerance levels in soils with different degrees of salinization. High-throughput 16S rRNA and ITS sequencing were employed to analyze the rhizosphere microbial communities. Undoubtedly, the increasing salinity significantly inhibited alfalfa growth and reduced rhizosphere microbial diversity. However, intriguingly, salt-tolerant varieties exhibited relatively lower susceptibility to salinity, maintaining more stable rhizosphere bacterial community structure, whereas the reverse was observed for salt-sensitive varieties. Bacillus emerged as the dominant species in alfalfa's adaptation to salinity stress, constituting 21.20% of the shared bacterial genera among the three varieties. The higher abundance of Bacillus, Ensifer, and Pseudomonas in the rhizosphere of salt-tolerant alfalfa varieties is crucial in determining their elevated salt tolerance. As salinity levels increased, salt-sensitive varieties gradually accumulated a substantial population of pathogenic fungi, such as Fusarium and Rhizoctonia. Furthermore, rhizosphere bacteria of salt-tolerant varieties exhibited increased activity in various metabolic pathways, including biosynthesis of secondary metabolites, carbon metabolism, and biosynthesis of amino acids. It is suggested that salt-tolerant alfalfa varieties can provide more carbon sources to the rhizosphere, enriching more effective plant growth-promoting bacteria (PGPB) such as Pseudomonas to mitigate salinity stress. In conclusion, our results highlight the variety-mediated enrichment of rhizosphere microbiota in response to salinity stress, confirming that the high-abundance enrichment of specific dominant rhizosphere microbes and their vital roles play a significant role in conferring high salt adaptability to these varieties.

Identifying microbiota community patterns important for plant protection using synthetic communities and machine learning

Plant-associated microbiomes contribute to important ecosystem functions such as host resistance to biotic and abiotic stresses. The factors that determine such community outcomes are inherently difficult to identify under complex environmental conditions. In this study, we present an experimental and analytical approach to explore microbiota properties relevant for a microbiota-conferred host phenotype, here plant protection, in a reductionist system. We screened 136 randomly assembled synthetic communities (SynComs) of five bacterial strains each, followed by classification and regression analyses as well as empirical validation to test potential explanatory factors of community structure and composition, including evenness, total commensal colonization, phylogenetic diversity, and strain identity. We find strain identity to be the most important predictor of pathogen reduction, with machine learning algorithms improving performances compared to random classifications (94-100% versus 32% recall) and non-modelled predictions (0.79-1.06 versus 1.5 RMSE). Further experimental validation confirms three strains as the main drivers of pathogen reduction and two additional strains that confer protection in combination. Beyond the specific application presented in our study, we provide a framework that can be adapted to help determine features relevant for microbiota function in other biological systems.

Allelopathy-selected microbiomes mitigate chemical inhibition of plant performance

Allelopathy is a common and important stressor that shapes plant communities and can alter soil microbiomes, yet little is known about the direct effects of allelochemical addition on bacterial and fungal communities or the potential for allelochemical-selected microbiomes to mediate plant performance responses, especially in habitats naturally structured by allelopathy. Here, we present the first community-wide investigation of microbial mediation of allelochemical effects on plant performance by testing how allelopathy affects soil microbiome structure and how these microbial changes impact germination and productivity across 13 plant species. The soil microbiome exhibited significant changes to 'core' bacterial and fungal taxa, bacterial composition, abundance of functionally important bacterial and fungal taxa, and predicted bacterial functional genes after the addition of the dominant allelochemical native to this habitat. Furthermore, plant performance was mediated by the allelochemical-selected microbiome, with allelopathic inhibition of plant productivity moderately mitigated by the microbiome. Through our findings, we present a potential framework to understand the strength of plant-microbial interactions in the presence of environmental stressors, in which frequency of the ecological stress may be a key predictor of microbiome-mediation strength.

Above- and belowground fungal biodiversity of Populus trees on a continental scale

Understanding drivers of terrestrial fungal communities over large scales is an important challenge for predicting the fate of ecosystems under climate change and providing critical ecological context for bioengineering plant-microbe interactions in model systems. We conducted an extensive molecular and microscopy field study across the contiguous United States measuring natural variation in the Populus fungal microbiome among tree species, plant niche compartments and key symbionts. Our results show clear biodiversity hotspots and regional endemism of Populus-associated fungal communities explained by a combination of climate, soil and geographic factors. Modelling climate change impacts showed a deterioration of Populus mycorrhizal associations and an increase in potentially pathogenic foliar endophyte diversity and prevalence. Geographic differences among these symbiont groups in their sensitivity to environmental change are likely to influence broader forest health and ecosystem function. This dataset provides an above- and belowground atlas of Populus fungal biodiversity at a continental scale.

Intraspecific variation in realized dispersal probability and host quality shape nectar microbiomes

Epiphytic microbes frequently affect plant phenotype and fitness, but their effects depend on microbe abundance and community composition. Filtering by plant traits and deterministic dispersal-mediated processes can affect microbiome assembly, yet their relative contribution to predictable variation in microbiome is poorly understood. We compared the effects of host-plant filtering and dispersal on nectar microbiome presence, abundance, and composition. We inoculated representative bacteria and yeast into 30 plants across four phenotypically distinct cultivars of Epilobium canum. We compared the growth of inoculated communities to openly visited flowers from a subset of the same plants. There was clear evidence of host selection when we inoculated flowers with synthetic communities. However, plants with the highest microbial densities when inoculated did not have the highest microbial densities when openly visited. Instead, plants predictably varied in the presence of bacteria, which was correlated with pollen receipt and floral traits, suggesting a role for deterministic dispersal. These findings suggest that host filtering could drive plant microbiome assembly in tissues where species pools are large and dispersal is high. However, deterministic differences in microbial dispersal to hosts may be equally or more important when microbes rely on an animal vector, dispersal is low, or arrival order is important.

Fossil-fuel-dependent scenarios could lead to a significant decline of global plant-beneficial bacteria abundance in soils by 2100

Exploiting the potential benefits of plant-associated microbes represents a sustainable approach to enhancing crop productivity. Plant-beneficial bacteria (PBB) provide multiple benefits to plants. However, the biogeography and community structure remain largely unknown. Here we constructed a PBB database to couple microbial taxonomy with their plant-beneficial traits and analysed the global atlas of potential PBB from 4,245 soil samples. We show that the diversity of PBB peaks in low-latitude regions, following a strong latitudinal diversity gradient. The distribution of potential PBB was primarily governed by environmental filtering, which was mainly determined by local climate. Our projections showed that fossil-fuel-dependent future scenarios would lead to a significant decline of potential PBB by 2100, especially biocontrol agents (-1.03%) and stress resistance bacteria (-0.61%), which may potentially threaten global food production and (agro)ecosystem services.

Influence of organic plant breeding on the rhizosphere microbiome of common bean (Phaseolus vulgaris L.)

Introduction

We now recognize that plant genotype affects the assembly of its microbiome, which in turn, affects essential plant functions. The production system for crop plants also influences the microbiome composition, and as a result, we would expect to find differences between conventional and organic production systems. Plant genotypes selected in an organic regime may host different microbiome assemblages than those selected in conventional environments. We aimed to address these questions using recombinant inbred populations of snap bean that differed in breeding history.

Methods

Rhizosphere microbiomes of conventional and organic common beans (Phaseolus vulgaris L.) were characterized within a long-term organic research site. The fungal and bacterial communities were distinguished using pooled replications of 16S and ITS amplicon sequences, which originated from rhizosphere samples collected between flowering and pod set.

Results

Bacterial communities significantly varied between organic and conventional breeding histories, while fungal communities varied between breeding histories and parentage. Within the organically-bred populations, a higher abundance of a plant-growth-promoting bacteria, Arthrobacter pokkalii, was identified. Conventionally-bred beans hosted a higher abundance of nitrogen-fixing bacteria that normally do not form functional nodules with common beans. Fungal communities in the organically derived beans included more arbuscular mycorrhizae, as well as several plant pathogens.

Discussion

The results confirm that the breeding environment of crops can significantly alter the microbiome community composition of progeny. Characterizing changes in microbiome communities and the plant genes instrumental to these changes will provide essential information about how future breeding efforts may pursue microbiome manipulation.

Crop adaptation to climate change: An evolutionary perspective

The disciplines of evolutionary biology and plant and animal breeding have been intertwined throughout their development, with responses to artificial selection yielding insights into the action of natural selection and evolutionary biology providing statistical and conceptual guidance for modern breeding. Here we offer an evolutionary perspective on a grand challenge of the 21st century: feeding humanity in the face of climate change. We first highlight promising strategies currently under way to adapt crops to current and future climate change. These include methods to match crop varieties with current and predicted environments and to optimize breeding goals, management practices, and crop microbiomes to enhance yield and sustainable production. We also describe the promise of crop wild relatives and recent technological innovations such as speed breeding, genomic selection, and genome editing for improving environmental resilience of existing crop varieties or for developing new crops. Next, we discuss how methods and theory from evolutionary biology can enhance these existing strategies and suggest novel approaches. We focus initially on methods for reconstructing the evolutionary history of crops and their pests and symbionts, because such historical information provides an overall framework for crop-improvement efforts. We then describe how evolutionary approaches can be used to detect and mitigate the accumulation of deleterious mutations in crop genomes, identify alleles and mutations that underlie adaptation (and maladaptation) to agricultural environments, mitigate evolutionary trade-offs, and improve critical proteins. Continuing feedback between the evolution and crop biology communities will ensure optimal design of strategies for adapting crops to climate change.

Plant beneficial microbiome a boon for improving multiple stress tolerance in plants

Beneficial microbes or their products have been key drivers for improving adaptive and growth features in plants under biotic and abiotic stress conditions. However, the majority of these studies so far have been utilized against individual stressors. In comparison to individual stressors, the combination of many environmental stresses that plants experience has a greater detrimental effect on them and poses a threat to their existence. Therefore, there is a need to explore the beneficial microbiota against combined stressors or multiple stressors, as this will offer new possibilities for improving plant growth and multiple adaptive traits. However, recognition of the multifaceted core beneficial microbiota from plant microbiome under stress combinations will require a thorough understanding of the functional and mechanistic facets of plant microbiome interactions under different environmental conditions in addition to agronomic management practices. Also, the development of tailored beneficial multiple stress tolerant microbiota in sustainable agriculture necessitates new model systems and prioritizes agricultural microbiome research. In this review, we provided an update on the effect of combined stressors on plants and their microbiome structure. Next, we discussed the role of beneficial microbes in plant growth promotion and stress adaptation. We also discussed how plant-beneficial microbes can be utilized for mitigating multiple stresses in plants. Finally, we have highlighted some key points that warrant future investigation for exploring plant microbiome interactions under multiple stressors.

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.

Exploring the Core Bacteria and Functional Traits in Pecan (Carya illinoinensis) Rhizosphere

Pecan (Carya illinoinensis) and Chinese hickory (Carya cathayensis) are important commercially cultivated nut trees. They are phylogenetically closely related plants; however, they exhibit significantly different phenotypes in response to abiotic stress and development. The rhizosphere selects core microorganisms from bulk soil, playing a pivotal role in the plant's resistance to abiotic stress and growth. In this study, we used metagenomic sequencing to compare the selection capabilities of seedling pecan and seedling hickory at taxonomic and functional levels in bulk soil and the rhizosphere. We observed that pecan has a stronger capacity to enrich rhizosphere plant-beneficial microbe bacteria (e.g., Rhizobium, Novosphingobium, Variovorax, Sphingobium, and Sphingomonas) and their associated functional traits than hickory. We also noted that the ABC transporters (e.g., monosaccharide transporter) and bacterial secretion systems (e.g., type IV secretion system) are the core functional traits of pecan rhizosphere bacteria. Rhizobium and Novosphingobium are the main contributors to the core functional traits. These results suggest that monosaccharides may help Rhizobium to efficiently enrich this niche. Novosphingobium may use a type IV secretion system to interact with other bacteria and thereby influence the assembly of pecan rhizosphere microbiomes. Our data provide valuable information to guide core microbial isolation and expand our knowledge of the assembly mechanisms of plant rhizosphere microbes. IMPORTANCE The rhizosphere microbiome has been identified as a fundamental factor in maintaining plant health, helping plants to fight the deleterious effects of diseases and abiotic stresses. However, to date, studies on the nut tree microbiome have been scarce. Here, we observed a significant "rhizosphere effect" on the seedling pecan. We furthermore demonstrated the core rhizosphere microbiome and function in the seedling pecan. Moreover, we deduced possible factors that help the core bacteria, such as Rhizobium, to efficiently enrich the pecan rhizosphere and the importance of the type IV system for the assembly of pecan rhizosphere bacterial communities. Our findings provide information for understanding the mechanism of the rhizosphere microbial community enrichment process.

Biogeography of Fungal Communities Associated with Pinus sylvestris L. and Picea abies (L.) H. Karst. along the Latitudinal Gradient in Europe

We assessed the diversity and composition of fungal communities in different functional tissues and the rhizosphere soil of Pinus sylvestris and Picea abies stands along the latitudinal gradient of these tree species distributions in Europe to model possible changes in fungal communities imposed by climate change. For each tree species, living needles, shoots, roots, and the rhizosphere soil were sampled and subjected to high-throughput sequencing. Results showed that the latitude and the host tree species had a limited effect on the diversity and composition of fungal communities, which were largely explained by the environmental variables of each site and the substrate they colonize. The mean annual temperature and mean annual precipitation had a strong effect on root fungal communities, isothermality on needle fungal communities, mean temperature of the warmest quarter and precipitation of the driest month on shoot fungal communities, and precipitation seasonality on soil fungal communities. Fungal communities of both tree species are predicted to shift to habitats with a lower annual temperature amplitude and with increasing precipitation during the driest month, but the suitability of these habitats as compared to the present conditions is predicted to decrease in the future.

The Microbial Connection to Sustainable Agriculture

Microorganisms are an important element in modeling sustainable agriculture. Their role in soil fertility and health is crucial in maintaining plants' growth, development, and yield. Further, microorganisms impact agriculture negatively through disease and emerging diseases. Deciphering the extensive functionality and structural diversity within the plant-soil microbiome is necessary to effectively deploy these organisms in sustainable agriculture. Although both the plant and soil microbiome have been studied over the decades, the efficiency of translating the laboratory and greenhouse findings to the field is largely dependent on the ability of the inoculants or beneficial microorganisms to colonize the soil and maintain stability in the ecosystem. Further, the plant and its environment are two variables that influence the plant and soil microbiome's diversity and structure. Thus, in recent years, researchers have looked into microbiome engineering that would enable them to modify the microbial communities in order to increase the efficiency and effectiveness of the inoculants. The engineering of environments is believed to support resistance to biotic and abiotic stressors, plant fitness, and productivity. Population characterization is crucial in microbiome manipulation, as well as in the identification of potential biofertilizers and biocontrol agents. Next-generation sequencing approaches that identify both culturable and non-culturable microbes associated with the soil and plant microbiome have expanded our knowledge in this area. Additionally, genome editing and multidisciplinary omics methods have provided scientists with a framework to engineer dependable and sustainable microbial communities that support high yield, disease resistance, nutrient cycling, and management of stressors. In this review, we present an overview of the role of beneficial microbes in sustainable agriculture, microbiome engineering, translation of this technology to the field, and the main approaches used by laboratories worldwide to study the plant-soil microbiome. These initiatives are important to the advancement of green technologies in agriculture.

Selection of rhizosphere communities of diverse rotation crops reveals unique core microbiome associated with reduced banana Fusarium wilt disease

Crop rotation can assemble distinct core microbiota as functionally specific barriers against the invasion of banana Fusarium oxysporum pathogens. However, the taxonomic identity of rotation-unique core taxa and their legacy effects are poorly understood under field conditions. Pepper and eggplant rotations were employed to reveal rotation crop- and banana-unique antagonistic core taxa by in situ tracking of the soil microbiome assembly patterns for 2 yr. The rotation crop-unique antagonistic taxa were isolated and functionally verified by culture-dependent techniques, high-throughput sequencing, and pot experiments. Pepper and eggplant rotations resulted in eight and one rotation-unique antagonistic core taxa out of 12 507 microbial taxa, respectively. These nine antagonistic taxa were retained the following year and significantly decreased banana wilt disease incidence via legacy effects, although the cultivated strains were exclusively of the genera Bacillus and Pseudomonas. The fermentation broth and volatiles of these two taxa showed strong antagonistic activity, and pot experiments demonstrated high suppression of wilt disease and significant promotion of banana growth. Our study provides a mechanistic understanding of the identification of rotation crop-unique antagonistic taxa and highlights the importance of targeted cultivation of beneficial microorganisms for optimizing crop rotation-based scenarios in support of banana agriculture sustainability.

Effects of above ground pathogen infection and fungicide application on the root-associated microbiota of apple saplings

BACKGROUND

The root-associated microbiome has been of keen research interest especially in the last decade due to the large potential for increasing overall plant performance in agricultural systems. Knowledge about the impact of above ground plant disturbances on the root-associated microbiome remains limited. We addressed this by focusing on two potential impacts, foliar pathogen infection alone and in combination with the application of a plant health protecting product. We hypothesized that these lead to plant-mediated responses in the rhizosphere microbiota.

RESULTS

The effects of an infection of greenhouse grown apple saplings with either Venturia inaequalis or Podosphaera leucotricha as foliar pathogen, as well as the combined effect of P. leucotricha infection and foliar application of the synthetic plant health protecting product Aliette (active ingredient: fosetyl-aluminum), were studied on the root-associated microbiota. The bacterial community structure of rhizospheric soil and endospheric root material was characterized post-infection, using 16S rRNA gene amplicon sequencing. With increasing disease severity both pathogens led to changes in the rhizosphere and endosphere bacterial communities in comparison to uninfected plants (explained variance up to 17.7%). While the preventive application of Aliette on healthy plants two weeks prior inoculation did not induce changes in the root-associated microbiota, a second later application on the diseased plants decreased disease severity and resulted in differences of the rhizosphere bacterial community between infected and several of the cured plants, though differences were overall not statistically significant.

CONCLUSIONS

Foliar pathogen infections can induce plant-mediated changes in the root-associated microbiota, indicating that above ground disturbances are reflected in the below-ground microbiome, even though these become evident only upon severe leaf infection. The application of the fungicide Aliette on healthy plants itself did not induce any changes, but the application to diseased plants helped the plant to regain the microbiota of a healthy plant. These findings indicate that above ground agronomic management practices have implications for the root-associated microbiome, which should be considered in the context of microbiome management strategies.

A core epiphytic bacterial consortia synergistically protect citrus from postharvest disease

Biological antagonists are a series of microbes that can control pathogens to reduce the incidence of disease or reduce symptoms. Herein, four varieties of citrus fruit were selected to perform an amplicon sequencing on their epiphytic microbiota to get a systematic understanding of them. Co-occurrence network, Venn, and LefSe analysis were performed to filter to 24 genera which represent the universality, specificity, and correlation among samples. Functional analysis hinted that the genes related to chitinase, which most of these 24 bacteria carry, might lead to a disease-suppressive phenotype. 115 strains of epiphytic bacteria were isolated, and the bacterial synthetic community was constructed by 8 strains. The in vivo test results indicated they were able to reduce pathogen development for a longer time than separate inoculation. Collectively, this study showed the disease control potential provided by native epiphytic bacteria of fruit and give a new strategy to sustainable agriculture.

Microorganisms Associated with the Ambrosial Beetle Xyleborus affinis with Plant Growth-Promotion Activity in Arabidopsis Seedlings and Antifungal Activity Against Phytopathogenic Fungus Fusarium sp. INECOL_BM-06

Plants interact with a great diversity of microorganisms or insects throughout their life cycle in the environment. Plant and insect interactions are common; besides, a great variety of microorganisms associated with insects can induce pathogenic damage in the host, as mutualist phytopathogenic fungus. However, there are other microorganisms present in the insect-fungal association, whose biological/ecological activities and functions during plant interaction are unknown. In the present work evaluated, the role of microorganisms associated with Xyleborus affinis, an important beetle species within the Xyleborini tribe, is characterized by attacking many plant species, some of which are of agricultural and forestry importance. We isolated six strains of microorganisms associated with X. affinis shown as plant growth-promoting activity and altered the root system architecture independent of auxin-signaling pathway in Arabidopsis seedlings and antifungal activity against the phytopathogenic fungus Fusarium sp. INECOL_BM-06. In addition, evaluating the tripartite interaction plant-microorganism-fungus, interestingly, we found that microorganisms can induce protection against the phytopathogenic fungus Fusarium sp. INECOL_BM-06 involving the jasmonic acid-signaling pathway and independent of salicylic acid-signaling pathway. Our results showed the important role of this microorganisms during the plant- and insect-microorganism interactions, and the biological potential use of these microorganisms as novel agents of biological control in the crops of agricultural and forestry is important.

A Synthetic Microbial Community of Plant Core Microbiome Can Be a Potential Biocontrol Tool

Microbes are accepted as the foremost drivers of the rhizosphere ecology that influences plant health in direct or indirect ways. In recent years, the rapid development of gene sequencing technology has greatly facilitated the study of plant microbiome structure and function, and various plant-associated microbiomes have been categorized. Additionally, there is growing research interest in plant-disease-related microbes, and some specific microflora beneficial to plant health have been identified. This Review discusses the plant-associated microbiome's biological control pathways and functions to modulate plant defense against pathogens. How do plant microbiomes enhance plant resistance? How does the plant core microbiome-associated synthetic microbial community (SynCom) improve plant health? This Review further points out the primary need to develop smart agriculture practices using SynComs against plant diseases. Finally, this Review provides ideas for future opportunities in plant disease control and mining new microbial resources.

The core fungal microbiome of banana (Musa spp.)

Here, we report a metabarcoding (ITS2) study to define the common core fungal microbiome (mycobiome) of healthy Musa spp. (bananas and plantains). To identify a list of 21 core fungal taxa, we first characterised the effects of edaphic conditions and host genotype – two factors that are likely to differ between farms – on the diversity of fungal communities in bulk soil and seven plant compartments. This experiment facilitated shortlisting of core ‘candidates’, which were then elevated to full core status if also found to frequent a wide-range of field-grown Musa spp. and exhibit hub-like characteristics in network analyses. Subsequently, we conducted a meta-analysis of eleven publicly available datasets of Musa spp. associated fungi demonstrating that the core fungi identified in our study have close relatives in other countries. The diversity and composition of mycobiomes differed between plant compartments and soils, but not genotypes. The core mycobiome included Fusarium oxysporum and its relatives, which dominated all plant compartments, as well as members of the Sordariomycetes, Dothideomycetes, and Mortierellomycota. Our study provides a robust list of common core fungal taxa for Musa spp. Further studies may consider how changes in the frequencies and activities of these taxa influence host fitness and whether they can be managed to improve banana production.

Alternative stable states, nonlinear behavior, and predictability of microbiome dynamics

BACKGROUND

Microbiome dynamics are both crucial indicators and potential drivers of human health, agricultural output, and industrial bio-applications. However, predicting microbiome dynamics is notoriously difficult because communities often show abrupt structural changes, such as "dysbiosis" in human microbiomes.

METHODS

We integrated theoretical frameworks and empirical analyses with the aim of anticipating drastic shifts of microbial communities. We monitored 48 experimental microbiomes for 110 days and observed that various community-level events, including collapse and gradual compositional changes, occurred according to a defined set of environmental conditions. We analyzed the time-series data based on statistical physics and non-linear mechanics to describe the characteristics of the microbiome dynamics and to examine the predictability of major shifts in microbial community structure.

RESULTS

We confirmed that the abrupt community changes observed through the time-series could be described as shifts between "alternative stable states" or dynamics around complex attractors. Furthermore, collapses of microbiome structure were successfully anticipated by means of the diagnostic threshold defined with the "energy landscape" analysis of statistical physics or that of a stability index of nonlinear mechanics.

CONCLUSIONS

The results indicate that abrupt microbiome events in complex microbial communities can be forecasted by extending classic ecological concepts to the scale of species-rich microbial systems. Video Abstract.

Indirect Enrichment of Desirable, but Less Fit Phenotypes, from a Synthetic Microbial Community Using Microdroplet Confinement

Spatial structure within microbial communities can provide nearly limitless opportunities for social interactions and are an important driver for evolution. As metabolites are often molecular signals, metabolite diffusion within microbial communities can affect the composition and dynamics of the community in a manner that can be challenging to deconstruct. We used encapsulation of a synthetic microbial community within microdroplets to investigate the effects of spatial structure and metabolite diffusion on population dynamics and to examine the effects of cheating by one member of the community. The synthetic community was composed of three strains: a "Producer" that makes the diffusible quorum sensing molecule (N-(3-oxododecanoyl)-l-homoserine lactone, C12-oxo-HSL) or AHL; a "Receiver" that is killed by AHL; and a Non-Producer or "cheater" that benefits from the extinction of the Receivers, but without the costs associated with the AHL synthesis. We demonstrate that despite rapid diffusion of AHL between microdroplets, the spatial structure imposed by the microdroplets allows a more efficient but transient enrichment of more rare and slower-growing Producer subpopulations. Eventually, the Non-Producer population drove the Producers to extinction. By including fluorescence-activated microdroplet sorting and providing sustained competition by the Receiver strain, we demonstrate a strategy for indirect enrichment of a rare and unlabeled Producer. The ability to screen and enrich metabolite Producers from a much larger population under conditions of rapid diffusion provides an important framework for the development of applications in synthetic ecology and biotechnology.

Responses of rhizosphere bacterial communities in newly reclaimed mudflat paddies to rice genotype and nitrogen fertilizer rate

The rhizosphere microbiome plays a vital role in crop growth and adaptation. However, the effects of rice genotype, nitrogen (N) fertilization, and their interactions on the rhizosphere bacterial communities in low fertility soil remain poorly understood. In this study, a two-factor field experiment was performed in newly reclaimed mudflat paddies characterized by poor fertility to analyze bacterial communities in the rhizosphere of Yongyou 2640 (japonica/indica hybrid rice, JIH) and Huaidao No.5 (japonica conventional rice, JC) under different N fertilizer rates. Results showed that genotype, followed by N fertilizer rate, was the primary factor affecting rhizobacteria diversity. Rhizobacteria diversity was higher in JIH than in JC and that of JIH and JC did not significantly change overall as N fertilizer rates but increased and decreased at N fertilizer rates of over 300 kg N ha^-1, respectively. The inconsistent response was probably attributed to the difference in the increase of ammonium and/or nitrate in the rhizosphere of JIH and JC. Genotype explained approximately 26% of the variation in rhizosphere bacterial communities. Rhizosphere bacterial communities with N fertilizer rates of over 300 kg N ha^-1 were more dissimilar to those without N fertilization relative to those with N fertilizer rates of below 300 kg N ha^-1, which was mainly attributed to changes in the concentration of ammonium and/or nitrate. The relative abundances of some potential beneficial genera such as Salinimicrobium, Salegentibacter, Gillisia, and Anaerolinea in the rhizosphere of JC and Salegentibacter, Lysobacter, Nocardioides, and Pontibacter in the rhizosphere of JIH were increased under N fertilizer rates of less than 300 kg N ha^-1 and positively correlated with rice yields, which indicate that changes in bacterial communities caused by N fertilization might be strongly associated with the improvement of rice yield. Overall, rhizosphere bacterial communities were more sensitive to genotype in newly reclaimed mudflat paddies and showed a consistent response to N fertilizer rates.

Seasonal activities of the phyllosphere microbiome of perennial crops

Understanding the interactions between plants and microorganisms can inform microbiome management to enhance crop productivity and resilience to stress. Here, we apply a genome-centric approach to identify ecologically important leaf microbiome members on replicated plots of field-grown switchgrass and miscanthus, and to quantify their activities over two growing seasons for switchgrass. We use metagenome and metatranscriptome sequencing and curate 40 medium- and high-quality metagenome-assembled-genomes (MAGs). We find that classes represented by these MAGs (Actinomycetia, Alpha- and Gamma- Proteobacteria, and Bacteroidota) are active in the late season, and upregulate transcripts for short-chain dehydrogenase, molybdopterin oxidoreductase, and polyketide cyclase. Stress-associated pathways are expressed for most MAGs, suggesting engagement with the host environment. We also detect seasonally activated biosynthetic pathways for terpenes and various non-ribosomal peptide pathways that are poorly annotated. Our findings support that leaf-associated bacterial populations are seasonally dynamic and responsive to host cues.

Interactive effects of intercropping and mulching under conservation tillage as sustainable agriculture increased cotton productivity

Climate change poses a significant risk to food security. Recent floods in Pakistan could serve as an example. In the current climate change scenario, there is a dire need to develop methods that increase crop productivity and reduce the threat of food insecurity in areas with low crop production. A detailed field experiment was conducted to check the effects of intercropping and straw mulching under conventional tillage (CT) and no tillage (NT) systems on soil health indicators and cotton productivity at the experimental area of Khwaja Fareed University of Engineering and Information Technology (KFUEIT), Rahim Yar Khan, Pakistan. The main plot treatments comprised CT and NT. The subplot treatments were sole cotton (C1), cotton + mung-bean intercropping (C2), cotton + mung-bean + straw mulching (C3) and cotton + straw mulching (C4) under CT, while sole cotton (N1), cotton + mung-bean intercropping (N2), cotton + mung-bean + straw mulching (N3) and cotton + straw mulching (N4) were the NT subplot treatments. Overall, NT increased plant height by 18.4 %, chlorophyll a and b contents by 28.2 and 21.1%, respectively, mean boll weight by 17.9%, and seed yield by 20.9% compared to CT (P < 0.05). The interaction of tillage and mulching increased plant height by 7.0% under CT and 21.8% under NT in comparison with no mulching. Similarly, straw mulching under NT increased chlorophyll a and b contents by 41.9 and 28.5%, respectively, mean boll weight by 26.9%, and cotton seed yield by 23.0% in comparison with no mulching under NT. Intercropping decreased crop yield without straw mulching but increased it under straw mulching. Further, straw mulching increased soil physicochemical properties under NT, which contributed to increasing crop productivity. We concluded that straw mulching under NT might be a promising practice for enhancing cotton yield, productivity, and soil health in low-productivity areas.

Indirect enrichment of desirable, but less fit phenotypes, from a synthetic microbial community using microdroplet confinement

Spatial structure within microbial communities can provide nearly limitless opportunities for social interactions and are an important driver for evolution. As metabolites are often molecular signals, metabolite diffusion within microbial communities can affect the composition and dynamics of the community in a manner that can be challenging to deconstruct. We used encapsulation of a synthetic microbial community within microdroplets to investigate the effects of spatial structure and metabolite diffusion on population dynamics and to examine the effects of cheating by one member of the community. The synthetic community was comprised of three strains: a 'Producer' that makes the diffusible quorum sensing molecule ( N -(3-Oxododecanoyl)-L-homoserine lactone, C12-oxo-HSL) or AHL; a 'Receiver' that is killed by AHL and a Non-Producer or 'cheater' that benefits from the extinction of the Receivers, but without the costs associated with the AHL synthesis. We demonstrate that despite rapid diffusion of AHL between microdroplets, the spatial structure imposed by the microdroplets allow a more efficient but transient enrichment of more rare and slower growing 'Producer' subpopulations. Eventually, the Non-Producer population drove the Producers to extinction. By including fluorescence-activated microdroplet sorting and providing sustained competition by the Receiver strain, we demonstrate a strategy for indirect enrichment of a rare and unlabeled Producer. The ability to screen and enrich metabolite Producers from a much larger population under conditions of rapid diffusion provides an important framework for the development of applications in synthetic ecology and biotechnology.

Abstract Figure

Treatment with organic manure inoculated with a biocontrol agent induces soil bacterial communities to inhibit tomato Fusarium wilt disease

Introduction

Organic manure, plant growth-promoting microorganisms, and biocontrol agents are widely used to sustainably control soil-borne diseases. However, how and whether organic manure inoculated with biocontrol agents alters soil microbiota and reduces disease severity is poorly understood.

Methods

Here, we examined changes to the soil microbial community, soil properties, and incidence of Fusarium wilt disease in response to several fertilization regimes. Specifically, we studied the effects of inorganic chemical fertilization (CF), organic manure fertilization (OF), and Erythrobacter sp. YH-07-inoculated organic manure fertilization (BF) on the incidence of Fusarium wilt in tomato across three seasons.

Results

BF-treated soils showed increased microbial abundance, richness, and diversity compared to other treatments, and this trend was stable across seasons. BF-treated soils also exhibited a significantly altered microbial community composition, including increased abundances of Bacillus, Altererythrobacter, Cryptococcus, and Saprospiraceae, and decreased abundances of Chryseolinea and Fusarium. Importantly, BF treatment significantly suppressed the incidence of Fusarium wilt in tomato, likely due to direct suppression by Erythrobacter sp. YH-07 and indirect suppression through changes to the microbial community composition and soil properties.

Discussion

Taken together, these results suggest that Erythrobacter sp. YH-07-inoculated organic manure is a stable and sustainable soil amendment for the suppression of Fusarium wilt diseases.

Uniting the Role of Endophytic Fungi against Plant Pathogens and Their Interaction

Endophytic fungi are used as the most common microbial biological control agents (MBCAs) against phytopathogens and are ubiquitous in all plant parts. Most of the fungal species have roles against a variety of plant pathogens. Fungal endophytes provide different services to be used as pathogen control agents, using an important aspect in the form of enhanced plant growth and induced systemic resistance, produce a variety of antifungal secondary metabolites (lipopeptides, antibiotics and enzymes) through colonization, and compete with other pathogenic microorganisms for growth factors (space and nutrients). The purpose of this review is to highlight the biological control potential of fungal species with antifungal properties against different fungal plant pathogens. We focused on the introduction, biology, isolation, identification of endophytic fungi, and their antifungal activity against fungal plant pathogens. The endosymbionts have developed specific genes that exhibited endophytic behavior and demonstrated defensive responses against pathogens such as antibiosis, parasitism, lytic enzyme and competition, siderophore production, and indirect responses by induced systemic resistance (ISR) in the host plant. Finally, different microscopic detection techniques to study microbial interactions (endophytic and pathogenic fungal interactions) in host plants are briefly discussed.

Root microbiome diversity and structure of the Sonoran desert buffelgrass (Pennisetum ciliare L.)

Buffelgrass (Pennisetum ciliare) is an invasive plant introduced into Mexico's Sonoran desert for cattle grazing and has converted large areas of native thorn scrub. One of the invasion mechanisms buffelgrass uses to invade is allelopathy, which consists of the production and secretion of allelochemicals that exert adverse effects on other plants' growth. The plant microbiome also plays a vital role in establishing invasive plants and host growth and development. However, little is known about the buffelgrass root-associated bacteria and the effects of allelochemicals on the microbiome. We used 16S rRNA gene amplicon sequencing to obtain the microbiome of buffelgrass and compare it between samples treated with root exacknudates and aqueous leachates as allelochemical exposure and samples without allelopathic exposure in two different periods. The Shannon diversity values were between H' = 5.1811-5.5709, with 2,164 reported bacterial Amplicon Sequence Variants (ASVs). A total of 24 phyla were found in the buffelgrass microbiome, predominantly Actinobacteria, Proteobacteria, and Acidobacteria. At the genus level, 30 different genera comprised the buffelgrass core microbiome. Our results show that buffelgrass recruits microorganisms capable of thriving under allelochemical conditions and may be able to metabolize them (e.g., Planctomicrobium, Aurantimonas, and Tellurimicrobium). We also found that the community composition of the microbiome changes depending on the developmental state of buffelgrass (p = 0.0366; ANOSIM). These findings provide new insights into the role of the microbiome in the establishment of invasive plant species and offer potential targets for developing strategies to control buffelgrass invasion.

Stable coexistence or competitive exclusion? Fern endophytes demonstrate rapid turnover favouring a dominant fungus

Fungal endophytes are critical members of the plant microbiome, but their community dynamics throughout an entire growing season are underexplored. Additionally, most fungal endophyte research has centred on seed-reproducing hosts, while spore-reproducing plants also host endophytes and may be colonized by unique community members. In order to examine annual fungal endophyte community dynamics in a spore-reproducing host, we explored endophytes in a single population of ferns, Polystichum munitum, in the Pacific Northwest. Through metabarcoding, we characterized the community assembly and temporal turnover of foliar endophytes throughout a growing season. From these results, we selected endophytes with outsized representations in sequence data and performed in vitro competition assays. Finally, we inoculated sterile fern gametophytes with dominant fungi observed in the field and determined their effects on host performance. Sequencing demonstrated that ferns were colonized by a diverse community of fungal endophytes in newly emerged tissue, but diversity decreased throughout the season leading to the preponderance of a single fungus in later sampling months. This previously undescribed endophyte appears to abundantly colonize the host to the detriment of other microfungi. Competition assays on a variety of media types failed to demonstrate that the dominant fungus was competitive against other fungi isolated from the same hosts, and inoculation onto sterile fern gametophytes did not alter growth compared to sterile controls, suggesting its effects are not antagonistic. The presence of this endophyte in the fern population probably demonstrates a case of repeated colonization driving competitive exclusion of other fungal community members.

Crop microbiome: their role and advances in molecular and omic techniques for the sustenance of agriculture

This review is an effort to provide in-depth knowledge of microbe's interaction and its role in crop microbiome using combination of advanced molecular and OMICS technology to translate this information for the sustenance of agriculture. Increasing population, climate change and exhaustive agricultural practices either influenced nutrient inputs of soil or generating biological and physico-chemical deterioration of the soils and affecting the agricultural productivity and agro-ecosystems. Alarming concerns toward food security and crop production claim for renewed attention in microbe-based farming practices. Microbes are omnipresent (soil, water, and air) and their close association with plants would help to accomplish sustainable agriculture goals. In the last few decades, the search for beneficial microbes in crop production, soil fertilization, disease management, and plant growth promotion is the thirst for eco-friendly agriculture. The crop microbiome opens new paths to utilize beneficial microbes and manage pathogenic microbes through integrated advanced biotechnology. The crop microbiome helps plants acquire nutrients, growth, resilience against phytopathogens, and tolerance to abiotic stresses, such as heat, drought, and salinity. Despite the emergent functionality of the crop microbiome as a complicated constituent of the plant fitness, our understanding of how the functionality of microbiome influenced by numerous factors including genotype of host, climatic conditions, mobilization of minerals, soil composition, nutrient availability, interaction between nexus of microbes, and interactions with other external microbiomes is partially understood. However, the structure, composition, dynamics, and functional contribution of such cultured and uncultured crop microbiome are least explored. The advanced biotechnological approaches are efficient tools for acquiring the information required to investigate the microbiome and extract data to develop high yield producing and resistant variety crops. This knowledge fills the fundamental gap between the theoretical concepts and the operational use of these advanced tools in crop microbiome studies. Here, we review (1) structure and composition of crop microbiome, (2) microbiome-mediated role associated with crops fitness, (3) Molecular and -omics techniques for exploration of crop microbiome, and (4) current approaches and future prospectives of crop microbiome and its exploitation for sustainable agriculture. Recent -omic approaches are influential tool for mapping, monitoring, modeling, and management of crops microbiome. Identification of crop microbiome, using system biology and rhizho-engineering, can help to develop future bioformulations for disease management, reclamation of stressed agro-ecosystems, and improved productivity of crops. Nano-system approaches combined with triggering molecules of crop microbiome can help in designing of nano-biofertilizers and nano-biopesticides. This combination has numerous merits over the traditional bioinoculants. They stimulate various defense mechanisms in plants facing stress conditions; provide bioavailability of nutrients in the soil, helps mitigate stress conditions; and enhance chances of crops establishment.

Bio-Organic Fertilizer Promotes Pear Yield by Shaping the Rhizosphere Microbiome Composition and Functions

Bio-organic fertilizers (BOF) containing both organic amendments and beneficial microorganisms have been consistently shown to improve soils fertility and yield. However, the exact mechanisms which link amendments and yields remain disputed, and the complexity of bio-organic fertilizers may work in parallel in several ways. BOF may directly improve yield by replenishing soil nutrients or introducing beneficial microbial genes or indirectly by altering the soil microbiome to enrich native beneficial microorganisms. In this work, we aim to disentangle the relative contributions of direct and indirect effects on pear yield. We treated pear trees with either chemical fertilizer or organic fertilizer with/without the plant-beneficial bacterium Bacillus velezensis SQR9. We then assessed, in detail, soil physicochemical and biological properties (metagenome sequencing) as well as pear yield. We then evaluated the relative importance of direct and indirect effects of soil amendments on pear yield. Both organic treatments increased plant yield by up to 20%, with the addition of bacteria tripling the increase driven by organic fertilizer alone. This increase could be linked to alterations in soil physicochemical properties, bacterial community function, and metabolism. Supplementation of organic fertilizer SQR9 increased rhizosphere microbiome richness and functional diversity. Fertilizer-sensitive microbes and functions responded as whole guilds. Pear yield was most positively associated with the Mitsuaria- and Actinoplanes-dominated ecological clusters and with gene clusters involved in ion transport and secondary metabolite biosynthesis. Together, these results suggested that bio-organic fertilizers mainly act indirectly on plant yield by creating soil chemical properties which promote a plant-beneficial microbiome. IMPORTANCE Bio-organic fertilization is a widely used, eco-friendly, sustainable approach to increasing plant productivity in the agriculture and fruit industries. However, it remains unclear whether the promotion of fruit productivity is related to specific changes in microbial inoculants, the resident microbiome, and/or the physicochemical properties of rhizosphere soils. We found that bio-organic fertilizers alter soil chemical properties, thus manipulating specific microbial taxa and functions within the rhizosphere microbiome of pear plants to promote yield. Our work unveils the ecological mechanisms which underlie the beneficial impacts of bio-organic fertilizers on yield promotion in fruit orchards, which may help in the design of more efficient biofertilizers to promote sustainable fruit production.

Characterization of Seed Mycobiota Using Culture-Dependent and Culture-Independent Approaches

Seed fungi are potentially important for their roles in seedling microbiome assembly and seedling health, but surveys of full seed fungal communities remain limited. While culture-dependent methods have been used to characterize some members of the seed mycobiota, recent culture-independent studies have improved the ease in identifying and characterizing full seed fungal communities. In this chapter, we describe how to survey seed fungi using both traditional culture-based methods and culture-free metabarcoding. We first describe protocols for the isolation and long-term preservation of fungal strains from individual seeds and for the extraction and amplification of DNA from such fungal isolates for identification with Sanger sequencing. We also detail how to extract, amplify, and sequence fungal DNA directly from individual seeds. Finally, we provide suggestions for troubleshooting media choices, PCR inhibition by isolates and plant tissue, and PCR limitation by low fungal DNA.

Genome-Wide Association Studies across Environmental and Genetic Contexts Reveal Complex Genetic Architecture of Symbiotic Extended Phenotypes

A goal of modern biology is to develop the genotype-phenotype (G→P) map, a predictive understanding of how genomic information generates trait variation that forms the basis of both natural and managed communities. As microbiome research advances, however, it has become clear that many of these traits are symbiotic extended phenotypes, being governed by genetic variation encoded not only by the host's own genome, but also by the genomes of myriad cryptic symbionts. Building a reliable G→P map therefore requires accounting for the multitude of interacting genes and even genomes involved in symbiosis. Here, we use naturally occurring genetic variation in 191 strains of the model microbial symbiont Sinorhizobium meliloti paired with two genotypes of the host Medicago truncatula in four genome-wide association studies (GWAS) to determine the genomic architecture of a key symbiotic extended phenotype-partner quality, or the fitness benefit conferred to a host by a particular symbiont genotype, within and across environmental contexts and host genotypes. We define three novel categories of loci in rhizobium genomes that must be accounted for if we want to build a reliable G→P map of partner quality; namely, (i) loci whose identities depend on the environment, (ii) those that depend on the host genotype with which rhizobia interact, and (iii) universal loci that are likely important in all or most environments. IMPORTANCE Given the rapid rise of research on how microbiomes can be harnessed to improve host health, understanding the contribution of microbial genetic variation to host phenotypic variation is pressing, and will better enable us to predict the evolution of (and select more precisely for) symbiotic extended phenotypes that impact host health. We uncover extensive context-dependency in both the identity and functions of symbiont loci that control host growth, which makes predicting the genes and pathways important for determining symbiotic outcomes under different conditions more challenging. Despite this context-dependency, we also resolve a core set of universal loci that are likely important in all or most environments, and thus, serve as excellent targets both for genetic engineering and future coevolutionary studies of symbiosis.

A Reproducible and Tunable Synthetic Soil Microbial Community Provides New Insights into Microbial Ecology

Microbial soil communities form commensal relationships with plants to promote the growth of both parties. The optimization of plant-microbe interactions to advance sustainable agriculture is an important field in agricultural research. However, investigation in this field is hindered by a lack of model microbial community systems and efficient approaches for building these communities. Two key challenges in developing standardized model communities are maintaining community diversity over time and storing/resuscitating these communities after cryopreservation, especially considering the different growth rates of organisms. Here, a model synthetic community (SynCom) of 16 soil microorganisms commonly found in the rhizosphere of diverse plant species, isolated from soil surrounding a single switchgrass plant, has been developed and optimized for in vitro experiments. The model soil community grows reproducibly between replicates and experiments, with a high community α-diversity being achieved through growth in low-nutrient media and through the adjustment of the starting composition ratios for the growth of individual organisms. The community can additionally be cryopreserved with glycerol, allowing for easy replication and dissemination of this in vitro system. Furthermore, the SynCom also grows reproducibly in fabricated ecosystem devices (EcoFABs), demonstrating the application of this community to an existing in vitro plant-microbe system. EcoFABs allow reproducible research in model plant systems, offering the precise control of environmental conditions and the easy measurement of plant microbe metrics. Our results demonstrate the generation of a stable and diverse microbial SynCom for the rhizosphere that can be used with EcoFAB devices and can be shared between research groups for maximum reproducibility. IMPORTANCE Microbes associate with plants in distinct soil communities to the benefit of both the soil microbes and the plants. Interactions between plants and these microbes can improve plant growth and health and are therefore a field of study in sustainable agricultural research. In this study, a model community of 16 soil bacteria has been developed to further the reproducible study of plant-soil microbe interactions. The preservation of the microbial community has been optimized for dissemination to other research settings. Overall, this work will advance soil microbe research through the optimization of a robust, reproducible model community.

Effects of Domestication on Plant-Microbiome Interactions

Through the process of domestication, selection is targeted on a limited number of plant traits that are typically associated with yield. As an unintended consequence, domesticated plants often perform poorly compared to their wild progenitors for a multitude of traits that were not under selection during domestication, including abiotic and biotic stress tolerance. Over the past decade, advances in sequencing technology have allowed for the rigorous characterization of host-associated microbial communities, termed the microbiome. It is now clear that nearly every conceivable plant interaction with the environment is mediated by interactions with the microbiome. For this reason, plant-microbiome interactions are an area of great promise for plant breeding and crop improvement. Here, we review the literature to assess the potential impact that domestication has had on plant-microbiome interactions and the current understanding of the genetic basis of microbiome variation to inform plant breeding efforts. Overall, we find limited evidence that domestication impacts the diversity of microbiomes, but domestication is often associated with shifts in the abundance and composition of microbial communities, including taxa of known functional significance. Moreover, genome-wide association studies and mutant analysis have not revealed a consistent set of core candidate genes or genetic pathways that confer variation in microbiomes across systems. However, such studies do implicate a consistent role for plant immunity, root traits, root and leaf exudates and cell wall integrity as key traits that control microbiome colonization and assembly. Therefore, selection on these key traits may pose the most immediate promise for enhancing plant-microbiome interactions through breeding.

Australian native Glycine clandestina seed microbiota hosts a more diverse bacterial community than the domesticated soybean Glycine max

BACKGROUND

Plant microbiome composition has been demonstrated to change during the domestication of wild plants and it is suggested that this has resulted in loss of plant beneficial microbes. Recently, the seed microbiome of native plants was demonstrated to harbour a more diverse microbiota and shared a common core microbiome with modern cultivars. In this study the composition of the seed-associated bacteria of Glycine clandestina is compared to seed-associated bacteria of Glycine max (soybean).

RESULTS

The seed microbiome of the native legume Glycine clandestina (crop wild relative; cwr) was more diverse than that of the domesticated Glycine max and was dominated by the bacterial class Gammaproteobacteria. Both the plant species (cwr vs domesticated) and individual seed accessions were identified as the main driver for this diversity and composition of the microbiota of all Glycine seed lots, with the effect of factor "plant species" exceeded that of "geographical location". A core microbiome was identified between the two Glycine species. A high percentage of the Glycine microbiome was unculturable [G. clandestina (80.8%) and G. max (75.5%)] with only bacteria of a high relative abundance being culturable under the conditions of this study.

CONCLUSION

Our results provided novel insights into the structure and diversity of the native Glycine clandestina seed microbiome and how it compares to that of the domesticated crop Glycine max. Beyond that, it also increased our knowledge of the key microbial taxa associated with the core Glycine spp. microbiome, both wild and domesticated. The investigation of this commonality and diversity is a valuable and essential tool in understanding the use of native Glycine spp. for the discovery of new microbes that would be of benefit to domesticated Glycine max cultivars or any other economically important crops. This study has isolated microbes from a crop wild relative that are now available for testing in G. max for beneficial phenotypes.