Towards a unified paradigm for sequence-based identification of fungi

Why are graminoid species more dominant? Trait-mediated plant-soil feedbacks shape community composition

Species traits may determine plant interactions along with soil microbiome, further shaping plant-soil feedbacks (PSFs). However, how plant traits modulate PSFs and, consequently, the dominance of plant functional groups remains unclear. We used a combination of field surveys and a two-phase PSF experiment to investigate whether forbs and graminoids differed in PSFs and in their trait-PSF associations. When grown in forb-conditioned soils, forbs experienced stronger negative feedbacks, while graminoids experienced positive feedbacks. Graminoid-conditioned soil resulted in neutral PSFs for both functional types. Forbs with thin roots and small seeds showed more-negative PSFs than those with thick roots and large seeds. Conversely, graminoids with acquisitive root and leaf traits (i.e., thin roots and thin leaves) demonstrated greater positive PSFs than graminoids with thick roots and tough leaves. By distinguishing overall and soil biota-mediated PSFs, we found that the associations between plant traits and PSFs within both functional groups were mainly mediated by soil biota. A simulation model demonstrated that such differences in PSFs could lead to a dominance of graminoids over forbs in natural plant communities, which might explain why graminoids dominate in grasslands. Our study provides new insights into the differentiation and adaptation of plant life-history strategies under selection pressures imposed by soil biota.

Improving crop salt tolerance through soil legacy effects

Soil salinization poses a critical problem, adversely affecting plant development and sustainable agriculture. Plants can produce soil legacy effects through interactions with the soil environments. Salt tolerance of plants in saline soils is not only determined by their own stress tolerance but is also closely related to soil legacy effects. Creating positive soil legacy effects for crops, thereby alleviating crop salt stress, presents a new perspective for improving soil conditions and increasing productivity in saline farmlands. Firstly, the formation and role of soil legacy effects in natural ecosystems are summarized. Then, the processes by which plants and soil microbial assistance respond to salt stress are outlined, as well as the potential soil legacy effects they may produce. Using this as a foundation, proposed the application of salt tolerance mechanisms related to soil legacy effects in natural ecosystems to saline farmlands production. One aspect involves leveraging the soil legacy effects created by plants to cope with salt stress, including the direct use of halophytes and salt-tolerant crops and the design of cropping patterns with the specific crop functional groups. Another aspect focuses on the utilization of soil legacy effects created synergistically by soil microorganisms. This includes the inoculation of specific strains, functional microbiota, entire soil which legacy with beneficial microorganisms and tolerant substances, as well as the application of novel technologies such as direct use of rhizosphere secretions or microbial transmission mechanisms. These approaches capitalize on the characteristics of beneficial microorganisms to help crops against salinity. Consequently, we concluded that by the screening suitable salt-tolerant crops, the development rational cropping patterns, and the inoculation of safe functional soils, positive soil legacy effects could be created to enhance crop salt tolerance. It could also improve the practical significance of soil legacy effects in the application of saline farmlands.

Local Community Assembly Mechanisms and the Size of Species Pool Jointly Explain the Beta Diversity of Soil Fungi

Fungi play vital regulatory roles in terrestrial ecosystems. Local community assembly mechanisms, including deterministic and stochastic processes, as well as the size of regional species pools (gamma diversity), typically influence overall soil microbial community beta diversity patterns. However, there is limited evidence supporting their direct and indirect effects on beta diversity of different soil fungal functional groups in forest ecosystems. To address this gap, we collected 1606 soil samples from a 25-ha subtropical forest plot in southern China. Our goal was to determine the direct effects and indirect effects of regional species pools on the beta diversity of soil fungi, specifically arbuscular mycorrhizal (AM), ectomycorrhizal (EcM), plant-pathogenic, and saprotrophic fungi. We quantified the effects of soil properties, mycorrhizal tree abundances, and topographical factors on soil fungal diversity. The beta diversity of plant-pathogenic fungi was predominantly influenced by the size of the species pool. In contrast, the beta diversity of EcM fungi was primarily driven indirectly through community assembly processes. Neither of them had significant effects on the beta diversity of AM and saprotrophic fungi. Our results highlight that the direct and indirect effects of species pools on the beta diversity of soil functional groups of fungi can significantly differ even within a relatively small area. They also demonstrate the independent and combined effects of various factors in regulating the diversities of soil functional groups of fungi. Consequently, it is crucial to study the fungal community not only as a whole but also by considering different functional groups within the community.

Impact of repeated fumigant applications on soil properties, crop yield, and microbial communities in a plastic-mulched tomato production system

Pre-plant soil fumigation is widely applied to control nematodes, soil-borne fungal pathogens, and weeds in vegetable crops. However, most of the research evaluating the effect of fumigants on crop yield and soil microbial communities has been done on single compounds despite growers mainly applying fumigant combinations. We studied the effect of different fumigant combinations (chloropicrin, 1,3-dichloropropene, and metam potassium) on soil properties, crop yield, and the soil bacterial and fungal microbiome for two consecutive years in a plastic-mulched tomato production system in Florida (United States). While combinations of fumigants did not improve plant productivity more than the individual application of these products, application of fumigants with >60 % chloropicrin did significantly increase yield. Fumigant combinations had no significant effect on bacterial diversity, but fumigants with >35 % chloropicrin reduced soil fungal diversity and induced temporary changes in the soil bacterial and fungal community composition. These changes included short-term increases in the relative abundance of Firmicutes and Ascomycota, as well as decreases in other bacterial and fungal taxa. Repeated fumigation reduced network complexity and the relative abundance of several predicted bacterial functions and fungal guilds, particularly after fumigation and at end of harvest (3-months post fumigation). A structural equation model (SEM) showed fumigants not only directly impact crop yield, but they can also indirectly determine variations in plant productivity through effects on the soil microbiome. Overall, this study increases our understanding of the environmental and agricultural impacts of fumigants in a plastic-mulched tomato production system.

Interactive effects between the invasive weed Stellera chamaejasme and grass: can arbuscular mycorrhizal fungi and fungal pathogens coregulate interspecific relationships?

The interaction between poisonous weeds and neighboring plants is complex. Poisonous weeds frequently have a competitive advantage in the interaction between poisonous weeds and neighboring plants. Arbuscular mycorrhizal fungi (AMF) and plant pathogenic fungi (PPF) are closely related to the interspecific relationships of plants. However, the role of AMF and PPF between poisonous weeds and neighboring grasses remains unclear. Here, we designed a pot experiment to determine the interspecific relationship between Leymus chinensis and Stellera chamaejasme and the regulation of AMF and PPF. The results showed that interactive effects between L. chinensis and S. chamaejasme significantly inhibited the aboveground growth of both but promoted the underground growth of L. chinensis. As the proportions of S. chamaejasme increased, the total nitrogen content and pH in the rhizosphere soil of L. chinensis were reduced, the soil pH of S. chamaejasme was reduced, and the relative abundance of AMF in the rhizosphere soil of L. chinensis significantly increased and that of S. chamaejasme decreased considerably. The relative abundances of PPF in the rhizosphere soil of both in the mono-cultures were significantly higher than those in the mixed cultures. Structural equation modeling indicated that soil abiotic (pH and N availability) and biotic (AMF and PPF) factors are major drivers explaining the interactive effects between L. chinensis and S. chamaejasme. We provided new evidence for the interspecific interactions between poisonous weeds and neighboring grasses and revealed the regulatory role of AMF and PPF in the interactive effects of both plants. This study will provide a scientific basis for the prevention and control of poisonous weeds and the vegetation restoration of degraded grasslands in the future.

Assessment of the impact of climate change on endangered conifer tree species by considering climate and soil dual suitability and interspecific competition

Climate change results in the habitat loss of many conifer tree species and jeopardizes species biodiversity and forest ecological functions. Delineating suitable habitats for tree species via climate niche model (CNM) is widely used to predict the impact of climate change and develop conservation and management strategies. However, the robustness of CNM is broadly debated as it usually does not consider soil and competition factors. Here we developed a new approach to combine soil variables with CNM and evaluate interspecific competition potential in the niche overlapping areas. We used an endangered conifer species - Chamaecyparis formosensis (red cypress) - as a case study to predict the impact of climate change. We developed a novel approach to integrate the climate niche model and soil niche model predictions and considered interspecific competition to predict the impacts of climate change on tree species. Our results show that the suitable habitat for red cypress would decrease significantly in the future with an additional threat from the competition of an oak tree species. Our approach and results may represent significant implications in making conservation strategies and evaluating the impacts of climate change, and providing the direction of the refinement of the ecological niche model.

Interspecific plant interaction via root exudates structures the disease suppressiveness of rhizosphere microbiomes

Terrestrial plants can affect the growth and health of adjacent plants via interspecific interaction. Here, we studied the mechanism by which plant root exudates affect the recruitment of the rhizosphere microbiome in adjacent plants-with implications for plant protection-using a tomato (Solanum lycopersicum)-potatoonion (Allium cepa var. agrogatum) intercropping system. First, we showed that the intercropping system results in a disease-suppressive rhizosphere microbiome that protects tomato plants against Verticillium wilt disease caused by the soilborne pathogen Verticillium dahliae. Second, 16S rRNA gene sequencing revealed that intercropping with potatoonion altered the composition of the tomato rhizosphere microbiome by promoting the colonization of specific Bacillus sp. This taxon was isolated and shown to inhibit V. dahliae growth and induce systemic resistance in tomato plants. Third, a belowground segregation experiment found that root exudates mediated the interspecific interaction between potatoonion and tomato. Moreover, experiments using split-root tomato plants found that root exudates from potatoonion, especially taxifolin-a flavonoid compound-stimulate tomato plants to recruit plant-beneficial bacteria, such as Bacillus sp. Lastly, ultra-high-pressure liquid chromatography-mass spectrometry analysis found that taxifolin alters tomato root exudate chemistry; thus, this compound acts indirectly in modulating root colonization by Bacillus sp. Our results revealed that this intercropping system can improve tomato plant fitness by changing rhizosphere microbiome recruitment via the use of signaling chemicals released by root exudates of potatoonion. This study revealed a novel mechanism by which interspecific plant interaction modulates the establishment of a disease-suppressive microbiome, thus opening up new avenues of research for precision plant microbiome manipulations.

Using root economics traits to predict biotic plant soil-feedbacks

Plant-soil feedbacks have been recognised as playing a key role in a range of ecological processes, including succession, invasion, species coexistence and population dynamics. However, there is substantial variation between species in the strength of plant-soil feedbacks and predicting this variation remains challenging. Here, we propose an original concept to predict the outcome of plant-soil feedbacks. We hypothesize that plants with different combinations of root traits culture different proportions of pathogens and mutualists in their soils and that this contributes to differences in performance between home soils (cultured by conspecifics) versus away soils (cultured by heterospecifics). We use the recently described root economics space, which identifies two gradients in root traits. A conservation gradient distinguishes fast vs. slow species, and from growth defence theory we predict that these species culture different amounts of pathogens in their soils. A collaboration gradient distinguishes species that associate with mycorrhizae to outsource soil nutrient acquisition vs. those which use a "do it yourself" strategy and capture nutrients without relying strongly on mycorrhizae. We provide a framework, which predicts that the strength and direction of the biotic feedback between a pair of species is determined by the dissimilarity between them along each axis of the root economics space. We then use data from two case studies to show how to apply the framework, by analysing the response of plant-soil feedbacks to measures of distance and position along each axis and find some support for our predictions. Finally, we highlight further areas where our framework could be developed and propose study designs that would help to fill current research gaps.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11104-023-05948-1.

Antagonistic Activity of Pseudomonas fluorescens Strain X1 Against Different Fusaria and it's In Vivo Analysis Against Fusarium udum Infected Pigeon Pea

A plant growth-promoting rhizobacterial strain, Pseudomonas fluorescens X1 isolated from the garden soil was employed for antagonistic activity against different species of fusaria. Strain X1 inhibited four different fusaria (Fusarium moniliforme, Fusarium oxysporum, Fusarium semitectum and Fusarium udum) in dual culture plate assay, and in broth culture using cell-free culture filtrate. Scanning electron microscopic (SEM) analysis revealed deformation and shrinkage in mycelia of fusaria after treatment with strain X1. Confocal micrographs showed degeneration of nuclei inside the cells of fusaria for the same effect. Strain X1 exhibited maximum antifungal activity, when it was grown in nutrient broth yeast (NBY) medium amended with 1 mM NH₄MoO₄ and 1% glucose. The antifungal extracts eluted from thin-layer chromatography (TLC) followed by high performance liquid chromatography (HPLC) showed two fractions active against different fusaria. Liquid chromatography-mass spectrometry (LCMS) analysis of the two fractions 1 and 2 corresponded to molecular ions at m/z 177.16 and m/z 177.09, respectively. Infra-red (IR) analysis showed five similar absorption bands in both the fractions analysed. In vivo analysis of strain X1 alone and along with fungicide inhibited the growth of F. udum and improved the biomass and growth of pigeon pea. These results indicated that strain X1 could be possibly used as a biocontrol agent to inhibit the growth of soil-borne diseases of different fusaria including F. udum that causes wilting in pigeon pea.

Dominant plant species play an important role in regulating bacterial antagonism in terrestrial Antarctica

In Antarctic terrestrial ecosystems, dominant plant species (grasses and mosses) and soil physicochemical properties have a significant influence on soil microbial communities. However, the effects of dominant plants on bacterial antagonistic interactions in Antarctica remain unclear. We hypothesized that dominant plant species can affect bacterial antagonistic interactions directly and indirectly by inducing alterations in soil physicochemical properties and bacterial abundance. We collected soil samples from two typical dominant plant species; the Antarctic grass Deschampsia antarctica and the Antarctic moss Sanionia uncinata, as well as bulk soil sample, devoid of vegetation. We evaluated bacterial antagonistic interactions, focusing on species from the genera Actinomyces, Bacillus, and Pseudomonas. We also measured soil physicochemical properties and evaluated bacterial abundance and diversity using high-throughput sequencing. Our results suggested that Antarctic dominant plants significantly influenced bacterial antagonistic interactions compared to bulk soils. Using structural equation modelling (SEM), we compared and analyzed the direct effect of grasses and mosses on bacterial antagonistic interactions and the indirect effects through changes in edaphic properties and bacterial abundance. SEMs showed that (1) grasses and mosses had a significant direct influence on bacterial antagonistic interactions; (2) grasses had a strong influence on soil water content, pH, and abundances of Actinomyces and Pseudomonas and (3) mosses influenced bacterial antagonistic interactions by impacting abundances of Actinomyces, Bacillus, and Pseudomonas. This study highlights the role of dominant plants in modulating bacterial antagonistic interactions in Antarctic terrestrial ecosystems.

Effect of fumigants and non-fumigants on nematode and weed control, crop yield, and soil microbial diversity and predicted functionality in a strawberry production system

Fumigants are commonly used to control soil-borne pathogens of high-value crops, but they may also impact non-target soil microorganisms. Increasing interest in the use of sustainable management practices to control plant- and root-parasitic nematodes has resulted in the formulation of non-fumigant nematicides (chemicals or bionematicides) which are considered environmentally friendly alternatives to fumigants. However, the impact of these new products compared to standard fumigants on soil-borne pathogens, plant production, and the diversity and composition of non-target microbial communities in all crops remains unclear. To begin to address this knowledge gap, we examined the effect of fumigants commonly used in Florida (United States) strawberry production and newly formulated non-fumigant nematicides on nematode and weed control, plant growth, crop yield, and bacterial and fungal community diversity and predicted functionality. We found the standard fumigants increased crop yields and reduced weed pressure more than non-fumigants. Both fumigants and non-fumigants were an efficient management strategy to control sting nematodes. Treatments also impacted the abundance of specific beneficial and antagonistic taxa. Both fumigants and non-fumigants reduced soil bacterial and fungal diversity, an effect that remained for six months, thus suggesting a potential residual impact of these products on soil microorganisms. However, only fumigants altered soil microbial community composition and reduced network complexity, inducing a decrease or even a loss of some predicted bacterial and fungal functions, particularly during the first weeks after fumigation. Nevertheless, soil collected at the end of the season showed significant levels of root-knot nematode suppression in a growth chamber experiment, irrespective of the previous treatment. By linking the effect of fumigants and non-fumigants on soil-borne pests, plant and production, and the soil microbiome, this study increases our knowledge regarding the environmental impact of these products.

Maize-soybean relay strip intercropping reshapes the rhizosphere bacterial community and recruits beneficial bacteria to suppress Fusarium root rot of soybean

Rhizosphere microbes play a vital role in plant health and defense against soil-borne diseases. Previous studies showed that maize-soybean relay strip intercropping altered the diversity and composition of pathogenic Fusarium species and biocontrol fungal communities in the soybean rhizosphere, and significantly suppressed soybean root rot. However, whether the rhizosphere bacterial community participates in the regulation of this intercropping on soybean root rot is not clear. In this study, the rhizosphere soil of soybean healthy plants was collected in the continuous cropping of maize-soybean relay strip intercropping and soybean monoculture in the fields, and the integrated methods of microbial profiling, dual culture assays in vitro, and pot experiments were employed to systematically investigate the diversity, composition, and function of rhizosphere bacteria related to soybean root rot in two cropping patterns. We found that intercropping reshaped the rhizosphere bacterial community and increased microbial community diversity, and meanwhile, it also recruited much richer and more diverse species of Pseudomonas sp., Bacillus sp., Streptomyces sp., and Microbacterium sp. in soybean rhizosphere when compared with monoculture. From the intercropping, nine species of rhizosphere bacteria displayed good antagonism against the pathogen Fusarium oxysporum B3S1 of soybean root rot, and among them, IRHB3 (Pseudomonas chlororaphis), IRHB6 (Streptomyces), and IRHB9 (Bacillus) were the dominant bacteria and extraordinarily rich. In contrast, MRHB108 (Streptomyces virginiae) and MRHB205 (Bacillus subtilis) were the only antagonistic bacteria from monoculture, which were relatively poor in abundance. Interestingly, introducing IRHB3 into the cultured substrates not only significantly promoted the growth and development of soybean roots but also improved the survival rate of seedlings that suffered from F. oxysporum infection. Thus, this study proves that maize-soybean relay strip intercropping could help the host resist soil-borne Fusarium root rot by reshaping the rhizosphere bacterial community and driving more beneficial microorganisms to accumulate in the soybean rhizosphere.

Root-knot nematode damage to a cucurbit double crop is increased by chloropicrin fumigation on the previous tomato crop

BACKGROUND

Double-cropping is a common practice in vegetable plasticulture whereby a second crop is planted on the same plastic bed as the first crop. Root-knot nematodes (Meloidogyne spp.) are one of the major soilborne constraints in double-cropped vegetables due to nematode population build-up on the first crop. We evaluated the effect of fumigant and non-fumigant nematicides applied on the first crop, on nematode infection and yield of the second crop in 10 field trials between 2017 and 2020. Fumigants were chloropicrin (Pic100), chloropicrin +1,3-D (PicClor60), and non-fumigant nematicides were oxamyl (Vydate), fluensulfone (Nimitz), fluopyram (Velum) and fluazaindolizine (Salibro). The first crop was tomato and double crops were cucumber, squash, zucchini, and cantaloupe.

RESULTS

Fumigation with chloropicrin on the first crop increased root-knot nematode damage on the double-crop at the end of the season in seven trials, while the opposite was noted in one trial, and no difference was noted in two trials. Fumigation with chloropicrin+1,3-D resulted in root-knot nematode damage less than chloropicrin but more than non-fumigated plots. Cucurbit yield was greater in non-fumigated beds in four trials, and in chloropicrin-treated beds in two trials. Fluensulfone reduced root-knot nematode damage on the second crop in five out of 10 trials.

CONCLUSION

Our results indicate that chloropicrin applied on the tomato crop may lead to increased root-knot nematode damage on the double crop. More research is needed to understand the processes behind this, but it is possibly related to a reduction in natural nematode soil suppressiveness due to the broad-spectrum fungicidal activity of chloropicrin. © 2022 Society of Chemical Industry.

Can multi-cropping affect soil microbial stoichiometry and functional diversity, decreasing potential soil-borne pathogens? A study on European organic vegetable cropping systems

Crop diversification in spatial and temporal patterns can optimize the synchronization of nutrients plant demand and availability in soils, as plant diversity and soil microbial communities are the main drivers of biogeochemical C and nutrient cycling. The introduction of multi-cropping in organic vegetable production can represent a key strategy to ensure efficient complementation mediated by soil microbiota, including beneficial mycorrhizal fungi. This study shows the effect of the introduction of multi-cropping in five European organic vegetable systems (South-West: Italy; North-West: Denmark and Belgium; North-East: Finland and Latvia) on: (i) soil physicochemical parameters; (ii) soil microbial biomass stoichiometry; (iii) crop root mycorrhization; (iv) bacterial and fungal diversity and composition in crop rhizosphere; (v) relative abundance of selected fungal pathogens species. In each site, three cropping systems were considered: (1) crop 1-monocropping; (2) crop 2-monocropping; (3) crop 1-crop 2-intercropping or strip cropping. Results showed that, just before harvest, multi-cropping can increase soil microbial biomass amount and shape microbial community toward a predominance of some bacteria or fungi phyla, in the function of soil nutrient availability. We mainly observed a selection effect of crop type on rhizosphere microbiota. Particularly, Bacteroidetes and Mortierellomycota relative abundances in rhizosphere soil resulted in suitable ecological indicators of the positive effect of plant diversity in field, the first ones attesting an improved C and P cycles in soil and the second ones a reduced soil pathogens' pressure. Plant diversity also increased the root mycorrhizal colonization between the intercropped crops that, when properly selected, can also reduce the relative abundance of potential soil-borne pathogens, with a positive effect on crop productivity in long term.

Warming shifts soil microbial communities and tropical tree seedling mortality

Plant-soil feedback (PSF), regulated by both mycorrhizae and soil-borne pathogens, is a primary mechanism maintaining high tree species diversity in the tropics. But how warming actually affects PSF is not well understood. We conducted a field warming experiment to test PSF on seedling mortality of two tree species: a rhizobia-associated tree (Ormosia semicastrata, Fabaceae) suffering from host-specific soil-borne pathogens and an ectomycorrhizal fungi-associated tree (Cyclobalanopsis patelliormis, Fagaceae) with low susceptibility to soil-borne pathogens. Soil fungi from the warming versus control seedling plots were identified by molecular sequencing. Results showed that the elevated temperature lowered seedling mortality of O. semicastrata, but had no effect on C. patelliormis seedlings. This indicates that warming weakened the negative PSF on O. semicastrata, presumably due to the observed decrease of the relative abundance of plant-pathogenic fungi and increase of ectomycorrhizal fungi but did not affect the PSF on C. patelliormis. The differential warming effects on seedling mortality of species with different microbial associations afford an example showcasing how the change in soil-borne microbes in response to global warming would in turn, through PSF, alters tropical tree species composition and diversity. This study helps shed mechanistic light on the debate of biodiversity change as driven by climate change.

Effects of Four Cropping Patterns of Lilium brownii on Rhizosphere Microbiome Structure and Replant Disease

Replant disease caused by continuous cropping obstacles commonly occurs in a Lilium brownii consecutive monoculture. To reveal the mechanisms contributing to the continuous cropping obstacles of L. brownii, four cropping patterns (fallow, L. brownii-rice rotation, newly planted L. brownii, and 2-year L. brownii consecutive monoculture) were designed, and Illumina MiSeq (16S rDNA and ITS) was utilized to detect shifts in the microbial community in the rhizosphere. Our result showed that planting of L. brownii significantly reduced soil pH. Consecutive monoculture of L. brownii can significantly decrease the diversity and abundance of soil bacteria, but markedly increase the diversity and abundance of soil fungi. Under the four planting pattern treatments, the changes in soil pH were consistent with the changes in the Shannon diversity index of soil bacterial communities, whereas we observed a negative correlation between soil pH and Shannon diversity index for fungi. The relative abundance of Lactobacillales significantly increased in soils of L. brownii consecutive monoculture, while Acidobacteriales, Solibacterales, and Xanthomonadales increased in soils of L. brownii-rice rotation and newly planted L. brownii. Collectively, this work aimed to elucidate the relationship between the L. brownii planting patterns and soil microbiome, thereby providing a theoretical basis for screening new biological agents that may contribute to resolving continuous cropping obstacles of L. brownii.

Enrichment of beneficial rhizosphere microbes in Chinese wheat yellow mosaic virus-resistant cultivars

The microbial community within the root system, the rhizosphere closely connected to the root, and their symbiotic relationship with the host are increasingly seen as possible drivers of natural pathogen resistance. Resistant cultivars have the most effective strategy in controlling the Chinese wheat yellow mosaic disease, but the roles of the root and rhizosphere microbial interactions among different taxonomic levels of resistant cultivars are still unknown. Thus, we aimed to investigate whether these microbial community composition and network characteristics are related to disease resistance and to analyze the belowground plant-associated microflora. Relatively high microbial diversity and stable community structure for the resistant cultivars were detected. Comparison analysis showed that some bacterial phyla were significantly enriched in the wheat root or rhizosphere of the resistant wheat cultivar. Furthermore, the root and rhizosphere of the resistant cultivars greatly recruited many known beneficial bacterial and fungal taxa. In contrast, the relative abundance of potential pathogens was higher for the susceptible cultivar than for the resistant cultivar. Network co-occurrence analysis revealed that a much more complex, more mutually beneficial, and a higher number of bacterial keystone taxa in belowground microbial networks were displayed in the resistant cultivar, which may have been responsible for maintaining the stability and ecological balance of the microbial community. Overall, compared with the susceptible cultivar, the resistant cultivar tends to recruit more potential beneficial microbial groups for plant and rhizosphere microbial community interactions. These findings indicate that beneficial rhizosphere microbiomes for cultivars should be targeted and evaluated using community compositional profiles. KEY POINTS: • Different resistance levels in cultivars affect the rhizosphere microbiome.. • Resistant cultivars tend to recruit more potential beneficial microbial groups. • Bacteria occupy a high proportion and core position in the microflora network.

From Microns to Meters: Exploring Advances in Legume Microbiome Diversity for Agroecosystem Benefits

Legumes are of primary importance for agroecosystems because they provide protein-rich foods and enhance soil fertility through fixed atmospheric nitrogen. The legume-rhizobia symbiosis that makes this possible has been extensively studied, from basic research on biochemical signaling to practical applications in cropping systems. While rhizobia are the most-studied group of associated microorganisms, the functional benefit they confer to their legume hosts by fixing nitrogen is not performed in isolation. Indeed, non-rhizobia members of the rhizosphere and nodule microbiome are now understood to contribute in multiple ways to nodule formation, legume fitness, and other agroecosystem services. In this review, we summarize advances contributing to our understanding of the diversity and composition of bacterial members of the belowground legume microbiome. We also highlight applied work in legume food and forage crops that link microbial community composition with plant functional benefits. Ultimately, further research will assist in the development of multi-species microbial inoculants and cropping systems that maximize plant nutrient benefits, while reducing sources of agricultural pollution.

Moderate plant-soil feedbacks have small effects on the biodiversity-productivity relationship: A field experiment

Plant-soil feedback (PSF) has gained attention as a mechanism promoting plant growth and coexistence. However, most PSF research has measured monoculture growth in greenhouse conditions. Translating PSFs into effects on plant growth in field communities remains an important frontier for PSF research. Using a 4-year, factorial field experiment in Jena, Germany, we measured the growth of nine grassland species on soils conditioned by each of the target species (i.e., 72 PSFs). Plant community models were parameterized with or without these PSF effects, and model predictions were compared to plant biomass production in diversity-productivity experiments. Plants created soils that changed subsequent plant biomass by 40%. However, because they were both positive and negative, the average PSF effect was 14% less growth on "home" than on "away" soils. Nine-species plant communities produced 29 to 37% more biomass for polycultures than for monocultures due primarily to selection effects. With or without PSF, plant community models predicted 28%-29% more biomass for polycultures than for monocultures, again due primarily to selection effects. Synthesis: Despite causing 40% changes in plant biomass, PSFs had little effect on model predictions of plant community biomass across a range of species richness. While somewhat surprising, a lack of a PSF effect was appropriate in this site because species richness effects in this study were caused by selection effects and not complementarity effects (PSFs are a complementarity mechanism). Our plant community models helped us describe several reasons that even large PSF may not affect plant productivity. Notably, we found that dominant species demonstrated small PSF, suggesting there may be selective pressure for plants to create neutral PSF. Broadly, testing PSFs in plant communities in field conditions provided a more realistic understanding of how PSFs affect plant growth in communities in the context of other species traits.

Commercialization, Diffusion and Adoption of Bioformulations for Sustainable Disease Management in Indian Arid Agriculture: Prospects and Challenges

Trichoderma spp. is one of the most popular genus of fungi commercially available as a plant growth promoting fungus (PGPF) and biological control agent. More than 80 species of Trichoderma are reported in the literature. However T. asperellum, T. harzianum, T. viride, and T. virens are most commonly utilized as biocontrol agents. Studies were initiated to explore the potential of biocontrol agents in order to develop a cost effective and practical management strategy. Analysis of large number of soil samples collected from western parts of the region led to isolation of native biocontrol agents viz., Trichoderma harzianum, Aspergillus versicolor, and Bacillus firmus from different agricultural systems. These biocontrol agents have proved their antagonistic ability in laboratory tests and field trials. In India, two species of Trichoderma i.e., T. viride and T. harzianum are commercially registered for usage against soil borne plant pathogens mostly as a seed treatment or soil application. There are published scientific papers on the efficacy of T. asperellum and T. virens in India for suppressing pathogens but these are not yet registered under Central Insecticide Board and Registration Committee (CIB & RC). This review article focuses on the uses, commercialization and adoption issues of various fungal and bacterial consortium products in sustainable disease management.

Plant-Microbiome Crosstalk: Dawning from Composition and Assembly of Microbial Community to Improvement of Disease Resilience in Plants

Plants host diverse but taxonomically structured communities of microorganisms, called microbiome, which colonize various parts of host plants. Plant-associated microbial communities have been shown to confer multiple beneficial advantages to their host plants, such as nutrient acquisition, growth promotion, pathogen resistance, and environmental stress tolerance. Systematic studies have provided new insights into the economically and ecologically important microbial communities as hubs of core microbiota and revealed their beneficial impacts on the host plants. Microbiome engineering, which can improve the functional capabilities of native microbial species under challenging agricultural ambiance, is an emerging biotechnological strategy to improve crop yield and resilience against variety of environmental constraints of both biotic and abiotic nature. This review highlights the importance of indigenous microbial communities in improving plant health under pathogen-induced stress. Moreover, the potential solutions leading towards commercialization of proficient bioformulations for sustainable and improved crop production are also described.

Revealing Microbiome Structure and Assembly Process in Three Rhizocompartments of Achyranthes bidentata Under Continuous Monoculture Regimes

The complex composition and interaction of root-associated microbes are critical to plant health and performance. In this study, we presented a detailed characterization of three rhizocompartment (rhizosphere, rhizoplane, and root) microbiomes of Achyranthes bidentata under different years of consecutive monoculture by deep sequencing in order to determine keystone microorganisms via co-occurrence network analysis. The network analysis showed that multiple consecutive monoculture (MCM, represented 5Y and 10Y) soils generated some distinct beneficial bacterial taxa such as Bacillus, Fictibacillus, Bradyrhizobium, Shinella, and Herbaspirillum. For fungi, Mortierella substituted for Fusarium in occupying an important position in different rhizocompartments under A. bidentate monoculture. Quantitative PCR analysis confirmed a significant increase in Bacillus, Pseudomonas, and Burkholderia spp. The results of the inoculation assay showed that addition of beneficial bacteria Bacillus subtilis 74 and Bacillus halodurans 75 significantly increased the root length and fresh weight of A. bidentata. Furthermore, three types of phytosterones, as the main allochemicals, were identified both in the rhizosphere soil and in culture medium under sterile conditions by LC-MS/MS. When looking at in vitro interactions, it was found that phytosterones displayed a positive interaction with dominant beneficial species (Bacillus amyloliquefaciens 4 and B. halodurans 75) and had a negative effect on the presence of the pathogenic fungi Fusarium solani and Fusarium oxysporum. Overall, this study demonstrated that consecutive monoculture of A. bidentata can alter the bacterial and fungal community by secreting root exudates, leading to recruitment of beneficial microbes and replacement of plant-specific pathogenic fungi with plant beneficial fungi.

Plant-Soil Feedbacks and Temporal Dynamics of Plant Diversity-Productivity Relationships

Plant-soil feedback (PSF) and diversity-productivity relationships are important research fields to study drivers and consequences of changes in plant biodiversity. While studies suggest that positive plant diversity-productivity relationships can be explained by variation in PSF in diverse plant communities, key questions on their temporal relationships remain. Here, we discuss three processes that change PSF over time in diverse plant communities, and their effects on temporal dynamics of diversity-productivity relationships: spatial redistribution and changes in dominance of plant species; phenotypic shifts in plant traits; and dilution of soil pathogens and increase in soil mutualists. Disentangling these processes in plant diversity experiments will yield new insights into how plant diversity-productivity relationships change over time.

Metagenomics Assessment of Soil Fertilization on the Chemotaxis and Disease Suppressive Genes Abundance in the Maize Rhizosphere

Soil fertility is a function of the level of organic and inorganic substances present in the soil, and it influences the activities of soil-borne microbes, plant growth performance and a host of other beneficial ecological functions. In this metagenomics study, we evaluated the response of maize microbial functional gene diversity involved in chemotaxis, antibiotics, siderophores, and antifungals producing genes within the rhizosphere of maize plants under compost, inorganic fertilizer, and unfertilized conditions. The results show that fertilization treatments at higher compost manure and lower inorganic fertilizer doses as well as maize plants itself in the unfertilized soil through rhizosphere effects share similar influences on the abundance of chemotaxis, siderophores, antifungal, and antibiotics synthesizing genes present in the samples, while higher doses of inorganic fertilizer and lower compost manure treatments significantly repress these genes. The implication is for a disease suppressive soil to be achieved, soil fertilization with high doses of compost manure fertilizer treatments as well as lower inorganic fertilizer should be used to enrich soil fertility and boost the abundance of chemotaxis and disease suppressive genes. Maize crops also should be planted sole or intercropped with other crops to enhance the rhizosphere effect of these plants in promoting the expression and abundance of these beneficial genes in the soil.

Plant Microbiota Beyond Farming Practices: A Review

Plants have always grown and evolved surrounded by numerous microorganisms that inhabit their environment, later termed microbiota. To enhance food production, humankind has relied on various farming practices such as irrigation, tilling, fertilization, and pest and disease management. Over the past few years, studies have highlighted the impacts of such practices, not only in terms of plant health or yields but also on the microbial communities associated with plants, which have been investigated through microbiome studies. Because some microorganisms exert beneficial traits that improve plant growth and health, understanding how to modulate microbial communities will help in developing smart farming and favor plant growth-promoting (PGP) microorganisms. With tremendous cost cuts in NGS technologies, metagenomic approaches are now affordable and have been widely used to investigate crop-associated microbiomes. Being able to engineer microbial communities in ways that benefit crop health and growth will help decrease the number of chemical inputs required. Against this background, this review explores the impacts of agricultural practices on soil- and plant-associated microbiomes, focusing on plant growth-promoting microorganisms from a metagenomic perspective.

Disease-Suppressive Soils-Beyond Food Production: a Critical Review

In the pursuit of higher food production and economic growth and increasing population, we have often jeopardized natural resources such as soil, water, vegetation, and biodiversity at an alarming rate. In this process, wider adoption of intensive farming practices, namely changes in land use, imbalanced fertilizer application, minimum addition of organic residue/manure, and non-adoption of site-specific conservation measures, has led to declining in soil health and land degradation in an irreversible manner. In addition, increasing use of pesticides, coupled with soil and water pollution, has led the researchers to search for an environmental-friendly and cost-effective alternatives to controlling soil-borne diseases that are difficult to control, and which significantly limit agricultural productivity. Since the 1960s, disease-suppressive soils (DSS) have been identified and studied around the world. Soil disease suppression is the reduction in the incidence of soil-borne diseases even in the presence of a host plant and inoculum in the soil. The disease-suppressive capacity is mainly attributed to diverse microbial communities present in the soil that could act against soil-borne pathogens in multifaceted ways. The beneficial microorganisms employ some specific functions such as antibiosis, parasitism, competition for resources, and predation. However, there has been increasing evidence on the role of soil abiotic factors that largely influence the disease suppression. The intricate interactions of the soil, plant, and environmental components in a disease triangle make this process complex yet crucial to study to reduce disease incidence. Increasing resistance of the pathogen to presently available chemicals has led to the shift from culturable microbes to unexplored and unculturable microbes. Agricultural management practices such as tillage, fertilization, manures, irrigation, and amendment applications significantly alter the soil physicochemical environment and influence the growth and behaviour of antagonistic microbes. Plant factors such as age, type of crop, and root behaviour of the plant could stimulate or limit the diversity and structure of soil microorganisms in the rhizosphere. Further, identification and in-depth of disease-suppressive soils could lead to the discovery of more beneficial microorganisms with novel anti-microbial and plant promoting traits. To date, several microbial species have been isolated and proposed as key contributors in disease suppression, but the complexities as well as the mechanisms of the microbial and abiotic interactions remain elusive for most of the disease-suppressive soils. Thus, this review critically explores disease-suppressive attributes in soils, mechanisms involved, and biotic and abiotic factors affecting DSS and also briefly reviewing soil microbiome for anti-microbial drugs, in fact, a consequence of DSS phenomenon.

Soil Microbiome Manipulation Gives New Insights in Plant Disease-Suppressive Soils from the Perspective of a Circular Economy: A Critical Review

This review pays attention to the newest insights on the soil microbiome in plant disease-suppressive soil (DSS) for sustainable plant health management from the perspective of a circular economy that provides beneficial microbiota by recycling agro-wastes into the soil. In order to increase suppression of soil-borne plant pathogens, the main goal of this paper is to critically discuss and compare the potential use of reshaped soil microbiomes by assembling different agricultural practices such as crop selection; land use and conservative agriculture; crop rotation, diversification, intercropping and cover cropping; compost and chitosan application; and soil pre-fumigation combined with organic amendments and bio-organic fertilizers. This review is seen mostly as a comprehensive understanding of the main findings regarding DSS, starting from the oldest concepts to the newest challenges, based on the assumption that sustainability for soil quality and plant health is increasingly viable and supported by microbiome-assisted strategies based on the next-generation sequencing (NGS) methods that characterize in depth the soil bacterial and fungal communities. This approach, together with the virtuous reuse of agro-wastes to produce in situ green composts and organic bio-fertilizers, is the best way to design new sustainable cropping systems in a circular economy system. The current knowledge on soil-borne pathogens and soil microbiota is summarized. How microbiota determine soil suppression and what NGS strategies are available to understand soil microbiomes in DSS are presented. Disturbance of soil microbiota based on combined agricultural practices is deeply considered. Sustainable soil microbiome management by recycling in situ agro-wastes is presented. Afterwards, how the resulting new insights can drive the progress in sustainable microbiome-based disease management is discussed.

Beneficial Effects of Mixing Kentucky Bluegrass With Red Fescue via Plant-Soil Interactions in Black Soil of Northeast China

Continuous monoculture of cool-season turfgrass causes soil degradation, and visual turf quality decline is a major concern in black soil regions of Northeast China. Turf mixtures can enhance turfgrass resistance to biotic and abiotic stresses and increase soil microbial diversity. Understanding mechanism by plant-soil interactions and changes of black soil microbial communities in turf mixture is beneficial to restoring the degradation of urbanized black soils and maintaining sustainable development of urban landscape ecology. In this study, based on the previous research of different sowing models, two schemes of turf monoculture and mixture were conducted in field plots during 2016-2018 in a black soil of Heilongjiang province of Northeast China. The mixture turf was established by mixing 50% Kentucky bluegrass "Midnight" (Poa pratensis L.) with 50% Red fescue "Frigg" (Festuca rubra L.); and the monoculture turf was established by sowing with pure Kentucky bluegrass. Turf performance, soil physiochemical properties, and microbial composition from rhizosphere were investigated. Soil microbial communities and abundance were analyzed by Illumina MiSeq sequencing and quantitative PCR methods. Results showed that turfgrass quality, turfgrass biomass, soil organic matter (SOM), urease, alkaline phosphatase, invertase, and catalase activities increased in PF mixture, but disease percentage and soil pH decreased. The microbial diversity was also significantly enhanced under turf mixture model. The microbial community compositions were significantly different between the two schemes. Turf mixtures obviously increased the abundances of Beauveria, Lysobacter, Chryseolinea, and Gemmatimonas spp., while remarkably reduced the abundances of Myrothecium and Epicoccum spp. Redundancy analysis showed that the compositions of bacteria and fungi were related to edaphic parameters, such as SOM, pH, and enzyme activities. Since the increasing of turf quality, biomass, and disease resistance were highly correlated with the changes of soil physiochemical parameters and microbial communities in turf mixture, which suggested that turf mixture with two species (i.e., Kentucky blue grass and Red fescue) changed soil microbial communities and enhanced visual turfgrass qualities through positive plant-soil interactions by soil biota.

The soil biotic community protects Rhododendron spp. across multiple clades from the oomycete Phytophthora cinnamomi at a cost to plant growth

The effects of whole soil biotic communities on plants is a result of positive and negative interactions from a complex suite of mutualists and pathogens. However, few experiments have evaluated the composite effects of whole soil biotic communities on plant growth and disease resistance. We conducted a factorial greenhouse experiment with 14 Rhododendron species grown with and without live conspecific soil biota and with and without the disease, Phytophthora cinnamomi. We tested the prediction that the presence of whole soil biotic communities influences survival in the presence of disease. We also explored functional trait correlations with disease susceptibility across the phylogeny. The presence of live soil biota led to higher survival in the presence of disease compared with sterilized soils, and the direction of this effect was consistent for seven species across four clades. The presence of live soil biota also significantly reduced plant growth rate and decreased shoot biomass, relative to plants grown in sterilized soil, indicating that live soil biota might influence plant allocation strategies. We found that Rhododendron species with higher Root Shoot Ratios were less susceptible to Phytophthora, suggesting that water relations influence disease susceptibility. Our findings that disease resistance and susceptibility occur independently across multiple clades and that whole soil biotic communities consistently enhance disease resistance across clades, suggest that soil biota may play an important role in disease resistance and can moderate disease-induced mortality.

Community context for mechanisms of disease dilution: insights from linking epidemiology and plant-soil feedback theory

In many natural systems, diverse host communities can reduce disease risk, though less is known about the mechanisms driving this "dilution effect." We relate feedback theory, which focuses on pathogen-mediated coexistence, to mechanisms of dilution derived from epidemiological models, with the central goal of gaining insights into host-pathogen interactions in a community context. We first compare the origin, structure, and application of epidemiological and feedback models. We then explore the mechanisms of dilution, which are grounded in single-pathogen, single-host epidemiological models, from the perspective of feedback theory. We also draw on feedback theory to examine how coinfecting pathogens, and pathogens that vary along a host specialist-generalist continuum, apply to dilution theory. By identifying synergies among the feedback and epidemiological approaches, we reveal ways in which organisms occupying different trophic levels contribute to diversity-disease relationships. Additionally, using feedbacks to distinguish dilution in disease incidence from dilution in the net effect of disease on host fitness allows us to articulate conditions under which definitions of dilution may not align. After ascribing dilution mechanisms to macro- or microorganisms, we propose ways in which each contributes to diversity-disease and productivity-diversity relationships. Our analyses lead to predictions that can guide future research efforts.

Cover Crop Diversity as a Tool to Mitigate Vine Decline and Reduce Pathogens in Vineyard Soils

Wine grape production is an important economic asset in many nations; however, a significant proportion of vines succumb to grapevine trunk pathogens, reducing yields and causing economic losses. Cover crops, plants that are grown in addition to main crops in order to maintain and enhance soil composition, may also serve as a line of defense against these fungal pathogens by producing volatile root exudates and/or harboring suppressive microbes. We tested whether cover crop diversity reduced disease symptoms and pathogen abundance. In two greenhouse experiments, we inoculated soil with a 106 conidia suspension of Ilyonectria liriodendri, a pathogenic fungus, then conditioned soil with cover crops for several months to investigate changes in pathogen abundance and fungal communities. After removal of cover crops, Chardonnay cuttings were grown in the same soil to assess disease symptoms. When grown alone, white mustard was the only cover crop associated with reductions in necrotic root damage and abundance of Ilyonectria. The suppressive effects of white mustard largely disappeared when paired with other cover crops. In this study, plant identity was more important than diversity when controlling for fungal pathogens in vineyards. This research aligns with other literature describing the suppressive potential of white mustard in vineyards.

Enrichment of potentially beneficial bacteria from the consistent microbial community confers canker resistance on tomato

The soil microbiota interacts with plants closely and exerts strong influences on plant health and productivity. However, the relationship between the microbiota and the bacterial canker of tomato that is caused by Clavibacter michiganensis subsp. michiganensis (Cmm) is still unclear. In order to establish causal relationship between the microbiota and plant phenotypes, the microbial communities of 49 tomato samples (including 15 cultivars) with different canker symptoms collected from the greenhouse in Gansu province, China were investigated via 16S ribosomal RNA sequencing. Roots exhibited a strong filter effect in the process of root colonization by microorganisms according to the α-diversity and the separation patterns of the microbiota in bulk soil, rhizosphere and endosphere. In addition, the gradually decreased cluster extent from bulk soil to endosphere indicating the selective effect of tomato on microbiota. Although the composition of the microbiota is similar, the potential beneficial bacteria and functions (e.g. antibiotics production, pollution degradation, nutrition acquisition) enriched in the rhizosphere and endosphere of healthy samples compared to those in the diseased ones. Furthermore, more robust networks occurred in the rhizosphere and endosphere of healthy samples compared to the diseased ones. Our research provided substantial evidence that although the plant genotype is the dominant factor of phenotype, the rhizosphere and endosphere microbiota, as part of phytobiomes or holobiont, could contribute to the host's phenotype. This causal relationship between microbiota and host phenotypes could guide us in rationally designing novel synthetic communities (SynComs) for tomato canker biocontrol in the near future.

The plant organs and rhizosphere determine the common bean mycobiome

The plant microbiota diversity is often underestimated when approaches developed mainly for the identification of cultivable microorganisms are used. High-throughput sequencing allows a deeper understanding of the microbial diversity associated with plants. The amplification of ITS1 was used to analyze fungal diversity in several plant organs and rhizosphere of three common bean (Phaseolus vulgaris) varieties grown in a greenhouse. The fungal diversity diverged between those plant organs and the rhizosphere, with the highest found in the rhizosphere and the lowest in the stem. In each organ different numbers of genus, OTUs were identified, in a total of 283 OTUs evenly distributed among the varieties. In the co-occurrence network, a larger number of positive interactions were found in the organs of the aerial part in all varieties. We observed that the diversity of the endophytic microbiota differed more between plant organs than between common bean varieties. Our results show that the diversity of endophytic fungi can be efficiently accessed with the sequencing of ITS amplicons and that this diversity may vary among distinct plant organs and the rhizosphere of a single plant variety.

Alteration of Bacterial Wilt Resistance in Tomato Plant by Microbiota Transplant

Plant-associated microbiota plays an important role in plant disease resistance. Bacterial wilt resistance of tomato is a function of the quantitative trait of tomato plants; however, the mechanism underlying quantitative resistance is unexplored. In this study, we hypothesized that rhizosphere microbiota affects the resistance of tomato plants against soil-borne bacterial wilt caused by Ralstonia solanacearum. This hypothesis was tested using a tomato cultivar grown in a defined soil with various microbiota transplants. The bacterial wilt-resistant Hawaii 7996 tomato cultivar exhibited marked suppression and induction of disease severity after treatment with upland soil-derived and forest soil-derived microbiotas, respectively, whereas the transplants did not affect the disease severity in the susceptible tomato cultivar Moneymaker. The differential resistance of Hawaii 7996 to bacterial wilt was abolished by diluted or heat-killed microbiota transplantation. Microbial community analysis revealed the transplant-specific distinct community structure in the tomato rhizosphere and the significant enrichment of specific microbial operational taxonomic units (OTUs) in the rhizosphere of the upland soil microbiota-treated Hawaii 7996. These results suggest that the specific transplanted microbiota alters the bacterial wilt resistance in the resistant cultivar potentially through a priority effect.

Modification of Rhizosphere Bacterial Community Structure and Functional Potentials to Control Pseudostellaria heterophylla Replant Disease

Replant disease caused by negative plant-soil feedback commonly occurs in a Pseudostellaria heterophylla monoculture regime. Here, barcoded pyrosequencing of 16S ribosomal DNA amplicons combined with phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analysis was applied to study the shifts in soil bacterial community structure and functional potentials in the rhizosphere of P. heterophylla under consecutive monoculture and different soil amendments (i.e., bio-organic fertilizer application [MF] and paddy-upland rotation [PR]). The results showed that the yield of tuberous roots decreased under P. heterophylla consecutive monoculture and then increased after MF and PR treatments, which was consistent with the changes in soil bacterial diversity. Both principal coordinate analysis and the unweighted pair-group method with arithmetic means cluster analysis showed the distinct difference in bacterial community structure between the consecutively monocultured soil (relatively unhealthy soil) and other relatively healthy soils (i.e., newly planted soil, MF, and PR). Furthermore, taxonomic analysis showed that consecutive monoculture of P. heterophylla significantly decreased the relative abundances of the families Burkholderiaceae and Acidobacteriaceae (subgroup 1), whereas it increased the population density of families Xanthomonadaceae, Phyllobacteriaceae, Sphingobacteriaceae, and Alcaligenaceae, and Fusarium oxysporum. In contrast, the MF and PR treatments recovered the soil microbiome and decreased F. oxysporum abundance through the different ways; for example, the introduction of beneficial microorganisms (in MF) or the switching between anaerobic and aerobic conditions (in PR). In addition, PICRUSt analysis revealed the higher abundances of membrane transport, cell motility, and DNA repair in the consecutively monocultured soil, which might contribute to the root colonization and survival for certain bacterial pathogens under monoculture. These findings highlight the close association between replant disease of P. heterophylla and the variations in structure and potential functions of rhizosphere bacterial community.

Cultivar-Dependent Variation of the Cotton Rhizosphere and Endosphere Microbiome Under Field Conditions

Verticillium wilt caused by Verticillium dahliae is a common soil-borne disease worldwide, affecting many economically important crop species. Soil microbes can influence plant disease development. We investigated rhizosphere and endosphere microbiomes in relation to cotton cultivars with differential susceptibility to Verticillium wilt. Soil samples from nine cotton cultivars were assessed for the density of V. dahliae microsclerotia; plants were assessed for disease development. We used amplicon sequencing to profile both bacterial and fungal communities. Unlike wilt severity, wilt inoculum density did not differ significantly among resistant and susceptible cultivars. Overall, there were no significant association of alpha diversity indices with wilt susceptibility. In contrast, there were clear differences in the overall rhizosphere and endosphere microbial communities, particularly bacteria, between resistant and susceptible cultivars. Many rhizosphere and endosphere microbial groups differed in their relative abundance between resistant and susceptible cultivars. These operational taxonomic units included several well-known taxonomy groups containing beneficial microbes, such as Bacillales, Pseudomonadales, Rhizobiales, and Trichoderma, which were higher in their relative abundance in resistant cultivars. Greenhouse studies with sterilized soil supported that beneficial microbes in the rhizosphere contribute to reduced wilt development. These findings suggested that specific rhizosphere and endosphere microbes may contribute to cotton resistance to V. dahliae.

Tree Diversity Reduces Fungal Endophyte Richness and Diversity in a Large-Scale Temperate Forest Experiment

Although decades of research have typically demonstrated a positive correlation between biodiversity of primary producers and associated trophic levels, the ecological drivers of this association are poorly understood. Recent evidence suggests that the plant microbiome, or the fungi and bacteria found on and inside plant hosts, may be cryptic yet important drivers of important processes, including primary production and trophic interactions. Here, using high-throughput sequencing, we characterized foliar fungal community diversity, composition, and function from 15 broadleaved tree species (N = 545) in a recently established, large-scale temperate tree diversity experiment using over 17,000 seedlings. Specifically, we tested whether increases in tree richness and phylogenetic diversity would increase fungal endophyte diversity (the “Diversity Begets Diversity” hypothesis), as well as alter community composition (the “Tree Diversity–Endophyte Community” hypothesis) and function (the “Tree Diversity–Endophyte Function” hypothesis) at different spatial scales. We demonstrated that increasing tree richness and phylogenetic diversity decreased fungal species and functional guild richness and diversity, including pathogens, saprotrophs, and parasites, within the first three years of a forest diversity experiment. These patterns were consistent at the neighborhood and tree plot scale. Our results suggest that fungal endophytes, unlike other trophic levels (e.g., herbivores as well as epiphytic bacteria), respond negatively to increasing plant diversity.

Feedbacks of plant identity and diversity on the diversity and community composition of rhizosphere microbiomes from a long-term biodiversity experiment

Soil microbes are known to be key drivers of several essential ecosystem processes such as nutrient cycling, plant productivity and the maintenance of plant species diversity. However, how plant species diversity and identity affect soil microbial diversity and community composition in the rhizosphere is largely unknown. We tested whether, over the course of 11 years, distinct soil bacterial communities developed under plant monocultures and mixtures, and if over this time frame plants with a monoculture or mixture history changed in the bacterial communities they associated with. For eight species, we grew offspring of plants that had been grown for 11 years in the same field monocultures or mixtures (plant history in monoculture vs. mixture) in pots inoculated with microbes extracted from the field monoculture and mixture soils attached to the roots of the host plants (soil legacy). After 5 months of growth in the glasshouse, we collected rhizosphere soil from each plant and used 16S rRNA gene sequencing to determine the community composition and diversity of the bacterial communities. Bacterial community structure in the plant rhizosphere was primarily determined by soil legacy and by plant species identity, but not by plant history. In seven of the eight plant species the number of individual operational taxonomic units with increased abundance was larger when inoculated with microbes from mixture soil. We conclude that plant species richness can affect below-ground community composition and diversity, feeding back to the assemblage of rhizosphere bacterial communities in newly establishing plants via the legacy in soil.

Linkage of forest productivity to tree diversity under two different bioclimatic regimes in Italy

We analyzed the Italian National Forest Inventory data set to evaluate the interdependence of forest productivity, tree species richness (used to indicate biodiversity), climate, and soil factors. We tested the hypotheses that the relationship between biodiversity and forest productivity is positive and significant for all forests in Italy and whether the relationship is the same for forests growing in the temperate and Mediterranean bioclimatic domains (regions) of Italy. We used generalized additive models to explore the univariate response curves for the data and then performed structural equation modeling (SEM) and multi-group SEM analyses to evaluate the relationship between biodiversity and productivity. We found that the SEM model for the entire dataset explained about 60% of the variation in forest productivity. In addition, the variation associated with species richness was greater than variation due to climatic factors and the variation in climate factors was greater than the variation in soil factors (all relative to their contributions to productivity). The multi-group SEM showed a more predominant effect of biodiversity and climate on productivity in Mediterranean compared to temperate forests. In both cases, we observed a moderate effect of soil (factors) on forest productivity. Our results support the hypothesis that increasing tree diversity in forests could help reduce the effects of climate warming and enhance ecosystem productivity in the Mediterranean region.

Biotic interactions, community assembly, and eco-evolutionary dynamics as drivers of long-term biodiversity–ecosystem functioning relationships

The functioning and service provisioning of ecosystems in the face of anthropogenic environmental and biodiversity change is a cornerstone of ecological research. The last three decades of biodiversity–ecosystem functioning (BEF) research have provided compelling evidence for the significant positive role of biodiversity in the functioning of many ecosystems. Despite broad consensus of this relationship, the underlying ecological and evolutionary mechanisms have not been well understood. This complicates the transition from a description of patterns to a predictive science. The proposed Research Unit aims at filling this gap of knowledge by applying novel experimental and analytical approaches in one of the longest-running biodiversity experiments in the world: the Jena Experiment. The central aim of the Research Unit is to uncover the mechanisms that determine BEF relationships in the short- and in the long-term. Increasing BEF relationships with time in long-term experiments do not only call for a paradigm shift in the appreciation of the relevance of biodiversity change, they likely are key to understanding the mechanisms of BEF relationships in general. The subprojects of the proposed Research Unit fall into two tightly linked main categories with two research areas each that aim at exploring variation in community assembly processes and resulting differences in biotic interactions as determinants of the long-term BEF relationship. Subprojects under “Microbial community assembly” and “Assembly and functions of animal communities” mostly focus on plant diversity effects on the assembly of communities and their feedback effects on biotic interactions and ecosystem functions. Subprojects under “Mediators of plant-biotic interactions” and “Intraspecific diversity and micro-evolutionary changes” mostly focus on plant diversity effects on plant trait expression and micro-evolutionary adaptation, and subsequent feedback effects on biotic interactions and ecosystem functions. This unification of evolutionary and ecosystem processes requires collaboration across the proposed subprojects in targeted plant and soil history experiments using cutting-edge technology and will produce significant synergies and novel mechanistic insights into BEF relationships. The Research Unit of the Jena Experiment is uniquely positioned in this context by taking an interdisciplinary and integrative approach to capture whole-ecosystem responses to changes in biodiversity and to advance a vibrant research field.

Culturing Simpler and Bacterial Wilt Suppressive Microbial Communities from Tomato Rhizosphere

Plant phenotype is affected by a community of associated microorganisms which requires dissection of the functional fraction. In this study, we aimed to culture the functionally active fraction of an upland soil microbiome, which can suppress tomato bacterial wilt. The microbiome fraction (MF) from the rhizosphere of Hawaii 7996 treated with an upland soil or forest soil MF was successively cultured in a designed modified M9 (MM9) medium partially mimicking the nutrient composition of tomato root exudates. Bacterial cells were harvested to amplify V3 and V4 regions of 16S rRNA gene for QIIME based sequence analysis and were also treated to Hawaii 7996 prior to Ralstonia solanacearum inoculation. The disease progress indicated that the upland MM9 1^st transfer suppressed the bacterial wilt. Community analysis revealed that species richness was declined by successive cultivation of the MF. The upland MM9 1^st transfer harbored population of phylum Proteobacteria (98.12%), Bacteriodetes (0.69%), Firmicutes (0.51%), Actinobacteria (0.08%), unidentified (0.54%), Cyanobacteria (0.01%), FBP (0.001%), OD1 (0.001%), Acidobacteria (0.005%). The family Enterobacteriaceae of Proteobacteria was the dominant member (86.76%) of the total population of which genus Enterobacter composed 86.76% making it a potential candidate to suppress bacterial wilt. The results suggest that this mixed culture approach is feasible to harvest microorganisms which may function as biocontrol agents.