Pseudomonas spp. diversity is negatively associated with suppression of the wheat take-all pathogen

Changes in the potato rhizosphere microbiota richness and diversity occur in a growth stage-dependent manner

Plant root and soil-associated microbiomes are influenced by niches, including bulk and rhizosphere soil. In this work, we collected bulk and rhizosphere soil samples at four potato developmental stages (leaf growth, flowering, tuber elongation and harvest) to identify whether rhizosphere microbiota are structured in a growth stage-dependent manner. The bacterial and fungal microbiota showed significant temporal differences in the rhizosphere and bulk soil. Rhizobacteria were most diverse at the tuber elongation stage, and dominant ASVs identified as Sphingomonas, Rhodanobacter, Sphingobium, Hyphomicrobium, and Solirubrobacter spp. In contrast, rhizosphere fungal diversity peaked at flowering stage, with Lecanicillium spp. being prominent. Furthermore, the abundance of saprophytic fungal genera, including Colletotrichum and Fusarium, and Alternaria, sharply increased at harvest stage, likely contributing to plant residue decomposition. Indicator taxa analysis highlighted the dominance of these genera at harvest. Network analysis revealed increased microbial complexity during the later growth stage, with 721 edges compared to 521 edges in the early growth stage. This increase included positive correlations between bacteria and negative correlations between bacteria and fungi. These changes suggest that microbial interactions become more interconnected and complex as potato plants mature. Our findings highlight the potential role of saprophytic fungi in shaping microbial dynamics during the later growth stage in rhizosphere soil.

Intercropping with Robinia pseudoacacia reduces soft rot incidence in konjac by modulating the root bacterial community

BACKGROUND

Soft rot (Pectobacterium aroidearum and Dickeya) is a devastating soil-borne bacterial disease that threatens konjac production. Intercropping with false acacia has been shown to significantly reduce soft rot incidence in konjac by shifting the microbial community. However, how intercropping shapes the root bacterial community and affects soft rot incidence remains unclear. To address this, we investigated three konjac intercropping systems (false acacia, paulownia, and maize) to explore the relationships among intercropping, soft rot incidence, root bacterial community, soil enzyme activity, and soil properties.

RESULTS

Konjac intercropped with false acacia exhibited the lowest soft rot incidence and the lowest abundance of pathogenic taxa. Soft rot incidence was negatively correlated with total soil nitrogen and potassium but positively correlated with total and available soil phosphorus. The bacterial community structure and function in konjac roots differed among intercropping types, mainly driven by available soil phosphorus. Beneficial microorganisms such as Bradyrhizobium and Variovorax were enriched under a false acacia intercropping system and were negatively correlated with soil-available phosphorus. Additionally, the stable bacterial community in healthy konjac roots under false acacia may make konjac less susceptible to pathogen invasion.

CONCLUSION

The study showed that intercropping reduced the soft rot incidence by regulating the structure and stability of the konjac root bacterial community, and soil-available phosphorus was the main factor affecting the difference in the konjac root bacterial community, which provided a basis for the management of soil fertilization in konjac cultivation. © 2024 Society of Chemical Industry.

Associations Among Cultivar Cropping Sequence, 2,4-Diacetlyphloroglucinol-Producing Pseudomonad Populations, and Take-All Disease of Winter Wheat in Oregon

Take-all of wheat (Triticum aestivum L.), caused by Gaeumannomyces tritici (syn. G. graminis var. tritici), is perhaps the most important soilborne disease of wheat globally and can cause substantial yield losses under several cropping scenarios in Oregon. Although resistance to take-all has not been identified in hexaploid wheat, continuous cropping of wheat for several years can reduce take-all severity through the development of suppressive soils, a process called "take-all decline" (TAD). Extensive work has shown that TAD is driven primarily by members of the Pseudomonas fluorescens complex that produce 2,4-diacetlyphloroglucinol (DAPG), an antibiotic that is associated with antagonism and induced host resistance against multiple pathogens. Field experiments were conducted to determine the influence of agronomically relevant first-year wheat cultivars on take-all levels and ability to accumulate DAPG-producing pseudomonads within their rhizospheres in second-year field trials and in greenhouse trials. One first-year wheat cultivar consistently resulted in less take-all in second-year wheat and accumulated significantly more DAPG-producing pseudomonads than other cultivars, suggesting a potential mechanism for take-all reduction associated with that cultivar. An intermediate level of take-all suppression in other cultivars was not clearly associated with population size of DAPG-producing pseudomonads, however. The first-year cultivar effect on take-all dominated in subsequent plantings, and its impact was not specific to the first-year cultivar. Our results confirm that wheat cultivars may be used to suppress take-all when deployed appropriately over cropping seasons, an approach that is cost-effective, sustainable, and currently being used by some wheat growers in Oregon to reduce take-all.

The UK Crop Microbiome Cryobank: a utility and model for supporting Phytobiomes research

Plant microbiomes are the microbial communities essential to the functioning of the phytobiome-the system that consist of plants, their environment, and their associated communities of organisms. A healthy, functional phytobiome is critical to crop health, improved yields and quality food. However, crop microbiomes are relatively under-researched, and this is associated with a fundamental need to underpin phytobiome research through the provision of a supporting infrastructure. The UK Crop Microbiome Cryobank (UKCMC) project is developing a unique, integrated and open-access resource to enable the development of solutions to improve soil and crop health. Six economically important crops (Barley, Fava Bean, Oats, Oil Seed Rape, Sugar Beet and Wheat) are targeted, and the methods as well as data outputs will underpin research activity both in the UK and internationally. This manuscript describes the approaches being taken, from characterisation, cryopreservation and analysis of the crop microbiome through to potential applications. We believe that the model research framework proposed is transferable to different crop and soil systems, acting not only as a mechanism to conserve biodiversity, but as a potential facilitator of sustainable agriculture systems.

Functional genomics analysis of a phyllospheric Pseudomonas spp with potential for biological control against coffee rust

Background

Pseudomonas spp. promotes plant growth and colonizes a wide range of environments. During the annotation of a Coffea arabica ESTs database, we detected a considerable number of contaminant Pseudomonas sequences, specially associated with leaves. The genome of a Pseudomonas isolated from coffee leaves was sequenced to investigate in silico information that could offer insights about bacterial adaptation to coffee phyllosphere. In parallel, several experiments were performed to confirm certain physiological characteristics that could be associated with phyllospheric behavior. Finally, in vivo and in vitro experiments were carried out to verify whether this isolate could serve as a biocontrol agent against coffee rust and how the isolate could act against the infection. 

Results

The isolate showed several genes that are associated with resistance to environmental stresses, such as genes encoding heat/cold shock proteins, antioxidant enzymes, carbon starvation proteins, proteins that control osmotic balance and biofilm formation. There was an increase of exopolysaccharides synthesis in response to osmotic stress, which may protect cells from dessication on phyllosphere. Metabolic pathways for degradation and incorporation into citrate cycle of phenolic compounds present in coffee were found, and experimentally confirmed. In addition, MN1F was found to be highly tolerant to caffeine. The experiments of biocontrol against coffee leaf rust showed that the isolate can control the progress of the disease, most likely through competition for resources.

Conclusion

Genomic analysis and experimental data suggest that there are adaptations of this Pseudomonas to live in association with coffee leaves and to act as a biocontrol agent.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-022-02637-4.

Genomic and physiological evaluation of two root associated Pseudomonas from Coffea arabica

Many Pseudomonas species promote plant growth and colonize a wide range of environments. The annotation of a Coffea arabica ESTs database revealed a considerable number of Pseudomonas sequences. To evaluate the genomic and physiology of Pseudomonas that inhabit coffee plants, fluorescent Pseudomonas from C. arabica root environment were isolated. Two of them had their genomes sequenced; one from rhizospheric soil, named as MNR3A, and one from internal part of the root, named as EMN2. In parallel, we performed biochemical and physiological experiments to confirm genomic analyses results. Interestingly, EMN2 has achromobactin and aerobactin siderophore receptors, but does not have the genes responsible for the production of these siderophores, suggesting an interesting bacterial competition strategy. The two bacterial isolates were able to degrade and catabolize plant phenolic compounds for their own benefit. Surprisingly, MNR3A and EMN2 do not contain caffeine methylases that are responsible for the catabolism of caffeine. In fact, bench experiments confirm that the bacteria did not metabolize caffeine, but were resistant and chemically attracted to it. Furthermore, both bacteria, most especially MNR3A, were able to increase growth of lettuce plants. Our results indicate MNR3A as a potential plant growth promoting bacteria.

Organic fertilizer activates soil beneficial microorganisms to promote strawberry growth and soil health after fumigation

Soil fumigants aim to control soil-borne diseases below levels that affect economic crop production, but their use also reduces the abundance of beneficial microorganisms. Previous studies have shown that adding various types of fertilizers to soil after fumigation can reshape the soil microbial community and regulate crop growth. We fumigated soil with dazomet (DZ) that had been cropped continuously for more than 20 years. After fumigation we applied silicon fertilizer, potassium humate organic fertilizer, Bacillus microbial fertilizer or a mixture of the last two. We studied the effects of different fertilizers treatments on the soil's physicochemical properties, enzyme activities, key soil pathogens and beneficial microbes. We found that fertilizers applied after fumigation promoted soil beneficial microorganisms (such as Fimicutes, Chloroflexi, Bacillus and Actinomadura) restoration; increased Fusarium and Phytophthora pathogen mortality, the content of ammonium nitrogen, sucrase enzyme activity; and increased strawberry fruit yield. A significant increase in strawberry yield was positively correlated with increases in beneficial microorganisms such as Gemmatimonadota, Firmicutes, Bacillus and Flavisolibacter. We concluded that organic fertilizer applied after fumigation significantly increased the number of beneficial microorganisms, improved the physicochemical properties of the soil, increased soil enzyme activities, inhibited the growth of soil pathogens to increase strawberry fruit yield. In summary, organic fertilizer activated soil beneficial microorganisms after soil fumigation, promoted soil health, and increased strawberry fruit yield.

The remediation effects of microbial organic fertilizer on soil microorganisms after chloropicrin fumigation

Soil fumigation with chloropicrin (CP) is an effective means of overcoming continuous cropping obstacles (CCO) in Panax notoginseng and improving its yield and quality. CP fumigation can change the microbial community of soil. Therefore, a key step after CP fumigation is the rapid restoration of soil microorganisms and the promotion of beneficial microorganism proliferation as the dominant flora. In this study, continuously cropped soil of P. notoginseng was fumigated with CP, and general organic fertilizer (GOF) or microbial organic fertilizer (MOF) was used to restore soil microorganisms after fumigation. Soil physical and chemical properties, soil microorganisms, and quality of P. notoginseng were investigated. The application of MOF and GOF after CP fumigation promoted increases in soil nitrogen (9.88% and 8.21%, respectively), phosphorus (21.39% and 11.57%, respectively), potassium (7.99% and 2.75%, respectively), and the quality of P. notoginseng; it also promoted the accumulation of saponins in the main roots (23.62% and 9.12%, respectively). Application of MOF and GOF can restore the diversity of microorganisms in the soil. MOF increased the relative abundance of the beneficial soil microorganisms Glomeromycota, Mortierellomycota, Humicola and Bacillus, thereby lowering the relative abundance of the harmful Ascomycota and Fusarium relative to GOF. In summary, CP fumigation reduces the diversity of microorganisms in the soil. The addition of organic fertilizer can promote microbial diversity and increase the relative abundance of beneficial species. Moreover, the promotion effect of MOF is better than that of GOF, thereby improving soil fertility and ultimately promoting the quality and yield of P. notoginseng.

An emerging chemical fumigant: two-sided effects of dazomet on soil microbial environment and plant response

Methyl bromide has been banned worldwide because it causes damage to the ozone layer and the environment. To find a substitute for methyl bromide, the relationships among fumigation, plant growth, and the microbial community in replant soil require further study. We performed pot and field experiments to investigate the effects of dazomet fumigation on soil properties and plant performance. Changes in soil microbial community structure and diversity were assessed using high-throughput sequencing, and plant physiological performance and soil physicochemical properties were also measured. Dazomet fumigation enhanced photosynthesis and promoted plant growth in replant soil; it altered soil physical and chemical properties and reduced soil enzyme activities, although these parameters gradually recovered over time. After dazomet fumigation, the dominant soil phyla changed, microbial diversity decreased significantly, the relative abundance of biocontrol bacteria such as Mortierella increased, and the relative abundance of pathogenic bacteria such as Fusarium decreased. Over the course of the experiment, the soil microbial flora changed dynamically, and soil enzyme activities and other physical and chemical properties also recovered to a certain extent. This result suggested that the effect of dazomet on soil microorganisms was temporary. However, fumigation also led to an increase in some resistant pathogens, such as Trichosporon, that affect soil function and health. Therefore, it is necessary to consider potential negative impacts of dazomet on the soil environment and to perform active environmental risk management in China.

Identification and Differentiation of Pseudomonas Species in Field Samples Using an rpoD Amplicon Sequencing Methodology

Species of the genus Pseudomonas are used for several biotechnological purposes, including plant biocontrol and bioremediation. To exploit the Pseudomonas genus in environmental, agricultural, or industrial settings, the organisms must be profiled at the species level as their bioactivity potential differs markedly between species. Standard 16S rRNA gene amplicon profiling does not allow for accurate species differentiation. Thus, the purpose of this study was to develop an amplicon-based high-resolution method targeting a 760-nucleotide (nt) region of the rpoD gene enabling taxonomic differentiation of Pseudomonas species in soil samples. The method was benchmarked on a 16-member Pseudomonas species mock community. All 16 species were correctly and semiquantitatively identified using rpoD gene amplicons, whereas 16S rRNA V3-V4 amplicon sequencing only correctly identified one species. We analyzed the Pseudomonas profiles in 13 soil samples in northern Zealand, Denmark, where samples were collected from grassland (3 samples) and agriculture soil (10 samples). Pseudomonas species represented up to 0.7% of the 16S rRNA gene abundance, of which each sampling site contained a unique Pseudomonas composition. Thirty culturable Pseudomonas strains were isolated from each grassland site and 10 from each agriculture site and identified by Sanger sequencing of the rpoD gene. In all cases, the rpoD amplicon approach identified more species than were found by cultivation, including hard-to-culture nonfluorescent pseudomonads, as well as more than were found by 16S rRNA V3-V4 amplicon sequencing. Thus, rpoD profiling can be used for species profiling of Pseudomonas, and large-scale prospecting of bioactive Pseudomonas may be guided by initial screening using this method.

IMPORTANCE A high-throughput sequencing-based method for profiling of Pseudomonas species in soil microbiomes was developed and identified more species than 16S rRNA gene sequencing or cultivation. Pseudomonas species are used as biocontrol organisms and plant growth-promoting agents, and the method will allow tracing of specific species of Pseudomonas as well as enable screening of environmental samples for further isolation and exploitation.

Take-All Disease: New Insights into an Important Wheat Root Pathogen

Take-all disease, caused by the fungal root pathogen Gaeumannomyces tritici, is considered to be the most important root disease of wheat worldwide. Here we review the advances in take-all research over the last 15 years, focusing on the identification of new sources of genetic resistance in wheat relatives and the role of the microbiome in disease development. We also highlight recent breakthroughs in the molecular interactions between G. tritici and wheat, including genome and transcriptome analyses. These new findings will aid the development of novel control strategies against take-all disease. In light of this growing understanding, the G. tritici-wheat interaction could provide a model study system for root-infecting fungal pathogens of cereals.

Multi-Trait Wheat Rhizobacteria from Calcareous Soil with Biocontrol Activity Promote Plant Growth and Mitigate Salinity Stress

Plant growth promoting rhizobacteria (PGPR) can be functional microbial fertilizers and/or biological control agents, contributing to an eco-spirit and safe solution for chemical replacement. Therefore, we have isolated rhizospheric arylsulfatase (ARS)-producing bacteria, belonging to Pseudomonas and Bacillus genus, from durum wheat crop grown on calcareous soil. These isolates harbouring plant growth promoting (PGP) traits were further evaluated in vitro for additional PGP traits, including indole compounds production and biocontrol activity against phytopathogens, limiting the group of multi-trait strains to eight. The selected bacterial strains were further evaluated for PGP attributes associated with biofilm formation, compatibility, salt tolerance ability and effect on plant growth. In vitro studies demonstrated that the multi-trait isolates, Bacillus (1.SG.7, 5.SG.3) and Pseudomonas (2.SG.20, 2.C.19) strains, enhanced the lateral roots abundance and shoots biomass, mitigated salinity stress, suggesting the utility of beneficial ARS-producing bacteria as potential microbial fertilizers. Furthermore, in vitro studies demonstrated that compatible combinations of multi-trait isolates, Bacillus sp. 1.SG.7 in a mixture coupled with 5.SG.3, and 2.C.19 with 5.SG.3 belonging to Bacillus and Pseudomonas, respectively, may enhance plant growth as compared to single inoculants.

Effect of Inorganic N Top Dressing and Trichoderma harzianum Seed-Inoculation on Crop Yield and the Shaping of Root Microbial Communities of Wheat Plants Cultivated Under High Basal N Fertilization

Wheat crop production needs nitrogen (N) for ensuring yield and quality. High doses of inorganic N fertilizer are applied to soil before sowing (basal dressing), with additional doses supplied along the cultivation (top dressing). Here, a long-term wheat field trial (12 plots), including four conditions (control, N top dressing, Trichoderma harzianum T34 seed-inoculation, and top dressing plus T34) in triplicate, was performed to assess, under high basal N fertilization, the influence of these treatments on crop yield and root microbial community shaping. Crop yield was not affected by top dressing and T. harzianum T34, but top dressing significantly increased grain protein and gluten contents. Twenty-seven-week old wheat plants were collected at 12 days after top dressing application and sampled as bulk soil, rhizosphere and root endosphere compartments in order to analyze their bacterial and fungal assemblies by 16S rDNA and ITS2 high-throughput sequencing, respectively. Significant differences for bacterial and fungal richness and diversity were detected among the three compartments with a microbial decline from bulk soil to root endosphere. The most abundant wheat root phyla were Proteobacteria and Actinobacteria for bacteria, and Ascomycota and Basidiomycota for fungi. An enrichment of genera commonly associated with soils subjected to chemical N fertilization was observed: Kaistobacter, Mortierella, and Solicoccozyma in bulk soil, Olpidium in rhizosphere, and Janthinobacterium and Pedobacter in root endosphere. Taxa whose abundance significantly differed among conditions within each compartment were identified. Results show that: (i) single or strain T34-combined application of N top dressing affected to a greater extent the bulk soil bacterial levels than the use of T34 alone; (ii) when N top dressing and T34 were applied in combination, the N fertilizer played a more decisive role in the bacterial microbiome than T34; (iii) many genera of plant beneficial bacteria, negatively affected by N top dressing, were increased by the application of T34 alone; (iv) bulk soil and rhizosphere fungal microbiomes were affected by any of the three treatments assayed; and (v) all treatments reduced Claroideoglomus in bulk soil but the single application of T34 raised the rhizosphere levels of this mycorrhizal fungus.

Microbial and volatile profiling of soils suppressive to Fusarium culmorum of wheat

In disease-suppressive soils, microbiota protect plants from root infections. Bacterial members of this microbiota have been shown to produce specific molecules that mediate this phenotype. To date, however, studies have focused on individual suppressive soils and the degree of natural variability of soil suppressiveness remains unclear. Here, we screened a large collection of field soils for suppressiveness to Fusarium culmorum using wheat (Triticum aestivum) as a model host plant. A high variation of disease suppressiveness was observed, with 14% showing a clear suppressive phenotype. The microbiological basis of suppressiveness to F. culmorum was confirmed by gamma sterilization and soil transplantation. Amplicon sequencing revealed diverse bacterial taxonomic compositions and no specific taxa were found exclusively enriched in all suppressive soils. Nonetheless, co-occurrence network analysis revealed that two suppressive soils shared an overrepresented bacterial guild dominated by various Acidobacteria. In addition, our study revealed that volatile emission may contribute to suppression, but not for all suppressive soils. Our study raises new questions regarding the possible mechanistic variability of disease-suppressive phenotypes across physico-chemically different soils. Accordingly, we anticipate that larger-scale soil profiling, along with functional studies, will enable a deeper understanding of disease-suppressive microbiomes.

Advances in the control of phytopathogenic fungi that infect crops through their root system

Productivity and economic sustainability of many herbaceous and woody crops are seriously threatened by numerous phytopathogenic fungi. While symptoms associated with phytopathogenic fungal infections of aerial parts (leaves, stems and fruits) are easily observable and therefore recognizable, allowing rapid or preventive action to control this type of infection, the effects produced by soil-borne fungi that infect plants through their root system are more difficult to detect. The fact that these fungi initiate infection and damage underground implies that the first symptoms are not as easily noticeable, and therefore both crop yield and plant survival are frequently severely compromised by the time the infection is found. In this paper we will review and discuss recent insights into plant-microbiota interactions in the root system crucial to understanding the beginning of the infectious process. We will also review different methods for diminishing and controlling the infection rate by phytopathogenic fungi penetrating through the root system including both the traditional use of biocontrol agents such as antifungal compounds as well as some new strategies that could be used because of their effective application, such as nanoparticles, virus-based nanopesticides, or inoculation of plant material with selected endophytes. We will also review the possibility of modeling and influencing the composition of the microbial population in the rhizosphere environment as a strategy for nudging the plant-microbiome interactions toward enhanced beneficial outcomes for the plant, such as controlling the infectious process.

More Than the Sum of Its Parts: Microbiome Biodiversity as a Driver of Plant Growth and Soil Health

Microorganisms drive several processes needed for robust plant growth and health. Harnessing microbial functions is thus key to productive and sustainable food production. Molecular methods have led to a greater understanding of the soil microbiome composition. However, translating species or gene composition into microbiome functionality remains a challenge. Community ecology concepts such as the biodiversity–ecosystem functioning framework may help predict the assembly and function of plant-associated soil microbiomes. Higher diversity can increase the number and resilience of plant-beneficial functions that can be coexpressed and unlock the expression of plant-beneficial traits that are hard to obtain from any species in isolation. We combine well-established community ecology concepts with molecular microbiology into a workable framework that may enable us to predict and enhance soil microbiome functionality to promote robust plant growth in a global change context.

Prokaryotic taxa play keystone roles in the soil microbiome associated with woody perennial plants in the genus Buxus

The microbiome associated with ornamental plants has largely been neglected, despite its potential for impacting plant health. This work characterized the composition, diversity, and microbial co-associations in the soil microbiome associated with species and cultivars of plant in the genus Buxus (common name boxwood), a group of woody perennial shrubs commonly used in residential landscapes and found in native ecosystems. Soil was collected from 82 individual curated boxwood accessions at the U.S. National Arboretum National Boxwood Collection. Amplicon libraries targeting archaea, bacteria, and fungi were generated and sequenced using the Illumina MiSeq platform. Identification of individual sequence variants resulted in 275 archaeal, 15,580 bacterial, and 7,525 fungal taxa. Neither spatial distance among samples nor association with different types of boxwood were significant predictors of soil microbiome composition. However, archaeal and bacterial diversity was significantly different in soil from distinct types of boxwood. Co-association networks indicated that archaea and bacteria show greater evidence of being keystone taxa than fungi. Overall, this work demonstrates the potential for targeting specific keystone taxa to shift the soil microbiome associated with these boxwood accessions and that planting different species or cultivars in the landscape may shift the diversity of prokaryotic microorganisms.

Impacts on soil microbial characteristics and their restorability with different soil disinfestation approaches in intensively cropped greenhouse soils

The different impacts, especially on soil physicochemical and microbial characteristics, among disinfestation methods based on different principles (including physical, chemical, and biological) have not been illustrated well. Here, we used steam sterilization, dazomet fumigation, and reductive soil disinfestation (RSD) methods representative of physical, chemical, and biological soil disinfestation, respectively, to disinfest seriously degraded greenhouse soils before watermelon cultivation in one season. Compared with the control, RSD significantly decreased the soil nitrate content by 85.9% and the electrical conductivity by 52.0% and increased the soil pH to 7.44. Although all three soil disinfestations significantly decreased the abundance of the pathogen Fusarium oxysporum by 83.0-99.2%, their impacts on soil microbial characteristics were variable. Briefly, steam sterilization significantly changed multiple bacterial and fungal properties. Dazomet fumigation impacted mainly fungal properties, such as abundance, diversity, and community structure, but RSD significantly decreased bacterial diversity and altered the bacterial community structure. Although the differences mentioned above got smaller after watermelon cultivation, the plant performances differed dramatically in different soils. The largest plant biomass, fruit ratio, and yield were found in the RSD-treated soil, whereas the lowest fruit ratio and yield were found in the steam-sterilized soil. The soil nitrate content, electrical conductivity, bacterial diversity and community structure, and some specific microbial agents, such as Aspergillus, Cladosporium, and Pseudomonas, were correlated with plant performance. RSD is a promising soil disinfestation strategy to support plant growth in intensively cultivated greenhouse soils with serious problems, such as acidification, salinization, and pathogen accumulation.

Facilitation promotes invasions in plant-associated microbial communities

While several studies have established a positive correlation between community diversity and invasion resistance, it is less clear how species interactions within resident communities shape this process. Here, we experimentally tested how antagonistic and facilitative pairwise interactions within resident model microbial communities predict invasion by the plant-pathogenic bacterium Ralstonia solanacearum. We found that facilitative resident community interactions promoted and antagonistic interactions suppressed invasions both in the lab and in the tomato plant rhizosphere. Crucially, pairwise interactions reliably explained observed invasion outcomes also in multispecies communities, and mechanistically, this was linked to direct inhibition of the invader by antagonistic communities (antibiosis), and to a lesser degree by resource competition between members of the resident community and the invader. Together, our findings suggest that the type and strength of pairwise interactions can reliably predict the outcome of invasions in more complex multispecies communities.

Exploring the resilience of wheat crops grown in short rotations through minimising the build-up of an important soil-borne fungal pathogen

Given the increasing demand for wheat which is forecast, cropping of wheat in short rotations will likely remain a common practice. However, in temperate wheat growing regions the soil-borne fungal pathogen Gaeumannomyces tritici becomes a major constraint on productivity. In cultivar rotation field experiments on the Rothamsted Farm (Hertfordshire, UK) we demonstrated a substantial reduction in take-all disease and grain yield increases of up to 2.4 tonnes/ha when a low take-all inoculum building wheat cultivar was grown in the first year of wheat cropping. Phenotyping of 71 modern elite wheat cultivars for the take-all inoculum build-up trait across six diverse trial sites identified a few cultivars which exhibited a consistent lowering of take-all inoculum build-up. However, there was also evidence of a significant interaction effect between trial site and cultivar when a pooled Residual Maximum Likelihood (REML) procedure was conducted. There was no evidence of an unusual rooting phenotype associated with take-all inoculum build-up in two independent field experiments and a sand column experiment. Together our results highlight the complex interactions between wheat genotype, environmental conditions and take-all inoculum build-up. Further work is required to determine the underlying genetic and mechanistic basis of this important phenomenon.

Antagonistic Interactions and Biofilm Forming Capabilities Among Bacterial Strains Isolated from the Egg Surfaces of Lake Sturgeon (Acipenser fulvescens)

Characterization of interactions within a host-associated microbiome can help elucidate the mechanisms of microbial community formation on hosts and can be used to identify potential probiotics that protect hosts from pathogens. Microbes employ various modes of antagonism when interacting with other members of the community. The formation of biofilm by some strains can be a defense against antimicrobial compounds produced by other taxa. We characterized the magnitude of antagonistic interactions and biofilm formation of 25 phylogenetically diverse taxa that are representative of isolates obtained from egg surfaces of the threatened fish species lake sturgeon (Acipenser fulvescens) at two ecologically relevant temperature regimes. Eight isolates exhibited aggression to at least one other isolate. Pseudomonas sp. C22 was found to be the most aggressive strain, while Flavobacterium spp. were found to be one of the least aggressive and the most susceptible genera. Temperature affected the prevalence and intensity of antagonism. The aggressive strains identified also inhibited growth of known fish pathogens. Biofilm formations were observed for nine isolates and were dependent on temperature and growth medium. The most aggressive of the isolates disrupted biofilm formation of two well-characterized isolates but enhanced biofilm formation of a fish pathogen. Our results revealed the complex nature of interactions among members of an egg associated microbial community yet underscored the potential of specific microbial populations as host probiotics.