Impact of soil heat on reassembly of bacterial communities in the rhizosphere microbiome and plant disease suppression

Long-Term Organic Farming Manipulated Rhizospheric Microbiome and Bacillus Antagonism Against Pepper Blight (Phytophthora capsici)

Soil-borne diseases are often less severe in organic farms, possibly because of the recruitment of beneficial microorganisms by crops. Here, the suppressiveness of organic, integrated, and conventionally managed soils to pepper blight (Phytophthora capsici) was studied in growth chamber experiments. Disease incidence was 41.3 and 34.1% lower in the soil from an organic farming system than in either the soil from the integrated or from the conventional farming systems, respectively. Beta-diversity of rhizospheric microbial communities differed among treatments, with enrichment of Bacillus, Sporosarcina, Acidobacteria Gp5, Gp6, Gp22, and Ignavibacterium by the organic soil. Cultivation-dependent analysis indicated that 50.3% of in vitro antagonists of P. capsici isolated from the rhizosphere of healthy peppers were affiliated to Bacillus. An integration of in vitro antagonists and bacterial diversity analyses indicated that Bacillus antagonists were higher in the rhizosphere of pepper treated by the organic soil. A microbial consortium of 18 in vitro Bacillus antagonists significantly increased the suppressiveness of soil from the integrated farming system against pepper blight. Overall, the soil microbiome under the long-term organic farming system was more suppressive to pepper blight, possibly owing to Bacillus antagonism in the rhizosphere. This study provided insights into microbiome management for disease suppression under greenhouse conditions.

Plant Host-Associated Mechanisms for Microbial Selection

Plants serve as host to numerous microorganisms. The members of these microbial communities interact among each other and with the plant, and there is increasing evidence to suggest that the microbial community may promote plant growth, improve drought tolerance, facilitate pathogen defense and even assist in environmental remediation. Therefore, it is important to better understand the mechanisms that influence the composition and structure of microbial communities, and what role the host may play in the recruitment and control of its microbiome. In particular, there is a growing body of research to suggest that plant defense systems not only provide a layer of protection against pathogens but may also actively manage the composition of the overall microbiome. In this review, we provide an overview of the current research into mechanisms employed by the plant host to select for and control its microbiome. We specifically review recent research that expands upon the role of keystone microbial species, phytohormones, and abiotic stress, and in how they relate to plant driven dynamic microbial structuring.

Temperature-mediated inhibition of a bumblebee parasite by an intestinal symbiont

Competition between organisms is often mediated by environmental factors, including temperature. In animal intestines, nonpathogenic symbionts compete physically and chemically against pathogens, with consequences for host infection. We used metabolic theory-based models to characterize differential responses to temperature of a bacterial symbiont and a co-occurring trypanosomatid parasite of bumblebees, which regulate body temperature during flight and incubation. We hypothesized that inhibition of parasites by bacterial symbionts would increase with temperature, due to symbionts having higher optimal growth temperatures than parasites. We found that a temperature increase over the range measured in bumblebee colonies would favour symbionts over parasites. As predicted by our hypothesis, symbionts reduced the optimal growth temperature for parasites, both in direct competition and when parasites were exposed to symbiont spent medium. Inhibitory effects of the symbiont increased with temperature, reflecting accelerated growth and acid production by symbionts. Our results indicate that high temperatures, whether due to host endothermy or environmental factors, can enhance the inhibitory effects of symbionts on parasites. Temperature-modulated manipulation of microbiota could be one explanation for fever- and heat-induced reductions of infection in animals, with consequences for diseases of medical and conservation concern.

Microbial Community Composition in Take-All Suppressive Soils

Gaeumannomyces graminis var. tritici (Ggt) is the main soilborne factor that affects wheat production around the world. Recently we reported the occurrence of six suppressive soils in monoculture areas from indigenous "Mapuche" communities, and evidenced that the suppression relied on the biotic component of those soils. Here, we compare the rhizosphere and endosphere microbial community structure (total bacteria, actinomycetes, total fungi, and ascomycetes) of wheat plants grown in suppressive and conducive soils. Our results suggested that Ggt suppression could be mediated mostly by bacterial endophytes, rather than rhizosphere microorganisms, since the community structure was similar in all suppressive soils as compared with conducive. Interestingly, we found that despite the lower incidence of take-all disease in suppressive soils, the Ggt concentration in roots was not significantly reduced in all suppressive soils compared to those growing in conducive soil. Therefore, the disease suppression is not always related to a reduction of the pathogen biomass. Furthermore, we isolated endophytic bacteria from wheat roots growing in suppressive soils. Among them we identified Serratia spp. and Enterobacter spp. able to inhibit Ggt growth in vitro. Since the disease, but not always pathogen amount, was reduced in the suppressive soils, we propose that take all disease suppressiveness is not only related to direct antagonism to the pathogen.

Developing climate-smart restoration: Can plant microbiomes be hardened against heat waves?

Heat waves are increasing in frequency and intensity, presenting a challenge for the already difficult practice of ecological restoration. We investigated whether pre-heating locally sourced rhizosphere soil (inoculum) could acclimatize plants to a field-imposed heat wave in a restoration setting. Soil heating in the laboratory caused a marked shift in rhizosphere bacterial community composition, accompanied by an increase in species evenness. Furthermore, pre-heated rhizosphere soil reduced plant height, number of leaves, and shoot mass of the C₄ grass, blue grama (Bouteloua gracilis), and it reduced the shoot mass of the C₃ grass, Arizona fescue (Festuca arizonica) in the glasshouse. Following transplantation and the application of a field heat wave, pre-heated inoculum did not influence heat wave survival for either plant species. However, there were strong species-level responses to the field heat wave. For instance, heat wave survivorship was over four times higher in blue grama (92%) than in Arizona fescue (22%). These results suggest that the use of C₄ seeds may be preferable for sites exhibiting high heat wave risk. Further research is needed to understand whether inocula are more effective in highly degraded soil in comparison with partially degraded soils.

Involvement of Burkholderiaceae and sulfurous volatiles in disease-suppressive soils

Disease-suppressive soils are ecosystems in which plants suffer less from root infections due to the activities of specific microbial consortia. The characteristics of soils suppressive to specific fungal root pathogens are comparable to those of adaptive immunity in animals, as reported by Raaijmakers and Mazzola (Science 352:1392-3, 2016), but the mechanisms and microbial species involved in the soil suppressiveness are largely unknown. Previous taxonomic and metatranscriptome analyses of a soil suppressive to the fungal root pathogen Rhizoctonia solani revealed that members of the Burkholderiaceae family were more abundant and more active in suppressive than in non-suppressive soils. Here, isolation, phylogeny, and soil bioassays revealed a significant disease-suppressive activity for representative isolates of Burkholderia pyrrocinia, Paraburkholderia caledonica, P. graminis, P. hospita, and P. terricola. In vitro antifungal activity was only observed for P. graminis. Comparative genomics and metabolite profiling further showed that the antifungal activity of P. graminis PHS1 was associated with the production of sulfurous volatile compounds encoded by genes not found in the other four genera. Site-directed mutagenesis of two of these genes, encoding a dimethyl sulfoxide reductase and a cysteine desulfurase, resulted in a loss of antifungal activity both in vitro and in situ. These results indicate that specific members of the Burkholderiaceae family contribute to soil suppressiveness via the production of sulfurous volatile compounds.

Suppression of the activity of arbuscular mycorrhizal fungi by the soil microbiota

Arbuscular mycorrhizal fungi (AMF) colonise roots of most plants; their extra-radical mycelium (ERM) extends into the soil and acquires nutrients for the plant. The ERM coexists with soil microbial communities and it is unresolved whether these communities stimulate or suppress the ERM activity. This work studied the prevalence of suppressed ERM activity and identified main components behind the suppression. ERM activity was determined by quantifying ERM-mediated P uptake from radioisotope-labelled unsterile soil into plants, and compared to soil physicochemical characteristics and soil microbiome composition. ERM activity varied considerably and was greatly suppressed in 4 of 21 soils. Suppression was mitigated by soil pasteurisation and had a dominating biotic component. AMF-suppressive soils had high abundances of Acidobacteria, and other bacterial taxa being putative fungal antagonists. Suppression was also associated with low soil pH, but this effect was likely indirect, as the relative abundance of, e.g., Acidobacteria decreased after liming. Suppression could not be transferred by adding small amounts of suppressive soil to conducive soil, and thus appeared to involve the common action of several taxa. The presence of AMF antagonists resembles the phenomenon of disease-suppressive soils and implies that ecosystem services of AMF will depend strongly on the specific soil microbiome.

Barcoded Pyrosequencing Reveals a Shift in the Bacterial Community in the Rhizosphere and Rhizoplane of Rehmannia glutinosa under Consecutive Monoculture

The production and quality of Rehmannia glutinosa can be dramatically reduced by replant disease under consecutive monoculture. The root-associated microbiome, also known as the second genome of the plant, was investigated to understand its impact on plant health. Culture-dependent and culture-independent pyrosequencing analysis was applied to assess the shifts in soil bacterial communities in the rhizosphere and rhizoplane under consecutive monoculture. The results show that the root-associated microbiome (including rhizosphere and rhizoplane microbiomes) was significantly impacted by rhizocompartments and consecutive monoculture. Consecutive monoculture of R. glutinosa led to a significant decline in the relative abundance of the phyla Firmicutes and Actinobacteria in the rhizosphere and rhizoplane. Furthermore, the families Flavobacteriaceae, Sphingomonadaceae, and Xanthomonadaceae enriched while Pseudomonadaceae, Bacillaceae, and Micrococcaceae decreased under consecutive monoculture. At the genus level, Pseudomonas, Bacillus, and Arthrobacter were prevalent in the newly planted soil, which decreased in consecutive monocultured soils. Besides, culture-dependent analysis confirmed the widespread presence of Pseudomonas spp. and Bacillus spp. in newly planted soil and their strong antagonistic activities against fungal pathogens. In conclusion, R. glutinosa monoculture resulted in distinct root-associated microbiome variation with a reduction in the abundance of beneficial microbes, which might contribute to the declined soil suppressiveness to fungal pathogens in the monoculture regime.

Disease-induced assemblage of a plant-beneficial bacterial consortium

Disease suppressive soils typically develop after a disease outbreak due to the subsequent assembly of protective microbiota in the rhizosphere. The role of the plant immune system in the assemblage of a protective rhizosphere microbiome is largely unknown. In this study, we demonstrate that Arabidopsis thaliana specifically promotes three bacterial species in the rhizosphere upon foliar defense activation by the downy mildew pathogen Hyaloperonospora arabidopsidis. The promoted bacteria were isolated and found to interact synergistically in biofilm formation in vitro. Although separately these bacteria did not affect the plant significantly, together they induced systemic resistance against downy mildew and promoted growth of the plant. Moreover, we show that the soil-mediated legacy of a primary population of downy mildew infected plants confers enhanced protection against this pathogen in a second population of plants growing in the same soil. Together our results indicate that plants can adjust their root microbiome upon pathogen infection and specifically recruit a group of disease resistance-inducing and growth-promoting beneficial microbes, therewith potentially maximizing the chance of survival of their offspring that will grow in the same soil.

Quality of Irrigation Water Affects Soil Functionality and Bacterial Community Stability in Response to Heat Disturbance

Anthropogenic activities alter the structure and function of a bacterial community. Furthermore, bacterial communities structured by the conditions the anthropogenic activities present may consequently reduce their stability in response to an unpredicted acute disturbance. The present mesocosm-scale study exposed soil bacterial communities to different irrigation water types, including freshwater, fertilized freshwater, treated wastewater, and artificial wastewater, and evaluated their response to a disturbance caused by heat. These effectors may be considered deterministic and stochastic forces common in agricultural operations of arid and semiarid regions. Bacterial communities under conditions of high mineral and organic carbon availability (artificial wastewater) differed from the native bacterial community and showed a proteobacterial dominance. These bacterial communities had a lower resistance to the heat treatment disturbance than soils under conditions of low resource availability (high-quality treated wastewater or freshwater). The latter soil bacterial communities showed a higher abundance of operational taxonomic units (OTUs) classified as Bacilli These results were elucidated by soil under conditions of high resource availability, which lost higher degrees of functional potential and had a greater bacterial community composition change. However, the functional resilience, after the disturbance ended, was higher under a condition of high resource availability despite the bacterial community composition shift and the decrease in species richness. The functional resilience was directly connected to the high growth rates of certain Bacteroidetes and proteobacterial groups. A high stability was found in samples that supported the coexistence of both resistant OTUs and fast-growing OTUs.IMPORTANCE This report presents the results of a study employing a hypothesis-based experimental approach to reveal the forces involved in determining the stability of a soil bacterial community to disturbance. The resultant postdisturbance bacterial community composition dynamics and functionality were analyzed. The paper demonstrates the relatedness of community structure and stability under cultivation conditions prevalent in an arid area under irrigation with water of different qualities. The use of common agricultural practices to demonstrate these features has not been described before. The combination of a fundamental theoretical issue in ecology with common and concerning disturbances caused by agricultural practice makes this study unique. Furthermore, the results of the present study have applicable importance regarding soil conservation, as it enables a better characterization and monitoring of stressed soil bacterial communities and possible intervention to reduce the stress. It will also be of valued interest in coming years, as fresh water scarcity and the use of alternative water sources are expected to rise globally.

Thermal remediation alters soil properties - a review

Contaminated soils pose a risk to human and ecological health, and thermal remediation is an efficient and reliable way to reduce soil contaminant concentration in a range of situations. A primary benefit of thermal treatment is the speed at which remediation can occur, allowing the return of treated soils to a desired land use as quickly as possible. However, this treatment also alters many soil properties that affect the capacity of the soil to function. While extensive research addresses contaminant reduction, the range and magnitude of effects to soil properties have not been explored. Understanding the effects of thermal remediation on soil properties is vital to successful reclamation, as drastic effects may preclude certain post-treatment land uses. This review highlights thermal remediation studies that have quantified alterations to soil properties, and it supplements that information with laboratory heating studies to further elucidate the effects of thermal treatment of soil. Notably, both heating temperature and heating time affect i) soil organic matter; ii) soil texture and mineralogy; iii) soil pH; iv) plant available nutrients and heavy metals; v) soil biological communities; and iv) the ability of the soil to sustain vegetation. Broadly, increasing either temperature or time results in greater contaminant reduction efficiency, but it also causes more severe impacts to soil characteristics. Thus, project managers must balance the need for contaminant reduction with the deterioration of soil function for each specific remediation project.

Current Insights into the Role of Rhizosphere Bacteria in Disease Suppressive Soils

Disease suppressive soils offer effective protection to plants against infection by soil-borne pathogens, including fungi, oomycetes, bacteria, and nematodes. The specific disease suppression that operates in these soils is, in most cases, microbial in origin. Therefore, suppressive soils are considered as a rich resource for the discovery of beneficial microorganisms with novel antimicrobial and other plant protective traits. To date, several microbial genera have been proposed as key players in disease suppressiveness of soils, but the complexity of the microbial interactions as well as the underlying mechanisms and microbial traits remain elusive for most disease suppressive soils. Recent developments in next generation sequencing and other 'omics' technologies have provided new insights into the microbial ecology of disease suppressive soils and the identification of microbial consortia and traits involved in disease suppressiveness. Here, we review the results of recent 'omics'-based studies on the microbial basis of disease suppressive soils, with specific emphasis on the role of rhizosphere bacteria in this intriguing microbiological phenomenon.

Steering Soil Microbiomes to Suppress Aboveground Insect Pests

Soil-borne microbes affect aboveground herbivorous insects through a cascade of molecular and chemical changes in the plant, but knowledge of these microbe-plant-insect interactions is mostly limited to one or a few microbial strains. Yet, the soil microbial community comprises thousands of unique taxa interacting in complex networks, the so-called 'microbiome', which provides plants with multiple beneficial functions. There has been little exploration of the role and management of whole microbiomes in plant-insect interactions, calling for the integration of this complexity in aboveground-belowground research. Here, we propose holistic approaches to select soil microbiomes that can be used to protect plants from aboveground attackers.

Upscaling of fungal-bacterial interactions: from the lab to the field

Fungal-bacterial interactions (FBI) are an integral component of microbial community networks in terrestrial ecosystems. During the last decade, the attention for FBI has increased tremendously. For a wide variety of FBI, information has become available on the mechanisms and functional responses. Yet, most studies have focused on pairwise interactions under controlled conditions. The question to what extent such studies are relevant to assess the importance of FBI for functioning of natural microbial communities in real ecosystems remains largely unanswered. Here, the information obtained by studying a type of FBI, namely antagonistic interactions between bacteria and plant pathogenic fungi, is discussed for different levels of community complexity. Based on this, general recommendations are given to integrate pairwise and ecosystem FBI studies. This approach could lead to the development of novel strategies to steer terrestrial ecosystem functioning.

Aboveground Whitefly Infestation-Mediated Reshaping of the Root Microbiota

Plants respond to various types of herbivore and pathogen attack using well-developed defensive machinery designed for self-protection. Infestation from phloem-sucking insects such as whitefly and aphid on plant leaves was previously shown to influence both the saprophytic and pathogenic bacterial community in the plant rhizosphere. However, the modulation of the root microbial community by plants following insect infestation has been largely unexplored. Only limited studies of culture-dependent bacterial diversity caused by whitefly and aphid have been conducted. In this study, to obtain a complete picture of the belowground microbiome community, we performed high-speed and high-throughput next-generation sequencing. We sampled the rhizosphere soils of pepper seedlings at 0, 1, and 2 weeks after whitefly infestation versus the water control. We amplified a partial 16S ribosomal RNA gene (V1-V3 region) by polymerase chain reaction with specific primers. Our analysis revealed that whitefly infestation reshaped the overall microbiota structure compared to that of the control rhizosphere, even after 1 week of infestation. Examination of the relative abundance distributions of microbes demonstrated that whitefly infestation shifted the proteobacterial groups at week 2. Intriguingly, the population of Pseudomonadales of the class Gammaproteobacteria significantly increased after 2 weeks of whitefly infestation, and the fluorescent Pseudomonas spp. recruited to the rhizosphere were confirmed to exhibit insect-killing capacity. Additionally, three taxa, including Caulobacteraceae, Enterobacteriaceae, and Flavobacteriaceae, and three genera, including Achromobacter, Janthinobacterium, and Stenotrophomonas, were the most abundant bacterial groups in the whitefly infested plant rhizosphere. Our results indicate that whitefly infestation leads to the recruitment of specific groups of rhizosphere bacteria by the plant, which confer beneficial traits to the host plant. This study provides a new framework for investigating how aboveground insect feeding modulates the belowground microbiome.

Development of alternative strategies for management of soilborne pathogens currently controlled with methyl bromide

The current standard treatment for management of soilborne pests in some high-value crop production systems is preplant fumigation with mixtures of methyl bromide and chloropicrin. With the impending phase-out of methyl bromide, the agricultural industries that rely on soil fumigation face the need for development of alternative pest management strategies. To maintain farm productivity, immediate term research has focused on evaluation of alternative fumigants, modification of current crop production practices to accommodate their use, and improvement of application technologies to reduce the environmental effects of fumigant applications. Longer-term research goals have focused on developing a more integrated approach for pest management that incorporates the use of cultural practices to reduce pathogen pressure, host resistance to disease, and biological approaches for stimulating plant growth and control of root diseases.