Biocontrol of Cereal Crop Diseases Using Streptomycetes

A growing world population and an increasing demand for greater food production requires that crop losses caused by pests and diseases are dramatically reduced. Concurrently, sustainability targets mean that alternatives to chemical pesticides are becoming increasingly desirable. Bacteria in the plant root microbiome can protect their plant host against pests and pathogenic infection. In particular, Streptomyces species are well-known to produce a range of secondary metabolites that can inhibit the growth of phytopathogens. Streptomyces are abundant in soils and are also enriched in the root microbiomes of many different plant species, including those grown as economically and nutritionally valuable cereal crops. In this review we discuss the potential of Streptomyces to protect against some of the most damaging cereal crop diseases, particularly those caused by fungal pathogens. We also explore factors that may improve the efficacy of these strains as biocontrol agents in situ, as well as the possibility of exploiting plant mechanisms, such as root exudation, that enable the recruitment of microbial species from the soil to the root microbiome. We argue that a greater understanding of these mechanisms may enable the development of protective plant root microbiomes with a greater abundance of beneficial bacteria, such as Streptomyces species.

Systems Biology of Plant-Microbiome Interactions

In natural environments, plants are exposed to diverse microbiota that they interact with in complex ways. While plant-pathogen interactions have been intensely studied to understand defense mechanisms in plants, many microbes and microbial communities can have substantial beneficial effects on their plant host. Such beneficial effects include improved acquisition of nutrients, accelerated growth, resilience against pathogens, and improved resistance against abiotic stress conditions such as heat, drought, and salinity. However, the beneficial effects of bacterial strains or consortia on their host are often cultivar and species specific, posing an obstacle to their general application. Remarkably, many of the signals that trigger plant immune responses are molecularly highly similar and often identical in pathogenic and beneficial microbes. Thus, it is unclear what determines the outcome of a particular microbe-host interaction and which factors enable plants to distinguish beneficials from pathogens. To unravel the complex network of genetic, microbial, and metabolic interactions, including the signaling events mediating microbe-host interactions, comprehensive quantitative systems biology approaches will be needed.

Evaluation of in-vitro methods to select effective streptomycetes against toxigenic fusaria

Biocontrol microorganisms are emerging as an effective alternative to pesticides. Ideally, biocontrol agents (BCAs) for the control of fungal plant pathogens should be selected by an in vitro method that is high-throughput and is predictive of in planta efficacy, possibly considering environmental factors, and the natural diversity of the pathogen. The purpose of our study was (1) to assess the effects of Fusarium strain diversity (N = 5) and culture media (N = 6) on the identification of biological control activity of Streptomyces strains (N = 20) against Fusarium pathogens of wheat in vitro and (2) to verify the ability of our in vitro screening methods to simulate the activity in planta. Our results indicate that culture media, Fusarium strain diversity, and their interactions affect the results of an in vitro selection by dual culture assay. The results obtained on the wheat-based culture media resulted in the highest correlation score (r = 0.5) with the in planta root rot (RR) inhibition, suggesting that this in vitro method was the best predictor of in planta performance of streptomycetes against Fusarium RR of wheat assessed as extension of the necrosis on the root. Contrarily, none of the in vitro plate assays using the media tested could appropriately predict the activity of the streptomycetes against Fusarium foot rot symptoms estimated as the necrosis at the crown level. Considering overall data of correlation, the activity in planta cannot be effectively predicted by dual culture plate studies, therefore improved in vitro methods are needed to better mimic the activity of biocontrol strains in natural conditions. This work contributes to setting up laboratory standards for preliminary screening assays of Streptomyces BCAs against fungal pathogens.

Insight into the Bacterial Endophytic Communities of Peach Cultivars Related to Crown Gall Disease Resistance

Crown gall disease caused by Agrobacterium tumefaciens severely impacts the production of peach and other fruit trees. Several peach cultivars are partially resistant to A. tumefaciens, but little is known about the roles of endophytic microbiota in disease resistance. In the present study, the endophytic bacterial communities of resistant and susceptible peach cultivars "Honggengansutao" and "Okinawa" were analyzed using universal 16S rRNA gene amplicon sequencing in parallel with the cultivation and characterization of bacterial isolates. A total of 1,357,088 high-quality sequences representing 3,160 distinct operational taxonomic units (OTUs; Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes) and 1,200 isolates of 20 genera and 305 distinct ribotypes were collected from peach roots and twigs. It was found that factors including plant developmental stage, cultivar, and A. tumefaciens invasion strongly influenced the peach endophytic communities. The community diversity of endophytic bacteria and the abundance of culturable bacteria were both higher in the roots of the resistant cultivar, particularly after inoculation. Strikingly, the pathogen antagonists Streptomyces and Pseudomonas in roots and Rhizobium in twigs were most frequently detected in resistant plants. Our results suggest that the higher abundance and diversity of endophytic bacteria and increased proportions of antagonistic bacteria might contribute to the natural defense of the resistant cultivar against A. tumefaciens This work reveals the relationships between endophytic bacteria and disease resistance in peach plants and provides important information for microbiome-based biocontrol of crown gall disease in fruit trees.IMPORTANCE Agrobacterium tumefaciens as the causal agent of peach crown gall disease can be controlled by planting resistant cultivars. This study profiles the endophytic bacteria in susceptible and resistant peach cultivars, advancing our understanding of the relationships between endophytic bacterial communities and peach crown gall disease, with potential implications for other complex microbiome-plant-pathogen interactions. The resistant cultivar may defend itself by increasing the diversity and abundance of beneficial endophytic bacteria. The antagonists identified among the genera Streptomyces, Pseudomonas, and Rhizobium may have application potential for biocontrol of crown gall disease in fruit trees.

Microbiome Diversity in Cotton Rhizosphere Under Normal and Drought Conditions

Climate change contributes to drought stress and subsequently affects crop growth, development, and yield. The microbial community, such as fungi and bacteria in the rhizosphere, is of special importance to plant productivity. In this study, soil collected from a cotton research field was used to grow cotton plants (Gossypium hirsutum cv. Jin668) under controlled environment conditions. Drought stress was applied at flowering stage, while control plants were regularly watered. At the same time, the soil without plants was also subjected to drought, while control pots were regularly watered. The soil was collected in sterilized tubes and microbial DNA was isolated and high-throughput sequencing of 16S rRNA genes was carried out. The alpha diversity of bacteria community significantly increased in the soil with cotton plants compared to the soil without cotton plants. Taxonomic analysis revealed that the bacterial community structure of the cotton rhizosphere predominantly consisted of the phyla Proteobacteria (31.7%), Actinobacteria (29.6%), Gemmatimonadetes (9.8%), Chloroflexi (9%), Cyanobacteria (5.6%), and Acidobacteria. In the drought-treated rhizosphere, Chloroflexi and Gemmatimonadetes were the dominant phyla. This study reveals that the cotton rhizosphere has a rich pool of bacterial communities even under drought stress, and which may improve drought tolerance in plants. These data will underpin future improvement of drought tolerance of cotton via the soil microbial community.

Sequential improvement of rimocidin production in Streptomyces rimosus M527 by introduction of cumulative drug-resistance mutations

Rimocidin is a polyene macrolide that exhibits a strong inhibitory activity against a broad range of plant-pathogenic fungi. In this study, fermentation optimization and ribosome engineering technology were employed to enhance rimocidin production in Streptomyces rimosus M527. After the optimization of fermentation, rimocidin production in S. rimosus M527 increased from 0.11 ± 0.01 to 0.23 ± 0.02 g/L during shake-flask experiments and reached 0.41 ± 0.05 g/L using 5-L fermentor. Fermentation optimization was followed by the generation of mutants of S. rimosus M527 through treatment of the strain with different concentrations of gentamycin (Gen) or rifamycin. One Gen^r mutant named S. rimosus M527-G37 and one Rif^r mutant named S. rimosus M527-R5 showed increased rimocidin production. Double-resistant (Gen^r and Rif^r) mutants were selected using S. rimosus M527-G37 and S. rimosus M527-R5, and subsequently tested. One mutant, S. rimosus M527-GR7, which was derived from M527-G37, achieved the greatest cumulative improvement in rimocidin production. In the 5-L fermentor, the maximum rimocidin production achieved by S. rimosus M527-GR7 was 25.36% and 62.89% greater than those achieved by S. rimosus M527-G37 and the wild-type strain S. rimosus M527, respectively. Moreover, in the mutants S. rimosus M527-G37 and S. rimosus M527-GR7 the transcriptional levels of ten genes (rimA_sr to rimK_sr) located in the gene cluster involved in rimocidin biosynthesis were all higher than those in the parental strain M527 to varying degrees. In addition, after expression of the single rimocidin biosynthetic genes in S. rimosus M527 a few recombinants showed an increase in rimocidin production. Expression of rimE led to the highest production.

Illumina-Based Sequencing Analysis Directed Selection for Actinobacterial Probiotic Candidates for Banana Plants

As potential probiotic candidates, plant vertically transmitted actinobacteria are beneficial to growth and health of host plants. New methods to isolate the actinobacterial taxa with low growth rates should be developed. Based on the actinobacterial population information, the probiotic actinobacterial taxa could be directly isolated from healthy banana shoot tips. However, actinobacterial DNAs with high GC contents could bias estimates of actinobacteria by PCR. In the study, two amplicon sequencing strategies were adopted to elucidate the endophytic actinobacterial community of banana plants. More than 92.5% bacterial OTUs were affiliated with actinobacteria by these two strategies, and total 14,289 actinobacterial OTUs with above 97% similarity were detected in banana shoot tips. Although the libraries generated by the two strategies differed in the abundance of some genera, Mycobacterium and Nocardia dominated both libraries and most actinobacterial taxa were overlapped. Higher phylogenetic resolution actinobacteriome of banana plants was successfully established. Based on the endophytic actinobacterial community information, the streptomycetes were isolated from shoot tips. Pot experiments illustrated that the strain could promote banana plantlet growth and elevate resistance to Fusarium oxysporum f. sp. cubense (FOC) under FOC infested soils. The results suggested that the selection for probiotic agents based on actinobacteriome analysis is reliable and feasible compared with present greenhouse selection.

Streptomyces: implications and interactions in plant growth promotion

With the impending increase of the world population by 2050, more activities have been directed toward the improvement of crop yield and a safe environment. The need for chemical-free agricultural practices is becoming eminent due to the effects of these chemicals on the environment and human health. Actinomycetes constitute a significant percentage of the soil microbial community. The Streptomyces genus, which is the most abundant and arguably the most important actinomycetes, is a good source of bioactive compounds, antibiotics, and extracellular enzymes. These genera have shown over time great potential in improving the future of agriculture. This review highlights and buttresses the agricultural importance of Streptomyces through its biocontrol and plant growth-promoting activities. These activities are highlighted and discussed in this review. Some biocontrol products from this genus are already being marketed while work is still ongoing on this productive genus. Compared to more focus on its biocontrol ability, less work has been done on it as a biofertilizer until recently. This genus is as efficient as a biofertilizer as it is as a biocontrol.

Deciphering differences in the chemical and microbial characteristics of healthy and Fusarium wilt-infected watermelon rhizosphere soils

Plant health is determined by the comprehensive effect of soil physicochemical and biological properties. In this study, we compared the chemical properties and microbiomes of the rhizosphere soils of healthy, Fusarium oxysporum-infected, and dead watermelon plants and attempted to assess their potential roles in plant health and Fusarium wilt expression. The rhizosphere soils were collected from watermelon plants grown in a greenhouse under the same field management practices, and various soil microbial and chemical characteristics were analyzed. The rhizosphere soil of healthy plants had the lowest abundance of F. oxysporum and pH and the highest contents of ammonium (NH₄⁺) and nitrate (NO₃^-). The relative content of hemicellulose was decreased in the rhizosphere soil of F. oxysporum-infected plants. The differences in soil microbial compositions among the watermelons at the three health statuses were obvious, and their microbiomes changed gradually along with plant health status. The microbiome in the rhizosphere soil of healthy plants had the highest relative abundances of potential antagonists and the lowest relative abundances of potential pathogens. The specific microbial composition together with some chemical properties of the rhizosphere soil of healthy plants might be responsible for inhibiting Fusarium wilt expression.

Mechanisms of bacterial attachment to roots

The attachment of bacteria to roots constitutes the first physical step in many plant-microbe interactions. These interactions exert both positive and negative influences on agricultural systems depending on whether a growth-promoting, symbiotic or pathogenic relationship transpires. A common biphasic mechanism of root attachment exists across agriculturally important microbial species, including Rhizobium, Agrobacterium, Pseudomonas, Azospirillum and Salmonella. Attachment studies have revealed how plant-microbe interactions develop, and how to manipulate these relationships for agricultural benefit. Here, we review our current understanding of the molecular mechanisms governing plant-microbe root attachment and draw together a common biphasic model.

Endophytic Actinomycetes from Tea Plants (Camellia sinensis): Isolation, Abundance, Antimicrobial, and Plant-Growth-Promoting Activities

Endophytic actinomycetes are a promising source of novel metabolites with diverse biological activities. Tea plants (Camellia sinensis) produce arsenals of phytochemicals, which are linked to a number of medicinal and nutritional properties. However, a systematic investigation into the abundance and diversity of cultivated actinomycetes residing in tea plants has not been performed. In this study, a total of 46 actinobacteria were recovered from leaf, stem, and root samples of 15 tea cultivars collected in Fujian province, China. Their abundance and diversity were shown to be influenced by both the genotypes and tissue types of tea plants. Based on 16S RNA sequence analysis, these isolates were taxonomically grouped into 11 families and 13 genera, including Streptomyces, Actinomadura, Kribbella, Nocardia, Kytococcus, Leifsonia, Microbacterium, Micromonospora, Mobilicoccus, Mycobacterium, Nocardiopsis, Piscicoccus, and Pseudonocardia. The genus Streptomyces was most prevalent whereas rare genera, Mobilicoccus and Piscicoccus, were reported for the first time to occur as plant endophytes. PCR screening of polyketide synthase genes (PKS-I and PKS-II) and nonribosomal peptide synthetase genes (NRPS), along with antimicrobial assays against a set of bacterial and fungal pathogens, showed that endophytic actinomycetes associated with tea plants have a high potential for producing antimicrobial metabolites. Furthermore, indole acetic acid (IAA) production and 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activities were recorded in 93.5% and 21.7% of all isolates, respectively. Overall, these results indicate that endophytic actinomycetes from tea plants represent a valuable source of bioactive metabolites with antibacterial, antifungal, and plant-growth-promoting properties.

Exploration of the Biosynthetic Potential of the Populus Microbiome

The plant root microbiome is one of the most diverse and abundant biological communities known. Plant-associated bacteria can have a profound effect on plant growth and development, and especially on protection from disease and environmental stress. These organisms are also known to be a rich source of antibiotic and antifungal drugs. In order to better understand the ways bacterial communities influence plant health, we evaluated the diversity and uniqueness of the natural product gene clusters in bacteria isolated from poplar trees. The complex molecule clusters are abundant, and the majority are unique, suggesting a great potential to discover new molecules that could not only affect plant health but also could have applications as antibiotic agents.

Natural products (NPs) isolated from bacteria have dramatically advanced human society, especially in medicine and agriculture. The rapidity and ease of genome sequencing have enabled bioinformatics-guided NP discovery and characterization. As a result, NP potential and diversity within a complex community, such as the microbiome of a plant, are rapidly expanding areas of scientific exploration. Here, we assess biosynthetic diversity in the Populus microbiome by analyzing both bacterial isolate genomes and metagenome samples. We utilize the fully sequenced genomes of isolates from the Populus root microbiome to characterize a subset of organisms for NP potential. The more than 3,400 individual gene clusters identified in 339 bacterial isolates, including 173 newly sequenced organisms, were diverse across NP types and distinct from known NP clusters. The ribosomally synthesized and posttranslationally modified peptides were both widespread and divergent from previously characterized molecules. Lactones and siderophores were prevalent in the genomes, suggesting a high level of communication and pressure to compete for resources. We then consider the overall bacterial diversity and NP variety of metagenome samples compared to the sequenced isolate collection and other plant microbiomes. The sequenced collection, curated to reflect the phylogenetic diversity of the Populus microbiome, also reflects the overall NP diversity trends seen in the metagenomic samples. In our study, only about 1% of all clusters from sequenced isolates were positively matched to a previously characterized gene cluster, suggesting a great opportunity for the discovery of novel NPs involved in communication and control in the Populus root microbiome.

IMPORTANCE The plant root microbiome is one of the most diverse and abundant biological communities known. Plant-associated bacteria can have a profound effect on plant growth and development, and especially on protection from disease and environmental stress. These organisms are also known to be a rich source of antibiotic and antifungal drugs. In order to better understand the ways bacterial communities influence plant health, we evaluated the diversity and uniqueness of the natural product gene clusters in bacteria isolated from poplar trees. The complex molecule clusters are abundant, and the majority are unique, suggesting a great potential to discover new molecules that could not only affect plant health but also could have applications as antibiotic agents.

Rhizosphere pseudomonads as probiotics improving plant health

Many root-colonizing microbes are multifaceted in traits that improve plant health. Although isolates designated as biological control agents directly reduce pathogen growth, many exert additional beneficial features that parallel changes induced in animal and other hosts by health-promoting microbes termed probiotics. Both animal and plant probiotics cause direct antagonism of pathogens and induce systemic immunity in the host to pathogens and other stresses. They also alter host development and improve host nutrition. The probiotic root-colonizing pseudomonads are generalists in terms of plant hosts, soil habitats and the array of stress responses that are ameliorated in the plant. This article illustrates how the probiotic pseudomonads, nurtured by the carbon (C) and nitrogen (N) sources released by the plant in root exudates, form protective biofilms on the root surface and produce the metabolites or enzymes to boost plant health. The findings reveal the multifunctional nature of many of the microbial metabolites in the plant-probiotic interplay. The beneficial effects of probiotics on plant function can contribute to sustainable yield and quality in agricultural production.

Assessment of the Detrimental Impact of Polyvalent Streptophages Intended to be Used as Biological Control Agents on Beneficial Soil Streptoflora

Streptophages are currently being investigated to control potato common scab, however, since a majority of streptophages are reported to be polyvalent, their potential to infect beneficial soil streptomycetes during the application process may have unintended consequences. To test this hypothesis, two phytopathogenic fungi, namely Fusarium solani and Rhizoctonia solani, were tested for their detrimental effect on the test crop wheat (Triticum aestivum cv. Gutha). F. solani caused a significant root weight reduction (34%) in the wheat plant and therefore was tested further in the pot trials with actinomycetes present. Sixty-seven streptomycete isolates from a Tasmanian potato farm were screened for their antifungal abilities against the two phytopathogenic fungi. Four actinomycetes found to be strongly antifungal were then tested for their disease-protective abilities against F. solani in pot trials again using wheat. Addition of the streptomycetes into the container media protected the plants against F. solani, indicating that streptomycetes have a disease-suppressive effect. A further pot trial was conducted to evaluate whether these beneficial streptomycete species would be affected by streptophage treatment and subsequently result in an increased risk of fungal infections. When streptophages were added to the pots, the shoot and root growth of wheat declined by 23.6% and 8.0%, respectively, in the pots with the pathogenic fungus compared to the control pots. These differences might suggest that removal of antifungal streptomycetes by polyvalent phages from plant rhizosphere when biocontrol of plant pathogenic streptomycetes (e.g. Streptomyces scabiei) is targeted might encourage secondary fungal infections in the farm environment. The presented data provide preliminary evidence that streptophage treatment of pathogenic streptomycetes may lead to an aggravated disease risk by soil-borne fungal pathogens when naturally present antagonists are removed. As a result, extensive farm site trials are required to determine the long-term detrimental impact of polyvalent streptophage treatments on beneficial soil streptoflora.

Plant Growth Promoting and Biocontrol Activity of Streptomyces spp. as Endophytes

There has been many recent studies on the use of microbial antagonists to control diseases incited by soilborne and airborne plant pathogenic bacteria and fungi, in an attempt to replace existing methods of chemical control and avoid extensive use of fungicides, which often lead to resistance in plant pathogens. In agriculture, plant growth-promoting and biocontrol microorganisms have emerged as safe alternatives to chemical pesticides. Streptomyces spp. and their metabolites may have great potential as excellent agents for controlling various fungal and bacterial phytopathogens. Streptomycetes belong to the rhizosoil microbial communities and are efficient colonizers of plant tissues, from roots to the aerial parts. They are active producers of antibiotics and volatile organic compounds, both in soil and in planta, and this feature is helpful for identifying active antagonists of plant pathogens and can be used in several cropping systems as biocontrol agents. Additionally, their ability to promote plant growth has been demonstrated in a number of crops, thus inspiring the wide application of streptomycetes as biofertilizers to increase plant productivity. The present review highlights Streptomyces spp.-mediated functional traits, such as enhancement of plant growth and biocontrol of phytopathogens.

Soil Bacterial Community Was Changed after Brassicaceous Seed Meal Application for Suppression of Fusarium Wilt on Pepper

Application of Brassicaceous seed meal (BSM) is a promising biologically based disease-control practice but BSM could directly and indirectly also affect the non-target bacterial communities, including the beneficial populations. Understanding the bacterial response to BSM at the community level is of great significance for directing plant disease management through the manipulation of resident bacterial communities. Fusarium wilt is a devastating disease on pepper. However, little is known about the response of bacterial communities, especially the rhizosphere bacterial community, to BSM application to soil heavily infested with Fusarium wilt pathogen and cropped with peppers. In this study, a 25-day microcosm incubation of a natural Fusarium wilt pathogen-infested soil supplemented with three BSMs, i.e., Camelina sativa 'Crantz' (CAME), Brassica juncea 'Pacific Gold' (PG), and a mixture of PG and Sinapis alba cv. 'IdaGold' (IG) (PG+IG, 1:1 ratio), was performed. Then, a further 35-day pot experiment was established with pepper plants growing in the BSM treated soils. The changes in the bacterial community in the soil after 25 days of incubation and changes in the rhizosphere after an additional 35 days of pepper growth were investigated by 454 pyrosequencing technique. The results show that the application of PG and PG+IG reduced the disease index by 100% and 72.8%, respectively, after 35 days of pepper growth, while the application of CAME did not have an evident suppressive effect. All BSM treatments altered the bacterial community structure and decreased the bacterial richness and diversity after 25 days of incubation, although this effect was weakened after an additional 35 days of pepper growth. At the phylum/class and the genus levels, the changes in specific bacterial populations resulting from the PG and PG+IG treatments, especially the significant increase in Actinobacteria-affiliated Streptomyces and an unclassified genus and the significant decrease in Chloroflexi, were suspected to be one of the microbial mechanisms involved in PG-containing BSM-induced disease suppression. This study is helpful for our understanding of the mechanisms that lead to contrasting plant disease severity after the addition of different BSMs.

Inter- and intracellular colonization of Arabidopsis roots by endophytic actinobacteria and the impact of plant hormones on their antimicrobial activity

Many actinobacteria live in close association with eukaryotes such as fungi, insects, animals and plants. Plant-associated actinobacteria display (endo)symbiotic, saprophytic or pathogenic life styles, and can make up a substantial part of the endophytic community. Here, we characterised endophytic actinobacteria isolated from root tissue of Arabidopsis thaliana (Arabidopsis) plants grown in soil from a natural ecosystem. Many of these actinobacteria belong to the family of Streptomycetaceae with Streptomyces olivochromogenes and Streptomyces clavifer as well represented species. When seeds of Arabidopsis were inoculated with spores of Streptomyces strain coa1, which shows high similarity to S. olivochromogenes, roots were colonised intercellularly and, unexpectedly, also intracellularly. Subsequent exposure of endophytic isolates to plant hormones typically found in root and shoot tissues of Arabidopsis led to altered antibiotic production against Escherichia coli and Bacillus subtilis. Taken together, our work reveals remarkable colonization patterns of endophytic streptomycetes with specific traits that may allow a competitive advantage inside root tissue.

Bacteria utilizing plant-derived carbon in the rhizosphere of Triticum aestivum change in different depths of an arable soil

Root exudates shape microbial communities at the plant-soil interface. Here we compared bacterial communities that utilize plant-derived carbon in the rhizosphere of wheat in different soil depths, including topsoil, as well as two subsoil layers up to 1 m depth. The experiment was performed in a greenhouse using soil monoliths with intact soil structure taken from an agricultural field. To identify bacteria utilizing plant-derived carbon, ¹³ C-CO₂ labelling of plants was performed for two weeks at the EC50 stage, followed by isopycnic density gradient centrifugation of extracted DNA from the rhizosphere combined with 16S rRNA gene-based amplicon sequencing. Our findings suggest substantially different bacterial key players and interaction mechanisms between plants and bacteria utilizing plant-derived carbon in the rhizosphere of subsoils and topsoil. Among the three soil depths, clear differences were found in ¹³ C enrichment pattern across abundant operational taxonomic units (OTUs). Whereas, OTUs linked to Proteobacteria were enriched in ¹³ C mainly in the topsoil, in both subsoil layers OTUs related to Cohnella, Paenibacillus, Flavobacterium showed a clear ¹³ C signal, indicating an important, so far overseen role of Firmicutes and Bacteriodetes in the subsoil rhizosphere.

Disease Suppressive Soils: New Insights from the Soil Microbiome

Soils suppressive to soilborne pathogens have been identified worldwide for almost 60 years and attributed mainly to suppressive or antagonistic microorganisms. Rather than identifying, testing and applying potential biocontrol agents in an inundative fashion, research into suppressive soils has attempted to understand how indigenous microbiomes can reduce disease, even in the presence of the pathogen, susceptible host, and favorable environment. Recent advances in next-generation sequencing of microbiomes have provided new tools to reexamine and further characterize the nature of these soils. Two general types of suppression have been described: specific and general suppression, and theories have been developed around these two models. In this review, we will present three examples of currently-studied model systems with features representative of specific and general suppressiveness: suppression to take-all (Gaeumannomyces graminis var. tritici), Rhizoctonia bare patch of wheat (Rhizoctonia solani AG-8), and Streptomyces. To compare and contrast the two models of general versus specific suppression, we propose a number of hypotheses about the nature and ecology of microbial populations and communities of suppressive soils. We outline the potential and limitations of new molecular techniques that can provide novel ways of testing these hypotheses. Finally, we consider how this greater understanding of the phytobiome can facilitate sustainable disease management in agriculture by harnessing the potential of indigenous soil microbes.

Symbiosis-inspired approaches to antibiotic discovery

Covering: 2010 up to 2017Life on Earth is characterized by a remarkable abundance of symbiotic and highly refined relationships among life forms. Defined as any kind of close, long-term association between two organisms, symbioses can be mutualistic, commensalistic or parasitic. Historically speaking, selective pressures have shaped symbioses in which one organism (typically a bacterium or fungus) generates bioactive small molecules that impact the host (and possibly other symbionts); the symbiosis is driven fundamentally by the genetic machineries available to the small molecule producer. The human microbiome is now integral to the most recent chapter in animal-microbe symbiosis studies and plant-microbe symbioses have significantly advanced our understanding of natural products biosynthesis; this also is the case for studies of fungal-microbe symbioses. However, much less is known about microbe-microbe systems involving interspecies interactions. Microbe-derived small molecules (i.e. antibiotics and quorum sensing molecules, etc.) have been shown to regulate transcription in microbes within the same environmental niche, suggesting interspecies interactions whereas, intraspecies interactions, such as those that exploit autoinducing small molecules, also modulate gene expression based on environmental cues. We, and others, contend that symbioses provide almost unlimited opportunities for the discovery of new bioactive compounds whose activities and applications have been evolutionarily optimized. Particularly intriguing is the possibility that environmental effectors can guide laboratory expression of secondary metabolites from "orphan", or silent, biosynthetic gene clusters (BGCs). Notably, many of the studies summarized here result from advances in "omics" technologies and highlight how symbioses have given rise to new anti-bacterial and antifungal natural products now being discovered.

Complete Genome Sequences of the Endophytic Streptomyces sp. Strains LUP30 and LUP47B, Isolated from Lucerne Plants

The complete genome sequences of two endophytic Streptomyces sp. strains, LUP30 and LUP47B, were analyzed. These strains were isolated from surface-sterilized roots of lucerne plants from South Australia and were found to promote the growth of the rhizobial partner in vitro and significantly increased nodulation and nitrogen fixation in lucerne plants.

Plenty Is No Plague: Streptomyces Symbiosis with Crops

Streptomyces spp. constitute a major clade of the phylum Actinobacteria. These Gram-positive, filamentous prokaryotes are ubiquitous in soils and marine sediments, and are commonly found in the rhizosphere or inside plant roots. Plant-interacting Streptomyces have received limited attention, in contrast to Streptomyces spp. extensively investigated for decades in medicine given their rich potential for secondary metabolite biosynthesis. Recent genomic, metabolomic, and biotechnological advances have produced key insights into Streptomyces spp., paving the way to the use of their metabolites in agriculture. In this Opinion article we propose how Streptomyces spp. could dominate future aspects of crop nutrition and protection. Risks and benefits of the use of these microorganisms in agriculture are also discussed.

Dynamics in the Strawberry Rhizosphere Microbiome in Response to Biochar and Botrytis cinerea Leaf Infection

Adding biochar, the solid coproduct of biofuel production, to peat can enhance strawberry growth, and disease resistance against the airborne fungal pathogen Botrytis cinerea. Additionally, biochar can induce shifts in the strawberry rhizosphere microbiome. However, the moment that this biochar-mediated shift occurs in the rhizosphere is not known. Further, the effect of an above-ground infection on the strawberry rhizosphere microbiome is unknown. In the present study we established two experiments in which strawberry transplants (cv. Elsanta) were planted either in peat or in peat amended with 3% biochar. First, we established a time course experiment to measure the effect of biochar on the rhizosphere bacterial and fungal communities over time. In a second experiment, we inoculated the strawberry leaves with B. cinerea, and studied the impact of the infection on the rhizosphere bacterial community. The fungal rhizosphere community was stabilized after 1 week, except for the upcoming Auriculariales, whereas the bacterial community shifted till 6 weeks. An effect of the addition of biochar to the peat on the rhizosphere microbiome was solely measured for the bacterial community from week 6 of plant growth onwards. When scoring the plant development, biochar addition was associated with enhanced root formation, fruit production, and postharvest resistance of the fruits against B. cinerea. We hypothesize that the bacterial rhizosphere microbiome, but also biochar-mediated changes in chemical substrate composition could be involved in these events. Infection of the strawberry leaves with B. cinerea induced shifts in the bacterial rhizosphere community, with an increased bacterial richness. This disease-induced effect was not observed in the rhizospheres of the B. cinerea-infected plants grown in the biochar-amended peat. The results show that an above-ground infection has its effect on the strawberry rhizosphere microbiome, changing the bacterial interactions in the root-substrate interface. This infection effect on the bacterial rhizosphere microbiome seems to be comparable to, but less pronounced than the effect of biochar-addition to the peat. The biological meaning of these observations needs further research, but this study indicates that biochar and an above-ground pathogen attack help the plant to recruit rhizosphere microbes that may aid them in their plant growth and health.

Recent advances in understanding Streptomyces

About 2,500 papers dated 2014–2016 were recovered by searching the PubMed database for Streptomyces, which are the richest known source of antibiotics. This review integrates around 100 of these papers in sections dealing with evolution, ecology, pathogenicity, growth and development, stress responses and secondary metabolism, gene expression, and technical advances. Genomic approaches have greatly accelerated progress. For example, it has been definitively shown that interspecies recombination of conserved genes has occurred during evolution, in addition to exchanges of some of the tens of thousands of non-conserved accessory genes. The closeness of the association of Streptomyces with plants, fungi, and insects has become clear and is reflected in the importance of regulators of cellulose and chitin utilisation in overall Streptomyces biology. Interestingly, endogenous cellulose-like glycans are also proving important in hyphal growth and in the clumping that affects industrial fermentations. Nucleotide secondary messengers, including cyclic di-GMP, have been shown to provide key input into developmental processes such as germination and reproductive growth, while late morphological changes during sporulation involve control by phosphorylation. The discovery that nitric oxide is produced endogenously puts a new face on speculative models in which regulatory Wbl proteins (peculiar to actinobacteria) respond to nitric oxide produced in stressful physiological transitions. Some dramatic insights have come from a new model system for Streptomyces developmental biology, Streptomyces venezuelae, including molecular evidence of very close interplay in each of two pairs of regulatory proteins. An extra dimension has been added to the many complexities of the regulation of secondary metabolism by findings of regulatory crosstalk within and between pathways, and even between species, mediated by end products. Among many outcomes from the application of chromosome immunoprecipitation sequencing (ChIP-seq) analysis and other methods based on “next-generation sequencing” has been the finding that 21% of Streptomyces mRNA species lack leader sequences and conventional ribosome binding sites. Further technical advances now emerging should lead to continued acceleration of knowledge, and more effective exploitation, of these astonishing and critically important organisms.