Combining in vitro and in vivo screening to identify efficient Pseudomonas biocontrol strains against the phytopathogenic bacterium Ralstonia solanacearum

Fungal Biocontrol Agents in the Management of Postharvest Losses of Fresh Produce-A Comprehensive Review

Postharvest decay of vegetables and fruits presents a significant threat confronting sustainable food production worldwide, and in the recent times, applying synthetic fungicides has become the most popular technique of managing postharvest losses. However, there are concerns and reported proofs of hazardous impacts on consumers' health and the environment, traceable to the application of chemical treatments as preservatives on fresh produce. Physical methods, on the other hand, cause damage to fresh produce, exposing it to even more infections. Therefore, healthier and more environmentally friendly alternatives to existing methods for managing postharvest decays of fresh produce should be advocated. There is increasing consensus that utilization of biological control agents (BCAs), mainly fungi, represents a more sustainable and effective strategy for controlling postharvest losses compared to physical and chemical treatments. Secretion of antifungal compounds, parasitism, as well as competition for nutrients and space are the most common antagonistic mechanisms employed by these BCAs. This article provides an overview of (i) the methods currently used for management of postharvest diseases of fresh produce, highlighting their limitations, and (ii) the use of biocontrol agents as an alternative strategy for control of such diseases, with emphasis on fungal antagonists, their mode of action, and, more importantly, their advantages when compared to other methods commonly used. We therefore hypothesize that the use of fungal antagonists for prevention of postharvest loss of fresh produce is more effective compared to physical and chemical methods. Finally, particular attention is given to the gaps observed in establishing beneficial microbes as BCAs and factors that hamper their development, particularly in terms of shelf life, efficacy, commercialization, and legislation procedures.

Defining the Secondary Metabolites in the Pseudomonas protegens PBL3 Secretome with Antagonistic Activity Against Burkholderia glumae

Rice production worldwide is threatened by the disease bacterial panicle blight (BPB) caused by Burkholderia glumae. Despite the threat, resources to control this disease, such as completely resistant cultivars or effective chemical methods, are still lacking. However, the need to control this disease has paved the way to explore biologically based approaches harnessing the antimicrobial activities of environmental bacteria. Previously, the bacterium Pseudomonas protegens PBL3 was identified as a potential biological control agent against B. glumae due to its antimicrobial activity against B. glumae. Such antimicrobial activity in vitro and in planta was associated with the P. protegens PBL3 bacteria-free secreted fraction (secretome), although the specific molecules responsible for this activity have remained elusive. In this work, we advance the characterization of the P. protegens PBL3 secretome by evaluating the antimicrobial activity in vitro of selected secondary metabolites predicted by the P. protegens PBL3 genomic sequence against B. glumae. In addition, using reversed-phase liquid chromatography tandem mass spectrometry of the P. protegens PBL3 secretome enabled us to successfully detect and quantify pyoluteorin, 2,4-diacetylphloroglucinol, and pyochelin. Among those, pyoluteorin and 2,4-diacetylphloroglucinol reduced the growth of B. glumae in vitro, along with reducing the symptoms of BPB and bacterial growth in planta, suggesting that these compounds could be effective as biopesticides to mitigate BPB.

Harnessing Pseudomonas spp. for sustainable plant crop protection

This review examines the role of Pseudomonas spp. bacteria as biocontrol agents against crop diseases, focusing on their mechanisms of action, efficacy, and potential applications in sustainable agriculture. Pseudomonas spp., ubiquitous in soil ecosystems and root microbiomes, have attracted attention for their ability to suppress phytopathogens and enhance plant health through various mechanisms. These include direct competition for nutrients, production of antimicrobial compounds and volatile organic compounds, competition using type VI secretion systems, and indirect induction of systemic resistance. Our review shows that Pseudomonas strains effectively control a wide range of diseases across diverse plant species, with some strains demonstrating efficacy comparable to chemical fungicides. However, the review also highlights challenges in achieving consistent performance when using Pseudomonas inoculants under field conditions due to various biotic and abiotic factors. Strategies to optimize biocontrol potential, such as formulation techniques, application methods, and integration with other management practices, are discussed. The advantages of Pseudomonas-based biocontrol for sustainable agriculture include reduced reliance on chemical pesticides, enhanced crop productivity, and improved environmental sustainability. Future research directions should focus on understanding the complex interactions within the plant microbiome, optimizing delivery systems, and addressing regulatory hurdles for commercial deployment. This review underscores the significant potential of Pseudomonas spp. in sustainable crop protection while acknowledging the need for further research to fully harness their capabilities in agricultural systems.

Antibacterial, Herbicidal, and Plant Growth-Promoting Properties of Streptomyces sp. STD57 from the Rhizosphere of Adenophora stricta

Bacterial wilt triggered by the soil-borne pathogenic bacterium Ralstonia solanacearum is one of the most serious diseases in tomato plants, leading to huge economic losses worldwide. Biological control is considered an environmentally friendly and sustainable way to manage soil-borne diseases. In this study, Streptomyces sp. STD57 isolated from the rhizosphere of Adenophora stricta showed strong antibacterial activity against R. solanacearum. Pot experiments showed that strain STD57 exhibited a significant biocontrol effect (81.7%) on tomato bacterial wilt in the greenhouse environment. Furthermore, strain STD57 could inhibit the growth of weeds (Amaranthus retroflexus, Portulaca oleracea, and Echinochloa crusgalli) but promote the growth of crops (wheat, rice, and tomato). The plant growth-promoting substance was identified as indoleacetic acid (IAA) by high-pressure liquid chromatography-mass spectrometry and genome analysis. Coarse separation of the fermented extracts revealed that the antibacterial and herbicidal substances were mainly in the fermentation supernatant and belonged to different products. These findings suggested that strain STD57 may be a potential biocontrol and bioherbicide agent useful in agriculture.

Evaluation of Resistance Induction Promoted by Bioactive Compounds of Pseudomonas aeruginosa LV Strain against Asian Soybean Rust

Pseudomonas are known as higher producers of secondary metabolites with antimicrobial properties and plant growth promoters, including resistance induction. These mechanisms should be an alternative to pesticide use in crop production. Phakopsora pachyrhizi causes Asian soybean rust, representing a high loss of yield around the world. The objective of this paper was to evaluate the application of secondary metabolites produced by Pseudomonas aeruginosa LV strain from the semi-purified fraction F4A in soybean plants to induce plant resistance against P. pachyrhizi in field conditions. The experimental design was performed in randomized blocks with three replicates using two F4A doses (1 and 10 μg mL-1) combined or not with fungicides (Unizeb Gold® or Sphere Max®). The control treatment, with Uni + Sph, saponins, flavonoids, and sphingolipids, showed higher intensities in the plants. In contrast, plants treated with the F4A fraction mainly exhibited fatty acid derivatives and some non-identified compounds with nitrogen. Plants treated with Sphere Max®, with or without F4A10, showed higher intensities of glycosylated flavonoids, such as kaempferol, luteolin, narigenin, and apigenin. Plants treated with F4A showed higher intensities of genistein and fatty acid derivatives. These increases in flavonoid compound biosynthesis and antioxidant properties probably contribute to the protection against reactive oxygen species (ROS).

Naringenin restricts the colonization and growth of Ralstonia solanacearum in tobacco mutant KCB-1

Bacterial wilt severely jeopardizes plant growth and causes enormous economic loss in the production of many crops, including tobacco (Nicotiana tabacum). Here, we first demonstrated that the roots of bacterial wilt-resistant tobacco mutant KCB-1 can limit the growth and reproduction of Ralstonia solanacearum. Secondly, we demonstrated that KCB-1 specifically induced an upregulation of naringenin content in root metabolites and root secretions. Further experiments showed that naringenin can disrupt the structure of R. solanacearum, inhibit the growth and reproduction of R. solanacearum, and exert a controlling effect on bacterial wilt. Exogenous naringenin application activated the resistance response in tobacco by inducing the burst of reactive oxygen species and salicylic acid deposition, leading to transcriptional reprogramming in tobacco roots. Additionally, both external application of naringenin in CB-1 and overexpression of the Nicotiana tabacum chalcone isomerase (NtCHI) gene, which regulates naringenin biosynthesis, in CB-1 resulted in a higher complexity of their inter-root bacterial communities than in untreated CB-1. Further analysis showed that naringenin could be used as a marker for resistant tobacco. The present study provides a reference for analyzing the resistance mechanism of bacterial wilt-resistant tobacco and controlling tobacco bacterial wilt.

Resistance towards and biotransformation of a Pseudomonas-produced secondary metabolite during community invasion

The role of antagonistic secondary metabolites produced by Pseudomonas protegens in suppression of soil-borne phytopathogens has been clearly documented. However, their contribution to the ability of P. protegens to establish in soil and rhizosphere microbiomes remains less clear. Here, we use a four-species synthetic community (SynCom) in which individual members are sensitive towards key P. protegens antimicrobial metabolites (DAPG, pyoluteorin, and orfamide A) to determine how antibiotic production contributes to P. protegens community invasion and to identify community traits that counteract the antimicrobial effects. We show that P. protegens readily invades and alters the SynCom composition over time, and that P. protegens establishment requires production of DAPG and pyoluteorin. An orfamide A-deficient mutant of P. protegens invades the community as efficiently as wildtype, and both cause similar perturbations to community composition. Here, we identify the microbial interactions underlying the absence of an orfamide A mediated impact on the otherwise antibiotic-sensitive SynCom member, and show that the cyclic lipopeptide is inactivated and degraded by the combined action of Rhodococcus globerulus D757 and Stenotrophomonas indicatrix D763. Altogether, the demonstration that the synthetic community constrains P. protegens invasion by detoxifying its antibiotics may provide a mechanistic explanation to inconsistencies in biocontrol effectiveness in situ.

Deciphering key factors in pathogen-suppressive microbiome assembly in the rhizosphere

In a plant-microbe symbiosis, the host plant plays a key role in promoting the association of beneficial microbes and maintaining microbiome homeostasis through microbe-associated molecular patterns (MAMPs). The associated microbes provide an additional layer of protection for plant immunity and help in nutrient acquisition. Despite identical MAMPs in pathogens and commensals, the plant distinguishes between them and promotes the enrichment of beneficial ones while defending against the pathogens. The rhizosphere is a narrow zone of soil surrounding living plant roots. Hence, various biotic and abiotic factors are involved in shaping the rhizosphere microbiome responsible for pathogen suppression. Efforts have been devoted to modifying the composition and structure of the rhizosphere microbiome. Nevertheless, systemic manipulation of the rhizosphere microbiome has been challenging, and predicting the resultant microbiome structure after an introduced change is difficult. This is due to the involvement of various factors that determine microbiome assembly and result in an increased complexity of microbial networks. Thus, a comprehensive analysis of critical factors that influence microbiome assembly in the rhizosphere will enable scientists to design intervention techniques to reshape the rhizosphere microbiome structure and functions systematically. In this review, we give highlights on fundamental concepts in soil suppressiveness and concisely explore studies on how plants monitor microbiome assembly and homeostasis. We then emphasize key factors that govern pathogen-suppressive microbiome assembly. We discuss how pathogen infection enhances plant immunity by employing a cry-for-help strategy and examine how domestication wipes out defensive genes in plants experiencing domestication syndrome. Additionally, we provide insights into how nutrient availability and pH determine pathogen suppression in the rhizosphere. We finally highlight up-to-date endeavors in rhizosphere microbiome manipulation to gain valuable insights into potential strategies by which microbiome structure could be reshaped to promote pathogen-suppressive soil development.

Collaborative impact of bacterial exometabolites governing root microbiota formation

The majority of the root microbiota formation derives from soil-dwelling microorganisms. The limited extent of thorough investigation leads to a dearth of knowledge concerning the intricate mechanisms of microbe-microbe interaction implicated in the establishment of root microbiota. Therefore, the taxonomic signatures in bacterial inhibition profiles were determined by in vitro testing of 39,204 binary interbacterial interactions. However, findings from genetic and metabolomic studies elucidated that co-functioning of the antimicrobial 2,4-d iacetylphloroglucinol (DAPG) and the iron chelator pyoverdine as exometabolites has significantly contributed to the potent inhibitory activities of the highly antagonistic Pseudomonas brassicacearum R401. Microbiota restoration with a core of Arabidopsis thaliana root commensals showed that these exometabolites possess a root niche-specific function in establishing root competence and inducing anticipated changes in root surroundings. Both biosynthetic operons are abundant in roots in natural habitats, indicating that these exometabolites co-functioning is an adaptive feature that helps Pseudomonad dominate the root microbiota.

Ralstonia solanacearum: An Arsenal of Virulence Strategies and Prospects for Resistance

The group of strains constituting the Ralstonia solanacearum species complex (RSSC) is a prominent model for the study of plant-pathogenic bacteria because of its impact on agriculture, owing to its wide host range, worldwide distribution, and long persistence in the environment. RSSC strains have led to numerous studies aimed at deciphering the molecular bases of virulence, and many biological functions and mechanisms have been described to contribute to host infection and pathogenesis. In this review, we put into perspective recent advances in our understanding of virulence in RSSC strains, both in terms of the inventory of functions that participate in this process and their evolutionary dynamics. We also present the different strategies that have been developed to combat these pathogenic strains through biological control, antimicrobial agents, plant genetics, or microbiota engineering.

Genome mining of Pseudomonas spp. hints towards the production of under-pitched secondary metabolites

The recent advances in omics and computational analysis have enabled the capacity to identify the exclusive strain-specific metabolites and novel biosynthetic gene clusters. This study analyzed eight strains of P. aurantiaca including GS1, GS3, GS4, GS6, GS7, FS2, ARS38, PBSt2, one strain of P. chlororaphis RP4, one strain of P. aeruginosa (At1RP4), and one strain of P. fluorescens (RS1) for the production of rhamnolipids, quorum-sensing signals, and osmolytes. Seven rhamnolipid derivatives were variably detected in fluorescent pseudomonads. These rhamnolipids included Rha-C10-C8, Rha-Rha-C10-C10, Rha-C10-C12db, Rha-C10-C10, Rha-Rha-C10-C12, Rha-C10-C12, and Rha-Rha-C10-C12db. Pseudomonas spp. also showed the variable production of osmoprotectants including N-acetyl glutaminyl glutamine amide (NAGGN), betaine, ectoine, and trehalose. Betaine and ectoine were produced by all pseudomonads, however, NAGGN and trehalose were observed by five and three strains, respectively. Four strains including P. chlororaphis (RP4), P. aeruginosa (At1RP4), P. fluorescens (RS1), and P. aurantiaca (PBSt2) were exposed to 1- 4% NaCl concentrations and evaluated for the changes in phenazine production profile which were negligible. AntiSMASH 5.0 platform showed 50 biosynthetic gene clusters in PB-St2, of which 23 (45%) were classified as putative gene clusters with ClusterFinder algorithm, five (10%) were classified as non-ribosomal peptides synthetases (NRPS), five (10%) as saccharides, and four (8%) were classified as putative fatty acids. The genomic attributes and comprehensive insights into the metabolomic profile of these Pseudomonas spp. strains showcase their phytostimulatory, phyto-protective, and osmoprotective effects of diverse crops grown in normal and saline soils.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03607-x.

Use of whey protein as a natural polymer for the encapsulation of plant biocontrol bacteria: A review

Climate changes, drought, the salinity of water and soil, the emergence of new breeds of pests and pathogens, the industrialization of countries, and environmental contamination are among the factors limiting the production of agricultural products. The use of chemicals (in the form of fertilizers, pesticides and fungicides) to enhance products against biotic and abiotic stresses has limitations. To eliminate the effects of agricultural chemicals, synthetic agrochemicals should be replaced with natural substances and useful microorganisms. To be more effective and efficient, plant biocontrol bacteria need a coating layer around themselves to protect them from adverse conditions. Whey protein, a valuable by-product of the cheese industry, is one of the important natural polymers. Due to its high protein content, safety, and biodegradability, whey can have many applications in agriculture and encapsulation of bacteria to resist pests and plant diseases. This compound is a rich source of amino acids that can activate plant defense systems and defense enzymes. Considering the amazing potentialities of formulation whey protein, this review attends to the efficiency of whey protein as coating layers on fruit and vegetables and in the packaging system to increase the shelf life of agricultural products against phytopathogens.

"What I cannot create, I do not understand": elucidating microbe-microbe interactions to facilitate plant microbiome engineering

Plant-microbe interactions are important for both physiological and pathological processes. Despite the significance of plant-microbe interactions, microbe-microbe interactions themselves represent an important, complex, dynamic network that warrants deeper investigation. To understand how microbe-microbe interactions affect plant microbiomes, one approach is to systematically understand all the factors involved in successful engineering of a microbial community. This follows the physicist Richard Feynman's declaration: "what I cannot create, I do not understand". This review highlights recent studies that focus on aspects that we believe are important for building (ergo understanding) microbe-microbe interactions in the plant environment, including pairwise screening, intelligent application of cross-feeding models, spatial distributions of microbes, and understudied interactions between bacteria and fungi, phages, and protists. We offer a framework for systematic collection and centralized integration of data of plant microbiomes that could organize all the factors that can help ecologists understand microbiomes and help synthetic ecologists engineer beneficial microbiomes.

Seaweed as a Natural Source against Phytopathogenic Bacteria

Plant bacterial pathogens can be devastating and compromise entire crops of fruit and vegetables worldwide. The consequences of bacterial plant infections represent not only relevant economical losses, but also the reduction of food availability. Synthetic bactericides have been the most used tool to control bacterial diseases, representing an expensive investment for the producers, since cyclic applications are usually necessary, and are a potential threat to the environment. The development of greener methodologies is of paramount importance, and some options are already available in the market, usually related to genetic manipulation or plant community modulation, as in the case of biocontrol. Seaweeds are one of the richest sources of bioactive compounds, already being used in different industries such as cosmetics, food, medicine, pharmaceutical investigation, and agriculture, among others. They also arise as an eco-friendly alternative to synthetic bactericides. Several studies have already demonstrated their inhibitory activity over relevant bacterial phytopathogens, some of these compounds are known for their eliciting ability to trigger priming defense mechanisms. The present work aims to gather the available information regarding seaweed extracts/compounds with antibacterial activity and eliciting potential to control bacterial phytopathogens, highlighting the extracts from brown algae with protective properties against microbial attack.