Comparative transcriptional profiling of orange fruit in response to the biocontrol yeast Kloeckera apiculata and its active compounds

Chromosome Genome Sequencing and Comparative Transcriptome-Based Analyses of Kloeckera apiculata 34-9 Unveil the Potential Biocontrol Mechanisms Against Citrus Green Mold

Biological control is an environmentally friendly, safe, and replaceable strategy for disease management. Genome sequences of a certain biocontrol agent could lay a solid foundation for the research of molecular biology, and the more refined the reference genome, the more information it provides. In the present study, a higher resolution genome of Kloeckera apiculata 34-9 was assembled using high-throughput chromosome conformation capture (Hi-C) technology. A total of 8.07 M sequences of K. apiculata 34-9 genome was anchored onto 7 pesudochromosomes, which accounting for about 99.51% of the whole assembled sequences, and 4,014 protein-coding genes were annotated. Meanwhile, the detailed gene expression changes of K. apiculata 34-9 were obtained under low temperature and co-incubation with Penicillium digitatum treatments, respectively. Totally 254 differentially expressed genes (DEGs) were detected with low temperature treatment, of which 184 and 70 genes were upregulated and downregulated, respectively. Some candidate genes were significantly enriched in ribosome biosynthesis in eukaryotes and ABC transporters. The expression of gene Kap003732 and Kap001595 remained upregulated and downregulated through the entire time-points, respectively, indicating that they might be core genes for positive and negative response to low temperature stress. When co-incubation with P. digitatum, a total of 2,364 DEGs were found, and there were 1,247 upregulated and 1,117 downregulated genes, respectively. Biosynthesis of lysine and arginine, and phenylalanine metabolism were the highest enrichment of the cluster and KEGG analyses of the co-DEGs, the results showed that they might be involved in the positive regulation of K. apiculata 34-9 response to P. digitatum. The completeness of K. apiculata 34-9 genome and the transcriptome data presented here are essential for providing a high-quality genomic resource and it might serve as valuable molecular properties for further studies on yeast genome, expression pattern of biocontrol system, and postharvest citrus storage and preservation.

Biological control of postharvest fungal decays in citrus: a review

Citrus (Citrus spp.) species produce a variety of fruits that are popular worldwide. Citrus fruits, however, are susceptible to postharvest decays caused by various pathogenic fungi, including Penicillium digitatum, Penicillium italicum, Geotrichum citri-aurantii, Aspergillus niger, and Aspergillus flavus. Decays resulting from infections by these pathogens cause a significant reduction in citrus quality and marketable yield. Biological control of postharvest decay utilizing antagonistic bacteria and fungi has been explored as a promising alternative to synthetic fungicides. In the present article, the isolation of antagonists utilized to manage postharvest decays in citrus is reviewed, and the mechanism of action including recent molecular and genomic studies is discussed as well. Several recently-postulated mechanisms of action, such as biofilm formation and an oxidative burst of reactive oxygen species have been highlighted. Improvements in biocontrol efficacy of antagonists through the use of a combination of microbial antagonists and additives are also reviewed. Biological control utilizing bacterial and yeast antagonists is a critical component of an integrated management approach for the sustainable development of the citrus industry. Further research will be needed, however, to explore and utilize beneficial microbial consortia and novel approaches like CRISPR/Cas technology for management of postharvest decays.

Paenibacillus brasilensis YS-1: A Potential Biocontrol Agent to Retard Xinyu Tangerine Senescence

The Xinyu tangerine (Citrus reticulata Blanco) is a non-climacteric fruit that is widely cultivated and consumed in China but highly susceptible to fungal infections. Antagonistic microorganisms can control postharvest diseases and extend the storage life of citrus fruits. However, little work has been done to investigate the effects of applying Paenibacillus brasilensis YS-1 by immersion to enhance the cold storability of Xinyu tangerines. Fruits were soaked with P. brasilensis YS-1 fermented filtrates for 10 min and in sterile water as the control. The decay incidence, weight loss, nutrient content, respiration rate, malondialdehyde (MDA) content, and defensive enzymes activities in citrus fruit were measured during cold storage at 5 ± 0.5 °C. The results showed that P. brasilensis YS-1 treatment significantly reduced postharvest decay and effectively maintained the nutritional quality compared to the control under cold storage. The weight loss, respiration rate, and MDA content were lower in P. brasilensis YS-1-treated fruits than the control fruits, indicating that P. brasilensis YS-1 treatment increased the activities of superoxide dismutase (SOD), peroxidase (POD), polyphenol oxidase (PPO), and phenylalnine ammonia-lyase (PAL). According to the results, a postharvest application of P. brasilensis YS-1 can control the postharvest decay and maintain fruit quality, as well as increase the defensive enzyme activity, so as to achieve the purpose of retarding postharvest senescence in citrus fruit.

The unknown soldier in citrus plants: polyamines-based defensive mechanisms against biotic and abiotic stresses and their relationship with other stress-associated metabolites

Citrus plants are challenged by a broad diversity of abiotic and biotic stresses, which definitely alter their growth, development, and productivity. In order to survive the various stressful conditions, citrus plants relay on multi-layered adaptive strategies, among which is the accumulation of stress-associated metabolites that play vital and complex roles in citrus defensive responses. These metabolites included amino acids, organic acids, fatty acids, phytohormones, polyamines (PAs), and other secondary metabolites. However, the contribution of PAs pathways in citrus defense responses is poorly understood. In this review article, we will discuss the recent metabolic, genetic, and molecular evidence illustrating the potential roles of PAs in citrus defensive responses against biotic and abiotic stressors. We believe that PAs-based defensive role, against biotic and abiotic stress in citrus, is involving the interaction with other stress-associated metabolites, particularly phytohormones. The knowledge gained so far about PAs-based defensive responses in citrus underpins our need for further genetic manipulation of PAs biosynthetic genes to produce transgenic citrus plants with modulated PAs content that may enhance the tolerance of citrus plants against stressful conditions. In addition, it provides valuable information for the potential use of PAs or their synthetic analogs and their emergence as a promising approach to practical applications in citriculture to enhance stress tolerance in citrus plants.

Characterization of the active fragments of Spodoptera litura Lebocin-1

Insects can produce various antimicrobial peptides (AMPs) upon immune stimulation. One class of AMPs are characterized by their high proline content in certain fragments. They are generally called proline-rich antimicrobial peptides (PrAMPs). We previously reported the characterization of Spodoptera litura lebocin-1 (SlLeb-1), a PrAMP proprotein. Preliminary studies with synthetic polypeptides showed that among the four deductive active fragments, the C-terminal fragment SlLeb-1 (124-158) showed strong antibacterial activities. Here, we further characterized the antibacterial and antifungal activities of 124-158 and its four subfragments: 124-155, 124-149, 127-158, and 135-158. Only 124-158 and 127-158 could agglutinate bacteria, while 124-158 and four subfragments all could agglutinate Beauveria bassiana spores. Confocal microscopy showed that fluorescent peptides were located on the microbial surface. Fragment 135-158 lost activity completely against Escherichia coli and Staphylococcus aureus, and partially against Bacillus subtilis. Only 124-149 showed low activity against Serratia marcescens. Negative staining, transmission, and scanning electron microscopy of 124-158 treated bacteria showed different morphologies. Flow cytometry analysis of S. aureus showed that 124-158 and four subfragments changed bacterial subpopulations and caused an increase of DNA content. These results indicate that active fragments of SlLeb-1 may have diverse antimicrobial effects against different microbes. This study may provide an insight into the development of novel antimicrobial agents.

Biocontrol yeasts: mechanisms and applications

Yeasts occur in all environments and have been described as potent antagonists of various plant pathogens. Due to their antagonistic ability, undemanding cultivation requirements, and limited biosafety concerns, many of these unicellular fungi have been considered for biocontrol applications. Here, we review the fundamental research on the mechanisms (e.g., competition, enzyme secretion, toxin production, volatiles, mycoparasitism, induction of resistance) by which biocontrol yeasts exert their activity as plant protection agents. In a second part, we focus on five yeast species (Candida oleophila, Aureobasidium pullulans, Metschnikowia fructicola, Cryptococcus albidus, Saccharomyces cerevisiae) that are or have been registered for the application as biocontrol products. These examples demonstrate the potential of yeasts for commercial biocontrol usage, but this review also highlights the scarcity of fundamental studies on yeast biocontrol mechanisms and of registered yeast-based biocontrol products. Yeast biocontrol mechanisms thus represent a largely unexplored field of research and plentiful opportunities for the development of commercial, yeast-based applications for plant protection exist.

Comparative genomics of Paraburkholderia kururiensis and its potential in bioremediation, biofertilization, and biocontrol of plant pathogens

Burkholderia harbors versatile Gram-negative species and is β-Proteobacteria. Recently, it was proposed to split the genus in two main branches: one of animal and plant pathogens and another, Paraburkholderia, harboring environmental and plant-beneficial species. Currently, Paraburkholderia comprises more than 70 species with ability to occupy very diverse environmental niches. Herein, we sequenced and analyzed the genome of Paraburkholderia kururiensis type strain KP23T , and compared to P. kururiensis M130, isolated in Brazil, and P. kururiensis susbp. thiooxydans, from Korea. This study focused on the gene content of the three genomes with special emphasis on their potential of plant-association, biocontrol, and bioremediation. The comparative analyses revealed several genes related to plant benefits, including biosynthesis of IAA, ACC deaminase, multiple efflux pumps, dioxygenases, and degradation of aromatic compounds. Importantly, a range of genes for protein secretion systems (type III, IV, V, and VI) were characterized, potentially involved in P. kururiensis well documented ability to establish endophytic association with plants. These findings shed light onto bacteria-plant interaction mechanisms at molecular level, adding novel information that supports their potential application in bioremediation, biofertilization, and biocontrol of plant pathogens. P. kururiensis emerges as a promising model to investigate adaptation mechanisms in different ecological niches.

Biocontrol of Penicillium digitatum on Postharvest Citrus Fruits by Pseudomonas fluorescens

The effectiveness of the bacteria antagonist Pseudomonas fluorescens to control green mold caused by Penicillium digitatum on oranges (Citrus sinensis Osbeck, cv. Jincheng) and the possible modes of action were evaluated. Whether in vitro or in vivo, treatments with cell-free autoclaved cultures or culture filtrate had limited capacity to suppress P. digitatum, while P. digitatum was significantly inhibited by bacterial fluid (P. fluorescens in the nutrient broth liquid medium) and bacterial suspension (P. fluorescens in sterile distilled water) with living cells. There was a positive relationship between the concentration of P. fluorescens in bacterial suspension and its biological efficacy. In addition, P. fluorescens was effective when applied preventatively but not when applied curatively. In the inoculated wounds, the population of P. fluorescens was an approximately 28- and 34-fold increase after being incubated at 20°C for 8 d and at 4°C for 16 d, respectively, and P. digitatum could effectively stimulate the growth and reproduction of P. fluorescens. Moreover, P. fluorescens was able to inhibit spore germination and germ tube elongation of P. digitatum as well as induce resistance on citrus peel by increasing the chitinase (CHI) activity and advancing the activities peaks of β-1,3-glucanase (GLU), peroxidase (POD), and phenylalanine ammonia lyase (PAL). All of these results support the potential application of P. fluorescens against green mold on postharvest citrus.

Genome-Wide Analysis of Multidrug and Toxic Compound Extrusion (MATE) Family in Gossypium raimondii and Gossypium arboreum and Its Expression Analysis Under Salt, Cadmium, and Drought Stress

The extrusion of toxins and substances at a cellular level is a vital life process in plants under abiotic stress. The multidrug and toxic compound extrusion (MATE) gene family plays a large role in the exportation of toxins and other substrates. We carried out a genome-wide analysis of MATE gene families in Gossypium raimondii and Gossypium arboreum and assessed their expression levels under salt, cadmium and drought stresses. We identified 70 and 68 MATE genes in G. raimondii and G. arboreum, respectively. The majority of the genes were predicted to be localized within the plasma membrane, with some distributed in other cell parts. Based on phylogenetic analysis, the genes were subdivided into three subfamilies, designated as M1, M2 and M3. Closely related members shared similar gene structures, and thus were highly conserved in nature and have mainly evolved through purifying selection. The genes were distributed in all chromosomes. Twenty-nine gene duplication events were detected, with segmental being the dominant type. GO annotation revealed a link to salt, drought and cadmium stresses. The genes exhibited differential expression, with GrMATE18, GrMATE34, GaMATE41 and GaMATE51 significantly upregulated under drought, salt and cadmium stress, and these could possibly be the candidate genes. Our results provide the first data on the genome-wide and functional characterization of MATE genes in diploid cotton, and are important for breeders of more stress-tolerant cotton genotypes.

Role of flagella and type four pili in the co-migration of Burkholderia terrae BS001 with fungal hyphae through soil

Burkholderia terrae BS001 has previously been found to be able to disperse along with growing fungal hyphae in soil, with the type-3 secretion system having a supportive role in this movement. In this study, we focus on the role of two motility- and adherence-associated appendages, i.e. type-4 pili (T4P) and flagella. Electron microcopy and motility testing revealed that strain BS001 produces polar flagella and can swim on semi-solid R2A agar. Flagellum- and T4P-negative mutants were then constructed to examine the ecological roles of the respective systems. Both in liquid media and on swimming agar, the mutant strains showed similar fitness to the wild-type strain in mixed culture. The flagellar mutant had completely lost its flagella, as well as its swimming capacity. It also lost its co-migration ability with two soil-exploring fungi, Lyophyllum sp. strain Karsten and Trichoderma asperellum 302, in soil microcosms. In contrast, the T4P mutant showed reduced surface twitching motility, whereas its co-migration ability in competition with the wild-type strain was slightly reduced. We conclude that the co-migration of strain BS001 with fungal hyphae through soil is dependent on the presence of functional flagella conferring swimming motility, with the T4P system having a minor effect.