The role of clp-regulated factors in antagonism against Magnaporthe poae and biological control of summer patch disease of Kentucky bluegrass by Lysobacter enzymogenes C3

The impact of utilizing oyster shell soil conditioner on the growth of tomato plants and the composition of inter-root soil bacterial communities in an acidic soil environment

Introduction

The objective of this study is to examine the impact of various oyster shell soil conditioners, which are primarily composed of oyster shells, on the growth of tomatoes in acidic soil. Moreover, the aim of this investigation is to analyze the variety and structure of soil bacterial populations in close proximity to tomato roots while also contributing to the understanding of the physical, chemical, and biological mechanisms of oyster shell soil conditioners.

Methods

Tomato plants were grown in acidic red soil in three groups: a control group and a treatment group that used two types of oyster shell soil conditioners, OS (oyster shell powder) and OSF (oyster shell powder with organic microbial fertilizer). A range of soil physicochemical properties were measured to study differences in inter-soil physicochemical parameters and the growth of tomato plantings. In addition, this study utilized the CTAB (Cetyltrimethylammonium Bromide) technique to extract DNA from the soil in order to investigate the effects of oyster shell soil conditioner on the composition and diversity of bacterial populations. Utilizing high-throughput sequencing technologies and diversity index analysis, the composition and diversity of bacterial populations in the soil adjacent to plant roots were then evaluated. Ultimately, correlation analysis was used in this study to explore the relationship between environmental factors and the relative abundance of soil bacteria in the inter-root zone of tomato plants.

Results

The findings indicated that the oyster shell soil conditioners were capable of modifying the physicochemical characteristics of the soil. This was evidenced by significant increases in soil total nitrogen (16.2 and 59.9%), soil total carbon (25.8 and 27.7%), pH (56.9 and 55.8%), and electrical conductivity (377.5 and 311.7%) in the OS and OSF groups, respectively, compared to the control group (p < 0.05). Additionally, data pertaining to tomato seed germination and seedling growth biomass demonstrated that both oyster shell soil conditioners facilitated the germination of tomato seeds and the growth of seedlings in an acidic red clay soil (p < 0.05). On the other hand, the application of two oyster shell soil conditioners resulted in a modest reduction in the diversity of inter-root soil bacteria in tomato plants. Specifically, the group treated with OSF exhibited the most substantial fall in the diversity index, which was 13.6% lower compared to the control group. The investigation carried out on the soil between tomato plant roots yielded findings about the identification of the ten most abundant phyla. These phyla together represented 91.00-97.64% of the overall abundance. In the inter-root soil of tomatoes, a study identified four major phyla, namely Proteobacteria, Bacteroidetes, Acidobacteria, and Actinobacteria, which collectively accounted for up to 85% of the total abundance. At the general level, the relative abundance of Massilia increased by 2.18 and 7.93%, Brevundimonas by 5.43 and 3.01%, and Lysobacter by 3.12 and 7.49% in the OS and OSF groups, respectively, compared to the control group. However, the pathogenic bacteria unidentified_Burkholderiaceae decreased by 5.76 and 5.05%, respectively. The correlation analysis yielded conclusive evidence indicating that, which involved the use of CCA (Canonical Correlation Analysis) graphs and Spearman correlation coefficients, pH exhibited a positive correlation (p < 0.05) with Shewanella and a negative correlation (p < 0.05) with Bradyrhizobium. The relative abundance of Lysobacter and Massilia exhibited a positive correlation with the levels of total soil nitrogen.

Discussion

The utilization of oyster shell soil conditioner on acidic red soil resulted in several positive effects. Firstly, it raised the pH level of the inter-root soil of tomato plants, which is typically acidic. This pH adjustment facilitated the germination of tomato seeds and promoted the growth of seedlings. In addition, the application of oyster shell soil conditioner resulted in changes in the structure of the bacterial community in the inter-root soil, leading to an increase in the relative abundance of Proteobacteria and Bacteroidetes and a decrease in the relative abundance of Acidobacteria. Furthermore, this treatment fostered the proliferation of genera of beneficial bacteria like Massilia, Brevundimonas, and Lysobacter, ultimately enhancing the fertility of the red soil.

Acetaminophen Levels Found in Recycled Wastewater Alter Soil Microbial Community Structure and Functional Diversity

The practice of using recycled wastewater (RWW) has been successfully adopted to address the growing demand for clean water. However, chemicals of emerging concern (CECs) including pharmaceutical products remain in the RWW even after additional cleaning. When RWW is used to irrigate crops or landscapes, these chemicals can enter these and adjacent environments. Unfortunately, the overall composition and concentrations of CECs found in different RWW sources vary, and even the same source can vary over time. Therefore, we selected one compound that is found frequently and in high concentrations in many RWW sources, acetaminophen (APAP), to use for our study. Using greenhouse grown eggplants treated with APAP concentrations within the ranges found in RWW effluents, we investigated the short-term impacts of APAP on the soil bacterial population under agricultural settings. Using Illumina sequencing-based approaches, we showed that APAP has the potential to cause shifts in the microbial community most likely by positively selecting for bacteria that are capable of metabolizing the breakdown products of APAP such as glycosides and carboxylic acids. Community-level physiological profiles of carbon metabolism were evaluated using Biolog EcoPlate as a proxy for community functions. The Biolog plates indicated that the metabolism of amines, amino acids, carbohydrates, carboxylic acids, and polymers was significantly higher in the presence of APAP. Abundance of microorganisms of importance to plant health and productivity was altered by APAP. Our results indicate that the soil microbial community and functions could be altered by APAP at concentrations found in RWW. Our findings contribute to the knowledge base needed to guide policies regulating RWW reuse in agriculture and also highlight the need to further investigate the effects of CECs found in RWW on soil microbiomes.

Characterization of Lysobacter enzymogenes B25, a potential biological control agent of plant-parasitic nematodes, and its mode of action

It is certainly difficult to estimate productivity losses due to the action of phytopathogenic nematodes but it might be about 12 % of world agricultural production. Although there are numerous tools to reduce the effect of these nematodes, there is growing concern about their environmental impact. Lysobacter enzymogenes B25 is an effective biological control agent against plant-parasitic nematodes, showing control over root-knot nematodes (RKN) such as Meloidogyne incognita and Meloidogyne javanica. In this paper, the efficacy of B25 to control RKN infestation in tomato plants (Solanum lycopersicum cv. Durinta) is described. The bacterium was applied 4 times at an average of concentration around 10⁸ CFU/mL showing an efficacy of 50-95 % depending on the population and the pressure of the pathogen. Furthermore, the control activity of B25 was comparable to that of the reference chemical used. L. enzymogenes B25 is hereby characterized, and its mode of action studied, focusing on different mechanisms that include motility, the production of lytic enzymes and secondary metabolites and the induction of plant defenses. The presence of M. incognita increased the twitching motility of B25. In addition, cell-free supernatants obtained after growing B25, in both poor and rich media, showed efficacy in inhibiting RKN egg hatching in vitro. This nematicidal activity was sensitive to high temperatures, suggesting that it is mainly due to extracellular lytic enzymes. The secondary metabolites heat-stable antifungal factor and alteramide A/B were identified in the culture filtrate and their contribution to the nematicidal activity of B25 is discussed. This study points out L. enzymogenes B25 as a promising biocontrol microorganism against nematode infestation of plants and a good candidate to develop a sustainable nematicidal product.

Comparative genomics provides insights into the potential biocontrol mechanism of two Lysobacter enzymogenes strains with distinct antagonistic activities

Lysobacter enzymogenes has been applied as an abundant beneficial microorganism to control plant disease; however, most L. enzymogenes strains have been mainly reported to control fungal diseases, not bacterial diseases. In this study, two L. enzymogenes strains were characterized, of which CX03 displayed a broad spectrum of antagonistic activities toward multiple bacteria, while CX06 exhibited a broad spectrum of antagonistic activities toward diverse fungi and oomycete, and the whole genomes of the two strains were sequenced and compared. The genome annotation showed that the CX03 genome comprised a 5,947,018 bp circular chromosome, while strain CX06 comprised a circular 6,206,196 bp chromosome. Phylogenetic analysis revealed that CX03 had a closer genetic relationship with L. enzymogenes ATCC29487T and M497-1, while CX06 was highly similar to L. enzymogenes C3. Functional gene annotation analyses of the two L. enzymogenes strains showed that many genes or gene clusters associated with the biosynthesis of different secondary metabolites were found in strains CX03 and CX06, which may be responsible for the different antagonistic activities against diverse plant pathogens. Moreover, comparative genomic analysis revealed the difference in bacterial secretory systems between L. enzymogenes strains CX03 and CX06. In addition, numerous conserved genes related to siderophore biosynthesis, quorum sensing, two-component systems, flagellar biosynthesis and chemotaxis were also identified in the genomes of strains CX03 and CX06. Most reported L. enzymogenes strains were proven mainly to suppress fungi, while CX03 exhibited direct inhibitory activities toward plant bacterial pathogens and showed an obvious role in managing bacterial disease. This study provides a novel understanding of the biocontrol mechanisms of L. enzymogenes, and reveals great potential for its application in plant disease control.

Biosynthesis, regulation, and engineering of natural products from Lysobacter

Covering: up to August 2021Lysobacter is a genus of Gram-negative bacteria that was classified in 1987. Several Lysobacter species are emerging as new biocontrol agents for crop protection in agriculture. Lysobacter are prolific producers of new bioactive natural products that are largely underexplored. So far, several classes of structurally interesting and biologically active natural products have been isolated from Lysobacter. This article reviews the progress in Lysobacter natural product research over the past ten years, including molecular mechanisms for biosynthesis, regulation and mode of action, genome mining of cryptic biosynthetic gene clusters, and metabolic engineering using synthetic biology tools.

Clp is a "busy" transcription factor in the bacterial warrior, Lysobacter enzymogenes

Cyclic AMP receptor protein (CRP) is a well-characterized group of global transcription factors in bacteria. They are known to regulate numerous cellular processes by binding DNA and/or cAMP (a ligand called bacterial second messenger) to control target gene expression. Gram-negative Lysobacter enzymogenes is a soilborne, plant-beneficial bacterium without flagella that can fight against filamentous fungi and oomycete. Driven by the type IV pilus (T4P) system, this bacterium moves to nearby pathogens and uses a “mobile-attack” antifungal strategy to kill them via heat-stable antifungal factor (HSAF) and abundant lyases. This strategy is controlled by a unique “busy” transcription factor Clp, which is a CRP-like protein that is inactivated by binding of c-di-GMP, another ubiquitous second messenger of bacteria. In this review, we summarize the current progress in how Clp initiates a “mobile-attack” strategy through a series of previously uncharacterized mechanisms, including binding to DNA in a unique pattern, directly interacting with or responding to various small molecules, and interacting specifically with proteins adopting distinct structure. Together, these characteristics highlight the multifunctional roles of Clp in L. enzymogenes, a powerful bacterial warrior against fungal pathogens.

Protein Expression Level Changes in Weissella koreensis during Garlic Media Fermentation

Simple Summary

Garlic is used in cooking and is known to have antibacterial properties due to various organic sulfur components. Weissella koreensis is one of the lactic acid bacteria used for fermentation with garlic and is a strain found in kimchi in Korea, one of foods to which garlic is added. In this study, the addition of garlic to the medium did not cause a difference in growth of W. koreensis. However, the addition of garlic to the growth medium did produce changes in the amount of specific W. koreensis proteins. This study provides basic information about the effect of garlic on fermentation using W. koreensis.

Abstract

This study investigated the changes in Weissella koreensis (WK) protein expression levels during fermentation in MRS medium supplemented with garlic of WK. WK was first discovered as lactic acid bacteria (LAB) in a Korean fermented cabbage dish known as kimchi. The number of WK cells in MRS medium with garlic (MBCG) and without (MB) after 7 days was 3.55 × 10¹⁰ and 2.55 × 10¹⁰ CFU/mL, respectively. To observe the changes in the carbon sources in the media, we measured the glucose, sucrose, lactic acid, and acetic acid levels in each medium (MB and MBCG). Thus, 67.2 ± 2.4 (MB) and 64.2 ± 4.7 (MBCG) mmol⁻¹ of glucose were consumed. For sucrose, the level was 3.5 ± 2.2 (MB), and 3.4 ± 2.5 (MBCG) mmol⁻¹. There was not much difference in the lactic acid and acetic acid levels at 160.8 ± 0.4 (MB) and 159.2 ± 0.2 (MBCG) and 2.4 ± 0.4 (MB) and 2.2 ± 8.1 (MBCG) mmol⁻¹, respectively. After the 7-day fermentation period, two-dimensional electrophoresis (2DE) was used to confirm the protein expression pattern in the WK strain. The results show that the fusA and ssb1 proteins were reduced, and the clpP protein was increased. Afterwards, the expression patterns of the above proteins were confirmed through qRT-PCR. Thus, this study confirms the changes in protein expression levels in Weissella koreensis when garlic was added to the media. This study provides basic data for future studies on the major biosynthetic pathways of WK.

Comparative Analysis of the Apple Root Transcriptome as Affected by Rootstock Genotype and Brassicaceae Seed Meal Soil Amendment: Implications for Plant Health

Brassicaceae seed meal (SM) soil amendment has been utilized as an effective strategy to control the biological complex of organisms, which includes oomycetes, fungi, and parasitic nematodes, that incites the phenomenon termed apple replant disease. Soil-borne disease control attained in response to Brassicaceae SM amendment is reliant on multiple chemical and biological attributes, including specific SM-generated modifications to the soil/rhizosphere microbiome. In this study, we conducted a comparative analyses of apple root gene expression as influenced by rootstock genotype combined with a seed meal (SM) soil amendment. Apple replant disease (ARD) susceptible (M.26) and tolerant (G.210) rootstocks cultivated in SM-amended soil exhibited differential gene expression relative to corresponding non-treated control (NTC) orchard soil. The temporal dynamics of gene expression indicated that the SM-amended soil system altered the trajectory of the root transcriptome in a genotype-specific manner. In both genotypes, the expression of genes related to plant defense and hormone signaling were altered in SM-amended soil, suggesting SM-responsive phytohormone regulation. Altered gene expression was temporally associated with changes in rhizosphere microbiome density and composition in the SM-treated soil. Gene expression analysis across the two rootstocks cultivated in the pathogen-infested NTC soil showed genotype-specific responses indicative of different defensive strategies. These results are consistent with previously described resistance mechanisms of ARD “tolerant” rootstock cultivars and also add to our understanding of the multiple mechanisms by which SM soil amendment and the resulting rhizosphere microbiome affect apple rootstock physiology. Future studies which assess transcriptomic and metagenomic data in parallel will be important for illuminating important connections between specific rhizosphere microbiota, gene-regulation, and plant health.

Impairment of cost-benefit decision making in morphine-dependent rats is partly mediated via the alteration of BDNF and p-CREB levels in the nucleus accumbens

The ability to choose goals based on decision usefulness or the time required to reach the goals chosen are important aspects of decision making. There is considerable evidence in the literature indicating the fact that drug abuse affects different aspects of cognition. In the current study, we assessed the effects of morphine dependence and its withdrawal on cost-benefit decision making and furthermore the involvement of BDNF and p-CREB in the nucleus accumbens, a key brain area involved in decision making was measured. Different groups of male Wistar rats were trained in an effort-based and/or delay-based form of cost-benefit T-maze decision-making task. Thereafter, the animals were morphine dependent and the percentage of the high reward preference was evaluated. After behavioral tests, the BDNF level, and p-CREB/CREB ratio were measured by Western blot analysis. The results showed that during effort-based but not delay-based decision making, BDNF and p-CREB levels increased. During effort-based decision making in morphine dependent rats, BDNF decreased but there was no significant change in p-CREB. Besides, during delay-based decision making in the morphine dependent group, both BDNF and p-CREB did not show any significant change. These findings revealed that BDNF and p-CREB/CREB ratio in the NAc are essential factors for effort-based but not delay-based decision making. In addition, impairment of effort-based decision making in morphine dependent rats is related to the decrease of BDNF level but not p-CREB/CREB ratio in the NAc. However, delay-based decision making defects in morphine dependent rats did not associate with the change in BDNF and p-CREB levels in the NAc.

Protecting books from mould damage by decreasing paper bioreceptivity to fungal attack using decoloured cell-free supernatant of Lysobacter enzymogenes C3

AIMS

To evaluate whether decoloured cell-free supernatant of Lysobacter enzymogenes C3 can decrease paper bioreceptivity to fungal attack.

METHODS AND RESULTS

To prepare colourless C3 supernatant, single-factor design and uniform design were applied. The optimum conditions with high decolouration degree and low antifungal activity loss were achieved as follows: carbon granule content 1·6% (M/V), temperature 27°C, decolouring time 1·2 h and pH 8·0. An agar plate bioassay was used to assess the antifungal activity of the decoloured supernatant against the fungal isolates obtained from contaminated books, and strong suppression was observed. Small-sacle laboratory test was further introduced, in which common book papers were artificially inoculated with the fungal isolates, and then sprayed uniformly with decoloured supernatant or water. The results showed that, after treatment, the paper showed a significantly low extent of fungal colonization and high tensile strength, and maintained the same colour before and after treatment.

CONCLUSION

These results suggest that the decoloured C3 supernatant inhibits fungal growth on types of paper commonly used in books.

SIGNIFICANCE AND IMPACT OF THE STUDY

Decoloured C3 supernatant could be used as a preventive agent to protect books and other paper-based items against fungal growth.

Evaluation of Bacillus Strains for Plant Growth Promotion and Predictability of Efficacy by In Vitro Physiological Traits

Bacilli are commonly used as plant growth-promoting agents but can be limited in effectiveness to certain crop and soil environments. The objectives of this study were to (1) identify Bacillus strains that can be consistent in promoting the growth of corn, wheat, and soybean and (2) determine whether physiological traits expressed in vitro can be predictive of growth promotion efficacy/consistency and be used for selecting effective strains. Twelve Bacillus strains isolated from wheat rhizospheres were evaluated in greenhouse pot tests with nonsterile soil for their effects on the growth of corn, soybean, and wheat. The strains also were assessed in vitro for multiple physiological traits. All 12 strains increased corn growth significantly compared to the controls. The four most efficacious strains on corn-Bacillus megaterium R181, B. safensis R173, B. simplex R180, and Paenibacillus graminis R200-also increased the growth of soybean and wheat. No set of traits was a predictor of growth promotion efficacy. The number of traits expressed by a strain also was not an indicator of efficacy as strain R200 that was positive for only one trait showed high growth promotion efficacy. Effective strains can be identified through pot tests on multiple crop plants, but in vitro physiological assays are unreliable for strain selection.

The impact of the omics era on the knowledge and use of Lysobacter species to control phytopathogenic micro-organisms

Omics technologies have had a tremendous impact on underinvestigated genera of plant disease biocontrol agents such as Lysobacter. Strong evidence of the association between Lysobacter spp. and the rhizosphere has been obtained through culture-independent methods, which has also contributed towards highlighting the relationship between Lysobacter abundance and soil suppressiveness. It is conceivable that the role played by Lysobacter spp. in soil suppressiveness is related to their ability to produce an impressive array of lytic enzymes and antibiotics. Indeed, genomics has revealed that biocontrol Lysobacter strains share a vast number of genes involved in antagonism activities, and the molecular pathways underlying how Lysobacter spp. interact with the environment and other micro-organisms have been depicted through transcriptomic analysis. Furthermore, omics technologies shed light on the regulatory pathways governing cell motility and the biosynthesis of antibiotics. Overall, the results achieved so far through omics technologies confirm that the genus Lysobacter is a valuable source of novel biocontrol agents, paving the way for studies aimed at making their application in field conditions more reliable.

Evidence of an Unidentified Extracellular Heat-Stable Factor Produced by Lysobacter enzymogenes (OH11) that Degrade Fusarium graminearum PH1 Hyphae

Lysobacter enzymogenes OH11 produces heat-stable antifungal factor (HSAF) and lytic enzymes possessing antifungal activity. This study bio-prospected for other potential antifungal factors besides those above. The cells and extracellular metabolites of L. enzymogenes OH11 and the mutants ΔchiA, ΔchiB, ΔchiC, Δclp, Δpks, and ΔpilA were examined for antifungal activity against Fusarium graminearum PH1, the causal agent of Fusarium head blight (FHB). Results evidenced that OH11 produces an unidentified extracellular heat-stable degrading metabolite (HSDM) that exhibit degrading activity on F. graminearum PH1 chitinous hyphae. Interestingly, both heat-treated and non-heat-treated extracellular metabolites of OH11 mutants exhibited hyphae-degrading activity against F. graminearum PH1. Enzyme activity detection of heat-treated metabolites ruled out the possibility of enzyme degradation activity. Remarkably, the PKS-NRPS-deficient mutant Δpks cannot produce HSAF or analogues, yet its metabolites exhibited hyphae-degrading activity. HPLC analysis confirmed no HSAF production by Δpks. Δclp lacks hyphae-degrading ability. Therefore, clp regulates HSDM and extracellular lytic enzymes production in L. enzymogenes OH11. ΔpilA had impaired surface cell motility and significantly reduced antagonistic properties. ΔchiA, ΔchiB, and ΔchiC retained hyphae-degrading ability, despite having reduced abilities to produce chitinase enzymes. Ultimately, L. enzymogenes OH11 can produce other unidentified HSDM independent of the PKS-NRPS genes. This suggests HSAF and lytic enzymes production are a fraction of the antifungal mechanisms in OH11. Characterization of HSDM, determination of its biosynthetic gene cluster and understanding its mode of action will provide new leads in the search for effective drugs for FHB management.

Salinity altered root distribution and increased diversity of bacterial communities in the rhizosphere soil of Jerusalem artichoke

The interaction between roots and bacterial communities in halophytic species is poorly understood. Here, we used Jerusalem artichoke cultivar Nanyu 1 (NY-1) to characterise root distribution patterns and determine diversity and abundance of bacteria in the rhizosphere soil under variable salinity. Root growth was not inhibited within the salinity range 1.2 to 1.9 g salt/kg, but roots were mainly confined to 0–20 cm soil layer vertically and 0–30 cm horizontally from the plant centre. Root concentrations of K⁺, Na⁺, Mg²⁺ and particularly Ca²⁺ were relatively high under salinity stress. High salinity stress decreased soil invertase and catalase activity. Using a next-generation, Illumina-based sequencing approach, we determined higher diversity of bacteria in the rhizosphere soil at high than low salinity. More than 15,500 valid reads were obtained, and Proteobacteria, Acidobacteria, Bacteroidetes and Actinobacteria predominated in all samples, accounting for >80% of the reads. On a genus level, 636 genera were common to the low and high salinity treatments at 0–5 cm and 5–10 cm depth. The abundance of Steroidobacter and Sphingomonas was significantly decreased by increasing salinity. Higher Shannon and Chao 1 indices with increasing severity of salt stress indicated that high salt stress increased diversity in the bacterial communities.

Transcriptomic analysis reveals new regulatory roles of Clp signaling in secondary metabolite biosynthesis and surface motility in Lysobacter enzymogenes OH11

Lysobacter enzymogenes is a bacterial biological control agent emerging as a new source of antibiotic metabolites, such as heat-stable antifungal factor (HSAF) and the antibacterial factor WAP-8294A2. The regulatory mechanism(s) for antibiotic metabolite biosynthesis remains largely unknown in L. enzymogenes. Clp, a cyclic adenosine monophosphate (cAMP)-receptor-like protein, is shown to function as a global regulator in modulating biocontrol-associated traits in L. enzymogenes. However, the genetic basis of Clp signaling remains unclear. Here, we utilized transcriptome/microarray analysis to determine the Clp regulon in L. enzymogenes. We showed that Clp is a global regulator in gene expression, as the transcription of 775 genes belonging to 19 functional groups was differentially controlled by Clp signaling. Analysis of the Clp regulon detected previously characterized Clp-modulated functions as well as novel loci. These include novel loci involved in antibiotic metabolite biosynthesis and surface motility in L. enzymogenes. We further showed experimentally that Clp signaling played a positive role in regulating the biosynthesis of HSAF and WAP-8294A2, as well as surface motility which is a type-IV-pilus-dependent trait. The regulation by Clp signaling of antibiotic (HSAF and WAP-8294A2) biosynthesis and surface motility was found to be independent. Importantly, we identified a factor Lysobacter acetyltransferase (Lat), a homologue of histone acetyltransferase Hpa2, which was regulated by Clp and involved in HSAF biosynthesis, but not associated with WAP-8294A2 production and surface motility. Overall, our study provided new insights into the regulatory role and molecular mechanism of Clp signaling in L. enzymogenes.

Naturally occurring tetramic acid products: isolation, structure elucidation and biological activity

Natural products containing the tetramic acid core scaffold have been isolated from an assortment of terrestrial and marine species and often display wide ranging and potent biological activities including antibacterial, antiviral and antitumoral activities.

Facile method for site-specific gene integration in Lysobacter enzymogenes for yield improvement of the anti-MRSA antibiotics WAP-8294A and the antifungal antibiotic HSAF

Lysobacter is a genus of Gram-negative gliding bacteria that are emerged as novel biocontrol agents and new sources of bioactive natural products. The bacteria are naturally resistant to many antibiotics commonly used in transformant selection, which has hampered the genetic manipulations. Here, we described a facile method for quick-and-easy identification of the target transformants from a large population of the wild type and nontarget transformants. The method is based on a distinct yellow-to-black color change as a visual selection marker for site-specific integration of the gene of interest. Through transposon random mutagenesis, we identified a black-colored strain from the yellow-colored L. enzymogenes . The black strain was resulted from a disruption of hmgA, a gene required for tyrosine/phenylalanine metabolism. The disruption of hmgA led to accumulation of dark brown pigments. As proof of principle, we constructed a series of expression vectors for a regulator gene found within the WAP-8294A biosynthetic gene cluster. The yield of WAP-8294A in the black strains increased by 2 fold compared to the wild type. Interestingly, the yield of another antibiotic (HSAF) increased up to 7 fold in the black strains. WAP-8294A is a family of potent anti-MRSA antibiotics and is currently in clinical studies, and HSAF is an antifungal compound with distinct structural features and a novel mode of action. This work represents the first successful metabolic engineering in Lysobacter. The development of this facile method opens a way toward manipulating antibiotic production in the largely unexplored sources.

Transcriptomics of the rice blast fungus Magnaporthe oryzae in response to the bacterial antagonist Lysobacter enzymogenes reveals candidate fungal defense response genes

Plants and animals have evolved a first line of defense response to pathogens called innate or basal immunity. While basal defenses in these organisms are well studied, there is almost a complete lack of understanding of such systems in fungal species, and more specifically, how they are able to detect and mount a defense response upon pathogen attack. Hence, the goal of the present study was to understand how fungi respond to biotic stress by assessing the transcriptional profile of the rice blast pathogen, Magnaporthe oryzae, when challenged with the bacterial antagonist Lysobacter enzymogenes. Based on microscopic observations of interactions between M. oryzae and wild-type L. enzymogenes strain C3, we selected early and intermediate stages represented by time-points of 3 and 9 hours post-inoculation, respectively, to evaluate the fungal transcriptome using RNA-seq. For comparative purposes, we also challenged the fungus with L. enzymogenes mutant strain DCA, previously demonstrated to be devoid of antifungal activity. A comparison of transcriptional data from fungal interactions with the wild-type bacterial strain C3 and the mutant strain DCA revealed 463 fungal genes that were down-regulated during attack by C3; of these genes, 100 were also found to be up-regulated during the interaction with DCA. Functional categorization of genes in this suite included those with roles in carbohydrate metabolism, cellular transport and stress response. One gene in this suite belongs to the CFEM-domain class of fungal proteins. Another CFEM class protein called PTH11 has been previously characterized, and we found that a deletion in this gene caused advanced lesion development by C3 compared to its growth on the wild-type fungus. We discuss the characterization of this suite of 100 genes with respect to their role in the fungal defense response.

Biosynthetic mechanism for sunscreens of the biocontrol agent Lysobacter enzymogenes

Lysobacter are ubiquitous environmental bacteria emerging as novel biocontrol agents and new sources of anti-infectives. So far, very little effort has been invested in the study of the biology of these Gram-negative gliding bacteria. Many Lysobacter species are characterized by their yellow-orange appearance. Using transposon mutagenesis, we identified a stand-alone polyketide synthase (PKS) gene cluster required for the pigment production in L. enzymogenes OH11. The yellow pigments were abolished in the "white" mutants generated by target-specific deletions of ketosynthase (KS), acyl carrier protein, or ketoreductase. Spectroscopic data suggested that the pigments belong to xanthomonadin-like aryl polyenes. Polyene-type polyketides are known to be biosynthesized by modular PKS (Type I), not by stand-alone PKS (Type II) which always contain the heterodimer KS-CLF (chain-length factor) as the key catalytic component. Remarkably, this aryl polyene PKS complex only contains the KS (ORF17), but not the CLF. Instead, a hypothetical protein (ORF16) is located immediately next to ORF17. ORF16-17 homologs are widespread in numerous uncharacterized microbial genomes, in which an ORF17 homolog is always accompanied by an ORF16 homolog. The deletion of ORF16 eliminated pigment production, and homology modeling suggested that ORF16 shares a structural similarity to the N-terminal half of CLF. A point-mutation of glutamine (Q166A) that is the conserved active site of known CLF abolished pigment production. The "white" mutants are significantly more sensitive to UV/visible light radiation or H2O2 treatment than the wild type. These results unveil the first example of Type II PKS-synthesized polyene pigments and show that the metabolites serve as Lysobacter "sunscreens" that are important for the survival of these ubiquitous environmental organisms.

Use of the tetrazolium salt MTT to measure cell viability effects of the bacterial antagonist Lysobacter enzymogenes on the filamentous fungus Cryphonectria parasitica

Despite substantial interest investigating bacterial mechanisms of fungal growth inhibition, there are few methods available that quantify fungal cell death during direct interactions with bacteria. Here we describe an in vitro cell suspension assay using the tetrazolium salt MTT as a viability stain to assess direct effects of the bacterial antagonist Lysobacter enzymogenes on hyphal cells of the filamentous fungus Cryphonectria parasitica. The effects of bacterial cell density, fungal age and the physiological state of fungal mycelia on fungal cell viability were evaluated. As expected, increased bacterial cell density correlated with reduced fungal cell viability over time. Bacterial effects on fungal cell viability were influenced by both age and physiological state of the fungal mycelium. Cells obtained from 1-week-old mycelia lost viability faster compared with those from 2-week-old mycelia. Likewise, hyphal cells obtained from the lower layer of the mycelial pellicle lost viability more quickly compared with cells from the upper layer of the mycelial pellicle. Fungal cell viability was compared between interactions with L. enzymogenes wildtype strain C3 and a mutant strain, DCA, which was previously demonstrated to lack in vitro antifungal activity. Addition of antibiotics eliminated contributions to MTT-formazan production by bacterial cells, but not by fungal cells, demonstrating that mutant strain DCA had lost complete capacity to reduce fungal cell viability. These results indicate this cell suspension assay can be used to quantify bacterial effects on fungal cells, thus providing a reliable method to differentiate strains during bacterial/fungal interactions.

Identification and characterization of the anti-methicillin-resistant Staphylococcus aureus WAP-8294A2 biosynthetic gene cluster from Lysobacter enzymogenes OH11

Lysobactor enzymogenes strain OH11 is an emerging biological control agent of fungal and bacterial diseases. We recently completed its genome sequence and found it contains a large number of gene clusters putatively responsible for the biosynthesis of nonribosomal peptides and polyketides, including the previously identified antifungal dihydromaltophilin (HSAF). One of the gene clusters contains two huge open reading frames, together encoding 12 modules of nonribosomal peptide synthetases (NRPS). Gene disruption of one of the NRPS led to the disappearance of a metabolite produced in the wild type and the elimination of its antibacterial activity. The metabolite and antibacterial activity were also affected by the disruption of some of the flanking genes. We subsequently isolated this metabolite and subjected it to spectroscopic analysis. The mass spectrometry and nuclear magnetic resonance data showed that its chemical structure is identical to WAP-8294A2, a cyclic lipodepsipeptide with potent anti-methicillin-resistant Staphylococcus aureus (MRSA) activity and currently in phase I/II clinical trials. The WAP-8294A2 biosynthetic genes had not been described previously. So far, the Gram-positive Streptomyces have been the primary source of anti-infectives. Lysobacter are Gram-negative soil/water bacteria that are genetically amendable and have not been well exploited. The WAP-8294A2 synthetase represents one of the largest NRPS complexes, consisting of 45 functional domains. The identification of these genes sets the foundation for the study of the WAP-8294A2 biosynthetic mechanism and opens the door for producing new anti-MRSA antibiotics through biosynthetic engineering in this new source of Lysobacter.

Bacterial/Fungal interactions: from pathogens to mutualistic endosymbionts

A fundamental issue in biology is the question of how bacteria initiate and maintain pathogenic relationships with eukaryotic hosts. Despite billions of years of coexistence, far less is known about bacterial/fungal interactions than the equivalent associations formed by either of these types of microorganisms with higher eukaryotes. This review highlights recent research advances in the field of bacterial/fungal interactions, and provides examples of the various forms such interactions may assume, ranging from simple antagonism and parasitism to more intimate associations of pathogenesis and endosymbiosis. Information derived from the associations of bacteria and fungi in the context of natural and agronomic ecosystems is emphasized, including interactions observed from biological control systems, endosymbiotic relationships, diseases of cultivated mushrooms, and model systems that expand our understanding of human disease. The benefits of studying these systems at the molecular level are also emphasized.

An antibiotic complex from Lysobacter enzymogenes strain C3: antimicrobial activity and role in plant disease control

Lysobacter enzymogenes C3 is a bacterial biological control agent that exhibits antagonism against multiple fungal pathogens. Its antifungal activity was attributed in part to lytic enzymes. In this study, a heat-stable antifungal factor (HSAF), an antibiotic complex consisting of dihydromaltophilin and structurally related macrocyclic lactams, was found to be responsible for antagonism by C3 against fungi and oomycetes in culture. HSAF in purified form exhibited inhibitory activity against a wide range of fungal and oomycetes species in vitro, inhibiting spore germination, and disrupting hyphal polarity in sensitive fungi. When applied to tall fescue leaves as a partially-purified extract, HSAF at 25 mug/ml and higher inhibited germination of conidia of Bipolaris sorokiniana compared with the control. Although application of HSAF at 12.5 mug/ml did not reduce the incidence of conidial germination, it inhibited appressorium formation and suppressed Bipolaris leaf spot development. Two mutant strains of C3 (K19 and DeltaNRPS) that were disrupted in different domains in the hybrid polyketide synthase-nonribosomal peptide synthetase gene for HSAF biosynthesis and had lost the ability to produce HSAF were compared with the wild-type strain for biological control efficacy against Bipolaris leaf spot on tall fescue and Fusarium head blight, caused by Fusarium graminearum, on wheat. Both mutant strains exhibited decreased capacity to reduce the incidence and severity of Bipolaris leaf spot compared with C3. In contrast, the mutant strains were as efficacious as the wild-type strain in reducing the severity of Fusarium head blight. Thus, HSAF appears to be a mechanism for biological control by strain C3 against some, but not all, plant pathogenic fungi.

Isolation of maize soil and rhizosphere bacteria with antagonistic activity against Aspergillus flavus and Fusarium verticillioides

Bacterial isolates from Mississippi maize field soil and maize rhizosphere samples were evaluated for their potential as biological control agents against Aspergillus flavus and Fusarium verticillioides. Isolated strains were screened for antagonistic activities in liquid coculture against A. flavus and on agar media against A. flavus and F. verticillioides. We identified 221 strains that inhibited growth of both fungi. These bacteria were further differentiated by their production of extracellular enzymes that hydrolyzed chitin and yeast cell walls and by production of antifungal metabolites. Based on molecular and nutritional identification of the bacterial strains, the most prevalent genera isolated from rhizosphere samples were Burkholderia and Pseudomonas, and the most prevalent genera isolated from nonrhizosphere soil were Pseudomonas and Bacillus. Less prevalent genera included Stenotrophomonas, Agrobacterium, Variovorax, Wautersia, and several genera of coryneform and enteric bacteria. In quantitative coculture assays, strains of P. chlororaphis and P. fluorescens consistently inhibited growth of A. flavus and F. verticillioides in different media. These results demonstrate the potential for developing individual biocontrol agents for simultaneous control of the mycotoxigenic A. flavus and F. verticillioides.

Structure and biosynthesis of heat-stable antifungal factor (HSAF), a broad-spectrum antimycotic with a novel mode of action

A screen for antifungal compounds from Lysobacter enzymogenes strain C3, a bacterial biological control agent of fungal diseases, has previously led to the isolation of heat-stable antifungal factor (HSAF). HSAF exhibits inhibitory activities against a wide range of fungal species and shows a novel mode of antifungal action by disrupting the biosynthesis of a distinct group of sphingolipids. We have now determined the chemical structure of HSAF, which is identical to that of dihydromaltophilin, an antifungal metabolite with a unique macrocyclic lactam system containing a tetramic acid moiety and a 5,5,6-tricyclic skeleton. We have also identified the genetic locus responsible for the biosynthesis of HSAF in strain C3. DNA sequencing of this locus revealed genes for a hybrid polyketide synthase-nonribosomal peptide synthetase (PKS-NRPS), a sterol desaturase, a ferredoxin reductase, and an arginase. The disruption of the PKS-NRPS gene generated C3 mutants that lost the ability to produce HSAF and to inhibit fungal growth, demonstrating a hybrid PKS-NRPS that catalyzed the biosynthesis of the unique macrolactam system that is found in many biologically active natural products isolated from marine organisms. In addition, we have generated mutants with disrupted sterol desaturase, ferredoxin reductase, and arginase and examined the metabolites produced in these mutants. The work represents the first study of the genetic basis for the biosynthesis of the tetramic acid-containing macrolactams. The elucidation of the chemical structure of HSAF and the identification of the genetic locus for its biosynthesis establish the foundation for future exploitation of this group of compounds as new fungicides or antifungal drugs.