A Mini-Review of Anti-Listerial Compounds from Marine Actinobacteria (1990-2023).

Among the foodborne illnesses, listeriosis has the third highest case mortality rate (20-30% or higher). Emerging drug-resistant strains of Listeria monocytogenes, a causative bacterium of listeriosis, exacerbate the seriousness of this public health concern. Novel anti-Listerial compounds are therefore needed to combat this challenge. In recent years, marine actinobacteria have come to be regarded as a promising source of novel antimicrobials. Hence, our aim was to provide a narrative of the available literature and discuss trends regarding bioprospecting marine actinobacteria for new anti-Listerial compounds. Four databases were searched for the review: Academic Search Ultimate, Google Scholar, ScienceDirect, and South African Thesis and Dissertations. The search was restricted to peer-reviewed full-text manuscripts that discussed marine actinobacteria as a source of antimicrobials and were written in English from 1990 to December 2023. In total, for the past three decades (1990-December 2023), only 23 compounds from marine actinobacteria have been tested for their anti-Listerial potential. Out of the 23 reported compounds, only 2-allyoxyphenol, adipostatins E-G, 4-bromophenol, and ansamycins (seco-geldanamycin B, 4.5-dihydro-17-O-demethylgeldanamycin, and seco-geldanamycin) have been found to possess anti-Listerial activity. Thus, our literature survey reveals the scarcity of published assays testing the anti-Listerial capacity of bioactive compounds sourced from marine actinobacteria during this period.

Auxin production and plant growth promotion by Microbacterium albopurpureum sp. nov. from the rhizoplane of leafless Chiloschista parishii Seidenf. orchid.

The strains of the genus Microbacterium, with more than 150 species, inhabit diverse environments; plant-associated bacteria reveal their plant growth-promoting activities due to a number of beneficial characteristics. Through the performance of diverse techniques and methods, including isolation of a novel Microbacterium strain from the aerial roots of leafless epiphytic orchid, Chiloschista parishii Seidenf., its morphological and biochemical characterization, chemotaxonomy, phylogenetic and genome analysis, as well as bioassays and estimation of its auxin production capacity, a novel strain of ET2T is described. Despite that it shared 16S rRNA gene sequence similarity of 99.79% with Microbacterium kunmingense JXJ CY 27-2T, so they formed a monophyletic group on phylogenetic trees, the two strains showed clear divergence of their genome sequences. The average nucleotide identity (ANI), average amino acid identity (AAI) and digital DNA-DNA hybridization (dDDH) values of ET2T differed greatly from phylogenetically close JXJ CY 27-2T. Based on the differences being below the threshold for species similarity, together with the unique chemotaxonomic characteristics, strain ET2T represents a novel species of the genus Microbacterium. Several genes, putatively involved in auxin biosynthesis were predicted. This strain revealed obvious plant growth-promoting activities, including diazotrophy and biosynthesis of tryptophan-dependent auxins (indole-3-acetic and indole-3-pyruvic acids). Microbial auxins directly stimulated the rhizogenesis, so that the ET2T-inoculated seeds of wheat, cucumber and garden cress showed evident promotion in their growth and development, both under optimal and under cold stress conditions. Based on phenotypic, chemotypic and genotypic evidences, the strain ET2T belongs to the genus Microbacterium, order Micrococcales, class Actinomycetes, and it represents a novel species, for which the name Microbacterium albopurpureum sp. nov. is proposed, with strain ET2T (VKPM Ac-2212, VKM Ас-2998) as the type strain.

Blastococcus brunescens sp. nov., a member of the Geodermatophilaceae isolated from sandstone collected from the Sahara Desert in Tunisia.

The taxonomic position of strain BMG 8361T, isolated from sandstone collected in the Sahara Desert of Southern Tunisia, was refined through a polyphasic taxonomic investigation. Colonies of BMG 8361T were pale-orange coloured, irregular with a dry surface and produced a diffusible pink or brown pigment depending on media. The Gram-positive cells were catalase-positive and oxidase-negative. The strain exhibited growth at 10-40 °C and pH values ranging from 5.5 to 9.0, with optima at 28-35 °C and pH 6.5-8.0. Additionally, BMG 8361T demonstrated the ability to grow in the presence of up to 1 % NaCl (w/v) concentration. The peptidoglycan of the cell wall contained meso-diaminopimelic acid, glucose, galactose, xylose, ribose, and rhamnose. The predominant menaquinones consisted of MK-9(H4) and MK-9. The main polar lipids were phosphatidylcholine, phosphatidylinositol, glycophosphatidylinositol, diphosphatidylglycerol, phosphatidylethanolamine, and two unidentified lipids. Major cellular fatty acids were iso-C16 : 0, iso-C16 : 1 h, and C17 : 1 ω8c. Phylogenetic analyses based on both the 16S rRNA gene and whole-genome sequences assigned strain BMG 8361T within the genus Blastococcus. The highest pairwise sequence similarity observed in the 16S rRNA gene was 99.5 % with Blastococcus haudaquaticus AT 7-14T. However, when considering digital DNA-DNA hybridization and average nucleotide identity, the highest values, 48.4 and 86.58 %, respectively, were obtained with Blastococcus colisei BMG 822T. These values significantly undershoot the recommended thresholds for establishing new species, corroborating the robust support for the distinctive taxonomic status of strain BMG 8361T within the genus Blastococcus. In conjunction with the phenotyping results, this compelling evidence leads to the proposal of a novel species we named Blastococcus brunescens sp. nov. with BMG 8361T (=DSM 46845T=CECT 8880T) as the type strain.

LogoMotif: A Comprehensive Database of Transcription Factor Binding Site Profiles in Actinobacteria.

Actinobacteria undergo a complex multicellular life cycle and produce a wide range of specialized metabolites, including the majority of the antibiotics. These biological processes are controlled by intricate regulatory pathways, and to better understand how they are controlled we need to augment our insights into the transcription factor binding sites. Here, we present LogoMotif (https://logomotif.bioinformatics.nl), an open-source database for characterized and predicted transcription factor binding sites in Actinobacteria, along with their cognate position weight matrices and hidden Markov models. Genome-wide predictions of binding site locations in Streptomyces model organisms are supplied and visualized in interactive regulatory networks. In the web interface, users can freely access, download and investigate the underlying data. With this curated collection of actinobacterial regulatory interactions, LogoMotif serves as a basis for binding site predictions, thus providing users with clues on how to elicit the expression of genes of interest and guide genome mining efforts.

Association between the relative abundance of phyla actinobacteria, vitamin C consumption, and DNA methylation of genes linked to immune response pathways.

Introduction: There is an emerging body of evidence that vitamin C consumption can modulate microbiota abundance and can also impact DNA methylation in the host, and this could be a link between diet, microbiota, and immune response. The objective of this study was to evaluate common CpG sites associated with both vitamin C and microbiota phyla abundance. Methods: Six healthy women participated in this cohort study. They were divided into two groups, according to the amount of vitamin C they ingested. Ingestion was evaluated using the 24-h recall method. The Illumina 450 k BeadChip was used to evaluate DNA methylation. Singular value decomposition analyses were used to evaluate the principal components of this dataset. Associations were evaluated using the differentially methylated position function from the Champ package for R Studio. Results and discussion: The group with higher vitamin C (HVC) ingestion also had a higher relative abundance of Actinobacteria. There was a positive correlation between those variables (r = 0.84, p = 0.01). The HVC group also had higher granulocytes, and regarding DNA methylation, there were 207 CpG sites commonly related to vitamin C ingestion and the relative abundance of Actinobacteria. From these sites, there were 13 sites hypomethylated and 103 hypermethylated. The hypomethylated targets involved the respective processes: immune function, glucose homeostasis, and general cellular metabolism. The hypermethylated sites were also enriched in immune function-related processes, and interestingly, more immune responses against pathogens were detected. These findings contribute to understanding the interaction between nutrients, microbiota, DNA methylation, and the immune response.

Harnessing regulatory networks in Actinobacteria for natural product discovery.

Microbes typically live in complex habitats where they need to rapidly adapt to continuously changing growth conditions. To do so, they produce an astonishing array of natural products with diverse structures and functions. Actinobacteria stand out for their prolific production of bioactive molecules, including antibiotics, anticancer agents, antifungals, and immunosuppressants. Attention has been directed especially towards the identification of the compounds they produce and the mining of the large diversity of biosynthetic gene clusters (BGCs) in their genomes. However, the current return on investment in random screening for bioactive compounds is low, while it is hard to predict which of the millions of BGCs should be prioritized. Moreover, many of the BGCs for yet undiscovered natural products are silent or cryptic under laboratory growth conditions. To identify ways to prioritize and activate these BGCs, knowledge regarding the way their expression is controlled is crucial. Intricate regulatory networks control global gene expression in Actinobacteria, governed by a staggering number of up to 1000 transcription factors per strain. This review highlights recent advances in experimental and computational methods for characterizing and predicting transcription factor binding sites and their applications to guide natural product discovery. We propose that regulation-guided genome mining approaches will open new avenues toward eliciting the expression of BGCs, as well as prioritizing subsets of BGCs for expression using synthetic biology approaches. ONE-SENTENCE SUMMARY: This review provides insights into advances in experimental and computational methods aimed at predicting transcription factor binding sites and their applications to guide natural product discovery.

The contribution of plasmids to trait diversity in a soil bacterium.

Plasmids are so closely associated with pathogens and antibiotic resistance that their potential for conferring other traits is often overlooked. Few studies consider how the full suite of traits encoded by plasmids is related to a host's environmental adaptation, particularly for Gram-positive bacteria. To investigate the role that plasmid traits might play in microbial communities from natural ecosystems, we identified plasmids carried by isolates of Curtobacterium (phylum Actinomycetota) from a variety of soil environments. We found that plasmids were common, but not ubiquitous, in the genus and varied greatly in their size and genetic diversity. There was little evidence of phylogenetic conservation among Curtobacterium plasmids even for closely related bacterial strains within the same ecotype, indicating that horizontal transmission of plasmids is common. The plasmids carried a wide diversity of traits that were not a random subset of the host chromosome. Furthermore, the composition of these plasmid traits was associated with the environmental context of the host bacterium. Together, the results indicate that plasmids contribute substantially to the microdiversity of a soil bacterium and that this diversity may play a role in niche differentiation and a bacterium's adaptation to its local environment.

Identification of bio-active secondary metabolites from Actinobacteria as potential drug targets against Porphyromonas gingivalis in oral squamous cell carcinoma using molecular docking and dynamics study.

Chronic periodontitis caused by the bacteria Porphyromonas gingivalis is thought to be a risk factor for the advancement of oral squamous cell carcinoma (OSCC). Virulence factors of P. gingivalis include gingipains, outer membrane surface lipoproteins, and fimbriae contribute to the activation of oncogenic pathways in OSCC by up-regulating different cytokines. Gingipains (Arg and Lys) proteases have an important role in the activation of proMMP-9, which promotes cellular invasion and metastatic ability of OSCC. Thus gingipains and MMP-9 were actively investigated as potential therapeutic targets in OSCC therapy. Various natural bioactive compounds from Actinobacteria have been explored for their anticancer potential in a variety of cancers, but very few studies have been reported in OSCC. Therefore, the current study is focused to identify potential actinobacterial compounds that can be considered as a therapeutic target against gingipains and inflammatory proteins in OSCC through high-throughput virtual screening, Molecular Docking (MD), and Molecular Dynamics Simulation (MDS) approaches. A total of 179 bioactive secondary metabolites of Actinobacteria were explored for their binding affinity against six virulence proteins of P. gingivalis. The Molecular Docking studies revealed that among 179 metabolites screened, Actinosporin G showed a highly acceptable binding affinity of -7.9 kcal/mol with RgpB (1CVR), and exhibited multi-protein targeting and drug-likeness property and passed level of toxicity. Comprehensive docking interaction of the best top-ranked Actinosporin G with OSCC-related protein targets illustrated high binding affinity towards MMP-9 and JAK-1 proteins among all targeted receptor proteins. The molecular dynamic (MD) simulation has been executed for the metabolite Actinosporin G for both bacterial gingipain (RgpB) and MMP-9 & JAK-1 showed stable intermolecular binding with both hydrogen and hydrophobic interactions. In conclusion, this work suggests that the bioactive secondary metabolite of Actinosporin G from Actinobacteria genera may serve as a promising therapy for P. gingivalis-induced OSCC. Supplementary Information: The online version contains supplementary material available at 10.1007/s40203-024-00209-0.

Harnessing artificial intelligence-driven approach for enhanced indole-3-acetic acid from the newly isolated Streptomyces rutgersensis AW08.

Indole-3-acetic acid (IAA) derived from Actinobacteria fermentations on agro-wastes constitutes a safer and low-cost alternative to synthetic IAA. This study aims to select a high IAA-producing Streptomyces-like strain isolated from Lake Oubeira sediments (El Kala, Algeria) for further investigations (i.e., 16S rRNA gene barcoding and process optimization). Subsequently, artificial intelligence-based approaches were employed to maximize IAA bioproduction on spent coffee grounds as high-value-added feedstock. The specificity was the novel application of the Limited-Memory Broyden-Fletcher-Goldfarb-Shanno Box (L-BFGS-B) optimization algorithm. The new strain AW08 was a significant producer of IAA (26.116 ± 0.61 µg/mL) and was identified as Streptomyces rutgersensis by 16S rRNA gene barcoding and phylogenetic inquiry. The empirical data involved the inoculation of AW08 in various cultural conditions according to a four-factor Box Behnken Design matrix (BBD) of Response surface methodology (RSM). The input parameters and regression equation extracted from the RSM-BBD were the basis for implementing and training the L-BFGS-B algorithm. Upon training the model, the optimal conditions suggested by the BBD and L-BFGS-B algorithm were, respectively, L-Trp (X1) = 0.58 %; 0.57 %; T° (X2) = 26.37 °C; 28.19 °C; pH (X3) = 7.75; 8.59; and carbon source (X4) = 30 %; 33.29 %, with the predicted response IAA (Y) =152.8; 169.18 µg/mL). Our findings emphasize the potential of the multifunctional S. rutgersensis AW08, isolated and reported for the first time in Algeria, as a robust producer of IAA. Validation investigations using the bioprocess parameters provided by the L-BFGS-B and the BBD-RSM models demonstrate the effectiveness of AI-driven optimization in maximizing IAA output by 5.43-fold and 4.2-fold, respectively. This study constitutes the first paper reporting a novel interdisciplinary approach and providing insights into biotechnological advancements. These results support for the first time a reasonable approach for valorizing spent coffee grounds as feedstock for sustainable and economic IAA production from S. rutgersensis AW08.

Biosynthesis of Silver Nanoparticles From Marine Actinobacterium Micromonospora sp. and Their Bioactive Potential.

Background The biosynthesis of nanoparticles represents a rapid, environmentally friendly, cost-effective, and straightforward technology. This approach allows for the production of nanoparticles with a wide range of chemical compositions, sizes, shapes, high uniformity, and scalability. One of the principal advantages of biogenic nanoparticles is their water solubility and compatibility with biological systems. Biologically synthesized nanoparticles have demonstrated superior efficiency compared to conventionally synthesized particles. Among biosynthesis, microbial-mediated biosynthesis is a promising one that has a selectively reducing ability on specific metal ions through electron transfer.  Objectives Evaluation of antimicrobial and antioxidant activity of silver nanoparticle synthesized by actinobacteria Micromonospora sp. which is isolated from marine environment. Materials and methods In this study, actinobacteria were isolated from the marine sediment using the spread plate method. The isolates were identified based on morphological observation, cell wall amino acids, sugar analysis, and micromorphological analysis. The silver nanoparticle synthesis from microbes and their inhibition against clinical pathogens have been evaluated by the disc diffusion method. Antioxidant efficiency was evaluated in terms of total antioxidant activity through ammonium molybdenum assay. Results A total of five isolates were isolated from the sediment sample. The cell-free extract of MBIT-MSA4 can synthesize silver nanoparticles that have potential antimicrobial activity against the clinical pathogens Streptococcus mutans at a zone of inhibition 6 mm, 10 mm inhibition zone of Klebsiella pneumonia, and 8 mm zone of inhibition of Staphylococcus aureus. Also, it has significant antioxidant activity up to 73% of free radical inhibition. Conclusion Marine microbial-mediated biosynthesized silver nanoparticles have potential antimicrobial activity against S. mutans and methicillin-resistant Staphylococcus aureus (MRSA) and inhibit the oxidation process through antioxidant activity. This enhanced efficient biosynthesised nanoparticle has significantly reduced the concentration of free radicals caused by pathogens.

Novel strains of Actinobacteria associated with neotropical social wasps (Vespidae; Polistinae, Epiponini) with antimicrobial potential for natural product discovery.

Antimicrobial resistance has been considered a public health threat. The World Health Organization has warned about the urgency of detecting new antibiotics from novel sources. Social insects could be crucial in the search for new antibiotic metabolites, as some of them survive in places that favor parasite development. Recent studies have shown the potential of social insects to produce antimicrobial metabolites (e.g. ants, bees, and termites). However, most groups of social wasps remain unstudied. Here, we explored whether Actinobacteria are associated with workers in the Neotropical Social Wasps (Epiponini) of Costa Rica and evaluated their putative inhibitory activity against other bacteria. Most isolated strains (67%) have antagonistic effects, mainly against Bacillus thuringensis and Escherichia coli ATCC 25992. Based on genome analysis, some inhibitory Actinobacteria showed biosynthetic gene clusters (BGCs) related to the production of antimicrobial molecules such as Selvamycin, Piericidin A1, and Nystatin. The Actinobacteria could be associated with social wasps to produce antimicrobial compounds. For these reasons, we speculate that Actinobacteria associated with social wasps could be a novel source of antimicrobial compounds, mainly against Gram-negative bacteria.

Genome sequences of actinobacteriophages JorRay, Blocker23, Nibbles, and OlgasClover.

JorRay, Blocker23, Nibbles, and OlgasClover are actinobacteriophages belonging to clusters G1, B2, CT, and DJ, respectively. JorRay and Blocker23 were identified in host bacterium Mycobacterium smegmatis mc2155. Nibbles and OlgasClover were identified in host bacterium Gordonia rubripertincta NRRL B-16540.

Desert diversity: genome sequence of Gordonia rubripertincta cluster DJ phage Mossy and cluster DV phage Erutan.

Lytic bacteriophages Mossy and Erutan were directly isolated from desert soil on Gordonia rubripertincta and characterized by their morphologies and genomes. Mossy, part of the DJ cluster of Actinobacteriophage, has a genome of 61,183 bp. The genome of Erutan, part of the DV cluster, is 66,957 bp.

Marine-Derived Anticancer Agents Targeting Apoptotic Pathways: Exploring the Depths for Novel Cancer Therapies.

Extensive research has been conducted on the isolation and study of bioactive compounds derived from marine sources. Several natural products have demonstrated potential as inducers of apoptosis and are currently under investigation in clinical trials. These marine-derived compounds selectively interact with extrinsic and intrinsic apoptotic pathways using a variety of molecular mechanisms, resulting in cell shrinkage, chromatin condensation, cytoplasmic blebs, apoptotic bodies, and phagocytosis by adjacent parenchymal cells, neoplastic cells, or macrophages. Numerous marine-derived compounds are currently undergoing rigorous examination for their potential application in cancer therapy. This review examines a total of 21 marine-derived compounds, along with their synthetic derivatives, sourced from marine organisms such as sponges, corals, tunicates, mollusks, ascidians, algae, cyanobacteria, fungi, and actinobacteria. These compounds are currently undergoing preclinical and clinical trials to evaluate their potential as apoptosis inducers for the treatment of different types of cancer. This review further examined the compound's properties and mode of action, preclinical investigations, clinical trial studies on single or combination therapy, and the prospective development of marine-derived anticancer therapies.

Endophytic Streptomyces sp. NEAU-DD186 from Moss with Broad-Spectrum Antimicrobial Activity: Biocontrol Potential Against Soilborne Diseases and Bioactive Components.

Soilborne diseases cause significant economic losses in agricultural production around the world. They are difficult to control because a host plant is invaded by multiple pathogens, and chemical control often does not work well. In this study, we isolated and identified an endophytic Streptomyces sp. NEAU-DD186 from moss, which showed broad-spectrum antifungal activity against 17 soilborne phytopathogenic fungi, with Bipolaris sorokiniana being the most prominent. The strain also exhibited strong antibacterial activity against soilborne phytopathogenic bacteria Ralstonia solanacearum. To evaluate its biocontrol potential, the strain was prepared into biofertilizer by solid-state fermentation. Response surface methodology was employed to optimize the fermentation conditions for maximizing spore production and revealed that the 1:1 ratio of vermicompost to wheat bran, a temperature of 28°C, and 50% water content with an inoculation amount of 15% represented the optimal parameters. Pot experiments showed that the application of biofertilizer with a spore concentration of 108 CFU/g soil could effectively suppress the occurrence of tomato bacterial wilt caused by R. solanacearum and wheat root rot caused by B. sorokiniana, and the biocontrol efficacy was 81.2 and 72.2%, respectively. Chemical analysis of strain NEAU-DD186 extracts using nuclear magnetic resonance spectrometry and mass analysis indicated that 25-O-malonylguanidylfungin A and 23-O-malonylguanidylfungin A were the main active constituents, which showed high activity against R. solanacearum (EC50 of 2.46 and 2.58 µg ml-1) and B. sorokiniana (EC50 of 3.92 and 3.95 µg ml-1). In conclusion, this study demonstrates that Streptomyces sp. NEAU-DD186 can be developed as biofertilizer to control soilborne diseases.

Endophytic Streptomyces sp. MSARE05 isolated from roots of Peanut plant produces a novel antimicrobial compound.

AIM: This study aimed to isolate, endophytic Streptomyces sp. MSARE05 isolated from root of a peanut (Arachis hypogaea) inhibits the growth of other bacteria. The research focused on characterizing the strain and the antimicrobial compound. METHODS AND RESULTS: The surface-sterilized peanut roots were used to isolate the endophytic bacterium Streptomyces sp. MSARE05. A small-scale fermentation was done to get the antimicrobial compound SM05 produced in highest amount in ISP-2 medium (pH 7) for 7 days at 30°C in shaking (180 rpm) condition. Extraction, purification, and chemical analysis of the antibacterial component revealed a novel class of antibiotics with a 485.54 Dalton molecular weight. The MIC was 0.4-0.8 µg ml-1 against the tested pathogens. It also inhibits multidrug-resistant (MDR) pathogens and Mycobacterium with 0.8-3.2 µg ml-1 MIC. SM05 was found to disrupt cell membrane of target pathogen as evident by significant leakage of intracellular proteins and nucleic acids. It showed synergistic activity with ampicillin, chloramphenicol, streptomycin, and kanamycin. CONCLUSIONS: The new-class antimicrobial SM05 consisting naphthalene core moiety was effective against drug-resistant pathogens but non-cytotoxic to human cells. This study underscores the significance of endophytic Streptomyces as a source of innovative antibiotics, contributing to the ongoing efforts to combat antibiotic resistance.

Multiphasic investigations imply transfer of orange-/red-pigmented strains of the bean pathogen Curtobacterium flaccumfaciens pv. flaccumfaciens to a new species as C. aurantiacum sp. nov., elevation of the poinsettia pathogen C. flaccumfaciens pv. poinsettiae to the species level as C. Poinsettiae sp. nov., and synonymy of C. albidum with C. citreum.

Curtobacterium flaccumfaciens (Microbacteriaceae), a plant-pathogenic coryneform species includes five pathovars with valid names and a number of proposed - but unvalidated - new members. In this study, phenotypic features and DNA similarity indexes were investigated among all C. flaccumfaciens members. Results showed that the C. flaccumfaciens pv. poinsettiae strains causing bacterial canker of Euphorbia pulcherrima in the USA as well as the orange-/red-pigmented strains of C. flaccumfaciens pv. flaccumfaciens pathogenic on dry beans in Iran are too distinct from each other and from the type strain of the species to be considered members of C. flaccumfaciens. Hence, the latter two groups were elevated at the species level as C. poinsettiae sp. nov. (ATCC 9682T = CFBP 2403T = ICMP 2566T = LMG 3715T = NCPPB 854T as type strain), and C. aurantiacum sp. nov. (50RT = CFBP 8819T = ICMP 22071T as type strain). Within the emended species C. flaccumfaciens comb. nov., yellow-pigmented strains causing bacterial wilt of dry beans and those causing bacterial canker of Euphorbia pulcherrima in Europe were retained as C. flaccumfaciens pv. flaccumfaciens and C. flaccumfaciens pv. poinsettiae, respectively; while taxonomic position of the sugar beet pathogen C. flaccumfaciens pv. beticola ATCC BAA144PT was confirmed. The newly described onion pathogen C. allii was also reclassified as C. flaccumfaciens pv. allii with the pathotype strain LMG 32517PT. Furthermore, C. flaccumfaciens pv. basellae causing bacterial leaf spot of malabar spinach (Basella rubra) was transferred to C. citreum pv. basellae with ATCC BAA143PT as pathotype.

The crystal structure of mycothiol disulfide reductase (Mtr) provides mechanistic insight into the specific low-molecular-weight thiol reductase activity of Actinobacteria.

Low-molecular-weight (LMW) thiols are involved in many processes in all organisms, playing a protective role against reactive species, heavy metals, toxins and antibiotics. Actinobacteria, such as Mycobacterium tuberculosis, use the LMW thiol mycothiol (MSH) to buffer the intracellular redox environment. The NADPH-dependent FAD-containing oxidoreductase mycothiol disulfide reductase (Mtr) is known to reduce oxidized mycothiol disulfide (MSSM) to MSH, which is crucial to maintain the cellular redox balance. In this work, the first crystal structures of Mtr are presented, expanding the structural knowledge and understanding of LMW thiol reductases. The structural analyses and docking calculations provide insight into the nature of Mtrs, with regard to the binding and reduction of the MSSM substrate, in the context of related oxidoreductases. The putative binding site for MSSM suggests a similar binding to that described for the homologous glutathione reductase and its respective substrate glutathione disulfide, but with distinct structural differences shaped to fit the bulkier MSSM substrate, assigning Mtrs as uniquely functioning reductases. As MSH has been acknowledged as an attractive antitubercular target, the structural findings presented in this work may contribute towards future antituberculosis drug development.

(Pan)genomic analysis of two Rhodococcus isolates and their role in phenolic compound degradation.

The genus Rhodococcus is recognized for its potential to degrade a large range of aromatic substances, including plant-derived phenolic compounds. We used comparative genomics in the context of the broader Rhodococcus pan-genome to study genomic traits of two newly described Rhodococcus strains (type-strain Rhodococcus pseudokoreensis R79T and Rhodococcus koreensis R85) isolated from apple rhizosphere. Of particular interest was their ability to degrade phenolic compounds as part of an integrated approach to treat apple replant disease (ARD) syndrome. The pan-genome of the genus Rhodococcus based on 109 high-quality genomes was open with a small core (1.3%) consisting of genes assigned to basic cell functioning. The range of genome sizes in Rhodococcus was high, from 3.7 to 10.9 Mbp. Genomes from host-associated strains were generally smaller compared to environmental isolates which were characterized by exceptionally large genome sizes. Due to large genomic differences, we propose the reclassification of distinct groups of rhodococci like the Rhodococcus equi cluster to new genera. Taxonomic species affiliation was the most important factor in predicting genetic content and clustering of the genomes. Additionally, we found genes that discriminated between the strains based on habitat. All members of the genus Rhodococcus had at least one gene involved in the pathway for the degradation of benzoate, while biphenyl degradation was mainly restricted to strains in close phylogenetic relationships with our isolates. The ~40% of genes still unclassified in larger Rhodococcus genomes, particularly those of environmental isolates, need more research to explore the metabolic potential of this genus.IMPORTANCERhodococcus is a diverse, metabolically powerful genus, with high potential to adapt to different habitats due to the linear plasmids and large genome sizes. The analysis of its pan-genome allowed us to separate host-associated from environmental strains, supporting taxonomic reclassification. It was shown which genes contribute to the differentiation of the genomes based on habitat, which can possibly be used for targeted isolation and screening for desired traits. With respect to apple replant disease (ARD), our isolates showed genome traits that suggest potential for application in reducing plant-derived phenolic substances in soil, which makes them good candidates for further testing against ARD.

Actinomycetospora lemnae sp. nov., A Novel Actinobacterium Isolated from Lemna aequinoctialis Able to Enhance Duckweed Growth.

Duckweed-associated actinobacteria are co-existing microbes that affect duckweed growth and adaptation. In this study, we aimed to report a novel actinobacterium species and explore its ability to enhance duckweed growth. Strain DW7H6T was isolated from duckweed, Lemna aequinoctialis. Phylogenetic analysis based on its 16S rRNA gene sequence revealed that the strain was most closely related to Actinomycetospora straminea IY07-55T (99.0%), Actinomycetospora chibensis TT04-21T (98.9%), Actinomycetospora lutea TT00-04T (98.8%) and Actinomycetospora callitridis CAP 335T (98.4%). Chemotaxonomic and morphological characteristics of strain DW7H6T were consistent with members of the genus Actinomycetospora, while average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) between the draft genomes of this strain and its closely related type strains were below the proposed threshold values used for species discrimination. Based on chemotaxonomic, phylogenetic, phenotypic, and genomic evidence obtained, we describe a novel Actinomycetospora species, for which the name Actinomycetospora lemnae sp. nov. is proposed. The type strain is DW7H6T (TBRC 15165T, NBRC 115294T). Additionally, the duckweed-associated actinobacterium strain DW7H6T was able to enhance duckweed growth when compared to the control, in which the number of fronds and biomass dry weight were increased by up to 1.4 and 1.3 fold, respectively. Moreover, several plant-associated gene features in the genome of strain DW7H6T potentially involved in plant-microbe interactions were identified.