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The potential of seed endophytic microbes to enhance plant growth and resilience is well recognized, yet their role in alleviating cold stress in rice remains underexplored due to the complexity of these microbial communities. In this study, we investigated the diversity of seed endophytic microbes in two rice varieties, the cold-sensitive CB9 and the cold-tolerant JG117. Our results revealed significant differences in the abundance of Microbacteriaceae, with JG117 exhibiting a higher abundance under both cold stress and room temperature conditions compared to CB9. Further analysis led to the identification of a specific cold-tolerant microbe, Microbacterium testaceum M15, in JG117 seeds. M15-inoculated CB9 plants showed enhanced growth and cold tolerance, with a germination rate increase from 40 % to 56.67 % at 14℃ and a survival rate under cold stress (4℃) doubling from 22.67 % to 66.67 %. Additionally, M15 significantly boosted chlorophyll content by over 30 %, increased total protein by 16.31 %, reduced malondialdehyde (MDA) levels by 37.76 %, and increased catalase activity by 26.15 %. Overall, our study highlights the potential of beneficial endophytic microbes like M. testaceum M15 in improving cold tolerance in rice, which could have implications for sustainable agricultural practices and increased crop productivity in cold-prone regions., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier GmbH. All rights reserved.)

Strain MP-1014 T , an obligate halophilic actinobacterium, was isolated from the mangrove soil of Thandavarayancholanganpettai, Tamil Nadu, India. A polyphasic approach was utilized to explore its phylogenetic position completely. The isolate was Gram-positive, filamentous, non-motile, and coccoid in older cultures. Ideal growth conditions were seen at 30 °C and pH 7.0, with 5% NaCl (W/V), and the DNA G + C content was 73.3%. The phylogenic analysis of this strain based upon 16S rRNA gene sequence revealed 97-99.8% similarity to the recognized species of the genus Isoptericola. Strain MP-1014 T exhibits the highest similarity to I. sediminis JC619 T (99.7%), I. chiayiensis KCTC19740 T (98.9%), and subsequently to I. halotolerans KCTC19646 T (98.6%), when compared with other members within the Isoptericola genus (< 98%). ANI scores of strain MP-1014 T are 86.4%, 84.2%, and 81.5% and dDDH values are 59.7%, 53.6%, and 34.8% with I. sediminis JC619 T , I. chiayiensis KCTC19740 T and I. halotolerans KCTC19646 T respectively. The major polar lipids of the strain MP-1014 T were phosphatidylinositol, phosphatidylglycerol, diphosphotidylglycerol, two unknown phospholipids, and glycolipids. The predominant respiratory menaquinones were MK 9 (H 4 ) and MK 9 (H 2 ). The major fatty acids were anteiso-C 15:0 , anteiso-C 17:0 , iso-C 14:0 , C 15:0, and C 16:0 . Also, initial genome analysis of the organism suggests it as a biostimulant for enhancing agriculture in saline environments. Based on phenotypic and genetic distinctiveness, the strain MP-1014 T represents the novel species of the genus Isoptericola assigned Isoptericola haloaureus sp. nov., is addressed by the strain MP-1014 T , given its phenotypic, phylogenetic, and hereditary uniqueness. The type strain is MP-1014 T [(NCBI = OP672482.1 = GCA&#95;036689775.1) ATCC = BAA 2646 T ; DSMZ = 29325 T ; MTCC = 13246 T ]., (© 2024. The Author(s), under exclusive licence to Springer Nature Switzerland AG.)

An Actinobacteria - Kitasatospora sp. K002 - was isolated from the soil of Cerrado, a savanna-like Brazilian biome. Herein, we conducted a phylogenetic, phenotypic and physiological characterization, revealing its potential for biotechnological applications. Kitasatospora sp. K002 is an aerobic, non-motile, Gram-positive bacteria that forms grayish-white mycelium on solid cultures and submerged spores with vegetative mycelia on liquid cultures. The strain showed antibacterial activity against Bacillus subtilis, Pseudomonas aeruginosa and Escherichia coli. Genomic analysis indicated that Kitasatospora xanthocidica JCM 4862 is the closest strain to K002, with a dDDH of 32.8-37.8% and an ANI of 86.86% and the pangenome investigations identified a high number of rare genes. A total of 60 gene clusters of 22 different types were detected by AntiSMASH, and 22 gene clusters showed low similarity (< 10%) with known compounds, which suggests the potential production of novel bioactive compounds. In addition, phylogenetic analysis and morphophysiological characterization clearly distinguished Kitasatospora sp. K002 from other related species. Therefore, we propose that Kitasatospora sp. K002 should be recognized as a new species of the genus Kitasatospora - Kitasatospora brasiliensis sp. nov. (type strains = K002)., (© 2024. The Author(s) under exclusive licence to Sociedade Brasileira de Microbiologia.)

Prokaryotic Argonautes (pAgos) play a vital role in host defense by utilizing short nucleic acid guides to recognize and target complementary nucleic acids. Despite being the majority of pAgos, short pAgos have only recently received attention. Short pAgos are often associated with proteins containing an APAZ domain and a nuclease domain including DUF4365, SMEK, or HNH domain. In contrast to long pAgos that specifically cleave the target DNA, our study demonstrates that the short pAgo from Thermocrispum municipal, along with its associated DUF4365-APAZ protein, forms a heterodimeric complex. Upon RNA-guided target DNA recognition, this complex is activated to nonspecifically cleave DNA. Additionally, we found that the TmuRE-Ago complex shows a preference for 5'-OH guide RNA, specifically requires a uridine nucleotide at the 5' end of the guide RNA, and is sensitive to single-nucleotide mismatches between the guide RNA and target DNA. Based on its catalytic properties, our study has established a novel nucleic acid detection method and demonstrated its feasibility. This study not only expands our understanding of the defense mechanism employed by short pAgo systems but also suggests their potential applications in nucleic acid detection., (© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Patescibacteria, also known as the candidate phyla radiation (CPR), are a diverse group of bacteria that constitute a disproportionately large fraction of microbial dark matter. Its few cultivated members, belonging mostly to Saccharibacteria, grow as epibionts on host Actinobacteria. Due to a lack of suitable tools, the genetic basis of this lifestyle and other unique features of Patescibacteira remain unexplored. Here, we show that Saccharibacteria exhibit natural competence, and we exploit this property for their genetic manipulation. Imaging of fluorescent protein-labeled Saccharibacteria provides high spatiotemporal resolution of phenomena accompanying epibiotic growth, and a transposon-insertion sequencing (Tn-seq) genome-wide screen reveals the contribution of enigmatic Saccharibacterial genes to growth on their hosts. Finally, we leverage metagenomic data to provide cutting-edge protein structure-based bioinformatic resources that support the strain Southlakia epibionticum and its corresponding host, Actinomyces israelii, as a model system for unlocking the molecular underpinnings of the epibiotic lifestyle., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)

Atrazine is used to control broad-leaved weeds in farmland and has negative impacts on soybean growth. Legume-rhizobium symbiosis plays an important role in regulating abiotic stress tolerance of plants, however, the mechanisms of rhizobia regulate the tolerance of soybean to atrazine based on the biochemical responses of the plant-soil system are limited. In this experiment, Glycine max (L.) Merr. Dongnong 252, planted in 20 mg kg -1 of atrazine-contaminated soil, was inoculated with Bradyrhizobium japonicum AC20, and the plant growth, rhizosphere soil microbial diversity and the expression of the genes related to soybean carbon and nitrogen metabolism were assessed. The results indicated that strain AC20 inoculation alleviated atrazine-induced growth inhibition via increasing the contents of leghemoglobin and total nitrogen in soybean seedlings. The psbA gene expression level of the soybean seedlings that inoculated strain AC20 was 1.4 times than that of no rhizobium inoculating treatments. Moreover, the inoculated AC20 increased the abundance of Acidobacteria and Actinobacteria in soybean rhizosphere. Transcriptome analysis demonstrated that strain AC20 regulated the genes expression of amino acid metabolism and carbohydrate metabolism of soybean seedlings. Correlation analysis between 16S rRNA and transcriptome showed that strain AC20 reduced Planctomycetes abundance so as to down-regulated the expression of genes Glyma. 13G087800, Glyma. 12G005100 and Glyma.12G098900 involved in starch synthesis pathway of soybean leaves. These results provide available information for the rhizobia application to enhance the atrazine tolerate in soybean seedlings., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023. Published by Elsevier Masson SAS.)

Purpose: To determine the possible microbiome related to Vogt-Koyanagi-Harada (VKH) disease in comparison to patients with noninfectious anterior scleritis and healthy people., Methods: Fecal samples were extracted from 42 individuals, including 11 patients with active VKH, 11 healthy people, and 20 patients with noninfectious anterior scleritis. We amplified the V3 to V4 16S ribosomal DNA (rDNA) region to obtain the target sequence. Then, the target sequence was amplified by polymerase chain reaction. The obtained target sequences were sequenced by high-throughput 16S rDNA analysis., Results: At the genus level, there were three enriched (Stomatobaculum, Pseudomonas, Lachnoanaerobaculum) and two depleted (Gordonibacter, Slackia) microbes that were detected only in patients with VKH. There were 10 enriched and 12 depleted microbes that were observed in both patients with VKH disease and noninfectious anterior scleritis (P < 0.05). The interactions of these microbes were graphed. Tyzzerella and Eggerthella were the nodes of interaction between these microorganisms, which were regulated by both positive and negative aspects, but the expression level in patients with active VKH was upregulated., Conclusions: Special or nonspecial enrichment and decreased intestinal microbes were observed in patients with active VKH. The action mechanism of these microbes needs further study.

Nowadays, the worldwide agriculture is experiencing a transition process toward more sustainable production, which requires the reduction of chemical inputs and the preservation of microbiomes' richness and biodiversity. Plants are no longer considered as standalone entities, and the future of agriculture should be grounded on the study of plant-associated microorganisms and all their potentiality. Moreover, due to the climate change scenario and the resulting rising incidence of abiotic stresses, an innovative and environmentally friendly technique in agroecosystem management is required to support plants in facing hostile environments. Plant-associated microorganisms have shown a great attitude as a promising tool to improve agriculture sustainability and to deal with harsh environments. Several studies were carried out in recent years looking for some beneficial plant-associated microbes and, on the basis of them, it is evident that Actinomycetes and arbuscular mycorrhizal fungi (AMF) have shown a considerable number of positive effects on plants' fitness and health. Given the potential of these microorganisms and the effects of climate change, this review will be focused on their ability to support the plant during the interaction with abiotic stresses and on multi-omics techniques which can support researchers in unearthing the hidden world of plant-microbiome interactions. These associated microorganisms can increase plants' endurance of abiotic stresses through several mechanisms, such as growth-promoting traits or priming-mediated stress tolerance. Using a multi-omics approach, it will be possible to deepen these mechanisms and the dynamic of belowground microbiomes, gaining fundamental information to exploit them as staunch allies and innovative weapons against crop abiotic enemies threatening crops in the ongoing global climate change context.

WhiB7/WblC is a transcriptional factor of actinomycetes conferring intrinsic resistance to multiple translation-inhibitory antibiotics. It positively autoregulates its own transcription in response to the same antibiotics. The presence of a uORF and a potential Rho-independent transcription terminator in the 5' leader region has suggested a possibility that the whiB7/wblC gene is regulated via a uORF-mediated transcription attenuation. However, experimental evidence for the molecular mechanism to explain how antibiotic stress suppresses the attenuator, if any, and induces transcription of the whiB7/wblC gene has been lacking. Here we report that the 5' leader sequences of the whiB7/wblC genes in sub-clades of actinomycetes include conserved antiterminator RNA structures. We confirmed that the putative antiterminator in the whiB7/wblC leader sequences of both Streptomyces and Mycobacterium indeed suppresses Rho-independent transcription terminator and facilitates transcription readthrough, which is required for WhiB7/WblC-mediated antibiotic resistance. The antibiotic-mediated suppression of the attenuator can be recapitulated by amino acid starvation, indicating that translational inhibition of uORF by multiple signals is a key to induce whiB7/wblC expression. Our findings of a mechanism leading to intrinsic antibiotic resistance could provide an alternative to treat drug-resistant mycobacteria., (© 2021 John Wiley & Sons Ltd.)

Background: The native potatoes (Solanum tuberosum subsp. tuberosum L.) grown in Chile (Chiloé) represent a new, unexplored source of endophytes to find potential biological control agents for the prevention of bacterial diseases, like blackleg and soft rot, in potato crops., Result: The objective of this study was the selection of endophytic actinobacteria from native potatoes for antagonistic activity against Pectobacterium carotovorum subsp. carotovorum and Pectobacterium atrosepticum, and their potential to suppress tissue maceration symptoms in potato tubers. This potential was determined through the quorum quenching activity using a Chromobacterium violaceaum ATCC 12472 Wild type (WT) bioassay and its colonization behavior of the potato plant root system (S. tuberosum) by means of the Double labeling of oligonucleotide probes for fluorescence in situ hybridization (DOPE-FISH) targeting technique. The results showed that although Streptomyces sp. TP199 and Streptomyces sp. A2R31 were able to inhibit the growth of the pathogens, only the Streptomyces sp. TP199 isolate inhibited Pectobacterium sp. growth and diminished tissue maceration in tubers (p ≤ 0.05). Streptomyces sp. TP199 had metal-dependent acyl homoserine lactones (AHL) quorum quenching activity in vitro and was able to colonize the root endosphere 10 days after inoculation., Conclusions: We concluded that native potatoes from southern Chile possess endophyte actinobacteria that are potential agents for the disease management of soft rot and blackleg., (© 2021. The Author(s).)

The mortality rates of COVID-19 vary widely across countries, but the underlying mechanisms remain unelucidated. We aimed at the elucidation of relationship between gut microbiota and the mortality rates of COVID-19 across countries. Raw sequencing data of 16S rRNA V3-V5 regions of gut microbiota in 953 healthy subjects in ten countries were obtained from the public database. We made a generalized linear model (GLM) to predict the COVID-19 mortality rates using gut microbiota. GLM revealed that low genus Collinsella predicted high COVID-19 mortality rates with a markedly low p-value. Unsupervised clustering of gut microbiota in 953 subjects yielded five enterotypes. The mortality rates were increased from enterotypes 1 to 5, whereas the abundances of Collinsella were decreased from enterotypes 1 to 5 except for enterotype 2. Collinsella produces ursodeoxycholate. Ursodeoxycholate was previously reported to inhibit binding of SARS-CoV-2 to angiotensin-converting enzyme 2; suppress pro-inflammatory cytokines like TNF-α, IL-1β, IL-2, IL-4, and IL-6; have antioxidant and anti-apoptotic effects; and increase alveolar fluid clearance in acute respiratory distress syndrome. Ursodeoxycholate produced by Collinsella may prevent COVID-19 infection and ameliorate acute respiratory distress syndrome in COVID-19 by suppressing cytokine storm syndrome., Competing Interests: The authors have declared that no competing interests exist.

Saccharibacteria (TM7) are obligate epibionts living on the surface of their host bacteria and are strongly correlated with dysbiotic microbiomes during periodontitis and other inflammatory diseases, suggesting they are putative pathogens. However, due to the recalcitrance of TM7 cultivation, causal research to investigate their role in inflammatory diseases is lacking. Here, we isolated multiple TM7 species on their host bacteria from periodontitis patients. These TM7 species reduce inflammation and consequential bone loss by modulating host bacterial pathogenicity in a mouse ligature-induced periodontitis model. Two host bacterial functions involved in collagen binding and utilization of eukaryotic sialic acid are required for inducing bone loss and are altered by TM7 association. This TM7-mediated downregulation of host bacterial pathogenicity is shown for multiple TM7/host bacteria pairs, suggesting that, in contrast to their suspected pathogenic role, TM7 could protect mammalian hosts from inflammatory damage induced by their host bacteria., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2021 Elsevier Inc. All rights reserved.)

Curtobacterium sp. GD1 was isolated from leaves of conventionally grown soybean in Brazil. It was noteworthy that among all bacteria previously isolated from the same origin, only Curtobacterium sp. GD1 showed a strong chitinase activity. The enzyme was secreted and its production was induced by the presence of colloidal chitin in the medium. The chitinase was partially purified and characterized: molecular weight was approximately 37 kDa and specific activity 90.8 U/mg. Furthermore, Curtobacterium sp. GD1 genome was sequenced and analyzed. Our isolate formed a phylogenetic cluster with four other Curtobacterium spp. strains, with ANIb/ANIm ≥ 98%, representing a new, still non described Curtobacterium species. The circular genome visualization and comparison of genome sequences of strains forming new cluster indicated that most regions within their genomes were highly conserved. The gene associated with chitinase production was identified and the distribution pattern of glycosyl hydrolases genes was assessed. Also, genes associated with catabolism of structural carbohydrates such as oligosaccharides, mixed polysaccharides, plant and animal polysaccharides, as well as genes or gene clusters associated with resistance to antibiotics, toxic compounds and auxin biosynthesis subsystem products were identified. The abundance of putative glycosyl hydrolases in the genome of Curtobacterium sp. GD1 suggests that it has the tools for the hydrolysis of different polysaccharides. Therefore, Curtobacterium sp. GD1 isolated from soybean might be a bioremediator, biocontrol agent, an elicitor of the plant defense responses or simply degrader., Competing Interests: The authors have declared that no competing interests exist.

The enzyme dextranase is widely used in the sugar and food industries, as well as in the medical field. Most land-derived dextranases are produced by fungi and have the disadvantages of long production cycles, low tolerance to environmental conditions, and low safety. The use of marine bacteria to produce dextranases may overcome these problems. In this study, a dextranase-producing bacterium was isolated from the Rizhao seacoast of Shandong, China. The bacterium, denoted as PX02, was identified as Cellulosimicrobium sp. and its growing conditions and the production and properties of its dextranase were investigated. The dextranase had a molecular weight of approximately 40 kDa, maximum activity at 40°C and pH 7.5, with a stability range of up to 45°C and pH 7.0-9.0. High-performance liquid chromatography showed that the dextranase hydrolyzed dextranT20 to isomaltotriose, maltopentaose, and isomaltooligosaccharides. Hydrolysis by dextranase produced excellent antioxidant effects, suggesting its potential use in the health food industry. Investigation of the action of the dextranase on Streptococcus mutans biofilm and scanning electron microscopy showed that it to be effective both for removing and inhibiting the formation of biofilms, suggesting its potential application in the dental industry., (© 2021 Wiley-VCH GmbH.)

Many wastewater treatment plants around the world suffer from the operational problem of foaming. This is characterized by a persistent stable foam that forms on the aeration basin, which reduces effluent quality. The foam is often stabilized by a highly hydrophobic group of Actinobacteria known as the Mycolata 1 . Gordonia amarae is one of the most frequently reported foaming members 1 . With no currently reliable method for treating foams, phage biocontrol has been suggested as an attractive treatment strategy 2 . Phages isolated from related foaming bacteria can destabilize foams at the laboratory scale 3,4 ; however, no phage has been isolated that lyses G. amarae. Here, we assemble the complete genomes of G. amarae and a previously undescribed species, Gordonia pseudoamarae, to examine mechanisms that encourage stable foam production. We show that both of these species are recalcitrant to phage infection via a number of antiviral mechanisms including restriction, CRISPR-Cas and bacteriophage exclusion. Instead, we isolate and cocultivate an environmental ultrasmall epiparasitic bacterium from the phylum Saccharibacteria that lyses G. amarae and G. pseudoamarae and several other Mycolata commonly associated with wastewater foams. The application of this parasitic bacterium, 'Candidatus Mycosynbacter amalyticus', may represent a promising strategy for the biocontrol of bacteria responsible for stabilizing wastewater foams.

Phosphate solubilizing microorganisms widely exist in plant rhizosphere soil, but report about the P solubilization and multiple growth-promoting properties of rare actinomycetes are scarce. In this paper, a phosphate solubilizing Tsukamurella tyrosinosolvens P9 strain was isolated from the rhizosphere soil of tea plants. Phosphorus-dissolving abilities of this strain were different under different carbon and nitrogen sources, the soluble phosphorus content was 442.41 mg/L with glucose and potassium nitrate as nutrient sources. The secretion of various organic acids, such as lactic acid, maleic acid, oxalic acid, etc., was the main mechanism for P solubilization and pH value in culture was very significant negative correlation with soluble P content. In addition, this strain had multiple growth-promoting characteristics with 37.26 μg/mL of IAA and 72.01% of siderophore relative content. Under pot experiments, P9 strain improved obviously the growth of peanut seedlings. The bacterial communities of peanut rhizoshpere soil were assessed after inoculated with P9 strain. It showed that there was no significant difference in alpha-diversity indices between the inoculation and control groups, but the P9 treatment group changed the composition of bacterial communities, which increased the relative abundance of beneficial and functional microbes, which relative abundances of Chitinophagaceae at the family level, and of Flavihumibacter, Ramlibacter and Microvirga at the genus level, were all siginificant increased. Specially, Tsukamurella tyrosinosolvens were only detected in the rhizosphere of the inoculated group. This study not only founded growth-promoting properties of T. tyrosinosolvens P9 strain and its possible phosphate solublizing mechanism, but also expected to afford an excellent strain resource in biological fertilizers.

Aims: This study aimed to isolate actinomycetes from marine environments and examine their antifungal activity against Talaromyces marneffei both in vitro and in vivo., Methods and Results: Nineteen out of 101 actinomycete extracts were active and further determined for their minimum inhibitory concentrations (MIC). Three extracts of AMA50 that isolated from sediment showed strong antifungal activity against T. marneffei yeast (MICs ≤0·03-0·25 µg ml -1 ) and mould (MICs 0·5-16 µg ml -1 ) forms. The hexane extract from the cells of AMA50 (AMA50CH) exhibited the best activity against both the forms (MIC ≤ 1 µg ml -1 ). Three extracts from AMA50 killed the melanized yeast cells at 0·5 µg ml -1 . The AMA50CH was further tested for protective effects in Caenorhabditis elegans model. At concentrations of 1-8 µg ml -1 , the AMA50CH prolonged survival of T. marneffei-infected C. elegans with a 60-70% survival rate. The composition of AMA50CH was determined by gas chromatography-mass spectrometry. The major components were n-hexadecanoic acid, tetradecanoic acid and pentadecanoic acid. Sequencing analysis revealed that isolate AMA50 belonged to the genus Streptomyces., Conclusions: The AMA50CH from Streptomyces sp. AMA50 was the most effective extract against T. marneffei., Significance and Impact of the Study: Talaromyces marneffei is one of the most important thermally dimorphic pathogenic fungi. These results indicated the potency of marine-derived actinomycete extracts against T. marneffei both in vitro and in vivo., (© 2020 The Society for Applied Microbiology.)

An alkaliphilic actinomycete, designated HAJB-30  T , was isolated from a soda alkali-saline soil in Heilongjiang, Northeast China. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain HAJB-30  T was most closely related to type strains of the genus Phytoactinopolyspora with sequence similarities ranging between 93.5 and 98.9%. Strain HAJB-30  T grew at pH 8.0-11.0 (optimum pH 9.5-10.0) and in the presence of 0-7.0% NaCl (optimum 1.0-3.0%). Whole-cell hydrolysates of the isolate contained LL-diaminopimelic acid as the diagnostic diamino acid and mannose and rhamnose as diagnostic sugars. The major fatty acids identified were iso-C 14:0 , iso-C 15:0 , anteiso-C 15:0 , iso-C 16:0 and anteiso-C 17:0 , while the menaquinone was MK-9(H4). The genome (6,589,901 bp), composed of 50 contigs, had a G + C content of 66.8%. Out of the 6074 predicted genes, 6020 were protein-coding genes, and 54 were ncRNAs. Digital DNA-DNA hybridization (dDDH) estimation and average nucleotide identity (ANI) of strain HAJB-30  T against genomes of the type strains of related species in the same family ranged between 19.7 and 22.0% and between 71.5 and 76.8%, respectively. From these results, it was concluded that strain HAJB-30  T possesses sufficient characteristics differentiated from all recognized Phytoactinopolyspora species, it is considered to be a novel species for which the name Phytoactinopolyspora limicola sp. nov. is proposed. The type strain is HAJB-30  T (= CGMCC 4.7591  T , = JCM 33694  T ).

Three novel bacterial strains, HDW9A T , HDW9B T , and HDW9C T , isolated from the intestine of the diving beetles Cybister lewisianus and Cybister brevis, were characterized as three novel species using a polyphasic approach. The isolates were Gram-staining-positive, strictly aerobic, non-motile, and rod-shaped. They grew optimally at 30°C (pH 7) in the presence of 0.5% (wt/vol) NaCl. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that they belong to the genus Leucobacter and are closely related to L. denitrificans M1T8B10 T (98.4-98.7% sequence similarity). Average nucleotide identity (ANI) values among the isolates were 76.4-84.1%. ANI values for the isolates and the closest taxonomic species, L. denitrificans KACC 14055 T , were 72.3-73.1%. The isolates showed ANI values of < 76.5% with all analyzable Leucobacter strains in the EzBioCloud database. The genomic DNA G + C content of the isolates was 60.3-62.5%. The polar lipid components were phosphatidylglycerol, diphosphatidylglycerol, and other unidentified glycolipids, phospholipids, and lipids. The major cellular fatty acids were anteiso-C 15:0 , iso-C 16:0 , and anteiso-C 17:0 . MK-10 was the major respiratory quinone, and MK-7 and MK-11 were the minor respiratory quinones. The whole-cell sugar components of the isolates were ribose, glucose, galactose, and mannose. The isolates harbored L-2,4-diaminobutyric acid, L-serine, L-lysine, L-aspartic acid, glycine, and D-glutamic acid within the cell wall peptidoglycan. Based on phylogenetic, phenotypic, chemotaxonomic, and genotypic analyses, strains HDW9A T , HDW9B T , and HDW9C T represent three novel species within the genus Leucobacter. We propose the name Leucobacter coleopterorum sp. nov. for strain HDW9A T (= KACC 21331 T = KCTC 49317 T = JCM 33667 T ), the name Leucobacter insecticola sp. nov. for strain HDW9B T (= KACC 21332 T = KCTC 49318 T = JCM 33668 T ), and the name Leucobacter viscericola sp. nov. for strain HDW9C T (= KACC 21333 T = KCTC 49319 T = JCM 33669 T ).

Sugarcane ratoon stunting disease (RSD) caused by Leifsonia xyli subsp. xyli (Lxx) is a common destructive disease that occurs around the world. Lxx is an obligate pathogen of sugarcane, and previous studies have reported some physiological responses of RSD-affected sugarcane. However, the molecular understanding of sugarcane response to Lxx infection remains unclear. In the present study, transcriptomes of healthy and Lxx-infected sugarcane stalks and leaves were studied to gain more insights into the gene activity in sugarcane in response to Lxx infection. RNA-Seq analysis of healthy and diseased plants transcriptomes identified 107,750 unigenes. Analysis of these unigenes showed a large number of differentially expressed genes (DEGs) occurring mostly in leaves of infected plants. Sugarcane responds to Lxx infection mainly via alteration of metabolic pathways such as photosynthesis, phytohormone biosynthesis, phytohormone action-mediated regulation, and plant-pathogen interactions. It was also found that cell wall defense pathways and protein phosphorylation/dephosphorylation pathways may play important roles in Lxx pathogeneis. In Lxx-infected plants, significant inhibition in photosynthetic processes through large number of differentially expressed genes involved in energy capture, energy metabolism and chloroplast structure. Also, Lxx infection caused down-regulation of gibberellin response through an increased activity of DELLA and down-regulation of GID1 proteins. This alteration in gibberellic acid response combined with the inhibition of photosynthetic processes may account for the majority of growth retardation occurring in RSD-affected plants. A number of genes associated with plant-pathogen interactions were also differentially expressed in Lxx-infected plants. These include those involved in secondary metabolite biosynthesis, protein phosphorylation/dephosphorylation, cell wall biosynthesis, and phagosomes, implicating an active defense response to Lxx infection. Considering the fact that RSD occurs worldwide and a significant cause of sugarcane productivity, a better understanding of Lxx resistance-related processes may help develop tools and technologies for producing RSD-resistant sugarcane varieties through conventional and/or molecular breeding., Competing Interests: No authors have competing interests.

Breast cancer is the second leading cause of cancer-related mortality in women. Various nutritional compounds possess anti-carcinogenic properties which may be mediated through their effects on the gut microbiota and its production of short-chain fatty acids (SCFAs) for the prevention of breast cancer. We evaluated the impact of broccoli sprouts (BSp), green tea polyphenols (GTPs) and their combination on the gut microbiota and SCFAs metabolism from the microbiota in Her2/neu transgenic mice that spontaneously develop estrogen receptor-negative [ER(-)] mammary tumors. The mice were grouped based on the dietary treatment: control, BSp, GTPs or their combination from beginning in early life (BE) or life-long from conception (LC). We found that the combination group showed the strongest inhibiting effect on tumor growth volume and a significant increase in tumor latency. BSp treatment was integrally more efficacious than the GTPs group when compared to the control group. There was similar clustering of microbiota of BSp-fed mice with combination-fed mice, and GTPs-fed mice with control-fed mice at pre-tumor in the BE group and at pre-tumor and post-tumor in the LC group. The mice on all dietary treatment groups incurred a significant increase of Adlercreutzia, Lactobacillus genus and Lachnospiraceae, S24-7 family in the both BE and LC groups. We found no change in SCFAs levels in the plasma of BSp-fed, GTPs-fed and combination-fed mice of the BE group. Marked changes were observed in the mice of the LC group consisting of significant increases in propionate and isobutyrate in GTPs-fed and combination-fed mice. These studies indicate that nutrients such as BSp and GTPs differentially affect the gut microbial composition in both the BE and LC groups and the key metabolites (SCFAs) levels in the LC group. The findings also suggest that temporal factors related to different time windows of consumption during the life-span can have a promising influence on the gut microbial composition, SCFAs profiles and ER(-) breast cancer prevention., Competing Interests: The authors have declared that no competing interests exist.

The use of actinomycetes for improving soil fertility and plant production is an attractive strategy for developing sustainable agricultural systems due to their effectiveness, eco-friendliness, and low production cost. Out of 17 species isolated from the soil rhizosphere of legume crops, 4 bioactive isolates were selected and their impact on 5 legumes: soybean, kidney bean, chickpea, lentil, and pea were evaluated. According to the morphological and molecular identification, these isolates belong to the genus Streptomyces. Here, we showed that these isolates increased soil nutrients and organic matter content and improved soil microbial populations. At the plant level, soil enrichment with actinomycetes increased photosynthetic reactions and eventually increased legume yield. Actinomycetes also increased nitrogen availability in soil and legume tissue and seeds, which induced the activity of key nitrogen metabolizing enzymes, e.g., glutamine synthetase, glutamate synthase, and nitrate reductase. In addition to increased nitrogen-containing amino acids levels, we also report high sugar, organic acids, and fatty acids as well as antioxidant phenolics, mineral, and vitamins levels in actinomycete treated legume seeds, which in turn improved their seed quality. Overall, this study shed the light on the impact of actinomycetes on enhancing the quality and productivity of legume crops by boosting the bioactive primary and secondary metabolites. Moreover, our findings emphasize the positive role of actinomycetes in improving the soil by enriching its microbial population. Therefore, our data reinforce the usage of actinomycetes as biofertilizers to provide sustainable food production and achieve biosafety.

Here we analyze the microbial community of healthy and diseased tomato plants to evaluate its impact on plant health. The organisms found in all samples mainly belonged to 4 phyla: Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. The Proteobacteria were the highest relative abundant within the endophytic communities of different plant organs of diseased tomato. Among endophytic bacteria of tomato, only a few taxa could be cultured. Here we showed that only a few taxa of bacteria inhabiting tomato plants could be cultured and that all plant organs have a highly diverse endophytic bacterial, whose activity might affect plant growth and development as well as health. The roots seem to be an important barrier for microbes and leaves appear to be the organs with the higher diversity which is incidentally related to plant health. Fruits also contain a complex bacterial community that appeared to be unaffected by foliar diseases such as gray leaf spot at least under the conditions studied.

Fungus-growing attine ants are under constant threat from fungal pathogens such as the specialized mycoparasite Escovopsis, which uses combined physical and chemical attack strategies to prey on the fungal gardens of the ants. In defence, some species assemble protective microbiomes on their exoskeletons that contain antimicrobial-producing Actinobacteria. Underlying this network of mutualistic and antagonistic interactions are an array of chemical signals. Escovopsis weberi produces the shearinine terpene-indole alkaloids, which affect ant behaviour, diketopiperazines to combat defensive bacteria, and other small molecules that inhibit the fungal cultivar. Pseudonocardia and Streptomyces mutualist bacteria produce depsipeptide and polyene macrolide antifungals active against Escovopsis spp. The ant nest metabolome is further complicated by competition between defensive bacteria, which produce antibacterials active against even closely related species., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

Background: Numerous studies have reported the health-promoting effects of exopolysaccharides (EPSs) in in vitro models; however, a functional evaluation of EPSs will provide additional knowledge of EPS-microbe interactions by in vivo intestinal microbial model. In the present study, high-throughput amplicon sequencing, short-chain fatty acid (SCFAs) and intestinal inflammation evaluation were performed to explore the potential benefits of exopolysaccharides (EPSs) and EPS-producing Lactobacillus (HNUB20 group) using the healthy zebrafish (Danio rerio) model., Results: The results based on microbial taxonomic analysis revealed that the abundance of four genera, Ochrobactrum, Sediminibacterium, Sphingomonas and Sphingobium, were increased in the control group in comparison to HNUB20 group. Pelomonas spp. levels were significantly higher and that of the genera Lactobacillus and Brachybacterium were significantly decreased in EPS group compared with control group. PICRUSt based functional prediction of gut microbiota metabolic pathways indicated that significantly lower abundance was found for transcription, and membrane transport, whereas folding, sorting and degradation and energy metabolism had significantly higher abundance after HNUB20 treatment. Two metabolic pathways, including metabolism and endocrine functions, were more abundant in the EPS group than control group. Similar to the HNUB20 group, transcription was also decreased in the EPS group compared with the control group. However, SCFAs and immune indexes indicated EPS and HNUB20 performed limited efficacy in the healthy zebrafish., Conclusions: The present intestinal microbial model-based study indicated that EPSs and high-yield EPS-producing Lactobacillus can shake the structure of intestinal microbiota, but cannot change SCFAs presence and intestinal inflammation.

Fungal-bacterial associations are present in nature, playing important roles in ecological, evolutionary and medicinal processes. Here we report a fungus-bacterial symbiont from marine sediment. The bacterium lives inside the fungal mycelium yet is robust enough to survive independent of its host; the independently grown bacterium can infect the fungal host in vitro and continue to grow progenitively. The bacterial symbiont modulates the fungal host to biosynthesize a polyketide antimicrobial, spiromarmycin. Spiromarmycin appears to endow upon the symbiont pair a protective/defensive means of warding off competitor organisms, be they prokaryotic or eukaryotic microorganisms. Genomic analyses revealed the spiromarmycin biosynthetic machinery to be encoded, not by the bacterium, but rather the fungal host. This unique fungal-bacterial symbiotic relationship and the molecule/s resulting from it dramatically expand our knowledge of marine microbial diversity and shed important insights into endosymbionts and fungal-bacterial relationships.

The bacterial pathogen Pseudomonas tolaasii severely damages white button mushrooms by secretion of the pore-forming toxin tolaasin, the main virulence factor of brown blotch disease. Yet, fungus-associated helper bacteria of the genus Mycetocola ( Mycetocola tolaasinivorans and Mycetocola lacteus ) may protect their host by an unknown detoxification mechanism. By a combination of metabolic profiling, imaging mass spectrometry, structure elucidation, and bioassays, we found that the helper bacteria inactivate tolaasin by linearizing the lipocyclopeptide. Furthermore, we found that Mycetocola spp. impair the dissemination of the pathogen by cleavage of the lactone ring of pseudodesmin. The role of pseudodesmin as a major swarming factor was corroborated by identification and inactivation of the corresponding biosynthetic gene cluster. Activity-guided fractionation of the Mycetocola proteome, matrix-assisted laser desorption/ionization (MALDI) analyses, and heterologous enzyme production identified the lactonase responsible for toxin cleavage. We revealed an antivirulence strategy in the context of a tripartite interaction that has high ecological and agricultural relevance., Competing Interests: The authors declare no competing interest., (Copyright © 2020 the Author(s). Published by PNAS.)

Actinobacteria produce antibacterial and antifungal specialized metabolites. Many insects harbour actinobacteria on their bodies or in their nests and use these metabolites for protection. However, some actinobacteria produce metabolites that are toxic to insects and the evolutionary relevance of this toxicity is unknown. Here we explore chemical interactions between streptomycetes and the fruit fly Drosophila melanogaster. We find that many streptomycetes produce specialized metabolites that have potent larvicidal effects against the fly; larvae that ingest spores of these species die. The mechanism of toxicity is specific to the bacterium's chemical arsenal: cosmomycin D producing bacteria induce a cell death-like response in the larval digestive tract; avermectin producing bacteria induce paralysis. Furthermore, low concentrations of volatile terpenes like 2-methylisoborneol that are produced by streptomycetes attract fruit flies such that they preferentially deposit their eggs on contaminated food sources. The resulting larvae are killed during growth and development. The phenomenon of volatile-mediated attraction and specialized metabolite toxicity suggests that some streptomycetes pose an evolutionary risk to insects in nature.

Soil-dwelling animals are at risk of pathogen infection in soils. When choosing nesting sites, animals could reduce this risk by avoiding contact with pathogens, yet there is currently little evidence. We tested this hypothesis using Solenopsis invicta as a model system. Newly mated queens of S. invicta were found to nest preferentially in soil containing more actinobacteria of Streptomyces and Nocardiopsis and to be attracted to two volatiles produced by these bacteria, geosmin and 2-methylisoborneol. Actinobacteria-rich soil was favored by S. invicta and this soil contained fewer putative entomopathogenic fungi than adjacent areas. Queens in such soil benefited from a higher survival rate. In culture, isolated actinobacteria inhibited entomopathogenic fungi, suggested that their presence may reduce the risk of fungal infection. These results indicated a soil-dwelling ant may choose nest sites presenting relatively low pathogen risk by detecting the odors produced by bacteria with anti-fungal properties., Competing Interests: The authors have declared that no competing interests exist.

Marine obligate actinobacteria produce a wide variety of secondary metabolites with biological activity, notably those with antibiotic activity urgently needed against multi-drug-resistant bacteria. Seventy-five marine actinobacteria were isolated from a marine sediment sample collected in Punta Arena de La Ventana, Baja California Sur, Mexico. The 16S rRNA gene identification, Multi Locus Sequence Analysis, and the marine salt requirement for growth assigned seventy-one isolates as members of the genus Salinispora , grouped apart but related to the main Salinispora arenicola species clade. The ability of salinisporae to inhibit bacterial growth of Staphylococcus epidermidis, Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacer baumannii, Pseudomonas aeruginosa , and Enterobacter spp. was evaluated by cross-streaking plate and supernatant inhibition tests. Ten supernatants inhibited the growth of eight strains of S. epidermidis from patients suffering from ocular infections, two out of the eight showed growth inhibition on ten S. epidermidis strains from prosthetic joint infections. Also, it inhibited the growth of the remaining six multi-drug-resistant bacteria tested. These results showed that some Salinispora strains could produce antibacterial compounds to combat bacteria of clinical importance and prove that studying different geographical sites uncovers untapped microorganisms with metabolic potential., Competing Interests: Conflict of interest The authors do not report any financial or personal connections with other persons or organizations, which might negatively affect the contents of this publication and/or claim authorship rights to this publication., (© 2020 Luis Contreras-Castro et al.)

Salt stress negatively affects growth and development of plants. However, it is hypothesized that plant growth-promoting endophytic bacteria can greatly alleviate the adverse effects of salinity and can promote growth and development of plants. In the present research, we aimed to isolate endophytic bacteria from halotolerant plants and evaluate their capacity for promoting crop plant growth. The bacterial endophytes were isolated from selected plants inhabiting sand dunes at Pohang beach, screened for plant growth-promoting traits and applied to rice seedlings under salt stress (NaCl; 150 mm). Out of 59 endophytic bacterial isolates, only six isolates, i.e. Curtobacterium oceanosedimentum SAK1, Curtobacterium luteum SAK2, Enterobacter ludwigii SAK5, Bacillus cereus SA1, Micrococcus yunnanensis SA2, Enterobacter tabaci SA3, resulted in a significant increase in the growth of Waito-C rice. The cultural filtrates of bacterial endophytes were tested for phytohormones, including indole-3-acetic acid, gibberellins and organic acids. Inoculation of the selected strains considerably reduced the amount of endogenous ABA in rice plants under NaCl stress, however, they increased GSH and sugar content. Similarly, these strains augmented the expression of flavin monooxygenase (OsYUCCA1) and auxin efflux carrier (OsPIN1) genes under salt stress. In conclusion, the pragmatic application of the above selected bacterial strains alleviated the adverse effects of NaCl stress and enhanced rice growth attributes by producing various phytohormones., (© 2020 German Society for Plant Sciences and The Royal Botanical Society of the Netherlands.)

Continuous cropping of tomato is increasingly practiced in greenhouse cultivation, leading to several soil-related obstacles. In this study, a type of microbial restoration substrate (MRS) was used to amend soils from the re-cropping of tomato for 8 years under greenhouse-cultivated conditions. Two treatments were established: using 1,500 kg hm -2 of MRS to amend soil as treatment (TR), and non-MRS as control (CK). The severity of bacterial wilt (BW), soil properties and rhizobacterial community composition under two different treatments were compared. The application of MRS led to an average 83.75% reduction in the severity of BW, and significantly increased the plant height, root activity and yield. Meanwhile, soil pH, soil organic contents (SOC), total nitrogen (TN) and exchangeable calcium were significantly increased (P < 0.05) by MRS treatment. Illumina-MiSeq sequencing analysis of the 16S rRNA genes revealed that MRS increased the diversity of the tomato rhizobacterial community. The relative abundances of Proteobacteria, Actinobacteria and Bacteroidetes were enhanced, whereas those of Acidobacteria, Chloroflexi, TM7 and Firmicutes were decreased by MRS. The redundancy analysis (RDA) revealed that the severity of tomato BW was negatively correlated with the relative abundances of Actinobacteria, Bacteroidetes and Proteobacteria, but positively correlated with those of Gemmatimonadetes, Firmicutes and Acidobacteria. In addition, the effects of MRS on rhizobacterial metabolic potentials were predicted using a Kyoto Encyclopedia of Genes and Genomes (KEGG) database, implying that MRS could significantly increase nitrogen metabolisms and reduce carbon metabolism. Together, our results indicated that the use of MRS could reestablish soil microbial communities, which was beneficial to plant health compared with the control.

It is now recognized that some diseases of aquatic animals are attributed to polymicrobial pathogens infection. Thus, the traditional view of "one pathogen, one disease" might mislead the identification of multiple pathogens, which in turn impedes the design of probiotics. To address this gap, we explored polymicrobial pathogens based on the origin and timing of increased abundance over shrimp white feces syndrome (WFS) progression. OTU70848 Vibrio fluvialis, OTU35090 V. coralliilyticus, and OTU28721 V. tubiashii were identified as the primary colonizers, whose abundances increased only in individuals that eventually showed disease signs but were stable in healthy subjects over the same timeframe. Notably, the random Forest model revealed that the profiles of the three primary colonizers contributed an overall 91.4% of diagnosing accuracy of shrimp health status. Additionally, NetShift analysis quantified that the three primary colonizers were important "drivers" in the gut microbiotas from healthy to WFS shrimp. For these reasons, the primary colonizers were potential pathogens that contributed to the exacerbation of WFS. By this logic, we further identified a few "drivers" commensals in healthy individuals, such as OUT50531 Demequina sediminicola and OTU&#95;74495 Ruegeria lacuscaerulensis, which directly antagonized the three primary colonizers. The predicted functional pathways involved in energy metabolism, genetic information processing, terpenoids and polyketides metabolism, lipid and amino acid metabolism significantly decreased in diseased shrimp compared with those in healthy cohorts, in concordant with the knowledge that the attenuations of these functional pathways increase shrimp sensitivity to pathogen infection. Collectively, we provide an ecological framework for inferring polymicrobial pathogens and designing antagonized probiotics by quantifying their changed "driver" feature that intimately links shrimp WFS progression. This approach might generalize to the exploring disease etiology for other aquatic animals.

The actinomycetes are Gram-positive bacteria belonging to the order Actinomycetales within the phylum Actinobacteria . They include members with significant economic and medical importance, for example filamentous actinomycetes such as Streptomyces species, which have a propensity to produce a plethora of bioactive secondary metabolites and form symbioses with higher organisms, such as plants and insects. Studying these bacteria is challenging, but also fascinating and very rewarding. As a Microbiology Society initiative, members of the actinomycete research community have been developing a Wikipedia-style resource, called ActinoBase, the purpose of which is to aid in the study of these filamentous bacteria. This review will highlight 10 publications from 2019 that have been of special interest to the ActinoBase community, covering 4 major components of actinomycete research: (i) development and regulation; (ii) specialized metabolites; (iii) ecology and host interactions; and (iv) technology and methodology.

The endophytic actinobacteria constitute a diverse community which has vast potential importance that may be exploited in pharmaceutical, agricultural, and biotechnological industries. However, the effects of seasonal changes on distribution of endophytic actinobacteria in medicinal plants of Meghalaya are largely uncharacterized. Here, we investigated host and seasonal influence on diversity of endophytic actinobacteria residing in roots of six medicinal plant species of Meghalaya. A total of 493 cultivable endophytic actinobacterial isolates representing 41 species were obtained from root segments of six plant species which had been collected during four different seasons of 2011-2012 and 2012-2013. Among the host plant species, maximum actinobacterial colonization was observed in Costus speciosus and minimum in Potentilla fulgens. In regard to seasons, the highest actinobacterial colonization and relative abundance were observed during summer season and least was recorded during the winter season. It was ascertained that though endophytic actinobacteria have varying capacity to colonize in different plant species during the seasons, colonization is not found to be species-specific. Culture-independent attempt also inferred that actinobacterial community varied amongst the six medicinal plants during the different seasons. Hence, seasons are influential factors in the colonization capacity of endophytic actinobacterial community. Furthermore, plant growth-promoting activities were recorded in 34.15% of the isolates. Hence, these results indicate that endophytic actinobacteria from the selected medicinal plants also represent an important source of plant growth-promoting bioactive metabolites.

Eggerthella lenta is an emerging and uncommon human pathogen that has been under recognized due to the limitations of phenotypic identification. Here we describe two cases of bacteremia caused by E. lenta and summarize the results of antimicrobial susceptibility testing according to some previous literatures, which illustrate the importance of identification and treatment of unusual organisms. The most reliable antibiotic treatment options to E. lenta appear to be metronidazole, amoxicillin-clavulanate, carbapenems, vancomycin, cefoxitin, chloramphenicol and clindamycin.

This article details emerging infectious diseases that have devastating impacts on captive and wild squamates. Treatment advances have been attempted for Cryptosporidium infections in squamates. Gram-positive bacteria, Devriesea agamarum and Austwickia chelonae, are contributing to severe disease in captive and now in wild reptiles, some critically endangered. Nannizziposis, Paranannizziopsis, and Ophidiomyces continue to cause fatal disease as primary pathogens in wild and captive populations of squamates and sphenodontids. Nidovirus, bornavirus, paramyxovirus, sunshine virus, and arenavirus have emerged to be significant causes of neurorespiratory disease in snakes. Controlled studies evaluating environmental stability, disinfection, transmission control, and treatment are lacking., Competing Interests: Disclosure The authors have nothing to disclose., (Copyright © 2020 Elsevier Inc. All rights reserved.)

Bacterial vaginosis (BV) is the most common vaginal infection among women of reproductive age. A hallmark of BV is the presence of a highly structured polymicrobial biofilm on the vaginal epithelium, presumably initiated by facultative anaerobes of the genus Gardnerella , which then becomes a scaffold for other species to adhere to. One of the species often found incorporated in Gardnerella mediated biofilms is Atopobium vaginae . Interestingly, A. vaginae is very rarely found without the presence of Gardnerella . However, not much is known regarding the interactions between A. vaginae and Gardnerella species. This study assessed biological interactions between Gardnerella vaginalis and A. vaginae . In our in vitro model, by using specific Gardnerella and A. vaginae Peptide Nucleic Acid (PNA)-Fluorescence In Situ Hybridization (FISH) probes, we confirmed that A. vaginae was able to incorporate a pre-formed G. vaginalis biofilm, accounting for up to 20% of the total number of biofilm cells. However, our findings showed that almost 92% of A. vaginae cells lost viability after 48 h of mono-species planktonic growth, but were able to maintain viability when co-cultured with Gardnerella or after pre-conditioning with cell-free supernatant of Gardnerella cultures. While the in vitro conditions are very different from the in vivo microenvironment, this study contributes to a better understanding of why A. vaginae vaginal colonization rarely occurs in the absence of Gardnerella . Overall, this highlights the importance of microbial interactions between BV-associated bacteria and demands more studies focused on the polymicrobial bacterial communities found in BV., (Copyright © 2020 Castro, Rosca, Cools, Vaneechoutte and Cerca.)

Although infrequent in our laboratory, growth of bacterial colonies has been observed on top of the purified cultures of yeasts. In this study, the likelihood of bacterial excision from yeast under aging and starvation stresses was assessed using 10 gastric and 10 food-borne yeasts. Yeasts were identified as members of Candida or Saccharomyces genus by amplification and sequencing of D1/D2 region of 26S rDNA. For aging stress, yeasts were cultured on brain heart infusion agar supplemented with sheep blood and incubated at 30 °C for 3-4 weeks. For starvation stress, yeasts were inoculated into distilled water and incubated similarly. After seven days, starved yeasts were cultured on yeast extract glucose agar, incubated similarly and examined daily for appearance of bacterial colonies on top of the yeast's growth. Outgrowth of excised bacteria was observed on top of the cultures of 4 yeasts (Y1, Y3, Y13 and Y18) after 3-7 days. The excised bacteria (B1, B3, B13 and B18) were isolated and identified at the genus level according to their biochemical characteristics as well as amplification and sequencing of 16S rDNA. B1 (Arthrobacter) were excised from Y1 (Candida albicans) upon aging and B3 (Staphylococcus), B13 (Cellulomonas) and B18 (Staphylococcus) were excised from their respective yeasts; Y3 (Candida tropicalis), Y13 (Saccharomyces cerevisiae) and Y18 (Candida glabrata) upon starvation. DNA from yeasts was used for detection of 16S rDNA of their intracellular bacteria and sequencing. Amplified products from yeasts showed sequence similarity to those of excised bacteria. Under normal conditions, yeast exerts tight control on multiplication of its intracellular bacteria. However, upon aging and starvation the control is no longer effective and bacterial outgrowth occurs. Unlimited multiplication of excised bacteria might provide yeast with plenty of food in close vicinity. This could be an evolutionary dialogue between yeast and bacteria that ensures the survival of both partners., Competing Interests: Declaration of Competing Interest None., (Copyright © 2019 Elsevier B.V. All rights reserved.)

Leifsonia xyli subsp. xyli (Lxx) colonizes the xylem vessels of sugarcane, a plant niche where microorganisms are highly exposed to oxidative and osmotic stresses. This study performed an in silico analysis of the genome of Lxx and characterized 16 genes related to the detoxification of oxidative species (peroxidases, O 2 - dismutases, and methionine reductases) and to the production and transport of osmolytes and analyzed their expression in vitro after 30, 60, and 120 min of exposure to H 2 O 2 or PEG. The PAGE activity of superoxide dismutase (Mn-SOD as confirmed by inhibition tests) and of catalase (CAT) and the accumulation of trehalose were also assessed. Exposure to H 2 O 2 increased the expression of most oxidative-responsive genes and decreased the expression of those related to osmotic responses, whereas the opposite occurred after exposure to PEG. The isoform profiles of CAT and Mn-SOD shifted in response to H 2 O 2 but not to PEG and Lxx cells accumulated more trehalose over time after exposure to PEG compared with non-exposed cells. The experimental results validated the in silico analysis and indicated that this obligate endophytic parasite has multiple and functional mechanisms to combat the stresses imposed by its host.

Background: Increased antibiotic resistant properties of pathogens has led to a pronounced search for new effective antibiotics from microbes in diverse ecological niches. This study focused on isolating actinomycetes from soil of reserved areas and profiling them for antibacterial potentials., Methods: The isolates (IS-2, IS-4, IS-6, IS-10, IS-14) were assessed for antagonistic activity against ten multi-drug resistant bacterial strains (Gram positive and negative) by cross streak and well diffusion methods., Results: During the primary screening, four of the isolates showed good antagonistic activity against the test strains. Notably, all the bacterial strains except Pseudomonas aeruginosa responded sensitively to at least one of the actinomycetes screened. The crude extracts of the secondary metabolites of the four actinomycetes (IS-2, IS-4, IS-6, IS-10) with considerably significant antagonistic activities inhibited the growth of all the bacterial strains efficiently. All the test bacterial strains were sensitive to at least one of the extracts at a concentration of 100µg/ml. The minimum inhibitory concentration of the extracts against the isolates ranged from 12.5 - 25µg/ml. The crude extracts of IS-4 and IS-6 identified as Streptomyces glauciniger NBRC 100913 and Streptomyces griseoplanus NRRL-ISP 5009 by I6s rRNA sequencing, showed higher antibacterial activities against the bacterial strains. Significantly, the ethyl acetate crude extract of the actinomycetes demonstrated better antibacterial activities than the standard antibiotics (ofloxacin, amoxicillin/clavulanate, cefuroxime and ceftriaxone)., Conclusion: This study reports remarkable anti-MRSA activities as well as broad spectrum antibacterial potentials of extracts of Streptomyces spp. worthy of further exploration., (© 2020 Ahmed RN, et al.)

The white leg Litopenaeus vannamei shrimp is of importance to the eastern Pacific fisheries and aquaculture industry but suffer from diseases such as the recently emerged early mortality syndrome. Many bacterial pathogens have been identified but the L. vannamei microbiota is still poorly known. Using a next-generation sequencing (NGS) approach, this work evaluated the impact of the inclusion in the diet of mannan oligosaccharide, (MOS, 0.5% w/w), over the L. vannamei microbiota and production behavior of L. vannamei under intensive cultivation in Ecuador. The MOS supplementation lasted for 60 days, after which the shrimp in the ponds were harvested, and the production data were collected. MOS improved productivity outcomes by increasing shrimp survival by 30%. NGS revealed quantitative differences in the shrimp microbiota between MOS and control conditions. In the treatment with inclusion of dietary MOS, the predominant phylum was Actinobacteria (28%); while the control group was dominated by the phylum Proteobacteria (30%). MOS has also been linked to an increased prevalence of Lactococcus- and Verrucomicrobiaceae-like bacteria. Furthermore, under the treatment of MOS, the prevalence of potential opportunistic pathogens, like Vibrio, Aeromonas, Bergeyella and Shewanella, was negligible. This may be attributable to MOS blocking the adhesion of pathogens to the surfaces of the host tissues. Together, these findings point to the fact that the performance (survival) improvements of the dietary MOS may be linked to the impact on the microbiota, since bacterial lines with pathogenic potential towards shrimps were excluded in the gut.

A multiplex real-time PCR method based on fluorescent TaqMan® probes was developed for the simultaneous detection of the tomato pathogenic bacteria Clavibacter michiganensis subsp. michiganensis, Pseudomonas syringae pv. tomato and bacterial spot-causing xanthomonads. The specificity of the multiplex assay was validated on 44 bacterial strains, including 32 target pathogen strains as well as closely related species and nontarget tomato pathogenic bacteria. The designed multiplex real-time PCR showed high sensitivity when positive amplification was observed for one pg of bacterial DNA in the cases of Clavibacter michiganensis subsp. michiganensis and Pseudomonas syringae pv. tomato bacteria and 100 pg for bacterial spot-causing xanthomonads. The reliability of the developed multiplex real-time PCR assay for in planta detection was verified by recognition of the target pathogens in 18 tomato plants artificially inoculated by each of the target bacteria and tomato samples from production greenhouses., Competing Interests: The authors have declared that no competing interests exist.

The aim of this study was identification features of cultivation representatives of genus Acanthamoeba isolated from bentonite using Cellulosimicrobium sp. as a bacteria-feeders. Identification of isolated bacteria was conducted by morphological, cultural and molecular-genetic methods. The cultivation of free-living „bentonite” amoeba on the lawn of Cellulosimicrobium sp. have gained significant advantages than using Escherichia coli as a bacteriafeeders was shown. “Bentonite” amoeba form crateroid plaques, which fit to the quantitative characteristic materials which contains amoeba, during deep co-cultivation Acanthamoeba sp. and Cellulosimicrobium sp. on 1% glucose meet-peptone agar.

A polyphasic study was undertaken to establish the taxonomic status of three Modestobacter strains isolated from a high altitude Atacama Desert soil. The isolates, strains 1G6 T , 1G14 and 1G50, showed chemotaxonomic and morphological properties characteristic of members of the genus Modestobacter. The peptidoglycan contained meso-diaminopimelic acid, the whole cell sugars were glucose and ribose (diagnostic sugars) and arabinose, the predominant menaquinone was MK-9(H 4 ), polar lipid patterns contained diphosphatidylglycerol, glycophosphatidylinositol, phosphatidylethanolamine (diagnostic component), phosphatidylglycerol and phosphatidylinositol while whole cellular fatty acid profiles consisted of complex mixtures of saturated, unsaturated iso- and anteiso-components. The isolates were shown to have different BOX-PCR fingerprint and physiological profiles. They formed a distinct phyletic line in Modestobacter 16S rRNA gene trees, were most closely related to the type strain of Modestobacter italicus (99.9 % similarity) but were distinguished from this and other closely related Modestobacter type strains using a combination of phenotypic properties. Average nucleotide identity and digital DNA:DNA hybridization similarities between the draft genome sequences of isolate 1G6 T and M. italicus BC 501 T were 90.9 % and 42.3 %, respectively, indicating that they belong to different species. Based on these phenotypic and genotypic data it is proposed that the isolates be assigned to a novel species in the genus Modestobacter, namely as Modestobacter excelsi with isolate 1G6 T (=DSM 107535 T =PCM 3004 T ) as the type strain. Analysis of the whole genome sequence of M. excelsi 1G6 T (genome size of 5.26 Mb) showed the presence of genes and gene clusters that encode for properties that are in tune with its adaptation to extreme environmental conditions that prevail in the Atacama Desert biome., (Copyright © 2019 The Author(s). Published by Elsevier GmbH.. All rights reserved.)

To avoid an antibiotic resistance crisis, we need to develop antibiotics at a pace that matches the rate of evolution of resistance. However, the complex functions performed by antibiotics-combining, e.g., penetration of membranes, counteraction of resistance mechanisms, and interaction with molecular targets-have proven hard to achieve with current methods for drug development, including target-based screening and rational design. Here, we argue that we can meet the evolution of resistance in the clinic with evolution of antibiotics in the laboratory. On the basis of the results of experimental evolution studies of microbes in general and antibiotic production in Actinobacteria in particular, we propose methodology for evolving antibiotics to circumvent mechanisms of resistance. This exploits the ability of evolution to find solutions to complex problems without a need for design. We review evolutionary theory critical to this approach and argue that it is feasible and has important advantages over current methods for antibiotic discovery., (Copyright © 2019 Wollein Waldetoft et al.)

Case Description: Five workers (2 males and 3 females) employed in a furniture factory located in eastern Poland developed hypersensitivity pneumonitis (HP) after the pine wood used for furniture production was replaced by birch wood. All of them reported onset of respiratory and general symptoms (cough, shortness of breath, general malaise) after inhalation exposure to birch dust, showed crackles at auscultation, ground-glass attenuations in HRCT examination, and lymphocytosis in the BAL examination. The diagnosis of acute HP was set in 4 persons and the diagnosis of subacute HP in one., Identification of Specific Allergen: Samples of birch wood associated with evoking disease symptoms were subjected to microbiological analysis with the conventional and molecular methods. Two bacterial isolates were found to occur in large quantities (of the order 10 8 CFU/g) in examined samples: Gram-negative bacterium of the species Pantoea agglomerans and a non-filamentous Gram-positive actinobacterium of the species Microbacterium barkeri . In the test for inhibition of leukocyte migration, 4 out of 5 examined patients showed a positive reaction in the presence of P. agglomerans and 2 in the presence of M. barkeri . Only one person showed the presence of precipitins to P. agglomerans and none to M. barkeri . In the inhalation challenge, which is the most relevant allergological test in the HP diagnostics, all patients reacted positively to P. agglomerans and only one to M. barkeri . The results indicate that P. agglomerans developing in birch wood was the main agent causing HP in the workers exposed to the inhalation of dust from this wood, while the etiologic role of M. barkeri is probably secondary., Conclusion: The results demonstrate that apart from fungi and filamentous actinobacteria, regarded until recently as causative agents of HP in woodworkers, Gram-negative bacteria and non-filamentous actinobacteria may also elicit disease symptoms in the workers processing wood infected with large amounts of these microorganisms. The results obtained also seem to indicate that cellular-mediated reactions are more significant for causing disease symptoms compared to those that are precipitin-mediated.

Background: The soybean cyst nematode Heterodera glycines (Ichinohe) is the most devastating pathogen affecting soybean production worldwide. Biocontrol agents have become eco-friendly candidates to control pathogens. The aim of this study was to discover novel biocontrol agents against H. glycines., Results: Microbacterium maritypicum Sneb159, screened from 804 strains, effectively reduced the number of females in field experiments conducted in 2014 and 2015. The stability and efficiency of H. glycines control by Sneb159 was further assessed in growth chamber and field experiments. Sneb159 decreased H. glycines population densities, especially the number of females by 43.9%-67.7%. To confirm Sneb159 induced plant resistance, a split-root assay was conducted. Sneb159 induced local and systemic resistance to suppress the penetration and development of H. glycines, and enhanced the gene expression of PR2, PR3b, and JAZ1, involved in the salicylic acid and jasmonic acid pathways., Conclusion: This is the first report of M. maritypicum Sneb159 suppressing H. glycines infection. This effect may be the result of Sneb159-induced resistance. Our study indicates that M. maritypicum Sneb159 is a promising biocontrol agent against H. glycines. © 2019 Society of Chemical Industry., (© 2019 Society of Chemical Industry.)

Aluminum (Al) bioaccumulation by a novel Al and drought tolerant Curtobacterium herbarum strain CAH5 isolated from rhizosphere soil of Beta vulgaris grown in acidic Andisols were examined. The rhizobacterial strain also presented important plant growth promoting traits even with Al and drought stresses under in-vitro conditions in broth. In experiments with a 2-6 mM as initial Al concentrations, the percentages of Al removal by bacteria were 89-93% and 78-91% within 72 h incubation under the normal and drought conditions, respectively. Cytogenotoxicity assay revealed that the toxicity of Al was reduced after bioaccumulation process. In the greenhouse study, formulated bio-inoculant CAH5 significantly improves the Lactuca sativa growth under Al and drought stress by reducing oxidative stress, lipid peroxidation and Al accumulation in plant parts. Our results highlighted that strain CAH5 could be used as a promising bioresource for restoration of agricultural soil with presence of phytotoxic Al improving crop production even under drought conditions., (Copyright © 2019 Elsevier Inc. All rights reserved.)