Current Microbiology

Isolation of extracellular enzyme degrading aerobic bacteria in the digestive tracts of fresh water prawn was carried out. Gut bacteria were isolated on carboxymethyl cellulose agar plates, starch agar media plates, gelatine peptone agar media plates. The isolated strain was qualitatively screen based on their extracellular enzyme on selective media. The strain was characterised based on morphological, physiological and biochemical characterization identified Bacillus species. Bacillus species was isolated by colony characterization carried out by using Gelatin agar Media, carboxymethyl cellulose media and congo red CMC media and starch agar media for different enzyms. Isolates are capable of hydrolysing proteins and carbohydrates indicating their importance in fish nutrition.

The stringent response has far-reaching consequences, with links to antimicrobial resistance, stress and virulence. This study assessed the role of relA in nutritional, environmental and antimicrobial stress in Klebsiella pneumoniae, the extent of polysaccharide capsule and biofilm formation, and the pathogenic effect on Drosophila melanogaster. Two single mutants (KP03DrelA and KPPR1DrelA) obtained using the Lambda Red Recombinase Technique were the focus of analyses. We assessed environmental (ethanol, osmotic, heat) and nutritional stress (carbon, phosphate, amino acid) tolerance, capsule formation, and cell size determination in wild-type (WT) and mutant bacteria. Biofilm and agar plate susceptibility assays were performed on both starved and non-starved strains using gentamicin and ceftazidime, and stress response genes were analyzed. Drosophila melanogaster was used to examine the pathogenic effect of the presence or deletion of relA on fly survival. DrelA mutants had reduced fitness to environmental and nutritional stress compared to WT strains. Mutant strains cell lengths were elongated and lacked a capsule versus WT and non-starved strains, and mutant strains exhibited enhanced biofilm formation or survival in the presence of ceftazidime and gentamicin. Stress response genes rpoD, phoR, phoU and pstB were absent during starvation, but rpoS was detected in C-, C+PO+ and serine hydroxamate (SHX) media; mrkA gene was not detected during starvation. Lastly, the animal model proved to be effective in showing infection levels associated with the presence of the relA gene.

Two yellow pigmented bacterial strains were isolated from healthy rice seeds. The strains designated as PPL560T and PPL568 were identified as members of genus Xanthomonas based on analysis of biochemical and 16S rRNA gene sequence retrieved from whole genome sequence. Isolates formed a distinct monophyletic lineage with X. sontii and X. sacchari as the closest relatives in the phylogenetic tree based on core gene content shared by reported species in genus Xanthomonas. Pairwise ortho Average Nucleotide Identity and digital DNA-DNA hybridisation values calculated against other species of Xanthomonas were below their respective cut-offs. In planta studies revealed that PPL560T and PPL568 are non-pathogenic to rice plants upon leaf clip inoculation. Absence of type III secretion system related genes and effectors further supported their non-pathogenic status. Herein, we propose Xanthomonas indica sp. nov. as novel species of genus Xanthomonas with PPL560T=MTCC13185 as its type strain and PPL568 as another constituent member.

Citrus is an economically important fruit crop grown in all provinces of Pakistan, while Punjab accounting for 95 percent of total production due to its favorable climate for citrus production. Commercially grown varieties in Pakistan include sweet oranges, grapefruits, Mandarine, Lime, and lemon. The goal of this research was to see how diverse the cultivable bacterial populations are found in citrus cultivars. Out of 90 isolated cultures, 37 endophytic bacterial species and 15 different genera of bacteria were characterized based on morphological, biochemical, and molecular methods from citrus leaves. All the isolated bacteria were subjected to PCR amplification through 16S rDNA followed by sequencing. RDP base classification revealed that class Bacilli has the largest percentage of isolates, whereas class Alpha, Beta, and Gamma Proteobacteria have the lowest percentage among all genotypes used. According to the findings, the phylum Firmicutes contains a common genus (Brevibacterium, 1%; Enterococcus, 6%; Staphylococcus, 7% and Bacillus, 60%). Alpha (Rhizobium) beta (Burkholderia cepacia; Comamonas terigena) gamma Proteobacteria (Enterobacter hermachei (1%), Klebsiella pneumoniae (1%), Proteus mirabilis (8%), Pseudomonas aeruginosa (5%), Psychrobacter pulmonis and Yersinia molalretti (1%) respectively. These results revealed that cultivars of the plants might contribute to the structure and endophytic bacterial communities associated with citrus. Endophytes extracted from leaf samples of different citrus cultivars in Pakistan are reported for the first time. The idea of employing endophytes bacteria to produce enzymes stimulate plant growth, and its purpose as a biological control agent will be investigated in the future.

Three novel bioluminescent bacterial strains, VNB-15T, VNB-16 and SChm4, were isolated from water of the Black Sea (Russia) and intestines of the Black Sea horse mackerel. Cells of the isolated strains are motile Gram negative slightly curved rods with single polar flagellum. The temperature range for growth was 10-35{degrees}C, the optimum being 20-25{degrees}C. The pH range for growth was 6.0-9.0, the optimum being 7.0-8.0. The bacteria were able to grow in the presence of 0.5 to 5.0% NaCl (w/v), the optimum being 1.0-4.0% (w/v). Phylogenetic analysis based on comparison of 16S rRNA sequences shows these strains to have kinship with the species Vibrio jasicida, Vibrio hyugaensis, Vibrio alginolyticus, Vibrio campbelli, Vibrio rotiferianus, Vibrio harveyi and Vibrio owensii with sequence similarity from 99.6 to 98.0%. Phylogenetic analysis based on comparison of the sequences of genes gyrB, recA, pyrH, gapA, rpoA, mreB, ftsZ, topA shows that the strains VNB-15T, VNB-16 and SChm4 to form a cluster within the V. harveyi clade and belong to a new species of the Vibrio genus. Comparison of the complete genomic sequence of VNB-15T with typical strains of nearby species also indicates that VNB-15T belongs to a separate species (maximum similarity 98% with V. hyugaensis and 96% with V. jasicida). VNB-15T differs from closely related species by its ability to utilize glucose, mannitol, inositol, sorbitol, rhamnose and sucrose, and to form lysine decarboxylase, ornithine decarboxylase, lipase, acid phosphatase, -glucosidase, {beta}-glucosidase and N-acetyl-{beta}-D-glucosaminidase enzymes. Based on phylogenetic analysis and phenotypic characteristics, Vibrio aquamarinus sp. nov. is proposed. The type strain is VNB-15T (= VKPM B-11245T = DSM 26054 T). RepositoriesThe GenBank accession numbers for the gapA, 16S rRNA, gyrB, pyrH, rpoA, recA, mreB, ftsZ, topA genes sequences of strain VNB-15T are JQ319116-JQ319121, KX242381, KX 242384, KX242387, respectively. The GenBank accession numbers for the gapA, gyrB, pyrH, recA, rpoA,16S rRNA, mreB, ftsZ, topA genes sequences of strain VNB-16 are KP221561-KP221566, KX242382, KX 242385, KX242388 respectively. The GenBank accession numbers for the 16S rRNA, gapA gyrB, rpoA, recA, pyrH, mreB, ftsZ, topA genes sequences of strain SChm4 are KX242375-KX242380, KX242383, KX 242386, KX242389, respectively. The GenBank/EMBL/DDBJ accession numbers for the housekeeping gene sequences used in this study are detailed in supplementary Table S1, Figures S1-S8. The genome of Vibrio aquamarinus sp. nov. VNB-15T, comprising two chromosomes and a plasmid, has been assembled and deposited in the NCBI database under the submission number SUB14585067

K. pneumoniae is a non-motile, encapsulated bacterium from the Enterobacteriaceae family. The illnesses related to this opportunistic pathogen are pneumonia, Urinary Tract Infection (UTI), pyogenic liver abscess, endophthalmitis, and meningitis. Among them, UTI is predominant due to its biofilm formation leading to the mortality of 150 million people worldwide. The function of monovalent and divalent ions on Klebsiella biofilm, aside from physiochemical variables, remains unclear. Hence the present study was performed to analyze the role of K+, Ca2+, Na+, Mg2+, NH+4 in biofilm formation and its influence on biofilm-related genes. Among the tested cations, K+ and Ca2+ yielded strong biofilm in clinical and environment isolates in pH between 6.5 to 9.5. Increasing Ca2+ ions concertation reduced the Klebsiella biofilm. When compared to the hypercalciuria condition (Ca2+ level > 5 mM), 2.5 mM resulted in high biofilm mass. Cations concurrently enhanced the size of the capsule and cell density of Klebsiella but were not correlated with biofilm mass. Expression of the LPS gene (WbaG) either in planktonic or biofilm stage promoted biofilm formation in the presence of K+, Ca2+ and Na+. Whereas, expression of fimbriae genes (FimH and mrkD) was co- regulation, and capsule genes (RmpA and Wcab) were absent. Stating, the primary component needed for the Klebsiella biofilm is not the capsule or fimbriae, rather LPS. Resulting as a potent target in the treatment of Klebsiella biofilm in UTI. To the best of our knowledge, this is the first kind of study on the effect of cation ions on biofilm and planktonic cells of Klebsiella spp. and demonstrating the role of LPS biosynthesis gene (WbaG) in biofilm development.

It has been hypothesized that AT-biased genotypes of Ophiocordyceps sinensis are generated through repeat-induced point mutation (RIP) and coexist as permanently nonfunctional internal transcribed spacer (ITS) pseudogenes in the genome of Hirsutella sinensis (GC-biased Genotype #1 of O. sinensis). This study examined the H. sinensis genome, which contains multiple repetitive ITS copies (GC content: 64.7{+/-}0.33%) with multiple insertion/deletion and transversion alleles, which were not generated through RIP mutagenesis that theoretically causes cytosine-to-thymine (C-to-T) and guanine-to-adenine (G-to-A) transitions. The repetitive ITS copies in the H. sinensis genome were found to be genetically and phylogenetically distinct from the AT-biased O. sinensis genotypes (GC content: 51.1{+/-}1.69%), which possess multiple transition alleles. The sequences of Genotypes #2-17, both GC- and AT-biased, are absent from the H. sinensis genome; these genotypes belong to interindividual O. sinensis fungi and differentially occur in different compartments of natural Cordyceps sinensis, with dynamic alterations in abundance occurring in an asynchronous, disproportional manner during C. sinensis maturation. Metatranscriptomic analyses of natural C. sinensis revealed the transcriptional silencing of 5.8S genes in all C. sinensis- colonizing fungi, including H. sinensis. The transcription assay reported by Li et al. [1] provided unsound, controversial evidence indicating that the 5.8S genes of AT-biased genotypes are nonfunctional pseudogenes. In addition to the single ITS locus analysis, repetitive genomic copies were also examined at multiple loci in the H. sinensis genome, and approximately 8.2% of the authentic genes had repetitive copies, including various transitions, transversions, and insertions/deletions. The transcripts for the repetitive copies, regardless of the decreases, increases, or bidirectional changes in the AT content, were identified in the H. sinensis transcriptome. These results are inconsistent with those of RIP mutagenesis, which generates pseudogenic, nonfunctional, repetitive copies. In conclusion, AT-biased genotypes of O. sinensis might have evolved through evolutionary mechanisms from a common ancestor over the long course of evolution, in parallel with GC-biased Genotype #1 H. sinensis.

The antibiotic stress on bacteria leads to initiation of adaptive mechanisms, including exploiting the available opportunity, if any, for cell survival. In order to use the opportunity for survival while under threat, the microbe undergoes various mechanisms which are not completely known e.g. homologous recombination, horizontal gene transfer etc. Our aim is to understand the adaptive mechanism for cell survival during stress, especially antibiotic stress, in E. coli in the presence of opportunity. Understanding this mechanism in bacteria that gained resistance will help in identifying alternative survival pathways. By subjecting a recombination deficient ({Delta}RecA) strain of bacteria to antibiotic stress, we expected cell death, due to its inability to repair DNA damage (1, 2). Here we show that providing an opportunity in the form of an antibiotic resistance gene with homologous ends aids bacterial survival. There was 3-fold increase in cell envelope thickness along with 2.5-fold increase in phosphatidylethanolamine (PE) content, and enhanced antibiotic resistance to >4000{micro}g/mL (Kan). We observed genome-wide alteration of methylation pattern that lead to changes in transcriptome, proteome, lipidome, and metabolite level, thus, leading to morphological and physiological changes. We prove that global methylation helps in survival of bacteria under stress that changes essential pathways like energy, cell envelope, lipids, amino acids acid, etc. leading to over production of cell wall components including synthesis of PE. By inhibiting the activity of methyltransferase, it is noticed that there is reduction in PE synthesis in agreement with demethylation. This proves that the phenotypic changes are caused due to the global methylation, and also demonstrates that demethylation could be used as a strategy to prevent antibiotic resistance in microbes. One Sentence SummaryGlobal methylation determines the survival of bacteria to gain the antimicrobial resistance with an opportunity

IntroductionRhizobacteria has the suppression ability to compete with pathogenic microorganisms and help for plant immunity and defense mechanism. Their growth and survival in rhizosphere ensure biological balance in favor of the host plant. MethodsIn our study, with agar diffusion assays, we found a rhizobacterium species belonging to Bacillus safensis, which can significantly suppress Phomopsis viticola. To elucidate the antagonistic mechanism, genome-wide gene expression profiling of B. safensis (strain MM19) was performed in the presence and absence of P. viticola. We used RNA-seq analysis to obtain a comprehensive overview of the responsive B. safensis whole gene expression classified according to biological and metabolic process to P. viticola concomitant growth in liquid culture. ResultsThe differential gene expression profiles of B. safensis (MM19) revealed significantly increased expression of prominent genes related to thiamine biosynthesis involving various metabolites and enzymes that play role in the suppression of mycelium growth and pathogen inhibition. Correspondingly, the expression of three major genes (HOG1, FUS3, SGI) involving in the virulence of P. viticola was followed using qPCR analysis. HOG1 was the highest expressed gene in the pathogen when it co-cultivated with MM19. Based on these findings, we performed molecular docking and dynamics analysis to explore the interaction between HOG1 and thiamine, besides expression of network analysis constructed using Cytoscape. DiscussionThe results proved that the functional genomic data related to thiamine biosynthesis and corresponding pathways ensure a priming role in the antagonistic behavior of B. safensis (MM19) against P. viticola as a supporter for plant immunity.

Vibrio cholerae is the bacteria responsible for the cholera disease and a natural inhabitant of aquatic environments. Biofilm formation is important for human colonization and environmental survival. Motility is essential for adhesion and biofilm formation by V. cholerae. In a previous study, we showed that motility and biofilm formation are altered in the presence of sub-inhibitory concentrations of polymyxin B in V. cholerae. In this study, we performed an experimental evolution to identify genes rescuing the motility in the presence of polymyxin B. Mutations in 5 genes have been identified: ihfA, vacJ (mlaA), mlaF, dacB and ccmH. The details of these mutations, their potential impact on the function of the proteins they encode and on the motility in presence of polymyxin B are discussed.

Due to their relatively small size and the lack of housekeeping genes, bacterial plasmids are very convenient models for studying DNA replication. So, for a long time, they had been intensively studied in this regard. Unfortunately, only a limited number of model plasmid replication systems were analyzed in detail. In the era of high-throughput DNA sequencing, we are faced with an increasing gap in our knowledge of bacterial plasmid replication and a rapidly growing number of deposited new plasmid genome sequences. For this reason, we decided to investigate the replication system of the pIGMS31 plasmid, a representative of the newly described pHW126-like plasmids family. They are small replicons isolated from different clinical and environmental strains of Gamma proteobacteria. Whole shares unique replication modules with no significant similarities to known model plasmid replication systems. In this study, we identified and characterized the basic elements of the pIGMS31 replication module. Studies on regulatory mechanisms of replication initiation of this plasmid as well as on pIGMS31 replication mode were also performed. We revealed that the pIGMS31 replication module is composed of elements typical for both theta and rolling circle replicons. This mosaic structure is reflected in the unique course of replication of this plasmid, with both modes of replication. What is more, our results led us to conclude that pHW126-like plasmids, despite DNA sequence similarity, are a highly diverse group of replicons.

The ciliated protist communities show richness as well as uniqueness. This is true both for aquatic and soil ciliates. Delhi region lies in the subtropical semi-arid zone wherein the temperatures are highest in May-June and lowest in January. It also receives its monsoonal rainfall during the month of July-August. Thus, the region offers ideal conditions for the growth and proliferation of aquatic living beings. During the past three decades, a series of investigation has been carried out on the freshwater free-living ciliate fauna from fourteen sites at the river Yamuna and different freshwater bodies in Delhi. Samples were brought to the laboratory, ciliates were identified using live-cell observations and silver staining methods. A large number of Spirotrich species and a lower proportion belonging to class Heterotrichea, Litostomaea, Phyllopharyngea, Oligohymenophorea, Prostomatea, and Colpodea were identified. A total of 55 species belonging to 7 classes, 16 orders, 26 families, 40 genera were identified and documented. Ciliate diversity was found to be highest in the water sample from Okhla bird sanctuary (OBS). All ciliate species recorded during the present study have been listed and their general characteristics have been discussed.

Serratia rubidaea a member of the Enterobacteriaceae family, is a Gram-negative opportunistic pathogen, known to survive harsh environmental conditions and responsible for hospital associated infections. Specifically, S. rubidaea can withstand desiccation and survive on hospital surfaces and equipments as well as have acquired antimicrobial resistance determinants for different commercial antibiotics. The expansion of this multidrug resistant pattern suggests that the treatment of S. rubidaea infections will become increasingly difficult in near future. Although some measures were taken to control this species, an inhibition mechanism is remaining unknown. To design effective means to control the dissemination of S. rubidaea, an in-depth analysis is required. In the present study, one possible candidate was isolated from the soil of Sundarban Mangroove Forest (Bangladesh) that has important physiological effects to inhibit this pathogenic bacterium. The bacterial isolate was initially identified as Bacillus amyloliquefaciens subsp. amyloliquefaciens using BIOLOG identification system and confirmed to be B. amyloliquefaciens strain through 16S rDNA sequence analysis. The growth and antagonistic activity of this potential strain was shown to be stable under wide range of pH, temperature and salinity (NaCl). Moreover, the novel B. amyloliquefaciens isolate can also inhibit Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa and other pathogenic bacteria. These results suggest that B. amyloliquefaciens might have potential antimicrobial properties and further research is required for future use of this bacterium as biological controls of S. rubidaea or development as new drugs for pathogenic bacteria.

The interspecific interactions play an important role in the establishment of a community phenotype. Furthermore, the evolution of a community can not only occur through an evolution of the species composing the community but also of the interactions among them. In this study, we investigated how widespread was the evolution of interspecific interactions in the evolutionary response of eight two-bacterial species communities regarding productivity. We found evidence for an evolution of the interactions in half of the studied communities which gave rise to a mean change of 15% in community productivity as compared to what was expected from the individual responses. Even when the interactions did not evolve themselves, they influenced the evolutionary responses of the bacterial strains within the communities which further affected community response. We found that the evolution within a community often promoted an adaptation of the bacterial strains to the abiotic environment, especially for the dominant strain in a community. Overall, this study suggested that the evolution of the interspecific interactions was frequent and that it could increase community response to evolution. We propose that the existence of an evolution of the interspecific interactions can justify the consideration of the community as a unit of selection.

Microbiome diversity and composition in mammals is affected by the hosts environment and has been linked to important immune and physiological host functions, yet most of these data come from the gut microbiome. Research on the oral and hair microbiome in nonhuman primates has been far less common, and information from wild primates is even rarer. These overlooked patterns of environmental effects on microbial communities across the body may have important implications for a range of host functions. Therefore, in this study we characterized the gut, oral, and hair microbiomes across nine different captive and wild lemur species: Eulemur collaris, Eulemur coronatus, Eulemur mongoz, Lemur catta, Microcebus griseorufus, Microcebus murinus, Propithecus coquereli, Propithecus verreauxi, and Varecia rubra. We explored how host environment affects the microbiome diversity of these three body regions using 16S rRNA sequencing and found significant differences in microbiome composition, diversity, and environmental influence across body regions. The oral microbiome was least diverse and most resilient to different environmental effects; conversely, the hair microbiome was both most diverse and most labile. Differentially abundant bacterial taxa across oral, gut, and hair microbiota may also reflect selective regimes unique to each body region. These results emphasize the importance of accounting for body region when conducting microbiome studies. ImportanceAn organisms microbiome plays important roles in a wide variety of the host animals physiological functions, yet how these microbial communities in body regions beyond the gut are affected by the hosts environment is not clearly understood. We therefore analyzed how the oral, gut, and hair microbiomes of nine lemur species (genera Eulemur, Lemur, Microcebus, Propithecus, and Varecia) varied across wild and captive environments. We found that host environment affected the microbiomes of each body region in distinct ways, with the oral microbiome appearing conserved and more resilient to environmental effects, particularly compared to the diverse and widely variable hair microbiome. To our knowledge, this study is the most comprehensive multi-body-region analysis of the lemur microbiome to date. Our results demonstrate that the environment does not have a universal effect on the microbiome across body regions, but is instead mediated by body-region specific factors.

Membrane cardiolipin (CL) phospholipids play a fundamental role in the adaptation of bacteria to various environmental conditions, including saline stress. Here, we constructed deletion mutants of two CL synthetase genes, clsA and clsB, in the rhizobacterium Pseudomonas fluorescens UM270, and evaluated their role in plant growth promotion under salt stress. P. fluorescens UM270 {Delta}clsA and {Delta}clsB mutants showed a significant reduction in CL synthesis compared to the UM270 wild-type strain (58% {Delta}clsA and 53% {Delta}clsB), and their growth rate was not affected, except when grown at 100 and 200 mM NaCl. Additionally, the root colonization capacity of both mutant strains was impaired compared with that of the wild type. Concomitant with the deletion of clsA and clsB, some physiological changes were observed in the UM270 {Delta}clsA and {Delta}clsB mutants, such as a reduction in indole acetic acid and biofilm production. By contrast, an increase in siderophore biosynthesis was observed. Further, inoculation of the UM270 wild-type strain in tomato plants (Lycopersicon esculentum Saladette) grown under salt stress conditions (100 and 200 mM NaCl) resulted in an increase in root and shoot length, chlorophyll content, and dry weight. On the contrary, when each of the mutants ({Delta}clsA and {Delta}clsB) were inoculated in tomato plants, a reduction in root length was observed when grown at 200 mM NaCl, but the shoot length, chlorophyll content, and total plant dry weight parameters were significantly reduced under normal or saline conditions (100 and 200 mM NaCl), compared to UM270 wild-type-inoculated plants. In conclusion, these results suggest that CL synthesis in P. fluorescens UM270 plays an important role in the promotion of tomato plant growth under normal conditions, but to a greater extent, under salt-stress conditions.

Nowadays, there is a significant gap in the knowledge of the diversity and patterns for marine heterotrophic culturable microorganisms. In addition, most of the bacterial isolation efforts have focused on the photic ocean leaving the deep ocean less explored. We have isolated 1561 bacterial strains covering both photic (817) and aphotic layers (744) including isolates from the oxygen minimum zone (362) and the bathypelagic (382) from a variety of oceanographic regions including the North Western Mediterranean Sea, the North and South Atlantic Oceans, the Indian, the Pacific, and the Arctic Oceans. The partial sequencing of the 16S rRNA gene of all isolates revealed that they mainly affiliate with the classes Alphaproteobacteria (35.9%) and Gammaproteobacteria (38.6%), as well as, phylum Bacteroidetes (16.5%). The genera Alteromonas and Erythrobacter were the most widespread heterotrophic bacteria in the ocean able to grow on solid agar media. When comparing the sequences of all isolates, 37% of them were 100% identical. In fact, we found that 59% of the total aphotic isolates were 100% identical to photic isolates, indicating the ubiquity of some bacterial isolates along the water column. Unweighted UniFrac distances did not show significant differences among stations regardless of their geographic distance or depth, reflecting the wide dispersion of the culturable bacterial assemblage. This isolates collection provides an overview of the distribution patterns of cosmopolitan marine culturable heterotrophic bacteria.

Deinococcus radiodurans, a natural transformation (NT) enabled bacterium renowned for its exceptional radiation resistance, employs unique DNA repair and oxidative stress mitigation mechanisms as a strategic response to DNA damage. This study excavate into the intricate roles of NT machinery in the stressed D. radiodurans, focusing on the genes comEA, comEC, endA, pilT and dprA, which are instrumental in the uptake and processing of extracellular DNA (eDNA). Our data reveals that NT not only supports the nutritional needs of D. radiodurans under stress but also have roles in DNA repair. The study findings establish that NT-specific proteins (ComEA, ComEC, and EndA) might contribute to support the nutritional requirements in unstressed and heavily DNA-damaged cells while DprA contribute differently and in a context-dependent manner to navigating through the DNA damage storm. Thus, this dual functionality of NT-specific genes is proposed to be one of factor in D. radiodurans remarkable ability to survive and thrive in environments characterized by high levels of DNA-damaging agents. Author SummaryDeinococcus radiodurans, a bacterium known for its extraordinary radiation resistance. This study explores the roles of natural transformation (NT) machinery in the radiation-resistant bacterium Deinococcus radiodurans, focusing on the genes comEA, comEC, endA, pilT, and dprA. These genes are crucial for the uptake and processing of extracellular DNA (eDNA) and contribute to the bacterium nutritional needs and DNA repair under stress. The findings suggest that the NT-specific proteins ComEA, ComEC, and EndA may help meet the nutritional needs of unstressed and heavily DNA-damaged cells, whereas DprA plays a distinct role that varies depending on the context in aiding cells to cope with DNA damage. The functionality of NT genes is proposed to enhance D. radiodurans survival in environments with high levels of DNA-damaging agents.

There have been theories presented on Azolla cyanobionts, known for voracious nitrogen fixation, vertical transmission of cyanobiont and helping transform a greenhouse planet to an icehouse one ~49 Mya. One such theory encapsulates the existence of two cyanobionts, named Major and Minor. We show here the identity of a possible minor cyanobiont of Azolla named Fischerella uthpalarensis. A likely cyanobiont with straight or curved filaments that were truly branched was isolated. Seven gene fragments, namely 16s rDNA (Forward and Reverse), RNA Polymerase, ITS1 region (Forward and Reverse), nifD and GroEL genes were utilized to identify the isolated cyanobiont. The best match based on BLASTn search tool was found in the RNA Polymerase beta subunit (rpoC) gene fragment, that showed 99.54% identity with 55% coverage to Fischerella muscicola. Phylogenetic inferences with the rpoC genetic locus and the GroEL protein sequence suggest a likely Fischerella genus identity. Furthermore, VnfDG and VnfN fragments too were amplified using PCR and sequenced to demonstrate that this cyanobiont has alternate nitrogenase genes, on top of the molybdenum counterpart, providing an advantage in lifestyle. We encountered a higher level of genomic-level synonymous substitutions, which was not reflected in protein sequences, namely VnfDG and VnfN gene products, which may be due to codon heterogeneity. We also propose for F. uthpalarensis atypicality in codon usage due to the likely acquisition of the V-nitrogenase operon from a presumed recent horizontal gene transfer (HGT) event. The cyanobiont from this study showcases a higher preference for AT over GC at the VnfDG composite locus again hinting at a symbiotic lifestyle.

Sponges (phylum Porifera) are ancient, filtering, multicellular metazoans. Freshwater sponges (Demosponges, Lubomirskiidae) dominate the fauna of the littoral zone of Lake Baikal. Over the last years, there have been mass diseases and death of endemic sponges. Previously, the strain Janthinobacterium sp. SLB01 was isolated from the diseased sponge Lubomirskia baicalensis. The studies of the pathogenicity of the strain Janthinobacterium sp. SLB01 for Baikal sponges has not been carried out. Therefore we infected experimentally in vitro to determine its pathogenicity by the cell culture of the primmorphs with subsequent isolation, sequencing, and analysis of the genomes. The purpose of the study is to show that the strain Janthinobacterium sp. SLB01 isolated from the diseased sponge L. baicalensis is a pathogen for the cell culture of primmorphs. The bacteria from the infected samples of the primmorphs were isolated and identified as strain Janthinobacterium sp. PLB02. A comparative analysis of the genomes of the strains Janthinobacterium sp. SLB01 and Janthinobacterium sp. PLB02 showed that they are practically identical. The genomes of both strains contain genes vioABCDE violacein, flok formation, and strong biofilm, and the type VI secretion system (T6SS), as the primary virulence factor. The bacterial strains Janthinobacterium sp. based on a comparison of complete genomes showed similarity with strain Janthinobacterium lividum MTR. Isolated our strains of Janthinobacterium sp. are pathogens for cell cultures of primmorphs and L. baicalensis sponges. The results of the study will help to expand the understanding of microbial relationships in the development of disease and the death of Baikal sponges.