Complete genome sequence of Euzebya sp. DY32-46, a marine Actinobacteria isolated from the Pacific Ocean

Transcriptomic responses of haloalkalitolerant bacterium Egicoccus halophilus EGI 80432T to highly alkaline stress

The haloalkalitolerant bacterium Egicoccus halophilus EGI 80432^T exhibits high adaptability to saline-alkaline environment. The salinity adaptation mechanism of E. halophilus EGI 80432^T was fully understood based on transcriptome analyses and physiological responses; however, the alkaline response mechanism has not yet been investigated. Here, we investigated the alkaline response mechanism of E. halophilus EGI 80432^T by a transcriptomic comparison. In this study, the genes involved in the glycolysis, TCA cycle, starch, and trehalose metabolism for energy production and storage, were up-regulated under highly alkaline condition. Furthermore, genes responsible for the production of acidic and neutral metabolites, i.e., acetate, pyruvate, formate, glutamate, threonine, and ectoine, showed increased expression under highly alkaline condition, compared with the control pH condition. In contrast, the opposite results were observed in proton capture or retention gene expression profiles, i.e., cation/proton antiporters and ATP synthases. The above results revealed that E. halophilus EGI 80432^T likely tended to adopt an "acidic metabolites production" strategy in response to a highly alkaline condition. These findings would pave the way for further studies in the saline-alkaline adaptation mechanisms of E. halophilus EGI 80432^T, and hopefully provide a new insight into the foundational theory and application in ecological restoration with saline-alkaline strains.

Euzebya pacifica sp. nov., a novel member of the class Nitriliruptoria

A Gram-stain-positive, aerobic, chemo-organotrophic, rod-shaped, non-spore-forming strain, which produced convex, circular, pink-pigmented colonies, designated as DY32-46^T, was isolated from seawater collected from the Pacific Ocean. DY32-46^T was found to grow at 20-40 °C (optimum, 30-35 °C), pH 6.0-8.0 (optimum, pH 6.5) and with 0-5 % (w/v) NaCl (optimum, 1-2 %). The results of chemotaxonomic analysis indicated that the respiratory quinone of DY32-46^T was MK-9(H₄), and major fatty acids (>10 %) were C_17 : 1 ω8c, summed feature 3 (C_16 : 1 ω7c and/or C_16 : 1 ω6c), C_16 : 0 and C_15 : 1 ω6c. The polar lipids included diphosphatidylglycerol, phosphatidylglycerol, one unidentified aminophospholipid, three unidentified glycolipids, three unidentified phospholipids, one unidentified phosphoglycolipid and five unidentified lipids. The DNA G+C content of DY32-46^T was 70.6 mol%. The results of phylogenetic analysis based on 16S rRNA gene sequences and genomic data indicated that DY32-46^T should be assigned to the genus Euzebya. ANI and in silico DNA-DNA hybridization values between strain DY32-46^T and type strains of Euzebya species were 73.1-87.2 % and 20.2-32.4 %, respectively. Different phenotypic properties, together with genetic distinctiveness, demonstrated that strain DY32-46^T was clearly distinct from recognized species of the genus Euzebya. Therefore, DY32-46^T represents a novel species within the genus Euzebya, for which the name Euzebya pacifica sp. nov is proposed. The type strain is DY32-46^T (=MCCC 1K03476^T=KCTC 49091^T).

Muriiphilus fusiformis gen. nov., sp. nov., a novel non-marine bacterium belonging to the Roseobacter group, and reclassification of Maritimibacter lacisalsi (Zhong et al. 2015) as Muriicola lacisalsi gen. nov., comb. nov

An aerobic, Gram-stain-negative, non-sporulating, flagellated and spindle-like bacterium, designated HY14^T, was isolated from a pickle-processing factory wastewater sample. The isolate chemoheterotrophically grew at 4-42 °C (optimum, 35 °C) and pH 5.5-9.0 (optimum, pH 6.0-6.5). Salt was required for growth (0.5-12 % NaCl, w/v). A deep brown and water-soluble uncharacterized pigment was produced when grown in certain media. The predominant fatty acids (>5 %) included C_16 : 0, C_18 : 1  ω7c, 11-methyl C_18 : 1  ω7c and C_19 : 0 cyclo ω8c. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, two unidentified aminolipids, two unidentified phospholipids, two unidentified glycolipids and five unknown lipids. The major isoprenoid quinone was ubiquinone-10. Pairwise alignment based on 16S rRNA gene sequences indicated that strain HY14^T had the highest sequence similarity to genera Maritimibacter (95.61-96.05 %) and Boseongicola (95.82 %). Phylogenetic analysis based on core genome illustrated that strain HY14^T formed a monophyletic lineage with members of the genus Maritimibacter in the clade of the Roseobacter group in the family Rhodobacteraeceae. The core-gene average amino acid identity used to define bacterial genera by a threshold of 60-80 % was calculated to be 68.56-76.5 % between HY14^T and closely related taxa. Several genomic characteristics, such as carrying two RuBisCO-mediated pathways and different osmoprotectant transport pathways, exhibited the genotypic discrepancies of strain HY14^T. Based on the polyphasic taxonomic characterization, strain HY14^T is considered to represent a novel species of a novel genus belonging to the family Rhodobacteraeceae, for which the name Muriiphilus fusiformis gen. nov., sp. nov. is proposed. The type strain is HY14^T (=CGMCC 1.15973^T=KCTC 52499^T). Maritimibacter lacisalsi (Zhong et al. 2015) is considered to diverge from Maritimibacter alkaliphilus at the genus level, and should be reassigned as a novel genus, for which the name Muriicola lacisalsi gen. nov., comb. nov. is proposed.

Revealing the salinity adaptation mechanism in halotolerant bacterium Egicoccus halophilus EGI 80432T by physiological analysis and comparative transcriptomics

Egicoccus halophilus EGI 80432^T, a halotolerant bacterium isolated from a saline-alkaline soil, belongs to a member of the class Nitriliruptoria, which exhibits high adaptability to salt environments. At present, the detailed knowledge of the salinity adaptation strategies of Nitriliruptoria was limited except for one research by using comparative genomics analysis. Here, we investigated the salinity adaptation mechanism of E. halophilus EGI 80432^T by comparative physiological and transcriptomic analyses. The results of physiological analyses showed that trehalose and glutamate were accumulated by salt stress and showed the maximum at moderate salinity condition. Furthermore, the contents of histidine, threonine, proline, and ectoine were increased with increasing salt concentration. We found that both 0% and 9% NaCl conditions resulted in increased expressions of genes involved in carbohydrate and energy metabolisms, but negatively affected the Na⁺ efflux, iron, and molybdate transport. Moreover, the high salt condition led to enhancement of transcription of genes required for the synthesis of compatible solutes, e.g., glutamate, histidine, threonine, proline, and ectoine, which agree with the results of physiological analyses. The above results revealed that E. halophilus EGI 80432^T increased inorganic ions uptake and accumulated trehalose and glutamate in response to moderate salinity condition, while the salinity adaptation strategy was changed from a "salt-in-cytoplasm" strategy to a "compatible solute" strategy under high salinity condition. The findings in this study would promote further studies in salt tolerance molecular mechanism of Nitriliruptoria and provide a theoretical support for E. halophilus EGI 80432^T's application in ecological restoration.Key Points• Salt stress affected gene expressions responsible for carbohydrate and energy metabolisms of E. halophilus EGI 8042^T.• E. halophilus EGI 80432^T significantly accumulated compatible solutes under salt stress.• E. halophilus EGI 80432^T adopted a "compatible solute" strategy to withstand high salt stress.

Complete genome sequence of Micromonospora craniellae LHW63014T, a potential metal ion-chelating agent producer

Micromonospora craniellae LHW63014^T is a novel marine Micromonospora, isolated from a Craniella species sponge collected in the South China Sea. In this study, we report the complete genome sequence of M. craniellae LHW63014^T, which is comprised of a circular chromosome of 6,839,926 bp with the G + C content of 70.9 mol%. The complete genome contained 6572 protein-coding genes, 48 tRNA genes, and 9 rRNA genes. Genomic annotations revealed that 79.09% of the protein-coding genes were assigned to the COG database, among which, the abundant genes were predicted to be involved in transcription, replication, recombination and repair, and amino acid transport and metabolism. Secondary metabolites prediction using antiSMASH revealed that 22 biosynthetic gene clusters (BGC) of secondary metabolites were located in the genome of M. craniellae LHW63014^T, 19 of which showed low similarity (<50%) to known BGCs and 5 of which showed the closest homology with BGCs encoding metal ion-chelating agents, indicating the immense potential of M. craniellae LHW63014^T to produce a wide variety of novel antibiotics, especially for metal ion-chelating agents.

Omics for Bioprospecting and Drug Discovery from Bacteria and Microalgae

"Omics" represent a combinatorial approach to high-throughput analysis of biological entities for various purposes. It broadly encompasses genomics, transcriptomics, proteomics, lipidomics, and metabolomics. Bacteria and microalgae exhibit a wide range of genetic, biochemical and concomitantly, physiological variations owing to their exposure to biotic and abiotic dynamics in their ecosystem conditions. Consequently, optimal conditions for adequate growth and production of useful bacterial or microalgal metabolites are critically unpredictable. Traditional methods employ microbe isolation and 'blind'-culture optimization with numerous chemical analyses making the bioprospecting process laborious, strenuous, and costly. Advances in the next generation sequencing (NGS) technologies have offered a platform for the pan-genomic analysis of microbes from community and strain downstream to the gene level. Changing conditions in nature or laboratory accompany epigenetic modulation, variation in gene expression, and subsequent biochemical profiles defining an organism's inherent metabolic repertoire. Proteome and metabolome analysis could further our understanding of the molecular and biochemical attributes of the microbes under research. This review provides an overview of recent studies that have employed omics as a robust, broad-spectrum approach for screening bacteria and microalgae to exploit their potential as sources of drug leads by focusing on their genomes, secondary metabolite biosynthetic pathway genes, transcriptomes, and metabolomes. We also highlight how recent studies have combined molecular biology with analytical chemistry methods, which further underscore the need for advances in bioinformatics and chemoinformatics as vital instruments in the discovery of novel bacterial and microalgal strains as well as new drug leads.

Genome-centric resolution of novel microbial lineages in an excavated Centrosaurus dinosaur fossil bone from the Late Cretaceous of North America

BACKGROUND

Exceptional preservation of endogenous organics such as collagens and blood vessels has been frequently reported in Mesozoic dinosaur fossils. The persistence of these soft tissues in Mesozoic fossil bones has been challenged because of the susceptibility of proteins to degradation and because bone porosity allows microorganisms to colonize the inner microenvironments through geological time. Although protein lability has been studied extensively, the genomic diversity of microbiomes in dinosaur fossil bones and their potential roles in bone taphonomy remain underexplored. Genome-resolved metagenomics was performed, therefore, on the microbiomes recovered from a Late Cretaceous Centrosaurus bone and its encompassing mudstone in order to provide insight into the genomic potential for microbial alteration of fossil bone.

RESULTS

Co-assembly and binning of metagenomic reads resulted in a total of 46 high-quality metagenome-assembled genomes (MAGs) affiliated to six bacterial phyla (Actinobacteria, Proteobacteria, Nitrospira, Acidobacteria, Gemmatimonadetes and Chloroflexi) and 1 archaeal phylum (Thaumarchaeota). The majority of the MAGs represented uncultivated, novel microbial lineages from class to species levels based on phylogenetics, phylogenomics and average amino acid identity. Several MAGs from the classes Nitriliruptoria, Deltaproteobacteria and Betaproteobacteria were highly enriched in the bone relative to the adjacent mudstone. Annotation of the MAGs revealed that the distinct putative metabolic functions of different taxonomic groups were linked to carbon, nitrogen, sulfur and iron metabolism. Metaproteomics revealed gene expression from many of the MAGs, but no endogenous collagen peptides were identified in the bone that could have been derived from the dinosaur. Estimated in situ replication rates among the bacterial MAGs suggested that most of the microbial populations in the bone might have been actively growing but at a slow rate.

CONCLUSIONS

Our results indicate that excavated dinosaur bones are habitats for microorganisms including novel microbial lineages. The distinctive microhabitats and geochemistry of fossil bone interiors compared to that of the external sediment enrich a microbial biomass comprised of various novel taxa that harbor multiple gene sets related to interconnected biogeochemical processes. Therefore, the presence of these microbiomes in Mesozoic dinosaur fossils urges extra caution to be taken in the science of paleontology when hunting for endogenous biomolecules preserved from deep time.