Complete genome analysis of type strain of a novel bacterial family Temperatibacteraceae fam. nov., isolated from surface seawater.

Novel bacterial resources are valuable for studying bacterial taxonomy, bacterial evolution, and genome mining of novel antibiotics, antitumor agents, and immune modulators. In this study, we de novo sequenced the type strain of a novel bacterial family, Temperatibacteraceae fam. Nov., belonging to class Alphaproteobacteria of phylum Pseudomonadota. The type strain, Temperatibacter marinus NBRC 110045T, is mesophilic and was isolated from surface seawater around Muroto city of Japan at a depth of 0.5 m. Here, the sequenced complete genome of strain NBRC 110045T is composed of a circular chromosome of 3,184,799 bp with a mean G + C content of 43.71%. Genome analysis was applied to reveal the genetic basis of its cellular activities. Cellular regulation and signaling was analyzed to infer the regulatory mechanism of its limited growth temperature range. Genomic features of the novel family Temperatibacteraceae may expand our knowledge on environmental adaptation, genetic evolution and natural product discovery of marine bacteria.

Genomic insights into secondary metabolites of pharmaceutical utility for Hyphococcus flavus MCCC 1K03223T, isolated from bathypelagic seawater.

During an attempt to screen secondary metabolites of pharmaceutical utility, we sequenced the complete genome of type strain of a novel marine bacterial genus, named genus Hyphococcus. The type strain, Hyphococcus flavus MCCC 1K03223T, was isolated from bathypelagic seawater of South China Sea at a depth of 2500 m. The complete genome of strain MCCC 1K03223T is composed of a circular chromosome of 3,472,649 bp with a mean G + C content of 54.8%. Functional genomic analysis showed that this genome encodes five biosynthetic gene clusters, which were annotated to synthesize medicinally important secondary metabolites. Secondary metabolites annotated include ectoine which acts cytoprotection, ravidomycin which is an antitumor antibiotic and three other different metabolites of terpene type. The secondary metabolic potentials of H. flavus revealed in this study provide more evidences on mining bioactive substances from marine bathypelagic microorganisms.

Complete genome of Pelagovum pacificum SM1903T isolated from the marine surface oligotrophic environment.

Pelagovum pacificum SM1903T, belonging to a novel genus of the family Rhodobacteraceae, was isolated from the surface seawater of the Mariana Trench. Here, we report the first complete genome sequence of the novel genus Pelagovum. The genome of strain SM1903T consists of a circular chromosome of 4,040,866 bp and two plasmids of 41,363 bp and 9705 bp, respectively. Gene annotation and metabolic pathway analyses showed that strain SM1903T possesses a series of genes related to adaptation to marine oligotrophic environments, which are involved in utilization of aromatic compounds, allantoin, and alkylphosphonate, and second messenger signaling in response to the oligotrophic stress. This strain also contains a variety of genes involved in coping with other stresses including osmotic stress, oxidative stress, cold shock, and heat shock. These features would assist this strain to survive under the natural nutrient limitation and other stresses from the environment. The genome of strain SM1903T of the novel genus Pelagovum would deepen our knowledge on marine bacterioplankton and their adaption strategies to marine oligotrophic environments.

Phylogenetic Distribution of Polysaccharide-Degrading Enzymes in Marine Bacteria.

Deconstruction is an essential step of conversion of polysaccharides, and polysaccharide-degrading enzymes play a key role in this process. Although there is recent progress in the identification of these enzymes, the diversity and phylogenetic distribution of these enzymes in marine microorganisms remain largely unknown, hindering our understanding of the ecological roles of marine microorganisms in the ocean carbon cycle. Here, we studied the phylogenetic distribution of nine types of polysaccharide-degrading enzymes in marine bacterial genomes. First, we manually compiled a reference sequence database containing 961 experimentally verified enzymes. With this reference database, we annotated 9,335 enzyme sequences from 2,182 high-quality marine bacterial genomes, revealing extended distribution for six enzymes at the phylum level and for all nine enzymes at lower taxonomic levels. Next, phylogenetic analyses revealed intra-clade diversity in the encoding potentials and phylogenetic conservation of a few enzymes at the genus level. Lastly, our analyses revealed correlations between enzymes, with alginate lyases demonstrating the most extensive correlations with others. Intriguingly, chitinases showed negative correlations with cellulases, alginate lyases, and agarases in a few genera. This result suggested that intra-genus lifestyle differentiation occurred many times in marine bacteria and that the utilization of polysaccharides may act as an important driver in the recent ecological differentiation of a few lineages. This study expanded our knowledge of the phylogenetic distribution of polysaccharide enzymes and provided insights into the ecological differentiation of marine bacteria.

Comparative genomics reveals broad genetic diversity, extensive recombination and nascent ecological adaptation in Micrococcus luteus.

BACKGROUND: Micrococcus luteus is a group of actinobacteria that is widely used in biotechnology and is being thought as an emerging nosocomial pathogen. With one of the smallest genomes of free-living actinobacteria, it is found in a wide range of environments, but intraspecies genetic diversity and adaptation strategies to various environments remain unclear. Here, comparative genomics, phylogenomics, and genome-wide association studies were used to investigate the genomic diversity, evolutionary history, and the potential ecological differentiation of the species. RESULTS: High-quality genomes of 66 M. luteus strains were downloaded from the NCBI GenBank database and core and pan-genome analysis revealed a considerable intraspecies heterogeneity. Phylogenomic analysis, gene content comparison, and average nucleotide identity calculation consistently indicated that the species has diverged into three well-differentiated clades. Population structure analysis further suggested the existence of an unknown ancestor or the fourth, yet unsampled, clade. Reconstruction of gene gain/loss events along the evolutionary history revealed both early events that contributed to the inter-clade divergence and recent events leading to the intra-clade diversity. We also found convincing evidence that recombination has played a key role in the evolutionary process of the species, with upto two-thirds of the core genes having been affected by recombination. Furthermore, distribution of mammal-associated strains (including pathogens) on the phylogenetic tree suggested that the last common ancestor had a free-living lifestyle, and a few recently diverged lineages have developed a mammal-associated lifestyle separately. Consistently, genome-wide association analysis revealed that mammal-associated strains from different lineages shared genes functionally relevant to the host-associated lifestyle, indicating a recent ecological adaption to the new host-associated habitats. CONCLUSIONS: These results revealed high intraspecies genomic diversity of M. luteus and highlighted that gene gain/loss events and extensive recombination events played key roles in the genome evolution. Our study also indicated that, as a free-living species, some lineages have recently developed or are developing a mammal-associated lifestyle. This study provides insights into the mechanisms that drive the genome evolution and adaption to various environments of a bacterial species.

Genomic insights into antioxidant activities of Pyruvatibacter mobilis CGMCC 1.15125T, a pyruvate-requiring bacterium isolated from the marine microalgae culture.

Pyruvate is a well-known scavenger of reactive oxygen species (ROS) like hydrogen peroxide and could prevent cells from oxidative damage. A pyruvate-requiring marine bacterium, Pyruvatibacter mobilis CGMCC 1.15125T (=KCTC 42509T), was isolated from the culture broth of a photosynthetic marine microalga. Here we report the complete genome sequence of Pyruvatibacter mobilis, which contained a circular chromosome of 3,333,914 bp with a mean G + C content of 63.9%. Through genomic analysis, we revealed that strain CGMCC 1.15125T encodes genes for some antioxidants like superoxide dismutase, glutathione, rubrerythrin and globin to relieve cellular oxidative stress, while pyruvate added to the medium may reduce extracellular ROS. The genome features of P. mobilis provide further insights into the antioxidant activities of bacteria surviving in oxygen-enriched habitats.

Evolutionary Trajectory of the Replication Mode of Bacterial Replicons.

As typical bacterial replicons, circular chromosomes replicate bidirectionally and circular plasmids replicate either bidirectionally or unidirectionally. Whereas the finding of chromids (plasmid-derived chromosomes) in multiple bacterial lineages provides circumstantial evidence that chromosomes likely evolved from plasmids, all experimentally assayed chromids were shown to use bidirectional replication. Here, we employed a model system, the marine bacterial genus Pseudoalteromonas, members of which consistently carry a chromosome and a chromid. We provide experimental and bioinformatic evidence that while chromids in a few strains replicate bidirectionally, most replicate unidirectionally. This is the first experimental demonstration of the unidirectional replication mode in bacterial chromids. Phylogenomic and comparative genomic analyses showed that the bidirectional replication evolved only once from a unidirectional ancestor and that this transition was associated with insertions of exogenous DNA and relocation of the replication terminus region (ter2) from near the origin site (ori2) to a position roughly opposite it. This process enables a plasmid-derived chromosome to increase its size and expand the bacterium's metabolic versatility while keeping its replication synchronized with that of the main chromosome. A major implication of our study is that the uni- and bidirectionally replicating chromids may represent two stages on the evolutionary trajectory from unidirectionally replicating plasmids to bidirectionally replicating chromosomes in bacteria. Further bioinformatic analyses predicted unidirectionally replicating chromids in several unrelated bacterial phyla, suggesting that evolution from unidirectionally to bidirectionally replicating replicons occurred multiple times in bacteria.IMPORTANCE Chromosome replication is an essential process for cell division. The mode of chromosome replication has important impacts on the structure of the chromosome and replication speed. Bidirectional replication is the rule for bacterial chromosomes, and unidirectional replication has been found only in plasmids. To date, no bacterial chromosomes have been experimentally demonstrated to replicate unidirectionally. Here, we showed that the chromids (plasmid-derived chromosomes) in Pseudoalteromonas replicate either uni- or bidirectionally and that a single evolutionary transition from uni- to bidirectionality explains this diversity. These uni- and bidirectionally replicating chromids likely represent two stages during the evolution from a small and unidirectionally replicating plasmid to a large and bidirectionally replicating chromosome. This study provides insights into both the physiology of chromosome replication and the early evolutionary history of bacterial chromosomes.

Complete Genomic Sequence of Pseudoalteromonas sp. Strain SAO4-4, a Protease-Producing Bacterium Isolated from Seawater of the Atlantic Ocean.

The complete genome of Pseudoalteromonas sp. strain SAO4-4, a protease-producing bacterium from seawater, is composed of two circular chromosomes and one plasmid. This genome sequence will provide a better understanding of the ecological roles of protease-producing bacteria in the degradation of organic matter in marine aquatic environments.

Complete genome sequence of Pseudoalteromonas espejiana DSM9414T, an amino-acid-requiring strain from seawater.

Strain DSM9414, the type strain of Pseudoalteromonas espejiana, is a Gram-negative, and amino-acid-requiring stain isolated from seawater off the coast of Northern California. In this study, we report the complete genome sequence of Pseudoalteromonas espejiana DSM9414T. The genome (4,500,451bp; 40.3% G+C) is composed of two circular chromosomes: chromosome I is 3,720,756bp with 40.4% G+C content and chromosome II is 779,695bp with 39.8% G+C content. Genomic analysis showed that chromosome I encodes a complete set of ABC transporters responsible for branched-chain amino acids, whose homologous proteins were not discovered in other Pseudoalteromonas genomes released. This result indicated the tight dependence of extracellular amino acids for strain DSM9414T, which is consistent with its phenotype. The complete genome sequence of P. espejiana provides further genetic insights into the diversity of dependence on extracellular amino acids for Pseudoalteromonas species.

Complete genome sequence of a marine bacterium with two chromosomes, Pseudoalteromonas translucida KMM 520(T).

Bacteria with multiple chromosomes provide new insights into the evolution of multipartite genome structures and bacterial survival strategies. In this study, we report the complete genome sequence of Pseudoalteromonas translucida KMM 520(T), which contains two circular chromosomes and comprises 4,147,593 bp with a mean G+C content of 40.1%. The two chromosomes have similar G+C contents and similar percentages of coding regions. Chromosome II of P. translucida possesses a plasmid-type replication initiator protein (RepA), which indicated that chromosome II is probably originated from a plasmid. COG functional categories revealed that the two chromosomes have divergent distributions of functional categories, which indicated that they bear different responsibilities for cellular functions. The complete genome sequence of P. translucida contributes to a better understanding of the origin and evolution of the additional chromosome and the physiology of Pseudoalteromonas genus.

Insight into the genome sequence of a sediment-adapted marine bacterium Neptunomonas antarctica S3-22(T) from Antarctica.

Neptunomonas antarctica S3-22(T) was isolated from marine sediment of the Nella Fjord, Antarctica. Here we report the draft genome sequence of N. antarctica, which comprises 4,568,828 bp with a mean G+C content of 45.7%. We found numerous genes related to resistance, motility and chemotaxis, nitrogen metabolism, aromatic compound metabolism and stress response. These metabolic features and related genes revealed genetic basis for the adaptation to the marine sediment environment in Antarctica. The genome sequence of N. antarctica S3-22(T) may also provide further insights into the ecological role of the genus Neptunomonas.

Deep RNA sequencing reveals a high frequency of alternative splicing events in the fungus Trichoderma longibrachiatum.

BACKGROUND: Alternative splicing is crucial for proteome diversity and functional complexity in higher organisms. However, the alternative splicing landscape in fungi is still elusive. RESULTS: The transcriptome of the filamentous fungus Trichoderma longibrachiatum was deep sequenced using Illumina Solexa technology. A total of 14305 splice junctions were discovered. Analyses of alternative splicing events revealed that the number of all alternative splicing events (10034), intron retentions (IR, 9369), alternative 5' splice sites (A5SS, 167), and alternative 3' splice sites (A3SS, 302) is 7.3, 7.4, 5.1, and 5.9-fold higher, respectively, than those observed in the fungus Aspergillus oryzae using Illumina Solexa technology. This unexpectedly high ratio of alternative splicing suggests that alternative splicing is important to the transcriptome diversity of T. longibrachiatum. Alternatively spliced introns had longer lengths, higher GC contents, and lower splice site scores than constitutive introns. Further analysis demonstrated that the isoform relative frequencies were correlated with the splice site scores of the isoforms. Moreover, comparative transcriptomics determined that most enzymes related to glycolysis and the citrate cycle and glyoxylate cycle as well as a few carbohydrate-active enzymes are transcriptionally regulated. CONCLUSIONS: This study, consisting of a comprehensive analysis of the alternative splicing landscape in the filamentous fungus T. longibrachiatum, revealed an unexpectedly high ratio of alternative splicing events and provided new insights into transcriptome diversity in fungi.

Comparative transcriptome analysis reveals that lactose acts as an inducer and provides proper carbon sources for enhancing exopolysaccharide yield in the deep-sea bacterium Zunongwangia profunda SM-A87.

Many marine bacteria secrete exopolysaccharides (EPSs) that have important ecological and physiological functions. Numerous nutritional and environmental factors influence bacterial EPS production. However, the regulatory mechanisms of EPS production are poorly understood. The deep-sea Bacteroidetes bacterium Zunongwangia profunda SM-A87 can produce high quantities of EPS, and its EPS production is enhanced significantly by lactose. Here, we studied the reasons behind the significant advantage that lactose has over other carbon sources in EPS production in SM-A87. RNA-seq technologies were used to study lactose-regulated genes in SM-A87. The expression level of genes within the EPS gene cluster was up-regulated when lactose was added. Supplement of lactose also influenced the expression of genes located outside the EPS gene cluster that are also involved in EPS biosynthesis. The major glycosyl components of SM-A87 EPS are mannose, glucose and galactose. Genomic metabolic pathway analyses showed that the EPS precursor GDP-mannose can be synthesized from glucose, while the precursor UDP-glucose must be synthesized from galactose. Lactose can provide glucose and galactose simultaneously and prevent glucose inhibition. Lactose can also greatly stimulate the growth of SM-A87. Taken together, lactose acts not only as an inducer but also as a carbohydrate source for EPS production. This research broadens our knowledge of the regulation of EPS production in marine bacteria.

Comparative genomics of the marine bacterial genus Glaciecola reveals the high degree of genomic diversity and genomic characteristic for cold adaptation.

To what extent the genomes of different species belonging to one genus can be diverse and the relationship between genomic differentiation and environmental factor remain unclear for oceanic bacteria. With many new bacterial genera and species being isolated from marine environments, this question warrants attention. In this study, we sequenced all the type strains of the published species of Glaciecola, a recently defined cold-adapted genus with species from diverse marine locations, to study the genomic diversity and cold-adaptation strategy in this genus.The genome size diverged widely from 3.08 to 5.96 Mb, which can be explained by massive gene gain and loss events. Horizontal gene transfer and new gene emergence contributed substantially to the genome size expansion. The genus Glaciecola had an open pan-genome. Comparative genomic research indicated that species of the genus Glaciecola had high diversity in genome size, gene content and genetic relatedness. This may be prevalent in marine bacterial genera considering the dynamic and complex environments of the ocean. Species of Glaciecola had some common genomic features related to cold adaptation, which enable them to thrive and play a role in biogeochemical cycle in the cold marine environments.

Comparative genomics provide insights into evolution of trichoderma nutrition style.

Saprotrophy on plant biomass is a recently developed nutrition strategy for Trichoderma. However, the physiology and evolution of this new nutrition strategy is still elusive. We report the deep sequencing and analysis of the genome of Trichoderma longibrachiatum, an efficient cellulase producer. The 31.7-Mb genome, smallest among the sequenced Trichoderma species, encodes fewer nutrition-related genes than saprotrophic T. reesei (Tr), including glycoside hydrolases and nonribosomal peptide synthetase-polyketide synthase. Homology and phylogenetic analyses suggest that a large number of nutrition-related genes, including GH18 chitinases, ß-1,3/1,6-glucanases, cellulolytic enzymes, and hemicellulolytic enzymes, were lost in the common ancestor of T. longibrachiatum (Tl) and Tr. dN/dS (ω) calculation indicates that all the nutrition-related genes analyzed are under purifying selection. Cellulolytic enzymes, the key enzymes for saprotrophy on plant biomass, are under stronger purifying selection pressure in Tl and Tr than in mycoparasitic species, suggesting that development of the nutrition strategy of saprotrophy on plant biomass has increased the selection pressure. In addition, aspartic proteases, serine proteases, and metalloproteases are subject to stronger purifying selection pressure in Tl and Tr, suggesting that these enzymes may also play important roles in the nutrition. This study provides insights into the physiology and evolution of the nutrition strategy of Trichoderma.

Genome sequence of proteorhodopsin-containing sea ice bacterium Glaciecola punicea ACAM 611T.

Here, we report the draft genome sequence of Antarctic sea ice bacterium Glaciecola punicea ACAM 611(T), the type species of the genus Glaciecola. A blue-light-absorbing proteorhodopsin gene is present in the 3.08-Mb genome. This genome sequence can facilitate the study of the physiological metabolisms and ecological roles of sea ice bacteria.

Genome sequences of type strains of seven species of the marine bacterium Pseudoalteromonas.

There are over 30 species in the marine bacterial genus Pseudoalteromonas. However, our knowledge about this genus is still limited. We sequenced the genomes of type strains of seven species in the genus, facilitating the study of the physiology, adaptation, and evolution of this genus.

Genome sequence of the cycloprodigiosin-producing bacterial strain Pseudoalteromonas rubra ATCC 29570(T).

The cycloprodigiosin biosynthetic gene cluster has not been reported. We sequenced the genome of a cycloprodigiosin-producing bacterial strain, Pseudoalteromonas rubra ATCC 29570(T). Analysis revealed a probable cycloprodigiosin biosynthetic cluster, providing a good model for the study of cycloprodigiosin synthesis and regulation.