Keshao Liu

Distribution and Functions of TonB-Dependent Transporters in Marine Bacteria and Environments: Implications for Dissolved Organic Matter Utilization

Background Bacteria play critical roles in marine nutrient cycles by incorporating and redistributing dissolved organic matter (DOM) and inorganic nutrients in the ocean. TonB-dependent transporter (TBDT) proteins allow Gram-negative bacteria to take up scarce resources from nutrient-limiting environments as well as siderophores, heme, vitamin B12, and recently identified carbohydrates. Thus, the characterization of TBDT distribution and functions is essential to better understand the contribution TBDT to DOM assimilation and its consequences on nutrient cycling in the environment. Methodology/Principal Findings This study presents the distribution of encoded known and putative TBDT proteins in the genomes of microorganisms and from the Global Ocean Survey data. Using a Lek clustering algorithm and substrate specificities, the TBDT sequences were mainly classified into the following three groups: (1) DOM transporters; (2) Siderophores/Vitamins transporters; and (3) Heme/Hemophores/Iron(heme)-binding protein transporters. Diverse TBDTs were found in the genomes of oligotroph Citromicrobium bathyomarinum JL354 and Citromicrobium sp JLT1363 and were highly expressed in the stationary phase of bacterial growth. The results show that the Gammaproteobacteria and the Cytophaga-Flavobacterium-Bacteroides (CFB) group bacteria accounted for the majority of the TBDT gene pool in marine surface waters. Conclusions/Significance The results of this study confirm the ecological importance of TBDTs in DOM assimilation for bacteria in marine environments owing to a wide range of substrate utilization potential in the ubiquitous Gammaproteobacteria and CFB group bacteria.

Functional Metagenomic Investigations of Microbial Communities in a Shallow-Sea Hydrothermal System

Little is known about the functional capability of microbial communities in shallow-sea hydrothermal systems (water depth of <200 m). This study analyzed two high-throughput pyrosequencing metagenomic datasets from the vent and the surface water in the shallow-sea hydrothermal system offshore NE Taiwan. This system exhibited distinct geochemical parameters. Metagenomic data revealed that the vent and the surface water were predominated by Epsilonproteobacteria (Nautiliales-like organisms) and Gammaproteobacteria ( Thiomicrospira -like organisms), respectively. A significant difference in microbial carbon fixation and sulfur metabolism was found between the vent and the surface water. The chemoautotrophic microorganisms in the vent and in the surface water might possess the reverse tricarboxylic acid cycle and the Calvin−Bassham−Benson cycle for carbon fixation in response to carbon dioxide highly enriched in the environment, which is possibly fueled by geochemical energy with sulfur and hydrogen. Comparative analyses of metagenomes showed that the shallow-sea metagenomes contained some genes similar to those present in other extreme environments. This study may serve as a basis for deeply understanding the genetic network and functional capability of the microbial members of shallow-sea hydrothermal systems.

Gramella flava sp nov., a member of the family Flavobacteriaceae isolated from seawater

A novel Gram-negative, yellow-pigmented, aerobic, motile by gliding, rod-shaped marine bacterium (JLT2011(T)) was isolated from surface seawater. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain JLT2011(T) could be assigned to the genus Gramella and was most closely related to Gramella gaetbulicola, with 96.2 % similarity. The genomic DNA G+C content was 42.1 %. The predominant fatty acids were C16 : 0, iso-C15 : 0, C18 : 0 and summed feature 3 (C16 : 1ω6c/C16 : 1ω7c). The major menaquinone was MK-6. The major components of the polar lipid profile were phosphatidylglycerol, diphosphatidylglycerol and sphingoglycolipid. On the basis of phenotypic, genotypic and taxonomic data presented, strain JLT2011(T) is considered to represent a novel species of the genus Gramella, for which the name Gramella flava sp. nov. is proposed; the type strain is JLT2011(T) ( = CGMCC 1.12375(T) = LMG 27360(T)).

Thiobacimonas profunda gen. nov., sp. nov., a member of the family Rhodobacteraceae isolated from deep-sea water

A bacterial strain, JLT2016(T), was isolated from a sample of South-eastern Pacific deep-sea water. Cells were Gram-stain-negative, aerobic, devoid of flagella, motile by gliding and rod-shaped. Colonies were mucoid and cream. Growth occurred at 1.0-11.0 % (w/v) NaCl, 10-40 °C and pH 4.0-9.0. The major fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) (60.5 %), C19 : 0 cyclo ω8c (10.9 %) and C16 : 0 (9.0 %). The polar lipids included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and two sphingoglycolipids. The DNA G+C content was 67.1 mol%. The closest relative of strain JLT2016(T) was Salipiger mucosus A3(T) (96.7 % 16S rRNA gene sequence similarity). The results of phylogenetic analyses with different treeing algorithms indicated that this strain belonged to the Roseobacter clade in the order Rhodobacterales. Based on polyphasic analysis, strain JLT2016(T) is considered to represent a novel genus and species, for which the name Thiobacimonas profunda gen. nov., sp. nov. is proposed. The type strain is JLT2016(T) ( = LMG 27365(T) = CGMCC 1.12377(T)).

Hymenobacter glacieicola sp nov., isolated from glacier ice

A Gram-stain-negative, rod-shaped, non-motile and red-pink-pigmented bacterial strain, designated B1909T, was isolated from an ice core drilled from Muztagh Glacier on the Tibetan Plateau, China. A phylogenetic tree based on 16S rRNA gene sequences showed that strain B1909T formed a lineage within the genus Hymenobacter and was closely related to Hymenobacter xinjiangensis X2-1gT (96.16 % similarity) and Hymenobacter psychrotolerans Tibet-IIU11T (95.99 %). The predominant fatty acids were iso-C15 : 0, summed feature 3 (C16 : 1ω7c/C16 : 1ω6c), summed feature 4 (iso-C17 : 1ω6c I/anteiso B), C16 : 1ω5c, anteiso-C15 : 0 and iso-C17 : 0 3-OH. The major menaquinone was MK-7. The major polar lipid was phosphatidylethanolamine. The DNA G+C content was 59 mol%. On the basis of the phenotypic, phylogenetic and chemotaxonomic data presented, strain B1909T is considered to represent a novel species of the genus Hymenobacter, for which the name Hymenobacterglacieicola sp. nov. is proposed; the type strain is B1909T (=JCM 30596T=CGMCC 1.12990T).

Oceanitalea nanhaiensis gen nov, sp nov, an actinobacterium isolated from seawater

A Gram-positive, motile, short-rod-shaped bacterium, designated strain JLT1488(T), was isolated from the South China Sea and investigated in a taxonomic study using a polyphasic approach. The peptidoglycan type determined for strain JLT1488(T) was A4α with lysine as the diagnostic cell-wall diamino acid and an interpeptide bridge of L-Lys-L-Glu. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides, an unknown glycolipid and an unknown phospholipid. The only detected menaquinone was MK-8(H(4)), and the major fatty acids were summed feature 8 (C(18 : 1)ω7c/C(18 : 1)ω6c) , C(16 : 0) and summed feature 3 (C(16 : 1)ω7c/C(16 : 1)ω6c); significant amounts of C(12 : 0) 3-OH, C(10 : 0) and C(19 : 0) cyclo ω8c were also present. The G+C content of the genomic DNA was 62.3 mol%. Comparison of the 16S rRNA gene sequence of strain JLT1488(T) with those of related type strains demonstrated that it represented a novel lineage within the family Bogoriellaceae, suborder Micrococcineae, being closely related to species of the genera Georgenia, Bogoriella and Cellulomonas (94.6-96.8 % sequence similarity). These results demonstrate that strain JLT1488(T) is a member of a new genus, for which the name Oceanitalea nanhaiensis gen. nov., sp. nov. is proposed. The type strain of the type species is JLT1488(T) ( = JCM 17755(T) = CGMCC 1.10826(T)).

Genomic, physiologic, and proteomic insights into metabolic versatility in Roseobacter clade bacteria isolated from deep-sea water

Roseobacter clade bacteria are ubiquitous in marine environments and now thought to be significant contributors to carbon and sulfur cycling. However, only a few strains of roseobacters have been isolated from the deep-sea water column and have not been thoroughly investigated. Here, we present the complete genomes of phylogentically closed related Thiobacimonas profunda JLT2016 and Pelagibaca abyssi JLT2014 isolated from deep-sea water of the Southeastern Pacific. The genome sequences showed that the two deep-sea roseobacters carry genes for versatile metabolisms with functional capabilities such as ribulose bisphosphate carboxylase-mediated carbon fixation and inorganic sulfur oxidation. Physiological and biochemical analysis showed that T. profunda JLT2016 was capable of autotrophy, heterotrophy, and mixotrophy accompanied by the production of exopolysaccharide. Heterotrophic carbon fixation via anaplerotic reactions contributed minimally to bacterial biomass. Comparative proteomics experiments showed a significantly up-regulated carbon fixation and inorganic sulfur oxidation associated proteins under chemolithotrophic conditions compared to heterotrophic conditions. Collectively, rosebacters show a high metabolic flexibility, suggesting a considerable capacity for adaptation to the marine environment.

Marivirga lumbricoides sp. nov., a marine bacterium isolated from the South China Sea.

A novel, aerobic, heterotrophic, orange-pigmented, Gram-staining-negative, rod-shaped, gliding bacterial strain, designated JLT2000(T), was isolated from surface water of the South China Sea. The strain was oxidase- and catalase-positive. The major cellular fatty acids of strain JLT2000 T: were C12 : 0, iso-C15 : 1 G, iso-C15 : 0, iso-C17 : 0 3-OH, summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 0. MK-7 was the major respiratory quinone and the major polar lipids were phosphatidylcholine and phosphatidylethanolamine. The genomic DNA G+C content of strain JLT2000(T) was 37.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain JLT2000(T) formed a branch within the genus Marivirga, but was clearly separated from the two established species of this genus, Marivirga tractuosa and Marivirga sericea. The 16S rRNA gene sequence similarity of strain JLT2000(T) with the type strains of these two species was 95.8 % and 96.1 %, respectively. Strain JLT2000(T) had a shorter cell length and wider growth range in different temperatures and salinities than those of Marivirga tractuosa NBRC 15989(T) and Marivirga sericea NBRC 15983(T). In addition, strain JLT2000(T) could utilize more carbon sources and hydrolyse more polymers than Marivirga tractuosa NBRC 15989(T) and Marivirga sericea NBRC 15983(T). Based on this polyphasic analysis, strain JLT2000(T) represents a novel species of the genus Marivirga, for which the name Marivirga lumbricoides sp. nov. is proposed. The type strain is JLT2000(T) ( = JCM 18012(T) = CGMCC 1.10832(T)).

Genomic, proteomic and bioinformatic analysis of two temperate phages in Roseobacter clade bacteria isolated from the deep-sea water

BackgroundMarine phages are spectacularly diverse in nature. Dozens of roseophages infecting members of Roseobacter clade bacteria were isolated and characterized, exhibiting a very high degree of genetic diversity. In the present study, the induction of two temperate bacteriophages, namely, vB_ThpS-P1 and vB_PeaS-P1, was performed in Roseobacter clade bacteria isolated from the deep-sea water, Thiobacimonas profunda JLT2016 and Pelagibaca abyssi JLT2014, respectively. Two novel phages in morphological, genomic and proteomic features were presented, and their phylogeny and evolutionary relationships were explored by bioinformatic analysis.ResultsElectron microscopy showed that the morphology of the two phages were similar to that of siphoviruses. Genome sequencing indicated that the two phages were similar in size, organization, and content, thereby suggesting that these shared a common ancestor. Despite the presence of Mu-like phage head genes, the phages are more closely related to Rhodobacter phage RC1 than Mu phages in terms of gene content and sequence similarity. Based on comparative genomic and phylogenetic analysis, we propose a Mu-like head phage group to allow for the inclusion of Mu-like phages and two newly phages. The sequences of the Mu-like head phage group were widespread, occurring in each investigated metagenomes. Furthermore, the horizontal exchange of genetic material within the Mu-like head phage group might have involved a gene that was associated with phage phenotypic characteristics.ConclusionsThis study is the first report on the complete genome sequences of temperate phages that infect deep-sea roseobacters, belonging to the Mu-like head phage group. The Mu-like head phage group might represent a small but ubiquitous fraction of marine viral diversity.