Kangiella koreensis gen. nov., sp. nov. and Kangiella aquimarina sp. nov., isolated from a tidal flat of the Yellow Sea in Korea

Degradation potential of alkanes by diverse oil-degrading bacteria from deep-sea sediments of Haima cold seep areas, South China Sea

Marine oil spills are a significant concern worldwide, destroying the ecological environment and threatening the survival of marine life. Various oil-degrading bacteria have been widely reported in marine environments in response to marine oil pollution. However, little information is known about culturable oil-degrading bacteria in cold seep of the deep-sea environments, which are rich in hydrocarbons. This study enriched five oil-degrading consortia from sediments collected from the Haima cold seep areas of the South China Sea. Parvibaculum, Erythrobacter, Acinetobacter, Alcanivorax, Pseudomonas, Marinobacter, Halomonas, and Idiomarina were the dominant genera. Further results of bacterial growth and degradation ability tests indicated seven efficient alkane-degrading bacteria belonging to Acinetobacter, Alcanivorax, Kangiella, Limimaricola, Marinobacter, Flavobacterium, and Paracoccus, whose degradation rates were higher in crude oil (70.3–78.0%) than that in diesel oil (62.7–66.3%). From the view of carbon chain length, alkane degradation rates were medium chains > long chains > short chains. In addition, Kangiella aquimarina F7, Acinetobacter venetianus F1, Limimaricola variabilis F8, Marinobacter nauticus J5, Flavobacterium sediminis N3, and Paracoccus sediminilitoris N6 were first identified as oil-degrading bacteria from deep-sea environments. This study will provide insight into the bacterial community structures and oil-degrading bacterial diversity in the Haima cold seep areas, South China Sea, and offer bacterial resources to oil bioremediation applications.

The microbial RNA metagenome of Aedes albopictus (Diptera: Culicidae) from Germany

Aedes albopictus is a highly invasive mosquito species that has become widespread across the globe. In addition, it is an efficient vector of numerous pathogens of medical and veterinary importance, including dengue, chikungunya and Zika viruses. Among others, the vector potential of mosquitoes is influenced by their microbiome. However, this influence is very dynamic and can vary between individuals and life stages. To obtain a rough overview on the microbiome of Ae. albopictus populations in Germany, pooled female and pooled male individuals from seven German locations were investigated by total RNA sequencing. The mosquito specimens had been collected as larvae in the field and processed immediately after adult emergence, i.e. without females having fed on blood. RNA fragments with high degrees of identity to a large number of viruses and microorganisms were identified, including, for example, Wolbachia pipientis and Acinetobacter baumannii, with differences between male and female mosquitoes. Knowledge about the natural occurrence of microorganisms in mosquitoes may be translated into new approaches to vector control, for example W. pipientis can be exploited to manipulate mosquito reproduction and vector competence. The study results show how diverse the microbiome of Ae. albopictus can be, and the more so needs to be adequately analysed and interpreted.

Kangiella shandongensis sp. nov., a novel species isolated from saltern in Yantai, China

A Gram-stain-negative, wheat, rod-shaped, non-motile, non-spore forming, and facultatively anaerobic bacterium strain, designated as PI^T, was isolated from saline silt samples collected in saltern in Yantai, Shandong, China. Growth was observed within the ranges 4-45 °C (optimally at 33 °C), pH 6.0-9.0 (optimally at pH 7.0) and 1.0-11.0% NaCl (optimally at 3.0%, w/v). Strain PI^T showed highest 16S rRNA gene sequence similarity to Kangiella sediminilitoris BB-Mw22^T (98.3%) and Kangiella taiwanensis KT1^T (98.3%). The major cellular fatty acids (> 10% of the total fatty acids) were iso-C_15:0 (52.7%) and summed featured 9 (iso-C_17:1ω9c/C_16:0 10-methyl, 11.8%). The major polar lipids identified were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine and phosphatidylglycerol. The major respiratory isoprenoid quinone was Q-8. The G + C content of the genomic DNA was 45.8%. Average Nucleotide Identity values between whole genome sequences of strain PI^T and next related type strains supported the novel species status. Based on physiological, biochemical, chemotaxonomic characteristics and genomic analysis, strain PI^T is considered to represent a novel species within the genus Kangiella, for which the name Kangiella shandongensis sp. nov. is proposed. The type strain is PI^T (= KCTC 82509 ^T = MCCC 1K04352^T).

Aliikangiella coralliicola sp. nov., a bacterium isolated from coral Porites lutea, and proposal of Pleioneaceae fam. nov. to accommodate Pleionea and Aliikangiella

A novel Gram-stain-negative, non-endospore-forming, motile, and aerobic bacterial strain, M105^T, was isolated from coral Porites lutea, and was subjected to a polyphasic taxonomic study. Global alignment based on 16S rRNA gene sequences indicated that M105^T shares the highest sequence identity of 94.5 % with Aliikangiella marina GYP-15^T. The average nucleotide identity (ANI) and average amino acid identity (AAI) between M105^T and A. marina GYP-15^T was 69.8 and 71.6 %, respectively. On the basis of the results of phenotypic, chemotaxonomic, phylogenetic, phylogenomic, and comparative genomic analyses, it is concluded that M105^T should represent a novel species in the genus Aliikangiella, for which the name Aliikangiella coralliicola sp. nov. is proposed. The type strain is M105^T (=MCCC 1K03773^T= KCTC 72442^T). Furthermore, the family Kangiellaceae was classified into two families on the basis of phylogenetic, phylogenomic, polar lipid profile and motility variations. The novel family Pleioneaceae fam. nov. is proposed to accommodate the genera Aliikangiella and Pleionea.

Reclassification of the Taxonomic Framework of Orders Cellvibrionales, Oceanospirillales, Pseudomonadales, and Alteromonadales in Class Gammaproteobacteria through Phylogenomic Tree Analysis

Orders Oceanospirillales and Pseudomonadales play important roles in various ecosystems as the keystone taxa of microbiomes. However, the two orders present a close evolutionary relationship, which might have caused taxonomic misinterpretation and resulted in an incorrect understanding of their evolutionary history. In this study, first, we used the 16S rRNA gene sequences of 2,049 species of Gammaproteobacteria to build a phylogenetic tree, which demonstrated that reports regarding the evolutionary relationship of orders Cellvibrionales, Oceanospirillales, and Pseudomonadales based on a single conserved gene with a poor resolution have been conflicting; in particular, the major families Moraxellaceae and Pseudomonadaceae of order Pseudomonadales were separated from orders Cellvibrionales and Oceanospirillales Subsequently, we constructed the bac120 trees of all representative reference genomes of class Gammaproteobacteria based on 120 ubiquitous single-copy proteins from bacteria and a phylogenomic tree based on the 119 core genes of 257 reference genomes obtained from orders Cellvibrionales, Oceanospirillales, and Pseudomonadales to cross validate and infer their intrinsic evolutionary relationships. These results indicated that two novel orders, Moraxellales ord. nov. and Kangiellales ord. nov., and three novel families, Marinobacteraceae fam. nov., Perlucidibacaceae fam. nov., and Zooshikellaceae fam. nov., should be proposed. Additionally, orders Cellvibrionales and Oceanospirillales were merged into the order Pseudomonadales except for families Moraxellaceae and Kangiellaceae in class Gammaproteobacteria, which currently includes 18 families. Our work sheds some light on the evolutionary history of class Gammaproteobacteria, which could facilitate the detection and taxonomic analysis of natural communities.IMPORTANCE The orders Cellvibrionales, Oceanospirillales, and Pseudomonadales, as three major orders of the largest bacterial class, Gammaproteobacteria, play important roles in various ecosystems as the keystone taxa of microbiomes, but their evolutionary relationship is currently polyphyletic and chaotic. Here, we constructed a bac120 tree and core-genome tree and calculated the amino acid identity (AAI) value to explore their intrinsic evolutionary history. In this study, we proposed two novel orders and three novel families. This evolution study vastly reconstructed the taxonomic framework of class Gammaproteobacteria and could provide a more distinct perspective on global distribution and evolutionary patterns of these environmental microorganisms.

Pelagibaculum spongiae gen. nov., sp. nov., isolated from a marine sponge in South-West Iceland

A Gram-stain-negative, motile, mesophilic, aerobic, rod-shaped bacterium, designated Hp12^T, was isolated from a marine sponge in the intertidal zone off the coast of Seltjarnarnes (64° 16' N 22° 00' W), Iceland. Strain Hp12^T grew optimally at 20-22 °C, at pH 7-8 and in the presence of 1-2 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences placed strain Hp12^T in the class Gammaproteobacteria, related to members of the genus Alcanivorax in the order Oceanospirillales with 90.3-88.5 % sequence similarity. The strain had a draft genome size of 4.99 Mbp with a DNA G+C content of 43.0 mol%. Cellular fatty acids were dominated by C16 : 1 ω7c, C18 : 1 ω7c and C16 : 0. The predominant polar lipids were phosphatidylglycerol and phosphatidylethanolamine. The major respiratory lipoquinones were ubiquinone Q8 and menaquinone MK8. From the taxonomic information and phenotypic properties obtained in this study, it is proposed that strain Hp12^T be placed into a novel genus and species named Pelagibaculum spongiae gen. nov., sp. nov. The type strain of Pelagibaculum spongiae is Hp12^T (=DSM 104963^T=CECT 9367^T).

Benefits of a Bacillus probiotic to larval fish survival and transport stress resistance

The need for sustainable bacterial management approaches in aquaculture is crucial for advancement of the industry. Probiotics are a promising strategy as evidenced by benefits demonstrated in intensive larviculture of various marine fish species. In this study we investigate the effects of a mixed Bacillus species (B. licheniformis and B. amyloliquefaciens) probiotic on rearing of larval common snook (Centropomus undecimalis). Experimental treatments included (1) probiotics supplemented to the water and live feed, (2) probiotics supplemented to the water only, and (3) no probiotic controls. Data from two separate trials indicated up to 2.5 times higher survival with probiotic addition, as well as 20% higher survival 7 days following a transport event. These benefits were not explained by faster growth, measured water quality parameters, or innate immune enzyme activities. Microbiota analysis indicated the importance of system stabilization prior to larval stocking to improve rearing success and probiotic performance. ied Potential probiotic benefits include accelerated gastrointestinal tract development, enhanced immunity, inhibition of opportunistic bacteria, and improvements to water quality parameters. Results suggest this probiotic should be tested in other marine fish species in order to reduce larval rearing bottlenecks.

Trophic Specialization Results in Genomic Reduction in Free-Living Marine Idiomarina Bacteria

The streamlining hypothesis is usually used to explain the genomic reduction events in free-living bacteria like SAR11. However, we find that the genomic reduction phenomenon in the bacterial genus Idiomarina is different from that in SAR11. Therefore, we propose a new hypothesis to explain genomic reduction in this genus based on trophic specialization that could result in genomic reduction, which would be not uncommon in nature. Not only can the trophic specialization hypothesis explain the genomic reduction in the genus Idiomarina, but it also sheds new light on our understanding of the genomic reduction processes in other free-living bacterial lineages.

The streamlining hypothesis is generally used to explain the genomic reduction events related to the small genome size of free-living bacteria like marine bacteria SAR11. However, our current understanding of the correlation between bacterial genome size and environmental adaptation relies on too few species. It is still unclear whether there are other paths leading to genomic reduction in free-living bacteria. The genome size of marine free-living bacteria of the genus Idiomarina belonging to the order Alteromonadales (Gammaproteobacteria) is much smaller than the size of related genomes from bacteria in the same order. Comparative genomic and physiological analyses showed that the genomic reduction pattern in this genus is different from that of the classical SAR11 lineage. Genomic reduction reconstruction and substrate utilization profile showed that Idiomarina spp. lost a large number of genes related to carbohydrate utilization, and instead they specialized on using proteinaceous resources. Here we propose a new hypothesis to explain genomic reduction in this genus; we propose that trophic specialization increasing the metabolic efficiency for using one kind of substrate but reducing the substrate utilization spectrum could result in bacterial genomic reduction, which would be not uncommon in nature. This hypothesis was further tested in another free-living genus, Kangiella, which also shows dramatic genomic reduction. These findings highlight that trophic specialization is potentially an important path leading to genomic reduction in some marine free-living bacteria, which is distinct from the classical lineages like SAR11.

Genome Sequence of the Halophilic Bacterium Kangiella spongicola ATCC BAA-2076 T

The Gram-negative genus Kangiella contains a number of halophilic species that display high levels of iso-branched fatty acids. Kangiella spongicola was isolated from a marine sponge, Chondrilla nucula, from the Florida Keys in the United States.

The Gram-negative genus Kangiella contains a number of halophilic species that display high levels of iso-branched fatty acids. Kangiella spongicola was isolated from a marine sponge, Chondrilla nucula, from the Florida Keys in the United States. A genome assembly of 2,825,399 bp with a 44.31% G+C content was generated from strain A79^T (=ATCC BAA-2076^T).

Comparative Genomics Reveals Evidence of Genome Reduction and High Extracellular Protein Degradation Potential in Kangiella

The genus Kangiella has recently been proposed within the family Kangiellaceae, belonging to order Oceanospirillales. Here, we report the complete genome sequence of a novel strain, Kangiella profundi FT102, which is the only Kangiella species isolated from a deep sea sediment sample. Furthermore, gaps in the publicly available genome scaffold of K. aquimarina DSM 16071 (NCBI Reference Sequence: NZ_ARFE00000000.1) were also filled using polymerase chain reaction (PCR) and Sanger sequencing. A comparative genomic analysis of five Kangiella and 18 non-Kangiella strains revealed insights into their metabolic potential. It was shown that low genomic redundancy and Kangiella-lineage-specific gene loss are the key reasons behind the genome reduction in Kangiella compared to that in any other free-living Oceanospirillales strain. The occurrence of relatively diverse and more frequent extracellular protease-coding genes along with the incomplete carbohydrate metabolic pathways in the genome suggests that Kangiella has high extracellular protein degradation potential. Growth of Kangiella strains has been observed using amino acids as the only carbon and nitrogen source and tends to increase with additional tryptone. Here, we propose that extracellular protein degradation and amino acid utilization are significant and prominent features of Kangiella. Our study provides more insight into the genomic traits and proteolytic metabolic capabilities of Kangiella.

Bacterial Succession on Sinking Particles in the Ocean's Interior

Sinking particles formed in the photic zone and moving vertically through the water column are a main mechanism for nutrient transport to the deep ocean, and a key component of the biological carbon pump. The particles appear to be processed by a microbial community substantially different from the surrounding waters. Single cell genomics and metagenomics were employed to describe the succession of dominant bacterial groups during particle processing. Sinking particles were extracted from sediment traps at Station Aloha in the North Pacific Subtropical Gyre (NPSG) during two different trap deployments conducted in July and August 2012. The microbial communities in poisoned vs. live sediment traps differed significantly from one another, consistent with prior observations by Fontanez et al. (2015). Partial genomes from these communities were sequenced from cells belonging to the genus Arcobacter (commensalists potentially associated with protists such as Radiolaria), and Vibrio campbellii (a group previously reported to be associated with crustacea). These bacteria were found in the particle-associated communities at specific depths in both trap deployments, presumably due to their specific host-associations. Partial genomes were also sequenced from cells belonging to Idiomarina and Kangiella that were enriched in live traps over a broad depth range, that represented a motile copiotroph and a putatively non-motile algicidal saprophyte, respectively. Planktonic bacterial cells most likely caught in the wake of the particles belonging to Actinomarina and the SAR11 clade were also sequenced. Our results suggest that similar groups of eukaryote-associated bacteria are consistently found on sinking particles at different times, and that particle remineralization involves specific, reproducible bacterial succession events in oligotrophic ocean waters.

Diversity of bacteria in ships ballast water as revealed by next generation DNA sequencing

The bacterial diversity in ballast water from five general cargo ships calling at the Port of Houston was determined with ion semiconductor DNA sequencing (Ion Torrent PGM) of PCR amplified 16S rRNA genes. Phylogenetic analysis revealed that the composition of bacteria in ballast water did not resemble that of typical marine habitats or even open ocean waters where BWEs occur. The predominant group of bacteria in ships conducting BWEs was the Roseobacter clade within the Alphaproteobacteria. In contrast, Gammaproteobacteria were predominant in the ship that did not conduct a BWE. All the ships contained human, fish, and terrestrial plant pathogens as well as bacteria indicative of fecal or activated sludge contamination. Most of the 60 pathogens had not been detected in ballast water previously. Among these were the human pathogens Corynebacterium diptheriae and several Legionella species and the fish pathogens Francisella piscicida and Piscirickettsia salmonis.

Aliikangiella marina gen. nov., sp. nov., a marine bacterium from the culture broth of Picochlorum sp. 122, and proposal of Kangiellaceae fam. nov. in the order Oceanospirillales

A Gram-stain-negative, non-motile, non-spore-forming, long rod-shaped bacterium, designated strain GYP-15T, was isolated from the culture broth of a marine microalga, Picochloruma sp. 122. Phylogenetic analyses revealed that strain GYP-15T shared 90.6 % 16S rRNA gene sequence similarity with its closest relative, Kangiella aquimarina KCTC 12183T, and represents a distinct phylogenetic lineage in a robust clade consisting of GYP-15T and members of the genera Kangiella and Pleionea in the order Oceanospirillales. Chemotaxonomic and physiological characteristics, including major cellular fatty acids, NaCl tolerance and pattern of carbon source utilization, could also readily distinguish strain GYP-15T from all established genera and species. Thus, it is concluded that strain GYP-15T represents a novel species of a new genus, for which the name Aliikangiella marina gen. nov., sp. nov. is proposed. The type strain of Aliikangiella marina is GYP-15T ( = MCCC 1K01163T = KCTC 42667T). Based on phylogenetic results, 16S rRNA gene signature nucleotide pattern and some physiological characteristics, the three genera Kangiella, Pleionea and Aliikangiella are proposed to make up a novel family, Kangiellaceae fam. nov., in the order Oceanospirillales.

Kangiella profundi sp. nov., isolated from deep-sea sediment

A taxonomic study employing a polyphasic approach was carried out on strain FT102(T), which was isolated from a deep-sea sediment sample collected in the south-west Indian Ocean at a depth of 2784 m. The strain was Gram-stain-negative, non-motile, rod-shaped and non-spore-forming. It grew optimally at 37-42 °C, pH 6.5-8.5 and in the presence of 1-4% (w/v) NaCl. Phylogenetic analysis of 16S rRNA gene sequences confirmed the separation of the novel strain from recognized members of the genus Kangiella that are available in public databases. Strain FT102(T) exhibited 95.5-98.6% 16S rRNA gene sequence similarity to the type strains of the eight recognized species of the genus Kangiella. The chemotaxonomically characteristic fatty acid iso-C15:0 and ubiquinone Q-8 were also detected. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylmonomethylethanolamine. The DNA G + C content of strain FT102(T) was 45.0 mol%. The mean DNA-DNA relatedness values between strain FT102(T) and the type strains of Kangiella aquimarina and Kangiella koreensis were 47.3% and 13.7%, respectively. The combined results of phylogenetic, physiological and chemotaxonomic studies indicated that strain FT102(T) was affiliated with the genus Kangiella but differed from the recognized species of the genus Kangiella. Therefore, strain FT102T represents a novel species of the genus Kangiella, for which the name Kangiella profundi sp. nov. is proposed. The type strain is FT102(T) ( = CGMCC 1.12959(T) = KCTC 42297(T) = JCM 30232(T)).

Kangiella chungangensis sp. nov. isolated from a marine sand

A Gram-negative bacterium, designated CAU 1040(T), which was isolated from marine sand obtained from Jeju Island in South Korea, was characterized as an aerobic rod-shaped organism that that was non-motile, non-spore-forming and halophilic. The bacterium grew optimally at 37 °C, at pH 8, and in the presence of 2% (w/v) NaCl. The taxonomic classification of CAU 1040(T) was investigated using a polyphasic characterization approach. While phylogenetic analysis of the 16S rRNA gene sequence revealed that CAU 1040(T) belongs to the genus Kangiella, the strain exhibited only 94.4-95.4% sequence similarity to the previously described Kangiella species. Similar to other Kangiella species, Q-8 was the predominant ubiquionone and iso-C(15:0) was the major cellular fatty acid detected in strain CAU 1040(T). The predominant polar lipids identified were diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. The G+C content of the CAU 1040(T) genome was 45.3 mol%. The phylogenetic, physiological, biochemical and chemotaxonomic data obtained in this study indicate that strain CAU 1040(T) represents a novel species of the genus Kangiella, for which the name Kangiella chungangensis sp. nov. is hereby proposed. The type strain is CAU 1040(T) (KCTC 42299(T), NBRC 110728(T)).

Characterization of alcohol dehydrogenase from Kangiella koreensis and its application to production of all-trans-retinol

A recombinant alcohol dehydrogenase (ADH) from Kangiella koreensis was purified as a 40 kDa dimer with a specific activity of 21.3 nmol min(-1) mg(-1), a K m of 1.8 μM, and a k cat of 1.7 min(-1) for all-trans-retinal using NADH as cofactor. The enzyme showed activity for all-trans-retinol using NAD (+) as a cofactor. The reaction conditions for all-trans-retinol production were optimal at pH 6.5 and 60 °C, 2 g enzyme l(-1), and 2,200 mg all-trans-retinal l(-1) in the presence of 5% (v/v) methanol, 1% (w/v) hydroquinone, and 10 mM NADH. Under optimized conditions, the ADH produced 600 mg all-trans-retinol l(-1) after 3 h, with a conversion yield of 27.3% (w/w) and a productivity of 200 mg l(-1) h(-1). This is the first report of the characterization of a bacterial ADH for all-trans-retinal and the biotechnological production of all-trans-retinol using ADH.

Lignocellulose-responsive bacteria in a southern California salt marsh identified by stable isotope probing

Carbon cycling by microbes has been recognized as the main mechanism of organic matter decomposition and export in coastal wetlands, yet very little is known about the functional diversity of specific groups of decomposers (e.g., bacteria) in salt marsh benthic trophic structure. Indeed, salt marsh sediment bacteria remain largely in a black box in terms of their diversity and functional roles within salt marsh benthic food web pathways. We used DNA stable isotope probing (SIP) utilizing ¹³C-labeled lignocellulose as a proxy to evaluate the fate of macrophyte-derived carbon in benthic salt marsh bacterial communities. Overall, 146 bacterial species were detected using SIP, of which only 12 lineages were shared between enriched and non-enriched communities. Abundant groups from the ¹³C-labeled community included Desulfosarcina, Spirochaeta, and Kangiella. This study is the first to use heavy-labeled lignocellulose to identify bacteria responsible for macrophyte carbon utilization in salt marsh sediments and will allow future studies to target specific lineages to elucidate their role in salt marsh carbon cycling and ultimately aid our understanding of the potential of salt marshes to store carbon.

Comparative analysis of amino acid sequences from mesophiles and thermophiles in respective of carbon-nitrogen hydrolase family

A comparative study of amino acid sequence and physicochemical properties indicates the affiliation of protein from the nitrilase/cyanide hydratase family. This family contains nitrilases that break carbon-nitrogen bonds and appear to be involved in the reduction of organic nitrogen compounds and ammonia production. They all have distinct substrate specificity and include nitrilase, cyanide hydratases, aliphatic amidases, beta-alanine synthase, and a few other proteins with unknown molecular function. These sequences were analyzed for different physical and chemical properties and to relate these observed differences to the thermostability properties, phylogenetic tree construction and the evolutionary relationship among them. In this work, in silico analysis of amino acid sequences of mesophilic (15) and thermophilic (archaea, 15 and bacteria, 15) proteins has been done. The physiochemical properties of these three groups of nitrilase/cyanide hydratase family also differ in number of amino acids, molecular weight, pI values, positively charged ions, i.e. Arg + Lys, aliphatic index and grand average of hydropathacity (GRAVY). The amino acid Ala (1.37-fold) was found to be higher in mesophilic bacteria as compared to thermophilic bacteria but Lys and Phe were found to be significantly high (1.43 and 1.39-fold, respectively) in case of thermophilic bacteria. The amino acids Ala, Cys, Gln, His and Thr were found to be significantly higher (1.41, 1.6, 1.77, 1.44 and 1.29-fold, respectively) in mesophilic bacteria as compared to thermophilic archaea, where Glu, Leu and Val were found significantly high (1.22, 1.19 and 1.26-fold, respectively).

Pleionea mediterranea gen. nov., sp. nov., a gammaproteobacterium isolated from coastal seawater

A Gram-negative, aerobic, cream-pigmented, non-motile, non-spore-forming straight rod, strain MOLA115T, was isolated from a coastal water sample from the Mediterranean Sea. On the basis of phylogenetic analysis of the 16S rRNA gene sequences, strain MOLA115T was shown to belong to the Gammaproteobacteria , adjacent to members of the genera Marinicella , Arenicella and Kangiella , sharing less than 89 % 16S rRNA gene sequence similarity with strains of all recognized species within the Gammaproteobacteria . The only isoprenoid quinone was ubiquinone-8. Polar lipids in strain MOLA115T included phosphatidylethanolamine, an aminolipid, phosphatidylglycerol and an aminophospholipid. Fatty acid analysis revealed iso-C15 : 0 and iso-C17 : 1ω9c to be the dominant components. The DNA G+C content was 44.5 mol%. Based upon the phenotypic and phylogenetic data, we propose that strain MOLA115T should be considered to represent a novel species in a new genus, for which the name Pleionea mediterranea gen. nov., sp. nov. is proposed. The type strain of Pleionea mediterranea is MOLA115T ( = CIP 110343T = DSM 25350T).

Kangiella sediminilitoris sp. nov., isolated from a tidal flat sediment

A Gram-stain-negative, non-motile, non-spore-forming, rod-shaped bacterial strain, BB-Mw22T, was isolated from a tidal flat sediment of the South Sea in South Korea. It grew optimally at 30–37 °C, at pH 7.0–7.5 and in the presence of 2–3 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain BB-Mw22T belonged to the genus Kangiella and the cluster comprising Kangiella species and strain BB-Mw22T was clearly separated from other taxa. Strain BB-Mw22T exhibited 95.3–98.7 % 16S rRNA gene sequence similarity to the type strains of recognized Kangiella species. Strain BB-Mw22T contained Q-8 as the predominant ubiquionone and iso-C15 : 0 and iso-C11 : 0 3-OH as the major fatty acids. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine and one unidentified aminolipid. The DNA G+C content of strain BB-Mw22T was 48.9 mol%, and its mean DNA–DNA hybridization values with Kangiella geojedonensis YCS-5T, Kangiella japonica JCM 16211T and Kangiella taiwanensis JCM 17727T were 14–28 %. Phylogenetic and genetic distinctiveness and differential phenotypic properties revealed that strain BB-Mw22T is distinguishable from all recognized Kangiella species. On the basis of the data presented, strain BB-Mw22T is considered to represent a novel species of the genus Kangiella , for which the name Kangiella sediminilitoris sp. nov. is proposed. The type strain is BB-Mw22T ( = KCTC 23892T  = CCUG 62217T).

Kangiella taiwanensis sp. nov. and Kangiella marina sp. nov., marine bacteria isolated from shallow coastal water

Two Gram-negative, heterotrophic, aerobic, marine bacteria, designated strains KT1T and KM1T, were isolated from seawater samples collected from the shallow coastal regions of northern Taiwan. Cells grown in broth cultures were non-flagellated rods. NaCl was required for growth. Optimal growth occurred with 2–5 % NaCl, at 25–30 °C and at pH 8. They grew aerobically and were not capable of anaerobic growth by fermenting d-glucose or other carbohydrates. Q-8 was the only isoprenoid quinone. The major polar lipid detected in strain KT1T was phosphatidylmonomethylethanolamine, whereas those detected in KM1T were phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine and an unidentified phospholipid. Cellular fatty acids were nearly all iso-branched, with iso-C15 : 0 as the most abundant component (54.6–57.2 % of the total). Strains KT1T and KM1T had DNA G+C contents of 43.9 and 46.3 mol%, respectively. The two strains shared 98.1 % 16S rRNA gene sequence similarity; levels of similarity with the type strains of species of the genus Kangiella were 95.6–98.4 %. Data from the present taxonomic study conducted using a polyphasic approach revealed that the isolates could be classified as representatives of two novel species of the genus Kangiella , for which the names Kangiella taiwanensis sp. nov. (type strain KT1T = BCRC 80330T = JCM 17727T) and Kangiella marina sp. nov. (type strain KM1T = BCRC 80329T = JCM 17728T) are proposed.

Functional diversity in the denitrifying biofilm of the methanol-fed marine denitrification system at the Montreal Biodome

Nitrate is a serious problem in closed-circuit public aquariums because its accumulation rapidly becomes toxic to many lifeforms. A moving bed biofilm denitrification reactor was installed at the Montreal Biodome to treat its 3,250-m(3) seawater system. Naturally occurring microorganisms from the seawater affluent colonized the reactor carriers to form a denitrifying biofilm. Here, we investigated the functional diversity of this biofilm by retrieving gene sequences related to narG, napA, nirK, nirS, cnorB, and nosZ. A total of 25 sequences related to these genes were retrieved from the biofilm. Among them, the corresponding napA1, nirK1, cnorB9, and nosZ3 sequences were identical to the corresponding genes found in Hyphomicrobium sp. NL23 while the narG1 and narG2 sequences were identical to the two corresponding narG genes found in Methylophaga sp. JAM1. These two bacterial strains were previously isolated from the denitrifying biofilm. To assess the abundance of denitrifiers and nitrate respirers in the biofilm, the gene copy number of all the narG, napA, nirS, and nirK sequences found in biofilm was determined by quantitative PCR. napA1, nirK1, narG1, and narG2, which were all associated with either Methylophaga sp. JAM1 or Hyphomicrobium sp. NL23, were the most abundant genes. The other genes were 10 to 10,000 times less abundant. nirK, cnorB, and nosZ but not napA transcripts from Hyphomicrobium sp. NL23 were detected in the biofilm, and only the narG1 transcripts from Methylophaga sp. JAM1 were detected in the biofilm. Among the 19 other genes, the transcripts of only two genes were detected in the biofilm. Our results show the predominance of Methylophaga sp. JAM1 and Hyphomicrobium sp. NL23 among the denitrifiers detected in the biofilm. The results suggest that Hyphomicrobium sp. NL23 could use the nitrite present in the biofilm generated by nitrate respirers such as Methylophaga sp. JAM1.

Kangiella geojedonensis sp. nov., isolated from seawater

A Gram-stain-negative, non-motile, non-spore-forming bacterial strain, YCS-5T, was isolated from seawater off the southern coast of Korea. Strain YCS-5T grew optimally at 30 °C and in the presence of 2 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain YCS-5T fell within the clade comprising Kangiella species. Strain YCS-5T exhibited 16S rRNA gene sequence similarity values of 96.6, 95.7 and 97.9 % to the type strains of Kangiella koreensis, Kangiella aquimarina and Kangiella japonica, respectively, and less than 89.8 % to strains of other species used in the phylogenetic analysis. Strain YCS-5T contained Q-8 as the predominant ubiquinone and iso-C17 : 0, iso-C15 : 0, iso-C11 : 0 3-OH and iso-C17 : 1ω9c as the major fatty acids. The polar lipid profile of strain YCS-5T was similar to that of K. koreensis SW-125T, with phosphatidylglycerol and an unidentified aminolipid as major polar lipids. The DNA G+C content was 47 mol%. The mean DNA–DNA relatedness value between strain YCS-5T and K. japonica JCM 16211T was 12 %. Differential phenotypic properties and the phylogenetic and genetic distinctiveness of strain YCS-5T demonstrated that this strain is distinguishable from other Kangiella species. On the basis of the data presented, strain YCS-5T is considered to represent a novel species of the genus Kangiella, for which the name Kangiella geojedonensis sp. nov. is proposed; the type strain is YCS-5T ( = KCTC 23420T = CCUG 60526T).

Going deeper: metagenome of a hadopelagic microbial community

The paucity of sequence data from pelagic deep-ocean microbial assemblages has severely restricted molecular exploration of the largest biome on Earth. In this study, an analysis is presented of a large-scale 454-pyrosequencing metagenomic dataset from a hadopelagic environment from 6,000 m depth within the Puerto Rico Trench (PRT). A total of 145 Mbp of assembled sequence data was generated and compared to two pelagic deep ocean metagenomes and two representative surface seawater datasets from the Sargasso Sea. In a number of instances, all three deep metagenomes displayed similar trends, but were most magnified in the PRT, including enrichment in functions for two-component signal transduction mechanisms and transcriptional regulation. Overrepresented transporters in the PRT metagenome included outer membrane porins, diverse cation transporters, and di- and tri-carboxylate transporters that matched well with the prevailing catabolic processes such as butanoate, glyoxylate and dicarboxylate metabolism. A surprisingly high abundance of sulfatases for the degradation of sulfated polysaccharides were also present in the PRT. The most dramatic adaptational feature of the PRT microbes appears to be heavy metal resistance, as reflected in the large numbers of transporters present for their removal. As a complement to the metagenome approach, single-cell genomic techniques were utilized to generate partial whole-genome sequence data from four uncultivated cells from members of the dominant phyla within the PRT, Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes and Planctomycetes. The single-cell sequence data provided genomic context for many of the highly abundant functional attributes identified from the PRT metagenome, as well as recruiting heavily the PRT metagenomic sequence data compared to 172 available reference marine genomes. Through these multifaceted sequence approaches, new insights have been provided into the unique functional attributes present in microbes residing in a deeper layer of the ocean far removed from the more productive sun-drenched zones above.

Kangiella spongicola sp. nov., a halophilic marine bacterium isolated from the sponge Chondrilla nucula

A novel halophilic bacterium of the genus Kangiella was isolated from a marine sponge collected from the Florida Keys, USA. Strain A79T, an aerobic, Gram-negative, non-motile, rod-shaped bacterium, grew in 2–15 % (w/v) NaCl, at a temperature of 10–49 °C and at pH 4.5–10. Phylogenetic analysis placed strain A79T in the family Alcanivoraceae in the class Gammaproteobacteria. Strain A79T showed 98.5 % 16S rRNA gene sequence similarity to Kangiella japonica KMM 3899T, 96.6 % similarity to Kangiella koreensis DSM 16069T and 95.6 % similarity to Kangiella aquimarina DSM 16071T. The major cellular fatty acids were iso-C11 : 0, iso-C11 : 0 3-OH, iso-C15 : 0, iso-C17 : 0 and iso-C17 : 1ω9c and the G+C content of the genomic DNA was 44.9 mol%. On the basis of physiological, chemotaxonomic and phylogenetic comparisons, strain A79T represents a novel species in the genus Kangiella, for which the name Kangiella spongicola sp. nov. is proposed. The type strain is A79T ( = ATCC BAA-2076T = DSM 23219T).

Kangiella japonica sp. nov., isolated from a marine environment

Three Gram-negative, aerobic, halophilic, non-motile, yellowish-pigmented bacteria, designated KMM 3896, KMM 3897 and KMM 3899T, were isolated from coastal seawater and sediment samples of the Sea of Japan, Russia. The isolates were shown to belong to the same species on the basis of 16S rRNA gene sequence similarities (99.6–99.9 %) and DNA–DNA relatedness (73–98 %). Phylogenetic analysis of 16S rRNA gene sequences demonstrated that the isolates formed a subcluster within the genus Kangiella in the class Gammaproteobacteria. 16S rRNA gene sequence similarities between strain KMM 3899T and its closest phylogenetic neighbours, Kangiella koreensis SW-125T and Kangiella aquimarina SW-154T, were 96.6 and 95.5 %, respectively. On the basis of phenotypic differences and phylogenetic distances, it is proposed that strains KMM 3896, KMM 3897 and KMM 3899T are assigned to a novel species of the genus Kangiella, Kangiella japonica sp. nov. The type strain is KMM 3899T (=NRIC 0764T =JCM 16211T).

Arenicella xantha gen. nov., sp. nov., a gammaproteobacterium isolated from a marine sandy sediment

A Gram-negative, aerobic, yellow-pigmented, rod-shaped, non-motile bacterium, strain KMM 3895T, was isolated from a marine sandy sample collected offshore from the Sea of Japan. Phylogenetic analysis based on the 16S rRNA gene sequence placed strain KMM 3895T in the class Gammaproteobacteria, forming a separate branch, sharing 89.5 % sequence similarity with Nitrincola lacisaponensis 4CAT and 88–87 % similarity with the other members of the cluster, including members of Kangiella, Spongiibacter, Alcanivorax and Microbulbifer. The major isoprenoid quinone was Q-8. Polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, aminophospholipid and an unknown phospholipid. Fatty acid analysis revealed C16 : 1 ω7, iso-C16 : 0, iso-C18 : 0 and C18 : 1 ω7 as dominant components. The DNA G+C content was determined to be 48.1 mol%. Based on its unique phenotypic characteristics and phylogenetic distance, the marine coastal sediment isolate KMM 3895T should be classified as a representative of a novel genus and species, for which the name Arenicella xantha gen. nov., sp. nov. is proposed. The type strain of Arenicella xantha is KMM 3895T (=NRIC 0759T =JCM 16153T).

Marinicella litoralis gen. nov., sp. nov., a gammaproteobacterium isolated from coastal seawater

A Gram-negative, aerobic, greyish–yellowish-pigmented, stenohaline, rod-shaped, non-motile bacterium, strain KMM 3900T, was isolated from a coastal seawater sample collected from the Sea of Japan. Based on phylogenetic analysis, strain KMM 3900T was positioned within the Gammaproteobacteria on a separate branch adjacent to members of the genera Reinekea and Kangiella, sharing less than 88 % 16S rRNA gene sequence similarity with all recognized species of the Gammaproteobacteria. The major isoprenoid quinone was Q-8. Polar lipids consisted of phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and two unknown phospholipids. Fatty acid analysis revealed iso-C15 : 0, C16 : 1 ω7c and C16 : 0 as the dominant components. The DNA G+C content was 43.8 mol%. Based on its unique phenotypic characteristics and phylogenetic remoteness, marine isolate KMM 3900T is considered to represent a novel genus and species, for which the name Marinicella litoralis gen. nov., sp. nov. is proposed. The type strain of Marinicella litoralis is KMM 3900T (=NRIC 0758T =JCM 16154T).

Complete genome sequence of Kangiella koreensis type strain (SW-125)

Kangiella koreensis (Yoon et al. 2004) is the type species of the genus and is of phylogenetic interest because of the very isolated location of the genus Kangiella in the gammaproteobacterial order Oceanospirillales. K. koreensis SW-125(T) is a Gram-negative, non-motile, non-spore-forming bacterium isolated from tidal flat sediments at Daepo Beach, Yellow Sea, Korea. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first completed genome sequence from the genus Kangiella and only the fourth genome from the order Oceanospirillales. This 2,852,073 bp long single replicon genome with its 2647 protein-coding and 48 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

Marinobacterium halophilum sp. nov., a marine bacterium isolated from the Yellow Sea

A moderately halophilic, aerobic, Gram-negative bacterium was isolated from a tidal flat area of Dae-Chun, Chung-Nam, Korea. The strain, designated mano11T, comprised rod-shaped cells that were motile by means of polar flagella. It grew with 3–12 % NaCl and at 4–37 °C and pH 5.3–9.3. The predominant menaquinone present in this strain was MK-7 and diaminopimelic acid was not found in the cell-wall peptidoglycan. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain mano11T belongs to the genus Marinobacterium. Strain mano11T exhibited 92.8–98.3 % 16S rRNA gene sequence similarity when compared with the type strains of three other species of the genus Marinobacterium. DNA–DNA hybridization between strain mano11T and Marinobacterium georgiense DSM 11526T, its closest relative in terms of 16S rRNA gene sequence similarity, was 13 %. On the basis of the phenotypic, genetic and phylogenetic data, strain mano11T represents a novel species of the genus Marinobacterium, for which the name Marinobacterium halophilum sp. nov. is proposed. The type strain is mano11T (=KCTC 12240T=DSM 17586T).

Halomonas alkaliphila sp. nov., a novel halotolerant alkaliphilic bacterium isolated from a salt pool in Campania (Italy)

A halotolerant and alkaliphilic Gram-negative bacterium, strain 18bAG(T), that grows aerobically at the optimum temperature of 37 degrees C, and at pH 7.5-10 (optimum 9.0), was isolated from a salt pool located in Montefredane in Campania Region (South of Italy). The isolate tolerated high concentration of NaCl up to 20%. Strain 18bAG(T) accumulated osmolytes and polyhydroxybutyrate, produced exopolysaccharide and possessed alpha-glucosidase activity. The predominant respiratory quinones were ubiquinones, Q8 and Q6(6H); phosphoethanolamine, phosphatidylglycerol and diphosphatidylglycerol were the predominant polar lipids. Major fatty acids were C16 : 1, C16 : 0, and C18 : 0. On the basis of 16S rRNA gene sequence similarity, 18bAG(T) was shown to belong to Halomonas genus. Analysis of 16S rRNA gene revealed a high similarity of strain 18bAG(T) to Halomonas venusta (DSM 4743(T)) and Halomonas hydrothermalis (DSM 15725(T)). Level of DNA-DNA relatedness between strain 18bAG(T) and the most related species Halomonas venusta and Halomonas hydrothermalis was 56.0% and 41.2%, respectively. The G+C content (mol%) of DNA was 53.0. The RiboPrinting patterns of Halomonas venusta and 18AG(T) showed a pattern similarity of 0.50. On the basis of genomic information and phenotypic characteristics strain 18bAG(T) represents a new species, for which the name Halomonas alkaliphila sp. nov. is proposed. The type strain is 18bAG(T) (=DSM 16354T =ATCC BAA-953T).