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.

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).

Successful bio-electrochemical treatment of nitrogenous mariculture wastewater by enhancing nitrogen removal via synergy of algae and cathodic photo-electro-catalysis

Systems with catalytic cathode in microbial fuel cell can achieve high treatment efficiency enhanced by the cathode. Such bio-electrochemical systems have potential applications in treating high-salinity nitrogenous mariculture wastewater. For sustainable development of the mariculture industry, enhancing inorganic nitrogen removal is of vital importance due to the low carbon to nitrogen (C/N) ratio of wastewater and strict discharge standard. Herein, simulated mariculture wastewater (high salinity, low COD/N ratio of 0.5-1.0) was successfully treated in an integrated self-biased bio-electrochemical system, with catalyst (TiO₂/Co-WO₃/SiC) on the cathode and natural-grown algae in the cathode chamber. Satisfactory nitrogen removal (94.05% NH₄⁺-N and 77.35% inorganic nitrogen) and favorable 76.66% removal of organics (UV₂₅₄) were both achieved, with visible light illumination. The NH₄⁺-N in the effluent was below 2 mg L^-1. The synergy of bacteria, algae and cathode, promoted pollutant removal, and made the system sustainable and efficient in treating mariculture wastewater.

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.

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.

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.

Complete genome of Kangiella geojedonensis KCTC 23420(T), putative evidence for recent genome reduction in marine environments

Kangiella geojedonensis KCTC 23420(T) is an aerobic, Gram-negative, non-motile, non-spore-forming, rod-shaped bacterium that was isolated from seawater off the southern coast of Korea. We here report the complete genome of K. geojedonensis KCTC 23420(T), which consists of 2,495,242 bp (G+C content of 43.78%) with 2,257 protein-coding genes, 41 tRNAs, 2 rRNA operons. The genome is smaller than the other closely related genomes, indicating that K. geojedonensis has recently experienced reductive evolution.

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)).

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.