Description of Spongiibacter borealis sp. nov., isolated from Arctic seawater, and reclassification of Melitea salexigens Urios et al. 2008 as a later heterotypic synonym of Spongiibacter marinus Graeber et al. 2008 with emended descriptions of the genus Spongiibacter and Spongiibacter marinus

In situ oil contamination in young mangroves: Biodegradation of petroleum hydrocarbons and effects on the microbial and benthic communities, an experimental study in French Guiana

An in-situ experiment was conducted in a young mangrove with no history of oil contamination (French Guiana). Control and oil-contaminated sediments were sampled one month after exposure and analyzed to a depth of 18 cm to assess natural oil depletion and changes in benthic communities. High biodegradation percentages (89-99 %) of n-alkanes and polycyclic aromatic hydrocarbons were measured. The microbiological results suggest that this degradation is strongly connected to several bacterial taxa. A 90 % decrease in the meso- (>250 mm) and macro-benthic organisms' (>1 mm) densities was observed. The oil has also significantly impacted the composition of the benthos, as well as the microorganisms responsible for mediating biogeochemical functions associated with nitrogen turnover. While chemical and microbiological analyses revealed a high bioremediation potential by the indigenous microbes, an oil spill would be a catastrophic event for the benthic fauna, which could, in turn, affect the microbial communities.

Insights into the prokaryotic communities of the abyssal-hadal benthic-boundary layer of the Kuril Kamchatka Trench

BACKGROUND

The Kuril-Kamchatka Trench (maximum depth 9604 m), located in the NW Pacific Ocean, is among the top seven deepest hadal trenches. The work aimed to investigate the unexplored abyssal-hadal prokaryotic communities of this fascinating, but underrated environment.

RESULTS

As for the bacterial communities, we found that Proteobacteria (56.1-74.5%), Bacteroidetes (6.5-19.1%), and Actinobacteria (0.9-16.1%) were the most represented bacterial phyla over all samples. Thaumarchaeota (52.9-91.1%) was the most abundant phylum in the archaeal communities. The archaeal diversity was highly represented by the ammonia-oxidizing Nitrosopumilus, and the potential hydrocarbon-degrading bacteria Acinetobacter, Zhongshania, and Colwellia were the main bacterial genera. The α-diversity analysis evidenced that both prokaryotic communities were characterized by low evenness, as indicated by the high Gini index values (> 0.9). The β-diversity analysis (Redundancy Analysis) indicated that, as expected, the depth significantly affected the structure of the prokaryotic communities. The co-occurrence network revealed seven prokaryotic groups that covaried across the abyssal-hadal zone of the Kuril-Kamchatka Trench. Among them, the main group included the most abundant archaeal and bacterial OTUs (Nitrosopumilus OTU A2 and OTU A1; Acinetobacter OTU B1), which were ubiquitous across the trench.

CONCLUSIONS

This manuscript represents the first attempt to characterize the prokaryotic communities of the KKT abyssal-hadal zone. Our results reveal that the most abundant prokaryotes harbored by the abyssal-hadal zone of Kuril-Kamchatka Trench were chemolithotrophic archaea and heterotrophic bacteria, which did not show a distinctive pattern distribution according to depth. In particular, Acinetobacter, Zhongshania, and Colwellia (potential hydrocarbon degraders) were the main bacterial genera, and Nitrosopumilus (ammonia oxidizer) was the dominant representative of the archaeal diversity.

Zhongshania aquimaris sp. nov., isolated from seawater

A Gram-negative, motile, rod-shaped, aerobic bacterial strain CAU 1632^T was isolated from a seawater sample collected in the Republic of Korea. The cells of strain CAU 1632^T grew optimally at 30 °C and pH 7.0 in 0% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CAU 1632^T formed a tight phyletic lineage with Zhongshania antarctica ZS-23^T, Zhongshania borealis CL-AS9^T, Zhongshania marina DSW25-10^T, Zhongshania guokunii ZS6-22^T, 'Zhongshania ponticola GM-8^T', Zhongshania aliphaticivorans SM-2^T and shared a high similarity between 97.2% and 97.7%. The whole genome of strain CAU 1632^T was 4.3-Mb with 3,780 protein-coding genes, 12 contigs, and a DNA G+C content of 49.4 mol%. The major fatty acids of strain CAU 1632^T were C_17:1 ω8c, C_19:1 ω6c and/or C_19:0 cyclo ω10c (summed feature 3), and C_18:1 ω6c and/or C_18:1 ω7c (summed feature 8). Q-8 was the only respiratory quinone. The polar lipids were composed of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two aminophospholipids, and two phospholipids. Based on the results of phenotypic, chemotaxonomic, and phylogenetic analyses, strain CAU 1632^T represents a novel species within the genus Zhongshania, for which the name Zhongshania aquimaris sp. nov. is proposed. The type strain is CAU 1632^T (= KCTC 82432^T = MCCC 1K06086^T).

Spongiibacter thalassae sp. nov., a marine gammaproteobacterium isolated from seawater

A bacterium, designated as KMU-166^T, belonging to the class Gammaproteobacteria, was isolated from seawater collected on the coastline of Dadaepo, Republic of Korea. Strain KMU-166^T was Gram-staining-negative, ovoid-shaped, motile, strictly aerobic, beige-colored, catalase-positive, and oxidase-negative; and had a chemoorganoheterotrophic metabolism. The novel isolate was found to grow at 1-4% NaCl concentrations (w/v), pH 6.5-9.5, and 10-40 °C. The 16S rRNA gene sequence-based phylogeny showed that strain KMU-166^T affiliates to the family Spongiibacteraceae and that it shared the greatest sequence similarity (96.4%) with Spongiibacter marinus HAL40b^T. The main (> 10%) cellular fatty acids were summed feature 3 (C16:1ω7c and/or C16:1ω6c), C17:1ω8c, and C18:1ω7c. The predominant respiratory quinone was ubiquinone-8 (Q-8). Strain KMU-166^T comprised phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, and two unidentified lipids. The assembled draft genome was 4.40 Mbp in size with a DNA G+C content of 55.7%. The average nucleotide identity, digital DNA-DNA hybridization, and average amino acid identity values of KMU-166^T and Spongiibacter marinus HAL40b^T, Spongiibacter tropicus CL-CB221^T, and "Spongiibacter pelagi" KMU-158^T were found to be 77.7-79.8%, 13.7-15.4%, and 66.1-70.9%, respectively. From the distinguishable polyphasic taxonomic results obtained, the strain is considered to represent a novel species of the genus Spongiibacter for which the name Spongiibacter thalassae sp. nov. is proposed. The type strain of S. thalassae sp. nov. is KMU-166^T (= KCCM 90449^T = NBRC 114308^T).

Diesel and Crude Oil Biodegradation by Cold-Adapted Microbial Communities in the Labrador Sea

Oil spills in the subarctic marine environment off the coast of Labrador, Canada, are increasingly likely due to potential oil production and increases in ship traffic in the region. To understand the microbiome response and how nutrient biostimulation promotes biodegradation of oil spills in this cold marine setting, marine sediment microcosms amended with diesel or crude oil were incubated at in situ temperature (4°C) for several weeks. Sequencing of 16S rRNA genes following these spill simulations revealed decreased microbial diversity and enrichment of putative hydrocarbonoclastic bacteria that differed depending on the petroleum product. Metagenomic sequencing revealed that the genus Paraperlucidibaca harbors previously unrecognized capabilities for alkane biodegradation, which were also observed in Cycloclasticus. Genomic and amplicon sequencing together suggest that Oleispira and Thalassolituus degraded alkanes from diesel, while Zhongshania and the novel PGZG01 lineage contributed to crude oil alkane biodegradation. Greater losses in PAHs from crude oil than from diesel were consistent with Marinobacter, Pseudomonas_D, and Amphritea genomes exhibiting aromatic hydrocarbon biodegradation potential. Biostimulation with nitrogen and phosphorus (4.67 mM NH4Cl and 1.47 mM KH2PO4) was effective at enhancing n-alkane and PAH degradation following low-concentration (0.1% [vol/vol]) diesel and crude oil amendments, while at higher concentrations (1% [vol/vol]) only n-alkanes in diesel were consumed, suggesting toxicity induced by compounds in unrefined crude oil. Biostimulation allowed for a more rapid shift in the microbial community in response to petroleum amendments, more than doubling the rates of CO2 increase during the first few weeks of incubation. IMPORTANCE Increases in transportation of diesel and crude oil in the Labrador Sea will pose a significant threat to remote benthic and shoreline environments, where coastal communities and wildlife are particularly vulnerable to oil spill contaminants. Whereas marine microbiology has not been incorporated into environmental assessments in the Labrador Sea, there is a growing demand for microbial biodiversity evaluations given the pronounced impact of climate change in this region. Benthic microbial communities are important to consider given that a fraction of spilled oil typically sinks such that its biodegradation occurs at the seafloor, where novel taxa with previously unrecognized potential to degrade hydrocarbons were discovered in this work. Understanding how cold-adapted microbiomes catalyze hydrocarbon degradation at low in situ temperature is crucial in the Labrador Sea, which remains relatively cold throughout the year.

Individual Physiological Adaptations Enable Selected Bacterial Taxa To Prevail during Long-Term Incubations

Enclosure experiments are frequently used to investigate the impact of changing environmental conditions on microbial assemblages. Yet, how the incubation itself challenges complex bacterial communities is thus far unknown. In this study, metaproteomic profiling, 16S rRNA gene analyses, and cell counts were combined to evaluate bacterial communities derived from marine, mesohaline, and oligohaline conditions after long-term batch incubations. Early in the experiment, the three bacterial communities were highly diverse and differed significantly in their compositions. Manipulation of the enclosures with terrigenous dissolved organic carbon resulted in notable differences compared to the control enclosures at this early phase of the experiment. However, after 55 days, bacterial communities in the manipulated and the control enclosures under marine and mesohaline conditions were all dominated by gammaproteobacterium Spongiibacter In the oligohaline enclosures, actinobacterial cluster I of the hgc group (hgc-I) remained abundant in the late phase of the incubation. Metaproteome analyses suggested that the ability to use outer membrane-based internal energy stores, in addition to the previously described grazing resistance, may enable the gammaproteobacterium Spongiibacter to prevail in long-time incubations. Under oligohaline conditions, the utilization of external recalcitrant carbon appeared to be more important (hgc-I). Enclosure experiments with complex natural microbial communities are important tools to investigate the effects of manipulations. However, species-specific properties, such as individual carbon storage strategies, can cause manipulation-independent effects and need to be considered when interpreting results from enclosures.IMPORTANCE In microbial ecology, enclosure studies are often used to investigate the effect of single environmental factors on complex bacterial communities. However, in addition to the manipulation, unintended effects ("bottle effect") may occur due to the enclosure itself. In this study, we analyzed the bacterial communities that originated from three different salinities of the Baltic Sea, comparing their compositions and physiological activities both at the early stage and after 55 days of incubation. Our results suggested that internal carbon storage strategies impact the success of certain bacterial species, independent of the experimental manipulation. Thus, while enclosure experiments remain valid tools in environmental research, microbial community composition shifts must be critically followed. This investigation of the metaproteome during long-term batch enclosures expanded our current understanding of the so-called "bottle effect," which is well known to occur during enclosure experiments.

Marortus luteolus gen. nov., sp. nov., isolated from surface seawater of the East Sea in China

A Gram-stain-negative, motile, aerobic, rod-shaped bacterium with flagella, designated ZX-21^T, was isolated from surface seawater of the East Sea in Zhoushan, China. Growth of strain ZX-21T was observed at 10--35  o°C (optimum, 30 °C), at pH 6.0-8.5 (pHoptimum 6.5-7.0) and in the presence of 0.5-8 % (w/v) NaCl (optimum 3-4 %). It was positive for oxidase and catalase activity. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain ZX-21T constituted an independent lineage within the family Spongiibacteraceae and was most closely related to Zhongshania guokunii (96.83 %). Strain ZX-21T contained ubiquinone-8 (Q-8) as the sole isoprenoid quinone and summed feature 3 (C16 : 1ω77c and/or C16 : 1ω66c), summed feature 8 (C18 : 1ω77c and/or C18 : 1ω66c) and C16 : 0 as the major fatty acids. Phosphatidylglycerol (), phosphatidylethanolamine (), diphosphatidylglycerol () and an unidentified glycolipid were the major cellular polar lipids. The DNA G+C content was 49.1 mol%. Based on itsthe morphological, physiological and chemotaxonomic characteristics, strain ZX-21Tis described as a novel species in a novel genus for whichwith the name Marortus luteolus gen. nov., sp. nov. (type strain ZX-21T = MCCC 1K03431T=KCTC 62160T) is proposed.

Zhongshania marina sp. nov., isolated from deep-sea water

A Gram-stain-negative, aerobic, catalase-positive, oxidase-positive, motile by a single polar flagellum, rod-shaped strain, designated DSW25-10^T, was isolated from the deep-sea water of the East Sea, Republic of Korea. Strain DSW25-10^Tgrew at 4-35 °C (optimum, 20-35 °C), at pH 5.5-9.0 (optimum, pH 7.0) and in the presence of 0-6.0 % NaCl (optimum, 0.5-2 %), and could assimilate valerate, but not assimilate d-mannitol and 3-hydroxy-butyrate. Comparative 16S rRNA gene sequence analysis showed that strain DSW25-10^T belongs to the genus Zhongshania in the family Spongiibacteraceae and is most closely related to Zhongshania guokunii ZS6-22^T, Zhongshania borealis CL-AS9^T, Zhongshania aliphaticivorans SM-2^T and Zhongshani antarctica ZS5-23^T with a similarities of 97.1, 97.0, 96.7 and 96.6 %, respectively. The G+C content of genomic DNA was 49.1 mol% and the major respiratory quinone was ubiquinone-8. Phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol were identified as the major cellular polar lipids. The predominant cellular fatty acids in strain DSW25-10^T were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c), C16 : 0 and C17 : 1ω8c. The DNA-DNA relatedness values between strain DSW25-10^T and related strains were clearly lower than 70 %. On the basis of evidence from a polyphasic analysis, strain DSW25-10^T is proposed to represent a novel species, Zhongshania marina sp. nov. The type strain is DSW25-10^T (=KCCM 43273^T=JCM 17372^T).

Zhongshania ponticola sp. nov., a novel lipolytic bacterium of the class Gammaproteobacteria isolated from seawater

A bacterial strain, designated GM-8^T, which was isolated from seawater around Pohang in Republic of Korea, was subjected to a polyphasic taxonomic study. It was lipolytic, Gram-stain-negative, aerobic, non-motile and coccoid, ovoid, or rod-shaped. Strain GM-8^T grew optimally at 30 °C and in the presence of 2.0-3.0% (w/v) NaCl. The phylogenetic trees of 16S rRNA gene sequences based on three algorithms showed that strain GM-8^T joined the clade comprising the type strains of Zhongshania species. The novel strain exhibited the highest 16S rRNA gene sequence similarity value (98.6%) to Zhongshania borealis CL-AS9^T and sequence similarities of 97.7-98.3% to the type strains of three other Zhongshania species. Strain GM-8^T contained Q-8 as the predominant ubiquinone and C_17:1 ω8c, summed feature 3 (C_16:1 ω7c and/or C_16:1 ω6c), and C_18:1 ω7c as the major fatty acids. Phosphatidylglycerol and phosphatidylethanolamine were major polar lipids found in strain GM-8^T and the type strain of Zhongshania antarctica. The DNA G + C content of strain GM-8^T was 50.9 mol%. Mean DNA-DNA relatedness values between strain GM-8^T and the type strains of four other Zhongshania species were 13.3-20.3%. Its differential phenotypic traits, together with the phylogenetic and genetic evidences, revealed that strain GM-8^T is distinct from recognized species of the genus Zhongshania. On the basis of the data presented, strain GM-8^T represents a novel species of the genus Zhongshania, for which the name Zhongshania ponticola sp. nov. is proposed. The type strain is GM-8^T (= KCTC 62425^T = KACC 19616^T = NBRC 113193^T).

A taxonomic framework for emerging groups of ecologically important marine gammaproteobacteria based on the reconstruction of evolutionary relationships using genome-scale data

In recent years a large number of isolates were obtained from saline environments that are phylogenetically related to distinct clades of oligotrophic marine gammaproteobacteria, which were originally identified in seawater samples using cultivation independent methods and are characterized by high seasonal abundances in coastal environments. To date a sound taxonomic framework for the classification of these ecologically important isolates and related species in accordance with their evolutionary relationships is missing. In this study we demonstrate that a reliable allocation of members of the oligotrophic marine gammaproteobacteria (OMG) group and related species to higher taxonomic ranks is possible by phylogenetic analyses of whole proteomes but also of the RNA polymerase beta subunit, whereas phylogenetic reconstructions based on 16S rRNA genes alone resulted in unstable tree topologies with only insignificant bootstrap support. The identified clades could be correlated with distinct phenotypic traits illustrating an adaptation to common environmental factors in their evolutionary history. Genome wide gene-content analyses revealed the existence of two distinct ecological guilds within the analyzed lineage of marine gammaproteobacteria which can be distinguished by their trophic strategies. Based on our results a novel order within the class Gammaproteobacteria is proposed, which is designated Cellvibrionales ord. nov. and comprises the five novel families Cellvibrionaceae fam. nov., Halieaceae fam. nov., Microbulbiferaceae fam. nov., Porticoccaceae fam. nov., and Spongiibacteraceae fam. nov.

Litorivivens lipolytica gen. nov., sp. nov., a lipolytic bacterium isolated from a tidal flat

A Gram-stain-negative, flagellated, aerobic and rod-shaped or ovoid bacterial strain, designated HJTF-7(T), was isolated from a tidal flat on the South Sea of South Korea, and its taxonomic position was investigated using a polyphasic approach. Strain HJTF-7(T) grew optimally at 25 °C, at pH 7.0-8.0 and in the presence of 2.0% (w/v) NaCl. Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees, based on 16S rRNA gene sequences, showed that strain HJTF-7(T) joined the cluster comprising the type strains of species of the genera Spongiibacter and Zhongshania. Strain HJTF-7(T) exhibited 16S rRNA gene sequence similarities of 90.4-92.5% to the type strains of species of the genera Spongiibacter and Zhongshania and of less than 91.5% to the type strains of other recognized species. Strain HJTF-7(T) contained Q-8 as the predominant ubiquinone. The major fatty acids were iso-C17:1ω9c, iso-C15:0, iso-C17:0, iso-C11:0 3-OH and C17:1ω8c and the major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. The fatty acid and polar lipid profiles of strain HJTF-7(T) were distinct from those of members of the genera Spongiibacter and Zhongshania. The DNA G+C content of strain HJTF-7(T) was 55.9 mol%. The phylogenetic data and differential chemotaxonomic and other phenotypic properties revealed that strain HJTF-7(T) represents a novel genus and species within the class Gammaproteobacteria, for which the name Litorivivens lipolytica gen. nov., sp. nov. is proposed. The type strain of Litorivivens lipolytica is HJTF-7(T) ( =KCTC 42157(T) =CECT 8654(T)).

Zhongshania aliphaticivorans sp. nov., an aliphatic hydrocarbon-degrading bacterium isolated from marine sediment, and transfer of Spongiibacter borealis Jang et al. 2011 to the genus Zhongshania as Zhongshania borealis comb. nov

A Gram-staining-negative, facultatively aerobic bacterium, designated SM-2(T), was isolated from a sea-tidal flat of Yellow Sea, South Korea. Cells were catalase- and oxidase-positive motile rods with a single polar flagellum. Growth of strain SM-2(T) was observed at 10-37 °C (optimum, 25-30 °C), at pH 5.5-8.5 (optimum, pH 7.0-7.5) and in the presence of 0-11% (w/v) NaCl (optimum, 2%). Strain SM-2(T) contained ubiquinone-8 (Q-8) as the sole isoprenoid quinone and C(17:1)ω8c, summed feature 3 (comprising C(16:1)ω7c and/or iso-C(15:0) 2-OH), C(17:0) and C(18:1)ω7c as the major fatty acids. Phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an unidentified lipid were identified as the major cellular polar lipids. The G+C content of the genomic DNA was 52.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain SM-2(T) formed a tight phyletic lineage with Zhongshania antarctica ZS5-23(T), Zhongshania guokunii ZS6-22(T) and Spongiibacter borealis CL-AS9(T), but that S. borealis CL-AS9(T) was distinct from other species of the genus Spongiibacter. Based on 16S rRNA gene sequence similarities, strain SM-2(T) was most closely related to S. borealis CL-AS9(T), Z. antarctica ZS5-23(T) and Z. guokunii ZS6-22(T), with similarities of 99.5%, 98.9% and 98.7%, respectively, but the DNA-DNA hybridization values among these species were clearly lower than 70%. On the basis of chemotaxonomic data and molecular properties, we propose strain SM-2(T) represents a novel species of the genus Zhongshania with the name Zhongshania aliphaticivorans sp. nov. (type strain SM-2(T) =KACC 18120(T) =JCM 30138(T)). We also propose the transfer of Spongiibacter borealis Jang et al. 2011 to the genus Zhongshania as Zhongshania borealis comb. nov. (type strain CL-AS9(T) =KCCM 90094(T) =JCM 17304(T)).

Alkane biodegradation genes from chronically polluted subantarctic coastal sediments and their shifts in response to oil exposure

Although sediments are the natural hydrocarbon sink in the marine environment, the ecology of hydrocarbon-degrading bacteria in sediments is poorly understood, especially in cold regions. We studied the diversity of alkane-degrading bacterial populations and their response to oil exposure in sediments of a chronically polluted Subantarctic coastal environment, by analyzing alkane monooxygenase (alkB) gene libraries. Sequences from the sediment clone libraries were affiliated with genes described in Proteobacteria and Actinobacteria, with 67 % amino acid identity in average to sequences from isolated microorganisms. The majority of the sequences were most closely related to uncultured microorganisms from cold marine sediments or soils from high latitude regions, highlighting the role of temperature in the structuring of this bacterial guild. The distribution of alkB sequences among samples of different sites and years, and selection after experimental oil exposure allowed us to identify ecologically relevant alkB genes in Subantarctic sediments, which could be used as biomarkers for alkane biodegradation in this environment. 16 S rRNA amplicon pyrosequencing indicated the abundance of several genera for which no alkB genes have yet been described (Oleispira, Thalassospira) or that have not been previously associated with oil biodegradation (Spongiibacter-formerly Melitea-, Maribius, Robiginitomaculum, Bizionia and Gillisia). These genera constitute candidates for future work involving identification of hydrocarbon biodegradation pathway genes.