Methanooceanicella nereidis gen. nov., sp. nov., the first oceanic Methanocellaceae methanogen, isolated from potential methane hydrate bearing area offshore southwestern Taiwan.

A novel mesophilic, hydrogenotrophic methanogen, strain CWC-04T, was obtained from a sediment sample extracted from a gravity core retrieved at station 22 within the KP-9 area off the southwestern coast of Taiwan during the ORIII-1368 cruise in 2009. Cells of strain CWC-04T were rod-shaped, 1.4-2.9 µm long by 0.5-0.6 µm wide, and occurred singly. Strain CWC-04Tutilized formate, H2/CO2, 2-propanol/CO2 or 2-butanol/CO2 as catabolic substrates. The optimal growth conditions were 42 °C, 0.17 M NaCl and pH 5.35. The genomic DNA G+C content calculated from the genome sequence of strain CWC-04T was 46.19 mol%. Phylogenetic analysis of 16S rRNA gene revealed that strain CWC-04T is affiliated with the genus Methanocella. The 16S rRNA gene sequences similarities within strains Methanocella arvoryzae MRE50T, Methanocella paludicola SANAET and Methanocella conradii HZ254T were 93.7, 93.0 and 91.3 %, respectively. In addition, the optical density of CWC-04T culture dropped abruptly upon entering the late-log growth phase, with virus-like particles (150 nm in diameter) being observed on and around the cells. This observation suggests that strain CWC-04T harbours a lytic virus. Based on these phenotypic, phylogenetic and genomic results, we propose that strain CWC-04T represents a novel species of a novel genus in the family Methanocellaceae, for which the name Methanooceanicella nereidis gen. nov., sp. nov. is proposed. The type strain is CWC-04T (=BCRC AR10050T=NBRC 113165T).

Methanovulcanius yangii gen. nov., sp. nov., a hydrogenotrophic methanogen, isolated from a submarine mud volcano in the offshore area of southwestern Taiwan.

A novel mesophilic, hydrogenotrophic methanogen, strain CYW5T, was isolated from a sediment sample of a piston core collected from submarine mud volcano MV5 located in the offshore area of southwestern Taiwan. Cells of strain CYW5T were irregular coccids, 0.5-1.0 µm in diameter and lysed easily by 0.01 % sodium dodecyl sulphate (SDS) treatment. Strain CYW5Tutilized formate or hydrogen plus carbon dioxide as catabolic substrates for methanogenesis. The optimal growth conditions were 37 °C, 0.043-0.085 M NaCl and pH 6.02-7.32. The genomic DNA G+C content calculated from the genome sequence of strain CYW5T was 56.2 mol%. The results of phylogenetic analysis of 16S rRNA gene sequences indicated that strain CYW5T represented a member of the family Methanomicrobiaceae in the order Methanomicrobiales, and was closely related to the members of the genus Methanogenium. The most closely related species was Methanogenium cariaci JR1T (94.9 % of 16S rRNA gene sequence identity). The average nucleotide identity and average amino acid identity values between strain CYW5T and members of the family Methanomicrobiaceae were 74.7-78.5 % and 49.1-64.9%, respectively. Although many of the morphological and physiological characteristics of strain CYW5T and the species of the genus Methanogenium were similar, they were distinguishable by the differences in genomic G+C content and temperature, NaCl and pH ranges for growth. Based on these phenotypic, phylogenetic and genomic results, we propose that strain CYW5T represents a novel species, of a novel genus, named Methanovulcanius yangii gen. nov., sp. nov. The type strain is CYW5T (=BCRC AR10048T=DSM 100756T=NBRC 111404T).

Discharge of deeply rooted fluids from submarine mud volcanism in the Taiwan accretionary prism.

Qualitative and quantitative assessments of fluid cycling are essential to address the role and transport of deeply sourced fluids in subduction systems. In this study, sediment cores distributed across a submarine mud volcano (SMV) offshore southwestern Taiwan were investigated to determine the characteristics of fluids generated through the convergence between the Eurasian and Phillippine Sea Plates. The low dissolved chloride concentration combined with the enrichment of 18O, and depletion of 2H of pore fluids suggest the discharge of deep freshwater formed by smectite dehydration at an equilibrium temperature of 100 to 150 °C. The upward fluid velocities, decreasing from 2.0 to 5.0 cm yr-1 at the center to a negligible value at margin sites, varied with the rate and efficiency of anaerobic methanotrophy, demonstrating the impact of fluid migration on biogeochemical processes and carbon cycling. By extrapolating the velocity pattern, the flux of fluids exported from 13 SMVs into seawater amounted up to 1.3-2.5 × 107 kg yr-1, a quantity accounting for 1.1-28.6% of the smectite-bound water originally stored in the incoming sediments. Our results imply that SMVs could act as a conduit to channel the fluids produced from great depth/temperature into seafloor environments in a subduction system of the western Pacific Ocean.

Spatial and temporal variations of sediment metals in the Tuul River, Mongolia.

Mongolia has been a pristine environment without much pollution. Our objective is to study a section of the Tuul River to evaluate the present condition of this pristine environment. Sediment metal (Al, Fe, Mn, Cu, Zn, Pb, Ni, Cd, Hg, and Cr) concentrations and Pb-210 were sampled and analyzed. Results showed that metal concentrations are much higher at areas near the capital city and municipal sewage outlet, with enrichment factor values up to 18 for Cu, and 26 for Cr. Higher copper concentrations were found at sites about ~ 50 km downstream from the source, an indication that pollutions are spreading further down the river. Vertical metal concentration profiles indicated that pollutions could be traced back to the 1960s. Inefficient sewage treatment plants and poorly managed power plant ash ponds were major sources of metals leaking into the Tuul River. Sewage wastewater is carrying metals through Tuul River to the lower river basin. Dusts from ash ponds are airborne and transport to greater area. These findings indicate that new and alternative measures have to be enforced to prevent further pollution entering the Tuul River drainage basin and airborne dust to other broader regions of the Asia and ocean.

Quantitative reconstruction of salinity history by otolith oxygen stable isotopes: An example of a euryhaline fish Lateolabrax japonicus.

RATIONALE: Otolith strontium:calcium (Sr:Ca) ratios have been extensively used to study fish migration across a river, estuary and ocean at each life stage. However, otolith Sr:Ca ratios only explain partial variations in salinity and quantitative reconstruction of salinity history of fishes remains a challenge. Using a euryhaline fish Lateolabrax japonicus as an example, this study demonstrated an isotopic method of quantitatively reconstructing the salinity histories and habitat uses of the fish. METHODS: Otolith oxygen stable isotopic ratios (δ18 Ooto values) were measured using a mass spectrometer for subsamples sequentially milled from the otolith core to the edge, and otolith Sr:Ca ratios were measured by an electron probe microanalyzer for the comparison. The mean water temperature within the studied area in the time period of each milled subsample was estimated from the Copernicus database. Based on an isotopic fractionation equation, each δ18 Ooto value and water temperature pair determined the water δ18 O value, which was then converted into salinity using published linear equations or an equation that was newly generated for this study. RESULTS: Individual fish clearly revealed different preferences in habitat use. The retrospectively reconstructed salinity history indicated that most L. japonicus inhabit and can spawn in seawater as well as in brackish estuaries. Few fish lived in freshwater during the young stage based on the analysis of δ18 Ooto profiles; however, otolith Sr:Ca ratios can only reveal freshwater residence and cannot distinguish residence in brackish water or seawater. CONCLUSIONS: This study demonstrated that otolith temporal microstructure and δ18 Ooto values are well-suited approaches for quantitative reconstruction of salinity histories of the fish. This method can improve the understanding of the habitat uses of other fishes inhabiting diverse habitats among the rivers, estuaries and oceans.

Dongshaea marina gen. nov., sp. nov., a facultatively anaerobic marine bacterium that ferments glucose with gas production.

Two isolates of heterotrophic, facultatively anaerobic, marine bacteria, designated DM1 and DM2T, were recovered from a lagoon sediment sample of Dongsha Island, Taiwan. Cells were Gram-reaction-negative rods. Nearly all of the cells were non-motile and non-flagellated during the late exponential to early stationary phase of growth, while a few of the cells exhibited motility with monotrichous flagellation. The two isolates required NaCl for growth and grew optimally at about 30 °C, 2-3 % NaCl and pH 7-8. They grew aerobically and could achieve anaerobic growth by fermenting d-glucose or other carbohydrates with production of acids and the gases, including CO2 and H2. Ubiquinone Q-8 was the only respiratory quinone. Cellular fatty acids were predominated by C16 : 0, C18 : 1ω7c and C16 : 1ω7c. The major polar lipid was phosphatidylethanolamine. Strains DM1 and DM2T had DNA G+C contents of 52.0 and 51.8 mol%, respectively, as determined by HPLC analysis. Phylogenetic analyses based on 16S rRNA gene sequences clearly indicated that the two isolates formed a distinct genus-level lineage in the family Aeromonadaceae of the class Gammaproteobacteria and was an outgroup with respect to a stable supragenic clade comprising species of the genera Oceanimonas, Oceanisphaera and Zobellella. The phylogenetic data and those from chemotaxonomic, physiological and morphological characterizations support the establishment of a novel species and genus inside the family Aeromonadaceae, for which the name Dongshaea marina gen. nov., sp. nov. is proposed. The type strain is DM2T (=BCRC 81069T=JCM 32096T).

Methanoculleus sediminis sp. nov., a methanogen from sediments near a submarine mud volcano.

A mesophilic, hydrogenotrophic methanogen, strain S3Fa(T), was isolated from sediments collected by Ocean Researcher I cruise ORI-934 in 2010 near the submarine mud volcano MV4 located at the upper slope of south-west Taiwan. The methanogenic substrates utilized by strain S3Fa(T) were formate and H2/CO2 but not acetate, secondary alcohols, methylamines, methanol or ethanol. Cells of strain S3Fa(T) were non-motile, irregular cocci, 0.5-1.0 µm in diameter. The surface-layer protein showed an Mr of 128,000.The optimum growth conditions were 37 °C, pH 7.1 and 0.17 M NaCl. The DNA G+C content of the genome of strain S3Fa(T) was 62.3 mol%. Phylogenetic analysis revealed that strain S3Fa(T) was most closely related to Methanoculleus marisnigri JR1(T) (99.3% 16S rRNA gene sequence similarity). Genome relatedness between strain S3Fa(T) and Methanoculleus marisnigri JR1(T) was computed using both genome-to-genome distance analysis (GGDA) and average nucleotide identity (ANI) with values of 46.3-55.5% and 93.08%, respectively. Based on morphological, phenotypic, phylogenetic and genomic relatedness data, it is evident that strain S3Fa(T) represents a novel species of the genus Methanoculleus, for which the name Methanoculleus sediminis sp. nov. is proposed. The type strain is S3Fa(T) ( = BCRC AR10044(T) = DSM 29354(T)).

Methanoculleus taiwanensis sp. nov., a methanogen isolated from deep marine sediment at the deformation front area near Taiwan.

A mesophilic, hydrogenotrophic methanogen, strain CYW4(T), was isolated from deep-sea sediment obtained by the Ocean Researcher I cruiser, ORI-961, in 2011. The sediment was from the deformation front area offshore of south-western Taiwan. Here, seismic reflections indicated that methane hydrates were abundant. The methanogenic substrates utilized by strain CYW4(T) were formate and H2/CO2, but not acetate, secondary alcohols, methylamines, methanol and ethanol. Cells of strain CYW4(T) were non-motile, irregular cocci and 0.6-1.5 µm in diameter. The S-layer protein had an Mr of 112 000. The optimum growth conditions were at 37 °C, pH 8.1 and 0.08 M NaCl. Growth of the strain was stimulated by acetate. The G+C content of the chromosomal DNA of strain CYW4(T) was 61 mol%. Phylogenetic analysis revealed that strain CYW4(T) was most closely related to Methanoculleus marisnigri JR1(T) (96.82 % 16S rRNA gene sequence similarity). Based on the morphological, phenotypic and phylogenetic characteristics presented here, it is evident that strain CYW4(T) represents a novel species of the genus Methanoculleus, and the name Methanoculleus taiwanensis sp. nov. is proposed. The type strain is CYW4(T) ( = BCRC AR10043(T) = NBRC 110782(T)). The optical density of cultures of strain CYW4(T) dropped abruptly upon entering the stationary growth phase. During this time numerous particles of approximately 50 nm in diameter were observed on and around the cells. This suggests that strain CYW4(T) harbours a lytic virus that is induced in the stationary phase, which is of interest because only a few lytic viruses have been reported in methanogens.

Reclassification of [Glaciecola] lipolytica and [Aestuariibacter] litoralis in Aliiglaciecola gen. nov., as Aliiglaciecola lipolytica comb. nov. and Aliiglaciecola litoralis comb. nov., respectively.

Following phylogenetic analysis based on 16S rRNA gene sequences, together with DNA G+C contents and differential chemotaxonomic and physiological characteristics, a new genus with the name Aliiglaciecola gen. nov. is proposed to more appropriately accommodate two recognized species of the genera Glaciecola and Aestuariibacter. Accordingly, [Glaciecola] lipolytica and [Aestuariibacter] litoralis should be reassigned to the novel genus as Aliiglaciecola lipolytica comb. nov. (type strain, E3(T) = JCM 15139(T) = CGMCC 1.7001(T)) and Aliiglaciecola litoralis comb. nov. (type strain, KMM 3894(T) = JCM 15896(T) = NRIC 0754(T)), respectively. Aliiglaciecola lipolytica is proposed as the type species of this new genus. Physiologically, the combined characteristics of positive reactions for nitrate reduction and growth at 4 °C and 36 °C distinguish the new genus from the genera Aestuariibacter and Glaciecola by one to three traits. Moreover, the new genus is also distinguished from the genus Glaciecola by the fatty acid profile and distinguished from the genus Aestuariibacter by the differences of major isoprenoid quinone (MK-7 vs Q-8) and DNA G+C content (40.8-43.0 mol% vs 48.0-54.0 mol%).

Munidopsis lauensis Baba & de Saint Laurent, 1992 (Decapoda, Anomura, Munidopsidae), a newly recorded squat lobster from a cold seep in Taiwan.

The squat lobster, Munidopsis lauensis Baba & de Saint Laurent, 1992, is recorded from Taiwan for the first time. This species was previously known only from deep-sea hydrothermal vents in the South-West Pacific but it was now found at a deep-sea cold seep site off southwestern Taiwan. The identity of the Taiwanese material is confirmed by comparison of sequences from the barcoding gene COI. Munidopsis lauensis can be easily separated from other congeners in Taiwanese waters by the eyes bearing a strong mesiodorsal spine and a small mesioventral spine, smooth carapace, fingers of the cheliped distally spooned and fixed finger without a denticulate carina on the distolateral margin. The discovery of this species in Taiwan increases the Munidopsis fauna of the island to 38 species. A color photograph and line drawings illustrating distinctive characters are provided for the Taiwanese material.

Geochemical speciation and risk assessment of heavy metals in the river estuarine sediments--a case study: Mahanadi basin, India.

Sequential extraction technique was used to study the mobility and dynamics of operationally determined chemical forms of heavy metals in the sediments and their ecological risk on the biotic species. The results reveal that high environmental risk of Cd, Ni, Co and Pb, are due to their higher availability in the exchangeable fraction. Substantial amount of Cd, Co, Mn, Cu, Zn, Ni and Pb, is observed as carbonate bound, which may result due to their special affinity towards carbonate and their co-precipitation with its minerals. Colloids of Fe-Mn oxides act as efficient scavengers for the heavy metals like Zn, Pb, Cu, Cr, Co, and Ni. Toxic metals like Ni, Pb and Cd are of concern, which occasionally may be associated with adverse biological effects based on the comparison with sediment quality guidelines (SQGs). The risk assessment code (RAC) suggests that the highest mobility of Cd poses a higher environmental risk and also threat to the aquatic biota. Factor analysis reveals that the enrichment of heavy metals in bioavailable fraction is mostly contributed from anthropogenic sources. These contributing sources are highlighted by cluster analysis.

Consequences and implication of heavy metal spatial variations in sediments of the Keelung River drainage basin, Taiwan.

A great deal of effort was enforced to reduce the pollution of the Keelung River in the past 20 years. A set of sediments covering most of the Keelung River drainage basin was analyzed for bulk sediment heavy metal concentrations, grain size content and Pb-210 dating in order to understand the spatial variations of sediment heavy metal contents as well as to evaluate the effectiveness of pollution control. The results showed that anthropogenic pollution and grain size are two of the most important factors in controlling spatial variations of metals in the Keelung River sediments. In addition, little reduction of sediment heavy metal concentrations was observed in the Keelung River drainage basin. Large spatial variations of metals and grain size were observed. High concentrations of zinc, copper, lead and cadmium were found in sediments near the main outlets of the adjacent Da-Wu-Lun Industrial Park and municipal waste drainage systems. Anthropogenic sources of heavy metal have altered the natural sediment heavy metal distributions. Positive linear relationships between aluminum, iron and fine-grained sediments showed that spatial grain size variations controlled the natural aluminum and iron concentrations in sediments. Zinc, copper, lead and cadmium contents were much higher than those measured 15 years ago. The unusually high concentrations of heavy metals, high enrichment factors and their rapid increases with time in Pb-210 dated core showed that the efforts in heavy metal reduction were futile. A proper regulation to prevent further heavy metals from entering into the river is urgently needed.