Whole-genome sequence of a marine bacterial strain, FRT2, belonging to the genus Leeuwenhoekiella, isolated from the seawater of the Obama Bay in Fukui, Japan.

A marine bacterial strain, FRT2, was isolated from the surface water of the Obama Bay in Fukui, Japan. Its complete genome comprises one circular chromosome (3,806,097 bp), harboring 3,269 predicted protein- and 44-tRNA-encoding genes and 3 rRNA operons.

Whole-genome sequence of the strictly anaerobic bacterial strain SANA belonging to the family Gottschalkiaceae, isolated from a xenic culture of an anaerobic protist.

An anaerobic bacterial strain SANA was isolated from a xenic culture of an anaerobic heterolobosean protist which was obtained from a saline lake in Japan. Its draft genome comprises 1 circular chromosome (3,490,293 bp), harboring 3,275 predicted protein-coding and 73 tRNA-encoding genes and 8 rRNA operons.

Pseudodesulfovibrio nedwellii sp. nov., a mesophilic sulphate-reducing bacterium isolated from a xenic culture of an anaerobic heterolobosean protist.

A novel sulphate-reducing bacterium, strain SYKT, was isolated from a xenic culture of an anaerobic protist obtained from a sulphidogenic sediment of the saline Lake Hiruga in Fukui, Japan. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that SYKT clustered with the members of the genus Pseudodesulfovibrio. The closest relative of strain SYKT was Pseudodesulfovibrio sediminis SF6T, with 16S rRNA gene sequence identity of 97.43 %. Digital DNA-DNA hybridisation and average nucleotide identity values between SYKT and species of the genus Pseudodesulfovibrio fell below the respective thresholds for species delineation, indicating that SYKT represents a novel species of the genus Pseudodesulfovibrio. Cells measured 1.7-3.7×0.2-0.5 µm in size and were Gram-stain-negative, obligately anaerobic, motile by means of a single polar flagellum and had a curved rod or sigmoid shape. Cell growth was observed under saline conditions from pH 6.0 to 9.5 (optimum pH 8.0-9.0) and at a temperature of 10-30 °C (optimum 25 °C). SYKT used lactate, pyruvate, fumarate, formate and H2 as electron donors. It used sulphate, sulphite, thiosulphate and sulphur as terminal electron acceptors. Pyruvate and fumarate were fermented. Major cellular fatty acids were anteiso-C15 : 0, C16 : 0, anteiso-C17 : 1ω9c, summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The DNA G+C content of SYKT was 49.4 mol%. On the basis of the the genetic and phenotypic features, SYKT was determined to represent a novel species of the genus Pseudodesulfovibrio for which the name Pseudodesulfovibrio nedwellii sp. nov. is proposed with type strain SYKT (=DSM 114958T=JCM 35746T).

Whole-Genome Sequence of the Sulfate-Reducing Bacterial Strain SYK, Isolated from a Xenic Culture of an Anaerobic Protist.

The sulfate-reducing bacterial strain SYK was isolated from a xenic culture of an anaerobic heterolobosean protist which was obtained from a saline lake in Japan. Its draft genome comprises 1 circular chromosome (3,762,062 bp), harboring 3,463 predicted protein- and 65 tRNA-encoding genes and 3 rRNA operons.

Genome Sequence of the Sulfate-Reducing Bacterium Pseudodesulfovibrio portus JCM 14722T.

Pseudodesulfovibrio portus JCM 14722T is a strictly anaerobic, mesophilic sulfate-reducing bacterium isolated from estuarine sediments in Japan. Its draft genome sequence comprises 1 circular chromosome (3,403,863 bp), harboring 3,182 predicted protein- and 60 tRNA-encoding genes, as well as 2 rRNA operons.

Revision of the phylogeny of Placididea (Stramenopiles): Molecular and morphological diversity of novel placidid protists from extreme aquatic environments.

Recent studies suggested that the diversity of microbial eukaryotes in hypersaline environments is widely underestimated. Placidids are a group of heterotrophic stramenopile flagellates that are frequently found in these environments, but up to now only very few species were isolated and fully described, mostly from marine or brackish water sites. In this study, we extend the known diversity of Placididea by three new genera (Allegra, Haloplacidia, and Placilonga) compromising nine new species, isolated from athalassic, mostly hypersaline environments (Allegra dunaii, Allegra atacamiensis, Allegra hypersalina, Haloplacidia cosmopolita, Suigetsumonas keniensis) and marine waters (Placilonga atlantica, Placidia azorensis, Placidia abyssalis, Wobblia pacifica) including a description of their morphology and molecular phylogeny. In total, 36 strains were comparatively analysed. Studies from athalassic waters revealed an especially high number of different genotypes. A multigene analysis based on a ten genes dataset revealed a clear separation into marine, athalassic and brackish water clades. Several representatives were found to cope with hypersaline conditions from 20 to 250 PSU, even up to 284 PSU, suggesting that they may form a halotolerant group.

Potential oxygen consumption and community composition of sediment bacteria in a seasonally hypoxic enclosed bay.

The dynamics of potential oxygen consumption at the sediment surface in a seasonally hypoxic bay were monitored monthly by applying a tetrazolium dye (2-(4-iodophenyl)-3-(4-nitrophenyl)-5-phenyl-2H-tetrazolium chloride [INT]) reduction assay to intact sediment core samples for two consecutive years (2012-2013). Based on the empirically determined correlation between INT reduction (INT-formazan formation) and actual oxygen consumption of sediment samples, we inferred the relative contribution of biological and non-biological (chemical) processes to the potential whole oxygen consumption in the collected sediment samples. It was demonstrated that both potentials consistently increased and reached a maximum during summer hypoxia in each year. For samples collected in 2012, amplicon sequence variants (ASVs) of the bacterial 16S rRNA genes derived from the sediment surface revealed a sharp increase in the relative abundance of sulfate reducing bacteria toward hypoxia. In addition, a notable shift in other bacterial compositions was observed before and after the INT assay incubation. It was Arcobacter (Arcobacteraceae, Campylobacteria), a putative sulfur-oxidizing bacterial genus, that increased markedly during the assay period in the summer samples. These findings have implications not only for members of Delta- and Gammaproteobacteria that are consistently responsible for the consumption of dissolved oxygen (DO) year-round in the sediment, but also for those that might grow rapidly in response to episodic DO supply on the sediment surface during midst of seasonal hypoxia.

Distribution of the Harmful Bloom-Forming Cyanobacterium, Microcystis aeruginosa, in 88 Freshwater Environments across Japan.

Microcystis aeruginosa was quantitatively surveyed in 88 freshwater environments across Japan within 3| |weeks in 2011. In order to clarify the distribution pattern of M. aeruginosa at the intra-species level, three major genotypes, which were defined by 16S-23S rRNA inter-transcribed-spacer (ITS) regions, were selectively detected using quantitative real-time PCR assays. Of the 68 sites at which the Microcystis intergenic-spacer region of the phycocyanin (IGS-PC) gene was detected, the M. aeruginosa morphotype-related genotype (MG1) dominated in 41 sites, followed by the non-toxic M. wesenbergii-related genotype (MG3). A correlation analysis showed that total nitrogen and phosphate positively correlated with the abundance of IGS-PC, which positively correlated with microcystin synthetase gene abundance. A redundancy analysis of genotype compositions showed that pH positively correlated with the dominance of MG3 and negatively correlated with MG1, i.e., both toxic and non-toxic genotypes. Our survey of Microcystis populations over a wide area revealed that MG1 is a dominant genotype in Japan.

Data on taxonomic annotation and diversity of 18S rRNA gene amplicon libraries derived from high throughput sequencing.

This Data in Brief article is a supporting information for the research article entitled "Protistan community composition in anoxic sediments from three salinity-disparate Japanese lakes" by Kataoka and Kondo (2019) [1]. Summary of 18S rRNA gene sequences originated from anoxic sediment of three lakes in two seasons using high throughput sequencing techniques (MiSeq, Illumina) was shown in this data article. Supergroup-level taxonomy was compared between the SILVA search for SILVA database and BLASTn search for the PR2 database. Alpha diversity was calculated in each sample, and beta-diversity was calculated among the six amplicon libraries. Partial sequence length between the primer set of 574*f and 1132R Hugerth et al., 2015 was compared between the forward read and the combined read.

Dynamics of Sulfate-Reducing Bacteria Community Structure in Surface Sediment of a Seasonally Hypoxic Enclosed Bay.

We herein report on the dynamics of a sulfate-reducing bacteria (SRB) community structure in the surface sediment of a seasonally hypoxic enclosed bay for two consecutive years (2012 and 2013). The uppermost (0-5 mm) and subsurface (5-10 mm) layers of sediment were examined with a terminal-restriction fragment length polymorphism (T-RFLP) analysis based on the dissimilatory sulfite reductase (dsrA) gene. The SRB community significantly differed between the two sediment layers over the sampling period. This difference was mainly attributed to operational taxonomic units (OTUs) that were unique to either of the sediment layers. However, nearly 70% of total OTUs were shared between the two layers, with a few predominating. Therefore, no significant shift was observed in the SRB community structure under varying dissolved oxygen (DO) conditions in bottom water overlying the sediment surface. An additional analysis of 16S rRNA gene amplicon sequences, conducted for three uppermost sediment samples (July, August, and September in 2012), revealed that Desulfococcus, a member of SRB with high tolerance to oxygen, was the predominant Deltaproteobacteria across the uppermost sediment samples. Based on the predominance of shared OTUs across the SRB community in the sediment (0-10 mm) regardless of bottom-water DO, some SRB that are physiologically tolerant of a wide range of DO conditions may have dominated and masked changes in responsive SRB to DO concentrations. These results suggest that the SRB community structure in the enclosed bay became stable under repeated cycles of seasonal hypoxia, but may be compromised if the severity of hypoxia increases in the future.

Effects of bottom-water hypoxia on sediment bacterial community composition in a seasonally hypoxic enclosed bay (Omura Bay, West Kyushu, Japan).

The bacterial community strongly drives carbon and other biogeochemical cycles in marine sediment. However, little is known about the impact of dissolved oxygen (DO) availability on bacterial community composition. To fill this gap, we examined diversity, richness and structure of the bacterial population for three consecutive years (2011-2013) in the uppermost (0-5 and 0-7 mm depth) and the subsurface layers (5-10 and 7-14 mm depth) of Omura Bay, Kyushu, Japan, a seasonally hypoxic enclosed bay. Automated ribosomal intergenic spacer analysis revealed a unimodal pattern of diversity indices with DO, peaking at the suboxic (11 µM O2) condition. Shifts in the bacterial communities were also evident in response to the availability of DO. Changes in the operational taxonomic units (OTUs) that were less abundant accounted for a large part of the community dissimilarity. It was further demonstrated that the relative abundance of OTUs affiliated with Gammaproteobacteria was correlated positively with DO, while that with Deltaproteobacteria was inversely correlated with DO. These results strongly suggest that DO availability of bottom water plays a fundamental role in shaping the bacterial community in sediment surfaces of shallow coastal areas.

Growth and Grazing Kinetics of the Facultative Anaerobic Nanoflagellate, Suigetsumonas clinomigrationis.

The functional and numerical responses of the facultative anaerobic heterotrophic nanoflagellate, Suigetsumonas clinomigrationis NIES-3647 to prey density were examined under oxic and anoxic conditions. S. clinomigrationis grew at temperatures between 10 and 30°C and in the salinity range of 3.9-36.9 psu. The maximum specific growth and ingestion rates of S. clinomigrationis were lower under anoxic conditions than under oxic conditions. Half-saturation constants for the growth of S. clinomigrationis were within or greater than the range of bacterial densities in the water column of Lake Suigetsu, suggesting that its growth rate is limited by bacterial prey densities in natural environments.

Sulfur Fertilization Changes the Community Structure of Rice Root-, and Soil- Associated Bacteria.

Under paddy field conditions, biological sulfur oxidation occurs in the oxidized surface soil layer and rhizosphere, in which oxygen leaks from the aerenchyma system of rice plants. In the present study, we examined community shifts in sulfur-oxidizing bacteria associated with the oxidized surface soil layer and rice roots under different sulfur fertilization conditions based on the 16S ribosomal RNA (rRNA) gene in order to explore the existence of oligotrophic sulfur-oxidizing bacteria in the paddy rice ecosystem. Rice plants were grown in pots with no fertilization (control) or CaCO3 or CaSO4 fertilization. A principal-coordinates analysis (PCoA) showed that CaSO4 fertilization markedly affected bacterial communities associated with rice roots and soil, whereas no significant differences were observed in plant growth among the fertilizer treatments examined. In rice roots, the relative abundance of Acidobacteria, Alphaproteobacteria, Gammaproteobacteria, and TM7 was significantly higher in CaSO4-fertilized pots than in control pots. Alphaproteobacteria, Bradyrhizobiaceae, and Methylocystaceae members were significantly more abundant in CaSO4-fertilized roots than in control roots. On the other hand, the abundance of Actinobacteria and Proteobacteria was lower in CaSO4-fertilized soil than in control soil. These results indicate that the bacteria associated with rice roots and soil responded to the sulfur amendment, suggesting that more diverse bacteria are involved in sulfur oxidation in the rice paddy ecosystem than previously considered.

Suigetsumonas clinomigrationis gen. et sp. nov., a Novel Facultative Anaerobic Nanoflagellate Isolated from the Meromictic Lake Suigetsu, Japan.

A novel facultative anaerobic bacterivorous nanoflagellate was isolated from the water just below the permanent oxic-anoxic interface of the meromictic Lake Suigetsu, Japan. We characterized the isolate using light and transmission electron microscopy and molecular phylogenetic analyses inferred from 18S rDNA sequences. The phylogenetic analyses showed that the isolate belonged to class Placididea (stramenopiles). The isolate showed key ultrastructural features of the Placididea, such as flagellar hairs with two unequal terminal filaments, microtubular root 2 changing in shape from an arced to an acute-angled shape, and a lack of an x-fiber in root 2. However, the isolate had a single helix in the flagellar transition region, which is a double helix in the two known placidid nanoflagellates Placidia cafeteriopsis and Wobblia lunata. Moreover, the isolate had different intracellular features compared with these two genera, such as the arrangement of basal bodies, the components of the flagellar apparatus, the number of mitochondria, and the absence (or presence) of paranuclear bodies. The 18S rDNA sequence was also phylogenetically distant from the clades of the known Placididae W. lunata and P. cafeteriopsis. Consequently, the newly isolated nanoflagellate was described as Suigetsumonas clinomigrationis gen. et sp. nov.

Dominance of green sulfur bacteria in the chemocline of the meromictic Lake Suigetsu, Japan, as revealed by dissimilatory sulfite reductase gene analysis.

This study investigated the spatiotemporal abundance and diversity of the α-subunit of the dissimilatory sulfite reductase gene (dsrA) in the meromictic Lake Suigetsu for assessing the sulfur-oxidizing bacterial community. The density of dsrA in the chemocline reached up to 3.1 × 10(6) copies ml(-1) in summer by means of quantitative real-time PCR and it was generally higher than deeper layers. Most of the dsrA clones sequenced were related to green sulfur bacteria such as Chlorobium phaeovibrioides, C. limicola, and C. luteolum. Below the chemocline of the lake, we also detected other dsrA clones related to the purple sulfur bacterium Halochromatium salexigens and some branching lineages of diverse sequences that were related to chemotrophic sulfur bacterial species such as Magnetospirillum gryphiswaldense, Candidatus Ruthia magnifica, and Candidatus Thiobios zoothamnicoli. The abundance and community compositions of sulfur-oxidizing bacteria changed depending on the water depth and season. This study indicated that the green sulfur bacteria dominated among sulfur-oxidizing bacterial population in the chemocline of Lake Suigetsu and that certain abiotic environmental variables were important factors that determined sulfur bacterial abundance and community structure.

Comparison of sulphate-reducing bacterial communities in Japanese fish farm sediments with different levels of organic enrichment.

Fish farm sediments receive a large amount of organic matter from uneaten food and fecal material. This nutrient enrichment, or organic pollution, causes the accumulation of sulphide in the sediment from the action of sulphate-reducing bacteria (SRB). We investigated the effect of organic enrichment around coastal fish farms comparing the SRB community structure in these sediments. Sediment samples with different levels of organic pollution classified based upon the contents of acid-volatile sulphide and chemical oxygen demand were collected at three stations on the coast of western Japan. The SRB community composition was assessed using PCR amplification, cloning, sequencing and phylogenetic analysis of the dissimilatory sulphite reductase b-subunit gene (dsrB) fragments using directly extracted sediment DNA. Sequencing of the cloned PCR products of dsrB showed the existence of different SRB groups in the sediments. The majority of dsrB sequences were associated with the families Desulfobacteraceae and Desulfobulbaceae. Clones related to the phylum Firmicutes were also detected from all sediment samples. Statistical comparison of sequences revealed that community compositions of SRB from polluted sediments significantly differed from those of moderately polluted sediments and unpolluted sediments (LIBSHUFF, p<0.05), showing a different distribution of SRB in the fish farm sediments. There is evidence showing that the organic enrichment of sediments influences the composition of SRB communities in sediments at marine fish farms.

Comprehensive detection of phototrophic sulfur bacteria using PCR primers that target reverse dissimilatory sulfite reductase gene.

A new set of primers for the detection of phototrophic sulfur bacteria in natural environments is described. The primers target the α-subunit of the reverse dissimilatory sulfite reductase gene (dsrA). PCR-amplification resulted in products of the expected size from all the phototrophic strains tested, including purple sulfur and green sulfur bacteria. Seventy-nine clones obtained from environmental DNA using the primers were sequenced and all found to be closely related to the dsrA of purple sulfur bacteria and green sulfur bacteria. This newly developed PCR assay targeting dsrA is rapid and simple for the detection of phototrophic sulfur bacteria in situ and superior to the use of culture-dependent techniques.

[Endarterectomy for cervical internal carotid artery stenosis accompanied with severe aortic valve stenosis--case report].

A 75-year-old man, who had undergone coronary artery bypass graft and repair for abdominal aortic aneurysm, suffered from angina pectoris due to severe aortic valve stenosis complicated with asymptomatic bilateral cervical internal carotid artery stenoses. Brain perfusion imaging revealed reduced cerebral blood flow and cerebrovascular reactivity to acetazolamide in the bilateral cerebral hemispheres. First, the patient underwent left carotid endarterectomy, and the postoperative course was uneventful. Postoperative brain perfusion imaging showed improvement of cerebrovascular reactivity to acetazolamide in the bilateral cerebral hemispheres. Seven weeks later, the patient underwent aortic valve replacement, and his postoperative course was uneventful. Carotid endarterectomy rather than carotid artery stenting should be preceded for cervical carotid stenosis complicated with severe aortic valve stenosis.

[Proximal ligation of the parent artery for symptomatic tandem stenosis of the extradural internal carotid artery: a case report].

A 72-year-old man suffered blindness due to right central retinal artery occlusion. Cerebral angiography revealed tandem stenosis in the cervical, petrosal and cavernous portions of the right internal carotid artery (ICA). Blood flow from the vertebrobasilar artery via the right posterior communicating artery mainly perfused the right cerebral hemisphere. In addition, significant stenosis was observed in the left cervical carotid artery and the origin of the left vertebral artety. First, the patient underwent left carotid endarterectomy and vertebral artery to subclavian artery transposition. Two months later, ligation of the right ICA at its origin was performed. Postoperative course was uneventful and the patient has not experienced further ischemic events. We suggest that proximal ligation of the parent artery is a useful procedure for medically-refractory extradural ICA stenosis when surgical direct revascularization and percutaneous transluminal angioplasty cannot be performed.

Genetic diversity of the toxic cyanobacterium Microcystis in Lake Mikata.

The aim of the present study was to clarify the bloom dynamics and community composition of hepatotoxin microcystin-producing and non-microcystin-producing Microcystis genotypes in the environment. In Lake Mikata (Fukui, Japan) from April 2003 to January 2004, seasonal variation in the number of cells with microcystin (mcy) genotypes and the genetic diversity of the total population were investigated using quantitative competitive PCR and a 16S rDNA clone library, respectively. Using competitive PCR, cells with mcyA genotypes were quantified in August and October, and the ratio of the number of these mcyA genotypes to colony-forming Microcystis cells was 0.37 and 2.37, respectively. The 16S rDNA clones obtained could be divided into 12 ribotypes: a-l. Sixty-one Microcystis strains isolated from Lake Mikata during the sampling period were subjected to toxicity tests using HPLC and ELISA, PCR-based detection of the mcyA gene, and sequence analysis of the 16S rDNA. All isolates could be differentiated into 11 ribotypes (a, b, d, f, h, i, and m-q). Ribotypes b, f, i, m, n, and p had at least one strain that was a microcystin producer. In natural communities ribotypes b and f accounted for 85% of the 16S rDNA clones in August, and ribotypes b and i accounted for 24% of the clones in October. Thus, in some bloom stages the presence of microcystin genotypes identified using the 16S rDNA clone library correlated with that of mcy genotypes determined using competitive PCR.