Trichome Lengths of the Heterocystous N\u3csub\u3e2\u3c/sub\u3e-Fixing Cyanobacteria in the Tropical Marginal Seas of the Western North Pacific

Calothrix rhizosoleniae and Richelia intracellularis are heterocystous cyanobacteria found in the tropical oceans. C. rhizosoleniae commonly live epiphytically on diatom genera Chaetoceros (C-C) and Bacteriastrum (B-C) while R. intracellularis live endosymbiotically within Rhizosolenia (R-R), Guinardia (G-R), and Hemiaulus (H-R); although, they occasionally live freely (FL-C and FL-R). Both species have much shorter trichomes than the other marine filamentous cyanobacteria such as Trichodesmium spp. and Anabaena gerdii. We investigated the trichome lengths of C. rhizosoleniae and R. intracellularis in the South China Sea (SCS) and the Philippine Sea (PS) between 2006 and 2014. On average, H-R had the shortest trichome lengths (3.5 cells/trichome), followed by B-C and C-C (4.9–5.2 cells/trichome) and FL-C (5.9 cells/trichome), and R-R, G-R, and FL-R had the longest trichome lengths (7.4–8.3 cells/trichome). Field results showed the trichome lengths of C-C and B-C did not vary seasonally or regionally. However, FL-C and H-R from the SCS and during the cool season had longer trichomes, where/when the ambient nutrient concentrations were higher. R-R, G-R, and FL-R also showed regional and seasonal variations in trichome length. Ultrastructural analysis found no gas vesicles within the C. rhizosoleniae cells to assist in buoyancy regulation. Results suggest that the trichome lengths of C. rhizosoleniae and R. intracellularis might be regulated by their diatom hosts’ symbiotic styles and by ambient nutrients. Short trichome length might help C. rhizosoleniae and R. intracellularis to stay in the euphotic zone regardless as to whether they are free-living or symbiotic

Controlling factors of large-scale harmful algal blooms with Karenia selliformis after record-breaking marine heatwaves

Unprecedented, large-scale harmful algal blooms (HABs) dominated by Karenia selliformis occurred off the southeastern coast of Hokkaido, Japan, from late September to early November 2021, about a month after intense and extensive marine heatwaves (MHWs) had subsided. The aims of the present study were to understand the mechanism of development, maintenance, and decay of the HABs as well as to investigate the effect of the MHWs on the HABs. We developed a one-dimensional, lower trophic-level ecosystem model (NEMURO+) to simulate the HABs. The model successfully simulated the 2021 HABs and indicated that their development, maintenance, and decay were controlled primarily by changes of water temperature. Nitrate supply from subsurface layers by seasonal vertical diffusion in autumn also helped to maintain the HABs. Vertical diffusion following MHWs in 2021 contributed to the long duration of the preferred temperature for K. selliformis and the occurrence of pre-bloom of K. selliformis, resulting in preconditioning and accelerating the HABs. However, simulations for normal years (i.e., the climatological mean during 2003–2018) showed that HABs could have occurred, even in the absence of MHWs. The simulations indicated that massive blooms of other phytoplankton species (e.g., diatoms) would not have occurred in 2021, even in the absence of a K. selliformis bloom. The implication was that the HABs in 2021 were the species-specific responses of K. selliformis. The proposed mechanism of the HABs was peculiar to our study area and differed from that previously reported for other K. selliformis blooms. Specifically, the preferred temperature for the HABs of K. selliformis was clearly lower than the previously reported preferred temperature of K. selliformis; thus, the physiological characteristics of the K. selliformis that bloomed in our study area differed from those of other K. selliformis strains. These discoveries provide the first evidence to explain how MHWs affect HABs, and to understand how inter-regional dissimilarities of K. selliformis can lead to large-scale, devastating outbreaks under different oceanographic conditions

Co-Occurrence of Marine Extremes Induced by Tropical Storms and an Ocean Eddy in Summer 2016: Anomalous Hydrographic Conditions in the Pacific Shelf Waters off Southeast Hokkaido, Japan

This study proposes an analysis methodology to address how very rare marine extremes can be understood using limited data. In summer 2016, extreme weather and marine events occurred simultaneously around the Pacific shelf off southeastern Hokkaido, Japan. Six successive tropical storms brought extreme precipitation and an anticyclonic mesoscale eddy of subtropical Kuroshio water closely approached the coast, locally causing marine heat waves. We examined how these compound extremes affected oceanographic conditions on the coastal shelf by analyzing data from ship surveys in October 2016 on the Pacific shelf and outputs from a realistic ocean model. Climatologically, warm, high-salinity (33.0–33.7) subtropical water from the Okhotsk Sea (modified Soya Warm Current water) is distributed near the sea surface on the Pacific shelf in October and transported by the along-shelf boundary current. In 2016, however, a vertically well-mixed low-salinity (<33.0) layer associated with the heavy rainfall was observed at 0–50 m depth on the shelf, salinity maxima (≥33.7) associated with Kuroshio water from the mesoscale eddy occurred at 50–150 m depth on the slope, and baroclinic jets formed along the salinity front near the shelfbreak. These observed salinity structures were reproduced by a 1/50° ocean model. Particle-tracking experiments revealed that the low-salinity water originated mainly off eastern Hokkaido, where heavy rainfall events occurred in August, and was modified by mixing with Soya Warm Current water before transport to the Pacific shelf

Spatial variation of bacterial community composition at the expiry of spring phytoplankton bloom in Sendai Bay, Japan

AbstractIn order to characterize how bacterial communities are propagated over spatial scales in a coastal area, the bacterial community composition was examined along with a transect line set in a bay at an expiry of spring phytoplankton bloom. Four distinctive bacterial communities were found within the bay by a fingerprinting method of 16S rRNA gene amplicons. The most widely distributed one was distributed in the surface and middle layers at whole area of the bay. The water was characterized by low inorganic nutrients concentration and high bacterial abundance, suggesting that the bacterial community had been developed in the bloom. Pyrosequencing analyses of the gene amplicons indicated that Rhodobacteriaceae and Flavobacteriaceae were abundant in the bacterial community, though the most abundant bacterial taxon was SAR11. The second group was distributed in the bottom water at the coastal side of the bay where considerably high Chl. a concentration was observed, probably because of the sedimentation of phytoplankton bloom. The community diversity was high and Alteromonadaceae, Saprospiraceae, and some families of Actinobacter existed more in this community than the others. The third group was distributed in the deep water near the border with the outside of the bay. The ratio of SAR11 was the highest in this community; besides, Burkholderianceae and Rhodospilliraceae existed in relatively high abundances. Another bacterial community having intermediate characters was observed in the middle to bottom layers around a central part of the bay where vertical water mixing was observed. These findings suggest that spatially different bacterial communities were formed under the influences of phytoplankton bloom and/or hydrographic events such as oceanic seawater intrusion of the bay

Subarctic-scale transport of 134Cs to ocean surface off northeastern Japan in 2020

Abstract We studied the spatiotemporal variations in 134Cs, 137Cs, and 228Ra concentrations at the sea surface off southeastern Hokkaido, Japan (off-Doto region) from 2018 to 2022 using low-background γ-spectrometry. The 134Cs concentrations in the off-Doto region, decay-corrected to the date of the Fukushima Dai-ichi Nuclear Power Plant (FDNPP) accident, exhibited wide lateral variation each year (e.g., 0.7–1.1 mBq/L in 2020). By studying the 228Ra concentrations and salinity, this variation was explained based on the current mixing patterns. Furthermore, the 134Cs concentrations in the waters highly affected by the Oyashio Current (OYC) gradually increased from 2018 to 2020, and subsequently decreased in 2022. This implies that the water mass maximally contaminated with 134Cs was transported back to the side of the Japanese islands 10 years after the FDNPP accident along with counter-clockwise currents (e.g., the OYC) in the northern North Pacific Ocean. The 134Cs concentrations in the OYC-affected waters in the off-Doto region in 2020 were ~ 1/6 times those in the 134Cs-enriched core of waters off the western American Coast in 2015, which can be ascribed to dilution via spatial dispersion during subarctic current circulation. Overall, we elucidated the ocean-scale subarctic current systems in the northwestern North Pacific Ocean, including water circulation timespans

Interannual variation of polycyclic aromatic hydrocarbons in surface seawater at adjacent seas of the Japanese archipelago

http://www.godac.jamstec.go.jp/darwin/cruise/mirai/mr19-03c/ehttp://www.godac.jamstec.go.jp/darwin/cruise/mirai/mr20-01/

A Preliminary Metagenome Analysis Based on a Combination of Protein Domains

Metagenomic data have mainly been addressed by showing the composition of organisms based on a small part of a well-examined genomic sequence, such as ribosomal RNA genes and mitochondrial DNAs. On the contrary, whole metagenomic data obtained by the shotgun sequence method have not often been fully analyzed through a homology search because the genomic data in databases for living organisms on earth are insufficient. In order to complement the results obtained through homology-search-based methods with shotgun metagenomes data, we focused on the composition of protein domains deduced from the sequences of genomes and metagenomes, and we utilized them in characterizing genomes and metagenomes, respectively. First, we compared the relationships based on similarities in the protein domain composition with the relationships based on sequence similarities. We searched for protein domains of 325 bacterial species produced using the Pfam database. Next, the correlation coefficients of protein domain compositions between every pair of bacteria were examined. Every pairwise genetic distance was also calculated from 16S rRNA or DNA gyrase subunit B. We compared the results of these methods and found a moderate correlation between them. Essentially, the same results were obtained when we used partial random 100 bp DNA sequences of the bacterial genomes, which simulated raw sequence data obtained from short-read next-generation sequences. Then, we applied the method for analyzing the actual environmental data obtained by shotgun sequencing. We found that the transition of the microbial phase occurred because the seasonal change in water temperature was shown by the method. These results showed the usability of the method in characterizing metagenomic data based on protein domain compositions

Development of a time-series shotgun metagenomics database for monitoring microbial communities at the Pacific coast of Japan

Abstract Although numerous metagenome, amplicon sequencing-based studies have been conducted to date to characterize marine microbial communities, relatively few have employed full metagenome shotgun sequencing to obtain a broader picture of the functional features of these marine microbial communities. Moreover, most of these studies only performed sporadic sampling, which is insufficient to understand an ecosystem comprehensively. In this study, we regularly conducted seawater sampling along the northeastern Pacific coast of Japan between March 2012 and May 2016. We collected 213 seawater samples and prepared size-based fractions to generate 454 subsets of samples for shotgun metagenome sequencing and analysis. We also determined the sequences of 16S rRNA (n = 111) and 18S rRNA (n = 47) gene amplicons from smaller sample subsets. We thereafter developed the Ocean Monitoring Database for time-series metagenomic data ( http://marine-meta.healthscience.sci.waseda.ac.jp/omd/ ), which provides a three-dimensional bird’s-eye view of the data. This database includes results of digital DNA chip analysis, a novel method for estimating ocean characteristics such as water temperature from metagenomic data. Furthermore, we developed a novel classification method that includes more information about viruses than that acquired using BLAST. We further report the discovery of a large number of previously overlooked (TAG)n repeat sequences in the genomes of marine microbes. We predict that the availability of this time-series database will lead to major discoveries in marine microbiome research