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Water-soluble organic nitrogen (WSON) in marine atmospheric aerosols affect the water solubility, acidity, and light-absorbing properties of aerosol particles, which are important parameters in assessing both the climate impact and the biogeochemical cycling of bioelements. Size-segregated aerosol and surface seawater (SSW) samples were simultaneously collected over the subtropical North Pacific to investigate the origin of WSON in the marine atmosphere. The fine-mode WSON concentration (7.5 ± 6.6 ngN m−3) at 200–240∘ E along 23∘ N, defined as the eastern North Pacific (ENP), was significantly higher than that (2.4 ± 1.9 ngN m−3) at 135–200∘ E, defined as the western North Pacific (WNP). Analysis of the stable carbon isotope ratio of water-soluble organic carbon (WSOC; δ13CWSOC) together with backward trajectory indicated that most of the observed WSON in the fine particles in the ENP originated from the ocean surface. We found positive relations among nitrogen-fixation rate, dissolved organic nitrogen (DON) in SSW, and the WSON concentrations. The result suggests that reactive nitrogen (DON and ammonium), produced and exuded by nitrogen-fixing microorganisms in SSW, contributed to the formation of WSON aerosols. This study provides new insights into the role of ocean-derived reactive nitrogen aerosols associated with marine microbial activity.

Dinitrogen (N2) fixation is the major source of reactive nitrogen in the ocean and has been considered to occur specifically in low-latitude oligotrophic oceans. Recent studies have shown that N2 fixation also occurs in the polar regions and thus is a global process, although the physiological and ecological characteristics of polar diazotrophs are not yet known. Here, we successfully reconstructed diazotroph genomes, including that of cyanobacterium UCYN-A (Candidatus ‘Atelocyanobacterium thalassa’), from metagenome data corresponding to 111 samples isolated from the Arctic Ocean. These diazotrophs were highly abundant in the Arctic Ocean (max., 1.28% of the total microbial community), suggesting that they have important roles in the Arctic ecosystem and biogeochemical cycles. Further, we show that diazotrophs within genera Arcobacter, Psychromonas, and Oceanobacter are prevalent in the 2 fixation. Diazotrophs in the Arctic Ocean were either Arctic-endemic or cosmopolitan species from their global distribution patterns. Arctic-endemic diazotrophs, including Arctic UCYN-A, were similar to low-latitude-endemic and cosmopolitan diazotrophs in genome-wide function, however, they had unique gene sets (e.g., diverse aromatics degradation genes), suggesting adaptations to Arctic-specific conditions. Cosmopolitan diazotrophs were generally non-cyanobacteria and commonly had the gene that encodes the cold-inducible RNA chaperone, which presumably makes their survival possible even in deep, cold waters of global ocean and polar surface waters. This study shows global distribution pattern of diazotrophs with their genomes and provides clues to answering the question of how diazotrophs can inhabit polar waters.

Many studies have investigated the ability of environmental DNA (eDNA) to identify the species. However, when individual species are to be identified, accurate estimation of their abundance using traditional eDNA analyses is still difficult. We previously developed a novel analytical method called HaCeD-Seq (haplotype count from eDNA by sequencing), which focuses on the mitochondrial D-loop sequence for eels and tuna. In this study, universal D-loop primers were designed to enable the comprehensive detection of multiple fish species by a single sequence. To sequence the full-length D-loop with high accuracy, we performed nanopore sequencing with unique molecular identifiers (UMI). In addition, to determine the D-loop reference sequence, whole genome sequencing was performed with thin coverage, and complete mitochondrial genomes were determined. We developed a UMI-based Nanopore D-loop sequencing analysis pipeline and released it as open-source software. We detected 5 out of 15 species (33%) and 10 haplotypes out of 35 individuals (29%) among the detected species. This study demonstrates the possibility of comprehensively obtaining information related to population size from eDNA. In the future, this method can be used to improve the accuracy of fish resource estimation, which is currently highly dependent on fishing catches.

Nitrogen fixation is the major source of reactive nitrogen in the ocean and has been considered to occur specifically in low-latitude oligotrophic oceans. Recent studies have shown that nitrogen fixation also occurs in the polar regions and thus is a global process, although the physiological and ecological characteristics of polar diazotrophs are not yet known. Here, we successfully reconstructed genomes, including that of cyanobacterium UCYN-A (Candidatus‘Atelocyanobacterium thalassa’), from metagenome data corresponding to 111 samples isolated from the Arctic Ocean. These diazotrophs were highly abundant in the Arctic Ocean (max., 1.28% of the total microbial community), suggesting that they have important roles in the Arctic ecosystem and biogeochemical cycles. Diazotrophs in the Arctic Ocean were either Arctic-specific or universal species. Arctic-specific diazotrophs, including Arctic UCYN-A, had unique gene sets (e.g., aromatics degradation) and/or a very small cell size (

Water-soluble organic nitrogen (WSON) in marine atmospheric aerosols affect the water solubility, acidity, and light-absorbing properties of aerosol particles, which are important parameters in assessing both the climate impact and the biogeochemical cycling of bioelements. Size-segregated aerosol and surface seawater (SSW) samples were simultaneously collected over the subtropical North Pacific to investigate the origin of WSON in the marine atmosphere. The fine-mode WSON concentration (7.5 ± 6.6 ngN m−3) at 200–240∘ E along 23∘ N, defined as the eastern North Pacific (ENP), was significantly higher than that (2.4 ± 1.9 ngN m−3) at 135–200∘ E, defined as the western North Pacific (WNP). Analysis of the stable carbon isotope ratio of water-soluble organic carbon (WSOC; δ13CWSOC) together with backward trajectory indicated that most of the observed WSON in the fine particles in the ENP originated from the ocean surface. We found positive relations among nitrogen-fixation rate, dissolved organic nitrogen (DON) in SSW, and the WSON concentrations. The result suggests that reactive nitrogen (DON and ammonium), produced and exuded by nitrogen-fixing microorganisms in SSW, contributed to the formation of WSON aerosols. This study provides new insights into the role of ocean-derived reactive nitrogen aerosols associated with marine microbial activity.

Euphausiids are abundant micronekton and important links between higher and lower trophic levels in marine ecosystems; however, their detailed diets cannot be fully understood by conventional microscopy, especially in subtropical areas. Here, we report the euphausiid community structure in the California Current (CC) area and the eastern/western North Pacific subtropical gyre (ESG and WSG) and detail the feeding ecology of the dominant species (Euphausia pacifica, E. brevis, and E. hemigibba) in each region using a combined approach of gut content analysis via 18S V9 metabarcoding and stable carbon and nitrogen isotope analysis. A pronounced omnivorous feeding of all studied euphausiid species was supported by both methods: phytoplanktonic taxonomic groups (Dinophyta, Stramenopiles, and Archaeplastida), Copepoda, and Hydrozoa were detected in the gut contents; all the three euphausiid species displayed an intermediate trophic position between the net plankton (0.2–1.0 mm) and the myctophid fish (15.2–85.5 mm). However, Hydrozoa found in euphausiid gut contents likely derived from a potential cod-end feeding, based on isotope analysis. E. pacifica in the CC province ingested more autotrophic prey, including pelagophyte and green algae, due to a greater abundance of Stramenopiles and Archaeplastida in shallow layers of CC water. On the other hand, non-autotrophic prey such as mixotrophic Kareniaceae dinoflagellates, Pontellidae and Clausocalanidae copepods, and Sphaerozoidae rhizarian contributed more to the diets of E. brevis and E. hemigibba because of a lower chlorophyll a concentration or potentially a scarcity of autotrophic prey availability in ESG and WSG. The feeding patterns of dominant euphausiid species conducting filter feeding were thus largely determined by phytoplankton prey availability in the environments. Dietary difference across three species was also indicated by stable isotope analysis, with a lower mean trophic level of E. pacifica (2.32) than E. brevis (2.48) and E. hemigibba (2.57). These results verify direct trophic interactions between euphausiids and primary production and suggest that the omnivorous feeding habit is a favorable character for dominant Euphausia species.

Here, we report the draft genome sequence of the aerobic anoxygenic phototrophic bacterium Roseobacter sp. strain OBYS 0001, isolated from coastal seawater in Ostuchi Bay, Japan. This genome sequence could be useful for our understanding of the variation in photosynthesis-related genes among aerobic anoxygenic phototrophs.

Here, we report the draft genome sequence of the aerobic anoxygenic phototrophic bacterium Roseobacter sp. strain OBYS 0001, isolated from coastal seawater in Ostuchi Bay, Japan. This genome sequence could be useful for our understanding of the variation in photosynthesis-related genes among aerobic anoxygenic phototrophs.

Although culture-independent studies have shown the presence of Verrucomicrobia in the deep sea, verrucomicrobial strains from deep-sea environments have been rarely cultured and characterized. Recently, Rubritalea profundi SAORIC-165T, a psychrophilic bacterium of the phylum Verrucomicrobia, was isolated from a depth of 2,000 m in the northwestern Pacific Ocean. In this study, the genome sequence of R. profundi SAORIC-165T, the first deep-sea verrucomicrobial isolate, is reported with description of the genome properties and comparison to surface-borne Rubritalea genomes. The draft genome consisted of four contigs with an entire size of 4,167,407 bp and G+C content of 47.5%. The SAORIC-165T genome was predicted to have 3,844 proteincoding genes and 45 non-coding RNA genes. The genome contained a repertoire of metabolic pathways, including the Embden-Meyerhof-Parnas pathway, pentose phosphate pathway, tricarboxylic acid cycle, assimilatory sulfate reduction, and biosynthesis of nicotinate/nicotinamide, pantothenate/coenzyme A, folate, and lycopene. The comparative genomic analyses with two surface-derived Rubritalea genomes showed that the SAORIC-165T genome was enriched in genes involved in transposition of mobile elements, signal transduction, and carbohydrate metabolism, some of which might be related to bacterial enhancement of ecological fitness in the deep-sea environment. Amplicon sequencing of 16S rRNA genes from the water column revealed that R. profundi-related phylotypes were relatively abundant at 2,000 m and preferred a particle-associated life style in the deep sea. These findings suggest that R. profundi represents a genetically unique and ecologically relevant verrucomicrobial group well adapted to the deep-sea environment.

The recent global spread of cloud computing has streamlined all kinds of tasks by allowing people to go online and get the services they need, when they need them. The cloud is a revolutionary system that saves time, effort, and money. On the other hand, devices connected to the cloud pose the risk of cyber-attacks. One example is Advanced Persistent Threats (APTs), which analyze a target over a long period of time and expose it to danger. The increase in this threat has led to the need for robustness against stealthy attacks. In this paper, we propose Moving Target Defense (MTD) as a defense strategy in the CloudControl game model, which models the interaction between the cloud-connected devices, the defender and the attacker struggling for control of the cloud. We also prove the convergence of this strategy against a static attacker by numerical experiments. Our results contribute to cyber insurance, commercial investment, and corporate policy.

Background Organic particles are hotspots for microbial activity and serve as sites of organic matter mineralisation in the water column of marine systems. In nutrient-limited surface water, degradation of organic matter and nutrient regeneration by marine microbes is crucial. Although free-living (FL) bacteria vastly outnumber those on particles, particle-associated (PA) bacteria can reach locally higher concentrations. Accordingly, to achieve a better understanding of marine microbial ecosystems, it is important to elucidate the differences in not only microbial community structures, but also functional traits, between PA and FL environmental sample fractions. In a previous study, we demonstrated that the Genomaple (formerly MAPLE) system could successfully differentiate the functional potentials and diversity of contributors to each function in four metagenomic datasets generated by the Global Ocean Sampling expedition. Hence, we also used this system to highlight functional traits in PA microbial assemblages. Results The PA and FL fractions could be distinguished from one another by their taxonomic compositions, inferred from ribosomal proteins and relative abundance of module functions. Module functions that were more abundant among PA assemblages than FL assemblages were shared between both subtropical gyres, and their taxonomic compositions were similar. Bacterial transport systems associated with adhesive molecules used for forming microbial assemblages through particulate organic matter were more abundant in the PA fractions. Bacterial regulatory system elements for C 4 -dicarboxylate transport and B-vitamin biosynthesis were also abundant among PA assemblages, suggesting mutual relationships between bacteria and algae involved in exchange of nutrient sources. On the other hand, module functions related to amino acid biosynthesis and bacterial transport systems for inorganic nitrogen, phosphorus, and urea were significantly more abundant in the PA assemblages of more oligotrophic North and South Pacific subtropical gyres than eastern equatorial Pacific regions. Conclusions Comprehensive functional metagenomic analyses based on functional abundance revealed some notable functional traits in PA assemblages related to cell adhesion and nutrient acquisition, enabling the microbes to survive in subtropical regions that are more oligotrophic than the equatorial regions.

Anaerobic ammonium-oxidizing (anammox) bacteria produce dinitrogen gas from nitrite and ammonium under anoxic conditions and significantly contribute nitrogen removal processes in marine environments. Distribution and activity of anammox bacteria in a marine water column have been well studied in some oxygen deficient waters such as Black Sea, Arabian Sea, Namibian upwelling and Peruvian upwelling systems. However, the habitable area of anammox bacteria in the Pacific Ocean is still an open question. Here, we report distribution, abundance and phylogeny of anammox bacteria in the water column along the north-south transect (40⁰S to 55⁰N, 170⁰W) of the Pacific Ocean in order to determine their habitable area in the open ocean. Anammox bacteria-specific 16S rRNA gene was detected at 10 locations mostly from oxygen minimum depths (OMD) where dissolved oxygen (DO) concentration ranged from 10.9 to 46.2 µmol Kg-1. Their abundance measured by qPCR ranged from 3.69 ± 1.35 × 102 copies L-1 to 474 ± 15 × 102 copies L-1. The phylogenetic analysis showed that anammox bacteria detected in this study were all related to Candidatus Scalindua species and clustered into three subgroups: the Scalindua brodae/sorokinii cluster, the sediment cluster and the Arabian Sea cluster. Relationship between the abundance of anammox bacteria and DO concentration varied among these 3 clusters, suggesting their difference in oxygen sensitivity. Although rate measurement of anammox reaction using 15N-labeled substrates failed for all OMD samples tested during the cruise, this study unveiled the distribution of anammox bacteria in the open ocean oxygen minimum zone (OMZ) where oxygen deficiency is not extreme but moderate, which provides an insight into the potential distribution of anammox bacteria in marine environments.

A rod-shaped, pale yellow-pigmented, aerobic, Gram-staining-negative strain with gliding motility, designated as strain SK-16T, was isolated from the coastal surface water of a semi-enclosed coastal inlet in Misaki, Japan. Analysis of 16S rRNA gene sequences revealed that SK-16T represented a member of the family Flavobacteriaceae and was closely related to the genus Algibacter , with sequence similarities ranging from 95.9 to 94.3 % to the type strains of species of the genus Algibacter . The major cellular fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 0 G and iso-C15 : 0 3-OH. Major polar lipids were phosphatidylethanolamine, an aminophospholipid and an unidentified phospholipid. The DNA G+C content of SK-16T was 32.3 mol% and MK-6 was the only predominant isoprenoid quinone. On the basis of the results of phenotypic, genotypic, chemotaxonomic and phylogenetic studies, it was suggested that SK-16T represents a novel species within the genus Algibacter , with the newly proposed name Algibacter aquaticus. The type strain is SK-16T (=NBRC 110220T=KCTC 32974T).

Nitrogen-fixing micro-organisms (diazotrophs) provide biologically available nitrogen to plankton communities and thereby greatly influence the productivity in many marine regions. Various cyanobacterial groups have traditionally been considered the major oceanic diazotrophs, but later non-cyanobacterial and presumably heterotrophic diazotrophs were also found to be widespread and potentially important in nitrogen fixation. However, the distribution and activity of different diazotroph groups is still poorly constrained for most oceanic ecosystems. Here, we examined diazotroph community structure and activity along a 7,500-km south-north transect between the central equatorial Pacific and the Bering Sea. Nitrogen fixation contributed up to 84% of new production in the upper waters of the subtropical gyre, where the diazotroph community included the gammaproteobacterium γ-24774A11 and highly active cyanobacterial phylotypes (>50% of total nifH transcript abundance). Nitrogen fixation was sometimes detectable down to 150 m depth and extended horizontally to the edge of the gyre at around 35°N. Nitrogen fixation was even detected far north on the Bering Sea shelf. In the Alaskan Coastal Waters on the Bering Sea shelf, low nitrate together with high dissolved iron concentrations seemed to foster diazotroph growth, including a prominent role of UCYN-A2, which was abundant near the surface (1.2 × 105 nifH gene copies L-1). Our study provides evidence for nitrogen fixation in the Bering Sea and suggests a clear contrast in the composition of diazotrophs between the tropical/subtropical gyre and the separate waters in the cold northern regions of the North Pacific.

The subtropical and tropical regions of the Pacific Ocean are less productive than other oceanic regions. Although particle association should be an important strategy for heterotrophic prokaryotes to survive in such environments, we have little information on particle-associated (PA) prokaryotes in these regions. The specific aim of this study was to determine bacterial and archaeal community structures in the PA assemblage in comparison to the free-living (FL) assemblage in the North Pacific Subtropical Gyre, the South Pacific Subtropical Gyre, and an eastern equatorial region of the Pacific Ocean. Community profiles and phylogenetic identities were obtained by denaturing gradient gel electrophoresis, 454-pyrosequencing, and cloning followed by Sanger sequencing of 16Sr RNA gene amplicons. The distribution patterns of some abundant groups in three regions and two lifestyles (PA and FL) are shown in this study. Also, the PA community structures of bacteria differed from the FL ones and exhibited higher diversity than the FL ones, while the archaeal community structures did not show significant differences between PA and FL assemblages. We found that specific phylotypes of Gammaproteobacteria and Flavobacteria were abundant in PA bacterial assemblages, suggesting that they prefer to attach and consume particulate organic matter. In summary, the surface seawater PA assemblages represent very different bacterial and archaeal community structures between three different oceanic regions, each of which had distinct PA and FL community structures. These results imply that environmental factors determine microbial community structures.

Dinitrogen fixation, the biological reduction in N2 gas to ammonia contributes to the supply of new nitrogen in the surface ocean. To understand the diversity and abundance of potentially diazotrophic (N2 fixing) microorganisms associated with marine zooplankton, especially copepods, the nifH gene was studied using zooplankton samples collected in the Pacific Ocean. In total, 257 nifH sequences were recovered from 23 nifH‐positive DNA extracts out of 90 copepod samples. The nifH genes derived from cyanobacteria related to Trichodesmium, α‐ and γ‐subdivisions of proteobacteria, and anaerobic euryarchaeota related to Methanosaeta concilii were detected. Our results indicated that Pleuromamma, Pontella, and Euchaeta were the major copepod genera hosting dinitrogen fixers, though we found no species‐specific association between copepods and dinitrogen fixers. Also, the digital PCR provided novel data on the number of copies of the nifH gene in individual copepods, which we report the range from 30 to 1666 copies per copepod. This study is the first systematic study of zooplankton‐associated diazotrophs, covering a large area of the open ocean, which provide a clue to further study of a possible new hotspot of N2 fixation.

How microbes respond to variable environmental conditions? This is a fundamental question to understand regulating mechanisms of biogeochemical cycles in the ocean. High coverage expression profiling (HiCEP) is an RNA fingerprinting method able to analyze microbial metabolic responses to various environmental conditions. Although HiCEP has been applied to various types of single organisms and revealed their responses to targeted conditions, there have been no reports on the application of this method to gene expression profiling of microbial communities. The HiCEP method can provide a unique way of analysis in metatranscriptomics. In this chapter, we provide a guidance of the HiCEP method for applying it to the omics-study of natural ecosystems. We experimentally obtained HiCEP data of prokaryotic communities in coastal surface seawater to show the feasibility of this application, indicating its methodological advantages in the analysis of metatranscriptome. In addition to high accuracy and reproducibility, this method can evaluate gene expression using either peak patterns or compositions of sequence clusters without annotation information, which enables us to highlight previously undescribed but showing distinctive expression in particular environmental conditions. The HiCEP-sequencing method can be a powerful tool for meta-omics studies in various types of environmental settings.

Although culture-independent studies have shown the presence of Verrucomicrobia in the deep sea, verrucomicrobial strains from deep-sea environments have been rarely cultured and characterized. Recently, Rubritalea profundi SAORIC-165

Archaea represent an important component of marine picoplankton. Marine archaeal communities are generally dominated by Marine Group I (MGI) and Marine Group II (MGII), which are affiliated to the phyla Thaumarchaeota and Euryarchaeota. We used pyrosequencing-based analysis of archaeal 16S rRNA genes to investigate archaeal community composition throughout the water column (0–5000 m) at the subarctic (station K2) and subtropical (station S1) stations in western North Pacific. Sampling was conducted on four occasions between 2010 and 2011 to examine seasonal variability in community composition. Four phylogenetic groups (MGI-α, MGI-γ, MGII-α, and MGII-β) belonging to Thaumarchaeota and Euryarchaeota were found throughout the water column, but the relative abundance of each group varied depending on depth. In the surface water, archaeal communities displayed marked seasonal variability at both stations, whereas in deeper waters (300–5000 m), temporal variability in community composition was less evident. Sequences similar to those of the uncultured Marine Benthic Group A, to date found only in marine sediments, were detected throughout the water column at station S1.

We examined nitrification in the euphotic zone, its impact on the nitrogen cycles, and the controlling factors along a 7500 km transect from the equatorial Pacific Ocean to the Arctic Ocean. Ammonia oxidation occurred in the euphotic zone at most of the stations. The gene and transcript abundances for ammonia oxidation indicated that the shallow clade archaea were the major ammonia oxidizers throughout the study regions. Ammonia oxidation accounted for up to 87.4% (average 55.6%) of the rate of nitrate assimilation in the subtropical oligotrophic region. However, in the shallow Bering and Chukchi sea shelves (bottom ⩽67 m), the percentage was small (0-4.74%) because ammonia oxidation and the abundance of ammonia oxidizers were low, the light environment being one possible explanation for the low activity. With the exception of the shallow bottom stations, depth-integrated ammonia oxidation was positively correlated with depth-integrated primary production. Ammonia oxidation was low in the high-nutrient low-chlorophyll subarctic region and high in the Bering Sea Green Belt, and primary production in both was influenced by micronutrient supply. An ammonium kinetics experiment demonstrated that ammonia oxidation did not increase significantly with the addition of 31-1560 nm ammonium at most stations except in the Bering Sea Green Belt. Thus, the relationship between ammonia oxidation and primary production does not simply indicate that ammonia oxidation increased with ammonium supply through decomposition of organic matter produced by primary production but that ammonia oxidation might also be controlled by micronutrient availability as with primary production.

After the passage of typhoon Malou in 2010, daily field samplings were conducted at both inshore (Sta. A) and offshore (Sta. M) stations in Sagami Bay, Japan, to evaluate responses of bacteria and phytoplankton to variations of physical-chemical environments induced by typhoon passage. Malou passage caused an abrupt decline of salinity and a large increase in the amount of nutrients at both stations. The relationships between salinity and nutrient concentrations suggested that major nutrient sources were terrestrial runoff at Sta. M and sediment resuspension in addition to terrestrial runoff at Sta. A. Bacterial production (BP) at Sta. A showed 114 ± 21 mg C m −3 d −1 one day after Malou passage, while primary production (PP) was 76 ± 8 mg C m −3 d −1 , suggesting the dominance of BP (BP/PP ratio = 1.5). PP exceeded BP two days after Malou passage, and then reached a maximum of 554 ± 32 mg C m −3 d −1 five days later (BP/PP ratio = 0.10). PP was always dominant at Sta. M throughout the study period (BP/PP ratio = 0.13 ± 0.05). The ratio of BP to bacterial abundance (BP/BA ratio) at Sta. M showed a positive correlation with PP, suggesting that bacterial productivity depended on autochthonous substrates derived from phytoplankton. The BP/BA ratio at Sta. A showed no relationship with PP, suggesting that bacterial productivity was enhanced not only by PP, but also loading of allochthonous substrates. BP/BA ratios at both stations increased exponentially with the increase of PO 4 and NH 4 concentrations; these concentrations are likely coming from sediment pore waters. The results suggest that sediment resuspension induced by typhoon passage enhanced bacterial productivity abruptly just after the passage at an inshore station. The bacterial response could be regulated by difference in relative contribution of nutrient sources after the passage of typhoon.

We analyzed the vertical distributions of ammonia-oxidizing archaea (AOA) in terms of abundance in Suruga Bay, Japan. We distinguished particle-associated (PA) from free-living (FL) assemblages. According to quantitative PCR measurements of the ammonia monooxygenase subunit A gene (amoA), most marine AOA were in an FL state. The vertical distributions of PA AOA ecotypes differed from the general trend; the Shallow Marine clade was dominant in both the surface and deep layers. Thus, although PA AOA account for a small percentage of AOA abundance, they have a community structure distinct from that of FL AOA in planktonic environments. Marine particles should be investigated further as an unexplored niche of AOA in the ocean.

Coral reef ecosystems are highly sensitive to microbial activities that result from dissolved organic matter (DOM) enrichment of their surrounding seawater. However, the response to particulate organic matter (POM) enrichment is less studied. In a microcosm experiment, we tested the response of bacterioplankton to a pulse of POM from the mass-spawning of Orbicella franksi coral off the Caribbean coast of Panama. Particulate organic carbon (POC), a proxy measurement for POM, increased by 40-fold in seawater samples collected during spawning; 68% degraded within 66 h. The elevation of multiple hydrolases presumably solubilized the spawn-derived POM into DOM. A carbon budget constructed for the 275 µM of degraded POC showed negligible change to the concentration of dissolved organic carbon (DOC), indicating that the DOM was readily utilized. Fourier transform ion cyclotron resonance mass spectrometry shows that the DOM pool became enriched with heteroatom-containing molecules, a trend that suggests microbial alteration of organic matter. Our sensitivity analysis demonstrates that bacterial carbon demand could have accounted for a large proportion of the POC degradation. Further, using bromodeoxyuridine immunocapture in combination with 454 pyrosequencing of the 16S ribosomal RNA gene, we surmise that actively growing bacterial groups were the primary degraders. We conclude that coral gametes are highly labile to bacteria and that such large capacity for bacterial degradation and alteration of organic matter has implications for coral reef health and coastal marine biogeochemistry.

A novel Gram-negative bacterium, designated 4G11T, was isolated from the sea surface microlayer of a marine inlet. On the basis of 16S rRNA gene sequence analysis, the strain showed the closest similarity to Amylibacter ulvae KCTC 32465T (99.0 %). However, DNA–DNA hybridization values showed low DNA relatedness between strain 4G11T and its close phylogenetic neighbours, Amylibacter marinus NBRC 110140T (8.0±0.4 %) and Amylibacter ulvae KCTC 32465T (52.9±0.9 %). Strain 4G11T had C18 : 1, C16 : 0 and C18 : 2 as the major fatty acids. The only isoprenoid quinone detected for strain 4G11T was ubiquinone-10. The major polar lipids were phosphatidylglycerol, phosphatidylcholine, one unidentified polar lipid, one unidentified phospholipid and one unidentified aminolipid. The DNA G+C content of strain 4G11T was 50.0 mol%. Based on phenotypic and chemotaxonomic characteristics and analysis of the 16S rRNA gene sequence, the novel strain should be assigned to a novel species, for which the name Amylibacter kogurei sp. nov. is proposed. The type strain of Amylibacter kogurei is 4G11T (KY463497=KCTC 52506T=NBRC 112428T).

This study proposed a non-radioactive quantitative measurement of bacterial production using stable isotope nitrogen-15-labeled deoxyadenosine ([15N5]-2′-deoxyadenosine; 15N-dA) by liquid chromatography mass spectrometry (LC–MS). The method of preparing 5N-dA described in this study included incubation of seawater or lake water with 15N-dA for 5–24 h, filtration onto a membrane filter, DNA extraction, enzymatic hydrolysis of DNA to nucleosides and quantification of 15N-dA by LC–MS. In the DNA extraction, the silica beads method was examined first, but a large amount of salts and enzymatic inhibitors used in the method caused failure of subsequent procedures, such as enzymatic hydrolysis and LC–MS analysis. On the other hand, the magnetic beads method showed much better results for the extraction. The incorporation rate of 15N-dA was significantly positively correlated to that of tritium-labeled thymidine (3H-TdR) in samples of coastal seawaters and lake waters. The average 15N-dA: 3H-TdR incorporation ratio for the seawater sample was 0.55 with 2.5 and 97.5 % confidence intervals of 0.51 and 0.58, respectively; the average ratio for the lake water sample was 0.28 with 2.5 and 97.5 % confidence intervals of 0.23 and 0.34, respectively. The results suggest that the 15N-dA method can be applied to the measurement of bacterial production in aquatic ecosystems, and that this method can accurately predict the DNA synthesis rates measured by the conventional method.

Aerobic anoxygenic phototrophic bacteria (AAnPB) are bacteriochlorophyll a-containing photoheterotrophic organisms that rely on phototrophy and heterotrophy processes for energy acquisition. Here, we demonstrate the ubiquitous distribution of AAnPB in the Uwa Sea and their relatively larger cell size among members of the bacteria community. The contribution of AAnPB in terms of cell number to the total bacterial abundance ranged from 3.5 % to 7.9 %. The mean cell volume for AAnPB was 2.78 ± 0.72 times larger than the mean cell volume of the total bacteria. The ratio of the contribution of their biovolume to the total bacteria was estimated to be 9.7–22 %.

This paper describes the photosynthetic response of a Roseobacter strain of marine aerobic anoxygenic phototrophic bacteria to an organic substrate limitation. In batch cultures, higher values of the spheroidenone/bacteriochlorophyll a ratio were observed under substrate-deficient conditions. Interestingly, the maximum photochemical quantum efficiencies of the photosystem under substrate-deficient conditions using blue or green excitation were significantly higher than those under substrate-replete conditions. These results indicate that spheroidenone, which can absorb green light, may play an important role in their photosynthesis as a light-harvesting antenna pigment, and the photosynthetic competence of the Roseobacter strain can increase in an organic substrate-deficient environment.

Here, we report the draft genome sequences of Fabibacter sp. strain 4D4 and F. misakiensis strain SK-8 T , isolated from surface seawater of a semienclosed inlet.

Biologically toxic arsenate is physicochemically similar to biologically essential phosphate. Because arsenate and phosphate are indiscriminately incorporated by microbes, their ambient concentration ratios can be an important factor controlling microbial growth and metabolism. This study investigated the spatial distributions of arsenate and phosphate and the associated biogeochemical dynamics in the subtropical North and South Pacific Ocean. Vertical arsenate and phosphate profiles (≤ 150 m) in most of the study areas showed a nutrient-type distribution where the concentrations increased below the euphotic zone. The arsenate and phosphate concentrations in the surface waters ranged from the detection limits (5 nM and 4 nM, respectively) to approximately 40 nM and 400 nM, respectively. The surface arsenate:phosphate ratios were typically lower than 1, but those in the western subtropical North Pacific (WSNP) were frequently higher than 1 due to phosphate depletion. In the WSNP surface waters, Prochlorococcus and Pelagibacter arsenic detoxification and phosphorus acquisition genes were abundant. Results of the onboard bioassays involving the addition of arsenate or phosphate to the surface water indicated that microbes throughout the study areas possessed arsenate resistance and those in the WSNP during summer were under serious phosphate limitation. Although phosphate limitation likely accelerates the relative cellular accumulation of toxic arsenate, the lowest particulate As:P ratios were observed in the summer WSNP, concurrent with the lowest dissolved organic P (DOP) concentrations and the highest alkaline phosphatase activities. These results imply that active As excretion and/or DOP utilization could alleviate As accumulation while maintaining the cellular P quota.

We investigated predatory behavior of sapphirinid copepods on doliolids around the Kuroshio Extension at stations experiencing blooms of Dolioletta gegenbauri. Onboard observations showed that adult Sapphirina nigromaculata was an active predator of doliolids, with a preference for internal tissues. When entering a doliolid body cavity, sapphirinids left a characteristic bite mark around the fringe of oral and atrial aperture or hole on the tunic of the doliolid. In situ observations with a video plankton recorder (VPR) revealed that association between sapphirinids and doliolids was common in the field. Adult sapphirinids and doliolids exhibiting the characteristic evidence of an attack (bite mark or hole) were found in sediment traps at a depth of 50 m, indicating that the association between these taxa was due to predation. Early copepodites, which were not observed in sedimenttrap samples, appeared in the VPR observations to have a semi-parasitic phase when they attached themselves to nurse chains. The maximal daily ration of sapphirinids estimated by onboard experiments ranged between 29% and 37% of their body carbon weight. Although the mean predation effect by sapphirinids on the doliolid population biomass was only 0.7% d21, sapphirinids potentially had a greater effect on doliolid abundance at the termination of doliolid blooms. Some of the attacked doliolids were discarded by the sapphirinids and contributed to the sinking flux below 150 m, the importance of which as a source of detritus likely increased with depth. Sapphirinids, despite their relatively low abundance in the water column, play a specific role in driving community succession and biogeochemical cycling.