Geographic Distribution of Ammonia-Oxidizing Archaea along the Kuril Islands in the Western Subarctic Pacific

Community composition and abundance of ammonia-oxidizing archaea (AOA) in the ocean were affected by different physicochemical conditions, but their responses to physical barriers (such as a chain of islands) were largely unknown. In our study, geographic distribution of the AOA from the surface photic zone to the deep bathypelagic waters in the western subarctic Pacific adjacent to the Kuril Islands was investigated using pyrosequencing based on the ammonia monooxygenase subunit A (amoA) gene. Genotypes of clusters A and B dominated in the upper euphotic zone and the deep waters, respectively. Quantitative PCR assays revealed that the occurrence and ammonia-oxidizing activity of ammonia-oxidizing archaea (AOA) reached their maxima at the depth of 200 m, where a higher diversity and abundance of actively transcribed AOA was observed at the station located in the marginal sea exposed to more terrestrial input. Similar community composition of AOA observed at the two stations adjacent to the Kuril Islands maybe due to water exchange across the Bussol Strait. They distinct from the station located in the western subarctic gyre, where sub-cluster WCAII had a specific distribution in the surface water, and this sub-cluster seemed having a confined distribution in the western Pacific. Habitat-specific groupings of different WCB sub-clusters were observed reflecting the isolated microevolution existed in cluster WCB. The effect of the Kuril Islands on the phylogenetic composition of AOA between the Sea of Okhotsk and the western subarctic Pacific is not obvious, possibly because our sampling stations are near to the Bussol Strait, the main gateway through which water is exchanged between the Sea of Okhotsk and the Pacific. The vertical and horizontal distribution patterns of AOA communities among stations along the Kuril Islands were essentially determined by the in situ prevailing physicochemical gradients along the two dimensions

Sadržaj

<p>A redundancy analysis (RDA) biplot based on total OTUs (97% sequence similarity as the cutoff value) for samples collected from five locations with (a) environmental parameters and (b) metals as explanatory variables. *<i>p</i> < 0.05.</p

Differential Distribution and Determinants of Ammonia Oxidizing Archaea Sublineages in the Oxygen Minimum Zone off Costa Rica

Ammonia oxidizing archaea (AOA) are microbes that are widely distributed in the ocean that convert ammonia to nitrite for energy acquisition in the presence of oxygen. Recent study has unraveled highly diverse sublineages within the previously defined AOA ecotypes (i.e., water column A (WCA) and water column B (WCB)), although the eco-physiology and environmental determinants of WCB subclades remain largely unclear. In this study, we examined the AOA communities along the water columns (40&ndash;3000 m depth) in the Costa Rica Dome (CRD) upwelling region in the eastern tropical North Pacific Ocean. Highly diverse AOA communities that were significantly different from those in oxygenated water layers were observed in the core layer of the oxygen minimum zone (OMZ), where the dissolved oxygen (DO) concentration was &lt; 2&mu;M. Moreover, a number of AOA phylotypes were found to be enriched in the OMZ core. Most of them were negatively correlated with DO and were also detected in other OMZs in the Arabian Sea and Gulf of California, which suggests low oxygen adaptation. This study provided the first insight into the differential niche partitioning and environmental determinants of various subclades within the ecotype WCB. Our results indicated that the ecotype WCB did indeed consist of various sublineages with different eco-physiologies, which should be further explored

Metagenomic Insights Into the Microbial Community and Nutrient Cycling in the Western Subarctic Pacific Ocean

The composition and metabolic functions of prokaryotic communities in the western subarctic Pacific (WSP), where strong mixing of waters from the Sea of Okhotsk and the East Kamchatka Current result in transfer to the Oyashio Current, were investigated using a shotgun metagenome sequencing approach. Functional metabolic genes related to nutrient cycling of nitrogen, sulfur, carbohydrates, iron and amino acids were differently distributed between the surface and deep waters of the WSP. Genes related to nitrogen metabolism were mainly found in deep waters, where Thaumarchaeaota, Sphingomonadales, and Pseudomonadales were closely associated and performing important roles in ammonia oxidation, assimilatory nitrate reduction, and dissimilatory nitrate reduction processes, respectively. In addition, orders affiliated to Spingobacteria and Alphaproteobacteria were crucial for sulfate reduction and abundant at 3000 m, whereas orders affiliated to Gammaproteobacteria, which harbored the most sulfate reduction genes, were abundant at 1000 m. Additionally, when compared with the East Kamchatka Current, the prokaryotes in the Oyashio Current were likely to consume more energy for synthesizing cellular components. Also, genes encoding iron transport and siderophore biosynthesis proteins were in low abundance, indicating that the iron was not a limiting factor in the Oyashio current. In contrast, in the East Kamchatka Current, prokaryotes were more likely to directly utilize the amino acids and absorb iron from the environment. Overall, our data indicated that the transformation from the East Kamchatka Current to the Oyashio Current reshapes not only the composition of microbial community, but also the function of the metabolic processes. These results extended our knowledge of the microbial composition and potential metabolism in the WSP

Distribution and Oxidation Rates of Ammonia-Oxidizing Archaea Influenced by the Coastal Upwelling off Eastern Hainan Island

Coastal upwelling causes variations in temperature, salinity and inorganic nutrients in the water column, consequently leading to the shift of microbial populations and their metabolic activities. Impacts of the eastern Hainan upwelling (EHU) on the ammonia-oxidizing archaea (AOA) were investigated based on the amoA gene using pyrosequencing and quantitative PCR at both DNA and cDNA levels, together with the determination of the ammonia oxidation (AO) rate measured with 15N-labelled ammonium. By comparing stations with and without upwelling influence, we found that coastal upwelling correlated with an increase in amoA gene abundance, the dominance of distinct clades for AOA communities at the respective gene and transcript levels, and a large increase in the proportion of the SCM1-like (Nitrosopumilus maritimus-like) cluster as well. The AO rates were generally higher in the deeper water (~25 m), which was in significant positive correlation with the proportion of cluster Water Column A (WCA) at the transcript level, indicating the potential contribution of this cluster to in situ ammonia oxidization. Our study demonstrated that coastal upwelling had a significant impact on the AOA community and ammonia oxidization rate; therefore, this physical forcing should be considered in the future assessment of the global nitrogen budgets and biogeochemical nitrogen cycles

Physical Forcing Controls the Basin-Scale Occurrence of Nitrogen-Fixing Organisms in the North Pacific Ocean

Biological nitrogen fixation is increasingly recognized as an important source of new nitrogen in a warming ocean. However, the basin-scale spatiotemporal distribution of nitrogen-fixing organisms (diazotrophs) in the ocean and its controlling environmental factors remain unclear. Here we examined the basin-scale seasonal distribution patterns of major diazotrophs (filamentous cyanobacterialTrichodesmium, unicellular cyanobacterial UCYN-A1, and proteobacterial Gamma-A) in surface waters of the North Pacific from 2014 to 2016 with unprecedented coverage and resolution. In general, UCYN-A1,Trichodesmium, and Gamma-A were abundant during spring-autumn, summer-autumn, and spring respectively. Regarding latitudinal patterns of abundance, UCYN-A1 showed dome shape;Trichodesmiumwas gradually decreasing from low- to high-latitude regions; and Gamma-A did not show a clear pattern, which were coincident with the distinct correlations between the diazotrophs and temperature. All three diazotrophs were abundant (reached 10(6)-10(7)nifHgene copy number L-1) in the North Pacific transition zone and subtropical gyre, where the cyanobacterial diazotrophs were more abundant in both the western and eastern North Pacific than in the central North Pacific. The diazotroph abundance in the western North Pacific was positively correlated with eddy kinetic energy and sea surface height anomaly, which implies an enhancement of diazotrophs in mesoscale eddies associated with the western boundary current Kuroshio and its extension. The cyanobacterial diazotrophs were positively correlated with wind stress curl, a measurable parameter of wind-driven upwelling, in the eastern North Pacific. Our study refines the biogeography of three major diazotrophs and highlights the importance of physical forcing in mediating their dynamics

Role of nutrients and temperature in shaping distinct summer phytoplankton and microzooplankton population dynamics in the western North Pacific and Bering Sea

Phytoplankton growth and microzooplankton grazing are two critical processes in marine food webs, but they remain understudied in the vast area of the subarctic western Pacific and the Bering Sea. In this study, we measured phytoplankton growth and microzooplankton grazing rates in these less-explored regions to demonstrate their spatial patterns and investigate underlying mechanisms driving the planktonic food web dynamics. Our results showed that the phytoplankton growth in these regions was determined by nutrient availability and temperature. In the high-nutrient, low-chlorophyll regions (HNLC), iron availability was the primary factor limiting phytoplankton growth. In contrast, phytoplankton growth in the Gulf of Anadyr and Kamchatka Strait was mainly limited by inorganic nitrogen exhausted by the summer blooms. We found that microzooplankton grazing rate was affected by temperature and prey availability, highlighting the positive effect of temperature. Strong top-down control on phytoplankton by microzooplankton in the Gulf of Anadyr and Kamchatka Strait indicated an active microbial food web with high turnover rates. In contrast, the decoupling of phytoplankton growth and microzooplankton grazing in the HNLC regions illustrates a weak role of microzooplankton in the marine food web. These results indicated different food web structures in the areas with and without riverine iron input. By revealing the roles of temperature and nutrient or prey availability in regulating the spatial variability of plankton rates, we expect that the plankton will respond differently to ocean warming between the HNLC and coastal regions of the subarctic Pacific due to different nutrient conditions. Our study helps understand how marine plankton will respond to environmental changes at high latitudes

Non-cyanobacterial diazotrophs: global diversity, distribution, ecophysiology, and activity in marine waters.

Biological dinitrogen (N2) fixation supplies nitrogen to the oceans, supporting primary productivity, and is carried out by some bacteria and archaea referred to as diazotrophs. Cyanobacteria are conventionally considered to be the major contributors to marine N2 fixation, but non-cyanobacterial diazotrophs (NCDs) have been shown to be distributed throughout ocean ecosystems. However, the biogeochemical significance of marine NCDs has not been demonstrated. This review synthesizes multiple datasets, drawing from cultivation-independent molecular techniques and data from extensive oceanic expeditions, to provide a comprehensive view into the diversity, biogeography, ecophysiology, and activity of marine NCDs. A NCD nifH gene catalog was compiled containing sequences from both PCR-based and PCR-free methods, identifying taxa for future studies. NCD abundances from a novel database of NCD nifH-based abundances were colocalized with environmental data, unveiling distinct distributions and environmental drivers of individual taxa. Mechanisms that NCDs may use to fuel and regulate N2 fixation in response to oxygen and fixed nitrogen availability are discussed, based on a metabolic analysis of recently available Tara Oceans expedition data. The integration of multiple datasets provides a new perspective that enhances understanding of the biology, ecology, and biogeography of marine NCDs and provides tools and directions for future research

Highly heterogeneous diazotroph communities in the Kuroshio Current and the Tokara Strait, Japan - Fig 3

<p>(A). A UPGMA dendrogram showing the relationship between samples, at 0.03 cutoff. (B). Shannon diversity indices and Chao richness estimators of the diazotroph community in the samples, at 0.03 cutoff.</p