Phylogenetic analysis of Archaea in the deep-sea sediments of west Pacific Warm Pool

Archaea are known to play important roles in carbon cycling in marine sediments. The main compositions of archaeal community in five deep-sea sediment samples collected from west Pacific Warm Pool area (WP-0, WP-1, WP-2, WP-3, WP-4), and in five sediment layers (1 cm-, 3 cm-, 6 cm-, 10 cm-, 12 cm- layer) of the 12 cm sediment core of WP-0 were checked and compared by denaturing gradient gel electrophoresis and 16 S rRNA gene sequencing. It was revealed that all the deep-sea sediment samples checked contained members of non-thermophilic marine group I crenarchaeota as the predominant archaeal group. To further detect groups of archaea possibly relating with C1 metabolism, PCR amplification was carried out using primers targeting methane-oxidizing archaea. Although no methane-oxidizing archaea was detected, a group of novel archaea (named as WPA) was instead identified from all these five WP samples by clone analysis. They could be placed in the euryarchaeota kingdom, separated into two distinct groups, the main group was peripherally related with methanogens, the other group related with Thermoplasma. The vertical distributions of WPA, archaea and bacteria along the WP-0 sediment column were determined by quantitative-PCR. It was found that bacteria dominated at all depths, the numbers of bacteria were 10–10⁴ times more than those of archaea. The proportion of archaea versus bacteria had a depth related increasing tendency, it was lowest at the first layer (0.01%), reached highest at the 12 cm- layer (10%). WPA only constituted a small proportion of the archaeal community (0.05% to 5%) of west Pacific Warm Pool sediment.Peng Wang and Xiang Xiao contributed equally to this paper     

中国南海部分深海沉积物真菌多样性及其抗菌活性

【目的】从南海4个站位的深海沉积物中分离真菌,揭示其多样性并测定抗菌活性。【方法】使用4种培养方法和8种培养基,从12个深海沉积物样本中分离培养真菌,通过菌落形态观察和ITS序列系统发育分析进行鉴定。采用滤纸片扩散法和生长速率法分别测试真菌小量发酵液粗浸膏的抗细菌和抗真菌活性。【结果】共分离到125株纯培养真菌,基于形态和ITS序列分析,排重后得到18个种类型,这些真菌可以划分到12个属,大多数属于子囊菌门(Ascomycota),只有2株属于担子菌门(Basidiomycota)。4个站位可培养真菌多样性具有差异性。抑菌活性筛选显示,大多数真菌具有较好的抑菌活性;链格孢属(Alternaria)、青霉属(Penicillium)、匐柄霉属(Stemphylium)这几个属的真菌表现出对多种指示细菌有抑制作用,尤其是Alternaria tenuissima DN09、Alternaria alternata DN14和Penicillium chrysogenum DN16对G~+和G~–细菌均表现出抑制作用。【结论】本研究揭示了南海深海沉积物可培养真菌多样性和抑菌活性,为进一步利用深海沉积物来源真菌奠定了基础。     

Coccolith distribution patterns in surface sediments of Equatorial and Southeastern Pacific Ocean

This study aims to contribute to a more detailed knowledge of the biogeography of coccolithophores in the Equatorial and Southeastern Pacific Ocean. Census data of fossil coccoliths are presented in a suite of core-top sediment samples from 15°N to 50.6°S and from 71°W to 93°W. Following standard preparation of smear slides, a total of 19 taxa are recognized in light microscopy and their relative abundances are determined for 134 surface sediment samples. Considering the multivariate character of oceanic conditions and their effects on phytoplankton, a Factor Analysis was performed and three factors were retained. Factor 1, dominated by Florisphaera profunda and Gephyrocapsa oceanica, includes samples located under warm water masses and indicates the occurrence of calcite dissolution in the water column in the area offshore Chile. Factor 2 is related to cold, low-salinity surface-water masses from the Chilean upwelling, and is dominated by Emiliania huxleyi, Gephyrocapsa sp. < 3 μm, Coccolithus pelagicus and Gephyrocapsa muellerae. Factor 3 is linked to more saline, coastal upwelling areas where Calcidiscus leptoporus and Helicosphaera carteri are the dominant species.     

Fine-scale vertical distribution of bacteria in the East Pacific deep-sea sediments determined via 16S rRNA gene T-RFLP and clone library analyses

Although the deep-sea sediments harbor diverse and novel bacteria with important ecological and environmental functions, a comprehensive view of their community characteristics is still lacking, considering the vast area and volume of the deep-sea sedimentary environments. Sediment bacteria vertical distribution and community structure were studied of the E272 site in the East Pacific Ocean with the molecular methods of 16S rRNA gene T-RFLP (terminal restriction fragment length polymorphism) and clone library analyses. Layered distribution of the bacterial assemblages was detected by both methods, indicating that the shallow sediments (40 cm in depth) harbored a diverse and distinct bacterial composition with fine-scale spatial heterogeneity. Substantial bacterial diversity was detected and nine major bacterial lineages were obtained, including Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Nitrospirae, Planctomycetes, Proteobacteria, and the candidate divisions OP8 and TM6. Three subdivisions of the Proteobacteria presented in our libraries, including the α-, γ- and δ-Proteobacteria. Most of our sequences have low similarity with known bacterial 16S rRNA genes, indicating that these sequences may represent as-yet-uncultivated novel bacteria. Most of our sequences were related to the GenBank nearest neighboring sequences retrieved from marine sediments, especially from deep-sea methane seep, gas hydrate or mud volcano environments. Several sequences were related to the sequences recovered from the deep-sea hydrothermal vent or basalt glasses-bearing sediments, indicating that our deep-sea sampling site might be influenced to certain degree by the nearby hydrothermal field of the East Pacific Rise at 13°N. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

The tropical history and future of the Mediterranean biota and the West African enigma

Aim Since the opening of the Suez Canal in 1869, many tropical taxa from the Indo‐West Pacific (IWP) realm have entered the Mediterranean Sea, which is experiencing rising temperatures. My aims are: (1) to compare biogeographically this tropical transformation of the Mediterranean biota with the tropical faunas of the Mediterranean and adjacent southern European and West African seas during the Late Oligocene to Pliocene interval; (2) to infer the relative contributions of the tropical eastern Atlantic and IWP to the tropical component of the marine biota in southern Europe; and (3) to understand why West Africa is not now a major source of warm‐water species. Location Southern Europe, including the Mediterranean Sea, and the coast of tropical West Africa. Methods I surveyed the literature on fossil and living shell‐bearing molluscs to infer the sources and fates of tropical subgenus‐level taxa living in southern Europe and West Africa during the Late Oligocene to Pliocene interval. Results Ninety‐four taxa disappeared from the tropical eastern Atlantic (including the Mediterranean) but persisted elsewhere in the tropics, mainly in the IWP (81 taxa, 86%) and to a lesser extent in tropical America (36 taxa, 38%). Nine taxa inferred to have arrived in the tropical eastern Atlantic from the west after the Pliocene did not enter the Mediterranean. The modern West African fauna is today isolated from that of other parts of the marine tropics. Main conclusions Taxa now entering the Mediterranean through the Suez Canal are re‐establishing a link with the IWP that last existed 16 million years ago. This IWP element, which evolved under oligotrophic conditions and under a regime of intense anti‐predatory selection, will continue to expand in the increasingly warm and increasingly oligotrophic Mediterranean. The IWP source fauna contrasts with the tropical West African biota, which evolved under productive conditions and in a regime of less anti‐predatory specialization. Until now, the post‐Pliocene West African source area has been isolated from the Mediterranean by cold upwelling. If further warming should reduce this barrier, as occurred during the productive and warm Early Pliocene, the Mediterranean could become a meeting place for two tropical faunas of contrasting source conditions.     

Features of the spatial distribution and size structure of the Pacific lamprey <Emphasis Type="Italic">Lampetra tridentata</Emphasis> in the North Pacific

Results of long-term research on the spatial and vertical distribution of the Pacific lamprey Lampetra tridentata (Richardson, 1836) (the family Petromyzontidae) in the North Pacific, and data on its size structure are submitted. It was shown, that L. tridentate reached its greatest number in the Bering Sea. The maximum concentration of the Pacific lamprey was observed all year round about Navarin Cape, in the Koryak shelf area, at the East Aleutian Islands and at the west coast of the USA, which, apparently, spoke of the increased number of its prey there. On the bottom, the Pacific lamprey was the most numerous at depths of less than 500 m, and in the pelagic, in the upper 100-meter layer. The length of individuals varied in catches from 12 up to 85 cm. The existence of several size groups may indicate that the Pacific lamprey spend several years in the sea. No correlation was revealed between the length of body and fishing depth. The correlations between body length and body weight, body length and condition factor were analyzed. Seasonal dynamics of these parameters were considered.     

Connectivity and the development of population genetic structure in Indo‐West Pacific coral reef communities

Aim To identify connectivity patterns among coral reefs of the Indo‐West Pacific. Projecting connectivity forward in time provides a framework for studying long‐term source–sink dynamics in the region, and makes it possible to evaluate the manner in which migration shapes population genetic structure at regional scales. This information is essential for addressing critical gaps in knowledge for conservation planning efforts in one of the most biologically diverse regions on earth. Location Coral reefs of the Indo‐West Pacific, ranging from 15° S to 30° N and 95° E to 140° E. Methods Individual‐based biophysical dispersal models were used in conjunction with matrix projection to identify the expected patterns of exchange between coral reefs over time. Results Present‐day oceanographic conditions lead to the transport of larvae from the South China Sea into the Coral Triangle region via the Sulu Sea, and from northern Papua New Guinea and the Solomon Islands via Halmahera. The directionality of the system leads to the expected accumulation of organisms from outlying areas into the Coral Triangle region over time, particularly in the vicinity of the Maluku Islands and eastern Sulawesi. Coral reefs in Papua New Guinea, the Sulu Archipelago and areas within the Philippines are expected to be areas of high diversity as well. Main conclusions Biophysical dispersal models, used in conjunction with matrix projection, provide an effective means of simulating connectivity structure across the Indo‐West Pacific and thereby evaluating the directionality of genetic diversity. Migration appears to have a significant influence on population genetic structure in the region. Based on present‐day ocean currents, coral reefs in the South China Sea, northern Papua New Guinea and the Solomon Islands are contributing to high levels of diversity in the Coral Triangle.     

Isolation of extremophiles with the detection and retrieval of<Emphasis Type="Italic"> Shewanella</Emphasis> strains in deep-sea sediments from the west Pacific

Tests to detect the presence of piezophilic Shewanella strains in the deep-sea sediments of the west, mid- and east Pacific at different depths were done by amplification of previously identified pressure-regulated operons (ORF1,2 and ORF3). The operon fragments were detected in all the deep-sea sediment samples, indicating the broad presence of piezophilic deep-sea Shewanella species or related species in the deep-sea sediments across the Pacific. Extremophiles were isolated from the deep-sea sediment of the west Pacific under atmospheric pressure. Two psychrophilic/psychrotrophic strains, WP2 and WP3, were assigned to the Shewanella genus as determined by their 16S rDNA sequences. WP2 and WP3 were both capable of amplifying pressure-regulated operons; the sequences of the pressure-regulated operons of WP2 and WP3 share high identity between each other, but have more differences from those of S. benthica and S. violacea. The major fatty acids of WP2 and WP3 are 3OH-i-13:0, 14:0, i-15:0, 16:0, 16:1, 18:1, and 20:5. Combined phenotypic analysis, 16S rDNA sequences, and DNA–DNA hybridization results suggest that WP2 and WP3 are two new deep-sea Shewanella species.Communicated by K. Horikoshi     

Diversity and distribution of foliose Bangiales (Rhodophyta) in West Greenland: a link between the North Atlantic and North Pacific

Greenland is a continental island in the northern part of the North Atlantic where the foliose Bangiales flora is poorly known. It is an important area for the study of algal biogeography because of the region’s glacial history, in which Greenland has been alternately exposed to or isolated from the North Pacific via the Bering Strait. A molecular study using 3′ rbcL + 5′ rbcL–S sequences was undertaken to assess the diversity of foliose Bangiales on the west coast of Greenland and rbcL sequences were used to study the Greenland flora in a larger phylogenetic and floristic context. New and historic collections document seven species in four genera from the west coast of Greenland. All species had a close link to North Pacific species, being either conspecific with them or North Atlantic–North Pacific vicariant counterparts.     

哥斯达黎加外海夏季表层浮游动物种类组成及分布

根据2009年7—8月在东热带太平洋哥斯达黎加外海(4°30’—10°24’N、91°20’—100°00’W)进行茎柔鱼探捕调查期间采集的表层浮游动物资料,对其种类组成、生物量及其分布进行了分析。结果表明,调查海域,鉴定出腔肠动物8目10科17属23种;甲壳动物8目30科43属74种;毛颚动物1目1科1属4种;尾索动物3目3科5属5种;环节动物为1目3科5属6种;软体动物1目1科3属3种;其他浮游动物有头足类的幼体、鱼卵和仔稚鱼以及浮游幼虫。调查海域总生物量和丰度的平均值分别为(124.78±176.83)mg/m3和(848±1219)个/m3,生物量较大的类群主要是甲壳动物的桡足类和毛颚动物的箭虫类其中桡足类的丰度(727个/m3)为最高,其次为箭虫类(373个/m3);出现频率较高的为桡足类、箭虫类、长尾类、头足类和鱼类仔稚鱼。     

Comparative analysis of archaeal 16S rRNA and <Emphasis Type="Italic">amoA</Emphasis> genes to estimate the abundance and diversity of ammonia-oxidizing archaea in marine sediments

Considering their abundance and broad distribution, non-extremophilic Crenarchaeota are likely to play important roles in global organic and inorganic matter cycles. The diversity and abundance of archaeal 16S rRNA and putative ammonia monooxygenase alpha-subunit (amoA) genes were comparatively analyzed to study genetic potential for nitrification of ammonia-oxidizing archaea (AOA) in the surface layers (0-1 cm) of four marine sediments of the East Sea, Korea. After analysis of a 16S rRNA gene clone library, we found various archaeal groups that include the crenarchaeotal group (CG) I.1a (54.8%) and CG I.1b (5.8%), both of which are known to harbor ammonia oxidizers. Notably, the 16S rRNA gene of CG I.1b has only previously been observed in terrestrial environments. The 16S rRNA gene sequence data revealed a distinct difference in archaeal community among sites of marine sediments. Most of the obtained amoA sequences were not closely related to those of the clones retrieved from estuarine sediments and marine water columns. Furthermore, clades of unique amoA sequences were likely to cluster according to sampling sites. Using real-time PCR, quantitative analysis of amoA copy numbers showed that the copy numbers of archaeal amoA ranged from 1.1 x 10(7) to 4.9 x 10(7) per gram of sediment and were more numerous than those of bacterial amoA, with ratios ranging from 11 to 28. In conclusion, diverse CG I.1a and CG I.1b AOA inhabit surface layers of marine sediments and AOA, and especially, CG I.1a are more numerous than other ammonia-oxidizing bacteria.     

Community structure and spatial distribution of benthic fauna in the Bellingshausen Sea (West Antarctica)

The structure and spatial distribution of the macrofauna community of the Bellingshausen Sea in the western sector of Antarctica was studied during the ‘BENTART–06’ oceanographic expedition. This is one of the least explored Antarctic seas. A total of 20 box cores were sampled at 11 stations ranging from 157 to 3,304 m depth, using an USNEL-type box corer (BC) dredge. Representatives of 25 higher taxa of invertebrates were collected. Deeper sampling sites were less rich in taxa (4–7 taxa), whereas the figures were higher at shallower sites (up to 17 taxa). Faunal density on the sea bottom revealed a horizontal spatial gradient from the western sites with extremely low figures (90 indiv./m²) towards the eastern ones with the highest figures (1,360 indiv./m²) close to the Antarctic Peninsula. Several abiotic factors (depth, redox, organic matter, carbonates and particle size of surficial sediments) were measured simultaneously on the sea floor to characterise the substrate preferences of the fauna. Positive correlations were found between the faunal distribution and a combination of depth, redox values, and organic matter content of sediments. This indicates decreasing availability of food in the deeper bottoms of the Bellingshausen Sea with a prevalence of depauperated bottoms dominated almost exclusively by a foraminiferans community.     

Skeletal morphogenesis and growth mode of modern and fossil deep-water isidid gorgonians (Octocorallia) in the West Pacific (New Zealand and Sea of Okhotsk)

Fabric and growth mode of deep-water isidid gorgonian skeletons showing bright Mg-calcitic internodes and dark proteinageous nodes were investigated on modern, subrecent and fossil skeletons. The internodial microstructure is characterised by three-dimensionally interfingering calcitic fascicles accreting around a central axis. Macroscopic colour banding results from varying orientations of organic-rich fascicle bundles and intercalated bands of organic-poor granular crystals. This skeletal structure of isidid gorgonians strikingly differs from the density banding of scleractinians. Radiocarbon dating of a fossil skeleton gave an age of 3,985±35 to 3,680±35 years before present (BP) with a record of 305±35 years (±range). Linear extension rates of 0.4 mm year⁻¹ average allow for an annual to sub-annual resolution on micrometer scale of colour bands or fascicles, respectively. The growth mode of branched skeletons is characterised by simultaneous secretion of vertically alternating nodes/internodes and lateral accretion of concentric increments enveloping the entire skeleton. Bifurcations at various growth stages imply that adjacent branches have different ages and show varying numbers of growth bands at any skeletal cross section. The scleroprotein gorgonin plays a crucial role in the formation of organic nodes and the secretion of calcitic internodes by providing a structural framework in the biomineralisation process.     

The relationship between Chironomus plumosus burrows and the spatial distribution of pore-water phosphate, iron and ammonium in lake sediments

1. To study the influence of chironomids on the distribution of pore‐water concentrations of phosphate, iron and ammonium, we conducted a laboratory experiment using mesocosms equipped with two‐dimensional pore‐water samplers, filled with lake sediment and populated with different densities of Chironomus plumosus. 2. Specially designed mesocosms were used in the study. A 6‐mm deep space between the front plate and the pore‐water sampler at the back plate was just thick enough to allow the chironomids to live undisturbed, yet thin enough to force all the burrows into a two‐dimensional plane. 3. The courses of the burrows were observed during the experiment as oxidised zones surrounding them, as well as being identified with an X‐ray image taken at the end of the experiment. 4. We investigated the relationship between C. plumosus burrows and spatial patterns of pore‐water composition. Concentrations of the three ions were significantly less around ventilated burrows (54% to 24%), as bioirrigation caused a convective exchange of pore‐water enriched with dissolved species compared with the overlying water, and also because oxygen imported into the sediment resulting in nitrification of ammonium, oxidation of iron(II) and a co‐precipitation of phosphate with Fe(III) oxyhydroxides. 5. In mesocosms with chironomids, new (redox) interfaces occurred with diffusive pore‐water gradients perpendicular to the course of burrows and the site of major phosphate, ammonium and iron(II) release shifted from the sediment surface to the burrow walls.     

Temporal distribution and spatial pattern of abundance of the Rift Valley fever and West Nile fever vectors in Barkedji, Senegal

The temporal distribution and spatial pattern of abundance of mosquito vectors of Rift Valley fever (RVf) and West Nile fever (WNf) were studied during the 2005 and 2006 rainy seasons at Barkedji, Senegal. Mosquitoes were collected every two weeks with CDC light traps with dry ice at 79 sites including temporary ponds, barren, shrubby savannah, wooded savannah, steppes, and villages at different distances (between 0 and 600 m) from the nearest pond. The temporal distributions of these vectors varied between 2005 and 2006 and were positively correlated with rainfall for Aedes (Aedimorphus) vexans Patton, with rainfall after a lag time of one month for Culex (Culex) poicilipes (Theobald) and Culex (Culex) neavei Theobald. All the vectors had their highest abundances and parity rates between September and November. The highest vector abundances were observed in the barren and temporary ponds. The distance of trap location to the nearest ponds was negatively correlated to the abundance of the vectors. Taking into account the linear regression equations, it was predicted that mosquitoes would not disperse and be collected by the light trap, up to 1,500 m to the nearest ponds. The implications of these findings in the epidemiology and control of RVF and WNF at Barkedji are discussed.     

Diversity, biomass and distribution pattern of Sargassum beds in the South West lagoon of New Caledonia (South Pacific)

Sargassum (Phaeophyceae, Fucales) is a genus of worldwide distribution recently recognised to proliferate in several regions of the South Pacific. In New Caledonia, species of this genus naturally structure one of the major lagoon habitats but their extent, composition and biomass remain largely unknown. To fill these gaps in our knowledge over large areas, we applied a combination of remote sensing and in situ methods applied to the Neo Caledonian South West Lagoon. Space borne high resolution Landsat (30-m resolution) and Quickbird (2.4-m resolution) images of the Neo Caledonian South West lagoon were used to estimate the spatial extent of the different beds of interest. Species composition was determined for 11 Sargassum beds and seasonal variations were investigated for four representative beds over an 18 month period using quadrats and transects. Relationships between surface cover and biomass were estimated from seasonal field data sets. Finally, four methods requiring variable levels of sampling effort were designed to estimate the total biomass at the scale of each bed, considering (or not) the specific composition, and spatial and temporal variations. Seven Sargassaceae species were identified. Mean surface cover (24.4–51.6%) and total biomass [3.4–1,461.9 t dry matter (DM)] varied widely between beds. Overall, biomass temporal variations were not significantly different, but species-level variations seemed to be bed-specific. The extent of the 11 beds was 9 km²; their total biomass was estimated and compared using each of the four methods, and the most precise method provided an estimate of 2,900 t DM. This study demonstrates a way of characterising Sargassum beds, efficiently and on a large scale, using a combination of remotely sensed and in situ data. These methods should be useful for possible future biomonitoring of Sargassum beds in New Caledonia, and in other areas worldwide.