Prokaryotic metabolic activity and community structure in Antarctic continental shelf sediments

The prokaryote community activity and structural characteristics within marine sediment sampled across a continental shelf area located off eastern Antarctica (66 degrees S, 143 degrees E; depth range, 709 to 964 m) were studied. Correlations were found between microbial biomass and aminopeptidase and chitinase rates, which were used as proxies for microbial activity. Biomass and activity were maximal within the 0- to 3-cm depth range and declined rapidly with sediment depths below 5 cm. Most-probable-number counting using a dilute carbohydrate-containing medium recovered 1.7 to 3.8% of the sediment total bacterial count, with mostly facultatively anaerobic psychrophiles cultured. The median optimal growth temperature for the sediment isolates was 15 degrees C. Many of the isolates identified belonged to genera characteristic of deep-sea habitats, although most appear to be novel species. Phospholipid fatty acid (PLFA) and isoprenoid glycerol dialkyl glycerol tetraether analyses indicated that the samples contained lipid components typical of marine sediments, with profiles varying little between samples at the same depth; however, significant differences in PLFA profiles were found between depths of 0 to 1 cm and 13 to 15 cm, reflecting the presence of a different microbial community. Denaturing gradient gel electrophoresis (DGGE) analysis of amplified bacterial 16S rRNA genes revealed that between samples and across sediment core depths of 1 to 4 cm, the community structure appeared homogenous; however, principal-component analysis of DGGE patterns revealed that at greater sediment depths, successional shifts in community structure were evident. Sequencing of DGGE bands and rRNA probe hybridization analysis revealed that the major community members belonged to delta proteobacteria, putative sulfide oxidizers of the gamma proteobacteria, Flavobacteria, Planctomycetales, and Archaea. rRNA hybridization analyses also indicated that these groups were present at similar levels in the top layer across the shelf region.     

Pelagic community respiration on the continental shelf off Georgia, USA

The South Atlantic Bight (SAB) has been a focus for the study of continental shelf ecosystem respiration during the past two decades. However, two questions concerning respiration in this area have yet to be answered. First, why do previous estimates of respiration in the SAB exceed measured carbon fixation rates by almost an order of magnitude? Second, considering that bacteria are responsible for most of the pelagic community respiration in the SAB, why is respiration almost uniform from the coastline to the shelf break, while bacterial production estimates decrease offshore? This study addresses these critical questions by presenting new pelagic community respiration data that were collected across the entire width of the continental shelf off Georgia, USA from June 2003 to May 2006. The respiration was calculated as in vitro changes of dissolved oxygen and dissolved inorganic carbon concentrations during deck incubations. The measured respiration rates ranged from 0.3(±0.1) to 21.2(±1.4) mmol m^?3 day^?1. They followed a clear seasonal pattern, being lowest over the entire shelf in winter and reaching maxima in summer. Summertime respiration rates were highest on the inner shelf and decreased with distance offshore. Consistent with this trend, bacterial abundance measurements taken during the sampling month of July 2005 followed a pattern of seaward decline. The SAB organic carbon fluxes calculated from the respiration data are close to the estimates for primary production, which resolves a long-standing mystery regarding perceived carbon imbalance in the SAB.     

Psychrophilic prokaryote structural-functional relationships, biogeography and evolution within marine sediment.

Prokaryote diversity has been found to be surprisingly high in cold marine sediments with numerous clades detected spread throughout many phyla. Marine benthic sediment clades are largely ecotypically distinct and autochthonous. Since almost all marine sediment prokaryotic taxa have yet to be cultivated, functionality is currently overwhelmingly cryptic for most benthic prokaryotic taxa except those falling into specific lineages for which there is cultivation or detailed biogeochemical data. Multivariate statistical comparisons of 16S rRNA gene sequence and denaturing gradient gel electrophoresis (DGGE) data show distinct distribution patterns of prokaryotic communities in sediment layers. By comparison geographical differences and differences related to the physical texture and organic content seem to result in generally smaller differences.     

High level of bacterial diversity and novel taxa in continental shelf sediment

The bacterial diversity of the continental shelf sediment in the Yellow Sea was investigated by the cloning and sequencing of PCR-amplified 16S rRNA genes. The majority of the cloned sequences were distinct phylotypes that were novel at the species level. The richness estimator indicated that the sediment sample might harbor up to 32 phylum-level taxa. A large number of low-abundance, phylum-level taxa accounted for most of the observed phylogenetic diversity at our study site, suggesting that these low-abundance taxa might play crucial roles in the shelf sediment ecosystem.     

Biodiversity, Community Structural Shifts, and Biogeography of Prokaryotes within Antarctic Continental Shelf Sediment

16S ribosomal DNA (rDNA) clone library analysis was conducted to assess prokaryotic diversity and community structural changes within a surficial sediment core obtained from an Antarctic continental shelf area (depth, 761 m) within the Mertz Glacier Polynya (MGP) region. Libraries were created from three separate horizons of the core (0- to 0.4-cm, 1.5- to 2.5-cm, and 20- to 21-cm depth positions). The results indicated that at the oxic sediment surface (depth, 0 to 0.4 cm) the microbial community appeared to be dominated by a small subset of potentially r-strategist (fast-growing, opportunistic) species, resulting in a lower-than-expected species richness of 442 operational taxonomic units (OTUs). At a depth of 1.5 to 2.5 cm, the species richness (1,128 OTUs) was much higher, with the community dominated by numerous gamma and delta proteobacterial phylotypes. At a depth of 20 to 21 cm, a clear decline in species richness (541 OTUs) occurred, accompanied by a larger number of more phylogenetically divergent phylotypes and a decline in the predominance of Proteobacteria. Based on rRNA and clonal abundance as well as sequence comparisons, syntrophic cycling of oxidized and reduced sulfur compounds appeared to be the dominant process in surficial MGP sediment, as phylotype groups putatively linked to these processes made up a large proportion of clones throughout the core. Between 18 and 65% of 16S rDNA phylotypes detected in a wide range of coastal and open ocean sediments possessed high levels of sequence similarity (>95%) with the MGP sediment phylotypes, indicating that many sediment prokaryote phylotype groups defined in this study are ubiquitous in marine sediment.     

Global diversity and biogeography of deep-sea pelagic prokaryotes

The deep-sea is the largest biome of the biosphere, and contains more than half of the whole ocean''s microbes. Uncovering their general patterns of diversity and community structure at a global scale remains a great challenge, as only fragmentary information of deep-sea microbial diversity exists based on regional-scale studies. Here we report the first globally comprehensive survey of the prokaryotic communities inhabiting the bathypelagic ocean using high-throughput sequencing of the 16S rRNA gene. This work identifies the dominant prokaryotes in the pelagic deep ocean and reveals that 50% of the operational taxonomic units (OTUs) belong to previously unknown prokaryotic taxa, most of which are rare and appear in just a few samples. We show that whereas the local richness of communities is comparable to that observed in previous regional studies, the global pool of prokaryotic taxa detected is modest (~3600 OTUs), as a high proportion of OTUs are shared among samples. The water masses appear to act as clear drivers of the geographical distribution of both particle-attached and free-living prokaryotes. In addition, we show that the deep-oceanic basins in which the bathypelagic realm is divided contain different particle-attached (but not free-living) microbial communities. The combination of the aging of the water masses and a lack of complete dispersal are identified as the main drivers for this biogeographical pattern. All together, we identify the potential of the deep ocean as a reservoir of still unknown biological diversity with a higher degree of spatial complexity than hitherto considered.     

3. Biodiversity, biogeography and conservation of diatoms

Recent morphometric and breeding studies of diatoms show that the present species classification is too coarse and hides significant diversity. Many species are subdivided into phenodemes, which often differ in cell size, shape, stria density and pattern, but may also have different ultrastructural features. In raphid diatoms these can include the form of the raphe endings, details of the pore occlusions, and the structure of the girdle, while chloroplast structure can also vary. The phenodemes can be sympatric or allopatric. In Sellaphora pupula and other species, sympatric phenodemes are reproductively isolated. It is recommended that such demes are recognized as separate species; the total number of diatom species worldwide may thus be at least 2 × 10⁵. Use of a fine-grained classification reveals that many diatom species may be endemics, some restricted to a single lake or catchment, others to wider areas. Environmental impact assessments and conservation strategies must begin to take account of endemism and rarity among microscopic algae and protists.     

Biodiversity and biogeography of the atmosphere

The variation of life has predominantly been studied on land and in water, but this focus is changing. There is a resurging interest in the distribution of life in the atmosphere and the processes that underlie patterns in this distribution. Here, we review our current state of knowledge about the biodiversity and biogeography of the atmosphere, with an emphasis on micro-organisms, the numerically dominant forms of aerial life. We present evidence to suggest that the atmosphere is a habitat for micro-organisms, and not purely a conduit for terrestrial and aquatic life. Building on a rich history of research in terrestrial and aquatic systems, we explore biodiversity patterns that are likely to play an important role in the emerging field of air biogeography. We discuss the possibility of a more unified understanding of the biosphere, one that links knowledge about biodiversity and biogeography in the lithosphere, hydrosphere and atmosphere.     

Biodiversity and biogeography of Henderson Island's insects

Henderson Island is an example of a raised coral atoll, and as such supports a much more diverse biota than geographically similar low atolls. It is also, due to its remote location, largely undisturbed by the activities of humans. It is therefore unique in the Pacific Ocean, and comparable to Aldabra in the Indian Ocean. Biogeographically it is also interesting as it is amongst the most easterly islands of the Indo-West Pacific region, and has been largely colonized by species dispersing from island to island across the ocean from the west. New and extensive collections of insects were made in 1991. Although not fully identified yet, it is clear that the fauna is depauperate, with only about 180 species known to date. Despite its easterly location almost all species are derived from the west, and much of the fauna is likely to be indigenous. The most diverse orders are the Lepidoptera ( c. 53 spp.), Coleoptera ( c. 38 spp.), Diptera ( c. 37 spp.), Hymenoptera ( c. 21 spp.), Homoptera ( c. 14 spp.) and Heteroptera (4 spp.). Of particular interest are the weevils, Heteroptera and Homoptera which exhibit considerable endemism with perhaps some examples of intra-island radiation. Although depauperate, Henderson supports a much larger insect fauna than that of nearby Ducie Atoll (total known insect fauna =15 spp).     

Biodiversity and biogeography of Southern Ocean pycnogonids

The pycnogonids of the Southern Ocean have been studied for almost two centuries and have played a key role in shaping previous biogeographic regions for the Antarctic benthos. The aim of this study was to assess the biogeographic patterns derived from the most current sample records of pycnogonids from the Southern Ocean and neighbouring areas. 332 species of pycnogonids from 1837 sample locations were analysed using 279 3° by 3° grid cells. We investigated richness patterns and the effect of sampling intensity at both local and regional scales, and used multivariate analysis of distribution patterns and species assemblages to define biogeographic trends. These analyses identified a distinct and isolated Antarctic pycnogonid shelf fauna which was different to that of the deep‐sea around Antarctica, the Sub‐Antarctic islands, South America or New Zealand. Within the Antarctic, we found the South Shetland Islands to be the most speciose region and a probable center of radiation for the pycnogonids. No latitudinal gradients in species richness were detected. We note that the distribution patterns observed are based upon classical taxonomy and discuss the potential for changes to these patterns with new insights from molecular techniques. We conclude that, even with the potential for cryptic species, the large‐scale biogeographic trends observed in the pycnogonids should hold true.     

The deep-water macroalgal community of the East Florida continental shelf (USA)

The deep-water macroalgal community of the continental shelf off the east coast of Florida was sampled by lock-out divers from two research submersibles as part of the most detailed year-round study of a macroalgal community extending below routine SCUBA depths. A total of 208 taxa (excluding crustose corallines) were recorded; of these, 42 (20.2%), 19 (9.1%), and 147 (70.7%) belonged to the Chlorophyta, Phaeophyta, and Rhodophyta, respectively. Taxonomic diversity was maximal during late spring and summer and minimal during late fall and winter. The number of reproductive taxa closely followed the number of taxa present; when reproductive frequency was expressed as a percentage of the species present during each month, two peaks (January and August) were observed. Most perennial species had considerable depth ranges, with the greatest number of taxa observed from 31 to 40 m in depth. Although most of the taxa present also grow in shallow water (i.e. <10 m), there were some species whose distribution is limited to deeper water. The latter are strongly dominated by rhodophytes. This community has a strong tropical affinity, but over half the taxa occur in warm-temperate areas. Forty-two new records (20% of the taxa identified) for Florida were listed; this includes 15 taxa which previously had been considered distributional disjuncts in this area. The phaeophyteHalopteris filicina is a new addition to the flora of the western Atlantic. Although more studies are needed, it appears that the deep-water flora may be relatively continuous over a large portion of the tropical and subtropical western North Atlantic. The traditional practice of considering Cape Canaveral as a biogeographical boundary may only be appropriate for shallow water. This study demonstrates the need for additional floristic work on macroalgal communities, especially from deep water, before more detailed biogeographical analyses can be performed and suggests that deep-water species could be important in experimental approaches to macroalgal biogeography.     

Diversity and composition of macrobenthic community associated with sandy shoals of the Louisiana continental shelf

Along the Louisiana, USA continental shelf, sandy shoals are shallow, possibly oxygen-rich “islands” surrounded by deeper muddy deposits prone to hypoxia. Shoals also contain significant quantities of fine sand that may be mined in the future for coastal restoration. The ecological role of shoals remains poorly understood and we hypothesized that shoals provide critical habitat for benthic invertebrates. Using Ship Shoal as a model system, we assessed the diversity and structure of macrobenthic assemblages and how community structure varies with season and environmental parameters. High biomass (averaging 26.7 g m⁻²) and high diversity (161 species) of macrobenthos was found in 2006. Polychaetes (45%—72 species) and crustaceans comprised most of the species (28%—46 species); spionids and amphipods dominated the polychaete and crustacean groups respectively, both in terms of number of species and abundances. Sharp decreases in diversity, abundance and biomass occurred from spring to autumn. Species diversity and total abundance significantly increased with decreasing sediment grain size and increasing bottom water dissolved oxygen. Across seasons, mole crabs Albunea paretii and amphioxus Branchiostoma floridae typified the community and contributed most of the biomass. The polychaetes Nephtys simoni, Neanthes micromma, Dispio uncinata, Mediomastus californiensis and Magelona sp. A, the amphipod Acanthohautorius sp. A and the burrowing shrimp Ogyrides alphaerostris also contributed to variation in community composition. Cluster analyses quantified seasonal variation, mainly based on sharp decreases in abundance, as well as spatial differences in species composition oriented along both east–west and north–south gradients. Variation in benthic assemblages was correlated with water depth and sediment characteristics (mean grain size and percentage of gravel-sized shell debris). We conclude that Ship Shoal is an unrecognized biodiversity hotspot and a hypoxia refuge compared to the immediate surrounding area where the benthic community is affected by seasonal hypoxia events and we discuss how sand-mining may influence this community.     

Biodiversity, phylogeography, biogeography and conservation: lemurs as an example

The lemurs of Madagascar represent a spectacular example of adaptive radiation among primates. Given the special setting under which they evolved (i.e. long isolation, geographical location, geological relief), they provide excellent models for study in many realms, and at different levels and scales, including diversity. At the same time, they occur in a 'hottest hot spot' region for biodiversity conservation. Although there is no single definition of biodiversity, the most commonly used units to measure biodiversity are species-species richness, species abundance and, for conservation purposes in particular, species endemism. However, what a species actually is or how, precisely, it should be defined are unresolved issues. Many species concepts have been proposed and several have been used in primatology in recent years. Nowadays, one of the more common approaches to measuring diversity, and eventually inferring species status, is to look at genetic diversity as reflected by mitochondrial DNA differences. Not enough attention has been paid, however, to the different levels at which genetic differences may occur. Lemurs provide instructive examples to highlight the questions involved in species recognition and definition. Using lemurs as examples, I will highlight the strengths and limitations of some analytical tools, including phylogeography and cladistic biogeography and, I will, in particular, emphasize the questions arising at the interface of scientific and conservation perceptions, both of which influence decisions in the field of biodiversity preservation.     

Biodiversity and emerging biogeography of the neutrophilic iron-oxidizing Zetaproteobacteria

Members of the neutrophilic iron-oxidizing candidate class Zetaproteobacteria have predominantly been found at sites of microbially mediated iron oxidation in marine environments around the Pacific Ocean. Eighty-four full-length (>1,400-bp) and 48 partial-length Zetaproteobacteria small-subunit (SSU) rRNA gene sequences from five novel clone libraries, one novel Zetaproteobacteria isolate, and the GenBank database were analyzed to assess the biodiversity of this burgeoning class of the Proteobacteria and to investigate its biogeography between three major sampling regions in the Pacific Ocean: Loihi Seamount, the Southern Mariana Trough, and the Tonga Arc. Sequences were grouped into operational taxonomic units (OTUs) on the basis of a 97% minimum similarity. Of the 28 OTUs detected, 13 were found to be endemic to one of the three main sampling regions and 2 were ubiquitous throughout the Pacific Ocean. Additionally, two deeply rooted OTUs that potentially dominate communities of iron oxidizers originating in the deep subsurface were identified. Spatial autocorrelation analysis and analysis of molecular variance (AMOVA) showed that geographic distance played a significant role in the distribution of Zetaproteobacteria biodiversity, whereas environmental parameters, such as temperature, pH, or total Fe concentration, did not have a significant effect. These results, detected using the coarse resolution of the SSU rRNA gene, indicate that the Zetaproteobacteria have a strong biogeographic signal.     

Biodiversity and biogeography of the avifauna of the Sierra Madre Occidental,Mexico

The Sierra Madre Occidental (SMOc) is located in the boundary between the Nearctic and Neotropical regions, area which has been considered as a complex transition zone. We analysed biogeographic patterns of its resident avifauna, including species richness, endemism, and biotic regionalization by analysing presence-absence matrices of 148 species of resident-terrestrial birds. We created the species richness maps by overlapping potential distribution maps obtained for each species via species distribution models (SDMs). To depict biogeographic patterns, we used strict consensus cladograms from parsimony analyses of endemicity (PAE) and phenograms from an unweighted pair-group method with arithmetic average clustering algorithm. The Pacific slope of the SMOc contains the highest species richness, decreasing towards the northeast, and reflected in endemic and endangered species richness patterns. The PAE resulted in one area of endemism represented by the whole SMOc, outlining a divided area in its Pacific slope. The cluster analyses divided the area into two. One group towards the Pacific slope, delimited by the mountain ridge and characterized by tropical vegetation types and Mexican-Mesoamerican affinities; the other group is located towards the east and northeast, characterized by arid and temperate types of vegetation and Nearctic affinities. These results evidence a transition from a tropical to a temperate composition of bird species. In this way the location for a boundary between the Nearctic and the transition zone, for birds in this part of Mexico, is restricted to these highest elevations.     

Modeling the effects of doliolids on the plankton community structure of the southeastern US continental shelf

A model of the lower trophic levels that consists of a system of coupled ordinary differential equations was developed to investigate the time-dependent behavior of doliolid populations associated with upwelling features on the outer southeastern US continental shelf. Model equations describe the interactions of doliolids with two phytoplankton size fractions, five copepod developmental states and detrital pool. Additional equations describe nitrate and ammonia. Model dynamics are based primarily upon data obtained from field and laboratory experiments for southeastern US continental shelf plankton populations. Variations on a reference simulation, which represents average upwelling conditions without doliolids, were carried out to determine the effect of inclusion of doliolids, temperature and nutrient variations, and variations in ambient food concentrations on the basic plankton community structure. These simulations provide a measure of the role of environmental versus biological interactions in structuring the planktonic food web on the southeastern US continental shelf. Simulations show that he copepod population is significantly reduce when doliolids are present. This happens primarily as a result of direct predation of the doliolids on copepod eggs and juveniles as opposed to an increase in competition for phytoplankton, the primary food source. Additional simulations show that the cooler temperatures associated with the newly upwelled water temporarily decrease the growth rates of doliolids and copepods, bestowing an event greater advantage on the rapidly reproducing doliolids.      

Primary production of ice algae on a seasonally-ice-covered,continental shelf

Summary Ice algae samples were collected from the winter pack ice off Labrador during March 1984. The population was dominated by centric diatoms. Chlorophyll concentrations ranged from 40 to 190 mg m^–3, and particulate organic carbon from 2 to 10 g m^–3. Assimilation numbers for the ice algae ranged from 1.4 to 2.8 mg C (mg chl)^–1 h^–1 with a mean of 2.3, and were not significantly different from the assimilation numbers of the pelagic community beneath the ice. The ice algae were not photoinhibited at light intensities approaching surface light intensities. It is postulated that the dynamic nature of the ice field permits near-surface light intensities to reach the ice algae community at irregular intervals thereby suppressing photoinhibition.     

海洋微型底栖生物的多样性与地理分布

海洋微型底栖生物是指生活于海洋沉积物中及表面的所有单细胞原核和真核微型生物,包括原核微生物、真核微藻及原生动物等光合自养和异养的类群.与水体相比,海洋底栖生境孕育了形态和功能多样性更高的微型生物,在陆架浅海单位体积沉积物中其丰度较之水体中同类生物高一至几个数量级,而深海则孕育着特殊进化环境下新奇多样且数量庞大的微型底栖生物,是维持海洋生物多样性、海洋生态系统结构和功能不可或缺的部分.迄今对于微型生物是全球性还是限定性分布一直存在争议,对其解答受到分类研究欠缺及采样不足的制约.分子生物学从正反两方面提供了理论依据,但无法得出一个普遍接受的观点.海洋微型底栖生物的多样性研究侧重于物种多样性及群落结构与分子多样性,较为显著的进展体现在原核微生物的分子多样性及底栖真核微藻的物种多样性研究,对于海洋底栖原生动物的多样性研究则相较滞后.本文综述了国内外对海洋微型底栖生物各主要类群的分类学和多样性研究进展,探讨了各类群在全球的潜在物种多样性,并就我国未来加强海洋微型底栖生物多样性构成、分布与变动及驱动变化的因子以及底栖微食物网的研究提出了建议.     

Species diversity and distribution within the deep-sea nematode genus Acantholaimus on the continental shelf and slope in Antarctica

Species diversity and distribution—in relation with biogeography, bathymetry and environmental characteristics—within the genus Acantholaimus were investigated on the shelf and slope (182–2,009 m) in the Weddell Sea (Kapp Norvegia and Vestkapp) and near the Antarctic Peninsula (Drake Passage and Bransfield Strait). The occurrence of the otherwise typical deep-sea genus Acantholaimus in high densities and diversity on the continental shelf is a unique feature of the Southern Ocean. Fifty-five Acantholaimus species (morpho-types) were distinguished in our study area, of which 39 were found on the shelf. The Acantholaimus communities were characterised by a high number of congeneric species and the presence of many rare species, similar to typical deep-sea communities. Fourteen species had a distribution extending from the shelf to the lower slope. High local and regional diversity was obvious and a considerable level of endemism was suggested. A negative impact of chlorophyll a concentrations, reflecting the availability of phytoplankton, was found on the Acantholaimus densities and species diversity.     

Growth of silver hake within the U.S. continental shelf ecosystem of the northwest Atlantic Ocean

Von Bertalanffy growth parameters were estimated for silver hake Merluccius bilinearis within four regions of the United States continental shelf ecosystem of the northwest Atlantic Ocean during 1975–1980, 1982–1987 and 1988–1992. Differences in silver hake growth were found between the Middle Atlantic and southern Georges Bank regions ( P <0–01) over all three time periods. Growth also differed between northern Georges Bank and the Gulf of Maine ( P <0–01) during 1975–1980 and 1982–1987, and significant differences between southern Georges Bank and northern Georges Bank were found only during 1982–1987. Silver hake in the Gulf of Maine exhibited larger asymptotic sizes, but attained their asymptotic size at slower rates (L₀₀= 47 cm and K =0–33) in comparison to silver hake in the Middle Atlantic ( L₀₀= 43 cm and K =0–51), while growth parameter estimates for silver hake on Georges Bank were intermediate between these. Although significant differences in growth of silver hake between the various regions are consistent with separate stocks in the U.S. continental shelf ecosystem, the growth characteristics from the different regions are inconsistent with the presently assigned stock boundaries. (c) 1996 The Fisheries Society of the British Isles