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.     

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.     

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.     

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.     

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.     

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 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.     

Diversity and biogeography of the Antarctic flora

Aim To establish how well the terrestrial flora of the Antarctic has been sampled, how well the flora is known, and to determine the major patterns in diversity and biogeography. Location Antarctica south of 60° S, together with the South Sandwich Islands, but excluding South Georgia, Bouvetøya and the periantarctic islands. Methods Plant occurrence data were collated from herbarium specimens and literature records, and assembled into the Antarctic Plant Database. Distributional patterns were analysed using a geographic information system. Biogeographical patterns were determined with a variety of multivariate statistics. Results Plants have been recorded from throughout the Antarctic, including all latitudes between 60° S and 86° S. Species richness declines with latitude along the Antarctic Peninsula, but there was no evidence for a similar cline in Victoria Land and the Transantarctic mountains. Multi‐dimensional scaling ordinations showed that the species compositions of the South Orkney, South Shetland Islands and the north‐western Antarctic Peninsula are very similar to each other, as are the floras of different regions in continental Antarctica. They also suggest, however, that the eastern Antarctic Peninsula flora is more similar to the flora of the southern Antarctic Peninsula than to the continental flora (with which it has traditionally been linked). The South Sandwich Islands have a flora that is very dissimilar to that in all Antarctic regions, probably because of their isolation and volcanic nature. Main conclusions The Antarctic flora has been reasonably well sampled, but certain areas require further floristic surveys. Available data do, however, allow for a number of robust conclusions. A diversity gradient exists along the Antarctic Peninsula, with fewer species (but not fewer higher taxa) at higher latitudes. Multi‐dimensional scaling ordination suggests three major floral provinces within Antarctica: northern maritime, southern maritime, and continental. Patterns of endemism suggest that a proportion of the lichen flora may have an ancient vicariant distribution, while most bryophytes are more recent colonists.     

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.     

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.     

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.     

南海西北部陆架区鱼类的种类组成与群落格局

根据2006-2007年在南海西北部陆架区海域进行的4航次底拖网调查数据,对该海域鱼类的种类组成和群落格局进行分析.调查共采获鱼类262种,隶属于20目102科.以冬季出现种类数最多,为166种;夏季和秋季次之,分别为161种和155种;春季最少,为135种.运用聚类分析和非度量多维标度(NMDS)方法分析了南海西北部陆架区鱼类群落结构的空间分布.研究表明,该海域鱼类可划分为5个群落,分别为粤西沿岸群落(群落Ⅰ)、海南岛东南沿岸群落(群落Ⅱ)、海南岛东部深海群落(群落Ⅲ)、过渡群落(群落Ⅳ)和混合群落(群落Ⅴ).ANOSIM检验表明,各群落间鱼类组成的差异极为显著(R=0.847-0.939,P＜0.001).鱼类群落格局的变化与海流和水深关系密切,有较明显的沿水深梯度分布的规律.咸淡水鱼类在雷州半岛东部的冷涡区域,形成群落Ⅰ;南海暖流控制区域内的深海鱼类,形成群落Ⅲ;在南海暖流最为强劲的冬季,研究区域内大部分鱼类集结为混合性群落Ⅴ;琼东南沿岸的上升流区内形成群落Ⅱ;沿岸流强劲的夏、秋季,在沿岸流和上升流交汇处,形成过渡性群落Ⅳ.     

Biodiversity and biogeography of southern temperate and polar bryozoans

Aim To describe the distribution of biodiversity and endemism of bryozoans in southern temperate and polar waters. We hypothesized that we would find: (1) no strong latitudinal richness gradient; (2) striking contrasts in richness and endemism between clades and between regions; and (3) that faunal similarity of regions would cluster geographically around each southern continent. Location South Atlantic, Indian and Pacific Oceans and the Southern Ocean. Methods We constructed a data base from known literature, regional data bases and recent finds. We regionalized each southern continent, calculated levels of richness and endemism for each region and continent, and used primer 5 to perform multivariate statistical analysis. Results A third (1681) of global bryozoan species described occur south of 30° S, of which c. 87% were cheilostomes. In richness we found no latitudinal cline and change across longitude was stronger. New Zealand was richest and had the most (60%) endemic species, followed by Antarctica at 57%. There were striking contrasts in regional richness and endemism between clades but the highest levels of between‐region similarity were around Antarctica. The timing of past continent connectivity was reflected. Main conclusions Bryozoans show strong hemispherical asymmetry in richness and, like molluscs and corals, decrease away from Australasia rather than with latitude. Species endemism is much lower in Antarctic bryozoans than previously thought, and as this taxon is not particularly dispersive and is now amongst the best studied regionally, maybe Antarctic endemism in general is lower and Antarctica less cut‐off to species dispersal than previously thought. However, Antarctic generic endemism is double the level previously calculated and regional faunal similarities are much higher than around other continents – both reflecting long‐term isolation. Bryozoans, in contrast to the paradigm of Antarctic fauna, may be fairly robust to predicted climate change. Paradoxically, they may also be one of the best taxa to monitor to sensitively detect marine benthic responses.     

The phylogeny and biogeography of Hakea (Proteaceae) reveals the role of biome shifts in a continental plant radiation

The frequency of evolutionary biome shifts during diversification has important implications for our ability to explain geographic patterns of plant diversity. Recent studies present several examples of biome shifts, but whether frequencies of biome shifts closely reflect geographic proximity or environmental similarity of biomes remains poorly known. We explore this question by using phylogenomic methods to estimate the phylogeny of Hakea, a diverse Australian genus occupying a wide range of biomes. Model‐based estimation of ancestral regions indicates that Hakea began diversifying in the Mediterranean biome of southern Australia in the Middle Eocene–Early Oligocene, and dispersed repeatedly into other biomes across the continent. We infer around 47 shifts between biomes. Frequencies of shifts between pairs of biomes are usually similar to those expected from their geographic connectedness or climatic similarity, but in some cases are substantially higher or lower than expected, perhaps reflecting how readily key physiological traits can be modified to adapt lineages to new environments. The history of frequent biome‐shifting is reflected in the structure of present‐day assemblages, which tend to be more phylogenetically diverse than null‐model expectations. The case of Hakea demonstrates that the radiation of large plant clades across wide geographic areas need not be constrained by dispersal limitation or conserved adaptations to particular environments.     

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.