Eukaryotic microbiota in the surface waters and sea ice of the Southern Ocean: aspects of physiology, ecology and biodiversity in a ‘two-phase’ ecosystem

The Southern Ocean provides a habitat for microplankton which is strongly influenced by physical factors. Of these, one of the most important and striking is the formation of sea ice. Organisms in the ice form a unique community with specific properties and adaptations. Material and organisms are exchanged between the water column and the ice during the annual cycle, and ice is an important factor in modifying biogeochemical processes and exchange between ocean and atmosphere. The coupled system, in which a range of organisms alternate between a fluid and a solid medium, provides an interesting exercise in community ecology, and has implications for the assessment of biodiversity in understanding large-scale change.     

Multiple, Novel Biologically Active Endophytic Actinomycetes Isolated from Upper Amazonian Rainforests

Microbial biodiversity provides an increasingly important source of medically and industrially useful compounds. We have isolated 14 actinomycete species from a collection of approximately 300 plant stem samples from the upper Amazonian rainforest in Peru. All of the cultured isolates produce substances with inhibitory activity directed at a range of potential fungal and bacterial pathogens. For some organisms, this activity is very broad in spectrum while other organisms show specific activity against a limited number of organisms. Two of these organisms preferentially inhibit bacterial test organisms over eukaryotic organisms. rDNA sequence analysis indicates that these organisms are not equivalent to any other cultured deposits in GenBank. Our results provide evidence of the untapped biodiversity in the form of biologically active microbes present within the tissues of higher plants.     

Degradation of nitroaromatic compounds by microorganisms

Nitroaromatic compounds are abundantly present in nature, but are in most cases highly toxic to living organisms. Several microorganisms, however, are capable of mineralizing or converting these compounds. Until now four pathways for the complete degradation of nitroaromatics have been described, which start with either the oxygenolytic or reductive removal of the nitro group from the aromatic ring or with this removal by means of replacement reactions. Besides these conversions many organisms are able to reduce nitroaromatics. The degradation of nitroaromatic compounds does not only occur in pure cultures but also in situ, for example in soil, water and sewage. However, several problems are associated with the application of microorganisms in the bioremediation of contaminated sites, as nitroaromatics or their conversion products may chemically interact with soil particles and cells. Besides the possibilities of applying microorganisms in the cleaning of sites contaminated with nitroaromatics, the use of microorganisms or enzymes in the biocatalytic production of industrially valuable products from nitroaromatics is also discussed.     

Patterns and controlling factors of species diversity in the Arctic Ocean

Aim The Arctic Ocean is one of the last near‐pristine regions on Earth, and, although human activities are expected to impact on Arctic ecosystems, we know very little about baseline patterns of Arctic Ocean biodiversity. This paper aims to describe Arctic Ocean‐wide patterns of benthic biodiversity and to explore factors related to the large‐scale species diversity patterns. Location Arctic Ocean. Methods We used large ostracode and foraminiferal datasets to describe the biodiversity patterns and applied comprehensive ecological modelling to test the degree to which these patterns are potentially governed by environmental factors, such as temperature, productivity, seasonality, ice cover and others. To test environmental control of the observed diversity patterns, subsets of samples for which all environmental parameters were available were analysed with multiple regression and model averaging. Results Well‐known negative latitudinal species diversity gradients (LSDGs) were found in metazoan Ostracoda, but the LSDGs were unimodal with an intermediate maximum with respect to latitude in protozoan foraminifera. Depth species diversity gradients were unimodal, with peaks in diversity shallower than those in other oceans. Our modelling results showed that several factors are significant predictors of diversity, but the significant predictors were different among shallow marine ostracodes, deep‐sea ostracodes and deep‐sea foraminifera. Main conclusions On the basis of these Arctic Ocean‐wide comprehensive datasets, we document large‐scale diversity patterns with respect to latitude and depth. Our modelling results suggest that the underlying mechanisms causing these species diversity patterns are unexpectedly complex. The environmental parameters of temperature, surface productivity, seasonality of productivity, salinity and ice cover can all play a role in shaping large‐scale diversity patterns, but their relative importance may depend on the ecological preferences of taxa and the oceanographic context of regions. These results suggest that a multiplicity of variables appear to be related to community structure in this system.     

From Sea to Sea: Canada's Three Oceans of Biodiversity

Evaluating and understanding biodiversity in marine ecosystems are both necessary and challenging for conservation. This paper compiles and summarizes current knowledge of the diversity of marine taxa in Canada''s three oceans while recognizing that this compilation is incomplete and will change in the future. That Canada has the longest coastline in the world and incorporates distinctly different biogeographic provinces and ecoregions (e.g., temperate through ice-covered areas) constrains this analysis. The taxonomic groups presented here include microbes, phytoplankton, macroalgae, zooplankton, benthic infauna, fishes, and marine mammals. The minimum number of species or taxa compiled here is 15,988 for the three Canadian oceans. However, this number clearly underestimates in several ways the total number of taxa present. First, there are significant gaps in the published literature. Second, the diversity of many habitats has not been compiled for all taxonomic groups (e.g., intertidal rocky shores, deep sea), and data compilations are based on short-term, directed research programs or longer-term monitoring activities with limited spatial resolution. Third, the biodiversity of large organisms is well known, but this is not true of smaller organisms. Finally, the greatest constraint on this summary is the willingness and capacity of those who collected the data to make it available to those interested in biodiversity meta-analyses. Confirmation of identities and intercomparison of studies are also constrained by the disturbing rate of decline in the number of taxonomists and systematists specializing on marine taxa in Canada. This decline is mostly the result of retirements of current specialists and to a lack of training and employment opportunities for new ones. Considering the difficulties encountered in compiling an overview of biogeographic data and the diversity of species or taxa in Canada''s three oceans, this synthesis is intended to serve as a biodiversity baseline for a new program on marine biodiversity, the Canadian Healthy Ocean Network. A major effort needs to be undertaken to establish a complete baseline of Canadian marine biodiversity of all taxonomic groups, especially if we are to understand and conserve this part of Canada''s natural heritage.     

New Caledonia: A ‘Hot Spot’ for Valuable Chemodiversity. Part 1: Gymnosperms

The flora of New Caledonia encompasses more than 3,000 species and almost 80% of them are endemic. New Caledonia is considered as a ‘hot spot’ for biodiversity. With the current global loss of biodiversity, and the fact that several drugs and pesticides are becoming obsolete, there is an urgent need to increase sampling and research on new natural products. In this context, we review the chemical information available on New Caledonian native flora from economical perspectives. We expect that a better knowledge of the economic potential will encourage the plantation of native plants for the development of a sustainable economy which will participate in the conservation of biodiversity. In the first part of this review, we discuss the results reported in 18 scientific articles on the chemicals isolated from 23 endemic conifers of New Caledonia. Several bioactive and original products, such as neocallitropsene or libocedrins, have been isolated from these conifers. This review also highlights several groups, such as Podocarpus spp., that are unexplored in New Caledonia despite the fact that they have been described in other countries to contain a wide range of original bioactive compounds. Those plants are considered as priority for future chemical investigations.     

Reef-associated crustacean fauna: biodiversity estimates using semi-quantitative sampling and DNA barcoding

The cryptofauna associated with coral reefs accounts for a major part of the biodiversity in these ecosystems but has been largely overlooked in biodiversity estimates because the organisms are hard to collect and identify. We combine a semi-quantitative sampling design and a DNA barcoding approach to provide metrics for the diversity of reef-associated crustacean. Twenty-two similar-sized dead heads of Pocillopora were sampled at 10 m depth from five central Pacific Ocean localities (four atolls in the Northern Line Islands and in Moorea, French Polynesia). All crustaceans were removed, and partial cytochrome oxidase subunit I was sequenced from 403 individuals, yielding 135 distinct taxa using a species-level criterion of 5% similarity. Most crustacean species were rare; 44% of the OTUs were represented by a single individual, and an additional 33% were represented by several specimens found only in one of the five localities. The Northern Line Islands and Moorea shared only 11 OTUs. Total numbers estimated by species richness statistics (Chao1 and ACE) suggest at least 90 species of crustaceans in Moorea and 150 in the Northern Line Islands for this habitat type. However, rarefaction curves for each region failed to approach an asymptote, and Chao1 and ACE estimators did not stabilize after sampling eight heads in Moorea, so even these diversity figures are underestimates. Nevertheless, even this modest sampling effort from a very limited habitat resulted in surprisingly high species numbers.     

Buried treasure: soil biodiversity and conservation

Soils are incredibly biodiverse habitats, yet soil-dwelling organisms have received little attention within the field of conservation biology. Due to difficulties involved in studying soil biota, and to taxonomic biases in conservation research, the full extent of soil biodiversity is not well understood, and soil-dwelling organisms are rarely candidates for conservation. The biogeography of soil biota differs significantly from that of plants or animals aboveground, and the taxonomic and functional diversity of soil-dwellers allows them to have a multitude of ecological effects on aboveground organisms. Soil organisms exhibit levels of biodiversity several orders of magnitude greater than those found in their aboveground counterparts on a per-area basis. The biodiversity of soils underpins many crucial ecosystem services which support the plants and animals typically targeted by conservation efforts. Strategies detailed in this paper provide practitioners with the ability to address many of the challenges related to incorporating soils and soil organisms into conservation planning.     

Influences of past climatic changes on historical population structure and demography of a cosmopolitan marine predator,the common dolphin (genus Delphinus)

Climatic oscillations during the Pleistocene have greatly influenced the distribution and connectivity of many organisms, leading to extinctions but also generating biodiversity. While the effects of such changes have been extensively studied in the terrestrial environment, studies focusing on the marine realm are still scarce. Here we used sequence data from one mitochondrial and five nuclear loci to assess the potential influence of Pleistocene climatic changes on the phylogeography and demographic history of a cosmopolitan marine predator, the common dolphin (genus Delphinus). Population samples representing the three major morphotypes of Delphinus were obtained from 10 oceanic regions. Our results suggest that short‐beaked common dolphins are likely to have originated in the eastern Indo‐Pacific Ocean during the Pleistocene and expanded into the Atlantic Ocean through the Indian Ocean. On the other hand, long‐beaked common dolphins appear to have evolved more recently and independently in several oceans. Our results also suggest that short‐beaked common dolphins had recurrent demographic expansions concomitant with changes in sea surface temperature during the Pleistocene and its associated increases in resource availability, which differed between the North Atlantic and Pacific Ocean basins. By proposing how past environmental changes had an effect on the demography and speciation of a widely distributed marine mammal, we highlight the impacts that climate change may have on the distribution and abundance of marine predators and its ecological consequences for marine ecosystems.     

Biodiversity in Mediterranean-climate streams of California

Although the California mediterranean climate region is widely considered a biodiversity hotspot for terrestrial plants and vertebrates, freshwater biodiversity in this region is generally not well known. Using information from museum specimen databases, published literature, biological assessment surveys, and specialist’s knowledge, we review freshwater biodiversity for several groups of stream organisms in the med-climate region of California, which includes 2,220 species in 292 families. The groups with the highest diversity of lotic species are aquatic insects and diatoms, which comprise 39 and 36 % of species in our lists, respectively. Sequential floods and drying periods limit the overall biodiversity of many stream organisms in California mediterranean rivers, and continued climate and land-use change may cause disproportionate biodiversity declines in the region. However, only 4 % of lotic species have been evaluated in the IUCN Red List of Threatened Species, and many assessments are outdated. Future development of online databases for botanical and zoological collections will significantly enhance biodiversity and distribution knowledge. This information will enable us to more accurately and efficiently assess the effects of global change on biodiversity of freshwater organisms, to evaluate conservation status of individual taxa, and to set conservation priorities for stream ecosystems.     

Meta‐analysis reveals complex marine biological responses to the interactive effects of ocean acidification and warming

Ocean acidification and warming are considered two of the greatest threats to marine biodiversity, yet the combined effect of these stressors on marine organisms remains largely unclear. Using a meta‐analytical approach, we assessed the biological responses of marine organisms to the effects of ocean acidification and warming in isolation and combination. As expected biological responses varied across taxonomic groups, life‐history stages, and trophic levels, but importantly, combining stressors generally exhibited a stronger biological (either positive or negative) effect. Using a subset of orthogonal studies, we show that four of five of the biological responses measured (calcification, photosynthesis, reproduction, and survival, but not growth) interacted synergistically when warming and acidification were combined. The observed synergisms between interacting stressors suggest that care must be made in making inferences from single‐stressor studies. Our findings clearly have implications for the development of adaptive management strategies particularly given that the frequency of stressors interacting in marine systems will be likely to intensify in the future. There is now an urgent need to move toward more robust, holistic, and ecologically realistic climate change experiments that incorporate interactions. Without them accurate predictions about the likely deleterious impacts to marine biodiversity and ecosystem functioning over the next century will not be possible.     

Phylogeography of Padina boryana (Dictyotales,Phaeophyceae) around the Thai-Malay Peninsula

The Indo-Pacific Ocean is a biodiversity hotspot for marine organisms. In this area, most of the research has focused on marine animals, such as reef fish, molluscs and other associated coral fauna, but very little has been done on macroalgae. The Thai-Malay Peninsula is an important north–south barrier in this area, which faces two different oceans – the Indian Ocean and the Pacific Ocean. This study aims to investigate genetic distribution patterns of Padina boryana Thivy around the Thai-Malay Peninsula, where it is common. Three DNA marker regions, the mitochondrion-encoded cytochrome c oxidase subunit 3 gene (cox3); the plastid rbcL, and the nuclear internal transcribed spacer 2 (ITS2) were used to evaluate genetic diversity and the relationships within and between populations. Samples were collected from both the Andaman Sea and Gulf of Thailand sides of the peninsula. Parsimony networks and maximum likelihood and Bayesian analyses showed clearly that there are two separated P. boryana lineages, one restricted to the Gulf of Thailand and the other to the Andaman Sea and other areas of the Indo-Pacific. The effect of different ocean currents along the Andaman Sea and Gulf of Thailand may have shaped these populations of P. boryana. This phylogeographic separation, based on persistent currents in the area, may affect other marine organisms along the Thai peninsula.     

Antibacterial and antitubercular activity of fosmidomycin, FR900098, and their lipophilic analogs

The nonmevalonate pathway (NMP) of isoprene biosynthesis is an exciting new route toward novel antibiotic development. Inhibitors against several enzymes in this pathway are currently under examination. A significant liability of many of these agents is poor cell penetration. To overcome and improve our understanding of this problem, we have synthesized a series of lipophilic, prodrug analogs of fosmidomycin and FR900098, inhibitors of the NMP enzyme Dxr. Several of these compounds show improved antibacterial activity against a panel of organisms relative to the parent compound, including activity against Mycobacterium tuberculosis (Mtb). Our results show that this strategy can be an effective way for improving whole cell activity of NMP inhibitors.     

Antarctic reptant decapods: more than a myth?

The impoverished Antarctic decapod fauna is one of the most conspicuous biodiversity phenomena in polar science. Although physiological and ecological approaches have tried to explain the reason for the low decapod biodiversity pattern in the Southern Ocean, the complexity of this problem is still not completely understood. The scant records of crabs south of the Polar Front were always considered as exceptional, and have mostly been ignored by marine biologists world-wide, creating one of the most dogmatic paradigms in polar science. We herein review the record of both adults and larvae of reptants from the Southern Ocean. At present, several species of only lithodid crabs maintain considerable adult populations in circum-Antarctic waters, although they remain absent from the high-Antarctic shelves.     

Linking aboveground and belowground diversity

Aboveground and belowground species interactions drive ecosystem properties at the local scale, but it is unclear how these relationships scale-up to regional and global scales. Here, we discuss our current knowledge of aboveground and belowground diversity links from a global to a local scale. Global diversity peaks towards the Equator for large, aboveground organisms, but not for small (mainly belowground) organisms, suggesting that there are size-related biodiversity gradients in global aboveground-belowground linkages. The generalization of aboveground-belowground diversity relationships, and their role in ecosystem functioning, requires surveys at scales that are relevant to the organisms and ecosystem properties. Habitat sizes and diversity gradients can differ significantly between aboveground and belowground organisms and between ecosystems. These gradients in biodiversity and plant community trait perception need to be acknowledged when studying aboveground-belowground biodiversity linkages.     

海洋生物多样性信息资源

海洋生物多样性甚高, 但却饱受人为的破坏及干扰。目前全球最大的含点位数据的在线开放性数据库是海洋生物地理信息系统(OBIS), 共约12万种3,700万笔资料; 另一个较大的数据库世界海洋生物物种登录(WoRMS)已收集全球22万种海洋生物之物种分类信息。除此之外, 以海洋生物为主的单一类群的数据库只有鱼库(FishBase)、藻库(AlgaeBase)及世界六放珊瑚(Hexacorallians of the World)3个。跨类群及跨陆海域的全球性物种数据库则甚多, 如网络生命大百科(EOL)、全球生物物种名录(CoL)、整合分类信息系统(ITIS)、维基物种(Wikispecies)、ETI生物信息(ETI Bioinformatics)、生命条形码(BOL)、基因库(GenBank)、生物多样性历史文献图书馆(BHL)、海洋生物库(SeaLifeBase); 海洋物种鉴定入口网(Marine Species Identification Portal)、FAO渔业及水产养殖概要(FAO Fisheries and Aquaculture Fact Sheets)等可查询以分类或物种解说为主的数据库。全球生物多样性信息网络(GBIF)、发现生命(Discover Life)、水生物图库(AquaMaps)等则是以生态分布数据为主, 且可作地理分布图并提供下载功能, 甚至于可以改变水温、盐度等环境因子的参数值, 利用既定的模式作参数改变后之物种分布预测。谷歌地球(Google Earth)及国家地理(National Geographic)网站中的海洋子网页, 以及珊瑚礁库(ReefBase)等官方机构或非政府组织之网站, 则大多以海洋保育的教育倡导为主, 所提供的信息及素材可谓包罗万象, 令人目不暇给。更令用户感到方便的是上述许多网站或数据库彼此间均已可交互链接及查询。另外, 属于搜索引擎的谷歌图片(Google Images)与谷歌学术(Google Scholar)透过海洋生物数据库所提供的直接链接, 在充实物种生态图片与学术论文上亦发挥极大帮助, 让用户获得丰富多样的信息。为了保育之目的, 生物多样性数据库除了整合与公开分享外, 还应鼓励并推荐大家来使用。本文乃举Rainer Froese在巴黎演讲之内容为例, 介绍如何使用海洋生物多样性之数据来预测气候变迁对鱼类分布的影响。最后就中国大陆与台湾目前海洋生物多样性数据库的现况、两岸的合作及如何与国际接轨作介绍。     

Distribution, ecology and morphology of Lytocarpia myriophyllum (Cnidaria: Hydrozoa), a Mediterranean Sea habitat former to protect

In the Mediterranean Sea, as well as in other parts of the word, intense bottom trawling threatens deep and mesophotic assemblages, compromising mainly the survivorship of erect organisms and of the habitat complexity they shape. Protection of species able to affect their habitats, by increasing spatial complexity and enhancing interspecific interactions, is crucial for biodiversity conservation. It is urgent to highlight the occurrence of those species which act as ecosystem engineers and/or habitat former to enhance awareness on their ecological role and to develop focused conservation strategies. Lytocarpia myriophyllum is the largest Leptomedusan hydroid of the Mediterranean Sea, with colonies up to 1 m high, and the most abundant Aglaopheniid in the eastern part of the North Atlantic Ocean. This species creates wide forests on soft bottoms stabilizing sediments, providing refuge and food for several other associated organisms and could be defined both a habitat former and an ecosystem engineer. Thanks to trimix diving here we report on new insights on the morphological, biological and ecological features of L. myriophyllum meadows from the Mediterranean Sea furnishing a baseline for protection plans focused on these facies. This work demonstrates that direct studies of mesophotic habitats allow to collect far more detailed information than grabs, ROVs, or towed camera arrays and highlights the urgent need to redefine the vertical extension of several marine protected areas.     

Fissidens monguilloni Thér. in England

Abstract

The 1996 Chagos Expedition provided an opportunity to study the archipelago's bryophyte flora: 25 of the 55 islands were ecologically investigated, some in more detail than others, and lists and representative collections of mosses, hepatics and other cryptogamic plants were assembled for many of them. Although the islands have a low biodiversity for most of these groups, as would be expected in terms of their relatively young age, remoteness and small terrestrial surface areas, those organisms that are present are often found in abundance and play significant ecological roles. Where the status of taxa on islands has been determined, there appears to be a good correlation between bryophyte biodiversity and island size. Epiphytic bryophytes were not host specific and no epiphyllous species was observed. Biogeographic details are provided, where possible, for the 19 taxa recorded, of which four are new to the Indian Ocean and seven are new to the Chagos Archipelago. A new taxon, Cololejeunea planissima var. chagosensis Pócs var. nov. is described, and notes and illustrations of a probably new Lejeunea species are provided.     

rRNA and rDNA based assessment of sea ice protist biodiversity from the central Arctic Ocean

Sea ice is a large and diverse ecosystem contributing significantly to primary production in ice-covered regions. In the Arctic Ocean, sea ice consists of mixed multi-year ice (MYI), often several metres thick, and thinner first-year ice (FYI). Current global warming is most severe in Arctic regions; as a consequence, summer sea ice cover is decreasing and MYI is disappearing at an alarming rate. Despite its apparent hostility, sea ice is inhabited by a diverse microbial community of bacteria and protists, many of which are photosynthetic. Here we present an assessment of eukaryotic biodiversity in MYI and FYI from the central Arctic Ocean using high-throughput 454 sequencing of 18S rRNA and rDNA amplicons. We compared the rDNA-based ‘total’ biodiversity with the ‘active’ biodiversity from rRNA amplicons and found differences between them including an over-representation of Ciliophora, Bicosoecida and Bacillariophyceae operational taxonomic units (OTUs) in the active part of the community. Differences between the two libraries are more pronounced at the lower taxonomic level: certain genera, such as Melosira, are more abundant in the rRNA library, indicating activity of these genera. Furthermore, we found that one FYI station showed a higher activity of potential grazers which was probably due to the advanced stage of melt evident by higher ice temperatures and highly porous ice compared with the other stations.     

Ocean and bio-medical research

On the Planet Earth, oceans and seas today correspond to the largest volume offered to Life. Roughly, 275,000 species have been described from marine environments, only representing some 15% of all the present known living. But marine biomass can be enormous. Life appeared in the ancestral ocean 3 800 million years ago and determining events occurred there: appearance of the nuclear membrane and cell nucleus, "pluricellularity", capture of bacteria transformed into organelles, then sexuality. On the 33 phyla existing today on the Earth, 12 never have left the ocean and are exclusively marine. Such biodiversity, archaism of characters, organisational and behavioural patterns make these marine organisms an excellent reservoir for identifying and extracting very interesting pharmacological and cosmetic molecules (>5 000 today) and/or to represent very pertinent "models" for basic and applied research. Relationships between ocean and public health are physical, chemical, biological and physiological. A few marine species as "models" set the base for major advances in life sciences recognized by several Nobel Prices: from the discovery of phagocytosis to anaphylactic shock, and including nervous influx transmission, memory molecular bases, cyclins discovery, eye organisation, neurotransmitter membrane receptors, bases of the specific immune system... These marine models are very useful to understand the origin and functioning of important living mechanisms in the human and sometimes to deduce applications for efficient treatments. Ocean supplies mankind with renewable living resources, much threatened today. We have to manage and protect these to maintain ecosystems, stocks and biodiversity. Only because of the greenhouse effect and anthropic emissions, temperature is globally increasing: and, what if (tomorrow?) one million species would disappear (before 2050) because of global warming?