Novel eukaryotes from the permanently anoxic Cariaco Basin (Caribbean Sea)

Present knowledge of microbial diversity is decidedly incomplete (S. J. Giovannoni and M. S. Rappé, p. 47-84, in D. Kirchman, ed., Microbial Ecology of the Oceans, 2000; E. Stackebrandt and T. M. Embley, p. 57-75, in R. R. Colwell and D. J. Grimes, ed., Nonculturable Microorganisms in the Environment, 2000). Protistan phylogenies are particularly deficient and undoubtedly exclude clades of principal ecological and evolutionary importance (S. L. Baldauf, Science 300:1703-1706, 2003). The rRNA approach has been extraordinarily successful in expanding the global prokaryotic record (S. J. Giovannoni and M. S. Rappé, p. 47-84, in D. Kirchman, ed., Microbial Ecology of the Oceans, 2000; E. Stackebrandt and T. M. Embley, p. 57-75, in R. R. Colwell and D. J. Grimes, ed., Nonculturable Microorganisms in the Environment, 2000) but has rarely been used in protistan discovery. Here we report the first application of the 18S rRNA approach to a permanently anoxic environment, the Cariaco Basin off the Venezuelan coast. On the basis of rRNA sequences, we uncovered a substantial number of novel protistan lineages. These included new clades of the highest taxonomic level unrelated to any known eukaryote as well as deep branches within established protistan groups. Three novel lineages branch at the base of the eukaryotic evolutionary tree preceding, contemporary with, or immediately following the earliest eukaryotic branches. These newly discovered protists may retain traits reminiscent of an early eukaryotic ancestor(s).     

Phylogenetic Diversity of Bacterial and Archaeal Communities in the Anoxic Zone of the Cariaco Basin

Microbial community samples were collected from the anoxic zone of the Cariaco Basin at depths of 320, 500, and 1,310 m on a November 1996 cruise and were used to construct 16S ribosomal DNA libraries. Of 60 nonchimeric sequences in the 320-m library, 56 belonged to the subdivision of the Proteobacteria (-Proteobacteria) and 53 were closely related to ectosymbionts of Rimicaris exoculata and Alvinella pompejana, which are referred to here as epsilon symbiont relatives (ESR). The 500-m library contained sequences affiliated with the fibrobacteria, the Flexibacter-Cytophaga-Bacteroides division, the division Verrucomicrobia, the division Proteobacteria, and the OP3 candidate division. The Proteobacteria included members of the γ, δ, and new candidate subdivisions, and γ-proteobacterial sequences were dominant (25.6%) among the proteobacterial sequences. As in the 320-m library, the majority of the -proteobacteria belonged to the ESR group. The genus Fibrobacter and its relatives were the second largest group in the library (23.6%), followed by the δ-proteobacteria and the -proteobacteria. The 1,310-m library had the greatest diversity; 59 nonchimeric clones in the library contained 30 unique sequences belonging to the planctomycetes, the fibrobacteria, the Flexibacter-Cytophaga-Bacteroides division, the Proteobacteria, and the OP3 and OP8 candidate divisions. The proteobacteria included members of new candidate subdivisions and the β, γ, δ, and -subdivisions. ESR sequences were still present in the 1,310-m library but in a much lower proportion (8.5%). One archaeal sequence was present in the 500-m library (2% of all microorganisms in the library), and eight archaeal sequences were present in the 1,310-m library (13.6%). All archaeal sequences fell into two groups; two clones in the 1,310-m library belonged to the kingdom Crenarchaeota and the remaining sequences in both libraries belonged to the kingdom Euryarchaeota. The latter group appears to be related to the Eel-TA1f2 sequence, which belongs to an archaeon suggested to be able to oxidize methane anaerobically. Based on phylogenetic inferences and measurements of dark CO₂ fixation, we hypothesized that (i) the ESR are autotrophic anaerobic sulfide oxidizers, (ii) sulfate reduction and fermentative metabolism may be carried out by a large number of bacteria in the 500- and 1,310-m libraries, and (iii) members of the Euryarchaeota found in relatively large numbers in the 1,310-m library may be involved in anaerobic methane oxidation. Overall, the composition of microbial communities from the Cariaco Basin resembles the compositions of communities from several anaerobic sediments, supporting the hypothesis that the Cariaco Basin water column is similar to anaerobic sediments.     

Comparison of Vertical Distributions of Prokaryotic Assemblages in the Anoxic Cariaco Basin and Black Sea by Use of Fluorescence In Situ Hybridization

Individual prokaryotic cells from two major anoxic basins, the Cariaco Basin and the Black Sea, were enumerated throughout their water columns using fluorescence in situ hybridization (FISH) with the fluorochrome Cy3 or horseradish peroxidase-modified oligonucleotide probes. For both basins, significant differences in total prokaryotic abundance and phylogenetic composition were observed among oxic, anoxic, and transitional (redoxcline) waters. Epsilon-proteobacteria, Crenarchaeota, and Euryarchaeota were more prevalent in the redoxclines, where previous studies reported high rates of chemoautotrophic production relative to those in waters above and below the redoxclines. Relative abundances of Archaea in both systems varied between 1% and 28% of total prokaryotes, depending on depth. The prokaryotic community composition varied between the two anoxic basins, consistent with distinct geochemical and physical conditions. In the Black Sea, the relative contributions of group I Crenarchaeota (median, 5.5%) to prokaryotic communities were significantly higher (P < 0.001; n = 20) than those of group II Euryarchaeota (median, 2.9%). In contrast, their proportions were nearly equivalent in the Cariaco Basin. Beta-proteobacteria were unexpectedly common throughout the Cariaco Basin's water column, accounting for an average of 47% of 4′,6′-diamidino-2-phenylindole (DAPI)-stained cells. This group was below the detection limit (<1%) in the Black Sea samples. Compositional differences between basins may reflect temporal variability in microbial populations and/or systematic differences in environmental conditions and the populations for which they select.     

欧科学家发现首个无氧生活的多细胞动物

<正>近日,来自意大利和丹麦的研究人员首次识别出一种完全不依赖氧气生活的多细胞生物,这种生物生活在地球最恶劣的环境中:地中海L'Atalante盆地,此地的盐水密度非常之高,含有氧气的水层只能留在上面,而在海底的它们则终日生活在无氧环境里。这一最新发现发表在新一期《BMCBiology》上。     

Spatial structure of the Caribbean lobster (Metanephrops binghami) in the Colombian Caribbean Sea

Crustaceans of the genus Metanephrops are of great commercial value in some tropical and subtropical regions. With the potential development of a new deep lobster fishery in the Colombian Caribbean Sea, the objective of this work is to describe for first time the patterns of spatial and bathymetric distribution, and diel migratory periodicity of the Caribbean lobster (M. binghami). Data were collected by trawling in depths between 200 and 550 m (100 m strata intervals) in the Colombian Caribbean Sea. Higher biomass and size of these crustaceans were found between 250 and 350 m, with a maximum at about 300 m. The study offers diel patterns of M. binghami, which suggests nocturnal activity and burrowing during daylight hours.     

Genetic Diversity of Microbial Eukaryotes in Anoxic Sediment of the Saline Meromictic Lake Namako-ike (Japan): On the Detection of Anaerobic or Anoxic-tolerant Lineages of Eukaryotes

Available sequence data on eukaryotic small-subunit ribosomal DNA (SSU rDNA) directly retrieved from various environments have increased recently, and the diversity of microbial eukaryotes (protists) has been shown to be much greater than previously expected. However, the molecular information accumulated to date does still not thoroughly reveal ecological distribution patterns of microbial eukaryotes. In the ongoing challenge to detect anaerobic or anoxic-tolerant lineages of eukaryotes, we directly extracted DNA from the anoxic sediment of a saline meromictic lake, constructed genetic libraries of PCR-amplified SSU rDNA, and performed phylogenetic analyses with the cloned SSU rDNA sequences. Although a few sequences could not be confidently assigned to any major eukaryotic groups in the analyses and are debatable regarding their taxonomic positions, most sequences obtained have affiliations with known major lineages of eukaryotes (Cercozoa, Alveolata, Stramenopiles, and Opisthokonta). Among these sequences, some branched with lineages predominantly composed of uncultured environmental clones retrieved from other anoxic environments, while others were closely related to those of eukaryotic parasites (e.g. Phytomyxea of Cercozoa, Gregarinea of Alveolata, and Ichthyosporea of Opisthokonta).     

Leptepsilonema gen. n. (Nematoda, Epsilonematidae) from Chile and the Caribbean Sea

The new genus Leptepsilonema is erected. L. procerum sp.n from intertidal sandy beaches of the Caribbean sea and L. macrum sp.n. and L. exile sp.n. from Chile are described. Postembryonal development of L. procerum , covering the juvenile stages II-IV, is presented. Some ecological data are added.     

New fatty acids from Colombian Caribbean Sea sponges

The fatty acid composition of whole phospholipids from marine sponges collected from the Colombian Caribbean Sea was determined as part of our studies on the order Halichondrida: Halichondria magniconulosa, Halichondria lutea, Petromica ciocalyptoides, Axinyssa ambrosia, Didiscus oxeata and Dragmaxia undata. Structure elucidation was accomplished by means of gas chromatography retention parameters and GCMS. Eight new fatty acids were identified by their methyl esters and N-acylpyrrolidide derivatives (i.e. 5-methyl-6-octadecenoic, 16-methyl-11-heptadecenoic, 8-methyl-4-tetracosenoic, 8,17-dimethyl-5-octadecenoic, 23-methyl-8-tetracosenoic, 20-methyl-18-tetracosenoic, 4,17-tetracosadienoic and 22,27-dimethyl-5,9-octacosadienoic acids). These findings establish alternative fatty acid biosynthetic possibilities for these organisms.     

Hermit crabs (Anomura: Paguroidea) distribution patterns in the Colombian Caribbean Sea

Hermit crabs represent the marine life in the Colombian Caribbean, and are important for the dynamic equilibrium maintenance in ecosystems, the ecological interactions and their impact on food web stability. Generally, in order to come up with some conservation strategies, strong bio-geographical information is needed for poll cies definition. With this aim, this study analyzed the distribution patterns of hermit crabs in the Colombian Caribbean Sea. through classification and spatial ordination multivariate analyses, using historical records from years 1916 to 2006. Besides, the world distribution of Colombian species and their geographic affinity in the Caribbean and Western Atlantic were identified. The results show deep differences between coastal and continental slope faunas, and latitudinal differences in the assemblages, with the identification of three groups: Northeast. Center and Southwest. The differences in faunal composition that support these three groups were determined. Based on maps of the Colombian marine ecosystems, it was found that the main factors affecting the distribution of hermit crabs were the Caribaná slope (depth), water-mass temperature, Guajira sea-grass beds, and particular conditions of "Coralline Archipelagos" and "Darién" eco-regions. Colombian hermit crab fauna is more related to the North Atlantic and the Antilles, than to the South Atlantic and the Gulf of Mexico. Additionally, geographical sub-provinces in which Colombia is included, these were found as transition zones among Northern and Austral subprovinces of the Greater Caribbean.     

Fingerprinting Microbial Assemblages from the Oxic/Anoxic Chemocline of the Black Sea

Biomass samples from the Black Sea collected in 1988 were analyzed for SSU genes from Bacteria and Archaea after 10 years of storage at −80°C. Both clonal libraries and direct fingerprinting by terminal restriction fragment length polymorphism (T-RFLP) analyses were used to assess the microbial community. Uniform and discrete depth distributions of different SSU phylotypes were observed. However, most recombinant clones were not restricted to a specific depth in the water column, and many of the major T-RFLP peaks remain uncharacterized. Of the clones obtained, an -Proteobacteria and a Pseudoalteromonas-like clone accounted for major peaks in the fingerprint, while deeply branching lineages of α- and γ-Proteobacteria were associated with smaller peaks. Additionally, members were found among both the δ-Proteobacteria related to sulfate reducers and the Archaea related to phylotypes from the ANME groups that anaerobically oxidize methane.     

Species of dinoflagellates of the genus Gambierdiscus (Dinophyceae) in the Mexican Caribbean Sea

Some dinoflagellates with benthic habits are related to ciguatera intoxication by fish consumption, especially in tropical areas. In the Mexican Caribbean, ciguatera is relatively common, but only one paper seems to have been published on the subject, and there are very few publicactions on phytoplankton and benthic microalgae. Material collected along the coast of the State of Quintana Roo with phytoplankton net (54 mm) and directly from sediment and epiphytes of macroscopic plants, was searched for toxic and other associated dinoflagellates. Samples were studied by light and scanning electron microscopy. Morphological characters were useful for species identification, but eventually physiological, ecological and molecular characters could also be used. Three species of Gambierdiscus, related to the production of ciguatera toxins, were identified: G. belizeanus, G. toxicus and G. yasumotoi. They are distributed in shallow coastal areas, including coastal lagoons.     

Cruoriella rhodoliths from shallow-water back reef environments in La Parguera, Puerto Rico (Caribbean Sea)

The occurrence of shallow-water (0.9 to 1.3 m) rhodoliths in back reef environments in southwest Puerto Rico is reported. The rhodoliths were generally cylindrical, discoidal or irregular in shape with an average longest dimension of 7.2 cm. They occurred at a maximum density of 524 m⁻². The rhodoliths were composed of mostly coral nuclei with concentric laminations of aragonite-producing Cruoriella armorica (Peyssonneliaceae, Rhodophyta). Maximum Cruoriella accretion around coral nuclei was 30 mm although accretions of 1 to 20 mm were more common. Based on measurements of Cruoriella accretion, these shallow water rhodoliths are estimated to have minimum ages of 12 to 24 years. It is further estimated that approximately 2% of the rhodoliths are turned over daily. Accepted: 1 October 1999     

Inclusion bodies in several species of Ceratium Schrank (Dinophyceae) from the Caribbean Sea examined with DNA-specific staining

Several dinoflagellate species in the genus Ceraiium Schrankwere examined, with the help of a DNA-specific dye, for thepresence of a nucleus, chloroplasts and inclusion bodies. Theabundance of Ceratium in the Caribbean Sea in April 1990 wasbetween 1.3 and 4.9 x 10⁵ cells m^–3 Most Ceratium teresKofoid contained 5–10 small chloroplasts and among 529C.teres cells. 8% possessed an inclusion body. The shape andsize of inclusion bodies varied, and 7% of the inclusions hada DNA-containing particle inside. Similar inclusion bodies werealso observed in Ceratium declinatum f. normale Jörgensen,Ceratium furca (Ehrenberg) Claparede and Lachmann, and Ceratiumfusus (Ehrenberg) Dujardin. Our observations indicated thatinclusion bodies are common in oceanic Ceratium. ¹Present address: Institute of Marine Biology, National TaiwanOcean University, Keelung 20224, Taiwan, ROC     

Sea surface temperatures and coral reef bleaching off La Parguera, Puerto Rico (northeastern Caribbean Sea)

 Much recent attention has been given to coral reef bleaching because of its widespread occurrence, damage to reefs, and possible connection to global change. There is still debate about the relationship between temperature and widespread bleaching. We compared coral reef bleaching at La Parguera, Puerto Rico to a 30-y (1966–1995) record of sea surface temperature (SST) at the same location. The last eight years of the La Parguera SST record have all had greater than average maximum temperatures; over the past 30 y maximum summer temperature has increased 0.7 °C. Coral reef bleaching has been particularly frequent since the middle 1980s. The years 1969, 1987, 1990, and 1995 were especially noteworthy for the severity of bleaching in Puerto Rico. Seven different annual temperature indices were devised to determine the extent to which they could predict severe coral bleaching episodes. Three of these, maximum daily SST, days >29.5 °C, and days >30 °C predict correctly the four years with severe bleaching. A log-log linear relationship was found between SST and the number of days in a given year above that SST at which severe coral beaching was observed. However, the intra-annual relationship between temperature and the incidence of bleaching suggests that no one simple predictor of the onset of coral bleaching within a year may be applicable. Accepted: 17 March 1998     

Phytoplankton observations in the Eastern Caribbean Sea

A total of 88 taxa were noted in these samples, of which there were 44 diatoms, 41 pyrrhophyceans, 2 cyanophyceans and 1 silicoflagellate. Totals of 37 and 38 different phytoplankters were observed during cruises E46K-67-68 and E1-C-70, respectively, with 58 species noted in the extensive samplings of E 5013-68-69. A diatomaceaous flora predominated in each series of collections. The phytoflagellates were well represented, but in low numbers. The overall phytoplankton concentrations were low for each of the areas studied during these three January cruises. Even the preliminary data on the coccolithophore concentration does not indicate a major development at this time of the year. Generally, phytoplankton counts were lowest at stations most distant from the island complex and especially in the shallow waters that passed between the islands, directly from the north Atlantic into the Caribbean Sea. Results from the 1969 and 1970 collections west of the Lesser Antilles correspond closely to the findings reported by Hargraves et al. (1970). There was considerable diversity of phytoplankton species, but they were present in low numbers. They have related this condition to the low nutrient concentrations in the oceanic waters of the Lesser Antilles region.The writer thanks Duke University Marine Laboratory for the use of the facilities of the R/V EASTWARD on cruises E46K-67-68, E50D-68-69, and E1C-70, in the Cooperative Oceanographic Program supported through National Science Foundation grant G17669.     

Comparison of vertical distributions of prokaryotic assemblages in the anoxic Cariaco Basin and Black Sea by use of fluorescence in situ hybridization

Individual prokaryotic cells from two major anoxic basins, the Cariaco Basin and the Black Sea, were enumerated throughout their water columns using fluorescence in situ hybridization (FISH) with the fluorochrome Cy3 or horseradish peroxidase-modified oligonucleotide probes. For both basins, significant differences in total prokaryotic abundance and phylogenetic composition were observed among oxic, anoxic, and transitional (redoxcline) waters. Epsilon-proteobacteria, Crenarchaeota, and Euryarchaeota were more prevalent in the redoxclines, where previous studies reported high rates of chemoautotrophic production relative to those in waters above and below the redoxclines. Relative abundances of Archaea in both systems varied between 1% and 28% of total prokaryotes, depending on depth. The prokaryotic community composition varied between the two anoxic basins, consistent with distinct geochemical and physical conditions. In the Black Sea, the relative contributions of group I Crenarchaeota (median, 5.5%) to prokaryotic communities were significantly higher (P < 0.001; n = 20) than those of group II Euryarchaeota (median, 2.9%). In contrast, their proportions were nearly equivalent in the Cariaco Basin. Beta-proteobacteria were unexpectedly common throughout the Cariaco Basin's water column, accounting for an average of 47% of 4',6'-diamidino-2-phenylindole (DAPI)-stained cells. This group was below the detection limit (<1%) in the Black Sea samples. Compositional differences between basins may reflect temporal variability in microbial populations and/or systematic differences in environmental conditions and the populations for which they select.