Novel uncultivated labyrinthulomycetes revealed by 18S rDNA sequences from seawater and sediment samples

Labyrinthulomycetes (Labyrinthulea) are ubiquitous marine osmoheterotrophic protists that appear to be important in decomposition of both allochthonous and autochthonous organic matter. We used a cultivation-independent method based on the labyrinthulomycete-specific primer LABY-Y to PCR amplify, clone, and sequence 68 nearly full-length 18S rDNA amplicons from 4 sediment and 3 seawater samples collected in estuarine habitats around Long Island, New York, USA. Phylogenetic analyses revealed that all 68 amplicons belonged to the Labyrinthulea. Only 15 of the 68 amplicons belonged to the thraustochytrid phylogenetic group (Thraustochytriidae). None of these 15 were similar to cultivated strains, and 11 formed a novel group. The remaining 53 amplicons belonged either to the labyrinthulid phylogenetic group (Labyrinthulidae) or to other families of Labyrinthulea. that have not yet been described. Of these amplicons, 37 were closely related to previously cultivated Aplanochytrium spp. and Oblongichytrium spp. Members of these 2 genera were also cultivated from 1 of the sediment samples. The 16 other amplicons were not closely related to cultivated strains, and 15 belonged to 5 groups of apparently novel labyrinthulomycetes. Most of the novel groups of amplicons also contained environmental sequences from surveys of protist diversity using universal 18S rDNA primers. Because the primer LABY-Y is biased against several groups of labyrinthulomycetes, particularly among the thraustochytrids, these results may underestimate the undiscovered diversity of labyrinthulomycetes.

Concurrence of cat and tet genes in multiple antibiotic-resistant bacteria isolated from a sea cucumber and sea urchin mariculture farm in China

A basic understanding of abundance and diversity of antibiotic-resistant microbes and their genetic determinants is necessary for finding a way to prevent and control the spread of antibiotic resistance. For this purpose, chloramphenicol and multiple antibiotic-resistant bacteria were screened from a mariculture farm in northern China. Both sea cucumber and sea urchin rearing ponds were populated with abundant antibiotic-resistant bacteria, especially marine vibrios. Sixty-five percent chloramphenicol-resistant isolates from sea cucumber harbored a cat gene, either cat IV or cat II, whereas 35% sea urchin isolates harbored a cat gene, actually cat II. The predominant resistance determinant cat IV gene mainly occurred in isolates related to Vibrio tasmaniensis or Pseudoalteromonas atlantica, and the cat II gene mainly occurred in Vibrio splendidus-like isolates. All the cat-positive isolates also harbored one or two of the tet genes, tet(D), tet(B), or tet(A). As no chloramphenicol-related antibiotic was ever used, coselection of the cat genes by other antibiotics, especially oxytetracycline, might be the cause of the high incidence of cat genes in the mariculture farm studied.

Surface sediment diatoms from the western Pacific marginal seas and their correlation to environmental variables

Diatom data of 192 surface sediment samples from the marginal seas in the western Pacific together with modern summer and winter sea surface temperature and salinity data were analyzed. The results of canonical correspondence analysis show that summer sea-surface salinity (SSS) is highly positively correlated with winter SSS and so is summer sea-surface temperature (SST) with winter SST. The correlations between SSSs and SSTs are less positively correlated, which may be due to interactions of regional current pattern and monsoon climate. The correlations between diatom species, sample sites and environmental variables concur with known diatom ecology and regional oceanographic characters. The results of forward selection of the environmental variables and associated Monte Carlo permutation tests of the statistical significance of each variable suggest that summer SSS and winter SST are the main environmental factors affecting the diatom distribution in the area and therefore preserved diatom data from down core could be used for reconstructions of summer SSS and winter SST in the region.

Diversity of Both the Cultivable Protease-Producing Bacteria and Their Extracellular Proteases in the Sediments of the South China Sea

Protease-producing bacteria are known to play an important role in degrading sedimentary particular organic nitrogen, and yet, their diversity and extracellular proteases remain largely unknown. In this paper, the diversity of the cultivable protease-producing bacteria and their extracellular proteases in the sediments of the South China Sea was investigated. The richness of the cultivable protease-producing bacteria reached 10(6) cells/g in all sediment samples. Analysis of the 16S rRNA gene sequences revealed that the predominant cultivated protease-producing bacteria are Gammaproteobacteria affiliated with the genera Pseudoalteromonas, Alteromonas, Marinobacter, Idiomarina, Halomonas, Vibrio, Shewanella, Pseudomonas, and Rheinheimera, with Alteromonas (34.6%) and Pseudoalteromonas (28.2%) as the predominant groups. Inhibitor analysis showed that nearly all the extracellular proteases from the bacteria are serine proteases or metalloproteases. Moreover, these proteases have different hydrolytic ability to different proteins, reflecting they may belong to different kinds of serine proteases or metalloproteases. To our knowledge, this study represents the first report of the diversity of bacterial proteases in deep-sea sediments.

Incidence of diverse integrons and beta-lactamase genes in environmental Enterobacteriaceae isolates from Jiaozhou Bay, China

Environmental microbiology investigation was performed to determine the molecular diversity of beta-lactamase genes among ampicillin-resistant bacteria from Jiaozhou Bay. beta-lactamase genes were detected in 93.8% of the bacterial isolates identified as Enterobacteriaceae. The most frequently detected gene was bla(TEM), followed by bla(SHV), bla(OAX-1), bla(MOX) and bla(CMY). Most of the isolates (68.8%) were positive for the intI1 integrase gene, and two isolates were also found for the intI2 gene. The dfr and aadA gene cassettes were predominant. Anthropogenic contamination from onshore sewage processing plants might contribute predominantly to the beta-lactamase gene reservoir in the studied coastal waters. Environmental antibiotic-resistant bacteria and resistance genes may serve as bioindicators of coastal environmental quality or biotracers of the potential contamination sources. This is the first report of the prevalence and characterization of beta-lactamase genes and integrons in coastal Enterobacteriaceae from China.

Spatial distribution of ciliates, copepod nauplii and eggs, Engraulis japonicus post-larvae and microzooplankton herbivorous activity in the Yellow Sea, China

The abundance of anchovy Engraulis japonicus larvae, >20 mum ciliates, copepod eggs and nauplii, and microzooplankton herbivorous activity were studied in the Yellow Sea in June 2000. Anchovy juveniles and larvae were found in only 6 of the 19 stations sampled. The ciliate communities were dominated by 2 species: Laboea strobila and Strombidium compressum. In the surface waters, the abundance of L. strobila ranged between 0 and 560 ind. l(-1). S. compressum only appeared at Stns 15 to 18 (20 to 3300 ind. l(-1)). L. strobila was found mainly in the top 20 m. The abundance of L. strobila was less than 50 ind, l(-1) in waters deeper than 25 m. S, compressum showed subsurface abundance peaks at the salinity abnormality. Tintinnids occurred occasionally with abundance lower than 100 ind. l(-1), The total ciliate abundance fell in the range of 40 to 3420 ind. l(-1). The ciliate biomass in the surface water and the water column ranged between 0,15 and 6.76 mug C l(-1) and 0.4 and 134.4 mg C m(-2), respectively, In the surface waters, the abundance of copepod eggs and nauplii ranged from 0,3 to 3.1 and 1,1 to 15.6 ind, l(-1), respectively. The average abundance of copepod eggs and nauplii in 4 depth (0, 5, 10 and 20 m) fell in the range of 0.2 to 2.8 and 1.0 to 29.4 ind. l(-1), respectively. As a food item of the E. japonicus post-larvae, the abundance of copepod nauplii and eggs appeared to be low. The abundance peaks of ciliate and E, japonicus post-larvae coincided. Although not found in the gut of E, japonicus post-larvae, aloricate ciliates might be ingested by first-feeding anchovy larvae, preventing initial starvation and prolonging the time to irreversible starvation. On the basis of dilution experiments with positive microzooplankton grazing rates, microzooplankton grazed at rates of 0 to 0.61 d(-1). Grazing pressure of microzooplankton on chlorophyll a standing stock (P-i) and potential chlorophyll a primary production (P-p) were 17 to 46% and 35 to 109% d(-1), respectively.