Steroids and anthraquinones from the deep-sea-derived fungus Aspergillus nidulans MCCC 3A00050

Aspergillus nidulans MCCC 3A00050 was isolated from a deep-sea sediment sample of the western Pacific Ocean. A systematic investigation on its chemical constituents led to the isolation of 19 compounds, including 13 steroids (1–13), four anthraquinones (14–17), one phenolics (18), and one chromanone (19). For the first time, three diosgenins (1–3) were isolated from fungi, three ergosterols (4–6) from the genus of Aspergillus, while other 11 miscellaneous compounds (7–11 and 14–19) from the species of Aspergillus nidulans. The isolation of diosgenins (1–3) and ergosterols (4–6) might be used as chemotaxonomic markers for the genus of Aspergillus and the species of Aspergillus nidulans, respectively.     

Abyssal NE Atlantic benthic foraminifera during the last 15 kyr: Relation to variations in seasonality of productivity

Benthic foraminiferal faunas (> 63 μm) and stable isotopes from the last 15 kyr were studied in BENGAL programme (high-resolution temporal and spatial study of the BENthic biology and Geochemistry of a north-eastern Atlantic abyssal Locality) kasten core 13078#16 from the Porcupine Abyssal Plain, NE Atlantic (48°49.91 N, 16°29.94 W, water depth 4844 m). Changes occurred in the accumulation rates, species composition, diversity, and stable isotopes during the last 15 kyr. Today, the area is strongly influenced by seasonal inputs of phytodetritus following the spring blooms in surface water primary productivity. Variations in the relative abundance of the two most abundant species, Epistominella exigua and Alabaminella weddellensis, which today show significant increases in abundance with the presence of phytodetritus on the sea-floor, are interpreted as resulting from changes in the seasonality of productivity. Seasonal productivity was higher during the Holocene than during the last deglaciation and Younger Dryas, probably coinciding with the retreat of the polar front to higher latitudes. This hypothesis is consistent with simultaneous decreases in the percentage of the polar planktic foraminifera Neogloboquadrina pachyderma (s), and increases in the percentage of Globigerina bulloides, a warmer water planktic foraminifera indicative of phytoplankton blooms and enhanced productivity. The relative abundance of the ‘phytodetritus species’ (E. exigua and A. weddellensis) covary between 14.7 and 8.1 kyr, but not between 7.8 and 1.2 kyr. Major decreases in the numbers per gram and accumulation rates of planktic and benthic foraminifera occurred at ∼ 12–8.5 kyr and at ∼ 4 kyr which correspond to decreases in the % sediment coarse fraction and published data on inorganic carbon contents suggesting that dissolution may have increased at these times. Relationships between benthic foraminiferal faunas and benthic stable isotope records suggest no simple relationship between faunal abundances and test isotope chemistry. For example, the abundances of phytodetritus species do not show strong correlations with either the δ¹³C values of E. exigua or the Δδ¹³C _{E. exigua − P. wuellerstorfi} record, which have previously been suggested as indicative of seasonality of productivity.     

Monophyly, phylogenetic position and inter-familial relationships of the Alepocephaliformes (Teleostei) based on whole mitogenome sequences

Recent mitogenomic studies suggest a new position for the deep-sea fishes of the order Alepocephaliformes, placing them within the Otocephala in contrast to their traditional placement within the Euteleostei. However, these studies included only two alepocephaliform taxa and left several questions unsolved about their systematics. Here we use whole mitogenome sequences to reconstruct phylogenetic relationships for 11 alepocephaliform taxa, sampled from all five nominal families, and a large selection of non-alepocephaliform teleosts, to address the following three questions: (1) is the Alepocephaliformes monophyletic, (2) what is its phylogenetic position within the Teleostei and (3) what are the relationships among the alepocephaliform families? Our character sets, including unambiguously aligned, concatenated mitogenome sequences that we have divided into four (first and second codon positions, tRNA genes, and rRNA genes) or five partitions (same as before plus the transversions at third codon positions, using "RY" coding), were analyzed by the partitioned maximum likelihood and Bayesian methods. Our result strongly supported the monophyly of the Alepocephaliformes and its close relationship to the Clupeiformes and Ostariophysi. Altogether, these three groups comprise the Otocephala. Statistical comparison using likelihood-based SH test confidently rejected the monophyly of the Euteleostei when including the Alepocephaliformes. However, increasing the taxonomic sampling within the Alepocephaliformes did not resolve its position relative to the Clupeiformes and Ostariophysi. Within the Alepocephaliformes, our results strongly supported the monophyly of the platytroctid genera but not that of the remaining taxa. From one analysis to other, platytroctids were either the sister group of the remaining taxa or nested within the alepocephalids. Inferred relationships among alepocephaliform taxa were not congruent with any of the previously published phylogenetic hypotheses based on morphological characters.     

Vision in the dimmest habitats on Earth

A very large proportion of the world's animal species are active in dim light, either under the cover of night or in the depths of the sea. The worlds they see can be dim and extended, with light reaching the eyes from all directions at once, or they can be composed of bright point sources, like the multitudes of stars seen in a clear night sky or the rare sparks of bioluminescence that are visible in the deep sea. The eye designs of nocturnal and deep-sea animals have evolved in response to these two very different types of habitats, being optimised for maximum sensitivity to extended scenes, or to point sources, or to both. After describing the many visual adaptations that have evolved across the animal kingdom for maximising sensitivity to extended and point-source scenes, I then use case studies from the recent literature to show how these adaptations have endowed nocturnal animals with excellent vision. Nocturnal animals can see colour and negotiate dimly illuminated obstacles during flight. They can also navigate using learned terrestrial landmarks, the constellations of stars or the dim pattern of polarised light formed around the moon. The conclusion from these studies is clear: nocturnal habitats are just as rich in visual details as diurnal habitats are, and nocturnal animals have evolved visual systems capable of exploiting them. The same is certainly true of deep-sea animals, as future research will no doubt reveal.     

Occurrence and antagonistic potential of Stenotrophomonas strains isolated from deep-sea invertebrates

Stenotrophomonas maltophilia is known to be of significance as opportunistic pathogen as well as a source of biocontrol and bioremediation activities. S. maltophilia strains have been isolated from rhizospheres, soil, clinical material, aquatic habitats, but little is known about Stenotrophomonas strains recovered from marine environments. During a survey of the biodiversity of Pseudomonas-like bacteria associated with deep-sea invertebrates six Stenotrophomonas strains were isolated from sponge, sea urchin, and ophiura specimens collected from differing Pacific areas, including the Philippine Sea, the Fiji Sea and the Bering Sea. 16S rRNA gene sequence analysis confirmed an assignment of marine isolates to the genus Stenotrophomonas as it placed four strains into the S. maltophilia CIP 60.77^T cluster and two related to the S. rhizophila DSM 14405^T. Together with a number of common characteristics typical of S. maltophilia and S. rhizophila marine isolates exhibited differences in pigmentation, a NaCl tolerance, a range of temperatures, which supported their growth, substrate utilization pattern, and antibiotics resistance. Strains displayed hemolytic and remarkable inhibitory activity against a number of fungal cultures and Gram-positive microorganisms, but very weak or none against Candida albicans. This is the first report on isolation, taxonomic characterization and antimicrobial activity of Stenotrophomonas strains isolated from deep-sea invertebrates.     

Lebetimonas natsushimae sp. nov., a novel strictly anaerobic,moderately thermophilic chemoautotroph isolated from a deep-sea hydrothermal vent polychaete nest in the Mid-Okinawa Trough

A moderately thermophilic, strictly anaerobic, chemoautotrophic bacterium, designated strain HS1857^T, was isolated from a deep-sea hydrothermal vent at the Noho site in the Mid-Okinawa Trough. Strain HS1857^T grew between 35 and 63 °C (optimum 55 °C), in the presence of 10–55 g l^?1 NaCl (optimum 25 g l^?1), and pH 5.5–7.1 (optimum 6.4). Growth occurred with molecular hydrogen as the electron donor and elemental sulfur, nitrate, or selenate as the electron acceptors. Formate could serve as an alternative electron donor with nitrate as an electron acceptor. During growth with nitrate as the electron acceptor, strain HS1857^T produced ammonium and formed a biofilm. CO₂ was utilized as the sole carbon source. The G + C content of the genomic DNA was 33.2 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain HS1857^T is a member of the order Nautiliales, showing a sequence similarity of 95.0% with Lebetimonas acidiphila Pd55^T. The fatty acid composition was similar to that of L. acidiphila, which was dominated by C_18:0 (47.0%) and C_18:1 (23.7%). Based on the genomic, chemotaxonomic, phenotypic characteristics, the name Lebetimonas natsushimae sp. nov., is proposed. The type strain is HS1857^T (= NBRC 112478^T = DSM 104102^T).     

Phylogenetic analysis of Archaea in the deep-sea sediments of west Pacific Warm Pool

Archaea are known to play important roles in carbon cycling in marine sediments. The main compositions of archaeal community in five deep-sea sediment samples collected from west Pacific Warm Pool area (WP-0, WP-1, WP-2, WP-3, WP-4), and in five sediment layers (1 cm-, 3 cm-, 6 cm-, 10 cm-, 12 cm- layer) of the 12 cm sediment core of WP-0 were checked and compared by denaturing gradient gel electrophoresis and 16 S rRNA gene sequencing. It was revealed that all the deep-sea sediment samples checked contained members of non-thermophilic marine group I crenarchaeota as the predominant archaeal group. To further detect groups of archaea possibly relating with C1 metabolism, PCR amplification was carried out using primers targeting methane-oxidizing archaea. Although no methane-oxidizing archaea was detected, a group of novel archaea (named as WPA) was instead identified from all these five WP samples by clone analysis. They could be placed in the euryarchaeota kingdom, separated into two distinct groups, the main group was peripherally related with methanogens, the other group related with Thermoplasma. The vertical distributions of WPA, archaea and bacteria along the WP-0 sediment column were determined by quantitative-PCR. It was found that bacteria dominated at all depths, the numbers of bacteria were 10–10⁴ times more than those of archaea. The proportion of archaea versus bacteria had a depth related increasing tendency, it was lowest at the first layer (0.01%), reached highest at the 12 cm- layer (10%). WPA only constituted a small proportion of the archaeal community (0.05% to 5%) of west Pacific Warm Pool sediment.Peng Wang and Xiang Xiao contributed equally to this paper     

深海微生物高压适应与生物地球化学循环

深海是典型的高压环境,嗜压微生物是深海生态系统中的重要类群.随着深海采样技术的发展及高压微生物特殊培养设备的开发,已从深海环境中分离到一系列嗜压微生物,包括一些常压环境不能生长的严格嗜压菌.对这些嗜压菌的研究,不仅对微生物适应极端高压环境的机制有一定了解,而且发现了一些特殊的代谢产物.研究微生物高压嗜压机理,还有助于探索地球生命的温度压力极限及生命起源和演化等科学问题.从深海嗜压微生物多样性、深海微生物高压环境适应机理及深海微生物在生物地球化学循环中的作用等方面对嗜压微生物的研究进展进行综述.     

Visual and lenticular pigments in the eyes of demersal deep-sea fishes

We report on the lens pigmentation and visual pigments of 52 species of demersal deep-sea fishes caught at depths ranging from 480 m to 4110 m in the Porcupine Seabight and Goban Spur area of the North-eastern Atlantic. Only one species, caught between 480 and 840 m, had a lens with large amounts of pigment, consistent with the hypothesis that heavily pigmented lenses in deep-sea fish serve to enhance the contrast of bioluminescent signals by removing much of the background radiance, which is only visible to fish living shallower than 1000 m. Low concentrations of lens pigmentation were also observed in a further two species (Rouleina attrita and Micromesisteus poutassou). The retinae of all species except five, contained only a single visual pigment, as determined by microspectrophotometry of individual rods, and/or spectrophotometry of retinal wholemounts and retinal extracts. Those fishes caught between 500 m and 1100 m had wavelengths of peak sensitivity (_max) ranging from 476 nm to 494 nm, while most fish living below 1100 m tended to be more conservative with (_max) values ranging from 475 nm to 485 nm. The only exceptions to this were three deep-living species caught between 1600 m and 2000 m whose retinae contain abnormally short-wave sensitive visual pigments (Cataetyx laticeps — _max 468 nm; Alepocephalus bairdii — _max 467 nm; Narcetes stomias _max 472 nm), suggesting adaptation for the detection of short-wave bioluminescence.