Expansion of the geographic distribution of a novel lineage of epsilon-Proteobacteria to a hydrothermal vent site on the Southern East Pacific Rise

The diversity associated with a microbial mat sample collected from a deep-sea hydrothermal vent on the Southern East Pacific Rise was determined using a molecular phylogenetic approach based on the comparison of sequences from the small subunit ribosomal RNA gene (16S rDNA). The DNA was extracted from the sample and the 16S rDNA was amplified by PCR. Sixteen different phylotypes were identified by restriction fragment length polymorphism analysis; four phylotypes were later identified as putative chimeras. Analysis of the 16S rDNA sequences placed all the phylotypes within the Proteobacteria. The majority of the sequences (98%) were most closely related to a new clade of epsilon-Proteobacteria that were initially identified from an in situ growth chamber deployed on a deep-sea hydrothermal vent on the Mid-Atlantic Ridge in 1995. The similarity between phylotypes identified from Atlantic and Pacific deep-sea hydrothermal vent sites indicates that this new clade of Proteobacteria may be endemic to and widely distributed among deep-sea hydrothermal vents.     

TAXONOMY OF QUATERNARY DEEP-SEA OSTRACODS FROM THE WESTERN NORTH ATLANTIC OCEAN

Abstract:  Late Quaternary sediments from Ocean Drilling Program (ODP) Hole 1055B, Carolina Slope, western North Atlantic (32°47.041' N, 76°17.179' W; 1798 m water depth) were examined for deep-sea ostracod taxonomy. A total of 13 933 specimens were picked from 207 samples and c . 120 species were identified. Among them, 87 species were included and illustrated in this paper. Twenty-eight new species are described. The new species are: Ambocythere sturgio , Argilloecia abba , Argilloecia caju , Argilloecia keigwini , Argilloecia robinwhatleyi , Aversovalva carolinensis , Bythoceratina willemvandenboldi , Bythocythere eugeneschornikovi , Chejudocythere tenuis , Cytheropteron aielloi , Cytheropteron demenocali , Cytheropteron didieae , Cytheropteron richarddinglei , Cytheropteron fugu , Cytheropteron guerneti , Cytheropteron richardbensoni , Eucytherura hazeli , Eucytherura mayressi , Eucytherura namericana , Eucytherura spinicorona , Posacythere hunti , Paracytherois bondi , Pedicythere atroposopetasi , Pedicythere kennettopetasi , Pedicythere klothopetasi , Pedicythere lachesisopetasi , Ruggieriella mcmanusi and Xestoleberis oppoae . Taxonomic revisions of several common species were made to reduce taxonomic uncertainty in the literature. This study provides a robust taxonomic baseline for application to palaeoceanographical reconstruction and biodiversity analyses in the deep and intermediate-depth environments of the North Atlantic Ocean.     

Fungal Diversity in Deep Sea Sediments from East Yap Trench and Their Denitrification Potential

Abstract

In recent years, the hadal trenches have been recognized as biological hot spots for deep sea researchers. Due to high hydrostatic pressure, low temperatures, high salinity and low nutrients, the microorganisms in hadal trenches may have unique community structure with potential for biotechnical application. Compared with bacteria and archaea, the diversity and ecological roles of fungi in hadal trenches remain largely unknown. The purpose of this study was to explore fungal diversity in deep-sea sediments of the Yap trench and their denitrification potential. In the present study, a total of 106 fungal strains were isolated from six sediment samples collected in the East Yap Trench. These fungi belonged to five classes (Dothideomycetes, Eurotiomycetes, Sordariomycetes, Cystobasidiomycetes, and Microbotryomycetes), thirteen genera (Acremonium, Alternaria, Aureobasidium, Aspergillus, Cladosporium, Cystobasidium, Engyodontium, Gliomastix, Lecanicillium, Penicillium, Phoma, Rhodotorula and Trichoderma) and eighteen species, based on morphological identification and ITS-rDNA sequence analysis. Among them, the dominant genus is Cladosporium, which accounting for 42.45% of the total fungal strains. Meanwhile, the denitrification potential of the fungal strains was also examined with two different denitrifying media (nitrate and nitrite as sole substrate, respectively). Two fungal strains (Acremonium sp. and Aspergillus versicolor), were found to be able to produce N₂O ex situ in the presence of nitrite. No fungus was found to produce N₂O by using nitrate. Our results suggest that fungi in hadal sediments, play important roles in nitrogen cycles.     

Cultivable Fungal Diversity in Deep-Sea Sediment of the East Pacific Ocean

The diversity of fungi in the marine environment has been extensively studied, but their denitrification activity has rarely been reported to date. In the present study, we used six different media to isolate fungi from 10 sediment samples collected at five different locations of the East Pacific Ocean with water depths ranging from 4545 to 7068?m. Fungal identification and phylogenetic diversity analysis were conducted based on morphological characteristics and internal transcribed spacers of ribosomal DNA (ITS-rRNA) sequencing. A total of 106 fungal isolates, belonging to 12 genera, including Aspergillus (five strains), Aureobasidium (three strains), Candida (two strains), Cladosporium (56 strains), Cystobasidium (one strain), Devriesia (nine strains), Knufia (one strain), Nigrospora (three strains), Penicillium (18 strains), Rhodotorula (four strains), Sarocladium (three strains), and unclassified Xylariales (one strain) were obtained. The most dominant culturable genus was Cladosporium. One possible novel fungal strains showed less than 97% similarity to their closest matches of unclassified Xylariales in the Genbank. In addition, we used nirK gene as the molecular marker to detect denitrifying fungi among the cultivable fungal isolates. The nirK gene was detected in Aspergillus niger and Penicillium chrysogenum. Our research indicated that diverse fungi from the deep sea sediments of the East Pacific Ocean and highlighted the involvement of these fungi in denitrification process.     

Ammonium content and buoyancy in midwater cephalopods

The majority of squid families (Teuthoidea: Cephalopoda) exchange sodium for ammonium, creating a low-density fluid that imparts lift for neutral buoyancy. However, previous methods for measuring ammonium did not distinguish between NH₄⁺ and various other amine compounds. The present study, using single column ion chromatography, reassessed the cation concentrations in several midwater cephalopod species. High NH₄⁺ levels were confirmed for histioteuthid, cranchiid, and chiroteuthid and related squids. A strong relationship is reported between ammonium content and body mass in Histioteuthis heteropsis, suggesting a gradual accumulation of ammonium coincident with an ontogenetic migration to greater depths. The bathypelagic squids Bathyteuthis abyssicola and Bathyteuthis berryi, on the other hand, contained very little ammonium but rather contained large quantities of an as yet unidentified cation. The ecological significance of this compound is not yet known. Morphology in Bathyteuthid squids suggests that the unknown cation is contained intracellularly and so, unlike sequestered ammonia, does not diminish the space available for muscle tissue. Accordingly, protein measurements in B. berryi mantle muscle are on par with shallower-living muscular squids, and in situ submersible observations reveal strong locomotory abilities relative to other deep-water squids.     

Gammaproteobacteria occurrence and microdiversity in Tyrrhenian Sea sediments as revealed by cultivation-dependent and -independent approaches

Bacterial diversity in Tyrrhenian Sea sediments was assessed using cultivation-dependent and -independent approaches. Samples collected from the different sediment layers (up to 30 cm) relative to four seamount and non-seamount stations, at depths from 3425 to 3580 m, were subjected to DNA extraction and 16S rRNA amplification targeting the V3 region. Denaturing gradient gel electrophoresis (DGGE) showed several heterogeneous profiles and 27 single bands were excised and sequenced. Sequence analysis revealed the presence of Firmicutes, Actinobacteria and Chloroflexi in 26% of the DGGE bands and a predominance of sequences affiliated to cultivable and uncultivable clones of Gammaproteobacteria (55%). To corroborate these findings, cultivation attempts were performed that allowed the isolation of 87 strains assigned to the proteobacterial classes. Identification was achieved by means of automated ribosomal intergenic spacer analysis (ARISA) and by 16S rDNA sequencing. The isolates were related to the gamma, alpha and beta subclasses of Proteobacteria with respective percentages of 77, 17 and 6%. The most predominant Gammaproteobacteria isolates, assigned to the Psychrobacter marincola and P. submarinus clade (n = 53) and to Halomonas aquamarina (n = 14), showed a huge intraspecific diversity with 29 distinct ARISA haplotypes. The detection by both approaches of these psychrophilic and moderately halophilic species and their extensive microdiversity indicated their predominance in Tyrrhenian Sea sediments where they constituted the indigenous microflora.     

Genetic characterization of ompH mutants in the deep-sea bacterium Photobacterium sp. strain SS9

OmpH is an outer membrane protein produced by the deep-sea bacterium Photobacterium species strain SS9 in response to elevated hydrostatic pressure. In order to facilitate studies of the function of this protein, a series of OmpH⁺ and OmpH^- strains were obtained from SS9 by Tn5 gene replacement mutagenesis. A previously isolated ompH::lacZ strain and a derivative of this strain harboring a plasmid expressing the wild-type ompH gene were also utilized. The acridine mutagen ICR 191 preferentially inhibited the growth of OmpH⁺ over OmpH^- cells. Indeed, OmpH⁺ cultures treated with the mutagen rapidly accumulated mutants producing reduced levels of OmpH. In addition. OmpH⁺ cells took up the peptide Met-Leu-Phe approximately 15 times more rapidly than OmpH^- cells. The results are consistent with the hypothesis that OmpH functions as a relatively large, nonspecific diffusion channel.Abbreviations OMP Outer membrane protein     

Cenozoic deep-sea ostracods from Maud Rise, Weddell Sea, Antarctica (ODP Site 689): a palaeoceanographical perspective

Cenozoic palaeoceanography of the Maude Rise, Weddell Sea, Antarctica, has been investigated using Palaeocene to Quaternary deep-sea ostracod faunas from 23 samples of ODP Site 689. The abundance of ostracods is high enough only during the Palaeogene (Palaeocene-Oligocene) to allow palaeoceanographical inferences based on changes in diversity, dominance, endemism and faunal turnover (first and last occurrences). The abundance is particularly high throughout the Palaeocene and Eocene, but declines irreversibly near the Eocene/Oligocene boundary. The diversity increases more or less continuously from the Early Palaeocene to the Middle Eocene, and then it generally decreases throughout the remaining part of the Palaeogene (Middle Eocene-Oligocene); an exception is a positive peak in the Shannon-Weaver index in a single sample in the Late Oligocene. No positive peaks in diversity and taxa originations (first occurrences) at c. 40-38 Ma, occurs at Site 689; so the site provides no evidence for the establishment of the psychrosphere at this time. This corroborates similar regional results from an earlier study of benthonic foraminifera. Explanations for this may be related to Late Eocene-Early Oligocene changes in sedimentology and clay-mineralogy (associated with the progressive cooling of the Antarctica) which could have negatively affected abundance and diversity locally at Site 689. Alternatively, by this time, the ostracod fauna could also have been subjected to selective removal (with possible local extinction) of taxa (due to increased ventilation) or to thanatocoenosis dissolution (due to a decrease in temperature and availability of CaCO₃). A further possibility may be related to the fact that Site 689 was at intermediate water depths and may have remained within older water masses near the Eocene/Oligocene boundary. Failing these explanations, the results could indicate that the Late Eocene-Early Oligocene palaeoenvironmental changes in the world oceans were more gradual and occurred over a longer time interval than the global ostracod data show, at least at southern high latitudes.     

Cold-water coral reef frameworks,megafaunal communities and evidence for coral carbonate mounds on the Hatton Bank,north east Atlantic

Offshore banks and seamounts sustain diverse megafaunal communities, including framework reefs formed by cold-water corals. Few studies have quantified environmental effects on the alpha or beta diversity of these communities. We adopted an interdisciplinary approach that used historical geophysical data to identify topographic highs on Hatton Bank, which were surveyed visually. The resulting photographic data were used to examine relationships between megafaunal communities and macrohabitat, the latter defined into six categories (mud, sand, cobbles, coral rubble, coral framework, rock). The survey stations revealed considerable small-scale variability in macrohabitat from exposed Late Palaeocene lava flows to quiescent muddy habitats and coral-built carbonate mounds. The first reported evidence for coral carbonate mound development in UK waters is presented, which was most pronounced near present-day or former sites of topographic change, suggesting that local current acceleration favoured coral framework growth and mound initiation. Alpha diversity varied significantly across macrohabitats, but not between rock and coral rubble, or between smaller grain sized categories of cobbles, sand and mud. Community composition differed between most macrohabitats, and variation in beta diversity across Hatton Bank was largely explained by fine-scale substratum. Certain megafauna were clearly associated with particular macrohabitats, with stylasterid corals notably associated with cobble and rock habitats and coral habitats characterized by a diverse community of suspension-feeders. The visual surveys also produced novel images of deep-water megafauna including a new photographic record of the gorgonian coral Paragorgia arborea, a species not previously reported from Rockall Plateau. Further interdisciplinary studies are needed to interpret beta diversity across these and other environmental gradients on Hatton Bank. It is clear that efforts are also needed to improve our understanding of the genetic connectivity and biogeography of vulnerable deep-water ecosystems and to develop predictive models of their occurrence that can help inform future conservation measures. An erratum to this article can be found at     

Paleocene Thalassinidea colonization in deep-sea environment and the coprolite Palaxius osaensis n. ichnosp. in Southern Costa Rica

Palaxius osaensis n. ichnosp., a new ichnospecies of crustacean coprolite is described. The coprolite is preserved in a 200-m thick Paleocene sequence in Southern Costa Rica that is largely dominated by pillow basalts. The studied sample is part of a seamount formed in the Pacific Ocean that was accreted to the Central American isthmus during the Eocene. The absence of lava vesicles, shallow-water deposits, and detrital sediments in the section suggest that the coprolites were deposited in a deep environment during the first stage of the development of the seamount. This represents one of the deepest occurrences of Thalassinidea coprolites reported in the literature and indicates that the producers of the coprolites, presumably some shrimps, developed the aptitude to colonize abyssal environments at least since Early Tertiary. The crustacean coprolites were encountered at a site which apparently lacked a food supply, although hydrothermal processes are believed to have provided the opportunity for a chemotrophic community to develop on the deepest part of the seamount. P. osaensis n. ichnosp. is also found in Colombia in late Cretaceous shallow-water sediments that notably contain Palaxius caucaensis coprolites (Micropaleontology 41 (1995) 85-88). Occurrences of P. osaensis n. ichnosp. deposited at both shallow and deep levels may possibly be related to an aptitude of some thalassinid organisms to have developed in various biotopes during the late Cretaceous-Paleocene.