David Gillan

Bio: David Gillan is an academic researcher from University of Mons. The author has contributed to research in topics: Asterias & Population. The author has an hindex of 22, co-authored 64 publications receiving 2241 citations. Previous affiliations of David Gillan include Université libre de Bruxelles.

First insights into the biodiversity and biogeography of the Southern Ocean deep sea

Abstract: Shallow marine benthic communities around Antarctica show high levels of endemism, gigantism, slow growth, longevity and late maturity, as well as adaptive radiations that have generated considerable biodiversity in some taxa. The deeper parts of the Southern Ocean exhibit some unique environmental features, including a very deep continental shelf and a weakly stratified water column, and are the source for much of the deep water in the world ocean. These features suggest that deep-sea faunas around the Antarctic may be related both to adjacent shelf communities and to those in other oceans. Unlike shallow-water Antarctic benthic communities, however, little is known about life in this vast deep-sea region. Here, we report new data from recent sampling expeditions in the deep Weddell Sea and adjacent areas (748-6,348 m water depth) that reveal high levels of new biodiversity; for example, 674 isopods species, of which 585 were new to science. Bathymetric and biogeographic trends varied between taxa. In groups such as the isopods and polychaetes, slope assemblages included species that have invaded from the shelf. In other taxa, the shelf and slope assemblages were more distinct. Abyssal faunas tended to have stronger links to other oceans, particularly the Atlantic, but mainly in taxa with good dispersal capabilities, such as the Foraminifera. The isopods, ostracods and nematodes, which are poor dispersers, include many species currently known only from the Southern Ocean. Our findings challenge suggestions that deep-sea diversity is depressed in the Southern Ocean and provide a basis for exploring the evolutionary significance of the varied biogeographic patterns observed in this remote environment.

Structure of Sediment-Associated Microbial Communities along a Heavy-Metal Contamination Gradient in the Marine Environment

Abstract: Microbial community composition and structure were characterized in marine sediments contaminated for >80 years with cadmium, copper, lead, and zinc. Four sampling sites that encompass a wide range of sediment metal loads were compared in a Norwegian fjord (Sorfjord). HCl-extractable metals and organic matter constantly decreased from the most contaminated site (S1) to the control site (S4). All sampling sites presented low polychlorinated biphenyl (PCB) concentrations (Sigma(7)PCB < 7.0 ng g [dry weight](-1)). The biomass ranged from 4.3 x 10(8) to 13.4 x 10(8) cells g (dry weight) of sediments(-1) and was not correlated to metal levels. Denaturing gradient gel electrophoresis indicated that diversity was not affected by the contamination. The majority of the partial 16S rRNA sequences obtained were classified in the gamma- and delta-Proteobacteria and in the Cytophaga-Flexibacter-Bacteroides (CFB) bacteria. Some sequences were closely related to other sequences from polluted marine sediments. The abundances of seven phylogenetic groups were determined by using fluorescent in situ hybridization (FISH). FISH was impaired in S1 by high levels of autofluorescing particles. For S2 to S4, the results indicated that the HCl-extractable Cu, Pb, and Zn were negatively correlated with the abundance of gamma-Proteobacteria and CFB bacteria. delta-Proteobacteria were not correlated with HCl-extractable metals. Bacteria of the Desulfosarcina-Desulfococcus group were detected in every site and represented 6 to 14% of the DAPI (4',6'-diamidino-2-phenylindole) counts. Although factors other than metals may explain the distribution observed, the information presented here may be useful in predicting long-term effects of heavy-metal contamination in the marine environment.

Genetic Diversity of the Biofilm Covering Montacuta ferruginosa (Mollusca, Bivalvia) as Evaluated by Denaturing Gradient Gel Electrophoresis Analysis and Cloning of PCR-Amplified Gene Fragments Coding for 16S rRNA†

Abstract: The shell of the bivalve Montacuta ferruginosa, a symbiont living in the burrow of an echinoid, is covered with a rust-colored biofilm. This biofilm includes different morphotypes of bacteria that are encrusted with a mineral rich in ferric ion and phosphate. The aim of this research was to determine the genetic diversity and phylogenetic affiliation of the biofilm bacteria. Also, the possible roles of the microorganisms in the processes of mineral deposition within the biofilm, as well as their impact on the biology of the bivalve, were assessed by phenotypic inference. The genetic diversity was determined by denaturing gradient gel electrophoresis (DGGE) analysis of short (193-bp) 16S ribosomal DNA PCR products obtained with primers specific for the domain Bacteria. This analysis revealed a diverse consortium; 11 to 25 sequence types were detected depending on the method of DNA extraction used. Individual biofilms analyzed by using the same DNA extraction protocol did not produce identical DGGE profiles. However, different biofilms shared common bands, suggesting that similar bacteria can be found in different biofilms. The phylogenetic affiliations of the sequence types were determined by cloning and sequencing the 16S rRNA genes. Close relatives of the genera Pseudoalteromonas, Colwellia, and Oceanospirillum (members of the γ-Proteobacteria lineage), as well as Flexibacter maritimus (a member of the Cytophaga-Flavobacter-Bacteroides lineage), were found in the biofilms. We inferred from the results that some of the biofilm bacteria could play a role in the mineral formation processes.

Fast Tree: Computing Large Minimum-Evolution Trees with Profiles instead of a Distance Matrix

Abstract: Gene families are growing rapidly, but standard methods for inferring phylogenies do not scale to alignments with over 10,000 sequences. We present FastTree, a method for constructing large phylogenies and for estimating their reliability. Instead of storing a distance matrix, FastTree stores sequence profiles of internal nodes in the tree. FastTree uses these profiles to implement neighbor-joining and uses heuristics to quickly identify candidate joins. FastTree then uses nearest-neighbor interchanges to reduce the length of the tree. For an alignment with N sequences, L sites, and a different characters, a distance matrix requires O(N^2) space and O(N^2 L) time, but FastTree requires just O( NLa + N sqrt(N) ) memory and O( N sqrt(N) log(N) L a ) time. To estimate the tree's reliability, FastTree uses local bootstrapping, which gives another 100-fold speedup over a distance matrix. For example, FastTree computed a tree and support values for 158,022 distinct 16S ribosomal RNAs in 17 hours and 2.4 gigabytes of memory. Just computing pairwise Jukes-Cantor distances and storing them, without inferring a tree or bootstrapping, would require 17 hours and 50 gigabytes of memory. In simulations, FastTree was slightly more accurate than neighbor joining, BIONJ, or FastME; on genuine alignments, FastTree's topologies had higher likelihoods. FastTree is available at http://microbesonline.org/fasttree.

Manganese- and Iron-Dependent Marine Methane Oxidation

Abstract: Anaerobic methanotrophs help regulate Earth’s climate and may have been an important part of the microbial ecosystem on the early Earth. The anaerobic oxidation of methane (AOM) is often thought of as a sulfate-dependent process, despite the fact that other electron acceptors are more energetically favorable. Here, we show that microorganisms from marine methane-seep sediment in the Eel River Basin in California are capable of using manganese (birnessite) and iron (ferrihydrite) to oxidize methane, revealing that marine AOM is coupled, either directly or indirectly, to a larger variety of oxidants than previously thought. Large amounts of manganese and iron are provided to oceans from rivers, indicating that manganese- and iron-dependent AOM have the potential to be globally important.