David Gillan

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

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 (Sørfjord). 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 (Σ7PCB < 7.0 ng g [dry weight]−1). The biomass ranged from 4.3 × 108 to 13.4 × 108 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 γ- and δ-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 γ-Proteobacteria and CFB bacteria. δ-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.

Co-occurrence of integrase 1, antibiotic and heavy metal resistance genes in municipal wastewater treatment plants.

The impact of human activities on the spread and on the persistence of antibiotic resistances in the environment is still far from being understood. The natural background of resistances is influenced by human activities, and the wastewater treatment plants (WWTPs) are among the main sources of the release of antibiotic resistance into the environment. The various treatments of WWTPs provide a number of different environmental conditions potentially favoring the selection of antibiotic resistance genes (ARGs) and thereby their well-documented spread in the environment. Although the distribution of different ARGs in WWTPs has been deeply investigated, very little is known on the ecology and on the molecular mechanisms underlying the selection of specific ARGs. This study investigates the fate of diverse ARGs, heavy metal resistance genes (HMRGs) and of a mobile element (the class I integron) in three WWTPs. Abundances of the different genetic markers were correlated to each other and their relation to biotic and abiotic factors (total organic carbon, total nitrogen, prokaryotic cell abundance and its relative distribution in single cells and aggregates) influencing the microbial communities in the different treatment phases in three WWTPs, were investigated. Water samples were analyzed for the abundance of six ARGs (tetA, sulII, blaTEM, blaCTXM,ermB, and qnrS), two HMRGs (czcA and arsB), and of the class I integron (int1). The measured variables clustered in two well-defined groups, the first including tetA, ermB, qnrS and the different biotic and abiotic factors, and a second group around the genes sulII, czcA, arsB and int1. Moreover, the dynamics of sulII, HMRGs, and int1 correlated strongly. Our results suggest a potentially crucial role of HMRGs in the spread, mediated by mobile elements, of some ARGs, i.e. sulII. The possibility of a relation between heavy metal contamination and the spread of ARGs in WWTPs calls for further research to clarify the mechanisms of co-selection and their ecology, in order to implement the removal efficiency of the applied treatments.

Adherent bacteria in heavy metal contaminated marine sediments

Abstract The eubacterial communities adherent to sediment particles were studied in heavy metal contaminated coastal sediments. Six sampling sites on the Belgian continental plate and presenting various metal loads, granulometries, and organic matter content, were compared. The results indicated that the total microbial biomass (attached + free-living bacteria) was negatively correlated to HCl-extractable metal levels (p < 0.05) and that the percentage of cells adherent to sediment particles was close to 100% in every site even in highly contaminated sediments. Consequently, it seems that heavy metal contamination does affect total bacterial biomass in marine sediments but that the ratio between attached and free living microorganisms is not affected. The composition of the eubacterial communities adherent to the fine fraction of the sediments (<150 µm) was determined using fluorescent in situ hybridisation (FISH). The FISH results indicated that the proportion of γ- and δ-Proteobacteria, and Cytophaga-Flexibacter-Bacteroides (CFB) bacteria, was not related to the HCl extractable metal levels. Most of the 79 complete 16S rRNA sequences obtained from the attached microbial communities were classified in the γ- and δ-Proteobacteria and in the CFB bacteria. A large proportion of the attached γ-Proteobacterial sequences found in this study (56%) was included in the uncultivated GMS clades that are indigenous to marine sediments.

Bacterial metal resistance genes and metal bioavailability in contaminated sediments.

In bacteria a metal may be defined as bioavailable if it crosses the cytoplasmic membrane to reach the cytoplasm. Once inside the cell, specific metal resistance systems may be triggered. In this research, specific metal resistance genes were used to estimate metal bioavailability in sediment microbial communities. Gene levels were measured by quantitative PCR and correlated to metals in sediments using five different protocols to estimate dissolved, particle-adsorbed and occluded metals. The best correlations were obtained with czcA (a Cd/Zn/Co efflux pump) and Cd/Zn adsorbed or occluded in particles. Only adsorbed Co was correlated to czcA levels. We concluded that the measurement of czcA gene levels by quantitative PCR is a promising tool which may complement the classical approaches used to estimate Cd/Zn/Co bioavailability in sediment compartments.

Iron microbial communities in Belgian Frasnian carbonate mounds

SummaryThe Belgian Frasnian carbonate mounds occur in three stratigraphic levels in an overall backstepping succession. Petit-Mont and Arche Members form the famous red and grey “marble” exploited for ornamental stone since Roman times. The evolution and distribution of the facies in the mounds is thought to be associated with ecologic evolution and relative sea-level fluctuations. Iron oxides exist in five forms in the Frasnian mounds; four are undoubtedly endobiotic organized structures: (1) microstromatolites and associated forms (blisters, veils...), possibly organized in “endostromatolites”; (2) hematitic coccoids and (3) non dichotomic filaments. The filaments resemble iron bacteria of theSphaerotilus-Leptothrix “group”; (4) networks of dichotomic filaments ascribable to fungi; (5) a red ferruginous pigment dispersed in the calcareous matrix whose distribution is related to the mound facies type. The endobiotic forms developed during the edification of the mounds, before cementation by fibrous calcite. The microbial precipitation of iron took place as long as the developing mounds were bathed by water impoverished in oxygen.

Validation of the asteroid Asterias rubens (Echinodermata) as a bioindicator of spatial and temporal trends of Pb, Cd, and Zn contamination in the field

The aim of the present study was to assess the value of Asterias rubens as a bioindicator of metal contamination in the field. Spatial gradients of Pb, Cd, and Zn contamination were identified along Sorfjord, and metal concentrations were consistently higher (1.7–8.3 times) in the body compartments of large asteroids sampled close to the smelters than in those sampled further away. Cd and Pb concentrations in the pyloric caeca varied along the fjord according to a decreasing sigmoidal relationship, while Cd and Pb concentrations in the body wall and the skeleton varied according to a decreasing exponential relationship. This suggests that the bioavailability of these metals has decreased over the last few years at the head of the fjord, which agrees generally with water chemistry data available from the State Pollution Monitoring Programme (Norway). The decrease in metal bioavailability could be a direct consequence of the 1992 remedial action taken in the fjord to reduce heavy metal release from the contaminated sediments. Lead concentrations in the skeletons of large asteroids (12–14cm; 154 ± 63 μg Pb g−1 dry wt) were eight times higher than those in the skeletons of juvenile individuals (0.5–4 cm; 19 ± 8 μg Pb g−1 dry wt) in the population located at the head of the fjord. Asteroids of 12–14 cm length were likely to be 4–7 y old (i.e. born before the remedial action) while small asteroids were born after the remedial action. According to comparisons with allometric relationships in an uncontaminated population and experimental exposures, results indicate that the half-life of Pb in the skeleton is long (i.e. several years) while the half-life of Cd and Zn is much shorter (i.e. several weeks for Cd, and short but not precisely known for Zn). A smaller size and unusual reduction of the skeleton of adult individuals at the head of the fjord were observed and may result from the effects of heavy metal pollution. A comparison between possible sources of contamination in the fjord (metals in water, food, and sediments) indicates that sediment-associated metals are likely to be an important source of contamination in this environment due to the microphagic activity of asteroids.

The long-term adaptation of bacterial communities in metal-contaminated sediments: a metaproteogenomic study

The aim of the study was to understand the effect of a long-term metal exposure (110 years) on sediment microbial communities. Two freshwater sites, Férin and MetalEurop, differing by one order of magnitude in metal levels (MetalEurop: 3218 mg Zn kg(-1) ; 913 mg Pb kg(-1) ) were compared by shotgun metaproteogenomics. A total of 69-118 Mpb of DNA and 943-1241 proteins were obtained. PhymmBL analysis of the DNA sequences indicated that the phylogenetic profile was similar in both stations and that β-Proteobacteria were dominant. However, subtle but significant changes were observed for some bacteria: e.g. Pseudomonas (+0.4%), Leptothrix (-0.4%), Thiobacillus (+0.36%) and Acidovorax (+0.48%). Using the stamp software, the two communities were found to be functionally very similar. However, significant genetic differences (10(-6)  < P < 10(-3) ) were observed for three SEED categories: synthesis of exopolymeric substances, virulence and defence mechanisms (including czcA metal efflux genes), and elements involved in horizontal gene transfer. The CzcA protein was found by metaproteomics in MetalEurop, but the levels were too low to allow comparisons. It is concluded that bacterial communities in freshwater sediments may adapt to high metal levels without broad changes in the structure of the population.

Novel epibiotic Thiothrix bacterium on a marine amphipod

ABSTRACT Comparative analysis of the 16S rRNA gene and fluorescent in situ hybridization (FISH) was used to identify epibiotic filamentous bacteria living on the marine amphipod crustacean Urothoe poseidonis. The epibionts belong to the gamma proteobacteria and represent a novel marine phylotype within the genus Thiothrix. FISH and denaturing gradient gel electrophoresis revealed that the Thiothrix filaments are present on the majority of the amphipods examined.

Field contamination of the starfish Asterias rubens by metals. Part 2: Effects on cellular immunity.

To study the effects of metals on starfish in field conditions, immune responses were measured in starfish from natural populations along a metal pollution gradient (long-term contamination) and in starfish that were transferred up the gradient (short-term contamination). Coelomic amoebocyte concentration (CAC) and production of reactive oxygen species (ROS) by amoebocytes were measured in two varieties of Asterias rubens occurring in the fjord: The black variety which lives only in the low salinity upper waters (22-26/1000) and the red variety which live both in the upper layer and in the deeper layer characterized by a salinity close to that of seawater (30/1000). The studied immune responses were stimulated in starfish living along the metal pollution gradient according to the contamination of these starfish by cadmium. However, the sensitivity of these responses toward metals appeared to be strongly modulated by the salinity stress. In red starfish living at 30/1000 and transferred up the contamination gradient, the immune responses were inhibited and closely followed the short-term accumulation of metals in the animal organs. Starfish transferred down the gradient did not recover normal immune responses in the short-term and appeared highly sensitive to caging stress. It is suggested that the impact of metals on the immune responses of A. rubens in field conditions occurs in three phases. Short-term inhibitory effects are exerted by a direct action of metals on the immune cells and are followed by a recovery due to the induction of protective mechanisms. Eventually, when these mechanisms are overwhelmed by a long-term contamination, indirect and durable stimulatory effects on the immune responses appear due to a global disruption of the animal physiology.