Antonio Dell'Anno

Major viral impact on the functioning of benthic deep-sea ecosystems

Viruses are the most abundant biological organisms of the world’s oceans. Viral infections are a substantial source of mortality in a range of organisms—including autotrophic and heterotrophic plankton—but their impact on the deep ocean and benthic biosphere is completely unknown. Here we report that viral production in deep-sea benthic ecosystems worldwide is extremely high, and that viral infections are responsible for the abatement of 80% of prokaryotic heterotrophic production. Virus-induced prokaryotic mortality increases with increasing water depth, and beneath a depth of 1,000 m nearly all of the prokaryotic heterotrophic production is transformed into organic detritus. The viral shunt, releasing on a global scale ∼0.37–0.63 gigatonnes of carbon per year, is an essential source of labile organic detritus in the deep-sea ecosystems. This process sustains a high prokaryotic biomass and provides an important contribution to prokaryotic metabolism, allowing the system to cope with the severe organic resource limitation of deep-sea ecosystems. Our results indicate that viruses have an important role in global biogeochemical cycles, in deep-sea metabolism and the overall functioning of the largest ecosystem of our biosphere.

Determination of virus abundance in marine sediments

ABSTRACT In this study, we optimized procedures to enumerate viruses from marine sediments by epifluorescence microscopy using SYBR Green I as a stain. The highest virus yields from the bulk of the sediments were obtained by utilizing pyrophosphate and 3 min of sonication. The efficiency of extraction benthic viruses by pyrophosphate-ultrasound treatment was about 60% of the extractable virus particles. Samples treated with nucleases had increased virus counts, suggesting a masking effect of extracellular DNA. No significant differences were observed between virus counts obtained by epifluorescence microscopy and transmission electron microscopy. Both formaldehyde and glutaraldehyde gave significant reductions of virus counts after only 24 h of sediment storage, but no further loss occurred after 7 days.

Comparison of Two Fingerprinting Techniques, Terminal Restriction Fragment Length Polymorphism and Automated Ribosomal Intergenic Spacer Analysis, for Determination of Bacterial Diversity in Aquatic Environments

ABSTRACT We investigated bacterial diversity in different aquatic environments (including marine and lagoon sediments, coastal seawater, and groundwater), and we compared two fingerprinting techniques (terminal restriction fragment length polymorphism [T-RFLP] and automated ribosomal intergenic spacer analysis [ARISA]) which are currently utilized for estimating richness and community composition. Bacterial diversity ranged from 27 to 99 phylotypes (on average, 56) using the T-RFLP approach and from 62 to 101 genotypes (on average, 81) when the same samples were analyzed using ARISA. The total diversity encountered in all matrices analyzed was 144 phylotypes for T-RFLP and 200 genotypes for ARISA. Although the two techniques provided similar results in the analysis of community structure, bacterial richness and diversity estimates were significantly higher using ARISA. These findings suggest that ARISA is more effective than T-RFLP in detecting the presence of bacterial taxa accounting for <5% of total amplified product. ARISA enabled also distinction among aquatic bacterial isolates of Pseudomonas spp. which were indistinguishable using T-RFLP analysis. Overall, the results of this study show that ARISA is more accurate than T-RFLP analysis on the 16S rRNA gene for estimating the biodiversity of aquatic bacterial assemblages.

Higher Abundance of Bacteria than of Viruses in Deep Mediterranean Sediments

ABSTRACT The interactions between viral abundance and bacterial density, biomass, and production were investigated along a longitudinal transect consisting of nine deep-sea stations encompassing the entire Mediterranean basin. The numbers of viruses were very low (range, 3.6 × 107 to 12.0 × 107 viruses g−1) and decreased eastward. The virus-to-bacterium ratio was always < 1.0, indicating that the deep-sea sediments of the Mediterranean Sea are the first example of a marine ecosystem not numerically dominated by viruses. The lowest virus numbers were found where the lowest bacterial metabolism and turnover rates and the largest cell size were observed, suggesting that bacterial doubling time might play an important role in benthic virus development.

Deep-sea ecosystem response to climate changes: the eastern Mediterranean case study

Abstract Climate change is significantly modifying ecosystem functioning on a global scale, but little is known about the response of deep-sea ecosystems to such change. In the past decade, extensive climate change has modified the physico–chemical characteristics of deep waters in the eastern Mediterranean. Climate change has caused an immediate accumulation of organic matter on the deep-sea floor, altered the carbon and nitrogen cycles and has had negative effects on deep-sea bacteria and benthic fauna. Evidence from a miniature ocean model provides new ways of interpreting signals from the deep sea and indicates that, contrary to what might have been expected, deep-sea ecosystems do respond quickly to climate change.

Enzymatically hydrolyzable protein and carbohydrate sedimentary pools as indicators of the trophic state of detritus sink systems: A case study in a Mediterranean coastal lagoon

In order to classify the trophic state of detritus sink systems, instead of the conventional indicators based on inorganic nutrient availability and algal biomass and productivity in the water column, we used new biochemical descriptors based on the amount of sedimentary organic carbon (C) and nitrogen (N) potentially available to heterotrophs. We investigated spatial and temporal changes in microphytobenthic biomass, organic matter biochemical composition, and enzymatically hydrolyzable protein and carbohydrate pools along a north-south transect in the Marsala lagoon (Mediterranean Sea, Italy) at three stations characterized by different hydrodynamic conditions and organic matter content in the sediment. In the Marsala lagoon water currents decreased from north to south and this pattern was reflected by organic matter distribution and composition. Sediment organic matter concentrations were among the highest reported in the literature and, in the central area where large meadows of the seagrassPosidonia oceanica were present, display a strong dominance of highly refractory carbohydrates. The protein to carbohydrate ratio was always < 1, indicating the dominance of aged organic detritus. Microphytobenthic biomass displayed an increasing pattern southward, and its contribution to the biopolymeric C pools ranged from negligible in the central sector of the lagoon to 50% in its northern part, indicating that sources of sediment organic C also changed along the hydrodynamic gradient. The percentage contribution of the enzymatically hydrolyzable fraction of proteins and carbohydrates was inversely related to total protein and total carbohydrate concentrations, respectively, suggesting that bioavailability of organic C and N increased with decreasing organic matter content in the sediment and with increasing hydrodynamic regime. Microphytobenthic contribution to biopolymeric C (as a proxy of autotrophic organic C) and the ratio of the enzymatically digestible fraction to biopolymeric C (as an indicator of organic matter liability) were significantly correlated, suggesting that chlorophylla sediment content might be used as an indicator of food promptly available to consumers. The present study also highlighted that the ratio of labile (i.e., enzymatically digestible) versus biopolymeric organic C in the sediments tends to decrease with increasing organic matter content, due to the increase of the refractory fraction of organic C.

Degradation and Turnover of Extracellular DNA in Marine Sediments: Ecological and Methodological Considerations

ABSTRACT Degradation rates of extracellular DNA determined in marine sediments were much higher than those in the water column. However, due to the high sediment DNA content, turnover times were much shorter in seawater. Results reported here provide new insights into the role of extracellular DNA in P cycling in marine ecosystems.

Organic matter composition of the continental shelf and bathyal sediments of the Cretan Sea (NE Mediterranean)

Abstract The seasonal, spatial and bathymetric changes in the distribution of chloroplastic pigments (Chl a, phaeopigments and CPE), TOC, TON, ATP, bottom water nutrient content and the main biochemical classes of organic compounds (lipids, proteins and carbohydrates) were recorded from May 1994 to September 1995 over the continental margin of northern Crete. The concentration of chloroplastic pigment equivalents (CPE) was always low, dropping dramatically along the shelf-slope gradient. Microbial activity (ATP) also dropped sharply beyond the continental shelf following a distribution pattern similar to TOC and TON. Lipid, protein and carbohydrate concentrations, as well as biopolymeric carbon were comparable to those reported for other more productive areas, however, the quality of the organic matter itself was rather poor. Thus, carbohydrates, the dominant biochemical class, were characterised by being highly (80–99%) refractory, as soluble carbohydrates represented (on annual average) only 6% of the total carbohydrate pool. Protein and lipid concentrations strongly decreased with depth, indicating depletion of trophic resources in the bathyal zone. Proteins appeared to be the more degradable compounds and indeed the protein to carbohydrate ratios were found to decrease strongly in the deeper stations. Organic matter content and quality decreased both with increasing distance from the coast and within the sediment. All sedimentary organic compounds were found to vary between sampling periods, with the changes being more pronounced over the continental shelf. The different temporal patterns of the various components suggest a different composition and/or origin of the OM inputs during the different sampling periods. The amount of material reaching the sediments below 540 m is extremely low, suggesting that most of the organic material is decomposed and/or utilised before reaching the sea floor. In conclusion, the continental shelf and bathyal sediments of the Cretan Sea can be considered, from a trophic point of view, as two different subsystems.

Heterotrophic nanoflagellates, bacteria, and labile organic compounds in continental shelf and deep-sea sediments of the Eastern Mediterranean

A bstractThe abundance and biomass of heterotrophic nanoflagellates were examined in continental and deep-sea sediments of the Cretan Sea (Eastern Mediterranean); at depths of 40 to 1540 m. Nanoflagellate distribution was compared to the composition of sedimentary organic matter and bacterial standing stocks to investigate trophic interactions and factors potentially affecting distribution. Quantitative estimates were obtained using different samplers for testing whether the box corer is as effective as the multiplecorer for bacterial and protozoan population estimates. The sediments of the deep Cretan Sea appeared extremely deficient in organic nutrients, and were composed mostly (more than 90%) of detritus. Labile organic compounds (such as lipids, proteins, and soluble carbohydrates) were present at extremely low concentrations, decreasing with water depth. Refractory and structural carbohydrates were the dominant biochemical class. The decrease in food quality with depth was associated with a strong decline of the RNA:DNA ratio. Benthic bacteria were constrained by food availability, and reacted to different organic matter inputs (especially total carbohydrates) at different depths. Large size bacteria were significantly correlated with the amounts of proteins and chloroplastic pigments. Heterotrophic nanoflagellate distribution in the continental shelf and deep-sea sediments of the Cretan Sea was controlled by available food sources (i.e., labile organic compounds and bacteria). Flagellate density was significantly correlated with the concentration of food indicators (chlorophyll a, soluble carbohydrates, and lipids), and to bacterial number and biomass. Despite the oligotrophy of the system, flagellate densities were high (40–119 × 103 g−1) and dominated by small cells (3 to 6 μm in length). These results, coupled with the high nanoflagellate to bacterial biomass ratio (up to 0.27 at 40 m depth), suggest that benthic nanoflagellates may contribute significantly to the direct transfer of detrital carbon and bacterial biomass to the metazoan component of the food web in the Cretan Sea.

Organic matter composition in coastal sediments at Terra Nova Bay (Ross Sea) during summer 1995

Abstract We illustrate the spatial and vertical distribution of sediment phytopigments and organic matter biochemical composition at Terra Nova Bay (Ross Sea) during summer 1995. Coastal sediments displayed high phytopigments concentrations associated with huge amounts of labile organic matter largely dominated by proteins. This result was opposite to previous observations in the same area. Such comparison suggested that whilst organic matter quantity in the sediments depended upon the vertical input from the water column, temporal changes in its biochemical composition were related to benthic processes. As considerably high concentrations of biopolymeric organic carbon were found even at 6-cm depth and according to the “loss type” functioning of the coastal waters of the Ross Sea, we stress the summer time occurrence in coastal sediments of an important organic matter burial.