Elena Manini

Large Fraction of Dead and Inactive Bacteria in Coastal Marine Sediments: Comparison of Protocols for Determination and Ecological Significance

ABSTRACT It is now universally recognized that only a portion of aquatic bacteria is actively growing, but quantitative information on the fraction of living versus dormant or dead bacteria in marine sediments is completely lacking. We compared different protocols for the determination of the dead, dormant, and active bacterial fractions in two different marine sediments and at different depths into the sediment core. Bacterial counts ranged between (1.5 ± 0.2) × 108 cells g−1 and (53.1 ± 16.0) × 108 cells g−1 in sandy and muddy sediments, respectively. Bacteria displaying intact membrane (live bacterial cells) accounted for 26 to 30% of total bacterial counts, while dead cells represented the most abundant fraction (70 to 74%). Among living bacterial cells, nucleoid-containing cells represented only 4% of total bacterial counts, indicating that only a very limited fraction of bacterial assemblage was actively growing. Nucleoid-containing cells increased with increasing sediment organic content. The number of bacteria responsive to antibiotic treatment (direct viable count; range, 0.3 to 4.8% of the total bacterial number) was significantly lower than nucleoid-containing cell counts. An experiment of nutrient enrichment to stimulate a response of the dormant bacterial fraction determined a significant increase of nucleoid-containing cells. After nutrient enrichment, a large fraction of dormant bacteria (6 to 11% of the total bacterial number) was “reactivated.” Bacterial turnover rates estimated ranged from 0.01 to 0.1 day−1 but were 50 to 80 times higher when only the fraction of active bacteria was considered (on average 3.2 day−1). Our results suggest that the fraction of active bacteria in marine sediments is controlled by nutrient supply and availability and that their turnover rates are at least 1 order of magnitude higher than previously reported.

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.

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.

Benthic microbial loop functioning in coastal lagoons: a comparative approach

Abstract Coastal lagoons are highly variable and dynamic systems that have been rarely investigated in terms of benthic microbial loop. We present here the results of a comparative study aimed at investigating factors and benthic processes potentially affecting microbial loop functioning in three lagoon systems (Goro, Lesina and Marsala lagoons). The three lagoons were characterised by different geo-morphological, trophic and ecological features. We determined organic matter quantity and biochemical composition, exo-enzymatic activities, bacterial biomass and bacterial carbon production together with heterotrophic nanoflagellate and meiofauna biomass. These variables allowed providing estimates of biomass ratios between different benthic compartments and gathering information on C transfer in different systems. The results of this study indicate that organic matter composition played a primary role on microbial loop ability of channelling C-biomass to higher trophic levels. In coastal lagoons, indeed, quantity and quality of sediment organic matter control rates of organic matter degradation, turnover rates (through breakdown of large macromolecules) and utilisation by benthic heterotrophic organisms (bacterial C production). Exo-enzymatic activities in all lagoons investigated were generally low, when compared to coastal marine systems, and lowest rates were observed in systems characterised by refractory organic pools. Our results indicate that the autotrophic contribution to the biopolymeric carbon pools, which influences the ratio of autotrophic to heterotrophic biomass, is a key factor regulating the functional efficiency of the benthic system. The structure of the benthic microbial loop varied according to the different characteristics of the lagoons: from a classical “detritus sink” system (i.e., the Marsala lagoon, where organic matter was highly refractory), to the “source” system (Lesina lagoon, which displayed an efficient C transfer to higher trophic levels, mediated by benthic bacteria).

Trophic state, ecosystem efficiency and biodiversity of transitional aquatic ecosystems: analysis of environmental quality based on different benthic indicators

Estuaries and coastal lagoons are characterized by a strong spatial and temporal variability of physicochemical characteristics and productivity patterns. In these environments, the magnitude and direction of the ecological responses to inorganic nutrient increase (i.e. eutrophication) are difficult to predict. In the framework of the project, New Indicators of Trophic state and environmental quality of marine coastal ecosystems and transitional environments (NITIDA), we analysed benthic indicators of trophic state, ecosystem efficiency, and environmental quality in four different transitional environments. The trophic state of the sediments was assessed in terms of quantity and bioavailability of sediment organic C pools; ecosystem efficiency was determined in terms of the prokaryote efficiency in exploiting enzymatycally degraded organic C; environmental quality was determined in terms of meiofaunal diversity. Here, we provide a synopsis of the results obtained and a meta-analysis of the scores assessments obtained using the different ecological indicators of environmental quality and demonstrate that trophic state, ecosystem efficiency, and biodiversity in transitional ecosystems are closely linked. We conclude that the assessment of the environmental quality of transitional ecosystems should be based upon a battery of trophic state indicators and ‘sensors’ of ecosystem functioning, efficiency, and quality.

Short-Term Impact of Clam Harvesting on Sediment Chemistry, Benthic Microbes and Meiofauna in the Goro Lagoon (Italy)

The effects of clam harvesting on sediment organic matter, bacteria, heterotrophic nanoflagellates, ciliates and meiofauna were investigated through a short-term experiment carried out in the Goro lagoon during summer 2000. Sediment samples were collected in two areas: an impacted and an undisturbed (both 25 m2), before and after (5, 24 and 48 h) clam harvesting. Immediately after sediment reworking, total organic matter content decreased for about 20%. Different organic compounds displayed different redeposition patterns resulting in the alteration of the biochemical composition of sediment organic matter. Bacterial abundance decreased significantly after clam harvesting, but microbial enzymatic activities and bacterial C production were relatively unaffected. Heterotrophic nanoflagellates displayed a positive response to sediment disturbance, whereas ciliate and meiofaunal abundance did not display any significant response. Results of this short-term field experiment suggest that clam harvesting determines a positive impact on nutritional availability of sediment organic matter, thus facilitating organic carbon transfer to higher trophic levels of the benthic microbial loop.

Diversity and phylogenetic analyses of bacteria from a shallow-water hydrothermal vent in Milos island (Greece)

Studies of shallow-water hydrothermal vents have been lagging behind their deep-sea counterparts. Hence, the importance of these systems and their contribution to the local and regional diversity and biogeochemistry is unclear. This study analyzes the bacterial community along a transect at the shallow-water hydrothermal vent system of Milos island, Greece. The abundance and biomass of the prokaryotic community is comparable to areas not affected by hydrothermal activity and was, on average, 1.34 × 108 cells g−1. The abundance, biomass and diversity of the prokaryotic community increased with the distance from the center of the vent and appeared to be controlled by the temperature gradient rather than the trophic conditions. The retrieved 16S rRNA gene fragments matched sequences from a variety of geothermal environments, although the average similarity was low (94%), revealing previously undiscovered taxa. Epsilonproteobacteria constituted the majority of the population along the transect, with an average contribution to the total diversity of 60%. The larger cluster of 16S rRNA gene sequences was related to chemolithoautotrophic Sulfurovum spp., an Epsilonproteobacterium so far detected only at deep-sea hydrothermal vents. The presence of previously unknown lineages of Epsilonproteobacteria could be related to the abundance of organic matter in these systems, which may support alternative metabolic strategies to chemolithoautotrophy. The relative contribution of Gammaproteobacteria to the Milos microbial community increased along the transect as the distance from the center of the vent increased. Further attempts to isolate key species from these ecosystems will be critical to shed light on their evolution and ecology.

Shallow hydrothermal vents in the southern Tyrrhenian Sea

Shallow hydrothermal systems represent particularly suitable fields for studying the interactions between fluids and microorganisms inhabiting extreme environments. Coastal zones of the southern Tyrrhenian Sea are home to shallow hydrothermal systems, related to both active and extinct volcanism, located in the Flegrean area, at Cape Palinuro and around the Eolian Islands. A great diversity of Archaea and Bacteria has been reported at shallow hydrothermal vents, where they are key elements in ecosystem functioning. When compared with deep-sea locations, photosynthetic microorganisms appear to be the main characteristic of shallow hydrothermal vents, where both light and hydrothermal energy support a complex microbial community displaying primary productivity (phototrophic and chemotrophic) of mixed origin. Viriobenthos abundances are low compared with other shallow marine systems, suggesting that viruses are less tolerant than prokaryotes of high temperatures and consequently are believed to have a low impact on prokaryotic abundance and biodiversity. Microorganisms from shallow hydrothermal vents represent an almost unexploited resource for thermostable enzymes and biomolecules potentially valuable in biotechnology.

Benthic-pelagic coupling: effects on nematode communities along southern European continental margins.

Along a west-to-east axis spanning the Galicia Bank region (Iberian margin) and the Mediterranean basin, a reduction in surface primary productivity and in seafloor flux of particulate organic carbon was mirrored in the in situ organic matter quantity and quality within the underlying deep-sea sediments at different water depths (1200, 1900 and 3000 m). Nematode standing stock (abundance and biomass) and genus and trophic composition were investigated to evaluate downward benthic-pelagic coupling. The longitudinal decline in seafloor particulate organic carbon flux was reflected by a reduction in benthic phytopigment concentrations and nematode standing stock. An exception was the station sampled at the Galicia Bank seamount, where despite the maximal particulate organic carbon flux estimate, we observed reduced pigment levels and nematode standing stock. The strong hydrodynamic forcing at this station was believed to be the main cause of the local decoupling between pelagic and benthic processes. Besides a longitudinal cline in nematode standing stock, we noticed a west-to-east gradient in nematode genus and feeding type composition (owing to an increasing importance of predatory/scavenging nematodes with longitude) governed by potential proxies for food availability (percentage of nitrogen, organic carbon, and total organic matter). Within-station variability in generic composition was elevated in sediments with lower phytopigment concentrations. Standing stock appeared to be regulated by sedimentation rates and benthic environmental variables, whereas genus composition covaried only with benthic environmental variables. The coupling between deep-sea nematode assemblages and surface water processes evidenced in the present study suggests that it is likely that climate change will affect the composition and function of deep-sea nematodes.

Biogeochemistry, grain size and mineralogy of the central and southern Adriatic Sea sediments: a review

This review aims to present the current status of studies on geochemical (major minor and trace elements), biochemical (total organic carbon, total nitrogen, isotopic carbon composition, Bacteria, Archaea, phytopigments, proteins, carbohydrates, lipids, humic and fulvic acids), mineralogical (light and heavy minerals, clay minerals) and pollutant (trace metals, polycyclic aromatic hydrocarbons, polychlorinated biphenyls, pesticides, organic stannic compounds) parameters, grain-size composition and sediment–water interactions (early diagenesis and benthic fluxes) for the bottom sediments of the central and southern Adriatic Sea. The review highlighted gaps in or completeness of the parameters needed for research, of areas in which the parameters were investigated, as well as the interdisciplinary nature of the studies. In general, biogeochemical, mineralogical, grain-size and pollutant studies in the central and southern Adriatic Sea are restricted to limited areas, consider only single parameters without an interdisciplinary approach and, except for some more recent projects, are predominatly out of date. On the whole, there is a lack of an organised study concerning the various parameters for the entire central and southern Adriatic Sea and their evolution over time.