Linking Microbial Functioning and Trophic Pathways to Ecological Status in a Coastal Mediterranean Ecosystem

Coastal marine ecosystems host complex microbial communities whose composition and metabolism are influenced by continental inputs and mesoscale properties of seawater masses. The identifying traits of the phytoplankton and bacteria such as biomass, size, shape and their metabolism related to organic matter production and degradation, recognized as indicators of the functioning of an ecosystem, were observed in the Gulf of Manfredonia (South Adriatic Sea, Italy) in late spring. This Gulf area is characterized by terrestrial inputs and mesoscale circulation influence such as coastal waters flowing southward from the North Adriatic and offshore waters interested by the Ionian Sea. Water samples were grouped in clusters (Coastal, Intermediate, Offshore and Deep Systems) according to the water column properties. Phytoplankton community biomass and composition, autotrophic and total prokaryotic abundances and microbial metabolism such as enzyme activity rates and prokaryotic heterotrophic production were analyzed to elucidate the trophic pathways with the objective to infer on the ecosystem status. As expected, size-fractionated phytoplankton biomass and production showed greater concentration in coastal waters with prevalence of the largest fractions (micro- and nano-) supported by the diatoms. Conversely, lower biomass and production were measured in all off-shore waters, mainly sustained by smallest fractions (nano-sized phytoflagellates and picophytoplankton). Total and autotrophic prokaryotic abundance decreased from coastal to offshore stations, inversely with respect to cell volume. Prokaryotic heterotrophic production was just below 50% compared to that of phytoplankton in all waters, evidencing an active biomass synthesis. High alkaline phosphatase and leucine aminopeptidase in coastal and offshore waters suggested the quick regeneration of Phosphorus and protein decomposition, respectively. Different levels of phytoplankton-bacteria association might provide a tool to define the ecological status of the studied system in the observed period; an approach to ecosystem assessment exportable to other coastal systems is proposed

Linking Microbial Functioning and Trophic Pathways to Ecological Status in a Coastal Mediterranean Ecosystem

Coastal marine ecosystems host complex microbial communities whose composition and metabolism are influenced by continental inputs and mesoscale properties of seawater masses. The identifying traits of the phytoplankton and bacteria such as biomass, size, shape and their metabolism related to organic matter production and degradation, recognized as indicators of the functioning of an ecosystem, were observed in the Gulf of Manfredonia (South Adriatic Sea, Italy) in late spring. This Gulf area is characterized by terrestrial inputs and mesoscale circulation influence such as coastal waters flowing southward from the North Adriatic and offshore waters interested by the Ionian Sea. Water samples were grouped in clusters (Coastal, Intermediate, Offshore and Deep Systems) according to the water column properties. Phytoplankton community biomass and composition, autotrophic and total prokaryotic abundances and microbial metabolism such as enzyme activity rates and prokaryotic heterotrophic production were analyzed to elucidate the trophic pathways with the objective to infer on the ecosystem status. As expected, size-fractionated phytoplankton biomass and production showed greater concentration in coastal waters with prevalence of the largest fractions (micro- and nano-) supported by the diatoms. Conversely, lower biomass and production were measured in all off-shore waters, mainly sustained by smallest fractions (nano-sized phytoflagellates and picophytoplankton). Total and autotrophic prokaryotic abundance decreased from coastal to offshore stations, inversely with respect to cell volume. Prokaryotic heterotrophic production was just below 50% compared to that of phytoplankton in all waters, evidencing an active biomass synthesis. High alkaline phosphatase and leucine aminopeptidase in coastal and offshore waters suggested the quick regeneration of Phosphorus and protein decomposition, respectively. Different levels of phytoplankton-bacteria association might provide a tool to define the ecological status of the studied system in the observed period; an approach to ecosystem assessment exportable to other coastal systems is proposed

Alternative Strategies for ICZM: an intelligent monitoring database

This document reports the SPICOSA-FP6 project work package 10 "Alternative Strategies” years 2010-2011 activity and particularly of the Work Task “Intelligent Monitoring”. We report the results of the experience collected dialoguing with the SPICOSA study sites in which, a new methodology, the System Approach Framework (SAF) has been tested, and where an intelligent monitoring database has been developed analyzing the issues and the impacts related to system modelling for Integrated Coastal Zone Management (ICZM). For more information and readings on “System Approach Framework-SAF” and on the "Alternative Strategies" please see the SPICOSA website (www.spicosa.eu)

Sensitivity analysis of CDOM spectral slope in artificialand natural samples: an application in the central easternMediterranean Basin

In the past two decades, optical properties of chromophoric dissolved organic matter (CDOM) in marine environments have been extensively studied. Many of these studies report CDOM properties for the offshore environment where this complex mixture of optically active compounds is strongly diluted. Nevertheless, autochthonous and allochthonous sources have been identified and sinks related to photodegradation and bacterial activity have been demonstrated. The calculation of the spectral slope of the CDOM absorption curve has been proven to be useful and is often reported. However, a rigorous uncertainty analysis of the slope calculation is rarely reported. In this paper, we propose a method to evaluate the uncertainty of CDOM spectral slope calculated between 270 and 400 nm, using both naturally sampled and artificial solutions. We use these results to study the ultra-oligotrophic waters of the Mediterranean Sea (central eastern basin), where little is known about CDOM spatial distribution. We show that dilutions of both artificial and natural samples produce a Gaussian distribution of spectral slopes, indicating that consistent values may be determined, with a typical uncertainty of ±0.0004 nm-1 when absorption at 300 nm was greater then 0.1 m-1 (0.1 m pathlength). Comparing the distribution of spectral slopes from central eastern basin samples to a Gaussian distribution, we show differences between measurements that were significantly different. These values allow us to distinguish possible sources (algal derived CDOM), sinks (e.g. photo-bleaching) at different depths. We propose a subdivision of CDOM compounds into refractory and semilabile/refractory pools and evaluate the CDOM spectral slope of algal derived CDOM released at or near deep chlorophyll maximum

The dark portion of the Mediterranean Sea is a bioreactor of organic matter cycling

Total prokaryotic abundance, prokaryotic heterotrophic production and enzymatic activities were investigated in epi-, meso- and bathypelagic waters along a longitudinal transect covering the entire Mediterranean Sea. The prokaryotic production and enzymatic activities in deep waters were among the highest reported worldwide at similar depths, indicating that the peculiar physico-chemical characteristics of the Mediterranean Sea, characterized by warm temperatures (typically 13°C also at abyssal depths), support high rates of organic carbon degradation and incorporation by prokaryotic assemblages. The higher trophic conditions in the epipelagic waters of the Western basin resulted in significantly higher prokaryotic production and enzymatic activities rates than in the Central-Eastern basin. While all of the variables decreased significantly from epi- to meso- and bathypelagic waters, cell-specific hydrolytic activity and cell-specific carbon production significantly increased. In addition, the deep-water layers were characterised by low half-saturation constants (Km) of all enzymatic activities. These findings suggest that prokaryotic assemblages inhabiting the dark portion of the Mediterranean Sea are able to channel degraded carbon into biomass in a very efficient way, and that prokaryotic assemblages of the deep Mediterranean waters work as a “bioreactor” of organic matter cycling. Since prokaryotic production and enzymatic activities in deep water masses were inversely related with oxygen concentration, we hypothesise a tight link between prokaryotic metabolism and oxygen consumption. As climate change is increasing deep-water temperatures, the predicted positive response of prokaryotic metabolism to temperature increases may accelerate oxygen depletion of deep Mediterranean waters, with cascade consequences on carbon cycling and biogeochemical processes on the entire deep basin

All-In-One: Microbial Response to Natural and Anthropogenic Forcings in a Coastal Mediterranean Ecosystem, the Syracuse Bay (Ionian Sea, Italy)

Bacterial and phytoplankton communities are known to be in close relationships, but how natural and anthropogenic stressors can affect their dynamics is not fully understood. To study the response of microbial communities to environmental and human-induced perturbations, phytoplankton and bacterial communities were seasonally monitored in a Mediterranean coastal ecosystem, Syracuse Bay, where multiple conflicts co-exist. Quali-quantitative, seasonal surveys of the phytoplankton communities (diatoms, dinoflagellates and other taxa), the potential microbial enzymatic activity rates (leucine aminopeptidase, beta-glucosidase and alkaline phosphatase) and heterotrophic culturable bacterial abundance, together with the thermohaline structure and trophic status in terms of nutrient concentrations, phytoplankton biomass (as Chlorophyll-a), and total suspended and particulate organic matter, were carried out. The aim was to integrate microbial community dynamics in the context of the environmental characterization and disentangle microbial patterns related to natural changes from those driven by the anthropic impact on this ecosystem. In spite of the complex relationships between the habitat characteristics, microbial community abundance and metabolic potential, in Syracuse Bay, the availability of organic substrates differently originated by the local conditions appeared to drive the distribution and activity of microbial assemblage. A seasonal pattern of microbial abundances was observed, with the highest concentrations of phytoplankton in spring and low values in winter, whereas heterotrophic bacteria were more abundant during the autumn period. The autumn peaks of the rates of enzymatic activities suggested that not only phytoplankton-derived but also allochthonous organic polymers strongly stimulated microbial metabolism. Increased microbial response in terms of abundance and metabolic activities was detected especially at the sites directly affected by organic matter inputs related to agriculture or aquaculture activities. Nitrogen salts such as nitrate, rather than orthophosphate, were primary drivers of phytoplankton growth. This study also provides insights on the different seasonal scenarios of water quality in Syracuse Bay, which could be helpful for management plans of this Mediterranean coastal environment

Microbial Abundance and Enzyme Activity Patterns: Response to Changing Environmental Characteristics along a Transect in Kongsfjorden (Svalbard Islands)

Svalbard archipelago is experiencing the effects of climate changes (i.e., glaciers’ thickness reduction and glacier front retreat), but how ice melting affects water biogeochemistry is still unknown. Microbial communities often act as environmental sentinels, modulating their distribution and activity in response to environmental variability. To assess microbial response to climate warming, within the ARctic: present Climatic change and pAst extreme events (ARCA) project, a survey was carried out along a transect in Konsfjorden from off-shore stations towards the Kronebreen glacier. Total bacterial abundance and the fraction of actively respiring cells (labelled by cyanotetrazolium chloride, CTC), cultivable heterotrophic bacterial abundance, and extracellular enzymatic activities (leucine aminopeptidase (LAP), beta-glucosidase (GLU), and alkaline phosphatase (AP)) were measured. In addition, water temperature, salinity, dissolved oxygen, turbidity, total suspended matter (TSM), particulate and chromophoric dissolved organic matter (CDOM), chlorophyll-a (Chl-a), and inorganic compounds were determined, in order to evaluate whether variations in microbial abundance and metabolism were related with changes in environmental variables. Colder waters at surface (3.5–5 m) depths and increased turbidity, TSM, and inorganic compounds found at some hydrological stations close to the glacier were signals of ice melting. CDOM absorption slope values (275–295 nm) varied from 0.0077 to 0.0109 nm−1, and total bacterial cell count and cultivable heterotrophic bacterial abundance were in the order of 106 cells/mL and 103 colony forming units/mL, respectively. Enzymatic rates <1.78, 1.25, and 0.25 nmol/L/h were recorded for AP, LAP, and GLU, respectively. Inorganic compounds, TSM, and turbidity correlated inversely with temperature; AP was significantly related with CDOM absorption spectra and heterotrophic bacteria (r = 0.59, 0.71, p < 0.05); and LAP with Chl-a, Particulate Organic Carbon (POC) and Particulate Organic Nitrogen (PON) (0.97, 0.780, 0.734, p < 0.01), suggesting that fresh material from ice melting stimulated the metabolism of the cultivable fraction

Heterotrophic bicarbonate assimilation is the main process of de novo organic carbon synthesis in hadal zone of the Hellenic Trench, the deepest part of Mediterranean Sea

Ammonium‐oxidizing chemoautotrophic members of Thaumarchaea are proposed to be the key players in the assimilation of bicarbonate in the dark (ABD). However, this process may also involve heterotrophic metabolic pathways, such as fixation of carbon dioxide (CO2) via various anaplerotic reactions. We collected samples from the depth of 4900 m at the Matapan‐Vavilov Deep (MVD) station (Hellenic Trench, Eastern Mediterranean) and used the multiphasic approach to study the ABD mediators in this deep‐sea ecosystem. At this depth, our analysis indicated the occurrence of actively CO2‐fixing heterotrophic microbial assemblages dominated by Gammaproteobacteria with virtually no Thaumarchaea present. [14C]‐bicarbonate incorporation experiments combined with shotgun [14C]‐proteomic analysis identified a series of proteins of gammaproteobacterial origin. More than quarter of them were closely related with Alteromonas macleodii ‘deep ecotype’ AltDE, the predominant organism in the microbial community of MVD. The present study demonstrated that in the aphotic/hadal zone of the Mediterranean Sea, the assimilation of bicarbonate is associated with both chemolithoauto‐ and heterotrophic ABD. In some deep‐sea areas, the latter may predominantly contribute to the de novo synthesis of organic carbon which points at the important and yet underestimated role heterotrophic bacterial populations can play the in global carbon cycle/sink in the ocean interior.This work wasdone; thanks to financial support of CNR in the frame ofESF Project 09-EuroEEFGFP-044 Deep_C; funds obtainedin the frame of EU Projects FP7-KBBE-2009-2B-226977 MAMBA, FP7-OCEAN.2011-2-287589 MICROB3 and in the frames of Italian National project FIRB 2008 EXPLODIVERBFR08AWP6_002; and funds of grant BIO2011–25012 from the Spanish Ministry of Economy and Competitiveness(formerly MICINN).Peer Reviewe

Contribution of Bicarbonate Assimilation to Carbon Pool Dynamics in the Deep Mediterranean Sea and Cultivation of Actively Nitrifying and CO2-Fixing Bathypelagic Prokaryotic Consortia

Covering two-thirds of our planet, the global deep ocean plays a central role in supporting life on Earth. Among other processes, this biggest ecosystem buffers the rise of atmospheric CO2. Despite carbon sequestration in the deep ocean has been known for a long time, microbial activity in the meso- and bathypelagic realm via the “assimilation of bicarbonate in the dark” (ABD) has only recently been described in more details. Based on recent findings, this process seems primarily the result of chemosynthetic and anaplerotic reactions driven by different groups of deep-sea prokaryoplankton. We quantified bicarbonate assimilation in relation to total prokaryotic abundance, prokaryotic heterotrophic production and respiration in the meso- and bathypelagic Mediterranean Sea. The measured ABD values, ranging from 133 to 370 μg C m−3 d−1, were among the highest ones reported worldwide for similar depths, likely due to the elevated temperature of the deep Mediterranean Sea (13–14°C also at abyssal depths). Integrated over the dark water column (≥200 m depth), bicarbonate assimilation in the deep-sea ranged from 396 to 873 mg C m−2 d−1. This quantity of produced de novo organic carbon amounts to about 85–424% of the phytoplankton primary production and covers up to 62% of deep-sea prokaryotic total carbon demand. Hence, the ABD process in the meso- and bathypelagic Mediterranean Sea might substantially contribute to the inorganic and organic pool and significantly sustain the deep-sea microbial food web. To elucidate the ABD key-players, we established three actively nitrifying and CO2-fixing prokaryotic enrichments. Consortia were characterized by the co-occurrence of chemolithoautotrophic Thaumarchaeota and chemoheterotrophic proteobacteria. One of the enrichments, originated from Ionian bathypelagic waters (3,000 m depth) and supplemented with low concentrations of ammonia, was dominated by the Thaumarchaeota “low-ammonia-concentration” deep-sea ecotype, an enigmatic and ecologically important group of organisms, uncultured until this study