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In many countries worldwide, inland shipping is a reliable and viable option to transport maritime containers inland. This modality comes with a set of operational challenges, among which the stowage of containers, i.e. the positioning of a set of containers onboard, is a complex and delicate task. In this paper, we develop a DSS to support the generation of feasible stowage plans, with the goal of maximizing the amount of containers onboard, while guaranteeing stability and complying with a set of rules. In this regard, we propose the case of inland shipping in the Netherlands. The stowage problem is modelled with a mixed integer linear programming mathematical formulation. Numerical experiments validate the model and give insights on the complexity of the problem for real-world size instances.

Africa is a continent of great natural resources, societal potential, and beauty. The rapid growth of population of people and cattle in sub-Saharan Africa has dramatically increased the pressure on the environmental resources, reducing their resilience and sustainability. To reverse this negative trend, ecohydrology needs to be implemented and this must start with a transfer of knowledge of ecohydrology, not only on a theoretical level but also in practical applications. Ecohydrology is about engineering a harmony between environment and society, ie it is a problem-solving science. It proposes low-cost, nature-based solutions. It often starts with the creation of demonstration sites, such as farmers' education centre in Asella, Ethiopia (Zalewski et al., 2010b).

Benthic communities inhabiting river lagoons are subjected to several natural (e.g. hypoxia and anoxia events) and anthropogenic disturbances such as excessive organic and nutrient loads from urban, industrial and agricultural discharges and high contamination levels. To investigate how benthic microbial communities (prokaryotes and microphytobenthos-MPB) respond to these disturbances, in the framework of the Project RITMARE, surface sediments from four coastal lagoons of the Po River delta were sampled in May 2016 (3 sampling sites in each lagoon): two with more marine features (Scardovari and Caleri) and two more directly affected by the Po River flow (Canarin and Vallona-Marinetta). Prokaryotes distribution was analyzed by hybridization techniques (CARD-FISH); MPB by inverted light microscopy (400x final magnification). The abundance and structure of benthic communities were related to physical-chemical parameters (grain-size, Organic C and synthetic organic contaminants: PAHs, PCBs, DDX). High densities of Bacteria and Archaea were observed at sites directly influenced by the freshwater input and a significant correlation between prokaryotes abundance and Organic C was highlighted. Delta-, Alpha- and Gamma-Proteobacteria were the dominant classes at all sites. Deltaproteobacteria, that include sulfate reducers typical of anoxic conditions, were more abundant in Canarin. Beta-Proteobacteria, a typically freshwater class, displayed the highest abundances at sites characterized by the lowest salinity where also Gamma-Proteobacteria, that include pathogens of fecal origin (e.g. Escherichia coli), were well represented. MPB abundances in Marinetta-Vallona and Canarin were almost double (81600±22735 and 81200±50938 cells cm-3, respectively) compared to Scardovari and Caleri (42350±19131 and 48700±10086 cells cm-3, respectively) likely due to freshwater nutrient loads. In Marinetta-Vallona and Canarin, the higher relative abundance of Chlorophyceae, Cyanobacteria and freshwater planktonic diatoms was a clear signature of the major river inflow. Cluster and nMDS analyses highlighted different MPB communities both at the intra-lagoonal level (among stations within the same lagoon), and inter-lagoonal level (among the four lagoons). Diversity indices revealed that the MPB community was more biodiverse at stations closest to the sea due to the concomitant presence of marine and brackish species, compared to the innermost stations where the lowest biodiversity was observed. Under organic enrichment conditions, as those encountered in Marinetta-Vallona due to intensive clam farming, Nitzschia tryblionella that prefers high organic loads was the most represented species (RA =19.1%).The benthic diatom community, through the selection of specific living forms, appeared to be affected by contaminants to some extent. In Canarin, the most contaminated lagoon, diatom living forms that are scarcely or not at all associated with the sediments prevailed over the typical benthic forms, suggesting a negative influence attributed to contaminants accumulated in the sediments. However, the contamination levels in Canarin did not seem to severely affect the microbial benthic communities that showed to be overall stimulated by the combined effect of high organic and nutrient loads.

The Chlamydiae are a phylum of obligate intracellular bacteria comprising important human and animal pathogens, yet their occurrence in the environment, their phylogenetic diversity and their host range has been largely underestimated. We investigated the seasonality of environmental chlamydiae in a Tyrrhenian coastal lake. By catalysed reporter deposition fluorescence in situ hybridization, we quantified the small planktonic cells and detected a peak in the abundance of environmental chlamydiae in early autumn with up to 5.9 × 10(4) cells ml(-1) . Super-resolution microscopy improved the visualization and quantification of these bacteria and enabled the detection of pleomorphic chlamydial cells in their protist host directly in an environmental sample. To isolate environmental chlamydiae together with their host, we applied a high-throughput limited dilution approach and successfully recovered a Vexillifera sp., strain harbouring chlamydiae (93% 16S rRNA sequence identity to Simkania negevensis), tentatively named 'Candidatus Neptunochlamydia vexilliferae'. Transmission electron microscopy in combination with fluorescence in situ hybridization was used to prove the intracellular location of these bacteria representing the first strain of marine chlamydiae stably maintained alongside with their host in a laboratory culture. Taken together, this study contributes to a better understanding of the distribution and diversity of environmental chlamydiae in previously neglected marine environments.

The presence of arsenic (As) in aquatic environments is often attributable to geogenic processes occurring within aquifers. Arsenic exists in two prevalent oxidation states, with the trivalent arsenite [As(III)] exerting stronger toxicity effects on the aquatic biota than the pentavalent arsenate [As(V)]. The review evaluates the literature available on the main arsenic removal technologies and the application of combined chemical and biological treatments. We provide a synthetic outlook on the potential strategies of biological As(III) oxidation to As(V) by means of cell-detoxifying mechanisms or metabolic processes with the aim to enhance As removal efficiency. Furthermore, the role of microorganisms in the mobility of arsenic in natural systems as well as the distribution of As-resistant bacteria, potentially suitable for arsenic removal, is discussed in the context of a case study carried out in Latium region (Italy), which is known for arsenic contamination of waters.

Arsenic contamination of soil and groundwater is a serious problem worldwide. Here we show that anaerobic oxidation of As(III) to As(V), a form which is more extensively and stably adsorbed onto metal-oxides, can be achieved by using a polarized (+497 mV vs. SHE) graphite anode serving as terminal electron acceptor in the microbial metabolism. The characterization of the microbial populations at the electrode, by using in situ detection methods, revealed the predominance of gammaproteobacteria. In principle, the proposed bioelectrochemical oxidation process would make it possible to provide As(III)-oxidizing microorganisms with a virtually unlimited, low-cost and low-maintenance electron acceptor as well as with a physical support for microbial attachment This work was supported by MIUR PRIN 2010-2011 project (grant agreement No 2010JBNLJ7-002). The authors thank the Advanced Centre for Microscopy "P. Albertano" of University of Rome "Tor Vergata" for CLSM analyses. Narcis Pous and Sebastia Puig were supported by a project grant from the Catalan Government (2012 FI-B 00941) and the Spanish Government (CTQ2011-23632). Narcis Pous was also supported by a COST Action ES1202 in the context of Water 2020 (COST-STSM-ECOST-STSM-ES1202-011013-035423)

In this paper, we present a DSS that generates schedules for the transportation of containers by barge in the hinterland, in particular from sea terminals to an inland terminal. As a case study, we propose the transportation from the ports of Rotterdam and Antwerp to a terminal in the south of the Netherlands, where the problem is typical. This problem is modeled as a heterogeneous fleet vehicle routing problem. The main decision is based on the trade-off of either consolidating containers to generate economies of scale with barges or alternatively dispatch, expensively and quickly, single containers by truck. The DSS is flexible as it can be applied to different settings by properly tuning the several parameters in the model. With numerical experiments, based on real world data, we evaluate the effectiveness of this system and its applicability. (C) 2015 Elsevier B.V. All rights reserved.

Groundwater plays a central role in the hydrological cycle and represents the utmost natural resource for human consumption and activities on a global scale. Therefore, any source of contamination of either geogenic or anthropogenic origin may provide a serious environmental health threat. Within the long list of organic and inorganic groundwater contaminants, arsenic, a toxic element retrieved in air, soils, rocks, waters and organisms, can occur at high concentrations in aquifers representing an issue of worldwide concern. Over the past years, research efforts aimed to elucidate the microorganisms and mechanisms involved in the biogeochemical cycling of this element. An emerging challenge is to identify and exploit microbial metabolic potentialities for arsenic-contaminated water treatment. The objective of this review is to outline the existing knowledge about ecology, biochemistry and genomics of arsenic-related microorganisms, with particular reference to their distribution and their capabilities to oxidize As(III) in groundwater. Moreover, a broad evaluation of the application potentialities of microbiological processes suitable for treatment strategies of arsenic-contaminated groundwater is provided.

Arsenic (As) is a toxic element released in aquatic environments by geogenic processes or anthropic activities. To counteract its toxicity, several microorganisms have developed mechanisms to tolerate and utilize it for respiratory metabolism. However, still little is known about identity and physiological properties of microorganisms exposed to natural high levels of As and the role they play in As transformation and mobilization processes. This work aims to explore the phylogenetic composition and functional properties of aquatic microbial communities in As-rich freshwater environments of geothermal origin and to elucidate the key microbial functional groups that directly or indirectly may influence As-transformations across a natural range of geogenic arsenic contamination. Distinct bacterial communities in terms of composition and metabolisms were found. Members of Proteobacteria, affiliated to Alpha- and Betaproteobacteria were mainly retrieved in groundwaters and surface waters, whereas Gammaproteobacteria were the main component in thermal waters. Most of the OTUs from thermal waters were only distantly related to 16S rRNA gene sequences of known taxa, indicating the occurrence of bacterial biodiversity so far unexplored. Nitrate and sulphate reduction and heterotrophic As(III)-oxidization were found as main metabolic traits of the microbial cultivable fraction in such environments. No growth of autotrophic As(III)-oxidizers, autotrophic and heterotrophic As(V)-reducers, Fe-reducers and oxidizers, Mn-reducers and sulfide oxidizers was observed. The ars genes, involved in As(V) detoxifying reduction, were found in all samples whereas aioA (As(III) oxidase) and arrA genes (As(V) respiratory reductase) were not found. Overall, we found that As detoxification processes prevailed over As metabolic processes, concomitantly with the intriguing occurrence of novel thermophiles able to tolerate high levels of As.

Understanding DOM transport and reactivity in rivers is essential to having a complete picture of the global carbon cycle. In this study, we explore the effects of hydrological variability and downstream transport on dissolved organic matter (DOM) dynamics in a Mediterranean river. We sampled the main stem of the river Tordera from the source to the sea, over a range of fifteen hydrological conditions including extreme events (flood and drought). By exploring spatial and temporal gradients of DOM fluorescence properties, river hydrology was found to be a significant predictor of DOM spatial heterogeneity. An additional space-resolved mass balance analysis performed on four contrasting hydrological conditions revealed that this was due to a shift in the biogeochemical function of the river. Flood conditions caused a conservative transport of DOM, generating a homogeneous, humic-like spatial profile of DOM quality. Lower flows induced a non-conservative, reactive transport of DOM, which enhanced the spatial heterogeneity of DOM properties. Moreover, the downstream evolution of DOM chemostatic behaviour revealed that the role of hydrology in regulating DOM properties increased gradually downstream, indicating an organised inter-dependency between the spatial and the temporal dimensions. Overall, our findings reveal that riverine DOM dynamics is in constant change owing to varying hydrological conditions, and emphasize that in order to fully understand the role of rivers in the global carbon cycle, it is necessary to take into account the full range of hydrological variability, from floods to droughts.

Background Recent studies have suggested that addition of electrically conductive biochar particles is an effective strategy to improve the methanogenic conversion of waste organic substrates, by promoting syntrophic associations between acetogenic and methanogenic organisms based on interspecies electron transfer processes. However, the underlying fundamentals of the process are still largely speculative and, therefore, a priori identification, screening, and even design of suitable biochar materials for a given biotechnological process are not yet possible. Results Here, three charcoal-like products (i.e., biochars) obtained from the pyrolysis of different lignocellulosic materials, (i.e., wheat bran pellets, coppiced woodlands, and orchard pruning) were tested for their capacity to enhance methane production from a food waste fermentate. In all biochar-supplemented (25 g/L) batch experiments, the complete methanogenic conversion of fermentate volatile fatty acids proceeded at a rate that was up to 5 times higher than that observed in the unamended (or sand-supplemented) controls. Fluorescent in situ hybridization analysis coupled with confocal laser scanning microscopy revealed an intimate association between archaea and bacteria around the biochar particles and provided a clear indication that biochar also shaped the composition of the microbial consortium. Based on the application of a suite of physico-chemical and electrochemical characterization techniques, we demonstrated that the positive effect of biochar is directly related to the electron-donating capacity (EDC) of the material, but is independent of its bulk electrical conductivity and specific surface area. The latter properties were all previously hypothesized to play a major role in the biochar-mediated interspecies electron transfer process in methanogenic consortia. Conclusions Collectively, these results of this study suggest that for biochar addition in anaerobic digester operation, the screening and identification of the most suitable biochar material should be based on EDC determination, via simple electrochemical tests. Electronic supplementary material The online version of this article (10.1186/s13068-017-0994-7) contains supplementary material, which is available to authorized users.

Sediment resuspension represents a key process in all natural aquatic systems, owing to its role in nutrient cycling and transport of potential contaminants. Although suspended solids are generally accepted as an important quality parameter, current monitoring programs cover quantitative aspects only. Established methodologies do not provide information on origin, fate, and risks associated with uncontrolled inputs of solids in waters. Here we discuss the analytical approaches to assess the occurrence and ecological relevance of resuspended particulate matter in freshwaters, with a focus on the dynamics of associated contaminants and microorganisms. Triggered by the identification of specific physical–chemical traits and community structure of particle-associated microorganisms, recent findings suggest that a quantitative determination of microorganisms can be reasonably used to trace the origin of particulate matter by means of nucleic acid-based assays in different aquatic systems.

The interaction of anaerobic dechlorinating cultures with soil and aquifer geochemical components is largely unknown, although this has potentially a major impact on the bioremediation of chlorinated solvent-contaminated sites. In this study, we found that addition of magnetite (Fe 3 O 4 ) – the end-product of Fe(III)-reduction by dissimilatory iron reducing bacteria – to anaerobic dechlorinating cultures enhances the kinetics of trichloroethene dechlorination up to 1.5-times, compared to unamended controls. Specifically, a low concentration (approx. 10 mg/L as total Fe) of small size particles (200 nm-filtered) resulted in a greater stimulatory effect compared to the addition of a higher concentration (approx. 300 mg/L as total Fe) of unfiltered particles. Notably, Desulforomonas spp. were substantially enriched in microcosms supplemented with magnetite, whereas Dehalococcoides mccartyi spp. was found to be markedly inhibited or outcompeted. Multiple lines of evidence, including the direct visualization of microbial cells and magnetite particles via Confocal Laser Scanning Microscopy (CLSM), suggest that electrically conductive particles promoted the establishment of a cooperative metabolism, based on direct interspecies electron transfer, between dechlorinating and non-dechlorinating microorganisms.

Groundwaters may act as sinks or sources of organic and inorganic solutes, depending on the relative magnitude of biochemical mobilizing processes and groundwater-surface water exchanges. The objective of this study was to link the lithological and hydrogeological gradients to the aquatic microbial community structure in the transition from aquifer recharge (volcanic formations) to discharge areas (alluvial deposits). A field-scale analysis was performed along a water table aquifer in which volcanic products decreased in thickness and areal extension, while alluvial deposits became increasingly important. We measured the main groundwater physical parameters and the concentrations of major and trace elements. In addition, the microbial community structure was assessed by estimating the occurrence of total coliforms and Escherichia coli, the prokaryotic abundance, the cytometric and phylogenetic community composition. The overall biogeochemical asset differed along the aquifer flow path. The concentration of total and live prokaryotic cells significantly increased in alluvial waters, together with the percentages of Beta- and Delta-Proteobacteria. The microbial propagation over a theoretical groundwater travel time allowed for the identification of microbial groups shifting significantly in the transition between the two different hydrogeochemical facies. The microbial community structure was intimately associated with geochemical changes, thus it should be further considered in view of a better understanding of groundwater ecology and sustainable management strategies. © 2014 Elsevier Ltd.

To understand to what extent depositional dynamics and riverine input contribute to shape the microbial benthic community structure in coastal systems, surface sediments were collected along one nearshore and two land-sea transects in the Po River prodelta, and analyzed for lithology, sediment structures, grain-size, short-lived radioisotopes (7Be and 137Cs) and organic matter (OM) quantity and origin (C, N, stable isotopes). The most recent surface supply (i.e. 5–6 mo = SUP layer) and the underneath, older sub-surface deposits (i.e. >6 mo = SUB layer) were analyzed at six selected sampling sites and checked for possible differences in the microbial community abundance and structure. According to different depositional dynamics, three distinct groups of sites were detected: nearshore muddy and sandy sites, and offshore sites. Sedimentary records reflected the interplay of different elements and/or processes acting in this complex and highly dynamic system. River-derived sediments, as depicted by high contribution of silty particles and recent riverine OM inputs, were confined to nearshore locations in front of the main river mouth. They resulted highly correlated to bacterial distribution and prokaryotic abundances in SUP layer. Nevertheless, in subsurface sediments affected by the delivery of high amount of mud, potential burial phenomena and/or the development of anoxic conditions occurred, leading to a change in the bacterial community structure. We speculated that the decrease of Gamma- and increase of Delta-Proteobacteria in the SUB layer could be related to their sulfur-oxidizing and sulfate-reducing activities, respectively. On the other hand, at offshore sites, the presence of a low, and regular sedimentary input and less intense hydrodynamic conditions favored a more stable microbial structure across surface and subsurface sediments. Four discriminating proxies, such as grain-size representing the system energy, Total N as an indicator of land-derived nutrient inputs, 7Be as a tracer of the freshness of riverine discharge, and stable C isotope as an indicator of the type and age of OM, mainly summarize the complex relationships between sedimentary dynamics and bacterial community structure in the Po River prodelta area.

Antibiotics are emerging contaminants, which wing to their bioactivity, may lead to short-term and long-term alterations of natural microbial communities in aquatic environment. We investigated the effects of antibiotics on biofilm bacterial communities in the Llobregat River (Northeast Spain). Three sampling sites were selected: two less polluted sites and one hotspot. River water was collected from each site and used both as inoculum and medium for growing biofilms in independent mesocosms. After 25 d of biofilm colonization, we exposed the colonized biofilms to river waters from the downstream sites (progressively contaminated by antibiotics). A control from each site was maintained where the growing biofilm was always exposed to water from the same site. The bacterial community composition, bacterial live/dead ratio and extracellular enzyme activities of the biofilms were measured before and 9 d after exposing the biofilms to increasing contaminated waters. Sixteen antibiotic compounds were detected in the water from the three sampling sites. At each site, the antibiotics present in the highest concentrations were sulfonamides, followed by quinolones and macrolides. Bacterial communities of biofilms grown with the three river waters differed markedly in their structure, but less so in terms of functional descriptors. After switching the medium water to increasing pollution, biofilms exhibited increased levels of actinobacteria (HGC), a trend that was associated to the higher antibiotic concentrations in the water. These biofilms also showed increased bacterial mortality, and decreased extracellular leucine-aminopeptidase and alkaline phosphatase. There was a significant correlation between antibiotic concentrations and biofilm responses. Our results indicate that the continuous entrance of antibiotics in running waters cause significant structural and functional changes in microbial attached communities.

Flow cytometry is suitable to discriminate and quantify aquatic microbial cells within a spectrum of fluorescence and light scatter signals. Using fixed operational and gating settings, a mixture model, coupled to Laplacian operator and Nelder-Mead optimization algorithm, allowed deconvolving bivariate cytometric profiles into single cell subgroups. This procedure was applied to outline recurrent patterns and quantitative changes of the aquatic microbial community along a river hydrologic continuum. We found five major persistent subgroups within each of the commonly retrieved populations of cells with Low and High content of Nucleic Acids (namely, LNA and HNA cells). Moreover, we assessed changes of the cytometric community profile over-imposed by water inputs from a wastewater treatment plant. Our approach for multiparametric data deconvolution confirmed that flow cytometry could represent a prime candidate technology for assessing microbial community patterns in flowing waters.

Among the bacterivorous protists, heterotrophic nanoflagellates (HNFs) are considered to be the main grazers of bacteria in freshwaters due to their size-selective grazing. In this work, we assessed the change of a riverine bacterial community in controlled incubations, where HNFs' predation pressure was initially released through filtration. Filtration did not prevent the passage of cysts, which grew in the enrichments afterwards. Data on the composition of the bacterial community were gathered by Catalyzed Reporter Deposition Fluorescent In situ Hybridization (CARD-FISH) using 16S probes targeting phylogenetic groups. Bacterial cell size was also examined using image analysis. Overall, the initial filtration directly (through release of predation pressure) or indirectly (through competition among bacterial groups) affected the bacterial community composition. When nanoflagellate abundance rose, a reduction of bacterial abundance and changes in cell size distribution were observed. Gamma-Proteobacteria and Actinobacteria were the groups showing the greatest reduction in abundance. Beta-Proteobacteria showed a reduction of cell size and were found in aggregates. Alpha-Proteobacteria and Actinobacteria developed two distinct filamentous morphotypes: short, segmented rods and long chains of rods. Our results showed that the release of the predation pressure and the successive rise of the nanoflagellates changed the bacterial community in terms of composition at large phylogenetic scale. HNF grazing is highly group-specific and seems to reconstruct the community based on cell size, and thus, not only drastically changing the bacterial community composition, but also increasing its functional diversity.

In this paper, we discuss, model and heuristically solve a particular container transport problem, related to the inland transport between a sea port and an inland terminal directly connected to it, called dry port. The transport is undertaken by a heterogeneous fleet. Similarly to the classical vehicle routing problem with pickup and delivery (VRPPD), vehicles can deliver containers to the different quays of the sea port and pick up others to bring to the dry port. The highly clustered setting, the strong heterogeneity of the fleet and time constraints add further features to the classical problem. After a detailed description of the setting, we develop the mathematical model and propose a heuristic approach.

L'elevata concentrazione di arsenico nelle acque destinate al consumo umano rappresenta un problema di forte interesse pubblico e scientifico su scala globale, considerando l'origine geogenica della contaminazione e i ben documentati effetti negativi sulla salute umana nel lungo termine. Tuttavia, gli aspetti microbiologici legati ai trattamenti di dearsenificazione sono raramente presi in considerazione. La citometria a flusso si è dimostrata una tecnologia adatta per il monitoraggio dei microrganismi, sia in forma di singola cellula che adesi al particolato in sospensione, fornendo informazioni di supporto per valutare in modo integrato il corretto funzionamento degli schemi impiantistici per il trattamento di acque contaminate.

The Po River runoff strongly affects the oceanographic and ecological characteristics of the Northern Adriatic Sea. Catalysed reported deposition - fluorescence in situ hybridization (CARD-FISH) analysis was employed to assess how the composition of the coastal bacterioplankton community is influenced by the river runoff in two different seasons (spring and autumn). Samples were collected from the water column along a coastal–offshore transect in the Northern Adriatic Sea at different depths. Four clone libraries were then constructed from coastal (0 m) and offshore waters (−65 m). Higher abundances of bacteria were recorded in coastal waters as compared with the offshore samples. This result was mainly due to the trophic state of the water column, and it was related to salinity. Particularly, Actinobacteria and Gammaproteobacteria were affected by the riverine inputs, whereas Bacteroidetes and Alphaproteobacteria showed only minor responses. This was particularly clear in the autumn sample, in which a clear difference between the coastal and the offshore samples was found due to a strong influence of the less saline river water with high nutrient concentrations. Analysis of 205 partial length 16S rRNA gene sequences indicated a high diversity with the dominance of Alphaproteobacteria, Bacteroidetes and Gammaproteobacteria mainly affiliated to coastal and marine bacterioplankton clades. Actinobacteria were also detected and, together with Gammaproteobacteria, strongly follow the freshwater intrusion. Overall, our results indicate that the seasonal difference in the Po River discharge greatly affects the bacterioplankton community. In spring we observed a smooth transition from coastal to open-sea conditions owing to the more superficial freshwater plume. In autumn the deeper freshwater intrusion in the coastal site and thermal stratification offshore resulted in a marked difference between the coastal and offshore microbial communities.

Different countries in Europe still suffer of elevated arsenic (As) concentration in groundwaters used for human consumption. In the case of households not connected to the distribution system, decentralized water supply systems, such as Point of Use (POU) and Point of Entry (POE), offer a direct benefit for the consumers. Field scale ex-situ treatment systems based on metallic iron (ZVI) are already available for the production of reduced volumes of drinking water in remote areas (village scale). To address drinking water needs at larger scale, we designed a pilot unit able to produce an elevated daily volume of water for human consumption. We tested the long-term As removal efficiency of a two steps ZVI treatment unit for the production of 400 L/day clean water based on the combination of ZVI corrosion process with sedimentation and retention of freshly formed Fe precipitates. The system treated 100 mu g/L As(V)-contaminated oxic groundwater in a discontinuous operation mode at a flow rate of 1 L/min for 31 days. Final removal was 77-96% and the most performing step was aeration/sedimentation (A/S) tank with a 60-94% efficiency. Arsenic in the outflow slightly exceeded the drinking water limit of 10 mu g/L only after 6000 L treated and Fe concentration was always below 0.2 mg/L. Under proposed operating conditions ZVI passivation readily occurred and, as a consequence, Fe production sharply decreased. Arsenic mobility attached to particulate was 13-60% after ZVI column and 37-100% after A/S tank. Uniform amorphous cluster of Fe nanoparticles (100 nm) formed during aeration drove As removal process with an adsorption capacity corresponding to 20.5 mgAs/gFe. Research studies often focus only on chemico-physical aspects disregarding the importance of biological processes that may co-occur and interfere with ZVI corrosion, As removal and safe water production. We explored the microbial transport dynamics by flow cytometry, proved as a suitable tool to monitor the fate of both single cells and bioactive particles along the treatment train of the pilot unit. A net release of bioactive particles, representing on average 26.5% of flow cytometric events, was promoted by the ZVI filter, with densities 10 times higher than those found in the inflow. In conclusion, the proposed system was efficient to treat large daily volumes of As contaminated groundwater. However, filter design and operating conditions should be carefully adapted to specific situation, since several key factors affect As removal efficiency. An effort in the optimization of ZVI filter design should be made to reduce fast observed ZVI passivation and low As adsorption capacity of the whole filter: More attention to biomass retention and bioactive particles travelling within the unit should be given in order to elucidate bacteria influences on As removal efficiency and related sanitary risks on long term basis. (C) 2016 Elsevier Ltd. All rights reserved.

Temporary rivers are characterized by dry-wet phases and represent an important water resource in semi-arid regions worldwide. The fate and effect of contaminants have not been firmly established in temporary rivers such as in other aquatic environments. In this study, we assessed the effects of sediment amendment with Polycyclic Aromatic Hydrocarbons (PAHs) on benthic microbial communities. Experimental microcosms containing natural (Control) and amended sediments (2 and 20 mg PAHs kg(-1) were incubated for 28 days. The PAH concentrations in sediments were monitored weekly together with microbial community structural (biomass and phylogenetic composition by TGGE and CARD-FISH) and functional parameters (ATP concentration, community respiration rate, bacterial carbon production rate, extracellular enzyme activities). The concentration of the PAH isomers did not change significantly with the exception of phenanthrene. No changes were observed in the TGGE profiles, whereas the occurrence of Alpha- and Beta-Proteobacteria was significantly affected by the treatments. In the amended sediments, the rates of carbon production were stimulated together with aminopeptidase enzyme activity. The community respiration rates showed values significantly lower than the Control after 1 day from the amendment then recovering the Control values during the incubation. A negative trend between the respiration rates and ATP concentration was observed only in the amended sediments. This result indicates a potential toxic effect on the oxidative phosphorylation processes. The impoverishment of the energetic resources that follows the PAH impact may act as a domino on the flux of energy from prokaryotes to the upper level of the trophic chain, with the potential to alter the temporary river functioning.

Fluvial corridors such as streams and urban canals are critical components of the landscape and are key ecohydrological assets. They are essential to landscape function and are vulnerable to anthropogenic pressures. Energy and nutrient budgets in such corridors are dominated by processes associated with detrital organic matter and are mediated by microorganisms that mainly reside in biofilms. Here, we review the major hydrologic factors shaping biofilms in natural and urban water corridors, and propose the integration of single-cell visualization techniques with other broad-scale approaches (genomics) to better understand structure-function coupling in such complex microbial communities. We, further, provide evidence that it is possible to visualize specific bacterial clusters and autotrophic microorganisms within the matrix of natural biofilms from urban canals. This can then guide the development of ecohydrological approaches and management interventions to harness ecological services mediated by biofilms, with enormous implications also by a sanitary point of view. (C) 2015 European Regional Centre for Ecohydrology of the Polish Academy of Sciences. Published by Elsevier Sp. z o.o. All rights reserved.

River and stream biofilms in mediterranean fluvial ecosystems face both extreme seasonality as well as arrhythmic fluctuations. The hydrological extremes (droughts and floods) impose direct changes in water availability but also in the quantity and quality of organic matter and nutrients that sustain the microbial growth. This review analyzes how these ecological pulses might determine unique properties of biofilms developing in mediterranean streams. The paper brings together data from heterotrophic and autotrophic community structure, and extracellular enzyme activities in biofilms in mediterranean streams. Mediterranean stream biofilms show higher use of peptides during the favorable period for epilithic algae development (spring), and preferential use of cellulose and hemicellulose in autumn as a response to allochthonous input. The drying process causes the reduction in bacterial production and chlorophyll biomass, but the rapid recovery of both autotrophs and heterotrophs with rewetting indicates their adaptability to fluctuations. Bacteria surviving the drought are mainly associated with sediment and leaf litter which serve as "humid refuges". Some algae and cyanobacteria show resistant strategies to cope with the drought stress. The resistance to these fluctuations is strongly linked to the streambed characteristics (e.g., sediment grain size, organic matter accumulation, nutrient content) This study was funded by the projects CGL2011-30151-C02-01, and SCARCE (Consolider-Ingenio 2010 CSD2009-00065) of the Spanish Ministry of Economy and Competitiveness; the Italy-Spain Exchange Project CNR-CSIC 2006IT0010; and the EU project MIRAGE (FP7-ENV-2007-1 n.211732)

Summary For a long time the bacterial phylum of Chlamydiae exclusively consisted of one family of obligate intracellular bacteria, the Chlamydiaceae, which encompassed causative agents of severe diseases. In the 1990s, environmental chlamydiae were discovered as symbionts of free-living amoebae and other eukaryotic hosts. During a sampling campaign in September 2008, while monitoring Planctomycetes, we retrieved 20 almost full-length 16S rRNA gene sequences affiliated with Chlamydiales from a lake at the Tyrrhenian coast of central Italy (Lago di Paola, Latium). Two main clusters were identified. The nine sequences within the tight cluster I shared ∼98% identity, just like the six sequences of cluster II. The 16S rRNA sequence identity between the two novel groups was with 88% higher than with all known families of the order Chlamydiales. Four types of less frequent chlamydial 16S rRNA sequences were also detected. Two oligonucleotide probes were designed, and optimized. Chl282 targets the cluster I and almost all other Chlamydiales, while Chl282bis targets the cluster II and few other sequences. By catalysed reporter deposition fluorescence in situ hybridization (CARD-FISH), we identified in the Lago di Paola picoplankton abundant tiny cells with dot-shaped morphology and, interestingly, rarely also protists with intracellular pleomorphic chlamydiae. Abundances of the novel chlamydial clusters were up to 5 × 104 cells per millilitre. The two clusters were also detected in similar numbers during a second sampling in October 2010. This confirmed the relevance of the two newly described clusters of chlamydiae in Lago di Paola, not only enlarging the knowledge on the biodiversity of environmental chlamydiae in aquatic habitats, but also raising sanitary issues that should be addressed in the future.

In Mediterranean regions, drought is one of the main factors shaping fluvial ecosystems. Droughts cause a shift from lotic to lentic conditions, triggering a gradual fragmentation of the longitudinal hydrological continuum, and a severe alteration of water chemical properties. However, within a biogeochemical perspective, little is known about how and to which extend droughts modify the chemical properties of dissolved organic matter (DOM). In this study, the variability of DOM properties along a fragmented fluvial system is explored, during a summer severe drought, by means of (a) the ratio between dissolved organic carbon and nitrogen concentrations (DOC:DON); (b) DOC bioavailability (BDOC) and (c) DOM optical properties (SUVA index, fluorescence index, and excitation–emission fluorescence matrices). DOM and water measurements were collected from isolated water parcels that became disconnected from the fluvial continuum at different times, and were compared with data obtained in the following autumn, when the fluvial continuum was re-established. Analysis of DOM chemical properties evidenced that these properties during drought clearly differed from those observed in autumn, but changes did not follow an arbitrary pattern. Thus, the sampling sites with lotic water bodies showed DOM properties similar to those observed in autumn reflecting the dominance of terrestrial inputs. But, once hydrological fragmentation occurred, there was a gradual increase in the contribution of autochthonous DOM as the time elapsed since the pools were established, and the geochemical conditions shifted from oxidized to reduced conditions. In consequence, the fragmentation of fluvial continuum generates a set of distinct biochemical hot spots (i.e., each water parcel), revealing that extreme drought greatly amplifies the qualitative heterogeneity of organic matter in a fluvial system.

Temporary rivers are characterized by recurrent dry phases, and global warming will stress their hydrology by amplifying extreme events. Microbial degradation and transformation of organic matter (OM) in riverbed sediment are key processes with regard to carbon and nutrient fluxes. In this study, we describe structural and functional changes of benthic microbial communities in a riverine environment subject to hydrological fluctuation. Sampling was carried out in the outlet section of the Mulargia River (Sardinia, Italy) under various water regimes, including one flood event. Overall, sediments were characterized by low bacterial cell abundance (range 0.6–1.8 × 109 cell g−1) as a consequence of their low nutrient and OM concentrations. No major differences were found in the community composition. Alpha-Proteobacteria dominated during the whole year (range 21–30%) followed by Beta-Proteobacteria, Gamma-Proteobacteria, and Cytophaga-Flavobacteria which always contributed

Efficient detachment and purification of bacterial cells associated with streambed sediments are required in order to quantify cell abundance and to assess community composition through the application of epifluorescence microscopy techniques. We applied chemical (i.e., sodium pyrophosphate and polysorbate) and physical treatments (i.e., shaking and sonication), followed by Nycodenz density gradient centrifugation to efficiently recover benthic bacteria. This procedure resulted in a highly purified cell suspension allowing for a precise cell quantification through the application of fluorescent dyes. About 93% of total cells were recovered from the original sediment, with higher recovery from the finer grain-size class (90%) in comparison to the coarse fraction (69%). The potential damaging effects of the applied procedures on cell integrity were assessed on planktonic bacteria in a pre-filtered water control. As a consequence of the high purity of the extracted bacteria, flow cytometry was successfully applied as counting method for sediment cell suspension. However, a significant decrease of protein synthesis in purified samples was measured by estimating the 3H-Leucine incorporation rates, rising uncertainties on the possibility to apply potential metabolic assays after Nycodenz purification.

We studied the diversity, community composition and activity of the primary microbial colonizers of the water above freshly re-wetted sediments from a temporary river. Dried sediments, collected from Mulargia River (Sardinia, Italy), were covered with sterile freshwater in triplicate microcosms, and changes of the planktonic microbial assemblage were monitored over a 48 h period. During the first 9 h bacterial abundance was low (1.5 x 10(4) cells ml(-1)); it increased to 3.4 x 10(6) cells ml(-1) after 28 h and did not change thereafter. Approximately 20% of bacteria exhibited DNA de novo synthesis already after 9 h of incubation. Changes of the ratios of (3)H-leucine to (3)H-thymidine incorporation rates indicated a shift of growth patterns during the experiment. Extracellular enzyme activity showed a maximum at 48 h with aminopeptidase activity (430.8 +/- 22.6 nmol MCA l(-1) h(-1)) significantly higher than alkaline phosphatase (98.6 +/- 4.3 nmol MUF l(-1) h(-1)). The primary microbial colonizers of the overlaying water - as determined by 16S rRNA gene sequence analysis - were related to at least six different phylogenetic lineages of Bacilli and to Alphaproteobacteria (Brevundimonas spp. and Caulobacter spp.). Large bacterial cells affiliated to one clade of Bacillus sp. were rare in the dried sediments, but constituted the majority of the planktonic microbial assemblage and of cells with detectable DNA-synthesis until 28 h after re-wetting. Their community contribution decreased in parallel with a rise of flagellated and ciliated protists. Estimates based on cell production rates suggested that the rapidly enriched Bacillus sp. suffered disproportionally high loss rates from selective predation, thus favouring the establishment of a more heterogenic assemblage of microbes (consisting of Proteobacteria, Actinobacteria and Cytophaga-Flavobacteria). Our results suggest that the primary microbial colonizers of the water above dried sediments are passively released into the plankton and that their high growth potential is counteracted by the activity of bacterivorous protists.

The trophic status classification of coastal waters at the European scale requires the availability of harmonised indicators and procedures. The composite trophic status index (TRIX) provides useful metrics for the assessment of the trophic status of coastal waters. It was originally developed for Italian coastal waters and then applied in many European seas (Adriatic, Tyrrhenian, Baltic, Black and Northern seas). The TRIX index does not fulfil the classification procedure suggested by the WFD for two reasons: (a) it is based on an absolute trophic scale without any normalization to type-specific reference conditions; (b) it makes an ex ante aggregation of biological (Chl- a ) and physico-chemical (oxygen, nutrients) quality elements, instead of an ex post integration of separate evaluations of biological and subsequent chemical quality elements. A revisitation of the TRIX index in the light of the European Water Framework Directive (WFD, 2000/60/EC) and new TRIX derived tools are presented in this paper. A number of Italian coastal sites were grouped into different types based on a thorough analysis of their hydro-morphological conditions, and type-specific reference sites were selected. Unscaled TRIX values (UNTRIX) for reference and impacted sites have been calculated and two alternative UNTRIX-based classification procedures are discussed. The proposed procedures, to be validated on a broader scale, provide users with simple tools that give an integrated view of nutrient enrichment and its effects on algal biomass (Chl- a ) and on oxygen levels. This trophic evaluation along with phytoplankton indicator species and algal blooms contribute to the comprehensive assessment of phytoplankton, one of the biological quality elements in coastal waters.

We studied the efficiency of two hybridization techniques for the analysis of benthic bacterial community composition under varying sediment water content. Microcosms were set up with sediments from four European temporary rivers. Wet sediments were dried, and dry sediments were artificially rewetted. The percentage of bacterial cells detected by fluorescence in situ hybridization with fluorescently monolabeled probes (FISH) significantly increased from dry to wet sediments, showing a positive correlation with the community activity measured via incorporation of 3H leucine. FISH and signal amplification by catalyzed reporter deposition (CARD-FISH) could significantly better detect cells with low activity in dried sediments. Through the application of an optimized cell permeabilization protocol, the percentage of hybridized cells by CARD-FISH showed comparable values in dry and wet conditions. This approach was unrelated to 3H leucine incorporation rates. Moreover, the optimized protocol allowed a significantly better visualization of Gram-positive Actinobacteria in the studied samples. CARD-FISH is, therefore, proposed as an effective technique to compare bacterial communities residing in sediments with contrasting water content, irrespective of differences in the activity state of target cells. Considering the increasing frequencies of flood and drought cycles in European temporary rivers, our approach may help to better understand the dynamics of microbial communities in such systems.

In the semiarid Mediterranean regions, water scarcity represents a common physiological stress for microbial communities residing in river sediments. However, the effect of drying has not yet adequately been evaluated when analyzing riverine microbiological processes. The bacterial community structure (abundance, biomass, composition) and functioning (carbon production, live cell percentage) were assessed during experimental desiccation in microcosms with sediments from different Mediterranean temporary rivers (Tagliamento, Krathis, Mulargia, Pardiela). Our results showed that the overall responses to drying of the bacterial community were independent from sediment origin and strictly related to water content. During desiccation, a prompt decline (up to 100%) of the initial bacterial carbon production was followed by a slower decrease in abundance and biomass, with an overall reduction of 74% and 78%, respectively. By the end of the experiment, live cells were still abundant but depressed in their main metabolic functions, thus resulting in a drastic increase in the community turnover time. Only 14% of the initial live cell biomass was available in dry sediments to immediately start the reactivation of the aquatic microbial food web after the arrival of new water. Community composition analysis showed a relative increase in alpha- and beta-Proteobacteria, when passing from wet to dry conditions. Our results suggest that the occurrence of drought events could affect carbon cycling through the freshwater microbial compartment, by temporarily limiting microbial mineralization and altering bacterial community structure.

The Chlamydiae are a phylum of obligate intracellular bacteria comprising important human and animal pathogens, yet their occurrence in the environment, their phylogenetic diversity and their host range has been largely underestimated. We investigated the seasonality of environmental chlamydiae in a Tyrrhenian coastal lake. By catalysed reporter deposition fluorescence in situ hybridization, we quantified the small planktonic cells and detected a peak in the abundance of environmental chlamydiae in early autumn with up to 5.9 × 10(4) cells ml(-1) . Super-resolution microscopy improved the visualization and quantification of these bacteria and enabled the detection of pleomorphic chlamydial cells in their protist host directly in an environmental sample. To isolate environmental chlamydiae together with their host, we applied a high-throughput limited dilution approach and successfully recovered a Vexillifera sp., strain harbouring chlamydiae (93% 16S rRNA sequence identity to Simkania negevensis), tentatively named 'Candidatus Neptunochlamydia vexilliferae'. Transmission electron microscopy in combination with fluorescence in situ hybridization was used to prove the intracellular location of these bacteria representing the first strain of marine chlamydiae stably maintained alongside with their host in a laboratory culture. Taken together, this study contributes to a better understanding of the distribution and diversity of environmental chlamydiae in previously neglected marine environments.

Interspecies electron transfer mechanisms between Bacteria and Archaea play a pivotal role during methanogenic degradation of organic matter in natural and engineered anaerobic ecosystems. Growing evidence suggests that in syntrophic communities electron transfer does not rely exclusively on the exchange of diffusible molecules and energy carriers such as hydrogen or formate, rather microorganisms have the capability to exchange metabolic electrons in a more direct manner. Here, we show that supplementation of micrometer-size magnetite (Fe3O4) particles to a methanogenic sludge enhanced (up to 33%) the methane production rate from propionate, a key intermediate in the anaerobic digestion of organic matter and a model substrate to study energy-limited syntrophic communities. The stimulatory effect most probably resulted from the establishment of a direct interspecies electron transfer (DIET), based on magnetite particles serving as electron conduits between propionate-oxidizing acetogens and carbon dioxide-reducing methanogens. Theoretical calculations revealed that DIET allows electrons to be transferred among syntrophic partners at rates which are substantially higher than those attainable via interspecies H2 transfer. Besides the remarkable potential for improving anaerobic digestion, which is a proven biological strategy for renewable energy production, the herein described conduction-based DIET could also have a role in natural methane emissions from magnetite-rich soils and sediments.

Jakarta Metropolitan Area (JMA) or Jabotabek is one of the most dynamic regions of Indonesia. At present, the JMA is the largest concentration of urban population in Indonesia and seventh largest urban agglomeration in the world. The massive demographic and economic growth taking place in the region have gone hand in hand with environmental destruction and poverty concentration. Jabotabek is experiencing a number of problems related to its coastal location: coastal littering, water pollution, saltwater intrusion, land subsidence, seafood contamination and the loss of habitat for birds, fish and other wild life. Poverty alleviation and the preservation of the coastal environment for sustainable development are becoming critical issues facing the Jabotabek. This is where the concept of wise coastal management practice becomes pertinent, where scientists and managers and local stakeholders co-operate in finding solutions to these various inter-related problems. A multiple-prong approach is employed to improve coastal environmental management among other: scientific campaign on coastal resources management, community-based development for sustainable coastal management including community-based waste management and recycling, social empowerment, and environmental education. The paper also proposes the strategy to strengthen the existing community-based environmental management activities.

The effect of macroinvertebrate detritivore density on the mass loss rates of leaf litter of Alnus glutinosa (alder) was assessed. Experimental freshwater macrocosms, with increasing densities of four species of macroinvertebrate detritivores belonging to two functional groups (shredders and scrapers), were set up outdoors. The litter bag technique was used to assess decomposition rates of alder leaves. Indirect effects of increasing density of macroinvertebrates on phytoplankton standing crop in the water column were investigated by analysing Chlorophyll a concentration. Decomposition rate increased as animal density increased, although a continuous increase in detritivores density resulted in a discrete, step-wise increase of the decomposition rates. Animal colonisation followed an exponential pattern in low-medium density treatments versus a typical `bell-shape' curve in high density treatments; animals started to leave the consumed patches when about 60% of the initial leaf mass was lost (35th day in high-density treatments). Diversity (Hs) of the simplified detritivore community decreased as decomposition proceeded, with a dominance of shredders during the last phase of decomposition. Faster decomposition rate of detritus in the benthic compartment lead to a higher microalgae standing crop in the water column emphasising the role of allochthonous detritus as a source of nutrients for algae primary production in coastal freshwater ecotones.

In sediments sampled in Northern Adriatic Sea invertebrate benthic macrofauna was examined in comparison with both substratum bulk parameters (average grain size, sorting, total organic matter content) and attributes of grain size classes (specific organic matter content of dimensional fractions). The aims were: 1) to determine whether variations of community overall parameters (total spatial density, number of taxa) and in numerically dominant feeding types (deposit-feeders and suspension-feeders) patterns were related to changes in sediment general properties; 2) to evaluate whether the observed patterns of abundance for deposit- and filter-feeders had more valid correlates in specific properties of substratum dimensional fractions. Number of taxa and animal spatial density resulted conventionally related to substratum bulk parameters while feeding types patterns in comparison with sediment total organic matter content exibited a reciprocal negative effect; only when both feeding types and sediment structure were resolved to their specific attributes in terms of prevalence of tubicolous taxa among deposit-feeders and organic matter richness of single dimensional fractions, the analysis emphasized patterns unequally affected by specific size fractions abundance and organic matter content: deposit feeders demonstrated to be related to the presence in the substrate of intermediate grain size classes necessary for tube-building. Those intermediate fractions proved to be more adequate descriptors than average grain size or other overall sediment parameters per se of relations actually established between feeding types and the complex nature of bottom sediments. Our results emphasize that in the Northern Adriatic Sea, sediment organic matter content may represent a factor of minor importance in comparison with other substrate attributes, for which it may be necessary a detailed analysis of sediment structure. Thus, we concluded that the complexity of soft-bottom communities may defy any simple paradigm relating macrobenthic patterns to any single sediment bulk attribute, and we propose a shift in focus towards an higher resolution of both functional groups in macrobenthic associations (as already suggested in other investigations) and of substratum structural description.

For a long time the bacterial phylum of Chlamydiae exclusively consisted of one family of obligate intracellular bacteria, the Chlamydiaceae, which encompassed causative agents of severe diseases. In the 1990s, environmental chlamydiae were discovered as symbionts of free-living amoebae and other eukaryotic hosts. During a sampling campaign in September 2008, while monitoring Planctomycetes, we retrieved 20 almost full-length 16S rRNA gene sequences affiliated with Chlamydiales from a lake at the Tyrrhenian coast of central Italy (Lago di Paola, Latium). Two main clusters were identified. The nine sequences within the tight cluster I shared ∼98% identity, just like the six sequences of cluster II. The 16S rRNA sequence identity between the two novel groups was with 88% higher than with all known families of the order Chlamydiales. Four types of less frequent chlamydial 16S rRNA sequences were also detected. Two oligonucleotide probes were designed, and optimized. Chl282 targets the cluster I and almost all other Chlamydiales, while Chl282bis targets the cluster II and few other sequences. By catalysed reporter deposition fluorescence in situ hybridization (CARD-FISH), we identified in the Lago di Paola picoplankton abundant tiny cells with dot-shaped morphology and, interestingly, rarely also protists with intracellular pleomorphic chlamydiae. Abundances of the novel chlamydial clusters were up to 5 × 10(4) cells per millilitre. The two clusters were also detected in similar numbers during a second sampling in October 2010. This confirmed the relevance of the two newly described clusters of chlamydiae in Lago di Paola, not only enlarging the knowledge on the biodiversity of environmental chlamydiae in aquatic habitats, but also raising sanitary issues that should be addressed in the future.

10 páginas, 6 figuras, 1 tabla., In Mediterranean intermittent streams, the hydrological fragmentation in summer and the successive water flow reconvergence in autumn allow exploring how local processes shape the microbial community within the same habitat. The objectives of this study were to determine how bacterial community composition responded to hydrological fragmentation in summer, and to evaluate whether the seasonal shifts in community composition predominate over the effects of episodic habitat fragmentation. The bacterial community was assessed along the intermittent stream Fuirosos (Spain), at different levels of phylogenetic resolution by in situ hybridization, fingerprinting, and 16S rRNA gene sequencing. The hydrological fragmentation of the stream network strongly altered the biogeochemical conditions with the depletion of oxidized solutes and caused changes in dissolved organic carbon characteristics. In the isolated ponds, beta-Proteobacteria and Actinobacteria increased their abundance with a gradual reduction of the alpha-diversity as pond isolation time increased. Moreover, fingerprinting analysis clearly showed a shift in community composition between summer and autumn. In the context of a seasonal shift, the temporary stream fragmentation simultaneously reduced the microbial dispersion and affected local environmental conditions (shift in redox regime and quality of the dissolved organic matter) tightly shaping the bacterioplankton community composition., Participation of AB and EV was supported by Project CGL2011-30151-C02-02/BTE, funded by Ministerio de Economı`a y Competitividad. AB, EOC and EV are members of the Graccie Consortium.

24 páginas, 2 figuras, 1 tabla., The protection, preservation and restoration of aquatic ecosystems and their functions are of global importance. For European states it became legally binding mainly through the EUWater Framework Directive (WFD). In order to assess the ecological status of a given water body, aquatic biodiversity data are obtained and compared to a reference water body. The quantified mismatch obtained determines the extent of potential management actions. The current approach to biodiversity assessment is based on morpho-taxonomy. This approach has many drawbacks such as being time consuming, limited in temporal and spatial resolution, and error-prone due to the varying individual taxonomic expertise of the analysts. Novel genomic tools can overcome many of the aforementioned problems and could complement or even replace traditional bioassessment. Yet, a plethora of approaches are independently developed in different institutions, thereby hampering any concerted routine application. The goal of this Action is to nucleate a group of researchers across disciplines with the task to identify gold-standard genomic tools and novel ecogenomic indices for routine application in biodiversity assessments of European fresh- and marine water bodies. Furthermore, DNAqua-Net will provide a platform for training of the next generation of European researchers preparing them for the new technologies. Jointly with water managers, politicians, and other stakeholders, the group will develop a conceptual framework for the standard application of eco-genomic tools as part of legally binding assessments.

Bacterial community composition was assessed during riverine biofilm development by the Catalyzed Reporter Deposition Fluorescence In Situ Hybridization (CARD-FISH) in combination with Confocal Laser Scanning Microscopy. Using artificial substrates, it was possible to follow the dynamics of specific bacterial clusters, while maintaining the unaltered structure and architecture of the biofilm.

International audience; The phylum Planctomycetes is involved in important processes, such as the mineralization of algal biomass and the removal of nitrogen. Using a combination of 16S rRNA sequence analysis and in situ hybridization, we analyzed the diversity and dynamics of Planctomycetes in a shallow meso-eutrophic lake, Lago di Paola, Italy. Planctomycetes detected by the probe PLA46 accounted for 1 to 5% of prokaryotic picoplankton. Abundances were higher in the coastal lake than in the adjacent marine waters. In the surface waters of the lake, the numbers of Planctomycetes fluctuated greatly, reaching a maximum of 1.5 x 10(6) cells ml(-1) in July. The hypoxic bottom waters had less variable cell abundances. The Planctomycetes counts were positively correlated with chlorophyll a concentrations, confirming the role of this phylum in the degradation of algal biomass. We obtained 70 almost full-length 16S rRNA gene sequences of Planctomycetes from 2 libraries. Four distinct clades could be identified. The Pirellula-related group F and the uncultured Planctomycetes group B both had the highest identity with sequences retrieved from marine habitats, whereas the Pirellula-related group E was affiliated with sequences known from freshwater and brackish water environments. The Planctomyces-related group A seems to have a wide habitat range. Catalyzed reported deposition fluorescence in situ hybridization with newly developed probes revealed abundances of the 4 clades in surface and bottom waters ranging from 1 x 10(3) to 5 x 10(4) cells ml(-1). Together, the 4 clade-specific probes identified only about a quarter of the Planctomycetes detected by probe PLA46. This indicates that the diversity of Planctomycetes has not yet been fully explored.

1. Knowledge about processes and dynamics underlying organic matter accumulation in transitional waters is crucial for the protection of these ecologically important coastal habitats. This study investigated the relationship between large particle accumulation and decomposition in a coastal lake included in a Site of Community Interest (SCI) using sediment trap and litterbag techniques. 2. Two sets of sediment traps were deployed at five sites along the longitudinal axis of the lake. One set was emptied once a month for 12 months, and the other twice a year. The contents of the monthly and the 6-monthly traps and the superficial sediments were then compared to estimate the organic matter accumulation and loss. To determine the mass loss rate of the three major allochthonous sources of detritus (the reed Phragmites australis, the cordgrass Spartina juncea, and the seagrass Posidonia oceanica), litterbags were placed near the sediment traps at three out of the five sites at the beginning of each 6-month period and retrieved monthly. 3. The amount of annual particulate organic matter (POM) deposition in the traps was 1320.2±58.5 g m−2 y−1 and consisted of 25% large particles (CPOM). Allochthonous litter comprised an important fraction of CPOM, and its breakdown rate changed with the plant species, site and season. Loss rate of CPOM accumulated at the lake bottom was significantly related with the mass loss rate of reed and cordgrass litter, but not with that of seagrass. 4. Due to slow litter breakdown and tidal landward advection, the lake acted as a sediment trap for allochthonous matter, especially from Posidonia. The important role of marine-derived litter in organic matter sedimentation suggests addressing conservation strategies of the lake functioning towards the selective control of allochthonous CPOM inputs, in particular at the mouth where the incoming tide brings suspended material and salinity decelerates matter flow to the sea and decomposition. This study supports the hypothesis that sedimentation and decomposition dynamics are important factors for coastal lake evolution, and shows litterbag and sediment trap techniques as simple useful investigation tools in management strategies aiming at conserving transitional waters. Copyright © 2008 John Wiley & Sons, Ltd.

We studied the diversity, community composition and activity of the primary microbial colonizers of the water above freshly re-wetted sediments from a temporary river. Dried sediments, collected from Mulargia River (Sardinia, Italy), were covered with sterile freshwater in triplicate microcosms, and changes of the planktonic microbial assemblage were monitored over a 48 h period. During the first 9 h bacterial abundance was low (1.5 x 10(4) cells ml(-1)); it increased to 3.4 x 10(6) cells ml(-1) after 28 h and did not change thereafter. Approximately 20% of bacteria exhibited DNA de novo synthesis already after 9 h of incubation. Changes of the ratios of (3)H-leucine to (3)H-thymidine incorporation rates indicated a shift of growth patterns during the experiment. Extracellular enzyme activity showed a maximum at 48 h with aminopeptidase activity (430.8 +/- 22.6 nmol MCA l(-1) h(-1)) significantly higher than alkaline phosphatase (98.6 +/- 4.3 nmol MUF l(-1) h(-1)). The primary microbial colonizers of the overlaying water - as determined by 16S rRNA gene sequence analysis - were related to at least six different phylogenetic lineages of Bacilli and to Alphaproteobacteria (Brevundimonas spp. and Caulobacter spp.). Large bacterial cells affiliated to one clade of Bacillus sp. were rare in the dried sediments, but constituted the majority of the planktonic microbial assemblage and of cells with detectable DNA-synthesis until 28 h after re-wetting. Their community contribution decreased in parallel with a rise of flagellated and ciliated protists. Estimates based on cell production rates suggested that the rapidly enriched Bacillus sp. suffered disproportionally high loss rates from selective predation, thus favouring the establishment of a more heterogenic assemblage of microbes (consisting of Proteobacteria, Actinobacteria and Cytophaga-Flavobacteria). Our results suggest that the primary microbial colonizers of the water above dried sediments are passively released into the plankton and that their high growth potential is counteracted by the activity of bacterivorous protists.

Chlorinated ethenes contamination of soil and groundwater is a widespread problem in most industrialized countries. To date, there is a general consensus in the literature that members of the genus Dehalococcoides are required for complete dechlorination of these compounds. The availability of specific identification tools to track their distribution in the field is therefore a topic of particular relevance in environmental studies. These microorganisms have been successfully visualized by fluorescence in situ hybridization (FISH) in highly active dechlorinating cultures. However, FISH detection of Dehalococcoides under low activity conditions can be strongly hampered by their small cell size and low ribosome content. In this study, catalyzed reporter deposition (CARD)-FISH was employed as an alternative detection method. In a trichloroethene (TCE) dechlorinating enrichment culture, CARD-FISH, using proteinase K as a permeabilization pre-treatment, was found to be significantly superior to conventional FISH in terms of both microscopic visualization and quantification efficiency (about 30%). An application of this method on contaminated aquifer samples is also presented and discussed.

Bacterial degradation of mucilaginous aggregates (creamy layers, stringers and macroflocs) collected during two summer events (2001-2002) was tested. The objective was to describe the temporal trend of the bacterial activity, abundance and composition in the aggregated and dissolved organic matter under different trophic conditions. In the native aggregates proteins and organic phosphorous were actively hydrolyzed as aminopeptidase and alkaline phosphatase activities represented up to 87% and 25% of total activity, respectively; polysaccharides were less hydrolyzed and the highest activities were observed for beta-glucosidase (5% of the total). This hydrolysation pattern tends to a progressive accumulation of long persistent polysaccharides. During short term incubations nutrient addition (P, N and Glucose) differently stimulated bacterial growth in the seawater: P played the main role in stimulating bacterial production from 3 to 6 folds higher than in the control, whereas a secondary C-limitation was observed only for bacteria growing on seawater from macroflocs. This scarce dissolved organic carbon (DOC) bioavailability was confirmed by the lower DOC removal (13% macroflocs, 36% stringers). The total amount of carbon incorporated by bacteria living on aggregates was similar (0.58 mg C L(-1)) both in the control and under P enrichments showing a more balanced condition with respect to the seawater. Hence the well-known P limitation in the Northern Adriatic Sea affects only dissolved organic carbon uptake without influencing the uptake of aggregated organic matter. Organic matter limitation was observed only on stringers--total C incorporated raised to 0.96 mg C L(-1) after PNG addition. Macroflocs release of refractory compounds leads to DOC accumulation (73 microM DOC) contributing to inflate the pool of refractory DOC in the surrounding waters. Several evidences, including different monosaccharide composition of stringers and macroflocs (glucose 15% and 56% on stringers and macroflocs, respectively), bring to the conclusion that stringers are in an older stage in comparison with macroflocs. Community composition described by fluorescence in situ hybridization did not show significant differences between free-living and attached bacteria but it was modified by the different enrichment conditions: Cytophaga-Flavobacteria increased after inorganic nutrients enrichments while organics advantaged gamma-Proteobacteria.

Summary Bacterial communities associated with a variety of benthic detritus types were studied in three streams in the context of the chemical characteristics of the sediment material and the stream water. A cell purification assay was developed for a quantitative microscopic evaluation of bacterial community structure in detritus samples by fluorescence in situ hybridization (FISH). The efficiency of FISH with fluorescently monolabelled probes was compared with FISH with signal amplification by catalysed reporter deposition (CARD-FISH). In detritus types poor in organic carbon and nitrogen, the numbers of prokaryotes were related to the chemical characteristics of the stream water column, whereas no such relationship was found for detritus types rich in organic carbon and nitrogen. These results might help to provide criteria for the selection of detritus types for river ecosystem assessment and monitoring. The percentage of bacteria detected by FISH with monolabelled probes was correlated with the detritus total organic matter (OM). This is likely attributed to a higher ribosome content of microbial cells on substrates rich in OM. Cell detection by CARD-FISH did not show any correlation with OM content, indicating that this technique renders the results more independent from the activity state of cells. Fluorescence in situ hybridization with four group-specific probes suggested a relationship between substrate quality and the composition of the microbial assemblages on the various types of detritus. The improved protocol for cell purification and CARD-FISH may facilitate future investigations on the relationship between the riverine benthic detritus quality and microbial community composition.