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Active hydrothermal travertine systems are ideal environments to investigate how abiotic and biotic processes affect mineralization mechanisms and mineral fabric formation. In this study, a biogeochemical characterization of waters, dissolved gases, and microbial mats was performed together with a mineralogical investigation on travertine encrustations occurring at the outflow channel of a thermal spring. The comprehensive model, compiled by means of TOUGHREACT computational tool from measured parameters, revealed that mineral phases were differently influenced by either abiotic conditions or microbially driven processes. Microbial mats are shaped by light availability and temperature gradient of waters flowing along the channel. Mineralogical features were homogeneous throughout the system, with euhedral calcite crystals, related to inorganic precipitation induced by CO

The construction of offshore wind farms requires solving more and more complex logistical problems due to the increasing sizes of turbines and changing environments. In particular, the installation of substructures requires attention due to their significant impact on capital expenditures and the limited literature and guidelines available. In this paper, we develop a decision support tool consisting of a discrete-event simulation that allows for comparing strategies for the installation of offshore wind turbine substructures in terms of time and costs. We identify several combinations of transportation and installation strategies for monopile and for jacket substructures. The differentiation is based on the deployed vessels and the installation sequence of the components. The strategies are applied to the case of a wind farm in the North Sea. For both substructure types, we find that strategies involving a second installation vessel result in the shortest installation times, and those in which the installation vessel(s) take(s) care of both transportation and installation result in the lowest costs. Additionally, we quantify the performance increases as a result of a reduction of the most prominent bottlenecks and the sensitivity of the project performance to the start date. Finally, the results are discussed in relation to future market and technological developments in the field.

Microbial communities are major players in the biogeochemical processes and ecosystem functioning of river networks. Despite their importance in the ecosystem, biomonitoring tools relying on prokaryotes are still lacking. Only a few studies have employed both metabarcoding and quantitative techniques such as catalysed reported deposition fluorescence in situ hybridization (CARD-FISH) to analyse prokaryotic communities of epilithic biofilms in river ecosystems. We intended to investigate the efficacy of both techniques in detecting changes in microbial community structure associated with environmental drivers. We report a significant correlation between the prokaryotic community composition and pH in rivers from two different geographical areas in Norway. Both CARD-FISH and metabarcoding data were following the pattern of the environmental variables, but the main feature distinguishing the community composition was the regional difference itself. Beta-dispersion analyses on both CARD-FISH abundance and metabarcoding data revealed higher accuracy of metabarcoding to differentiate regions and river systems. The CARD-FISH results showed high variability, even for samples within the same river, probably due to some unmeasured microscale ecological variability which we could not resolve. We also present a statistical method, which uses variation coefficient and overall prevalence of taxonomic groups, to detect possible biological indicators among prokaryotes using metabarcoding data. The development of new prokaryotic bioindicators would benefit from both techniques used in this study, but metabarcoding seems to be faster and more reliable than CARD-FISH for large scale bio-assessment.

Supplementary data to this article can be found online at https://doi. org/10.1016/j.scitotenv.2021.151783, Environmental DNA (eDNA) metabarcoding (parallel sequencing of DNA/RNA for identification of whole communities within a targeted group) is revolutionizing the field of aquatic biomonitoring. To date, most metabarcoding studies aiming to assess the ecological status of aquatic ecosystems have focused on water eDNA and macroinvertebrate bulk samples. However, the eDNA metabarcoding has also been applied to soft sediment samples, mainly for assessing microbial or meiofaunal biota. Compared to classical methodologies based on manual sorting and morphological identification of benthic taxa, eDNA metabarcoding offers potentially important advantages for assessing the environmental quality of sediments. The methods and protocols utilized for sediment eDNA metabarcoding can vary considerably among studies, and standardization efforts are needed to improve their robustness, comparability and use within regulatory frameworks. Here, we review the available information on eDNA metabarcoding applied to sediment samples, with a focus on sampling, preservation, and DNA extraction steps. We discuss challenges specific to sediment eDNA analysis, including the variety of different sources and states of eDNA and its persistence in the sediment. This paper aims to identify good-practice strategies and facilitate method harmonization for routine use of sediment eDNA in future benthic monitoring., The work is the result of the DNAqua-Net workshop held in Rome, on June 10–12, 2019, organised by IRSA-CNR and supported by European Cooperation in Science and Technology (COST) grant CA15219 (DNAqua-Net). It largely benefited from the discussions with DNAqua-Net members during this event as well as other DNAqua-Net conferences.This study was carried out within the UNIVPM VIRIDE Project (n. 2017EKFA98) funded by the Ministry of University and Research of Italy (MUR) and the Italian National Project on the use of environmental DNA for the identification of marine non-indigenous species funded by the Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA). JP, TC, and LAPG were supported by the Swiss National Science Foundation (grant 31003A_179125) as well as FL with an Early Postdoc.Mobility grant (P2GEP3_171829). MS-M was supported by the Ministry of Education, Youth and Sports of the Czech Republic, European Regional Development Fund-Project CZ.02.1.01/0.0/0.0/16_019/0000845 and LTC 20063. KP was supported by the European Regional Development Fund within National Programme for Addressing Socio-Economic Challenges through R&D (L190003VLVI RITA1/02-60-05) and base financed project P190250PKKH of Estonian University of Life Sciences, IM was supported by the Slovenian Research Agency (ARRS) programme P4-0085. SD was supported by the Portuguese Foundation for Science and Technology (FCT) (CEECIND/00667/2017). LC was supported by the PON AIM 1854833 – PON Ricerca e Innovazione 2014–2020 – Azione I.2 – D.D. n. 407, 27/02/2018 – Attraction and International Mobility.VK was supported by grants PUT1389 (ETAg) and Institute of Technology, University of Tartu basic funding grant.

Although terrestrial hydrothermal systems are considered among the most fascinating environments, how their unique and extreme conditions can affect microorganisms selection and the role in biogeochemical cycles has not yet been well elucidated. A combined geochemical and microbiological exploration in waters and sediments from 10 sampling points along a sharp temperature gradient (15–90°C) within an extremely acidic hydrothermal system (Pisciarelli Spring, Campi Flegrei area, southern Italy) displayed how hydrothermal fluids influence the microbial dynamics. This area was characterized by high levels of reduced gaseous species (e.g. H2S, H2, CH4, CO) and very low pH values (

We study a typical problem within the air cargo supply chain, concerning the transportation of standard Unit Load Devices (ULDs) from freight forwarders’ to ground handlers’ warehouses. First, ULDs are picked up by a set of available trucks at the freight forwarders’ premises within a time window. Next, they are delivered to the ground handlers, also within a time window, and discharged according to a Last In First Out (LIFO) policy. Due to space constraints, ground handlers have limited capacity to serve the trucks and waiting times may arise, especially in case freight forwarders do not coordinate their operations. Therefore, in this paper we consider a cooperative framework where this transportation is coordinated by a central planner. The goal of the planner is to find a proper routing and scheduling that minimizes the sum of the transportation and waiting times at the ground handlers’ warehouses, while satisfying the capacity of the trucks. We propose two mathematical formulations, one based on the routing and the other based on the packing aspect of the problem. To solve large instances of the problem, an Adaptive Large Neighborhood Search algorithm is also developed. With numerical experiments, we compare the performances of the two models and the metaheuristic, and we quantify the benefits of the proposed framework to reduce waiting times.

The typical voyage of a barge transporting maritime containers inland, consists of visiting a set of terminals where loading/unloading operations occur. The required stowage plans must meet stability requirements during all transport phases and avoid costly re-handling operations. In this paper, we formalize this problem and consider a typical dry-port transport system. We propose a comprehensive mathematical model that seeks to maximize stowed containers. To solve it, we develop a hybrid metaheuristic approach, based on local search and an industrial solver. Numerical experiments, based on real-world data, provide insights into the performances of the proposed framework and current stowage practices.

BACKGROUND: Microbial electrochemical technologies (METs) represent a novel platform to harvest the energy trapped in municipal wastewater. At the anode of METs, electro‐active bacteria (EAB) anaerobically oxidize wastewater constituents using the electrode as the terminal electron acceptor and, by so doing, generate an electric current. To convert complex wastewater constituents into electricity, EAB must not only establish syntrophic relationships with other members of the microbial community, but also compete with methanogens for consumption of hydrogen and acetate. Here, we examined the addition of magnetite nanoparticles (NPs) (250 mg Fe L⁻¹) as a novel strategy to manipulate such metabolic interactions and in turn maximize the efficiency of wastewater treatment and the yield of electric current generation. RESULTS: Batch experiments carried out either in the presence of a mixture of volatile fatty acids or of a synthetic sewage demonstrated that magnetite addition accelerate the rate of electrogenic oxidation of specific compounds, particularly propionate (up to 120%), an intermediate which frequently accumulates during anaerobic treatment processes, while correspondingly enhancing electric current generation (up to 90%), and diminishing the rate of competing methane generation (up to 50%). Notably, the composition of the microbial community was not substantially affected by the presence of magnetite nanoparticles, possibly suggesting that these latter facilitated extracellular electron transfer mechanisms (among microbes and with the electrode), rather than enriching conditions for specific microorganisms. CONCLUSION: The addition of magnetite NPs may represent a practical strategy to kick‐start a bioelectrochemical system designed for wastewater treatment and improve the effectiveness of electrogenic substrate oxidation processes. © 2019 Society of Chemical Industry

Offshore wind energy is recognised globally as a viable alternative to finite energy sources. However, large cost reductions are still needed, particularly in the Operations & Maintenance (O&M) phase, which currently accounts for about 30% of the cost of offshore wind. For large component replacements, a jack-up vessel is often leased from the spot market, resulting in high costs and low utilisation. These costs can be lowered when multiple wind farm service providers would share the resources needed to employ jack-up vessels. In this paper, we analyse two types of resource sharing, as an alternative to each service provider leasing its own vessel: (i) vessel purchasing and sharing and (ii) the combined use of vessel and harbour sharing. We design a simulation model and include stochastic processes such as weather patterns and component failures. Results show that cost benefits up to 45% can be achieved compared to a leasing policy, depending on the number of wind farm service providers involved and on the geographical distance between offshore wind farms. Moreover, it is shown that the jack-up vessel should not be fully utilised to minimise costs. The performance benefits of harbour sharing in addition to vessel sharing are generally small, but become more significant if the network faces considerable congestion. Results are illustrated using a case study based on a setting in the Western North Sea.

International audience; Bioindication has become an indispensable part of water quality monitoring in most countries of the world, with the presence and abundance of bioindicator taxa, mostly multicellular eukaryotes, used for biotic indices. In contrast, microbes (bacteria, archaea and protists) are seldom used as bioindicators in routine assessments, although they have been recognized for their importance in environmental processes. Recently, the use of molecular methods has revealed unexpected diversity within known functional groups and novel metabolic pathways that are particularly important in energy and nutrient cycling. In various habitats, microbial communities respond to eutrophication, metals, and natural or anthropogenic organic pollutants through changes in diversity and function. In this review, we evaluated the common trends in these changes, documenting that they have value as bioindicators and can be used not only for monitoring but also for improving our understanding of the major processes in lotic and lentic environments. Current knowledge provides a solid foundation for exploiting microbial taxa, community structures and diversity, as well as functional genes, in novel monitoring programs. These microbial community measures can also be combined into biotic indices, improving the resolution of individual bioindicators. Here, we assess particular molecular approaches complemented by advanced bioinformatic analysis, as these are the most promising with respect to detailed bioindication value. We conclude that microbial community dynamics are a missing link important for our understanding of rapid changes in the structure and function of aquatic ecosystems, and should be addressed in the future environmental monitoring of freshwater ecosystems.

This book represents a synthesis of knowledge and best practice in the field of DNA-based biomonitoring at the time of writing. It has been written with end-users of molecular tools in mind, as well as those who are new to the field in research settings and are looking to gain an overall grounding in the subject area. For each of the main types of sample (water, soil / sediment, bulk invertebrates and diatoms), and for each stage of the field and laboratory processes, we outline key considerations, decisions that need to be made, factors that might influence those decisions, and trade-offs inherent in the choices made. We hope that this will help users, practitioners, and those commissioning DNA-based monitoring programmes to navigate this large field and critically evaluate the strengths and weaknesses of different analysis workflows based on context, project aims and available resources., ISBN:978-619-248-052-3, ISBN:978-619-248-053-0

In this paper, we will study a typical problem in inland container shipping, concerning the barge transportation of maritime containers between a dry port and a set of seaport terminals. The barges depart from the dry port and visit a set of sea terminals, where containers need either to be dropped off or picked up. The goal is to achieve economies of scale with barges and avoid trucking as much as possible. The decision thus involves finding the best allocation of containers to barges in order to guarantee on-time delivery and meet capacity restrictions. The problem will be modeled as a variant of the split vehicle routing problem with simultaneous pickups and deliveries coupled with time features. The model includes parameters that can be tuned to improve barge utilization and travelling distance. A hybrid local search meta-heuristic algorithm, combined with a branch-and-cut solver, will be developed to solve the model. Numerical experiments have been conducted to test the performance of the algorithm and provide solution analysis for practical insights. Real-world data has been collected from a local barge operator based in the Port of Rotterdam region and will be used as input for the experiments. This will result in an in-depth analysis into current planning practices. The proposed framework complements existing models in the literature and contributes to the development of a comprehensive set of decision support tools, which help in the decision-making process for inland terminals.

Lago Exsnia-Viscosa is located in the eastern part of Rome, on the left bank of Tiber river, close to the historical centre of the city and in a highly urbanized area. The lake takes its name from the factory of artificial silk, the SNIA Viscosa, active there from 1923 to 1954. The industrial plant, located close to the Marranella ditch, used its water for the production processes, also after its channelled and covered. The Marranella ditch was named also Acqua Bullicante (in English “Bubbling water”). It is supposed that the ditch was hosted along a fault where bubbling waters and diffuse degassing from soil were recognized. These manifestations were dominated in CO2 but due to the intensive post-war (Second World War) building expansion, no trace remain. These phenomena are typically recognizable in volcanic areas characterized by active hydrothermalis, such as the neighbour volcanic district of Alban Hills. The proximity of this volcanic district to Rome and the fact that it cannot be considered extinct have moved our motivation to study the Lake Exsnia-Viscosa to investigate on possible degassing phenomena in the city centre. The lake appeared in the ‘90s, after illegal excavations (deep up to 10-13 meters) to build unlawfully a shopping center. This caused a leakage of groundwater and the emergence of a small lake (about 7,000 m2 large, around 7 meters deep). Due to the citizen protests, the works were immediately blocked and the whole area was expropriated and closed. The site, has remained closed, from ‘90s to today, favouring re-naturalization processes, new ecological systems and forbidding anthropogenic transformations. Currently, it represents a precious green area for the city, but is still in danger of being threatened by speculation. For this reason, the citizen is fighting for its recognition as natural heritage supported by cultural and professional associations. In this framework, our study, moved at the beginning to investigate on degassing phenomena, proved to be an important step in the process of recognition of the site as natural heritage. The lake has been used by us as an open-air laboratory collecting water along a vertical profile from the lake surface to the maximum depth, for a geochemical and microbial characterization of the groundwaters. Currently, the results are supporting the community and the local administration in order to make this green site a protected area to donate to their citizens.

Urban lakes have become increasingly important in the planning of urban ecology, green infrastructure and green areas in European cities. This paper describes the chemical, isotope and microbial features of Lake Bullicante, a small artificial lake located within the urban area of the city of Rome. It has an anthropogenic origin due to excavation works that intercepted the underlying aquifer, giving rise to a water body. The lake area is 7.000 m2, with a maximum depth of 7 m and located on the distal deposits of the Alban Hills Volcanic District in an area named "Acqua Bullicante" (i.e. Bubbling Water), where degassing phenomena were historically recorded. The proximity of this volcanic district motivated the study on Lake Bullicante as a potential open-air laboratory to trace possible degassing phenomena in a highly urbanized area. A preliminary geochemical and microbial sampling survey was carried out in winter 2018. Samples were collected along a vertical profile of the lake from the surface to the maximum depth. Major, minor, trace elements, dissolved gases and stable isotopes (deltaD-H2O, delta18OH 2O, delta13C-CO2) were analyzed, along with the analysis of 87Sr/86Sr ratio. The microbial community characteristics were analysed by epifluorescence microscopy (CARD-FISH) and flow cytometry. The chemical composition and water isotopes suggest that lake water has a meteoric origin and is related to a Ca-HCO3 shallow aquifer hosted in volcanic rocks. This is confirmed by both the 87Sr/86Sr ratio of lake water, which falls in the range of values of Alban Hills volcanites, and the chemical-isotopic composition of neighboring wells. A relatively high concentration of dissolved CO2, its isotopic signature (delta13C-CO2 20%o V-PDB), and the high content in organic matter (DOC 10-30 mg/L) suggest for the lake an eutrophication state with denitrification also occurring. Considering the relatively high concentrations of dissolved CO2, an external input of carbon dioxide cannot be completely excluded and as a consequence, not even the hypothesis of mixing processes between biotic and inorganic CO2. This makes further investigations necessary especially during the summer, when the lake is stratified. A summer survey could be also useful to better understand the microbial processes into the lake, its eutrophication evolution and health status, and to plan eventual proper remediation strategies, providing important tools to the local administration and stakeholders to improve, protect and preserve this ecological niche.

In this work, an untargeted approach based on ultra-high performance liquid chromatography coupled to high-resolution tandem mass spectrometry (UHPLC-HRMS/MS) was employed for the analysis of contaminants in surface water samples, possibly deriving from an ineffective removal by wastewater treatment plants or illicit release. First, solid-phase extraction (SPE) conditions for 30 target compounds were optimized for two different sorbents, namely the commercial Oasis HLB and graphitized carbon black (GCB), by Box-Behnken designs of experiments. Upon identification of optimal conditions, the two SPE materials yielded comparable extraction recoveries, ranging between 52-110% and 55-100% for Oasis HLB and GCB, respectively. Thereafter, river water samples collected in five locations near Rome (Italy) were extracted using both sorbents and then analyzed by UHPLC-HRMS/MS in both positive and negative electrospray (ESI) ion polarities. The retrieved raw data files were submitted to Compound Discoverer software and compound identification was tentatively assigned by matching their tandem mass spectra with the mzCloud mass spectral library and manual validation, resulting in a total of 241 identified compounds (211 and 40 in positive and negative ESI mode, respectively), mainly belonging to pharmaceuticals.

Increase of congestion at container deep seaports and shortage of capacity has led inland transport systems worldwide to rely more and more on inland terminals, and on the use of high capacity modes of transport to generate economies of scale and reduce negative effects of trucking. In this setting, planning the transport of maritime containers between a deep seaport and a final inland destination must also consider due dates and soft time windows, the latter known as Demurrage and Detention (D&D). In this paper, we formalize the concept of D&D, model the multimodal planning problem, and assess the impact of different D&D regimes on the emerging inland transport systems. By means of an experimental framework, we compare different D&D policies and provide managerial insights. The experiments highlight the effects of existing D&D regimes on transport efficiency and provide guidelines for their choice in practice. D&D are shown to have a twofold effect: first to limit consolidation opportunities and force the use of trucks as buffer, and second to push containers to dwell unnecessarily at the seaports.

The volcanic and tectonic lakes of the eastern branch of the African Great Rift Valley are exposed to multiple stressors and characterised by different levels of hydrological connectivity. Past volcanic activity generated endorheic basins, in which the nature of the bedrock, its connection with groundwater, and local climatic conditions, favoured the formation of highly alkaline soda waters. While little is known about their nutrient dynamics, most lakes in this area experience considerable microbial blooms and harbour diverse and specifically adapted microbial populations, some of which could embody novel biotechnological potential. Here we review the geochemical and (micro)biological features of a cluster of lakes distributed within the East African Rift, ranging from fresh to hypersaline, under different levels of hydrological connectivity. Possibly no other location on Earth has a comparable range of lake types in close proximity to each other and representing such a remarkable microbial biodiversity. Environmental heterogeneity and habitat connectivity among adjacent aquatic ecosystems may have positive implications in terms of regional environmental stability by enhancing the overall carrying capacity, i.e. the resilience to various forms of impact, contributing to biodiversity protection. Within these ecosystems, microbial processes encompass the entire basis of their primary production, in particular those driven by cyanobacteria. Combining a multi-disciplinary ecohydrological approach with a biogeochemical investigation of the principles underlying their functioning, our study can contribute to the development of appropriate environmental protection measures to effectively maintain their natural capital.

Flow cytometry is suitable to discriminate and quantify aquatic microbial cells within a spectrum of fluorescence and light scatter signals. Using fixed gating and operational settings, we developed a finite distribution mixture model, followed by the Voronoi tessellation, to resolve bivariate cytometric profiles into cohesive subgroups of events. 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 subgroups within each of the commonly retrieved populations of cells with Low and High content of Nucleic Acids (namely, LNA, and HNA cells). Moreover, the advanced analysis allowed assessing changes of community patterns perturbed by a wastewater feed. Our approach for cytometric data deconvolution confirmed that flow cytometry could represent a prime candidate technology for assessing microbial community patterns in flowing waters. © 2017 International Society for Advancement of Cytometry.

Direct and indirect effects of extremely high geogenic CO2 levels, commonly occurring in volcanic and hydrothermal environments, on biogeochemical processes in soil are poorly understood. This study investigated a sinkhole in Italy where long-term emissions of thermometamorphic-derived CO2 are associated with accumulation of carbon in the topsoil and removal of inorganic carbon in low pH environments at the bottom of the sinkhole. The comparison between interstitial soil gasses and those collected in an adjacent bubbling pool and the analysis of the carbon isotopic composition of CO2 and CH4 clearly indicated the occurrence of CH4 oxidation and negligible methanogenesis in soils at the bottom of the sinkhole. Extremely high CO2 concentrations resulted in higher microbial abundance (up to 4 × 109 cell g-1 DW) and a lower microbial diversity by favoring bacteria already reported to be involved in acetogenesis in mofette soils (i.e., Firmicutes, Chloroflexi, and Acidobacteria). Laboratory incubations to test the acetogenic and methanogenic potential clearly showed that all the mofette soil supplied with hydrogen gas displayed a remarkable CO2 fixation potential, primarily due to the activity of acetogenic microorganisms. By contrast, negligible production of acetate occurred in control tests incubated with the same soils, under identical conditions, without the addition of hydrogen. In this study, we report how changes in diversity and functions of the soil microbial community - induced by high CO2 concentration - create peculiar biogeochemical profile. CO2 emission affects carbon cycling through: (i) inhibition of the decomposition of the organic carbon and (ii) promotion of CO2-fixation via the acetyl-CoA pathway. Sites naturally exposed to extremely high CO2 levels could potentially represent an untapped source of microorganisms with unique capabilities to catalytically convert CO2 into valuable organic chemicals and fuels.

This study represents the first example in which benthic heterotrophic and photoautotrophic microbial communities (prokaryotes and microphytobenthos-MPB, respectively) were simultaneously investigated. To explore how they synergistically respond to multiple natural and anthropogenic stressors, in the framework of the Project RITMARE four lagoons of the Po River Delta were sampled in May 2016: two with more marine features, i.e. Scardovari (SC) and Caleri (CL), and two more directly affected by the Po River flow, i.e. Canarin (CN) and Vallona-Marinetta (MV). The abundance and structure of benthic communities were related to physical-chemical parameters i.e. grain-size, total N, total organic C, stable C and N isotopes, and synthetic organic contaminants. Stations were gathered into three distinct groups (R-ansosim = 0.540 p < 0.001) according to their different physical-chemical features: outer, inner-freshwater and inner-marine sites. Contamination levels did not seem to severely affect the microbial abundances that were overall stimulated by the combined effect of high organic and nutrient loads: prokaryotes up to + 42% and MPB up to +93%. Bacteria and Archaea displayed high densities at sites directly influenced by the freshwater input and anthropogenically derived nitrogen. Delta- (30.8%), Alpha- (12.8%), Gamma- (11.8%) and Beta-Proteobacteria (7.1%) were the dominant classes at all sites. For both communities, a significant inter-lagoonal (among different lagoons) and infra-lagoonal (among stations within the same lagoon) pattern was highlighted by PERMANOVA. nMDS and SIMPER analyses revealed distinct assemblages in the inner and outer parts of the lagoons. We applied a novel functional approach based on diatom life modes. At inner and outer sites, different diatom living forms developed: epipsammic (on sand) nearby the lagoonal mouths, epipelic (on mud) at the innermost sites and non-benthic forms (planktonic, tychopelagic and epiphytic) at sites directly influenced by freshwater. Distance-based Linear Models further indicated that salinity, clay and temperature were the significant drivers of the prokaryotic spatial distribution whereas clay, PAHs, PCBs and salinity best explained the MPB structure. The dominance of non-benthic diatom life modes in the more polluted lagoon (CN) suggests a negative influence of contamination on the MPB structure. Two diatom keystone species likely contribute to restore the oxic gradient in sediments frequently exposed to anoxia, allowing the subsequent microbial aerobic degradation and the recolonization of higher trophic organisms. The capacity of re-oxygenation after anoxia has important ecological and economic implications in lagoons exploited for aquaculture.

Heterotrophic bacteria play a key role in the degradation of organic matter and carbon cycling in river sediments. These bacterial communities are directly influenced by environmental variables that differ spatially and temporally in rivers. Here, we studied the longitudinal patterns of sediment bacterial community composition and dissolved organic matter utilization under base flow and drought conditions in a Mediterranean river. Our results indicated that sediment microbial communities were affected by dissolved organic matter quality and origin along the river continuum. In headwaters the potential degradation of cellulose and hemicellulose was greater (i.e., higher β-glucosidase and β-xylosidase activities), suggesting higher microbial utilization of allochthonous detritus from terrestrial origin. Conversely, the accumulation and transport of more recalcitrant compounds (i.e., decrease in the recalcitrant index) became potentially relevant downstream. Furthermore, discharge fluctuations had clear effects on bacterial community composition and dissolved organic matter use. The hydrological fragmentation of the river continuum during drought period generated sediment microhabitats dominated by gamma and delta-Proteobacteria, with a greater potential capacity to degrade a wide range of compounds, particularly nitrogen containing moieties. During base flow conditions, we observed a higher occurrence of alpha-Proteobacteria and a greater potential use of more recalcitrant carbon compounds, mostly of terrestrial origin. Overall, our findings suggest an upstream-downstream longitudinal transition of sediment microbial communities that rely on allochthonous to autochthonous dissolved organic matter, and a shift toward autochthonous dissolved organic matter reliance during drought.

Microorganisms play an important role in speciation and mobility of arsenic in the environment, by mediating redox transformations of both inorganic and organic species. Since arsenite [As(III)] is more toxic than arsenate [As(V)] to the biota, the microbial driven processes of As(V) reduction and As(III) oxidation may play a prominent role in mediating the environmental impact of arsenic contamination. However, little is known about the ecology and dynamics of As(III)-oxidizing populations within native microbial communities exposed to natural high levels of As. In this study, two techniques for single cell quantification (i.e., flow cytometry, CARD-FISH) were used to analyze the structure of aquatic microbial communities across a gradient of arsenic (As) contamination in different freshwater environments (i.e., groundwaters, surface and thermal waters). Moreover, we followed the structural evolution of these communities and their capacity to oxidize arsenite, when experimentally exposed to high As(III) concentrations in experimental microcosms. Betaproteobacteria and Deltaproteobacteria were the main groups retrieved in groundwaters and surface waters, while Beta and Gammaproteobacteria dominated the bacteria community in thermal waters. At the end of microcosm incubations, the communities were able to oxidize up to 95 % of arsenite, with an increase of Alphaproteobacteria in most of the experimental conditions. Finally, heterotrophic As(III)-oxidizing strains (one Alphaproteobacteria and two Gammaproteobacteria) were isolated from As rich waters. Our findings underlined that native microbial communities from different arsenic-contaminated freshwaters can efficiently perform arsenite oxidation, thus contributing to reduce the overall As toxicity to the aquatic biota.

Quorum sensing signals regulate various functions within activated sludge processes such as formation of microbial aggregates. Disturbance of this signaling system, known as quorum quenching (QQ), provides opportunities for eliminating some problems related to biological wastewater treatment (e.g., biofouling and excess sludge production). However, it is poorly understood how and to what extent QQ systems can affect the microbial aggregation processes and the following floc formation. In particular, an in-depth structural characterization at the scale of microbial aggregate while considering nutrient conditions in the reactor is still largely disregarded. Here, we evaluated the QQ effects at the short-term time scale (i.e., after 4 h for the exogenous period and 19 h for exogenous/endogenous period), by combining advanced techniques for microbial characterization (flow cytometry, CARD-FISH, and confocal laser scanning microscopy) and conventional physical-chemical assessments. The results indicated that by implementing QQ agents (immobilized Acylase I enzyme in porous alginate beads) the abundance of single cells and suspended microbial aggregates in the supernatant did not show significant changes during the exogenous period. Conversely, at the end of the exogenous/endogenous period a significant increase of single prokaryotic cells, small and large microbial aggregates favored the growth of grazers, including free-living nanoflagellates and ciliates. Flocs became looser and thinner than those in the control reactor, thus affecting the sludge settling behavior. Inability of microbial community in degradation of soluble protein during the endogenous period confirmed that the QQ agents are likely to inhibit the secretion of protease enzyme within microbial communities of activated sludge.

The influence of the freshwater runoff on marine prokaryotes has been largelly studied in the pelagic environment, little is known about the effects on the prokaryotes in coastal sediments. We investigated the distribution of benthic prokaryotes in the northern Adriatic Sea, when an extreme Po River flood event determined high heterogeneity along the estuarine salinity gradient (from mainly freshwater to marine). The microbial diversity was assessed by 16S rRNA gene Illumina sequencing, the quantification of the dominant taxa of Bacteria and Archaea by microscopy techniques (CARD-FISH). Our results showed dominance of Bacteria (eight-fold higher) over Archaea, and highlighted Proteobacteria as the most represented phylum, followed by Bacteroidetes. Prokaryotic abundance, quantified by DAPI staining, was mainly affected by sediment characteristics (Total Organic C and Total N contents, and silt fraction). Abundance reached the highest values in sites directly affected by the plume (range 7.3 × 108 - 2.8 × 109 cell g−1). A considerable difference in prokaryotes composition was observed along the salinity gradient, with an increasing presence of freshwater taxa at stations more influenced by the river discharge. CARD-FISH analyses corroborated these findings, showing higher abundance of beta-Proteobacteria and Planctomycetes at stations closest to the river mouths. Nevertheless, a core microbiome (about 10% of the total OTUs) was present across all the study areas, indicating the ability of this assemblage to survive in rather diverse environmental conditions, differently impacted by the river plume. Our results show that the river plume can affect the diversity and distribution patterns of benthic prokaryotes far into the pro-delta, although further investigations are needed in order to understand how the mixing of bacterial communities of different origin might reflect on ecosystem functioning.

Glyphosate-based herbicides are widely used for several crops, such as transgenic soybean and forestry. The aim of this study was to determine the effect of glyphosate on the community structure of riverine bacterioplankton and to evaluate the potential of bacterioplankton to degrade the herbicide. River water to which 13C-labelled glyphosate (10, 100µgL–1) was added or not (control) was incubated for 6 days at the temperature measured in situ (20°C). Significant differences in bacterioplankton community composition, as assessed by microfluidics-based automated ribosomal intergenic spacer analysis, were found among treatments, with differences in the presence of 100µgL–1 of glyphosate being more pronounced, namely significant decreases in bacterial richness and diversity. The glyphosate degradation product aminomethylphosphonic acid (AMPA) was detected, accounting for 1.2% of glyphosate conversion in water with 100µgL–1 of 13C-labelled glyphosate, together with a significant enrichment of 13C in the bacterial biomass. These findings suggest that glyphosate had a direct detrimental effect on most bacterioplankton taxa, but enriched those that were able to degrade the herbicide. Together, the results indicate that glyphosate degradation in the river assessed would be a slow process (months–years), taking place through the AMPA degradation pathway and meaning glyphosate accumulate in the ecosystem.

An integrated geochemical and microbiological investigation of soils from the Solfatara Crater (Campi Flegrei, southern Italy) demonstrated that interstitial soil gases dominated by CO2 and other typical hydrothermal gaseous species (e.g. H2S, CH4, ethane, benzene, alkenes and S-bearing organic compounds) influenced the composition of microbial communities. The relatively high concentrations of hydrothermal fluids permeating the soil produced acidic conditions and whitish deposits that characterize the Solfatara Crater floor. Archaea and Bacteria showed almost equal cell abundance (up to 3.2 x 10(7) and 4.2 x 10(7) cell/g, respectively) with relatively low levels of biodiversity and equitability in sites characterized by elevated temperatures (up to 70 degrees C), very low pH values (up to 2.2) and reducing conditions. In these sites, high-throughput sequencing showed the marked selection of microorganisms, mainly affiliated with the genera Thermoplasma, Ferroplasma and Acidithiobacillus. A relatively high biodiversity and concomitant distinctive structure of the microbial community were observed in soils poorly affected by fumarolic emissions that were oxic and rich in organic matter.

Arsenic (As) contamination in drinking water represents a worldwide threat to human health. During last decades, the exploitation of microbial As-transformations has been proposed for bioremediation applications. Among biological methods for As-contaminated water treatment, microbial As(III)-oxidation is one of the most promising approaches since it can be coupled to commonly used adsorption removal technologies, without requiring the addition of chemicals and producing toxic by-products. Despite the As(III) oxidation capability has been described in several bacterial pure or enrichment cultures, very little is known about the real potentialities of this process when mixed microbial communities, naturally occurring in As contaminated waters, are used. This study highlighted the contribution of native groundwater bacteria to As(III)-oxidation in biofilters, under conditions suitable for a household-scale treatment system. This work elucidated the influence of a variety of experimental conditions (i.e., various filling materials, flow rates, As(III) inflow concentration, As(III):As(V) ratio, filter volumes) on the microbially-mediated As(III)-oxidation process in terms of oxidation efficiency and rate. The highest oxidation efficiencies (up to 90% in 3 h) were found on coarse sand biofilters treating total initial As concentration of 100 μg L−1. The detailed microbial characterization of the As(III) oxidizing biofilms revealed the occurrence of several OTUs affiliated with families known to oxidize As(III) (e.g., Burkholderiaceae, Comamonadaceae, Rhodobacteraceae, Xanthomonadaceae). Furthermore, As-related functional genes increased in biofilter systems in line with the observed oxidative performances.

Uncertainties exist regarding the magnitude of in situ dissolved organic matter (DOM) processing in lotic systems. In addition, little is known about the effects of extreme hydrological events on in-stream DOM retention or release during downriver transport. This study quantified the net in-stream retention/release efficiencies (η) of dissolved organic carbon (DOC) and its humic and protein-like fluorescent fractions along a Mediterranean river during drought, baseflow and flood conditions. High performance size exclusion chromatography was used to describe the apparent size distributions of the humic and protein-like DOM moieties. A snapshot mass balance allowed estimating the η values of DOC and humic and protein-like fractions. Significant DOM net retention (η < 0) was detected during the drought condition and the protein-like fraction was more retained than the humic-like fraction and bulk DOC. In addition, small substances were more efficiently retained than larger substances. DOC retention decreased under baseflow conditions, but it remained significant. The humic and protein-like net efficiencies exhibited high variability, but the net retention were not significant. From a longitudinal perspective, the entire fluvial corridor contributed net retention of DOC and humic and protein-like moieties net retention during drought condition. In contrast, net retention/release efficiencies exhibited spatial variability during baseflow condition. The flood preferentially mobilized large size DOM molecules and the fluvial corridor behaved as a homogeneous passive DOM (η = 0) conduit. This research highlights the relevance of hydrological extreme events on the magnitude of DOM retention/release mass balance and emphasizes the need to perform measurements during these conditions to quantify the impact of fluvial corridors on DOM fate and transport This research is funded by the Spanish Ministry of Education and Science (MEC) (CGL2011-30151-C02 and CGL2014-5876-C3-R) and European Community 7th Framework Programme (No. 603629- ENV-2013-6.2.1-Globaqua)

Microbial electrochemical systems (MES) represent an innovative reagent-free technology for in situ remediation of groundwater contaminated by petroleum hydrocarbons. Here we describe the long-term (>160 days) anaerobic treatment of synthetic groundwater containing toluene (25 mg L−1) in a novel laboratory-scale, continuous-flow bioelectrochemical reactor, termed the “bioelectric well”. Under optimal operating conditions (i.e., anode potential potentiostatically controlled at +0.2 V vs. SHE and recycle flow-rate set at 75 mL min−1), the observed electrogenic toluene oxidation rate was 67.2 ± 5.7 mg L d−1, a value which is among the highest reported in the literature for laboratory-scale anaerobic treatment systems. Correspondingly, electric current was 5.1 ± 0.1 mA and the Coulombic efficiency (i.e., the yield of toluene conversion into electric current) was 79 ± 7%. Electrogenic toluene oxidation was most likely catalyzed by Geobacter species, which were found to dominate the surface of the graphite anode. The combined application of GC-MS (for detection and identification of metabolites) and qPCR (for quantification of functional genes) revealed that toluene degradation was initiated by fumarate addition, an activation pathway that is widely distributed among anaerobic hydrocarbon-degrading microorganisms. Collectively, the results of this study indicate that the bioelectric well holds remarkable potential for in situ treatment of groundwater contaminated by petroleum hydrocarbons.