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The contribution of oxic methane production to greenhouse gas emissions from lakes is globally relevant, yet uncertainties remain about the levels up to which methanogenesis can counterbalance methanotrophy by leading to CH4 oversaturation in productive surface waters. Here, we explored the biogeochemical and microbial community variation patterns in a meromictic soda lake, in the East African Rift Valley (Kenya), showing an extraordinarily high concentration of methane in oxic waters (up to 156 µmol L−1). Vertical profiles of dissolved gases and their isotopic signature indicated a biogenic origin of CH4. A bloom of Oxyphotobacteria co-occurred with abundant hydrogenotrophic and acetoclastic methanogens, mostly found within suspended aggregates promoting the interactions between Bacteria, Cyanobacteria, and Archaea. Moreover, aggregate sedimentation appeared critical in connecting the lake compartments through biomass and organic matter transfer. Our findings provide insights into understanding how hydrogeochemical features of a meromictic soda lake, the origin of carbon sources, and the microbial community profiles, could promote methane oversaturation and production up to exceptionally high rates., Fazi et al. report on an extraordinarily high biogenic methane concentration detected in the surface water of Lake Sonachi, Kenya. Using gas chromatography and microbiome profiling, they determine that these high concentrations are associated with cyanobacterial blooms and help provide insight to methanogenesis in meromictic soda lakes.

The Pasvik River experiences chemical, physical, and biological stressors due to the direct discharges of domestic sewage from settlements located within the catchment, runoff from smelter and mine wastes. Sediments, as a natural repository of organic matter and associated contaminants, are of global concern for the possible release of pollutants in the water column, with detrimental effects on aquatic organisms. The present study was aimed at characterizing the riverine benthic microbial community, evaluating its ecological role in relation to the contamination level. Sediments were sampled along the river during two contrasting environmental periods (i.e., beginning and ongoing phases of ice-melting). Microbial enzymatic activities, cell abundance, and morphological traits were evaluated, along with the phylogenetic community composition. Bacterial 16S rRNA genes were amplified and sequenced using next-generation sequencing technology. Sediments were also analyzed for a variety of chemical features, namely particulate material characteristics and concentration of polychlorobiphenyls, polycyclic aromatic hydrocarbons and pesticides. Riverine and brackish sites did not affect the microbial community in terms of main phylogenetic diversity (at phylum level), morphometry, enzymatic activities and abundance. Instead, bacterial diversity in the river sediments appeared to be influenced by the micro-niche conditions, with differences in the relative abundance of selected taxa. In particular, our results highlighted the occurrence of bacterial taxa directly involved in the C, Fe, and N cycles, as well as in the degradation of organic pollutants and toxic compounds.

The effects of climate change-induced ice melting on the microbial communities in different glacial-fed aquatic systems have been reported, but seasonal dynamics remain poorly inves-tigated. In this study, the structural and functional traits of the aquatic microbial community were assessed along with the hydrological and biogeochemical variation patterns of the Arctic Pasvik River under riverine and brackish conditions at the beginning (May = Ice-melt(-)) and during the ice-melting season (July = Ice-melt(+)). The microbial abundance and morphometric analysis showed a spatial diversification between the riverine and brackish stations. Results highlighted different levels of microbial respiration and activities with different carbon and phosphorous utilization pathways, thus suggesting an active biogeochemical cycling along the river especially at the beginning of the ice-melting period. At Ice-melt(-), Gammaproteobacteria and Alphaproteobacteria were dominant in riverine and brackish stations, respectively. Conversely at Ice-melt(+), the microbial community composition was more homogeneously distributed along the river (Gammaproteobacteria>Alphaproteobacteria> Bacteroidetes). Our findings provide evidence on how riverine microbial communities adapt and respond to seasonal ice melting in glacial-fed aquatic ecosystems.

Little is known about the quantity and quality of dissolved organic matter (DOM) in waters from continental geothermal systems, with only a few reports available from the Yellowstone US National Park. In this study, we explored the chemodiversity of DOM in water samples collected from two geothermal hot springs from the Kenyan East African Rift Valley, a region extremely rich in fumaroles, geysers, and spouting springs, located in close proximity to volcanic lakes. The DOM characterization included in-depth assessments performed by negative electrospray ionization Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). Reduced, saturated and little aromatic DOM compounds were dominant in the hot spring waters collected from either the Ol Njorowa gorge (ON) or the south shore of the soda-saline Lake Elementaita (ELM). Oxygen-poor and sulfur-bearing DOM molecules prevailed in ON, probably reflecting abiotic sulfurization from sulfide-rich geofluids. Nitrogen-bearing aliphatic and protein-like molecules were abundant in ELM, possibly perfusing through the organic-rich sediments of the adjacent Lake Elementaita. Notably, the heat-altered DOM of ancient autochthonous derivation could represent an overlooked source of aliphatic organic carbon for connected lentic environments, with a potential direct impact on nutrient cycling in lakes that receive geothermal water inputs.

Aquifers represent the largest accessible and fragile resource of freshwater on Earth. The municipal solid waste disposal in landfills, followed by the dispersion of leachate, is among the major threats for groundwater ecosystems, which harbour different microbial taxa generally adapted to low availability of organic carbon and nutrients. The aim of this study was to explore how groundwater quality can influence major microbial community characteristics, and particularly the functional diversity and metabolic responsiveness to a spectrum of organic carbon inputs. We hypothesized that the landfill-induced water quality changes will represent relevant stress factor for the ecological dynamics of groundwater microbial communities. A comprehensive study of a deep aquifer underlying a municipal solid waste landfill was performed in Central Italy across a network of twelve piezometers. Along with major physical-chemical parameters, the microbial community structure and the microbiological contamination (total coliforms and Escherichia coli), were assessed respectively by flow cytometry and the test Colilert-18. The BIOLOG EcoPlates(TM) assay was used to analyze the metabolic potential and the organic substrate utilization profiles. Three groundwater groups with distinct hydrogeochemical characteristics (pristine, mixed and altered conditions) were identified across the landfill area. Relatively higher total cell counts and the presence of E. coli under altered conditions suggested the occurrence of land-derived inputs. The kinetic analysis of the BIOLOG profiles showed that the aquatic microorganisms in samples from altered conditions were relatively more efficient in metabolizing a larger number of organic substrates, including complex structural molecules of xenobiotic origin. Our outcomes showed that the landfill-induced groundwater quality changes can directly affect the oxidation-reduction potential and the overall carbon cycle. Moreover, a multidisciplinary methodological approach is likely to represent a supportive tool to better characterize the impact of groundwater quality alterations, with potential consequences on the ecosystem functioning.

The spatial and temporal distribution of microbial biomass and metabolic rates were investigated in water samples collected along the Pasvik River (Arctic Norway) from 9 stations during two sampling campaigns (May and July 2014). Water samples were analyzed for physico-chemical parameters, viable bacterial abundance (VCs), prokaryotic abundance (PA), microbial enzymatic and respiratory activity. All data were statistically analyzed. VCs were generally homogeneous in May and July. PA showing enhanced abundance in July and higher values in the outer than in inner stations. Microbial respiration was higher in July than in May. Pearson's correlation coefficients showed that physical and chemical parameters affected both the PA and functionality. Respiration was significantly related to Temperature, suggesting its stimulation on the oxidation process. ANOSIM analysis showed seasonal significant differences (R=0.231, p=0.002), with temperature accounting for 11.4% of total variability. Psychrophilic microorganisms of the Pasvik river appear to be quite plastic to acclimate to seasonal changes of the cold habitat in which they live, modifying their abundance and metabolism, although further research is needed for a deepen knowledge of this Arctic ecosystem.

Polar Regions are experiencing multiple environmental stressors and the increasing contaminant influxes are likely becoming more severe. As filter-feeders, in Porifera ingestion becomes the primary route in the uptake and accumulation of particle-associated contaminants, which may accumulate in animal tissues. Porifera also provide an important habitat for aquatic prokaryotes that colonize outer surfaces and interstices of ostia and oscula, and may be particularly responsive against contaminants accumulated in the sponge tissues. Symbiotic microorganisms can adhere to the sponge surfaces by forming biofilm with complex 3D-structures, composed by microbial consortia encased in an extracellular polymeric substances. The exopolymeric substances possess high biotechnological potentialities with applications in biomedical, cosmetic, food and environmental fields. Despite Porifera are abundant invertebrates in Antarctica, the associated prokaryotic communities and their biotechnological potentialities were largely disregarded. Funded by the Italian PNRA, the P3 project "Antarctic Porifera: Hot-spots for Prokaryotic diversity and biotechnological Potentialities"" (PNRA16_00020) will aim at linking the ecological traits (e.g., phylogenetic diversity and metabolic activities) and biotechnological potential (e.g., biofilm production, pollutant degradation) of prokaryotes associated with Antarctic Porifera by applying a multidisciplinary approach.

PERSEUS EU FP7 Project aims to identify the interacting patterns of natural and human-derived pressures on the Mediterranean and Black Seas, to assess their impact on marine ecosystems and, using the objectives and principles of the Marine Strategy Framework Directive (MSFD) as a vehicle, to design an effective and innovative research governance framework based on sound scientific knowledge. In the frame of this Project (subtask 1.3.3 ADREX: Adriatic and Ionian Seas Experiment), a preliminary monitoring survey has been conducted in the Adriatic Sea (Italy) in order to verify the occurrence and the variation of selected classes of organic priority substances in sediments and to study the structural and functional characteristics of native bacterial communities. The study site represented a good natural laboratory sensitive to climate variability and human pressure, owing to the semi-enclosed nature of the Adriatic Sea and to the increasing trend of human activities in the coastal regions. During the cruise ADRI-13 (November 2013), we sampled three coastal areas nearby Ancona, Gargano Promontory and Bari. Surface sediments were collected in all areas, while sediment cores were sampled in selected sites. The sediment contamination level was determined by measuring the concentration of contaminants included in the list of organic priority substances: PAHs, PCBs, organochlorine pesticides (OCs), bisphenol A (BPA), alkylphenols (Aps), selected on the basis of the anthropogenic pressure. The extraction-clean-up for the PAHs, BPA and Aps was performed by ultrasonic bath with the appropriate solvent, followed by analytical determination with LC-MS and HPLC UV-fluorescence. The extraction of PCBs and OCs was performed by Soxhlet extraction and the concentrated extracts were cleaned-up using acidic silica chromatographic column, followed by determination on GC-ECD. The sediment bacterial abundance was determined by epifluorescence microscopy; the rate of bacterial carbon production was determined by measuring the 3H-leucine uptake rates and the community respiration was estimated by the measurement of the electron transport system (ETS) activity. The analyses of organic pollutants and microbial functional properties in marine sediments described the impact of anthropic pressure on the selected coastal areas. Microbes associated with marine sediments play an important role in the C-flux being responsible for the transformation of organic carbon (autochthonous and allochthonous) into biomass. At the surface layers, the microbial carbon assimilation and mineralization rates were affected by the increasing concentration of pollutants. The higher concentrations of organic pollutants were measured in the deeper sediment analysed (20 cm), along with the reduction of microbial metabolic activities. The results of this study can contribute to acquire information to improve MSFD and to reach the good environmental status.

Freshwater cyanobacteria of the genus Synechococcus are ubiquitous and organized either as single cells of diverse morphology or as microcolonies of different size. We studied the formation of microcolonies induced by the mixotrophic nanoflagellate Poterioochromonas sp. grazing on two Synechococcus strains belonging to phylotypes with different content of phycobiliproteins (PE: phycoerythrin-rich cells, L.Albano Group A; PC: phycocyanin-rich cells, MW101C3 Group I). The quantitative variations in cell abundance, morphological and physiological conditions were assessed on short-term incubations in semi-continuous cultures, single culture (PE, PC) and co-culture (PE+PC), with and without predators, by flow cytometry, and PhytoPAM. Under grazing pressure, we observed that (i) the abundance of PE single cells decreased over time with a concomitant formation of PE microcolonies; (ii) in PC single cultures, no significant variation in single cells was found and microcolonies did not form; (iii) both PE and PC formed monoclonal microcolonies in co-culture; (iv) PC cells increased the photosynthetic efficiency of the PSII (higher Fv/Fm) in co-culture. In the aftermath of microcolony formation as a predation-induced adaptation, our findings indicated a different response of Synechococcus phylotypes potentially co-existing in natural environment and the importance of their interaction.

River waters are classified worldwide in relation to their chemical quality status, which is assessed by the presence of inorganic and organic pollutants. Meanwhile, microbiological quality evaluations are based mainly on the occurrence of pathogens and faecal contaminants, which are indirectly retrieved by standard cultivation methods. In this study, the structural dynamics of a riverine bacterioplankton community were investigated through a quantitative single-cell approach with the use of flow cytometry for the quantification of total, viable and active cells. Furthermore, catalyzed reporter deposition (CARD)-FISH was used for the evaluation of Proteobacteria and Cytophaga-Flavobacteria bacterial classes. The aim was to identify the major cytometric and phylogenetic cell groups that most representatively reflect the physical and chemical changes occurring in an upland-to-lowland transect along a human-impacted river (the Foglia River, Italy). The use of CARD-FISH to obtain cell abundance measurements of specific taxonomic clusters enabled different microbial propagation dynamics along the river transects to be identified. Furthermore, our results highlighted that the multiparametric approach with flow cytometry produces basic microbiological parameters in a reasonable time span that is consistent with the requirements for an early warning monitoring strategy with respect to integrated riverine water quality assessments.

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.

1 - Coastal lagoons are particularly vulnerable to strong anthropogenic pressure. These environments can act as sink for allochthonous material, including harmful bacteria, with the ability to reduce their impact to adjacent coastal waters. 2 - This study investigates fecal pollution impairment in two Italian coastal lagoons and adjacent coastal waters. We utilised methodological approaches to gain fast and more precise information on the contamination and viability of fecal indicator bacteria. 3 - The analyses of total coliforms (TC) and Escherichia coli (E. coli) were performed in situ by enzyme assays. E. coli live/dead cells were enumerated by immunofluorescence technique (combined with propidium iodide) for the specific detection of enteropathogenic serotypes (12 EPEC and 2 EIEC). 4 - Overall TC enzyme activity showed a high degree of temporal variation whereas E. coli enzyme activity peaked in summer in both lagoons (beta-glucuronidase, 84 and 47 nmol MUFL-1h-1, Sabaudia and Orbetello respectively). Beta-glucuronidase activity showed a high correlation with viable cells counts of E. coli enteropathogenic strains (p