Stream hydrological fragmentation drives bacterioplankton community composition

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

Single culture and co-culture of two Synechococcus phylotypes respond differently to nanoflagellate grazing

Cyanobacteria belonging to the genus Synechococcus are found in lake waters typically as planktonic single cells and monospecific microcolonies. In oligotrophic lakes, single cells dominate in spring, while microcolonies are mostly found in late summer-autumn when the large colonial cyanobacteria increase in number. Since grazing activity is known as one of the major factors inducing microbial phenotypical changes, the formation of Synechococcus microcolonies was proposed as an efficient defence strategy against sizeselective predators. To better understand this ecological interaction, we explored the effect of grazing by the mixotrophic nanoflagellate Poteriochromonas sp. on the aggregation of two freshwater Synechococcus strains belonging to different phylogenetic clades (phycoerythrin-rich cells, PE, Group A; phycocyanin-rich cells, PC, Group I). During four days of incubation, we followed the dynamics of single-cells, microcolonies, and flagellates in semicontinuous cultures under different treatments (single culture and co-culture, with and without predators) by flow cytometry, epifluorescence microscopy and PhytoPAM. In single culture with the addition of Poteriochromonas, we observed the formation of grazing-induced monoclonal PE microcolonies, conversely limited in PC. In co-culture, there was an interaction between PE and PC, with an active microcolony formation by both PE and PC, and an increase of PC photosynthetic fitness (Fv/Fm). In co-culture, the microenvironment, generated by the formation of PE microcolonies, PC cells, bacteria and Poteriochromonas, can be the site of a beneficial "communication signalling" among Synechococcus cells for attaining the best spatial distribution for the fitness of the group

Physiological Profiling and Functional Diversity of Groundwater Microbial Communities in a Municipal Solid Waste Landfill Area

The disposal of municipal solid wastes in landfills represents a major threat for aquifer environments at the global scale. The aim of this study was to explore how groundwater geochemical characteristics can influence the microbial community functioning and the potential degradation patterns of selected organic substrates in response to different levels of landfill-induced alterations. Groundwaters collected from a landfill area were monitored by assessing major physical-chemical parameters and the microbiological contamination levels (total coliforms and fecal indicators—Colilert-18). The aquatic microbial community was further characterized by flow cytometry and Biolog EcoPlatesTM assay. Three groundwater conditions (i.e., pristine, mixed, and altered) were identified according to their distinct geochemical profiles. The altered groundwaters showed relatively higher values of organic matter concentration and total cell counts, along with the presence of fecal indicator bacteria, in comparison to samples from pristine and mixed conditions. The kinetic profiles of the Biolog substrate degradation showed that the microbial community thriving in altered conditions was relatively more efficient in metabolizing a larger number of organic substrates, including those with complex molecular structures. We concluded that the assessment of physiological profiling and functional diversity at the microbial community level could represent a supportive tool to understand the potential consequences of the organic contamination of impacted aquifers, thus complementing the current strategies for groundwater management

Quality and reactivity of dissolved organic matter in a Mediterranean river across hydrological and spatial gradients.

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

Artificial intelligence applied to software testing:a tertiary study

Context: Artificial intelligence (AI) methods and models have extensively been applied to support different phases of the software development lifecycle, including software testing (ST). Several secondary studies investigated the interplay between AI and ST but restricted the scope of the research to specific domains or sub-domains within either area.Objective: This research aims to explore the overall contribution of AI to ST, while identifying the most popular applications and potential paths for future research directions.Method: We executed a tertiary study following well-established guidelines for conducting systematic literature mappings in software engineering and for answering nine research questions.Results: We identified and analyzed 20 relevant secondary studies. The analysis was performed by drawing from well-recognized AI and ST taxonomies and mapping the selected studies according to them. The resulting mapping and discussions provide extensive and detailed information on the interplay between AI and ST.Conclusion: The application of AI to support ST is a well-consolidated and growing interest research topic. The mapping resulting from our study can be used by researchers to identify opportunities for future research, and by practitioners looking for evidence-based information on which AI-supported technology to possibly adopt in their testing processes

Zooplankton as refuge for invading bacteria

Nonetheless, studies on the impact of non-parasitic bacteria are still scarce. In this study we analysed the consequences of this colonisation on the distribution of potentially pathogenic and antibiotic resistant bacteria in freshwater systems. This is based on the hypothesis that potential pathogens have a selective advantage when growing in biofilms, as has been shown in clinical settings. Thus we postulate that attaching to animals might allow potential pathogens, e.g. deriving from the efflux of a waste water treatment plant (WWTP), to survive in freshwaters. Additionally the movement of the animal transports the bacteria away from the point-contamination to more pristine waters. We experimentally show that, if added to a natural bacterial community, Escherichia coli attaches to daphnids and derives particularly well in the gut of the animals, where they naturally do not form part of their microflora, whilst decreasing in abundance in the surrounding water. Moreover, the presence of daphnids decreased the abundance of a tetracycline resistance gene (tetA) in the surrounding water, whilst a higher number of tetA gene copies were detected in the animals. In addition we tested whether zooplankton species form a surface for the horizontal gene transfer, of e.g. antibiotic resistant genes, from one E. coli strain to another. In order to expand our hypothesis to natural environment we sampled Lake Maggiore at three points with increasing distance to an inflow of a WWTP and compared the microbial community on various zooplankton species as well as on stones and in the sediment. Whereas similar relationships have been described in marine systems, e.g. Vibrio cholera and Copepods, this is the first study that confronts the potential role of zooplankton in the spread of potential pathogens in freshwater systems

Bacterial uptake of DOM released from P-limited phytoplankton

The growth and the structure of a coastal bacterioplankton community were monitored in short-term bottle experiments in order to investigate the bacterial uptake of extracellular organic carbon released by the diatom Cylindrotheca closterium grown under P-balanced and P-depleted conditions. Bacterial specific growth rates and carbon demand were significantly lower in the exudates from P-depleted algae (24% and 30% reduction, respectively). The origin of the extracellular carbon appeared also to affect the taxonomic composition of the bacterioplankton assemblage, mainly reducing the development of Q-Proteobacteria. This pattern of bacterial carbon uptake could contribute to a longer persistence of the exudates released in P-depleted conditions affecting the dynamics of the carbon cycle in marine environments

Six artificial recharge pilot replicates to gain insight into water quality enhancement processes

The processes that control water quality improvement during artificial recharge (filtering, degradation, and adsorption) can be enhanced by adding a reactive barrier containing different types of sorption sites and promoting diverse redox states along the flow path, which increases the range of pollutants degraded. While this option looks attractive for renaturazing reclaimed water, three issues have to be analyzed prior to broad scale application: (1) a fair comparison between the system with and without reactive barrier; (2) the role of plants in prevention of clogging and addition of organic carbon; and (3) the removal of pathogens. Here, we describe a pilot installation built to address these issues within a waste water treatment plant that feeds on water reclaimed from the secondary outflow. The installation consists of six systems of recharge basin and aquifer with some variations in the design of the reactive barrier and the heterogeneity of the aquifer. We report preliminary results after one year of operation. We find that (1) the systems are efficient in obtaining a broad range of redox conditions (at least iron and manganese reducing), (2) contaminants of emerging concern are significantly removed (around 80% removal, but very sensitive to the compound), (3) pathogen indicators (E. coli and Enterococci) drop by some 3–5 log units, and (4) the recharge systems maintained infiltration capacity after one year of operation (only the system without plants and the one without reactive barrier displayed some clogging). Overall, the reactive barrier enhances somewhat the performance of the system, but the gain is not dramatic, which suggests that barrier composition needs to be improved.This study was supported by the Water Joint Programming Initiative (JPI)Water Challenges for a ChangingWorld 2014 through the project ACWAPUR (ACcelerated Water PURification during artificial recharge of aquifers: A tool to restore drinking water sources) and partially funded by the Spanish Ministry of Science, Innovation and Universities through PCIN-2015-245. We are very grateful to the staff of ‘Aguas de la Costa Brava' for their assistance, and to Ma Pau Serra-Roig and Ana Julia Acunha for their contribution to the chemical analysis and to Juli_a Garcia for his effort with the field site work.Peer ReviewedPostprint (published version

Dissolved organic matter in continental hydro-geothermal systems: insights from two hot springs of the East African Rift valley

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

Milk metagenomics and cheese-making properties as affected by indoor farming and summer highland grazing

The study of the complex relationships between milk metagenomics and milk composition and cheese-making efficiency as affected by indoor farming and summer highland grazing was the aim of the present work. The experimental design considered monthly sampling (over 5 mo) of the milk produced by 12 Brown Swiss cows divided into 2 groups: the first remained on a lowland indoor farm from June to October, and the second was moved to highland pastures in July and then returned to the lowland farm in September. The resulting 60 milk samples (2 kg each) were used to analyze milk composition, milk coagulation, curd firming, and syneresis processes, and to make individual model cheeses to measure cheese yields and nutrient recoveries in the cheese. After DNA extraction and Illumina Miseq sequencing, milk microbiota amplicons were also processed by means of an open-source pipeline called Quantitative Insights Into Microbial Ecology (Qiime2, version 2018.2; https://qiime2.org). Out of a total of 44 taxa analyzed, 13 bacterial taxa were considered important for the dairy industry (lactic acid bacteria, LAB, 5 taxa; and spoilage bacteria, 4) and for human (other probiotics, 2) and animal health (pathogenic bacteria, 2). The results revealed the transhumant group of cows transferred to summer highland pastures showed an increase in almost all the LAB taxa, bifidobacteria, and propionibacteria, and a reduction in spoilage taxa. All the metagenomic changes disappeared when the transhumant cows were moved back to the permanent indoor farm. The relationships between 17 microbial traits and 30 compositional and technological milk traits were investigated through analysis of correlation and latent explanatory factor analysis. Eight latent factors were identified, explaining 75.3% of the total variance, 2 of which were mainly based on microbial traits: pro-dairy bacteria (14% of total variance, improving during summer pasturing) and pathogenic bacteria (6.0% of total variance). Some bacterial traits contributed to other compositional-technological latent factors (gelation, udder health, and caseins)