Do fish gut microbiotas vary across spatial scales? A case study of Diplodus vulgaris in the Mediterranean Sea.

BACKGROUND: Biogeography has been linked to differences in gut microbiota in several animals. However, the existence of such a relationship in fish is not clear yet. So far, it seems to depend on the fish species studied. However, most studies of fish gut microbiotas are based on single populations. In this study, we investigated the gut microbiota of fish from three wild populations of the two-banded sea bream Diplodus vulgaris (Geoffroy Saint-Hilaire, 1817) to determine whether its diversity, structure and potential functionality reflect the geographic origin of the fish, at large and small geographical scale. Additionally, we explored the host- and environmental-related factors explaining this relationship. RESULTS: We showed that the taxonomy and potential functionality of the mucosa-associated gut microbiota of Diplodus vulgaris differ to varying degrees depending on the spatial scale considered. At large scale, we observed that both the taxonomical structure and the potential functionality of the fish microbiota differed significantly between populations. In contrast, the taxonomical diversity of the microbial community displayed a significant relationship with factors other than the geographic origin of the fish (i.e. sampling date). On the other hand, at small scale, the different composition and diversity of the microbiota differ according to the characteristics of the habitat occupied by the fish. Specifically, we identified the presence of Posidonia oceanica in the benthic habitat as predictor of both the microbiota composition and diversity. Lastly, we reported the enrichment of functions related to the metabolism of xenobiotics (i.e. drugs and 4-aminobenzoate) in a population and we indicated it as a potential target of future monitoring. CONCLUSIONS: With this study, we confirmed the importance of investigating the gut microbiota of wild fish species using multiple populations, taking into account the different habitats occupied by the individuals. Furthermore, we underscored the use of the biodegradation potential of the gut microbiota as an alternative means of monitoring emerging contaminants in Mediterranean fish.

Bactericidal effect of bacteria isolated from the marine sponges Hymeniacidon perlevis and Halichondria panicea against carbapenem-resistant Acinetobacter baumannii.

In this study, we evaluated the antimicrobial activity of bacteria isolated from the marine sponges Hymeniacidon perlevis and Halichondria panicea against seven Acinetobacter baumannii strains, the majority of which were clinically relevant carbapenem-resistant A. baumannii strains. We observed the inhibitory activity of 18 (out of 114) sponge-isolated bacterial strains against all A. baumanii strains using medium-throughput solid agar overlay assays. These inhibitory strains belonged to the genera Lactococcus, Pseudomonas, and Vagococcus. In addition, this antimicrobial activity was validated through a liquid co-cultivation challenge using an inhibitory strain of each genus and a green fluorescent protein-tagged A. baumanii strain. Fluorescence measurements indicated that the growth of A. baumanii was inhibited by the sponge isolates. In addition, the inability of A. baumanii to grow after spreading the co-cultures on solid medium allowed us to characterize the activity of the sponge isolates as bactericidal. In conclusion, this study demonstrates that marine sponges are a reservoir of bacteria that deserves to be tapped for antibiotic discovery against A. baumanii.

Human health risk attributed to consumption of seafood and recreation swimming in Negombo Lagoon, Sri Lanka: An assessment on lagoon water and inhabitant oysters (Crassostrea cucullata Born, 1778).

The Negombo Lagoon is a coastal lagoon influenced by local communities that introduce waste into its ecosystem. This study examined seven sewage entry points, out of which five sites were chosen for oyster sampling based on availability. Physicochemical and microbiological parameters of water (measured in triplicate at each site, n = 84) and oyster samples (total length, TL > 6 cm, n = 30) were assessed. Variation in regional coliform contamination was analyzed employing a one-way analysis of variance (ANOVA). Results indicated that the northern part of the lagoon exceeded recommended coliform thresholds for swimming (total coliform concentration (TCC) < 126 most probable number (MPN)) and seafood consumption (TCC < 100 MPN/g), indicating the presence of Escherichia coli. Water quality indices affirmed fecal pollution, except in the southern part of the lagoon. Furthermore, the study found high oyster consumption (76.7 %), elucidating that oysters from the northern part of Negombo Lagoon pose health risks.

Deciphering Interactions Within a 4-Strain Riverine Bacterial Community.

The dynamics of a community of four planktonic bacterial strains isolated from river water was followed in R2 broth for 72 h in batch experiments. These strains were identified as Janthinobacterium sp., Brevundimonas sp., Flavobacterium sp. and Variovorax sp. 16S rRNA gene sequencing and flow cytometry analyses were combined to monitor the change in abundance of each individual strain in bi-cultures and quadri-culture. Two interaction networks were constructed that summarize the impact of the strains on each other's growth rate in exponential phase and carrying capacity in stationary phase. The networks agree on the absence of positive interactions but also show differences, implying that ecological interactions can be specific to particular growth phases. Janthinobacterium sp. was the fastest growing strain and dominated the co-cultures. However, its growth rate was negatively affected by the presence of other strains 10 to 100 times less abundant than Janthinobacterium sp. In general, we saw a positive correlation between growth rate and carrying capacity in this system. In addition, growth rate in monoculture was predictive of carrying capacity in co-culture. Taken together, our results highlight the necessity to take growth phases into account when measuring interactions within a microbial community. In addition, evidence that a minor strain can greatly influence the dynamics of a dominant one underlines the necessity to choose population models that do not assume a linear dependency of interaction strength to abundance of other species for accurate parameterization from such empirical data.

Shifting microbial communities can enhance tree tolerance to changing climates.

Climate change is pushing species outside of their evolved tolerances. Plant populations must acclimate, adapt, or migrate to avoid extinction. However, because plants associate with diverse microbial communities that shape their phenotypes, shifts in microbial associations may provide an alternative source of climate tolerance. Here, we show that tree seedlings inoculated with microbial communities sourced from drier, warmer, or colder sites displayed higher survival when faced with drought, heat, or cold stress, respectively. Microbially mediated drought tolerance was associated with increased diversity of arbuscular mycorrhizal fungi, whereas cold tolerance was associated with lower fungal richness, likely reflecting a reduced burden of nonadapted fungal taxa. Understanding microbially mediated climate tolerance may enhance our ability to predict and manage the adaptability of forest ecosystems to changing climates.

Comparative genome analysis of Vagococcus fluvialis reveals abundance of mobile genetic elements in sponge-isolated strains.

BACKGROUND: Vagococcus fluvialis is a species of lactic acid bacteria found both free-living in river and seawater and associated to hosts, such as marine sponges. This species has been greatly understudied, with no complete genome assembly available to date, which is essential for the characterisation of the mobilome. RESULTS: We sequenced and assembled de novo the complete genome sequences of five V. fluvialis isolates recovered from marine sponges. Pangenome analysis of the V. fluvialis species (total of 17 genomes) showed a high intraspecific diversity, with 45.5% of orthologous genes found to be strain specific. Despite this diversity, analyses of gene functions clustered all V. fluvialis species together and separated them from other sequenced Vagococcus species. V. fluvialis strains from different habitats were highly similar in terms of functional diversity but the sponge-isolated strains were enriched in several functions related to the marine environment. Furthermore, sponge-isolated strains carried a significantly higher number of mobile genetic elements (MGEs) compared to previously sequenced V. fluvialis strains from other environments. Sponge-isolated strains carried up to 4 circular plasmids each, including a 48-kb conjugative plasmid. Three of the five strains carried an additional circular extrachromosomal sequence, assumed to be an excised prophage as it contained mainly viral genes and lacked plasmid replication genes. Insertion sequences (ISs) were up to five times more abundant in the genomes of sponge-isolated strains compared to the others, including several IS families found exclusively in these genomes. CONCLUSIONS: Our findings highlight the dynamics and plasticity of the V. fluvialis genome. The abundance of mobile genetic elements in the genomes of sponge-isolated V. fluvialis strains suggests that the mobilome might be key to understanding the genomic signatures of symbiosis in bacteria.

Deprivation of direct adult contact during development affects social representation in a songbird.

Social cognition involves a wide array of skills that are built largely through interactions with conspecifics and therefore depend upon early social experience. Motivation for social stimuli is a key feature of social behavior and an operant conditioning task showed that isolated wild-caught adult starlings (Sturnus vulgaris) are highly motivated to access pictures of other starlings. Here, we show that hand-raised adult starlings maintained in groups of peers throughout development but without any contact with adult models were not or only poorly motivated to access pictures of conspecifics. Moreover, they did not prefer pictures of starlings to pictures of landscapes, unlike birds wild-caught as adults. These results raise questions about the role of social experience during development, particularly with adult models, in the development of social motivation and of social representation in general.

Biogas residues in the battle for terrestrial carbon sequestration: A comparative decomposition study in the grassland soils of the Greater Region.

The recycling of biogas residues resulting from the anaerobic digestion of organic waste on agricultural land is among the means to reduce chemical fertilizer use and combat climate change. This in sacco decomposition study investigates (1) the potential of the granulated biogas residue fraction to provide nutrients and enhance soil carbon sequestration when utilized as exogenous organic matter in grassland soils, and (2) the impact of different nitrogen fertilizers on the organic matter decomposition and nutrient release processes. The experiment was conducted in two permanent grasslands of the Greater Region over one management period using rooibos tea as a comparator material. The decomposition and chemical changes of the two materials after incubation in the soil were assessed by measuring the mass loss, total carbon and nitrogen status, and fibre composition in cellulose, hemicellulose and lignin. Overall, after the incubation period, granulated biogas residue maintained up to 68% of its total mass, organic matter and total carbon; increased its content in recalcitrant organic matter by up to 45% and released 45% of its total nitrogen. Granulated biogas residue demonstrated resilience and a higher response uniformity when exposed to different nitrogen fertilizers, as opposed to the comparator material of rooibos tea. However, the magnitude of fertilizer-type effect varied, with ammonium nitrate and the combinatorial treatment of raw biogas residue mixed with urea leading to the highest organic matter loss from the bags. Our findings suggest that granulated biogas residue is a biofertilizer with the potential to supply nutrients to soil biota over time, and promote carbon sequestration in grassland soils, and thereby advance agricultural sustainability while contributing to climate change mitigation.

A 3D In Vitro Model of the Human Airway Epithelium Exposed to Tritiated Water: Dosimetric Estimate and Cytotoxic Effects.

Tritium has been receiving worldwide attention, particularly because of its production and use in existing fission reactors and future nuclear fusion technologies, leading to an increased risk of release in the environment. Linking human health effects to low-dose tritium exposures presents a challenge for many reasons. Among these: biological effects strongly depend on the speciation of tritiated products and exposure pathway; large dosimetric uncertainties may exist; measurements using in vitro cell cultures generally lack a description of effects at the tissue level, while large-scale animal studies might be ethically questionable and too highly demanding in terms of resources. In this context, three-dimensional models of the human airway epithelium are a powerful tool to investigate potential toxicity induced upon inhalation of radioactive products in controlled physiological conditions. In this study we exposed such a model to tritiated water (HTO) for 24 h, with a range of activity levels (up to ∼33 kBq µl-1 cm-2). After the exposures, we measured cell viability, integrity of epithelial layer and pro-inflammatory response at different post-exposure time-points. We also quantified tritium absorption and performed dosimetric estimates considering HTO passage through the epithelial layer, leading to reconstructed upper limits for the dose to the tissue of less than 50 cGy cumulative dose for the highest activity. Upon exposure to the highest activity, cell viability was not decreased; however, we observed a small effect on epithelial integrity and an inflammatory response persisting after seven days. These results represent a reference condition and will guide future experiments using human airway epithelium to investigate the effects of other peculiar tritiated products.

Lateralization of social signal brain processing correlates with the degree of social integration in a songbird.

Group cohesion relies on the ability of its members to process social signals. Songbirds provide a unique model to investigate links between group functioning and brain processing of social acoustic signals. In the present study, we performed both behavioral observations of social relationships within a group of starlings and individual electrophysiological recordings of HVC neuronal activity during the broadcast of either familiar or unfamiliar individual songs. This allowed us to evaluate and compare preferred partnerships and individual electrophysiological profiles. The electrophysiological results revealed asymmetric neuronal activity in the HVC and higher responsiveness to familiar than to unfamiliar songs. However, most importantly, we found a correlation between strength of cerebral asymmetry and social integration in the group: the more preferred partners a bird had, the more its HVC neuronal activity was lateralized. Laterality is likely to give advantages in terms of survival. Our results suggest that these include social skill advantages. Better knowledge of links between social integration and lateralization of social signal processing should help understand why and how lateralization has evolved.

Toxicological Assessment of ITER-Like Tungsten Nanoparticles Using an In Vitro 3D Human Airway Epithelium Model.

The International Thermonuclear Experimental Reactor (ITER) is an international project aimed at the production of carbon-free energy through the use of thermonuclear fusion. During ITER operation, in case of a loss-of-vacuum-accident, tungsten nanoparticles (W-NPs) could potentially be released into the environment and induce occupational exposure via inhalation. W-NPs toxicity was evaluated on MucilAir™, a 3D in vitro cell model of the human airway epithelium. MucilAir™ was exposed for 24 h to metallic ITER-like milled W-NPs, tungstate (WO42-) and tungsten carbide cobalt particles alloy (WC-Co). Cytotoxicity and its reversibility were assessed using a kinetic mode up to 28 days after exposure. Epithelial tightness, metabolic activity and interleukin-8 release were also evaluated. Electron microscopy was performed to determine any morphological modification, while mass spectrometry allowed the quantification of W-NPs internalization and of W transfer through the MucilAir™. Our results underlined a decrease in barrier integrity, no effect on metabolic activity or cell viability and a transient increase in IL-8 secretion after exposure to ITER-like milled W-NPs. These effects were associated with W-transfer through the epithelium, but not with intracellular accumulation. We have shown that, under our experimental conditions, ITER-like milled W-NPs have a minor impact on the MucilAir™ in vitro model.

Biogas residues in substitution for chemical fertilizers: A comparative study on a grassland in the Walloon Region.

To provide sufficient quantities of food and feed, farming systems have to overcome limiting factors such as the nutrient depletion of arable soils. Nitrogen being the main mineral element required for plant growth, has led to the extensive use of chemical fertilizers causing nitrogen pollution of the ecosystems. This field study investigates the use of biogas residues (BRs) as biofertilizers and their contribution to the mitigation of nitrate leaching in agricultural soils, while also demonstrating the polluting nature of chemical fertilizers. Nine different fertilization treatments classified in three schemes and two nitrogen doses were tested for three consecutive years on a grassland in the Walloon Region of Belgium. Residual soil mineral nitrogen, percentage contribution of treatments in residual nitrate and agronomic performance were assessed for each fertilization treatment. The results obtained showed significant differences on treatment and scheme level regarding nitrate accumulation in the soil, with chemical fertilizers posing the highest nitrate leaching risk. BRs did not cause nitrate accumulation in the soil, and were N rate and rainfall independent, while the chemical treatments indicated a cumulative tendency under high N rate and low precipitation. Forage yield did not demonstrate statistical differences on treatment and scheme level but varied with changing precipitation, while the maximum application rate suggested a plateau. Aboveground nitrogen content was significantly higher after the application of chemical fertilizers only in the first year, while all the chemical treatments indicated a dilution effect under elevated annual rainfall. Finally, the partial substitution of chemical fertilizers by raw digestate reduced the concentration of NO3- in the soil without having a negative impact on the yield and N content of the biomass. These results strongly advocate for the environmental benefits of BRs over chemical fertilizers and underline their suitability as biofertilizers and substitutes for chemical fertilizers in similar agricultural systems.

The Dynamic of a River Model Bacterial Community in Two Different Media Reveals a Divergent Succession and an Enhanced Growth of Most Strains Compared to Monocultures.

The dynamic of a community of 20 bacterial strains isolated from river water was followed in R2 broth and in autoclaved river water medium for 27 days in batch experiments. At an early stage of incubation, a fast-growing specialist strain, Acinetobater sp., dominated the community in both media. Later on, the community composition in both media diverged but was highly reproducible across replicates. In R2, several strains previously reported to degrade multiple simple carbon sources prevailed. In autoclaved river water, the community was more even and became dominated by several strains growing faster or exclusively in that medium. Those strains have been reported in the literature to degrade complex compounds. Their growth rate in the community was 1.5- to 7-fold greater than that observed in monoculture. Furthermore, those strains developed simultaneously in the community. Together, our results suggest the existence of cooperative interactions within the community incubated in autoclaved river water.

Application of a multidisciplinary and integrative weight-of-evidence approach to a 1-year monitoring survey of the Seine River.

Quality assessment of environments under high anthropogenic pressures such as the Seine Basin, subjected to complex and chronic inputs, can only be based on combined chemical and biological analyses. The present study integrates and summarizes a multidisciplinary dataset acquired throughout a 1-year monitoring survey conducted at three workshop sites along the Seine River (PIREN-Seine program), upstream and downstream of the Paris conurbation, during four seasonal campaigns using a weight-of-evidence approach. Sediment and water column chemical analyses, bioaccumulation levels and biomarker responses in caged gammarids, and laboratory (eco)toxicity bioassays were integrated into four lines of evidence (LOEs). Results from each LOE clearly reflected an anthropogenic gradient, with contamination levels and biological effects increasing from upstream to downstream of Paris, in good agreement with the variations in the structure and composition of bacterial communities from the water column. Based on annual average data, the global hazard was summarized as "moderate" at the upstream station and as "major" at the two downstream ones. Seasonal variability was also highlighted; the winter campaign was least impacted. The model was notably improved using previously established reference and threshold values from national-scale studies. It undoubtedly represents a powerful practical tool to facilitate the decision-making processes of environment managers within the framework of an environmental risk assessment strategy.

Phylogeny and Antagonistic Activities of Culturable Bacteria Associated with the Gut Microbiota of the Sea Urchin (Paracentrotus lividus).

In this study, we have investigated the phylogeny and the antagonistic interactions of culturable bacteria isolated from the sea urchin Paracentrotus lividus collected from Aber and Morgat, both located in Crozon peninsula, France. Bacteria were isolated from the gastrointestinal tracts of ten specimens by using conventional culture-dependent method and then investigated by using phylogenetic analysis based on 16S rRNA gene sequence comparisons. Assays for antagonistic interactions among the bacterial strains were performed; bacteria (including at least one strain representative of each OTU identified) were screened for antimicrobial substance production. So, 367 bacterial strains were isolated on marine-agar. On the basis of morphological characteristics, 180 strains were sequenced and 94 OTUs were classified. The dominant phyla were Proteobacteria, Firmicutes and Actinobacteria, with a high abundance of the strains belonging to the genus Psychrobacter. From the antagonistic interactions assays, it could be determined that 22.7% strains were positive for at least one antagonism interaction, 18.3% of them isolated from the sea urchins collected in Morgat. We hypothesize that the bacteria isolated in this study may represent the transitory microbiota of the gastrointestinal tract of P. lividus, and that this microbiota may be related to the diet of this marine invertebrate. Furthermore, our results suggest that chemical antagonism could play a significant role in shaping the bacterial communities within gastrointestinal tract of the sea urchins. In addition, most isolated bacteria may have promising biotechnology applications.

Carbon utilization profiles of river bacterial strains facing sole carbon sources suggest metabolic interactions.

Microbial communities play a key role in water self-purification. They are primary drivers of biogenic element cycles and ecosystem processes. However, these communities remain largely uncharacterized. In order to understand the diversity-heterotrophic activity relationship facing sole carbon sources, we assembled a synthetic community composed of 20 'typical' freshwater bacterial species mainly isolated from the Zenne River (Belgium). The carbon source utilization profiles of each individual strain and of the mixed community were measured in Biolog Phenotype MicroArrays PM1 and PM2A microplates that allowed testing 190 different carbon sources. Our results strongly suggest interactions occurring between our planktonic strains as our synthetic community showed metabolic properties that were not displayed by its single components. Finally, the catabolic performances of the synthetic community and a natural community from the same sampling site were compared. The synthetic community behaved like the natural one and was therefore representative of the latter in regard to carbon source consumption.

Culturable bacterial communities associated to Brazilian Oscarella species (Porifera: Homoscleromorpha) and their antagonistic interactions.

Sponges offer an excellent model to investigate invertebrate-microorganism interactions. Furthermore, bacteria associated with marine sponges represent a rich source of bioactive metabolites. The aim of this study was to characterize the bacteria inhabiting a genus of sponges, Oscarella, and their potentiality for antimicrobial production. Bacterial isolates were recovered from different Oscarella specimens, among which 337 were phylogenetically identified. The culturable community was dominated by Proteobacteria and Firmicutes, and Vibrio was the most frequently isolated genus, followed by Shewanella. When tested for antimicrobial production, bacteria of the 12 genera isolated were capable of producing antimicrobial substances. The majority of strains were involved in antagonistic interactions and inhibitory activities were also observed against bacteria of medical importance. It was more pronounced in some isolated genera (Acinetobacter, Bacillus, Photobacterium, Shewanella and Vibrio). These findings suggest that chemical antagonism could play a significant role in shaping bacterial communities within Oscarella, a genus classified as low-microbial abundance sponge. Moreover, the identified strains may contribute to the search for new sources of antimicrobial substances, an important strategy for developing therapies to treat infections caused by multidrug-resistant bacteria. This study was the first to investigate the diversity and antagonistic activity of bacteria isolated from Oscarella spp. It highlights the biotechnological potential of sponge-associated bacteria.

Metagenomics: Probing pollutant fate in natural and engineered ecosystems.

Polluted environments are a reservoir of microbial species able to degrade or to convert pollutants to harmless compounds. The proper management of microbial resources requires a comprehensive characterization of their genetic pool to assess the fate of contaminants and increase the efficiency of bioremediation processes. Metagenomics offers appropriate tools to describe microbial communities in their whole complexity without lab-based cultivation of individual strains. After a decade of use of metagenomics to study microbiomes, the scientific community has made significant progress in this field. In this review, we survey the main steps of metagenomics applied to environments contaminated with organic compounds or heavy metals. We emphasize technical solutions proposed to overcome encountered obstacles. We then compare two metagenomic approaches, i.e. library-based targeted metagenomics and direct sequencing of metagenomes. In the former, environmental DNA is cloned inside a host, and then clones of interest are selected based on (i) their expression of biodegradative functions or (ii) sequence homology with probes and primers designed from relevant, already known sequences. The highest score for the discovery of novel genes and degradation pathways has been achieved so far by functional screening of large clone libraries. On the other hand, direct sequencing of metagenomes without a cloning step has been more often applied to polluted environments for characterization of the taxonomic and functional composition of microbial communities and their dynamics. In this case, the analysis has focused on 16S rRNA genes and marker genes of biodegradation. Advances in next generation sequencing and in bioinformatic analysis of sequencing data have opened up new opportunities for assessing the potential of biodegradation by microbes, but annotation of collected genes is still hampered by a limited number of available reference sequences in databases. Although metagenomics is still facing technical and computational challenges, our review of the recent literature highlights its value as an aid to efficiently monitor the clean-up of contaminated environments and develop successful strategies to mitigate the impact of pollutants on ecosystems.

Antibiotic resistance genes detected in the marine sponge Petromica citrina from Brazilian coast

ABSTRACT Although antibiotic-resistant pathogens pose a significant threat to human health, the environmental reservoirs of the resistance determinants are still poorly understood. This study reports the detection of resistance genes (ermB, mecA, mupA, qnrA, qnrB and tetL) to antibiotics among certain culturable and unculturable bacteria associated with the marine sponge Petromica citrina. The antimicrobial activities elicited by P. citrina and its associated bacteria are also described. The results indicate that the marine environment could play an important role in the development of antibiotic resistance and the dissemination of resistance genes among bacteria.

Antibiotic resistance genes detected in the marine sponge Petromica citrina from Brazilian coast.

Although antibiotic-resistant pathogens pose a significant threat to human health, the environmental reservoirs of the resistance determinants are still poorly understood. This study reports the detection of resistance genes (ermB, mecA, mupA, qnrA, qnrB and tetL) to antibiotics among certain culturable and unculturable bacteria associated with the marine sponge Petromica citrina. The antimicrobial activities elicited by P. citrina and its associated bacteria are also described. The results indicate that the marine environment could play an important role in the development of antibiotic resistance and the dissemination of resistance genes among bacteria.