Toxicity of Silver-Chitosan Nanocomposites to Aquatic Microcrustaceans Daphnia magna and Thamnocephalus platyurus and Naturally Luminescent Bacteria Vibrio fischeri

All novel materials should be analyzed for their potential environmental hazard. In this study, the toxicity of different silver-chitosan nanocomposites-potential candidates for wound dressings or antimicrobial surface coatings-was evaluated using environmentally relevant aquatic microcrustaceans Daphnia magna and Thamnocephalus platyurus and naturally luminescent bacteria Vibrio fischeri. Three silver-chitosan nanocomposites (nAgCSs) with different weight ratios of Ag to CS were studied. Citrate-coated silver nanoparticles (nAg-Cit), AgNO3 (ionic control) and low molecular weight chitosan (LMW CS) were evaluated in parallel. The primary size of nAgCSs was ~50 nm. The average hydrodynamic sizes in deionized water were ≤100 nm, and the zeta potential values were positive (16-26 mV). The nAgCSs proved very toxic to aquatic crustaceans: the 48-h EC50 value for D. magna was 0.065-0.232 mg/L, and the 24-h LC50 value for T. platyurus was 0.25-1.04 mg/L. The toxic effect correlated with the shedding of Ag ions (about 1%) from nAgCSs. Upon exposure of V. fischeri to nAgCSs for 30 min, bacterial luminescence was inhibited by 50% at 13-33 mg/L. However, the inhibitory effect (minimum bactericidal concentration, MBC) on bacterial growth upon 1 h exposure was observed at higher concentrations of nAgCSs, 40-65 mg/L. LMW CS inhibited bacterial luminescence upon 30-min exposure at 5.6 mg/L, but bacterial growth was inhibited at a much higher concentration (1 h MBC > 100 mg/L). The multi-trophic test battery, where D. magna was the most sensitive test organism, ranked the silver-chitosan nanocomposites from 'extremely toxic' [L(E)C50 ≤ 0.1 mg/L] to 'very toxic' [L(E)C50 > 0.1-1 mg/L]. Chitosan was toxic (EC(L)50) to crustaceans at ~12 mg/L, and ranked accordingly as 'harmful' [L(E)C50 > 10-100 mg/L]. Thus, silver-chitosan nanocomposites may pose a hazard to aquatic organisms and must be handled accordingly.

Lighting the way: how the Vibrio fischeri model microbe reveals the complexity of Earth's "simplest" life forms

Vibrio (Aliivibrio) fischeri's initial rise to fame derived from its alluring production of blue-green light. Subsequent studies to probe the mechanisms underlying this bioluminescence helped the field discover the phenomenon now known as quorum sensing. Orthologs of quorum-sensing regulators (i.e., LuxR and LuxI) originally identified in V. fischeri were subsequently uncovered in a plethora of bacterial species, and analogous pathways were found in yet others. Over the past three decades, the study of this microbe has greatly expanded to probe the unique role of V. fischeri as the exclusive symbiont of the light organ of the Hawaiian bobtail squid, Euprymna scolopes. Buoyed by this optically amenable host and by persistent and insightful researchers who have applied novel and cross-disciplinary approaches, V. fischeri has developed into a robust model for microbe-host associations. It has contributed to our understanding of how bacteria experience and respond to specific, often fluxing environmental conditions and the mechanisms by which bacteria impact the development of their host. It has also deepened our understanding of numerous microbial processes such as motility and chemotaxis, biofilm formation and dispersal, and bacterial competition, and of the relevance of specific bacterial genes in the context of colonizing an animal host. Parallels in these processes between this symbiont and bacteria studied as pathogens are readily apparent, demonstrating functional conservation across diverse associations and permitting a reinterpretation of "pathogenesis." Collectively, these advances built a foundation for microbiome studies and have positioned V. fischeri to continue to expand the frontiers of our understanding of the microbial world inside animals.

SecMet-FISH: labeling, visualization, and enumeration of secondary metabolite producing microorganisms

Our understanding of the role of secondary metabolites in microbial communities is challenged by intrinsic limitations of culturing bacteria under laboratory conditions and hence cultivation independent approaches are needed. Here, we present a protocol termed Secondary Metabolite FISH (SecMet-FISH), combining advantages of gene-targeted fluorescence in situ hybridization (geneFISH) with in-solution methods (in-solution FISH) to detect and quantify cells based on their genetic capacity to produce secondary metabolites. The approach capitalizes on the conserved nature of biosynthetic gene clusters (BGCs) encoding adenylation (AD) and ketosynthase (KS) domains, and thus selectively targets the genetic basis of non-ribosomal peptide and polyketide biosynthesis. The concept relies on the generation of amplicon pools using degenerate primers broadly targeting AD and KS domains followed by fluorescent labeling, detection, and quantification. Initially, we obtained AD and KS amplicons from Pseuodoalteromonas rubra, which allowed us to successfully label and visualize BGCs within P. rubra cells, demonstrating the feasibility of SecMet-FISH. Next, we adapted the protocol and optimized it for hybridization in both Gram-negative and Gram-positive bacterial cell suspensions, enabling high-throughput single cell analysis by flow cytometry. Ultimately, we used SecMet-FISH to successfully distinguish secondary metabolite producers from non-producers in a five-member synthetic community.

Extending the Shelf Life of Atlantic Salmon (Salmo salar) with Sub-Chilled Storage and Modified Atmosphere Packaging in Recyclable Mono-Material Trays

This study investigated the effect of sub-chilling whole gutted salmon and sub-chilled storage at -1 °C in modified-atmosphere packaging in two recyclable mono-material trays (CPET, HDPE). Quality parameters were measured, including water-holding properties, salt content, color, texture, lipid oxidation, and sensory and microbiological shelf life. The oxygen transmission rate was measured for the packages. Compared to traditional fish storage on ice, sub-chilling gave a 0.4% weight gain, better water-holding capacity, and higher salt content. The sub-chilled fish gave a significantly better sensory quality and microbiological shelf life of up to 49 days. Photobacterium was the dominating bacteria during storage. Salmon packaged in CPET trays had a higher drip loss than HDPE trays, but a lower rate of lipid oxidation (1-penten-3-ol). Our results showed the feasibility of significantly extending shelf life with sub-chilling, removing the need for ice. Moreover, using recyclable trays for packaging contributes to a circular economy without compromising food quality.

Bioactivity Profiling and Untargeted Metabolomics of Microbiota Associated with Mesopelagic Jellyfish Periphylla periphylla

The marine mesopelagic zone extends from water depths of 200 m to 1000 m and is home to a vast number and diversity of species. It is one of the least understood regions of the marine environment with untapped resources of pharmaceutical relevance. The mesopelagic jellyfish Periphylla periphylla is a well-known and widely distributed species in the mesopelagic zone; however, the diversity or the pharmaceutical potential of its cultivable microbiota has not been explored. In this study, we isolated microorganisms associated with the inner and outer umbrella of P. periphylla collected in Irminger Sea by a culture-dependent approach, and profiled their chemical composition and biological activities. Sixteen mostly gram-negative bacterial isolates were selected and subjected to an OSMAC cultivation regime approach using liquid and solid marine broth (MB) and glucose-yeast-malt (GYM) media. Their ethyl acetate (EtOAc) extracts were assessed for cytotoxicity and antimicrobial activity against fish and human pathogens. All, except one extract, displayed diverse levels of antimicrobial activities. Based on low IC₅₀ values, four most bioactive gram-negative strains; Polaribacter sp. SU124, Shewanella sp. SU126, Psychrobacter sp. SU143 and Psychrobacter sp. SU137, were prioritized for an in-depth comparative and untargeted metabolomics analysis using feature-based molecular networking. Various chemical classes such as diketopiperazines, polyhydroxybutyrates (PHBs), bile acids and other lipids were putatively annotated, highlighting the biotechnological potential in P. periphylla-associated microbiota as well as gram-negative bacteria. This is the first study providing an insight into the cultivable bacterial community associated with the mesopelagic jellyfish P. periphylla and, indeed, the first to mine the metabolome and antimicrobial activities of these microorganisms.

Vibrio amylolyticus sp. nov. and Vibrio gelatinilyticus sp. nov., two marine bacteria isolated from surface seawater of Qingdao

Two Gram-stain-negative, oxidase-positive, facultative anaerobic and rod-shaped motile bacteria, designated strains ZSDZ34 and ZSDE26, were isolated from offshore surface seawater collected near Qingdao. Phylogenetic analysis based on 16S rRNA gene sequences placed ZSDE26^T and ZSDZ34^T within the genus Vibrio, family Vibrionaceae, class Gammaproteobacteria. Strain ZSDE26^T was most closely related to Vibrio gallaecicus VB 8.9^T with 97.3 % sequence similarity, whereas ZSDZ34^T was most closely related to Vibrio aestuarianus subsp. cardii DSM 109723^T with 97.8 % sequence similarity. Strain ZSDE26^T grew with 1-5 % (w/v) NaCl (optimum, 4 %), at 16-28 °C (optimum, 28 °C) and at pH 6.0-9.0 (optimum, pH 7.0). Growth of strain ZSDZ34^T occurred with 1-6 % (w/v) NaCl (optimum, 3 %), at 16-37 °C (optimum, 28 °C) and at pH 6.0-9.0 (optimum, pH 7.0). Both strains shared the same major fatty acid components (more than 10 % of total fatty acids) of summed feature 3 (C_16 : 1 ω7c and/or C_16 : 1 ω6c), summed feature 8 (C_18 : 1 ω7c and/or C_18 : 1 ω6c) and C_16 : 0. Additionally, strain ZSDZ34^T contained a higher proportion of iso-C_16 : 0. The DNA G+C contents of strains ZSDE26^T and ZSDZ34^T were 42.8 and 44.5 mol%, respectively. On the basis of the results of polyphasic analysis, ZSDE26^T and ZSDZ34^T are considered to represent novel species within the genus Vibrio, for which the names Vibrio amylolyticus sp. nov. (type strain, ZSDE26^T=KCTC 82890^T=MCCC 1K06290^T) and Vibrio gelatinilyticus sp. nov. (type strain, ZSDZ34^T=KCTC 82888^T=MCCC 1K06292^T) are proposed, respectively.

Review of ecologically relevant in vitro bioassays to supplement current in vivo tests for whole effluent toxicity testing - Part 1: Apical endpoints

Whole effluent toxicity (WET) testing is commonly used to ensure that wastewater discharges do not pose an unacceptable risk to receiving environments. Traditional WET testing involves exposing animals to (waste)water samples to assess four major ecologically relevant apical endpoints: mortality, growth, development, and reproduction. Recently, with the widespread implementation of the 3Rs to replace, reduce and refine the use of animals in research and testing, there has been a global shift away from in vivo testing towards in vitro alternatives. However, prior to the inclusion of in vitro bioassays in regulatory frameworks, it is critical to establish their ecological relevance and technical suitability. This is part 1 of a two-part review that aims to identify in vitro bioassays that can be used in WET testing and relate them to ecologically relevant endpoints through toxicity pathways, providing the reader with a high-level overview of current capabilities. Part 1 of this review focuses on four apical endpoints currently included in WET testing: mortality, growth, development, and reproduction. For each endpoint, the link between responses at the molecular or cellular level, that can be measured in vitro, and the adverse outcome at the organism level were established through simplified toxicity pathways. Additionally, literature from 2015 to 2020 on the use of in vitro bioassays for water quality assessments was reviewed to identify a list of suitable bioassays for each endpoint. This review will enable the prioritization of relevant endpoints and bioassays for incorporation into WET testing.

Bacterial survivors: evaluating the mechanisms of antibiotic persistence

Bacteria withstand antibiotic onslaughts by employing a variety of strategies, one of which is persistence. Persistence occurs in a bacterial population where a subpopulation of cells (persisters) survives antibiotic treatment and can regrow in a drug-free environment. Persisters may cause the recalcitrance of infectious diseases and can be a stepping stone to antibiotic resistance, so understanding persistence mechanisms is critical for therapeutic applications. However, current understanding of persistence is pervaded by paradoxes that stymie research progress, and many aspects of this cellular state remain elusive. In this review, we summarize the putative persister mechanisms, including toxin-antitoxin modules, quorum sensing, indole signalling and epigenetics, as well as the reasons behind the inconsistent body of evidence. We highlight present limitations in the field and underscore a clinical context that is frequently neglected, in the hope of supporting future researchers in examining clinically important persister mechanisms.

Vibriosis Outbreaks in Aquaculture: Addressing Environmental and Public Health Concerns and Preventive Therapies Using Gilthead Seabream Farming as a Model System

Bacterial and viral diseases in aquaculture result in severe production and economic losses. Among pathogenic bacteria, species belonging to the Vibrio genus are one of the most common and widespread disease-causing agents. Vibrio infections play a leading role in constraining the sustainable growth of the aquaculture sector worldwide and, consequently, are the target of manifold disease prevention strategies. During the early, larval stages of development, Vibrio species are a common cause of high mortality rates in reared fish and shellfish, circumstances under which the host organisms might be highly susceptible to disease preventive or treatment strategies such as vaccines and antibiotics use, respectively. Regardless of host developmental stage, Vibrio infections may occur suddenly and can lead to the loss of the entire population reared in a given aquaculture system. Furthermore, the frequency of Vibrio-associated diseases in humans is increasing globally and has been linked to anthropic activities, in particular human-driven climate change and intensive livestock production. In this context, here we cover the current knowledge of Vibrio infections in fish aquaculture, with a focus on the model species gilthead seabream (Sparus aurata), a highly valuable reared fish in the Mediterranean climatic zone. Molecular methods currently used for fast detection and identification of Vibrio pathogens and their antibiotic resistance profiles are addressed. Targeted therapeutic approaches are critically examined. They include vaccination, phage therapy and probiotics supplementation, which bear promise in supressing vibriosis in land-based fish rearing and in mitigating possible threats to human health and the environment. This literature review suggests that antibiotic resistance is increasing among Vibrio species, with the use of probiotics constituting a promising, sustainable approach to prevent Vibrio infections in aquaculture.

Synergistic Interaction of Low Salinity Stress With Vibrio Infection Causes Mass Mortalities in the Oyster by Inducing Host Microflora Imbalance and Immune Dysregulation

A sudden drop in salinity following extreme precipitation events usually causes mass mortality of oysters exposed to pathogens in ocean environment. While how low salinity stress interacts with pathogens to cause mass mortality remains obscure. In this study, we performed an experiment by low salinity stress and pathogen infection with Vibrio alginolyticus to investigate their synergistic effect on the mortality of the Pacific oyster toward understanding of the interaction among environment, host, and pathogen. We showed that low salinity stress did not significantly affect proliferation and virulence of V. alginolyticus, but significantly altered microbial composition and immune response of infected oysters. Microbial community profiling by 16S rRNA amplicon sequencing revealed disrupted homeostasis of digestive bacterial microbiota with the abundance of several pathogenic bacteria being increased, which may affect the pathogenesis in infected oysters. Transcriptome profiling of infected oysters revealed that a large number of genes associated with apoptosis and inflammation were significantly upregulated under low salinity, suggesting that low salinity stress may have triggered immune dysregulation in infected oysters. Our results suggest that host-pathogen interactions are strongly affected by low salinity stress, which is of great significance for assessing future environmental risk of pathogenic diseases, decoding the interaction among environment, host genetics and commensal microbes, and disease surveillance in the oyster.

Vibrio spp.: Life Strategies, Ecology, and Risks in a Changing Environment

Vibrios are ubiquitous bacteria in aquatic systems, especially marine ones, and belong to the Gammaproteobacteria class, the most diverse class of Gram-negative bacteria. The main objective of this review is to update the information regarding the ecology of Vibrio species, and contribute to the discussion of their potential risk in a changing environment. As heterotrophic organisms, Vibrio spp. live freely in aquatic environments, from marine depths to the surface of the water column, and frequently may be associated with micro- and macroalgae, invertebrates, and vertebrates such as fish, or live in symbiosis. Some Vibrio spp. are pathogenic to humans and animals, and there is evidence that infections caused by vibrios are increasing in the world. This rise may be related to global changes in human behavior (increases in tourism, maritime traffic, consumption of seafood, aquaculture production, water demand, pollution), and temperature. Most likely in the future, Vibrio spp. in water and in seafood will be monitored in order to safeguard human and animal health. Regulators of the microbiological quality of water (marine and freshwater) and food for human and animal consumption, professionals involved in marine and freshwater production chains, consumers and users of aquatic resources, and health professionals will be challenged to anticipate and mitigate new risks.

Efficiency and specificity of CARD-FISH probes in detection of marine vibrios

Vibrio is a bacterial genus widely distributed in natural aquatic systems. Some Vibrio species can cause severe diseases in both marine organisms and humans. Previous studies revealed a link between the current climate change and increased incidence of the Vibrio-associated diseases recently causing sanitary, economic and/or ecological problems worldwide. The conventional culture-based methods (e.g. selection on TCBS agar) used to monitor the presence of Vibrio spp. in environmental samples are not always straightforward and can underestimate the number of cells, especially in microbial populations containing a fraction of 'dormant' cells (e.g. cells in the Viable but Non Culturable [VBNC] state). This problem can be overcome by using alternative culture-free approaches such as Catalysed Reporter Deposition-Fluorescence In situ Hybridization (CARD-FISH). To select an efficient CARD-FISH probe for detection of Vibrio spp. in environmental samples, we have assessed the most promising probes described in the literature by using both computer-assisted and experimental approaches. Our results demonstrate that the use of the optimized protocol along with a very specific probe, ViB572a, can offer the high sensitivity and selectivity of CARD-FISH detection of marine vibrios in natural seawater.

Diversity of the Tryptophanase Gene and Its Evolutionary Implications in Living Organisms

Tryptophanase encoded by the gene tnaA is a pyridoxal phosphate-dependent enzyme that catalyses the conversion of tryptophan to indole, which is commonly used as an intra- and interspecies signalling molecule, particularly by microbes. However, the production of indole is rare in eukaryotic organisms. A nucleotide and protein database search revealed tnaA is commonly reported in various Gram-negative bacteria, but that only a few Gram-positive bacteria and archaea possess the gene. The presence of tnaA in eukaryotes, particularly protozoans and marine organisms, demonstrates the importance of this gene in the animal kingdom. Here, we document the distribution of tnaA and its acquisition and expansion among different taxonomic groups, many of which are usually categorized as non-indole producers. This study provides an opportunity to understand the intriguing role played by tnaA, and its distribution among various types of organisms.

The Role of SprIR Quorum Sensing System in the Regulation of Serratia proteamaculans 94 Invasion

The bacteria Serratia proteamaculans 94 have a LuxI/LuxR type QS system consisting of AHL synthase SprI and the regulatory receptor SprR. We have previously shown that inactivation of the AHL synthase sprI gene resulted in an increase in the invasive activity of S. proteamaculans correlated with an increased bacterial adhesion. In the present work, the effects of inactivation of the S. proteamaculans receptor SprR are studied. Our results show that inactivation of the receptor sprR gene leads to an increase in bacterial invasion without any increase in their adhesion. On the other hand, inactivation of the sprR gene increases the activity of the extracellular protease serralysin. Inactivation of the QS system does not affect the activity of the pore-forming toxin ShlA and prevents the ShlA activation under conditions of a limited concentration of iron ions typical of the human body. While the wild type strain shows increased invasion in the iron-depleted medium, deletion of its QS system leads to a decrease in host cell invasion, which is nevertheless similar to the level of the wild type S. proteamaculans grown in the iron-rich medium. Thus, inactivation of either of the two component of the S. proteamaculans LuxI/LuxR-type QS system leads to an increase in the invasive activity of these bacteria through different mechanisms and prevents invasion under the iron-limited conditions.

Quorum sensing in Aliivibrio wodanis 06/09/139 and its role in controlling various phenotypic traits

Background

Quorum Sensing (QS) is a cell-to-cell communication system that bacteria utilize to adapt to the external environment by synthesizing and responding to signalling molecules called autoinducers. The psychrotrophic bacterium Aliivibrio wodanis 06/09/139, originally isolated from a winter ulcer of a reared Atlantic salmon, produces the autoinducer N-3-hydroxy-decanoyl-homoserine-lactone (3OHC10-HSL) and encodes the QS systems AinS/R and LuxS/PQ, and the master regulator LitR. However, the role of QS in this bacterium has not been investigated yet.

Results

In the present work we show that 3OHC10-HSL production is cell density and temperature-dependent in A. wodanis 06/09/139 with the highest production occurring at a low temperature (6 °C). Gene inactivation demonstrates that AinS is responsible for 3OHC10-HSL production and positively regulated by LitR. Inactivation of ainS and litR further show that QS is involved in the regulation of growth, motility, hemolysis, protease activity and siderophore production. Of these QS regulated activities, only the protease activity was found to be independent of LitR. Lastly, supernatants harvested from the wild type and the ΔainS and ΔlitR mutants at high cell densities show that inactivation of QS leads to a decreased cytopathogenic effect (CPE) in a cell culture assay, and strongest attenuation of the CPE was observed with supernatants harvested from the ΔlitR mutant.

Conclusion

A. wodanis 06/09/139 use QS to regulate a number of activities that may prove important for host colonization or interactions. The temperature of 6 °C that is in the temperature range at which winter ulcer occurs, plays a role in AHL production and development of CPE on a Chinook Salmon Embryo (CHSE) cell line.

Veronia nyctiphanis gen. nov., sp. nov., Isolated from the Stomach of the Euphausiid Nyctiphanes simplex (Hansen, 1911) in the Gulf of California, and Reclassification of Enterovibrio pacificus as Veronia pacifica comb. nov

The bacterial strain 42Xb2 ^T was isolated from a female adult krill Nyctiphanes simplex infected with the apostome parasitoid ciliate Pseudocollinia brintoni in January 2007 in the Gulf of California. The strain has the morphological, phenotypic, and molecular characteristics of the bacteria of the family Vibrionaceae. The 16S rRNA gene sequence has a similarity of 97.7% with Enterovibrio pacificus SW014 ^T and 96.1% similarity with Enterovibrio norvegicus LMG 19839 ^T. A phylogenomic and a multilocus sequence analyses placed this strain close to the genera Enterovibrio, Grimontia, and Salinivibrio, but clearly forming a separate branch from these bacterial genera. Genomic analyses presented further support this result. A novel genus Veronia gen. nov. and a species Veronia nyctiphanis sp. nov. is here described with CAIM 600 ^T (= DSM 24592 ^T = CECT 7578 ^T) as the type strain. Morphological, physiological, and genetic evidence presented here support the unification of Enterovibrio pacificus and Veronia nyctiphanis in the new genus Veronia. Enterovibrio pacificus is reclassified as Veronia pacifica. V. pacifica is assigned as the type species of the new genus Veronia.Genome Sequencing Data The GenBank/EMBL/DDBJ accession numbers for the genome sequence of Veronia nyctiphanis CAIM 600 ^T is PEIB01 and of Enterovibrio pacificus CAIM 1920 ^T is LYBM01. The 16S rRNA gene sequence of V. nyctiphanis CAIM 600 ^T is JX129353.

Phylogenomics illuminates the evolution of bobtail and bottletail squid (order Sepiolida)

Bobtail and bottletail squid are small cephalopods with striking anti-predatory defensive mechanisms, bioluminescence, and complex morphology; that inhabit nektobenthic and pelagic environments around the world's oceans. Yet, the evolution and diversification of these animals remain unclear. Here, we used shallow genome sequencing of thirty-two bobtail and bottletail squids to estimate their evolutionary relationships and divergence time. Our phylogenetic analyses show that each of Sepiadariidae, Sepiolidae, and the three subfamilies of the Sepiolidae are monophyletic. We found that the ancestor of the Sepiolinae very likely possessed a bilobed light organ with bacteriogenic luminescence. Sepiolinae forms a sister group to Rossinae and Heteroteuthinae, and split into Indo-Pacific and Atlantic-Mediterranean lineages. The origin of these lineages coincides with the end of the Tethys Sea and the separation of these regions during the Eocene and the beginning of the Oligocene. We demonstrated that sepiolids radiated after the Late Cretaceous and that major biogeographic events might have shaped their distribution and speciation.

Vibrio fischeri: Laboratory Cultivation, Storage, and Common Phenotypic Assays

Vibrio fischeri is a nonpathogenic organism related to pathogenic Vibrio species that can be readily grown and stored with common laboratory equipment. In this article, protocols for routine growth, storage, and phenotypic assessment of V. fischeri, as well as recipes for useful media, are included. Specifically, this article describes procedures and considerations for growth of this microbe in complex and minimal media. It also describes assays for biofilm formation, motility, and bioluminescence, three commonly assessed phenotypes of V. fischeri. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Growth of V. fischeri from frozen stocks Basic Protocol 2: Growth of V. fischeri in rich, undefined liquid medium Alternate Protocol 1: Growth of V. fischeri in minimal medium Basic Protocol 3: Storage of V. fischeri in frozen stocks Basic Protocol 4: Biofilm assay on solid agar Alternate Protocol 2: Biofilm assay in shaking liquid culture Alternate Protocol 3: Biofilm assay in static liquid culture Basic Protocol 5: Motility assay Basic Protocol 6: Luminescence assay.

Salmon gut microbiota correlates with disease infection status: potential for monitoring health in farmed animals

BACKGROUND

Infectious diseases cause significant production losses in aquaculture every year. Since the gut microbiota plays an essential role in regulating the host immune system, health and physiology, altered gut microbiota compositions are often associated with a diseased status. However, few studies have examined the association between disease severity and degree of gut dysbiosis, especially when the gut is not the site of the primary infection. Moreover, there is a lack of knowledge on whether bath treatment with formalin, a disinfectant commonly used in aquaculture to treat external infections, might affect the gut microbiome as a consequence of formalin ingestion. Here we investigate, through 16S rRNA gene metabarcoding, changes in the distal gut microbiota composition of a captive-reared cohort of 80 Atlantic salmon (Salmo salar L.), in consequence of an external bacterial skin infection due to a natural outbreak and subsequent formalin treatment.

RESULTS

We identified Tenacibaculum dicentrarchi as the causative disease pathogen and we show that the distal gut of diseased salmon presented a different composition from that of healthy individuals. A new, yet undescribed, Mycoplasma genus characterized the gut of healthy salmon, while in the sick fish we observed an increase in terms of relative abundance of Aliivibrio sp., a strain regarded as opportunistic. We also noticed a positive correlation between fish weight and Mycoplasma sp. relative abundance, potentially indicating a beneficial effect for its host. Moreover, we observed that the gut microbiota of fish treated with formalin was more similar to those of sick fish than healthy ones.

CONCLUSIONS

We conclude that external Tenacibaculum infections have the potential of indirectly affecting the host gut microbiota. As such, treatment optimization procedures should account for that. Formalin treatment is not an optimal solution from a holistic perspective, since we observe an altered gut microbiota in the treated fish. We suggest its coupling with a probiotic treatment aimed at re-establishing a healthy community. Lastly, we have observed a positive correlation of Mycoplasma sp. with salmon health and weight, therefore we encourage further investigations towards its potential utilization as a biomarker for monitoring health in salmon and potentially other farmed fish species.

Host-specific symbioses and the microbial prey of a pelagic tunicate (Pyrosoma atlanticum)

Pyrosomes are widely distributed pelagic tunicates that have the potential to reshape marine food webs when they bloom. However, their grazing preferences and interactions with the background microbial community are poorly understood. This is the first study of the marine microorganisms associated with pyrosomes undertaken to improve the understanding of pyrosome biology, the impact of pyrosome blooms on marine microbial systems, and microbial symbioses with marine animals. The diversity, relative abundance, and taxonomy of pyrosome-associated microorganisms were compared to seawater during a Pyrosoma atlanticum bloom in the Northern California Current System using high-throughput sequencing of the 16S rRNA gene, microscopy, and flow cytometry. We found that pyrosomes harbor a microbiome distinct from the surrounding seawater, which was dominated by a few novel taxa. In addition to the dominant taxa, numerous more rare pyrosome-specific microbial taxa were recovered. Multiple bioluminescent taxa were present in pyrosomes, which may be a source of the iconic pyrosome luminescence. We also discovered free-living marine microorganisms in association with pyrosomes, suggesting that pyrosome feeding impacts all microbial size classes but preferentially removes larger eukaryotic taxa. This study demonstrates that microbial symbionts and microbial prey are central to pyrosome biology. In addition to pyrosome impacts on higher trophic level marine food webs, the work suggests that pyrosomes also alter marine food webs at the microbial level through feeding and seeding of the marine microbial communities with their symbionts. Future efforts to predict pyrosome blooms, and account for their ecosystem impacts, should consider pyrosome interactions with marine microbial communities.

The Effects of Forest Litter and Waterlogging on the Ecotoxicity of Soils Strongly Enriched in Arsenic in a Historical Mining Site

This study examined the effects of waterlogging and forest litter introduced to soil on chemical properties of soil pore water and ecotoxicity of soils highly enriched in As. These effects were examined in a 21-day incubation experiment. Tested soil samples were collected from Złoty Stok, a historical centre of arsenic and gold mining: from a forested part of the Orchid Dump (19,600 mg/kg As) and from a less contaminated site situated in a neighboring forest (2020 mg/kg As). An unpolluted soil was used as control. The concentrations of As, Fe and Mn in soil pore water were measured together with a redox potential Eh. A battery of ecotoxicological tests, including a bioassay with luminescence bacteria Vibrio fischeri (Microtox) and several tests on crustaceans (Rapidtox, Thamnotox and Ostracodtox tests), was used to assess soil ecotoxicity. The bioassays with crustaceans (T. platyurus, H. incongruens) were more sensitive than the bacterial test Microtox. The study confirmed that the input of forest litter into the soil may significantly increase the effects of toxicity. Waterlogged conditions facilitated a release of As into pore water, and the addition of forest litter accelerated this effect thus causing increased toxicity.

Vibrio agarilyticus sp. nov., an agar-digesting marine bacterium isolated from coastal seawater in Daya Bay (Guangdong, China)

A Gram-strain-negative, facultatively anaerobic, motile, rod-shaped and flagellated marine bacterium, designated SM6^T, was isolated from surface seawater collected in Daya Bay (Guangdong, China). Phylogenetic analysis based on 16S rRNA gene sequences, multilocus sequence analysis, phylogenomic analysis of single-copy gene families and whole genome data showed that strain SM6^T belonged to the genus Vibrio. The closest phylogenetic relatives of SM6^T were Vibrio plantisponsor MSSRF60^T (97.38 % 16S rRNA gene sequence pairwise similarity), Vibrio variabilis R-40492^T (97.27 %), Vibrio aestuarianus ATCC 35048^T (97.21 %) and Vibrio sagamiensis LC2-047^T (97.3 %). Growth of strain SM6^T occurred at 10-45 °C (optimum 30 °C), at pH 6.0-9.0 (optimum 6.0) and in the presence of 0-10 % (w/v) NaCl (optimum 3-8 %). The predominant fatty acids (>10 %) were summed feature 3 (C_{16 : 1} ω7c or/and C_{16 : 1} ω6c), C_{16 : 0} and summed feature 8 (C_{18 : 1} ω7c or/and C_{18 : 1} ω6c). The DNA G+C content of the assembled genomic sequences was 47.37 % for strain SM6^T. Average nucleotide identity values between SM6^T and its reference species were lower than the threshold for species delineation (95-96 %); in silico DNA-DNA hybridization further showed that the strains shared less than 70 % similarity. On the basis of evidence from the present polyphasic study, strain SM6^T is considered to represent a novel species of the genus Vibrio, for which the name Vibrio agarilyticus sp. nov. is proposed. The type strain is SM6^T (=KCTC 82076^T=MCCC 1K04327 ^T).

Phylogenetic Revision of the Genus Aliivibrio: Intra- and Inter-Species Variance Among Clusters Suggest a Wider Diversity of Species

Genus Aliivibrio is known to harbor species exhibiting bioluminescence as well as pathogenic behavior affecting the fish farming industry. Current phylogenetic understanding of Aliivibrio has largely remained dormant after reclassification disentangled it from the Vibrio genus in 2007. There is growing evidence of wider diversity, but until now the lack of genomes and selective use of type strains have limited the ability to compare and classify strains firmly. In this study, a total of 143 bacterial strains, including 51 novel sequenced strains, were used to strengthen phylogenetic relationships in Aliivibrio by exploring intra-species and inter-species relations. Multilocus sequence analysis (MLSA), applying the six housekeeping genes 16S ribosomal RNA (rRNA), gapA, gyrB, pyrH, recA, and rpoA, inferred 12 clades and a singular branch in Aliivibrio. Along with four new phylogenetic clades, the MLSA resolved prior inconsistencies circumscribing Aliivibrio wodanis and formed a unique clade we propose as the novel species Aliivibrio sp. “friggae.” Furthermore, phylogenetic assessment of individual marker genes showed gyrB, pyrH, and recA superior to the 16S rRNA gene, resolving accurately for most species clades in Aliivibrio. In this study, we provide a robust phylogenetic groundwork for Aliivibrio as a reference point to classification of species.

Quantitative determination of aloin, antioxidant activity, and toxicity of Aloe vera leaf gel products from Greece

BACKGROUND

Aloe vera is a popular medicinal plant used widely by the cosmetic, pharmaceutical, and food industries. The A. vera leaf gel, which is used mostly for its positive effects on human health, contains over 75 different bioactive compounds, including aloin. Aloin is a toxic compound, and its content in A. vera leaf gel products depends on the different cultivation conditions and especially on leaf processing.

RESULTS

In this study, A. vera leaf gel products, varied in terms of leaf processing, were analyzed using liquid chromatography for their aloin content, their antioxidant activity by 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonate) radical cation (ABTS^·+ ) and the 2,2-diphenyl-1-picrylhydrazyl radical (DPPH^· ) antioxidant activity assays and their toxicity against Aliivibrio fisheri and SH-SY5Y cells. In the samples processed with industrial methods and in those filtered in the lab, the content of aloin was found below the limit (0.1 mg L^-1 ) of the EU legislation however, the unprocessed and unfiltered samples were found to contain more than 10 mg L^-1 . Antioxidant activity was estimated to vary from 1.64 to 9.21 μmol Trolox mL^-1 for DPPH^· and from 0.73 to 5.14 μmol Trolox mL^-1 for ABTS^·+ . Toxicity values on A. fisheri, expressed as the concentration at 50% loss of initial luminescence, ranged from 0.03 to 0.09 mg mL^-1 . The cytotoxic study indicated that aloin A at low concentrations (1 and 10 μg mL^-1 ) protects SH-SY5Y cells from toxicity induced by hydrogen peroxide.

CONCLUSIONS

Consequently, the filtration process of A. vera leaf gels, either laboratory or industrial, resulted in aloin A content below the EU legislation detection limits. © 2020 Society of Chemical Industry.

Differential response of digesta- and mucosa-associated intestinal microbiota to dietary insect meal during the seawater phase of Atlantic salmon

Background

Intestinal digesta is commonly used for studying responses of microbiota to dietary shifts, yet evidence is accumulating that it represents an incomplete view of the intestinal microbiota. The present work aims to investigate the differences between digesta- and mucosa-associated intestinal microbiota in Atlantic salmon (Salmo salar) and how they may respond differently to dietary perturbations. In a 16-week seawater feeding trial, Atlantic salmon were fed either a commercially-relevant reference diet or an insect meal diet containing ~ 15% black soldier fly (Hermetia illucens) larvae meal. The digesta- and mucosa-associated distal intestinal microbiota were profiled by 16S rRNA gene sequencing.

Results

Regardless of diet, we observed substantial differences between digesta- and mucosa-associated intestinal microbiota. Microbial richness and diversity were much higher in the digesta than the mucosa. The insect meal diet altered the distal intestinal microbiota resulting in higher microbial richness and diversity. The diet effect, however, depended on the sample origin. Digesta-associated intestinal microbiota showed more pronounced changes than the mucosa-associated microbiota. Multivariate association analyses identified two mucosa-enriched taxa, Brevinema andersonii and Spirochaetaceae, associated with the expression of genes related to immune responses and barrier function in the distal intestine, respectively.

Conclusions

Our data show that salmon intestinal digesta and mucosa harbor microbial communities with clear differences. While feeding insects increased microbial richness and diversity in both digesta- and mucosa-associated intestinal microbiota, mucosa-associated intestinal microbiota seems more resilient to variations in the diet composition. To fully unveil the response of intestinal microbiota to dietary changes, concurrent profiling of digesta- and mucosa-associated intestinal microbiota is recommended whenever feasible. Specific taxa enriched in the intestinal mucosa are associated to gene expression related to immune responses and barrier function. Detailed studies are needed on the ecological and functional significance of taxa associated to intestinal microbiota dwelling on the mucosa.

Supplementary Information

The online version contains supplementary material available at 10.1186/s42523-020-00071-3.

Application of a standard risk assessment scheme to a North Africa contaminated site (Sfax, Tunisia) -Tier 1

Phosphorus is a critical element to agriculture, consequently global phosphate rock demand will remain rising to feed a growing world population. The beneficiation of phosphorous ore gives rise to several tons of a waste by-product [phosphogypsum (PG)] which valorisation is limited, within other reasons, by the risks posed to environment and human health. Although threatening, the accumulation in stacks is the only procedure so far practiced by several countries as a means to get rid of this industrial externality. As part of a NATO Science for Peace Project (SfP 983311) this study describes the application of an environmental risk assessment (ERA) framework, to assess the risks posed by a PG stack to the surrounding soils, in Sfax, Republic of Tunisia. The ERA followed a weight of evidence approach, supported by two lines of evidence (LoE): the chemical (ChemLoE) and the ecotoxicological (EcotoxLoE). Integrated risks point for risk values greater than 0.5 in soils collected in PG stack surrounding area. Soil salinization, has likely contributed to the exacerbation of risks, as well as to the lack of consistency between both LoEs. This study highlights the need of rethinking the weight given to each LoE in ERA, in areas where soil salinization is a reality.

Direct Comparison of Fecal and Gut Microbiota in the Blue Mussel (Mytilus edulis) Discourages Fecal Sampling as a Proxy for Resident Gut Community

Bivalves have ecological and economic importance but information regarding their associated microbiomes is lacking. As suspension feeders, bivalves capture and ingest a myriad of particles, and their digestive organs have a high throughput of particle-associated microbiota. To better understand the complement of transient and resident microbial communities, standard methods need to be developed. For example, fecal sampling could represent a convenient proxy for the gut microbiome and is simple, nondestructive, and allows for sampling of individuals through time. The goal of this study was to evaluate fecal sampling as a reliable proxy for gut microbiome assessment in the blue mussel (Mytilus edulis). Mussels were collected from the natural environment and placed into individual sterilized microcosms for 6 h to allow for fecal egestion. Feces and gut homogenates from the same individuals were sampled and subjected to 16S rRNA gene amplicon sequencing. Fecal communities of different mussels resembled each other but did not resemble gut communities. Fecal communities were significantly more diverse, in terms of amplicon sequence variant (ASV) richness and evenness, than gut communities. Results suggested a mostly transient nature for fecal microbiota. Nonetheless, mussels retained a distinct resident microbial community in their gut after fecal egestion that was dominated by ASVs belonging to Mycoplasma. The use of fecal sampling as a nondestructive substitute for direct sampling of the gut is strongly discouraged. Experiments that aim to study solely resident bivalve gut microbiota should employ an egestion period prior to gut sampling to allow time for voidance of transient microbes.

Gut Symbiotic Microbial Communities in the IUCN Critically Endangered Pinna nobilis Suffering from Mass Mortalities, Revealed by 16S rRNA Amplicon NGS

Mass mortality events due to disease outbreaks have recently affected almost every healthy population of fan mussel, Pinna nobilis in Mediterranean Sea. The devastating mortality of the species has turned the interest of the research towards the causes of these events. After the haplosporidan infestation and the infection by Mycobacterium sp., new emerging pathogens have arisen based on the latest research. In the present study, a metagenomic approach of 16S rRNA next generation sequencing (NGS) was applied in order to assess the bacterial diversity within the digestive gland of diseased individuals as well as to carry out geographical correlations among the biodiversity of microbiome in the endangered species Pinna nobilis. The specimens originated from the mortalities occurred in 2019 in the region of Greece. Together with other bacterial genera, the results confirmed the presence of Vibrio spp., assuming synergistic effects in the mortality events of the species. Alongside with the presence of Vibrio spp., numerous bacterial genera were detected as well, including Aliivibrio spp., Photobacterium spp., Pseudoalteromonas spp., Psychrilyobacter spp. and Mycoplasma spp. Bacteria of the genus Mycoplasma were in high abundance particularly in the sample originated from Limnos island representing the first time recorded in Pinna nobilis. In conclusion, apart from exclusively the Haplosporidan and the Mycobacterium parasites, the presence of potentially pathogenic bacterial taxa detected, such as Vibrio spp., Photobactrium spp. and Alivibrio spp. lead us to assume that mortality events in the endangered Fan mussel, Pinna nobilis, may be attributed to synergistic effects of more pathogens.

Impacts of anthropogenic gadolinium on the activity of the ammonia oxidizing bacterium Nitrosomonas europaea

Widespread use of gadolinium-based contrast agents in medical imaging has resulted in increased Gd inputs to municipal wastewater treatment plants. Others have reported that typical wastewater treatment does not attenuate Gd, resulting in discharges to natural waters. However, whether elevated Gd impacts the performance of biological treatment has not been investigated. We examined whether gadolinium chloride or Gd chelated with diethylenetriaminepentaacetic acid (DTPA) affected the activity of the model nitrifying bacterium Nitrosomonas europaea. At nominal GdCl₃ additions ranging from 1 to 500 μM, no impact was observed compared to the control. Most (>98%) of the added Gd precipitated, and extracellular GdPO₄ nanoparticles were observed. When chelated with DTPA, Gd remained soluble, but no statistically significant impact on ammonia oxidation was observed until the highest concentrations tested. At 300 and 500 μM Gd-DTPA, a temporary reduction of nitrite production relative to the control (effect size 1.3 mg l^-1 and 1.5 mg l^-1, respectively, at 24 h) was seen. By itself, DTPA was highly inhibitory. Modeling suggested that DTPA likely chelated other metals, but adjusting the concentrations of the most abundant metals in the medium, calcium and magnesium, indicated that lowering their free ion activities was probably not the cause of inhibition. Complexation of other essential metals was more likely. Our studies indicate that while the low bioavailability of Gd may limit its ecosystem impacts, the role of synthetic ligands used with Gd and other rare earth elements should be considered as the production, use and disposal of these elements increases.

Mathematical Modeling Approaches for Assessing the Joint Toxicity of Chemical Mixtures Based on Luminescent Bacteria: A Systematic Review

Developments in industrial applications inevitably accelerate the discharge of enormous substances into the environment, whereas multi-component mixtures commonly cause joint toxicity which is distinct from the simple sum of independent effect. Thus, ecotoxicological assessment, by luminescent bioassays has recently brought increasing attention to overcome the environmental risks. Based on the above viewpoint, this review included a brief introduction to the occurrence and characteristics of toxic bioassay based on the luminescent bacteria. In order to assess the environmental risk of mixtures, a series of models for the prediction of the joint effect of multi-component mixtures have been summarized and discussed in-depth. Among them, Quantitative Structure-Activity Relationship (QSAR) method which was widely applied in silico has been described in detail. Furthermore, the reported potential mechanisms of joint toxicity on the luminescent bacteria were also overviewed, including the Trojan-horse type mechanism, funnel hypothesis, and fishing hypothesis. The future perspectives toward the development and application of toxicity assessment based on luminescent bacteria were proposed.

Ecotoxicity of Pore Water in Meadow Soils Affected by Historical Spills of Arsenic-Rich Tailings

This study was carried out in Złoty Stok, a historical centre of gold and arsenic mining. Two kinds of soil material, containing 5020 and 8000 mg/kg As, represented a floodplain meadow flooded in the past by tailings spills and a dry meadow developed on the plateau built of pure tailings, respectively. The effects of soil treatment with a cattle manure and mineral fertilizers were examined in an incubation experiment. Soil pore water was collected after 2, 7, 21, 90, and 270 days, using MacroRhizon samplers and analyzed on As concentrations and toxicity, and assessed in three bioassays: Microtox, the Microbial Assay for Risk Assessment (MARA), and Phytotox, with Sinapis alba as a test plant. In all samples, As concentrations were above 4.5 mg/L. Fertilization with manure caused an intensive release of As, and its concentration in pore water of floodplain soil reached 81.8 mg/L. Mineral fertilization caused a release of As only from the pure tailings soil. The results of bioassays, particularly of Phytotox and MARA, correlated well with As concentrations, while Microtox indices depended additionally on other factors. Very high toxicity was associated with As > 20 mg/L. Despite an effect of “aging”, pore water As remained at the level of several mg/L, causing a potential environmental risk.

Sequence analysis of nonulosonic acid biosynthetic gene clusters in Vibrionaceae and Moritella viscosa

Nonulosonic acid (NulO) biosynthesis in bacteria is directed by nab gene clusters that can lead to neuraminic, legionaminic or pseudaminic acids. Analysis of the gene content from a set mainly composed of Aliivibrio salmonicida and Moritella viscosa strains reveals the existence of several unique nab clusters, for which the NulO products were predicted. This prediction method can be used to guide tandem mass spectrometry studies in order to verify the products of previously undescribed nab clusters and identify new members of the NulOs family.

Molecular Identification and Characterization of Vibrio Species and Mycobacterium Species in Wild and Cultured Marine Fish from the Eastern Mediterranean Sea

In contrast to numerous documented pathogens and infectious diseases of aquaculture, there is a lack of baseline data and information regarding pathogenic agents' prevalence in wild marine fish populations. This study focused on two common fish pathogenic microorganisms, namely Mycobacterium species and Vibrio species, both of which are known to be major causes of fish loss, occasionally to the extent of being a limiting factor in fish production. Both microorganisms are known as zoonotic agents. In total, 210 wild marine indigenous and Lessepsian fish from four different species from the eastern Mediterranean Sea were sampled and tested for Vibrio species and Mycobacterium species during a two-year period (2016-2017). Using PCR with 16S rRNA primers, we detected different strain variations of Mycobacterium species and Vibrio species and, based on the sequencing results, the overall prevalence for Vibrio species in wild fish in 2016 was significantly higher compared to 2017. No significant difference was detected for Mycobacterium species prevalence in wild fish between 2016 and 2017. In addition, 72 gilthead seabream (Sparus aurata) from an Israeli offshore marine farm were also examined during the two-year period (2017-2018). The results suggest that Mycobacterium species prevalence was significantly higher in 2018, while in 2017 there was no positive results for Mycobacterium species. In addition, there was no significant difference between both years in regard to the prevalence of Vibrio species for maricultured fish. These results highlight the necessity of continuous molecular monitoring in order to evaluate the prevalence of pathogenic microorganisms in both wild and cultured fish populations.

The strains of bioluminescent bacteria isolated from the White Sea finfishes: genera Photobacterium, Aliivibrio, Vibrio, Shewanella, and first luminous Kosakonia

Bioluminescence is a spectacular feature of some prokaryotes. In the present work, we address the distribution of bioluminescence among bacteria isolated from the White Sea finfishes. Luminous bacteria are widely distributed throughout the World Ocean. Many strains have been isolated and described for tropical latitudes, while Nordic seas still remain quite a white spot in studying bioluminescence of bacteria. We describe the strains related to the two main genera of luminous bacteria, Photobacterium and Aliivibrio, as well as Shewanella and Vibrio. They are related to families Vibrionaceae and Shewanellaceae of the Gammaproteobacteria class. Here, we at the first time, report the bioluminescence of the Enterobacteriaceae Kosakonia cowanii. Moreover, we applied the polyphasic approach to identify and describe the isolated microorganisms. The data on sequencing, diversity of cell fine structure, and light emission spectra at room temperature on the solid medium are discussed. The bacteria are characterized by features in their light emission spectra. It may reflect possible molecular mechanisms of bioluminescence as well as features of bacterial composition. The obtained data expands the existing body of knowledge about the bioluminescence spread among the bacteria of Nordic latitudes and provides complex information that is crucial for their precise identification.

The Marine Bacterium Shewanella woodyi Produces C8-HSL to Regulate Bioluminescence

Quorum sensing (QS), a cell-to-cell communication system involved in the synchronization of bacterial behavior in a cell-density-dependent manner has been shown to control phenotypes such as luminescence, virulence, and biofilm formation. The marine strain, Shewanella woodyi MS32 has been identified as a luminous bacterium. Very little information is known on this bacterium, in particular if its luminescence and biofilm formation are controlled by QS. In this study, we have demonstrated that S. woodyi MS32 emits luminescence in planktonic and sessile conditions. The putative QS regulatory genes homologous to luxI and luxR identified in the S. woodyi MS32 genome, named swoI and swoR, are divergently transcribed and are not genetically linked to the lux operon in contrast with its closest parent Shewanella hanedai and with Aliivibrio fischeri. Interestingly, the phylogenetic analysis based on the SwoI and SwoR sequences shows that a separate horizontal gene transfer (HGT) occurred for the regulatory genes and for the lux operon. Functional analyses demonstrate that the swoI and swoR mutants were non-luminescent. Expression of lux genes was impaired in the QS regulatory mutants. N-octanoyl-L-homoserine lactone (C₈-HSL) identified using liquid chromatography mass spectrometry in the wild-type strain (but not in ΔswoI) can induce S. woodyi luminescence. No significant difference has been detected between the wild-type and mutants on adhesion and biofilm formation in the conditions tested. Therefore, we have demonstrated that the luxCDABEG genes of S. woodyi MS32 are involved in luminescence emission and that the swoR/swoI genes, originated from a separate HGT, regulate luminescence through C₈-HSL production.

Improving biotreatability of hazardous effluents combining ZVI, electrolysis and photolysis

In this work, nine types of combination advanced oxidation processes/zero-valent iron (AOP-ZVI) were tested, in order to determine if any of these combinations demonstrate good chances as pretreatment for the biological degradation processes of organochlorinated pollutants. To do this, the changes undergone in the respirometric behavior, toxicity and short-term biodegradability were compared. The three AOPs studied were anodic oxidation with mixed metal oxides anodes (AO-MMO), with boron doped diamond anodes (AO-BDD) and photolysis and they were evaluated in three different modes: without any addition of ZVI, with ZVI-dehalogenation as pre-treatment and with ZVI-dehalogenation simultaneous to the AOP treatment. Clopyralid has been used as a model of chlorinated hydrocarbon pollutant. Results show that technologies proposed can successfully treat wastes polluted with clopyralid and the biological characteristics of the waste are significantly modified by dehalogenating the waste with ZVI, either previously to the treatment or simultaneously to the treatment, being the information provided by the three techniques very important in order to evaluate later combinations of the advanced oxidation technologies with biological treatments.

Extension of biotic ligand model to account for the effects of pH and phosphate in accurate prediction of arsenate toxicity

Biotic ligand model (BLM) was extended to predict the toxicity of inorganic arsenate (iAs(V)) to the luminescent bacteria, Aliivibrio fischeri. As the pH increased from 5 to 9, the HAsO₄^2- form predominated more than the H₂AsO₄^- form did, and the EC₅₀[As]_T (50% effective iAs(V) concentration) decreased drastically from 3554 ± 393 to 39 ± 6 μM; thus, the HAsO₄^2- form was more toxic to A. fischeri than H₂AsO₄^-. As the HPO₄^2- activity increased from 0 to 0.44 mM, the EC₅₀{HAsO₄^2-} values (50% effective HAsO₄^2- activity) increased from 31 ± 6 to 859 ± 128 μM, indicating that the toxicity of iAs(V) decreased, owing to the competition caused by the structural similarity between iAs(V) and phosphate ions. However, activities of Ca²⁺, Mg²⁺, K⁺, SO₄^2-, NO₃^-, and HCO₃^- did not significantly affect the EC₅₀{HAsO₄^2-} values. The BLM was reconstructed to take into account the effects of pH and phosphate, and the conditional binding constants for H₂PO₄^-, HPO₄^2-, H₂AsO₄^-, and HAsO₄^2- to the active binding sites of A. fischeri were obtained; 3.424 for logK_XH2PO4, 4.588 for logK_XHPO4, 3.067 for logK_XH2AsO4, and 4.802 for logK_XHAsO4. The fraction of active binding sites occupied by iAs(V) to induce 50% toxicity (f_mix^50%) was found to be 0.616.

Using Colonization Assays and Comparative Genomics To Discover Symbiosis Behaviors and Factors in Vibrio fischeri

The luminous marine Gram-negative bacterium Vibrio (Aliivibrio) fischeri is the natural light organ symbiont of several squid species, including the Hawaiian bobtail squid, Euprymna scolopes, and the Japanese bobtail squid, Euprymna morsei Work with E. scolopes has shown how the bacteria establish their niche in the light organ of the newly hatched host. Two types of V. fischeri strains have been distinguished based upon their behavior in cocolonization competition assays in juvenile E. scolopes, i.e., (i) niche-sharing or (ii) niche-dominant behavior. This study aimed to determine whether these behaviors are observed with other V. fischeri strains or whether they are specific to those isolated from E. scolopes light organs. Cocolonization competition assays between V. fischeri strains isolated from the congeneric squid E. morsei or from other marine animals revealed the same sharing or dominant behaviors. In addition, whole-genome sequencing of these strains showed that the dominant behavior is polyphyletic and not associated with the presence or absence of a single gene or genes. Comparative genomics of 44 squid light organ isolates from around the globe led to the identification of symbiosis-specific candidates in the genomes of these strains. Colonization assays using genetic derivatives with deletions of these candidates established the importance of two such genes in colonization. This study has allowed us to expand the concept of distinct colonization behaviors to strains isolated from a number of squid and fish hosts.IMPORTANCE There is an increasing recognition of the importance of strain differences in the ecology of a symbiotic bacterial species and, in particular, how these differences underlie crucial interactions with their host. Nevertheless, little is known about the genetic bases for these differences, how they manifest themselves in specific behaviors, and their distribution among symbionts of different host species. In this study, we sequenced the genomes of Vibrio fischeri isolated from the tissues of squids and fishes and applied comparative genomics approaches to look for patterns between symbiont lineages and host colonization behavior. In addition, we identified the only two genes that were exclusively present in all V. fischeri strains isolated from the light organs of sepiolid squid species. Mutational studies of these genes indicated that they both played a role in colonization of the squid light organ, emphasizing the value of applying a comparative genomics approach in the study of symbioses.

The Analysis of Bifenox and Dichlobenil Toxicity in Selected Microorganisms and Human Cancer Cells

Bifenox and Dichlobenil belong to the commonly used in Poland in agriculture group of herbicides and their residues are often detected in the environment. They are poorly known regarding their possible carcinogenic and antibacterial effect at the cellular level. Therefore, we decided to study their activity in bacterial strains Aliivibrio fisheri, E. coli, P. aeruginosa, and C. albicans (yeast) and human cancer ZR-75-1 cells. Compounds under study exhibit stimulatory effect on analyzed bacterial strains. The study performed on mammalian cells better reflects the influence of environmental pollutants on human organism, therefore we evaluated the effect of herbicides on ZR-75-1 cells. Cells viability, apoptosis and selected oxidative stress parameters in ZR-75-1 cells were investigated. Both analyzed substances exhibit stimulatory effects on analyzed parameters, however they do not stimulate apoptosis which correlate positively with the induction of oxidative stress. Bifenox and Dichlobenil enhance oxidative stress parameters by the generation of high levels of ROS, which can lead to their adaptation and resistance to the standard treatment regimen.

Seasonal changes in luminescent intestinal microflora of the fish inhabiting the Bering and Okhotsk seas

Here, we present a study of luminescent intestinal microflora of the fish inhabiting Bering and Okhotsk seas in summer and winter seasons. Sampling of intestinal luminescent microflora was carried for several years, with all recovered species belonging to psychrophilic bacteria of either Aliivibrio logei or Photobacterium phosphoreum species. A seasonal change in fish intestinal luminescent microflora detected include an increase in prevalence of P. phosphoreum bacteria in summer and an increase in prevalence of A. logei bacteria in winter seasons. In fact, 90% of all luminescent bacteria isolated in winter period (January-March) were A. logei, while 88% of luminescent isolates recovered in summer period (July-September) were that of P. phosphoreum species. Seasonal changes were similar across all six sampling expeditions, three in winter and three in summer seasons, evenly spread through 2010-2018 period.

Ecotoxicity of pore water in soils developed on historical arsenic mine dumps: The effects of forest litter

Arsenic release from dump soils in historical mining sites poses the environmental risk. Decomposing forest litter can affect mobilization of As and other toxic elements, change their speciation in pore water and influence the toxicity to biota. This study examined the chemistry and ecotoxicity of pore water acquired from four soils that developed on the dumps in former As mining sites, in the presence and absence of forest litter collected from beech and spruce stands. Soils contained 1540-19600 mg/kg of As. Pore water was collected after 2, 7, 21 and 90 days of incubation, using MacroRhizon suction samplers. Its chemical analysis involved determination of pH, the concentrations of As, Cu and Pb (the elements with high enrichment factor Igeo>3), as well as metals considered most mobile: Cd, Zn and Mn. Ecotoxicity of pore water was examined in three bioassays: Microtox, MARA and Phytotox with Sinapis alba as test plant. The release of As, unlike heavy metals, was particularly intensive from the soils with neutral and alkaline pH. The concentrations of toxic elements in pore water were in broad ranges, up to dozens mg/L. The results of Phytotox had a poor precision, but their means correlated well with As concentrations in pore water, which indicates that As made a crucial factor of phytotoxicity. The outcomes of Microtox bioassay indicated poorer relationships between As concentrations and toxicity, and other factors contributed to ecotoxicity at very low and very high As concentrations. The highest toxicity was recorded from the soils treated with forest litter. MARA turned out to be not sensitive enough to give reproducible results in experimental conditions. The PCA analysis confirmed that the growth of microbes in MARA bioassay was poorly dependent on As and metals in pore water except for a yeast Pichia anomala (No 11). The results let us conclude that the bioassays Phytotox and Microtox can provide useful information on ecotoxicity of pore water in soils that develop on As-rich dumps whereas applicability of MARA in those conditions proved limited.

Application of the bacteriophage pVco-14 to prevent Vibrio coralliilyticus infection in Pacific oyster (Crassostrea gigas) larvae

Vibrio coralliilyticus infects a variety of shellfish larvae, including Pacific oyster (Crassostrea gigas) larvae worldwide, and remains a major constraint in marine bivalve aquaculture practice, especially in artificial seed production facilities. In this study, we isolated and characterized the bacteriophage (phage) that specifically infects V. coralliilyticus. The phage was designated pVco-14 and classified as Siphoviridae. We also investigated the potential efficacy of the isolated phage against V. coralliilyticus infection. We conducted a survey to replace the overuse of antibiotics, which generate multi-antibiotic-resistant strains and causes environmental pollution. The latent period of pVco-14 was estimated to be approximately 30 min, whereas the burst size was 13.3 PFU/cell. The phage was found to infect four strains of tested V. coralliilyticus. pVco-14 was stable at wide temperature (4-37 °C) and pH (5.0-9.0) ranges. Eighty-one percent of oyster larvae died in an immersion challenge at a dose 1.32 × 10⁵ CFU/ml of virulent V. coralliilyticus (strain 58) within 24 h. When oyster larvae were pre-treated with the phage before the bacterial challenge (bacterial conc.: 1.32 × 10⁴ and 1.32 × 10⁵ CFU/ml), mortality of the phage-treated oyster larvae was lower than that of the untreated control. These results suggest that pVco-14 has potential to be used as a prophylactic agent for preventing V. coralliilyticus infection in marine bivalve hatcheries and can reduce the overuse of antibiotics.

Saline Environments as a Source of Potential Quorum Sensing Disruptors to Control Bacterial Infections: A Review

Saline environments, such as marine and hypersaline habitats, are widely distributed around the world. They include sea waters, saline lakes, solar salterns, or hypersaline soils. The bacteria that live in these habitats produce and develop unique bioactive molecules and physiological pathways to cope with the stress conditions generated by these environments. They have been described to produce compounds with properties that differ from those found in non-saline habitats. In the last decades, the ability to disrupt quorum-sensing (QS) intercellular communication systems has been identified in many marine organisms, including bacteria. The two main mechanisms of QS interference, i.e., quorum sensing inhibition (QSI) and quorum quenching (QQ), appear to be a more frequent phenomenon in marine aquatic environments than in soils. However, data concerning bacteria from hypersaline habitats is scarce. Salt-tolerant QSI compounds and QQ enzymes may be of interest to interfere with QS-regulated bacterial functions, including virulence, in sectors such as aquaculture or agriculture where salinity is a serious environmental issue. This review provides a global overview of the main works related to QS interruption in saline environments as well as the derived biotechnological applications.

Variability in the Composition of Pacific Oyster Microbiomes Across Oyster Families Exhibiting Different Levels of Susceptibility to OsHV-1 μvar Disease

Oyster diseases are a major impediment to the profitability and growth of the oyster aquaculture industry. In recent years, geographically widespread outbreaks of disease caused by ostreid herpesvirus-1 microvariant (OsHV-1 μvar) have led to mass mortalities among Crassostrea gigas, the Pacific Oyster. Attempts to minimize the impact of this disease have been largely focused on breeding programs, and although these have shown some success in producing oyster families with reduced mortality, the mechanism(s) behind this protection is poorly understood. One possible factor is modification of the C. gigas microbiome. To explore how breeding for resistance to OsHV-1 μvar affects the oyster microbiome, we used 16S rRNA amplicon sequencing to characterize the bacterial communities associated with 35 C. gigas families, incorporating oysters with different levels of susceptibility to OsHV-1 μvar disease. The microbiomes of disease-susceptible families were significantly different to the microbiomes of disease-resistant families. OTUs assigned to the Photobacterium, Vibrio, Aliivibrio, Streptococcus, and Roseovarius genera were associated with low disease resistance. In partial support of this finding, qPCR identified a statistically significant increase of Vibrio-specific 16S rRNA gene copies in the low disease resistance families, possibly indicative of a reduced host immune response to these pathogens. In addition to these results, examination of the core microbiome revealed that each family possessed a small core community, with OTUs assigned to the Winogradskyella genus and the Bradyrhizobiaceae family consistent members across most disease-resistant families. This study examines patterns in the microbiome of oyster families exhibiting differing levels of OsHV-1 μvar disease resistance and reveals some key bacterial taxa that may provide a protective or detrimental role in OsHV-1 μvar disease outbreaks.

Vibriosis in Fish: A Review on Disease Development and Prevention

Current growth in aquaculture production is parallel with the increasing number of disease outbreaks, which negatively affect the production, profitability, and sustainability of the global aquaculture industry. Vibriosis is among the most common diseases leading to massive mortality of cultured shrimp, fish, and shellfish in Asia. High incidence of vibriosis can occur in hatchery and grow-out facilities, but juveniles are more susceptible to the disease. Various factors, particularly the source of fish, environmental factors (including water quality and farm management), and the virulence factors of Vibrio, influence the occurrence of the disease. Affected fish show weariness, with necrosis of skin and appendages, leading to body malformation, slow growth, internal organ liquefaction, blindness, muscle opacity, and mortality. A combination of control measures, particularly a disease-free source of fish, biosecurity of the farm, improved water quality, and other preventive measures (e.g., vaccination) might be able to control the infection. Although some control measures are expensive and less practical, vaccination is effective, relatively cheap, and easily implemented. In this review, the latest knowledge on the pathogenesis and control of vibriosis, including vaccination, is discussed.