An outbreak of Shewanella putrefaciens group in wild eels Anguilla anguilla L. favoured by hypoxic aquatic environments

Network-based integration of omics, physiological and environmental data in real-world Elbe estuarine Zander

Coastal and estuarine environments are under endogenic and exogenic pressures jeopardizing survival and diversity of inhabiting biota. Information of possible synergistic effects of multiple (a)biotic stressors and holobiont interaction are largely missing in estuaries like the Elbe but are of importance to estimate unforeseen effects on animals' physiology. Here, we seek to leverage host-transcriptional RNA-seq and gill mucus microbial 16S rRNA metabarcoding data coupled with physiological and abiotic measurements in a network analysis approach to decipher the impact of multiple stressors on the health of juvenile Sander lucioperca along one of the largest European estuaries. We find mesohaline areas characterized by gill tissue specific transcriptional responses matching osmosensing and tissue remodeling. Liver transcriptomes instead emphasized that zander from highly turbid areas were undergoing starvation which was supported by compromised body condition. Potential pathogenic bacteria, including Shewanella, Acinetobacter, Aeromonas and Chryseobacterium, dominated the gill microbiome along the freshwater transition and oxygen minimum zone. Their occurrence coincided with a strong adaptive and innate transcriptional immune response in host gill and enhanced energy demand in liver tissue supporting their potential pathogenicity. Taken together, we show physiological responses of a fish species and its microbiome to abiotic factors whose impact is expected to increase with consequences of climate change. We further present a method for the close-meshed detection of the main stressors and bacterial species with disease potential in a highly productive ecosystem.

Shewanella xiamenensis-associated ulcerative dermatitis in koi carp (Cyprinus rubrofuscus)

Ulcerative dermatitis (UD) is common in ornamental fish collections and is typically associated with a wide range of bacterial aetiologies. Clinical reports describing Shewanella xiamenensis-associated UD are limited, however, despite growing attention to pathogenic Shewanella species in fish. Two out of 95 koi carp with UD were presented for clinical assessment by a commercial collection (n = 3000 fish) and subsequently killed on welfare grounds for necropsy. Both specimens exhibited extensive cutaneous ulcers and coelomic fat necrosis with petechial haemorrhages on post-mortem examination. Shewanella xiamenensis was cultured from ulcerated skin tissues taken from both fish, with consistent intralesional gram-negative rod-like bacteria seen on skin scrape cytology. Histology also confirmed intralesional gram-negative rod-like bacteria within multiple ulcerative and erosive dermatitis lesions, plus myofibre necrosis and necrotising coelomic steatitis, in both specimens. Features associated with impaired generalised osmoregulation secondary to UD were detected within the striated muscle underlying the ulcers, the gills, and the caudal aspects of the kidneys. Additional histological features suggestive of sepsis were also seen in one of the fish. In the interim period, morbidity had increased from 3.2% to around 30% of the entire stock. Following culture results, increased pond water changes were implemented (q.2-3d) and the remaining stock was treated with florfenicol, resulting in complete resolution of UD in the collection (as per client). This article highlights the first description of S. xiamenensis-associated UD in koi carp/diseased ornamental fish in the United Kingdom.

Climate change can impair bacterial pathogen defences in sablefish via hypoxia-mediated effects on adaptive immunity

Low-oxygen levels (hypoxia) in aquatic habitats are becoming more common because of global warming and eutrophication. However, the effects on the health/disease status of fishes, the world's largest group of vertebrates, are unclear. Therefore, we assessed how long-term hypoxia affected the immune function of sablefish, an ecologically and economically important North Pacific species, including the response to a formalin-killed Aeromonas salmonicida bacterin. Sablefish were held at normoxia or hypoxia (100% or 40% air saturated seawater, respectively) for 6-16 weeks, while we measured a diverse array of immunological traits. Given that the sablefish is a non-model organism, this involved the development of a species-specific methodological toolbox comprised of qPCR primers for 16 key immune genes, assays for blood antibacterial defences, the assessment of blood immunoglobulin (IgM) levels with ELISA, and flow cytometry and confocal microscopy techniques. We show that innate immune parameters were typically elevated in response to the bacterial antigens, but were not substantially affected by hypoxia. In contrast, hypoxia completely prevented the ∼1.5-fold increase in blood IgM level that was observed under normoxic conditions following bacterin exposure, implying a serious impairment of adaptive immunity. Since the sablefish is naturally hypoxia tolerant, our results demonstrate that climate change-related deoxygenation may be a serious threat to the immune competency of fishes.

Gradual effects of gradient concentrations of perfluorooctane sulfonate on the antioxidant ability and gut microbiota of red claw crayfish (Cherax quadricarinatus)

Perfluorooctane sulfonate (PFOS) is a typical persistent organic pollutant that is characterized by environmental persistence, bioaccumulation, and toxicity. In this study, we investigated the gut microbial response of the red claw crayfish Cherax quadricarinatus after 28 days of exposure to 0 ng/L, 1 ng/L, 10 μg/L, or 10 mg/L of PFOS as a stressor. We measured oxidative stress-related enzyme activities and expression of molecules related to detoxification mechanisms to evaluate the toxic effects of PFOS. We found that PFOS disturbed microbial homeostasis in the gut of C. quadricarinatus, resulting in increased abundance of the pathogen Shewanella and decreased abundance of the beneficial bacterium Lactobacillus. The latter especially disturbed amino acid transport and carbohydrate transport. We also found that the activities of glutathione S-transferase and glutathione peroxidase were positively correlated with the expression levels of cytochrome P450 genes (GST1-1, GSTP, GSTK1, HPGDS, UGT5), which are products of PFOS-induced oxidative stress and play an antioxidant role in the body. The results of this study provided valuable ecotoxicological data to better understand the biological fate and effects of PFOS in C. quadricarinatus.

Phylogenetic analysis of Shewanella spp. isolated from fish

Different species of Shewanella spp. widely inhabit freshwater and marine environments. Some of them are opportunistic fish pathogens. The application of high-throughput sequencing enabled the characterization and taxonomic reclassification of many Shewanella spp. species. Still, some strains collected from fish need to be better recognized. The aim of the present study was to classify and determine the phylogenetic relationships of Shewanella spp. collected from fish. The complete genomes of 94 strains of Shewanella spp. from different fish species were sequenced using Illumina platform (MiSeq). The 16S rRNA gene, genomic features and whole-genome relationships of those bacteria were comprehensively analysed in comparison to reference strains. Whole-genome analysis showed that the tested Shewanella spp. strains were clustered into six groups similar to reference strains of S. xiamenensis, S. oneidensis, S. glacialipiscicola, S. hafniensis, S. baltica and S. oncorhynchi. Our study indicates that the whole-genome sequence analysis enabled taxonomic classification and assessment of the diversity of the Shewanella spp. strains, as opposed to recently the gold standard method of 16S rRNA amplicon sequencing. The high genetic diversity and low similarity to the reference genome of S. oneidensis indicate that the group of strains may be a subspecies or even new species. Furthermore, we showed that the most frequent Shewanella spp. species occurring in freshwater fish in our study is the recently described species S. oncorhynchi.

Integration of microbiome and Koch's postulates to reveal multiple bacterial pathogens of whitish muscle syndrome in mud crab, Scylla paramamosain

BACKGROUND

For more than a century, the Koch's postulates have been the golden rule for determining the causative agents in diseases. However, in cases of multiple pathogens-one disease, in which different pathogens can cause the same disease, the selection of microorganisms that regress infection is hard when Koch's postulates are applied. Microbiome approaches can obtain relatively complete information about disease-related microorganisms and can guide the selection of target microorganisms for regression infection. In the present study, whitish muscle syndrome (WMS) of Scylla paramamosain, which has typical symptoms with whitish muscle and blackened hemolymph was used as an example to establish a new research strategy that integrates microbiome approaches and Koch's postulates to determinate causative agents of multiple pathogens-one disease.

RESULTS

Microbiome results revealed that Aeromonas, Acinetobacter, Shewanella, Chryseomicrobium, Exiguobacterium, Vibrio and Flavobacterium, and Kurtzmaniella in hemolymph were bacterial and fungal indicators for WMS. A total of 23 bacteria and 14 fungi were isolated from hemolymph and muscle tissues, and among the bacteria, Shewanella chilikensis, S. xiamenensis, Vibrio alginolyticus, S. putrefaciens, V. fluvialis, and V. parahaemolyticus were present in hemolymph and/or muscle tissues in each WMS crab, and the last three species were also present in three Healthy crabs. The target bacteria and fungi were further screened to regression infections based on two criteria: whether they belonged to the indicator genera for WMS, whether they were isolated from both hemolymph and muscle tissues in most WMS crabs. Only S. chilikensis, S. putrefaciens, S. xiamenensis, V. alginolyticus, V. fluvialis, and V. parahaemolyticus met both two criteria. The six bacteria that met both two criteria and six fungi and another bacterium that unmatched any of two criteria were used to perform regression infection experiments based on Koch's postulates. S. chilikensis, S. putrefaciens, S. xiamenensis, V. alginolyticus, V. fluvialis, and V. parahaemolyticus met both two criteria, and the results indicate that they cause WMS in crabs independently.

CONCLUSIONS

This study fully demonstrated that our research strategy that integrates the microbiome and Koch's postulates can maximize the ability to catch pathogens in one net for the situation of multiple pathogens-one disease. Video Abstract.

Shewanella septentrionalis sp. nov. and Shewanella holmiensis sp. nov., isolated from Baltic Sea water and sediments

Two bacterial strains, SP1W3^T and SP1S2-7^T, were isolated from samples of water and sediments collected in Vaxholm, a town located on the Stockholm archipelago in the Baltic Sea, in November 2021. The strains were identified as novel genomic species within the genus Shewanella, based upon comparative analysis of whole genome sequence data. Strain SP1W3^T (genome size, 5.20 Mbp; G+C content, 46.0 mol%), isolated from water, was determined to be most closely related to S. hafniensis ATCC-BAA 1207^T and S. baltica NCTC 10735^T, with digital DNA-DNA hybridization (dDDH) values of 61.7% and 60.4 %, respectively. Strain SP1S2-7^T (genome size, 4.26 Mbp; G+C content, 41.5 mol%), isolated from sediments, was observed to be most closely related to S. aestuarii JCM17801^T, with a pairwise dDDH value of 33.8 %. Polyphasic analyses of physiological and phenotypic characteristics, in addition to genomic analyses, confirmed that each of these two strains represent distinct, novel species within the genus Shewanella, for which the names Shewanella septentrionalis sp. nov. (type strain SP1W3^T=CCUG 76164^T=CECT 30651^T) and Shewanella holmiensis sp. nov. (type strain SP1S2-7^T=CCUG 76165^T=CECT 30652^T) are proposed.

Shewanella spp. from wastewater treatment plant-affected environment: isolation and characterization

Bacteria from the genus Shewanella are inhabitants of marine and freshwater ecosystems, recognized fish spoilage bacteria, but less known as fish disease agents. Shewanella spp. isolated from fish living in waters close to effluents of a wastewater treatment plant (WWTP) were not previously characterized. We have tested Shewanella isolates from WWTP-affected waters and related fish. Genotypic characterization identified most strains as S. baltica and S. oneidensis. In order to investigate the sensibility and accuracy of their MALDI-TOF MS identification, they were grown on two culture media enriched by various NaCl concentrations, incubated at different temperatures and duration. We analyzed their antimicrobial susceptibility on a panel of antimicrobial drugs and capacity for biofilm production. With a view to demonstrate their capacity to produce fatty acids, we assessed the impact of different culture media on their lipid profile. We performed zebrafish embryotoxicity tests to simulate the environmental infection of the earliest life stages in S. baltica-contaminated waters. The best MALDI-TOF MS identification scores were for strains cultivated on TSA for 24 h at 22 °C and with supplementation of 1.5% NaCl. Less than 17% of isolates demonstrated antimicrobial resistance. Most isolates were weak biofilm producers. Strain-to-strain variation of MIC and MBC was low. The major fatty acids were C15:0, C16:0, C16:1, C17:1, and iC15:0. Exposure of Danio rerio to different S. baltica concentrations induced severe effects on zebrafish development: decreased heartbeat rate, locomotor activity, and melanin pigmentation. S. baltica passed through chorionic pores of zebrafish.

Pathogenic strains of Shewanella putrefaciens contain plasmids that are absent in the probiotic strain Pdp11

Shewanella putrefaciens Pdp11 is a strain described as a probiotic for use in aquaculture. However, S. putrefaciens includes strains reported to be pathogenic or saprophytic to fish. Although the probiotic trait has been related to the presence of a group of genes in its genome, the existence of plasmids that could determine the probiotic or pathogenic character of this bacterium is unknown. In the present work, we searched for plasmids in several strains of S. putrefaciens that differ in their pathogenic and probiotic character. Under the different conditions tested, plasmids were only found in two of the five pathogenic strains, but not in the probiotic strain nor in the two saprophytic strains tested. Using a workflow integrating Sanger and Illumina reads, the complete consensus sequences of the plasmids were obtained. Plasmids differed in one ORF and encoded a putative replication initiator protein of the repB family, as well as proteins related to plasmid stability and a toxin-antitoxin system. Phylogenetic analysis showed some similarity to functional repB proteins of other Shewanella species. The implication of these plasmids in the probiotic or pathogenic nature of S. putrefaciens is discussed.

The Innate Immune Response of Atlantic Salmon (Salmo salar) Is Not Negatively Affected by High Temperature and Moderate Hypoxia

Climate change is predicted to increase water temperatures and decrease oxygen levels in freshwater and marine environments, however, there is conflicting information regarding the extent to which these conditions may impact the immune defenses of fish. In this study, Atlantic salmon were exposed to: (1) normoxia (100–110% air saturation) at 12°C; (2) an incremental temperature increase (1°C per week from 12 to 20°C), and then held at 20°C for an additional 4 weeks; and (3) “2” with the addition of moderate hypoxia (~65–75% air saturation). These conditions realistically reflect what farmed salmon in some locations are currently facing, and future conditions in Atlantic Canada and Europe, during the summer months. The salmon were sampled for the measurement of head kidney constitutive anti-bacterial and anti-viral transcript expression levels, and blood parameters of humoral immune function. Thereafter, they were injected with either the multi-valent vaccine Forte V II (contains both bacterial and viral antigens) or PBS (phosphate-buffer-saline), and the head kidney and blood of these fish were sampled at 6, 12, 24, and 48 h post-injection (HPI). Our results showed that: (1) neither high temperature, nor high temperature + moderate hypoxia, adversely affected respiratory burst, complement activity or lysozyme concentration; (2) the constitutive transcript expression levels of the anti-bacterial genes il1β, il8-a, cox2, hamp-a, stlr5-a, and irf7-b were up-regulated by high temperature; (3) while high temperature hastened the peak in transcript expression levels of most anti-bacterial genes by 6–12 h following V II injection, it did not affect the magnitude of changes in transcript expression; (4) anti-viral (viperin-b, mx-b, and isg15-a) transcript expression levels were either unaffected, or downregulated, by acclimation temperature or V II injection over the 48 HPI; and (5) hypoxia, in addition to high temperature, did not impact immune transcript expression. In conclusion, temperatures up to 20°C, and moderate hypoxia, do not impair the capacity of the Atlantic salmon's innate immune system to respond to bacterial antigens. These findings are surprising, and highlight the salmon's capacity to mount robust innate immune responses (i.e., similar to control fish under optimal conditions) under conditions approaching their upper thermal limit.

The Shewanella genus: ubiquitous organisms sustaining and preserving aquatic ecosystems

The Gram-negative Shewanella bacterial genus currently includes about 70 species of mostly aquatic γ­-proteobacteria, which were isolated around the globe in a multitude of environments such as surface freshwater and the deepest marine trenches. Their survival in such a wide range of ecological niches is due to their impressive physiological and respiratory versatility. Some strains are among the organisms with the highest number of respiratory systems, depending on a complex and rich metabolic network. Implicated in the recycling of organic and inorganic matter, they are important components of organism-rich oxic/anoxic interfaces, but they also belong to the microflora of a broad group of eukaryotes from metazoans to green algae. Examples of long-term biological interactions like mutualism or pathogeny have been described, although molecular determinants of such symbioses are still poorly understood. Some of these bacteria are key organisms for various biotechnological applications, especially the bioremediation of hydrocarbons and metallic pollutants. The natural ability of these prokaryotes to thrive and detoxify deleterious compounds explains their use in wastewater treatment, their use in energy generation by microbial fuel cells and their importance for resilience of aquatic ecosystems.

Phenotypic Diversity and Potential Virulence Factors of the Shewanella Putrefaciens Group Isolated from Freshwater Fish

Introduction

The Shewanella putrefaciens group are ubiquitous microorganisms recently isolated from different freshwater fish species and causing serious health disorders. The purpose of the study was to characterise isolates of the S. putrefaciens group with special emphasis on elucidating serological diversity and determining putative virulence factors.

Material and Methods

Isolates collected from freshwater fish (n = 44) and reference strains were used. The identification of bacteria was carried out using biochemical kits and 16S rRNA sequencing. Polyclonal antibodies were prepared against the S. putrefaciens group. The bacterium’s susceptibility to antimicrobial agents, its enzymatic properties, and its adhesion ability to fish cell lines were also tested. Finally, selected isolates were used in challenge experiments in common carp and rainbow trout.

Results

Excluding six isolates undeterminable for species, the bacteria were classified to three species: S. putrefaciens, S. xiamenensis, and S. oneidensis, and showed some phenotypic diversity. Fourteen serological variants of the S. putrefaciens group were determined with the newly developed serotyping scheme.

Conclusion

Serodiversity may play an important role in the virulence of particular isolates. Further, S. putrefaciens group members adhere to epithelial cells and produce enzymes which may contribute to their virulence. Challenge tests confirmed the pathogenicity of the S. putrefaciens group for fish.

Genotypic diversity among Shewanella spp. collected from freshwater fish

Different Shewanella species are isolated both from healthy and from diseased fish. To date, contemporary methods do not provide sufficient insight to determine species and detail differentiation between tested strains. Bacteria isolated from cultured (n = 33), wild (n = 12) and ornamental (n = 6) fish, as well as several reference strains, were tested by 16S rRNA gene sequencing, ERIC-PCR and pulsed-field gel electrophoresis (PFGE) assays. Our study indicates that isolates collected from freshwater fish were genetically diverse. Based on 16S rRNA gene sequences, bacteria were clustered into groups S. putrefaciens, S. xiamenensis and S. oneidensis. Some isolates were classified only to genus Shewanella; thus, 16S rRNA gene analyses were not enough to determine the species. ERIC-PCR revealed 49 different genotype profiles indicating that the method might be useful for differentiation of Shewanella isolates irrespectively to species identification, contrary to PFGE which is not suitable for Shewanella typing.

TarSynFlow, a workflow for bacterial genome comparisons that revealed genes putatively involved in the probiotic character of Shewanella putrefaciens strain Pdp11

Probiotic microorganisms are of great interest in clinical, livestock and aquaculture. Knowledge of the genomic basis of probiotic characteristics can be a useful tool to understand why some strains can be pathogenic while others are probiotic in the same species. An automatized workflow called TarSynFlow (Targeted Synteny Workflow) has been then developed to compare finished or draft bacterial genomes based on a set of proteins. When used to analyze the finished genome of the probiotic strain Pdp11 of Shewanella putrefaciens and genome drafts from seven known non-probiotic strains of the same species obtained in this work, 15 genes were found exclusive of Pdp11. Their presence was confirmed by PCR using Pdp11-specific primers. Functional inspection of the 15 genes allowed us to hypothesize that Pdp11 underwent genome rearrangements spurred by plasmids and mobile elements. As a result, Pdp11 presents specific proteins for gut colonization, bile salt resistance and gut pathogen adhesion inhibition, which can explain some probiotic features of Pdp11.

Seasonal recovery of Edwardsiella piscicida from wild European eels and natural waters: Isolation methods, virulence and reservoirs

A total of 127 wild eels caught in the L'Albufera Lake (Spain) and 24 samples of lagoon freshwater were analysed for 1-year period. Edwardsiella strains were isolated from liver/kidney on TSA-1 plates in 31.9% of total diseased specimens, and the edwardsiellosis prevalence in the fishery was of 11.8%. The use of double-strength Salmonella-Shigella (DSSS) broth and SS agar yielded Edwardsiella isolation from intestine in 100% of those edwardsiellosis-diseased eels, but also in 40.4% of other sick fish with vibriosis or aeromonosis and in 28.8% of healthy eels, as well as from freshwater in 8.3% of samples. Pure cultures were isolated on SS agar from the former, but motile Aeromonas, Plesiomonas shigelloides and Hafnia alvei were recovered along with Edwardsiella in the other samples. Edwardsiella isolates identification at species level revealed that E. piscicida was distributed between wild eels and freshwater but E. tarda only did in freshwater. All E. piscicida strains were virulent for eels (LD  < 1.0 × 10⁶ CFU/fish) but that of E. tarda was not. This is the first report of E. piscicida in wild eel intestines and natural freshwater, highlighting its role as potential reservoirs for the bacterium. A seasonal recovery was found for E. piscicida at water temperature above 20°C.