Absolute quantification of priority bacteria in aquaculture using digital PCR.

Modern aquaculture systems are designed for intensive rearing of fish or other species. Both land-based and offshore systems typically contain high loads of biomass and the water quality in these systems is of paramount importance for fish health and production. Microorganisms play a crucial role in removal of organic matter and nitrogen-recycling, production of toxic hydrogen sulfide (H2S), and can affect fish health directly if pathogenic for fish or exerting probiotic properties. Methods currently used in aquaculture for monitoring certain bacteria species numbers still have typically low precision, specificity, sensitivity and are time-consuming. Here, we demonstrate the use of Digital PCR as a powerful tool for absolute quantification of sulfate-reducing bacteria (SRB) and major pathogens in salmon aquaculture, Moritella viscosa, Yersinia ruckeri and Flavobacterium psychrophilum. In addition, an assay for quantification of Listeria monocytogenes, which is a human pathogen bacterium and relevant target associated with salmonid cultivation in recirculating systems and salmon processing, has been assessed. Sudden mass mortality incidents caused by H2S produced by SRB have become of major concern in closed aquaculture systems. An ultra-sensitive assay for quantification of SRB has been established using Desulfovibrio desulfuricans as reference strain. The use of TaqMan® probe technology allowed for the development of multi-plex assays capable of simultaneous quantification of these aquaculture priority bacteria. In single-plex assays, limit of detection was found to be at around 20 fg DNA for M. viscosa, Y. ruckeri and F. psychrophilum, and as low as 2 fg DNA for L. monocytogenes and D. desulfuricans.

Co-cultivation and transcriptome sequencing of two co-existing fish pathogens Moritella viscosa and Aliivibrio wodanis.

BACKGROUND: Aliivibrio wodanis and Moritella viscosa have often been isolated concurrently from fish with winter-ulcer disease. Little is known about the interaction between the two bacterial species and how the presence of one bacterial species affects the behaviour of the other. RESULTS: The impact on bacterial growth in co-culture was investigated in vitro, and the presence of A. wodanis has an inhibitorial effect on M. viscosa. Further, we have sequenced the complete genomes of these two marine Gram-negative species, and have performed transcriptome analysis of the bacterial gene expression levels from in vivo samples. Using bacterial implants in the fish abdomen, we demonstrate that the presence of A. wodanis is altering the gene expression levels of M. viscosa compared to when the bacteria are implanted separately. CONCLUSIONS: From expression profiling of the transcriptomes, it is evident that the presence of A. wodanis is altering the global gene expression of M. viscosa. Co-cultivation studies showed that A. wodanis is impeding the growth of M. viscosa, and that the inhibitorial effect is not contact-dependent.

Host specificity and clade dependent distribution of putative virulence genes in Moritella viscosa.

Moritella viscosa is the aetiological agent of winter-ulcer disease in farmed salmonids in the North Atlantic. Previously, two major (typical and variant) genetic clades have been demonstrated within this bacterial species, one of which is almost solely related to disease in Atlantic salmon (Salmo salar). In the present study infection trials demonstrated that 'typical' M. viscosa isolated from Norwegian Atlantic salmon was highly virulent in this fish species but resulted in lower levels of mortality in rainbow trout. 'Variant' M. viscosa isolated from rainbow trout resulted in modest mortality levels in both Atlantic salmon and rainbow trout. To investigate the possible genetic background for inter-strain virulence differences, 38 M. viscosa isolates of diverse geographical origin and host species and a number of other Moritella spp. were investigated for the presence/absence of putative virulence related homologs. All isolates were positive for DNA sequences coding for; the Type VI secretion ATPase (clpV), hemolysin co-regulated protein (hcp), bacterioferritins (bfrA and bfrB), lectin (hemG), phospholipase D (pld), multifunctional autoprocessing repeats-in-toxin (martxA), aerolysin (aer), invasin (inv), and cytotoxic necrotizing factor (cnf), with the exception of one isolate in which cnf could not be confirmed. The product of an ABC transporter metal-binding lipoprotein (mat) was consistently detected although 11 isolates, all phylogenetically related, appear to produce a truncated version. A putative insecticidal toxin complex (mitABC) was detected almost exclusively in 'typical' Atlantic salmon isolates, and our data indicate that this complex of genes is expressed and co-transcribed. Transmission electron microscopy investigation revealed pili and flagella surface structures on nine M. viscosa representing both typical and variant isolates. Our results provide strong support for the existence of host specificity/high virulence in 'typical' M. viscosa related to Atlantic salmon. The gene distribution also provides further support for the genetic division within M. viscosa, and constitutes a basis for further study of the importance of the mitABC complex in winter-ulcer pathogenesis.

Characterisation of an extracellular vibriolysin of the fish pathogen Moritella viscosa.

Moritella viscosa causes winter ulcer disease in salmonids. The aim of the present work was to isolate and partially characterise an extracellular peptidase from M. viscosa, and to study its role in virulence. The peptidase, termed MvP1, was a 38-kDa metallopeptidase produced in late exponential growth. The optimum temperature for MvP1 was 40 degrees C, but the enzyme was active over a broad range of temperatures. MvP1 was non-lethal to salmon at concentrations up to 0.22microg/g fish, but extracellular products were lethal to salmon. MvP1 degraded casein, gelatin and collagen from lumpfish skin. It caused considerable tissue necrosis and hemorrhages at the site of injection, and affected cell-cell adhesions in EPC and BF-2 cell lines, but was not highly cytotoxic. The peptidase partially degraded fish IgM heavy chain but was non-hemolytic. The mvp1 gene was sequenced and encoded a 734-aa polypeptide containing a signal sequence, an N-terminal propeptide, a mature peptidase domain and a C-terminal propeptide. The MvP1 propeptide undergoes both N-terminal and C-terminal processing and different C-terminal processing results in the formation of several active isoforms of the mature peptidase. The catalytic domain showed highest sequence similarity with several vibriolysins (EC 3.4.24.25) originating from Pseudoalteromonas strains, showing up to 80% aa identity. The results indicate that MvP1 is a previously unknown vibriolysin that might affect M. viscosa virulence by aiding in the invasion and dissemination of the bacterium in its host, by causing tissue destruction.

Moritella dasanensis sp. nov., a psychrophilic bacterium isolated from the Arctic ocean.

An aerobic, motile, Gram-negative, ice-active substance-producing, rod-shaped psychrophile, designated strain ArB 0140T, was isolated from seawater collected from near a glacier in Kongsfjorden, Svalbard Archipelago, Norway. Phylogenetic analysis using 16S rRNA gene sequences indicated that strain ArB 0140T showed a distinct phyletic line within the genus Moritella. Characteristic chemotaxonomic data [predominant isoprenoid quinone, Q8; major fatty acids, C14 : 0, C14 : 1, C16 : 0, C16 : 1 and C22 : 6 (docosahexaenoic acid; DHA)] also corroborated the affiliation of strain ArB 0140T to the genus Moritella. The maximal growth rate of the novel strain was observed at 9 degrees C, with a maximum temperature for growth of 18 degrees C. The genomic DNA G+C content was 46.9 mol%. Based on the data obtained from this polyphasic study, including DNA-DNA relatedness, physiological and biochemical tests and ice-controlling activity, strain ArB 0140T was found to be genetically and phenotypically different from other recognized species of the genus Moritella. Therefore strain ArB 0140T represents a novel species, for which the name Moritella dasanensis sp. nov. is proposed. The type strain is ArB 0140T (=KCTC 10814T=KCCM 42845T=JCM 14759T).

Real-time PCR detection of Moritella viscosa, the likely causal agent of winter-ulcer in Atlantic salmon Salmo salar and rainbow trout Oncorhynchus mykiss.

We report the development of a real-time PCR protocol for specific detection of Moritella viscosa. This bacterium is considered to be the main aetiological agent in development of winter-ulcer, a disease severely affecting salmonid aquaculture in Norway. From a newly elaborated draft version of the genome of M. viscosa, the tonB gene sequence was selected as a suitable basis for the development of the real-time PCR assay. The real-time PCR demonstrated the presence of M. viscosa DNA sequences in 88.1% of samples collected from 35 outbreaks of winter-ulcer in Norwegian fish farms. In contrast, standard culturing on blood agar identified M. viscosa in only 39.7% of fish. While the culturing method revealed a similar prevalence (26 to 27%) of M. viscosa in kidney and ulcer samples, substantially more ulcer (81.5%) than kidney (49.7%) samples were shown positive by real-time PCR.

Growth and lysis of the fish pathogen Moritella viscosa.

AIMS: The sensitivity to lysis is a profound bottleneck to studies of the fish pathogen Moritella viscosa. The aim of this study was to examine the growth and the lysis process of M. viscosa cells under different physical and chemical conditions. METHODS AND RESULTS: Growth and cell lysis were studied under different conditions. The growth rate was highest at 15 degrees C and lowest at 4 degrees C, but the cells reached a higher density at 4 degrees than at 15 degrees C and the cells were more stable. The presence of minerals reduced lysis. CONCLUSIONS: Premature lysis of the cells is dependent on environmental factors. Moritella viscosa should be cultivated and kept in media containing a certain set of minerals and at temperatures as low as 4 degrees C. Formalin favours the stability of cells. The instability of the M. viscosa cells at temperatures above 10 degrees C might be one of the factors responsible for their inability to infect fish at higher temperatures. The presence of DHA in the cell membranes is predicted to be responsible for the susceptibility of the cells to lysis. SIGNIFICANCE AND IMPACT OF THE STUDY: The cultivation of M. viscosa cells is a key factor in studying the pathogenicity of the bacteria and in making an effective vaccine to prevent winter ulcers in farmed fish. The study provided recommendations on how to cultivate M. viscosa and how lysis of the cells can be minimized.

Amino acid substitutions in malate dehydrogenases of piezophilic bacteria isolated from intestinal contents of deep-sea fishes retrieved from the abyssal zone.

To examine the occurrence in other deep-sea bacteria of two amino acid substitutions (Ala-180 and His-229) in malate dehydrogenase (MDH) found previously in the deep-sea piezophilic Moritella sp. strain 2D2, we cloned and sequenced MDH genes of deep-sea piezophilic Moritella and Shewanella strains isolated from intestinal contents of deep-sea fishes, as well as other Moritella species from deep-sea water and sediments: M. marina, M. japonica, and M. yayanosii. The piezophilic Moritella strains had a Val residue or an Ala residue at position 180 and all the Moritella strains except for one had a His residue at position 229. However, four piezophilic-strain-specific substitutions at positions 103, 111, 229, and 283 were found to be completely conserved in the MDH of the intestinal Moritella strains of deep-sea fishes, indicating the substitutions may be habitat-specific. The piezophilic Shewanella strains had a Val residue and a Gln residue at positions 180 and 229, respectively. However, the MDHs of the Shewanella strains had five piezophilic-strain-specific substitutions at positions 61, 65, 107, 161, and 202. Therefore, the enzymatic strategies for responding to deep-sea high pressure environments of the MDHs between the genera Moritella and Shewanella are potentially different. Moreover, homology modeling shows these substitutions found in the MDHs of both genera except for position 229 in the subunit interface are located on the exposed region of the MDH molecules, indicating the substitutions may be related to the hydration state of the molecules.

Moritella profunda sp. nov. and Moritella abyssi sp. nov., two psychropiezophilic organisms isolated from deep Atlantic sediments.

Strains 2674T (=LMG 21259T =JCM 11435T) and 2693T (=LMG 21258T =JCM 11436T) were isolated from Atlantic sediments at a temperature of 2 degrees C and a depth of 2815 m off the West African coast. Polyphasic evidence indicates that the two strains belong to the genus Moritella and represent distinct species, for which the names Moritella profunda sp. nov. (for strain 2674T) and Moritella abyssi sp. nov. (for strain 2693T) are proposed. The moderate piezophily of the two organisms is intermediate between that of the type species, Moritella marina, which is not piezophilic, and Moritella yayanosii, an obligate piezophile. Both are strict psychrophiles with slightly different cardinal temperatures: at 0.1 MPa, maximal growth rates are observed at 2 degrees C (M. profunda) and 4 degrees C (M. abyssi) with maximum temperatures of 12 degrees C (M. profunda) or 14 degrees C (M. abyssi). The optimal pressure is lower than that at the site of isolation, and raising the temperature to 10 degrees C makes the organisms more piezophilic.