Mechanisms and the role of probiotic Bacillus in mitigating fish pathogens in aquaculture

Diseases are natural components of the environment, and many have economic implications for aquaculture and fisheries. Aquaculture is a fast-growing industry with the aim to meet the high protein demand of the ever-increasing global population; however, the emergence of diseases is a major setback to the industry. Probiotics emerged as a better solution to curb the disease problem in aquaculture among many alternatives. Probiotic Bacillus has been proven to better combat a wide range of fish pathogens relative to other probiotics in aquaculture; therefore, understanding the various mechanisms used by Bacillus in combating diseases will help improve their mode of action hence yielding better results in their combat against pathogens in the aquaculture industry. Thus, an overview of the mechanisms (production of bacteriocins, suppression of virulence gene expression, competition for adhesion sites, production of lytic enzymes, production of antibiotics, immunostimulation, competition for nutrients and energy, and production of organic acids) used by Bacillus probiotics in mitigating fish pathogens ranging from Aeromonas, Vibrio, Streptococcus, Yersinia, Pseudomonas, Clostridium, Acinetobacter, Edwardsiella, Flavobacterium, white spot syndrome virus, and infectious hypodermal and hematopoietic necrosis virus proven to be mitigated by Bacillus have been provided.

Expression of immune genes in Indian major carp, Catla catla challenged with Flavobacterium columnare

Columnaris disease, caused by Flavobacterium columnare, is one of the important bacterial diseases responsible for large-scale mortalities in numerous freshwater fishes globally. This disease can cause up to 100% mortality within 24 h of infection and is considered to be a cause of concern for aquaculture industry. Despite being a serious disease, scarce information is available regarding host-pathogen interaction, particularly the modulation of different immune genes in response to F. columnare infection. Therefore, in the present study, an attempt has been made to study expression of important immune regulatory genes, namely IL-1β, iNOS, INF-γ, IL-10, TGF-β, C3, MHC-I and MHC-II in gills and kidney of Catla catla following experimental infection with F. columnare. The expression analysis of immune genes revealed that transcript levels of IL-1β, iNOS, IL-10, TGF-β, C3 and MHC-I were significantly up-regulated (p < 0.05) in both the organs of the infected catla. IFN-γ and MHC-II were up-regulated in gills of infected catla whereas, both the genes showed down-regulation in kidney. The results indicate that important immune genes of C. catla are modulated following infection with F. columnare. The knowledge thus generated will strengthen the understanding of molecular pathogenesis of F. columnare in Indian major carp C. catla.

Multiplex PCR for genotyping Flavobacterium columnare

Recent research has identified four distinct genetic groups among isolates of Flavobacterium columnare through multilocus phylogenetic analyses; however, there are no quick methods to determine the genotype of an isolate. The objective of this research was to develop a multiplex PCR to rapidly genotype F. columnare to genetic group. Comparative bacterial genomics was used to identify regions in the genomes unique to each genetic group, and primers were designed to specifically amplify different sized amplicons for each genetic group. The optimized assay was demonstrated to be specific for each genetic group and F. columnare, and no specific amplicons were generated using gDNA from a panel of other Flavobacterium spp. and bacterial fish pathogens. The analytical sensitivity of the assay ranged from 209 to 883 genome equivalents depending on the genetic group. The multiplex PCR was evaluated by genotyping a panel of 22 unknown F. columnare isolates and performing DNA sequencing of the dnaK gene in parallel. The results demonstrated 100% accordance between multiplex PCR results and assignment to genetic group via phylogenetic analysis. The multiplex PCR provides a useful tool for assigning an unknown isolate to genetic group and may be used to determine which genetic groups of F. columnare are circulating and most predominant in different aquaculture industries.

Retrospective and Predictive Investigation of Fish Kill Events

Fish kill investigations are critical to understanding threats to aquatic ecosystems and can serve as a measure of environmental disruption as well as an early indicator of emerging disease. The goal of this study was to analyze historical data related to such events among wild fish populations in Minnesota in order to assess the quality and completeness of the data and potential trends in fish kills. After excluding events with incomplete data (e.g., in which the location was not reported), we analyzed 225 unique fish kills from 2003 to 2013 that were recorded in two Minnesota Department of Natural Resources databases. The most reported fish kills occurred during 2007 (n = 41) and during the month of June (n = 81) across all years. Centrarchid species were present in the most fish kills (138), followed by cyprinid and ictalurid species, which were present in 53 and 40 events, respectively. Environmental factors were the most common cause of death reported. Models of environmental factors revealed that the maximum nighttime land surface temperature was the most critical factor in fish mortality, followed by changes in primary productivity and human disturbances. During the course of this study, data gaps were identified, including underreporting, inconsistent investigation, and the lack of definitive diagnoses, making interpretation of our results challenging. Even so, understanding these historical trends and data gaps can be useful in generating hypotheses and advancing data collection systems for investigating future fish kills. Our study is a primer investigation of fish kills providing information on the plausible areas, seasons, and fish groups at risk that can guide active environmental monitoring and epidemiological surveillance of fishes.

Comparative genome analysis of fish pathogen Flavobacterium columnare reveals extensive sequence diversity within the species

Flavobacterium columnare is one of the deadliest fish pathogens causing devastating mortality in various freshwater fish species globally. To gain an insight into bacterial genomic contents and structures, comparative genome analyses were performed using the reference and newly sequenced genomes of F. columnare including genomovar I, II and I/II strains isolated from Thailand, Europe and the USA. Bacterial genomes varied in size from 3.09 to 3.39Mb (2714 to 3101 CDSs). The pan-genome analysis revealed open pan-genome nature of F. columnare strains, which possessed at least 4953 genes and tended to increase progressively with the addition of a new genome. Genomic islands (GIs) present in bacterial genomes were diverse, in which 65% (39 out of 60) of possible GIs were strain-specific. A CRISPR/cas investigation indicated at least two different CRISPR systems with varied spacer profiles. On the other hand, putative virulence genes, including those related to gliding motility, type IX secretion system (T9SS), outer membrane proteins (Omp), were equally distributed among F. columnare strains. The MLSA scheme categorized bacterial strains into nine different sequence types (ST 9-17). Phylogenetic analyses based on either 16S rRNA, MLSA and concatenated SNPs of core genome revealed the diversity of F. columnare strains. DNA homology analysis indicated that the estimated digital DNA-DNA hybridization (dDDH) between strains of genomovar I and II can be as low as 42.6%, while the three uniquely tilapia-originated strains from Thailand (1214, NK01 and 1215) were clearly dissimilar to other F. columnare strains as the dDDH values were only 27.7-30.4%. Collectively, this extensive diversity among bacterial strains suggested that species designation of F. columnare would potentially require re-emendation.

New host record of five Flavobacterium species associated with tropical fresh water farmed fishes from North India

Yellow pigmented, filamentous, Gram-negative bacteria belonging to genus Flavobacterium are commonly associated with infections in stressed fish. In this study, inter-species diversity of Flavobacterium was studied in apparently healthy freshwater farmed fishes. For this, ninety one yellow pigmented bacteria were isolated from skin and gill samples (n = 38) of three farmed fish species i.e. Labeo rohita, Catla catla and Cyprinus carpio. Among them, only twelve bacterial isolates (13.18%) were identified as Flavobacterium spp. on the basis of morphological, biochemical tests, partial 16S rDNA gene sequencing and phylogenetic analysis. On the basis of 16S rDNA gene sequencing, all the 12 isolates were 97.6-100% similar to six different formally described species of genus Flavobacterium. The 16S rDNA based phylogenetic analysis grouped these strains into six different clades. Of the 12 isolates, six strains (Fl9S1-6) grouped with F. suncheonense, two strains (Fl6I2, Fl6I3) with F. indicum and the rest four strains (Fl1A1, Fl2G1, Fl3H1 and Fl10T1) clustered with F. aquaticum, F. granuli, F. hercynium and F. terrae, respectively. None of these species except, F. hercynium were previously reported from fish. All the isolated Flavobacterium species possessed the ability of adhesion and biofilm formation to colonize the external surface of healthy fish. The present study is the first record of tropical freshwater farmed fishes as hosts to five environmentally associated species of the Flavobacterium.

Virulence assay of rhizoid and non-rhizoid morphotypes of Flavobacterium columnare in red tilapia, Oreochromis sp., fry

Numerous isolates of Flavobacterium columnare were previously recovered from red tilapia, Oreochromis sp., exhibiting columnaris-like disease in Thai farms, and the phenotypic and genetic characteristics were described. The objective of this study was to determine the virulence of two morphotypes (rhizoid and non-rhizoid colonies) of F. columnare and to determine their ability to adhere to and persist in red tilapia fry. The results showed that the typical rhizoid isolate (CUVET1214) was a highly virulent isolate and caused 100% mortality within 24 h following bath challenge of red tilapia with three different doses. The non-rhizoid isolate (CUVET1201) was avirulent to red tilapia fry. Both morphotypes adhered to and persisted in tilapia similarly at 0.5 and 6 h post-challenge as determined by whole fish bacterial loads. At 24 and 48 h post-challenge, fry challenged with the rhizoid morphotype exhibited significantly higher bacterial loads than the non-rhizoid morphotype. The results suggested that an inability of the non-rhizoid morphotype to persist in tilapia fry may explain lack of virulence.

Antibacterial activity of aquatic gliding bacteria

The study aimed to screen and isolate strains of freshwater aquatic gliding bacteria, and to investigate their antibacterial activity against seven common pathogenic bacteria. Submerged specimens were collected and isolated for aquatic gliding bacteria using four different isolation media (DW, MA, SAP2, and Vy/2). Gliding bacteria identification was performed by 16S rRNA gene sequencing and phylogenetic analysis. Crude extracts were obtained by methanol extraction. Antibacterial activity against seven pathogenic bacteria was examined by agar-well diffusion assay. Five strains of aquatic gliding bacteria including RPD001, RPD008, RPD018, RPD027 and RPD049 were isolated. Each submerged biofilm and plastic specimen provided two isolates of gliding bacteria, whereas plant debris gave only one isolate. Two strains of gliding bacteria were obtained from each DW and Vy/2 isolation medium, while one strain was obtained from the SAP2 medium. Gliding bacteria strains RPD001, RPD008 and RPD018 were identified as Flavobacterium anhuiense with 96, 82 and 96 % similarity, respectively. Strains RPD049 and RPD027 were identified as F. johnsoniae and Lysobacter brunescens, respectively, with similarity equal to 96 %. Only crude extract obtained from RPD001 inhibited growth of Listeria monocytogenes (MIC 150 µg/ml), Staphylococcus aureus (MIC 75 µg/ml) and Vibrio cholerae (MIC 300 µg/ml), but showed weak inhibitory effect on Salmonella typhimurium (MIC > 300 µg/ml). Gliding bacterium strain RPD008 should be considered to a novel genus separate from Flavobacterium due to its low similarity value. Crude extract produced by RPD001 showed potential for development as a broad antibiotic agent.

Phenotypic characterization and genetic diversity of Flavobacterium columnare isolated from red tilapia, Oreochromis sp., in Thailand

Flavobacterium columnare is the aetiological agent of columnaris disease and severely affects various freshwater aquaculture fish species worldwide. The objectives of this study were to determine the phenotypic characteristics and genetic variability among F. columnare isolates isolated from red tilapia in Thailand. Forty-four F. columnare isolates were recovered from diseased fish in different geographical locations. The isolates exhibited homologous phenotypic characteristics but exhibited genetic diversity. One isolate was assigned to genomovar I, and the remainder were assigned to genomovar II, indicating the coexistence of these genomovars but predominance of genomovar II. Phylogenetic analysis of the 16S-23S ISR sequences revealed that a subset of the Thai isolates (n = 25) contained a smaller intergenic spacer region (ISR) (523-537 bp) and formed a unique ISR phylogenetic group. Phylogenetic analysis of the 16S rRNA gene supported the unique cluster of Thai isolates. This is the first description of the phenotypic and molecular characteristics of F. columnare isolated from red tilapia in Thailand as well as five isolates of F. columnare derived from other fish species including Nile tilapia, koi carp and striped catfish.