An improved in situ hybridization method for the detection of fish pathogens

A fluorescent in situ hybridization (FISH) method was developed for detection of infectious pancreatic necrosis virus (IPNV) in paraffin-embedded tissues of Atlantic salmon, Salmo salar L. Several methods of probe labelling and detection were evaluated and found unsuitable for FISH because of tissue autofluorescence. Likewise, the use of avidin to detect biotin-labelled probe was obviated by the presence of endogenous biotin. An existing approach, using digoxigenin (DIG)-labelled probes and detection by anti-DIG antibody-labelled with alkaline phosphatase, was modified to use a fluorescent substrate, 2-hydroxy-3-naphthoic acid-2'-phenylanilide phosphate/4-chloro-2-methylbenzene diazonium hemi-zinc chloride salt (HNPP/Fast Red TR). This improved method allowed sensitive detection of IPNV target, without interference from autofluorescence or endogenous alkaline phosphatase. Furthermore, the reporter produces a discrete, non-fading signal, which is particularly suitable for analysis by confocal microscopy.     

Exploring the microbial diversity of the distal intestinal lumen and mucosa of farmed rainbow trout Oncorhynchus mykiss (Walbaum) using next generation sequencing (NGS)

In this study, next generation sequencing (NGS) was used to survey the 16S rRNA ribotypes of the distal intestinal lumen and mucosal epithelium of farmed rainbow trout. This approach yielded a library consisting of 2 979 715 quality filtered paired sequences, assigned to genus level of taxonomy using the Ribosomal Database Project (RDP). A high level of diversity was observed in both regions. A total of 90 bacterial genera were identified in the lumen of all fish sampled, compared with 159 in the mucosa. The allochthonous microflora was dominated by sequences belonging to the γ Proteobacteria (mean sequence abundance 54.3%), in particular the Enterobacteriaceae, with Yersinia, Serratia, Hafnia and Obesumbacterium the most abundant genera. Fewer γ Proteobacteria (mean sequence abundance 37%) were present in the mucosa, and autochthonous communities consisted of a more even split among the bacterial classes, with increases in sequences assigned to members of the β Proteobacteria (mean sequence abundance 18.4%) and Bacilli (mean sequence abundance 16.8%). The principal bacterial genera recorded in the mucosa were Cetobacterium, Yersinia, Ralstonia, Hafnia and Carnobacterium. The results of this study demonstrate that the luminal and mucosal bacterial communities may be different in their respective structures, and that the mucosal microflora of rainbow trout may be more diverse than previous research has suggested. This research also demonstrated a degree of conservation of bacterial genera between individual fish sampled, and is to the author's knowledge the first time the MiSeq^® NGS platform has been used to explore the rainbow trout intestinal microflora.     

Detection of the intranuclear microsporidian Enterospora nucleophila in gilthead sea bream by in situ hybridization

Enterospora nucleophila is an intranuclear microsporidian responsible for emaciative microsporidiosis of gilthead sea bream (GSB). Its minute size and cryptic nature make it easily misdiagnosed. An in situ hybridization (ISH) technique based on antisense oligonucleotide probes specific for the parasite was developed and used in clinically infected GSB in combination with calcofluor white stain (CW) and other histopathological techniques. The ISH method was found to label very conspicuously the cells containing parasite stages, with the signal concentrating in merogonial and sporogonial plasmodia within the infected cell nuclei. Comparison with CW demonstrated limited ISH signal in cells containing mature spores, which was attributed mostly to the scarcity of probe targets present in these stages. Although spores were detected in other organs of the digestive system as well as in the peripheral blood, proliferative stages or parasite reservoirs were not found in this work outside the intestines. The study demonstrated a frequent disassociation between the presence of abundant spores and the intensity of the infections as determined by the parasite activity. The ISH allows confirmatory diagnosis of GSB microsporidiosis and estimation of infection intensity and will be a valuable tool for a more precise determination of parasite dissemination pathways and pathogeny mechanisms.     

杂交三倍体泥鳅染色体C带及rDNA序列的FISH定位

对杂交三倍体泥鳅(4n♀×2n♂)的胚胎染色体进行了C带及染色体荧光原位杂交(FISH)分析,首次探讨了杂交三倍体泥鳅C带特征,为准确鉴别染色体提供依据,研究了核糖体5.8S+28S r DNA在杂交三倍体泥鳅胚胎中期染色体上的数目和位置。C带结果表明,杂交三倍体泥鳅的染色体C带包括臂端C带和着丝粒C带,没有发现臂间C带。M染色体只有1号染色体既有臂端C带又有着丝粒C带,但臂端C带均比着丝粒C带大,信号也比着丝粒的强;而其他M染色体及SM染色体、T染色体只有着丝粒C带。FISH分析显示,核糖体5.8S+28S r DNA清楚地定位在杂交三倍体泥鳅中期染色体中部着丝粒染色体(M)的端部区域,在杂交三倍体泥鳅中期染色体上可以检测到三簇杂交信号。该结果从分子细胞遗传学层面进一步证实了杂交三倍体泥鳅是含有三套染色体组的遗传三倍体。     

Cellulase‐producing bacteria of Aeromonas are dominant and indigenous in the gut of Ctenopharyngodon idellus (Valenciennes)

Herbivorous grass carp (Ctenopharyngodon idella) has a powerful capability to digest aquatic weed. Cellulase activity or cellulase‐producing bacteria were found in the gut of grass carp. However, it remains uncertain whether the cellulase‐producing bacteria were a part of indigenous intestinal microbiota that the fish harboured or were introduced with food. In the present study, the bacterial diversities and population abundance in the gut of starved grass carps have been investigated by sequencing 16S rRNA gene libraries. The 16S rRNA gene libraries revealed that 28 parasitic bacteria from gut were affiliated to seven genera of Vibrio, Acinetobacter, Providencia, Yersinia, Pseudominas, Morganella or Aeromonas, respectively, and Aeromonas was identified as the most dominant genus in the gut of C. idella. All of cellulase‐producing bacteria isolated from the gut of C. idella in this research belonged to Aeromonas. On the whole, the results in this research showed that cellulase activity within C. idella should be at least partially resulting from bacteria of Aeromonas with cellulase‐producing capabilities, which were indigenous and dominant intestinal species.     

皱纹盘鲍染色体C带和rDNA定位

为了提高对皱纹盘鲍染色体的辨识水平,实验利用 Ba(OH)₂ 处理显示了皱纹盘鲍染色体的C带,并用荧光原位杂交分析(fluorescence in situ hybridization,FISH)研究了核糖体大亚基rDNA在皱纹盘鲍中期染色体上的数目与位置。核型结果显示,皱纹盘鲍染色体组包含7对中部着丝粒染色体和8对亚中部着丝粒染色体,另有3对染色体介于中部着丝粒染色体与亚中着丝粒染色体之间(m/sm)。C显带结果显示,8对染色体有稳定的着丝粒C带,5～7对染色体上有中期相间多态的端部C带,3对染色体上有同源染色体异态的臂间C带。FISH 分析显示,皱纹盘鲍中期染色体上分布着4个大亚基 rDNA位点,分别位于2号短臂(2S)、7号短臂(7S)、12号短臂(12S)和18号长臂(18L)的端部。研究结果为皱纹盘鲍染色体辨识提供了新的特征与标记,为进一步研究皱纹盘鲍种群的染色体多态和鲍属染色体进化提供了基础资料。     

Assessment of microbial diversity in the river trout Salmo trutta fario L. intestinal tract identified by partial 16S rRNA gene sequence analysis

ABSTRACT:   The microbial diversity of the intestinal tract content of the river trout from two Lithuanian rivers has been investigated by molecular methods: polymerase chain reaction amplification and sequencing of partial 16S rRNA genes. Predominant bacterial populations detected in the river trout intestinal tract from the Skroblus River were Rahnella (21%), from the Žeimena River, Aeromonas (41.7%) and Plesiomonas (22.9%). Buttiauxella agrestis, Budvicia aquatica, Erwinia persicinus , Yersinia mollaretii , Y. kristensenii , Y. rohdei , Moellerella wisconsensis , Obesumbacterium proteus , Pantoea cedenensis , Rahnella aquatilis , and Rahnella sp. from the Enterobacteriaceae family have been detected in the intestinal tract of freshwater salmonid fish for the first time.     

Examination of the early infection stages of koi herpesvirus (KHV) in experimentally infected carp,Cyprinus carpio L. using in situ hybridization

Koi herpesvirus (KHV) causes a highly infectious disease afflicting common carp and koi, Cyprinus carpio L. Various molecular and antibody‐based detection methods have been used to elucidate the rapid attachment and dissemination of the virus throughout carp tissues, facilitating ongoing development of effective diagnostic approaches. In situ hybridization (ISH) was used here to determine the target tissues of KHV during very early infection, after infecting carp with a highly virulent KHV isolate. Analysis of paraffin‐embedded tissues (i.e. gills, skin, spleen, kidney, gut, liver and brain) during the first 8 h and following 10 days post‐infection (hpi; dpi) revealed positive signals in skin mucus, gills and gut sections after only 1 hpi. Respiratory epithelial cells were positive as early as 2 hpi. Viral DNA was also detected within blood vessels of various tissues early in the infection. Notable increases in signal abundance were observed in the gills and kidney between 5 and 10 dpi, and viral DNA was detected in all tissues except brain. This study suggests that the gills and gut play an important role in the early pathogenesis of this Alloherpesvirus, in addition to skin, and demonstrates ISH as a useful diagnostic tool for confirmation of acutely infected carp.     

Karyotype analysis of Oreochromis mossambicus,O. urolepis hornorum and their hybrid based on Cot‐1 DNA bands by fluorescence in situ hybridization

Chromosomal karyotypes of Oreochromis mossambicus and O. urolepis hornorum and their hybrid were analysed by means of Cot‐1 DNA bandings through fluorescence in situ hybridization (FISH). To identify all chromosomes, Cot‐1 DNA – which contains highly and moderately repetitive DNA – was extracted from genomic DNA, labelled as a probe with Dig‐11‐dUTP, and in situ hybridized to spreads of mitotic chromosomes of the three samples. The hybridized signals were detected by means of Cy3‐conjugated antidigoxigenin. The FISH results indicated that the three samples had the same diploid number (2n=44) of chromosomes. Specific fluorescence signal bands were detected on all individual chromosome pairs. On the basis of Cot‐1 DNA FISH banding patterns and chromosome morphology, the karyotypes of the three samples have been constructed; no remarkable differences were detected between the karyotypes of these species using this method. These results – which are similar to those reported previously, with respect to chromosome number, morphology and Cot‐1 DNA FISH patterns – suggest chromosomal stasis during speciation and hybridization of tilapia (Oreochromis, Cichlidae). Such a molecular cytogenetic procedure, if used in conjunction with other genomic research methods, could facilitate the study of genomic structure and be adapted for chromosome studies of other animal species.     

Bacterial community of pond's water,sediment and in the guts of tilapia (Oreochromis niloticus) juveniles characterized by fluorescent in situ hybridization technique

Information about bacterial community structure and functioning in fish farming ponds remains scarce, mainly due to methodological difficulties in counting and identifying uncultured bacteria. The main objective of this study was to evaluate the degree of similarity between the bacterial community of the digestive tract of tilapia (Oreochromis niloticus) juveniles and that of the test pond's water and sediment, using the Fluorescent In Situ Hybridization (FISH) technique. Samples of water, sediment and gut content of 30 tilapia juveniles from a single nursery ground were collected in January 2010. Potentially probiotic and pathogenic bacteria of the species Bacillus, Lactobacillus brevis, Lactobacillus collinoides, Lactobacillus coryniformis, Lactobacillus farciminis, Vibrio and Pseudomonas fluorescens were found in different samples using specific fluorescent probes. The similarity between bacterial community environments and gastrointestinal tracts was determined using the Morisita‐Horn index. The fish guts presented higher abundances of Pseudomonas fluorescens, Bacillus, Lactobacillus brevis and Lactobacillus collinoides. The bacterial community composition of tilapia gastrointestinal tract was more similar to the water than the sediment of the pond. The results of this study showed that the FISH technique can be easily used for monitoring of probiotics and pathogen detection in aquaculture systems.     

Development and application of fluorescence in situ hybridization (FISH) method for simple and rapid identification of the toxic dinoflagellates Alexandrium tamarense and Alexandrium catenella in cultured and natural seawater

ABSTRACT:   The toxic dinoflagellates Alexandrium tamarense (Lebour) Balech and A. catenella (Whedon and Kofoid) Balech produce potent neurotoxins, such as saxitoxin and gonyautoxin and have been mainly responsible for paralytic shellfish poisoning (PSP) in Japan. To prevent a negative effect on the fishery industry, it is necessary to identify these toxic species precisely and rapidly before and during the bloom. In this paper, a rapid and simple protocol of a fluorescence in situ hybridization (FISH) method using ribosomal RNA (rRNA)-targeted probes has been established for identifying the cultured strains and natural cells of A. tamarense and A. catenella . Using the FISH method established in this study, it was possible to identify these toxic species species-specifically and rapidly, within 30 min. The procedure of detection constituted three steps: (i) fixation/dehydration; (ii) hybridization; and (iii) washing; this made the identification simple. Moreover, this method did not require either special techniques or equipment, and the cost for detection was low. The specificity, rapidity, and simplicity of the developed method suggest that it might be useful for routine monitoring of these toxic microalgae.     

Direct visualization of the novel pathogen,Spiroplasma eriocheiris,in the freshwater crayfish Procambarus clarkii (Girard) using fluorescence in situ hybridization

Spiroplasma eriocheiris is the first spiroplasma strain known to be pathogenic to freshwater crustaceans. It has caused considerable economic losses both in the freshwater crayfish Procambarus clarkii (Girard) and in some other crustaceans. The monitoring of the pathogen in crustacean populations and study of its behaviour in the laboratory require the development of reliable diagnostic tools. In this article, we improved microscopic identification of S. eriocheiris by combining in situ hybridization with specific fluorescently labelled oligonucleotide probes. The established fluorescence in situ hybridization (FISH) allowed simultaneous visualization, identification and localization of S. eriocheiris in the tissues of diseased crayfish P. clarkii and exhibited low background autofluorescence and ideal signal‐to‐noise ratio. With the advantages of better tissue penetration, potentially more specific and stable, we designed three species‐specific oligonucleotide probes utilizing the sequences of 16S‐23S rRNA intergenic spacer regions (ISRs) of S. eriocheiris. Positive hybridization signals were visualized in haemocytes and connective tissues of hepatopancreas, cardiac muscle and gill from diseased crayfish. This unique distribution pattern matched the pathological changes when diagnosed by H&E staining and indicated that S. eriocheiris probably spread throughout the tissues in P. clarkii by hemokinesis. This assay will facilitate our understanding of the pathogenesis of S. eriocheiris and enhance the early diagnosis of the novel pathogen.     

Common specific indigenous bacteria reside in the intestinal tract of Chinese mitten crab (Eriocheir sinensis)

In our previous study, five bacterial phylotypes of Mollicutes group 1, Mollicutes group 2, Bacteroides, Meniscus and Marinifilum were found to be dominant (abundance > 0.5%) in the intestine of Chinese mitten crab (CMC, Eriocheir sinensis) farmed in Lake Tai, China. To shed light on whether these five bacterial lineages are common specific indigenous intestinal bacteria, samples of adult CMCs collected from eight geographically separated farms in China, juvenile crabs, farming water and crab feed are subjected to analysing by using 16S rRNA gene sequencing and phylotype‐specific, real‐time quantitative PCR (qPCR). Four phylotypes of the Mollicutes group 1, the Mollicutes group 2, Bacteroides and Meniscus are detected, with relatively higher number, in all crab samples, including adults and juveniles. The Mollicutes group 1 and 2 are more dominant, with the group 1 more abundant in midgut while the group 2 in hindgut. The Marinifilum phylotype is almost undetectable in crab samples but abundant in the farming water and feed. By contrast, phylotypes of the Mollicutes group 1, the Mollicutes group 2, Bacteroides and Meniscus are neither detectable in the water nor in feed. These four lineages appear to be the common specific indigenous intestinal bacteria in the entire CMC species, with the Mollicutes group 1 and 2 likely serving as the major symbiotic players in CMCs. Their beneficial contributions to CMC host await future deep investigation.