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首页> 外文期刊>BMC research notes >Diversity and relative abundance of the bacterial pathogen, Flavobacterium spp., infecting reproductive ecotypes of kokanee salmon
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Diversity and relative abundance of the bacterial pathogen, Flavobacterium spp., infecting reproductive ecotypes of kokanee salmon

机译：细菌病原体黄杆菌属菌种的多样性和相对丰度，感染了科卡尼鲑鱼的生殖生态型

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Background Understanding the distribution and abundance of pathogens can provide insight into the evolution and ecology of their host species. Previous research in kokanee, the freshwater form of sockeye salmon ( Oncorhynchus nerka ), found evidence that populations spawning in streams may experience a greater pathogen load compared with populations that spawn on beaches. In this study we tested for differences in the abundance and diversity of the gram-negative bacteria, Flavobacterium spp ., infecting tissues of kokanee in both of these spawning habitats (streams and beaches). Molecular assays were carried out using primers designed to amplify a ~200 nucleotide region of the gene encoding the ATP synthase alpha subunit ( AtpA ) within the genus Flavobacterium. Using a combination of DNA sequencing and quantitative PCR (qPCR) we compared the diversity and relative abundance of Flavobacterium AtpA amplicons present in DNA extracted from tissue samples of kokanee collected from each spawning habitat. Results We identified 10 Flavobacterium AtpA haplotypes among the tissues of stream-spawning kokanee and seven haplotypes among the tissues of beach-spawning kokanee, with only two haplotypes shared between spawning habitats. Haplotypes occurring in the same clade as F. psychrophilum were the most prevalent (92% of all reads, 60% of all haplotypes), and occurred in kokanee from both spawning habitats (streams and beaches). Subsequent qPCR assays did not find any significant difference in the relative abundance of Flavobacterium AtpA amplicons between samples from the different spawning habitats. Conclusions We confirmed the presence of Flavobacterium spp. in both spawning habitats and found weak evidence for increased Flavobacterium diversity in kokanee sampled from stream-spawning sites. However, the quantity of Flavobacterium DNA did not differ between spawning habitats. We recommend further study aimed at quantifying pathogen diversity and abundance in population-level samples of kokanee combined with environmental sampling to better understand the ecology of pathogen infection in this species.
机译：背景技术了解病原体的分布和丰富程度可以深入了解其宿主物种的进化和生态。以前在kokanee中进行的研究是红鲑鱼（Oncorhynchus nerka）的淡水形式，发现有证据表明，与在海滩上繁殖的种群相比，在河流中产生的种群可能承受更大的病原体负荷。在这项研究中，我们测试了革兰氏阴性细菌黄杆菌属细菌在这两个产卵栖息地（河流和海滩）中感染科卡尼组织的丰度和多样性差异。使用引物进行分子分析，所述引物被设计为扩增黄杆菌属中编码ATP合酶α亚基（AtpA）的基因的〜200个核苷酸区域。使用DNA测序和定量PCR（qPCR）的组合，我们比较了从每个产卵栖息地收集的kokanee组织样本中提取的DNA中存在的黄杆菌AtpA扩增子的多样性和相对丰度。结果我们在产卵科卡尼的组织中鉴定出10种黄杆菌AtpA单倍型，在海滩产卵科卡尼的组织中鉴定出7种单倍体，在产卵栖息地之间仅共享两种单倍型。在与嗜热镰刀菌相同的进化枝中出现的单倍型是最普遍的（占所有读物的92％，占所有单倍型的60％），并且来自两个产卵生境（河流和海滩）的科卡尼。随后的qPCR分析未发现来自不同产卵栖息地的样品之间黄杆菌属AtpA扩增子的相对丰度有任何显着差异。结论我们证实了黄杆菌属的存在。在两个产卵的生境中，发现从流产卵地点取样的kokanee中黄细菌多样性增加的证据不充分。但是，产卵生境之间黄杆菌DNA的数量没有差异。我们建议进行进一步的研究，以定量分析kokanee种群水平样本中的病原体多样性和丰度，并结合环境采样，以更好地了解该物种的病原体感染生态。

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