Department of Nematology, University of California, Riverside, Riverside, CA, USA.
School of Fisheries and Ocean Sciences, University of Alaska, Fairbanks, AK, USA.
Mol Ecol. 2018 Apr;27(8):1930-1951. doi: 10.1111/mec.14539. Epub 2018 Mar 29.
Studies of host-associated microbes are critical for advancing our understanding of ecology and evolution across diverse taxa and ecosystems. Nematode worms are ubiquitous across most habitats on earth, yet little is known about host-associated microbial assemblages within the phylum. Free-living nematodes are globally abundant and diverse in marine sediments, with species exhibiting distinct buccal cavity (mouth) morphologies that are thought to play an important role in feeding ecology and life history strategies. Here, we investigated patterns in marine nematode microbiomes, by characterizing host-associated microbial taxa in 281 worms isolated from a range of habitat types (deep-sea, shallow water, methane seeps, Lophelia coral mounds, kelp holdfasts) across three distinct geographic regions (Arctic, Southern California and Gulf of Mexico). Microbiome profiles were generated from single worms spanning 33 distinct morphological genera, using a two-gene metabarcoding approach to amplify the V4 region of the 16S ribosomal RNA (rRNA) gene targeting bacteria/archaea and the V1-V2 region of the 18S rRNA gene targeting microbial eukaryotes. Contrary to our expectations, nematode microbiome profiles demonstrated no distinct patterns either globally (across depths and ocean basins) or locally (within site); prokaryotic and eukaryotic microbial assemblages did not correlate with nematode feeding morphology, host phylogeny or morphological identity, ocean region or marine habitat type. However, fine-scale analysis of nematode microbiomes revealed a variety of novel ecological interactions, including putative parasites and symbionts, and potential associations with bacterial/archaeal taxa involved in nitrogen and methane cycling. Our results suggest that in marine habitats, free-living nematodes may utilize diverse and generalist foraging strategies that are not correlated with host genotype or feeding morphology. Furthermore, some abiotic factors such as geographic region and habitat type do not appear to play an obvious role in structuring host-microbe associations or feeding preferences.
宿主相关微生物的研究对于推进我们对不同分类群和生态系统的生态和进化的理解至关重要。线虫在地球上的大多数栖息地都很普遍，但对于门内的宿主相关微生物组合知之甚少。自由生活的线虫在海洋沉积物中广泛存在且种类繁多，其具有独特的口腔（嘴）形态，这些形态被认为在摄食生态学和生活史策略中发挥着重要作用。在这里，我们通过对来自不同生境类型（深海、浅水区、甲烷渗漏、Lophelia 珊瑚丘、海带固着器）的 281 个线虫样本进行宿主相关微生物类群的特征描述，研究了海洋线虫微生物组的模式，这些样本来自于三个不同地理区域（北极、南加州和墨西哥湾）。使用靶向细菌/古菌的 16S 核糖体 RNA（rRNA）基因 V4 区和靶向微生物真核生物的 18S rRNA 基因 V1-V2 区的双基因代谢组学方法，对来自 33 个不同形态属的单个线虫进行微生物组谱分析。与我们的预期相反，线虫微生物组谱在全球（跨越深度和海洋盆地）或局部（在同一地点）均无明显模式；原核和真核微生物组合与线虫摄食形态、宿主系统发育或形态特征、海洋区域或海洋生境类型均无相关性。然而，对线虫微生物组的精细分析揭示了各种新的生态相互作用，包括潜在的寄生虫和共生体，以及与参与氮和甲烷循环的细菌/古菌类群的潜在关联。我们的研究结果表明，在海洋生境中，自由生活的线虫可能利用多样化和通用的觅食策略，这些策略与宿主基因型或摄食形态无关。此外，一些非生物因素，如地理位置和生境类型，似乎并没有在构建宿主-微生物关联或摄食偏好方面发挥明显作用。
