Bird Clare, Darling Kate F, Russell Ann D, Fehrenbacher Jennifer S, Davis Catherine V, Free Andrew, Ngwenya Bryne T
School of Geosciences, University of Edinburgh, Edinburgh, United Kingdom.
School of Geography and Sustainable Development, University of St Andrews, St Andrews, United Kingdom.
PLoS One. 2018 Jan 29;13(1):e0191653. doi: 10.1371/journal.pone.0191653. eCollection 2018.
Uncovering the complexities of trophic and metabolic interactions among microorganisms is essential for the understanding of marine biogeochemical cycling and modelling climate-driven ecosystem shifts. High-throughput DNA sequencing methods provide valuable tools for examining these complex interactions, although this remains challenging, as many microorganisms are difficult to isolate, identify and culture. We use two species of planktonic foraminifera from the climatically susceptible, palaeoceanographically important genus Neogloboquadrina, as ideal test microorganisms for the application of 16S rRNA gene metabarcoding. Neogloboquadrina dutertrei and Neogloboquadrina incompta were collected from the California Current and subjected to either 16S rRNA gene metabarcoding, fluorescence microscopy, or transmission electron microscopy (TEM) to investigate their species-specific trophic interactions and potential symbiotic associations. 53-99% of 16S rRNA gene sequences recovered from two specimens of N. dutertrei were assigned to a single operational taxonomic unit (OTU) from a chloroplast of the phylum Stramenopile. TEM observations confirmed the presence of numerous intact coccoid algae within the host cell, consistent with algal symbionts. Based on sequence data and observed ultrastructure, we taxonomically assign the putative algal symbionts to Pelagophyceae and not Chrysophyceae, as previously reported in this species. In addition, our data shows that N. dutertrei feeds on protists within particulate organic matter (POM), but not on bacteria as a major food source. In total contrast, of OTUs recovered from three N. incompta specimens, 83-95% were assigned to bacterial classes Alteromonadales and Vibrionales of the order Gammaproteobacteria. TEM demonstrates that these bacteria are a food source, not putative symbionts. Contrary to the current view that non-spinose foraminifera are predominantly herbivorous, neither N. dutertrei nor N. incompta contained significant numbers of phytoplankton OTUs. We present an alternative view of their trophic interactions and discuss these results within the context of modelling global planktonic foraminiferal abundances in response to high-latitude climate change.
揭示微生物之间营养和代谢相互作用的复杂性对于理解海洋生物地球化学循环和模拟气候驱动的生态系统变化至关重要。高通量DNA测序方法为研究这些复杂相互作用提供了有价值的工具，尽管这仍然具有挑战性，因为许多微生物难以分离、鉴定和培养。我们使用了来自气候敏感、古海洋学上重要的新球藻属的两种浮游有孔虫，作为应用16S rRNA基因代谢条形码的理想测试微生物。从加利福尼亚洋流中采集了杜氏新球藻和不完全新球藻，并对其进行16S rRNA基因代谢条形码分析、荧光显微镜检查或透射电子显微镜（TEM）检查，以研究它们物种特异性的营养相互作用和潜在的共生关系。从两个杜氏新球藻标本中回收的16S rRNA基因序列，有53 - 99%被归入来自不等鞭毛门叶绿体的单个操作分类单元（OTU）。TEM观察证实宿主细胞内存在大量完整的球藻，这与藻类共生体一致。基于序列数据和观察到的超微结构，我们将推定的藻类共生体分类为褐藻纲而非金藻纲，这与该物种先前的报道不同。此外，我们的数据表明，杜氏新球藻以颗粒有机物（POM）中的原生生物为食，但不以细菌作为主要食物来源。完全相反的是，从三个不完全新球藻标本中回收的OTU，83 - 95%被归入γ-变形菌纲的交替单胞菌目和弧菌目细菌类。TEM表明这些细菌是食物来源，而非推定的共生体。与目前认为无刺有孔虫主要为草食性的观点相反，杜氏新球藻和不完全新球藻都没有大量的浮游植物OTU。我们提出了它们营养相互作用的另一种观点，并在模拟全球浮游有孔虫丰度对高纬度气候变化响应的背景下讨论了这些结果。
