Marine Microbiology Group, Department of Ecology and Marine Resources, Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Esporles, Spain; Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany.
Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany.
Syst Appl Microbiol. 2020 Mar;43(2):126066. doi: 10.1016/j.syapm.2020.126066. Epub 2020 Jan 27.
On-going studies of phytoplankton-bacterioplankton interactions at the long-term ecological research site Helgoland Roads have indicated that many of the heterotrophic bacterial taxa have not yet been cultivated. A high-throughput approach combining whole cell matrix-assisted laser desorption ionization - time of flight mass spectroscopy with 16S rRNA gene sequencing was applied to the spring bloom of 2016. Aiming at an assessment of cultivability during a spring bloom, cultivation on solid marine media had to be used since dilution to extinction would not have been feasible for a high-throughput approach, as performed in this study. A total of 5023 isolates were obtained from nine weekly samples on eight different solid media between the early-bloom and post-bloom periods. Most of the 4136 strains identified affiliated with Bacteroidetes (13.3%), Gammaproteobacteria (26.9%), Alphaproteobacteria (40.6%) and Actinobacteria (6.7%). Of the 271 operational phylogenetic units (OPUs) identified, 13 are likely to represent novel genera and 143 novel species. A comparison with 16S rRNA gene tag data indicated that most of the isolates were rather rare in surface waters, with the exception of five OPUs affiliating with Rhodobacteraceae, Polaribacter, Psychromonas and Pseudoalteromonas. The effort yielded many novel isolates, yet most of the abundant heterotrophic bacteria still remained elusive. The large strain collection obtained will not only provide insights into the succession of the cultivable fraction of the bacterioplankton, but also enable fine-tuned taxonomic and physiological follow-up studies for improving our knowledge on heterotrophic bacteria in North Sea waters.
在黑尔戈兰湾长期生态研究站进行的浮游植物-细菌相互作用的研究表明，许多异养细菌类群尚未被培养。本研究采用高通量方法，将全细胞基质辅助激光解吸电离-飞行时间质谱与 16S rRNA 基因测序相结合，应用于 2016 年的春季水华。由于在高通量方法中稀释至灭绝不可行，因此必须使用固体海洋培养基进行培养，以评估春季水华期间的可培养性。在早期水华和后期水华期间，从八种不同固体培养基的九周样品中总共获得了 5023 个分离株。在鉴定的 4136 株菌株中，大多数属于拟杆菌门（13.3%）、γ-变形菌纲（26.9%）、α-变形菌纲（40.6%）和放线菌纲（6.7%）。在所鉴定的 271 个操作分类单元（OPU）中，有 13 个可能代表新属，143 个为新种。与 16S rRNA 基因标签数据的比较表明，除了与红杆菌科、极地杆菌属、Psychromonas 和假交替单胞菌属相关的 5 个 OPU 外，大多数分离株在表层水中都相当罕见。该研究成果获得了许多新的分离株，但大多数丰富的异养细菌仍然难以捉摸。获得的大量菌株不仅为研究细菌浮游生物可培养部分的演替提供了依据，而且还为进一步进行分类和生理研究提供了可能，从而有助于提高我们对北海水域异养细菌的认识。
