Tizabi Daniela, Hill Russell T, Bachvaroff Tsvetan
Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD, USA.
Genome Biol Evol. 2025 Mar 6;17(3). doi: 10.1093/gbe/evaf022.
The dinoflagellate parasite Amoebophrya sp. ex Karlodinium veneficum plays a major role in controlling populations of the toxic bloom-forming dinoflagellate K. veneficum and is one of the few cultured representatives of Marine Alveolate Group II. The obligate parasitic nature of this Amoebophrya spp. precludes isolation in culture, and therefore, genomic characterization of this parasite relies on metagenomic sequencing. Whole-genome sequencing of an Amoebophrya sp. ex K. veneficum-infected culture using Nanopore long reads revealed a diverse community of novel bacteria as well as several species previously reported to be associated with algae. In sum, 39 metagenome-assembled genomes were assembled, and less than half of these required binning of multiple contigs. Seven were abundant but of unknown genera, 13 were identifiable at the generic level by BLAST (8 of which were apparently complete single-contig genomes), and the remaining 19 comprised less abundant (individually accounting for <2% of the total bacterial reads in the culture) and often rarer and/or novel species. Attempts to culture strains identified through sequencing revealed that only two of these bacterial isolates were readily amenable to cultivation, stressing the importance of a dual culture- and sequencing-based approach for robust community analysis. Functional annotations of metagenome-assembled genomes are presented here to support the characterization of a microbial community associated with K. veneficum and/or Amoebophrya sp. ex K. veneficum cultured from the Chesapeake Bay and give preliminary insights into the nature of the associations these bacteria have with this parasite-host complex.
源自剧毒卡尔藻（Karlodinium veneficum）的甲藻寄生虫阿米巴藻（Amoebophrya sp.）在控制形成有毒水华的卡尔藻种群方面发挥着重要作用，并且是海洋纤毛虫类群II中少数可培养的代表物种之一。这种阿米巴藻的专性寄生特性使其无法在培养中分离，因此，对这种寄生虫的基因组特征分析依赖于宏基因组测序。使用纳米孔长读长对受源自卡尔藻的阿米巴藻感染的培养物进行全基因组测序，揭示了一个多样的新型细菌群落以及几种先前报道与藻类相关的物种。总之，共组装了39个宏基因组组装基因组，其中不到一半需要对多个重叠群进行分箱。7个丰度较高但属未知，13个可通过BLAST在属水平上鉴定（其中8个显然是完整的单重叠群基因组），其余19个丰度较低（单个占培养物中细菌总读数的<2%），且通常是更罕见和/或新的物种。对通过测序鉴定的菌株进行培养的尝试表明，这些细菌分离物中只有两个易于培养，这强调了基于培养和测序的双重方法对稳健的群落分析的重要性。本文展示了宏基因组组装基因组的功能注释，以支持对与卡尔藻和/或源自卡尔藻的阿米巴藻相关的微生物群落的特征分析，这些微生物群落是从切萨皮克湾培养得到的，并初步洞察了这些细菌与这种寄生虫-宿主复合体之间关联的性质。
