Hiralal Anwar, Geelhoed Jeanine S, Hidalgo-Martinez Silvia, Smets Bent, van Dijk Jesper R, Meysman Filip J R
Geobiology Research Group, University of Antwerp, Antwerp, Belgium.
Department of Biotechnology, Delft University of Technology, Delft, Netherlands.
Microb Genom. 2024 Feb;10(2). doi: 10.1099/mgen.0.001197.
Many environmentally relevant micro-organisms cannot be cultured, and even with the latest metagenomic approaches, achieving complete genomes for specific target organisms of interest remains a challenge. Cable bacteria provide a prominent example of a microbial ecosystem engineer that is currently unculturable. They occur in low abundance in natural sediments, but due to their capability for long-distance electron transport, they exert a disproportionately large impact on the biogeochemistry of their environment. Current available genomes of marine cable bacteria are highly fragmented and incomplete, hampering the elucidation of their unique electrogenic physiology. Here, we present a metagenomic pipeline that combines Nanopore long-read and Illumina short-read shotgun sequencing. Starting from a clonal enrichment of a cable bacterium, we recovered a circular metagenome-assembled genome (5.09 Mbp in size), which represents a novel cable bacterium species with the proposed name Electrothrix scaldis. The closed genome contains 1109 novel identified genes, including key metabolic enzymes not previously described in incomplete genomes of cable bacteria. We examined in detail the factors leading to genome closure. Foremost, native, non-amplified long reads are crucial to resolve the many repetitive regions within the genome of cable bacteria, and by analysing the whole metagenomic assembly, we found that low strain diversity is key for achieving genome closure. The insights and approaches presented here could help achieve genome closure for other keystone micro-organisms present in complex environmental samples at low abundance.
许多与环境相关的微生物无法进行培养，即使采用最新的宏基因组学方法，要获得感兴趣的特定目标生物的完整基因组仍然是一项挑战。索细菌就是目前无法培养的微生物生态系统工程师的一个突出例子。它们在自然沉积物中含量较低，但由于其具备长距离电子传输能力，它们对其所处环境的生物地球化学产生了 disproportionately large 的影响。目前海洋索细菌的可用基因组高度碎片化且不完整，这阻碍了对其独特产电生理学的阐明。在此，我们提出了一种结合纳米孔长读长和 Illumina 短读长鸟枪法测序的宏基因组学流程。从索细菌的克隆富集开始，我们获得了一个环状的宏基因组组装基因组（大小为 5.09 Mbp），它代表了一个新的索细菌物种，提议命名为 Electrothrix scaldis。这个封闭的基因组包含 1109 个新鉴定的基因，包括先前在索细菌不完整基因组中未描述的关键代谢酶。我们详细研究了导致基因组封闭的因素。首先，天然的、未扩增的长读长对于解析索细菌基因组内的许多重复区域至关重要，并且通过分析整个宏基因组组装，我们发现低菌株多样性是实现基因组封闭的关键。本文提出的见解和方法有助于实现对复杂环境样本中低丰度存在的其他关键微生物的基因组封闭。
