海洋生态与环境科学重点实验室知识库

  趋磁细菌（Magnetotactic bacteria，MTB）是一类可以感知地磁场，并沿着磁力线运动的微好氧或厌氧的革兰氏阴性菌。趋磁细菌具有由基因调控胞内矿化合成的磁铁矿（Fe₃O₄）或胶黄铁矿（Fe₃S₄）纳米磁性颗粒，即磁小体，它为趋磁细菌的趋磁运动导航。趋磁细菌形态多样，包括单细胞的球菌、杆菌、弧菌、螺菌及多细胞聚集体形式的趋磁原核生物（Multicellular magnetotactic prokaryotes，MMPs）。趋磁细菌在淡水、内陆咸水、海洋等全球范围多种生境中广泛分布，但对其生态调查研究多集中在温带地区，对热带海区趋磁细菌的生态调查及多样性、分布特征及磁小体矿化特点的研究不足。本论文综合利用显微镜观察、显微操作、高通量测序和宏基因组组装分析等技术方法，探究了西太平洋卡罗琳海山（Caroline seamount，CM4）生境沉积物中趋磁细菌的多样性、分布特征及群落组成特点；另外，在中国南海金沙湾潮间带发现鉴定了多种桑葚状MMPs的新种类（Spherical mulberry-like multicellular magnetotactic prokaryotes，sMMPs），对其中一类优势度较高的sMMPs的菌体形态、磁小体矿化及基因簇特征进行了研究。

  调查发现趋磁细菌广泛分布在卡罗琳海山沉积物中，在13个沉积物采样站位中，有12个站位（水深90-1545 m）都观察到了活的趋磁细菌，其丰度为1.1×10³-43.7×10³ inds./dm³。观察发现该海山沉积物中趋磁球菌占据优势，此外还有趋磁弧菌、趋磁螺菌等。利用透射电子显微镜观察根据其形态特征将趋磁球菌分成了两类，一类是典型的球菌，平均直径为1.5 ± 0.4 μm，少数个体着生着周生鞭毛；另一类是形似“水滴”的近似球菌，大小约2.1 ± 0.3 μm×1.7 ± 0.3 μm，在菌体的一端通常生有一簇长长的鞭毛，约为菌体长度的5.7倍。该海山生境中趋磁球菌皆矿化合成八面体型磁小体，成分为Fe₃O₄，在细胞内成单链、双链或多链排列。通过高通量测序手段，从该海山9个站位的沉积物样品中共获得了41个属于趋磁细菌的OTUs，包含2,702条序列，分别占细菌种类及数量的0.83%和0.73%，其中有39个OTUs属于α-变形菌纲，包含2,691条序列；有1个OTU属于η-变形菌纲，包含4条序列；还有1个属于硝化螺旋菌门，包含7条序列。属于海洋趋磁螺菌属的趋磁细菌序列占据绝对优势，这与它临近的马里亚纳M2海山趋磁细菌优势类群相似，但多样性更加丰富。这两座海山共有的趋磁细菌细菌OTUs有11个，相似序列的丰度分别占到CM4和M2海山趋磁细菌序列的63.6%和54.8%，可以发现两座海山共有的趋磁细菌种类较多，群落组成较为相似，这可能与海山相似的由珊瑚砂及有孔虫砂等组成的沉积物类型等生境环境有关。

  在针对南海金沙湾潮间带趋磁细菌的调查研究中，我们首次在该区域发现种类丰富的桑葚状MMPs，有5属6种，包括了1个新属和4个新种。其中有一类sMMPs丰度占据优势，约为304 inds./cm³，完整的sMMPs菌体的直径为4.78 ± 0.67 μm，由14-40个卵球形的直径约1.03 ± 0.15 μm的小细胞成放射状排列而成。显微镜下观察发现该sMMPs中超过80%的个体表现出趋北极性，其进行趋磁运动时的速度约为78.0 ± 41.4 μm/s，运动轨迹为直线形或螺旋形；在进行乒乓运动时，快速漂移和回归的平均速度分别为223.9 ± 54.5 μm/s和102.2 ± 19.0 μm/s。透射电镜观察，该sMMPs可同时矿化合成子弹头型和不规则型磁小体，磁小体成链排列或成簇分布，其中子弹头型磁小体成分为Fe₃O₄而不规则型磁小体成分为Fe₃S₄。利用16S rRNA基因序列分析，发现该sMMPs属于脱硫菌门趋磁细菌中的一个新属。通过比较基因组学研究，在该sMMPs的基因组上发现了两套磁小体基因簇，分别调控磁铁矿和胶黄铁矿磁小体的矿化。其中，我们还发现由磁小体基因簇编码的两套Mam蛋白具有同源性，两套Mad蛋白也具有同源性，并且同源Mam蛋白之间的蛋白序列相似性与同源Mad蛋白之间的蛋白序列相似性接近，推测它们可以独立行使磁小体矿化的功能。

  本论文通过对热带西太平洋卡罗琳海山生境中趋磁细菌的多样性及分布特点和中国南海金沙湾潮间带中桑葚状MMPs的物种多样性及磁小体基因簇的分析，弥补了热带弱磁场的地理环境下趋磁细菌的研究，为海洋趋磁细菌的多样性及适应生境进化提供了新认识，为解析磁小体的矿化机制和磁小体基因簇的进化起源提供了新依据。

Magnetotactic bacteria (MTB) are a group of Gram-negative microbes that have the ability to sense the Earth’s magnetic field and swim along the magnetic field lines. They are capable of microaerophilic or anaerobic growth. MTB could biomineralize the membrane-enveloped magnetite (Fe₃O₄) and/or greigite (Fe₃S₄) crystals termed magnetosome, which is regulated by the magnetosome gene clusters. And the magnetosomes act as a compass orientating the magnetotactic behavior. MTB display a morphological diversity, and numerous morphotypes have been described including unicellular cocci, rods, vibrios, spirilla, and multicellular magnetotactic prokaryotes (MMPs). MTB are cosmopolitan in freshwater, brackish, and marine habitats, but the investigations of MTB were mainly performed in temperate regions, and fewer researches were conducted on the diversity, distribution pattern, and magnetosome biomineralization characteristics of MTB which inhabited in tropical marine areas. In this study, using a combination of diverse experimental techniques, such as microscopic observation, micromanipulation, high-throughput sequencing, and metagenomic assembly, we investigated the diversity, distribution, and community structure of MTB dwelled in the sediments of the Caroline seamount (CM4) in the western Pacific Ocean; and we also discovered and identified several new types of spherical mulberry-like multicellular magnetotactic prokaryotes (sMMPs) from the intertidal sediments of Jinsha Bay in the South China Sea. And the bacterial morphology, magnetosome biomineralization characteristics, and features of magnetosome gene clusters (MGCs) of one of the dominant sMMPs were also revealed.

Here, we noticed that MTB were ubiquitous in the sediments of the Caroline seamount, and living cells were observed at 12 of the 13 sampling stations ranging in depth from 90 to 1545 m. The abundance of MTB varied from 1.1×10³ to 43.7×10³ inds./dm³ among these 12 stations. Magnetotactic cocci were the dominant morphotype, and rod-shaped and spiral MTB were also detected. Using transmission electron microscopy (TEM) observation, magnetotactic cocci were classified into two types according to their morphological characteristics, one was the typical cocci with an average diameter of 1.5 ± 0.4 μm, and a few individuals appeared to possess peritrichous flagella; the other was drop-like cocci with a size of 2.1 ± 0.3 μm×1.7 ± 0.3 μm approximately, and had a single bundle of flagella at one end of the cell whose length was 5.7 times longer than the cell length in average. All observed magnetotactic cocci biomineralized octahedral magnetosomes that were composed of magnetite (Fe₃O₄) and arranged in single, double, or multiple chains. Using high-throughput sequencing, a total of 41 operational taxonomic units (OTUs) affiliated with putative MTB (2,702 reads) were acquired from nine stations, which accounted for 0.83% of total bacterial OTUs (the MTB reads accounted for 0.73% of total bacterial reads). Among 41 MTB OTUs, 39 of these belonged to Alphaproteobacteria (including 2,691 reads); one belonged to Etaproteobacteria (including 4 reads); and one belonged to Nitrospirae (including 7 reads). The dominant group of MTB was Magnetospira, which was similar to the dominant group of MTB in sediments of the neighboring Mariana M2 seamount. But the diversity of MTB on Caroline seamount was much richer than that on the Mariana M2 seamount. In addition, there are 11 MTB OTUs shared between the two seamounts, and the MTB reads of the 11 OTUs accounted for 63.6% and 54.8% at the Caroline and M2 seamounts, respectively. Our results showed that the two seamounts shared numerous species of MTB and the community structure of MTB on these two seamounts was also similar, which might be related to the similar environmental conditions of the seamounts, such as the sediment content mainly composed of coral and foraminiferan sands.

In another investigation, we firstly observed and identified 6 sMMPs species inhabited in the intertidal sediments of Jinsha Bay in the South China Sea, which belonged to 5 genera, including one novel genus and 4 novel species. It has showed a rich phylogenetical diversity. And one of the new types of sMMPs was dominant and had an abundance of about 304 inds./cm³. The sMMPs were 4.78 ± 0.67 μm in diameter and composed of 14-40 individual units of approximately 1.03 ± 0.15 μm in diameter arranged with radial symmetry. Microscopic observation showed that more than 80% of enriched sMMPs exhibited north-seeking polarity. The average velocity of the magnetotaxis motility of the sMMPs was approximately 78.0 ± 41.4 μm/s and showed a straight or helical trajectory. The average speeds of the excursion and return of the “ping-pong” motility were 223.9 ± 54.5 μm/s and 102.2 ± 19.0 μm/s, respectively. TEM observation showed the sMMPs could biomineralize both bullet-shaped and irregular magnetosomes arranged in chains or clusters. The bullet-shaped crystals were composed of magnetite (Fe₃O₄) and the irregular crystals were composed of greigite (Fe₃S₄). Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the sMMPs belonged to a new genus of Desulfobacterota. Using comparative genomic analysis, two sets of magnetosome gene clusters were identified, which regulated the biomineralization of magnetite and greigite magnetosomes, respectively. Furthermore, two sets of paralogous Mam and Mad proteins were also identified, and the degree of the paralogous Mam proteins similarities was similar to that of the paralogous Mad proteins similarities, which might perform the function of magnetosome biomineralization separately and independently.

In brief, this study depicted the diversity and distribution characteristics of MTB inhabited in the Caroline seamount habitat in the tropical western Pacific Ocean, and it also described the species diversity and MGCs of sMMPs inhabited in the intertidal zone of Jinsha Bay, the South China Sea, which remedied the research of MTB in tropical geography with a weak magnetic field. This study has provided new knowledge of the diversity and adaptive evolutions of marine MTB, and also provided new insights into the mechanism of biomineralization of magnetosomes in MMPs, and the evolutionary origin of MGCs.