海洋生态与环境科学重点实验室知识库

趋磁细菌（magnetotactic bacteria，MTB）是一类能够沿磁力线运动的特殊细菌，在海洋与淡水生境的有氧-无氧过渡区（oxic-anoxic transition zone, OATZ）中广泛存在。趋磁细菌具有一类特殊的细胞器——磁小体，使之能够感知磁场。趋磁细菌在遗传发育学上分属变形菌门下的α-变形菌纲、γ-变形菌纲、δ-变形菌纲、η-变形菌纲，以及硝化螺旋菌门等。自1975年美国学者Blakemore在Science上报道了趋磁细菌之后，科学家陆续在海洋、湖泊以及土壤等不同生境中发现了形态多样的趋磁细菌，其中对海洋趋磁细菌的研究主要集中在潮间带，对海底沉积物中趋磁细菌的报道较少，尚未有对大陆架趋磁细菌的系统调查研究。本论文结合生态调查、光学显微镜、电子显微镜与高通量测序等手段，对黄、东海大陆架沉积物趋磁细菌进行了系统的生态调查研究，分别研究了趋磁细菌的多样性，水平分布、垂直分布、季节变化，并分析了它们与环境因子的关系。

结果显示，无论近岸站位还是远岸站位，趋磁细菌在黄海大陆架沉积物中广泛存在。其中黄海夏冬春三个航次发现趋磁细菌的站位比例分别为27.27%、30.43%、60.00%，平均丰度分别为260 ind./dm³、130 ind./dm³、470 ind./dm³，最高丰度分别为2400 ind./dm³、820 ind./dm³、5000 ind./dm³，均出现在H17(H19)站位（121.33ºE，35.00ºN）。在大多数站位趋磁球菌占优势，在H17(H19)站位趋磁杆菌为优势。趋磁细菌垂直分布不均，最大丰度位于上层，分别是表层0-2 cm丰度为22 ind./dm³，次表层2-4 cm丰度为19 ind./dm³。随深度增加，趋磁细菌丰度下降，4-6 cm丰度为13 ind./dm³，6-8 cm与8-10 cm的丰度皆为12 ind./dm³，丰度与氧化还原电位相关。研究发现，黄海大陆架沉积物趋磁细菌在水平方向上的丰度主要受沉积物粒度影响，趋磁细菌丰度与沉积物中值粒径呈显著正相关关系。各元素含量或浓度都有随沉积物中值粒径增大而降低的趋势。MTB最高丰度的站位中值粒径远高于其他站位，粒径谱曲线显著异于其他站位，粒径高于190 μm的比例至少是其他站位的2倍，其TC、TN、TS、TOC、Fe等含量或浓度也近乎全部是各站位最低。运动对趋磁细菌的生理代谢至关重要，沉积物粒度会影响趋磁细菌的运动空间，进而影响趋磁细菌生存。此外，趋磁细菌更适合寡营养的环境，Cu、Co、Zn等元素会抑制趋磁细菌运动能力，可能也是造成趋磁细菌丰度与沉积物中值粒径正相关的原因。

使用通用引物338F与806R以PCR技术扩增细菌16S rRNA 基因的可变区V3–V5区并进行高通量测序。测序结果显示，夏冬季黄海趋磁细菌分为72个OTU，其中26个属于α-变形菌纲、7个属于δ-变形菌纲、38个属于硝化螺旋菌门。每个站位有19-46个OTU。夏季与冬季分别发现趋磁细菌序列数为2447、3271，各站位分别有序列71-439条。属于硝化螺旋菌门的趋磁细菌序列比例约75%。硝化螺旋菌门趋磁细菌在黄海大陆架趋磁细菌群落中占绝对优势。

在东海大陆架，趋磁细菌在近岸站位与远岸站位都有分布。2014、2016两年的平均丰度分别为2290 ind./dm³、590 ind./dm³。2014年丰度最大值在6-5站位，为11000 ind./dm³，2016年丰度最大值在DH4-4站位，为6500 ind./dm³，两站位位置接近。近岸站位以趋磁球菌为优势菌，而在远岸站位是趋磁球菌和趋磁杆菌同为优势菌。东海沉积物近岸多为黏土质、颗粒小，远岸多为砂质、颗粒大，趋磁细菌受沉积物类型及粒度的影响，在丰度上呈现远岸丰度高、近岸丰度低的趋势。黄、东海大陆架沉积物趋磁细菌的丰度均主要受沉积物粒度影响。

本研究首次对大陆架沉积物趋磁细菌进行了较系统生态学调查，研究了解其群落结构与时空分布，首次发现并解释了陆架沉积物粒度对趋磁细菌丰度的影响显著，为寻找海底沉积物趋磁细菌资源提供了重要参考。

Prokaryotes that exhibit magnetotaxis, collectively known as magnetotactic bacteria (MTB), have directional motility that is influenced by the Earth’s geomagnetic field and by externally applied magnetic fields. They are cosmopolitan in sediments of freshwater and marine habitats. They form variously shaped intracellular biomineral magnetic crystals, either magnetite (Fe₃O₄) or greigite (Fe₃S₄), termed magnetosomes, which cause the MTB to passively align along magnetic field lines as they swim. MTB have been classified into the phyla Proteobacteria, Nitrospirae and so forth. Different morphological types of MTB were found in marine, limnetic and pedologic environments since MTB were reported in Science by Richard P. Blakemore. Most studies of marine MTB have concerned intertidal zones, and there have been few reports of MTB from seafloor sediments. There is no systematic research focusing on MTB in sediments of continent shelf. In this study, a combination of ecological investigation and experimental technique, such as light microscopic observation, transmission electron microscopic observation, and high-throughput sequencing, were utilized to study the ecology of marine MTB inhabiting in sediments of the continent shelf of the Yellow Sea and East China Sea, including horizontal distribution, vertical distribution, seasonal variation, diversity and the relationship between MTB and environmental factors.

MTB were ubiquitous in sediments of continent shelf of Yellow Sea, from near-shore to far off-shore. The percentage of stations where MTB occurred in summer, winter and spring was 27.27%, 30.43% and 60.00% and the average abundance in these three seasons was 260 ind./dm³, 130 ind./dm³ and 470 ind./dm³. The highest abundance of MTB in these three seasons was 2400 ind./dm³, 820 ind./dm³ and 5000 ind./dm³ at station H17(H19) (121.33ºE，35.00ºN). At most stations except H17(H19) the dominant morphology of MTB was coccoid whereas at H17(H19) rod-shaped MTB dominated in three seasons. The abundance of MTB varied vertically，with the highest abundance in top layer (0-2 cm, 22 ind./dm³; 2-4 cm, 19 ind./dm³). With depth increasing, the abundance of MTB decreased (4-6 cm, 13 ind./dm³; 6-8 cm and 8-10 cm, 12 ind./dm³) and correlated to redox potential. The horizontal distribution of MTB in sediments of the Yellow Sea continent shelf was influenced by the grain size of sediments, with the abundance being positive correlated with the median sediment grain size. A trend of increasing MTB abundance with decreasing percentages of TC, TN, TS, and TOC, and a decreasing concentration of Fe, was also observed. The sediments at station H17(H19) were significantly coarser than at any other station. Percentages or concentration of some chemical elements at station H17(H19) were almost the lowest of all stations. Sediment grain size can influence the MTB motility which is indispensable for the metabolism and survival of MTB. Relative low concentrations of nutrients appear more favorable for MTB and Cu, Co and Zn inhibit the motility of MTB. These comprehensive factors can make a contribution to the negative correlation between MTB abundance and median sediment grain size.

The hypervariable region V3–V5 of bacterial 16S rRNA genes was amplified by PCR using the bar-coded universal primers 338F and 806R and then library construction and high-throughput sequencing were performed. High-throughput sequencing showed MTB of the Yellow Sea in summer and winter can be divided into 72 OTUs (26 OTUs belonged to Alphaproteobacteria; 7 Deltaproteobacteria; 38 Nitrospirae). There were 19-46 OTUs at each station. The number of reads was 2447 and 3271 in summer and winter respectively. There were 71-439 reads at each station. The proportion of reads of MTB affiliated to Nitrospirae was approximately 75%. The dominant group of MTB in sediments of the Yellow Sea continent was Nitrospirae.

In sediments of continent shelf of East China Sea, MTB distributed in both near-shore and far off-shore stations. The average abundance of MTB was 290 ind./dm³ and 590 ind./dm³ in 2014 and 2016. The highest abundance in 2014 was 11,000 ind./dm³ at station 6-5 and the highest abundance in 2016 was 6,500 ind./dm³ at station DH4-4. These two stations were adjacent. The dominant morphology of MTB at near-shore stations was coccoid while that at far off-shore stations was coccoid and rod-shaped. The types of sediments distribute were paralleled with coastline and sediment in near-shore region is clay which composed with smaller particles while that in far off-shore region is sand which is composed with larger particles. MTB abundance was influenced by sediment type and sediment grain size and thus MTB abundance was higher at near-shore region and lower at far off-shore region.

This is the first systematic report of spatial and temporal distribution and diversity of MTB in sediments of a continental shelf and propose that sediment grain size is the most important factor which influences MTB abundance and explain the mechanism. Knowledge of the distribution of MTB on the continental shelf of the Yellow Sea may serve as a general guideline to investigate the locations of MTB in seafloor habitats.

第一章  引言. 1

1.1 趋磁细菌的定义与特征. 1

1.2 趋磁细菌的形态. 1

1.3 趋磁细菌的磁小体. 2

1.3.1 铁氧型磁小体与铁硫型磁小体. 3

1.3.2 磁小体链. 4

1.3.3 磁小体的合成. 4

1.3.4 磁小体的膜. 6

1.4 趋磁细菌的趋性运动. 6

1.4.1 趋南与趋北. 6

1.4.2 极性趋磁性与轴向趋磁性. 7

1.4.3 趋磁趋氧性的机制. 7

1.4.4 趋光性. 9

1.5 趋磁细菌生态分布. 9

1.6 趋磁细菌的系统发育多样性. 11

1.6.1 α-变形菌纲. 11

1.6.2 γ-变形菌纲. 12

1.6.3 δ-变形菌纲. 12

1.6.4 硝化螺旋菌门. 13

1.6.5 其他类群. 14

1.7 趋磁细菌的研究手段. 14

1.7.1 趋磁细菌的检测与富集. 14

1.7.2 趋磁细菌的观察. 17

1.7.3 高通量测序技术在趋磁细菌多样性研究中的应用. 18

1.8 趋磁细菌的研究意义. 18

1.9本论文的研究内容与意义. 20

第二章  材料与方法. 22

2.1 样品采集. 22

2.1.1 采样海域. 22

2.1.2 采样站位布设. 22

2.1.3 沉积物的获取与趋磁细菌的收集. 23

2.2 趋磁细菌的计数、形态观察与磁小体成分测定. 26

2.3 趋磁细菌遗传多样性分析. 26

2.3.1 提取沉积物中微生物DNA 26

2.3.2 测序与结果分析. 27

2.4 环境因子的测定. 28

第三章  黄海大陆架沉积物趋磁细菌形态与分布及影响因素. 29

3.1 趋磁细菌形态与趋性. 29

3.2 磁小体形态与化学成分. 30

3.3 垂直分布. 30

3.4 水平分布. 31

3.5 温度. 35

3.6 氧化还原电位. 35

3.7 化学元素浓度. 36

3.7.1 TC含量. 36

3.7.2 TN含量. 36

3.7.3 TS含量. 36

3.7.4 TOC含量. 37

3.7.5 Fe浓度. 37

3.7.6 Mn浓度. 37

3.8 沉积物粒度. 41

3.9 讨论. 41

第四章  黄海趋磁细菌的遗传发育多样性. 47

4.1 夏季测序结果. 47

4.2 冬季测序结果. 47

4.3 相似序列. 54

4.4 讨论. 57

第五章  东海大陆架沉积物趋磁细菌形态与分布及影响因素. 60

5.1 趋磁细菌形态与趋性. 60

5.2 磁小体形态与化学成分. 60

5.3 水平分布. 62

5.4 化学元素浓度. 67

5.4.1 TC含量. 67

5.4.2 TN含量. 67

5.4.3 TS含量. 67

5.4.4 TOC含量. 67

5.4.5 Fe浓度. 67

5.4.6 Mn浓度. 68

5.5 沉积物粒度. 68

5.6 讨论. 68

5.7 黄、东海大陆架沉积物趋磁细菌的比较. 70

5.7.1 趋磁细菌形态与趋性. 70

5.7.2 分布. 70

第六章  结论、创新点与展望. 72

6.1 结论. 72

6.2 创新点. 73

6.3 展望. 73

参考文献. 74

致  谢. 87

作者简历及攻读学位期间发表的学术论文与研究成果. 88