© The Author(s) 2011. This article is published with open access at Springerlink.com csb.scichina.com www.springer.com/scp

Letter

SPECIAL TOPICS:

Geobiology February 2011 Vol.56 No.6: 476–478

doi: 10.1007/s11434-010-4275-0

DMTB: A comprehensive online resource of 16S rRNA genes, ecological metadata, oligonucleotides, and magnetic properties of magnetotactic bacteria

LIN Wei1,2, LI Bi1,2 & PAN YongXin1,2

1 Paleomagnetism and Geochronology Laboratory, Key Laboratory of the Earth’s Deep Interior, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing 100029, China;

2 France-China Bio-Mineralization and Nano-Structures Laboratory, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing 100029, China

Magnetotactic bacteria (MTB) are of interest in microbiology, biomineralization, advanced magnetic materials, and bio-geo-sciences because of their ability to form highly ordered intracellular magnetic minerals. Great strides for MTB studies have been made in the past four decades. In this paper we complied the first internet-accessible database for MTB, Database of Magnesto-tactic Bacteria (DMTB). It contains information of 16S rRNA gene sequences, corresponding ecological metadata, oligonucleo-tides, and magnetic properties of MTB. The comprehensive information contained in DMTB will provide a very useful data re-source for researchers from different disciplines. The website of DMTB is at http://database.biomnsl.com/.

magnetotactic bacteria, biomineralization, database

Citation: Lin W, Li B, Pan Y X. DMTB: A comprehensive online resource of 16S rRNA genes, ecological metadata, oligonucleotides, and magnetic properties of magnetotactic bacteria. Chinese Sci Bull, 2011, 56: 476−478, doi: 10.1007/s11434-010-4275-0

Magnetotactic bacteria (MTB) can sense the Earth’s mag-netic field and navigate the oxic-anoxic transition zone in chemically stratified environments through intracellular organelles termed magnetosomes [1]. Magnetosomes are ferrimagnetic nano-sized iron minerals, magnetite (Fe3O4) or greigite (Fe3S4), that are surrounded by a lipid bilayer membrane, and are arranged into one or more chains. Be-cause of their distinctive genetic control on the synthesis of magnetosomes, MTB have served as a model for under-standing biologically controlled mineralization processes [1]. The superior crystalline structure and uniform grain size (35–120 nm) make magnetosomes potentially novel bioma-terials for a number of applications. Moreover, given their widespread distribution in fresh, brackish and marine waters, and their production of iron minerals, MTB may play signifi-cant roles in geological iron and sulfur cycling, as well as in bulk magnetism of sediments [2].

In the past decades, research efforts from various fields have greatly advanced our understanding of MTB, especially with regard to tractable genetic systems and genome analyses of several pure cultures, morphological and molecular *Corresponding author (email: yxpan@mail.iggcas.ac.cn)

diversity and ecology of uncultivated MTB, and magnetic properties of MTB cells (for a recent review see [3]). Based on phylogenetic results, all currently known MTB are clas-sified within the Proteobacteria and Nitrospirae phyla. More than two hundred 16S rRNA gene sequences of MTB have been reported from more than 30 sampling locations, and 20 probes have been designed for identification of MTB through fluorescence in situ hybridization (FISH). Because magnetic approaches are fast, effective, and nondestructive in distinguishing bacterial crystals from abiogenic magnetic minerals in different environments, many magnetic methods have been applied. Currently, more than 600 articles con-cerning MTB have been published in peer-reviewed jour-nals. The rapidly-growing data on MTB are stimulating broadening interdisciplinary studies in such fields as global biogeography, comparative genomics, evolutionary analysis, and paleoenvironmental research. However, to our knowl-edge, no database specifically focused on MTB has yet been established. The great amount of data in different publica-tions and several general databases (e.g. GenBank) make it difficult and time-consuming to screen and compile data for multi-disciplinary studies. Thus, a comprehensive and easily accessible database of MTB is needed for multi-disciplinary

Lin W, et al. Chinese Sci Bull February (2011) Vol.56 No.6 477

scientists. Through the present study, we developed the Database of

Magnetotactic Bacteria (DMTB) containing published 16S rRNA gene sequences, ecological metadata, oligonucleotides (PCR primers and FISH probes), and magnetic properties of MTB. This database provides easy and fast access to com-prehensive information on MTB.

For compiling 16S rRNA gene sequences, a complex combination of keywords [(SSU OR 16S OR small subunit) AND (rRNA OR rDNA OR ribosomal RNA OR rRNA gene) AND (magnetic bacterium OR magnetotactic bacte-rium OR magneto*)] was used to search available se-quences in GenBank database. The retrieved sequences were then examined and selected based on their definitions. A total of 264 sequences were selected for the DMTB (up to the end of October, 2009). Seven sequences from the scien-tific literature, which were missing from the above search strategy, were manually added to the DMTB. Among all selected 271 sequences, 23 were defined as uncultivated MTB sequences by submitters; however, our analysis shows low sequence identities (<75%) with known MTB se-quences that were from pure cultures or non-cultured with confirmation by FISH. We marked these sequences as ‘Po-tential MTB’ in the DMTB, and their origins need to be confirmed by further studies. All data for ecological meta-data of sampling sites, oligonucleotides, and magnetic properties were collected from the scientific literature.

Data catalogs of the DMTB are summarized in Figure 1. By the initial release of the DMTB (November, 2009), the database contained 271 16S rRNA gene sequences, envi-ronmental information on 29 sampling sites, 3 sets of spe-cific primers, 20 FISH probes, and 10 entries of magnetic information. The data are accessible through four main in-terfaces: Site Sort, Phylo Sort, Oligonucleotides (PCR prim- ers and FISH probes), and Magnetic Properties.

Because of the rapidly increasing accumulation of se-quence information and ecological metadata, environmental

microbiology has become increasingly more important in this area of research, especially studies on the biogeography of microorganisms [4,5]. In the database, therefore, we pro-vided information of site- and phylogeny-based arrange-ments of 16S rRNA genes of MTB.

Site Sort interface contains a complete list of sampling sites in alphabetical order, listing the country and the num-ber of sequences. The entry of each site name is linked to an individual page containing detailed information about envi-ronmental metadata. Each number of sequence entries con-sists of information on 16S rRNA gene sequences of MTB. Sequence names also are linked to individual FASTA files for each 16S rRNA gene sequence. GenBank accession numbers and references are directed to the corresponding GenBank description interface and PubMed abstracts, re-spectively.

Phylo Sort interface lists taxonomic phyla and classes with which MTB are affiliated. Each entry includes a list of MTB sequence information, which is classified using the Greengenes “classify” utility. Identified MTB belong to six classes, including Alphaproteobacteria (153 sequences), Betaproteobacteria (2 sequences), Gammaproteobacteria (20 sequences), Deltaproteobacteria (65 sequences), Epsi-lonproteobacteria (3 sequences), and Nitrospirales (5 se-quences). Sequence names, GenBank accession numbers, and references in each entry serve as links to specific pages within public databases.

Oligonucleotides interface includes FISH probes and PCR primers specific for MTB. Each entry consists of the oligonucleotide name, target position, sequence, length, degeneracy, G+C content, and basic usage information for probes or primers. The corresponding reference is linked to the PubMed database.

Magnetic Properties interface contains magnetic informa-tion. Each MTB sample entry contains a variety of relevant information, including the Verwey transition temperature (Tv), delta ratio (δFC/δZFC), saturation magnetization (Ms),

Figure 1 The database structure of DMTB. FISH, fluorescence in situ hybridization; Ms, saturation magnetization; Mrs, saturation remanence; Bc, coercive force; and Bcr, coercivity of remanence.

478 Lin W, et al. Chinese Sci Bull February (2010) Vol.56 No.6

saturation remanence (Mrs), coercive force (Bc), coercivity of remanence (Bcr), ratios of Mrs/Ms and Bcr/Bc, and related references.

Search queries of the entire DMTB can be initiated easily with various keywords, such as site name, sequence name, accession number, and the last name of the first author.

In summary, the new DMTB offers an online accessible database, including comprehensive information on 16S rRNA gene sequences, ecological metadata, oligonucleo-tides, and magnetic properties of MTB. This database will be a valuable resource for microbiologists, ecologists, bio- mineralogists, biogeophysicists, and physicists for further study the biogeography, diversity, community structure, evolution, mineralogy, and physical characteristics of MTB.

The DMTB can be accessed freely through the Web at http://database.biomnsl.com/.

We sincerely thank Prof. Long-Fei Wu at CNRS-Marseille, France, for his valuable comments. This work was supported by the Knowledge Innovation Program of the Chinese Academy of Sciences (80912910), the National Natu-ral Science Foundation of China (40821091), and the CAS/SAFEA Interna-tional Partnership Program for Creative Research Teams (KZCX2-YW-T10).

1 Faivre D, Schüler D. Chem Rev, 2008, 108: 4875–4898 2 Pan Y, Deng C, Liu Q, et al. Chinese Sci Bull, 2004, 49: 2563–2568 3 Schüler D. Magnetoreception and Magnetosomes in Bacteria. New

York: Springer Verlag, 2007 4 Martiny J B H, Bohannan B J M, Brown J H, et al. Nat Rev Micro-

biol, 2006, 4: 102–112 5 Green J L, Bohannan B J M, Whitaker R J. Science, 2008, 320:

1039–1043

Open Access This article is distributed under the terms of the Creative commons Attribution License which permits any use, distribution, and reproduction

in any medium, provided the original author(s) and source are credited.

2011 年 第 56 卷 第 1 期：16 ~ 17

www.scichina.com csb.scichina.com

英文版见: Lin W, Li B, Pan Y X. DMTB: A comprehensive online resource of 16S rRNA genes, ecological metadata, oligonucleotides, and magnetic properties of

magnetotactic bacteria. Chinese Sci Bull, 2011, 55, doi: 10.1007/s11434-010-4275-0

快 讯

《中国科学》杂志社 SCIENCE CHINA PRESS

全球趋磁细菌数据库的建立

林巍①②, 李陛①②, 潘永信①②

① 中国科学院地质与地球物理研究所, 中国科学院地球深部重点实验室, 北京 100029;

② 中-法生物矿化与纳米结构联合实验室, 北京 100029

2010-09-13 收稿, 2010-11-05 接受

国家自然科学基金(40821091)、中国科学院知识创新工程青年人才领域前沿项目(80912910)和中国科学院创新团队国际合作伙伴计划

(KZCX2-YW-T10)资助

摘要 趋磁细菌是研究生物矿化的模式微生物. 鉴于磁小体在生物矿化、Fe 生物地球化学循

环、沉积剩磁、环境指示和磁性材料方面的重要性, 趋磁细菌研究已成为微生物学、地球科学

和材料科学共同关注的重要课题. 本文搜集并整理了截至目前全球趋磁细菌的实验观测数据,

建立了首个综合性的趋磁细菌数据库. 数据库包括了已发表的趋磁细菌 16S rRNA 基因序列、

特异性探针、特异性 PCR 引物、磁学性质以及采样地点环境物理化学性质等信息. 数据库为

趋磁细菌的数据共享和学科交叉研究提供了重要平台.

关键词

超磁细菌

生物矿化

数据库

微生物矿化(即微生物参与矿物

形成的过程)是当前国际上最为活跃

的前沿研究方向之一[1]. 微生物矿化

在自然界十分普遍, 根据微生物对矿

物形成调控机制的不同, 可以简单划

分为微生物诱导矿化和微生物控制

矿化 2 种类型[2]. 趋磁细菌是微生物

控制矿化的代表性微生物, 它们是一

类能够沿着磁场方向定向运动的细

菌, 广泛分布在湖泊和海洋环境中[3].

趋磁细菌的显著特征是在细胞内控

制矿化合成纳米级(35~120 nm)的磁

性矿物 , 通常是磁铁矿 (Fe3O4)或胶

黄铁矿(Fe3S4), 被称为磁小体. 磁小

体颗粒粒度均一、化学纯度高、由生

物膜包裹并在细胞内呈链状排列, 它

们在趋磁细菌的生理活动和进化中

发挥重要作用 [3]. 目前, 趋磁细菌已

成为研究生物矿化机制、生物感知地

磁场机理、早期地球或地外生命等重

大科学问题的焦点. 此外, 趋磁细菌

还在元素地球化学循环、沉积物剩

磁、古环境重建和现代生物医学等方

面具有重要的研究价值.

自 20 世纪 70 年代发现趋磁细菌

以来, 中外科学家对趋磁细菌的生态

学、分子生物学、基因组学、磁学等

研究已取得一系列重要进展, 磁小体

在医学和材料学领域也展现出诱人

的应用潜力[2,3]. 截止到 2010 年 3 月,

已发表 600 多篇研究论文; 全世界已

有 7 个国家超过 30 个地点发现趋磁

细菌; 已有 10 余株趋磁细菌在实验

室成功培养; 已公布 200 余条趋磁细

菌的 16S rRNA 基因序列; 已有 5 株

趋磁细菌基本完成全基因组测序 ;

已发表 3 对趋磁细菌特异性 PCR 引

物和 20 个荧光原位杂交(FISH)探针;

对已培养和未培养趋磁细菌也进行

了详细的磁学性质研究. 对趋磁细菌

的研究同时促进了一些新的学科交

叉研究领域的产生, 如趋磁细菌的生

物矿化、趋磁细菌的微生物地理学、

趋磁细菌的比较基因组学与进化分

析, 以及基于化石磁小体的古环境和

古气候重建研究等.

由于趋磁细菌研究所涉及的学

科多、领域广、信息量大, 使得相关

原始数据和科研信息的查找和搜集较

为困难, 耗时且易出错, 这在一定程

度上限制了趋磁细菌研究. 20 世纪 60

年代后期发展起来的数据库技术为综

合信息管理提供了重要保障, 建立多

学科共享的趋磁细菌研究的综合性数

据库不仅必要, 而且可行. 但目前国

际上尚无此类数据库. 最近, 中国科

学院地质与地球物理研究所生物地磁

学与生物矿化实验室系统搜集并整理

了已有的趋磁细菌研究的实验数据 ,

建立了第一个全球综合性趋磁细菌数

据库(database of magnetotactic bacte-

ria, DMTB), 其宗旨就是促进趋磁细

菌研究的信息共享, 及时准确地提供

17

快 讯

趋磁细菌研究的最新进展, 推动趋磁

细菌相关的多学科交叉研究的进步.

图 1 概括了趋磁细菌数据库所

涵盖的主要内容 . 该数据库于 2009

年 10 月 22 日首次发布, 截至 2010

年 3月 28日更新, 数据库的内容已包

括 262 条趋磁细菌 16S rRNA 基因序

列及详细信息、 23 条“暂定趋磁细

菌” (Potential MTB)16S rRNA 基因序

列、30 个采样地点的基本信息和环境

物理化学性质、20 条趋磁细菌的特异

性 FISH 探针、3 对趋磁细菌的特异

性 PCR 引物和 10 组趋磁细菌样品的

详细磁学性质. 数据库所涵盖的主要

内容可通过 4 个主要一级目录 Site

sort, Phylo sort, Oligonucleotides 和

Magnetic properties 获得.

为了方便使用, 本趋磁细菌数据

库支持关键词搜索, 包括地点名称、

序列名称、序列 GenBank 登录号、系

统发育地位、探针名称、引物名称、

菌种名称和参考文献第一作者名等 .

数据库还支持用户递交趋磁细菌相关

信息, 进入网站Submission页面, 下载

数据递交表单(Excel 格式), 填写相关

信息后可直接递交到管理员邮箱. 数

据库还具有用户在线反馈(Feedback)

功能, 用户可向数据库管理员反馈意

见和建议, 用户只需在反馈栏中填写

意见, 点击递交(submit comments)即

可直接发送给数据库管理员.

趋磁细菌数据库将根据趋磁细

菌文献的发表进行及时的更新. 数据

库每年会进行 1~2 次系统升级. 近期

计划添加下列内容: (1) 趋磁细菌研

究方法(protocols), 如趋磁细菌培养

方法、常用培养基成分、未培养趋磁

细菌的收集方法、趋磁细菌 FISH 技

术、用于分子生物学和磁学测量的样

品准备方法以及磁学测量流程等; (2)

北京地区趋磁细菌的光学和电子显

微镜照片; (3) BLAST 搜索同源序列

功能和序列多重比对功能等.

近年来由于微生物生物地理学的

兴起和发展, 微生物的多样性与环境

因素的关系逐渐成为研究的热点 [4,5].

因此, 在本趋磁细菌数据库中, 除了对

趋磁细菌进行系统发育分类(phylo sort)

外, 还依据不同采集地点进行分类(site

sort), 并搜集整理了采集地点的环境

信息, 这为研究趋磁细菌生物地理学

提供了基础数据, 也便于读者全面了

解趋磁细菌样品的环境信息.

本趋磁细菌数据库还提供了其

他常用数据库以及趋磁细菌与生物

矿化研究单位网站的链接. 目前包括

2 个综合性数据库即美国国立生物技

术信息中心 (NCBI)和法国 Magne-fying Genomes Microbial Genome Annotation System (MeGa), 6 个

rRNA相关的数据库和 11个趋磁细菌

与生物矿化研究组网站的链接. 此外,

本数据库还及时发布与趋磁细菌和

生物矿化相关的国内外会议信息.

综上 , 本数据库包含了与趋磁

细菌相关的 16S rRNA 基因序列、细

菌发现地点及环境信息、PCR 特异性

引物、FISH 特异性探针和磁学性质

等 详 细 数 据 和 信 息 , 还 链 接 了

GenBank 数据库和 PudMed 数据库,

构成了一个全面的、非冗余的趋磁细

菌数据库. 趋磁细菌数据库中信息经

过人工检查, 保证了数据的可靠性和

准确性. 该数据库为生物学家、生态

学家、地球物理学家、地质学家、物

理学家、化学家和材料学家研究趋磁

细菌与生物矿化提供了一个快捷而

实用的数据共享 /综合研究的平台 .

根据 CNZZ 数据统计, 趋磁细菌数据

库自 2009 年 10 月 22 日发布至今

(2010 年 3 月 28 日), 已有 17 个国家

或地区 632 位访客访问该网站, 总浏

览量超过 4000 次.

本趋磁细菌数据库的访问网址

为 http://database. biomnsl.com/.

致谢 作者诚挚地感谢法国科研中心马赛结构生物学-微生物学研究所吴龙飞研究员对初稿提出的宝贵意见.

参考文献

1 崔福斋. 生物矿化. 北京: 清华大学出版社, 2007

2 潘永信, 邓成龙, 刘青松, 等. 趋磁细菌磁小体的生物矿化作用和磁学性质研究进展. 科学通报, 2004, 49: 2505−2510

3 Faivre D, Schüler D. Magnetotactic bacteria and magnetosomes. Chem Rev, 2008, 108: 4875−4898

4 Martiny J B H, Bohannan B J M, Brown J H, et al. Microbial biogeography: Putting microorganisms on the map. Nat Rev Microbiol, 2006,

4: 102−112

5 Green J L, Bohannan B J M, Whitaker R J. Microbial biogeography: From taxonomy to traits. Science, 2008, 320: 1039−1043

图 1 趋磁细菌数据库所涵盖的主要内容 FISH, 荧光原位杂交; Ms, 饱和磁化强度, Mrs, 剩余饱和磁化强度; Bc, 矫顽力;

Bcr, 剩磁矫顽力