|本期目录/Table of Contents|

[1]李祎,杨彩云,郑天凌.自然环境中细菌的生存方式及其群落特征[J].应用与环境生物学报,2013,19(04):553-560.[doi:10.3724/SP.J.1145.2013.00553]
 LI Yi,YANG Caiyun,ZHENG Tianling.Bacterial Survival Modes and Community Characteristics in Natural Environment[J].Chinese Journal of Applied & Environmental Biology,2013,19(04):553-560.[doi:10.3724/SP.J.1145.2013.00553]
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自然环境中细菌的生存方式及其群落特征()
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《应用与环境生物学报》[ISSN:1006-687X/CN:51-1482/Q]

卷:
19卷
期数:
2013年04期
页码:
553-560
栏目:
综述
出版日期:
2013-08-25

文章信息/Info

Title:
Bacterial Survival Modes and Community Characteristics in Natural Environment
作者:
李祎杨彩云郑天凌
(1厦门大学生命科学学院,滨海湿地生态系统教育部重点实验室 厦门 361005)
(2厦门大学近海海洋环境科学国家重点实验室 厦门 361005)
Author(s):
LI Yi YANG Caiyun ZHENG Tianling
(1Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361005, China)
(2State Key Laboratory for Marine Environmental Sciences, Xiamen University, Xiamen 361005, China)
关键词:
自然环境细菌生存方式细菌群落结构生态功能
Keywords:
ecological environment bacterial survival mode bacterial community structure ecological function
分类号:
Q938
DOI:
10.3724/SP.J.1145.2013.00553
文献标志码:
A
摘要:
细菌在环境中是以群落的形式存在的,群落中的细菌有多种生存方式. 当处于适宜的环境中,细菌通过互作而快速生长,而营养物质的消耗又造成细菌之间的竞争. 不同细菌通过复杂的作用形成的群落容易受到外界环境的影响,并且特殊的功能基因也改变了原有的群落结构. 细菌群落在环境中有着重要的生态功能及理论与应用价值. 本文介绍了细菌的生存方式,结合作者相关研究阐述了细菌群落结构及其生态功能,并予以展望,旨在为细菌群落的深入研究、开发和应用提供参考. 图3 参76
Abstract:
Bacteria in the environment live in communities with multiple survival modes. Bacteria in a suitable environment grow rapidly through cooperation, whereas nutrient consumption cause competition. Bacterial communities are vulnerable to the impact of the external environment, and the special functional gene can also change the community structure. Bacterial communities have important ecological functions in the environment and they are both complex and valuable. This paper, by combining the work of our group with literature, tried to elaborate on bacterial survival modes as well as the formation and ecological function of bacterial communities, to provide a reference for the study of bacterial community and to look into the future direction of this field of research. Fig 3, Ref 76

参考文献/References:

Mckay CP, Friedmann EI, Frankel RB, Bazylinski DA. Magnetotactic bacteria on Earth and on Mars [J]. Astrobiology, 2003, 3 (2): 263-270
Chardin B, Giudici-Orticoni MT, Luca GD, Guigliarelli B, Bruschi M. Hydrogenases in sulfate-reducing bacteria function as chromium reductase [J]. Appl Microbiol Biotechnol, 2003, 63 (3): 315-321
Wang BX, Yang XR, Lu HJ, Zhou YY, Su JQ, Tian Y, Zhang J, Wang G, Zheng TL. A marine bacterium producing protein with algicidal activity against Alexandrium tamarense [J]. Harmful Algae, 2011, 1 (13): 83-88
Tian Y, Liu HJ, Zheng TL, Kwon KK, Kim SJ, Yan CL. PAHs contamination and bacterial communities in mangrove surface sediments of the Jiulong River Estuary, China [J]. Mar Pollut Bull, 2008, 57 (6): 707-715
Harrison F, Paul J, Massey RC, Buckling A. Interspecific competition and siderophore-mediated cooperation in Pseudomonas aeruginosa [J]. ISME J, 2007, 2 (1): 49-55
West SA, Diggle SP, Buckling A, Gardner A, Griffin AS. The social lives of microbes [J]. Annu Rev Ecol Evol Syst, 2007, 38: 53-77
Griffin AS, West SA, Buckling A. Cooperation and competition in pathogenic bacteria [J]. Nature, 2004, 430 (7003): 1024-1027
He Z, Kan J, Mansfeld F, Angenent LT, Nealson KH. Self-sustained phototrophic microbial fuel cells based on the synergistic cooperation between photosynthetic microorganisms and heterotrophic bacteria [J]. Environ Sci Technol, 2009, 43 (5): 1648-1654
Taga ME, Bassler BL. Chemical communication among bacteria [J]. PNAS, 2003, 100 (l2): 14549-14554
Stecher B, Robbiani R, Walker AW, Westendorf AM, Barthel M, Kremer M, Chaffron S, Macpherson AJ, Buer J, Parkhill J. Salmonella enterica serovar typhimurium exploits inflammation to compete with the intestinal microbiota [J]. PLoS Biol, 2007, 5 (10): 2177-2189
Brockhurst MA, Buckling A, Racey D, Gardner A. Resource supply and the evolution of public-goods cooperation in bacteria [J]. BMC Biol, 2008, 6 (1): 20
Frank SA. Foundations of Social Evolution [M]. Princeton: Princeton University Press, 1998
West SA, Buckling A. Cooperation, virulence and siderophore production in bacterial parasites [J]. Proc R Soc London B: Biol Sci, 2003, 270 (1510): 37-44
Harrison F, Browning LE, Vos M, Buckling A. Cooperation and virulence in acute Pseudomonas aeruginosa infections [J]. BMC Biol, 2006, 4 (1): 21
Cherif M, Loreau M. Stoichiometric constraints on resource use, competitive interactions, and elemental cycling in microbial decomposers [J]. Am Nat, 2007, 169 (6): 709-724
Chow SS, Wilke CO, Ofria C, Lenski RE, Adami C. Adaptive radiation from resource competition in digital organisms [J]. Science, 2004, 305 (5680): 84-86
Be’er A, Zhang HP, Florin EL, Payne SM, Ben-Jacob E, Swinney HL. Deadly competition between sibling bacterial colonies [J]. PNAS, 2009, 106 (2): 428-433
Tsuno H, Hidaka T, Nishimura F. A simple biofilm model of bacterial competition for attached surface [J]. Water Res, 2002, 36 (4): 996-1006
Saikaly PE, Oerther DB. Bacterial competition in activated sludge: theoretical analysis of varying solids retention times on diversity [J]. Microb Ecol, 2004, 48 (2): 274-284
Behkam B, Sitti M. Bacterial flagella-based propulsion and on/off motion control of microscale objects [J]. Appl Phys Lett, 2007, 90 (2): 23902-23903
Sokolov A, Aranson IS, Kessler JO, Goldstein RE. Concentration dependence of the collective dynamics of swimming bacteria [J]. Phys Rev Lett, 2007, 98 (15): 158102
Pham VD, Shebelut CW, Diodati ME, Bull CT, Singer M. Mutations affecting predation ability of the soil bacterium Myxococcus xanthus [J]. Microbiology, 2005, 151 (6): 1865-1874
An D, Danhorn T, Fuqua C, Parsek MR. Quorum sensing and motility mediate interactions between Pseudomonas aeruginosa and Agrobacterium tumefaciens in biofilm cocultures [J]. PNAS, 2006, 103 (10): 3828-3833
Turnbull GA, Morgan JAW, Whipps JM, Saunders JR. The role of bacterial motility in the survival and spread of Pseudomonas fluorescens in soil and in the attachment and colonisation of wheat roots [J]. FEMS Microbiol Ecol, 2006, 36 (1): 21-31
Lennon JT, Jones SE. Microbial seed banks: the ecological and evolutionary implications of dormancy [J]. Nat Rev Microbiol, 2011, 9 (2): 119-130
Oliver JD. The viable but nonculturable state in bacteria [J]. J Microbiol, 2005, 43 (1): 93-100
Oliver JD. The viable but nonculturable state and cellular resuscitation [A]. Microbial Biosystems: New Frontiers [C]. Atlantic Canada Society for Microbial Ecology, Halifax, Canada, 2000. 723-730
Oliver JD. Viable but nonculturable bacteria in food environments [A]. Food Borne Pathogens: Microbiology and Molecular Biology [C]. Norfolk: Horizon Scientific Press, 2005. 99-112
Gunasekera TS, Sørensen A, Attfield PV, Sørensen SJ, Veal DA. Inducible gene expression by nonculturable bacteria in milk after pasteurization [J]. Appl Environ Microbiol, 2002, 68 (4): 1988-1993
Gong XC, Liu ZS, Guo P, Chi CQ, Chen J, Wang XB, Tang YQ, Wu XL, Liu CZ. Bacteria in crude oil survived autoclaving and stimulated differentially by exogenous bacteria [J]. PloS ONE, 2012, 7 (9): e40842
Sonia RV, Richard MP, William GW. Strategies for culture of unculturable bacteria [J]. FEMS Microbiol Lett, 2010, 309: 1-7
Wang H, Laughinghouse HD, Anderson MA, Chen F, Willliams E, Place AR, Zmora O, Zohar Y, Zheng TL, Hill RT. Novel bacterial isolate from Permian groundwater, capable of aggregating potential biofuel-producing microalga Nannochloropsis oceanica IMET1 [J]. Appl Environ Microbiol, 2012, 78 (5): 1445-1453
Bhaya D, Grossman AR, Steunou AS. Population level functional diversity in a microbial community revealed by comparative genomic and metagenomic analyses [J]. ISME J, 2007, 1 (8): 703-713
Tang YQ, Li Y, Zhao JY, Chi CQ, Huang LX, Dong HP, Wu XL. Microbial communities in long-term, water-flooded petroleum reservoirs with different in situ temperatures in the Huabei oilfield, China [J]. PloS ONE, 2012, 7 (3): e33535
Wang X, Gong L, Liang S, Han X, Zhu C, Li Y. Algicidal activity of rhamnolipid biosurfactants produced by Pseudomonas aeruginosa [J]. Harmful Algae, 2005, 4 (2): 433-443
杨小茹, 苏建强, 郑小伟, 周月霞, 田蕴, 宁修仁, 郑天凌. 基于分子技术的 1 株产毒藻藻际细菌多样性分析[J]. 环境科学, 2009, 30 (1): 271-279 [Yang XR, Su JQ, Zheng XW, Zhou YX, Tian Y, Ning XR, Zheng TL. 16S rDNA clone library analysis of microbial diversity associated with the PSP-producing dinoflagellate Alexandrium tamarense [J]. Environ Sci, 2009, 30 (1): 271-279]
刘慧杰, 杨彩云, 田蕴, 林光辉, 郑天凌. 基于PCR-DGGE 技术的红树林区微生物群落结构[J]. 微生物学报, 2010, 50 (7): 923-930 [Liu HJ, Yang CY, Tian Y, Lin GH, Zheng TL. Analysis of microbial community structure in mangrove sediments by PCR-DGGE technique [J]. Acta Microbiol Sin, 2010, 50 (7): 923-930]
Pettersson M, Bååth E. Temperature-dependent changes in the soil bacterial community in limed and unlimed soil [J]. FEMS Microbiol Ecol, 2006, 45 (1): 13-21
Yoshie S, Makino H, Hirosawa H, Shirotani K, Tsuneda S, Hirata A. Molecular analysis of halophilic bacterial community for high-rate denitrification of saline industrial wastewater [J]. Appl Microbiol Biotechnol, 2006, 72 (1): 182-189
Zeglin LH, Dahm CN, Barrett JE, Gooseff MN, Fitpatrick SK, Takacs-Vesbach CD. Bacterial community structure along moisture gradients in the parafluvial sediments of two ephemeral desert streams [J]. Microb Ecol, 2011, 61 (3): 543-556
Xiong J, Wu L, Tu S, Van Nostrand JD, He Z, Zhou J, Wang G. Microbial communities and functional genes associated with soil arsenic contamination and the rhizosphere of the arsenic-hyperaccumulating plant Pteris vittata L. [J]. Appl Environ Microbiol, 2010, 76 (21): 7277-7284
陈明霞, 李和阳, 李刚, 郑天凌, 焦昆, 韩永胜. 深圳海域弧菌种类组成, 数量分布及其与环境因子的关系研究[J]. 海洋学报, 2011, 32 (5): 117-126 [Chen MX, Li HY, Li G, Zheng TL, Jiao K, Han YS. The study on the diversity and distribution of vibrios and the correlation between them and their ambient environmental factors in Shenzhen coastal waters [J]. Acta Oceanol Sin, 2011, 32 (5): 117-126]
Hong YG, Yin B, Zheng TL. Diversity and abundance of anammox bacterial community in the deep-ocean surface sediment from equatorial Pacific [J]. Appl Microbiol Biotechnol, 2011, 89 (4): 1233-1241
李祎, 杨彩云, 李东, 田蕴, 郑天凌. 厦门海域2011年中肋骨条藻和血红哈卡藻藻华期间细菌群落结构变化[J]. 微生物学报, 2012, 52 (10): 1268-1281 [Li Y, Yang CY, Li D, Tian Y, Zheng TL. Dynamics of bacterial community during the bloom caused by Skeletonema costatum and Akashiwo sanguinea in Xiamen sea area [J]. Acta Microbiol Sin, 2012, 52 (10): 1268-1281]
Indest KJ, Crocker FH, Athow RA. TaqMan polymerase chain reaction method for monitoring RDX-degrading bacteria based on the xplA functional gene [J]. J Microbiol Methods, 2007, 68 (2): 267-274
Borodina E, Cox MJ, Mcdonald IR, Murrell JC. Use of DNA-stable isotope probing and functional gene probes to investigate the diversity of methyl chloride-utilizing bacteria in soil [J]. Environ Microbiol, 2005, 7 (9): 1318-1328
Burke C, Steinberg P, Rusch D, Kjelleberg S, Thomas T. Bacterial community assembly based on functional genes rather than species [J]. PNAS, 2011, 108 (34): 14288-14293
Shokralla S, Spall JL, Gibson JF, Hajibabaei M. Next-generation sequencing technologies for environmental DNA research [J]. Mol Ecol, 2012, 21 (8): 1794-1805
Rinta-Kanto JM, Bürgmann H, Gifford SM, Sun S, Sharma S, Del Valle DA, Kiene RP, Moran MA. Analysis of sulfur-related transcription by Roseobacter communities using a taxon-specific functional gene microarray [J]. Environ Microbiol, 2011, 13 (2): 453-467
He Z, Deng Y, Van Nostrand JD, Tu Q, Xu M, Hemme CL, Li X, Wu L, Gentry TJ, Yin Y. GeoChip 3.0 as a high-throughput tool for analyzing microbial community composition, structure and functional activity [J]. ISME J, 2010, 4 (9): 1167-1179
Werner JJ, Knights D, Garcia ML, Scalfone NB, Smith S, Yarasheski K, Cummings TA, Beers AR, Knight R, Angenent LT. Bacterial community structures are unique and resilient in full-scale bioenergy systems [J]. PNAS, 2011, 108 (10): 4158-4163
Kostka JE, Prakash O, Overholt WA, Green SJ, Freyer G, Canion A, Delgardio J, Norton N, Hazen TC, Huettel M. Hydrocarbon-degrading bacteria and the bacterial community response in Gulf of Mexico beach sands impacted by the Deepwater Horizon oil spill [J]. Appl Environ Microbiol, 2011, 77 (22): 7962-7974
Zeng YX, Zou Y, Chen B, Grebmeier JM, Li H, Yu Y, Zheng TL. Phylogenetic diversity of sediment bacteria in the northern Bering Sea [J]. Polar Biol, 2011, 34 (6): 907-919
Tuzen M, Saygi KO, Soylak M. Solid phase extraction of heavy metal ions in environmental samples on multiwalled carbon nanotubes [J]. J Hazard Mat, 2008, 152 (2): 632-639
Ma M, Feng Z, Guan C, Ma Y, Xu H, Li H. DDT, PAH and PCB in sediments from the intertidal zone of the Bohai Sea and the Yellow Sea [J]. Mar Pollut Bull, 2001, 42 (2): 132-136
Sandaa RA, Torsvik V, Enger, Daae FL, Castberg T, Hahn D. Analysis of bacterial communities in heavy metal-contaminated soils at different levels of resolution [J]. FEMS Microbiol Ecol, 2006, 30 (3): 237-251
Hazen TC, Dubinsky EA, Desantis TZ, Andersen GL, Piceno YM, Singh N, Jansson JK, Probst A, Borglin SE, Fortney JL. Deep-sea oil plume enriches indigenous oil-degrading bacteria [J]. Science, 2010, 330 (6001): 204-208
丛利泽, 董磊, 谢忠, 郑天凌. 基于微生物技术的厨余垃圾资源化研究[J]. 厦门大学学报, 2010, 49 (1): 134-138 [Cong LZ, Dong L, Xie Z, Zheng TL. Study on the re-utilization of food wastes based on microbial technique [J]. J Xiamen Univ (Nat Sci), 2010, 49 (1): 134-138]
Liang YT, Van Nostrand JD, Deng Y, He ZL, Wu L, Zhang X, Li G, Zhou JZ. Functional gene diversity of soil microbial communities from five oil-contaminated fields in China [J]. ISME J, 2010, 5 (3): 403-413
Liu HJ, Yang CY, Tian Y, Lin GH, Zheng TL. Screening of PAH-degrading bacteria in a mangrove swamp using PCR-RFLP [J]. Mar Pollut Bull, 2010, 60 (11): 2056-2061
吕意华, 田蕴, 郑天凌. 生物组学在污染环境微生物修复研究中的应用[J]. 微生物学报, 2011, 51 (5): 579-585 [Lü YH, Tian Y, Zheng TL. The application of “omics” in the bioremediation of polluted environment [J]. Acta Microbiol Sin, 2011, 51 (5): 579-585]
Bai SJ, Li JW, He ZL, Van Nostrand JD, Tian Y, Zhou JZ, Zheng TL. GeoChip-based analysis of the functional gene diversity and metabolic potential of microbial communities in different mangrove habitats [J]. Appl Microbiol Biotechnol, 2012, DOI 10.1007/s00253-012-4496-z
王新, 周艳艳, 郑天凌. 海洋细菌生态学的若干前沿课题及其研究新进展[J]. 微生物学报, 2010, 50 (3): 291-297 [Wang X, Zhou YY, Zheng TL. Recent advances in mar ine bacter ial ecology-a review [J]. Acta Microbiol Sin, 2010, 50 (3): 291-297]
王新, 李志江, 郑天凌. 海洋浮游细菌在东海藻华高发区的分布与活性[J]. 环境科学, 2010, 31 (2): 287-295. [Wang X, Li ZJ, Zheng TL. Distribution and activity of marine bacterioplankton at frequent HAB area of east China sea [J]. Environ Sci, 2010, 31 (2): 287-295]
Anderson DM. Turning back the harmful red tide [J]. Nature, 1997, 388 (6642): 513-514
郑天凌, 吕静琳, 周艳艳, 苏建强, 杨小茹, 张金龙, 田蕴, 熊小京, 章军, 蔡明刚. 海洋有害藻华调控功能菌的发现与研究[J].厦门大学学报: 自然科学版, 2011, 50 (2): 445-454 [Zheng TL, Lü JL, Zhou YY, Su JQ, Yang XR, Zhang JL, Tian Y, Xiong XJ, Zhang J, Cai MG. Advance in study on microbial control of harmful algae blooms exploitation and research on marine algicidal bacteria [J]. J Xiamen Univ (Nat Sci), 2011, 50 (2): 445-454]
Malmstrom RR, Kiene RP, Cottrell MT, Kirchman DL. Contribution of SAR11 bacteria to dissolved dimethylsulfoniopropionate and amino acid uptake in the North Atlantic ocean [J]. Appl Environ Microbiol, 2004, 70 (7): 4129-4135
Anderson DM, Cembella AD, Hallegraeff GM. Progress in understanding harmful algal blooms: paradigm shifts and new technologies for research, monitoring, and management [J]. Annu Rev Mar Sci, 2012, (4): 143-176
Di HJ, Cameron KC, Shen JP, Winefield CS, O’callaghan M, Bowatte S, He JZ. Ammonia-oxidizing bacteria and archaea grow under contrasting soil nitrogen conditions [J]. FEMS Microbiol Ecol, 2010, 72 (3): 386-394
Chon K, Chang JS, Lee E, Lee J, Ryu J, Cho J. Abundance of denitrifying genes coding for nitrate (narG), nitrite (nirS), and nitrous oxide (nosZ) reductases in estuarine versus wastewater effluent-fed constructed wetlands [J]. Ecol Eng, 2011, 37 (1): 64-69
Witt V, Wild C, Anthony K, Diaz-Pulido G, Uthicke S. Effects of ocean acidification on microbial community composition of, and oxygen fluxes through, biofilms from the Great Barrier Reef [J]. Environ Microbiol, 2011, 13 (11): 2976-2989
原雅纬, 傅莲英, 刘国生, 郑天凌. 海水养殖沉积环境细菌多样性PCR-DGGE分析[J]. 河南师范大学学报: 自然科学版, 2010, 38 (5): 150-166 [Yuan YW, Fu LY, Liu GS, Zheng TL. Bacterial diversity in sediments of aquaculture environment using PCR-DGGE [J]. J Henan Norm Univ (Nat Sci), 2010, 38 (5): 150-166]
郑天凌, 陈瑛, 李福东, 蔡立哲. 控制对虾弧菌病药物的实验研究[J]. 水产学报, 1994, 18 (3): 215-220 [Zheng TL, Chen Y, Li FD, Cai LZ. Experimental studies on the controlling of effective drugs towards the prawn vibriosis [J]. J Fish China, 1994, 18 (3): 215-220]
蔡莹, 李志江, 田蕴, 郑天凌. 虾池沉积物细菌多样性分析和若干可培养技术的优化探讨[J]. 厦门大学学报(自然科学版), 2010, 49 (5): 731-737 [Cai Y, Li ZJ, Tian Y, Zheng TL. Bacterial diversity in aquaculture environment and optimization of culturing technique [J]. J Xiamen Univ (Nat Sci), 2010, 49 (5): 731-737]
Celik I, Ortasa I, Kilic S. Effects of compost, mycorrhiza, manure and fertilizer on some physical properties of a Chromoxerert soil [J]. Soil Tillage Res, 2004, 78 (1): 59-67
Wagner SC. Biological Nitrogen Fixation [J]. Nat Educ Knowl, 2011, 3 (10): 15

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备注/Memo

备注/Memo:
国家自然科学基金重点项目、面上项目(40930847,31070442)、福建省自然科学基金项目(2012J01150)和海洋公益性行业科研专项(201305016,201305041,201305022)资助
更新日期/Last Update: 2013-08-22