疣孢菌的生物勘探、分离与鉴定
|
摘要
分子生物学、生物信息学技术及各种组学技术的发展与应用,不仅为微生物资源研究提供了新的技术方法,也为微生物资源研究提供了新的策略与思路。因此,本课题以具有天然产物合成潜力的疣孢菌(Verrucosispora)属放线菌为目标,应用“生物勘探-多样性分析-选择性分离”的策略,获取疣孢菌菌株,为挖掘疣孢菌资源,研究其生态作用奠定基础。
根据疣孢菌属16S rRNA基因的序列特征设计了一对疣孢菌属特异性引物(S-G-Verr-0195-a-S-20和S-G-Verr-1152-a-A-19)。序列水平、模式菌株纯培养物水平的评价显示该引物与疣孢菌属所有种的代表菌株匹配,而与小单孢菌科的其它属模式种都不能匹配,具有属特异性。利用该引物对来自红树林、海洋沉积物的20个样品进行PCR扩增,发现除3个深海沉积物样品外,其余17个样品都有扩增产物。挑选其中的5个阳性样品构建16S rRNA基因文库,进行序列聚类分析,发现所有序列均落在疣孢菌属,超过40%的克隆子可能属于疣孢菌属新种。不但进一步验证了疣孢菌属引物特异性,而且也揭示出这些环境中蕴藏着多样性丰富的疣孢菌。
用9种选择性培养基对PCR检测阳性的10个样品和3个阴性样品进行选择性分离,获得794株放线菌。经疣孢菌特异性PCR快速鉴定,有21株属于疣孢菌属(18株来自MG,3株来自WC)。其中5株具有抗金黄色葡萄球菌活性,3株具有抗耐甲氧西林的金黄色葡萄球菌(MRSA)活性,菌株2603PH03对这两种病原菌生长的抑制率性都很强,分别为91.87%和74.78%。经PKS基因和NRPS基因检测,发现菌株2603PH03与已报道的疣孢菌菌株基因类型不同,显示该菌株具有进一步开发的潜力。
通过多相分类鉴定,菌株234402和菌株2603PH03是分别邻近V.lutea和V.gifhornensis的两个新种,而菌株232076和菌株234606是属于V.sediminis种的不同菌株。
Development and application of molecular biology, bioinformatics and "omics" technologies provides not only new technologies but also new strategies for exploring microbial resources. The primary aim of this study was to isolate members of the genus Verrucosispora that has been proved to be a rich resource of new bioactive compounds, using the strategy of'bioprospecting-biodiversity-selective isolation', highlighting the biotechnological potential and ecological significance of the members of this taxon.
A set of genus-specific oligonucleotide primers was generated based on signatural nucleotides sequences of the16S rRNA genes of Verrucosispora strains deposited in GenBank. In silico and pure culture studies showed that the primers matched perfectly with target sequences of16S rRNA gene of representatives of the genus Verrucosispora. The primers, designated S-G-Verr-0195-a-S-20and S-G-Verr-1152-a-A-18, amplified an≈960bp stretch of16S rRNA genes of Verrucosispora strains, but not those of representatives of other genera classified in the family Micromonosporaceae. Genus-specific amplicons were detected in17out of20community DNA samples prepared from diverse marine sediments and coastal soils. Phylogenetic analysis of over40%of clones derived from5of the samples belonged to novel Verrucosispora species. The primers were also used to confirm the identity of794Verrucosispora-like strains isolated from10positive samples and3negative samples using9selective media. Twenty one isolates,18from the Megas Gialos sediment and3from the Wenchang mangrove sample, were provisionally assigned to the genus Verrucosispora on the basis of colony morphology gave the genus-specific amplification product with primers S-G-Verr-0195-a-S-20and S-G-Verr-1152-a-A-19.
Metabolites of5Verrucosispora strains inhibited Staphylococcus aureus strain SO14, and3out of5strains inhibited MRSA (Methicillin Resistant Staphylococcus aureus) strain9551. The novel candidate species2603PH03was found significant active against these two pathogen strains with inhibition ratio of91.87%and74.78%, respectively. Moreover, this strain was different from other members of the genus Verrucosispora on patterns of PKSs and NRPSs genes, which showed a potential for further research on drug discovery against MRSA.
Polyphasic taxonomic study of strain234402and strain2603PH03gave result in two novel candidate species, near to V. lutea and V. gifhornensis, respectively. Strain232076and strain234606were assigned to the species V. sediminis.
根据疣孢菌属16S rRNA基因的序列特征设计了一对疣孢菌属特异性引物(S-G-Verr-0195-a-S-20和S-G-Verr-1152-a-A-19)。序列水平、模式菌株纯培养物水平的评价显示该引物与疣孢菌属所有种的代表菌株匹配,而与小单孢菌科的其它属模式种都不能匹配,具有属特异性。利用该引物对来自红树林、海洋沉积物的20个样品进行PCR扩增,发现除3个深海沉积物样品外,其余17个样品都有扩增产物。挑选其中的5个阳性样品构建16S rRNA基因文库,进行序列聚类分析,发现所有序列均落在疣孢菌属,超过40%的克隆子可能属于疣孢菌属新种。不但进一步验证了疣孢菌属引物特异性,而且也揭示出这些环境中蕴藏着多样性丰富的疣孢菌。
用9种选择性培养基对PCR检测阳性的10个样品和3个阴性样品进行选择性分离,获得794株放线菌。经疣孢菌特异性PCR快速鉴定,有21株属于疣孢菌属(18株来自MG,3株来自WC)。其中5株具有抗金黄色葡萄球菌活性,3株具有抗耐甲氧西林的金黄色葡萄球菌(MRSA)活性,菌株2603PH03对这两种病原菌生长的抑制率性都很强,分别为91.87%和74.78%。经PKS基因和NRPS基因检测,发现菌株2603PH03与已报道的疣孢菌菌株基因类型不同,显示该菌株具有进一步开发的潜力。
通过多相分类鉴定,菌株234402和菌株2603PH03是分别邻近V.lutea和V.gifhornensis的两个新种,而菌株232076和菌株234606是属于V.sediminis种的不同菌株。
Development and application of molecular biology, bioinformatics and "omics" technologies provides not only new technologies but also new strategies for exploring microbial resources. The primary aim of this study was to isolate members of the genus Verrucosispora that has been proved to be a rich resource of new bioactive compounds, using the strategy of'bioprospecting-biodiversity-selective isolation', highlighting the biotechnological potential and ecological significance of the members of this taxon.
A set of genus-specific oligonucleotide primers was generated based on signatural nucleotides sequences of the16S rRNA genes of Verrucosispora strains deposited in GenBank. In silico and pure culture studies showed that the primers matched perfectly with target sequences of16S rRNA gene of representatives of the genus Verrucosispora. The primers, designated S-G-Verr-0195-a-S-20and S-G-Verr-1152-a-A-18, amplified an≈960bp stretch of16S rRNA genes of Verrucosispora strains, but not those of representatives of other genera classified in the family Micromonosporaceae. Genus-specific amplicons were detected in17out of20community DNA samples prepared from diverse marine sediments and coastal soils. Phylogenetic analysis of over40%of clones derived from5of the samples belonged to novel Verrucosispora species. The primers were also used to confirm the identity of794Verrucosispora-like strains isolated from10positive samples and3negative samples using9selective media. Twenty one isolates,18from the Megas Gialos sediment and3from the Wenchang mangrove sample, were provisionally assigned to the genus Verrucosispora on the basis of colony morphology gave the genus-specific amplification product with primers S-G-Verr-0195-a-S-20and S-G-Verr-1152-a-A-19.
Metabolites of5Verrucosispora strains inhibited Staphylococcus aureus strain SO14, and3out of5strains inhibited MRSA (Methicillin Resistant Staphylococcus aureus) strain9551. The novel candidate species2603PH03was found significant active against these two pathogen strains with inhibition ratio of91.87%and74.78%, respectively. Moreover, this strain was different from other members of the genus Verrucosispora on patterns of PKSs and NRPSs genes, which showed a potential for further research on drug discovery against MRSA.
Polyphasic taxonomic study of strain234402and strain2603PH03gave result in two novel candidate species, near to V. lutea and V. gifhornensis, respectively. Strain232076and strain234606were assigned to the species V. sediminis.
引文
[1]陈宝三,黄春兰,张丽华.土壤全氮测定中消化方法对测定结果的影响[J].热带农业科学,1982,(4)：19-21.
[2]洪葵,谢晴宜编著.药用微生物资源研究技术[M].北京：中国农业大学出版社,2006.
[3]黄春兰.测定土壤有机质的一点改进[J].热作科技通讯,1978,(4)：25.
[4]蒋云霞 郑天凌.红树林土壤微生物的研究：过去、现在、未来[J].微生物学报,2006,46(5)：77-83.
[5]焦瑞身.新世纪微生物学者的一项重要任务-未培养微生物的分离培养[J].生物工程学报,2004,20(5)：641-645.
[6]李翔,秦岭,戴世鲲等.海洋微生物宏基因组工程进展与展望[J].微生物学报,2007,47(3)：548-553.
[7]刘颖.红树林环境具有生物活性共附生微生物群体培养物的研究.海南大学博士学位论文,2010.
[8]鲁如坤.土壤农业化学分析方法[M].北京：中国农业科技出版社：198-199,2000.
[9]聂毅磊,林如,郑永标,等,海绵疣孢菌FIM06031产生的2’-脱氧尿嘧啶核苷[J].中国抗生素杂志,2010,35(6)：426-430
[10]曲直.红树林放线菌的化学分类鉴定.海南大学硕士论文,2009
[11]沈定树,戴冬玲,余素飞,等.金黄色葡萄球菌耐药性分析[J].中国微生态学杂志,2005,17(5)：381-382。
[12]隋金蕾.红树林土壤链霉菌的选择性分离和菌株219820的鉴定.海南大学硕士论文,2010.
[13]王成.文昌红树林根际土壤小单孢菌的分离与菌株211018的鉴定.海南大学硕士论文,2010
[14]王凡.一株红树林稀有放线菌新种的鉴定.华中农业大学硕士论文,2010.
[15]王海龙.红树林细胞毒活性链霉菌061324的分子鉴定及定种.海南大学硕士论文,2009
[16]王平.测定放线菌菌体中氨基酸和单糖的快速方法—薄层层析法[J].微生物通报,1986,13：228-2301.
[17]王蓉.老鼠筋内生放线菌的分离鉴定活性评价及其类群分析.海南大学硕士论文,2008.
[18]王岳坤,洪葵.红树林土壤因子对土壤微生物的影响.热带作物学报.2005,26(3)：109-114.
[19]徐丽华,李文均,刘志恒,等.放线菌系统学——原理、方法及实践[M].北京：科学出版社,pp400-402,2007.
[20]徐平,李文均,高慧英,等.产生芳香环聚酮类天然产物放线菌的分子筛选研究[J].中国抗生素杂志,2005,30(3)：134-137.
[21]徐小雄.23种红树植物根际土壤小双孢菌的选择性分离.海南大学大学硕士论文,2009.
[22]闫莉萍.抗肿瘤活性放线菌的分离筛选及其16S rDNA多样性分析.华南热带农业大学硕士论文,2005.
[23]阎冰.红树林土壤16S rDNA多样性的研究.华中农业大学博士论文,2006.
[24]杨建,洪葵.红树林土壤总DNA不同提取方法比较研究生物技术通报[J].2006a,增刊：366-371.
[25]杨建.红树林土壤总DNA不同提取方法比较研究以及Ⅰ型聚酮合成酶基因检测.华南热带农业大学硕士论文,2006b.
[26]袁干军.红树林放线菌大环内酯化合物产生菌的筛选、产物的分离鉴定及活性研究.海南大学博士学位论文,2010.
[27]曾胤新,陈波,邹扬,等.极地微生物---新天然药物的潜在来源[J].微生物学报,2008,(5)：695-700.
[28]张致平.微生物药物学[M].北京：化学工业出版社,2003.
[29]中国科学院南京土壤研究所主编.土壤理化分析[M].上海：上海科学技术出版社,1978,97-101,114.
[30]朱义明.尼龙膜杂交检测放线菌基因组DNA同源性方法的建立.华南热带农业大学硕士论文,2007
[31]Achtman M, Wagner M. Microbial diversity and the genetic nature of microbial species[J]. Nature Reviews Microbiology,2008,6(6):431-440.
[32]Alm EW, Oerther DB, Larsen N, et al. The oligonucleotide probe database[J]. Appl Environ Microbiol,1996,62:3557-3559.
[33]Amann RI, Ludwig W, et al. Phylogenetic identification and in situ detection of individual microbial cells without cultivation[J]. Microbiol Rev,1995,59(1):143-169.
[34]Angle JS, McGrath SP, Chaney RL. New culture medium containing ionic concentrations of nutrients similar to concentrations found in the soil solution[J]. Appl Environ Microbiol,1991,57:3674-3676.
[35]Antony-Babu S, Stach JE, Goodfellow M. Computer-assisted numerical analysis of colour-group data for dereplication of streptomycetes for bioprospecting and ecological purposes[J]. Antonie Van Leeuwenhoek,2010,97:231-239.
[36]Anzai Y, Okuda T, Watanabe J. Application of the random amplified polymorphic DNA using the polymerase chain reaction for efficient elimination of duplicate strains in microbial screening. Ⅱ. Actinomycetes[J]. JAntibiot (Tokyo),1994,47:183-193.
[37]Ara I, Bakir MA, Kudo T, et al. Pseudosporangium ferrugineum gen. nov., sp. nov., a new member of the family Micromonosporaceae[J]. Int J Syst Evol Microbiol,2008a, 58:1644-1652.
[38]Ara I, Bakir MA, Kudo T. Transfer of Catellatospora koreensis Lee et al.2000 as Catelliglobosispora koreensis gen. nov., comb. nov. and Catellatospora tsunoense Asano et al.1989 as Hamadaea tsunoense gen. nov., comb, nov., and emended description of the genus Catellatospora Asano and Kawamoto 1986 emend. Lee and Hah 2002[J]. Int J Syst Evol Microbiol,2008b,58:1950-1960.
[39]Ara I, Kudo T. Luedemannella gen. nov., a new genus of the family Micromonosporaceae and description of Luedemannella helvata sp. nov. and Luedemannella flava sp. nov[J]. J Gen Appl Microbiol,2007a,53:39-51.
[40]Ara I, Kudo T. Krasilnikovia gen. nov., a new member of the family Micromonosporaceae and description of Krasilnikovia cinnamonea sp. nov[J]. Actinomycetologica,2007b,21:1-10.
[41]Ara I, Kudo T. Three novel species of the genus Catellatospora, Catellatospora chokoriensis sp. nov., Catellatospora coxensis sp. nov. and Catellatospora bangladeshensis sp. nov, and transfer of Catellatospora citrea subsp.
[42]Methionotrophica Asano and Kawamoto 1988 to Catellatospora methionotrophica sp. nov., comb. nov[J]. Int JSyst Evol Microbiol,2006,56:393-400.
[43]Ariesyady HD, Ito T, et al. Phylogenetic and functional diversity of propionate-oxidizing bacteria in an anaerobic digester sludge[J]. Appl. Microbiol. Biotechnol^ 2007, 75:673-683.
[44]Arnold L. Demain, Foreword in "Microbial Diversity and Bioprospecting". Ed. Bull AT, ASM Press, Washington, D.C.,2004.
[45]Asano K, Kawamoto I. Catellatospora, a new genus of the Actinomycetales[J]. Int J Syst Bacteriol,1986,36:512-517.
[46]Atalan E, GP Manfio, AC Ward, et al. Biosystematic studies on novel streptomycetes from soil. Antonie van Leeuwenhoek,2000,77:337-353.
[47]Avarre JC, De Lajudie P, Bena G. Hybridization of genomic DNA to microarrays:a challenge for the analysis of environmental samples[J]. J. Microbiol. Methods,2007, 57:269-278.
[48]Ayuso A, Clark D, Gonzalez I, et al. A novel actinomycete strain dereplication approach based on the diversity of polyketide synthase and nonribosomal peptide synthetase biosynthetic[J]. Appl Microbiol Biotechnol,2005,67:795-806.
[49]Bains W. Company strategies for using bioinformatics[J]. Trends Biotechnol.1996,14: 312-317.
[50]Baltz R H. Antimicrobials from Actinomycetes:Back to the Future[J]. Microbe,2007, 2(3):125-131.
[51]Bartscht K, Cypionka H, Overmann J. Evaluation of cell activity and of methods for the cultivation of bacteria from a natural lake community[J]. FEMS Microbiol Ecol,1999, 28:249-259.
[52]Bcrcczky K, Laatsch H, Wagner Dobler I, et al. Cluster analysis as selection and dereplication tool for identification of new natural compounds from large sample sets[J]. Chem Biodiv,2006,3:622-634.
[53]Berdy J. Bioactive microbial metabolites[J]. JAntibiot,2005,58:1-26
[54]Bister B, Bischoff D, Strobele M, et al. Abyssomicin C-A polycyclicantibiotic from a marine Verrucosispora strain as an inhibitor of the p-aminobenzoic acid/ tetrahydrofolate biosynthesis pathway [J]. Angew Chem Int Ed Engl,2004,43: 2574-2576.
[55]Bode HB, Bethe B, Hofs R, et al. Big effects from small changes:possible ways to explore nature's chemical diversity[J]. Chembiochem,2002,3:619-627.
[56]Bond PL, Smriga SP, Banfield JF. Phylogeny of microorganisms populating a thick, subaerial, predominantly lithotrophic biofilm at an extreme acid mine drainage site[J]. Appl Environ Microbiol,2000,6:3842-3849.
[57]Bouck A, Vision T. The molecular ecologist's guide to expressed sequence tags[J]. Molecular Ecology,2007,16:907-924.
[58]Brandao P. Dereplication for biotechnology screening:PyMS analysis and PCR-RFLP-SSCP (PRS) profiling of 16S rRNA genes of marine and terrestrial actinomycetes [J]. Appl Microbiol Biotechnol,2002,58:77-83.
[59]Bredholdt H, Tjaervik E, Johnsen G, et al. Actinomycetes from sediments in the Trondheim fjord, Norway:diversity and biological activity[J]. Mar Drugs,2008,6: 12-24
[60]Brosius J, Palmer ML, Kennedy PJ, et al. Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli [J]. Proc Natl Acad Sci USA,1978,75: 4801-4805.
[61]Bruns A, et al. Cyclic AMP and acyl homoserine lactones increase the cultivation efficiency of heterotrophic bacteria from the central Baltic Sea[J]. Appl. Environ. Microbiol,2002,68:3978-3987.
[62]Bull AT, Stach J. Marine actinobacteria:new opportunities for natural product search and discovery[J]. Trends Microbiol,2007,15:491-499.
[63]Bull AT, Ward AC, Goodfellow M. Search and discovery strategies for biotechnology: the paradigm shift[J]. Micro Mol Biol Rev.2000,64(3):573-606.
[64]Bull AT. The paradigm shift in microbial prospecting. in (ed.) Microbial Diversity and Bioprospecting. ASM Press, Washington, D.C,2004.
[65]Byron F, Brehm S, Eric AJ. Single-Cell Microbiology:Tools, Technologies, and Applications [J]. Microbioloy and Molecular Biology Reviews,2004,68:538-559.
[66]Cai H, Archambault M, John F. Prescott 16S ribosomal RNA sequence-based identification of veterinary clinical bacteria [J]. J Vet Diagn Invest,2003,15:465-469
[67]Castiglione F, Lazzarini A, Carrano L, et al. Determining the Structure and Mode of Action of Microbisporicin, a Potent Lantibiotic Active Against Multiresistant Pathogens[J]. Chemistry & Biology,2008,15:22-31.
[68]Chun J, Lee JH, Jung Y, et al. EzTaxon:a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences[J]. Int J Syst Evol Microbiol,2007,57:2259-2261.
[69]Collins MD, Pirouz T, Goodfellow M, et al. Distribution of menaquinones in actinomycetes and corynebacteria [J]. J Gen Microbiol,1977,100:221-230.
[70]Colquhoun JA, Zulu J, Goodfellow M, Horikoshi K, et al. Rapid characterisation of deep-sea actinomycetes for biotechnology screening programmes[J]. Antonie van Leeuwenhoek,2004,77:359-367.
[71]Colwell RR. Polyphasic taxonomy of the genus Vibrio:numerical taxonomy of Vibrio cholerae, lrbrio parahaemolyticus, and related Ybrio species[J]. Bacteriol,1970, 104:410-433.
[72]Coolen MJL, Overmann J. Functional exoenzymes as indicators of metabolicallly active bacteria in 124,000-year-old sapropel layers of the eastern Mediterranean sea [J]. Appl Environ Microbiol,2000,66:2589-2598.
[73]Couch JN. Actinoplanes. A new genus of the Actinomycetales [J]. J Elisha Mitchell.Sci Soc,1950,66:87-92.
[74]Czaran TL, Hoekstra RE, Page L. Chemical warfare between microbes promotes biodiversity [J]. Proc Natl Acad Sci USA,2002,99:786-790
[75]Dai HQ, Wang J, Xin YH, et al. Verrucosispora sediminis sp. nov., a novel cyclodipeptide-producing actinomycete from the South China Sea[J]. Int J Syst Evol Microbiol,2010,60:1807-1812
[76]Druschel GK, Baker BJ, Gihring TM, et al. Biogeochemistry of acid mine drainage at Iron Mountain, California [J]. Geochem Trans.2004,5:13-32.
[77]Duangmal K. Systematics and Comparative Genomics of Members of the Streptomyces violaceoruber 16S rRNA Gene Clade[M]. Thesis for the Degree of Doctor of Philosophy,2004.
[78]Dubey SK, Tripathi A K, Upadhyay SN. Exploration of soil bacterial communities for their potential as bioresource [J]. Bioresource Technology.2006,97(17):2217-2224.
[79]Elandalloussi LM, Rodrigues PM, Afonso R, et al. Shikimate and folate pathways in the protozoan parasite, Perkinsus olseni[J]. Molecular & Biochemical Parasitology,2005, 142:106-109.
[80]Feling RH, Buchanan GO, Mincer TJ, et al. Salinosporamide A:a highly cytotoxic proteasome inhibitor from a novel microbial source, a marine bacterium of the new genus Salinospora[J]. Angew Chem Int Ed.2003,42(3):355-357.
[81]Felsenstein J. Confidence limits on phylogenies:an approach using the bootstrap[J]. Evolution,1985,39:783-789.
[82]Felsenstein J. PHYLIP (phylogenetic inference package) version 3.2[J]. Cladistics, 1989,5:164-166.
[83]Felsenstein J. PHYLIP (phylogeny inference package) Version 3.68, Department of Genome Sciences, Unversity of Washington, Seattle, USA,2008.
[84]Fiedler HP, Bruntner C, Riedlinger J, et al. Proximicin A, B and C, novel aminofuran antibiotic and anticancer compounds isolated from marine strains of the actinomycete Verrucosispora[J]. J Antibiot,2008,61:158-163.
[85]Fischbach M, Walsh T. Antibiotics from emerging pathogens[J]. Science,2009,325: 1089-1093.
[86]Frohlich J, Konig H. New techniques for isolation of single prokaryotic cells[J]. FEMS Microbiol. Rev.,2000,24:567-572.
[87]Ginolhac A, Jarrin C, Gillet B, et al. Phylogenetic Analysis of Polyketide Synthase I Domains from Soil Metagenomic Libraries Allows Selection of Promising Clones[J]. Appl Environ Microbiol,2004,70(9):5522-5527.
[88]Good IL. The population frequencies of species and the estimation of population parameters[J]. Biometrika,1953,40:237-264.
[89]Goodacre R, Timmins EM, Burton R, et al. Rapid identification of urinary tract infection bacteria using hyperspectral whole-organism fingerprinting and artificial neural networks[J]. Microbiol,1998,144:1157-1170.
[90]Goodfellow M, Fiedler H. A guide to successful bioprospecting:informed by actinobacterial systematics[J]. Antonie van Leeuwenhoek.2010,98:119-142.
[91]Goodfellow M, Manfio GP, Chun J.Towards a practical species concept for cultivable bacteria, p.25-59. In Species:the units of biodiversity. Edited by Claridge H, Dawah A, Wilson MR. Chapman and Hall, London,1997.
[92]Goodfellow M, Stanton J, Simpson KE. et al. Numerical and chemical classification of Actinoplanes and some related actinomycetes[J]. J Gen Microbiol,1990,136:19-36.
[93]Hall UA. BioEdit, a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT[J]. Nucl Acids Symp Ser,1999,41:95-98.
[94]Handelsman J. Metagenomics:application of genomics to uncultured microorganisms [J]. Microbiol Mol Biol Rev,2004,68:669-685.
[95]Haugland RA, Vesper SJ, Wymer LJ. Quantitative measurement of Stachybotrys chartarum conidia using real time detection of PCR products with the TaqMan fluorogenic probe system[J]. Mol Cell Probes,1999,13:329-340.
[96]Haugland, RA, Heckman JL. Identification of putative sequence specific PCR primers for detection of the toxigenic fungal species Stachybotrys chartarum[J]. Mol Cell Probes,1998,12:387-396.
[97]Hayakawa M, Kajiura J, Nonomura H. New methods for the highly selective isolation of Streptosporangium and Dactylosporangium from soil[J]. J Ferm Bioeng,1991a,12: 327-333.
[98]Hayakawa M, Nonomura, H. Humic acid-vitamin agar, a new medium for selective isolation of soil actinomycetes, J Ferment Technol 1987,65:501-509.
[99]Hayakawa M, Otoguro M, Takeuchi T, et al. Application of a method incorporating differential centrifugation for selective isolation of motile actinomycetes in soil and plant litter[J]. Antonie van Leeuwenhoek,2000,78:171-185.
[100]Hayakawa M, Takeuchi T, Yamazaki T. Combined use of treimethoprim and nalidixic acid for the selective isolation of actinomycetes from soil[J]. Actinomycetologia,1996, 10:80-90.
[101]Hayakawa M, Tamura T, H. Nonomura. Selective isolation of Actinoplanes and Dactylosporangium from soil using colldine as the chemoattractant[J]. J Ferm Bioeng, 1991b,72:426-432.
[102]Hayakawa, M, lino H, Takeuchi S, et al. Application of a method incorporating treatment with chloramine-T for the selective isolation of Streptosporangiaceae from soil[J]. J. Ferm Bioeng,1997,84:599-602.
[103]Heuer H, Krsek M, Baker P, et al. Analysis of actinomycete communities by specific amplification of genes encoding 16S rRNA and gel electrophoretic separation in denaturing gradients[J]. Appl Environ Microbiol,1997,63:3233-3241.
[104]Hill RT,Mohamed NM, Montalvo NF, et al. Symbionts of marine invertebrates:Biodiversity and biomedical potential.13th International Biotechnology Symposium. Dalian, China,2008.
[105]Hong K, Gao AH, Xie QY, et al. Actinomycetes for marine drug discovery isolated from mangrove soils and plants in China[J]. Mar Drugs,2009,7:24-44
[106]Hopkins DW, MacNaughton SJ, et al. A dispersion and differential centrifugation technique for representatively sampling microorganisms from soil[J]. Soil Biol. Biochem,1991,23:217-225.
[107]Huber R, Burggraf S, Mayer T, et al. Isolation of a hyperthermophilic archaeum predicted by in situ RNA analysis[J]. Nature,1995,376:57-58.
[108]Huber T, Faulkner G, Hugenholtz P. Bellerophon:a program to detect chimeric sequence in multiple sequence alignments[J]. Bioinformatics,2004,20:2317-2319.
[109]Inahashi Y, Matsumoto A, Danbara H, et al. Phytohabitans suffuscus gen. nov., sp. nov., an actinomycete of the family Micromonosporaceae isolated from plant roots[J]. Int J Syst Evol Microbiol,2010,60:2652-2658.
[110]Jensen PR, Mincer TJ, Williams PG, et al. Marine actinomycete diversity and natural product discovery[J]. Antonie van Leeuwenhoek,2005,87:43-48.
[111]Jensen PR. Linking species concepts to natural product discovery in the post-genomic era[J]. J Ind Microbiol Biotechnol,2010,37:219-224.
[112]Jiang S, Sun W, Chen M, et al. Diversity of culturable actinobacteria isolated from marine sponge Haliclona sp [J]. Antonie van Leeuwenhoek,2007,92:405-416.
[113]Joseph SJ, Hugenholtz P, Sangwan P, et al. Laboratory cultivation of widespreadand previously uncultured soil bacteria[J]. Appl. Environ.Microbiol,2003,69:7210-7215.
[114]Kane WD. A new genus of the Actinoplanaceae, Pilimelia, with a description of two species, Pilimelia terevasa and Pilimelia anulata[J]. J Elisha Mitchell Sci Soc,1966, 82:220-230.
[115]Keller S, Nicholson G, Drahl C, et al. Abyssomicins G and H and a/rop-abyssomicin C from the marine Verrucosispora strain AB-18-032[J]. JAntibiot,2007,60:391-394.
[116]Kelly KL. Inter-Society Color Council-National Bureau of Standards Color Name Charts Illustrated with Centroid Colors. Washington, DC:US Government Printing Office,1964.
[117]Kim BY, Stach JEM, Weon HY, et al. Dactylosporangium luridium sp. nov., Dactylosporangium luteum sp. nov. and Dactylosporangium salmoneum sp. nov. nom. rev., isolated from soil [J]. Int JSyst Evol Microbiol,2010,60:1813-1823.
[118]Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences[J]. J Mol Evol,1980,16: 111-120.
[119]Koch C, Kroppenstedt RM, Rainey FA, et al.16S ribosomal DNA analysis of the genera Micromonospora, Actinoplanes, Catellatospora, Catenuloplanes, Couchioplanes, Dactylosporangium, and Pilimelia and emendation of the family Micromonosporaceae[J]. Int J Syst Bacteriol,1996,46:765-768.
[120]Kopke B, Wilms R, Engelen B, et al. Microbial diversity in coastal subsurface sediments:a cultivation approach using various electron acceptors and substrate gradients [J]. Appl Environ Microbiol,2005,71:7819-7830.
[121]Krasil'nikov NA. Ray Fungi and Related Organisms -Actinomycetales. Moscow: Izdatel'stvo Akademii Nauk SSSR (in Russian),1938.
[122]Kroppenstedt RM. Fatty acid and menaquinone analysis of actinomycetes and related organisms. In Chemical Methods in Bacterial Systematics (Society for Applied Bacteriology Technical Series vol.20), pp.173-199. Edited by Goodfellow M.& Minnikin D. E. New York:Academic Press,1985.
[123]Kudo T, Nakajima Y, Suzuki K. Catenuloplanes crispus (Petrolini et al.1993) comb, nov.:incorporation of the genus Planopolyspora Petrolini 1993 into the genus Catenuloplanes Yokota et al.1993 with an amended description of the genus Catenuloplanes[J]. Int JSyst Bacteriol,1999,49:1853-1860.
[124]Kumar Y, Aiemsum-Ang P, Ward AC, et al. Diversity and geographical distribution of members of the Streptomyces violaceusniger 16S rRNA gene clade detected by clade-specific PCR primers[J]. Fems Microbiol Ecol,2007,62(1):54-63.
[125]Kumar Y, Goodfellow M. Five new members of the Streptomyces violaceusniger 16S rRNA gene clade:Streptomyces castelarensis sp. nov., comb, nov., Streptomyces himastatinicus sp. nov., Streptomyces mordarskii sp. nov., Streptomyces rapamycinicus sp. nov. and Streptomyces ruanii sp. nov[J]. Int J Syst Evol Micr,2008,58(6):1369.
[126]Labeda, D P. Isolation of biotechnological organisms from nature. New York, NY: McGraw-Hill Publishing Company,1990.
[127]Lam KS. Discovery of novel metabolites from marine actinomycetes[J]. Curr Opin Microbiol,2006,9:245-251
[128]Lane DJ, Stackebrandt E, Goodfellow M.16S/23S rRNA sequencing. In "Nucleic Acid Techniques in Bacterial Systematics" Wiley:New York NY USA,115-175,1991.
[129]Lechevalier HA, Lechevalier MP, Starr P, et al. Spinger-verlag Berling, Heidelbery, 1981.
[130]Lechevalier MP, De Bie'vre C, Lechevalier HA. Chemotaxonomy of aerobic actinomycetes:phospholipid composition [J]. Biochem Syst Ecol,1977,5:249-260.
[131]Lechevalier MP, Lechevalier HA. The chemotaxonomy of actinomycetes. In Actinomycete Taxonomy (Special Publication no.6), pp.227-291. Edited by Dietz, A. & Thayer, J. Arlington, VA:Society for Industrial Microbiology,1980.
[132]Lee DW, Lee SD. Allocatelliglobosispora scoriae gen. nov., sp. nov., isolated from volcanic ash[J]. Int J Syst Evol Microbiol,2010, (IJSEM, in press).
[133]Lee SD, Hah YC. Proposal to transfer Catellatospora ferrugineum and 'Catellatospora ishikariense' to Asanoa gen. nov. as Asanoa ferrugineum comb. Nov. and Asanoa ishikariensis sp. Nov., with the emended description of the genus Catellatospora[J]. Int J Syst Evol Microbiol,2002,52:967-972.
[134]Li J, Zhao GZ, Zhu WY, et al. Phytomonospora endophytica gen. nov., sp 1. nov., a novel actinomycete of the family Micromonosporaceae isolated from the roots of Artemisia annua L [J]. Int J Syst Evol Microbiol.2011, doi:10.1099/ijs.0.030205-0
[135]Li YV, Terekhova LP, Alferova IV, et al. The application of succession analysis in combination with EHF irradiation to the selective isolation of actinomycetes from soil[J]. Microbiology,2003,72(1):114-117.
[136]Liao ZL, Tang SK, Guo L, et al. Verrucosispora lutea sp. nov., isolated from a mangrove sediment sample[J]. Int J Syst Evol Microbiol,2009,59:2269-2273.
[137]MacNaughton SJ, O'Donnell AG. Tuberculostearic acid as a means of estimating the recovery (using dispersion and differential centrifugation) of actinomycetes from soil[J]. J. Microbiol. Methods,1994,20:69-77.
[138]Maldonado L, Pathom-aree W, Beil W, et al. Proximicin A, B and C, novel aminofuran antibiotic and anticancer compounds isolated from marine strains of the actinomycete Verrucosispora[J]. JAntibiot,2008,61:158-163
[139]Maldonado LA, Fenical W, Jensen PR, et al. Salinispora arenicola gen. nov., sp. nov. and Salinispora tropica sp. nov., obligate marine actinomycetes belonging to the family Micromonosporaceae[J]. Int JSyst Evol Microbiol,2005a,55:1759-1766.
[140]Maldonado LA, Stach JEM, Pathom-aree W, et al. Diversity of cultivable actinobacteria in geographically widespread marine sediments[J]. Antonie van Leeuwenhoek,2005b,87:11-18
[141]Matsumoto A, Takahashi Y, Shinose M, et al. Longispora albida gen. nov., sp. nov., a novel genus of the family Micromonosporaceae[J]. Int J Syst Evol Microbiol,2003, 53:1553-1559.
[142]McVeigh HP, Divers M, Warwick S, et al. Exploration of actinomycete diversity using ribosomal RNA sequences[J]. Biotechnologia,1994,7-8:253-260.
[143]McVeigh HP, Munro J, Embley TM. Molecular evidence for the presence of novel actinomycete lineages in a temperate forest soil[J]. J Ind Microbiol,1996,17:197-204.
[144]Metsa-Ketela M, Salo V, Halo L, et al. An efficient approach for screening minimal PKS genes from Streptomyces[J]. FEMS Microbiol Lett,1999,180:1-6
[145]Mincer TJ, Fenical W, Jensen PR. Cultured and culture independent diversity within the obligate marine actinomycete genus Salinispora [J]. Appl Environ Microbiol,2005,71: 7019-7028
[146]Minnikin DE, O'Donnell AG, Goodfellow M, et al. An integrated procedure for the extraction of isoprenoid 111aponica and polar lipids[J]. J Microbiol Methods,1984, 2:233-241.
[147]Monciardini P, Cavaletti L, Ranghetti A, et al. Two novel members of the family Micromonosporaceae, Rugosimanospora acidiphila gen. nov, sp. nov. and Rugosimonospora japonica sp. nov[J]. Int J Syst Evol Microbiol,2009,59: 2752-2758.
[148]Monciardini P, Sosio M, Cavaletti L, et al. New PCR primers for the selective amplification of 16S rDNA from different groups of actinomycetes[J]. FEMS Microbiol Ecol,2002,42:419-429.
[149]Moron R, Gonzalez L, Genilloud O. New genus-specific primers for the PCR identification of members of the genera Pseudonocardia and Saccharopolyspora[J]. Int J Syst Bacteriol,1999,49:149-162
[150]Nett M, Ikeda H, Moore BS. Genomic basis for natural product biosynthetic diversity in the actinomycetes[J]. Nat. Prod. Rep,2009,26:1362-1384.
[151]Newmann DJ. Natural products as leads to potential drugs:an old process or the hope for drug discovery? [J]. JMed Chem,2008,61:2589-2599
[152]Niepold F, R Conrad H, G Schlegel. Evaluation of the efficiency of extraction for quantitative estimation of hydrogen bacteria in soil[J]. Antonie van Leeuwenhoek,1979, 45:485-497.
[153]Nonomura H, Hayakawa M. New methods for the selective isolation of soil actinomycetes, p.288-293. In Y. Okami, Y. Beppu, and K. Ogawara (eds.), Biology of Actinomycetes'88, Japan Scietific Societies Press, Tokyo,1988.
[154]Okoro CK, Brown R, Jones AL, et al. Diversity of culturable actinomycetes in hyper-arid soils of the Atacama Desert, Chile[J]. Antonie van Leeuwenhoek,2009,95: 121-133
[155]Olano C, Mendez C, Salas JA. Antitumor compounds from actinomycetes from gene clusters to new derivatives by combinatorial synthesis[J]. Nat Prod Rep,2009a 26:628-660
[156]Olano C, Mendez C, Salas JA. Antitumor compounds from marine actinomycetes[J]. Mar Drugs,2009b,7:210-248.
[157]0rskov J. Investigations into the morphology of the ray fungi. Enhagen:Levin and Munksgaard,1923.
[158]Overmann J. Novel cultivation strategies for environmentally important microorganisms. IN geomicrobiology:molecular and environmental perspective,69-89, 2010.
[159]Palleroni NJ. A chemotactic method for the isolation of Actinoplanceae[J]. A rch Microbiol,1980,128:53
[160]Pathom-Aree W, Stach JE, Ward AC, et.al. Diversity of actinomycetes isolated from Challenger Deep sediment (10,898 m) from the Mariana Trench[J]. Extremophiles, 2006,10(3):181-189.
[161]Phung N T, Lee J, Kang KH, et al. Analysis of microbial diversity in oligotrophic microbial fuel cells using 16S rDNA sequences[J]. FEMS Microbiology Letters,2004, 233(1):77-82.
[162]Pierr-alain M, Lionel R, Christophe M, et al. Metaproteomics:A new approach for studying functional microbial ecology[J]. Microbial Ecology.2007,53:486-493.
[163]Pospiech A, Neumann B. A versatile quick-prep of genomic DNA from gram-positive bacteria[J]. Trends Gene,1995,11:217-218
[164]Qin S, Li J, Zhang Y Q, et al. Plantactinospora mayteni gen. nov., sp. nov., a new member of the family Micromonosporaceae[J]. Int J Syst Evol Microbiol,2009,59: 2527-2533.
[165]Ramsay A J. Extraction of bacteria from soil:efficiency of shaking or ultrasonication as indicated by direct counts and autoradiography[J]. Soil Biol.Biochem,1984,16: 475-481.
[166]Rath JP, Kinast S, Maier ME. Synthesis of the full functionalized core structure of the antibiotic abyssomicin C[J]. Org Lett,2005,7:3089-3092.
[167]Rheims H, Schumann P, Rohde M, et al. Verrucosispora gifhornensis gen. nov., sp. Nov., a new member of the actinobacterial family Micromonosporaceae[J]. Int J Syst Bacteriol,1998,48:1119-1127.
[168]Riedlinger J, Reicke A, Zahner H, et al. Abyssomicins, inhibitors of the para-aminobenzoic acid pathway produced by the marine Verrucosispora strain AB-18-032[J]. JAntibiot,2004,57:271-279.
[169]Rintala H, Nevalainen A, Ronka E, et al. PCR primers targeting the 16S rRNA gene for the specific detection of streptomycetes[J]. Mol Cell Probes,2001,15:337-347.
[170]Robe P, Nalin R, Capellano C, et al. Extraction of DNA from soil[J]. European Journal of Soil Biology,2003,39:183-190.
[171]Roose-Amsaleg CL, Garnier-sillam E, Harry M. Extraction and purification of microbial DNA from soil and sediment samples[J]. Applied soil Ecology,2001, 18:47-60.
[172]Rothschild L. A microbiologist explodes the myth of the unculturables[J]. Nature,2006, 443:249.
[173]Rowbotham TJ, Cross T. Ecology of rhodococcus coprophilus and associated actinomycetes in fresh water and agricultural habitats[J]. J Gen Microbio.1977,100: 231-240.
[174]Saitou N, Nei M. The neighbor-joining method:a new method for reconstructing phylogenetic trees[J]. Mol Bio Evol,1987,4:406-425
[175]Salazar O, Gonzalez I, Genilloud O. New genus-specific primers for the PCR identification of new isolates of the genera Nocardiopsis and Saccharothrix[J]. Int J Syst Evol Microbiol,2002,52:1411-1421.
[176]Salazar O, Moron R, Genilloud O. New genus-specific primers for the PCR identification of members of the genus Saccharomonospora and evaluation of the microbial diversity of wild-type isolates of Saccharomonospora detected from soil DNAs[J]. Int J Syst Evol Microbiol,2000,50:2043-2055
[177]Sambrook J, Fritsch EF, Maniatis T. Molecular Cloning:A Laboratory Manual,2nd edn. Cold Spring Harbor Laboratory, New York,1989.
[178]Schafer J, Jackel U, Kampfer P. Development of a new PCR primer system for selective amplification of Actinobacteria[J]. FEMS Microbiol Lett,2010,311: 103-112.
[179]Schneider K, Keller S, Wolter FE, et al. Proximicins A, B, and C-antitumor furan analogues of netropsin from the marine actinomycete Verrucosispora Tnduce upregulation of p53 and the cyclin kinase inhibitor p21[J]. Angew Chem Int Ed Engl, 2008,47:3258-61
[180]Schuler GD. Sequence mapping by electronic PCR[J]. Genome Res,1997,7:541-550.
[181]Sekiguchi Y, Takahashi H, Kamagata Y, et al. In situ detection, isolation, and physiological properties of a thin filamentous microorganism abundant in methanogenic granular sludges:a novel isolate affiliated with a clone cluster, the green non-sulfur bacteria, subdivision I[J]. Appl Environ Microb,2001,67(12):5740.
[182]Sekiguchi Y, Kamagata Y, et al. Fluorescence in situ hybridization using 16S rRNA-targeted oligonucleotides reveals localization of methanogens and selected uncultured bacteria in mesophilic and thermophilic sludge granules[J]. Appl. Environ. Microbiol,1999,65:1280-1288.
[183]Sembiring L, Ward AC, Goodfellow M. Selective isolation and characterisation of members of the Streptomyces violaceusniger clade associated with the roots of Paraserianthes falcataria[J]. Antonie van Leeuwenhoek,2000,78:353-366.
[184]Shen FT, Young CC. Rapid detection and identification of the metabolically diverse genus Gordonia by 16S rRNA-gene-targeted genus-specific primers [J]. FEMS Microbiol Lett,2006,250:221-227
[185]Shirai M, Okuda M, Motohashi K, et al.Imoto M, Furihata K, Matsuo Y, Katsuta A, Shizuri Y, Seto H. Terpenoids produced by actinomycetes:isolation, structural elucidation and biosynthesis of new diterpenes, gifhornenolones A and B from Verrucosispora gifhornensis YM28-088[J]. JAntibiot (Tokyo).2010,63(5):245-50.
[186]Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species [J]. Int J Syst Bacteriol,1966,16:313-340.
[187]Stach JE, Maldonado LA, Masson DG, et al. Statistical approaches for estimating actinobacterial diversity in marine sediments[J]. Appl Environ Microbiol,2003a, 69(10):6189-6200.
[188]Stach JE, Maldonado LA, Ward AC, et al. New primers for the class Actinobacteria: application to marine and terrestrial environments [J]. Environ Microbiol,2003b, 5(10):828-841.
[189]Stackebrandt E, Liesack W. Nucleic acids and classification. In.Goodfellow M, O'Donell A G ed.Handbook of New Baetrial Systematics.London:Academic Press Ltd, 1993.
[190]Stackebrandt E, Rainey FA, Ward-Rainey NL. Proposal for a new hierarchic classification system, Actinobacteria classis nov[J]. Int J Syst Bacteriol,1997, 47:479-491.
[191]Staley JT, Konopka A. Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats [J]. Annu Rev Microbiol,1985,39: 321-346.
[192]Susannah GT, Edward MR. Metagenomics:DNA sequencing of environmental samples[J]. Nature Genetics.2005,6:805-814.
[193]Tamura K, Dudley J, Nei M, Kumar S. MEGA4, Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0 [J]. Mol Biol Evol,2007,24:1596-1599
[194]Tamura T, Hatano K, Suzuki, K. A new genus of the family Micromonosporaceae, Polymorphospora gen. nov., with description of Polymorphospora rubra sp. nov[J]. Int J Syst Evol Microbiol,2006,56,1959-1964.
[195]Tamura T, Hayakawa M, Hatano K. A new genus of the order Actinomycetales, Spirilliplanes gen. nov., with description of Spirilliplanes yamanashiensis sp. nov[J]. Int J Syst Bacteriol,1997,47:97-102.
[196]Tamura T, Hayakawa M, Hatano K. A new genus of the order Actinomycetales, Virgosporangium gen. nov., with descriptions of Virgosporangium ochraceum sp. nov. and Virgosporangium aurantiacum sp. nov[J]. Int J Syst Evol Microbiol,2001, 51:1809-1816.
[197]Tamura T, Nakagaito Y, Nishii T, et al. A new genus of the order Actinomycetales, Couchioplanes gen. nov., with descriptions of Couchioplanes caeruleus (Horan and Brodsky 1986) comb. Nov. and Couchioplanes caeruleus subsp. Azureus subsp. nov[J]. Int J Syst Bacteriol,1994,44:193-203.
[198]Tan GYA, Robinson S, Lacey E, et al. Amycolatopsis regifaucium sp. nov., a novel actinomycete that produces kigamicins[J]. Int J Syst Evol Microbiol,2007,57: 2562-2567.
[199]Tan GYA, Ward AC, Goodfellow M. Exploration of Amycolatopsis diversity in soil using genus-specific primers and novel selective media[J]. Syst Appl Microbiol 2006, 29:557-569.
[200]Thawai C, Tanasupawat S, Itoh T, et al. Actinocatenispora thailandica gen. nov., sp. nov., a new member of the family Micromonosporaceae[J]. Int J Syst Evol Microbiol, 2006,56:1789-1794.
[201]Thawai C, Tanasupawat S, Kudo T. Actinaurispora gen. nov., a new member of the family Micromonosporaceae, with description of Actinoaurantispora siamensis sp. nov[J]. Int J Syst Evol Microbiol,2010, (IJSEM, in press).
[202]Thiemann JE, Pagani H, Beretta G. A new genus of the Actinoplanaceae: Dactylosporangium gen. nov[J]. Arch Mikrobiol,1967,58,42-52.
[203]Thomas T, Egan S, Burg D, et al. Integration of genomics and proteomics into marine microbial ecology[J]. Mar Ecol Prog Ser,2007,332:291-299.
[204]Thompson JD, Gibson TJ, Plewniak F, et al. The CLUSTAL-X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools[J]. Nucleic Acids Res,1997,25:4876-4876
[205]Tiedje JM. Approaches to the comprehensive evaluation of prokaryotic diversity of a habitat, p73-87. In D Allsopp RR, Colwell DL, Hawksworth. Microbial diversity and ecosystem function. Wallingford, UK:CAB International,1995.
[206]Torsvik V, Goksoyr J, Daae FL. High diversity in DNA of soil bacteria[J]. Appl Environ Microbiol,1990,56:782-787.
[207]Tyson GW, Banfield JF. Cultivating the uncultivated:a community genomics perspective [J]. Trends Microbiol,2005,13:411-415.
[208]Tyson GW, Chapman J, Hugenholtz P, et al. Community structure and metabolism through reconstruction of microbial genomes from the environment[J]. Nature,2004, 428:37-43.
[209]Wang Q, Garrity GM, Tiedje JM, et al. Naive bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy [J]. Appl Environ Microbiol,2007, 73:5261-5267.
[210]Ward AC, Goodfellow M. Phylogeny and functionality:taxonomy as a roadmap to genes. In:Bull AT (ed) Microbial diversity, bioprospecting. ASM Press, Washington, DC, pp 288-313,2004.
[211]Ward DC, White DC. The new omics era [J]. Curr.Opin.Biotechnol,2002,13:11-13.
[212]Watanabe A, Ebizuka Y. Unprecedented Mechanism for Chain Length Determination in Fungal Aromatic Polyketide Synthases, Chemistry and Biology Vol.11, pp. 1101-1106A,2004.
[213]Wawrik B, Kutliev D, Abdivasievna UA, et al. Biogeography of actinomycete communities and type Ⅱ polyketide synthase genes in soils collected in New Jersey and central asia[J]. Appl. Environ. Microbiol.2007,73(9):2982-2989.
[214]Wayne LG, Brenner DJ, Colwell RR, et al. Report of the ad hoc committee on reconcilation of approaches to bacterial sytematics[J]. Int J Syst Bacteriol,1987,37: 463-464
[215]Wiese J, Jiang Y, Tang SK, et al. A new member of the family Micromonosporaceae, Planosporangium flavigriseum gen. nov., sp. nov[J]. Int J Syst Evol Microbiol,2008, 58:1324-1331.
[216]Williams PG, Buchanan GO, Feling RH, et al. New cytotoxic salinosporamides from the marine actinomycete Salinispora tropica [J]. J Org Chem,2005,70(16): 6196-6203.
[217]Williams ST, Lanning S, Wellington, et al. Ecology of actinomycetes. In "The Biology of the Actinomycetes", Goodfellow M, Mordarski M, Williams ST, Eds, Academic Press:London, UK, pp.481-528,1984a.
[218]Williams ST, Goodfellow M, Vickers JC. New microbes from old habitats, p. 219-256.In D P Kelly, N R Carr (ed.), The microbe 1984. Cambridge, UK:Cambridge University Press,1984b.
[219]Wilmes PT, Bond PL. Metaproteomics:studying functional gene wspression in mcriobial ecosystems [J]. Trends microbial,2006,14:92-97.
[220]Xie QY, Wang C, Wang R, et al. Jishengella endophytica gen. nov., sp. nov., a new member of the family Micromonosporaceae [J]. Int J Syst Evol Microbiol.2010, doi:10.1099/ijs.0.025288-0.
[221]Yokota A, Tamura T, Hasegawa T, et al. Catenuloplanes japonicas gen. nov., sp. nov., nom. Rev., a new genus of the order Actinomycetales[J]. Int J Syst Bacteriol,1993,43: 805-812.
[222]Yu Y, Lee C, et al. Analysis of community structures in anaerobic processes using a quantitative real-time PCR method." [J].Water Sci. Technol,2005,52:85-91.
[223]Zengler K, Toledo G, Rappe M, et al. Cultivating the uncultured [J]. Proc. Natl. Acad. Sci.,2002,99:15681-15696.
[224]Zhi XY, Li WJ, Stackebrandt E. An update of the structure and 16S rRNA gene sequence-based definition of higher ranks of the class Actinobacteria, with the proposal of two new suborders and four new families and emended descriptions of the existing higher taxa[J]. Int J Syst Evol Microbiol,2009,59:589-608.
[2]洪葵,谢晴宜编著.药用微生物资源研究技术[M].北京：中国农业大学出版社,2006.
[3]黄春兰.测定土壤有机质的一点改进[J].热作科技通讯,1978,(4)：25.
[4]蒋云霞 郑天凌.红树林土壤微生物的研究：过去、现在、未来[J].微生物学报,2006,46(5)：77-83.
[5]焦瑞身.新世纪微生物学者的一项重要任务-未培养微生物的分离培养[J].生物工程学报,2004,20(5)：641-645.
[6]李翔,秦岭,戴世鲲等.海洋微生物宏基因组工程进展与展望[J].微生物学报,2007,47(3)：548-553.
[7]刘颖.红树林环境具有生物活性共附生微生物群体培养物的研究.海南大学博士学位论文,2010.
[8]鲁如坤.土壤农业化学分析方法[M].北京：中国农业科技出版社：198-199,2000.
[9]聂毅磊,林如,郑永标,等,海绵疣孢菌FIM06031产生的2’-脱氧尿嘧啶核苷[J].中国抗生素杂志,2010,35(6)：426-430
[10]曲直.红树林放线菌的化学分类鉴定.海南大学硕士论文,2009
[11]沈定树,戴冬玲,余素飞,等.金黄色葡萄球菌耐药性分析[J].中国微生态学杂志,2005,17(5)：381-382。
[12]隋金蕾.红树林土壤链霉菌的选择性分离和菌株219820的鉴定.海南大学硕士论文,2010.
[13]王成.文昌红树林根际土壤小单孢菌的分离与菌株211018的鉴定.海南大学硕士论文,2010
[14]王凡.一株红树林稀有放线菌新种的鉴定.华中农业大学硕士论文,2010.
[15]王海龙.红树林细胞毒活性链霉菌061324的分子鉴定及定种.海南大学硕士论文,2009
[16]王平.测定放线菌菌体中氨基酸和单糖的快速方法—薄层层析法[J].微生物通报,1986,13：228-2301.
[17]王蓉.老鼠筋内生放线菌的分离鉴定活性评价及其类群分析.海南大学硕士论文,2008.
[18]王岳坤,洪葵.红树林土壤因子对土壤微生物的影响.热带作物学报.2005,26(3)：109-114.
[19]徐丽华,李文均,刘志恒,等.放线菌系统学——原理、方法及实践[M].北京：科学出版社,pp400-402,2007.
[20]徐平,李文均,高慧英,等.产生芳香环聚酮类天然产物放线菌的分子筛选研究[J].中国抗生素杂志,2005,30(3)：134-137.
[21]徐小雄.23种红树植物根际土壤小双孢菌的选择性分离.海南大学大学硕士论文,2009.
[22]闫莉萍.抗肿瘤活性放线菌的分离筛选及其16S rDNA多样性分析.华南热带农业大学硕士论文,2005.
[23]阎冰.红树林土壤16S rDNA多样性的研究.华中农业大学博士论文,2006.
[24]杨建,洪葵.红树林土壤总DNA不同提取方法比较研究生物技术通报[J].2006a,增刊：366-371.
[25]杨建.红树林土壤总DNA不同提取方法比较研究以及Ⅰ型聚酮合成酶基因检测.华南热带农业大学硕士论文,2006b.
[26]袁干军.红树林放线菌大环内酯化合物产生菌的筛选、产物的分离鉴定及活性研究.海南大学博士学位论文,2010.
[27]曾胤新,陈波,邹扬,等.极地微生物---新天然药物的潜在来源[J].微生物学报,2008,(5)：695-700.
[28]张致平.微生物药物学[M].北京：化学工业出版社,2003.
[29]中国科学院南京土壤研究所主编.土壤理化分析[M].上海：上海科学技术出版社,1978,97-101,114.
[30]朱义明.尼龙膜杂交检测放线菌基因组DNA同源性方法的建立.华南热带农业大学硕士论文,2007
[31]Achtman M, Wagner M. Microbial diversity and the genetic nature of microbial species[J]. Nature Reviews Microbiology,2008,6(6):431-440.
[32]Alm EW, Oerther DB, Larsen N, et al. The oligonucleotide probe database[J]. Appl Environ Microbiol,1996,62:3557-3559.
[33]Amann RI, Ludwig W, et al. Phylogenetic identification and in situ detection of individual microbial cells without cultivation[J]. Microbiol Rev,1995,59(1):143-169.
[34]Angle JS, McGrath SP, Chaney RL. New culture medium containing ionic concentrations of nutrients similar to concentrations found in the soil solution[J]. Appl Environ Microbiol,1991,57:3674-3676.
[35]Antony-Babu S, Stach JE, Goodfellow M. Computer-assisted numerical analysis of colour-group data for dereplication of streptomycetes for bioprospecting and ecological purposes[J]. Antonie Van Leeuwenhoek,2010,97:231-239.
[36]Anzai Y, Okuda T, Watanabe J. Application of the random amplified polymorphic DNA using the polymerase chain reaction for efficient elimination of duplicate strains in microbial screening. Ⅱ. Actinomycetes[J]. JAntibiot (Tokyo),1994,47:183-193.
[37]Ara I, Bakir MA, Kudo T, et al. Pseudosporangium ferrugineum gen. nov., sp. nov., a new member of the family Micromonosporaceae[J]. Int J Syst Evol Microbiol,2008a, 58:1644-1652.
[38]Ara I, Bakir MA, Kudo T. Transfer of Catellatospora koreensis Lee et al.2000 as Catelliglobosispora koreensis gen. nov., comb. nov. and Catellatospora tsunoense Asano et al.1989 as Hamadaea tsunoense gen. nov., comb, nov., and emended description of the genus Catellatospora Asano and Kawamoto 1986 emend. Lee and Hah 2002[J]. Int J Syst Evol Microbiol,2008b,58:1950-1960.
[39]Ara I, Kudo T. Luedemannella gen. nov., a new genus of the family Micromonosporaceae and description of Luedemannella helvata sp. nov. and Luedemannella flava sp. nov[J]. J Gen Appl Microbiol,2007a,53:39-51.
[40]Ara I, Kudo T. Krasilnikovia gen. nov., a new member of the family Micromonosporaceae and description of Krasilnikovia cinnamonea sp. nov[J]. Actinomycetologica,2007b,21:1-10.
[41]Ara I, Kudo T. Three novel species of the genus Catellatospora, Catellatospora chokoriensis sp. nov., Catellatospora coxensis sp. nov. and Catellatospora bangladeshensis sp. nov, and transfer of Catellatospora citrea subsp.
[42]Methionotrophica Asano and Kawamoto 1988 to Catellatospora methionotrophica sp. nov., comb. nov[J]. Int JSyst Evol Microbiol,2006,56:393-400.
[43]Ariesyady HD, Ito T, et al. Phylogenetic and functional diversity of propionate-oxidizing bacteria in an anaerobic digester sludge[J]. Appl. Microbiol. Biotechnol^ 2007, 75:673-683.
[44]Arnold L. Demain, Foreword in "Microbial Diversity and Bioprospecting". Ed. Bull AT, ASM Press, Washington, D.C.,2004.
[45]Asano K, Kawamoto I. Catellatospora, a new genus of the Actinomycetales[J]. Int J Syst Bacteriol,1986,36:512-517.
[46]Atalan E, GP Manfio, AC Ward, et al. Biosystematic studies on novel streptomycetes from soil. Antonie van Leeuwenhoek,2000,77:337-353.
[47]Avarre JC, De Lajudie P, Bena G. Hybridization of genomic DNA to microarrays:a challenge for the analysis of environmental samples[J]. J. Microbiol. Methods,2007, 57:269-278.
[48]Ayuso A, Clark D, Gonzalez I, et al. A novel actinomycete strain dereplication approach based on the diversity of polyketide synthase and nonribosomal peptide synthetase biosynthetic[J]. Appl Microbiol Biotechnol,2005,67:795-806.
[49]Bains W. Company strategies for using bioinformatics[J]. Trends Biotechnol.1996,14: 312-317.
[50]Baltz R H. Antimicrobials from Actinomycetes:Back to the Future[J]. Microbe,2007, 2(3):125-131.
[51]Bartscht K, Cypionka H, Overmann J. Evaluation of cell activity and of methods for the cultivation of bacteria from a natural lake community[J]. FEMS Microbiol Ecol,1999, 28:249-259.
[52]Bcrcczky K, Laatsch H, Wagner Dobler I, et al. Cluster analysis as selection and dereplication tool for identification of new natural compounds from large sample sets[J]. Chem Biodiv,2006,3:622-634.
[53]Berdy J. Bioactive microbial metabolites[J]. JAntibiot,2005,58:1-26
[54]Bister B, Bischoff D, Strobele M, et al. Abyssomicin C-A polycyclicantibiotic from a marine Verrucosispora strain as an inhibitor of the p-aminobenzoic acid/ tetrahydrofolate biosynthesis pathway [J]. Angew Chem Int Ed Engl,2004,43: 2574-2576.
[55]Bode HB, Bethe B, Hofs R, et al. Big effects from small changes:possible ways to explore nature's chemical diversity[J]. Chembiochem,2002,3:619-627.
[56]Bond PL, Smriga SP, Banfield JF. Phylogeny of microorganisms populating a thick, subaerial, predominantly lithotrophic biofilm at an extreme acid mine drainage site[J]. Appl Environ Microbiol,2000,6:3842-3849.
[57]Bouck A, Vision T. The molecular ecologist's guide to expressed sequence tags[J]. Molecular Ecology,2007,16:907-924.
[58]Brandao P. Dereplication for biotechnology screening:PyMS analysis and PCR-RFLP-SSCP (PRS) profiling of 16S rRNA genes of marine and terrestrial actinomycetes [J]. Appl Microbiol Biotechnol,2002,58:77-83.
[59]Bredholdt H, Tjaervik E, Johnsen G, et al. Actinomycetes from sediments in the Trondheim fjord, Norway:diversity and biological activity[J]. Mar Drugs,2008,6: 12-24
[60]Brosius J, Palmer ML, Kennedy PJ, et al. Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli [J]. Proc Natl Acad Sci USA,1978,75: 4801-4805.
[61]Bruns A, et al. Cyclic AMP and acyl homoserine lactones increase the cultivation efficiency of heterotrophic bacteria from the central Baltic Sea[J]. Appl. Environ. Microbiol,2002,68:3978-3987.
[62]Bull AT, Stach J. Marine actinobacteria:new opportunities for natural product search and discovery[J]. Trends Microbiol,2007,15:491-499.
[63]Bull AT, Ward AC, Goodfellow M. Search and discovery strategies for biotechnology: the paradigm shift[J]. Micro Mol Biol Rev.2000,64(3):573-606.
[64]Bull AT. The paradigm shift in microbial prospecting. in (ed.) Microbial Diversity and Bioprospecting. ASM Press, Washington, D.C,2004.
[65]Byron F, Brehm S, Eric AJ. Single-Cell Microbiology:Tools, Technologies, and Applications [J]. Microbioloy and Molecular Biology Reviews,2004,68:538-559.
[66]Cai H, Archambault M, John F. Prescott 16S ribosomal RNA sequence-based identification of veterinary clinical bacteria [J]. J Vet Diagn Invest,2003,15:465-469
[67]Castiglione F, Lazzarini A, Carrano L, et al. Determining the Structure and Mode of Action of Microbisporicin, a Potent Lantibiotic Active Against Multiresistant Pathogens[J]. Chemistry & Biology,2008,15:22-31.
[68]Chun J, Lee JH, Jung Y, et al. EzTaxon:a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences[J]. Int J Syst Evol Microbiol,2007,57:2259-2261.
[69]Collins MD, Pirouz T, Goodfellow M, et al. Distribution of menaquinones in actinomycetes and corynebacteria [J]. J Gen Microbiol,1977,100:221-230.
[70]Colquhoun JA, Zulu J, Goodfellow M, Horikoshi K, et al. Rapid characterisation of deep-sea actinomycetes for biotechnology screening programmes[J]. Antonie van Leeuwenhoek,2004,77:359-367.
[71]Colwell RR. Polyphasic taxonomy of the genus Vibrio:numerical taxonomy of Vibrio cholerae, lrbrio parahaemolyticus, and related Ybrio species[J]. Bacteriol,1970, 104:410-433.
[72]Coolen MJL, Overmann J. Functional exoenzymes as indicators of metabolicallly active bacteria in 124,000-year-old sapropel layers of the eastern Mediterranean sea [J]. Appl Environ Microbiol,2000,66:2589-2598.
[73]Couch JN. Actinoplanes. A new genus of the Actinomycetales [J]. J Elisha Mitchell.Sci Soc,1950,66:87-92.
[74]Czaran TL, Hoekstra RE, Page L. Chemical warfare between microbes promotes biodiversity [J]. Proc Natl Acad Sci USA,2002,99:786-790
[75]Dai HQ, Wang J, Xin YH, et al. Verrucosispora sediminis sp. nov., a novel cyclodipeptide-producing actinomycete from the South China Sea[J]. Int J Syst Evol Microbiol,2010,60:1807-1812
[76]Druschel GK, Baker BJ, Gihring TM, et al. Biogeochemistry of acid mine drainage at Iron Mountain, California [J]. Geochem Trans.2004,5:13-32.
[77]Duangmal K. Systematics and Comparative Genomics of Members of the Streptomyces violaceoruber 16S rRNA Gene Clade[M]. Thesis for the Degree of Doctor of Philosophy,2004.
[78]Dubey SK, Tripathi A K, Upadhyay SN. Exploration of soil bacterial communities for their potential as bioresource [J]. Bioresource Technology.2006,97(17):2217-2224.
[79]Elandalloussi LM, Rodrigues PM, Afonso R, et al. Shikimate and folate pathways in the protozoan parasite, Perkinsus olseni[J]. Molecular & Biochemical Parasitology,2005, 142:106-109.
[80]Feling RH, Buchanan GO, Mincer TJ, et al. Salinosporamide A:a highly cytotoxic proteasome inhibitor from a novel microbial source, a marine bacterium of the new genus Salinospora[J]. Angew Chem Int Ed.2003,42(3):355-357.
[81]Felsenstein J. Confidence limits on phylogenies:an approach using the bootstrap[J]. Evolution,1985,39:783-789.
[82]Felsenstein J. PHYLIP (phylogenetic inference package) version 3.2[J]. Cladistics, 1989,5:164-166.
[83]Felsenstein J. PHYLIP (phylogeny inference package) Version 3.68, Department of Genome Sciences, Unversity of Washington, Seattle, USA,2008.
[84]Fiedler HP, Bruntner C, Riedlinger J, et al. Proximicin A, B and C, novel aminofuran antibiotic and anticancer compounds isolated from marine strains of the actinomycete Verrucosispora[J]. J Antibiot,2008,61:158-163.
[85]Fischbach M, Walsh T. Antibiotics from emerging pathogens[J]. Science,2009,325: 1089-1093.
[86]Frohlich J, Konig H. New techniques for isolation of single prokaryotic cells[J]. FEMS Microbiol. Rev.,2000,24:567-572.
[87]Ginolhac A, Jarrin C, Gillet B, et al. Phylogenetic Analysis of Polyketide Synthase I Domains from Soil Metagenomic Libraries Allows Selection of Promising Clones[J]. Appl Environ Microbiol,2004,70(9):5522-5527.
[88]Good IL. The population frequencies of species and the estimation of population parameters[J]. Biometrika,1953,40:237-264.
[89]Goodacre R, Timmins EM, Burton R, et al. Rapid identification of urinary tract infection bacteria using hyperspectral whole-organism fingerprinting and artificial neural networks[J]. Microbiol,1998,144:1157-1170.
[90]Goodfellow M, Fiedler H. A guide to successful bioprospecting:informed by actinobacterial systematics[J]. Antonie van Leeuwenhoek.2010,98:119-142.
[91]Goodfellow M, Manfio GP, Chun J.Towards a practical species concept for cultivable bacteria, p.25-59. In Species:the units of biodiversity. Edited by Claridge H, Dawah A, Wilson MR. Chapman and Hall, London,1997.
[92]Goodfellow M, Stanton J, Simpson KE. et al. Numerical and chemical classification of Actinoplanes and some related actinomycetes[J]. J Gen Microbiol,1990,136:19-36.
[93]Hall UA. BioEdit, a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT[J]. Nucl Acids Symp Ser,1999,41:95-98.
[94]Handelsman J. Metagenomics:application of genomics to uncultured microorganisms [J]. Microbiol Mol Biol Rev,2004,68:669-685.
[95]Haugland RA, Vesper SJ, Wymer LJ. Quantitative measurement of Stachybotrys chartarum conidia using real time detection of PCR products with the TaqMan fluorogenic probe system[J]. Mol Cell Probes,1999,13:329-340.
[96]Haugland, RA, Heckman JL. Identification of putative sequence specific PCR primers for detection of the toxigenic fungal species Stachybotrys chartarum[J]. Mol Cell Probes,1998,12:387-396.
[97]Hayakawa M, Kajiura J, Nonomura H. New methods for the highly selective isolation of Streptosporangium and Dactylosporangium from soil[J]. J Ferm Bioeng,1991a,12: 327-333.
[98]Hayakawa M, Nonomura, H. Humic acid-vitamin agar, a new medium for selective isolation of soil actinomycetes, J Ferment Technol 1987,65:501-509.
[99]Hayakawa M, Otoguro M, Takeuchi T, et al. Application of a method incorporating differential centrifugation for selective isolation of motile actinomycetes in soil and plant litter[J]. Antonie van Leeuwenhoek,2000,78:171-185.
[100]Hayakawa M, Takeuchi T, Yamazaki T. Combined use of treimethoprim and nalidixic acid for the selective isolation of actinomycetes from soil[J]. Actinomycetologia,1996, 10:80-90.
[101]Hayakawa M, Tamura T, H. Nonomura. Selective isolation of Actinoplanes and Dactylosporangium from soil using colldine as the chemoattractant[J]. J Ferm Bioeng, 1991b,72:426-432.
[102]Hayakawa, M, lino H, Takeuchi S, et al. Application of a method incorporating treatment with chloramine-T for the selective isolation of Streptosporangiaceae from soil[J]. J. Ferm Bioeng,1997,84:599-602.
[103]Heuer H, Krsek M, Baker P, et al. Analysis of actinomycete communities by specific amplification of genes encoding 16S rRNA and gel electrophoretic separation in denaturing gradients[J]. Appl Environ Microbiol,1997,63:3233-3241.
[104]Hill RT,Mohamed NM, Montalvo NF, et al. Symbionts of marine invertebrates:Biodiversity and biomedical potential.13th International Biotechnology Symposium. Dalian, China,2008.
[105]Hong K, Gao AH, Xie QY, et al. Actinomycetes for marine drug discovery isolated from mangrove soils and plants in China[J]. Mar Drugs,2009,7:24-44
[106]Hopkins DW, MacNaughton SJ, et al. A dispersion and differential centrifugation technique for representatively sampling microorganisms from soil[J]. Soil Biol. Biochem,1991,23:217-225.
[107]Huber R, Burggraf S, Mayer T, et al. Isolation of a hyperthermophilic archaeum predicted by in situ RNA analysis[J]. Nature,1995,376:57-58.
[108]Huber T, Faulkner G, Hugenholtz P. Bellerophon:a program to detect chimeric sequence in multiple sequence alignments[J]. Bioinformatics,2004,20:2317-2319.
[109]Inahashi Y, Matsumoto A, Danbara H, et al. Phytohabitans suffuscus gen. nov., sp. nov., an actinomycete of the family Micromonosporaceae isolated from plant roots[J]. Int J Syst Evol Microbiol,2010,60:2652-2658.
[110]Jensen PR, Mincer TJ, Williams PG, et al. Marine actinomycete diversity and natural product discovery[J]. Antonie van Leeuwenhoek,2005,87:43-48.
[111]Jensen PR. Linking species concepts to natural product discovery in the post-genomic era[J]. J Ind Microbiol Biotechnol,2010,37:219-224.
[112]Jiang S, Sun W, Chen M, et al. Diversity of culturable actinobacteria isolated from marine sponge Haliclona sp [J]. Antonie van Leeuwenhoek,2007,92:405-416.
[113]Joseph SJ, Hugenholtz P, Sangwan P, et al. Laboratory cultivation of widespreadand previously uncultured soil bacteria[J]. Appl. Environ.Microbiol,2003,69:7210-7215.
[114]Kane WD. A new genus of the Actinoplanaceae, Pilimelia, with a description of two species, Pilimelia terevasa and Pilimelia anulata[J]. J Elisha Mitchell Sci Soc,1966, 82:220-230.
[115]Keller S, Nicholson G, Drahl C, et al. Abyssomicins G and H and a/rop-abyssomicin C from the marine Verrucosispora strain AB-18-032[J]. JAntibiot,2007,60:391-394.
[116]Kelly KL. Inter-Society Color Council-National Bureau of Standards Color Name Charts Illustrated with Centroid Colors. Washington, DC:US Government Printing Office,1964.
[117]Kim BY, Stach JEM, Weon HY, et al. Dactylosporangium luridium sp. nov., Dactylosporangium luteum sp. nov. and Dactylosporangium salmoneum sp. nov. nom. rev., isolated from soil [J]. Int JSyst Evol Microbiol,2010,60:1813-1823.
[118]Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences[J]. J Mol Evol,1980,16: 111-120.
[119]Koch C, Kroppenstedt RM, Rainey FA, et al.16S ribosomal DNA analysis of the genera Micromonospora, Actinoplanes, Catellatospora, Catenuloplanes, Couchioplanes, Dactylosporangium, and Pilimelia and emendation of the family Micromonosporaceae[J]. Int J Syst Bacteriol,1996,46:765-768.
[120]Kopke B, Wilms R, Engelen B, et al. Microbial diversity in coastal subsurface sediments:a cultivation approach using various electron acceptors and substrate gradients [J]. Appl Environ Microbiol,2005,71:7819-7830.
[121]Krasil'nikov NA. Ray Fungi and Related Organisms -Actinomycetales. Moscow: Izdatel'stvo Akademii Nauk SSSR (in Russian),1938.
[122]Kroppenstedt RM. Fatty acid and menaquinone analysis of actinomycetes and related organisms. In Chemical Methods in Bacterial Systematics (Society for Applied Bacteriology Technical Series vol.20), pp.173-199. Edited by Goodfellow M.& Minnikin D. E. New York:Academic Press,1985.
[123]Kudo T, Nakajima Y, Suzuki K. Catenuloplanes crispus (Petrolini et al.1993) comb, nov.:incorporation of the genus Planopolyspora Petrolini 1993 into the genus Catenuloplanes Yokota et al.1993 with an amended description of the genus Catenuloplanes[J]. Int JSyst Bacteriol,1999,49:1853-1860.
[124]Kumar Y, Aiemsum-Ang P, Ward AC, et al. Diversity and geographical distribution of members of the Streptomyces violaceusniger 16S rRNA gene clade detected by clade-specific PCR primers[J]. Fems Microbiol Ecol,2007,62(1):54-63.
[125]Kumar Y, Goodfellow M. Five new members of the Streptomyces violaceusniger 16S rRNA gene clade:Streptomyces castelarensis sp. nov., comb, nov., Streptomyces himastatinicus sp. nov., Streptomyces mordarskii sp. nov., Streptomyces rapamycinicus sp. nov. and Streptomyces ruanii sp. nov[J]. Int J Syst Evol Micr,2008,58(6):1369.
[126]Labeda, D P. Isolation of biotechnological organisms from nature. New York, NY: McGraw-Hill Publishing Company,1990.
[127]Lam KS. Discovery of novel metabolites from marine actinomycetes[J]. Curr Opin Microbiol,2006,9:245-251
[128]Lane DJ, Stackebrandt E, Goodfellow M.16S/23S rRNA sequencing. In "Nucleic Acid Techniques in Bacterial Systematics" Wiley:New York NY USA,115-175,1991.
[129]Lechevalier HA, Lechevalier MP, Starr P, et al. Spinger-verlag Berling, Heidelbery, 1981.
[130]Lechevalier MP, De Bie'vre C, Lechevalier HA. Chemotaxonomy of aerobic actinomycetes:phospholipid composition [J]. Biochem Syst Ecol,1977,5:249-260.
[131]Lechevalier MP, Lechevalier HA. The chemotaxonomy of actinomycetes. In Actinomycete Taxonomy (Special Publication no.6), pp.227-291. Edited by Dietz, A. & Thayer, J. Arlington, VA:Society for Industrial Microbiology,1980.
[132]Lee DW, Lee SD. Allocatelliglobosispora scoriae gen. nov., sp. nov., isolated from volcanic ash[J]. Int J Syst Evol Microbiol,2010, (IJSEM, in press).
[133]Lee SD, Hah YC. Proposal to transfer Catellatospora ferrugineum and 'Catellatospora ishikariense' to Asanoa gen. nov. as Asanoa ferrugineum comb. Nov. and Asanoa ishikariensis sp. Nov., with the emended description of the genus Catellatospora[J]. Int J Syst Evol Microbiol,2002,52:967-972.
[134]Li J, Zhao GZ, Zhu WY, et al. Phytomonospora endophytica gen. nov., sp 1. nov., a novel actinomycete of the family Micromonosporaceae isolated from the roots of Artemisia annua L [J]. Int J Syst Evol Microbiol.2011, doi:10.1099/ijs.0.030205-0
[135]Li YV, Terekhova LP, Alferova IV, et al. The application of succession analysis in combination with EHF irradiation to the selective isolation of actinomycetes from soil[J]. Microbiology,2003,72(1):114-117.
[136]Liao ZL, Tang SK, Guo L, et al. Verrucosispora lutea sp. nov., isolated from a mangrove sediment sample[J]. Int J Syst Evol Microbiol,2009,59:2269-2273.
[137]MacNaughton SJ, O'Donnell AG. Tuberculostearic acid as a means of estimating the recovery (using dispersion and differential centrifugation) of actinomycetes from soil[J]. J. Microbiol. Methods,1994,20:69-77.
[138]Maldonado L, Pathom-aree W, Beil W, et al. Proximicin A, B and C, novel aminofuran antibiotic and anticancer compounds isolated from marine strains of the actinomycete Verrucosispora[J]. JAntibiot,2008,61:158-163
[139]Maldonado LA, Fenical W, Jensen PR, et al. Salinispora arenicola gen. nov., sp. nov. and Salinispora tropica sp. nov., obligate marine actinomycetes belonging to the family Micromonosporaceae[J]. Int JSyst Evol Microbiol,2005a,55:1759-1766.
[140]Maldonado LA, Stach JEM, Pathom-aree W, et al. Diversity of cultivable actinobacteria in geographically widespread marine sediments[J]. Antonie van Leeuwenhoek,2005b,87:11-18
[141]Matsumoto A, Takahashi Y, Shinose M, et al. Longispora albida gen. nov., sp. nov., a novel genus of the family Micromonosporaceae[J]. Int J Syst Evol Microbiol,2003, 53:1553-1559.
[142]McVeigh HP, Divers M, Warwick S, et al. Exploration of actinomycete diversity using ribosomal RNA sequences[J]. Biotechnologia,1994,7-8:253-260.
[143]McVeigh HP, Munro J, Embley TM. Molecular evidence for the presence of novel actinomycete lineages in a temperate forest soil[J]. J Ind Microbiol,1996,17:197-204.
[144]Metsa-Ketela M, Salo V, Halo L, et al. An efficient approach for screening minimal PKS genes from Streptomyces[J]. FEMS Microbiol Lett,1999,180:1-6
[145]Mincer TJ, Fenical W, Jensen PR. Cultured and culture independent diversity within the obligate marine actinomycete genus Salinispora [J]. Appl Environ Microbiol,2005,71: 7019-7028
[146]Minnikin DE, O'Donnell AG, Goodfellow M, et al. An integrated procedure for the extraction of isoprenoid 111aponica and polar lipids[J]. J Microbiol Methods,1984, 2:233-241.
[147]Monciardini P, Cavaletti L, Ranghetti A, et al. Two novel members of the family Micromonosporaceae, Rugosimanospora acidiphila gen. nov, sp. nov. and Rugosimonospora japonica sp. nov[J]. Int J Syst Evol Microbiol,2009,59: 2752-2758.
[148]Monciardini P, Sosio M, Cavaletti L, et al. New PCR primers for the selective amplification of 16S rDNA from different groups of actinomycetes[J]. FEMS Microbiol Ecol,2002,42:419-429.
[149]Moron R, Gonzalez L, Genilloud O. New genus-specific primers for the PCR identification of members of the genera Pseudonocardia and Saccharopolyspora[J]. Int J Syst Bacteriol,1999,49:149-162
[150]Nett M, Ikeda H, Moore BS. Genomic basis for natural product biosynthetic diversity in the actinomycetes[J]. Nat. Prod. Rep,2009,26:1362-1384.
[151]Newmann DJ. Natural products as leads to potential drugs:an old process or the hope for drug discovery? [J]. JMed Chem,2008,61:2589-2599
[152]Niepold F, R Conrad H, G Schlegel. Evaluation of the efficiency of extraction for quantitative estimation of hydrogen bacteria in soil[J]. Antonie van Leeuwenhoek,1979, 45:485-497.
[153]Nonomura H, Hayakawa M. New methods for the selective isolation of soil actinomycetes, p.288-293. In Y. Okami, Y. Beppu, and K. Ogawara (eds.), Biology of Actinomycetes'88, Japan Scietific Societies Press, Tokyo,1988.
[154]Okoro CK, Brown R, Jones AL, et al. Diversity of culturable actinomycetes in hyper-arid soils of the Atacama Desert, Chile[J]. Antonie van Leeuwenhoek,2009,95: 121-133
[155]Olano C, Mendez C, Salas JA. Antitumor compounds from actinomycetes from gene clusters to new derivatives by combinatorial synthesis[J]. Nat Prod Rep,2009a 26:628-660
[156]Olano C, Mendez C, Salas JA. Antitumor compounds from marine actinomycetes[J]. Mar Drugs,2009b,7:210-248.
[157]0rskov J. Investigations into the morphology of the ray fungi. Enhagen:Levin and Munksgaard,1923.
[158]Overmann J. Novel cultivation strategies for environmentally important microorganisms. IN geomicrobiology:molecular and environmental perspective,69-89, 2010.
[159]Palleroni NJ. A chemotactic method for the isolation of Actinoplanceae[J]. A rch Microbiol,1980,128:53
[160]Pathom-Aree W, Stach JE, Ward AC, et.al. Diversity of actinomycetes isolated from Challenger Deep sediment (10,898 m) from the Mariana Trench[J]. Extremophiles, 2006,10(3):181-189.
[161]Phung N T, Lee J, Kang KH, et al. Analysis of microbial diversity in oligotrophic microbial fuel cells using 16S rDNA sequences[J]. FEMS Microbiology Letters,2004, 233(1):77-82.
[162]Pierr-alain M, Lionel R, Christophe M, et al. Metaproteomics:A new approach for studying functional microbial ecology[J]. Microbial Ecology.2007,53:486-493.
[163]Pospiech A, Neumann B. A versatile quick-prep of genomic DNA from gram-positive bacteria[J]. Trends Gene,1995,11:217-218
[164]Qin S, Li J, Zhang Y Q, et al. Plantactinospora mayteni gen. nov., sp. nov., a new member of the family Micromonosporaceae[J]. Int J Syst Evol Microbiol,2009,59: 2527-2533.
[165]Ramsay A J. Extraction of bacteria from soil:efficiency of shaking or ultrasonication as indicated by direct counts and autoradiography[J]. Soil Biol.Biochem,1984,16: 475-481.
[166]Rath JP, Kinast S, Maier ME. Synthesis of the full functionalized core structure of the antibiotic abyssomicin C[J]. Org Lett,2005,7:3089-3092.
[167]Rheims H, Schumann P, Rohde M, et al. Verrucosispora gifhornensis gen. nov., sp. Nov., a new member of the actinobacterial family Micromonosporaceae[J]. Int J Syst Bacteriol,1998,48:1119-1127.
[168]Riedlinger J, Reicke A, Zahner H, et al. Abyssomicins, inhibitors of the para-aminobenzoic acid pathway produced by the marine Verrucosispora strain AB-18-032[J]. JAntibiot,2004,57:271-279.
[169]Rintala H, Nevalainen A, Ronka E, et al. PCR primers targeting the 16S rRNA gene for the specific detection of streptomycetes[J]. Mol Cell Probes,2001,15:337-347.
[170]Robe P, Nalin R, Capellano C, et al. Extraction of DNA from soil[J]. European Journal of Soil Biology,2003,39:183-190.
[171]Roose-Amsaleg CL, Garnier-sillam E, Harry M. Extraction and purification of microbial DNA from soil and sediment samples[J]. Applied soil Ecology,2001, 18:47-60.
[172]Rothschild L. A microbiologist explodes the myth of the unculturables[J]. Nature,2006, 443:249.
[173]Rowbotham TJ, Cross T. Ecology of rhodococcus coprophilus and associated actinomycetes in fresh water and agricultural habitats[J]. J Gen Microbio.1977,100: 231-240.
[174]Saitou N, Nei M. The neighbor-joining method:a new method for reconstructing phylogenetic trees[J]. Mol Bio Evol,1987,4:406-425
[175]Salazar O, Gonzalez I, Genilloud O. New genus-specific primers for the PCR identification of new isolates of the genera Nocardiopsis and Saccharothrix[J]. Int J Syst Evol Microbiol,2002,52:1411-1421.
[176]Salazar O, Moron R, Genilloud O. New genus-specific primers for the PCR identification of members of the genus Saccharomonospora and evaluation of the microbial diversity of wild-type isolates of Saccharomonospora detected from soil DNAs[J]. Int J Syst Evol Microbiol,2000,50:2043-2055
[177]Sambrook J, Fritsch EF, Maniatis T. Molecular Cloning:A Laboratory Manual,2nd edn. Cold Spring Harbor Laboratory, New York,1989.
[178]Schafer J, Jackel U, Kampfer P. Development of a new PCR primer system for selective amplification of Actinobacteria[J]. FEMS Microbiol Lett,2010,311: 103-112.
[179]Schneider K, Keller S, Wolter FE, et al. Proximicins A, B, and C-antitumor furan analogues of netropsin from the marine actinomycete Verrucosispora Tnduce upregulation of p53 and the cyclin kinase inhibitor p21[J]. Angew Chem Int Ed Engl, 2008,47:3258-61
[180]Schuler GD. Sequence mapping by electronic PCR[J]. Genome Res,1997,7:541-550.
[181]Sekiguchi Y, Takahashi H, Kamagata Y, et al. In situ detection, isolation, and physiological properties of a thin filamentous microorganism abundant in methanogenic granular sludges:a novel isolate affiliated with a clone cluster, the green non-sulfur bacteria, subdivision I[J]. Appl Environ Microb,2001,67(12):5740.
[182]Sekiguchi Y, Kamagata Y, et al. Fluorescence in situ hybridization using 16S rRNA-targeted oligonucleotides reveals localization of methanogens and selected uncultured bacteria in mesophilic and thermophilic sludge granules[J]. Appl. Environ. Microbiol,1999,65:1280-1288.
[183]Sembiring L, Ward AC, Goodfellow M. Selective isolation and characterisation of members of the Streptomyces violaceusniger clade associated with the roots of Paraserianthes falcataria[J]. Antonie van Leeuwenhoek,2000,78:353-366.
[184]Shen FT, Young CC. Rapid detection and identification of the metabolically diverse genus Gordonia by 16S rRNA-gene-targeted genus-specific primers [J]. FEMS Microbiol Lett,2006,250:221-227
[185]Shirai M, Okuda M, Motohashi K, et al.Imoto M, Furihata K, Matsuo Y, Katsuta A, Shizuri Y, Seto H. Terpenoids produced by actinomycetes:isolation, structural elucidation and biosynthesis of new diterpenes, gifhornenolones A and B from Verrucosispora gifhornensis YM28-088[J]. JAntibiot (Tokyo).2010,63(5):245-50.
[186]Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species [J]. Int J Syst Bacteriol,1966,16:313-340.
[187]Stach JE, Maldonado LA, Masson DG, et al. Statistical approaches for estimating actinobacterial diversity in marine sediments[J]. Appl Environ Microbiol,2003a, 69(10):6189-6200.
[188]Stach JE, Maldonado LA, Ward AC, et al. New primers for the class Actinobacteria: application to marine and terrestrial environments [J]. Environ Microbiol,2003b, 5(10):828-841.
[189]Stackebrandt E, Liesack W. Nucleic acids and classification. In.Goodfellow M, O'Donell A G ed.Handbook of New Baetrial Systematics.London:Academic Press Ltd, 1993.
[190]Stackebrandt E, Rainey FA, Ward-Rainey NL. Proposal for a new hierarchic classification system, Actinobacteria classis nov[J]. Int J Syst Bacteriol,1997, 47:479-491.
[191]Staley JT, Konopka A. Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats [J]. Annu Rev Microbiol,1985,39: 321-346.
[192]Susannah GT, Edward MR. Metagenomics:DNA sequencing of environmental samples[J]. Nature Genetics.2005,6:805-814.
[193]Tamura K, Dudley J, Nei M, Kumar S. MEGA4, Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0 [J]. Mol Biol Evol,2007,24:1596-1599
[194]Tamura T, Hatano K, Suzuki, K. A new genus of the family Micromonosporaceae, Polymorphospora gen. nov., with description of Polymorphospora rubra sp. nov[J]. Int J Syst Evol Microbiol,2006,56,1959-1964.
[195]Tamura T, Hayakawa M, Hatano K. A new genus of the order Actinomycetales, Spirilliplanes gen. nov., with description of Spirilliplanes yamanashiensis sp. nov[J]. Int J Syst Bacteriol,1997,47:97-102.
[196]Tamura T, Hayakawa M, Hatano K. A new genus of the order Actinomycetales, Virgosporangium gen. nov., with descriptions of Virgosporangium ochraceum sp. nov. and Virgosporangium aurantiacum sp. nov[J]. Int J Syst Evol Microbiol,2001, 51:1809-1816.
[197]Tamura T, Nakagaito Y, Nishii T, et al. A new genus of the order Actinomycetales, Couchioplanes gen. nov., with descriptions of Couchioplanes caeruleus (Horan and Brodsky 1986) comb. Nov. and Couchioplanes caeruleus subsp. Azureus subsp. nov[J]. Int J Syst Bacteriol,1994,44:193-203.
[198]Tan GYA, Robinson S, Lacey E, et al. Amycolatopsis regifaucium sp. nov., a novel actinomycete that produces kigamicins[J]. Int J Syst Evol Microbiol,2007,57: 2562-2567.
[199]Tan GYA, Ward AC, Goodfellow M. Exploration of Amycolatopsis diversity in soil using genus-specific primers and novel selective media[J]. Syst Appl Microbiol 2006, 29:557-569.
[200]Thawai C, Tanasupawat S, Itoh T, et al. Actinocatenispora thailandica gen. nov., sp. nov., a new member of the family Micromonosporaceae[J]. Int J Syst Evol Microbiol, 2006,56:1789-1794.
[201]Thawai C, Tanasupawat S, Kudo T. Actinaurispora gen. nov., a new member of the family Micromonosporaceae, with description of Actinoaurantispora siamensis sp. nov[J]. Int J Syst Evol Microbiol,2010, (IJSEM, in press).
[202]Thiemann JE, Pagani H, Beretta G. A new genus of the Actinoplanaceae: Dactylosporangium gen. nov[J]. Arch Mikrobiol,1967,58,42-52.
[203]Thomas T, Egan S, Burg D, et al. Integration of genomics and proteomics into marine microbial ecology[J]. Mar Ecol Prog Ser,2007,332:291-299.
[204]Thompson JD, Gibson TJ, Plewniak F, et al. The CLUSTAL-X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools[J]. Nucleic Acids Res,1997,25:4876-4876
[205]Tiedje JM. Approaches to the comprehensive evaluation of prokaryotic diversity of a habitat, p73-87. In D Allsopp RR, Colwell DL, Hawksworth. Microbial diversity and ecosystem function. Wallingford, UK:CAB International,1995.
[206]Torsvik V, Goksoyr J, Daae FL. High diversity in DNA of soil bacteria[J]. Appl Environ Microbiol,1990,56:782-787.
[207]Tyson GW, Banfield JF. Cultivating the uncultivated:a community genomics perspective [J]. Trends Microbiol,2005,13:411-415.
[208]Tyson GW, Chapman J, Hugenholtz P, et al. Community structure and metabolism through reconstruction of microbial genomes from the environment[J]. Nature,2004, 428:37-43.
[209]Wang Q, Garrity GM, Tiedje JM, et al. Naive bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy [J]. Appl Environ Microbiol,2007, 73:5261-5267.
[210]Ward AC, Goodfellow M. Phylogeny and functionality:taxonomy as a roadmap to genes. In:Bull AT (ed) Microbial diversity, bioprospecting. ASM Press, Washington, DC, pp 288-313,2004.
[211]Ward DC, White DC. The new omics era [J]. Curr.Opin.Biotechnol,2002,13:11-13.
[212]Watanabe A, Ebizuka Y. Unprecedented Mechanism for Chain Length Determination in Fungal Aromatic Polyketide Synthases, Chemistry and Biology Vol.11, pp. 1101-1106A,2004.
[213]Wawrik B, Kutliev D, Abdivasievna UA, et al. Biogeography of actinomycete communities and type Ⅱ polyketide synthase genes in soils collected in New Jersey and central asia[J]. Appl. Environ. Microbiol.2007,73(9):2982-2989.
[214]Wayne LG, Brenner DJ, Colwell RR, et al. Report of the ad hoc committee on reconcilation of approaches to bacterial sytematics[J]. Int J Syst Bacteriol,1987,37: 463-464
[215]Wiese J, Jiang Y, Tang SK, et al. A new member of the family Micromonosporaceae, Planosporangium flavigriseum gen. nov., sp. nov[J]. Int J Syst Evol Microbiol,2008, 58:1324-1331.
[216]Williams PG, Buchanan GO, Feling RH, et al. New cytotoxic salinosporamides from the marine actinomycete Salinispora tropica [J]. J Org Chem,2005,70(16): 6196-6203.
[217]Williams ST, Lanning S, Wellington, et al. Ecology of actinomycetes. In "The Biology of the Actinomycetes", Goodfellow M, Mordarski M, Williams ST, Eds, Academic Press:London, UK, pp.481-528,1984a.
[218]Williams ST, Goodfellow M, Vickers JC. New microbes from old habitats, p. 219-256.In D P Kelly, N R Carr (ed.), The microbe 1984. Cambridge, UK:Cambridge University Press,1984b.
[219]Wilmes PT, Bond PL. Metaproteomics:studying functional gene wspression in mcriobial ecosystems [J]. Trends microbial,2006,14:92-97.
[220]Xie QY, Wang C, Wang R, et al. Jishengella endophytica gen. nov., sp. nov., a new member of the family Micromonosporaceae [J]. Int J Syst Evol Microbiol.2010, doi:10.1099/ijs.0.025288-0.
[221]Yokota A, Tamura T, Hasegawa T, et al. Catenuloplanes japonicas gen. nov., sp. nov., nom. Rev., a new genus of the order Actinomycetales[J]. Int J Syst Bacteriol,1993,43: 805-812.
[222]Yu Y, Lee C, et al. Analysis of community structures in anaerobic processes using a quantitative real-time PCR method." [J].Water Sci. Technol,2005,52:85-91.
[223]Zengler K, Toledo G, Rappe M, et al. Cultivating the uncultured [J]. Proc. Natl. Acad. Sci.,2002,99:15681-15696.
[224]Zhi XY, Li WJ, Stackebrandt E. An update of the structure and 16S rRNA gene sequence-based definition of higher ranks of the class Actinobacteria, with the proposal of two new suborders and four new families and emended descriptions of the existing higher taxa[J]. Int J Syst Evol Microbiol,2009,59:589-608.
© 2004-2018 中国地质图书馆版权所有 京ICP备05064691号 京公网安备11010802017129号 地址：北京市海淀区学院路29号 邮编：100083 电话：办公室：(+86 10)66554848；文献借阅、咨询服务、科技查新：66554700 |