海洋細菌可能生存於海洋中的各個角落，在不同的環境下，會發展出不同的細菌群落，所以可藉著採集不同地區的樣品，分析菌相組成與差異。本研究主要針對高雄港附近海域之不同深度以及東沙島海域等採樣點進行未經培養部分的分析，在高雄港另外進行培養的菌相分析。在實驗部分主要是利用聚合酶連鎖反應(PCR)，配合基因選殖(Cloning)與變性梯度膠體電泳(Denaturing gradient gel electrophoresis, DGGE)等分子生物技術，對微生物的16S rDNA 序列進行菌相分析。結果顯示高雄港培養的海水及底泥的菌相多樣性是相近的，皆有Bacilli綱及Gammaproteobacteria綱的菌種，但組成的比例是不同的；高雄港未經培養樣品的菌相多樣性，皆明顯的多於培養樣品。高雄港培養與未經培養的底泥樣品菌相，皆是以Bacilli綱為最多；而海水樣品菌相，培養以Gammaproteobacteria綱為最多，未經培養以Alphaproteobacteria綱為最多。高雄港與東沙島的未經培養海水菌相多樣性是相近的，但Deltaproteobacteria、Fibrobacteres/Acidobacteria group、Lactobacillales、Prochlorales 、Verrucomicrobia等綱，只出現於高雄港未經培養海水的菌相中；而Epsilonproteobacteria、Anaerolineae 、(Cytophaga-Flexibacter-Bacteroides, CFB) group、Chloroflexi、Thermomicrobia等綱，只出現於東沙島海水的菌相中。

Marine bacteria may live in the ocean everywhere, that the difference bacterial structure will breed in the different environment. So we can analyze the bacterial structure and the difference by sampling from different environment. In this study, various seawater and sediment samples in the offshore of Kaohsiung Harbor in southern Taiwan and Dongsha island were collected and analyzed for the non-cultivated bacteria in each sample. In addition, various seawater and sediment samples in the offshore of Kaohsiung Harbor were analyzed for the cultivated bacteria. Molecular techniques including PCR, denaturing gradient gel electrophoresis (DGGE), cloning and 16S rDNA sequencing were used to reveal the microbial diversities. The results showed that the bacterial isolated found in the non-cultivated samples of Kaohsiung Harbor were similiar, however, with different proportions. Gammaproteobacteria were predominant species in the cultivated schemes, the next abundant species were Bacilli. The bacterial community diversity are much in the non-cultivated schemes of Kaohsiung Harbor than in the cultivated schemes. In the sediment bacterial community of the both cultivated and non-cultivated are the most in the Bacilli specie. But the Gammaproteobacteria specie is predominant in the seawater bacterial community of the cultivated scheme, and the non-cultivated is the Alphaproteobacteria specie. The non-cultivated bacterial community diversity of seawater of the Kaohsiung and Dongsha island are smiliar. However, the species of Deltaproteobacteria, Fibrobacteres/Acidobacteria group, Lactobacillales, Prochlorales, Verrucomicrobia are only found in the samples of Kaohsiung Harbor, and the species of Epsilonproteobacteria, Anaerolineae, CFB group, Chloroflexi, Thermomicrobia are only existed in the Dongsha Island.

論文審定書................................................................................................................i
誌謝.........................................................................................................................ii
摘要 ........................................................................................................................iii
Abstract...................................................................................................................iv
圖次 .......................................................................................................................ix
表次 .......................................................................................................................xi
第一章前言 ..............................................................................................................1
1.1 高雄港介紹..........................................................................................................1
1.2東沙島介紹...........................................................................................................2
1.3 海洋細菌.............................................................................................................4
1.3.1 海洋細菌多樣性.................................................................................................4
1.3.2 海洋細菌之工業應用..........................................................................................5
1.3.3 海洋細菌之醫藥應用..........................................................................................5
1.4海洋潟湖細菌........................................................................................................6
1.5 微生物多樣性.......................................................................................................6
1.6 16S rDNA之應用與特性........................................................................................7
1.7 分子生物技術與海洋微生物分析.............................................................................8
1.7.1小單元的RNA (SSU,Small subunit of the rRNA): ..................................................8
1.7.2單股構形的多形性(SSCP, Single-strand Conformation Polymorphism):....................8
1.7.3隨機擴增多型性DNA (RAPD, Random Amplified Polymorphic DNA):.......................8
1.7.4限制片段長度多型性(RFLP ,Restriction Fragment Length Polymorphism): ..............8
1.7.5擴增片段長度多型性(AFLP ,Amplified Fragment Length Polymorphism): ................9
1.7.6溫度梯度膠體電泳(TGGE ,Temperature Gradient Gel Electrophoresis):....................9
1.7.7螢光原位雜合(FISH, Fluorescent in-situ Hybridisation):..........................................9
1.7.8分子選殖(Molecular Cloning):...............................................................................9
1.8 PCR配合DGGE技術之應用...................................................................................9
1.8.1聚合酶連鎖反應-Polymerase Chain Reaction (PCR) ..............................................9
1.8.2變性梯度膠體電泳- Denaturing Gradient Gel Electrophoresis (DGGE) ...................10
1.8.3 利用16S rDNA配合PCR-DGGE技術之菌相分析..................................................10
1.8.4 DGGE配合Cloning技術之16S rDNA菌相分析......................................................11
1.9研究目的............................................................................................................13
實驗流程 ................................................................................................................14
第二章實驗材料方法 ................................................................................................15
2.1 採樣..................................................................................................................15
2.1.1高雄港採樣......................................................................................................15
2.1.2東沙島採樣......................................................................................................15
2.2 細菌DNA萃取....................................................................................................15
2.2.1培養的海水細菌DNA萃取前處理.........................................................................15
2.2.2培養的底泥細菌DNA萃取前處理.........................................................................16
2.2.3東沙島、高雄港海水未經培養細菌DNA萃取前處理...............................................16
2.2.4高雄港未經培養海水及底泥細菌DNA萃取前處理..................................................17
2.2.5以agarose瓊脂膠體電泳檢視DNA.......................................................................17
2.3 聚合酶連鎖反應(PCR)放大16S rDNA....................................................................18
2.3.1瓊脂膠體電泳確認16S rDNA片段........................................................................19
2.4 變性梯度電泳-Denaturing Gradient Gel Electrophoresis (DGGE).............................20
2.4.1變性梯度膠體製作37.5%-57.5%.........................................................................20
2.4.2進行變性梯度膠體電泳......................................................................................21
2.4.3 SYBR greenⅠ染色............................................................................................21
2.4.4 DGGE膠體圖譜分析.........................................................................................22
2.5 DNA選殖(Cloning) .............................................................................................22
2.5.1純化回收PCR產物............................................................................................22
2.5.2 Ligation .........................................................................................................23
2.5.3 Transformation................................................................................................23
2.5.4篩選相同clone .................................................................................................25
2.5.5 Nested PCR反應.............................................................................................25
2.6 生化測試...........................................................................................................26
2.7 定序、序列比對、序列提交.................................................................................27
2.7.1序列比對分析...................................................................................................28
2.7.2序列提交至NCBI ..............................................................................................28
第三章 結果與討論 ..................................................................................................29
3.1高雄港培養菌相...................................................................................................29
3.1.1沿岸表層海水之菌相分析結果:...........................................................................30
3.1.2 100M海水之菌相分析結果: ..............................................................................30
3.1.3 300M海水之菌相分析結果: ..............................................................................31
3.1.4 500M海水之菌相分析結果: ..............................................................................31
3.1.5 100M底泥之菌相分析結果: ..............................................................................32
3.1.6 300M底泥之菌相分析結果: ..............................................................................32
3.1.7 500M底泥之菌相分析結果: ..............................................................................33
3.2高雄港未經培養菌相............................................................................................34
3.2.1沿岸表層海水之菌相分析...................................................................................34
3.2.2 100M表層海水部分之菌相分析..........................................................................36
3.2.3 300M表層海水之菌相分析................................................................................37
3.2.4 300M深度100M海水之菌相分析........................................................................37
3.2.5 500M表層海水之菌相分析................................................................................38
3.2.6 500M深度100M海水之菌相分析........................................................................39
3.2.7 300M底泥之菌相分析.......................................................................................39
3.2.8 500M底泥之菌相分析.......................................................................................40
3.2.9 高雄港序列提交結果........................................................................................41
3.3東沙島未經培養菌相............................................................................................41
3.3.1 東沙島周圍西之菌相分析..................................................................................41
3.3.2 東沙島周圍北之菌相分析..................................................................................43
3.3.3 東沙島周圍東之菌相分析..................................................................................44
3.3.4 東沙島周圍南之菌相分析..................................................................................45
3.3.5 東沙島小潟湖西之菌相分析...............................................................................46
3.3.6 東沙島小潟湖東北之菌相分析...........................................................................46
3.3.7 東沙島小潟湖東南之菌相分析...........................................................................47
3.3.8東沙島序列提交結果.........................................................................................48
3.4菌相差異............................................................................................................48
3.4.1高雄港培養海水及底泥之菌相比較......................................................................48
3.4.2高雄港未經培養海水及底泥之菌相比較...............................................................49
3.4.3高雄港培養與未經培養海水之菌相比較...............................................................51
3.4.4高雄港培養與未經培養底泥之菌相比較...............................................................51
3.4.5東沙島之菌相比較.............................................................................................52
3.4.6高雄港未經培養海水與東沙島海水之菌相比較......................................................52
第四章 結論.............................................................................................................56
參考文獻 ................................................................................................................58

白緹薇，2011。高雄港廢汙水排放區底棲生物之群聚結構及四種底棲動物蛋白質表現之研究。國立中山大學海洋生物研究所碩士論文。
方孟德，1996。台灣西南海域沈積物中重金屬及氯苯類化合物含量分佈之研究。國立中山大學海洋環境研究所碩士論文。
李瑋承，2013。高雄港蟹類重金屬蓄積之研究。國立高雄海洋科技大學。海洋環
境工程研究所碩士論文。
劉大綱，2008。高雄港海域船舶壓艙水導入外來種生物污染之研究。行政院國家
科學委員會研究報告。
海洋國家公園管理處網站。2010-05-12。
陳俊廷，2012。高雄港底泥污染調查及處理技術評估。國立中山大學環境工程研
究所碩士論文。
陳仲玉，1995。中央研究院歷史語言研究所。
羅文增，洪佳章，王玉懷。2011. 東沙環礁潟湖生態系統研究-物理、化學水文與
基礎生產力之時空變化探討。海洋國家公園管理處委託辦理報告。
高雄、台中、基隆、花蓮港務局。營運紀錄2008-2012。
宋克義，陳昭倫，王志騰，野澤洋耕。2009。東沙環礁珊瑚群聚調查分析與復育
策略研究(一)。海洋國家公園管理處委託辦理報告。
邵廣昭，陳義雄。2011。東沙環礁瀉湖魚卵及稚魚種類組成及分布調查計畫。海
洋國家公園管理處委託辦理報告。
汪谷威，夏復國。2011。秋季東沙環礁及南海季菌群聚結構及空間分布。國立台
灣海洋大學海洋環境化學與生態研究所。
梁
至希，夏復國。2012。東沙環礁潟湖內異營性細菌生產力時空變異及其生長限
制因子探討。國立台灣海洋大學海洋環境化學與生態研究所。
許峻嵐，2000。高屏海域沉積物重金屬之分布與污染史。中山大學海洋地質及化學研究所碩士論文。
謝濬澤。2011。從打狗到高雄：日治時期高雄港的興築與管理（1895—1945）。臺灣文獻。第六十二卷，第二期211-244頁。
謝濬澤。2008。國家與港口發展---高雄港的建構與管理(1985-1975)。暨南國際大學歷史系研究所碩士論文。
鄭春發，鄭國泰。2008。高雄海洋城市的發展機制之研究。臺北市立教育大學學報。第39卷，第一期1-44頁。
楊秉煌。2009。高雄港。台灣大百科全書。
Asao M, Takaichi S, Madigan MT (2007) Thiocapsa imhoffii, sp. nov., an alkaliphilic purple sulfur bacterium of the family Chromatiaceae from Soap Lake, Washington (USA). Arch Microbiol. 188: 665-675.
Abreu PC, Odebrecht C, Gonzalez A (1994) Particulate and dissolved phytoplankton production of the Patos Lagoon Estuary, southern Brazil: comparison of methods and influencing factors. J. Plankton Res. 16: 737-753.
Aiyar SE, Gaal T, Gourse RL (2002) rRNA promoter activity in the fast-growing bacterium Vibrio natriegens. J Bacteriol. 184:1349-1358.
Anil Kumar P, Srinivas TN, Sasikala C, Ramana CV (2007) Rhodobacter changlensis sp. nov., a psychrotolerant, phototrophic alphaproteobacterium from the Himalayas of India. Int J Syst Evol Microbiol. 57:2568-2571.
Alquezar R, Anastasi A (2013) The use of the cyanobacteria, Cyanobium sp., as a suitable organism for toxicity testing by flow cytometry. Bull Environ Contam Toxicol. 90: 684-690.
Adeleke AA, Fields BS, Benson RF, Daneshvar MI, Pruckler JM, Ratcliff RM, Harrison TG, Weyant RS, Birtles RJ, Raoult D, Halablab MA (2001) Legionella drozanskii sp. nov., Legionella rowbothamii sp. nov. and Legionella fallonii sp. nov.: three unusual new Legionella species. Int J Syst Evol Microbiol. 51:1151-1160.
Allers E, Gómez-Consarnau L, Pinhassi J, Gasol JM, Simek K, Pernthaler J (2007) Response of Alteromonadaceae and Rhodobacteriaceae to glucose and phosphorus manipulation in marine mesocosms. Environ Microbiol. 9: 2417-2429.
Attoui H, Jaafar FM, Belhouchet M, Micco P, Lamballerie X, Brussaard CP (2006) Micromonas pusilla reovirus: a new member of the family Reoviridae assigned to a novel proposed genus (Mimoreovirus). J Gen Virol. 87:1375-1383.
Arahal DR, Macián MC, Garay E, Pujalte MJ (2005) Thalassobius mediterraneus gen. nov., sp. nov., and reclassification of Ruegeria gelatinovorans as Thalassobius gelatinovorus comb. Int J Syst Evol Microbiol 55: 2371-2376.
Altinok I, Kayis S, Capkin E (2006) Pseudomonas putida infection in rainbow trout. Aquaculture. 261: 850-855.
Amarger N, Macheret V, Laguerre G (1997) Rhizobium gallicum sp. nov. and Rhizobium giardinii sp. nov., from Phaseolus vulgaris Nodules. Int J Syst Bacteriol. 47: 996-1006.
Ajithkumar B, Ajithkumar VP, Iriye R, Doi Y, Sakai T (2003) Spore-forming Serratia
marcescens subsp. sakuensis subsp. nov., isolated from a domestic wastewater treatment tank. Int J Syst Evol Microbiol. 53: 253-258
Alcaide E, Amaro C, Todolí R, Oltra R (1999) Isolation and characterization of Vibrio
parahaemolyticus causing infection in Iberian toothcarp Aphanius iberus. Dis Aquat Organ. 35:77-80.
Bozal N, Montes MJ, Tudela E, Guinea J (2003) Characterization of several Psychrobacter strains isolated from Antarctic environments and description of Psychrobacter luti sp. nov. and Psychrobacter fozii sp. nov. Int J Syst Evol Microbiol. 53: 1093-1100.
Brosius J, Palmer ML, Kennedy RJ, and Noller HF (1978) Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli. Proc Natl Acad Sci USA. 75: 4801-4805.
Brons JK, Elsas JD (2008) Analysis of bacterial communities in soil by use of
denaturing gradient gel electrophoresis and clone libraries, asinfluenced by different reverse primers. Appl Environ Microbiol. 74:2717-2127.
Burr FA, West JA (1971) Protein bodies in Bryopsis hypnoides: Their relationship to wound-healing and branch septum development. J Ultrastruct Res. 35: 476-498.
Biebl H, Pukall R, Lünsdorf H, Schulz S, Allgaier M, Tindall BJ,Wagner I (2007) Description of Labrenzia alexandriigen. nov., sp. nov., a novel alphaproteobacterium containing bacteriochlorophyll a, and a proposal for reclassification of Stappia aggregata as Labrenzia aggregata comb. nov., of Stappia marina as Labrenzia marinacomb. nov. and of Stappia alba as Labrenzia alba comb. nov., and emended descriptions of the genera Pannonibacter, Stappia and Roseibium, and of the species Roseibium denhamense and Roseibium hamelinense. Int J Syst Evol Microbiol. 57: 1095-1107.
Barns SM, Fundyga RE, Jeffries MW, Pace NR (1994) Remarkable archaeal diversity detected in a Yellowstone National Park hot spring environment. Proc Natl Acad Sci USA. 91: 1609-1613.
Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet. 32: 314-331.
Brown TA (2006) Gene cloning and DNA analysis: an introduction, 5th Edition. Cambridge, MA: Blackwell Pub.
Benlloch S, Rodríguez F, Martinez AJ (1995) Bacterial diversity in two coastal lagoons deduced from 16s rDNA PCR amplification and partial sequencing. FEMS Microbiol Ecol. 18: 267 -280.
Bjornsson L, Hugenholtz P, Tyson GW, Blackall LL (2002) Filamentous Chloroflexi (green non-sulfur bacteria) are abundant in wastewater treatment processes with biological nutrient removal. Microbiology. 148: 2309-2318.
Baldwin A, Mahenthiralingam E, Drevinek P, Vandamme P, Govan JR, Waine DJ, LiPuma JJ, Chiarini L, Dalmastri C, Henry DA, Speert DP, Honeybourne D, Maiden MCJ, and Dowson CG (2007) Environmental Burkholderia cepacia complex isolates in human infection. Emerg Infect Dis. 13: 458-461.
Breda V, Jolly N, Wyk J (2013) Characterisation of commercial and natural Torulaspora delbrueckii wine yeast strains. Int J Food Microbiol 163: 80-88.
Banciu HL, Sorokin DY, Tourova TP, Galinski EA, Muntyan MS, Kuenen JG, Muyzer G. (2008) Influence of salts and pH on growth and activity of a novel facultatively alkaliphilic, extremely salt-tolerant, obligately chemolithoautotrophic sufur-oxidizing Gammaproteobacterium Thioalkalibacter halophilus gen. nov., sp. nov. from South-Western Siberian soda lakes. Extremophiles. 12: 391-404.
Bond PL, Hugenholtz P, Keller J, Blackall LL (1995) Bacterial community structures of phosphate-removing and non-phosphate-removing activated sludges from sequencing batch reactors. Appl Environ Microbiol. 61: 1910-1916.
Berry C (2012) The bacterium, Lysinibacillus sphaericus, as an insect pathogen. J Invertebr Pathol. 109: 1-10.
Budinoff CR, Dunlap JR, Hadden M, Buchan A (2011) Marivita roseacus sp. nov., of the family Rhodobacteraceae, isolated from a temperate estuary and an emended description of the genus Marivita. J Gen Appl Microbiol. 57: 259-267.
Brown GR, Sutcliffe IC, Cummings SP (2001) Reclassification of [Pseudomonas]
doudoroffii (Baumann et al. 1983) into the genus Oceanomonas gen. nov. as Oceanomonas doudoroffii comb. nov., and description of a phenol-degrading bacterium from estuarine water as Oceanomonas baumannii sp. nov. Int J Syst Evol Microbiol. 51: 67-72
Brettar I, Christen R, Höfle MG (2004b). Belliella baltica gen. nov., sp. nov., a novel marine bacterium of the Cytophaga–Flavobacterium–Bacteroides group isolated from surface water of the central Baltic Sea. Int J Syst Evol Microbiol. 54: 2335-2341.
Bax CJ, Oostvogel PM, Mutsaers JA, Brand R, Craandijk M, Trimbos JB, Dörr PJ
(2002) Clinical characteristics of Chlamydia trachomatis infections in a general outpatient department of obstetrics and gynaecology in the Netherlands. Sex Transm Infect. 78:e6
Cappuccino JG and Sherman N (2001) Microbiology - A laboratory manual (sixth
edition), Pearson international edition, 143-185
Chang YJ, Stephen JR, Richter AP, Venosa AD, Bruggemann J, Macnaughton SJ, Kowalchuk GA, Haines JR, Kline E, White DC (2000) Phylogenetic analysis of aerobic freshwater and marine enrichment cultures efficient in hydrocarbon degradation: effect of profiling method. J Microbiol Methods. 40: 19-31.
Copeland C, Beers B, Thompson M, Pinkerton R, Barrett L, Sevilleja JE, Alencar S, Lima A, Guerrant R (2009) Faecal contamination of drinking water in a Brazilian shanty town: Importance of household storage and new human faecal marker testing. J Water Health. 7: 324-331.
Choi A, Cho JC (2010) Reinekea aestuarii sp. nov., isolated from tidal flat sediment. Int J Syst Evol Microbiol. 60: 2813-2817.
Choi DH, Hwang CY, Cho BC (2009) Pelagibius litoralis gen. nov., sp. nov., a marine bacterium in the family Rhodospirillaceae isolated from coastal seawater. Int J Syst Evol Microbiol. 59: 818-823.
Choi A, Yang SJ, Cho JC (2013) Lutibacter flavus sp. nov., a marine bacterium isolated
from a tidal flat sediment. Int J Syst Evol Microbiol. 63: 946-951.
Casas V, Kline DI, Wegley L, Yu Y, Breitbart M, Rohwer F (2004) Widespread association of a Rickettsiales-like bacterium with reef-building corals. Environ Microbiol. 6: 1137-1148.
Cabral, JPS (2010) Water Microbiology. Bacterial Pathogens and Water. Int J Environ Res Public Health. 7: 3657-3703.
Champs C, Le Seaux S, Dubost JJ, Boisgard S, Sauvezie B, Sirot J (2000) Isolation of Pantoea agglomerans in two cases of septic monoarthritis after plant thorn and wood sliver injuries. J Clin Microbiol. 38: 460-461.
Chung YH, Cho BC (2008) Cohaesibacter gelatinilyticus gen. nov., sp. nov., a marine bacterium that forms a distinct branch in the orderRhizobiales, and proposal ofCohaesibacteraceae fam. nov. Int J Syst Evol Microbiol. 58: 267-277.
Chiu HH, Shieh WY, Lin SY, Tseng CM, Chiang PW, Wagner I (2007) Alteromonas tagae sp. nov. and Alteromonas simiduii sp. nov., mercury-resistant bacteria isolated from a Taiwanese estuary. Int J Syst Evol Microbiol. 57: 1209-1216.
Colwell RR (1994) Biodiversity and release of genetically engineered organisms: a partnership of value. Curr Opin Biotechnol. 5: 244-246.
Choi A, Lee K, Oh HM, Feng J, Cho JC (2010) Litoricola marina sp. Int J Syst Evol Microbiol. 60:1303-1306.
Caumette P (1993) Ecology and physiology of phototrophic bacteria and sulfate-reducing bacteria in marine salterns. Experientia 49:473-481.
Chen WM , James EK , Prescott AR , Kierans M, Sprent JI (2003) Nodulation of Mimosa spp. by the β-Proteobacterium Ralstonia taiwanensis. Mol Plant Microbe Interact. 16: 1051-1061.
Choo YJ, Lee K, Song J, Cho JC (2007) Puniceicoccus vermicola gen. nov., sp. nov., a novel marine bacterium, and description of Puniceicoccaceae fam. nov., Puniceicoccales ord. nov., Opitutaceae fam. nov., Opitutales ord. nov. and Opitutae classis nov. in the phylum ‘Verrucomicrobia’. Int J Syst Evol Microbiol. 57: 532-537.
Carvalho FM, Souza RC, Barcellos FG, Hungria M, Vasconcelos AT (2010) Genomic and evolutionary comparisons of diazotrophic and pathogenic bacteria of the order Rhizobiales. BMC Microbiol. 10: 37.
Collado L, Figueras MJ (2011) Taxonomy, epidemiology, and clinical relevance of the genus Arcobacter. Clin Microbiol Rev. 24: 174-192.
Cai S, Li J, Hu FZ, Zhang K, Luo Y, Janto B, Boissy R, Ehrlich G, Dong X (2010) Cellulosilyticum ruminicola, a newly described rumen bacterium that possesses redundant fibrolytic- protein-encoding genes and degrades lignocellulose with multiple carbohydrate-borne fibrolytic enzymes. Appl Environ Microbiol. 76: 123818-3824.
Chen YG, Zhang YQ, Huang K, Tang SK, Cao Y, Shi JX, Xiao HD, Cui XL, Li WJ (2009) Pigmentiphaga litoralis sp. nov., a facultatively anaerobic bacterium isolated from a tidal flat sediment. Int J Syst Evol Microbiol. 59: 521-525.
Choroszy IC, Frej M, Jama A, Bober T, Jolanta Sarowska J (2012) Characteristics of
the Chlamydia trachomatis species - immunopathology and infections. Adv Clin Exp Med. 21:799-808.
Dilling W, Liesack W, Pfennig N (1995) Rhabdochromatium marinum gen. nom. rev., sp. nov., a purple sulfur bacterium from a salt marsh microbial mat. Arch Microbiol. 164: 125-131.
Dash HR, Mangwani N, Chakraborty J, Kumari S, Das S (2013) Marine bacteria: potential candidates for enhanced bioremediation. Appl Microbiol Biotechnol. 97: 561-571.
DeBoy RT, Mongodin EF, Fouts DE, Tailford LE, Khouri H, Emerson JB, Mohamoud
Y,Watkins K, Henrissat B, Gilbert HJ, Nelson KE (2008) Insights into plant cell wall degradation from the genome sequence of the soil bacterium Cellvibrio japonicus. J Bacteriol. 190: 5455-5463.
Dai X, Wang YN, Wang BJ, Liu SJ, Zhou YG (2005) Planomicrobium chinense sp. nov., isolated from coastal sediment, and transfer of Planococcuspsychrophilus and Planococcus alkanoclasticus to Planomicrobium as Planomicrobium psychrophilum comb. nov. and Planomicrobium alkanoclasticum comb. nov. Int J Syst Evol Microbiol. 55: 699-702.
Du ZJ, Zhang DC, Liu SN, Chen JX, Tian XL, Zhang ZN, Liu HC, Chen GJ (2009) Gilvimarinus chinensis gen. nov., sp. nov., an agar-digesting marine bacterium within the class Gammaproteobacteriaisolated from coastal seawater in Qingdao, China. Int J Syst Evol Microbiol. 59: 2987-2990.
De Clerck O, Kraft GT, Coppejans E (2002) Morphology and systematic of Sciurothamnion stegengae gen. et sp. nov. (ceramiaceae, rhodopgyta) from the Indo-Pacific. J Phycol. 38: 1176-1189.
Espinosa UM, Salido A, Ramos JL (2000) Genetic analysis of functions involved in adhesion of Pseudomonas putida to seeds. J Bacteriol. 182:2363-2369.
Eom SH, Kim YM, Kim SK (2013) Marine bacteria: potential sources for compounds to overcome antibiotic resistance. Appl Microbiol Biotechnol. 97: 4763-4773
Eder W, Ludwig W, Huber R (1999) Novel 16S rRNA gene sequences retrieved from highly saline brine sediments of Kebrit Deep, Red Sea. Arch Microbiol. 172: 213-218.
Emerson D, Rentz JA, Lilburn TG, Davis RE, Aldrich H, Chan C, Moyer CL (2007) A novel lineage of Proteobacteria involved in formation of marine fe-oxidizing microbial mat communities. PLoS One. 2: e667.
Ewing WH and Fife MA (1968) Enterobacter hafniae. Int J Syst Evol Microbiol.
18:263-271.
Eldere J (2003) Multicentre surveillance of Pseudomonas aeruginosa susceptibility patterns in nosocomial infections. J Antimicrob Chemother. 51: 347-352.
Fuhrman JA, McCallum K, Davis AA (1993) Phylogenetic diver sity of subsurface marine microbial communities from the Atlantic and Pacific oceans. Appl Environ Microbiol. 59: 1294-1302.
Ferreira AC, Nobre MF, Moore E, Rainey FA, Battista JR, Costa MS (1999) Characterization and radiation resistance of new isolates of Rubrobacter radiotolerans and Rubrobacter xylanophilus. Extremophiles. 3: 235-238.
Flombaum P, Gallegos JL, Gordillo RA, Rincón J, Zabala LL, Jiao N, Karl DM, Li
WK, Lomas MW, Veneziano D, Vera CS, Vrugt JA, Martiny AC (2013) Present and future global distributions of the marine Cyanobacteria Prochlorococcus and Synechococcus. Proc Natl Acad Sci USA. 110:9824-9829.
Fenical W, Jensen PR (2006) Developing a new resource for drug discovery: marine actinomycete bacteria. Nat Chem Biol. 2: 666- 673.
Gillespie JJ, Brayton KA, Williams KP, Quevedo Diaz MA, Brown WC, Brown WC, Azad AF, Sobral BW (2010) Phylogenomics reveals a diverse Rickettsiales Type IV Secretion System. Infect Immun. 78: 1809-1823.
Gomez B, Thompson FL, Thompson CC, Swings J (2003) Vibrio rotiferianus sp. nov., isolated from cultures of the rotifer Brachionus plicatilis. Int J Syst Evol Microbiol 53: 239-243.
Gilardi GL (1972) In frequently encountered Pseudomonas species causing infection in humans. Ann Intern Med. 77: 211-215.
Graeber I, Kaesler I, Borchert MS, Dieckmann R, Pape T, Lurz R, Nielsen P, von Döhren H, Michaelis W, Szewzyk U (2008) Spongiibacter marinus gen. nov., sp. nov., a halophilic marine bacterium isolated from the boreal sponge Haliclona sp. 1. Int J Syst Evol Microbiol. 58: 585-590.
Garrity GM, Holt JG (2001) Phylum BVII. Thermomicrobia phy. nov. Bergey’s Manual of Systematic Bacteriology. 2nd 1: 447-450.
Gonzalez-Lozano MC, Mendez-Rodriguez LC, Maeda-Martinez AM, Murugan G, Vazquez-Botello A (2010) Evaluation of toxicity of polluted marine sediments from Bahia Salina Cruz, Mexico. J Environ Sci Health A Tox Hazard Subst Environ Eng. 45: 121-7.
Grant WD, Gemmell RT, McGenity TJ, Halophiles, Horikoshi K (1998) Extremophiles: microbial life in extreme environments. New York, Wiley-Liss, 93-132.
Guiry MD, Guiry GM (2007) Genus: Trichosarcina taxonomy browser. AlgaeBase version 4.2 World-wide electronic publication, National University of Ireland, Galway.
Gauthier G., Gauthier M., Christen R (1995) Phylogenetic analysis of the genera Alteromonas, Shewanella, and Moritella using genes coding for small-subunit rRNA sequences and division of the genus Alteromonas into two genera, Alteromonas (emended) and Pseudoalteromonas gen. nov., and proposal of twelve new species combinations. Int J Syst Bacteriol. 45: 755–761.
Gandhi NM, Patell JR, Gandhi J, De Souza NJ, Kohl H. (1976) Prodigiosin metabolites of a marine Pseudomonas species. Mar Biol. 34: 223-227.
Garrity GM, Brenner DJ, Krieg NR, Staley JT (2005) The proteobacteria, Part C: The alpha-, beta-, Ddelta-, and epsilonproteobacteria. Bergey's Manual of Systematic Bacteriology, volume 2. New York, Springer. ISBN 978-0-387-24145-6.
Gremion F, Chatzinotas A, Harms H (2003) Comparative 16S rDNA and 16S rRNA
sequence analysis indicates that Actinobacteria might be a dominant part of the
metabolically active bacteria in heavy metalcontaminated bulk and rhizosphere
soil. Environ Microbiol. 5: 896-907
Gong J, Forster RJ, Yu H, Chambers JR, Sabour PM, Wheatcroft R , Chen S (2002)
Diversity and phylogenetic analysis of bacteria in the mucosa of chicken ceca
and comparison with bacteria in the cecal lumen. FEMS Microbiology. 208: 1-7
Galand PE, Bourrain M, De Maistre E, Catala P, Desdevises Y, Elifantz H, Kirchman DL, Lebaron P (2012) Phylogenetic and functional diversity of bacteria and archaea in a unique stratified lagoon, the Clipperton atoll (N Pacific). FEMS Microbiol Ecol. 79: 203-17.
Goh BPL, Chou LM (1997) Heavy Metal Levels in Marine Sediments of Singapore. Environmental Monitoring and Assessment 44: 67-80.
Gillan DC, Danis B, Pernet P, Joly G, Dubois P (2005) Structure of sediment-associated microbial communities along a heavy-metal contamination gradient in the marine environment. Appl Environ Microbiol 71: 679-690.
Gillan DC, Pernet P (2007) Adherent bacteria in heavy metal contaminated marine sediments. Biofouling. 23:1-13.
Hawksworth DL, Mound LA (1991) Biodiversity databases: the crucial significance of collections. In: The biodiversity of microorganisms and invertebrates: Its role in sustainable agriculture. CAB International, Wallingford, UK. 17-29.
Hájek J, Váczi P, Barták M, Jahnová L (2012) Interspecific differences in cryoresistance of lichen symbiotic algae of genus Trebouxia assessed by cell viability and chlorophyll fluorescence. Cryobiology. 64: 215-22.
Hobbie JE, Daley RJ, Jasper S (1977) Use of nuclepore filters for counting bacteria by fluorescence microscopy. Appl Environ Microbiol. 33: 1225-1228.
Haygood MG, Distel DL (1993) Bioluminescent symbionts of flashlight fishes and deep-sea anglerfishes form unique lineages related to the genus Vibrio. Nature. 363: 154-156.
Hardoim CC, Costa R, Araújo FV, Hajdu E, Peixoto R, Lins U, Rosado AS, Elsas JD
(2009) Diversity of bacteria in the marine sponge Aplysina fulva in Brazilian coastal waters. Appl Environ Microbiol. 75:3331-3343.
Hauahsy K (1992) PCR-SSCP: A simple and sensitive method foe detection of mutations in the genomic DNA. PCR Method Appl. 1:34-38.
Hadrys H, Balick M, Schierwater B (1992) Applications of random amplified polymorphic DNA (RAPD) in molecular ecology. Mol Ecol. 1: 55-63.
Hansen GH, Bergh O, Michaelsen J, Knappskog D (1992) Flexibacter ovolyticus sp. nov., a pathogen of eggs and larvae of Atlantic halibut, Hippoglossus hippoglossus L. Int J Syst Bacteriol. 42: 451-458.
Hernández-Eugenio G, Fardeau ML, Cayol JL, Patel BK, Thomas P, Macarie H, Garcia JL, Ollivier B (2002) Clostridium thiosulfatireducens sp. nov, a proteolytic, thiosulfate- and sulfur-reducing bacterium isolated from an upflow anaerobic sludge blanket (UASB) reactor. Int J Syst Evol Microbiol. 52: 1461-1468.
Hoffmann H, Stindl S, Stumpf A, Mehlen A, Monget D, Heesemann J, Schleifer KH, Roggenkamp A (2005) Description of Enterobacter ludwigii sp. nov., a novel Enterobacter species of clinical relevance. Syst Appl Microbiol. 28: 206-212.
Holmström C, Kjelleberg S (1999) Marine Pseudoalteromonas species are associated with higher organisms and produce biologically active extracellular agents. FEMS Microbiol Ecol. 30: 285-293.
Henke JM, Bassler BL (2004) Three parallel quorum-sensing systems regulate gene expression in Vibrio harveyi. J Bacteriol. 186: 6902-6914.
Hugenholtz P, Goebel BM, Pace NR (1998) Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol. 180: 4765-4774.
Hogan CM (2010) Bacteria. Encyclopedia of Earth. eds. Sidney Draggan and C.J.Cleveland, National Council for Science and the Environment, Washington DC
Hwang CY, Cho BC (2008) Cohaesibacter gelatinilyticus gen. nov., sp. nov., a marine bacterium that forms a distinct branch in the order Rhizobiales, and proposal of Cohaesibacteraceae fam. nov. Int J Syst Evol Microbiol. 58: 267-77.
Haake DA (2000) Spirochaetal lipoproteins and pathogenesis. Microbiology. 146: 1491-1504.
Hoyles L, Lawson PA, Foster G, Falsen E, Grainger JM, Collins MD (2000) Vagococcus fessus sp. nov., isolated from a seal and a harbour porpoise. Int J Syst Evol Microbiol. 50: 1151-1154.
Hafner LM, Pelzer ES (2011) Tubal damage, infertility and tubal ectopic pregnancy: chlamydia trachomatis and other microbial aetiologies. In Ectopic Pregnancy. Open Access Publisher. Ivars-Martinez E, Martin-Cuadrado AB, D'Auria G, Mira A, Ferriera S, Friedman R, Rodriguez-Valera F (2008) Comparative genomics of two ecotypes of the marine planktonic copiotroph Alteromonas macleodii suggests alternative lifestyles associated with different kinds of particulate organic matter. ISME J. 2: 1194-1212.
Imhoff JF, Pfennig N (2001) Thioflavicoccus mobilis gen. nov., sp. nov., a novel purple sulfur bacterium with bacteriochlorophyll b. Int J Syst Evol Microbiol. 51: 105-110.
Islam T, Jensen S, Reigstad LJ, Larsen O, Birkeland NK (2008) Methane oxidation
at 55 degrees C and pH 2 by a thermoacidophilic bacterium belonging to the Verrucomicrobia phylum. Proc Natl Acad Sci USA. 105: 300-304.
Inoue K, Habe H, Yamane H, Omori T, Nojiri H (2005) Diversity of carbazole-degrading bacteria having the car gene cluster: isolation of a novel gram-positive carbazole-degrading bacterium. FEMS Microbiol Lett. 245:145-153.
Ireland MM, Karty JA, Quardokus EM, Reilly JP, Brun YV (2002) Proteomic analysis of the Caulobacter crescentus stalk indicates competence for nutrient uptake. Mol Microbiol. 45: 1029-1041.
Ivanova EP, Flavier S and Christen R (2004) Phylogenetic relationships among marine Alteromonas-like proteobacteria: emended description of the family Alteromonadaceae and proposal of Pseudoalteromonadaceae fam. nov., Colwelliaceae fam. nov., Shewanellaceae fam. nov., Moritellaceae fam. nov., Ferrimonadaceae fam. nov., Idiomarinaceae fam. nov. and Psychromonadaceae fam. nov. Int J Syst Evol Microbiol. 54: 1773-1788.
Jun HS, Qi M, Ha1 JK, Forsberg CW (2007) Fibrobacter succinogenes, a dominant fibrolytic ruminal bacterium: transition to the post genomic era. Asian-Aust. J. Anim. Sci. 20: 802 - 810.
Jiang S, Kim MG, Kim IY, Hwangc SJ, Hur HG (2013) Biological synthesis of free-standing uniformed goethite nanowires by Shewanella sp. HN-41. J Mater Chem A 1: 1646-1650.
Juni E (1972) Interspecies transformation of Acinetobacter: genetic evidence for a ubiquitous genus. J Bacteriol. 112: 917.
Kikani BA, Singh SP (2012) The stability and thermodynamic parameters of a very thermostable and calcium-independent α-amylase from a newly isolated bacterium, Anoxybacillus beppuensis TSSC-1. Process Biochem 47: 1791-1798.
Kim H, Choo YJ, Cho JC (2007) Litoricolaceae fam. nov., to include Litoricola lipolytica gen. nov., sp. nov., a marine bacterium belonging to the order Oceanospirillales. Int J Syst Evol Microbiol. 57: 1793-1798.
Kang I, Lee K, Yang SJ, Choi A, Kang D, Lee YK, Cho JC (2012) Genome sequence of “Candidatus Aquiluna” sp. strain IMCC13023, a marine member ofthe Actinobacteria isolated from an Arctic Fjord. J Bacteriol. 194: 3550-3551.
KGC, 2004. Plan and design sanitary sewage system of Kaohsiung city. Kaohsiung city Government ,Taiwan , ROC.
Kämpfer P (2006). The family Streptomycetaceae. Part I. Taxonomy. In the prokaryotes, 3rd edn, 3: 538-604. Edited by M. Dworkin, S. Falkow, E. Rosenberg, K. H. Schleifer & E. Stackebrandt. New York: Springer.
Kurahashi M, Fukunaga Y, Sakiyama Y, Harayama S, Yokota A (2009) Iamia majanohamensis gen. nov., sp. nov., an actinobacterium isolated from sea cucumber Holothuria edulis, and proposal of Iamiaceae fam. nov. Int J Syst Evol Microbiol. 59: 869-873.
Koizumi Y, Kojima H, FuKui M (2003) Characterization of depth-related microbial community structure in lake sediment by denaturing gradient gel electrophoresis of amplified 16S rDNA and reversely transcribed 16S rRNA fragments. FEMS Microbiol Ecol .46: 147-157.
Kolton M, Green SJ, Harel YM, Sela N, Elad Y, Cytryn E (2012) Draft Genome Sequence of Flavobacterium sp. Strain F52, Isolated from the Rhizosphere of Bell Pepper (Capsicum annuum L. cv. Maccabi). J Bacteriol. 194: 5462-5463.
Ko KS, Oh WS, Lee MY, Lee JH, Lee H, Peck K R, Lee NY, Song JH (2006) Bacillus
infantis sp. nov. and Bacillus idriensis sp. nov., isolated from a patient with neonatal sepsis. Int J Syst Evol Microbiol. 56: 2541-2544.
Kishimoto N, Kosako Y, Tano T (1991) Acidobacterium capsulatum gen. nov., sp. nov.: an acidophilic chemoorganotrophic bacterium containing menaquinone from acidic mineral environment. Curr Microbiol. 22: 1-7.
Kainth P, Gupta RS (2005) Signature proteins that are distinctive of alpha proteobacteria. BMC Genomics. 6: 94.
Kersters K, Devos P, Gillis M, Swings J, Vandamme P, Stackebrandt E (2006)Introduction to the Proteobacteria. In The Prokaryotes: A Handbook on the Biology of Bacteria. 3rd edition, Release 3.12 edition. Edited by Dworkin M, Falkow S, Rosenberg E, Schleifer KH and Stackebrandt E. New York, Springer.
Lee CL, Coyle HM, Lee HC (2007) Genetic analysis of individual seeds by amplified fragment length polymorphism. Croat Med J. 248: 563-565.
Lee CL, Fang MD (1997) Sources and distribution of chlorobenzenes and hexachlorobutadiene in surficial sediments along the coast of Southwestern Taiwan. Chemosphere. 35: 2039-2050.
Lee CL, Fang MD, Hsieh MT (1998) Characterization and distribution of metals in surficial sediments in Southwestern Taiwan. Mar Pollut Bull. 36: 464-471.
Lee CL, Fang MD, Hsieh MT (1998) Characterization and distribution of metals in surficial sediments in southwestern Taiwan. Mar Pollut Bull 36: 464-471.
Larsen N, Olsen GJ, Maidak BL, McCaughey MJ, Overbeek R, Macke TJ, Marsh TL,Woese CR (1993) The ribosomal database project. Nucleic Acids Res. 21: 3021-3023.
Lim JM, Jeon CO, Lee JC, Song SM, Kim KY, Kim CJ (2006) Marinimicrobium koreense gen. nov., sp. nov. and Marinimicrobium agarilyticum sp. nov., novel moderately halotolerant bacteria isolated from tidal flat sediment in Korea. Int J Syst Evol Microbiol. 56: 653-657.
Lau KW, Ng CY, Ren J, Lau SC, Qian PY, Wong PK, Lau TC, Wu M (2005) Owenweeksia hongkongensis gen. nov., sp. nov., a novel marine bacterium of the phylum 'Bacteroidetes'. Int J Syst Evol Microbiol. 55: 1051-1057.
Lee YS, Lee DH, Kahng HY, Sohn SH, Jung JS (2011) Polaribacter gangjinensis sp. nov., isolated from seawater. Int J Syst Evol Microbiol. 61: 1425-1429.
Lee KB, Liu CT, Anzai Y, Kim H, Aono T, Oyaizu H (2005) The hierarchical system of the Alphaproteobacteria: description of Hyphomonadaceae fam. nov.,Xanthobacteraceae fam. nov. and Erythrobacteraceae fam. nov. Int J Syst Evol Microbiol. 55: 1907-1919.
Lee DH, Kahng HY, Lee YS, Jung JS, Kim JM, Chung BS, Park SK, Jeon CO (2009) Jejuia pallidilutea gen. nov., sp. nov., a new member of the family Flavobacteriaceae isolated from seawater. Int J Syst Evol Microbiol. 59: 2148-2152.
Li Q, Xu Y, Liu K, Cai L, Fu Y, Fu Y, Sun J, Zhang R (2013) Pelagibacterium nitratireducens sp.nov., a marine Alphaproteobacterium isolated from the East China Sea. Curr Microbiol. 66: 450-455.
Lee JS, Lee KC, Ahn JS, Mheen TI, Pyun YR, Park YH (2002) Weissella koreensis sp. nov., isolated from kimchi. Int J Syst Evol Microbiol. 52: 1257-1261.
Lim JM, Jeon CO, Song SM, Kim CJ (2005) Pontibacillus chungwhensis gen. nov., sp. nov., a moderately halophilic Gram-positive bacterium from a solar saltern in Korea. Int J Syst Evol Microbiol. 55: 165-170.
Labuzek S, Hupert-Kocurek KT, Skurnik M (2003) Isolation and characterisation of new Planococcus sp. strain able for aromatic hydrocarbons degradation. Acta Microbiol Pol. 52: 395-404.
Lai Q, Qiao N, Wu C, Sun F, Yuan J, Yuan J, Shao Z (2010) Stappia indica sp. nov., isolated from deep seawater of the Indian Ocean. Int J Syst Evol Microbiol. 60: 733-736.
Lee K, Lee HK, Choi TH, Kim KM, Cho JC (2007) Granulosicoccaceae fam. nov., to include Granulosicoccus antarcticus gen. nov., sp. nov., a non-phototrophic, obligately aerobic chemoheterotroph in the order Chromatiales, isolated from Antarctic seawater. J Microbiol Biotechnol. 17: 1483-1490.
Liu MY, Kjelleberg S, Thomas T (2011) Functional genomic analysis of an uncultured δ-proteobacterium in the sponge Cymbastela concentrica. ISME J. 5: 427-35.Li H, Liao JC (2013) Engineering a cyanobacterium as the catalyst for the photosynthetic conversion of CO2 to 1,2-propanediol. Microb Cell Fact. 12: 4.
Labrenz M, Lawson PA, Tindall BJ, Collins MD, Hirsch P (2003) Saccharospirillum impatiens gen. nov., sp. nov., a novel γ-Proteobacterium isolated from hypersaline Ekho Lake (East Antarctica). Int J Syst Evol Microbiol. 53: 653-660.
Liu MY, Kjelleberg S, Thomas T (2010) Functional genomic analysis of an uncultured δ-proteobacterium in the sponge Cymbastela concentrica. ISME J. 5: 427-435.
Lin SY, Shieh WY, Chen JS, Tang SL (2013) Complete Genome Sequence of Simiduia agarivorans SA1T, a marine bacterium able to degrade a variety of polysaccharides. Genome Announc 1: e00039-12.
Muyzer G, Kraan GM (2008) Bacteria from hydrocarbon seep areas growing on short-chain alkanes. Trends Microbiol. 16: 138-141.
Kennish MJ (1996) Practical Handbook of Estuarine and Marine Pollution (Marine Science) .
Madigan M, Cox SS, Stegeman RA (1984) Nitrogen fixation and nitrogenase activities in members of the family Rhodospirillaceae. J Bacteriol. 157: 73-78.
Mandelbaum RT, Allan DL, Wackett LP (1995) Isolation and characterization of a Pseudomonas sp. that mineralizes the s-Triazine herbicide atrazine. Appl Environ Microbiol. 61: 41451-41457
Math RK, Jin HM, Kim JM, Hahn Y, Park W, Madsen EL, Jeon CO (2012) Comparative genomics reveals adaptation by Alteromonas sp. SN2 to marine tidal-flat conditions: cold tolerance and aromatic hydrocarbon metabolism. PLoS One. 7: e35784.
Mayilraj S, Prasad GS, Suresh K, Saini HS, Shivaji S, Chakrabarti T (2005) Planococcus stackebrandtii sp. nov., isolated from a cold desert of the Himalayas, India. Int J Syst Evol Microbiol. 55: 91-94.Maya G, Neethu C, Aswathi N, Mohamed HA (2011) Diversity of Bacillus and Actinomycetes in the water and sediment samples from Kumarakom region of Vembanadu lake. Indian J Geo-Marine Sci. 40: 430-437.
McDonald WL, Jamaludin R, Mackereth G, Hansen M, Humphrey S, Short P, Taylor T, Swingler J, Dawson CE,Whatmore AM, Stubberfield E, Perrett LL, Simmons G (2006) Characterization of a Brucella sp. strain as a marine-mammal type despite isolation from a patient with spinal osteomyelitis in New Zealand. J Clin Microbiol. 4363-4370.
Manz W,Wagner M, Amann R, Schleifer KH (1994) In situ characterization of the microbial consortia active in two wastewater treatment plants. Water Res. 28: 1715-1723.
Musa N,Wei LS, Wee W (2008) Phenotypic and genotypic characteristics of Vibrio
harveyi isolated from black tiger shrimp (Penaeus Monodon). World Applied Sciences J. 3: 885-902 Mariat D, Firmesse O, Levenez F, Guimarăes V, Sokol H, Doré J, Corthier G, Furet JP (2009) The Firmicutes/Bacteroidetes ratio of the human microbiota changes with age. BMC Microbiol. 9: 123.
Marques AM, Burgos C, Aranda FJ, Teruel JA, Manresa A, Ortiz A, Farfán M (2012) Sphingobacterium detergens sp. nov., a surfactant-producing bacterium isolated from soil. Int J Syst Evol Microbiol. 62: 3036-3041.
McDonald IR, Kämpfer P, Topp E, Warner KL, Cox MJ, Hancock TL, Miller LG, Larkin MJ, Ducrocq V, Coulter C, Harper DB, Murrell JC, Oremland RS (2005) Aminobacter ciceronei sp. nov. and Aminobacter lissarensis sp. nov., isolated from various terrestrial environments. Int J Syst Evol Microbiol. 55: 1827-1832.
Mohamed NM, Enticknap JJ, Lohr JE, McIntosh SM, Hill RT (2008) Changes inbacterial communities of the marine sponge Mycale laxissima on transfer into aquaculture. Appl Environ Microbiol. 74:1209-1222.
Mergaert J, Lednická D, Goris J, Cnockaert MC, Vos P, Swings J (2003). Taxonomic study of Cellvibrio strains and description of Cellvibrio ostraviensis sp. nov., Cellvibrio fibrivorans sp. nov. and Cellvibrio gandavensis sp. nov. Int J Syst Evol Microbiol. 53: 465-471.
Makino K, Oshima K, Kurokawa K, Yokoyama K, Uda T, Tagomori K, Iijima Y, Najima M, Nakano M, Yamashita A, Kubota Y, Kimura S, Yasunaga T, Honda T,Shinagawa H, Hattori M, Iida T (2003) Genome sequence of Vibrio parahaemolyticus: a pathogenic mechanism distinct from that of Vibrio cholerae. Lancet 36: 743-749.
Muyzer G, Smalla K (1998) Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie van Leeuwenhoek 73: 127-141.
Muyzer G, Waal EC, Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol. 59: 695-700.
Muyzer G, Teske A, Wirsen CO, Jannasch HW (1995) Phylogenetic relationships of Thiomicrospira species and their identification in deep-sea hydrothermal vent samples by denaturing gradient gel electrophoresis of 16S rDNA fragments. Arch Microbiol. 164: 165-72.
Muyzer G (1999) DGGE/TGGE a method for identifying genes from natural ecosystems. Microbiol. 2:317-322.
Mountford DO (1993) Ecophysiological significance of anaerobes in the gastro-intestinal tracts of marine fish. In: Trends in Microbial Ecol ogy (RGuerrero and C Pedros-Alio, eds), pp 213-216, Spanish Society for Microbiology, Barcelona, Spain.
MacGregor BJ, Brüchert V, Fleischer S, Amann R (2002) Isolation of small-subunit rRNA for stable isotopic characterization. Environ Microbiol. 4: 451-64.
Mashiyama S, Sekiya T, Hayashi K (1990) Screening of multiple DNA samples for dectection of sequences changes. Technique 2: 304-306.
Medlin LK, Valentin K, Metfies K, Tobe K, Groben R (2006) Molecular tools for the study of marine microbial diversity. In: Doelle, H. W., (ed.) Encyclopedia of life support systems: biotechnology theme. Oxford, Eolss Publishers.
Madigan M and Martinko J. 2005. Brock Biology of Microorganisms (11th ed.). Prentice Hall.
Morillo J, Usero J, Gracia I (2004) Heavy metal distribution in marine sediments from the southwest coast of Spain. Chemosphere. 55:431-442.
Not F, Latasa M, Marie D, Cariou T, Vaulot D, Simon N (2004) A single species, Micromonas pusilla (Prasinophyceae), dominates the eukaryotic picoplankton in the Western English channel. Appl Environ Microbiol. 70: 4064-4072.
Nevin KP, Holmes DE, Woodard TL, Hinlein ES, Ostendorf DW, Lovley DR (2005) Geobacter bemidjiensis sp. nov. and Geobacter psychrophilus sp. nov., two novel Fe (III)-reducing subsurface isolates. Int J Syst Evol Microbiol. 55: 1667-1674.
Novak HR, Sayer C, Isupov MN, Paszkiewicz K, Gotz D, Gotz D, Spragg AM, Littlechild JA (2013) Marine Rhodobacteraceae L-haloacid dehalogenase contains a novel His/Glu dyad that could activate the catalytic water. FEBS J. 280: 1664-1680.
Nakatsu CH, Torsvik V, Øvreås L (2000) Soil community analysis using DGGE of 16S rDNA polymerase chain reaction products. Soil Sci Soc Am J. 64: 1382-1388.
Nithya C, Gnanalakshmi B, Pandian SK (2011) Assessment and characterization of heavy metal resistance in Palk Bay sedimentbacteria. Mar Environ Res. 71: 283-94.
Naiara RE, Embley TM (2012) The SAR11 group of alpha-proteobacteria is not related to the origin of mitochondria. PLoS One. 7: e30520.
Naas T, Coignard B, Carbonne A, Blanckaert K, Bajolet O, Bernet C, Verdeil X, Astagneau P, Desenclos JC, Nordmann P, French Nosocomial Infection Early Warning Investigation and Surveillance Network (2006) VEB-1 extended-spectrum beta-lactamase-producing Acinetobacter baumannii, France. Emerg Infect Dis 12: 1214-1222.
Nedashkovskaya OI, Kim SB, Han SK, Snauwaert C, Vancanneyt M, Kim KO, Lysenko AM, Rohde M, Frolova GM, Mikhailov VV, Bae KS (2005) Winogradskyella thalassocola gen. nov., sp. nov., Winogradskyella epiphytica sp. nov. and Winogradskyella eximia sp. nov., marine bacteria of the family Flavobacteriaceae. Int J Syst Evol Microbiol. 55: 49-55.
Olembo R (1991) Importance of microorganisms and invertebrates as components of biodiversity. In: The biodiversity of microorganisms and Invertebrates: Its role in Sustainable Agriculture. CAB International, Wallingford, UK.7-15.
Olsen GJ, Lane DJ, Giovannoni SJ, Pace NR, Stahl DA (1986) Microbial ecology and evolution: a ribosomal RNA approach. Annu Rev Microbiol. 40: 337-365.
Orata FD, Hedreyda CT (2011) Isolation and sequence analysis of the full-length toxR gene of type strain Vibrio campbellii and use of the toxR gene sequence to evaluate variation and relatedness with other Vibrio species. Philipp Sci Lett. 4: 70-80.
Ouellette SP, Dorsey FC, Moshiach S, Cleveland JL, CarabeoRA (2011) Chlamydia Species-Dependent Differences in the Growth Requirement for Lysosomes. PLoS One. 6: e16783.
Ogino A, Koshikawa H, Nakahara T, Uchiyama H (2001) Succession of microbial communities during a biostimulation process as evaluated by DGGE and clone library analyses. J Appl Microbiol. 91: 625-635.
Oh YS, Park AR, Lee JK, Lim CS, Yoo JS, Roh DH (2011) Pseudoalteromonas
donghaensis sp. nov., isolated from seawater. Int J Syst Evol Microbiol. 61: 351-355.
Orphan VJ, Taylor LT, Hafenbradl D, Delong EF (2000) Culture-dependent and
culture-independent characterization of microbial assemblages associated with high-temperature petroleum reservoirs. Appl. Environ. Microbiol. 66: 700-711
Petroutsos D. Petroutsos, P. Katapodis, P. Christakopoulos, D. Kekos (2007) Removal of p -chlorophenol by the marine microalga Tetraselmis marina. J Appl Phycol. 19: 485-490.
Petursdottir SK, Bjornsdottir SH, Hreggvidsson GO, Hjorleifsdottir S, Kristjansson
JK (2009) Analysis of the unique geothermal microbial ecosystem of the Blue
Lagoon. FEMS Microbiol Ecol. 70:425-432.
Partensky F, Hess WR, Vaulot D (1999) Prochlorococcus, a Marine Photosynthetic Prokaryote of Global Significance. Microbiol Mol Biol Rev 63: 106-127.
Pinhassi J, Pujalte MJ, Macián MC, Lekunberri I, González JM, Arahal DR (2007) Reinekea blandensis sp. nov., a marine, genome-sequenced gammaproteobacterium. Int J Syst Evol Microbiol. 57: 2370-2375.
Pandey J, Sharma NK, Khan F, Ghosh A, Oakeshott JG, Jain RK, Pandey G (2012) Chemotaxis of Burkholderia sp. strain SJ98 towards chloronitroaromatic compounds that it can metabolise. BMC Microbiol. 12: 19
Porter KG, Feig YS (1980) The use of DAPI for identifying and counting aquatic microflora. Limnol Oceanogr. 25: 943-948.
Powell JL (1999) Vibrio species. Clin Lab Med. 19: 537-552.
Palleroni N, Bradbury J (1993) Stenotrophomonas, a new bacterial genus for Xanthomonas maltophilia. Int J Syst Bacteriol. 43: 606-609.
Park S, Lee MH, Lee JS, Oh TK, Yoon JH (2011) Thalassobius maritimus sp. nov., isolated from seawater. Int J Syst Evol Microbiol. 62: 8-12.
Pisciotta JM, Zou Y, Baskakov IV (2010) Light-dependent electrogenic activity of cyanobacteria. PLoS One. 5: e10821.
Prescott LM, Harley JP, Klein DA (2005) Fundamentals of microbiology. 1st edition. McGraw-Hill Companies, Inc., USA.
Prescott LM, Harley JP, Klein DA (2008) Microbiology. 7th edition. McGraw-Hill Companies, Inc., USA.
Perry JJ, Staley JT, Lory S (2002) Microbial Life. Sinauer Associates, Inc., USA.
Pandey S, Ghosh PK, Ghosh S, De TK, Maiti TK (2013) Role of heavy metal resistantOchrobactrum sp. and Bacillus spp. strains in bioremediation of a rice cultivar and their PGPR like activities. J Microbiol. 51: 11-17.
Qin S, Zhang H, Zheng H (2012) Draft genome sequence of marine Streptomyces sp. strain W007, which produces angucyclinone antibiotics with a benz anthracene skeleton. J Bacteriol. 194: 1628-1629.
Rickert AA, Soria MA, Correa OS (2000) The adaptive acid response in Mesorhizobium sp. World J Microbiol Biotechnol 16:475-480
Rivas AJ, Balado M, Lemos ML, Osorio CR (2011) The Photobacterium damselae subsp. damselae hemolysins damselysin and HlyA are encoded within a new virulence plasmid. Infect Immun. 79: 4617-4627.
Romalde JL (2002) Photobacterium damselae subsp. piscicida: an integrated view of a bacterial fish pathogen. Int Microbiol 5: 3-9.
Rapala J, Berg KA, Lyra C, Niemi RM, Manz W, Manz W, Suomalainen S, Paulin L, Lahti K (2005) Paucibacter toxinivorans gen. nov., sp. nov., a bacterium that degrades cyclic cyanobacterial hepatotoxins microcystins and nodularin. Int J Syst Evol Microbiol. 55: 1563-1568.
Reinhold B, Hurek T, Gillis M, Hoste B, Vancanneyt M, Kersters K, De Ley J (1993) Azoarcus gen. nov., nitrogen-fixing proteobacteria associated with roots of kallar grass (Leptochloa fusca (L.) Kunth), and description of two species, Azoarcus indigens sp. nov. and Azoarcus communis sp. Int J Food Microbiol 43: 574-584.
Rasmussen LD, Sørensen SJ (1998) The effect of longterm exposure to mercury on the bacterial community in marine sediment. Curr Microbiol. 36: 291-297.
Riess O, Neorremoelle A, Collins C, Mah D, Weber B, Hayden MR (1992) Exclusion of DNA changes in the β–subunit of c-GMP phophodiesterase gene as the cause for Huntington’s disease. Nat Genet. 1: 104-113.
Rappé MS, Gordon DA, Vergin KL, Giovannoni SJ (1999) Phylogeny of actinobacteria small subunit (SSU) rRNA gene clones recovered from marine bacterioplankton. Syst Appl Microbiol. 22: 106–112.
Rhee YJ, Han CR, Kim WC, Jun DY, Rhee IK, Kim YH (2010) Isolation of a novel freshwater agarolytic Cellvibrio sp. KY-YJ-3 and characterization of its extracellular beta-agarase. J Microbiol Biotechnol. 20: 1378-1385.
Remans R, Snoeck C, Verreth C, Croonenborghs A, Luyten E, Ndayizeye M, Martínez E, Michiels J, Vanderleyden J (2007) Inactivation of the nodH gene in Sinorhizobium sp. BR816 enhances symbiosis with Phaseolus vulgaris L. FEMS Microbiol Lett. 266: 210-217.
Raja CE, Omine K (2012) Characterization of boron resistant and accumulating bacteria Lysinibacillus fusiformis M1, Bacillus cereus M2,Bacillus cereus M3, Bacillus pumilus M4 isolated from former mining site, Hokkaido, Japan. J Environ Sci Health A Tox Hazard Subst Environ Eng. 47:1341-1349.
Rothrock MJ, Garcla F (2005) Microbial diversity of benthic mats along a tidal desiccation gradient. Environ Microbiol. 7: 593-601.
Rodríguez V, Green C, Gómez B (2012) Cu and Pb biosorption on Bacillus thioparans strain U3 in aqueous solution: Kinetic and equilibrium studies. Chem Engine J. 181-182: 352-359.
Satomi M, Kimura B, Hamada T, Harayama S, Fujii T (2002) Phylogenetic study of the genus Oceanospirillum based on 16S rRNA and gyrB genes: emended description of the genus Oceanospirillum, description of Pseudospirillum gen. nov., Oceanobacter gen. nov. and Terasakiella gen. nov. and transfer of Oceanospirillum jannaschii and Pseudomonas stanieri to Marinobacterium as Marinobacterium jannaschii comb. nov. and Marinobacterium stanieri comb. nov. Int J Syst Evol Microbiol. 52: 739-747.
Schmidt U, Chmel H, Cobbs C (1979) Vibrio alginolyticus infections in humans. J
Clin Microbiol. 10: 666-668.
Sambasiva Rao KRS, Tripathy NK, Mahalaxmi Y, PrakashamRS(2012)Biochemical
characterization and identification of extracellular tyrosinase biosynthesis in Streptomyces antibioticus. Int Res J Bioche Bioinformatics. 2: 90-92.
Sogin ML, Morrison HG, Huber JA, Mark Welch D, Huse SM, Neal PR, Arrieta JM, Herndl GJ (2006) Microbial diversity in the deep sea and the underexplored "rare biosphere". Proc Natl Acad Sci U S A. 103:12115-12120.
Suresh K, Prabagaran SR, Sengupta S, Shivaji S (2004) Bacillus indicus sp. nov., an arsenic-resistant bacterium isolated from an aquifer in West Bengal, India. Int J Syst Evol Microbiol. 54: 1369-1375.
Seghers D, Wittebolle L, Top EM, Verstraete W and Siciliano SD (2004) Impact of agricultural practices on the Zea mays L. endophytic community. Appl Environ Microbiol. 70: 1475-1482.
Soliev AB, Hosokawa K, Enomoto K (2011) Bioactive pigments from marine bacteria: applications and physiological roles. Evid Based Complement Alternat Med. 1-17.
Souza BWS, Andrade FK, Teixeira DIA, Mansilla A, Freitas ALP (2010) Haemagglutinin of the antarctic seaweed Georgiella confluens (Reinsch) Kylin: isolation and partial characterization. Polar Biology. 33: 1311-1318.
Stronkhorst J, Schipper C, Brils J, Dubbeldam M, Postma J, Hoeven N (2003) Using marine bioassays to classify the toxicity of Dutch harbor sediments. Environ Toxicol Chem. 22: 1535-1547.
Suárez A, Lopez A, Tovar-Sanchez A, Yarza P, Orfila A, Arnds J, Marqués S, Niemann H, Schmitt P, Amann R, Rosselló R (2011) Response of sulfate-reducing bacteria to an artificial oil-spill in a coastal marine sediment. Environ Microbiol. 13: 1488-1499.
Suzuki Y, Orita M, Shiraihshi M, Hayashi K, Sekiya T (1990) Detection of ras gene mutations in human lung cancers by single-strand conformation polymorphism analysis of polymerase chain reaction pruductions. Oncogene. 5: 1037-1043.
Salunkhe D, Tiwari N, Walujkar S, Bhadekar R (2011) Halomonas sp. nov., an EPA-producing mesophilic marine isolate from the Indian Ocean. Pol J Microbiol. 60: 73-78.
Servin JA, Herbold CW, Skophammer RG, Lake JA (2008) Evidence excluding the root of the tree of life from the actinobacteria. Mol Biol Evol. 25: 1-4.
Sasidharan S, Logeswaran S, Latha LY (2012) Wound Healing Activity of Elaeis guineensis Leaf Extract Ointment. Int J Mol Sci. 13: 336-347.
Shieh WY, Lin YT, Jean WD (2004) Pseudovibrio denitrificans gen. nov., sp. nov., a marine, facultatively anaerobic, fermentative bacterium capable of denitrification.Int J Syst Evol Microbiol. 54: 2307-2312.
Shivaji S, Chaturvedi P, Suresh K, Reddy GS, Dutt CB, Wainwright M, Narlikar JV, Bhargava PM (2006) Bacillus aerius sp. nov., Bacillus aerophilus sp. nov., Bacillus stratosphericus sp. nov. and Bacillus altitudinis sp. nov., isolated from cryogenic tubes used for collecting air samples from high altitudes. Int J Syst Evol Microbiol. 56: 1465-1473.
Sekiguchi H,Watanabe M, Nakahara T, Xu B, Uchiyama H (2002) Succession of bacterial community structure along the Changjiang River determined by denaturing gradient gelelectrophoresis and clone library analysis. Appl Environ Microbiol. 68: 5142-5150.
Sawabe T, Hayashi K, Moriwaki J, Thompson FL, Swings J, Potin P, Christen R, Ezura Y (2004) Vibrio gallicus sp. nov., isolated from the gut of the French abalone Haliotis tuberculata. Int J Syst Evol Microbiol. 54: 843-846.
Saito T, Ishii S, Otsuka S, Nishiyama M, Senoo K (2008) Identification of novel Betaproteobacteria in a succinate-assimilating population in denitrifying rice paddy soil by using stable isotope probing. Microbes Environ. 23: 192-200.
Shelobolina ES, Vrionis HA, Findlay RH, Lovley DR (2008) Geobacter uraniireducens sp. nov., isolated from subsurface sediment undergoing uranium bioremediation. Int J Syst Evol Microbiol. 58:1075–1078.
Tagwerker C, Dupont CL, Karas BJ, Ma L, Chuang RY, Benders GA, Ramon A, Novotny M, Montague MG, Venepally P, Brami D, Schwartz A, Andrews C, Gibson DG, Glass JI, Smith HO, Venter JC, Hutchison CA 3rd (2012) Sequence analysis of a complete 1.66 Mb Prochlorococcus marinus MED4 genome cloned in yeast. Nucleic Acids Res. 40: 10375-10383.
Tappe D, Valenza G, Duwe T, Koebe HG, Frosch M, Abele M (2009) Clostridium subterminale - Infection Secondary to an Open Fracture. Infect Med. 26: 28-30.
Tena D, Martínez-Torres JA, María Pérez-Pomata T, Sáez-Nieto JA, Rubio V, Bisquert J (2007) Cutaneous Infection Due to Bacillus pumilus:Report of 3 Cases. Clin Infect Dis. 44: 40-42.
Thompson FL, Thompson CC, Li Y, Gomez B, Vandenberghe J, Hoste B, Swings J (2003) Vibrio kanaloae sp. nov., Vibrio pomeroyi sp. nov. and Vibrio chagasii sp. nov., from sea water and marine animals. Int J Syst Evol Microbiol. 53: 753-759.
Thomas F, Hehemann JH, Rebuffet E, Czjzek M, Michel G (2011) Environmental and gut bacteroidetes: the food connection. Front Microbiol 2:93.
Tiirola MA, Männistö MK, Puhakka JA, Kulomaa MS (2002) Isolation and characterization of Novosphingobium sp. strain MT1, a dominant polychlorophenol-degrading strain in a groundwater bioremediation system. Appl Environ Microbiol. 68: 173-180.
Tannock GW (1990) The microecology of lactobacilli inhabiting the gastrointestinal tract. In: Advances in Microbial Ecology, Vol 11 (KC Marshall, ed), 147-171, Plenum Press, New York.
Thomas Haaf. 2006. Encyclopedia of Analytical Chemistry.
Thompson FL, Gevers D, Thompson CC, Dawyndt P, Naser S, B. Hoste,Munn CB, Swings J (2005) Phylogeny and molecular identification of vibrios on the basis of multilocus sequence analysis. Appl Environ Microbiol. 71: 5107-5115.
Townsend SM, Hurrell E, Caubilla-Barron J, Loc-Carrillo C, Forsythe SJ (2008) Characterization of an extended-spectrum beta-lactamase Enterobacter hormaechei nosocomial outbreak, and other Enterobacter hormaechei misidentified as Cronobacter (Enterobacter) sakazakii. Microbiology. 154: 3659-3667.
Temmerman R, Huys G, Swings J (2004) Identification of lactic acid bacteria:
culture-dependent and culture-independent methods. Trends in Food Sci Technology 15: 348-359.
Vandecandelaere I, Nercessian O, Segaert E, Achouak W, Mollica A, De Vos P, Vandamme P (2008) Alteromonas genovensis sp. nov., isolated from amarine electroactive biofilm and emended description of Alteromonas macleodii Baumann et al. 1972 (approved lists 1980). Int J Syst Evol Microbiol. 58: 2589-2596.
Ventura M, Canchaya C, Tauch A, Chandra G, Fitzgerald GF, Chater KF, Sinderen D (2007) Genomics of Actinobacteria: tracing the evolutionary history of an ancient phylum. Microbiol Mol Biol Rev. 71: 495-548.
Vijay Kumar E, Srijana M, Kiran Kumar K, Harikrishna N, Reddy G (2011) A novel serine alkaline protease from Bacillus altitudinis GVC11 and its application as a dehairing agent. Bioprocess Biosyst Eng. 34: 403-409.
Vuković Ž, Radenković M, Stanković SJ, Vuković D (2011) Raspodela i akumulacija teških metala u vodi i sedimentu reke Save. J Serbian Chem Soci 76: 795-803.
Viggor S, Juhanson J, Jõesaar M, Mitt M, Truu J, Vedler E, Heinaru A (2013)
Dynamic changes in the structure of microbial communities in Baltic Sea coastal seawater microcosms modified by crude oil, shale oil or diesel fuel. Microbiol Res. 168:415-27.
Williams KP, Gillespie JJ, Sobral BWS, Nordberg EK, Snyder EE, Shallom JM, Dickerman AW (2010) Phylogeny of gammaproteobacteria. J Bacteriol. 192: 2305-2314.
Wright TD, Vergin KL, Boyd PW, Giovannoni SJ (1997) A novel delta-subdivision proteobacterial lineage from the lower ocean surface layer. Appl Environ Microbiol. 63: 41441-1448.
Weber DJ, Rutala WA (1988) Bacillus Species. Infect Control Hosp Epidemiol 9: 368-373.
Wang XH, Müller WEG (2009) Marine biominerals: perspectives and challenges for polymetallic nodules and crusts. Trends Biotechnol. 27: 375-383.
Wang CS, Liao L, Xu HX, Xu XW, Wu M, Zhu LZ (2010) Bacterial diversity in the sediment from polymetallic nodule fields of the Clarion-Clipperton Fracture Zone. J Microbiol. 48: 573-585.
Welsh J, McClelland M (1990) Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res. 18: 7213-7218.
Williams JG, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res. 18: 6531-6535.
Woese CR (1987) Bacterial evolution. Wzrobiol Rev 51: 221-271.
Weiner RM, Melick M, O'Neill K, Quintero E (2000) Hyphomonas adhaerens sp. nov., Hyphomonas johnsonii sp. nov. and Hyphomonas rosenbergii sp. nov., marine budding and prosthecate bacteria. Int J Syst Evol Microbiol. 50: 459-469.
Wang L, Cui YS, Kwon CS, Lee ST, Lee JS, Im WT (2011) Vagococcus acidifermentans sp. nov., isolated from an acidogenic fermentation bioreactor. Int J Syst Evol Microbiol. 61: 1123-1126.
Wei Y, Yang Y, Zhou L, Liu Z, Wang X, Yang R, Su Q, Zhou Y, Zhao J, Yang J (2013) Genome Sequence of Enterobacter cancerogenus YZ1. Genome Announc 1: e00023-13.
Xu XW,Wu YH, Wang CS, Gao XH,Wang XG, Wu M (2010) Pseudoalteromonas
lipolytica sp. nov., isolated from the Yangtze River estuary. Int J Syst Evol Microbiol. 60: 2176-2181.
Yoon JH, Kim IG, Kang KH, Oh TK, Park YH. (2004). Alteromonas litorea sp. nov., a slightly halophilic bacterium isolated from an intertidal sediment of the Yellow Sea in Korea. Int J Syst Evol Microbiol. 54: 1197-1201.
Yoon JH, Oh TK, Park YH (2004) Kangiella koreensis gen.nov., sp. nov. and Kangiella aquimarina sp. nov., isolated from a tidal flat of the Yellow Sea in Korea. Int J Syst Evol Microbiol. 54: 1829-1835.
Yang JC, Madupu R, Durkin AS, Ekborg NA, Pedamallu CS, Hostetler JB, Radune D, Toms BS, Henrissat B, Coutinho PM, Schwarz S, Field L, Trindade AE, Soares CA, Elshahawi S, Hanora A, Schmidt EW, Haygood MG, Posfai J, Benner J, Madinger C, Nove J, Anton B, Chaudhary K, Foster J, Holman A, Kumar S, Lessard PA, Luyten YA, Slatko B,Wood N, Wu B, Teplitski M, Mougous JD, Ward N, Eisen JA, Badger JH, Distel DL (2009) The complete genome of Teredinibacter turnerae T7901: an intracellular endosymbiont of marine wood-boring bivalves (Shipworms). PLoS One. 4: e6085.
Yoon JH, Kang SS, Lee KC, Lee ES, Kho YH, Kang KH, Park YH (2001) Planomicrobium koreense gen. nov., sp. nov., a bacterium isolated from the Korean traditional fermented seafood jeotgal, and transfer of Planococcus okeanokoites (Nakagawa et al. 1996) and Planococcus mcmeekinii (Junge et al. 1998) to the genus Planomicrobium. Int J Syst Evol Microbiol. 51: 1511–1520.
Yoon J, Matsuo Y, Adachi K, Nozawa M., Matsuda, S., Kasai, H. & Yokota, A. (2008). Description of Persicirhabdus sediminis gen. nov., sp. nov., Roseibacillus ishigakijimensis gen. nov., sp. nov., Roseibacillus ponti sp. nov., Roseibacillus persicicus sp. nov., Luteolibacter pohnpeiensis gen. nov., sp. nov. and Luteolibacter algae sp. nov., six marine members of the phylum ‘Verrucomicrobia’, and emended descriptions of the class Verrucomicrobiae, the order Verrucomicrobiales and the family Verrucomicrobiaceae. Int J Syst Evol Microbiol. 58: 998-1007.
Yoon JH, Kim IG, Kang KH, Oh TK, Park, YH (2003) Alteromonas marina sp. nov., isolated from sea water of the East Sea in Korea. Int J Syst Evol Microbiol. 53: 1625-1630.
Yoon JH, Lee CH, Oh TK (2005). Bacillus cibi sp. nov., isolated from jeotgal, a traditional Korean fermented seafood. Int J Syst Evol Microbiol 55: 733-736.
Yoon JH, Kim IG, Oh TK, Park YH (2004) Microbulbifer maritimus sp. nov., isolated from an intertidal sediment from the Yellow Sea, Korea. Int J Syst Evol Microbiol. 54: 1111-1116.
Yuan J, Lai Q, Wang B, Sun F, Liu X, Du Y, Li G, Gu L, Zheng T, Shao Z (2009) Oceanicola pacificus sp. nov., isolated from a deep-sea pyrene-degrading consortium. Int J Syst Evol Microbiol. 59: 1158-1161.
Yamamoto M, Takai K (2011) Sulfur metabolisms in epsilon- and gamma-proteobacteria in deep-sea hydrothermal fields. Front Microbiol 2: 192.
Yamada T, Sekiguchi Y, Hanada S, Imachi H, Ohashi A, Harada H, Kamagata Y (2006) Anaerolinea thermolimosa sp. nov., Levilinea saccharolytica gen. nov., sp. nov. and Leptolinea tardivitalis gen. nov., sp. nov., novel filamentous anaerobes, and description of the new classes Anaerolineae classis nov. and Caldilineae classis nov. in the bacterial phylum Chloroflexi. Int J Syst Evol Microbiol. 56: 1331-1340.
Yee B, Oertli GE, Fuerst JA, Staley JT (2010) Reclassification of the polyphyletic genus Prosthecomicrobium to form two novel genera, Vasilyevaea gen. nov. and Bauldia gen. nov. with four new combinations: Vasilyevaea enhydra comb. nov., Vasilyevaea mishustinii comb. nov., Bauldia consociata comb. nov. and Bauldia litoralis comb. nov. Int J Syst Evol Microbiol. 60: 2960-2966.
Yoo SH,Weon HY, Kim BY, Hong SB, Kwon SW, Cho YH, Go SJ, Stackebrandt E.2006. Devosia soli sp. nov., isolated from greenhouse soil in Korea. Int J Syst Evol Microbiol. 56:2689-2692.
Yoon JH, Kang SJ, Lee MH, Oh TK (2008) Tamlana agarivorans sp. nov., isolated from seawater off Jeju Island in Korea. Int J Syst Evol Microbiol. 58: 1892-1895.
Yoon JH, Lee SY (2012) Winogradskyella multivorans sp. nov., a polysaccharide-degrading bacterium isolated from seawater of an oyster farm. Antonie Van Leeuwenhoek. 102: 231-238.
Yoon JH,Weiss N, Kang KH, Oh TK, Park YH (2003) Planococcus maritimus sp. nov., isolated from sea water of a tidal flat in Korea. Int J Syst Evol Microbiol. 53: 2013-2017.
Yashiro E, Spear RN, McManus PS (2011) Culture-dependent and culture-
independent assessment of bacteria in the apple phyllosphere. J Appl Microbiol. 110: 1284-1296.
Zhang XY, Xie BB, Qin QL, Liu A, Chen XL, Zhou BC, Zhang YZ (2012) Draft Genome Sequence of Strain P7-3-5, a new Flavobacteriaceae bacterium isolated from intertidal sand. J Bacteriol. 194: 6632.
Zhang CX, Yang SY, Xu MX, Sun J, Liu H, Liu H, Kan F, Sun J, Lai R, Zhang KY (2009) Serratia nematodiphila sp. nov., associated symbiotically with the entomopathogenic nematode Heterorhabditidoides chongmingensis (Rhabditida: Rhabditidae). Int J Syst Evol Microbiol. 59: 1603-1608.
Zuo G, Roberts DJ, Lehman SG, Jackson GW, Fox GE,Willson RC (2009) Molecular assessment of salt-tolerant, perchlorate- and nitrate-reducing microbial cultures. Water Sci Technol. 60: 1745-1756.
Zhenyu X, Shaowen K, Chaoqun H, Zhixiong Z, Shifeng W, Yongcan Z (2013) First
characterization of bacterial pathogen, Vibrio alginolyticus, for porites andrewsi white syndrome in the South China Sea. PLoS One. 8: e75425.