臺灣博碩士論文加值系統

甲烷古菌(Methanogen)為在地球上唯一能夠產生大量甲烷的微生物族群，甲烷古菌具有獨特的代謝方式以及能量守恆模式且廣泛分佈於地球上各個棲地中，在形態及生理方面展現其高度的多樣性。甲烷與二氧化碳皆為造成溫室效應的主要氣體之一，據估計，全球每年約有1 Gt (1015 g)的甲烷排放至大氣中，北半球中高緯度的湖泊為重要的甲烷排放地，為瞭解此類棲地的甲烷古菌多樣性，此研究藉由分離純化甲烷古菌，並與已知物種進行親緣關係比對，探討北半球中高緯度湖泊中甲烷古菌的多樣性及其對環境的適應性。本論文研究所分析的樣品主要位於俄羅斯聯邦哈卡斯共和國境內的圖斯湖(Lake Tus)，此湖為高鹽湖。取湖下不同深度的底泥樣品，以厭氧方式增殖培養以純化甲烷古菌株。從圖斯湖增殖樣品中成功純化分離一株甲烷裂菌屬(Methanolobus)的甲烷古菌。菌株SY-01與Methanolobus zinderi SD1T的16S rRNA基因序列達97.30%相似性，與其它Methanolobus屬已發表菌株的16S rRNA基因序列相似性達95.47-97.30%。菌株SY-01為直徑約0.8-1.0 μm的球菌。菌株SY-01為甲基利用型的甲烷古菌，僅可利用甲醇行甲烷化作用。菌株SY-01最適的生長條件為30C、0.51 M NaCl與pH 8.0，從低溫培養的實驗中發現菌株SY-01可生長於4C的環境。從菌株SY-01的基因體確認具有甲基轉移酶相關的基因，為甲基利用型產甲烷古菌重要的基因。此外，菌株SY-01的基因體中也有發現編碼聚半乳醣酸醛酶(Polygalacturonase)以及果膠裂解酶(Pectate lyase)的功能性基因，能夠將果膠降解轉為甲基化物以進行甲烷化作用產生甲烷，菌株SY-01的基因體中也有發現分子伴護蛋白如DnaK、DnaJ、GrpE和ClpB等，以及分子伴護因子GroEL/ES、Thermosome以及prefoldin等幫助菌株SY-01能夠在面臨環境逆境的適應和生存。進一步比較菌株SY-01全基因體序列與其他已有全基因體序列的甲烷裂菌屬菌株分析基因體差異性，結果支持菌株SY-01為Methanolobus屬的新種。從中高緯度鹽鹼湖純化的甲烷古菌，可以進一步瞭解生存於低溫鹽鹼環境的甲烷古菌與環境之間的關聯性，增加微生物多樣化分析的資訊。

Methanogens are the only group of microorganisms on earth producing significant amounts of methane. The are unique in terms of metabolism and energy conservation, are widespread in different habitats and show a high diversity in morphology and physiological parameters.
Methane and carbon dioxide are important greenhouse gas, and northern lakes are the significant methane emission sites. To investigate the biodiversity of methanogen at northern lakes, sediment sample were collected from saline meromictic lake Tus. Partially puried cultures and purified isolates were obtained after anaerobic enrichment and serial diluted sub-transfer. An alkaliphile, halotolerant and methylotrophic novel Methanolobus species, strain SY-01, was isolated from the hypersaline Lake Tus in Siberia. Cells of strain SY-01 were non-motile, irregular cocci and 0.8–1.0 µm in diameter. The methanogenic substrates utilized by strain SY-01 were methanol only. The temperature range of growth for strain SY-01 was from 4 to 40°C. The optimum growth conditions were 30°C, pH 8.0 and 0.51 M NaCl. The G+C content of the genome of strain SY-01 was 43.6 mol%. Phylogenetic analysis revealed that strain SY-01 was most closely related to Methanolobus zinderi SD1T (97.30 % similarity in 16S rRNA gene sequence). The genome of strain SY-01 contains the genes of methyltransferase system, which is essential for methanol and methyl compound utilization for methane production and growth of Methanolobus sp. SY-01. Furthermore, this genome contains genes for pectate lyase and polygalacturonase, which degrades pectin into methyl compound. This genome also comprises complete gene sets of heat shock proteins, including DnaK, DnaJ, GrpE, GroEL/ES, prefoldin subunits, and small heat shock proteins. Based on the morphological, phenotypic, phylogenetic and genomic relatedness data presented here, it is evident that strain SY-01 represents a novel species of the genus Methanolobus.

摘要 i
Abstract ii
目錄 iii
表目錄 vii
圖目錄 viii
壹、前言 1
貳、前人研究 3
一、古菌 3
二、甲烷古菌與其分類 3
(一)Methanobacteria (甲烷桿菌綱) 4
1.Order Methanobacteriales (甲烷桿菌目) 4
(二)Methanococci (甲烷球菌綱) 5
1.Order Methanococcales (甲烷球菌目) 6
(三)甲烷微菌綱(Methanomicrobia) 6
1.Order Methanocellas(甲烷細胞目) 6
2.Order Methanomicrobiales (甲烷微菌目) 6
3.Order Methanosarcinales (甲烷八疊球菌目) 8
(四)甲烷火菌綱(Methanopyri) 9
1.Order Methanopyrales(甲烷火菌目) 9
(五)熱源體古菌綱(Thermoplasmata) 9
1.Order Methanoplasmatales(甲烷熱源體菌目) 9
三、甲烷古菌對生態及人類的影響與應用 10
(一)甲烷古菌在生態上的功能 10
1.碳循環(Carbon cycle) 10
2.氮循環(Nitrogen cycle) 11
3.硫循環(Sulfer cycle) 12
(二)甲烷古菌對於人類的影響 12
四、地球上的甲烷與溫室效應 13
五、湖泊與其微生物生態系 14
(一)鹽鹼湖 14
(二)極端環境下的甲烷古菌 14
(三)西伯利亞鹽湖區內發現的甲烷古菌 16
六、圖斯湖(Lake Tus) 16
七、微生物鑑定與分類 17
八、研究目的與重要結果 17
參、材料與方法 19
一、採樣時間與地點 19
二、除氧操作系統、藥劑與培養基 19
(一)除氧操作系統(Hungate station) 19
(二)MB/W與MM/W液態與固態培養基配製 19
(三)還原劑與碳源製備 20
(四)抗生素溶液製備 21
(五)TGC (thioglycollate)培養基配製 21
三、甲烷古菌增殖培養(enrichment)與厭氧轉殖接種 22
(一)接菌 22
(二)氣相層析儀偵測樣本之甲烷氣體 22
(三)抗生素添加 22
(四)連續稀釋法 23
(五)Roll-tube方法 23
四、Roll-tube菌株篩選 23
(一)厭氧操作箱 23
(二)挑選Roll-tube內菌落 24
五、微生物形態觀察 24
(一)位相差顯微鏡觀察細胞形態 24
(二)穿透式電子顯微鏡觀察細胞形態 24
(三)場發式掃描電子顯微鏡觀察細胞形態 24
六、生長與生理特性分析 25
(一)碳源使用測試 25
(二)抗生素抗性測試 25
(三)生長曲線測量 26
(四)溫度生長範圍測試 26
(五)鹽度範圍測試 27
(六)不同酸鹼值的生長範圍測試 27
七、核酸萃取與分析 27
(一)甲烷古菌染色體DNA萃取 27
(二)核酸純度與定量分析 28
(三)聚合酶連鎖反應 28
(四)核酸膠體電泳 29
(五)PCR增幅樣品回收 30
(六)DNA接合反應 30
八、質體轉型作用 30
(一)勝任細胞製備 30
(二)質體轉形作用 31
(三)質體DNA萃取與純化 31
九、核酸定序、親緣關係與基因體分析 32
(一)16S rRNA基因定序與序列分析 32
(二)染色體DNA定序與序列比較 33
(三)甲烷古菌基因體分析與比較 33
肆、結果與討論 35
一、西伯利亞希拉湖(Lake Shira)、舒涅特湖(Lake Shunet)與圖斯湖(Lake Tus)之甲烷古菌增殖培養與純化 35
(一)希拉湖、舒涅特湖增殖培養之甲烷古菌 35
(二)自圖斯湖增殖培養與純化之甲烷古菌 36
二、甲烷裂菌屬(Methanolobus)新種菌株SY-01的細胞形態 36
三、甲烷裂菌屬(Methanolobus)新種菌株SY-01親緣歸屬 37
四、 甲烷裂菌屬(Methanolobus)新種菌株SY-01生長與生理特性分析 38
(一)Mehthanolobus sp. SY-01可利用碳源 38
(二)Mehthanolobus sp. SY-01抗生素抗性 38
(三)Mehthanolobus sp. SY-01溫度生長範圍 39
(四)Mehthanolobus sp. SY-01鹽度生長範圍測試 39
(五)Mehthanolobus sp. SY-01酸鹼值生長範圍測試 40
五、甲烷裂菌屬(Methanolobus)新種菌株SY-01基因體特色 40
(一)基因組特徵 40
(二)碳源利用與甲烷化作用代謝途徑分析 41
(三)能量守恆與其他代謝途徑 42
(四)菌株SY-01基因組中發現的獨特COGs 43
六、部分純化甲烷古菌 43
(ㄧ)菌株Shunet 15-20F 43
(二)菌株Tus 15-20F 44
伍、結論 45
陸、表與圖 46
柒、參考文獻 65
捌、附錄 80
附錄一、圖斯湖、希拉湖與舒涅特湖位置圖 81
附錄二、Methanolobus sp. SY-01 16S rRNA基因序列 82
附錄三、根據MIGS建議所整理的的Methanolobus sp. SY-01分類以及特徵 84
附錄四、Methanolobus sp. SY-01其他項目資訊 85
附錄五、Methanolobus sp. SY-01基因體中25個一般COGs功能類別的基因數量與比例 86
附錄六、Methanolobus sp. SY-01基因體中29個獨特COGs 87
附錄七、菌株SY-01基因體中參與甲烷化作用與能量守恆的基因 89
附錄八、菌株SY-01基因體中參與其他代謝途徑的基因 91
附錄九、不同厭氧環境中的甲烷裂菌屬物種全基因體比較 93
 

翁杰愔。2014。台灣西南海域深海底泥Methanoculleus及Methanosarcina之純化與特性分析。國立中興大學生命科學系碩士學位論文。
陳眉霏。2013。台灣西南海域甲烷水合物賦存區底泥甲烷太古生物之純化與特性分析。國立中興大學生命科學所碩士學位論文。
黃星華。2016。西伯利亞不完全對流鹹水湖之甲烷太古生物純化及特性分析。國立中興大學生命科學所碩士學位論文。
Abram, F., A. M. Enright, J. O’Reilly, C. H. Botting, G. Collins and V. O’Flaherty. 2011. A metaproteomic approach gives functional insights into anaerobic digestion. J. Appl. Microbiol. 110:1550-1560.
Albers, S. and B. H. Meyer. 2011. The archaeal cell envelope. Nat. Rev. Microbiol. 9:414-426.
Antony, C. P., J. C. Murrell, Y. S. Shouche. 2012. Molecular diversity of methanogens and identification of Methanolobus sp. as active methylotrophic Archaea in Lonar crater lake sediments. FEMS Microbiol Ecol. 81:43–51.
Antunes, A., M. Taborda, R. Huber, C. Moissl, M. F. Nobre and M. S. da Costa. 2008. Halorhabdus tiamatea sp. nov., a non-pigmented, extremely halophilic archaeon from a deeo-sea, hypersaline anoxic basin of the Red Sea, and emended description if the genus Halorhabdus. Int. J. Syst. Evol. Microbiol. 58: 215-220
Appenzeller, T. 1991. Fire and ice under the deep-sea floor. Science. 252:1790-1792.
Aravalli, R. N., Q. She and R. A. Garrett. 1998. Archaea and the new age of microorganisms. Trends. Ecol. Evol. 13:190-194.
Attaluri, A., M. Jackson, J. Valestin and S. S. Rao. 2010. Methanogenic flora is associated with altered colonic transit but not stool characteristics in constipation without IBS. Am J Gastroenterol. 105:1407-1411.
Baatar, B., P. W. Chiang, D. Y. Rogozin, Y. T. Wu, C. H. Tseng, C. Y. Yang, H. H. Chiu, B. Oyuntsetseg, A. G. Degermendzhy and S. L. Tang. 2016. Bacterial communities of three saline meromictic lakes in central Asia. PLOS ONE. 11:e150847.
Balch, W. E., G. E. Fox, C. J. Magrum, C. R. Woese, and R. S. Wolfe. 1979. Methanogens: revalutation of a unique biological group. Microbial. Rev. 43: 260-296.
Barker, H. A. 1936. Studies upon the methane-producing bacteria. Arch. Microbiol. 7:947-960.
Biavati, B., M. Vasta and J. G. Ferry. 1988. Isolation and characterization of “Methanosphaera cuniculi” sp. nov. Appl Environ Microbiol. 54:768-771.
Boone, D. R. 1987. Request for an opinion: replacement of the type strain of Methanobacterium formicicum and reinstatement of Methanobacterium bryantii sp. nov. nom. rev. (ex Balch and Wolfe, 1981) with M.o.H. (DSM 863) as the type strain. Int J Syst Bacteriol. 37:172–173.
Boone, D. R., I. M. Mathrani, Y. Liu, J. A. G. F. Menaia, R. A. Mah and J. E. Boone. 1993. Isolation and characterization of Methanohalophilus portucalensis sp. nov. and DNA reassociation study of the genus Methanohalophilus. Intl. J. Syst. Bacteriol. 43: 430-437.
Boone, D. R., W. B. Whiteman and P. Rouviere. 1993. Diversity and taxonomy of methanogens. P. 35-80., In J. G. Ferry (ed.) Methanogenesis. Chapman and Hall, New York, USA.
Boone, D. R., W. B. Whiteman and Y Koga. 2001. Methanobateriales, p.213-235., In D. R. Boone, D. R., W. Castenholtz, G. M. Garrity (eds.) In Bergey’s Manual of systematic Bacteriology, 2nd edn. Springer-Verlag, New York, USA.
Borrel, G., A. C. Lehours, O. Crouzet, D. Jézéquel, K. Rockne, A. Kulczak, E. Duffaud, K. Joblin and G. Fonty. 2012. Stratification of Archaea in the deep sediments of a freshwater meromictic lake: vertical shift from methanogenic to uncultured archaeal lineages. PLoS One. 7:e43346.
Bowers, K. J. and J. Wiegel. 2011. Temperature and pH optima of extremely halophilic archaea: a mini-review. Extremophiles. 15:119-128.
Bräuer, S. L., H. Cadillo-Quiroz, R. J. Ward, J. B. Yavitt and S. H. Zinder. 2011. Methanoregula boonei gen. nov., sp. nov., an acidiphilic methanogen isolated from an acidic peat bog. Int. J. Syst. Evol. Microbiol. 61:45-52.
Bult, C.J., O. White, G. J. Olsen, L. Zhou, R. D. Fleischmann, G. G. Sutton, J. A. Blake, L. M. FitzGerald, R. A. Clayton, J. D. Gocayne, A. R. Kerlavage, B. A. Dougherty, J. F. Tomb, M. D. Adams, C. I. Reich, R. Overbeek, E. F. Kirkness, K. G. Weinstock, J. M. Merrick, A. Glodek, J. L. Scott, N. S. Geoghagen and J. C. Venter. 1996. Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science. 273:1058-1073.
Burke, S. A and J. A. Krzycki. 1997. Reconstitution of monomethylamine: coenzyme M methyl transfer with a corrinoid protein and two methyltransferases purified from Methanosarcina barkeri. J Biol Chem. 272:16570–16577.
Carr, S. A., Schubota, R., Dunbar, R. B., Mills, C. T., Dias, R., Summons, R. E., and Mandwenack, K. W. 2017. Acetoclastic Methanosaeta are dominant methanogens in organic-rich Antarctic marine sediments. ISME J. 12:330–342.
Chatelier E. L., T. Nielsen., J. Qin., E. Prifti., F. Hildebrand., G. Falony., M. Almeida., M. Arumugam., J-M. Batto., S. Kennedy., P. Leonard., J. Li., K. Burgdorf., N. Grarup., T. Jørgensen., I. Brandslund., H. B. Nielsen., A. S. Juncker., M. Bertalan., F. Levenez., N. Pons., S. Rasmussen., S. Sunagawa., J. Tap., S. Tims., E. G. Zoetendal., S. Brunak., K. Clément., J. Doré., M. Kleerebezem., K. Kristiansen., P. Renault., T. Sicheritz-Ponten., W. M. de Vos., J-D. Zucker., J. Raes., T. Hansen., MetaHIT consortium, P. Bork., J. Wang., S. D. Ehrlich. and O. Pedersen. 2013. Richness of human gut microbiome correlates with metabolic markers. Nature. 500: 541–546.
Chen, S. C., H. H. Huang., M. C. Lai., C. Y. Weng., H. H. Chiu., S. L. Tang., D. Y. Rogozin. and A. G. Degermendzhy. 2018. Methanolobus psychrotolerans sp. nov., a psychrotolerant methanoarchaeon isolated from a saline meromictic lake in Siberia. Int J Syst Evol Microbiol. 4:1378-1383.
Cheng. L.,T. L. Qiu, X. B. Yin, X. L. Wu, G. Q. Hu, Y. Deng, and H. Zhang. 2007. Methermicoccus shengliensis gen. nov., sp. nov., a thermophilic, methylotrophic methanogen isolated from oil-production water, and proposal of Methermicoccaceae fam. nov. 57:2964-2969.
Comeau, A. M., T. Harding, P. E. Galand, W. F. Vincent and C. Lovejoy. 2012. Vertical distribution of microbial communities in a perennially stratified Arctic lake with saline, anoxic bottom waters. Sci. Rep. doi: 10.1038/srep00604. Epub 2012 Aug 28.
De Maayer, P., D. Anderson, C. Cary and D. A. Cowan. 2014. Some like it cold: understanding the survival strategies of psychrophiles. EMBO Rep. 15:508-517
Dean, J. F., J. J. Middelburg, T. Röckmann, R. Aerts, L.G. Blauw, M. Egger, M. S. M. Jerren, A. E. E. de Jong, O. H. Meisel, O. Rasigraf, C. P. Slomp, M. H. in’t Zandt and A. J. Dolman. 2018. Methane Feedbacks to the Global Climate System in a warm world. Reviews of Geophysis. 56:207-250.
Delong, E. F. 1992. Archaea in coastal marine environments. Proc. Natl. Acad. Sci. 89: 5685-5689.
Doerfert, S. N., M. Reichlen, P. Iyer, M. Wang and J. G. Ferry. 2009. Methanolobus zinderi sp. nov., a methylotrophic methanogen isolated from a deep subsurface coal seam. Int. J. Syst. Evol. Microbiol. 59: 1064-1069.
Dridi B., M. Henry., A. EI. Khéchine., D. Raoult. and M. Drancourt. 2009. High prevalence of Methanobrevibacter smithii and Methanosphaera stadtmanae detected in the human gut using an improved DNA detection protocol. PLoS One 4:e7063.
Dridi, B., M. Fardeau, B. Ollivier, D. Raoult and M. Drancourt. 2012. Methanomassiliicoccus luminyensis gen. nov., sp. nov., a methanogenic archaeon isolated from human faeces. Int J Syst Evol Microbiol. 62: 1902-1907.
Eme, L., A. Spang, J. Lombard, C. W. Stairs and T. J. G. Ettema. 2017. Archaea and the origin of eukaryotes. Nat. Rev. Microbiol. 12:711-723.
Enzmann, F., F. Mayer, M. Rother and D. Holtmann. 2018. Methanogens: biochemical background and biotechnological applications. AMP exp. 8:1.
Erkkilä, K. M., A. Ojala, D. Bastviken, T. Biermann, J. J. Heiskanen, A. Lindroth, O. Peltola, M. Rantakari, T. Vesala and I. Mammare. 2018. Methane and carbon dioxide fluxes over a lake: comparison between eddy covariance, floating chambers and boundary layer method. Biogeosciences. 15:429–445.
Ferguson, T. J. and R. A Mah. 1983. Isolation and characterization of a H2-oxidizing thermophilic methanogen. Appl. Environ. Microbiol. 45: 265-274.
Ferry, J. G., P. H. Smith and R. S. Wolfe. 1974. Methanospirillum, a new genus of methanogenic bacteria, and characterization of Methanospirillum hungatii sp.nov. Int. J. Syst. Evol. Microbiol. 24: 465-469.
Firtel, M. and T. J. Beveridge. 1995. Scanning probe microscopy in microbiology. Micron. 26:347-362.
Firtel, M., G. Southam, T. Mok, R. Harris, and T. J. Beveridge. 1995. Electron microscopy techniques for the Archaea. p. 123-139. In K. R. Sowers & H. T. Schreier (ed.), Archaea: a Laboratory Manual, vol. 2, Methanogens. Cold Spring Habor, NY: Cold Spring Harbor Laboratory.
Gaci, N., G. Borrel, W. Tottey, P. W. O’Toole and J-F. Brugère. 2014. Archaea and the human gut: New beginning of an old story. World J. Gastroenterol. 20:16062-16078.
Garcia, J. L., B. K. Patel, and B. Ollivier. 2000. Taxonomic, phylogenetic, and ecological diversity of methanogenic Archaea. Anaerobe. 6: 205-226.
Garcia, J-L, Ollivier B, Whitman W. 2006. The order Methanomicrobiales. P. 208-230. In: Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E (eds), The Prokaryotes. Springer: New York, USA.
Ghoshal, U., R. Shukla., D. Srivastava., U. C. Ghoshal. 2016. Irritable bowel syndrome, particularly the constipation-predominant form, involves an increase in Methanobrevibacter smithii, which is associated with higher methane production. Gut Liver. 10:932–938.
Gray, M. W., G. Burger and B. F. Lang. 1999. Mitochondrial evolution. Science. 283: 1476–1481.
Grossman, E. L., L. A. Cifuentes and I. M. Cozzarelli. 2002. Anaerobic methane oxidation in a landfill-leachate plume. Environ. Sci. Technol. 36:2436-2442.
Guseva, N. V., N. G. Nalivayko, Yu. G. Kopylova, A. A. Khvaschevskaya and O. B. Vaishlya. 2014. Chemical and Microbial Composition of Khakassia Saline Lakes with Regard to Their Ecological State. IERI Procedia. 8:130-135.
Hajishengallis, G., R. P. Darveau and M. A. Curtis. 2012. The keystone-pathogen hypothesis. Nat Rev Microbiol. 10:717–725.
Henckel, T., M. Friedrich and R. Conrad. 1999. Molecular analyses of the methane-oxidizing microbial community in rice field soil by targeting the genes of the 16S rRNA, particulate methane monooxygenase, and methanol dehydrogenase. Appl Enviro Microbiol. 65:1980-1990.
Horz, H.-P. and G. Conrads. 2010. The discussion goes on: what is the role of Euryarchaeota in humans? Archaea. 2010:967271
Horz, H.-P. and G. Conrads. 2011. Methanogenic Archaea and oral infections – ways to unravel the black box. Oral Microl.Immunol. 3: 221-236.
Human Microbiome Project Consortium. 2012. A framework for human microbiome research. Nature. 486:215–221.
Hung, C. C. and M. C. Lai. 2013. The phylogenetic analysis and putative function of lysine 2,3-aminomutase from methanoarchaea infers the potential biocatalysts for the synthesis of -lysine. J. Microbiol. Immunol. Infect. 46:1-10.
Hungate, R. E. 1969. A rolltube method for cultivation of strict anaerobes, p117-132. In J. R. Norris and D. W. Ribbons (ed.) Method in microbiology, vol 3B. Academic press Inc., New York, USA.
Ito, M., M. Masato and T. A. Krulwich. 2017. Mrp Antiporters Have Important Roles in Diverse Bacteria and Archaea. Front Microbiol. 8:2325.
Jarrell, K. F., D. Faguy, A. M. Hebert and M. L. Kalmokoff. 1992. A general method of isolating high molecular weight DNA from methanogenic archaea (archaebacteria). Can. J. Microbiol. 38:65-68.
Jeanthon, C., S. L'Haridon, A. L. Reysenbach, M. Vernet, P. Messner, U. B. Sleytr and D. Prieur. 1998. Methanococcus infernus sp. nov., a novel hyperthermophilic lithotrophic methanogen isolated from a deep-sea hydrothermal vent. Int. J. Syst. Bacteriol. 3:913-919.
Joshi, A., V. Lanjekar, P. K. Dhakephalkar and S. S. Dagar. 2018. Cultivation of multiple genera of hydrogenotrophic methanogens from different environmental niches. Anerobe. 50:64-68.
Kadam, P. C., D. R. Wade, L. Mandelco and D. R. Boone. 1994. Isolation and characterization of Methanolobus bornbayensis sp. nov., a methylotrophic methanogen that requires high concentrations of divalent cations. Int. J. Syst. Bacteriol. 44:603-607.
Kadnikov, V. V., A. V. Mardanov, A. V. Beletsky, O. V. Shubenkova, T. V. Pogodaeva, T. I. Zemskaya, N. V. Ravin and K. G. Skryabin. 2012. Microbial community structure in methane hydrate-bearing sediments of freshwater Lake Baikal. FEMS Microbiol. Ecol. 79:348-358.
Kashefi, K. and D. R. Lovley. 2003. Extending the upper temperature limit for life. Science. 301:934.
Kendall, M. M. , Y. Liu, M. Sieprawska-Lupa, K. O. Stetter, W. B. Whitman and D. R. Boone. 2006. Methanococcus aeolicus sp. nov., a mesophilic, methanogenic archaeon from shallow and deep marine sediments. Int. J. Syst. Evol. Microbiol. 56:1525-1529.
Khelaifia, S. and D. Raoult. 2016. Haloferax massiliensis sp. nov., the first human-associated halophilic archaea. New Microbes New Infect. 12:96–98.
Kiene, R. P., R.S. Oremland, A. Catena, L. G. Miller, and D. G. Capone. 1986. Metabolism of reduced methylated sulfur compounds in anaerobic sediments and by a pure culture of an estuarine methanogen. Appl. Environ.Microbiol. 52:1037–1045.
Kim, M., H.-S. Oh, S.-C. Park, J. Chun. 2014. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int. J. Syst. Evol. Microbiol. 64:346-351.
King, G. M. 1984. Metabolism of trimethylamine, choline, and glycine betaine by sulfate-reducing and methanogenic bacteria in marine sediments. Appl. Environ. Microbiol. 48:719–725.
Kirk, E. 1949. The quantity and composition of human colonic flatus. Gastroenterology. 12:782-794.
Knittel, K. and A. Boetius. 2009. Anaerobic oxidation of methane: Progress with an unknown process. Annu. Rev. Microbiol. 63:311-334.
König, K. and K. O. Stetter. 1982. Isolation and characterization of Methanolobus tindarius sp. nov., a coccoid methanogen growing only on methanol and methylamines. Zentralbl. Bakteriol. Parasitenkd. Infektionskr. Hyg. Abt. 1 Orig. Reihe C 3:478-490.
Koskinen, K., M. R. Pausan, A. K. Perras, M. Beck, C. Bang, M. Mora, A. Schilhabel, R. Schmitz and C. Moissl-Eichingera. 2017. First Insights into the Diverse Human Archaeome: Specific Detection of Archaea in the Gastrointestinal Tract, Lung, and Nose and on Skin. Mbio. 6: e00824-17.
Kurr, M., R. Huber, H. König, H. W. Jannasch, H. Fricke, A. Trincone, J. K. Kristjansson and K. O. Stetter. 1991. Methanopyrus kandleri, gen. and sp. nov. represents a novel group of hyperthermophilic methanogens, growing at 110°C. Arch. Microbiol. 156:239-247.
Lai, M. C. and C. J. Shih. 2001. Characterization of Methanococcus voltaei strain P2F9701a, a new methanogen isolated from estuarine environment. Current Microbiology. 242: 432-437.
Lai, M. C. and S. C. Chen. 2001. Methanofollis aquaemaris sp. nov., a methanogen isolated from an aquaculture fish pond. Int. J. Syst. Evol. Microbiol. 51:1873-1880.
Lai, M. C., C. C. Lin, P. H. Yu, Y. F. Huang and S. C. Chen. 2004. Methanocalculus chungshingensis sp. nov., isolated from an estuary and a marine fishpond in Taiwan. Int. J. Syst. Evol. Microbiol. 54:183-189.
Lai, M. C., C. M. Shu, M. S. Chiou, T. Y. Hong, M. J. Chuang and J. J. Hua. 1999. Characterization of Methanosarcina mazei N2M9705 isolate from an aquaculture fishpond. Curr. Microbiol. 39:79-84.
Lai, M. C., D. R. Yang, and M. J. Chuang. 1999. Regulatory factors associated with synthesis of the osmolyte glycine betaine in the halophilic methanoarchaeon Methanohalophilus portucalensis. Appl. Envi. Microbiol. 65: 828-833.
Lai, M. C., K. R. Sowers, D. E. Robertson, M. F. Roberts and R. P. Gunsalus. 1991. Distribution of compatible solutes in the halophilic methanogenic archaebacteria. J. Bacteriol. 173:5352-5358
Lai, M. C., S. C. Chen, C. M. Shu, M. S. Chiou, C. C. Wang, M. J. Chuang, T. Y. Hong, C. C. Liu, L. J. Lai and J. J. Hua. 2002. Methanocalculus taiwanensis sp. nov., isolated from an estuarine environment. Int. J. Syst. Evol. Microbiol. 52:1799-1806.
Lai, S. J. and M. C. Lai. 2011. Characterization and Regulation of the Osmolyte Betaine Synthesizing Enzymes GSMT and SDMT from Halophilic Methanogen Methanohalophilus portucalensis. PloS one. 9:e25090.
Lang, K., J. Schuldes, A. Klingl, A. Poehlein, R. Daniel and A. Brune. 2015. New mode of energy metabolism in the seventh order of methanogens as revealed by comparative genome analysis of ‘Candidatus Methanoplasma termitum’. Appl. Environ. Microbiol. 81:1338–1352.
Lazar, C. S., R. J. Parkes, B. A. Cragg, S. L′Haridon, and L. Toffin. 2012. Methanogenic diversity and activity in hypersaline sediments of the centre of the Napoli mud volcano, Eastern Mediterranean Sea. Environ. Microbiol. 13: 2078-2091.
Lee, O. O., Y. Wang, J. Yang, F. F. Lafi, A. Al-Suwailem and P. Y. Qian. 2011. Pyrosequencing reveals highly diverse and species-specific microbial communities in sponges from the Red Sea. ISME. 5: 650-664.
Lehner, B. and P. Döll. 2004. Development and validation of a global database of lakes, reservoirs and wetlands. J. Hydrol. 296:1-22.
Leigh, J. A. 2000. Nitrogen fixation in methanogens: the archaeal perspective. Curr. Issues Mol. Biol. 2:125-131.
Lewis, W. M. 1983. A revised classification of lakes based on mixing. Can. J. Fish. Aquat. Sci. 40:1779-1787.
Lin, L. H., L. W. Wu, T. W. Cheng, W. X. Tu, J. R. Lin, T F. Yang, P. C. Chen, Y. Wang and P. L. Wang. 2014. Distributions and assemblages of microbial communities along a sediment core retrieved from a potential hydrate-bearing region offshore southwestern Taiwan. Journal of Asian Earth Sciences. 90:276-292.
Liu, Y. T., D. R. Boone and C. Choy. 1990. Methanohalophilus oregonense sp. nov. a methylotrophic methanogen from an alkaline, saline aquifer. Int. J. Syst. Bacteriol. 40:111-116.
Lloyd, K. G. L. Schreiber, D. G. Petersen, K. U Kjeldsen, M. A. Lever, A. D. Steen, R. Stepanauskas, M. Richter, A. Kleindienst, S. Lenk, A. Schramm and B. B. Jorgensen. 2013. Predominant archaea in marine sediments degrade detrital proteins. Nature Letter. 496: 215-220.
Lloyd, K. G., L. Lapham and A. Teske. 2006. An anaerobic methane-oxidizing community of ANME-1b archaea in hypersaline Gulf of Mexico Sediments. Appl. Environ. Microbiol. 72: 7218-7230.
Lovley, D. R., and M. J. Klug. 1983. Sulfate reducers can outcompete methanogens at freshwater sulfate concentrations. Appl. Environ. Microbiol. 45: 187–192.
Luton, P. E., Jonathan, M. W., Richard, J. S. and Riley, P. W. 2002. The mcrA gene as an alternative to 16S rRNA in the phylogenetic analysis of methanogen populations in landfill. Microbiology. 148:3521-3530.
Ma, K., X. Liu and X. Dong. 2006. Methanosaeta harundinacea sp. nov., a novel acetate-scavenging methanogen isolated from a UASB reactor. Int. J. Syst. Evol. Microbiol. 56:127-131.
Madsen, E. L. 2011. Microorganisms and their roles in fundamental biogeochemical cycles. Curr. Opin. Biotechnol. 22:456-464.
Mathrani, I. M., D. R. Boone, R. A. Mah, G. E. Fox and P. P. Lau. 1988. Methanohalophilus zhilinae sp. nov., an alkaliphilic, halophilic, methylotrophic methanogen. Int. J. Syst. Bacteriol. 38:139-142.
Meier-Kolthoff, J. P., A. F. Auch, H. Klenk and M. Goker. 2013. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics. doi: 10.1186/1471-2105-14-60
Meng, J., J. Xu, D. Qin, Y. He, X. Xiao and F. Wang . 2014. Genetic and functional properties of uncultivated MCG archaea assessed by metagenome and gene expression analyses. ISME J. 8:650-659.
Mikucki, J. A., Y. Liu, M. Delwiche, F. S. Colwell and D. R. Boone. 2003. Isolation of a methanogen from deep marine sediments that contain methane hydrates, and description of Methanoculleus submarinus sp. nov. Appl. Environ. Microbiol. 69:3311-3316.
Miller, T. L. and M. J. Wolin. 1985. Methanosphaera stadtmaniae gen. nov., sp. nov.: a species that forms methane by reducing methanol with hydrogen. Arch. Microbiol. 141:116-122.
Mochimaru, H., H. Tamaki, S. Hanada, H. Imachi, K. Nakamura, S. Sakata and Y. Kamagata. 2009. Methanolobus profundi sp. nov., a methylotrophic methanogen isolated from deep subsurface sediments in a natural gas field. Int. J. Syst. Evol. Microbiol. 59:714-718.
Moissl-Eichinger, C., M. Pausan, J. Taffner, G. Berg, C. Bang and R. A. Schmitz. 2018. Archaea Are Interactive Components of Complex Microbiomes. Trends Micorboi. 26:70-85.
Mori, K., T. Iino, K. Suzuki, K. Yamaguchi and Y. Kamagata. 2012. Aceticlastic and NaCl-requiring methanogen “Methanosaeta pelagica” sp. nov., isolated from marine tidal flat sediment. Appl. Environ. Microbiol. doi:10.1128/AEM.07484-11.
Muyzer, G. and A. J. M. Stams. 2008. The ecology and biotechnology of sulphate-reducing bacteria. Nat Rev Microbiol. 6:441-454.
Naor, A., P. Lapierre, M. Mevarech, R. T. Papke, U. Gophna. 2012. Low Species Barriers in Halophilic Archaea and the Formation of Recombinant Hybrids. Curr. Biol. 22:1444-1448.
Navid, D. 1989. The international law of migratory species: the Ramsar Convention. Nat. Resour. J. 29:1001-1016.
Nazaries, L., J. C. Murrell, P. Millard, L. Baggs and Brajesh K. Singh. 2013. Methane, microbes and models: fundamental understanding of the soil methane cycle for future predictions. Environ Microbiol. 15:2395-2417.
Nolla-Ard`evol, V., M. Strous, D. Y. Sorokin, A. Y Merkel, H. E. Tegetmeyer. 2012. Activity and diversity of haloalkaliphilic methanogens in Central Asian soda lakes. J. Biotechnology. 161:67– 173.
Nunoura, T, Y. Takaki, J. Kakuta, S. Nishi, J. Sugahara, H. Kazama, G. J. Chee, M. Hattori, A. Kanai, H. Atomi, K. Takai and H. Takami. 2011. Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group. Nucleic Acids Res. 39:3204-3223.
Ollivier, B., J. L. Cayol, B. K. Patel, M. Magot, M. L. Fardeau and J. L. Garcia. 1997. Methanoplanus petrolearius sp. nov., a novel methanogenic bacterium from an oil-producing well. FEMS Microbiol. Lett. 147:51-56.
Oremland, R. S., L. M. Marsh, S. Polcin. 1982. Methane production and simultaneous sulphate reduction in anoxic, salt marsh sediments. Nature. 296:143–145.
Pachiadaki, M. G., V. Lykousis, E. G. Stefanou, and K. A. Kormas. 2010. Prokaryotic community structure and diversity in the sediments of an active submarine mud volcano (Kazan mud volcano, East Mediterranean Sea). FEMS Microbiol. Ecol. 72: 429-444.
Padan, E., E. Bibi, M. Ito and T. A. Krulwich. 2005. Alkaline pH homeostasis in bacteria: New insights. Biochim. Biophys. Acta. 1717:67-88.
Parfrey, L. W., W. A. Walters and R. Knight. 2011. Microbial eukaryotes in the human microbiome: ecology, evolution, and future directions. Front Microbiol. 2:153.
Parnachev, V. P. and A. G. Degermendzhy. 2002. Geographical, geological and hydrochemical distribution of saline lakes in Khakasia, Southern Siberia. Aquatic Ecology. 36:107–122.
Parshina, S. N., A. V. Ermakova, M. Bomberg and E. N. Detkova. 2014. Methanospirillum stamsii sp. nov., a psychrotolerant, hydrogenotrophic, methanogenic archaeon isolated from an anaerobic expanded granular sludge bed bioreactor operated at low temperature. Int. J. Syst. Evol. Microbiol. 64:180-186.
Patel, G. B. and G. D. Sprott. 1990. Methanosaeta concilii gen. nov., sp. nov. ("Methanothrix concilii") and Methanosaeta thermoacetophila nom. rev., comb. nov. Int. J. Syst. Bacteriol. 40:79-82.
Paul, K., J. O. Nonoh, L. Mikulski, and A. Brune. 2012. "Methanoplasmatales," Thermoplasmatales-related archaea in termite guts and other environments, are the seventh order of methanogens. Appl. Environ. Microbiol. 78:8245-8253.
Pimentel, M., R. P. Gunsalus, S. S. C. Rao, and H. Zhang. 2012. Methanogens in human health and disease. Am. J. Gastroenterol. 1: 28-33.
Raymond, J., J. L. Siefert, C. R. Staples and R. E. Blankenship. 2003. The natural history of nitrogen fixation. Mol. Biol. Evol. 21:541-554.
Reed, D. W., Y. Fujita, M. E. Delwiche, D. B. Blackweder, P. P. Sheridan, T. Uchida and F. S. Colwell. 2002. Microbial communities from methane hydrate-bearing deep marine sediments in a forearc basin. Appl. Environ. Microbiol. 68: 3759-3770.
Reysenbach, A. L. 2001. Thermoplasmta, p. 335-340., In D. R. Boone, D. R., W. Castenholtz, G. M. Garrity (eds.), In Bergey’s Manual of Systematic Bacteriology, 2nd edn. Springer-Verlag, New York, N. Y.
Rotaru, A. E., P. M. Shrestha, Fanghua, L., Minita, S., Devesh, S., Mallory, E., Karsten, Z., Colin, W., Kelly, P. N., and Derek, R. Lovley. 2014. A new model for electron flow during anaerobic digestion: direct interspecies electron transfer to Methanosaeta for the reduction of carbon dioxide to methane. Energ Environ Sci. 7:408-415
Russkikh, I. V., E. B. Strelnikova, O. V. Serebrennikova, and E. A. Elchaninova. 2017. Bioorganic Components and Compounds of Petroleum Series in Bottom Sediments in Lake Tus and Lake Chyornoye (Khakassia). Contemp. Probl. Ecol. 2:184-192.
Sakai S., H. Imachi, S. Hanada, A. Ohashi, H. Harada and Y. Kamagata. 2008. Methanocella paludicola gen. nov., sp. nov., a methane-producing archaeon, the first isolate of the lineage ‘Rice Cluster I’, and proposal of the new archaeal order Methanocellales ord. nov. Int. J. Syst. Evol. Microbiol. 58:929-936.
Sakai, S., M. Ehara, I. C. Tseng, T. Yamaguchi, S. L. Bräuer, H. Cadillo-Quiroz, S. H. Zinder and H. Imachi. 2012. Methanolinea mesophila sp. nov., a hydrogenotrophic methanogen isolated from rice field soil, and proposal of the archaeal family Methanoregulaceae fam. nov. within the order Methanomicrobiales. Int. J. Syst. Evol. Microbiol. 62:1389-1395.
Sambrook, J. and D. W. Russell. 2001. Preparation and transformation of competent E. coli using calcium chloride. In Molecular cloning: A Laboratory Mannual, 3rd edition, Cold Spring Laboratory, Cold Spring Habor, New York.
Sasaki, H., T. Hara, S. Ito, S. Miura, M. M. Hoque, M. Lieffering, H. Y. Kim, M. Okada, and K. Kobayashi. 2005. Seasonal changes in canopy photosynthesis and respiration, and partitioning of photosynthate, in rice (Oryza sativa L.) grown under free-Air CO2 enrichment. Plant Cell Physiol. 46: 1704–1712.
Scanlan, P.D., F. Shanahan, J. R. Marchesi. 2008. Human methanogen diversity and incidence in healthy and diseased colonic groups using mcrA gene analysis. BMC Microbiology. 8:79.
Schink, B. 1997. Energetics of syntrophic cooperation in methanogenic degradation. Microbiol. Mol. Biol. Rev. 61:262-280
Schönheit, P., J. K. Kristjansson, J. and R. K. Thauer. 1982. Kinetic mechanism for the ability of sulfate reducers to out-compete methanogens for acetate. Arch. Microbiol. 132: 285–288.
Schubert, C. J. , F. Vazquez, T. Lösekann-Behrens, K. Knittel, M. Tonolla and A. Boetius. 2011. Evidence for anaerobic oxidation of methane in sediments of a freshwater system (Lago di Cadagno). FEMS Microbiol. Ecol. 76:26-38.
Schuldiner, S., V. Agmon, J. Brandsma, A. Cohen, E. Friedman and E. Padan. 1986. Induction of SOS functions by alkaline intracellular pH in Escherichia coli. J. Bacteriol. 168:936-939.
Sharma, A., Y. Kawarabayasi, T. Satyanarayana. 2012. Acidophilic bacteria and archaea: acid stable biocatalysts and their potential applications. Extremophiles. 16:1-19.
Simankova, M. V., O. R. Kotsyurbenko, T. Lueders, A. N. Nozhevnikova, B. Wagner, R. Conrad and M. W. Friedrich. 2003. Isolation and characterization of new strains of methanogens from cold terrestrial habitats. System. Appl. Microbiol. 26: 312-318.
Sorokin D.Y., I. I. Rusanov, N. V. Pimenov, T. P. Tourova, B. Abbas and G. Muyzer. 2010. Sulfidogenesis under extremely haloalkaline conditions in soda lakes of Kulunda steppe (Altai, Russia). FEMS Microbiol Ecol . 73:278–90.
Sorokin D.Y., J. G. Kuenen, G. Muyzer. 2011. The microbial sulfur cycle at extremely haloalkaline conditions of soda lakes. Front Microbiol. 2:44.
Sorokin, D. Y., B. Abbas, A. Y. Merke, W. I. C. Rijpstra, J. S. S. Damsté, M. V. Sukhacheva and M. C. M. van Loosdrecht. 2015. Methanosalsum natronophilum sp. nov., and Methanocalculus alkaliphilus sp. nov., haloalkaliphilic methanogens from hypersaline soda lakes. Int. J. Syst. Evol. Microbiol. 10:3739-3745.
Spang, A., J. H. Saw, S. L. Jørgensen, K. Zaremba-Niedzwiedzka, J. Martijn, A. E. Lind, R. van Eijk, C. Schleper, L. Guy and T. J. G. Ettema. 2015. Complex archaea that bridge the gap between prokaryotes and eukaryotes. Nature. doi:10.1038/nature14447.
Stams, A. J. M., S. J. W. H. O. Elferink and P. Westermann. 2003. Metabolic interactions between methanogenic consortia and anaerobic respiring bacteria. Adv. Biochem. Eng. Biotechnol. 81:32-45.
Stetter, K. O., M. Thomm, J Winter, G Wildgruber, H. Huber, W. Zilling, D. Jané-Covic, H. König, P Palm and S. Wunderl. 1981. Methanothermus fervidus, sp. Nov., a novel extremely thermophilic methanogen isolated from an Icelandic hot spring. Zentralbl. Bakeriol. Mikrobiol. Hyg. I. Abt. Orig. 2:166-178.
Surakasi, V. P., A. A. Wani, Y. S. Shouche, Dilip, R. R. 2007 . Phylogenetic analysis of methanogenic enrichment cultures obtained from Lonar Lake in India: isolation of Methanocalculus sp. and Methanoculleus sp. Microb Ecol. 54:697–704.
Tajima, K., T. Nagamine, H. Matsui, M. Nakamura and R. I. Aminov. 2001. Phylogenetic analysis of archaeal 16S rRNA libraries from the rumen suggests the existence of a novel group of archaea not associated with known methanogens. FEMS Microbiol. Lett. 200:67-72.
Takai, K., A. Inoue and K. Horikoshi. 2002. Methanothermococcus okinawensis sp. nov., a thermophilic, methane-producing archaeon isolated from a Western Pacific deep-sea hydrothermal vent system. Int. J. Syst. Evol. Microbiol. 52:1089-1095.
Takishita, K., Y. Takaki, Y. Chikaraishi, T. Ikuta, G. Ozawa, T. Yoshida, N. Ohkouchi, and K. Fujikura. 2017. Genomic Evidence Endosymbionts Likely Provide Deep-Sea Bathymodiolus Mussels with a Sterol Intermediate in Cholesterol Biosynthesis. Genome Biol. Evol. 5:1148-1160.
Taubert, M., C. Grob, A. M. Howat, O. J. Burns, J. Pratscher, N. Jehmlich, M. von Bergen, H. H. Richnow, Y. Chen and J. C. Murrell. 2017. Methylamine as a Nitrogen Source for Microorganisms from a Coastal Marine Environment. Environ Microbiol. 6:2246-2257.
Thauer, R. K., A. K. Kaster, H. Seedorf, W. Buckel and R. Hedderich. 2008. Methanogenic archaea: ecologically relevant differences in energy conservation. Nat. Rev. Microbiol. 6:579-591.
Timmers, P. H. A, C. U. Welte, J. J. Koehorst, C. M. Plugge, M. S. M. Jetten and A. J. M. Stams. 2017. Reverse methanogenesis and respiration in methanotrophic archaea. Archaea. 2017:1–22
Torres-Talamante, O., J. Alcocer, P. A. Beddows, E. G. Escobar-Briones and A. Lugo. 2011. The key role of the chemolimnion in meromictic cenotes of the Yucatan Peninsula, Mexico. Hydrobiologia. 677:107-127.
Tu, Q., Z. He, L. Wu, K. Xue, G. Xie, P. Chain, P. B. Reich, S. E. Hobbie and J. Zhou. 2017. Metagenomic reconstruction of nitrogen cycling pathways in a CO2- enriched grassland ecosystem. Soil Biology & Biochemistry. 106:99-108.
Utsumi, M., S. E. Belova, G. M. King, and H. Uchiyama. 2003. Phylogentic comparison of methanogen diversity in different wetland soils. J. Gen. Appl. Microbiol. 49:75-83.
Valentine, D. L. and W. S. Reeburgh. 2000. New perspectives on anaerobic methane oxidation. Environ Microbiol. 2:477-484.
van de Peer. Y., I. van den Broeck., P. de Rijk and R. de Wachter. 1994. Database on the structure of small ribosomal subunit RNA. Nucleic Acids Res. 22:3488-94.
van Teeseling, M. C., A. Pol, H. R. Harhangi, S. van der Zwart, M. S. M. Jetten, H. J. M. O. den Camp and L. van Niftrik. 2014. Expanding the verrucomicrobial methanotrophic world: Description of three novel species of Methylacidimicrobium gen. nov. Appl. Environ. Microbiol. 80:6782-6791.
Wagner, T., Carl-Eric, W., Jörg, K., Ulrich, E. and Seigo, S. 2017. Phylogenetic and Structural Comparisons of the Three Types of Methyl Coenzyme M Reductase from Methanococcales and Methanobacteriales. J. Bacteriol. 199:e00197-17.
Wasserfallen, A., J. Nölling, P. Pfister, J. Reeve and M. E. Conway. 2000. Phylogenetic analysis of 18 thermophilic Methanobacterium isolates supports the proposals to create a new genus, Methanothermobacter gen. nov., and to reclassify several isolates in three species, Methanothermobacter thermautotrophicus comb. nov., Methanothermobacter wolfeii comb. nov., and Methanothermobacter marburgensis sp. nov. Int. J. Syst. Evol. Microbiol. 50:43-53.
Welte, C. and U. Deppenmeier. 2014. Bioenergetics and anaerobic respiratory chains of aceticlastic methanogens. Biochim Biophys Acta Bioenerg. 1837:1130–1147.
Wen, X., S. Yang, F. Horn, M. Winkel, D. Wagner and S. Liebner. 2017. Global biogeographical analysis of methanogenic archaea identifies community-shaping envriomental factors of natural enviroments. Front. Microbiol. 8:1399.
Weng, C. Y., S. C. Chen, M. C. Lai, S. Y. Wu, S. Lin, T. F. Yang and P. C. Chen. 2015. Methanoculleus taiwanensis sp. nov., a methanogen isolated from deep marine sediment at the deformation front area near Taiwan. Int. J. Syst. Evol. Microbiol. 65:1044-1049.
Whitman, W. B. and C. Jeanthon. 2006. The order Methanococcales. P.257-273., In M. Dworkin, S Falkow, E. Rosenberg, K. H. Schleifer, E. Stackebrandt (Eds.) In The Prokaryotes, 3rd edn. Springer-Verlag New York, NY.
Wik, M., R. K. Varner, K. W. Anthony, S. Maclntyre and D. Bastviken. 2016. Climate-sensitive northern lakes and ponds are critical components of methane release. Nature Geoscience. 9:99-105.
Woese, C. R., L. J. Magrum and G. E. Fox. 1978. Archaebacteria. J. Mol. Evol. 11:245-252.
Wolin, E. A., M. J. Wolin, and R. S. Wolfe. 1963. Formation of methane by bacterial extracts. J. Biol. Chem. 238:2882-2886.
Wu, S. Y. and M. C. Lai. 2011. Methanogenic archaea isolated from Taiwan's Chelungpu fault. Appl. Environ. Microbiol. 77:830-838.
Yanagawa, K., M. Kouduka, Y. Nakamura, A. Hachikubo, H. Tomaru, Y. Suzuki. 2013. Distinct microbial communities thriving in gas hydrate-associated sediments from the eastern Japan Sea. Journal of Asian Earth Sciences. 90:43-249.
Yanagita, K., Y. Kamagata, M. Kawaharasaki, T. Suzuki, Y. Nakamura and H. Minato. 2000. Phylogenetic analysis of methanogens in sheep rumen ecosystem and detection of Methanomicrobium mobile by fluorescence in situ hybridization. Biosci. Biotechnol. Biochem. 64:1737-1742.
Youssef, N. H., K. N. Ashlock-Savage and M. S. Elshahed. 2011. Extremely halophilic archeae (order Halobacteriales) in multiple saline sediment habitats. Appl. Envi. Microbiol. 78:1332-1344.
Zaremba-Niedzwiedzka, K., E. F. Caceres, J. H. Saw, D. Bäckström, L. Juzokaite, E. Vancaester, K. W. Seitz, K. Anantharaman, P. Starnawski, K. U. Kjeldsen, M. B. Stott, T. Nunoura, J. F. Banfield, A. Schramm, B. J. Baker, A. Spang and T. J. G. Ettema. 2017. Asgard archaea illuminate the origin of eukaryotic cellular complexity. Natura. 541:353-358.
Zhang, G., N. Jiang, X. Liu, and X. Dong. 2008. Methanogenesis from Methanol at Low Temperatures by a Novel Psychrophilic Methanogen, “Methanolobus psychrophilus” sp. nov., Prevalent in Zoige Wetland of the Tibetan Plateau. Appl. Environ. Microbiol. 74:6114-6120
Zhilina, T. N., D. G. Zavarzina, V. V. Kevbrin, V. V. Kolganov. 2013. Methanocalculus natronophilus sp. nov., a new alkaliphilic hydogenotrophic methanogenic archaeon from soda lake and proposal of the new family Methanocalculaceae. Microbiology. 82:698–706.
Zhou, J. Z., K. Xue, J. P. Xie, Y. Deng, L. Wu, X. Cheng, S. Fei, S. Deng, Z. He, J. D. van Nostrand and Y. Luo. 2012. Microbial mediation of carbon-cycle feedbacks to climate warming. Nature Climate Change. 2:106-110.
Zhou, L., X. Liu and X. Dong. 2014. Methanospirillum psychrodurum sp. nov., isolated from wetland soil. Int. J. Syst. Evol. Microbiol. 64:638-641.
Zinder, S. H., K. R. Sowers and J. G. Ferry. 1985. Methanosarcina thermophila sp. nov., a thermophilic, acetotrophic, methane-producing bacterium. Int. J. Syst. Bacteriol. 35:522-523.
Zou, S., L. Caler, S. Colombini-Hatch, S. Glynn, P. Srinivas. 2016. Research on the human virome: where are we and what is next. Microbiome. 4:32.