臺灣博碩士論文加值系統

湧泉坑是地下水從地表流出而使地面產生凹坑之現象，常見於水陸交界之水岸線淺水處，推測是由於地下水頭壓力所造成之地下水湧升使底床沖積層之細顆粒發生流體化，而湧水沖刷帶出細顆粒在其出口周圍沈積形成湧泉坑，可能具有更新河水的功能。湧泉坑在地質學的研究上有一定的基礎，但於微生物生態與功能影響仍不清楚。本研究分析大台北地區景美溪的湧泉坑中河水及底泥的微生物相，並以不含湧泉坑的景美溪樣本做為對照組；以16S rRNA基因序列，分析樣區中的太古生物(古菌, Archaea)與細菌的群落架構變化與功能。共獲得229條太古生物及473條細菌的16S rRNA基因序列，若以97% 16S rRNA基因序列相似性定義為一個分類單位(OTUs)，在太古生物序列可分成55個不同OTUs，細菌序列可分成373個不同的OTUs。新湧泉坑與中期湧泉坑旁的控制組的底泥及河床底泥的太古生物相，以Methanosaetaceae為主要親緣型，而在湧泉坑及老化型湧泉坑的太古生物相大部分屬於rich minerotrophic fen親緣型。在細菌部分，除了新湧泉坑以Chloroflexi 及 Firmicutes親緣型為主之外，其餘樣品主要以 Bacteriodetes 及 Betaproteobacteria為優勢親緣型，且以中期湧泉坑具有顯著較高的多樣性與完整微生物碳、氮、硫元素的完整循環功能。研究顯示湧泉坑的形成除帶來新的菌群之外，亦改變環境溫度、還原電位、氧氣及營養源的濃度梯度，提高微生物物種與功能的多樣性，應具有更新河流生態系的功效。

Spring pits are bowl-shaped depressions formed near the shoreline. The occurrence of the spring pits may be formed by the upwelling ground water after heavy rains in Jing-Mei River at the southeastern Taipei basin. Spring pit may play a role to refresh the river water. Spring pits have been studied on the basis of their geography, but little is known about the ecology and community structure of microbial organisms (both archaea and bacteria). Total cell from samples were also determined using 4',6-diamidino-2-phenylindole (DAPI). The microbial communities associated with spring pits and control were investigated using 16S rRNA genes and phylogenetic analyses of clone libraries derived from DNA extracted from water and sediment samples. The significant difference in microbial abundance were found between inside and outside of spring pit sample. Totally 229 archaeal and 473 bacterial clones were obtained. All sequences could be defined as 55 archaeal and 373 bacterial operational taxonomic unit (OTUs) base on the 97% 16S rRNA gene sequence similarity. The archaeal 16S rRNA gene sequences retrieved from intermediate and old spring pits were mostly affiliated to a rich minerotrophic fen type subaqueous cluster, however Methanosaetaceae is the major group detected in the new spring pit, sediment nearby intermediate spring pit and control riverine sediment. The bacterial phyla Bacteriodetes and Betaproteobacteria were dominance in almost all of samples, except new spring pit which abundance by Chloroflexi and Firmicutes.The statistical analysis of 16S rRNA clone libraries found highest diversity in intermediate spring and revealed lower in new and old spring pit and control river in spring pit study site.The phylogeny-based microbial function in nitrogen (N), carbon (C) and sulfur (S) were also investigated and suggest that the occurrence of spring pit associated microbes can promote the complete of N, C, and S cycling. These results suggest that microbial community of the newly fromed spring pit will immediately mix with nearly river water and sediment which herely contribute the most diverse microbial community and function of intermediate spring pits. Further the spring pit microbial gradually aged with less diverse microbial community and limited functions as part of the river sediment. The spring pit formation bring in the new microbes and changing gradients in abiotic temperature, redox, oxygen and nutrients promote more diverse microbial functions which should be effectively refresh the river ecosystem.

Table of Contents
Chinese abstract i
English abstract ii
Table of Contents vi
List of Tables viii
List of Figures ix
1. Introduction 1
2. Literature reviews 2
2.1. The ecology of urban river 2
2.2. Spring pit 3
2.3. The application of molecular technologies to study the microbes in natural environments 4
2.3.1. Ribosomal RNA as a key to molecular phylogeny 5
2.3.1.1. Molecular microbial ecology approaches to accessing natural diversity 6
2.3.1.2. Genetic finger printing 6
2.3.1.3. PCR, Cloning and sequencing techniques 8
2.3.2. Single-cell identification in microbial community by fluorescence techniques 9
2.4. Common microbial group in freshwater habitat 12
2.4.1. Archaea 12
2.4.1.1. Features distinguishing Archaea from Bacteria and Eukarya 12
2.4.1.2. Archaeal phenotype and phylogenetic division 13
2.4.1.2.1. Phylum Crenarchaeota 13
2.4.1.2.2. Phylum Euryarchaeota 13
2.4.1.2.2.1. Class Methanomicrobia 14
2.4.1.2.2.1.1. Order Methanosarcinales 14
2.4.1.2.2.1.2. Order Methanomicrobiales 15
2.4.1.2.2.1.3. Unclassified Methanomicrobia 16
2.4.1.2.2.2. Class Methanobacteria 17
2.4.1.2.2..3. Uncultured Archaea 17
2.4.1.2.3. Phylum Thaumarchaeota 18
2.4.2. Bacteria 18
2.4.2.1. Phylum Acidobacteria 19
2.4.2.2. Phylum Bacteroidetes 19
2.4.2.3. Phylum Cyanobacteria 20
2.4.2.4. Phylum Proteobacteria 20
2.4.2.4.1. Class Alphaproteobacteria 20
2.4.2.4.2. Class Betaproteobacteria 21
2.4.2.4.3. Class Gammaproteobacteria 21
2.4.2.4.4. Class Deltaproteobacteria 21
2.4.2.5. Phylum Chloroflexi 22
2.4.2.6. Phylum Verrucomicrobia 22
2.4.2.7. Phylum Acidobacteria 23
2.4.2.8. Phylum Firmicutes 24
2.4.2.9. Phylum Plantomycetes 24
2.4.2.10. Phylum Deinococcus-Thermus 24
2.4.2.11 Phylum Fusobacteria 25
2.4.2.12. Phylum Gemmatimonadetes 25
2.4.2.13. Phylum Lentisphaerae 25
2.4.2.14. Phylum Armatimonadetes 26
2.4.2.15. Phylum Elusimicrobia 26
2.4.2.16. Phylum Chlorobi 26
2.4.2.17. Phylum Nitrospirae 26
2.4.2.18. Candidate division OP11 27
2.4.2.19. Candidate division OD1 27
2.4.2.20. Candidate division TM7 27
2.4.2.21. Candidate division WS3 27
3. Materials and Methods 29
3.1. Sample location and period 29
3.2. Sampling method 30
3.3. Cultivation of E. coli DH5α 30
3.3.1. Medium content 30
3.3.2. Recombinant E. coli clone selection 31
3.3.3. E. coli stock 31
3.3.4. Competent cell preparation 32
3.4. DNA extraction 32
3.5. 16S rRNA gene amplification 33
3.6. Recover and purified 16S rRNA gene fragment 34
3.7. 16S rDNA ligation 35
3.8. Transformation 35
3.9. Plasmid extraction and purification 36
3.10. Nucleic acid sequence analysis 37
3.11. Sequence analysis, phylotype analysis and phylogeny-based microbial function 38
3.12. Biodiversity 39
3.13. DAPI (4',6-diamidino-2-phenylindole) staining 40
3.13.1 Standard curve 40
3.13.2 Cell abundance observation 42
4. Results and discussion 43
4.1. Microbial abundance 43
4.1.1. Microbial abundance in Jing-Mei river sediments 43
4.1.2 Microbial abundance in spring pit and associated 43
4.2. Microbial diversity 44
4.2.1. Bacterial diversity in Jing-Mei River sediments 44
4.2.2. Microbial community in spring pits site at Jing-Mei River 44
4.2.2.1. Archaeal community in spring pits site at Jing-Mei River 44
4.2.2.2. Bacterial community in spring pits site at Jing-Mei River 48
4.2.2.3. Bacterial community assemblages in spring pit associated habitats 51
5. Discussion 54
5.1. Diversity measures and rarefaction curve analysis 54
5.2. Environmental gradient on the microbial distribution and metabolic function 56
5.2.1 Control along Jing-Mei River VS. Control Jing-Mei River at spring pit site 56
5.2.2 Microbial community in spring pit 57
5.3. Phylogeny-based microbial function in nutrient cycle in spring pit study site 57
5.3.1 Phylogeny-based microbial function in nitrogen cycle in spring pit study site 57
5.3.2 Phylogeny-based microbial function in carbon cycle in spring pit study site 58
5.3.3 Phylogeny-based microbial function in sulfur cycle in spring pit study site 58
6. Conclusions and Future Prospects 60
7. Tables and Figures 61
8. References 96

Allgaier, M., and H. P. Grossart. 2006. Diversity and seasonal dynamics of Actinobacteria populations in four lakes in northeastern Germany. Appl. Environ. Microbiol. 72:3489-3497.
Amann, R., and B. M. Fuchs. 2008. Single-cell identification in microbial communities by improved fluorescence in situ hybridization techniques. Nat. Rev. Microbiol. 6:339-348.
Anderson, R. T., H. A. Vrionis, I. Ortiz-Bernad, C. T. Resch, P. E. Long, R. Dayvault, K. Karp, S. Marutzky, D. R. Metzler, A. Peacock, D. C. White, M. Lowe, and D. R. Lovley. 2003. Stimulating the in situ activity of Geobacter species to remove uranium from the groundwater of a uranium-contaminated aquifer. Appl. Environ. Microbiol. 69:5884-5891.
Barns, S. M., S. L. Takala, and C. R. Kuske. 1999. Wide distribution and diversity of members of the bacterial kingdom Acidobacterium in the environment. Appl. Environ. Microbiol. 65:1731-1737.
Battin, T. J., A. Wille, B. Sattler, and R. Psenner. 2001. Phylogenetic and functional heterogeneity of sediment biofilms along environmental gradients in a glacial stream. Appl. Environ. Microbiol. 67:799-807.
Bennett, K. W., and A. Eley. 1993. Fusobacteria: new taxonomy and related diseases. J. Med. Microbiol. 39:246-254.
Bockelmanna, U., W. Manza, T. R. Neub, and U. Szewzyka. 2000. Characterization of the microbial community of lotic organic aggregates ('river snow') in the Elbe River of Germany by cultivation and molecular methods. FEMS Microbiol. Ecol. 33:157-170.
Boone, D. R., and R. A. Mah. 2001. The Archaea and the deeply branching and phototrophic In D. R. Boone and R. W. Castenholz (ed.), Bergey's manual of systematic bacteriology vol. 1. Springer, New York.
Brauer, S. L., H. Cadillo-Quiroz, E. Yashiro, J. B. Yavitt, and S. H. Zinder. 2006. Isolation of a novel acidiphilic methanogen from an acidic peat bog. Nature 442:192-194.
Brauer, S. L., E. Yashiro, N. G. Ueno, J. B. Yavitt, and S. H. Zinder. 2006. Characterization of acid-tolerant H2/CO2-utilizing methanogenic enrichment cultures from an acidic peat bog in New York State. FEMS Microbiol. Ecol. 57:206-216.
Briee, C., D. Moreira, and P. Lopez-Garcia. 2007. Archaeal and bacterial community composition of sediment and plankton from a suboxic freshwater pond. Res. Microbiol. 158:213-227.
Briggs, B. R., J. W. Pohlman, M. Torres, M. Riedel, E. L. Brodie, and F. S. Colwell. 2011. Macroscopic biofilms in fracture-dominated sediment that anaerobically oxidize methane. Appl. Environ. Microbiol. 77:6780-6787.
Brochier-Armanet, C., B. Boussau, S. Gribaldo, and P. Forterre. 2008. Mesophilic Crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota. Nat. Rev. Microbiol. 6:245-252.
Brochier-Armanet, C., S. Gribaldo, and P. Forterre. 2012. Spotlight on the Thaumarchaeota. Isme J 6:227-230.
Bruggemann, J., J. R. Stephen, Y. J. Chang, S. J. Macnaughton, G. A. Kowalchuk, E. Kline, and D. C. White. 2000. Competitive PCR-DGGE analysis of bacterial mixtures: an internal standard and an appraisal of template enumeration accuracy. J. Microbiol. Methods 40:111-123.
Burr, M. D., S. J. Clark, C. R. Spear, and A. K. Camper. 2006. Denaturing gradient gel electrophoresis can rapidly display the bacterial diversity contained in 16S rDNA clone libraries. Microb. Ecol. 51:479-486.
Cadillo-Quiroz, H., S. Brauer, E. Yashiro, C. Sun, J. Yavitt, and S. Zinder. 2006. Vertical profiles of methanogenesis and methanogens in two contrasting acidic peatlands in central New York State, USA. Environ. Microbiol. 8:1428-1440.
Cadillo-Quiroz, H., E. Yashiro, J. B. Yavitt, and S. H. Zinder. 2008. Characterization of the archaeal community in a minerotrophic fen and terminal restriction fragment length polymorphism-directed isolation of a novel hydrogenotrophic methanogen. Appl. Environ. Microbiol. 74:2059-2068.
Cadillo-Quiroz, H., J. B. Yavitt, and S. H. Zinder. 2009. Methanosphaerula palustris gen. nov., sp. nov., a hydrogenotrophic methanogen isolated from a minerotrophic fen peatland. Int. J. Syst. Evol. Microbiol. 59:928-935.
Castenholz, R. W. 2001. Phylum BX. Cyanobacteria, p. 473-487. In D. R. Boone and R. W. Castenholz (ed.), Bergey's Manual of Systematic Bacteriology, vol. 1. Springer, New York.
Chan, O. C., M. Wolf, D. Hepperle, and P. Casper. 2002. Methanogenic archaeal community in the sediment of an artificially partitioned acidic bog lake. FEMS Microbiol. Ecol. 42:119-129.
Chao, A. 1987. Estimating the population size for capture-recapture data with unequal catchability. Biometrics 43:783-791.
Chauhan, A., and A. Ogram. 2006. Phylogeny of acetate-utilizing microorganisms in soils along a nutrient gradient in the Florida Everglades. Appl. Environ. Microbiol. 72:6837-6840.
Chen, C. L., H. Macarie, I. Ramirez, A. Olmos, S. L. Ong, O. Monroy, and W. T. Liu. 2004. Microbial community structure in a thermophilic anaerobic hybrid reactor degrading terephthalate. Microbiology 150:3429-3440.
Chin, K. J., W. Liesack, and P. H. Janssen. 2001. Opitutus terrae gen. nov., sp. nov., to accommodate novel strains of the division 'Verrucomicrobia' isolated from rice paddy soil. Int. J. Syst. Evol. Microbiol. 51:1965-1968.
Chouari, R., D. Le Paslier, C. Dauga, P. Daegelen, J. Weissenbach, and A. Sghir. 2005. Novel major bacterial candidate division within a municipal anaerobic sludge digester. Appl. Environ. Microbiol. 71:2145-2153.
Christiansen, N., and B. K. Ahring. 1996. Desulfitobacterium hafniense sp nov, an anaerobic, reductively dechlorinating bacterium. Int. J. Syst. Bacteriol. 46:442-448.
Conrad, R., M. Klose, P. Claus, and A. Enrich-Prast. 2010. Methanogenic pathway, C-13 isotope fractionation, and archaeal community composition in the sediment of two clear-water lakes of Amazonia. Limnol. Oceanogr. 55:689-702.
Crump, B. C., and J. E. Hobbie. 2005. Synchrony and seasonality in bacterioplankton communities of two temperate rivers. Limnol. Oceanogr. 50:1718-1729.
Dahllof, I., H. Baillie, and S. Kjelleberg. 2000. rpoB-based microbial community analysis avoids limitations inherent in 16S rRNA gene intraspecies heterogeneity. Appl. Environ. Microbiol. 66:3376-3380.
Dedysh, S. N., T. A. Pankratov, S. E. Belova, I. S. Kulichevskaya, and W. Liesack. 2006. Phylogenetic analysis and in situ identification of bacteria community composition in an acidic Sphagnum peat bog. Appl. Environ. Microbiol. 72:2110-2117.
Delbes, C., R. Moletta, and J. J. Godon. 2000. Monitoring of activity dynamics of an anaerobic digester bacterial community using 16S rRNA polymerase chain reaction-single-strand conformation polymorphism analysis. Environ. Microbiol. 2:506-515.
DeLong, E. F. 1992. Archaea in coastal marine environments. Proc. Natl. Acad. Sci. USA 89:5685-5689.
DeLong, E. F. 1998. Everything in moderation: archaea as 'non-extremophiles'. Curr. Opin. Genet. Dev. 8:649-654.
Dettling, M. D., J. B. Yavitt, H. Cadillo-Quiroz, C. Sun, and S. H. Zinder. 2007. Soil-methanogen interactions in two peatlands (bog, fen) in central New York State. Geomicrobiol. J. 24:247-259.
Diaz, E. E., A. J. Stams, R. Amils, and J. L. Sanz. 2006. Phenotypic properties and microbial diversity of methanogenic granules from a full-scale upflow anaerobic sludge bed reactor treating brewery wastewater. Appl. Environ. Microbiol. 72:4942-4949.
Dinis, J. M., D. E. Barton, J. Ghadiri, D. Surendar, K. Reddy, F. Velasquez, C. L. Chaffee, M. C. Lee, H. Gavrilova, H. Ozuna, S. A. Smits, and C. C. Ouverney. 2011. In search of an uncultured human-associated TM7 bacterium in the environment. PLoS One 6:e21280.
Dojka, M. A., P. Hugenholtz, S. K. Haack, and N. R. Pace. 1998. Microbial diversity in a hydrocarbon- and chlorinated-solvent-contaminated aquifer undergoing intrinsic bioremediation. Appl. Environ. Microbiol. 64:3869-3877.
Draganits, E., C. Janda. 2003. Subaqueous artesian springs and associated spring pits in a Himalayan pond. Boreas 32:436-442.
Dridi, B., M. L. 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.
Earl, J., G. Hall, R. W. Pickup, D. A. Ritchie, and C. Edwards. 2003. Analysis of methanogen diversity in a hypereutrophic lake using PCR-RFLP analysis of mcr sequences. Microb. Ecol. 46:270-278.
Ehrich, S., D. Behrens, E. Lebedeva, W. Ludwig, and E. Bock. 1995. A new obligately chemolithoautotrophic, nitrite-oxidizing bacterium, Nitrospira moscoviensis sp. nov. and its phylogenetic relationship. Arch. Microbiol. 164:16-23.
Eickhorst, T., and R. Tippkotter. 2008. Detection of microorganisms in undisturbed soil by combining fluorescence in situ hybridization (FISH) and micropedological methods. Soil Biol. Biochem. 40:1284-1293.
Eiler, A., and S. Bertilsson. 2007. Flavobacteria blooms in four eutrophic lakes: linking population dynamics of freshwater bacterioplankton to resource availability. Appl. Environ. Microbiol. 73:3511-3518.
Eiler, A., J. A. Olsson, and S. Bertilsson. 2006. Diurnal variations in the auto- and heterotrophic activity of cyanobacterial phycospheres (Gloeotrichia echinulata) and the identity of attached bacteria. Freshwat. Biol. 51:298-311.
Ferris, M. J., G. Muyzer, and D. M. Ward. 1996. Denaturing gradient gel electrophoresis profiles of 16S rRNA-defined populations inhabiting a hot spring microbial mat community. Appl. Environ. Microbiol. 62:340-346.
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. Bacteriol. 24:465-469.
Fox, G. E., L. J. Magrum, W. E. Balch, R. S. Wolfe, and C. R. Woese. 1977. Classification of methanogenic bacteria by 16S ribosomal RNA characterization. Proc. Natl. Acad. Sci. USA. 74:4537-4541.
Fuerst, J. A. 2010. Beyond Prokaryotes and Eukaryotes : Planctomycetes and Cell Organization. Nature Education 3:44
Furtado, A. L. D., and P. Casper. 2000. Different methods for extracting bacteria from freshwater sediment and a simple method to measure bacterial production in sediment samples. J. Microbiol. Methods 41:249-257.

Galand, P. E., H. Fritze, R. Conrad, and K. Yrjala. 2005. Pathways for methanogenesis and diversity of methanogenic archaea in three boreal peatland ecosystems. Appl. Environ. Microbiol. 71:2195-2198.
Geissinger, O., D. P. Herlemann, E. Morschel, U. G. Maier, and A. Brune. 2009. The ultramicrobacterium "Elusimicrobium minutum" gen. nov., sp. nov., the first cultivated representative of the termite group 1 phylum. Appl. Environ. Microbiol. 75:2831-2840.
Glockner, F. O., E. Zaichikov, N. Belkova, L. Denissova, J. Pernthaler, A. Pernthaler, and R. Amann. 2000. Comparative 16S rRNA analysis of lake bacterioplankton reveals globally distributed phylogenetic clusters including an abundant group of actinobacteria. Appl. Environ. Microbiol. 66:5053.
Gonzalez, J. M., and C. Saiz-Jimenez. 2004. Microbial diversity in biodeteriorated monuments as studied by denaturing gradient gel electrophoresis. J. Sep. Sci. 27:174-180.
Good, I. J. 1953. The population frequencies of species and the estimation of population parameters. Biometrika 40:237-264.
Gotelli, N. J., and R. K. Colwell. 2001. Quantifying biodiversity: procedures and pitfalls in the measurement and comparison of species richness. Ecol. Lett. 4:379-391.
Gough, H. L., and D. A. Stahl. 2003. Optimization of direct cell counting in sediment. J. Microbiol. Methods 52:39-46.
Gray, J. P., and R. P. Herwig. 1996. Phylogenetic analysis of the bacterial communities in marine sediments. Appl. Environ. Microbiol. 62:4049-4059.
Gutell, R. R., N. Larsen, and C. R. Woese. 1994. Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective. Microbiol Rev 58:10-26.
Harris, J. K., S. T. Kelley, and N. R. Pace. 2004. New perspective on uncultured bacterial phylogenetic division OP11. Appl. Environ. Microbiol. 70:845-849.
Hedlund, B., J.-C. Cho, M. Derrien, and K. Costa. 2010. Phylum XXII. Lentisphaerae Cho, Vergin, Morris and Giovannoni 2004a, 1005VP (Effective publication: Cho, Vergin, Morris and Giovannoni 2004b, 617.), p. 785-793. In N. Krieg, J. Staley, D. Brown, B. Hedlund, B. Paster, N. Ward, W. Ludwig, and W. Whitman (ed.), Bergey’s ManualR of Systematic Bacteriology. Springer New York.
Herlemann, D. P., O. Geissinger, W. Ikeda-Ohtsubo, V. Kunin, H. Sun, A. Lapidus, P. Hugenholtz, and A. Brune. 2009. Genomic analysis of "Elusimicrobium minutum," the first cultivated representative of the phylum "Elusimicrobia" (formerly termite group 1). Appl. Environ. Microbiol. 75:2841-2849.
Holmes, D. E., K. T. Finneran, R. A. O'Neil, and D. R. Lovley. 2002. Enrichment of members of the family Geobacteraceae associated with stimulation of dissimilatory metal reduction in uranium-contaminated aquifer sediments. Appl. Environ. Microbiol. 68:2300-2306.
Huang, L. N., Y. Q. Chen, H. Zhou, S. Luo, C. Y. Lan, and L. H. Qu. 2003. Characterization of methanogenic Archaea in the leachate of a closed municipal solid waste landfill. FEMS Microbiol. Ecol. 46:171-177.
Huang, W. E., K. Stoecker, R. Griffiths, L. Newbold, H. Daims, A. S. Whiteley, and M. Wagner. 2007. Raman-FISH: combining stable-isotope Raman spectroscopy and fluorescence in situ hybridization for the single cell analysis of identity and function. Environ Microbiol 9:1878-1889.
Huang, Z. H. 2012. Biological community metabolism of spring pits in Jingmei River. M. S. thesis. National Chung-Hsing University, Taichung.
Hugenholtz, P., B. M. Goebel, and N. R. Pace. 1998. Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J. Bacteriol. 180:4765-4774.
Hugenholtz, P., G. W. Tyson, R. I. Webb, A. M. Wagner, and L. L. Blackall. 2001. Investigation of candidate division TM7, a recently recognized major lineage of the domain bacteria with no known pure-culture representatives. Appl. Environ. Microbiol. 67:411-419.
Iino, T., K. Mori, and K. Suzuki. 2010. Methanospirillum lacunae sp. nov., a methane-producing archaeon isolated from a puddly soil, and emended descriptions of the genus Methanospirillum and Methanospirillum hungatei. Int. J. Syst. Evol. Microbiol. 60:2563-2566.
Iino, T., K. Mori, Y. Uchino, T. Nakagawa, S. Harayama, and K. Suzuki. 2010. Ignavibacterium album gen. nov., sp. nov., a moderately thermophilic anaerobic bacterium isolated from microbial mats at a terrestrial hot spring and proposal of Ignavibacteria classis nov., for a novel lineage at the periphery of green sulfur bacteria. Int. J. Syst. Evol. Microbiol. 60:1376-1382.
Imachi, H., S. Sakai, Y. Sekiguchi, S. Hanada, Y. Kamagata, A. Ohashi, and H. Harada. 2008. Methanolinea tarda gen. nov., sp. nov., a methane-producing archaeon isolated from a methanogenic digester sludge. Int. J. Syst. Evol. Microbiol. 58:294-301.
Ishii, K., M. Mussmann, B. J. MacGregor, and R. Amann. 2004. An improved fluorescence in situ hybridization protocol for the identification of bacteria and archaea in marine sediments. FEMS Microbiol. Ecol. 50:203-213.
James, D. 2000. Fish use of upwellings. Alaska Department of Fish and Game's Habitat Division. (An Annotated Bibliography.)
Jetten, M. S. M., A. J. M. Stams, and A. J. B. Zehnder. 1992. Methanogenesis from acetate: a comparison of the acetate metabolism in Methanothrix Soehngenii and Methaosarcina spp. . FEMS Microbiol. Ecol. 88:181-197.
Jiang, B., S. N. Parshina, W. van Doesburg, B. P. Lomans, and A. J. Stams. 2005. Methanomethylovorans thermophila sp. nov., a thermophilic, methylotrophic methanogen from an anaerobic reactor fed with methanol. Int. J. Syst. Evol. Microbiol. 55:2465-2470.
Jiang, H., H. Dong, B. Yu, Q. Ye, J. Shen, H. Rowe, and C. Zhang. 2008. Dominance of putative marine benthic Archaea in Qinghai Lake, north-western China. Environ. Microbiol. 10:2355-2367.
Johnson N., C. Revenga and J. Echeverria. 2001. Managing Water for People and Nature. Science 292:1071-107.
Jones, W. J. 1991. Diversity and physiology of methanogens. ASM, Washington, DC.
Kasai, Y., Y. Takahata, T. Hoaki, and K. Watanabe. 2005. Physiological and molecular characterization of a microbial community established in unsaturated, petroleum-contaminated soil. Environ. Microbiol. 7:806-818.
Kirchman, D. L. 2002. The ecology of Cytophaga-Flavobacteria in aquatic environments. FEMS Microbiol. Ecol. 39:91-100.
Knittel, K., T. Losekann, A. Boetius, R. Kort, and R. Amann. 2005. Diversity and distribution of methanotrophic archaea at cold seeps. Appl. Environ. Microbiol. 71:467-479.
Konneke, M., A. E. Bernhard, J. R. de la Torre, C. B. Walker, J. B. Waterbury, and D. A. Stahl. 2005. Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437:543-546.
Kuenen, J. G. 2008. Anammox bacteria: from discovery to application. Nat. Rev. Microbiol. 6:320-326.
Kumar, P. S., A. L. Griffen, J. A. Barton, B. J. Paster, M. L. Moeschberger, and E. J. Leys. 2003. New bacterial species associated with chronic periodontitis. J. Dent. Res. 82:338-344.
Lai, M. C., C. M. Shu, S. C. Chen, L. J. Lai, M. S. Chiou, and J. J. Hua. 2000. Methanosarcina mazei strain O1M9704, methanogen with novel tubule isolated from estuarine environment. Curr. Microbiol. 41:15-20.
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 isolated from an aquaculture fishpond. Curr. Microbiol. 39:79-84.
Lechene, C. P., Y. Luyten, G. McMahon, and D. L. Distel. 2007. Quantitative imaging of nitrogen fixation by individual bacteria within animal cells. Science 317:1563-1566.
Lee, N., P. H. Nielsen, K. H. Andreasen, S. Juretschko, J. L. Nielsen, K. H. Schleifer, and M. Wagner. 1999. Combination of fluorescent in situ hybridization and microautoradiography-a new tool for structure-function analyses in microbial ecology. Appl Environ Microbiol 65:1289-1297.
Li, D., M. Yang, Z. Li, R. Qi, J. He, and H. Liu. 2008ge of bacterial communities in sediments along Songhua River in Northeastern China after a nitrobenzene pollution event. FEMS Microbiol. Ecol. 65:494-503.
Li, L., C. Kato, and K. Horikoshi. 1999. Bacterial diversity in deep-sea sediments from different depths. Biodivers. Conserv. 8:659-677.
Lin, X., D. Kennedy, J. Fredrickson, B. Bjornstad, and A. Konopka. 2012. Vertical stratification of subsurface microbial community composition across geological formations at the Hanford Site. Environ. Microbiol. 14:414-425.
Liu, Z., N. U. Frigaard, K. Vogl, T. Iino, M. Ohkuma, J. Overmann, and D. A. Bryant. 2012. Complete Genome of Ignavibacterium album, a Metabolically Versatile, Flagellated, Facultative Anaerobe from the Phylum Chlorobi. Front Microbiol 3:185.
Liu, Z., S. Huang, G. Sun, Z. Xu, and M. Xu. 2012. Phylogenetic diversity, composition and distribution of bacterioplankton community in the Dongjiang River, China. FEMS Microbiol. Ecol. 80:30-44.
Lliros, M., E. O. Casamayor, and C. Borrego. 2008. High archaeal richness in the water column of a freshwater sulfurous karstic lake along an interannual study. FEMS Microbiol. Ecol. 66:331-342.
Lomans, B. P., R. Luderer, P. Steenbakkers, A. Pol, C. van Der Drift, G. D. Vogels, and H. J. Op den Camp. 2001. Microbial populations involved in cycling of dimethyl sulfide and methanethiol in freshwater sediments. Appl. Environ. Microbiol. 67:1044-1051.
Lomans, B. P., R. Maas, R. Luderer, H. J. Op den Camp, A. Pol, C. van der Drift, and G. D. Vogels. 1999. Isolation and characterization of Methanomethylovorans hollandica gen. nov., sp. nov., isolated from freshwater sediment, a methylotrophic methanogen able to grow on dimethyl sulfide and methanethiol. Appl. Environ. Microbiol. 65:3641-3650.
Lovley, D. R. 2006.Dissimilatory Fe(III)- and Mn(IV)- reducing prokaryotes. In M. Dworkin, S. Falkow, E. Rosenberg, and E. Stackebrandt (eds). The Prokaryotes. Springer New York. 279: (http://www.prokaryotes.com)
Lueders, T., K. J. Chin, R. Conrad, and M. Friedrich. 2001. Molecular analyses of methyl-coenzyme M reductase alpha-subunit (mcrA) genes in rice field soil and enrichment cultures reveal the methanogenic phenotype of a novel archaeal lineage. Environ. Microbiol. 3:194-204.
Luton, P. E., J. M. Wayne, R. J. Sharp, and P. W. Riley. 2002. The mcrA gene as an alternative to 16S rRNA in the phylogenetic analysis of methanogen populations in landfill. Microbiology 148:3521-3530.
Maksimenko, S., T. I. Zemskaia, O. N. Pavlova, V. G. Ivanov, and S. P. Buriukhaev. 2008. Microbial community of the water column of the Selenga River-Lake Baikal biogeochemical barrier. Mikrobiologiia 77:660-667.
Merlino, G., A. Rizzi, F. Villa, C. Sorlini, M. Brambilla, P. Navarotto, B. Bertazzoni, M. Zagni, F. Araldi, and D. Daffonchio. 2012. Shifts of microbial community structure during anaerobic digestion of agro-industrial energetic crops and food industry byproducts. J. Chem. Technol. Biotechnol. 87:1302-1311.
Mizukami, S., K. Takeda, S. Akada, and T. Fujita. 2006. Isolation and characteristics of methanosaeta in paddy field soils. Biosci., Biotechnol., Biochem. 70:828-835.
Muyodi, F. J. 2000. Microbiological analysis of the waters of Lake Victoria in relation to the invasion of the water hyacinth. Ph. D. thesis. University of Dar es Salaam, Tanzania.
Muyzer, G., E. C. de Waal, and A. G. Uitterlinden. 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., and K. Smalla. 1998. Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Anton. Leeuw. 73:127-141.
Nakamura, K., T. Terada, Y. Sekiguchi, N. Shinzato, X. Y. Meng, M. Enoki, and Y. Kamagata. 2006. Application of pseudomurein endoisopeptidase to fluorescence in situ hybridization of methanogens within the family Methanobacteriaceae. Appl. Environ. Microbiol. 72:6907-6913.
Newton, R. J., S. E. Jones, A. Eiler, K. D. McMahon, and S. Bertilsson. 2011. A Guide to the Natural History of Freshwater Lake Bacteria. Microbiol. Mol. Biol. Rev. 75:14-49.
Nold, S. C., J. B. Pangborn, H. A. Zajack, S. T. Kendall, R. R. Rediske, and B. A. Biddanda. 2010. Benthic bacterial diversity in submerged sinkhole ecosystems. Appl Environ Microbiol 76:347-351.
North, N. N., S. L. Dollhopf, L. Petrie, J. D. Istok, D. L. Balkwill, and J. E. Kostka. 2004. ge in bacterial community structure during in situ biostimulation of subsurface sediment cocontaminated with uranium and nitrate. Appl. Environ. Microbiol. 70:4911-4920.
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.
Okabe, S., T. Kindaichi, and T. Ito. 2004. MAR-FISH—An Ecophysiological Approach to Link Phylogenetic Affiliation and In Situ Metabolic Activity of Microorganisms at a Single-Cell Resolution. Microbes Environ. 19:83-98.
Olsen, G. J., D. J. Lane, S. J. Giovannoni, N. R. Pace, and D. A. Stahl. 1986. Microbial ecology and evolution: a ribosomal RNA approach. Annu. Rev. Microbiol. 40:337-365.
Olsen, G. J., and C. R. Woese. 1993. Ribosomal RNA: a key to phylogeny. Faseb J 7:113-123.
Ouverney, C. C., G. C. Armitage, and D. A. Relman. 2003. Single-cell enumeration of an uncultivated TM7 subgroup in the human subgingival crevice. Appl. Environ. Microbiol. 69:6294-6298.
Orphan, V. J., C. H. House, K. U. Hinrichs, K. D. McKeegan, and E. F. DeLong. 2002. Multiple archaeal groups mediate methane oxidation in anoxic cold seep sediments. Proc Natl. Acad. Sci. USA 99:7663-7668.
Paul, M. J., and J. L. Meyer. 2001. Streams in the urban landscape. Annu. Rev. Ecol. Syst. 32:333-365.
Peng, T.-R. 2011. Using hydrogen and oxygen isotopes to assess contribution of groundwater to stream water: A case study of Jing Mei Creek, Taipei. M.S. thesis. National Chung-Hsing University, Taichung, Taiwan.
Pernthaler, A., J. Pernthaler, and R. Amann. 2002. Fluorescence in situ hybridization and catalyzed reporter deposition for the identification of marine bacteria. Appl. Environ. Microbiol. 68:3094-3101.
Pernthaler, A., and R. Amann. 2004. Simultaneous fluorescence in situ hybridization of mRNA and rRNA in environmental bacteria. Appl. Environ. Microbiol. 70:5426-5433.
Pester, M., C. Schleper, and M. Wagner. 2011. The Thaumarchaeota: an emerging view of their phylogeny and ecophysiology. Curr. Opin. Microbiol. 14:300-306.
Peura, S., A. Eiler, S. Bertilsson, H. Nykanen, M. Tiirola, and R. I. Jones. 2012. Distinct and diverse anaerobic bacterial communities in boreal lakes dominated by candidate division OD1. Isme J 6:1640-1652.
Plumb, J. J., J. Bell, and D. C. Stuckey. 2001. Microbial populations associated with treatment of an industrial dye effluent in an anaerobic baffled reactor. Appl. Environ. Microbiol. 67:3226-3235.
Porat, I., T. A. Vishnivetskaya, J. J. Mosher, C. C. Brandt, Z. K. Yang, S. C. Brooks, L. Liang, M. M. Drake, M. Podar, S. D. Brown, and A. V. Palumbo. 2010. Characterization of archaeal community in contaminated and uncontaminated surface stream sediments. Microb. Ecol. 60:784-795.
Prescott, L. M., J. P. Harley, and D. A. Klein. 2005. Bacteria: the Deinococci and nonproteobacteria gram negatives. p. 455-456. In Microbiology (6th ed). McGraw-Hill Singapore.
Prescott, L. M., J. P. Harley, and D. A. Klein. 2005. Bacteria: The Proteobacteria. p. 495-499. In Microbiology (6th ed). McGraw-Hill Singapore.
Prescott, L. M., J. P. Harley, and D. A. Klein. 2005. Bacteria: the low G + C gram positives. p. 515-518. In Microbiology (6th ed). McGraw-Hill Singapore.
Putkinen, A., H. Juottonen, S. Juutinen, E. S. Tuittila, H. Fritze, and K. Yrjala. 2009. Archaeal rRNA diversity and methane production in deep boreal peat. FEMS Microbiol. Ecol. 70:87-98.
Qiu, Y. L., Y. Sekiguchi, H. Imachi, Y. Kamagata, I. C. Tseng, S. S. Cheng, A. Ohashi, and H. Harada. 2004. Identification and isolation of anaerobic, syntrophic phthalate isomer-degrading microbes from methanogenic sludges treating wastewater from terephthalate manufacturing. Appl. Environ. Microbiol. 70:1617-1626.
Quirke, T. T. 1930. Spring pits; sedimentation phenomena. J. Geol. 38:88–91.
Rabus, R., D. Gade, R. Helbig, M. Bauer, F. O. Glockner, M. Kube, H. Schlesner, R. Reinhardt, and R. Amann. 2002. Analysis of N-acetylglucosamine metabolism in the marine bacterium Pirellula sp strain 1 by a proteomic approach. Proteomics 2:649-655.
Raghoebarsing, A. A., A. Pol, K. T. van de Pas-Schoonen, A. J. Smolders, K. F. Ettwig, W. I. Rijpstra, S. Schouten, J. S. Damste, H. J. Op den Camp, M. S. Jetten, and M. Strous. 2006. A microbial consortium couples anaerobic methane oxidation to denitrification. Nature 440:918-921.
Ranjard, L., F. Poly, and S. Nazaret. 2000. Monitoring complex bacterial communities using culture-independent molecular techniques: application to soil environment. Res. Microbiol. 151:167-177.
Raymond, L., J. Kepner, and R. P. Lame. 1994. Use of fluorochromes for direct enumeration of total bacteria in environmental samples: past ans present. Microbiol. Mol. Biol. Rev. 58:603-615.
Read, D. S., and A. S. Whiteley. 2011. Identity and function of single microbial cells within a community by raman microspectroscopy and relate single cell techniques, p. 163-176. In K. Sen and N. J. Ashbolt (eds.), Environmental Microbiology: Current Technology and Water Applications. Caister Academic Press, Norfolk
Rooney-Varga, J. N., R. T. Anderson, J. L. Fraga, D. Ringelberg, and D. R. Lovley. 1999. Microbial communities associated with anaerobic benzene degradation in a petroleum-contaminated aquifer. Appl. Environ. Microbiol. 65:3056-3063.
Sakai, S., M. Ehara, I. C. Tseng, T. Yamaguchi, S. L. Brauer, 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.
Sakai, S., H. Imachi, Y. Sekiguchi, I. C. Tseng, A. Ohashi, H. Harada, and Y. Kamagata. 2009. Cultivation of methanogens under low-hydrogen conditions by using the coculture method. Appl. Environ. Microbiol. 75:4892-4896.
Sambrook, J. and D. W. Russell. 2001. Molecular Cloning: A laboratory Mannual. Spring Harbor, New York. p. 1.123-1.125, 1.149-1.150 A 1.29
Sangwan, P., X. Chen, P. Hugenholtz, and P. H. Janssen. 2004. Chthoniobacter flavus gen. nov., sp. nov., the first pure-culture representative of subdivision two, Spartobacteria classis nov., of the phylum Verrucomicrobia. Appl. Environ. Microbiol. 70:5875-5881.
Schloss, P. D. 2008. Evaluating different approaches that test whether microbial communities have the same structure. Isme J 2:265-275.
Schloss, P. D., and J. Handelsman. 2006. Introducing SONS, a tool for operational taxonomic unit-based comparisons of microbial community memberships and structures. Appl. Environ. Microbiol. 72:6773-6779.
Schlotelburg, C., C. Wintzingerode, R. Hauck, F. Wintzingerode, W. Hegemann, and U. B. Gobel. 2002. Microbial structure of an anaerobic bioreactor population that continuously dechlorinates 1,2-dichloropropane. FEMS Microbiol. Ecol. 39:229-237.
Schuster, K. C., I. Reese, E. Urlaub, J. R. Gapes, and B. Lendl. 2000. Multidimensional information on the chemical composition of single bacterial cells by confocal Raman microspectroscopy. Analytical chemistry 72:5529-5534.
Sekar, R., B. M. Fuchs, R. Amann, and J. Pernthaler. 2004. Flow sorting of marine bacterioplankton after fluorescence in situ hybridization. Appl. Environ. Microbiol. 70:6210-6219.
Sheffield, V. C., J. S. Beck, E. M. Stone, and R. M. Myers. 1992. A simple and efficient method for attachment of a 40-base pair, GC-rich sequence to PCR-amplified DNA. BioTechniques 12:386-388.
Shinzato, N., T. Matsumoto, I. Yamaoka, T. Oshima, and A. Yamagishi. 1999. Phylogenetic diversity of symbiotic methanogens living in the hindgut of the lower termite Reticulitermes speratus analyzed by PCR and in situ hybridization. Appl. Environ. Microbiol. 65:837-840.
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. Syst. Appl. Microbiol. 26:312-318.
Simek, K., K. Hornak, J. Jezbera, M. Masin, J. Nedoma, J. M. Gasol, and M. Schauer. 2005. Influence of top-down and bottom-up manipulations on the R-BT065 subcluster of beta-proteobacteria, an abundant group in bacterioplankton of a freshwater reservoir. Appl. Environ. Microbiol. 71:2381-2390.
Spring, S., R. Amann, W. Ludwig, K.-H. Schleifer, H. van Gemerden, and N. Petersen. 1993. Dominating Role of an Unusual Magnetotactic Bacterium in the Microaerobic Zone of a Freshwater Sediment. Appl. Environ. Microbiol. 59:2397-2403.
Stackebrandt, E., and C. Woese. 1981. The evolution of prokaryotes. Cambridge University Press, Cambridge.
Staley, J. T., and W. B. Whitman. 2010. Phylum XIX. Fusobacteria. p. 747-774. In N. R. Krieg, J. T. Staley, D. R. Brown, B. P. Hedlund, B. J. Paster, N. L. Ward, W. Ludwig, and W. B. Whitman (eds.), Bergey’s Manual of Systematic Bacteriology, vol. 4. Springer New York, New York.
Stein, L. Y., G. Jones, B. Alexander, K. Elmund, C. Wright-Jones, and K. H. Nealson. 2002. Intriguing microbial diversity associated with metal-rich particles from a freshwater reservoir. FEMS Microbiol. Ecol. 42:431-440.
Stein, L. Y., M. T. La Duc, T. J. Grundl, and K. H. Nealson. 2001. Bacterial and archaeal populations associated with freshwater ferromanganous micronodules and sediments. Environ. Microbiol. 3:10-18.
Strous, M., J. A. Fuerst, E. H. Kramer, S. Logemann, G. Muyzer, K. T. van de Pas-Schoonen, R. Webb, J. G. Kuenen, and M. S. Jetten. 1999. Missing lithotroph identified as new Planctomycete. Nature 400:446-449.
Swofford, D.L., G.J. Olsen, P.J. Waddell, and D.M Hillis. 1996. Phylogeny reconstruction. In D.M. Hillis , C. Moritz, and B.K. Mable (eds.), Molecular Systematics, Sunderland, MA: Sinauer, pp. 407-514.
Taipale, S., R. I. Jones, and M. Tiirola. 2009. Vertical diversity of bacteria in an oxygen-stratified humic lake, evaluated using DNA and phospholipid analyses. Aquat. Microb. Ecol. 55:1-16.
Takai, K., and K. Horikoshi. 1999. Genetic diversity of archaea in deep-sea hydrothermal vent environments. Genetics 152:1285-1297.
Takai, K., D. P. Moser, M. DeFlaun, T. C. Onstott, and J. K. Fredrickson. 2001. Archaeal diversity in waters from deep South African gold mines. Appl. Environ. Microbiol. 67:5750-5760.
Tamaki, H., Y. Tanaka, H. Matsuzawa, M. Muramatsu, X. Y. Meng, S. Hanada, K. Mori, and Y. Kamagata. 2011. Armatimonas rosea gen. nov., sp nov., of a novel bacterial phylum, Armatimonadetes phyl. nov., formally called the candidate phylum OP10. Int. J. Syst. Evol. Microbiol. 61:1442-1447.
Tamura, K., D. Peterson, N. Peterson, G. Stecher, M. Nei, and S. Kumar. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28:2731-2739.
Taylor, K. G. 2007. Urban environments. In C. T. Perry and K. G. Taylor (eds.) Environmental sedimentology. Blackwell, Oxford. p.191-222.
Taylor, K. G., and P. N. Owens. 2009. Sediments in urban river basins: a review of sediment-contaminant dynamics in an environmental system conditioned by human activities. J. Soils Sed. 9:281-303.
Teske, A., and K. B. Sorensen. 2008. Uncultured archaea in deep marine subsurface sediments: have we caught them all? Isme J 2:3-18.
Tian, J., H. Chen, X. Dong, and Y. Wang. 2012. Relationship between archaeal community structure and vegetation type in a fen on the Qinghai–Tibetan Plateau. Biol. Fertility Soils 48:349-356.
Ueda, T., Y. Suga, and T. Matsuguchi. 1995. Molecular phylogenetic analysis of a soil microbial community in a soybean field. Eur. J. Soil Sci. 46:415-421.
UNFPA. 2011. State of the world population 2011: people and possibilities in a world of 7 billion. United Nation.
Utsumi, M., S. E. Belova, G. M. King, and H. Uchiyama. 2003. Phylogenetic comparison of methanogen diversity in different wetland soils. J Gen Appl Microbiol 49:75-83.
Van de Peer, Y., S. Chapelle, and R. De Wachter. 1996. A quantitative map of nucleotide substitution rates in bacterial rRNA. Nucleic Acids Res. 24:3381-3391.
Van Kessel, M. A., B. E. Dutilh, K. Neveling, M. P. Kwint, J. A. Veltman, G. Flik, M. S. Jetten, P. H. Klaren, and H. J. Op den Camp. 2011. Pyrosequencing of 16S rRNA gene amplicons to study the microbiota in the gastrointestinal tract of carp (Cyprinus carpio L.). AMB Express 1:41.
Ventura, M., C. Canchaya, A. Tauch, G. Chandra, G. F. Fitzgerald, K. F. Chater, and D. van Sinderen. 2007. Genomics of Actinobacteria: tracing the evolutionary history of an ancient phylum. Microbiol. Mol. Biol. R. 71:495-548.
Vergin, K. L., E. Urbach, J. L. Stein, E. F. DeLong, B. D. Lanoil, and S. J. Giovannoni. 1998. Screening of a fosmid library of marine environmental genomic DNA fragments reveals four clones related to members of the order Planctomycetales. Appl. Environ. Microbiol. 64:3075-3078.
Vetriani, C., H. W. Jannasch, B. J. MacGregor, D. A. Stahl and A.-L. Reysenbach. 1999. Population structure and phylogenetic characterization of marine benthic archaea in deep-sea sediments. Appl. Environ. Microbiol. 65;4375–4384.
Wagner, M. 2009. Single-cell ecophysiology of microbes as revealed by Raman microspectroscopy or secondary ion mass spectrometry imaging. Annu. Rev. Microbiol. 63:411-429.
Wagner, M., and M. Horn. 2006. The Planctomycetes, Verrucomicrobia, Chlamydiae and sister phyla comprise a superphylum with biotechnological and medical relevance. Curr. Opin. Biotechnol. 17:241-249.
Wallner, G., B. Fuchs, S. Spring, W. Beisker, and R. Amann. 1997. Flow sorting of microorganisms for molecular analysis. Appl. Environ. Microbiol. 63:4223-4231.
Wang, W. H. 2011. Using hydrogen and oxygen isotopes to assess contribution of groundwater to stream water: A case study of Jing Mei Creek, Taipei. M. S. thesis. National Chung Hsing University, Taichung.
Ward, N. L., J. F. Challacombe, P. H. Janssen, B. Henrissat, P. M. Coutinho, M. Wu, G. Xie, D. H. Haft, M. Sait, J. Badger, R. D. Barabote, B. Bradley, T. S. Brettin, L. M. Brinkac, D. Bruce, T. Creasy, S. C. Daugherty, T. M. Davidsen, R. T. DeBoy, J. C. Detter, R. J. Dodson, A. S. Durkin, A. Ganapathy, M. Gwinn-Giglio, C. S. Han, H. Khouri, H. Kiss, S. P. Kothari, R. Madupu, K. E. Nelson, W. C. Nelson, I. Paulsen, K. Penn, Q. Ren, M. J. Rosovitz, J. D. Selengut, S. Shrivastava, S. A. Sullivan, R. Tapia, L. S. Thompson, K. L. Watkins, Q. Yang, C. Yu, N. Zafar, L. Zhou, and C. R. Kuske. 2009. Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils. Appl. Environ. Microbiol. 75:2046-2056.
Watanabe, K., Y. Kodama, N. Hamamura, and N. Kaku. 2002. Diversity, abundance, and activity of archaeal populations in oil-contaminated groundwater accumulated at the bottom of an underground crude oil storage cavity. Appl. Environ. Microbiol. 68:3899-3907.
Weber, S., T. Lueders, M. W. Friedrich, and R. Conrad. 2001. Methanogenic populations involved in the degradation of rice straw in anoxic paddy soil. FEMS Microbiol. Ecol. 38:11-20.
Whitton, B. A. 1992. Diversity, ecology and taxonomy of the cyanobacteria. In N. H. Mann and N. G. Carr (eds.) Photosynthetic Prokaryotes. p. 1-52. Plenum Press, New York.
Wu, F. C. 2009. Assessment of the effectiveness of spring pits on restoration of urban river ecosystem: Studies on potential ecological benefit of removing streambed pavement. [Grant 98WFA0100267 proposal to the National Science Council].
Woese, C. R., O. Kandler, and M. L. Wheelis. 1990. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc. Natl. Acad. Sci. USA 87:4576-4579.
Xie, C. H., and A. Yokota. 2006. Sphingomonas azotifigens sp. nov., a nitrogen-fixing bacterium isolated from the roots of Oryza sativa. Int. J. Syst. Evol. Microbiol. 56:889-893.
Xu, J. 2006. Microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances. Mol. Ecol. 15:1713-1731.
Yamada, T., and Y. Sekiguchi. 2009. Cultivation of uncultured Chloroflexi subphyla: significance and ecophysiology of formerly uncultured Chloroflexi 'subphylum i' with natural and biotechnological relevance. Microbes and environments / JSME 24:205-216.
Yashiro, Y., S. Sakai, M. Ehara, M. Miyazaki, T. Yamaguchi, and H. Imachi. 2011. Methanoregula formicica sp. nov., a methane-producing archaeon isolated from methanogenic sludge. Int. J. Syst. Evol. Microbiol. 61:53-59.
Ye, W., X. Liu, S. Lin, J. Tan, J. Pan, D. Li, and H. Yang. 2009. The vertical distribution of bacterial and archaeal communities in the water and sediment of Lake Taihu. FEMS Microbiol. Ecol. 70:107-120.
Zhang, H., Y. Sekiguchi, S. Hanada, P. Hugenholtz, H. Kim, Y. Kamagata, and K. Nakamura. 2003. Gemmatimonas aurantiaca gen. nov., sp nov., a gram-negative, aerobic, polyphosphate-accumulating micro-organism, the first cultured representative of the new bacterial phylum Gemmatimonadetes phyl. nov. Int. J. Syst. Evol. Microbiol. 53:1155-1163.
Zhang, X. F., L. Zhao, S. J. Xu, Y. Z. Liu, H. Y. Liu, and G. D. Cheng. 2012. The influence of soil moisture on bacterial and fungal communities in Beilu River (Tibetan Plateau) permafrost soils with different vegetation types. J. Appl. Microbiol. DOI: 10.1111/jam.12106
Zhong, J. H., Z. F. Wen, G. M. Wang, X. B. Wang, H. B. Lu, and X. H. Shen. 2004. Air-discharge pits on the Yellow River delta plain. Sediment. Geol. 170:1-20.
Zhou, J., B. Xia, D. S. Treves, L. Y. Wu, T. L. Marsh, R. V. O'Neill, A. V. Palumbo, and J. M. Tiedje. 2002. Spatial and resource factors influencing high microbial diversity in soil. Appl. Environ. Microbiol. 68:326-334.
Zhu, J., H. Zheng, G. Ai, G. Zhang, D. Liu, X. Liu, and X. Dong. 2012. The genome characteristics and predicted function of methyl-group oxidation pathway in the obligate aceticlastic methanogens, Methanosaeta spp. PLoS One 7:e36756.
Zwart, G., B. C. Crump, M. P. K. V. Agterveld, F. Hagen, and S. K. Han. 2002. Typical freshwater bacteria: an analysis of available 16S rRNA gene sequences from plankton of lakes and rivers. Aquat. Microb. Ecol. 28:141-155.
Zwart, G., W. D. Hiorns, B. A. Methe, M. P. Van Agterveld, R. Huismans, S. C. Nold, J. P. Zehr, and H. J. Laanbroek. 1998. Nearly identical 16S rRNA sequences recovered from lakes in North America and Europe indicate the existence of clades of globally distributed freshwater Bacteria. Syst. Appl. Microbiol. 21:546-556.