1 |
Bottomley, P.J. 1992. Ecology of Bradyrhizobium, and Gluconoacetobacter diazotrophicusobium, p. 293-348. In G. Stacey, R.H. Burris and H.J. Evans (eds.), Biological Nitrogen Fixation. Chapman, and Hall New York, London, UK
|
2 |
Groth, I. and C. Saiz-Jimenez. 1999. Actinomycetes in hypogean environments. Geomicrobiol. J. 16, 1-8
DOI
|
3 |
Holmes, A.J., N.A. Tujula, M. Holley, A. Contos, J.M. James, P. Rogers, and M.R. Gillings. 2001. Phylogenetic structure of unusual aquatic microbial formations in Nullarbor Caves, Australia. Environ. Microbiol. 3, 256-264n
DOI
ScienceOn
|
4 |
Juretschko, S., A. Loy, A. Lehner, and M. Wagner. 2002. The microbial community composition of a nitrifying-denitrifying activated sludge from an industrial sewage treatment plant analyzed by the full-cycle rRNA approach. Syst. Appl. Microbiol. 25, 84-99
DOI
ScienceOn
|
5 |
Lane, D.J. 1991. 16S/23S rRNA sequencing, p. 115-175. In E. Stackebrandt, and M. Goodfellow (eds.), Nucleic Acid Techniques in Bacterial. Wiley, New York, USA
|
6 |
Liesack, W. and K. Finster. 1994. Phylogenetic analysis of five strains of Gram-negative, obligately anaerobic, sulfur-reducing bacteria, and description of Desulfuromusa gen. nov., including Desulfuromusa kysingii sp. nov., Desulfuromusa bakii sp. nov., and Desulfuromusa succinoxidans sp. nov. Int. J. Syst. Bacteriol. 44, 753-758
DOI
ScienceOn
|
7 |
Liesack, W., P.H. Janssen, F.A. Rainey, N. Ward-Rainey, and E. Stackebrandt. 1997. Microbial diversity in soil, the need for a combined approach using molecular, and cultivation techniques, p. 375-439. In J.D. van Elsas, J.T. Trevors, and E.M.H. Wellington (eds.), Modern Soil Microbiology. Marcel Dekker, New York, USA
|
8 |
Saitou, N., M. Nei, and L.S. Lerman. 1987. The neighbor-joining method, a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406-425
PUBMED
|
9 |
Schirmer, A., R. Gadkari, C.D. Reeves, F. Ibrahim, E.F. DeLong, and C.R. Hutchinson. 2005. Metagenomic analysis reveals diverse polyketide synthase gene clusters in microorganisms associated with the marine sponge Discodermia dissoluta. Appl. Environ. Microbiol. 71, 4840-4849
DOI
ScienceOn
|
10 |
Schmid, M., U. Twachtmann, M. Klein, M. Strous, S. Juretschko, and M. Jetten. 2000. Molecular evidence for a genus-level diversity of bacteria capable of catalyzing anaerobic ammonium oxidation. System. Appl. Microbiol. 23, 93-106
DOI
ScienceOn
|
11 |
Huang, L.N., H. Zhou, S. Zhu, and L.H. Qu. 2004. Phylogenetic. diversity of bacteria in the leachate of a full-scale recirculating landfill. FEMS Microbiol. Ecol. 50, 175-183
DOI
ScienceOn
|
12 |
Quaiser, A., T. Ochsenreiter, C. Lanz, S. C. Schuster, A. H. Treusch, J. Eck, and C. Schleper. 2003. Acidobacteria form a coherent but highly diverse group within the bacterial domain: evidence from environmental genomics. Mol. Microbiol. 50, 563-575
DOI
ScienceOn
|
13 |
Vlasceanu, L., S.M. Sarbu, A.S. Engel, and B.K. Kinkle. 2000. Acidic cave-wall biofilms located in the Frasassi Gorge, Italy. Geomicrobiol. J. 17, 125-140
DOI
ScienceOn
|
14 |
Kimura, M. 1980. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16, 111-120
DOI
|
15 |
Head, I.M., J.R. Saunders, and R.W. Pickup. 1998. Microbial evolution, diversity, and ecology, a decade of ribosomal RNA analysis of uncultivated microorganisms. Microb. Ecol. 35, 1-21
DOI
|
16 |
Laiz, L., I. Groth, P. Schumann, F. Zezza, A. Felske, B. Hermosin, and C. Saiz-Jimenez. 2000. Microbiology of the stalactites from Grotta dei Cervi, Porto Badisco, Italy. Int. Microbiol. 3, 25-30
PUBMED
|
17 |
Ozeki, S., I. Baba, N. Takaya, and H. Shoun. 2001. A novel C1- using denitrifier Alcaligenes sp. STC1, and its genes for coppercontaining nitrite reductase, and azurin. Biosci. Biotechnol. Biochem. 65, 1206-12101
DOI
ScienceOn
|
18 |
Groth, I., R.B. Vetterman, Schuetzte, P. Schumann, and C. Saiz- Jimenez. 1999. Actinomycetes in karstic caves of northern Spain Altamira, and Tito Bustillo. J. Microbiol. Methods 36, 115-122
DOI
ScienceOn
|
19 |
Suzuki, I., U. Dular, and S.C. Kwok. 1974. Ammonia or ammonium ion as substrate for oxidation by Nitrosomonas cells, and extracts. J. Bacteriol. 120, 556-558
PUBMED
|
20 |
Engel, A.S., M.I. Porter, B.K. Kinkle, and T.C. Kane. 2001. Ecological assessment, and geological significance of microbial communities from Cesspool Cave, Virginia. Geomicrobiol. J. 18, 259-274
DOI
|
21 |
Kumar, S., K. Tamura, and M. Nei. 2004. MEGA3, Integrated software for molecular evolutionary genetics analysis, and sequence alignment. Briefings in Bioinformatics 5, 150-163
DOI
ScienceOn
|
22 |
Asami, H., M. Aida, and K. Watanabe. 2005. Accelerated sulfur cycle in coastal marine sediment beneath areas of intensive shellfish aquaculture. Appl. Environ. Microbiol. 716, 2925-2933
|
23 |
Ghiorse, W.C. and P. Hirsch. 1979. An ultrastructural study of iron, and manganese deposition associated with extracellular polymers of Pedomicrobium-like budding bacteria. Arch. Microbiol. 123, 213-226
DOI
|
24 |
Peck, S.B. 1986. Bacterial deposition of iron, and manganese oxides in North American caves. NSS. Bull 48, 26-30
|
25 |
Jetten, M., M. Wagner, J. Fuerst, M. van Loosdrecht, G. Kuenen, and M. Strous. 2001. Microbiology, and application of the anaerobic ammonium oxidation 'anamox' process. Curr. Opin. Biotechnol. 12, 283-288
DOI
ScienceOn
|
26 |
Maidak, B.L., G.J. Olsen, N. Larsen, R. Overbeek, M.J. Mc- Caughey, and C.R. Woese. 1997. The RDP ribosomal database project. Nucleic Acids Res. 25, 109-110
DOI
|
27 |
Sarbu S.M., T.C. Kane, and B.K. Kinkle. 1996. A chemoautotrophically based cave ecosystem. Science 272, 1953-1954
DOI
ScienceOn
|
28 |
Schabereiter-Gurtner, C., C. Saiz-Jimenez, G. Pinar, W. Lubitz, and S. Rolleke. 2002a. Altamira Cave Paleolithic paintings harbour partly unknown bacterial communities. FEMS Microbiol. Lett. 211, 7-11
DOI
|
29 |
Canaveras, J.C., S. Sanchez-Moral, V. Soler, and C. Saiz-Jimenez. 2001. Microorganisms, and microbially induced fabrics in cave walls. Geomicrobiol. J. 18, 223-240
DOI
|
30 |
Engel, A.S., M.L. Porter, L.A. Stern, S. Quinlan, and P.C. Bennett. 2004. Bacterial diversity, and ecosystem function of filamentous microbial mats from aphotic (cave) sulfidic springs dominated by chemolithoautotrophic 'Epsilonproteobacteria'. FEMS Microbiol.Ecol. 51, 31-53,
DOI
ScienceOn
|
31 |
Zhang Y.J., M.D. Yang, and C.H. He. 1992. Karst geomorphology, and environmental implication in Guizhou. Cave Science 19, 13-20
|
32 |
Cramm, R., R.A. Siddiqui, and B. Friedrich. 1997. Two isofunctional nitric oxide reductases in Alcaligenes eutrophus H16. J. Bacteriol. 179, 6769-6777
DOI
PUBMED
|
33 |
Northup, D.E., C.N. Dahm, L.A. Melim, M.N. Spilde, L.J. Crossey, and K.H. Lavoie. 2000. Evidence for geomicrobiological interactions in Guadalupe Caves. J. Caves Kars.t Stud. 62, 80-90
|
34 |
Schabereiter-Gurtner, C., C. Saiz-Jimenez, G. Pin.ar, W. Lubitz, and S. Rolleke. 2002b. Phylogenetic 16S rRNA analysis reveals the presence of complex, and partly unknown bacterial communities in Tito Bustillo Cave, Spain, and on its Paleolithic paintings. Environ. Microbiol. 4, 392-400
DOI
ScienceOn
|
35 |
Amann, R.I., W. Ludwig, and K.H. Schleifer. 1995. Phylogenetic identification, and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59, 143-169
PUBMED
|
36 |
Hiorns, W.D., R.C. Hastings, I.M. Head, G.R. Hall, A.J. Mc- Carthy, J.R. Saunders, and R.W. Pickup. 1995. Amplification of 16S ribosomal RNA genes of autotrophic ammonia-oxidizing bacteria demonstrates the ubiquity of Nitrosospiras in the environment. Microbiology 141, 2793-2800
DOI
ScienceOn
|
37 |
Altschul, S.F., W. Gish, W. Miller, E.W. Myers, and D.J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215, 403-410
DOI
PUBMED
|
38 |
Groth, I., P. Schumann, L. Laiz, S. Sanchez-Moral, J.C. Canaveras, and C. Saiz-Jimenez. 2001. Geomicrobiological study of the Grotta dei Cervi, Porto Badisco, Italy. Geomicrobiol. J. 18, 241-258
DOI
|
39 |
Kuske, C.R., S.M. Barns, and J.D. Busch. 1997. Diverse uncultivated bacterial groups from soils of the arid southwestern United States that are present in many geographic regions. Appl. Environ. Microbiol. 63, 3614-3621
PUBMED
|
40 |
Northup, D.E., S.M. Barns, L.E. Yu, M.N. Spilde, R.T. Schelble, and K.E. Dano. 2003. Diverse microbial communities inhabiting ferromanganese deposits in Lechuguilla and Spider Caves. Environ. Microbiol. 5, 1071-1086
DOI
ScienceOn
|
41 |
Glockner, F.O., M. Kube, M. Bauer, H. Teeling, T. Lombardot, W. Ludwig, D. Gade, A. Beck, K. Borzym, K. Heitmann, R. Rabus, H. Schlesner, R. Amann, and R. Reinhardt. 2003. Complete genome sequence of the marine planctomycete Pirellula sp. strain 1. PNAS 14, 8298-8303
|
42 |
Ludwig, W., S.H. Bauer, M. Bauer, I. Held, I. Kirchhof, R. Schulze, and K.H. Schleifer. 1997. Detection, and in situ identification of representatives of a widely distributed new bacterial phylum. FEMS Microbiol. Lett. 153, 181-190
DOI
|
43 |
Northup, D.E. and K.H. Lavoie. 2001. Geomicrobiology of caves, a review. Geomicrobiol. J. 18, 199-222
DOI
|
44 |
Neef, A., R. Amann, H. Schlesner, and K.H. Schleifer. 1998. Monitoring a widespread bacterial group, in situ detection of planctomycetes with 16S rRNA-targeted probes. Microbiology 144, 3257-3266
DOI
ScienceOn
|
45 |
Schabereiter-Gurtner, C., C. Saiz-Jimenez, G. Pinar, W. Lubitz, and S. Rolleke. 2003. Phylogenetic diversity of bacteria associated with Paleolithic paintings, and surrounding rock walls in two Spanish caves Llonin, and La Garma. FEMS Microbiol. Ecol. 1606, 1-13
|
46 |
Chen, W.M., S. Laevens, T.M. Lee, T. Coenye, P. De Vos, M. Mergeay, and P. Vandamme. 2001. Ralstonia taiwanensis sp. nov., isolated from root nodules of Mimosa species, and sputum of a cystic fibrosis patient. Int. J. Syst. Evol. Microbiol. 51, 1729-1735
DOI
PUBMED
ScienceOn
|
47 |
Gillieson, D. 1996. Caves, processes, development, and management, p. 324. Blackwell Publishers, Oxford, UK
|
48 |
Hose L.D., A.N. Palmer, M.V. Palmer, D.E. Northup, P.J. Boston, and H.R. Duchene. 2000. Microbiology, and geochemistry in a hydrogen-sulphide-rich karst environment. Chem. Geol. 169, 399-423
DOI
ScienceOn
|
49 |
Laiz, L., I. Groth, I. Gonzalez, and C. Saiz-Jimenez. 1999. Microbiological study of the dripping water in Altamira Cave Santillana del Mar, Spain. J. Microbiol. Methods 36, 129-138
DOI
ScienceOn
|
50 |
Moore, G.W. 1981. Manganese deposition in limestone caves, p. 642-645. In B.F. Beck (eds.), Proceedings 8th International Congress of Speleology, II. Kentucky, USA
|
51 |
Smart, P.L, A.C. Waltham, M.D. Yang, and Y.J. Zhang. 1986. Karst geomorphology of western Guizhou, China. Cave Science 13, 89-104
|
52 |
Gonzalez, I., L. Laiz, B. Hermosin, B. Guerrero, C. Incerti, and C. Saiz-Jimenez. 2003. Microbial communities of the rock paintings of Atlanterra shelter South Spain. J. Microbiol. Methods 36, 123-127
DOI
ScienceOn
|
53 |
Hugenholtz, P., M.B. Goebel, and N.R. Pace. 1998. Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J. Bacteriol. 180, 4765-4774
PUBMED
|
54 |
Nealson, K.H. and D. Saffarini. 1994. Iron, and manganese in anaerobic respiration: environmental significance, physiology, and regulation. Ann. Rev. Microbiol. 48, 311-343
DOI
ScienceOn
|
55 |
Burrell, P.C., J. Keller, and L.L. Blackall. 1998. Microbiology of a nitrite-oxidizing bioreactor. Appl. Environ. Microbiol. 64, 1878- 1883
PUBMED
|
56 |
Cunningham, K.I., D.E. Northup, R.M. Pollastro, W.G. Wright, and E.J. LaRock. 1995. Bacteria, fungi, and biokarst in Lechuguilla Cave, Carlsbad Caverns National Park, New Mexico. Environ. Geol. 25, 2-8
DOI
|
57 |
Thompson, J.D., T.J. Gibson, F. Plewniak, F. Jeanmougin, and D.G. Higgens. 1997. The Clustal X windows interface, flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 24, 4876-4882
|