publication . Article . 2015

Bacterial diversity differences along an epigenic cave stream reveal evidence of community dynamics, succession, and stability

Brannen-Donnelly, Kathleen; Engel, Annette S.;
Open Access English
  • Published: 01 Jul 2015 Journal: Frontiers in Microbiology, volume 6 (issn: 1664-302X, eissn: 1664-302X, Copyright policy)
  • Publisher: Frontiers Media S.A.
Abstract
Unchanging physicochemical conditions and nutrient sources over long periods of time in cave and karst subsurface habitats, particularly aquifers, can support stable ecosystems, termed autochthonous microbial endokarst communities (AMEC). AMEC existence is unknown for other karst settings, such as epigenic cave streams. Conceptually, AMEC should not form in streams due to faster turnover rates and seasonal disturbances that have the capacity to transport large quantities of water and sediment and to change allochthonous nutrient and organic matter sources. Our goal was to investigate whether AMEC could form and persist in hydrologically active, epigenic cave str...
Subjects
free text keywords: succession, cave, environmental disturbance, stream, microorganisms, community dynamics, streams, Microbiology, Original Research, QR1-502, Bio-Traps®, community assembly
71 references, page 1 of 5

Alfreider A. Krossbacher M. Psenner R. (1997). Groundwater samples do not reflect bacterial densities and activity in subsurface systems. Water Res. 31, 832–840.

American Public Health A. Eaton A. D. American Water Works A. Water Environment F. (2005). Standard Methods for the Examination of Water and Wastewater. Washington, DC: APHA-AWWA-WEF.

ASTM. (2008). D5373-08. Standard test methods for instrumental determination of carbon, hydrogen, and nitrogen in laboratory samples of coal, in Annual Book of ASTM Standards (West Conshohocken, PA), 19428–12959.

Besemer K. Peter H. Logue J. B. Langenheder S. Lindstrom E. S. Tranvik L. J. . (2012). Unraveling assembly of stream biofilm communities. ISME J. 6, 1459–1468. 10.1038/ismej.2011.205 22237539 [OpenAIRE] [PubMed] [DOI]

Besemer K. Singer G. Limberger R. Chlup A. K. Hochedlinger G. Hodl I. . (2007). Biophysical controls on community succession in stream biofilms. Appl. Environ. Microbiol. 73, 4966–4974. 10.1128/AEM.00588-07 17557861 [OpenAIRE] [PubMed] [DOI]

Birdwell J. E. Engel A. S. (2010). Characterization of dissolved organic matter in cave and spring waters using UV–Vis absorbance and fluorescence spectroscopy. Org. Geochem. 41, 270–280. 10.1016/j.orggeochem.2009.11.002 [DOI]

Bonacci O. Pipan T. Culver D. C. (2008). A framework for karst ecohydrology. Environ. Geol. 56, 891–900. 10.1007/s00254-008-1189-0 [DOI]

Caporaso J. G. Kuczynski J. Stombaugh J. Bittinger K. Bushman F. D. Costello E. K. . (2010). QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7, 335–336. 10.1038/nmeth.f.303 20383131 [OpenAIRE] [PubMed] [DOI]

Chapelle F. H. (2000). The significance of microbial processes in hydrogeology and geochemistry. Hydrogeol. J. 8, 41–46. 10.1007/PL00010973 [DOI]

Coble P. (1996). Characterization of marine and terrestrial DOM in seawater using excitation-emission spectroscopy. Mar. Chem. 51, 325–346.

Crawford P. A. Crowley J. R. Sambandam N. Muegge B. D. Costello E. K. Hamady M. . (2009). Regulation of myocardial ketone body metabolism by the gut microbiota during nutrient deprivation. Proc. Natl. Acad. Sci. U.S.A. 106, 11276–11281. 10.1073/pnas.0902366106 19549860 [OpenAIRE] [PubMed] [DOI]

Desantis T. Z. Hugenholtz P. Larsen N. Rojas M. Brodie E. L. Keller K. . (2006). Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl. Environ. Microbiol. 72, 5069–5072. 10.1128/AEM.03006-05 16820507 [OpenAIRE] [PubMed] [DOI]

Dogwiler T. Wicks C. M. (2004). Sediment entrainment and transport in fluviokarst systems. J. Hydrol. 295, 163–172. 10.1016/j.jhydrol.2004.03.002 [DOI]

Dougherty P. H. (1985). An overview of the geology and physical geography of Kentucky, in Caves and Karst of Kentucky, ed Percy H. (Dougherty, KY: Geol. Survey Special Publication XI), 79–80.

Dowd S. E. Callaway T. R. Wolcott R. D. Sun Y. McKeehan T. Hagevoort R. G. . (2008). Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP). BMC Microbiol. 8:125. 10.1186/1471-2180-8-125 18652685 [OpenAIRE] [PubMed] [DOI]

71 references, page 1 of 5
Abstract
Unchanging physicochemical conditions and nutrient sources over long periods of time in cave and karst subsurface habitats, particularly aquifers, can support stable ecosystems, termed autochthonous microbial endokarst communities (AMEC). AMEC existence is unknown for other karst settings, such as epigenic cave streams. Conceptually, AMEC should not form in streams due to faster turnover rates and seasonal disturbances that have the capacity to transport large quantities of water and sediment and to change allochthonous nutrient and organic matter sources. Our goal was to investigate whether AMEC could form and persist in hydrologically active, epigenic cave str...
Subjects
free text keywords: succession, cave, environmental disturbance, stream, microorganisms, community dynamics, streams, Microbiology, Original Research, QR1-502, Bio-Traps®, community assembly
71 references, page 1 of 5

Alfreider A. Krossbacher M. Psenner R. (1997). Groundwater samples do not reflect bacterial densities and activity in subsurface systems. Water Res. 31, 832–840.

American Public Health A. Eaton A. D. American Water Works A. Water Environment F. (2005). Standard Methods for the Examination of Water and Wastewater. Washington, DC: APHA-AWWA-WEF.

ASTM. (2008). D5373-08. Standard test methods for instrumental determination of carbon, hydrogen, and nitrogen in laboratory samples of coal, in Annual Book of ASTM Standards (West Conshohocken, PA), 19428–12959.

Besemer K. Peter H. Logue J. B. Langenheder S. Lindstrom E. S. Tranvik L. J. . (2012). Unraveling assembly of stream biofilm communities. ISME J. 6, 1459–1468. 10.1038/ismej.2011.205 22237539 [OpenAIRE] [PubMed] [DOI]

Besemer K. Singer G. Limberger R. Chlup A. K. Hochedlinger G. Hodl I. . (2007). Biophysical controls on community succession in stream biofilms. Appl. Environ. Microbiol. 73, 4966–4974. 10.1128/AEM.00588-07 17557861 [OpenAIRE] [PubMed] [DOI]

Birdwell J. E. Engel A. S. (2010). Characterization of dissolved organic matter in cave and spring waters using UV–Vis absorbance and fluorescence spectroscopy. Org. Geochem. 41, 270–280. 10.1016/j.orggeochem.2009.11.002 [DOI]

Bonacci O. Pipan T. Culver D. C. (2008). A framework for karst ecohydrology. Environ. Geol. 56, 891–900. 10.1007/s00254-008-1189-0 [DOI]

Caporaso J. G. Kuczynski J. Stombaugh J. Bittinger K. Bushman F. D. Costello E. K. . (2010). QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7, 335–336. 10.1038/nmeth.f.303 20383131 [OpenAIRE] [PubMed] [DOI]

Chapelle F. H. (2000). The significance of microbial processes in hydrogeology and geochemistry. Hydrogeol. J. 8, 41–46. 10.1007/PL00010973 [DOI]

Coble P. (1996). Characterization of marine and terrestrial DOM in seawater using excitation-emission spectroscopy. Mar. Chem. 51, 325–346.

Crawford P. A. Crowley J. R. Sambandam N. Muegge B. D. Costello E. K. Hamady M. . (2009). Regulation of myocardial ketone body metabolism by the gut microbiota during nutrient deprivation. Proc. Natl. Acad. Sci. U.S.A. 106, 11276–11281. 10.1073/pnas.0902366106 19549860 [OpenAIRE] [PubMed] [DOI]

Desantis T. Z. Hugenholtz P. Larsen N. Rojas M. Brodie E. L. Keller K. . (2006). Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl. Environ. Microbiol. 72, 5069–5072. 10.1128/AEM.03006-05 16820507 [OpenAIRE] [PubMed] [DOI]

Dogwiler T. Wicks C. M. (2004). Sediment entrainment and transport in fluviokarst systems. J. Hydrol. 295, 163–172. 10.1016/j.jhydrol.2004.03.002 [DOI]

Dougherty P. H. (1985). An overview of the geology and physical geography of Kentucky, in Caves and Karst of Kentucky, ed Percy H. (Dougherty, KY: Geol. Survey Special Publication XI), 79–80.

Dowd S. E. Callaway T. R. Wolcott R. D. Sun Y. McKeehan T. Hagevoort R. G. . (2008). Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP). BMC Microbiol. 8:125. 10.1186/1471-2180-8-125 18652685 [OpenAIRE] [PubMed] [DOI]

71 references, page 1 of 5
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publication . Article . 2015

Bacterial diversity differences along an epigenic cave stream reveal evidence of community dynamics, succession, and stability

Brannen-Donnelly, Kathleen; Engel, Annette S.;