Assessing impacts of unconventional natural gas extraction on microbial communities in headwater stream ecosystems in northwestern Pennsylvania

Frontiers in Microbiology

Volumn 5, Issue SEP, 2014, Pages

  Trexler, Ryan ^a   Solomon, Caroline ^a   McClure, Erin E ^a   Brislawn, Colin J ^a   Grube, Alyssa M ^a   Wright, Justin R ^a   Rosenberger, Abigail ^a   Peterson, Mark P ^a,f   Keddache, Mehdi ^b   Mason, Olivia U ^c   Hazen, Terry C ^d,e   Grant, Christopher J ^a   Lamendella, Regina ^a  

^a JUNIATA COLLEGE   (United States)

^b CINCINNATI CHILDREN'S HOSPITAL MEDICAL CENTER   (United States)

^c FLORIDA STATE UNIVERSITY   (United States)

^d University of Tennessee Knoxville   (United States)

^e OAK RIDGE NATIONAL LABORATORY   (United States)

^f PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CARBON; NATURAL GAS; RNA 16S;

ACETOBACTERACEAE; AQUATIC ENVIRONMENT; ARTICLE; BIOFILM; COMMUNITY STRUCTURE; CONTROLLED STUDY; DNA EXTRACTION; GENE SEQUENCE; HIGH THROUGHPUT SEQUENCING; ISOTOPE ANALYSIS; METHYLOCYSTACEAE; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; NONHUMAN; OIL SHALE; PH; POLYMERASE CHAIN REACTION; PROTEOBACTERIA; RNA GENE; SPECIES RICHNESS; STRUCTURAL BIOINFORMATICS; UNITED STATES; WATERSHED;

ACIDOBACTERIACEAE; BRYOPHYTES; METHYLOCYSTACEAE; OTUS; PHENYLOBACTERIUM;

EID: 84928321769     PISSN: None     EISSN: 1664302X     Source Type: Journal    
DOI: 10.3389/fmicb.2014.00522     Document Type: Article

References (90)

1. Sweeney, B. (1992). Streamside Forests and the Physical, Chemical, and Trophic Characteristics of Piedmont Streams in Eastern North America. Available at: http://www.iwaponline.com/wst/02612/wst026122653.htm.
2. Pusch, M., Fiebig, D., Brettar, I., Eisenmann, H., Ellis, B. K., Lake, F., Station, B., Kaplan, L. A., Water, S., Lock, M. A., et al. (1998). The role of micro-organisms in the ecological connectivity of running waters. Freshw. Biol. 40, 453-495.
3. Lemke, M., Brown, B., and Leff, L. (1997). The response of three bacterial populations to pollution in a stream. Microb. Ecol. 34, 224-231. Available at: http://link.springer.com/article/10.1007/s002489900051 [Accessed July 14, 2014].
4. Lemke, M. J., and Leff, L. G. (1999). Bacterial populations in an anthropogenically disturbed stream: Comparison of different seasons. Microb. Ecol. 38, 234-243.
5. Janisch, J. E., Wondzell, S. M., and Ehinger, W. J. (2012). Headwater stream temperature: Interpreting response after logging, with and without riparian buffers, Washington, USA. For. Ecol. Manage. 270, 302-313. doi:10.1016/j.foreco.2011.12.035.
6. Ding, S., Xhang, Y., Liu, B., Kong, W., and Meng, W. (2013). Effects of riparian land use on water quality and fish communities in the headwater stream of the Taizi River in China. Front. Environ. Sci. Eng. 7, 699-708. doi:10.1007/s11783-013-0528-x.
7. Webber, J. S. (2012). Water Quality Condition Assessment of Streams in National Parks of the Mid-Atlantic USA Integrating Physical, Chemical, and Biological Datasets Pennsylvania State University.
8. Maloney, K. O., and Weller, D. E. (2011). Anthropogenic disturbance and streams: land use and land-use change affect stream ecosystems via multiple pathways. Freshw. Biol. 56, 611-626. doi:10.1111/j.1365-2427.2010.02522.x.
9. Meyer, J. L., Strayer, D. L., Wallace, J. B., Eggert, S. L., Helfman, G. S., and Leonard, N. E. (2007). The Contribution of Headwater Streams to Biodiversity in River Networks1. JAWRA J. Am. Water Resour. Assoc. 43, 86-103. doi:10.1111/j.1752-1688.2007.00008.x.
10. Freeman, M. C., Pringle, C. M., and Jackson, C. R. (2007). Hydrologic Connectivity and the Contribution of Stream Headwaters to Ecological Integrity at Regional Scales1. JAWRA J. Am. Water Resour. Assoc. 43, 5-14. doi:10.1111/j.1752-1688.2007.00002.x.
11. Wipfli, M. S., Richardson, J. S., and Naiman, R. J. (2007). Ecological Linkages Between Headwaters and Downstream Ecosystems: Transport of Organic Matter. J. Am. Water Resour. 43, 72-85.
12. Alexander, R. B., Boyer, E. W., Smith, R. a, Schwarz, G. E., and Moore, R. B. (2007). The Role of Headwater Streams in Downstream Water Quality. J. Am. Water Resour. Assoc. 43, 41-59. doi:10.1111/j.1752-1688.2007.00005.x.
13. Peterson, B. J., Wollheim, W. M., Mulholland, P. J., Webster, J. R., Meyer, J. L., Tank, J. L., Marti, E., Bowden, W. B., Valett, H. M., Hershey, a E., et al. (2001). Control of nitrogen export from watersheds by headwater streams. Science 292, 86-90. doi:10.1126/science.1056874.
14. Findlay, S., Tank, J., Dye, S., and Valett, H. (2002). A cross-system comparison of bacterial and fungal biomass in detritus pools of headwater streams. Microb. Ecol. 43, 55-66. doi:10.1007/10.007/s00248-001-1020-x.
15. Gulis, V., and Suberkropp, K. (2003). Leaf litter decomposition and microbial activity in nutrient-enriched and unaltered reaches of a headwater stream. Freshw. Biol. 48, 123-134. Available at: http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2427.2003.00985.x/full [Accessed July 10, 2014].
16. Wright, M. S., and Covich, a P. (2005). Relative importance of bacteria and fungi in a tropical headwater stream: leaf decomposition and invertebrate feeding preference. Microb. Ecol. 49, 536-46. doi:10.1007/s00248-004-0052-4.
17. Schelker, J., Eklöf, K., Bishop, K., and Laudon, H. (2012). Effects of forestry operations on dissolved organic carbon concentrations and export in boreal first-order streams. J. Geophyical Res. 117, G01011. Available at: http://adsabs.harvard.edu/abs/2012JGRG.117.1011S.
18. Hall, E. K., Besemer, K., Kohl, L., Preiler, C., Riedel, K., Schneider, T., Wanek, W., and Battin, T. J. (2012). Effects of resource chemistry on the composition and function of stream hyporheic biofilms. Front. Microbiol. 3, 35. doi:10.3389/fmicb.2012.00035.
19. Hall, R. O., and Tank, J. L. (2003). Ecosystem metabolism controls nitrogen uptake in streams in Grand Teton National Park, Wyoming. Limnol. Oceanogr. 48, 1120-1128. doi:10.4319/lo.2003.48.3.1120.
20. Puddu, A., Zoppini, A., Fazi, S., Rosati, M., Amalfitano, S., and Magaletti, E. (2003). Bacterial uptake of DOM released from P-limited phytoplankton. FEMS Microbiol. Ecol. 46, 257-68. doi:10.1016/S0168-6496(03)00197-1.
21. Wassel, R., and Mills, A. (1983). Changes in water and sediment bacterial community structure in a lake receiving acid mine drainage. Microb. Ecol. 9, 155-169. Available at: http://link.springer.com/article/10.1007/BF02015128 [Accessed July 14, 2014].
22. Clivot, H., Danger, M., Pagnout, C., Wagner, P., Rousselle, P., Poupin, P., and Guérold, F. (2013). Impaired leaf litter processing in acidified streams: learning from microbial enzyme activities. Microb. Ecol. 65, 1-11. doi:10.1007/s00248-012-0107-x.
23. Sun, M. Y., Dafforn, K. a, Johnston, E. L., and Brown, M. V (2013). Core sediment bacteria drive community response to anthropogenic contamination over multiple environmental gradients. Environ. Microbiol. 15, 2517-31. doi:10.1111/1462-2920.12133.
24. Hubbert, M. K., and Willis, D. G. (1954). Mechanics of Hydraulic Fracturing.
25. Arthur, J., Langhus, B., and Alleman, D. (2008). An overview of modern shale gas development in the United States. All Consult., 1-21. Available at: http://www.lexisnexis.com/documents/pdf/20100210093849_large.pdf [Accessed July 14, 2014].
26. Council, G. W. P., and LLC, A. C. (2009). Modern shale gas development in the United States: A primer. Available at: http://www.netl.doe.gov/technologies/oil gas/publications/EPreports/Shale_Gas_Primer_2009.pdf.
27. Pennsylvania drives Northeast natural gas production growth (2011). Available at: http://www.eia.gov/todayinenergy/detail.cfm?id=2870.
28. United States Energy Information Administration (2012). Horizontal drilling boosts Pennsylvania's natural gas production. Available: http://www.eia.gov/todayinenergy/detail.cfm?id=6390.
29. Ground Water Protection Council, All Consulting and LLC. (2009). M. shale gas development in the U. S. A. A primer. Available: http://www. netl. doe.gov/technologies/oil-gas/publications/EPreports/Shale_Gas_Primer_2009. pdf. (2013). Pennsylvania is the fastest-growing natural gas-producing state.
30. Davies, R. (2011). Methane contamination of drinking water caused by hydraulic fracturing remains unproven. Proc. Natl. Acad. Sci. U. S. A. 108, E871; author reply E872
31. DiGiulion, D., Wilkin, R., Miller, C., and Oberley, G. (2011). Investigation of Ground Water Contamination Near Pavillion, Wyoming.
32. Vengosh, A., Jackson, R., Warner, N., Darrah, T., and Kondash, A. (2014). A Critical Review of the Risks to Water Resources from Unconcentional Shale Gas Development and Hydraulic Fracturing in the United States. Environ. Sci. Technol. Available at: http://dx.doi.org/10.1021/es405118 [Accessed March 21, 2014].
33. Warner, N., Jackson, R., Darrah, T., Osborn, S., Down, A., Zhao, K., White, A., and Vengosh, A. (2012). Geochemical evidence for possible natural migration of Marcellus Formation brine to shallow aquifers in Pennsylvania. Proc. Natl. Acad. Sci. U. S. A. 109, 11961-11966.
34. Davies, R. (2011). Methane contamination of drinking water caused by hydraulic fracturing remains unproven. Proc. Natl. Acad. Sci. U. S. A. 108, E871; author reply E872.
35. Jackson, R., Vengosh, A., Darrah, T., Warner, N., Down, A., and Al., E. (2013). Increased stray gas abundance in a subset of drinking water wells near Marcellus shale gas extraction. Proc. Natl. Acad. Sci. U. S. A. 110, 11250-11255. Available at: http://www.pnas.org/content/110/28/11250.full?utm_source=buffer&utm_campaign=Buffer &utm_content=bufferfad6a&utm_medium=facebook.
36. Olmstead, S., Muehlenbachs, L., Shih, J.-S., Chu, Z., and Krupnick, A. (2013). Shale gas development impacts on surface water quality in Pennsylvania. Proc. Natl. Acad. Sci. U. S. A. 110, 4962-4967. Available at: http://www.pnas.org/content/110/13/4962.long.
37. Entrekin, S., Evans-White, M., Johnson, B., and Hagenbuch, E. (2011). Rapid expansion of natural gas development poses a threat to surface waters. Front. Ecol. Environ. 9, 503-511. Available at: http://dx.doi.org/10.1890/110053.
38. Barbot, E., Vidic, N. S., Gregory, K. B., and Vidic, R. D. (2013). Spatial and temporal correlation of water quality parameters of produced waters from devonian-age shale following hydraulic fracturing. Environ. Sci. Technol. 47, pp 2562-2569. doi:10.1021/es304638h.
39. Øvreås, L., and Jensen, S. (1998). Microbial community changes in a perturbed agricultural soil investigated by molecular and physiological approaches. Appl... Available at: http://aem.asm.org/content/64/7/2739.short [Accessed July 14, 2014].
40. Pacsi, A. P., Alhajeri, N. S., Zavala-Araiza, D., Webster, M. D., and Allen, D. T. (2013). Regional Air Quality Impacts of Increased Natural Gas Production and Use in Texas. Environ. Sci. Technol. 47, 3521-3527. doi:10.1021/es3044714.
41. Roy, A. A., Adams, P. J., and Robinson, A. L. (2014). Air pollutant emissions from the development, production, and processing of Marcellus Shale natural gas. J. Air Waste Manage. Assoc. 64, 19-37.
42. Entrekin, S., Evans-White, M., Johnson, B., and Hagenbuch, E. (2011). Rapid expansion of natural gas development poses a threat to surface waters. Front. Ecol. Environ. 9, 503-511. Available at: http://dx.doi.org/10.1890/110053.
43. Waxman, H., Markey, E., and DeGette, D. (2011). Chemicals used in hydraulic fracturing. Available at: http://democrats.energycommerce.house.gov/index.php?q=news/committee democrats-release-new-report-detailing-hydraulic-fracturing-products.
44. Drohan, P., Brittingham, M., Bishop, J., and Yoder, K. (2011). Early trends in landcover change and forest fragmentation due to shale-gas development in Pennsylvania: a potential outcome for the Northcentral Appalachians. Environ. Manage. 49, 1061-1075.
45. Johnson, N., Gangnolet, T., Ralls, R., Zimmerman, E., and Eichelberger, B. (2010). Pennsylvania Energy Impacts Assessment. Available at: http://www.marcellus.psu.edu/resources/PDFs/tncenergy.pdf.
46. Grant, C., Weimer, A., Marks, N., Perow, E., and Oster, J. (in revision) Marcellus and mercury: assessing potential impacts of unconventional natural gas extraction on aquatic ecosystems in northwestern Pennsylvania.
47. Meyer, J., and Tate, C. (1983). The effects of watershed disturbance on dissolved organic carbon dynamics of a stream. Ecology 64, 33-44. Available at: http://www.jstor.org/stable/1937326 [Accessed July 14, 2014].
48. Sollins, P., and McCorison, F. (1981). Nitrogen and carbon solution chemistry of an old growth coniferous forest watershed before and after cutting. Water Resour. Res. 17, 1409-1418. doi:10.1029/WR017i005p01409.
49. Palviainen, M., Finér, L., Laurén, A., Launiainen, S., Piirainen, S., Mattsson, T., and Starr, M. (2014). Nitrogen, phosphorus, carbon, and suspended solids loads from forest clear cutting and site preparation: long-term paired catchment studies from eastern Finland. Ambio 43, 218-233.
50. Schelker, J., Eklöf, K., Bishop, K., and Laudon, H. (2012). Effects of forestry operations on dissolved organic carbon concentrations and export in boreal first-order streams. J. Geophyical Res. 117, G01011. Available at: http://adsabs.harvard.edu/abs/2012JGRG.117.1011S.
51. Jardine, T. D., Kidd, K. a, and Rasmussen, J. B. (2012). Aquatic and terrestrial organic matter in the diet of stream consumers: implications for mercury bioaccumulation. Ecol. Appl. 22, 843-55. Available at: http://www.ncbi.nlm.nih.gov/pubmed/22645815.
52. Bryce, S. a., Lomnicky, G. a., and Kaufmann, P. R. (2010). Protecting sediment-sensitive aquatic species in mountain streams through the application of biologically based streambed sediment criteria. J. North Am. Benthol. Soc. 29, 657-672. doi:10.1899/09-061.1.
53. Struchtemeyer, C., Davis, J., and Elshahed, M. (2011). Influence of the drilling mud formulation process on the bacterial communities in thermogenic natural gas wells of the Barnett Shale. Appl. Environ. Microbiol. 77, 4744-4753. Available at: http://aem.asm.org/content/77/14/4744.full.
54. Murali Mohan, A., Hartsock, A., Hammack, R. W., Vidic, R. D., and Gregory, K. B. (2013). Microbial communities in flowback water impoundments from hydraulic fracturing for recovery of shale gas. FEMS Microbiol. Ecol. 86, 567-80. doi:10.1111/1574-6941.12183.
55. Wuchter, C., Banning, E., Mincer, T., Drenzek, N., and Coolen, M. (2013). Microbial diversity and methanogenic activity of Antrim Shale formation waters from recently fractured wells. Front. Microbiol. 4, 367. Available at: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3853793&tool=pmcentrez&ren dertype=abstract.
56. PADEP (2012). Permits Issued Detail Report. Harrisburg, PA. Available at: http://www.depreportingservices.state.pa.us/ReportServer/Pages/ReportViewer.aspx?/Oil_ Gas/Permits_Issued_Detail.
57. Hazen, T. C., Dubinsky, E. a, DeSantis, T. Z., Andersen, G. L., Piceno, Y. M., Singh, N., Jansson, J. K., Probst, A., Borglin, S. E., Fortney, J. L., et al. (2010). Deep-sea oil plume enriches indigenous oil-degrading bacteria. Science 330, 204-8. doi:10.1126/science.1195979.
58. Caporaso, J., and Lauber, C. (2011). Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc. Natl. Acad. Sci. 108, 4516-4522. doi:10.1073/pnas.1000080107/-/DCSupplemental.www.pnas.org/cgi/doi/10.1073/pnas.1000080107.
59. Edgar, R. C. (2013). UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat. Methods 10, 996-998. doi:10.1038/nmeth.2604.
60. Caporaso, J., Kuczynski, J., and Stombaugh, J. (2010). QIIME allows analysis of high throughput community sequencing data. Nat. 7, 335-336. doi:10.1038/nmeth.f.303.QIIME.
61. Edgar, R. C. (2010). Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460-1. doi:10.1093/bioinformatics/btq461.
62. DeSantis, T. Z., Hugenholtz, P., Larsen, N., Rojas, M., Brodie, E. L., Keller, K., Huber, T., Dalevi, D., Hu, P., and Andersen, G. L. (2006). Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl. Environ. Microbiol. 72, 5069-72. doi:10.1128/AEM.03006-05.
63. R Core Team (2014). R: A language and environment for statistical computing. Available at: http://www.r-project.org/.
64. McMurdie, P. J., and Holmes, S. (2013). phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One 8, e61217. doi:10.1371/journal.pone.0061217.
65. Vázquez-Baeza, Y., Pirrung, M., Gonzalez, A., and Knight, R. (2013). EMPeror: a tool for visualizing high-throughput microbial community data. Gigascience 2, 16. doi:10.1186/2047-217X-2-16.
66. Segata, N., Izard, J., Waldron, L., Gevers, D., Miropolsky, L., Garrett, W. S., and Huttenhower, C. (2011). Metagenomic biomarker discovery and explanation. Genome Biol. 12, R60. doi:10.1186/gb-2011-12-6-r60.
67. Baker, J., Van Sickle, J., Gagen, C., DeWalle, D., Sharpe, W., Carline, R., Baldigo, B., Murdoch, P., Bath, B., Krester, W., et al. (1996). Episodic Acidification of Small Streams in the Northeastern United States: Effects on Fish Populations. Ecol. Appl. 6, 422-437. Available at: http://www.jstor.org/stable/25153313.
68. Hammarstrom, J., Brady, K., and Cravotta, C. (2005). Acid-Rock Drainage at Skytop, Centre County, Pennsylvania, 2004. Available at: http://pubs.usgs.gov/of/2005/1148/.
69. Huckabee, J., Goodyear, C., and Jones, R. D. (1975). Acid Rock in the Great Smokies: Unanticipated Impact on Aquatic Biota of Road Construction in Regions of Sulfide Mineralization. Transatctions Am. Fish. Soc. 104, 677-684.
70. Fierer, N., and Jackson, R. B. (2006). The diversity and biogeography of soil bacterial communities. Proc. Natl. Acad. Sci. U. S. A. 103, 626-31. doi:10.1073/pnas.0507535103.
71. Rousk, J., Bååth, E., Brookes, P. C., Lauber, C. L., Lozupone, C., Caporaso, J. G., Knight, R., and Fierer, N. (2010). Soil bacterial and fungal communities across a pH gradient in an arable soil. ISME J. 4, 1340-51. doi:10.1038/ismej.2010.58.
72. Mulholland, P. J., Discoll, C. T., Elwood, J. W., Osgood, M. P., Palumbo, A. V, Rosemond, A. D., Smith, M. E., and Schofield, C. (1992). Relationships between stream acidity and bacteria, macroinvertebrates, and fish: a comparison of north temperate and south temperate mountain streams, USA. Hydrobiologia 239, 7-24.
73. Dangles, O., and Gessner, M. (2004). Impacts of stream acidification on litter breakdown: implications for assessing ecosystem functioning. J. Appl.. 41, 365-378. Available at: http://onlinelibrary.wiley.com/doi/10.1111/j.0021-8901.2004.00888.x/full [Accessed July 14, 2014].
74. Fierer, N., Morse, J., and Berthrong, S. (2007). E nvironmental controls on the landscape scale biogeography of stream bacterial communities. Ecology 88, 2162-2173. Available at: http://www.esajournals.org/doi/abs/10.1890/06-1746.1 [Accessed July 11, 2014].
75. Simon, K., Simon, M., and Benfield, E. (2009). Variation in ecosystem function in Appalachian streams along an acidity gradient. Ecol. Appl. 19, 1147-1160. Available at: http://www.esajournals.org/doi/abs/10.1890/08-0571.1 [Accessed July 14, 2014].
76. McKnight, D. M., and Feder, G. L. (1984). The ecological effect of acid conditions and precipitation of hydrous metal oxides in a Rocky Mountain stream. Hydrobiologia 119, 129-138.
77. Liebner, S., Rublack, K., Stuehrmann, T., and Wagner, D. (2009). Diversity of aerobic methanotrophic bacteria in a permafrost active layer soil of the Lena Delta, Siberia. Microb. Ecol. 57, 25-35. doi:10.1007/s00248-008-9411-x.
78. Uhlig, H., Karbaum, K., and Steudel, A. (1986). Acetobacter methanolicus sp. nov., an Acidophilic Faculatively Methylotrophic Bacterium. Int. J. Syst. Bacterology 36, 317-322.
79. Fuss, C., and Smock, L. (2003). Spatial and temporal variation of microbial respiration rates in a blackwater stream. Freshw. Biol. 36, 339-349.
80. Nogales, B., and Moore, E. (2001). Combined use of 16S ribosomal DNA and 16S rRNA to study the bacterial community of polychlorinated biphenyl-polluted soil. Appl... doi:10.1128/AEM.67.4.1874
81. Serkebaeva, Y. M., Kim, Y., Liesack, W., and Dedysh, S. N. (2013). Pyrosequencing-based assessment of the bacteria diversity in surface and subsurface peat layers of a northern wetland, with focus on poorly studied phyla and candidate divisions. PLoS One 8, e63994. doi:10.1371/journal.pone.0063994.
82. Costello, E. K., Halloy, S. R. P., Reed, S. C., Sowell, P., and Schmidt, S. K. (2009). Fumarole-supported islands of biodiversity within a hyperarid, high-elevation landscape on Socompa Volcano, Puna de Atacama, A ndes. Appl. Environ. Microbiol. 75, 735-47. doi:10.1128/AEM.01469-08.
83. Sharp, C. E., Stott, M. B., and Dunfield, P. F. (2012). Detection of autotrophic verrucomicrobial methanotrophs in a geothermal environment using stable isotope probing. Front. Microbiol. 3, 303. doi:10.3389/fmicb.2012.00303.
84. Grasby, S. E., Richards, B. C., Sharp, C. E., Brady, A. L., Jones, G. M., Dunfield, P. F., and Williamson, M.-C. (2013). The Paint Pots, Kootenay National Park, Canada - a natural acid spring analogue for Mars 1, 2. Can. J. Earth Sci. 50, 94-108. doi:10.1139/e2012-060.
85. Eberspacher, J., and Lingens, F. (2006). "The Genus Phenylobacterium," in The Prokaryotes, 250-256.
86. Oh, Y.-S., and Roh, D.-H. (2012). Phenylobacterium muchangponense sp. nov., isolated from beach soil, and emended description of the genus Phenylobacterium. Int. J. Syst. Evol. Microbiol. 62, 977-83. doi:10.1099/ijs.0.028902-0.
87. Yang, S., Wen, X., Zhao, L., Shi, Y., and Jin, H. (2014). Crude oil treatment leads to shift of bacterial communities in soils from the deep active layer and upper permafrost along the China-Russia Crude Oil Pipeline route. PLoS One 9, e96552. doi:10.1371/journal.pone.0096552.
88. Marušincová, H., Husárová, L., Ružicka, J., Ingr, M., Navrátil, V., Bunková, L., and Koutny, M. (2013). Polyvinyl alcohol biodegradation under denitrifying conditions. Int. Biodeterior. Biodegradation 84, 21-28. doi:10.1016/j.ibiod.2013.05.023.
89. Baeseman, J. L., Smith, R. L., and Silverstein, J. (2006). Denitrification potential in stream sediments impacted by acid mine drainage: effects of pH, various electron donors, and iron. Microb. Ecol. 51, 232-41. doi:10.1007/s00248-005-5155-z.
90. Kantor, R., Wrighton, K., and Handley, K. (2013). Small genomes and sparse metabolisms of sediment-associated bacteria from four candidate phyla. MBio 4. doi:10.1128/mBio.00708-13.Updated.