Dissolved organic carbon influences microbial community composition and diversity in managed aquifer recharge systems

Applied and Environmental Microbiology

Volumn 78, Issue 19, 2012, Pages 6819-6828

  Li, Dong ^a,b   Sharp, Jonathan O ^b   Saikaly, Pascal E ^a   Ali, Shahjahan ^a   Alidina, Mazahirali ^a   Alarawi, Mohammed S ^a   Keller, Stephanie ^a   Hoppe Jones, Christiane ^b   Drewes, Jörg E ^a,b  

^a KING ABDULLAH UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Saudi Arabia)

^b Department of Geology and Geological Engineering   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

16S RRNA GENE; AQUIFER RECHARGE; BETAPROTEOBACTERIA; CANONICAL CORRESPONDENCE ANALYSIS; COLUMN STUDY; COMBINED ANALYSIS; DISSOLVED ORGANIC CARBON; FIELD SCALE; GAMMAPROTEOBACTERIA; GEOCHEMICAL PROPERTIES; MICROBIAL ASSEMBLAGE; MICROBIAL COMMUNITIES; MICROBIAL COMMUNITY COMPOSITION; MICROBIAL COMMUNITY STRUCTURES; MICROBIAL DENSITY; PRINCIPAL COORDINATE ANALYSIS; PYROSEQUENCING; SAMPLING ZONES; SATURATED ZONE; SAUDI ARABIA; SEDIMENT COLUMN; SOUTH PLATTE RIVER;

AQUIFERS; LABORATORIES; MICROORGANISMS; PLANTS (BOTANY); RECHARGING (UNDERGROUND WATERS); RNA; SEDIMENTOLOGY; STREAM FLOW;

INFILTRATION;

CARBON; GROUND WATER;

AQUIFER; CONCENTRATION (COMPOSITION); DISSOLVED ORGANIC CARBON; GEOCHEMICAL METHOD; INFILTRATION; MICROBIAL COMMUNITY; PHYLOGENETICS; RECHARGE; RIVER BED; SATURATION; SPECIES DIVERSITY;

ARTICLE; BACTERIAL COUNT; BACTERIUM; BIOTA; CHEMISTRY; CLASSIFICATION; DNA SEQUENCE; GENETICS; MICROBIOLOGY; SAUDI ARABIA; UNITED STATES;

BACTERIA; BIOTA; CARBON; COLONY COUNT, MICROBIAL; COLORADO; GROUNDWATER; SAUDI ARABIA; SEQUENCE ANALYSIS, DNA;

SAUDI ARABIA; SOUTH PLATTE RIVER; UNITED STATES;

BETAPROTEOBACTERIA; GAMMAPROTEOBACTERIA;

EID: 84865978143     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.01223-12     Document Type: Article

References (56)

1. Aelion CM, Swindoll CM, Pfaender FK. 1987. Adaptation to and biodegradation of xenobiotic compounds by microbial communities from a pristine aquifer. Appl. Environ. Microbiol. 53:2212-2217.
2. Ajwa HA, Rice CW, Sotomayor D. 1998. Carbon and nitrogen mineralization in tallgrass prairie and agricultural soil profiles. Soil Sci. Soc. Am. J. 62:942-951.
3. Albuquerque L, et al. 2005. Truepera radiovictrix gen. nov., sp. nov., a new radiation resistant species and the proposal of Trueperaceae fam. nov. FEMS Microbiol. Lett. 247:161-169.
4. American Public Health Association. 1998. Standard methods for the examination of water and wastewater. American Public Health Association, Washington, DC.
5. Amy G, Drewes JE. 2007. Soil aquifer treatment (SAT) as a natural and sustainable wastewater reclamation/reuse technology: fate of wastewater effluent organic matter (EfOM) and trace organic compounds. Environ. Monit. Assess. 129:19-26.
6. Andrews JS, Rolfe SA, Huang WE, Scholes JD, Banwart SA. 2010. Biofilm formation in environmental bacteria is influenced by different macromolecules depending on genus and species. Environ. Microbiol. 12:2496-2507.
7. Angert ER. 2005. Alternatives to binary fission in bacteria. Nat. Rev. Microbiol. 3:214-224.
8. Benson AK, et al. 2010. Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors. Proc. Natl. Acad. Sci. U. S. A. 107:18933-18938.
9. Blume E, et al. 2002. Surface and subsurface microbial biomass, community structure and metabolic activity as a function of soil depth and season. Appl. Soil Ecol. 20:171-181.
10. Bossio DA, Scow KM. 1995. Impact of carbon and flooding on the metabolic diversity of microbial communities in soils. Appl. Environ. Microbiol. 61:4043-4050.
11. Bundt M, Widmer F, Pesaro M, Zeyer J, Blaser P. 2001. Preferential flow paths: biological 'hot spots' in soils. Soil Biol. Biochem. 33:729-738.
12. Caporaso JG, et al. 2010. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7:335-336.
13. Caporaso JG, et al. 2011. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc. Natl. Acad. Sci. U. S. A. 108: 4516-4522.
14. Dantas G, Sommer MOA, Oluwasegun RD, Church GM. 2008. Bacteria subsisting on antibiotics. Science 320:100-103.
15. Elliott DR, et al. 2010. Dynamic changes in microbial community structure and function in phenol degrading microcosms inoculated with cells from a contaminated aquifer. FEMS Microbiol. Ecol. 71:247-259.
16. Fierer N, Hamady M, Lauber CL, Knight R. 2008. The influence of sex, handedness, and washing on the diversity of hand surface bacteria. Proc. Natl. Acad. Sci. U. S. A. 105:17994-17999.
17. Fierer N, Jackson RB. 2006. The diversity and biogeography of soil bacterial communities. Proc. Natl. Acad. Sci. U. S. A. 103:626-631.
18. Foulquier A, Mermillod-Blondin F, Malard F, Gibert J. 2011. Response of sediment biofilm to increased dissolved organic carbon supply in groundwater artificially recharged with stormwater. J. Soils Sediments 11: 382-393.
19. Galand PE, Casamayor EO, Kirchman DL, Lovejoy C. 2009. Ecology of the rare microbial biosphere of the Arctic Ocean. Proc. Natl. Acad. Sci. U. S. A. 106:22427-22432.
20. Grunheid, S, Amy G, Jekel M. 2005. Removal of bulk dissolved organic carbon (DOC) and trace organic compounds by bank filtration and artificial recharge. Water Res. 39:3219-3228.
21. Hamady M, Walker JJ, Harris JK, Gold NJ, Knight R. 2008. Errorcorrecting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nat. Methods 5:235-237.
22. Hamady M, Knight R. 2009. Microbial community profiling for human microbiome projects: tools, techniques, and challenges. Genome Res. 19: 1141-1152.
23. Hammer Ø, Harper DAT, Ryan PD. 2001. Past: paleontological statistics software package for education and data analysis. Palaeont. Elec. 4:e1-e9.
24. Hansel CM, Fendorf S, Jardine PM, Francis CA. 2008. Changes in bacterial and archaeal community structure and functional diversity along a geochemically variable soil profile. Appl. Environ. Microbiol. 74:1620-1633.
25. Holden PA, Fierer N. 2005. Microbial processes in the vadose zone. Vadose Zone J. 4:1-21.
26. Hoppe-Jones C, Oldham G, Drewes JE. 2010. Attenuation of total organic carbon and unregulated trace organic chemicals in U.S. riverbank filtration systems. Water Res. 44:4643-4659.
27. Janssen PH. 2006. Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl. Environ. Microbiol. 72:1719-1728.
28. Kieft TL, et al. 1993. Microbial abundance and activities in relation to water potential in the vadose zones of arid and semiarid sites. Microb. Ecol. 26:59-78.
29. Kim JM, et al. 2008. Influence of soil components on the biodegradation of benzene, toluene, ethylbenzene, and o-, m-, and p-xylenes by the newly isolated bacterium Pseudoxanthomonas spadix BD-a59. Appl. Environ. Microbiol. 74:7313-7320.
30. Konings WN, Albers S-V, Koning S, Driessen AJM. 2002. The cell membrane plays a crucial role in survival of bacteria and archaea in extreme environments. Antonie Van Leeuwenhoek 81:61-72.
31. Konopka A, Turco R. 1991. Biodegradation of organic compounds in vadose zone and aquifer sediments. Appl. Environ. Microbiol. 57:2260-2268.
32. Langenheder S, Prosser JI. 2008. Resource availability influences the diversity of a functional group of heterotrophic soil bacteria. Environ. Microbiol. 10:2245-2256.
33. Lauber CL, Hamady M, Knight R, Fierer N. 2009. Pyrosequencingbased assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl. Environ. Microbiol. 75:5111-5120.
34. Lennon JT, Pfaff LE. 2005. Source and supply of terrestrial organic matter affects aquatic microbial metabolism. Aquat. Microb. Ecol. 39:107-119.
35. Li D, et al. 2010. Characterization of bacterial community structure in a drinking water distribution system during an occurrence of red water. Appl. Environ. Microbiol. 76:7171-7180.
36. Lozupone CA, Knight R. 2007. Global patterns in bacterial diversity. Proc. Natl. Acad. Sci. U. S. A. 104:11436-11440.
37. Martiny JB, et al. 2006. Microbial biogeography: putting microorganisms on the map. Nat. Rev. Microbiol. 4:102-112.
38. Moore ERB, et al. 2006. Nonmedical: Pseudomonas, p 646-703. In Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E (ed), The prokaryotes, 3rd ed. Springer-Verlag, New York, NY.
39. Oppenheimer J, Eaton A, Badruzzaman M, Haghani AW, Jacangelo JG. 2011. Occurrence and suitability of sucralose as an indicator compound of wastewater loading to surface waters in urbanized regions. Water Res. 45:4019-4027.
40. Potts M. 1994. Desiccation tolerance of prokaryotes. Microbiol. Mol. Biol. Rev. 58:755-805.
41. Rauch-Williams T, Drewes JE. 2006. Using soil biomass as an indicator for the biological removal of effluent-derived organic carbon during soil infiltration. Water Res. 40:961-968.
42. Rauch-Williams T, Hoppe-Jones C, Drewes JE. 2010. The role of organic matter in the removal of emerging trace organic contaminants during managed aquifer recharge. Water Res. 44:449-460.
43. Ray C, et al. 2008. Riverbank filtration for drinking water supply. In Encyclopedia of hydrological sciences. John Wiley & Sons, Inc., New York, NY.
44. Roesch LFW, et al. 2007. Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J. 1:283-290.
45. Rousk J, et al. 2010. Soil bacterial and fungal communities across a pH gradient in an arable soil. ISME J. 4:1340-1351.
46. Schütz K, Nagel P, Vetter W, Kandeler E, Ruess L. 2009. Flooding forested groundwater recharge areas modifies microbial communities from top soil to groundwater table. FEMS Microbiol. Ecol. 67:171-182.
47. Sharp JO, Sales C, Alvarez-Cohen L. 2010. Functional insights towards propane-enhanced n-nitrosodimethylamine removal by two actinomycetes. Biotechnol. Bioeng. 107:924-932.
48. Shinoda Y, et al. 2004. Aerobic and anaerobic toluene degradation by a newly isolated denitrifying bacterium, Thauera sp. strain DNT-1. Appl. Environ. Microbiol. 70:1385-1392.
49. Smoot M, Ono K, Ruscheinski J, Wang P-L, Ideker T. 2011. Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 27:431-432.
50. Torsvik V, Goksoyr J, Daae FL. 1990. High diversity in DNA of soil bacteria. Appl. Environ. Microbiol. 56:782-787.
51. Tšertova N, Kisand A, Tammert H, Kisand V. 2011. Low seasonal variability in community composition of sediment bacteria in large and shallow lake. Environ. Microbiol. Rep. 3:270-277.
52. Wakelin SA, Colloff MJ, Kookana RS. 2008. Effect of wastewater treatment plant effluent on microbial function and community structure in the sediment of a freshwater stream with variable seasonal flow. Appl. Environ. Microbiol. 74:2659-2668.
53. Willems A, Vos PD. 2006. Comamonas, p 723-736. In Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E. (ed), The prokaryotes, 3rd ed. Springer-Verlag, New York, NY.
54. Yagi JM, Neuhauser EF, Ripp JA, Mauro DM, Madsen EL. 2010. Subsurface ecosystem resilience: long-term attenuation of subsurface contaminants supports a dynamic microbial community. ISME J. 4:131-143.
55. Zhang H, Ziv-El M, Rittmann BE, Krajmalnik-Brown R. 2010. Effect of dechlorination and sulfate reduction on the microbial community structure in denitrifying membrane-biofilm reactors. Environ. Sci. Technol. 44:5159-5164.
56. Zhou J, et al. 2002. Spatial and resource factors influencing high microbial diversity in soil. Appl. Environ. Microbiol. 68:326-334.