Influence of Wastewater Discharge on the Metabolic Potential of the Microbial Community in River Sediments

Microbial Ecology

Volumn 71, Issue 1, 2016, Pages 78-86

  Li, Dong ^a,b   Sharp, Jonathan O ^a   Drewes, Jörg E ^a,b,c  

^a Department of Metallurgical and Materials Engineering   (United States)

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

^c TECHNICAL UNIVERSITY OF MUNICH   (Germany)

Author keywords

Functional genes; Metagenomics; Phylogenetics; Sediment; Wastewater discharge

Indexed keywords

BACTERIAL DNA; RIBOSOME DNA; RNA 16S; WASTE WATER;

BACTERIUM; BIODIVERSITY; CHEMISTRY; CLASSIFICATION; GENETICS; ISOLATION AND PURIFICATION; METABOLISM; MICROBIOLOGY; PHYLOGENY; RIVER; SEDIMENT; WASTE WATER;

BACTERIA; BIODIVERSITY; DNA, BACTERIAL; DNA, RIBOSOMAL; GEOLOGIC SEDIMENTS; PHYLOGENY; RIVERS; RNA, RIBOSOMAL, 16S; WASTE WATER;

EID: 84951569470     PISSN: 00953628     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00248-015-0680-x     Document Type: Article

References (28)

1. 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
2. APHA (2012) Standard methods for the examination of water and wastewater. Washington, DC
3. Arumugam M, Raes J, Pelletier E, Le PD, Yamada T, Mende DR (2011) Enterotypes of the human gut microbiome. Nature 473:174–180
4. Brock G, Pihur V, Datta S, Datta S (2008) clValid: an R package for cluster validation. J Stat Softw 25:i04
5. Chakraborty R, Wu CH, Hazen TC (2012) Systems biology approach to bioremediation. Curr Opin Biotechnol 23:483–490
6. Clarke KR, Gorley RN (2006) PRIMER v6: user manual/tutorial. PRIMER-E, Plymouth
7. Culhane AC, Thioulouse J, Perriere G, Higgins DG (2005) MADE4: an R package for multivariate analysis of gene expression data. Bioinformatics 21:2789–2790
8. DeLong EF (2009) The microbial ocean from genomes to biomes. Nature 459:200–206
9. Drewes JE, Khan S (2015) Contemporary design, operation and monitoring of potable reuse systems. J Water Reuse Desalination 5(1):2–7
10. Fierer N, Lauber CL, Ramirez KS, Zaneveld J, Bradford MA, Knight R (2012) Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients. ISME J 6:1007–1017
11. Fredrickson JK, Garland TR, Hicks RJ, Thomas JM, Li SW, McFadden KM (1989) Lithotrophic and heterotrophic bacteria in deep subsurface sediments and their relation to sediment properties. Geomicrobiol J 7:53–66
12. Grünheid 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
13. Hamady M, Knight R (2009) Microbial community profiling for human microbiome projects: tools, techniques, and challenges. Genome Res 19:1141–1152
14. Hammer Ø, Harper DAT, Ryan PD (2001) Past: paleontological statistics software package for education and data analysis. Palaeontol Elec 4:e1–e9
15. Kristiansson E, Hugenholtz P, Dalevi D (2009) ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes. Bioinformatics 25:2737–2738
16. Labrie SJ, Samson JE, Moineau S (2010) Bacteriophage resistance mechanisms. Nat Rev Microbiol 8:317–327
17. Langfelder P, Horvath S (2008) WGCNA: an R package for weighted correlation network analysis. BMC Bioinforma 9:559
18. Li D, Alidina M, Ouf M, Sharp JO, Saikaly PE, Drewes JE (2013) Microbial community evolution during simulated managed aquifer recharge in response to different biodegradable dissolved organic carbon (BDOC) concentrations. Water Res 47:2421–2430
19. Li D, Sharp JO, Saikaly PE, Ali S, Alidina M, Alarawi MS, Keller S, Hoppe-Jones C, Drewes JE (2012) Dissolved organic carbon influences microbial community composition and diversity in managed aquifer recharge systems. Appl Environ Microbiol 78:6819–6828
20. Löffler FE, Edwards EA (2006) Harnessing microbial activities for environmental cleanup. Curr Opin Biotechnol 17:274–284
21. Lovley DR (2003) Cleaning up with genomics: applying molecular biology to bioremediation. Nat Rev Microbiol 1:35–44
22. Lozupone CA, Knight R (2007) Global patterns in bacterial diversity. Proc Natl Acad Sci U S A 104:11436–11440
23. Martino DP, Grossman EL, Ulrich GA, Burger KC, Schlichenmeyer JL, Suflita JM, Ammerman JW (1998) Microbial abundance and activity in a low-conductivity aquifer system in east-central Texas. Microb Ecol 35:224–234
24. Meyer F, Paarmann D, D’Souza M, Olson R, Glass EM, Kubal M (2008) The metagenomics RAST server—a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinforma 9:386
25. Saito R, Smoot ME, Ono K, Ruscheinski J, Wang PL, Lotia S et al (2012) A travel guide to Cytoscape plugins. Nat Methods 9:1069–1076
26. Segata N, Izard J, Walron L, Gevers D, Miropolsky L, Garrett W, Huttenhower C (2011) Metagenomic biomarker discovery and explanation. Genome Biol 12:R60
27. Vogel TM, Simonet P, Jansson JK, Hirsch PR, Tiedje JM, van Elsas JD et al (2009) TerraGenome: a consortium for the sequencing of a soil metagenome. Nat Rev Microbiol 7:252
28. Winter C, Bouvier T, Weinbauer MG, Thingstad TF (2010) Trade-offs between competition and defense specialists among unicellular planktonic organisms: the “killing the winner” hypothesis revisited. Microbiol Mol Biol Rev 74:42–57