Effect of CH4/O2 ratio on fatty acid profile and polyhydroxybutyrate content in a heterotrophic-methanotrophic consortium

Chemosphere

Volumn 141, Issue , 2015, Pages 235-242

  Karthikeyan, Obulisamy P ^a   Chidambarampadmavathy, Karthigeyan ^a   Nadarajan, Saravanan ^a   Lee, Patrick K H ^b   Heimann, Kirsten ^a  

^a JAMES COOK UNIVERSITY   (Australia)

^b CITY UNIVERSITY OF HONG KONG   (Hong Kong)

Author keywords

Bioproducts; Fatty acids; Heterotrophs; Methane remediation; Microbial community; Polyhydroxybutyrate

Indexed keywords

BIOMOLECULES; BIOPOLYMERS; BIOPRODUCTS; METHANE; SUBMARINE GEOLOGY;

FATTY ACID CONTENTS; FATTY ACID PROFILES; HETEROTROPHS; MARINE SEDIMENTS; MICROBIAL COMMUNITIES; NEXT-GENERATION SEQUENCING; OXIDATION CAPACITY; POLYHYDROXYBUTYRATE;

FATTY ACIDS;

BACTERIAL DNA; BIOPOLYMER; DNA 16S; FATTY ACID; GENOMIC DNA; HYDROXYBUTYRIC ACID; METHANE; OXYGEN; POLY-BETA-HYDROXYBUTYRATE; POLYESTER; RIBOSOME DNA;

BACTERIUM; BIOREMEDIATION; FATTY ACID; GENE; HETEROTROPHY; MARINE SEDIMENT; METHANE; MICROBIAL COMMUNITY; OXYGEN; POCKMARK; POLYMER;

ARTICLE; BACTERIAL GENE; BACTERIAL GROWTH; BACTERIUM CULTURE; BIOFILTER; BIOMASS; CONTROLLED STUDY; FATTY ACID ANALYSIS; HETEROTROPHY; MARINE BACTERIUM; METHANOTROPHIC BACTERIUM; METHYLOBACTERIUM; METHYLOCAPSA; METHYLOCELLA; METHYLOCOCCACEAE; METHYLOCYSTIS; METHYLOMARINUM; METHYLOMICROBIUM; METHYLOMONAS; METHYLOPHAGA; METHYLOSARCINA; METHYLOSINUS; MICROBIAL CONSORTIUM; NEXT GENERATION SEQUENCING; NONHUMAN; OXIDATION; PRODUCT DEVELOPMENT; PSEUDOXANTHOMONAS; SEDIMENT; TOTAL ORGANIC CARBON; BIOREACTOR; CHEMISTRY; GENETICS; GROWTH, DEVELOPMENT AND AGING; HIGH THROUGHPUT SEQUENCING; ISOLATION AND PURIFICATION; METHYLOCYSTACEAE; MICROBIOLOGY; OXIDATION REDUCTION REACTION;

METHYLOCYSTIS; METHYLOPHAGA; PSEUDOXANTHOMONAS;

BIOMASS; BIOREACTORS; DNA, RIBOSOMAL; FATTY ACIDS; GEOLOGIC SEDIMENTS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HYDROXYBUTYRATES; METHANE; METHYLOCYSTACEAE; MICROBIAL CONSORTIA; OXIDATION-REDUCTION; OXYGEN; POLYESTERS;

EID: 84955287219     PISSN: 00456535     EISSN: 18791298     Source Type: Journal    
DOI: 10.1016/j.chemosphere.2015.07.054     Document Type: Article

References (66)

1. Abdallah R.Z., Adel M., Ouf A., Sayed A., Ghazy M.A., Alam I., Essack M., Lafi F.F., Bajic V.B., El-Dorry H. Aerobic methanotrophic communities at the Red Sea brine-seawater interface. Front. Microbiol. 2014, 5. 10.3389/fmicb.2014.00487.
2. Acha V., Alba J., Thalasso F. The absolute requirement for carbon dioxide for aerobic methane oxidation by a methanotrophic-heterotrophic soil community of bacteria. Biotechnol. Lett. 2002, 24:675-679.
3. APHA, A.P.H.A., 2005. Standard Methods for the Examination of Water and Wastewater APHA, Washington, DC.
4. Baani M., Liesack W. Two isozymes of particulate methane monooxygenase with different methane oxidation kinetics are found in Methylocystis sp. strain SC2. Proc. Natl. Acad. Sci. 2008, 105:10203-10208.
5. Beck D.A., Kalyuzhnaya M.G., Malfatti S., Tringe S.G., del Rio T.G., Ivanova N., Lidstrom M.E., Chistoserdova L. A metagenomic insight into freshwater methane-utilizing communities and evidence for cooperation between the Methylococcaceae and the Methylophilaceae. PeerJ 2013, 1:e23.
6. Benstead J., King G.M. Response of methanotrophic activity in forest soil to methane availability. FEMS Microbiol. Ecol. 1997, 23:333-340.
7. Blankenberg D., Gordon A., Von Kuster G., Coraor N., Taylor J., Nekrutenko A. Manipulation of FASTQ data with galaxy. Bioinformatics 2010, 26:1783-1785.
8. Bodelier P.L., Gillisen M.-J.B., Hordijk K., Damsté J.S.S., Rijpstra W.I.C., Geenevasen J.A., Dunfield P.F. A reanalysis of phospholipid fatty acids as ecological biomarkers for methanotrophic bacteria. ISME J. 2009, 3:606-617.
9. Bowman J. The family Methylococcaceae, the Prokaryotes - Gammaproteobacteria. The Prokaryotes: Prokaryotic Biology and Symbiotic Associations 2014, 411-441. Springer, New York, USA. E.F.D. Eugene Rosenberg, L. Stephen, E. Stackenbrandt, F. Thompson (Eds.).
10. Bowman J.P., Skerratt J.H., Nichols P.D., Sly L.I. Phospholipid fatty acid and lipopolysaccharide fatty acid signature lipids in methane-utilizing bacteria. FEMS Microbiol. Lett. 1991, 85:15-21.
11. Bull I.D., Parekh N.R., Hall G.H., Ineson P., Evershed R.P. Detection and classification of atmospheric methane oxidizing bacteria in soil. Nature 2000, 405:175-178.
12. Caporaso J., Kuczynski J., Stombaugh J., Bittinger K., Bushman F.D., Costello E.K., Fierer N., Peña A.G., Goodrich J.K., Gordon J.I., Huttley G.A., Kelley S.T., Knights D., Koenig J.E., Ley R.E., Lozupone C.A., McDonald D., Muegge B.D., Pirrung M., Reeder J., Sevinsky J.R., Turnbaugh P.J., Walters W.A., Widmann J., Yatsunenko T., Zaneveld J.R.K. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 2010, 7:335-336.
13. Caporaso J.G., Lauber C.L., Walters W.A., Berg-Lyons D., Huntley J., Fierer N., Owens S.M., Betley J., Fraser L., Bauer M., Gormley N., Gilbert J.A., Smith G., Knight R. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 2012, 6:1621-1624.
14. Chidambarampadmavathy K., Karthikeyan O.P., Heimann K. Role of copper and iron in methane oxidation and bacterial biopolymer accumulation. Eng. Life Sci. 2015, 15:387-399.
15. Chidambarampadmavathy K., Karthikeyan O.P., Heimann K. Biopolymers made from methane in bioreactors. Eng. Life Sci. 2015, 10.1002/elsc.201400203.
16. Cole J.R., Wang Q., Fish J.A., Chai B., McGarrell D.M., Sun Y., Brown C.T., Porras-Alfaro A., Kuske C.R., Tiedje J.M. Ribosomal database project: data and tools for high throughput rRNA analysis. Nucleic Acids Res. 2013, 42:633-642.
17. Cruz A.P.S., Barbosa C.F., Ayres-Neto A., Albuquerque A.L.S. Physical and geochemical properties of centennial marine sediments of the continental shelf of southeast Brazil. Geochim. Bras. 2013, 27:1-12.
18. Dedysh S.N., Dunfield P.F. Facultative and obligate methanotrophs how to identify and differentiate them. Methods Enzymol. 2011, 495:31-44.
19. Duan Y.F., Al-Soud W.A., Brejnrod A., Sørensen S.J., Elsgaard L., Petersen S.O., Boon N. Methanotrophs, methanogens and microbial community structure in livestock slurry surface crusts. J. Appl. Microbiol. 2014, 117:1066-1078.
20. Dunfield P.F., Liesack W., Henckel T., Knowles R., Conrad R. High-affinity methane oxidation by a soil enrichment culture containing a type II methanotroph. Appl. Environ. Microbiol. 1999, 65:1009-1014.
21. Edgar R.C., Haas B.J., Clemente J.C., Quince C., Knight R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 2011, 27:2194-2200.
22. Figueroa, R., 1993. Methane oxidation in landfill top soils. In: Christensen, T.H., Cossu, R., Stegmann, R. (Eds.). Sardinia Fourth International Landfill Symposium (Cagliari, Sardinia, October 1993). CISA Environmental Sanitary Engineering Centre, St. Margherita di Pula, Cagliari, Sardinia, Italy, pp. 701-713.
23. Gutierrez T., Aitken M.D. Role of methylotrophs in the degradation of hydrocarbons during the deepwater horizon oil spill. ISME J. 2014, 8:2543-2545.
24. Hanson R.S., Hanson T.E. Methanotrophic bacteria. Microbiol. Rev. 1996, 60:439-471.
25. Håvelsrud O.E., Haverkamp T.H., Kristensen T., Jakobsen K.S., Rike A.G. A metagenomic study of methanotrophic microorganisms in coal oil point seep sediments. BMC Microbiol. 2011, 11:221.
26. Helm J., Wendlandt K.D., Jechorek M., Stottmeister U. Potassium deficiency results in accumulation of ultra-high molecular weight poly-β-hydroxybutyrate in a methane-utilizing mixed culture. J. Appl. Microbiol. 2008, 105:1054-1061.
27. Helm J., Wendlandt K.D., Rogge G., Kappelmeyer U. Characterizing a stable methane-utilizing mixed culture used in the synthesis of a high-quality biopolymer in an open system. J. Appl. Microbiol. 2006, 101:387-395.
28. 4 on presence and activity of the indigenous methanotrophic community in rice field soil. Environ. Microbiol. 2000, 2:666-679.
29. Hilger H., Humer M. Biotic landfill cover treatments for mitigating methane emissions. Environ. Monit. Assess. 2003, 84:71-84.
30. Ho A., De Roy K., Thas O., De Neve J., Hoefman S., Vandamme P., Heylen K., Boon N. The more, the merrier: heterotroph richness stimulates methanotrophic activity. ISME J. 2014.
31. Hršak D., Begonja A. Possible interactions within a methanotrophic-heterotrophic groundwater community able to transform linear alkylbenzenesulfonates. Appl. Environ. Microbiol. 2000, 66:4433-4439.
32. Jang I., Lee S., Zoh K.-D., Kang H. Methane concentrations and methanotrophic community structure influence the response of soil methane oxidation to nitrogen content in a temperate forest. Soil Biol. Biochem. 2011, 43:620-627.
33. Kalyuzhnaya M.G., Yang S., Rozova O.N., Smalley N.E., Clubb J., Lamb A., Nagana Gowda G.A., Raftery D., Fu Y., Bringel F., Vuilleumier S., Beck D.A.C., Trotsenko Y.A., Khmelenina V.N., Lidstrom M.E. Highly efficient methane biocatalysis revealed in a methanotrophic bacterium. Nat. Commun. 2013, 4:2785.
34. Karthikeyan O., Karthigeyan C., Cirés S., Heimann K. Review of sustainable methane mitigation and bio-polymer production. Crit. Rev. Environ. Sci. Technol. 2015, 44:1579-1610.
35. Kim T.G., Lee E.-H., Cho K.S. Microbial community analysis of a methane-oxidizing biofilm using ribosomal tag pyrosequencing. J. Microbiol. Biotechnol. 2012, 22:360-370.
36. Limbri H., Gunawan C., Rosche B., Scott J. Challenges to developing methane biofiltration for coal mine ventilation air: a review. Water Air Soil Pollut. 2013, 224:1-15.
37. Liu J., Sun F., Wang L., Ju X., Wu W., Chen Y. Molecular characterization of a microbial consortium involved in methane oxidation coupled to denitrification under micro-aerobic conditions. Microb. Biotechnol. 2014, 7:64-76.
38. López J.C., Quijano G., Pérez R., Muñoz R. Assessing the influence of CH4 concentration during culture enrichment on the biodegradation kinetics and population structure. J. Environ. Manage. 2014, 146:116-123.
39. Lüke C., Frenzel P. Potential of pmoA amplicon pyrosequencing for methanotroph diversity studies. Appl. Environ. Microbiol. 2011, 77:6305-6309.
40. Mohanty S.R., Bodelier P.L., Conrad R. Effect of temperature on composition of the methanotrophic community in rice field and forest soil. FEMS Microbiol. Ecol. 2007, 62:24-31.
41. Nichols P.D., Mancuso C.A., White D.C. Measurement of methanotroph and methanogen signature phosopholipids for use in assessment of biomass and community structure in model systems. Org. Geochem. 1987, 11:451-461.
42. Oshkin I.Y., Beck D.A.C., Lamb A.E., Tchesnokova V., Benuska G., McTaggart T.L., Kalyuzhnaya M.G., Dedysh S.N., Lidstrom M.E., Chistoserdova L. Methane-fed microbial microcosms show differential community dynamics and pinpoint taxa involved in communal response. ISME J. 2014.
43. Pfluger A.R., Wu W.-M., Pieja A.J., Wan J., Rostkowski K.H., Criddle C.S. Selection of Type I and Type II methanotrophic proteobacteria in a fluidized bed reactor under non-sterile conditions. Bioresour. Technol. 2011, 102:9919-9926.
44. Pieja A.J., Rostkowski K.H., Criddle C.S. Distribution and selection of poly-3-hydroxybutyrate production capacity in methanotrophic proteobacteria. Microb. Ecol. 2011, 62:564-573.
45. Plieskatt J.L., Deenonpoe R., Mulvenna J.P., Krause L., Sripa B., Bethony J.M., Brindley P.J. Infection with the carcinogenic liver fluke Opisthorchis viverrini modifies intestinal and biliary microbiome. FASEB J. 2013, 27:4572-4584.
46. Rahnama F., Vasheghani-Farahani E., Yazdian F., Shojaosadati S.A. PHB production by Methylocystis hirsuta from natural gas in a bubble column and a vertical loop bioreactor. Biochem. Eng. J. 2012, 65:51-56.
47. Redmond M.C., Valentine D.L., Sessions A.L. Identification of novel methane, ethane and propane-oxidizing bacteria at marine hydrocarbon seeps by stable isotope probing. Appl. Environ. Microbiol. 2010, 76:6412-6422.
48. 2 ratios. Proc. Environ. Sci. 2012, 16:697-704.
49. Roslev P., Iversen N. Radioactive fingerprinting of microorganisms that oxidize atmospheric methane in different soils. Appl. Environ. Microbiol. 1999, 65:4064-4070.
50. Rostkowski K.H., Criddle C.S., Lepech M.D. Cradle-to-gate life cycle assessment for a cradle-to-cradle cycle: biogas-to-bioplastic (and back). Environ. Sci. Technol. 2012, 46:9822-9829.
51. Scheutz C., Bogner J., De Visscher A., Gebert J., Hilger H., Huber-Humer M., Kjeldsen P., Spokas K. Microbial methane oxidation processes and technologies for mitigation of landfill gas emissions. Waste Manage. Res. 2009, 27:409-455.
52. Semrau J.D., DiSpirito A.A., Yoon S. Methanotrophs and copper. FEMS Microbiol. Rev. 2010, 34:496-531.
53. Smith K., Ball T., Conen F., Dobbie K., Massheder J., Rey A. Exchange of greenhouse gases between soil and atmosphere: interactions of soil physical factors and biological processes. Eur. J. Soil Sci. 2003, 54:779-791.
54. Smith T.J., Murrell J.C. Methanotrophs. Encyclopedia of Industrial Biotechnology: Bioprocess, Bioseparation, and Cell Technology 2010, 1-13. John Wiley and Sons. 10.1002/9780470054581. M.C. Flickenger (Ed.).
55. Stepniewska Z., Goraj W., Kuźniar A., Pytlak A., Ciepielski J., Fraczek P. Biosynthesis of ectoine by the methanotrophic bacterial consortium isolated from Bogdanka coalmine (Poland). Appl. Biochem. Microbiol. 2014, 50:594-600.
56. Sundh I., Börjesson G., Tunlid A. Methane oxidation and phospholipid fatty acid composition in a podzolic soil profile. Soil Biol. Biochem. 2000, 32:1025-1028.
57. Van Bodegom P., Stams F., Mollema L., Boeke S., Leffelaar P. Methane oxidation and the competition for oxygen in the rice rhizosphere. Appl. Environ. Microbiol. 2001, 67:3586-3597.
58. von Alvensleben N., Stookey K., Magnusson M., Heimann K. Salinity tolerance of Picochlorum atomus and the use of salinity for contamination control by the freshwater cyanobacterium Pseudanabaena limnetica. PLoS One 2013, 8:e63569. 10.1371/journal.pone.0063569.
59. Wang Q., Garrity G.M., Tiedje J.M., Cole J.R. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 2007, 73:5261-5267.
60. Wendlandt K.-D., Jechorek M., Helm J., Stottmeister U. Producing poly-3-hydroxybutyrate with a high molecular mass from methane. J. Biotechnol. 2001, 86:127-133.
61. Wendlandt K.D., Stottmeister U., Helm J., Soltmann B., Jechorek M., Beck M. The potential of methane-oxidizing bacteria for applications in environmental biotechnology. Eng. Life Sci. 2010, 10:87-102.
62. Whittenbury R., Phillips K., Wilkinson J. Enrichment, isolation and some properties of methane-utilizing bacteria. J. Gen. Microbiol. 1970, 61:205-218.
63. Wilshusen J., Hettiaratchi J., De Visscher A., Saint-Fort R. Methane oxidation and formation of EPS in compost: effect of oxygen concentration. Environ. Pollut. 2004, 129:305-314.
64. Yamamoto M., Kayanne H., Yamamuro M. Characteristics of organic matter in lagoonal sediments from the Great Barrier Reef. Geochem. J. 2001, 35:385-401.
65. Yoon S., Carey J.N., Semrau J.D. Feasibility of atmospheric methane removal using methanotrophic biotrickling filters. Appl. Microbiol. Biotechnol. 2009, 83:949-956.
66. Zúñiga C., Morales M., Le Borgne S., Revah S. Production of poly-β-hydroxybutyrate (PHB) by Methylobacterium organophilum isolated from a methanotrophic consortium in a two-phase partition bioreactor. J. Hazard. Mater. 2011, 190:876-882.