Microbial CO2 Fixation Bioprocesses and Desert as Future Carbon Sink

  • Leena Agarwal
  • Nishant A. Dafale
  • Hemant J. Purohit
Chapter

Abstract

Increasing levels of carbon dioxide (CO2) in the atmosphere are causing serious effect on climatic changes. Thereby the most concerned environmental issue is global warming these days. The same culprit carbon dioxide is also involved in the most important process called autotrophy, which supports life on earth. Autotrophy could be one of the probable answers for the management of atmospheric CO2 in an eco-friendly manner. Plants contribute a major part in CO2 fixation but often ignored microbes are also involved in CO2 fixation by different CO2 fixation pathways. Since desert represents sparse green cover, we cannot ignore the microbes present in such soil, which would be contributing for carbon fixation. Oligotrophic soil like desert harbours microbes that are capable of surviving in low-carbon conditions, thus opening an area of research for the study of CO2 fixation by oligotrophs. Since microbes require carbon for their growth, and hence under carbon starvation, they might have the mechanism for autotrophy. By exploring CO2 fixation through oligotrophs of desert, we could probably enrich the desert soil by carbon in near future. Such microbe-based CO2 fixation studies could help us to channelize CO2 for the synthesis of some important bioproducts.

Keywords

Desert CO2 fixation Autotroph Oligotrophs Carbon sink Carbon cycles 

Notes

Acknowledgement

Authors are thankful to the Director, CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur for providing necessary facilities and support. The manuscript has been checked for plagiarism by Knowledge Resource Centre, CSIR-NEERI, Nagpur and assigned KRC No.: CSIR-NEERI/KRC/2017/JULY/EBGD/17.

References

  1. Agarwal L, Purohit HJ (2013) Genome sequence of Rhizobium lupini HPC(L) isolated from saline desert soil, Kutch (Gujarat). Genome Announc 1:e00071–e00012. https://doi.org/10.1128/genomeA.00071-12 CrossRefPubMedPubMedCentralGoogle Scholar
  2. Agarwal L, Qureshi A, Kalia VC, Kapley A, Purohit HJ, Singh RN (2014) Arid ecosystem: future option for carbon sinks using microbial community intelligence. Curr Sci 106:1357–1363Google Scholar
  3. Ambardar S, Gupta R, Trakroo D, Lal R, Vakhlu J (2016) High throughput sequencing: an overview of sequencing chemistry. Indian J Microbiol 56:394–404. https://doi.org/10.1007/s12088-016-0606-4 CrossRefPubMedPubMedCentralGoogle Scholar
  4. Atomi H (2002) Microbial enzymes involved in carbon dioxide fixation. J Biosci Bioeng 94:497–505. https://doi.org/10.1016/S1389-1723(02)80186-4 CrossRefPubMedGoogle Scholar
  5. Auguet J, Borrego CM, Bañeras L, Casamayor EO (2008) Fingerprinting the genetic diversity of the biotin carboxylase gene (accC) in aquatic ecosystems as a potential marker for studies of carbon dioxide assimilation in the dark. Environ Microbiol 10:2527–2536. https://doi.org/10.1111/j.1462-2920.2008.01677.x CrossRefPubMedGoogle Scholar
  6. Badger MR, Bek EJ (2008) Multiple rubisco forms in proteobacteria: their functional significance in relation to CO2 acquisition by the CBB cycle. J Exp Bot 59:1525–1541. https://doi.org/10.1093/jxb/erm297 CrossRefPubMedGoogle Scholar
  7. Beh M, Strauss G, Huber R, Stetter KO, Fuchs G (1993) Enzymes of the reductive citric acid cycle in the autotrophic eubacterium Aquifex pyrophilus and in the archaebacterium Thermoproteus neutrophilus. Arch Microbiol 160:306–311. https://doi.org/10.1007/BF00292082 CrossRefGoogle Scholar
  8. Berberoglu H, Barra N, Pilon L, Jay J (2008) Growth, CO2 consumption and H2 production of Anabaena variabilis ATCC 29413-U under different irradiances and CO2 concentrations. J Appl Microbiol 104:105–121. https://doi.org/10.1111/j.1365-2672.2007.03559.x
  9. Berg IA (2011) Ecological aspects of the distribution of different autotrophic CO2 fixation pathways. Appl Environ Microbiol 77:1925–1936. https://doi.org/10.1128/AEM.02473-10
  10. Berg IA, Kockelkorn D, Ramos-Vera WH, Say RF, Zarzycki J, Hügler M, Alber BE, Fuchs G (2010) Autotrophic carbon fixation in archaea. Nat Rev Microbiol 8(6):447–460. https://doi.org/10.1038/nrmicro2365 CrossRefPubMedGoogle Scholar
  11. Borrel G, Adam PS, Gribaldo S (2016) Methanogenesis and the Wood-Ljungdahl pathway: an ancient, versatile, and fragile association. Gen Biol Evol 8(6):1706–1711. https://doi.org/10.1093/gbe/evw114 CrossRefGoogle Scholar
  12. Campbell BJ, Cary SC (2004) Abundance of reverse tricarboxylic acid cycle genes in free-living microorganisms at deep-sea hydrothermal vents. Appl Environ Microbiol 70:6282–6289. https://doi.org/10.1128/AEM.70.10.6282-6289.2004 CrossRefPubMedPubMedCentralGoogle Scholar
  13. Campbell BJ, Stein JL, Cary SC (2003) Evidence of chemolithoautotrophy in the bacterial community associated with Alvinella pompejana, a hydrothermal vent polychaete. Appl Environ Microbiol 69:5070–5078. https://doi.org/10.1128/AEM.69.9.5070-5078.2003 CrossRefPubMedPubMedCentralGoogle Scholar
  14. Chowdhury SP, Schmid M, Hartmann A, Tripathi AK (2007) Identification of diazotrophs in the culturable bacterial community associated with roots of Lasiurus sindicus, a perennial grass of Thar Desert. India. Microb Ecol 54:82–90. https://doi.org/10.1007/s00248-006-9174-1 CrossRefPubMedGoogle Scholar
  15. Connon SA, Lester ED, Shafaat HS, Obenhuber DC, Ponce A (2007) Bacterial diversity in hyperarid Atacama Desert soils. J Geophys Res 112:1–9. https://doi.org/10.1029/2006JG000311 CrossRefGoogle Scholar
  16. Ding L, Yokota A (2004) Proposals of Curvibacter gracilis gen. nov., sp. nov. and Herbaspirillum putei sp. nov. for bacterial strains isolated from well water and reclassification of [Pseudomonas] huttiensis, [Pseudomonas] lanceolata, [Aquaspirillum] delicatum and [Aquaspirillum] autotrophicum as Herbaspirillum huttiense comb. nov., Curvibacter lanceolatus comb. nov., Curvibacter delicatus comb. nov. and Herbaspirillum autotrophicum comb. Nov. Int J Syst Evol Microbiol 54:2223–2230. https://doi.org/10.1099/ijs.0.02975-0 CrossRefPubMedGoogle Scholar
  17. Dong H, Rech JA, Jiang H, Sun H, Buck BJ (2007) Endolithic cyanobacteria in soil gypsum: occurrences in Atacama (Chile), Mojave (United States), and Al-Jafr Basin (Jordan) Deserts. J Geophys Res 112:1–11. https://doi.org/10.1029/2006JG000385 Google Scholar
  18. Erb TJ (2011) Carboxylases in natural and synthetic microbial pathways. Appl Environ Microbiol 77:8466–8477. https://doi.org/10.1128/AEM.05702-11 CrossRefPubMedPubMedCentralGoogle Scholar
  19. Evans MC, Buchanan BB, Arnon DI (1966) A new ferredoxin-dependent carbon reduction cycle in a photosynthetic bacterium. Proc Natl Acad Sci U S A 55(4):928–934CrossRefPubMedPubMedCentralGoogle Scholar
  20. Ferrera I, Longhorn S, Banta AB, Liu Y, Preston D, Reysenbach AL (2007) Diversity of 16S rRNA gene, ITS region and aclB gene of the aquificales. Extremophiles 11:57–64. https://doi.org/10.1007/s00792-006-0009-2 CrossRefPubMedGoogle Scholar
  21. Fuhrmanna S, Fernera M, Jeffke T, Henne A, Gottschalk G, Meyer O (2003) Complete nucleotide sequence of the circular megaplasmid pHCG3 of Oligotropha carboxidovorans: function in the chemolithoautotrophic utilization of CO, H2 and CO2. Gene 322:67–75. https://doi.org/10.1016/j.gene.2003.08.027
  22. Hanson TE, Tabita FR (2001) A ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) like protein from Chlorobium tepidum that is involved with sulfur metabolism and the response to oxidative stress. Proc Natl Acad Sci U S A 98:4397–4402. https://doi.org/10.1073/pnas.081610398 CrossRefPubMedPubMedCentralGoogle Scholar
  23. Holo H (1989) Chloroflexus aurantiacus secretes 3-hydroxypropionate, a possible intermediate in the assimilation of CO2 and acetate. Arch Microbiol 151:252–256. https://doi.org/10.1007/BF00413138
  24. Hu Y, Holden JF (2006) Citric acid cycle in the hyperthermophilic archaeon Pyrobaculum islandicum grown autotrophically, heterotrophically, and mixotrophically with acetate. J Bacteriol 188:4350–4355. https://doi.org/10.1128/JB.00138-06 CrossRefPubMedPubMedCentralGoogle Scholar
  25. Hügler M, Sievert SM (2011) Beyond the calvin cycle: autotrophic carbon fixation in the ocean. Annu Rev Mar Sci 3:261–289. https://doi.org/10.1146/annurev-marine-120709-142712 CrossRefGoogle Scholar
  26. Hügler M, Wirsen CO, Fuchs G, Taylor CD, Sievert SM (2005) Evidence for autotrophic CO2 fixation via the reductive tricarboxylic acid cycle by members of the -subdivision of proteobacteria. J Bacteriol 187:3020–3027. https://doi.org/10.1128/JB.187.9.3020-3027.2005
  27. Hügler M, Huber H, Molyneaux SJ, Vetriani C, Sievert SM (2007) Autotrophic CO2 fixation via the reductive tricarboxylic acid cycle in different lineages within the phylum Aquificae: evidence for two ways of citrate cleavage. Environ Microbiol 9:81–92. https://doi.org/10.1111/j.1462-2920.2006.01118.x
  28. Kanao T, Fukui T, Atomi H, Imanaka T (2001) ATP-citrate lyase from the green sulfur bacterium Chlorobium limicola is a heteromeric enzyme composed of two distinct gene products. Eur J Biochem 268:1670–1678. https://doi.org/10.1046/j.1432-1327.2001.02034.x CrossRefPubMedGoogle Scholar
  29. Köberl M, Müller H, Ramadan EM, Berg G (2011) Desert farming benefits from microbial potential in arid soils and promotes diversity and plant health. PLoS One 6:e24452. https://doi.org/10.1371/journal.pone.0024452 CrossRefPubMedPubMedCentralGoogle Scholar
  30. Kuhlman KR, Fusco WG, La Duc MT, Allenbach LB, Ball CL, Kuhlman GM, Anderson RC, Erickson IK, Stuecker T, Benardini J, Strap JL (2006) Diversity of microorganisms within rock varnish in the Whipple Mountains, California. Appl Environ Microbiol 72:1708–1715. https://doi.org/10.1128/AEM.72.2.1708-1715.2006 CrossRefPubMedPubMedCentralGoogle Scholar
  31. Kuznetsov BB, Ivanovsky RN, Keppen OI, Sukhacheva MV, Bumazhkin BK, Patutina EO, Beletsky AV, Mardanov AV, Baslerov RV, Panteleeva AN, Kolganova TV (2011) Draft genome sequence of the anoxygenic filamentous phototrophic bacterium Oscillochloris trichoides subsp. DG-6. J Bacteriol 193:321–322. https://doi.org/10.1128/JB.00931-10 CrossRefPubMedGoogle Scholar
  32. Lacap DC, Warren-Rhodes KA, McKay CP, Pointing SB (2011) Cyanobacteria and chloroflexi-dominated hypolithic colonization of quartz at the hyper-arid core of the Atacama Desert, Chile. Extremophiles 15:31–38. https://doi.org/10.1007/s00792-010-0334-3 CrossRefPubMedGoogle Scholar
  33. Lester ED, Satomi M, Ponce A (2007) Microflora of extreme arid Atacama desert soil. Soil Biol Biochem 39:704–708. https://doi.org/10.1016/j.soilbio.2006.09.020 CrossRefGoogle Scholar
  34. Navarro-González R, Rainey FA, Molina P, Bagaley DR, Hollen BJ, de la Rosa J, Small AM, Quinn RC, Grunthaner FJ, Cáceres L, Gomez-Silva B (2003) Mars-like soils in the Atacama Desert, Chile, and the dry limit of microbial life. Science 302:1018–1021. https://doi.org/10.1126/science.1089143 CrossRefPubMedGoogle Scholar
  35. Ohhata N, Yoshida N, Egami H, Katsuragi T, Tani Y, Takagi H (2007) An extremely oligotrophic bacterium, Rhodococcus erythropolis N9T-4, isolated from crude oil. J Bacteriol 189:6824–6831. https://doi.org/10.1128/JB.00872-07 CrossRefPubMedPubMedCentralGoogle Scholar
  36. Piubeli F, de Lourdes Moreno M, Kishi LT, Henrique-Silva F, García MT, Mellado E (2015) Phylogenetic profiling and diversity of bacterial communities in the Death Valley, an extreme habitat in the Atacama Desert. Indian J Microbiol 55:392–399. https://doi.org/10.1007/s12088-015-0539-3 CrossRefPubMedPubMedCentralGoogle Scholar
  37. Pointing SB, Chan Y, Lacap DC, Lau MCY, Jurgens JA, Farrell RL (2009) Highly specialized microbial diversity in hyper-arid polar desert. Proc Natl Acad Sci U S A 106:19964–19969. https://doi.org/10.1073/pnas.0908274106 CrossRefPubMedPubMedCentralGoogle Scholar
  38. Rao S, Chan Y, Bugler-Lacap DC, Bhatnagar A, Bhatnagar M, Pointing SB (2016) Microbial diversity in soil, sand dune and rock substrates of the Thar Monsoon Desert, India. Indian J Microbiol 56:35–45. https://doi.org/10.1007/s12088-015-0549-1 CrossRefPubMedGoogle Scholar
  39. Saini R, Kapoor R, Kumar R, Siddiqi TO, Kumar A (2011) CO2 utilizing microbes—a comprehensive review. Biotechnol Adv 29:949–960. https://doi.org/10.1016/j.biotechadv.2011.08.009
  40. Schafer S, Gotz M, Elsenreich W, Bacher A, Fuchs G (1989) 13C-NMR study of autotrophic CO2 fixation in Therrnoproteus neutrophilus. Eur J Biochem 184:151–156. https://doi.org/10.1111/j.1432-1033.1992.tb16850.x
  41. Selesi D, Schmid M, Hartmann A (2005) Diversity of green-like and red-like ribulose-1,5-bisphosphate carboxylase/oxygenase large-subunit genes (cbbL) in differently managed agricultural soils. Appl Environ Microbiol 71:175–184. https://doi.org/10.1128/AEM.71.1.175-184.2005 CrossRefPubMedPubMedCentralGoogle Scholar
  42. Shively JM, van Keulen G, Meijer WG (1998) Something from almost nothing: carbon dioxide fixation in chemoautotrophs. Annu Rev Microbiol 52:191–230. https://doi.org/10.1146/annurev.micro.52.1.191 CrossRefPubMedGoogle Scholar
  43. Sintsov NV, Ivanovskii RN, Kondrat’eva EN (1980) ATP-dependent citrate lyase in the green phototrophic bacterium, Chlorobium limicola. Mikrobiologiia 49(4):514–516PubMedGoogle Scholar
  44. Smith JJ, Tow LA, Stafford W, Cary C, Cowan DA (2006) Bacterial diversity in three different Antarctic Cold Desert mineral soils. Microb Ecol 51:413–421. https://doi.org/10.1007/s00248-006-9022-3 CrossRefPubMedGoogle Scholar
  45. Souza V, Espinosa-Asuar L, Escalante AE, Eguiarte LE, Farmer J, Forney L, Lloret L, Rodríguez-Martínez JM, Soberón X, Dirzo R, Elser JJ (2006) An endangered oasis of aquatic microbial biodiversity in the Chihuahuan desert. Proc Natl Acad Sci U S A 103:6565–6570. https://doi.org/10.1073/pnas.0601434103 CrossRefPubMedPubMedCentralGoogle Scholar
  46. Suárez EB, Matta J, Rolón M, Maldonado L, Detrés Y, De la Motta A, Gelado M, Ramos J, Armstrong R (2008) Molecular identification of the bacterial burden in Sahara Dust samples using a new method to improve the evidence for the effective management of public health measures during an SD event. J Environ Health Res 7:99–106Google Scholar
  47. Tang KH, Blankenship RE (2010) Both forward and reverse TCA cycles operate in green sulfur bacteria. J Biol Chem 285:35848–35854. https://doi.org/10.1074/jbc.M110.157834 CrossRefPubMedPubMedCentralGoogle Scholar
  48. Thauer RK, Kaster AK, Seedorf H, Buckel W, Hedderich R (2008) Methanogenic archaea: ecologically relevant differences in energy conservation. Nat Rev Microbiol 6:579–591. https://doi.org/10.1038/nrmicro1931 CrossRefPubMedGoogle Scholar
  49. Ueda K, Tagami Y, Kamihara Y, Shiratori H, Takano H, Beppu T (2008) Isolation of bacteria whose growth is dependent on high levels of CO2 and implications of their potential diversity. Appl Environ Microbiol 74:4535–4538. https://doi.org/10.1128/AEM.00491-08
  50. Warren-Rhodes KA, Rhodes KL, Pointing SB, Ewing SA, Lacap DC, Gomez-Silva B, Amundson R, Friedmann EI, McKay CP (2006) Hypolithic cyanobacteria, dry limit of photosynthesis, and microbial ecology in the hyperarid Atacama Desert. Microb Ecol 52:389–398. https://doi.org/10.1007/s00248-006-9055-7 CrossRefPubMedGoogle Scholar
  51. Williams TJ, Zhang CL, Scott JH, Bazylinski DA (2006) Evidence for autotrophy via the reverse tricarboxylic acid cycle in the marine Magnetotactic coccus strain MC-1. Appl Environ Microbiol 72:1322–1329. https://doi.org/10.1128/AEM.72.2.1322-1329.2006 CrossRefPubMedPubMedCentralGoogle Scholar
  52. Wood SA, Rueckert A, Cowan DA, Cary SC (2008) Sources of edaphic cyanobacterial diversity in the dry valleys of eastern Antarctica. ISME J 2:308–320. https://doi.org/10.1038/ismej.2007.104 CrossRefPubMedGoogle Scholar
  53. Yang C, Hua Q, Shimizu K (2002) Integration of the information from gene expression and metabolic fluxes for the analysis of the regulatory mechanisms in Synechocystis. Appl Microbiol Biotechnol 58:813–822. https://doi.org/10.1007/s00253-002-0949-0 CrossRefPubMedGoogle Scholar
  54. Yano T, Yoshida N, Yu F, Wakamatsu M, Takagi H (2015) The glyoxylate shunt is essential for CO2 requiring oligotrophic growth of Rhodococcus erythropolis N9T-4. Appl Microbiol Biotechnol 99:5627–5637. https://doi.org/10.1007/s00253-015-6500-x
  55. Yergeau E, Schoondermark-Stolk SA, Brodie EL, Déjean S, DeSantis TZ, Gonçalves O, Piceno YM, Andersen GL, Kowalchuk GA (2009) Environmental microarray analyses of Antarctic soil microbial communities. ISME J 3:340–351. https://doi.org/10.1038/ismej.2008.111 CrossRefPubMedGoogle Scholar
  56. Yoshida N, Ohhata N, Yoshino Y, Katsuragi T, Tani Y, Takagi H (2007) Screening of carbon dioxide extreme oligotrophs from soil. Biosci Biotechnol Biochem 71:2830–2832. https://doi.org/10.1271/bbb.70042 CrossRefPubMedGoogle Scholar
  57. Yoshida N, Hayasaki T, Takagi H (2011) Gene expression analysis of methylotrophic oxidoreductases involved in the oligotrophic growth of Rhodococcus erythropolis N9T-4. Biosci Biotechnol Biochem 75:123–127. https://doi.org/10.1271/bbb.100700 CrossRefPubMedGoogle Scholar
  58. Yousuf B, Sanadhya P, Keshri J, Jha B (2012) Comparative molecular analysis of chemolithotrophic bacterial diversity and community structure from coastal saline soils, Gujarat, India. BMC Microbiol 12:150. https://doi.org/10.1186/1471-2180-12-150 CrossRefPubMedPubMedCentralGoogle Scholar
  59. Yuan H, Ge T, Chen C, O’Donnell AG, Wu J (2012) Significant role for microbial autotrophy in the sequestration of soil carbon. Appl Environ Microbiol 78:2328–2336. https://doi.org/10.1128/AEM.06881-11 CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2017

Authors and Affiliations

  • Leena Agarwal
    • 1
  • Nishant A. Dafale
    • 1
  • Hemant J. Purohit
    • 1
  1. 1.Environmental Biotechnology and Genomics DivisionCSIR – National Environmental Engineering and Research Institute (CSIR-NEERI)NagpurIndia

Personalised recommendations