Linking Microbial Genomics to Renewable Energy Production and Global Carbon Management

  • Neha
  • Abhishek Singh
  • Suman Yadav
  • Yashpal BhardwajEmail author


The diminishing concentration of available fossil fuels and increasing global demand of energy have obligated the need for the production of alternate fuels to current petroleum-based fuels. Microbes have the potential to render renewable and sustainable energy sources that are carbon-neutral to counter the elevated concentration of greenhouse gases in the substantial climate changes. Various advancements in sequencing technologies have enabled the study of the microbial diversity and interpreting the variations within the entire genome of organisms and concluding the most feasible pathway of substrate utilization in a comparatively cheaper and faster way. To completely exploit the biofuel-producing potential of these microbes, various genomes have been sequenced and are now available for study. Computational approaches like functional genomics, genome-scale metabolic engineering, and flux balance analysis can be used to improve the H2-producing efficiencies of microbes. Many microorganisms like Enterobacter sp. IIT-BT 08 are reported to have a high rate of H2 production, and its draft genome was generated at DOE Joint Genome Institute (JGI) using Illumina data. The C. perfringens strain JJC was sequenced using the Illumina MiSeq benchtop sequencer which uses a vast variety of carbohydrates producing acetate, butyrate, lactate, ethanol, H2, and carbon dioxide and has various industrial applications. Access to multiple microalgal genome sequences now provides opportunities for application of “omic” approaches to decipher algal lipid metabolism and identify gene targets for the development of potentially engineered strains with optimized lipid content from which biofuel can be produced.


Microorganisms Biofuel Genomics Carbon management Biomass 


  1. Angenent LT, Karim K, Al-Dahhan MH, Wrenn BA, Domíguez-Espinosa R (2004) Production of bioenergy and biochemicals from industrial and agricultural wastewater. Trends Biotechnol 22(9):477–485CrossRefPubMedPubMedCentralGoogle Scholar
  2. Aro EM (2016) From first generation biofuels to advanced solar biofuels. Ambio 45:24–31CrossRefGoogle Scholar
  3. Bakonyi P, Nemestóthy N, Simon V, Bélafi-Bakó K (2014) Review on the start-up experiences of continuous fermentative hydrogen producing bioreactors. Renew Sust Energ Rev 40:806–813CrossRefGoogle Scholar
  4. Bao G, Wang R, Zhu Y, Dong H, Mao S, Zhang Y, Chen Z, Li Y, Ma Y (2011) Complete genome sequence of Clostridium acetobutylicum DSM 1731, a solvent-producing strain with multireplicon genome architecture. J Bacteriol 193(18):5007–5008CrossRefPubMedPubMedCentralGoogle Scholar
  5. Bardgett RD, Freeman C, Ostle NJ (2008) Microbial contributions to climate change through carbon cycle feedbacks. ISME J 2:805CrossRefPubMedPubMedCentralGoogle Scholar
  6. Beer LL, Boyd ES, Peters JW, Posewitz MC (2009) Engineering algae for biohydrogen and biofuel production. Curr Opin Biotechnol 20(3):264–271CrossRefPubMedPubMedCentralGoogle Scholar
  7. Boden R, Cunliffe M, Scanlan J, Moussard H, Kits KD, Klotz MG, Jetten MSM, Vuilleumier S, Han J, Peters L, Mikhailova N, Teshima H, Tapia R, Kyrpides N, Ivanova N, Pagani I, Cheng J-F, Goodwin L, Han C, Hauser L, Land ML, Lapidus A, Lucas S, Pitluck S, Woyke T, Stein L, Murrell JC (2011) Complete genome sequence of the aerobic marine methanotroph Methylomonas methanica MC09. J Bacteriol 193:7001CrossRefPubMedPubMedCentralGoogle Scholar
  8. Brown SD, Begemann MB, Mormile MR, Wall JD, Han CS, Goodwin LA, Pitluck S, Land ML, Hauser LJ, Elias DA (2011) Complete genome sequence of the haloalkaliphilic, hydrogen-producing bacterium Halanaerobium hydrogeniformans. J Bacteriol 193:3682–3683CrossRefPubMedPubMedCentralGoogle Scholar
  9. Burk MJ (2010) Sustainable production of industrial chemicals from sugars. Int Sugar J 112:30–35Google Scholar
  10. Canadell JG, Le Quéré C, Raupach MR, Field CB, Buitenhuis ET, Ciais P, Conway TJ, Gillett NP, Houghton RA, Marland G (2007) Contributions to accelerating atmospheric CO2 growth from economic activity, carbon intensity, and efficiency of natural sinks. Proc Natl Acad Sci 104:18866–18870CrossRefPubMedPubMedCentralGoogle Scholar
  11. Carere CR, Rydzak T, Verbeke TJ, Cicek N, Levin DB, Sparling R (2012) Linking genome content to biofuel production yields: a meta-analysis of major catabolic pathways among select H2 and ethanol-producing bacteria. BMC Microbiol 12:295CrossRefPubMedPubMedCentralGoogle Scholar
  12. de Vrije T, Mars AE, Budde MA, Lai MH, Dijkema C, de Waard P, Claassen PA (2007) Glycolytic pathway and hydrogen yield studies of the extreme thermophile Caldicellulosiruptor saccharolyticus. Appl Microbiol Biotechnol 74:1358–1367CrossRefPubMedPubMedCentralGoogle Scholar
  13. Desiniotis A, Kouvelis VN, Davenport K, Bruce D, Detter C, Tapia R, Han C, Goodwin LA, Woyke T, Kyrpides NC, Typas MA, Pappas KM (2012) Complete genome sequence of the ethanol-producing Zymomonas mobilis subsp. mobilis centrotype ATCC 29191. J Bacteriol 194(21):5966–5967CrossRefPubMedPubMedCentralGoogle Scholar
  14. Dubey S (2005) Microbial ecology of methane emission in rice Agroecosystem: a review. Appl Ecol Environ Res 3:1–27CrossRefGoogle Scholar
  15. Dutaur L, Verchot LV (2007) A global inventory of the soil CH4 sink. Glob Biogeochem Cy 21Google Scholar
  16. Falkowski P, Scholes RJ, Boyle E, Canadell J, Canfield D, Elser J, Gruber N, Hibbard K, Högberg P, Linder S, Mackenzie FT, Moore B III, Pedersen T, Rosenthal Y, Seitzinger S, Smetacek V, Steffen W (2000) The Global Carbon Cycle: A Test of Our Knowledge of Earth as a System. Science 290:291–296CrossRefGoogle Scholar
  17. Fierer N, Bradford MA, Jackson RB (2007) Toward an ecological classification of soil bacteria. Ecology 88:1354–1364CrossRefPubMedPubMedCentralGoogle Scholar
  18. Georgianna DR, Mayfield SP (2012) Exploiting diversity and synthetic biology for the production of algal biofuels. NatureGoogle Scholar
  19. Hanson RS, Hanson TE (1996) Methanotrophic bacteria. Microbiol Rev 60:439–471PubMedPubMedCentralGoogle Scholar
  20. Hashimoto K, Yoshizawa AC, Okuda S, Kuma K, Goto S, Kanehisa M (2008) The repertoire of desaturases and elongases reveals fatty acid variations in 56 eukaryotic genomes. J Lipid Res 49(1):183–191CrossRefPubMedPubMedCentralGoogle Scholar
  21. He Z, Xu M, Deng Y, Kang S, Kellogg L, Wu L, Van Nostrand JD, Hobbie SE, Reich PB, Zhou J (2010) Metagenomic analysis reveals a marked divergence in the structure of belowground microbial communities at elevated CO2. Ecol Lett 13(5):564–575CrossRefPubMedPubMedCentralGoogle Scholar
  22. Kalia VC, Lal S, Ghai R, Mandal M, Chauhan A (2003) Mining genomic databases to identify novel hydrogen producers. Trends Biotechnol 21:152–156CrossRefPubMedPubMedCentralGoogle Scholar
  23. Kanehisa M, Goto S, Furumichi M, Tanabe M, Hirakawa M (2010) KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res 38(Database issue):D355–D360CrossRefPubMedPubMedCentralGoogle Scholar
  24. Kataeva IA, Yang SJ, Dam P, Poole FL 2nd, Yin Y, Zhou F, Chou W-C, Xu Y, Goodwin L, Sims DR, Detter JC, Hauser LJ, Westpheling J, Adams MW (2009) Genome sequence of the anaerobic, thermophilic, and cellulolytic bacterium “Anaerocellum thermophilum” DSM 6725. J Bacteriol 191(11):3760–3761CrossRefPubMedPubMedCentralGoogle Scholar
  25. Kaufmann F, Lovley DR (2001) Isolation and characterization of a soluble NADPH-dependent Fe(III) reductase from Geobacter sulfurreducens. J Bacteriol 183:4468CrossRefPubMedPubMedCentralGoogle Scholar
  26. Khanna N, Ghosh AK, Huntemann M, Deshpande S, Han J, Chen A, Kyrpides N, Mavrommatis K, Szeto E, Markowitz V, Ivanova N, Pagani I, Pati A, Pitluck S, Nolan M, Woyke T, Teshima H, Chertkov O, Daligault H, Davenport K, Gu W, Munk C, Zhang X, Bruce D, Detter C, Xu Y, Quintana B, Reitenga K, Kunde Y, Green L, Erkkila T, Han C, Brambilla E-M, Lang E, Klenk H-P, Goodwin L, Chain P, Das D (2013) Complete genome sequence of Enterobacter sp. IIT-BT 08: A potential microbial strain for high rate hydrogen production. Stand Genomic Sci 9:359–369CrossRefPubMedPubMedCentralGoogle Scholar
  27. Kim BH, Kim HJ, Hyun MS, Park DH (1999) Direct electrode reaction of Fe(III)-reducing bacterium, Shewanella putrefaciens. J Microbiol Biotechnol 9:127–131Google Scholar
  28. Kimble JM, Lal R, Follett RF (2002) Agricultural practices and policies for carbon sequestration in soil. CRC Press, Boca RatonGoogle Scholar
  29. King GM (2011) Enhancing soil carbon storage for carbon remediation: potential contributions and constraints by microbes. Trends Microbiol 19:75–84CrossRefPubMedPubMedCentralGoogle Scholar
  30. Knothe G (2009) Improving biodiesel fuel properties by modifying fatty ester composition. Energy Environ Sci 2:759–766CrossRefGoogle Scholar
  31. Kumar R, Singh S, Singh OV (2008) Bioconversion of lignocellulosic biomass: biochemical and molecular perspectives. J Ind Microbiol Biotechnol 35(5):377–391CrossRefPubMedPubMedCentralGoogle Scholar
  32. Kumar G, Bakonyi P, Periyasamy S, Kim SH, Nemestóthy N, Bélafi-Bakó K (2015) Lignocellulose biohydrogen: Practical challenges and recent progress. Renew Sust Energ Rev 44:728–737CrossRefGoogle Scholar
  33. Lal R (2004) Soil carbon sequestration impacts on global climate change and food security. Science 304:1623–1627CrossRefPubMedPubMedCentralGoogle Scholar
  34. Larsen PE, Field D, Gilbert JA (2012) Predicting bacterial community assemblages using an artificial neural network approach. Nat Methods 9:621CrossRefPubMedPubMedCentralGoogle Scholar
  35. Li X, Huang S, Yu J, Wang Q, Wu S (2013) Improvement of hydrogen production of Chlamydomonas reinhardtii by co-cultivation with isolated bacteria. Int J Hydrog Energy 38:10779–10787CrossRefGoogle Scholar
  36. Liao JC, Mi L, Pontrelli S, Luo S (2016) Fuelling the future: microbial engineering for the production of sustainable biofuels. Nat Rev Microbiol 14(5):288–304CrossRefGoogle Scholar
  37. Logan BE (2004) Peer reviewed: extracting hydrogen and electricity from renewable resources. Environ Sci Technol 38:160A–167ACrossRefPubMedPubMedCentralGoogle Scholar
  38. Misra N, Panda PK, Parida BK (2013) Agrigenomics for microalgal biofuel production: an overview of various bioinformatics resources and recent studies to link OMICS to bioenergy and bioeconomy. OMICS 17(11):537–549CrossRefPubMedPubMedCentralGoogle Scholar
  39. Mukhopadhyay A, Redding AM, Rutherford BJ, Keasling JD (2008) Importance of systems biology in engineering microbes for biofuel production. Curr Opin Biotechnol 19(3):228–234CrossRefPubMedPubMedCentralGoogle Scholar
  40. Nielsen AT, Amandusson H, Bjorklund R, Dannetun H, Ejlertsson J, Ekedahl L-G, Lundström I, Svensson BH (2001) Hydrogen production from organic waste. Int J Hydrog Energy 26:547–550CrossRefGoogle Scholar
  41. O-Thong S, Khongkliang P, Mamimin C, Singkhala A, Prasertsan P, Birkeland NK (2017) Draft genome sequence of Thermoanaerobacterium sp. strain PSU-2 isolated from thermophilic hydrogen producing reactor. Genom Data 12:49–51CrossRefPubMedPubMedCentralGoogle Scholar
  42. Ouhib-Jacobs O, Lindley ND, Schmitt P, Clavel T (2009) Fructose and glucose mediates enterotoxin production and anaerobic metabolism of Bacillus cereus ATCC14579(T). J Appl Microbiol 107(3):821–829CrossRefPubMedPubMedCentralGoogle Scholar
  43. Patil SA, Surakasi VP, Koul S, Ijmulwar S, Vivek A, Shouche YS, Kapadnis BP (2009) Electricity generation using chocolate industry wastewater and its treatment in activated sludge based microbial fuel cell and analysis of developed microbial community in the anode chamber. Bioresour Technol 100:5132–5139CrossRefPubMedPubMedCentralGoogle Scholar
  44. Pfaltzgraff LA, De bruyn M, Cooper EC, Budarin V, Clark JH (2013) Food waste biomass: a resource for high-value chemicals. Green Chem 15:307–314CrossRefGoogle Scholar
  45. Reuter JA, Spacek DV, Snyder MP (2015) High-throughput sequencing technologies. Mol Cell 58(4):586–597CrossRefPubMedPubMedCentralGoogle Scholar
  46. Rismani-Yazdi H, Haznedaroglu BZ, Bibby K, Peccia J (2011) Transcriptome sequencing and annotation of the microalgae Dunaliella tertiolecta: Pathway description and gene discovery for production of next-generation biofuels. BMC Genomics 12:148CrossRefPubMedPubMedCentralGoogle Scholar
  47. Rittmann BE, Krajmalnik-Brown R, Halden RU (2008) Pre-genomic, genomic and post-genomic study of microbial communities involved in bioenergy. Nat Rev Microbiol 6:604CrossRefPubMedPubMedCentralGoogle Scholar
  48. Rivkin RB, Legendre L (2001) Biogenic carbon cycling in the upper ocean: effects of microbial respiration. Science 291(5512):2398–2400CrossRefPubMedPubMedCentralGoogle Scholar
  49. Rodríguez-Moyá M, Gonzalez R (2010) Systems biology approaches for the microbial production of biofuels. Biofuels 1:291–310CrossRefGoogle Scholar
  50. Roh H, Ko H-J, Kim D, Choi DG, Park S, Kim S, Chang IS, Choi I-G (2011) Complete Genome Sequence of a Carbon Monoxide-Utilizing Acetogen, Eubacterium limosum KIST612. J Bacteriol 193:307–308CrossRefPubMedPubMedCentralGoogle Scholar
  51. Rydzak T, Levin DB, Cicek N, Sparling R (2009) Growth phase-dependant enzyme profile of pyruvate catabolism and end-product formation in Clostridium thermocellum ATCC 27405. J Biotechnol 140(3–4):169–175CrossRefPubMedPubMedCentralGoogle Scholar
  52. Schmidt MWI, Torn MS, Abiven S, Dittmar T, Guggenberger G, Janssens IA, Kleber M, Kögel-Knabner I, Lehmann J, Manning DAC, Nannipieri P, Rasse DP, Weiner S, Trumbore SE (2011) Persistence of soil organic matter as an ecosystem property. Nature 478:49CrossRefPubMedPubMedCentralGoogle Scholar
  53. Shendure J, Ji HL (2008) Next-generation DNA sequencing. Nat Biotechnol 26:1135–1145CrossRefPubMedPubMedCentralGoogle Scholar
  54. Singh BK, Bardgett RD, Smith P, Reay DS (2010) Microorganisms and climate change: terrestrial feedbacks and mitigation options. Nat Rev Microbiol 8:779–790CrossRefPubMedPubMedCentralGoogle Scholar
  55. Smith SR, Abbriano RM, Hildebrand M (2012) Comparative analysis of diatom genomes reveals substantial differences in the organization of carbon partitioning pathways. Algal Res 1:2–16CrossRefGoogle Scholar
  56. Stein LY, Bringel F, DiSpirito AA, Han S, Jetten MSM, Kalyuzhnaya MG, Kits KD, Klotz MG, Op den Camp HJM, Semrau JD, Vuilleumier S, Bruce DC, Cheng J-F, Davenport KW, Goodwin L, Han S, Hauser L, Lajus A, Land ML, Lapidus A, Lucas S, Médigue C, Pitluck S, Woyke T (2011) Genome sequence of the methanotrophic Alphaproteobacterium Methylocystis sp. Strain Rockwell (ATCC 49242). J Bacteriol 193:2668CrossRefPubMedPubMedCentralGoogle Scholar
  57. Strickland MS, Rousk J (2010) Considering fungal:bacterial dominance in soils – Methods, controls, and ecosystem implications. Soil Biol Biochem 42:1385–1395CrossRefGoogle Scholar
  58. Su H, Zhang T, Bao M, Jiang Y, Wang Y, Tan T (2014) Genome Sequence of a Promising Hydrogen-Producing Facultative Anaerobic Bacterium, Brevundimonas naejangsanensis Strain B1. LID - 10.1128/genomeA.00542-14 [doi] LID - e00542-14 [pii]. Genome, AnnouncGoogle Scholar
  59. Vignais PM, Billoud B, Meyer J (2001) Classification and phylogeny of hydrogenases. FEMS Microbiol Rev 25(4):455–501CrossRefPubMedPubMedCentralGoogle Scholar
  60. Wang J, Suzuki T, Dohra H, Takigami S, Kako H, Soga A, Kamei I, Mori T, Kawagishi H, Hirai H (2016) Analysis of ethanol fermentation mechanism of ethanol-producing white-rot fungus Phlebia sp. MG-60 by RNA-seq. BMC Genomics 17(1):616CrossRefPubMedPubMedCentralGoogle Scholar
  61. Wong YM, Juan JC, Gan HM, Austin CM (2014) Draft Genome Sequence of Clostridium perfringens Strain JJC, a Highly Efficient Hydrogen Producer Isolated from Landfill Leachate Sludge. Genome Announc 2:e00064–e00014PubMedPubMedCentralGoogle Scholar
  62. Woodward FI, Bardgett RD, Raven JA, Hetherington AM (2009) Biological approaches to global environment change mitigation and remediation. Curr Biol 19:R615–R623CrossRefPubMedPubMedCentralGoogle Scholar
  63. Yadav S, Dubey SK (2018) Cellulose degradation potential of Paenibacillus lautus strain BHU3 and its whole genome sequence. Bioresour Technol 262:124–131CrossRefPubMedPubMedCentralGoogle Scholar
  64. Yu W-L, Ansari W, Schoepp NG, Hannon MJ, Mayfield SP, Burkart MD (2011) Modifications of the metabolic pathways of lipid and triacylglycerol production in microalgae. Microb Cell Factories 10:91CrossRefGoogle Scholar
  65. Zhao XQ, Zi LH, Bai FW, Lin HL, Hao XM, Yue GJ, Ho NWY (2012) Bioethanol from lignocellulosic biomass. Adv Biochem Eng Biotechnol 128:25–51PubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2019

Authors and Affiliations

  • Neha
    • 1
  • Abhishek Singh
    • 1
  • Suman Yadav
    • 1
  • Yashpal Bhardwaj
    • 1
    Email author
  1. 1.Laboratory of Molecular Ecology, Centre of Advanced Study in BotanyBanaras Hindu UniversityVaranasiIndia

Personalised recommendations