Synthetic circuit designs for earth terraformation

Biology Direct

Volumn 10, Issue 1, 2015, Pages

  Solé, Ricard V ^a,b   Montañez, Raúl ^a   Duran Nebreda, Salva ^a  

^a UNIVERSITAT POMPEU FABRA   (Spain)

^b SANTA FE INSTITUTE   (United States)

Author keywords

Catastrophic shifts; Climate change; Ecological engineering; Mutualism; Synthetic biology

Indexed keywords

BIOLOGICAL MODEL; BIOLOGY; BIOREACTOR; CARBON SEQUESTRATION; CLIMATE CHANGE; ECOSYSTEM; ENVIRONMENTAL PROTECTION; PHYSIOLOGY; SYMBIOSIS; TRANSGENIC ORGANISM;

BIOREACTORS; CARBON SEQUESTRATION; CLIMATE CHANGE; COMPUTATIONAL BIOLOGY; CONSERVATION OF NATURAL RESOURCES; ECOSYSTEM; MODELS, BIOLOGICAL; ORGANISMS, GENETICALLY MODIFIED; SYMBIOSIS;

EID: 84937562242     PISSN: None     EISSN: 17456150     Source Type: Journal    
DOI: 10.1186/s13062-015-0064-7     Document Type: Article

References (71)

1. Afshinnekoo E, Meydan C, Chowdhury S, Jaroudi D, Boyer C, Bernstein N, et al. Geospatial resolution of human and bacterial diversity with city-scale metagenomics. Cell Syst. 2015;1:1-15.
2. Barnes D. Invasions by marine life on plastic debris. Nature. 2002;416:808-9.
3. Barnosky AD, Hadly EA, Bascompte J, Berlow EL, Brown JH, Fortelius M, et al. Approaching a state of shift in earths biosphere. Nature. 2012;486:52-8.
4. Belnap J. The world at your feet: desert biological soil crusts. Front Ecol Environ. 2003;1:181-9.
5. Belnap J, Lange O, editors. Biological soil crusts: structure. Berlin: Function and Management. Springer; 2003.
6. Bowker M. Biological soil crust rehabilitation in theory and practice: An underexploited opportunity. Restor Ecol. 2007;15:13-23.
7. Bowker MA, Mau RL, Maestre FT, Escolar C, Castillo-Monroy AP. Functional profiles reveal unique ecological roles of various biological soil crust organisms. Funct Ecol. 2011;25:787-95.
8. Braude S, Low BS. An introduction to methods and models in ecology, evolution and conservation biology. 41 William Street, Princeton, New Jersey, USA: Princeton University Press; 2009.
9. Brooker RW, Maestre FT, Callaway RM, Lortie CL, Cavieres LA, Kunstler G, et al. Facilitation in plant communities: the past, the present, and the future. J Ecol. 2008;96:18-34.
10. Caldeira K, Bala G, Cao L. The science of geoengineering. Annu Rev Earth Planet Sci. 2013;41:231-56.
11. Cases I, de Lorenzo V. Genetically modified organisms for the environment: stories of success and failure and what we have learnt from them. Int Microbiol. 2005;8:213-22.
12. Cho I, Blaser M. The human micro biome: at the interface of health and disease. Nat Rev Genet. 2010;13:260-70.
13. Costello E. The application of ecological theory toward an understanding of the human microbiome. Science. 2012;336:1255-62.
14. Crichton M. Jurassic park. New York: Ballantine Books; 2012.
15. de Lorenzo V. Systems biology approaches to bioremediation. Curr Opin Biotechnol. 2008;19:579-89.
16. de Lorenzo V. Recombinant bacteria for environmental release: what went wrong and what we have learnt from it. Clin Microbiol Infect. 2009;15:63-5.
17. Edenhofer O, Pichsf-Madruga R, Sokona Y, editors. IPCC special report on renewable energy sources and climate change mitigation. Cambridge, New York: Cambridge University Press; 2011.
18. Ellis EC, Kaplan JO, Fuller DQ, Vavrusd S, Goldewijke KK, Verburgf PH. Used planet: A global history. Proc Natl Acad Sci USA. 2013;110:7978-85.
19. Esvelt, KM, Smidler AL, Catteruccia, F, Church G. Concerning RNA-guided gene drives for the alteration of wild populations. eLIFE. 2014;3:e03401.
20. Glavovic B, Smith G, editors. Adaptating to climate change: Lessons from natural hazards planning. Dortrech: Springer; 2014.
21. Gregory M. Environmental implications of plastic debris in marine setting. Phil Trans R Soc London B. 2009;364:2013-25.
22. Guan SH, Gris C, Cruveiller S, Pouzet C, Tasse L, Leru A, et al. Experimental evolution of nodule intracellular infection in legume symbionts. ISME J. 2013;7:1367-1377
23. Hillesland KL, Lim S, Flowers JJ, Turkarslan S, Pinel N, Zane GM, et al. Erosion of functional independence early in the evolution of a microbial mutualism. Proc Natl Acad Sci USA. 2014;111:14822-2827.
24. Hom E, Murray A. Niche engineering demonstrates a latent capacity for fungal-algal mutualism. Science. 2014;345:94-8.
25. Hughes TP, Carpenter S, Rockström J, Scheffer M, Walker B. Multiscale regime shifts and planetary boundaries. Trends Ecol Evol. 2013;28:389-95.
26. Huttenhower C, Gevers D, Knight R, Abubucker S, Badger JH, Chinwalla AT, et al. Structure, function and diversity of the healthy human microbiome. Nature. 2012;486:207-14.
27. Jones C, Lawton J, Shachak M. Organisms as ecosystem engineers. Oikos. 1994;69:373-86.
28. Jones C, Lawton J, Shachak M. Positive and negate effects of organism as physical ecosystem engineers. Ecology. 1997;78:1946-57.
29. Jonkersa HM, Thijssena A, Muyzerb G, Copuroglua O, Schlangen E. Application of bacteria as self-healing agent for the development of sustainable concrete. Ecol Eng. 2010;36:230-5.
30. Jordan III W, Gilpin M, Aber J. Restoration ecology: a synthetic approach to ecological research. New York: Cambridge University Press; 1987.
31. Kéfi S, Rietkerk M, Alados CL, Pueyo Y, Papanastasis VP, Elaich A, et al. Spatial vegetation patterns and imminent desertification in mediterranean arid ecosystems. Nature. 2007;449:213-7.
32. Kiers ET, Duhamel M, Beesetty Y, Mensah JA, Franken O, Verbruggen E. Geoengineering the climate: history and prospect. Annu Rev Energy Environ. 2000;25:245-84.
33. Kiers E, Duhamet M, Beesetty Y, et al. Reciprocal rewards stabilize cooperation in the mycrorrizal symbiosis. Science. 2011;333:880-2.
34. Kitching R. Systems ecology: an introduction to ecological modelling. St Lucia, New York and London: University of Queensland Press; 1983.
35. Law KL, Morét-Ferguson S, Maximenko NA, Proskurowski G, Peacock EE, Hafner J, et al. Plastic accumulation in the north Atlantic subtropical gyre. Science. 2010;329:1185-8.
36. Lenton TM, Held H, Kriegler E, Hall JW, Lucht W, Rahmstorf S, et al. Tipping elements in the earths climate system. Proc Natl Acad Sci USA. 2008;105:1786-93.
37. Levin S. The biosphere as a complex adaptive system. Ecosystems. 2002;1:431-6.
38. Mager D, Thomas A. Extracellular polysaccharides from cyanobacterial soil crusts: A review of their role in dryland soil processes. J Arid Environ. 2011;75:91-7.
39. Mandell DJ, Lajoie MJ, Mee MT, Takeuchi R, Kuznetsov G, Norville JE, et al. Biocontainment of genetically modified organisms by synthetic protein design. Nature. 2015;518:55-60.
40. Marchetti M, Capela D, Glew M, Cruveiller S, Chane-Woon-Ming B, Gris C, et al. Experimental evolution of a plant pathogen into a legume symbiont. PLoS Biol. 2010;8:1000280.
41. Marris E. Rambunctious garden. Bloombsbury, New York: Saving Nature in a Post-wild World; 2011.
42. Moe-Behrens, GHG, Davis R, Haynes KA. Preparing synthetic biology for the world. Frontiers in Microbiology. 2013;4(5):doi: 10.3389/fmicb.2013.00005.
43. Müller M, Neugeboren B, Nelson D, Murray A. Genetic drift opposes mutualism during spatial population expansion. Proc Natl Acad Sci USA. 2014;111:1037-42.
44. Newton RJ, McLellan SL, Dila DK, Vineis JH, Morrison HG, Eren AM, et al. Sewage reflects the microbiomes of human populations. MBio. 2015;6:e02574-14.
45. Nica D, Davis J, Kirby L, Zuo G, Roberts DJ. Isolation and characterization of microorganisms involved in the biodeterioration of concrete in sewers. Int Biodeter Biodegr. 2000;46:61-8.
46. Park C, Li X, Liang Jia R, Hur J. Effects of superabsorbent polymer on cyanobacterial biological soil crust formation in laboratory. Arid Land Res Manage. 2015;29:55-71.
47. Pepper J, Rosenfeld S. The emerging medical ecology of the human gut micro biome. Trends Ecol Evol. 2012;27:381-4.
48. Pointing S, Belnap J. Microbial colonization and controls in dryland ecosystems. Nat Rev Microbiol. 2012;10:551-62.
49. Poulter B, Frank D, Ciais P, Myneni RB, Andela N, Bi J, et al. Contribution of semi-arid ecosystems to interannual variability of the global carbon cycle. Nature. 2014;509:600-3.
50. Rao MVS, Reddy VS, Hafsa M, Veena P, Anusha P. Bioengineered concrete: A sustainable self-healing construction material. Res J Eng Sci. 2013;2:45-51.
51. Renda B, Hammerling M, Barrick J. Engineering reduced evolutionary potential for synthetic biology. Mol Biosys. 2014;10:1668-878.
52. Rietkerk M, Van de Koppe J. Regular pattern formation in real ecosystems. Trends Ecol Evol. 2008;23:169-75.
53. Rogelj J, McCollum DL, Reisinger A, Meinshausen M, Riahi K. Probabilistic cost estimates for climate change mitigation. Nature. 2014;493:79-83.
54. Sax DF, Stachowicz JJ, Brown JH, Bruno JF, Dawson MN, Gaines SD, et al. Ecological and evolutionary insights from species invasions. Trends Ecol Evol. 2007;22:465-71.
55. Scanlon T, Caylor K, Levin S, Rodriguez-Iturbe I. Positive feedbacks promote power-law clustering of kalahari vegetation. Nature. 2007;449:209-12.
56. Scheffer M. Critical transitions in nature and society. Princeton: Princeton U Press; 2009.
57. Scheffer M, Carpenter S, Foley JA, Folke C, Walker B. Catastrophic shifts in ecosystems. Nature. 2001;413:591-6.
58. Scheffer M, Westley F, Brock W. Slow response of societies to new problems: causes and costs. Ecosystems. 2003;6:493-502.
59. Schneider S. Geoengineering: could we or should we make it work? Phil Trans R Soc. 2008;366:3843-62.
60. Seastedt T, Hobbs R, Suding K. Management of novel ecosystems: are novel approaches required? Front Ecol Environ. 2008;6:547-53.
61. Shou W, Ram S, Vilar J. Synthetic cooperation in engineered yeast populations. Proc Natl Acad Sci USA. 2007;104:1877-82.
62. Simberloff D, Rejmánek M, editors. Encyclopedia of biological invasions. Berkeley CA: University of California Press; 2011.
63. Solé R. Scaling laws in the drier. Nature. 2007;449:151-3.
64. Solé R. Bioengineering the biosphere? Ecol Complex. 2015;22:40-9.
65. Solé RV, Bascompte J. Self-organization in complex ecosystems. 41 William Street, Princeton, New Jersey, USA: Princeton University Press; 2006.
66. Suding K, Gross K, Houseman G. Alternative states and positive feedbacks in restoration ecology. Trends Ecol Evol. 2004;19:46-53.
67. Vaughan N, Lenton T. A review of climate geoengineering proposals. Clim Change. 2011;109:745-90.
68. Watt KE. Systems analysis in ecology. New York and London: Academic; 1966.
69. Weber W, Fussenegger M. Emerging biomedical applications of synthetic biology. Nat Rev Genet. 2012;13:21-35.
70. Zettler E, Mincer T, Amaral-Zettler L. Life in the plastisphere: Microbial communities on plastic marine debris. Environ Sci Technol. 2013;47:7127-46.
71. BacillaFilla: Fixing Cracks in Concrete. http://2010.igem.org/Team:Newcastlelinks.html.