Bioengineering microbial communities: Their potential to help, hinder and disgust

References

• Madsen EL. Microorganisms and their roles in fundamental biogeochemical cycles. Curr Opinion Biotechnol 2011; 22:456-64; PMID:21333523; http://dx.doi.org/10.1016/j.copbio.2011.01.008.
   PubMed Web of Science ®Google Scholar
• Curtis TP, Sloan WT, Scannell JW. Estimating prokaryotic diversity and its limits. Proc Natl Acad Sci U S A 2002; 99:10494-9; PMID:12097644; http://dx.doi.org/10.1073/pnas.142680199.
   PubMed Web of Science ®Google Scholar
• Grosskopf T, Soyer OS. Synthetic microbial communities. Curr Opin Microbiol 2014; 18:72-7; PMID:24632350; http://dx.doi.org/10.1016/j.mib.2014.02.002.
   PubMed Web of Science ®Google Scholar
• Dworkin M. Sergei Winogradsky: a founder of modern microbiology and the first microbial ecologist. FEMS Microbiol Rev 2012; 36:364-79; PMID:22092289; http://dx.doi.org/10.1111/j.1574-6976.2011.00299.x.
   PubMed Web of Science ®Google Scholar
• Guhathakurta H, Biswas R, Dey P, Mahapatra PG, Mondal B. Effect of organic forms of phosphorus and variable concentrations of sulfide on the metabolic generation of soluble-reactive phosphate by sulfur chemolithoautotrophs: a laboratory study. ISME J 2007; 1:545-50; PMID:18043655; http://dx.doi.org/10.1038/ismej.2007.61.
   PubMed Web of Science ®Google Scholar
• Loss RA, Fontes ML, Reginatto V, and Antonio, RV. Biohydrogen production by a mixed photoheterotrophic culture obtained from a Winogradsky column prepared from the sediment of a southern Brazilian lagoon. Renewable Energy 2013; 50:648-54; http://dx.doi.org/10.1016/j.renene.2012.07.011
   Web of Science ®Google Scholar
• Rundell EA, Banta LM, Ward DV, Watts CD, Birren B, Esteban DJ. 16S rRNA gene survey of microbial communities in winogradsky columns. Plos One 2014; 9:e104134; http://dx.doi.org/10.1371/journal.pone.0104134.
   Google Scholar
• Anderson RT, Vrionis HA, Ortiz-Bernad I, Resch CT, Long PE, Dayvault R, Karp K, Marutzky S, Metzler DR, Peacock A, et al. Stimulating the in situ activity of Geobacter species to remove uranium from the groundwater of a uranium-contaminated aquifer. Appl Environ Microbiol 2003; 69:5884-91; PMID:14532040; http://dx.doi.org/10.1128/AEM.69.10.5884-5891.2003.
   PubMed Web of Science ®Google Scholar
• Stams AJM, Plugge CM. Electron transfer in syntrophic communities of anaerobic bacteria and archaea. Nat Rev Microbiol 2009; 7:568-77; PMID:19609258; http://dx.doi.org/10.1038/nrmicro2166.
   PubMed Web of Science ®Google Scholar
• Summers ZM, Fogarty HE, Leang C, Franks AE, Malvankar NS, Lovley DR. Direct exchange of electrons within aggregates of an evolved syntrophic coculture of anaerobic bacteria. Science 2010; 330:1413-5; PMID:21127257; http://dx.doi.org/10.1126/science.1196526.
   PubMed Web of Science ®Google Scholar
• Morita M, Malvankar NS, Franks AE, Summers ZM, Giloteaux L, Rotaru AE, Rotaru C, Lovley DR. Potential for direct interspecies electron transfer in methanogenic wastewater digester aggregates. Mbio 2011; 2:e00159-11; PMID:21862629.
   PubMed Web of Science ®Google Scholar
• Zhao Z, Zhang Y, Holmes DE, Dang Y, Woodard TL, Nevin KP, Lovley DR. Potential enhancement of direct interspecies electron transfer for syntrophic metabolism of propionate and butyrate with biochar in up-flow anaerobic sludge blanket reactors. Bioresour Technol 2016; 209:148-56; PMID:26967338; http://dx.doi.org/10.1016/j.biortech.2016.03.005.
   PubMed Web of Science ®Google Scholar
• Embree M, Liu JK, Al-Bassam MM, Zengler K. Networks of energetic and metabolic interactions define dynamics in microbial communities. Proc Natl Acad Sci U S A 2015; 112:15450-5; PMID:26621749; http://dx.doi.org/10.1073/pnas.1506034112.
   PubMed Web of Science ®Google Scholar
• Curtis TP, Sloan WT. Towards the design of diversity: stochastic models for community assembly in wastewater treatment plants. Water Sci Technol 2006; 54:227-36; PMID:16898156; http://dx.doi.org/10.2166/wst.2006.391.
   PubMed Web of Science ®Google Scholar
• Ofiteru ID, Lunn M, Curtis TP, Wells GF, Criddle CS, Francis CA, Sloan WT. Combined niche and neutral effects in a microbial wastewater treatment community. Proc Natl Acad Sci U S A 2010; 107:15345-50; PMID:20705897; http://dx.doi.org/10.1073/pnas.1000604107.
   PubMed Web of Science ®Google Scholar
• Ward AJ, Hobbs PJ, Holliman PJ, Jones DL. Optimisation of the anaerobic digestion of agricultural resources. Bioresour Technol 2008; 99:7928-40; PMID:18406612; http://dx.doi.org/10.1016/j.biortech.2008.02.044.
   PubMed Web of Science ®Google Scholar
• Mao CL, Feng YZ, Wang XJ, Ren, G. Review on research achievements of biogas from anaerobic digestion. Renewable Sustainable Energy Rev 2015; 45:540-55; http://dx.doi.org/10.1016/j.rser.2015.02.032.
   Web of Science ®Google Scholar
• Aracic S, Manna S, Petrovski S, Wiltshire JL, Mann G, Franks AE. Innovative biological approaches for monitoring and improving water quality. Front Microbiol 2015; 6:826; PMID:26322034; http://dx.doi.org/10.3389/fmicb.2015.00826.
   PubMed Web of Science ®Google Scholar
• Semenec L, Franks AE. Delving through electrogenic biofilms: from anodes to cathodes to microbes. AIMS Bioengineering 2015; 2:222-48; http://dx.doi.org/10.3934/bioeng.2015.3.222.
   Google Scholar
• Rosenbaum MA, Franks AE. Microbial catalysis in bioelectrochemical technologies: status quo, challenges and perspectives. Appl Microbiol Biotechnol 2014; 98:509-18; PMID:24270896; http://dx.doi.org/10.1007/s00253-013-5396-6.
   PubMed Web of Science ®Google Scholar
• De Vrieze J, Gildemyn S, Arends JBA, Vanwonterghem I, Verbeken K, Boon N, Verstraete W, Tyson GW, Hennebel T, Rabaey K. Biomass retention on electrodes rather than electrical current enhances stability in anaerobic digestion. Water Res 2014; 54:211-21; PMID:24576697; http://dx.doi.org/10.1016/j.watres.2014.01.044.
   PubMed Web of Science ®Google Scholar
• Sabra W, Dietz D, Tjahjasari D, Zeng, AP. Biosystems analysis and engineering of microbial consortia for industrial biotechnology. Engineering Life Sci 2010; 10:407-21; http://dx.doi.org/10.1002/elsc.201000111.
   Web of Science ®Google Scholar
• Williams DC, Van Frank RM, Muth WL, Burnett JP. Cytoplasmic inclusion bodies in Escherichia coli producing biosynthetic human insulin proteins. Science 1982; 215:687-9; PMID:7036343; http://dx.doi.org/10.1126/science.7036343.
   PubMed Web of Science ®Google Scholar
• Leonard E, Nielsen D, Solomon K, Prather KJ. Engineering microbes with synthetic biology frameworks. Trends Biotechnol 2008; 26:674-81; PMID:18977048; http://dx.doi.org/10.1016/j.tibtech.2008.08.003.
   PubMed Web of Science ®Google Scholar
• Zhang C, Tsoi R, You L. Addressing biological uncertainties in engineering gene circuits. Integr Biol (Camb) 2015; 8(4):456-64.
   PubMed Web of Science ®Google Scholar
• Gibson DG, Glass JI, Lartigue C, Noskov VN, Chuang RY, Algire MA, Benders GA, Montague MG, Ma L, Moodie MM, et al. Creation of a bacterial cell controlled by a chemically synthesized genome. Science 2010; 329:52-6; PMID:20488990; http://dx.doi.org/10.1126/science.1190719.
   PubMed Web of Science ®Google Scholar
• Nielsen AA, Der BS, Shin J, Vaidyanathan P, Paralanov V, Strychalski EA, Ross D, Densmore D, Voigt CA. Genetic circuit design automation. Science 2016; 352:aac7341.
   PubMed Web of Science ®Google Scholar
• Smanski MJ, Zhou H, Claesen J, Shen B, Fischbach MA, Voigt CA. Synthetic biology to access and expand nature's chemical diversity. Nat Rev Microbiol 2016; 14:135-49; PMID:26876034; http://dx.doi.org/10.1038/nrmicro.2015.24.
   PubMed Web of Science ®Google Scholar
• Medema MH, Kottmann R, Yilmaz P, Cummings M, Biggins JB, Blin K, de Bruijn I, Chooi YH, Claesen J, Coates RC, et al. Minimum information about a biosynthetic gene cluster. Nat Chem Biol 2015; 11:625-31; PMID:26284661; http://dx.doi.org/10.1038/nchembio.1890.
   PubMed Web of Science ®Google Scholar
• Temme K, Zhao D, Voigt CA. Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca. Proc Natl Acad Sci U S A 2012; 109:7085-90; PMID:22509035; http://dx.doi.org/10.1073/pnas.1120788109.
   PubMed Web of Science ®Google Scholar
• Freestone TS, Zhao H. Combinatorial pathway engineering for optimized production of the anti-malarial FR900098. Biotechnol Bio Eng 2016; 113:384-92; PMID:26245694; http://dx.doi.org/10.1002/bit.25719.
   PubMed Web of Science ®Google Scholar
• Selle K, Barrangou R. Harnessing CRISPR-Cas systems for bacterial genome editing. Trends Microbiol 2015; 23:225-32; PMID:25698413; http://dx.doi.org/10.1016/j.tim.2015.01.008.
   PubMed Web of Science ®Google Scholar
• Dibden J, Gibbs D, Cocklin C. Framing GM crops as a food security solution. J Rural Studies 2013; 29:59-70; http://dx.doi.org/10.1016/j.jrurstud.2011.11.001.
   Web of Science ®Google Scholar
• Hudson J, Caplanova A, Novak M. Public attitudes to GM foods. The balancing of risks and gains. Appetite 2015; 92:303-13; PMID:26026248; http://dx.doi.org/10.1016/j.appet.2015.05.031.
   PubMed Web of Science ®Google Scholar
• Rozin P, Fischler C, Shields-Argelès C. European and American perspectives on the meaning of natural. Appetite 2012; 59:448-55; PMID:22698976; http://dx.doi.org/10.1016/j.appet.2012.06.001.
   PubMed Web of Science ®Google Scholar
• Rozin P. The meaning of “natural” process more important than content. Psychological Sci 2005; 16:652-8; PMID:16102069; http://dx.doi.org/10.1111/j.1467-9280.2005.01589.x.
   PubMed Web of Science ®Google Scholar
• Rozin P, Haidt J. The domains of disgust and their origins: contrasting biological and cultural evolutionary accounts. Trends Cognitive Sci 2013; 17:367-8; PMID:23773551; http://dx.doi.org/10.1016/j.tics.2013.06.001.
   PubMed Web of Science ®Google Scholar
• Slovic P. Perception of risk. Science 1987; 236:280-5; PMID:3563507; http://dx.doi.org/10.1126/science.3563507.
   PubMed Web of Science ®Google Scholar
• Covello VT, von Winterfeldt D, Slovic P. Communicating scientific information about health and environmental risks: Problems and opportunities from a social and behavioral perspective. Uncertainty in risk assessment, risk management, and decision making: Springer. 1987:pp. 221-39.
   Google Scholar
• Rozin P, Spranca M, Krieger Z, Neuhaus R, Surillo D, Swerdlin A, Wood K. Preference for natural: instrumental and ideational/moral motivations, and the contrast between foods and medicines. Appetite 2004; 43:147-54; PMID:15458801; http://dx.doi.org/10.1016/j.appet.2004.03.005.
   PubMed Web of Science ®Google Scholar
• Myskja BK. The moral difference between intragenic and transgenic modification of plants. J Agricultural Environmental Ethics 2006; 19:225-38; PMID:17061380; http://dx.doi.org/10.1007/s10806-005-6164-0.
   PubMed Web of Science ®Google Scholar
• Biel A, Nilsson A. Religious values and environmental concern: harmony and detachment*. Social Science Quarterly 2005; 86:178-91; http://dx.doi.org/10.1111/j.0038-4941.2005.00297.x.
   Web of Science ®Google Scholar
• Savadori L, Savio S, Nicotra E, Rumiati R, Finucane M, Slovic P. Expert and public perception of risk from biotechnology. Risk Analysis 2004; 24:1289-99; PMID:15563295; http://dx.doi.org/10.1111/j.0272-4332.2004.00526.x.
   PubMed Web of Science ®Google Scholar
• Siegrist M, Cvetkovich G. Perception of hazards: The role of social trust and knowledge. Risk analysis 2000; 20:713-20; PMID:11110217; http://dx.doi.org/10.1111/0272-4332.205064.
   PubMed Web of Science ®Google Scholar
• Marques MD, Critchley CR, Walshe J. Attitudes to genetically modified food over time: How trust in organizations and the media cycle predict support. Public Understanding Sci 2015; 24:601-18; PMID:25063421; http://dx.doi.org/10.1177/0963662514542372.
   PubMed Web of Science ®Google Scholar
• Barnett J, Cooper H, Senior V. Belief in public efficacy, trust, and attitudes toward modern genetic science. Risk Anal 2007; 27:921-33; PMID:17958501; http://dx.doi.org/10.1111/j.1539-6924.2007.00932.x.
   PubMed Web of Science ®Google Scholar
• Lang JT, Hallman WK. Who does the public trust? The case of genetically modified food in the United States. Risk Analysis 2005; 25:1241-52; PMID:16297228; http://dx.doi.org/10.1111/j.1539-6924.2005.00668.x.
   PubMed Web of Science ®Google Scholar
• Starr C. Social benefit versus technological risk. Readings in Risk Science 1969; 165(3899):1232-8; 183-194.
   Google Scholar
• Zepeda L, Douthitt R, You SY. Consumer risk perceptions toward agricultural biotechnology, self‐protection, and food demand: the case of milk in the United States. Risk Analysis 2003; 23:973-84; PMID:12969412; http://dx.doi.org/10.1111/1539-6924.00374.
   PubMed Web of Science ®Google Scholar