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Engineering Synthetic Microbial Communities for Biomethane Production

Publications

Linkage of community composition and function over short response time in anaerobic digestion systems with food fermentation wastewater

Cai, Weiwei, Zhao, Mingxing, Kong, Jianyao, Riggio, Silvio, Finnigan, Tim, Stuckey, David & Guo, Miao

iScience (2021) 24: 102958. LinkLink opens in a new window

Sewage treatment at 4 °C in anaerobic upflow reactors with and without a membrane – performance, function and microbial diversity

Petropoulos, Evangelos, Shamurad, Burhan, Tabraiz, Shamas, Yu, Yongjie, Davenport, Russell, Curtis, Thomas P. & Dolfing, Jan.

Environmental Science: Water Research & Technology (2021) 7:156-171. LinkLink opens in a new window

Thermodynamic modelling of synthetic communities predicts minimum free energy requirements for sulfate reduction and methanogenesis

Hadrien Delattre, Jing Chen, Matthew Wade, Orkun S Soyer

Journal of the Royal Society Interface (2020) 17:20200053. LinkLink opens in a new window

Biogas productivity of anaerobic digestion process is governed by a core bacterial microbiota

Yu Tao, Mustafa Evren Ersahin, Dara S.M. Ghasimi, Hale Ozgun, Haoyu Wang, Xuedong Zhang, Miao Guo, Yunfeng Yang, David C. Stuckey, Jules B. van Lier,

Chemical Engineering Journal. 380:122425 (2020) LinkLink opens in a new window

High rate domestic wastewater treatment at 15 °C using anaerobic reactors inoculated with cold-adapted sediments/soils – shaping robust methanogenic communities

Petropoulos, Evangelos, Yu, Yongjie, Tabraiz, Shamas, Yakubu, Aminu, Curtis, Thomas P. & Dolfing, Jan

Environmental Science: Water Research & Technology (2019) 5:70-82. LinkLink opens in a new window

Growth Characteristics and Thermodynamics of Syntrophic Acetate Oxidizers
Maria Westerholm, Jan Dolfing, Anna Schnürer.
Environ. Sci. Technol. 53:5512-5520 (2019) LinkLink opens in a new window

Increasing sulfate levels show a differential impact on synthetic communities comprising different methanogens and asulfate reducer
Chen J, Wade MJ, Dolfing J,Soyer OS.
J. R. Soc. Interface 16:20190129 (2019) LinkLink opens in a new window
The effect of cheats on siderophore diversity in Pseudomonas aeruginosa
Peter Stilwell, Chris Lowe, Angus Buckling
J. Evol. Biol., 31: 1330-1339 (2018) LinkLink opens in a new window
Biodiversity-function relationships in methanogenic communities
Sierocinski P, Bayer F, Yvon-Durocher G, Burdon M, Grosskopf T, Alston M, Swarbreck D, Hobbs PJ, Soyer OS, and Buckling A.
Molecular Ecology 27:4641-4651 (2018) LinkLink opens in a new window
Impact of spatial organization on a novel auxotrophic interaction among soil microbes
Jiang X, Zerfass C, Feng S, Eichmann R, Asally M, Schafer P, Soyer OS.
ISME Journal 12:1443-1456 (2018) LinkLink opens in a new window
Ecological selection of siderophore-producing microbial taxa in response to heavy metal contamination
Hesse E, O'Brien S, Tromas N, Bayer F, Lujan AM, van Veen EM, Hodgson DJ and Buckling A.
Ecology Letters 21:117-127 (2018) LinkLink opens in a new window
Engineering microbial communities using thermodynamic principles and electrical interfaces
Zerfass C, Chen J and Soyer OS.
Current Opinion in Biotechnology 50:121-127 (2018) LinkLink opens in a new window
A Single Community Dominates Structure and Function of a Mixture of Multiple Methanogenic Communities
Sierocinski P, Milferstedt K, Bayer F, Grosskopf T, Alston M, Bastkowski S, Swarbreck D, Hobbs PJ, Soyer OS, Hamelin J and Buckling A.
Current Biology 27(21):3390-3395 (2017) LinkLink opens in a new window
Dynamics of two methanogenic microbiomes incubated in polycyclic aromatic hydrocarbons, naphthenic acids, and oil field produced water
Oko B, Tao Y and Stuckey DC.
Biotechnology for Biofuels 10:123 (2017) LinkLink opens in a new window
MI-Sim: A MATLAB package for the numerical analysis of microbial ecological interactions
Wade MJ, Oakley J, Harbisher S, Parker NG, Dolfing J.
PLoS ONE 12(3): e0173249 (2017) LinkLink opens in a new window
Predicting the dynamics and heterogeneity of genomic DNA content within bacterial populations across variable growth regimes
du Lac M, Scarpelli AH, Bates DG, and Leonard JN
ACS Synthetic biology 6(7):1131-1139 (2017) Link Link opens in a new window
Generalised approach to modelling a three-tiered microbial food-web
Sari T. and Wade M.
Mathematical Biosciences 291:21-37 (2017) LinkLink opens in a new window
Local adaptation of a bacterium is as important as its presence in structuring a natural microbial community
Gomez P, Paterson S, De Meester L, Liu X, Lenzi L, Sharma MD, McElroy K and Buckling A.
Nature Communications 7:12453 (2016) LinkLink opens in a new window
Metabolic modelling in a dynamic evolutionary framework predicts adaptive diversification of bacteria in a long-term evolution experiment
Grosskopf T, Consuegra J, Gaffe J, Willison JC, Lenski RE, Soyer OS, and Schneider D.
BMC Evolutionary Biology 16:163 (2016) LinkLink opens in a new window
A stable genetic polymorphism underpinning microbial syntrophy
Grosskopf T, Simone Z, Alston M, Folkes L, Swarbreck D, Soyer OS.
ISME Journal 10:2844-2853 (2016) LinkLink opens in a new window
Microbial diversity arising from thermodynamic constraints
Grosskopf T. and Soyer OS.
ISME Journal 10:2725-2733 (2016) LinkLink opens in a new window
Challenges in microbial ecology: building predictive understanding of community function and dynamics.
Widder S, Curtis TP, Grosskopf T, et. al and Soyer OS.
ISME Journal 10:2557-2568 (2016) LinkLink opens in a new window
Perspectives in mathematical modelling for microbial ecology
M.J. Wade, J. Harmand, B. Benyahia, T. Bouchez, S. Chaillou, B. Cloez, J.-J. Godon, B. Moussa Boudjemaa, A. Rapaport, T. Sari, R. Arditi, C. Lobry.
Ecological Modelling 321, 64-74 (2016) LinkLink opens in a new window
Emergent behaviour in a chlorophenol-mineralising three-tiered microbial `food web'
M. J. Wade, R. W. Pattinson, N. G. Parker and J. Dolfing.
Journal of Theoretical Biology 389:171-186 (2016) LinkLink opens in a new window
Draft Genome Sequences of Achromobacter piechaudii GCS2, Agrobacterium sp. Strain SUL3, Microbacterium sp. Strain GCS4, Shinella sp. Strain GWS1, and Shinella sp. Strain SUS2 Isolated from Consortium with the Hydrocarbon-Producing Alga Botryococcus braunii
K.J. Jones, K. Moore, C. Sambles, J. Love, D.J. Studholme, S.J. Aves.
Genome Announcements 4(1):e01527-15 (2016) LinkLink opens in a new window
Microbial population dynamics during long-term sludge adaptation of thermophilic and mesophilic sequencing batch digesters treating sewage fine sieved fraction at varying organic loading rates
D.S.M. Ghasimi1, Y. Tao, M. de Kreuk1, M. H. Zandvoort and J. B. van Lier.
Biotechnol Biofuels 8:171 (2015) Link
The Gibbs free energy of formation of halogenated benzenes, benzoates and phenols and their potential role as electron acceptors in anaerobic environments
Jan Dolfing and Igor Novak.
Biodegradation 26(1):15-27 (2015) LinkLink opens in a new window
Some (bacilli) like it hot: genomics of Geobacillus species
David Studholme
Microbial Biotechnology 8(1):40-48 (2015) LinkLink opens in a new window
Syntrophy in Microbial Fuel Cells
Jan Dolfing.
The ISME Journal 8(1):4-5 (2014) LinkLink opens in a new window
Synthetic Microbial Communities
Tobias Grosskopf and Orkun Soyer.
Current Opinion in Microbiology 18:72-77 (2014) LinkLink opens in a new window
The interplay between microevolution and community structure in microbial populations
Siobhan O'Brien, David J Hodgson and Angus Buckling
Current Opinion in Biotechnology 24:821-825 (2013) LinkLink opens in a new window
Syntrophic Propionate Oxidation via Butyrate: a Novel Window of Opportunity under Methanogenic Conditions
Dolfing, J.
Applied and Environmental Microbiology 79(14):4515-4516 (2013) LinkLink opens in a new window