Publications

Find me on Google Scholar.

Silica ecosystem for synergistic biotransformation

Baris R. Mutlu, Jonathan K. Sakkos, Sujin Yeom, Lawrence P. Wackett, and Alptekin Aksan (2016)

Synergistical bacterial species can perform more varied and complex transformations of chemical substances than either species alone, but this is rarely used commercially because of technical difficulties in maintaining mixed cultures. Typical problems with mixed cultures on scale are unrestrained growth of one bacterium, which leads to suboptimal population ratios, and lack of control over bacterial spatial distribution, which leads to inefficient substrate transport. To address these issues, we designed and produced a synthetic ecosystem by co-encapsulation in a silica gel matrix, which enabled precise control of the microbial populations and their microenvironment. As a case study, two greatly different microorganisms: Pseudomonas sp. NCIB 9816 and Synechococcus elongatus PCC 7942 were encapsulated. NCIB 9816 can aerobically biotransform over 100 aromatic hydrocarbons, a feat useful for synthesis of higher value commodity chemicals or environmental remediation. In our system, NCIB 9816 was used for biotransformation of naphthalene (a model substrate) into CO2 and the cyanobacterium PCC 7942 was used to provide the necessary oxygen for the biotransformation reactions via photosynthesis. A mathematical model was constructed to determine the critical cell density parameter to maximize oxygen production, and was then used to maximize the biotransformation rate of the system. DOI: 10.1038/srep27404


Reddit AMA (2016)

Jonathan K. Sakkos, r/Science , Science AMA Series: I'm Jonathan Sakkos, a graduate student in mechanical engineering at the University of Minnesota. I trap bacteria within porous materials for cleaning pollutants from water. AMA! DOI: 10.15200/winn.145830.01028


Engineering of a silica encapsulation platform for hydrocarbon degradation using Pseudomonas sp. NCIB 9816-4

Jonathan K. Sakkos, Daniel P. Kieffer, Baris R. Mutlu, Lawrence P. Wackett, and Alptekin Aksan (2015)

Industrial application of encapsulated bacteria for biodegradation of hydrocarbons in water requires mechanically stable materials. A silica gel encapsulation method was optimized for Pseudomonas sp. NCIB 9816-4, a bacterium that degrades more than 100 aromatic hydrocarbons. The design process focused on three aspects: (i) mechanical property enhancement; (ii) gel cytocompatibility; and (iii) reduction of the diffusion barrier in the gel. Mechanical testing indicated that the compressive strength at failure (σf) and elastic modulus (E) changed linearly with the amount of silicon alkoxide used in the gel composition. Measurement of naphthalene biodegradation by encapsulated cells indicated that the gel maintained cytocompatibility at lower levels of alkoxide. However, significant loss in activity was observed due to methanol formation during hydrolysis at high alkoxide concentrations, as measured by FTIR spectroscopy. The silica gel with the highest amount of alkoxide (without toxicity from methanol) had a biodegradation rate of 285 ± 42 nmol/L-s, σf = 652 ± 88 kPa, and E = 15.8 ± 2.0 MPa. Biodegradation was sustained for 1 month before it dropped below 20% of the initial rate. In order to improve the diffusion through the gel, polyvinyl alcohol (PVA) was used as a porogen and resulted in a 48 ± 19% enhancement in biodegradation, but it impacted the mechanical properties negatively. This is the first report studying how the silica composition affects biodegradation of naphthalene by Pseudomonas sp. NCIB 9816-4 and establishes a foundation for future studies of aromatic hydrocarbon biodegradation for industrial application. Biotechnol. Bioeng. 2016;113: 513–521. © 2015 Wiley Periodicals, Inc. DOI: 10.1002/bit.25821


Patents

Adi Radian, Baris R. Mutlu, Jonathan K. Sakkos, Alptekin Aksan, Lawrence P. Wackett, “Compositions Including A Silica Matrix And Biomaterial, Methods Regarding The Same And Uses Thereof”, U.S. Patent Application Number 14/883,053