Custom fabrication of biomass containment devices using 3-D printing enables bacterial growth analyses with complex insoluble substrates

Nelson, Cassandra E.; Beri, Nina R.; Gardner, Jeffrey G.

doi:10.1016/j.mimet.2016.09.013

Title: Custom fabrication of biomass containment devices using 3-D printing enables bacterial growth analyses with complex insoluble substrates

Journal Article · Wed Sep 21 00:00:00 EDT 2016 · Journal of Microbiological Methods

DOI:https://doi.org/10.1016/j.mimet.2016.09.013· OSTI ID:1326371

Nelson, Cassandra E. ^[1]; Beri, Nina R. ^[1];

^[1]

Univ. of Maryland Baltimore County (UMBC), Baltimore, MD (United States)

Physiological studies of recalcitrant polysaccharide degradation are challenging for several reasons, one of which is the difficulty in obtaining a reproducibly accurate real-time measurement of bacterial growth using insoluble substrates. Current methods suffer from several problems including (i) high background noise due to the insoluble material interspersed with cells, (ii) high consumable and reagent cost and (iii) significant time delay between sampling and data acquisition. A customizable substrate and cell separation device would provide an option to study bacterial growth using optical density measurements. To test this hypothesis we used 3-D printing to create biomass containment devices that allow interaction between insoluble substrates and microbial cells but do not interfere with spectrophotometer measurements. Evaluation of materials available for 3-D printing indicated that UV-cured acrylic plastic was the best material, being superior to nylon or stainless steel when examined for heat tolerance, reactivity, and ability to be sterilized. Cost analysis of the 3-D printed devices indicated they are a competitive way to quantitate bacterial growth compared to viable cell counting or protein measurements, and experimental conditions were scalable over a 100-fold range. The presence of the devices did not alter growth phenotypes when using either soluble substrates or insoluble substrates. Furthermore, we applied biomass containment to characterize growth of Cellvibrio japonicus on authentic lignocellulose (non-pretreated corn stover), and found physiological evidence that xylan is a significant nutritional source despite an abundance of cellulose present.

View Accepted Manuscript (DOE)

View Accepted Manuscript (Publisher)

Cite

Export

Save

Research Organization:: Univ. of Maryland Baltimore County (UMBC), Baltimore, MD (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: SC0014183

OSTI ID:: 1326371

Alternate ID(s):: OSTI ID: 1359567

Journal Information:: Journal of Microbiological Methods, Vol. 130, Issue C; ISSN 0167-7012

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

Citation Metrics:

Cited by: 6 works

Citation information provided by
Web of Science

References (36)

Direct Image-Based Enumeration of Clostridium phytofermentans Cells on Insoluble Plant Biomass Growth Substrates Alvelo-Maurosa, Jesús G.; Lee, Scott J.; Hazen, Samuel P. Applied and Environmental Microbiology, Vol. 82, Issue 3 https://doi.org/10.1128/AEM.03119-15	journal	February 2016
Open Labware: 3-D Printing Your Own Lab Equipment Baden, Tom; Chagas, Andre Maia; Gage, Greg PLOS Biology, Vol. 13, Issue 3 https://doi.org/10.1371/journal.pbio.1002086	journal	March 2015
Silica Gel Plates for Culture of Marine and Nonmarine Organisms Bazylinski, Dennis A.; Rosenberg, F. A. Applied and Environmental Microbiology, Vol. 39, Issue 4 https://doi.org/10.1128/AEM.39.4.934-934.1980	journal	April 1980
Bacterial chitin degradation—mechanisms and ecophysiological strategies Beier, Sara; Bertilsson, Stefan Frontiers in Microbiology, Vol. 4 https://doi.org/10.3389/fmicb.2013.00149	journal	January 2013
Studies on Lysogenesis i. Bertani, G. Journal of Bacteriology, Vol. 62, Issue 3 https://doi.org/10.1128/JB.62.3.293-300.1951	journal	January 1951
Lysogeny at Mid-Twentieth Century: P1, P2, and Other Experimental Systems Bertani, G. Journal of Bacteriology, Vol. 186, Issue 3 https://doi.org/10.1128/JB.186.3.595-600.2004	journal	January 2004
A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding Bradford, Marion M. Analytical Biochemistry, Vol. 72, Issue 1-2 https://doi.org/10.1016/0003-2697(76)90527-3	journal	May 1976
The Structure and Function of an Arabinan-specific α-1,2-Arabinofuranosidase Identified from Screening the Activities of Bacterial GH43 Glycoside Hydrolases Cartmell, Alan; McKee, Lauren S.; Peña, Maria J. Journal of Biological Chemistry, Vol. 286, Issue 17 https://doi.org/10.1074/jbc.M110.215962	journal	February 2011
Recent advances in 3D printing of biomaterials Chia, Helena N.; Wu, Benjamin M. Journal of Biological Engineering, Vol. 9, Issue 1 https://doi.org/10.1186/s13036-015-0001-4	journal	March 2015
3D printing of microscopic bacterial communities Connell, J. L.; Ritschdorff, E. T.; Whiteley, M. Proceedings of the National Academy of Sciences, Vol. 110, Issue 46 https://doi.org/10.1073/pnas.1309729110	journal	October 2013
Making sense of 3-D printing: Creating a map of additive manufacturing products and services Conner, Brett P.; Manogharan, Guha P.; Martof, Ashley N. Additive Manufacturing, Vol. 1-4 https://doi.org/10.1016/j.addma.2014.08.005	journal	October 2014
Insights into Plant Cell Wall Degradation from the Genome Sequence of the Soil Bacterium Cellvibrio japonicus DeBoy, R. T.; Mongodin, E. F.; Fouts, D. E. Journal of Bacteriology, Vol. 190, Issue 15, p. 5455-5463 https://doi.org/10.1128/JB.01701-07	journal	June 2008
Primary Production of the Biosphere: Integrating Terrestrial and Oceanic Components Field, C. B. Science, Vol. 281, Issue 5374 https://doi.org/10.1126/science.281.5374.237	journal	July 1998
Polysaccharide degradation systems of the saprophytic bacterium Cellvibrio japonicus Gardner, Jeffrey G. World Journal of Microbiology and Biotechnology, Vol. 32, Issue 7 https://doi.org/10.1007/s11274-016-2068-6	journal	June 2016
Requirement of the Type II Secretion System for Utilization of Cellulosic Substrates by Cellvibrio japonicus Gardner, J. G.; Keating, D. H. Applied and Environmental Microbiology, Vol. 76, Issue 15 https://doi.org/10.1128/AEM.00454-10	journal	June 2010
A high-throughput solid phase screening method for identification of lignocellulose-degrading bacteria from environmental isolates Gardner, Jeffrey G.; Zeitler, Laura A.; Wigstrom, Wendy Jo S. Biotechnology Letters, Vol. 34, Issue 1 https://doi.org/10.1007/s10529-011-0742-1	journal	September 2011
Systems biology defines the biological significance of redox‐active proteins during cellulose degradation in an aerobic bacterium Gardner, Jeffrey G.; Crouch, Lucy; Labourel, Aurore Molecular Microbiology, Vol. 94, Issue 5 https://doi.org/10.1111/mmi.12821	journal	October 2014
Pseudomonas fluorescens subsp. cellulosa : an alternative model for bacterial cellulase Hazlewood, G. P.; Laurie, J. I.; Ferreira, L. M. A. Journal of Applied Bacteriology, Vol. 72, Issue 3 https://doi.org/10.1111/j.1365-2672.1992.tb01830.x	journal	March 1992
3D printed microfluidics for biological applications Ho, Chee Meng Benjamin; Ng, Sum Huan; Li, King Ho Holden Lab on a Chip, Vol. 15, Issue 18 https://doi.org/10.1039/C5LC00685F	journal	January 2015
Chitinase 3-like-1 enhances bacterial adhesion to colonic epithelial cells through the interaction with bacterial chitin-binding protein Kawada, Mayumi; Chen, Chun-Chuan; Arihiro, Atsuko Laboratory Investigation, Vol. 88, Issue 8 https://doi.org/10.1038/labinvest.2008.47	journal	May 2008
Configurable 3D-Printed millifluidic and microfluidic ‘lab on a chip’ reactionware devices Kitson, Philip J.; Rosnes, Mali H.; Sans, Victor Lab on a Chip, Vol. 12, Issue 18 https://doi.org/10.1039/c2lc40761b	journal	January 2012
Cellulose Degradation in Anaerobic Environments Leschine, S. B. Annual Review of Microbiology, Vol. 49, Issue 1 https://doi.org/10.1146/annurev.mi.49.100195.002151	journal	October 1995
Microbial Cellulose Utilization: Fundamentals and Biotechnology Lynd, L. R.; Weimer, P. J.; van Zyl, W. H. Microbiology and Molecular Biology Reviews, Vol. 66, Issue 3, p. 506-577 https://doi.org/10.1128/MMBR.66.3.506-577.2002	journal	September 2002
Genome analyses highlight the different biological roles of cellulases Medie, Felix Mba; Davies, Gideon J.; Drancourt, Michel Nature Reviews Microbiology, Vol. 10, Issue 3 https://doi.org/10.1038/nrmicro2729	journal	January 2012
Do Rumen Bacteroidetes Utilize an Alternative Mechanism for Cellulose Degradation? Naas, A. E.; Mackenzie, A. K.; Mravec, J. mBio, Vol. 5, Issue 4 https://doi.org/10.1128/mBio.01401-14	journal	August 2014
In-Frame Deletions Allow Functional Characterization of Complex Cellulose Degradation Phenotypes in Cellvibrio japonicus Nelson, Cassandra E.; Gardner, Jeffrey G. Applied and Environmental Microbiology, Vol. 81, Issue 17 https://doi.org/10.1128/AEM.00847-15	journal	June 2015
Recent progress in consolidated bioprocessing Olson, Daniel G.; McBride, John E.; Joe Shaw, A. Current Opinion in Biotechnology, Vol. 23, Issue 3, p. 396-405 https://doi.org/10.1016/j.copbio.2011.11.026	journal	June 2012
Carbon catabolite repression in Pseudomonas : optimizing metabolic versatility and interactions with the environment Rojo, Fernando FEMS Microbiology Reviews, Vol. 34, Issue 5 https://doi.org/10.1111/j.1574-6976.2010.00218.x	journal	September 2010
Escherichia coli Physiology in Luria-Bertani Broth Sezonov, G.; Joseleau-Petit, D.; D'Ari, R. Journal of Bacteriology, Vol. 189, Issue 23 https://doi.org/10.1128/JB.01368-07	journal	September 2007
A simple and fast method for determining colony forming units Sieuwerts, S.; de Bok, F. A. M.; Mols, E. Letters in Applied Microbiology, Vol. 47, Issue 4 https://doi.org/10.1111/j.1472-765X.2008.02417.x	journal	October 2008
Measurement of protein using bicinchoninic acid Smith, P. K.; Krohn, R. I.; Hermanson, G. T. Analytical Biochemistry, Vol. 150, Issue 1 https://doi.org/10.1016/0003-2697(85)90442-7	journal	October 1985
Integrated 3D-printed reactionware for chemical synthesis and analysis Symes, Mark D.; Kitson, Philip J.; Yan, Jun Nature Chemistry, Vol. 4, Issue 5 https://doi.org/10.1038/nchem.1313	journal	April 2012
Classification of 'Anaerocellum thermophilum' strain DSM 6725 as Caldicellulosiruptor bescii sp. nov. Yang, S. -J.; Kataeva, I.; Wiegel, J. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 60, Issue 9 https://doi.org/10.1099/ijs.0.017731-0	journal	October 2009
Cellodextrin preparation by mixed-acid hydrolysis and chromatographic separation Zhang, Yi-Heng Percival; Lynd, Lee R. Analytical Biochemistry, Vol. 322, Issue 2 https://doi.org/10.1016/j.ab.2003.07.021	journal	November 2003
Open-Source 3D-Printable Optics Equipment Zhang, Chenlong; Anzalone, Nicholas C.; Faria, Rodrigo P. PLoS ONE, Vol. 8, Issue 3 https://doi.org/10.1371/journal.pone.0059840	journal	March 2013
Combining C6 and C5 sugar metabolism for enhancing microbial bioconversion Zhang, Guo-Chang; Liu, Jing-Jing; Kong, In Iok Current Opinion in Chemical Biology, Vol. 29 https://doi.org/10.1016/j.cbpa.2015.09.008	journal	December 2015

Cited By (4)

The complex physiology of Cellvibrio japonicus xylan degradation relies on a single cytoplasmic β-xylosidase for xylo-oligosaccharide utilization : Xylan degradation in Blake, Andrew D.; Beri, Nina R.; Guttman, Hadassa S. Molecular Microbiology, Vol. 107, Issue 5 https://doi.org/10.1111/mmi.13903	journal	January 2018
Systems analysis of the glycoside hydrolase family 18 enzymes from Cellvibrio japonicus characterizes essential chitin degradation functions Monge, Estela C.; Tuveng, Tina R.; Vaaje-Kolstad, Gustav Journal of Biological Chemistry, Vol. 293, Issue 10 https://doi.org/10.1074/jbc.ra117.000849	journal	January 2018
Comprehensive functional characterization of the glycoside hydrolase family 3 enzymes from Cellvibrio japonicus reveals unique metabolic roles in biomass saccharification : Complex glucan utilization in Nelson, Cassandra E.; Attia, Mohamed A.; Rogowski, Artur Environmental Microbiology, Vol. 19, Issue 12 https://doi.org/10.1111/1462-2920.13959	journal	December 2017
High-throughput screening of environmental polysaccharide-degrading bacteria using biomass containment and complex insoluble substrates Monge, Estela C.; Levi, Marios; Forbin, Joseph N. Applied Microbiology and Biotechnology, Vol. 104, Issue 8 https://doi.org/10.1007/s00253-020-10469-3	journal	February 2020

Similar Records

High-throughput screening of environmental polysaccharide-degrading bacteria using biomass containment and complex insoluble substrates

Journal Article · Sat Feb 29 00:00:00 EST 2020 · Applied Microbiology and Biotechnology · OSTI ID:1326371

Monge, Estela C.; Levi, Marios; Forbin, Joseph N.; +4 more

Polysaccharide degradation systems of the saprophytic bacterium Cellvibrio japonicus

Journal Article · Sat Jun 04 00:00:00 EDT 2016 · World Journal of Microbiology and Biotechnology · OSTI ID:1326371

Gardner, Jeffrey G.

The complex physiology of Cellvibrio japonicus xylan degradation relies on a single cytoplasmic β-xylosidase for xylo-oligosaccharide utilization

Journal Article · Thu Dec 21 00:00:00 EST 2017 · Molecular Microbiology · OSTI ID:1326371

Blake, Andrew D.; Beri, Nina R.; Guttman, Hadassa S.; +2 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
3-D printing
biomass containment
Cellvibrio japonicus
lignocellulose
polysaccharide degradation

Title: Custom fabrication of biomass containment devices using 3-D printing enables bacterial growth analyses with complex insoluble substrates

Citation Formats

References (36)

Cited By (4)

Similar Records

Related Subjects