Preservation of microbial communities enriched on lignocellulose under thermophilic and high-solid conditions

Yu, Chaowei; Reddy, Amitha P.; Simmons, Christopher W.; Simmons, Blake A.; Singer, Steven W.; VanderGheynst, Jean S.

doi:10.1186/s13068-015-0392-y

Title: Preservation of microbial communities enriched on lignocellulose under thermophilic and high-solid conditions

Abstract

Microbial communities enriched from diverse environments have shown considerable promise for the targeted discovery of microorganisms and enzymes for bioconversion of lignocellulose to liquid fuels. While preservation of microbial communities is important for commercialization and research, few studies have examined storage conditions ideal for preservation. The goal of this study was to evaluate the impact of preservation method on composition of microbial communities enriched on switchgrass before and after storage. The enrichments were completed in a high-solid and aerobic environment at 55 °C. Community composition was examined for each enrichment to determine when a stable community was achieved. Preservation methods included cryopreservation with the cryoprotective agents DMSO and glycerol, and cryopreservation without cryoprotective agents. Revived communities were examined for their ability to decompose switchgrass under high-solid and thermophilic conditions. High-throughput 16S rRNA gene sequencing of DNA extracted from enrichment samples showed that the majority of the shift in composition of the switchgrass-degrading community occurred during the initial three 2-week enrichments. Shifts in community structure upon storage occurred in all cryopreserved samples. Storage in liquid nitrogen in the absence of cryoprotectant resulted in variable preservation of dominant microorganisms in enriched samples. Cryopreservation with either DMSO or glycerol provided consistent and equivalentmore »« less

Authors:

Yu, Chaowei; Reddy, Amitha P.; Simmons, Christopher W.; Simmons, Blake A.; Singer, Steven W.;

Publication Date:: Wed Dec 02 00:00:00 EST 2015

Research Org.:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

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

OSTI Identifier:: 1618629

Alternate Identifier(s):: OSTI ID: 1257272

Grant/Contract Number:: AC02-05CH11231; CA-D-BAE-2228-RR; 12-LR-237496

Resource Type:: Published Article

Journal Name:: Biotechnology for Biofuels

Additional Journal Information:: Journal Name: Biotechnology for Biofuels Journal Volume: 8 Journal Issue: 1; Journal ID: ISSN 1754-6834

Publisher:: Springer Science + Business Media

Country of Publication:: Netherlands

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES; biological lignocellulose deconstruction; cryopreservation; microbial community enrichment

Citation Formats


                    Yu, Chaowei, Reddy, Amitha P., Simmons, Christopher W., Simmons, Blake A., Singer, Steven W., and VanderGheynst, Jean S. Preservation of microbial communities enriched on lignocellulose under thermophilic and high-solid conditions.  Netherlands: N. p., 2015. 
Web.  doi:10.1186/s13068-015-0392-y.

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                    Yu, Chaowei, Reddy, Amitha P., Simmons, Christopher W., Simmons, Blake A., Singer, Steven W., & VanderGheynst, Jean S. Preservation of microbial communities enriched on lignocellulose under thermophilic and high-solid conditions.  Netherlands.  https://doi.org/10.1186/s13068-015-0392-y

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                    Yu, Chaowei, Reddy, Amitha P., Simmons, Christopher W., Simmons, Blake A., Singer, Steven W., and VanderGheynst, Jean S. Wed .  
"Preservation of microbial communities enriched on lignocellulose under thermophilic and high-solid conditions".  Netherlands.  https://doi.org/10.1186/s13068-015-0392-y.

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@article{osti_1618629,

  title        = {Preservation of microbial communities enriched on lignocellulose under thermophilic and high-solid conditions},

  author       = {Yu, Chaowei and Reddy, Amitha P. and Simmons, Christopher W. and Simmons, Blake A. and Singer, Steven W. and VanderGheynst, Jean S.},

  abstractNote = {Microbial communities enriched from diverse environments have shown considerable promise for the targeted discovery of microorganisms and enzymes for bioconversion of lignocellulose to liquid fuels. While preservation of microbial communities is important for commercialization and research, few studies have examined storage conditions ideal for preservation. The goal of this study was to evaluate the impact of preservation method on composition of microbial communities enriched on switchgrass before and after storage. The enrichments were completed in a high-solid and aerobic environment at 55 °C. Community composition was examined for each enrichment to determine when a stable community was achieved. Preservation methods included cryopreservation with the cryoprotective agents DMSO and glycerol, and cryopreservation without cryoprotective agents. Revived communities were examined for their ability to decompose switchgrass under high-solid and thermophilic conditions. High-throughput 16S rRNA gene sequencing of DNA extracted from enrichment samples showed that the majority of the shift in composition of the switchgrass-degrading community occurred during the initial three 2-week enrichments. Shifts in community structure upon storage occurred in all cryopreserved samples. Storage in liquid nitrogen in the absence of cryoprotectant resulted in variable preservation of dominant microorganisms in enriched samples. Cryopreservation with either DMSO or glycerol provided consistent and equivalent preservation of dominant organisms. In conclusion, a stable switchgrass-degrading microbial community was achieved after three 2-week enrichments. Dominant microorganisms were preserved equally well with DMSO and glycerol. DMSO-preserved communities required more incubation time upon revival to achieve pre-storage activity levels during high-solid thermophilic cultivation on switchgrass. Despite shifts in the community with storage, the samples were active upon revival under thermophilic and high-solid conditions. The results suggest that the presence of microorganisms may be more important than their relative abundance in retaining an active microbial community.},

  doi          = {10.1186/s13068-015-0392-y},

  journal      = {Biotechnology for Biofuels},

  number       = 1,

  volume       = 8,

  place        = {Netherlands},

  year         = {Wed Dec 02 00:00:00 EST 2015},

  month        = {Wed Dec 02 00:00:00 EST 2015}

}

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Cited by: 18 works

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Figures / Tables:

Fig. 1: Carbon dioxide evolution rate (CER) profiles for a the first (T1) 2 weeks and b sixth (T6) 2 weeks of the enrichment study for individual reactors (R20, R21 and R23)

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Works referenced in this record:

Identification of microbial communities that assimilate substrate from root cap cells in an aerobic soil using a DNA-SIP approach
journal, September 2011

Li, Yong; Lee, Chol Gyu; Watanabe, Takeshi
Soil Biology and Biochemistry, Vol. 43, Issue 9
DOI: 10.1016/j.soilbio.2011.05.016

Effect of DNA extraction and sample preservation method on rumen bacterial population
journal, October 2014

Fliegerova, Katerina; Tapio, Ilma; Bonin, Aurelie
Anaerobe, Vol. 29
DOI: 10.1016/j.anaerobe.2013.09.015

Feedstocks for Lignocellulosic Biofuels
journal, August 2010

Somerville, Cris; Youngs, Heather; Taylor, Caroline
Science, Vol. 329, Issue 5993, p. 790-792
DOI: 10.1126/science.1189268

Characterization of wheat straw-degrading anaerobic alkali-tolerant mixed cultures from soda lake sediments by molecular and cultivation techniques: Lignocellulolytic methanogenic cultures from soda lakes
journal, March 2015

Porsch, Katharina; Wirth, Balázs; Tóth, Erika M.
Microbial Biotechnology, Vol. 8, Issue 5
DOI: 10.1111/1751-7915.12272

Fertility Cryopreservation
book, May 2010

Chian, Ri-Cheng; Quinn, Patrick
Cambridge University Press
DOI: 10.1017/CBO9780511730207

Optimization of protective media for actinomycetes storage in liquid nitrogen
journal, August 2007

Filippova, S. N.; Surgucheva, N. A.; Kuznetsov, V. D.
Microbiology, Vol. 76, Issue 4
DOI: 10.1134/S0026261707040194

Environmental life cycle assessment of lignocellulosic conversion to ethanol: A review
journal, September 2012

Borrion, Aiduan Li; McManus, Marcelle C.; Hammond, Geoffrey P.
Renewable and Sustainable Energy Reviews, Vol. 16, Issue 7
DOI: 10.1016/j.rser.2012.04.016

Optimized Cryopreservation of Mixed Microbial Communities for Conserved Functionality and Diversity
journal, June 2014

Kerckhof, Frederiek-Maarten; Courtens, Emilie N. P.; Geirnaert, Annelies
PLoS ONE, Vol. 9, Issue 6
DOI: 10.1371/journal.pone.0099517

Analysis of a thermophilic lignocellulose degrading microbial consortium and multi-species lignocellulolytic enzyme system
journal, November 2010

Wongwilaiwalin, Sarunyou; Rattanachomsri, Ukrit; Laothanachareon, Thanaporn
Enzyme and Microbial Technology, Vol. 47, Issue 6
DOI: 10.1016/j.enzmictec.2010.07.013

In-Depth Characterization of Wastewater Bacterial Community in Response to Algal Growth Using Pyrosequencing
journal, September 2013

Lee, Jangho
Journal of Microbiology and Biotechnology, Vol. 23, Issue 10
DOI: 10.4014/jmb.1303.03022

Kinetics and energetics of electron transfer in reaction centers of the photosynthetic bacterium Roseiflexus castenholzii
journal, March 2011

Collins, Aaron M.; Kirmaier, Christine; Holten, Dewey
Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1807, Issue 3
DOI: 10.1016/j.bbabio.2010.11.011

Unveiling the metabolic potential of two soil-derived microbial consortia selected on wheat straw
journal, September 2015

Jiménez, Diego Javier; Chaves-Moreno, Diego; van Elsas, Jan Dirk
Scientific Reports, Vol. 5, Issue 1
DOI: 10.1038/srep13845

Chelatococcus caeni sp. nov., isolated from a biofilm reactor sludge sample
journal, December 2014

Jin, L.; Ko, S. -R.; Lee, H. -G.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 65, Issue Pt 3
DOI: 10.1099/ijs.0.000032

Causes of death of bacteria in frozen suspensions
journal, December 1956

Harrison, Arthur P.
Antonie van Leeuwenhoek, Vol. 22, Issue 1
DOI: 10.1007/bf02538353

The protective action of neutral solutes against haemolysis by freezing and thawing
journal, February 1954

Lovelock, J. E.
Biochemical Journal, Vol. 56, Issue 2
DOI: 10.1042/bj0560265

Freezing Injury and its Prevention in Living Cells
journal, June 1974

Meryman, H. T.
Annual Review of Biophysics and Bioengineering, Vol. 3, Issue 1
DOI: 10.1146/annurev.bb.03.060174.002013

Comparison of dilute acid and ionic liquid pretreatment of switchgrass: Biomass recalcitrance, delignification and enzymatic saccharification
journal, July 2010

Li, Chenlin; Knierim, Bernhard; Manisseri, Chithra
Bioresource Technology, Vol. 101, Issue 13
DOI: 10.1016/j.biortech.2009.10.066

A metagenomic approach for the identification and cloning of an endoglucanase from rice straw compost
journal, May 2013

Yeh, Yi-Fang; Chang, Samuel Chia-yu; Kuo, Hsion-Wen
Gene, Vol. 519, Issue 2
DOI: 10.1016/j.gene.2012.07.076

Construction of a stable microbial community with high cellulose-degradation ability
journal, January 2002

S., Haruta; Z., Cui; Z., Huang
Applied Microbiology and Biotechnology, Vol. 59, Issue 4-5
DOI: 10.1007/s00253-002-1026-4

Strategies for Enhancing the Effectiveness of Metagenomic-based Enzyme Discovery in Lignocellulolytic Microbial Communities
journal, March 2010

DeAngelis, Kristen M.; Gladden, John M.; Allgaier, Martin
BioEnergy Research, Vol. 3, Issue 2
DOI: 10.1007/s12155-010-9089-z

Het mechanism of the protective action of glycerol against haemolysis by freezing and thawing
journal, January 1953

Lovelock, J. E.
Biochimica et Biophysica Acta, Vol. 11
DOI: 10.1016/0006-3002(53)90005-5

Development of a biorefinery optimized biofuel supply curve for the Western United States
journal, November 2010

Parker, Nathan; Tittmann, Peter; Hart, Quinn
Biomass and Bioenergy, Vol. 34, Issue 11
DOI: 10.1016/j.biombioe.2010.06.007

The challenge of enzyme cost in the production of lignocellulosic biofuels
journal, November 2011

Klein-Marcuschamer, Daniel; Oleskowicz-Popiel, Piotr; Simmons, Blake A.
Biotechnology and Bioengineering, Vol. 109, Issue 4
DOI: 10.1002/bit.24370

Cultivation of Uncultured Chloroflexi Subphyla: Significance and Ecophysiology of Formerly Uncultured Chloroflexi 'Subphylum I' with Natural and Biotechnological Relevance
journal, January 2009

Yamada, Takeshi; Sekiguchi, Yuji
Microbes and Environments, Vol. 24, Issue 3
DOI: 10.1264/jsme2.ME09151S

Isolation and screening of potential actinobacteria for rapid composting of rice straw
journal, August 2010

Kausar, H.; Sariah, M.; Mohd Saud, H.
Biodegradation, Vol. 22, Issue 2
DOI: 10.1007/s10532-010-9407-3

Discovery of Microorganisms and Enzymes Involved in High-Solids Decomposition of Rice Straw Using Metagenomic Analyses
journal, October 2013

Reddy, Amitha P.; Simmons, Christopher W.; D’haeseleer, Patrik
PLoS ONE, Vol. 8, Issue 10
DOI: 10.1371/journal.pone.0077985

Cryobiology: The Freezing of Biological Systems
journal, May 1970

Mazur, P.
Science, Vol. 168, Issue 3934
DOI: 10.1126/science.168.3934.939

Bacterial populations assimilating carbon from 13C-labeled plant residue in soil: Analysis by a DNA-SIP approach
journal, April 2011

Lee, Chol Gyu; Watanabe, Takeshi; Sato, Yutaka
Soil Biology and Biochemistry, Vol. 43, Issue 4
DOI: 10.1016/j.soilbio.2010.12.016

The effect of storage on microbial activity and bacterial community structure of drained and flooded paddy soil
journal, December 2014

Wang, Juan; Chapman, Stephen J.; Yao, Huaiying
Journal of Soils and Sediments, Vol. 15, Issue 4
DOI: 10.1007/s11368-014-1053-7

Prokaryotic successions and diversity in composts as revealed by 454-pyrosequencing
journal, April 2013

de Gannes, Vidya; Eudoxie, Gaius; Hickey, William J.
Bioresource Technology, Vol. 133
DOI: 10.1016/j.biortech.2013.01.138

Characterization of bacterial communities in solarized soil amended with lignocellulosic organic matter
journal, January 2014

Simmons, Christopher W.; Claypool, Joshua T.; Marshall, Megan N.
Applied Soil Ecology, Vol. 73
DOI: 10.1016/j.apsoil.2013.08.014

Non-parametric multivariate analyses of changes in community structure
journal, March 1993

Clarke, K. R.
Austral Ecology, Vol. 18, Issue 1
DOI: 10.1111/j.1442-9993.1993.tb00438.x

Soil microbiomes vary in their ability to confer drought tolerance to Arabidopsis
journal, June 2013

Zolla, Gaston; Badri, Dayakar V.; Bakker, Matthew G.
Applied Soil Ecology, Vol. 68
DOI: 10.1016/j.apsoil.2013.03.007

Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples: Influence of short-term storage conditions on microbiota
journal, March 2010

Lauber, Christian L.; Zhou, Nicholas; Gordon, Jeffrey I.
FEMS Microbiology Letters, Vol. 307, Issue 1
DOI: 10.1111/j.1574-6968.2010.01965.x

Taxonomic Diversity of Actinomycetes Isolated from Swine Manure Compost
journal, January 2010

Hayakawa, Masayuki; Yamamura, Hideki; Nakagawa, Youji
Actinomycetologica, Vol. 24, Issue 2
DOI: 10.3209/saj.SAJ240202

Isolation of bacterial strains able to metabolize lignin from screening of environmental samples
journal, June 2012

Taylor, C. R.; Hardiman, E. M.; Ahmad, M.
Journal of Applied Microbiology, Vol. 113, Issue 3
DOI: 10.1111/j.1365-2672.2012.05352.x

Novel multispecies microbial consortia involved in lignocellulose and 5-hydroxymethylfurfural bioconversion
journal, October 2013

Jiménez, Diego Javier; Korenblum, Elisa; van Elsas, Jan Dirk
Applied Microbiology and Biotechnology, Vol. 98, Issue 6
DOI: 10.1007/s00253-013-5253-7

Genomics of cellulolytic bacteria
journal, October 2014

Koeck, Daniela E.; Pechtl, Alexander; Zverlov, Vladimir V.
Current Opinion in Biotechnology, Vol. 29
DOI: 10.1016/j.copbio.2014.07.002

Improving Enzymes for Biomass Conversion: A Basic Research Perspective
journal, January 2010

Banerjee, Goutami; Scott-Craig, John S.; Walton, Jonathan D.
BioEnergy Research, Vol. 3, Issue 1
DOI: 10.1007/s12155-009-9067-5

Practice and prospects of microbial preservation
journal, November 2012

Prakash, Om; Nimonkar, Yogesh; Shouche, Yogesh S.
FEMS Microbiology Letters, Vol. 339, Issue 1
DOI: 10.1111/1574-6968.12034

Production of cellulase and β-glucosidase activity during growth of the actinomycete Micromonospora chalcae on cellulose-containing media
journal, May 1996

Gallagher, J.; Winters, A.; Barron, N.
Biotechnology Letters, Vol. 18, Issue 5
DOI: 10.1007/BF00140199

Effect of preservation method on the assessment of bacterial community structure in soil and water samples
journal, June 2014

Tatangelo, Valeria; Franzetti, Andrea; Gandolfi, Isabella
FEMS Microbiology Letters, Vol. 356, Issue 1
DOI: 10.1111/1574-6968.12475

The Critical Moisture Range for Rapid Microbial Decomposition of Rice Straw During Storage
journal, January 2009

A. P. Reddy,
Transactions of the ASABE, Vol. 52, Issue 2
DOI: 10.13031/2013.26806

Isolation and characterization of root-associated bacteria from agricultural crops in the Kavango region of Namibia
journal, May 2011

Grönemeyer, Jann Lasse; Burbano, Claudia Sofía; Hurek, Thomas
Plant and Soil, Vol. 356, Issue 1-2
DOI: 10.1007/s11104-011-0798-7

Anaerolinea thermophila gen. nov., sp. nov. and Caldilinea aerophila gen. nov., sp. nov., novel filamentous thermophiles that represent a previously uncultured lineage of the domain Bacteria at the subphylum level
journal, November 2003

Sekiguchi, Y.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 53, Issue 6
DOI: 10.1099/ijs.0.02699-0

Aerobic and facultatively anaerobic cellulolytic bacteria from the gut of the termite Zootermopsis angusticollis
journal, January 2002

Wenzel, M.; Schonig, I.; Berchtold, M.
Journal of Applied Microbiology, Vol. 92, Issue 1
DOI: 10.1046/j.1365-2672.2002.01502.x

Influence of Fecal Sample Storage on Bacterial Community Diversity
journal, April 2009

Roesch, Luiz F. W.; Casella, George; Simell, Olli
The Open Microbiology Journal, Vol. 3, Issue 1
DOI: 10.2174/1874285800903010040

Molecular and biochemical characterization of a novel xylanase from the symbiotic Sphingobacterium sp. TN19
journal, June 2009

Zhou, Junpei; Huang, Huoqing; Meng, Kun
Applied Microbiology and Biotechnology, Vol. 85, Issue 2
DOI: 10.1007/s00253-009-2081-x

Effect of inoculum source on the enrichment of microbial communities on two lignocellulosic bioenergy crops under thermophilic and high-solids conditions
journal, August 2014

Simmons, C. W.; Reddy, A. P.; Simmons, B. A.
Journal of Applied Microbiology, Vol. 117, Issue 4
DOI: 10.1111/jam.12609

Metataxonomic profiling and prediction of functional behaviour of wheat straw degrading microbial consortia
journal, January 2014

Jiménez, Diego; Dini-Andreote, Francisco; van Elsas, Jan
Biotechnology for Biofuels, Vol. 7, Issue 1
DOI: 10.1186/1754-6834-7-92

Micromonospora eburnea sp. nov., isolated from a Thai peat swamp forest
journal, January 2005

Thawai, C.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 55, Issue 1
DOI: 10.1099/ijs.0.63217-0

Safeguarding bacterial resources promotes biotechnological innovation
journal, March 2012

Heylen, Kim; Hoefman, Sven; Vekeman, Bram
Applied Microbiology and Biotechnology, Vol. 94, Issue 3
DOI: 10.1007/s00253-011-3797-y

Next-generation biomass feedstocks for biofuel production
journal, January 2008

Simmons, Blake A.; Loque, Dominique; Blanch, Harvey W.
Genome Biology, Vol. 9, Issue 12
DOI: 10.1186/gb-2008-9-12-242

Niche partitioning of bacterial communities in biological crusts and soils under grasses, shrubs and trees in the Kalahari
journal, April 2014

Elliott, David R.; Thomas, Andrew D.; Hoon, Stephen R.
Biodiversity and Conservation, Vol. 23, Issue 7
DOI: 10.1007/s10531-014-0684-8

Steroidobacter denitrificans gen. nov., sp. nov., a steroidal hormone-degrading gammaproteobacterium
journal, September 2008

Fahrbach, M.; Kuever, J.; Remesch, M.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 58, Issue 9
DOI: 10.1099/ijs.0.65342-0

Investigating the Impact of Storage Conditions on Microbial Community Composition in Soil Samples
journal, July 2013

Rubin, Benjamin E. R.; Gibbons, Sean M.; Kennedy, Suzanne
PLoS ONE, Vol. 8, Issue 7
DOI: 10.1371/journal.pone.0070460

Pretreatment: the key to unlocking low-cost cellulosic ethanol
journal, January 2008

Yang, Bin; Wyman, Charles E.
Biofuels, Bioproducts and Biorefining, Vol. 2, Issue 1
DOI: 10.1002/bbb.49

Bioenergy feedstock-specific enrichment of microbial populations during high-solids thermophilic deconstruction
journal, May 2011

Reddy, Amitha P.; Allgaier, Martin; Singer, Steven W.
Biotechnology and Bioengineering, Vol. 108, Issue 9
DOI: 10.1002/bit.23176

Targeted Discovery of Glycoside Hydrolases from a Switchgrass-Adapted Compost Community
journal, January 2010

Allgaier, Martin; Reddy, Amitha; Park, Joshua I.
PLoS ONE, Vol. 5, Issue 1
DOI: 10.1371/journal.pone.0008812

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