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Li XY, Li ZF, Zhang XL, Yang MQ, Wu PQ, Huang MJ, Huang HQ. Adaptation mechanism of three Impatiens species to different habitats based on stem morphology, lignin and MYB4 gene. BMC PLANT BIOLOGY 2024; 24:453. [PMID: 38789944 PMCID: PMC11127381 DOI: 10.1186/s12870-024-05115-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024]
Abstract
BACKGROUND Impatiens is an important genus with rich species of garden plants, and its distribution is extremely extensive, which is reflected in its diverse ecological environment. However, the specific mechanisms of Impatiens' adaptation to various environments and the mechanism related to lignin remain unclear. RESULTS Three representative Impatiens species,Impatiens chlorosepala (wet, low degree of lignification), Impatiens uliginosa (aquatic, moderate degree of lignification) and Impatiens rubrostriata (terrestrial, high degree of lignification), were selected and analyzed for their anatomical structures, lignin content and composition, and lignin-related gene expression. There are significant differences in anatomical parameters among the stems of three Impatiens species, and the anatomical structure is consistent with the determination results of lignin content. Furthermore, the thickness of the xylem and cell walls, as well as the ratio of cell wall thickness to stem diameter have a strong correlation with lignin content. The anatomical structure and degree of lignification in Impatiens can be attributed to the plant's growth environment, morphology, and growth rate. Our analysis of lignin-related genes revealed a negative correlation between the MYB4 gene and lignin content. The MYB4 gene may control the lignin synthesis in Impatiens by controlling the structural genes involved in the lignin synthesis pathway, such as HCT, C3H, and COMT. Nonetheless, the regulation pathway differs between species of Impatiens. CONCLUSIONS This study demonstrated consistency between the stem anatomy of Impatiens and the results obtained from lignin content and composition analyses. It is speculated that MYB4 negatively regulates the lignin synthesis in the stems of three Impatiens species by regulating the expression of structural genes, and its regulation mechanism appears to vary across different Impatiens species. This study analyses the variations among different Impatiens plants in diverse habitats, and can guide further molecular investigations of lignin biosynthesis in Impatiens.
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Affiliation(s)
- Xin-Yi Li
- Southwest Forestry University, College of Landscape Architecture and Horticulture Sciences, Southwest Research Center for Engineering Technology of Landscape Architecture (State Forestry and Grassland Administration), Yunnan Engineering Research Center for Functional Flower Resources and Industrialization, Research and Development Center of Landscape Plants and Horticulture Flowers, Kunming, Yunnan, 650224, China
| | - Ze-Feng Li
- Southwest Forestry University, College of Landscape Architecture and Horticulture Sciences, Southwest Research Center for Engineering Technology of Landscape Architecture (State Forestry and Grassland Administration), Yunnan Engineering Research Center for Functional Flower Resources and Industrialization, Research and Development Center of Landscape Plants and Horticulture Flowers, Kunming, Yunnan, 650224, China
| | - Xiao-Li Zhang
- Southwest Forestry University, College of Landscape Architecture and Horticulture Sciences, Southwest Research Center for Engineering Technology of Landscape Architecture (State Forestry and Grassland Administration), Yunnan Engineering Research Center for Functional Flower Resources and Industrialization, Research and Development Center of Landscape Plants and Horticulture Flowers, Kunming, Yunnan, 650224, China
| | - Meng-Qing Yang
- Southwest Forestry University, College of Landscape Architecture and Horticulture Sciences, Southwest Research Center for Engineering Technology of Landscape Architecture (State Forestry and Grassland Administration), Yunnan Engineering Research Center for Functional Flower Resources and Industrialization, Research and Development Center of Landscape Plants and Horticulture Flowers, Kunming, Yunnan, 650224, China
| | - Pei-Qing Wu
- Southwest Forestry University, College of Landscape Architecture and Horticulture Sciences, Southwest Research Center for Engineering Technology of Landscape Architecture (State Forestry and Grassland Administration), Yunnan Engineering Research Center for Functional Flower Resources and Industrialization, Research and Development Center of Landscape Plants and Horticulture Flowers, Kunming, Yunnan, 650224, China
| | - Mei-Juan Huang
- Southwest Forestry University, College of Landscape Architecture and Horticulture Sciences, Southwest Research Center for Engineering Technology of Landscape Architecture (State Forestry and Grassland Administration), Yunnan Engineering Research Center for Functional Flower Resources and Industrialization, Research and Development Center of Landscape Plants and Horticulture Flowers, Kunming, Yunnan, 650224, China.
| | - Hai-Quan Huang
- Southwest Forestry University, College of Landscape Architecture and Horticulture Sciences, Southwest Research Center for Engineering Technology of Landscape Architecture (State Forestry and Grassland Administration), Yunnan Engineering Research Center for Functional Flower Resources and Industrialization, Research and Development Center of Landscape Plants and Horticulture Flowers, Kunming, Yunnan, 650224, China.
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2
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Happs R, Hanes RJ, Bartling AW, Field JL, Harman-Ware AE, Clark RJ, Pendergast TH, Devos KM, Webb EG, Missaoui A, Xu Y, Makaju S, Shrestha V, Mazarei M, Stewart CN, Millwood RJ, Davison BH. Economic and Sustainability Impacts of Yield and Composition Variation in Bioenergy Crops: Switchgrass ( Panicum virgatum L.). ACS SUSTAINABLE CHEMISTRY & ENGINEERING 2024; 12:1897-1910. [PMID: 38333206 PMCID: PMC10848292 DOI: 10.1021/acssuschemeng.3c05770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 12/20/2023] [Accepted: 12/20/2023] [Indexed: 02/10/2024]
Abstract
Economically viable production of biobased products and fuels requires high-yielding, high-quality, sustainable process-advantaged crops, developed using bioengineering or advanced breeding approaches. Understanding which crop phenotypic traits have the largest impact on biofuel economics and sustainability outcomes is important for the targeted feedstock crop development. Here, we evaluated biomass yield and cell-wall composition traits across a large natural variant population of switchgrass (Panicum virgatum L.) grown across three common garden sites. Samples from 331 switchgrass genotypes were collected and analyzed for carbohydrate and lignin components. Considering plant survival and biomass after multiple years of growth, we found that 84 of the genotypes analyzed may be suited for commercial production in the southeastern U.S. These genotypes show a range of growth and compositional traits across the population that are apparently independent of each other. We used these data to conduct techno-economic analyses and life cycle assessments evaluating the performance of each switchgrass genotype under a standard cellulosic ethanol process model with pretreatment, added enzymes, and fermentation. We find that switchgrass yield per area is the largest economic driver of the minimum fuel selling price (MSFP), ethanol yield per hectare, global warming potential (GWP), and cumulative energy demand (CED). At any yield, the carbohydrate content is significant but of secondary importance. Water use follows similar trends but has more variability due to an increased dependence on the biorefinery model. Analyses presented here highlight the primary importance of plant yield and the secondary importance of carbohydrate content when selecting a feedstock that is both economical and sustainable.
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Affiliation(s)
- Renee
M. Happs
- Renewable
Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
- Center
for Bioenergy Innovation, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Rebecca J. Hanes
- Strategic
Energy Analysis Center, National Renewable
Energy Laboratory, Golden, Colorado 80401, United States
- Center
for Bioenergy Innovation, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Andrew W. Bartling
- Catalytic
Carbon and Transformation Center, National
Renewable Energy Laboratory, Golden, Colorado 80401, United States
- Center
for Bioenergy Innovation, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37830, United States
| | - John L. Field
- Environmental
Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
- Center
for Bioenergy Innovation, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Anne E. Harman-Ware
- Renewable
Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
- Center
for Bioenergy Innovation, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Robin J. Clark
- Environmental
Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
- Center
for Bioenergy Innovation, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Thomas H. Pendergast
- Institute
of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, Georgia 30602, United States
- Department
of Crop and Soil Sciences, University of
Georgia, Athens, Georgia 30602, United States
- Department
of Plant Biology, University of Georgia, Athens, Georgia 30602, United States
- Center
for Bioenergy Innovation, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Katrien M. Devos
- Institute
of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, Georgia 30602, United States
- Department
of Crop and Soil Sciences, University of
Georgia, Athens, Georgia 30602, United States
- Department
of Plant Biology, University of Georgia, Athens, Georgia 30602, United States
- Center
for Bioenergy Innovation, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Erin G. Webb
- Environmental
Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
- Center
for Bioenergy Innovation, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Ali Missaoui
- Institute
of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, Georgia 30602, United States
- Department
of Crop and Soil Sciences, University of
Georgia, Athens, Georgia 30602, United States
- Center
for Bioenergy Innovation, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Yaping Xu
- Department
of Plant Sciences, University of Tennessee
Knoxville, Knoxville, Tennessee 37919, United States
- Center
for Bioenergy Innovation, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Shiva Makaju
- Institute
of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, Georgia 30602, United States
- Department
of Crop and Soil Sciences, University of
Georgia, Athens, Georgia 30602, United States
- Center
for Bioenergy Innovation, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Vivek Shrestha
- Department
of Plant Sciences, University of Tennessee
Knoxville, Knoxville, Tennessee 37919, United States
- Center
for Bioenergy Innovation, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Mitra Mazarei
- Department
of Plant Sciences, University of Tennessee
Knoxville, Knoxville, Tennessee 37919, United States
- Center
for Bioenergy Innovation, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Charles Neal Stewart
- Department
of Plant Sciences, University of Tennessee
Knoxville, Knoxville, Tennessee 37919, United States
- Center
for Bioenergy Innovation, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Reginald J. Millwood
- Department
of Plant Sciences, University of Tennessee
Knoxville, Knoxville, Tennessee 37919, United States
- Center
for Bioenergy Innovation, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Brian H. Davison
- Biosciences
Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
- Center
for Bioenergy Innovation, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37830, United States
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Wagner ER, Gasch AP. Advances in S. cerevisiae Engineering for Xylose Fermentation and Biofuel Production: Balancing Growth, Metabolism, and Defense. J Fungi (Basel) 2023; 9:786. [PMID: 37623557 PMCID: PMC10455348 DOI: 10.3390/jof9080786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/19/2023] [Accepted: 07/24/2023] [Indexed: 08/26/2023] Open
Abstract
Genetically engineering microorganisms to produce chemicals has changed the industrialized world. The budding yeast Saccharomyces cerevisiae is frequently used in industry due to its genetic tractability and unique metabolic capabilities. S. cerevisiae has been engineered to produce novel compounds from diverse sugars found in lignocellulosic biomass, including pentose sugars, like xylose, not recognized by the organism. Engineering high flux toward novel compounds has proved to be more challenging than anticipated since simply introducing pathway components is often not enough. Several studies show that the rewiring of upstream signaling is required to direct products toward pathways of interest, but doing so can diminish stress tolerance, which is important in industrial conditions. As an example of these challenges, we reviewed S. cerevisiae engineering efforts, enabling anaerobic xylose fermentation as a model system and showcasing the regulatory interplay's controlling growth, metabolism, and stress defense. Enabling xylose fermentation in S. cerevisiae requires the introduction of several key metabolic enzymes but also regulatory rewiring of three signaling pathways at the intersection of the growth and stress defense responses: the RAS/PKA, Snf1, and high osmolarity glycerol (HOG) pathways. The current studies reviewed here suggest the modulation of global signaling pathways should be adopted into biorefinery microbial engineering pipelines to increase efficient product yields.
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Affiliation(s)
- Ellen R. Wagner
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Audrey P. Gasch
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA
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4
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Roni MS, Lin Y, Hartley DS, Thompson DN, Hoover AN, Emerson RM. Importance of incorporating spatial and temporal variability of biomass yield and quality in bioenergy supply chain. Sci Rep 2023; 13:6813. [PMID: 37100831 PMCID: PMC10133216 DOI: 10.1038/s41598-023-28671-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 01/23/2023] [Indexed: 04/28/2023] Open
Abstract
Biofuels made from biomass and waste residues will largely contribute to United States' 2050 decarbonization goal in the aviation sector. While cellulosic biofuels have the potential fuel performance equivalent to petroleum-based jet fuel, the biofuel industry needs to overcome the supply chain barrier caused by temporal and spatial variability of biomass yield and quality. This study highlights the importance of incorporating spatial and temporal variability during biomass supply chain planning via optimization modeling that incorporates 10 years of drought index data, a primary factor contributing to yield and quality variability. The results imply that the cost of delivering biomass to biorefinery may be significantly underestimated if the multi-year temporal and spatial variation in biomass yield and quality is not captured. For long term sustainable biorefinery operations, the industry should optimize supply chain strategy by studying the variability of yield and quality of biomass in their supply sheds.
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Affiliation(s)
- Mohammad S Roni
- System Science & Engineering Department, Idaho National Laboratory, Idaho Falls, ID, USA
| | - Yingqian Lin
- System Science & Engineering Department, Idaho National Laboratory, Idaho Falls, ID, USA.
| | - Damon S Hartley
- System Science & Engineering Department, Idaho National Laboratory, Idaho Falls, ID, USA
| | - David N Thompson
- Biomass Characterization Department, Idaho National Laboratory, Idaho Falls, ID, USA
| | - Amber N Hoover
- Biomass Characterization Department, Idaho National Laboratory, Idaho Falls, ID, USA
| | - Rachel M Emerson
- Biomass Characterization Department, Idaho National Laboratory, Idaho Falls, ID, USA
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5
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Water-soluble saponins accumulate in drought-stressed switchgrass and may inhibit yeast growth during bioethanol production. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:116. [PMID: 36310161 PMCID: PMC9620613 DOI: 10.1186/s13068-022-02213-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 10/17/2022] [Indexed: 11/23/2022]
Abstract
BACKGROUND Developing economically viable pathways to produce renewable energy has become an important research theme in recent years. Lignocellulosic biomass is a promising feedstock that can be converted into second-generation biofuels and bioproducts. Global warming has adversely affected climate change causing many environmental changes that have impacted earth surface temperature and rainfall patterns. Recent research has shown that environmental growth conditions altered the composition of drought-stressed switchgrass and directly influenced the extent of biomass conversion to fuels by completely inhibiting yeast growth during fermentation. Our goal in this project was to find a way to overcome the microbial inhibition and characterize specific compounds that led to this inhibition. Additionally, we also determined if these microbial inhibitors were plant-generated compounds, by-products of the pretreatment process, or a combination of both. RESULTS Switchgrass harvested in drought (2012) and non-drought (2010) years were pretreated using Ammonia Fiber Expansion (AFEX). Untreated and AFEX processed samples were then extracted using solvents (i.e., water, ethanol, and ethyl acetate) to selectively remove potential inhibitory compounds and determine whether pretreatment affects the inhibition. High solids loading enzymatic hydrolysis was performed on all samples, followed by fermentation using engineered Saccharomyces cerevisiae. Fermentation rate, cell growth, sugar consumption, and ethanol production were used to evaluate fermentation performance. We found that water extraction of drought-year switchgrass before AFEX pretreatment reduced the inhibition of yeast fermentation. The extracts were analyzed using liquid chromatography-mass spectrometry (LC-MS) to detect compounds enriched in the extracted fractions. Saponins, a class of plant-generated triterpene or steroidal glycosides, were found to be significantly more abundant in the water extracts from drought-year (inhibitory) switchgrass. The inhibitory nature of the saponins in switchgrass hydrolysate was validated by spiking commercially available saponin standard (protodioscin) in non-inhibitory switchgrass hydrolysate harvested in normal year. CONCLUSIONS Adding a water extraction step prior to AFEX-pretreatment of drought-stressed switchgrass effectively overcame inhibition of yeast growth during bioethanol production. Saponins appear to be generated by the plant as a response to drought as they were significantly more abundant in the drought-stressed switchgrass water extracts and may contribute toward yeast inhibition in drought-stressed switchgrass hydrolysates.
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6
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Vanacloig-Pedros E, Fisher KJ, Liu L, Debrauske DJ, Young MKM, Place M, Hittinger CT, Sato TK, Gasch AP. Comparative chemical genomic profiling across plant-based hydrolysate toxins reveals widespread antagonism in fitness contributions. FEMS Yeast Res 2022; 21:6650360. [PMID: 35883225 PMCID: PMC9508847 DOI: 10.1093/femsyr/foac036] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/06/2022] [Accepted: 07/21/2022] [Indexed: 11/15/2022] Open
Abstract
The budding yeast Saccharomyces cerevisiae has been used extensively in fermentative industrial processes, including biofuel production from sustainable plant-based hydrolysates. Myriad toxins and stressors found in hydrolysates inhibit microbial metabolism and product formation. Overcoming these stresses requires mitigation strategies that include strain engineering. To identify shared and divergent mechanisms of toxicity and to implicate gene targets for genetic engineering, we used a chemical genomic approach to study fitness effects across a library of S. cerevisiae deletion mutants cultured anaerobically in dozens of individual compounds found in different types of hydrolysates. Relationships in chemical genomic profiles identified classes of toxins that provoked similar cellular responses, spanning inhibitor relationships that were not expected from chemical classification. Our results also revealed widespread antagonistic effects across inhibitors, such that the same gene deletions were beneficial for surviving some toxins but detrimental for others. This work presents a rich dataset relating gene function to chemical compounds, which both expands our understanding of plant-based hydrolysates and provides a useful resource to identify engineering targets.
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Affiliation(s)
- Elena Vanacloig-Pedros
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 53726, Madison, WI, United States
| | - Kaitlin J Fisher
- Laboratory of Genetics, University of Wisconsin-Madison, 53706, Madison, WI, United States
- Center for Genomic Science Innovation, University of Wisconsin-Madison, 53706, Madison, WI, United States
- J.F. Crow Institute for the Study of Evolution, 53706, Madison, WI, United States
| | - Lisa Liu
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 53726, Madison, WI, United States
| | - Derek J Debrauske
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 53726, Madison, WI, United States
| | - Megan K M Young
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 53726, Madison, WI, United States
| | - Michael Place
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 53726, Madison, WI, United States
| | - Chris Todd Hittinger
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 53726, Madison, WI, United States
- Laboratory of Genetics, University of Wisconsin-Madison, 53706, Madison, WI, United States
- Center for Genomic Science Innovation, University of Wisconsin-Madison, 53706, Madison, WI, United States
- J.F. Crow Institute for the Study of Evolution, 53706, Madison, WI, United States
| | - Trey K Sato
- Corresponding author: Trey K. Sato, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 4117 Wisconsin Energy Institute, 1552 University Ave, Madison, WI 53726. Tel: (608) 890-2546; E-mail:
| | - Audrey P Gasch
- Corresponding author: Audrey P. Gasch, Center for Genomic Science Innovation, University of Wisconsin-Madison, 3422 Genetics-Biotechnology Center, 425 Henry Mall, Madison, WI 53704, United States. Tel: (608)265-0859; E-mail:
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7
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Wadler CS, Wolters JF, Fortney NW, Throckmorton KO, Zhang Y, Miller CR, Schneider RM, Wendt-Pienkowski E, Currie CR, Donohue TJ, Noguera DR, Hittinger CT, Thomas MG. Utilization of lignocellulosic biofuel conversion residue by diverse microorganisms. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:70. [PMID: 35751080 PMCID: PMC9233362 DOI: 10.1186/s13068-022-02168-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Lignocellulosic conversion residue (LCR) is the material remaining after deconstructed lignocellulosic biomass is subjected to microbial fermentation and treated to remove the biofuel. Technoeconomic analyses of biofuel refineries have shown that further microbial processing of this LCR into other bioproducts may help offset the costs of biofuel generation. Identifying organisms able to metabolize LCR is an important first step for harnessing the full chemical and economic potential of this material. In this study, we investigated the aerobic LCR utilization capabilities of 71 Streptomyces and 163 yeast species that could be engineered to produce valuable bioproducts. The LCR utilization by these individual microbes was compared to that of an aerobic mixed microbial consortium derived from a wastewater treatment plant as representative of a consortium with the highest potential for degrading the LCR components and a source of genetic material for future engineering efforts. RESULTS We analyzed several batches of a model LCR by chemical oxygen demand (COD) and chromatography-based assays and determined that the major components of LCR were oligomeric and monomeric sugars and other organic compounds. Many of the Streptomyces and yeast species tested were able to grow in LCR, with some individual microbes capable of utilizing over 40% of the soluble COD. For comparison, the maximum total soluble COD utilized by the mixed microbial consortium was about 70%. This represents an upper limit on how much of the LCR could be valorized by engineered Streptomyces or yeasts into bioproducts. To investigate the utilization of specific components in LCR and have a defined media for future experiments, we developed a synthetic conversion residue (SynCR) to mimic our model LCR and used it to show lignocellulose-derived inhibitors (LDIs) had little effect on the ability of the Streptomyces species to metabolize SynCR. CONCLUSIONS We found that LCR is rich in carbon sources for microbial utilization and has vitamins, minerals, amino acids and other trace metabolites necessary to support growth. Testing diverse collections of Streptomyces and yeast species confirmed that these microorganisms were capable of growth on LCR and revealed a phylogenetic correlation between those able to best utilize LCR. Identification and quantification of the components of LCR enabled us to develop a synthetic LCR (SynCR) that will be a useful tool for examining how individual components of LCR contribute to microbial growth and as a substrate for future engineering efforts to use these microorganisms to generate valuable bioproducts.
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Affiliation(s)
- Caryn S Wadler
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Dr, Madison, WI, 53706, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
| | - John F Wolters
- Wisconsin Energy Institute, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
- Laboratory of Genetics, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, 425-g Henry Mall, Madison, WI, 53706, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
| | - Nathaniel W Fortney
- Wisconsin Energy Institute, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
| | - Kurt O Throckmorton
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Dr, Madison, WI, 53706, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
| | - Yaoping Zhang
- Wisconsin Energy Institute, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
| | - Caroline R Miller
- Wisconsin Energy Institute, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
- Laboratory of Genetics, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, 425-g Henry Mall, Madison, WI, 53706, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
| | - Rachel M Schneider
- Wisconsin Energy Institute, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
- Laboratory of Genetics, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, 425-g Henry Mall, Madison, WI, 53706, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
| | - Evelyn Wendt-Pienkowski
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Dr, Madison, WI, 53706, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
| | - Cameron R Currie
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Dr, Madison, WI, 53706, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
| | - Timothy J Donohue
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Dr, Madison, WI, 53706, USA
- Wisconsin Energy Institute, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
| | - Daniel R Noguera
- Wisconsin Energy Institute, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, 1415 Engineering Dr, Madison, WI, 53706, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
| | - Chris Todd Hittinger
- Wisconsin Energy Institute, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
- Laboratory of Genetics, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, 425-g Henry Mall, Madison, WI, 53706, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
| | - Michael G Thomas
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Dr, Madison, WI, 53706, USA.
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA.
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8
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Chandrasekar M, Joshi L, Krieg K, Chipkar S, Burke E, Debrauske DJ, Thelen KD, Sato TK, Ong RG. A high solids field-to-fuel research pipeline to identify interactions between feedstocks and biofuel production. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:179. [PMID: 34507592 PMCID: PMC8431876 DOI: 10.1186/s13068-021-02033-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 08/30/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Environmental factors, such as weather extremes, have the potential to cause adverse effects on plant biomass quality and quantity. Beyond adversely affecting feedstock yield and composition, which have been extensively studied, environmental factors can have detrimental effects on saccharification and fermentation processes in biofuel production. Only a few studies have evaluated the effect of these factors on biomass deconstruction into biofuel and resulting fuel yields. This field-to-fuel evaluation of various feedstocks requires rigorous coordination of pretreatment, enzymatic hydrolysis, and fermentation experiments. A large number of biomass samples, often in limited quantity, are needed to thoroughly understand the effect of environmental conditions on biofuel production. This requires greater processing and analytical throughput of industrially relevant, high solids loading hydrolysates for fermentation, and led to the need for a laboratory-scale high solids experimentation platform. RESULTS A field-to-fuel platform was developed to provide sufficient volumes of high solids loading enzymatic hydrolysate for fermentation. AFEX pretreatment was conducted in custom pretreatment reactors, followed by high solids enzymatic hydrolysis. To accommodate enzymatic hydrolysis of multiple samples, roller bottles were used to overcome the bottlenecks of mixing and reduced sugar yields at high solids loading, while allowing greater sample throughput than possible in bioreactors. The roller bottle method provided 42-47% greater liquefaction compared to the batch shake flask method for the same solids loading. In fermentation experiments, hydrolysates from roller bottles were fermented more rapidly, with greater xylose consumption, but lower final ethanol yields and CO2 production than hydrolysates generated with shake flasks. The entire platform was tested and was able to replicate patterns of fermentation inhibition previously observed for experiments conducted in larger-scale reactors and bioreactors, showing divergent fermentation patterns for drought and normal year switchgrass hydrolysates. CONCLUSION A pipeline of small-scale AFEX pretreatment and roller bottle enzymatic hydrolysis was able to provide adequate quantities of hydrolysate for respirometer fermentation experiments and was able to overcome hydrolysis bottlenecks at high solids loading by obtaining greater liquefaction compared to batch shake flask hydrolysis. Thus, the roller bottle method can be effectively utilized to compare divergent feedstocks and diverse process conditions.
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Affiliation(s)
- Meenaa Chandrasekar
- DOE Great Lakes Bioenergy Research Center, Michigan Technological University, Houghton, MI, USA
- Department of Chemical Engineering, Michigan Technological University, Houghton, MI, USA
| | - Leela Joshi
- DOE Great Lakes Bioenergy Research Center, Michigan Technological University, Houghton, MI, USA
- Department of Chemical Engineering, Michigan Technological University, Houghton, MI, USA
| | - Karleigh Krieg
- DOE Great Lakes Bioenergy Research Center, Michigan Technological University, Houghton, MI, USA
- Department of Chemical Engineering, Michigan Technological University, Houghton, MI, USA
| | - Sarvada Chipkar
- DOE Great Lakes Bioenergy Research Center, Michigan Technological University, Houghton, MI, USA
- Department of Chemical Engineering, Michigan Technological University, Houghton, MI, USA
| | - Emily Burke
- DOE Great Lakes Bioenergy Research Center, Michigan Technological University, Houghton, MI, USA
- Department of Chemical Engineering, Michigan Technological University, Houghton, MI, USA
| | - Derek J Debrauske
- DOE Great Lakes Bioenergy Research Center, Univ. of Wisconsin-Madison, Madison, USA
| | - Kurt D Thelen
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, USA
| | - Trey K Sato
- DOE Great Lakes Bioenergy Research Center, Univ. of Wisconsin-Madison, Madison, USA
| | - Rebecca G Ong
- DOE Great Lakes Bioenergy Research Center, Michigan Technological University, Houghton, MI, USA.
- Department of Chemical Engineering, Michigan Technological University, Houghton, MI, USA.
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9
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Zhang Y, Vera JM, Xie D, Serate J, Pohlmann E, Russell JD, Hebert AS, Coon JJ, Sato TK, Landick R. Multiomic Fermentation Using Chemically Defined Synthetic Hydrolyzates Revealed Multiple Effects of Lignocellulose-Derived Inhibitors on Cell Physiology and Xylose Utilization in Zymomonas mobilis. Front Microbiol 2019; 10:2596. [PMID: 31787963 PMCID: PMC6853872 DOI: 10.3389/fmicb.2019.02596] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 10/25/2019] [Indexed: 01/14/2023] Open
Abstract
Utilization of both C5 and C6 sugars to produce biofuels and bioproducts is a key goal for the development of integrated lignocellulosic biorefineries. Previously we found that although engineered Zymomonas mobilis 2032 was able to ferment glucose to ethanol when fermenting highly concentrated hydrolyzates such as 9% glucan-loading AFEX-pretreated corn stover hydrolyzate (9% ACSH), xylose conversion after glucose depletion was greatly impaired. We hypothesized that impaired xylose conversion was caused by lignocellulose-derived inhibitors (LDIs) in hydrolyzates. To investigate the effects of LDIs on the cellular physiology of Z. mobilis during fermentation of hydrolyzates, including impacts on xylose utilization, we generated synthetic hydrolyzates (SynHs) that contained nutrients and LDIs at concentrations found in 9% ACSH. Comparative fermentations of Z. mobilis 2032 using SynH with or without LDIs were performed, and samples were collected for end product, transcriptomic, metabolomic, and proteomic analyses. Several LDI-specific effects were observed at various timepoints during fermentation including upregulation of sulfur assimilation and cysteine biosynthesis, upregulation of RND family efflux pump systems (ZMO0282-0285) and ZMO1429-1432, downregulation of a Type I secretion system (ZMO0252-0255), depletion of reduced glutathione, and intracellular accumulation of mannose-1P and mannose-6P. Furthermore, when grown in SynH containing LDIs, Z. mobilis 2032 only metabolized ∼50% of xylose, compared to ∼80% in SynH without LDIs, recapitulating the poor xylose utilization observed in 9% ACSH. Our metabolomic data suggest that the overall flux of xylose metabolism is reduced in the presence of LDIs. However, the expression of most genes involved in glucose and xylose assimilation was not affected by LDIs, nor did we observe blocks in glucose and xylose metabolic pathways. Accumulations of intracellular xylitol and xylonic acid was observed in both SynH with and without LDIs, which decreased overall xylose-to-ethanol conversion efficiency. Our results suggest that xylose metabolism in Z. mobilis 2032 may not be able to support the cellular demands of LDI mitigation and detoxification during fermentation of highly concentrated lignocellulosic hydrolyzates with elevated levels of LDIs. Together, our findings identify several cellular responses to LDIs and possible causes of impaired xylose conversion that will enable future strain engineering of Z. mobilis.
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Affiliation(s)
- Yaoping Zhang
- DOE-Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Jessica M Vera
- DOE-Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Dan Xie
- DOE-Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Jose Serate
- DOE-Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Edward Pohlmann
- DOE-Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Jason D Russell
- DOE-Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Alexander S Hebert
- DOE-Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Joshua J Coon
- DOE-Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Trey K Sato
- DOE-Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Robert Landick
- DOE-Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States
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10
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Sethupathy A, Sivashanmugam P. Investigation on ultrasonication mediated biosurfactant disintegration method in sludge flocs for enhancing hydrolytic enzymes activity and polyhydroxyalkanoates. ENVIRONMENTAL TECHNOLOGY 2019; 40:3547-3560. [PMID: 29806787 DOI: 10.1080/09593330.2018.1481887] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 05/22/2018] [Indexed: 06/08/2023]
Abstract
In this study, a novel biosurfactant potential bacterial strain Pseudomonas pachastrellae RW43 was isolated from pulp and paper sludge and the biosurfactant namely rhamnolipid produced by Pseudomonas pachastrellae RW43 was investigated by varying pH and incubation time in batch liquid fermentation process. The maximal yield of rhamnolipid was found to be 12.1 g/L at an optimized condition of pH 7 and incubation time of 168 h. NMR analysis was performed for identification of molecular structure of produced rhamnolipid and its results concluded that the product was identified as di rhamnolipid. Then, statistically the global optimum conditions for hydrolytic enzymes extraction parameters (sonication power (100 W), extraction time (15 min) and rhamnolipid dosage (2% v/v)) were established. At 30,456 kJ/kg TS specific energy, ultrasonication with rhamnolipid disintegration method extracted maximal consortium activity of hydrolytic enzymes from mixed sludge (municipal and pulp & paper sludge) and the maximum observed were found to be 42.22, 51.75, 34.26, 24.21, 11.35 Units/g VSS respectively for protease, α-amylase, cellulase, lipase and α-glucosidase. Polyhydroxyalkanoates was recovered from enzymes extracted sludge using various solvents namely chloroform, sodium hypochlorite with chloroform and sodium lauryl sulfate with sodium hypochlorite. The maximum recovery was found to be 74 g/kg using sodium hypochlorite and chloroform extraction solvents.
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Affiliation(s)
- A Sethupathy
- Department of Chemical Engineering, National Institute of Technology , Tiruchirappalli , India
| | - P Sivashanmugam
- Department of Chemical Engineering, National Institute of Technology , Tiruchirappalli , India
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11
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Li Y, Zhai R, Jiang X, Chen X, Yuan X, Liu Z, Jin M. Boosting Ethanol Productivity of Zymomonas mobilis 8b in Enzymatic Hydrolysate of Dilute Acid and Ammonia Pretreated Corn Stover Through Medium Optimization, High Cell Density Fermentation and Cell Recycling. Front Microbiol 2019; 10:2316. [PMID: 31636624 PMCID: PMC6787488 DOI: 10.3389/fmicb.2019.02316] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 09/23/2019] [Indexed: 12/19/2022] Open
Abstract
The presence of toxic degradation products in lignocellulosic hydrolysate typically reduced fermentation rates and xylose consumption rate, resulting in a decreased ethanol productivity. In the present study, Zymomonas mobilis 8b was investigated for high cell density fermentation with cell recycling to improve the ethanol productivity in lignocellulosic hydrolysate. The fermentation performances of Z. mobilis 8b at various conditions were first studied in yeast extract-tryptone medium. It was found that nutrient level was essential for glucose and xylose co-fermentation by Z. mobilis 8b and high cell density fermentation with cell recycling worked well in yeast extract-tryptone medium for 6 rounds fermentation. Z. mobilis 8b was then studied in enzymatic hydrolysates derived from dilute acid (DA) pretreated corn stover (CS) and ammonia pretreated CS for high cell density fermentation with cell recycling. Ethanol productivity obtained was around three times higher compared to traditional fermentation. Ethanol titer and metabolic yield were also enhanced with high cell density fermentation. Z. mobilis 8b cells showed high recyclability in ammonia pretreated CS hydrolysate.
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Affiliation(s)
- Ying Li
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, China
| | - Rui Zhai
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, China
| | - Xiaoxiao Jiang
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, China
| | - Xiangxue Chen
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, China
| | - Xinchuan Yuan
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, China
| | - Zhihua Liu
- Department of Plant Pathology and Microbiology, College of Agriculture and Life Sciences, Texas A&M University, College Station, TX, United States
| | - Mingjie Jin
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, China
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12
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Grady KL, Sorensen JW, Stopnisek N, Guittar J, Shade A. Assembly and seasonality of core phyllosphere microbiota on perennial biofuel crops. Nat Commun 2019; 10:4135. [PMID: 31515535 PMCID: PMC6742659 DOI: 10.1038/s41467-019-11974-4] [Citation(s) in RCA: 122] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 08/15/2019] [Indexed: 12/17/2022] Open
Abstract
Perennial grasses are promising feedstocks for biofuel production, with potential for leveraging their native microbiomes to increase their productivity and resilience to environmental stress. Here, we characterize the 16S rRNA gene diversity and seasonal assembly of bacterial and archaeal microbiomes of two perennial cellulosic feedstocks, switchgrass (Panicum virgatum L.) and miscanthus (Miscanthus x giganteus). We sample leaves and soil every three weeks from pre-emergence through senescence for two consecutive switchgrass growing seasons and one miscanthus season, and identify core leaf taxa based on occupancy. Virtually all leaf taxa are also detected in soil; source-sink modeling shows non-random, ecological filtering by the leaf, suggesting that soil is an important reservoir of phyllosphere diversity. Core leaf taxa include early, mid, and late season groups that were consistent across years and crops. This consistency in leaf microbiome dynamics and core members is promising for microbiome manipulation or management to support crop production. Microbial communities of plant leaf surfaces are ecologically important, but how they assemble and vary in time is unclear. Here, the authors identify core leaf microbiomes and seasonal patterns for two biofuel crops and show with source-sink models that soil is a reservoir of phyllosphere diversity.
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Affiliation(s)
- Keara L Grady
- Department of Microbiology and Molecular Genetics, Michigan State University, 567 Wilson Road, East Lansing, MI, 48824, USA.,The DOE Great Lakes Bioenergy Research Center, Michigan State University, 1129 Farm Lane, East Lansing, MI, 48824, USA
| | - Jackson W Sorensen
- Department of Microbiology and Molecular Genetics, Michigan State University, 567 Wilson Road, East Lansing, MI, 48824, USA.,The DOE Great Lakes Bioenergy Research Center, Michigan State University, 1129 Farm Lane, East Lansing, MI, 48824, USA
| | - Nejc Stopnisek
- The DOE Great Lakes Bioenergy Research Center, Michigan State University, 1129 Farm Lane, East Lansing, MI, 48824, USA.,Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, 293 Farm Lane, East Lansing, MI, 48824, USA
| | - John Guittar
- Department of Microbiology and Molecular Genetics, Michigan State University, 567 Wilson Road, East Lansing, MI, 48824, USA.,Kellogg Biological Station, Michigan State University, 3700 E. Gull Lake Dr, Hickory Corners, MI, 49060, USA
| | - Ashley Shade
- Department of Microbiology and Molecular Genetics, Michigan State University, 567 Wilson Road, East Lansing, MI, 48824, USA. .,The DOE Great Lakes Bioenergy Research Center, Michigan State University, 1129 Farm Lane, East Lansing, MI, 48824, USA. .,Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, 293 Farm Lane, East Lansing, MI, 48824, USA. .,The Plant Resilience Institute, Michigan State University, East Lansing, MI, 48840, USA. .,Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA.
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13
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Cell Aggregation and Aerobic Respiration Are Important for Zymomonas mobilis ZM4 Survival in an Aerobic Minimal Medium. Appl Environ Microbiol 2019; 85:AEM.00193-19. [PMID: 30877116 DOI: 10.1128/aem.00193-19] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 03/09/2019] [Indexed: 12/30/2022] Open
Abstract
Zymomonas mobilis produces ethanol from glucose near the theoretical maximum yield, making it a potential alternative to the yeast Saccharomyces cerevisiae for industrial ethanol production. A potentially useful industrial feature is the ability to form multicellular aggregates called flocs, which can settle quickly and exhibit higher resistance to harmful chemicals than single cells. While spontaneous floc-forming Z. mobilis mutants have been described, little is known about the natural conditions that induce Z. mobilis floc formation or about the genetic factors involved. Here we found that wild-type Z. mobilis forms flocs in response to aerobic growth conditions but only in a minimal medium. We identified a cellulose synthase gene cluster and a single diguanylate cyclase that are essential for both floc formation and survival in a minimal aerobic medium. We also found that NADH dehydrogenase 2, a key component of the aerobic respiratory chain, is important for survival in a minimal aerobic medium, providing a physiological role for this enzyme, which has previously been found to be disadvantageous in a rich aerobic medium. Supplementation of the minimal medium with vitamins also promoted survival but did not inhibit floc formation.IMPORTANCE The bacterium Zymomonas mobilis is best known for its anaerobic fermentative lifestyle, in which it converts glucose into ethanol at a yield surpassing that of yeast. However, Z. mobilis also has an aerobic lifestyle, which has confounded researchers with its attributes of poor growth, accumulation of toxic acetic acid and acetaldehyde, and respiratory enzymes that are detrimental for aerobic growth. Here we show that a major Z. mobilis respiratory enzyme and the ability to form multicellular aggregates, called flocs, are important for survival, but only during aerobic growth in a medium containing a minimum set of nutrients required for growth. Supplements, such as vitamins or yeast extract, promote aerobic growth and, in some cases, inhibit floc formation. We propose that Z. mobilis likely requires aerobic respiration and floc formation in order to survive in natural environments that lack protective factors found in supplements such as yeast extract.
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14
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Ralph J, Lapierre C, Boerjan W. Lignin structure and its engineering. Curr Opin Biotechnol 2019; 56:240-249. [PMID: 30921563 DOI: 10.1016/j.copbio.2019.02.019] [Citation(s) in RCA: 291] [Impact Index Per Article: 58.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/02/2019] [Accepted: 02/22/2019] [Indexed: 02/06/2023]
Abstract
Studies on lignin structure and its engineering are inextricably and bidirectionally linked. Perturbations of genes on the lignin biosynthetic pathway may result in striking compositional and structural changes that in turn suggest novel approaches for altering lignin and even 'designing' the polymer to enhance its value or with a view toward its simpler removal from the cell wall polysaccharides. Basic structural studies on various native lignins increasingly refine our knowledge of lignin structure, and examining lignins in different species reveals the extent to which evolution and natural variation have resulted in the incorporation of 'non-traditional' phenolic monomers, including phenolics from beyond the monolignol biosynthetic pathway. As a result, the very definition of lignin continues to be expanded and refined.
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Affiliation(s)
- John Ralph
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA; Department of Energy Great Lakes Bioenergy Research Center, The Wisconsin Energy Institute, University of Wisconsin, Madison, WI 53726, USA.
| | - Catherine Lapierre
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - Wout Boerjan
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, B-9052, Gent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 927, B-9052, Gent, Belgium
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15
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Scarborough MJ, Lynch G, Dickson M, McGee M, Donohue TJ, Noguera DR. Increasing the economic value of lignocellulosic stillage through medium-chain fatty acid production. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:200. [PMID: 30034526 PMCID: PMC6052542 DOI: 10.1186/s13068-018-1193-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 07/06/2018] [Indexed: 05/14/2023]
Abstract
BACKGROUND Lignocellulosic biomass is seen as an abundant renewable source of liquid fuels and chemicals that are currently derived from petroleum. When lignocellulosic biomass is used for ethanol production, the resulting liquid residue (stillage) contains large amounts of organic material that could be further transformed into recoverable bioproducts, thus enhancing the economics of the biorefinery. RESULTS Here we test the hypothesis that a bacterial community could transform the organics in stillage into valuable bioproducts. We demonstrate the ability of this microbiome to convert stillage organics into medium-chain fatty acids (MCFAs), identify the predominant community members, and perform a technoeconomic analysis of recovering MCFAs as co-products of ethanol production. Steady-state operation of a stillage-fed bioreactor showed that 18% of the organic matter in stillage was converted to MCFAs. Xylose and complex carbohydrates were the primary substrates transformed. During the MCFA production period, the five major genera represented more than 95% of the community, including Lactobacillus, Roseburia, Atopobium, Olsenella, and Pseudoramibacter. To assess the potential benefits of producing MCFAs from stillage, we modeled the economics of ethanol and MCFA co-production, at MCFA productivities observed during reactor operation. CONCLUSIONS The analysis predicts that production of MCFAs, ethanol, and electricity could reduce the minimum ethanol selling price from $2.15 to $1.76 gal-1 ($2.68 gal-1 gasoline equivalents) when compared to a lignocellulosic biorefinery that produces only ethanol and electricity.
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Affiliation(s)
- Matthew J. Scarborough
- The Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI USA
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI USA
| | - Griffin Lynch
- The Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI USA
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI USA
| | - Mitch Dickson
- The Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI USA
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI USA
| | - Mick McGee
- The Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI USA
| | - Timothy J. Donohue
- The Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI USA
| | - Daniel R. Noguera
- The Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI USA
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI USA
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16
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Wu W, Rondon V, Weeks K, Pullammanappallil P, Ingram LO, Shanmugam KT. Phosphoric acid based pretreatment of switchgrass and fermentation of entire slurry to ethanol using a simplified process. BIORESOURCE TECHNOLOGY 2018; 251:171-180. [PMID: 29274857 DOI: 10.1016/j.biortech.2017.12.041] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 12/13/2017] [Accepted: 12/14/2017] [Indexed: 05/21/2023]
Abstract
Switchgrass (Alamo) was pretreated with phosphoric acid (0.75 and 1%, w/w) at three temperatures (160, 175 and 190 °C) and time (5, 7.5 and 10 min) using a steam gun. The slurry after pretreatment was liquefied by enzymes and the released sugars were fermented in a simultaneous saccharification and co-fermentation process to ethanol using ethanologenic Escherichia coli strain SL100. Among the three variables in pretreatment, temperature and time were critical in supporting ethanol titer and yield. Enzyme hydrolysis significantly increased the concentration of furans in slurries, apparently due to release of furans bound to the solids. The highest ethanol titer of 21.2 ± 0.3 g/L ethanol obtained at the pretreatment condition of 190-1-7.5 (temperature-acid concentration-time) and 10% solids loading accounted for 190 ± 2.9 g ethanol/kg of raw switch grass. This converts to 61.7 gallons of ethanol per ton of dry switchgrass, a value that is comparable to other published pretreatment conditions.
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Affiliation(s)
- Wei Wu
- Department of Microbiology and Cell Science, Gainesville, FL 32611, United States; Department of Agricultural and Biological Engineering, Gainesville, FL 32611, United States
| | - Vanessa Rondon
- Department of Microbiology and Cell Science, Gainesville, FL 32611, United States; Stan Mayfield Biorefinery, University of Florida, Gainesville, FL 32611, United States
| | - Kalvin Weeks
- Stan Mayfield Biorefinery, University of Florida, Gainesville, FL 32611, United States
| | | | - Lonnie O Ingram
- Department of Microbiology and Cell Science, Gainesville, FL 32611, United States; Stan Mayfield Biorefinery, University of Florida, Gainesville, FL 32611, United States
| | - K T Shanmugam
- Department of Microbiology and Cell Science, Gainesville, FL 32611, United States.
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17
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Yang S, Vera JM, Grass J, Savvakis G, Moskvin OV, Yang Y, McIlwain SJ, Lyu Y, Zinonos I, Hebert AS, Coon JJ, Bates DM, Sato TK, Brown SD, Himmel ME, Zhang M, Landick R, Pappas KM, Zhang Y. Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:125. [PMID: 29743953 PMCID: PMC5930841 DOI: 10.1186/s13068-018-1116-x] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 04/11/2018] [Indexed: 05/19/2023]
Abstract
BACKGROUND Zymomonas mobilis is a natural ethanologen being developed and deployed as an industrial biofuel producer. To date, eight Z. mobilis strains have been completely sequenced and found to contain 2-8 native plasmids. However, systematic verification of predicted Z. mobilis plasmid genes and their contribution to cell fitness has not been hitherto addressed. Moreover, the precise number and identities of plasmids in Z. mobilis model strain ZM4 have been unclear. The lack of functional information about plasmid genes in ZM4 impedes ongoing studies for this model biofuel-producing strain. RESULTS In this study, we determined the complete chromosome and plasmid sequences of ZM4 and its engineered xylose-utilizing derivatives 2032 and 8b. Compared to previously published and revised ZM4 chromosome sequences, the ZM4 chromosome sequence reported here contains 65 nucleotide sequence variations as well as a 2400-bp insertion. Four plasmids were identified in all three strains, with 150 plasmid genes predicted in strain ZM4 and 2032, and 153 plasmid genes predicted in strain 8b due to the insertion of heterologous DNA for expanded substrate utilization. Plasmid genes were then annotated using Blast2GO, InterProScan, and systems biology data analyses, and most genes were found to have apparent orthologs in other organisms or identifiable conserved domains. To verify plasmid gene prediction, RNA-Seq was used to map transcripts and also compare relative gene expression under various growth conditions, including anaerobic and aerobic conditions, or growth in different concentrations of biomass hydrolysates. Overall, plasmid genes were more responsive to varying hydrolysate concentrations than to oxygen availability. Additionally, our results indicated that although all plasmids were present in low copy number (about 1-2 per cell), the copy number of some plasmids varied under specific growth conditions or due to heterologous gene insertion. CONCLUSIONS The complete genome of ZM4 and two xylose-utilizing derivatives is reported in this study, with an emphasis on identifying and characterizing plasmid genes. Plasmid gene annotation, validation, expression levels at growth conditions of interest, and contribution to host fitness are reported for the first time.
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Affiliation(s)
- Shihui Yang
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, 430062 China
- DOE-National Bioenergy Center, National Renewable Energy Laboratory (NREL), Golden, CO 80401 USA
| | - Jessica M. Vera
- DOE-Great Lakes Bioenergy Research Center (GLBRC), University of Wisconsin-Madison, Madison, WI USA
| | - Jeff Grass
- DOE-Great Lakes Bioenergy Research Center (GLBRC), University of Wisconsin-Madison, Madison, WI USA
| | - Giannis Savvakis
- Department of Genetics & Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens (NKUA), Panepistimiopolis, 15701 Athens, Greece
| | - Oleg V. Moskvin
- DOE-Great Lakes Bioenergy Research Center (GLBRC), University of Wisconsin-Madison, Madison, WI USA
| | - Yongfu Yang
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Sean J. McIlwain
- DOE-Great Lakes Bioenergy Research Center (GLBRC), University of Wisconsin-Madison, Madison, WI USA
| | - Yucai Lyu
- DOE-Great Lakes Bioenergy Research Center (GLBRC), University of Wisconsin-Madison, Madison, WI USA
- Present Address: China Three Gorges University, Yichang, 443002 Hubei China
| | - Irene Zinonos
- Department of Genetics & Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens (NKUA), Panepistimiopolis, 15701 Athens, Greece
| | - Alexander S. Hebert
- DOE-Great Lakes Bioenergy Research Center (GLBRC), University of Wisconsin-Madison, Madison, WI USA
| | - Joshua J. Coon
- DOE-Great Lakes Bioenergy Research Center (GLBRC), University of Wisconsin-Madison, Madison, WI USA
| | - Donna M. Bates
- DOE-Great Lakes Bioenergy Research Center (GLBRC), University of Wisconsin-Madison, Madison, WI USA
| | - Trey K. Sato
- DOE-Great Lakes Bioenergy Research Center (GLBRC), University of Wisconsin-Madison, Madison, WI USA
| | - Steven D. Brown
- DOE-BioEnergy Science Center, Oak Ridge National Laboratory (ORNL), Oak Ridge, TN 37831 USA
- DOE-Biosciences Division, Oak Ridge National Laboratory (ORNL), Oak Ridge, TN 37831 USA
- Present Address: LanzaTech, Inc., Skokie, IL 60077 USA
| | - Michael E. Himmel
- DOE-Biosciences Center, National Renewable Energy Laboratory (NREL), Golden, CO 80401 USA
| | - Min Zhang
- DOE-National Bioenergy Center, National Renewable Energy Laboratory (NREL), Golden, CO 80401 USA
| | - Robert Landick
- DOE-Great Lakes Bioenergy Research Center (GLBRC), University of Wisconsin-Madison, Madison, WI USA
| | - Katherine M. Pappas
- Department of Genetics & Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens (NKUA), Panepistimiopolis, 15701 Athens, Greece
| | - Yaoping Zhang
- DOE-Great Lakes Bioenergy Research Center (GLBRC), University of Wisconsin-Madison, Madison, WI USA
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18
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Crowe JD, Feringa N, Pattathil S, Merritt B, Foster C, Dines D, Ong RG, Hodge DB. Identification of developmental stage and anatomical fraction contributions to cell wall recalcitrance in switchgrass. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:184. [PMID: 28725264 PMCID: PMC5512841 DOI: 10.1186/s13068-017-0870-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 07/06/2017] [Indexed: 05/08/2023]
Abstract
BACKGROUND Heterogeneity within herbaceous biomass can present important challenges for processing feedstocks to cellulosic biofuels. Alterations to cell wall composition and organization during plant growth represent major contributions to heterogeneity within a single species or cultivar. To address this challenge, the focus of this study was to characterize the relationship between composition and properties of the plant cell wall and cell wall response to deconstruction by NaOH pretreatment and enzymatic hydrolysis for anatomical fractions (stem internodes, leaf sheaths, and leaf blades) within switchgrass at various tissue maturities as assessed by differing internode. RESULTS Substantial differences in both cell wall composition and response to deconstruction were observed as a function of anatomical fraction and tissue maturity. Notably, lignin content increased with tissue maturity concurrently with decreasing ferulate content across all three anatomical fractions. Stem internodes exhibited the highest lignin content as well as the lowest hydrolysis yields, which were inversely correlated to lignin content. Confocal microscopy was used to demonstrate that removal of cell wall aromatics (i.e., lignins and hydroxycinnamates) by NaOH pretreatment was non-uniform across diverse cell types. Non-cellulosic polysaccharides were linked to differences in cell wall response to deconstruction in lower lignin fractions. Specifically, leaf sheath and leaf blade were found to have higher contents of substituted glucuronoarabinoxylans and pectic polysaccharides. Glycome profiling demonstrated that xylan and pectic polysaccharide extractability varied with stem internode maturity, with more mature internodes requiring harsher chemical extractions to remove comparable glycan abundances relative to less mature internodes. While enzymatic hydrolysis was performed on extractives-free biomass, extractible sugars (i.e., starch and sucrose) comprised a significant portion of total dry weight particularly in stem internodes, and may provide an opportunity for recovery during processing. CONCLUSIONS Cell wall structural differences within a single plant can play a significant role in feedstock properties and have the potential to be exploited for improving biomass processability during a biorefining process. The results from this work demonstrate that cell wall lignin content, while generally exhibiting a negative correlation with enzymatic hydrolysis yields, is not the sole contributor to cell wall recalcitrance across diverse anatomical fractions within switchgrass.
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Affiliation(s)
- Jacob D. Crowe
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI USA
| | - Nicholas Feringa
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI USA
| | - Sivakumar Pattathil
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA USA
- Bioenergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Brian Merritt
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA USA
| | - Cliff Foster
- DOE-Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI USA
| | - Dayna Dines
- DOE-Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI USA
| | - Rebecca G. Ong
- Department of Chemical Engineering, Michigan Technological University, Houghton, MI USA
| | - David B. Hodge
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI USA
- DOE-Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI USA
- Department of Biosystems & Agricultural Engineering, Michigan State University, East Lansing, MI USA
- Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, Luleå, Sweden
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