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Gorenz B, Oelschlager ML, Jespersen JC, Cao C, Smith AH, Mackie RI, Dilger RN. Organ growth and fermentation profiles of broilers differing in body growth rate. Poult Sci 2024; 103:103628. [PMID: 38518667 DOI: 10.1016/j.psj.2024.103628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/02/2024] [Accepted: 03/04/2024] [Indexed: 03/24/2024] Open
Abstract
This study sought to determine the relationship among broiler performance, organ development, and indicators of microbiota colonization. A total of 1,200 two-day-old male Ross 308 broiler chicks, divided among 3 cohorts of equal size, were housed in battery cages, and allotted based on body weight. On study d 11, birds were weighed, and birds with BW gain within the 10th and 90th percentiles were assigned to the Slow and Fast groups, respectively. Birds (n = 30 for each group) selected on d 11 were provided water and a corn-soybean meal-based diet ad libitum while maintained individually through study d 25 (i.e., a 14-d growth period). Parameters regarding growth performance, organ and intestine weights and lengths, and intestinal volatile fatty acid concentrations were measured. All data were analyzed by one-way ANOVA using the Mixed procedure of SAS. Fast birds exhibited greater (P < 0.001) BW gain and feed intake than slow birds, but feed conversion ratio (FCR) did not differ (P = 0.19). Additionally, Slow birds had higher (P < 0.05) relative weights (% of BW) for nearly all organs on d 11 and 25, most notably the gizzard, proventriculus, pancreas, and liver. Conversely, intestinal sections were longer (P < 0.05) in the Fast birds. Measurement of gut histomorphology did not show any notable differences between growth rate groups in terms of villi height, crypt depth, or their ratio for either time-point (P > 0.05). In terms of volatile fatty acid concentrations of luminal contents, acetate concentrations were 10.2% higher (P < 0.001) in the ileum of the Slow birds compared with Fast birds on d 25. Overall, the findings suggest that total BW gain is influenced by the development of metabolically active organs, as supported by lower weight gain in Slow birds with relatively larger organ weights and shorter intestinal lengths than their Fast counterparts. The general lack of differences in fermentation end-product concentrations in luminal contents does not rule out influence of the microbiota on growth rate of broilers, which warrants further investigation.
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Affiliation(s)
- Brad Gorenz
- Department of Animal Sciences, University of Illinois, Urbana, IL 61801, USA
| | - Maci L Oelschlager
- Department of Animal Sciences, University of Illinois, Urbana, IL 61801, USA
| | | | - Chang Cao
- Department of Animal Sciences, University of Illinois, Urbana, IL 61801, USA
| | - Alexandra H Smith
- Arm & Hammer Animal and Food Production, Church & Dwight Co., Inc., Waukesha, WI 53186, USA
| | - Roderick I Mackie
- Department of Animal Sciences, University of Illinois, Urbana, IL 61801, USA
| | - Ryan N Dilger
- Department of Animal Sciences, University of Illinois, Urbana, IL 61801, USA.
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Mackie RI, Kim H, Kim NK, Cann I. - Invited Review - Hydrogen production and hydrogen utilization in the rumen: key to mitigating enteric methane production. Anim Biosci 2024; 37:323-336. [PMID: 38186257 PMCID: PMC10838669 DOI: 10.5713/ab.23.0294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 10/13/2023] [Accepted: 11/08/2023] [Indexed: 01/09/2024] Open
Abstract
Molecular hydrogen (H2) and formate (HCOO-) are metabolic end products of many primary fermenters in the rumen ecosystem. Both play a vital role in fermentation where they are electron sinks for individual microbes in an anaerobic environment that lacks external electron acceptors. If H2 and/or formate accumulate within the rumen, the ability of primary fermenters to regenerate electron carriers may be inhibited and microbial metabolism and growth disrupted. Consequently, H2- and/or formate-consuming microbes such as methanogens and possibly homoacetogens play a key role in maintaining the metabolic efficiency of primary fermenters. There is increasing interest in identifying approaches to manipulate the rumen ecosystem for the benefit of the host and the environment. As H2 and formate are important mediators of interspecies interactions, an understanding of their production and utilization could be a significant starting point for the development of successful interventions aimed at redirecting electron flow and reducing methane emissions. We conclude by discussing in brief ruminant methane mitigation approaches as a model to help understand the fate of H2 and formate in the rumen ecosystem.
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Affiliation(s)
- Roderick I. Mackie
- Department of Animal Sciences, University of Illinois, Urbana, IL 61801,
USA
- Carle R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801,
USA
| | - Hyewon Kim
- Department of Animal Sciences, University of Illinois, Urbana, IL 61801,
USA
| | - Na Kyung Kim
- Department of Animal Sciences, University of Illinois, Urbana, IL 61801,
USA
| | - Isaac Cann
- Department of Animal Sciences, University of Illinois, Urbana, IL 61801,
USA
- Carle R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801,
USA
- Department of Microbiology, University of Illinois, Urbana, IL 61801,
USA
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Bedekar AA, Deewan A, Jagtap SS, Parker DA, Liu P, Mackie RI, Rao CV. Transcriptional and metabolomic responses of Methylococcus capsulatus Bath to nitrogen source and temperature downshift. Front Microbiol 2023; 14:1259015. [PMID: 37928661 PMCID: PMC10623323 DOI: 10.3389/fmicb.2023.1259015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/10/2023] [Indexed: 11/07/2023] Open
Abstract
Methanotrophs play a significant role in methane oxidation, because they are the only biological methane sink present in nature. The methane monooxygenase enzyme oxidizes methane or ammonia into methanol or hydroxylamine, respectively. While much is known about central carbon metabolism in methanotrophs, far less is known about nitrogen metabolism. In this study, we investigated how Methylococcus capsulatus Bath, a methane-oxidizing bacterium, responds to nitrogen source and temperature. Batch culture experiments were conducted using nitrate or ammonium as nitrogen sources at both 37°C and 42°C. While growth rates with nitrate and ammonium were comparable at 42°C, a significant growth advantage was observed with ammonium at 37°C. Utilization of nitrate was higher at 42°C than at 37°C, especially in the first 24 h. Use of ammonium remained constant between 42°C and 37°C; however, nitrite buildup and conversion to ammonia were found to be temperature-dependent processes. We performed RNA-seq to understand the underlying molecular mechanisms, and the results revealed complex transcriptional changes in response to varying conditions. Different gene expression patterns connected to respiration, nitrate and ammonia metabolism, methane oxidation, and amino acid biosynthesis were identified using gene ontology analysis. Notably, key pathways with variable expression profiles included oxidative phosphorylation and methane and methanol oxidation. Additionally, there were transcription levels that varied for genes related to nitrogen metabolism, particularly for ammonia oxidation, nitrate reduction, and transporters. Quantitative PCR was used to validate these transcriptional changes. Analyses of intracellular metabolites revealed changes in fatty acids, amino acids, central carbon intermediates, and nitrogen bases in response to various nitrogen sources and temperatures. Overall, our results offer improved understanding of the intricate interactions between nitrogen availability, temperature, and gene expression in M. capsulatus Bath. This study enhances our understanding of microbial adaptation strategies, offering potential applications in biotechnological and environmental contexts.
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Affiliation(s)
- Ashwini Ashok Bedekar
- Energy and Biosciences Institute, Materials Research Laboratory, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - Anshu Deewan
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - Sujit S. Jagtap
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - David A. Parker
- Energy and Biosciences Institute, Materials Research Laboratory, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Shell Exploration and Production Inc., Westhollow Technology Center, Houston, TX, United States
| | - Ping Liu
- Energy and Biosciences Institute, Materials Research Laboratory, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Shell Exploration and Production Inc., Westhollow Technology Center, Houston, TX, United States
| | - Roderick I. Mackie
- Energy and Biosciences Institute, Materials Research Laboratory, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - Christopher V. Rao
- Energy and Biosciences Institute, Materials Research Laboratory, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Champaign, IL, United States
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Kim HW, Kim NK, Phillips APR, Parker DA, Liu P, Whitaker RJ, Rao CV, Mackie RI. Genomic insight and physiological characterization of thermoacidophilic Alicyclobacillus isolated from Yellowstone National Park. Front Microbiol 2023; 14:1232587. [PMID: 37822751 PMCID: PMC10562698 DOI: 10.3389/fmicb.2023.1232587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 09/14/2023] [Indexed: 10/13/2023] Open
Abstract
Introduction Alicyclobacillus has been isolated from extreme environments such as hot springs, volcanoes, as well as pasteurized acidic beverages, because it can tolerate extreme temperatures and acidity. In our previous study, Alicyclobacillus was isolated during the enrichment of methane oxidizing bacteria from Yellowstone Hot Spring samples. Methods Physiological characterization and genomic exploration of two new Alicyclobacillus isolates, AL01A and AL05G, are the main focus of this study to identify their potential relationships with a thermoacidophilic methanotroph (Methylacidiphilum) isolated from the same hot spring sediments. Results and discussion In the present study, both Alicyclobacillus isolates showed optimal growth at pH 3.5 and 55°C, and contain ω-alicyclic fatty acids as a major lipid (ca. 60%) in the bacterial membrane. Genomic analysis of these strains revealed specific genes and pathways that the methanotroph genome does not have in the intermediary carbon metabolism pathway such as serC (phosphoserine aminotransferase), comA (phosphosulfolactate synthase), and DAK (glycerone kinase). Both Alicyclobacillus strains were also found to contain transporter systems for extracellular sulfate (ABC transporter), suggesting that they could play an important role in sulfur metabolism in this extreme environment. Genomic analysis of vitamin metabolism revealed Alicyclobacillus and Methylacidiphilum are able to complement each other's nutritional deficiencies, resulting in a mutually beneficial relationship, especially in vitamin B1(thiamin), B3 (niacin), and B7 (biotin) metabolism. These findings provide insights into the role of Alicyclobacillus isolates in geothermal environments and their unique metabolic adaptations to these environments.
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Affiliation(s)
- Hye Won Kim
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Materials Research Laboratory, Energy and Biosciences Institute, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - Na Kyung Kim
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Materials Research Laboratory, Energy and Biosciences Institute, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - Alex P. R. Phillips
- Department of Microbiology, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - David A. Parker
- Materials Research Laboratory, Energy and Biosciences Institute, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Westhollow Technology Center, Shell Exploration and Production Inc., Houston, TX, United States
| | - Ping Liu
- Materials Research Laboratory, Energy and Biosciences Institute, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Westhollow Technology Center, Shell Exploration and Production Inc., Houston, TX, United States
| | - Rachel J. Whitaker
- Department of Microbiology, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - Christopher V. Rao
- Materials Research Laboratory, Energy and Biosciences Institute, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - Roderick I. Mackie
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Materials Research Laboratory, Energy and Biosciences Institute, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, United States
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Tondini SM, Mackie RI, McCann JC. Polyclonal antibodies inhibit growth of key cellulolytic rumen bacterial species. Front Microbiol 2023; 14:1196492. [PMID: 37408639 PMCID: PMC10318403 DOI: 10.3389/fmicb.2023.1196492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 05/22/2023] [Indexed: 07/07/2023] Open
Abstract
Antibodies targeting specific bacterial species could allow for modification of the rumen microbial population to enhance rumen fermentation. However, there is limited knowledge of targeted antibody effects on rumen bacteria. Therefore, our objective was to develop efficacious polyclonal antibodies to inhibit the growth of targeted cellulolytic bacteria from the rumen. Egg-derived, polyclonal antibodies were developed against pure cultures of Ruminococcus albus 7 (anti-RA7), Ruminococcus albus 8 (anti-RA8), and Fibrobacter succinogenes S85 (anti-FS85). Antibodies were added to a cellobiose-containing growth medium for each of the three targeted species. Antibody efficacy was determined via inoculation time (0 h and 4 h) and dose response. Antibody doses included: 0 (CON), 1.3 × 10-4 (LO), 0.013 (MD), and 1.3 (HI) mg antibody per ml of medium. Each targeted species inoculated at 0 h with HI of their respective antibody had decreased (P < 0.01) final optical density and total acetate concentration after a 52 h growth period when compared with CON or LO. Live/dead stains of R. albus 7 and F. succinogenes S85 dosed at 0 h with HI of their respective antibody indicated a decrease (≥ 96%; P < 0.05) in live bacterial cells during the mid-log phase compared with CON or LO. Addition of HI of anti-FS85 at 0 h in F. succinogenes S85 cultures reduced (P < 0.01) total substrate disappearance over 52 h by at least 48% when compared with CON or LO. Cross-reactivity was assessed by adding HI at 0 h to non-targeted bacterial species. Addition of anti-RA8 or anti-RA7 to F. succinogenes S85 cultures did not affect (P ≥ 0.45) total acetate accumulation after 52 h incubation, indicating that antibodies have less of an inhibitory effect on non-target strains. Addition of anti-FS85 to non-cellulolytic strains did not affect (P ≥ 0.89) OD, substrate disappearance, or total VFA concentrations, providing further evidence of specificity against fiber-degrading bacteria. Western blotting with anti-FS85 indicated selective binding to F. succinogenes S85 proteins. Identification by LC-MS/MS of 8 selected protein spots indicated 7 were outer membrane proteins. Overall, polyclonal antibodies were more efficacious at inhibiting the growth of targeted cellulolytic bacteria than non-targeted bacteria. Validated polyclonal antibodies could serve as an effective approach to modify rumen bacterial populations.
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Affiliation(s)
- Sara M. Tondini
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Roderick I. Mackie
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- Carle R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Joshua C. McCann
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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Tondini SM, Mackie RI, McCann JC. 207 Polyclonal Antibodies Inhibit Growth of Key Cellulolytic Rumen Bacterial Species. J Anim Sci 2022. [DOI: 10.1093/jas/skac064.161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
The objective was to develop efficacious polyclonal antibodies to inhibit growth of targeted cellulolytic rumen bacterial species. Many rumen microorganisms have overlapping functions, so inhibiting the activity of targeted bacterial species may help elucidate their dynamic contributions to rumen fermentation. Egg-derived, polyclonal antibodies were developed against whole-cell cultures of Ruminococcus albus 7 (anti-RA7), Ruminococcus albus 8 (anti-RA8), and Fibrobacter succinogenes S85 (anti-FS85). Antibodies were added to a cellobiose-containing growth medium of pure cultures of the 3 targeted species. Antibody efficacy was determined via an inoculation time (0 and 4 h) and dose response. Antibody doses included: 0 (CON), 0.013 (LO), 1.3 (MD), 13 (HI) mg antibody per 10 mL of medium. Each targeted species inoculated at 0 h with HI of their respective antibody had decreased (P < 0.01) final optical density and total volatile fatty acid (VFA) concentration after a 52-h growth period when compared with CON or LO. Live/dead stains of R. albus 7 and F. succinogenes S85 dosed at 0 h with HI of their respective antibody indicated a decrease (≥ 96%; P < 0.05) of live bacterial cells during mid-log phase compared with CON or LO. Addition of HI of anti-FS85 at 0 h in F. succinogenes S85 cultures reduced (P < 0.01) total substrate disappearance over 52 h by at least 48% when compared with CON or LO. Cross-reactivity was assessed by adding HI at 0 h to non-targeted bacterial species. Addition of anti-RA8 or anti-RA7 to F. succinogenes S85 cultures did not affect (P ≥ 0.45) total VFA accumulation after 52 h incubation. Overall, polyclonal antibodies were more efficacious at inhibiting growth of targeted cellulolytic bacteria than non-targeted bacteria. Specific polyclonal antibodies can be used to further characterize functional contributions of bacterial species to rumen fermentation.
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Kelly WJ, Mackie RI, Attwood GT, Janssen PH, McAllister TA, Leahy SC. Hydrogen and formate production and utilisation in the rumen and the human colon. Anim Microbiome 2022; 4:22. [PMID: 35287765 PMCID: PMC8919644 DOI: 10.1186/s42523-022-00174-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 03/02/2022] [Indexed: 12/31/2022] Open
Abstract
Molecular hydrogen (H2) and formate (HCOO−) are metabolic end products of many primary fermenters in the mammalian gut. Both play a vital role in fermentation where they are electron sinks for individual microbes in an anaerobic environment that lacks external electron acceptors. If H2 and/or formate accumulate within the gut ecosystem, the ability of primary fermenters to regenerate electron carriers may be inhibited and microbial metabolism and growth disrupted. Consequently, H2- and/or formate-consuming microbes such as methanogens and homoacetogens play a key role in maintaining the metabolic efficiency of primary fermenters. There is increasing interest in identifying approaches to manipulate mammalian gut environments for the benefit of the host and the environment. As H2 and formate are important mediators of interspecies interactions, an understanding of their production and utilisation could be a significant entry point for the development of successful interventions. Ruminant methane mitigation approaches are discussed as a model to help understand the fate of H2 and formate in gut systems.
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Leahy SC, Janssen PH, Attwood GT, Mackie RI, McAllister TA, Kelly WJ. Electron flow: key to mitigating ruminant methanogenesis. Trends Microbiol 2022; 30:209-212. [PMID: 35027237 DOI: 10.1016/j.tim.2021.12.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 12/07/2021] [Accepted: 12/08/2021] [Indexed: 10/19/2022]
Abstract
Disposal of electrons generated during the fermentation of ingested feed is a fundamental feature of anaerobic microbial gut ecosystems. Here, we focus on the well-studied rumen environment to highlight how electrons are transferred through anaerobic fermentation pathways and how manipulating this electron flow is important to reducing methane emissions from ruminants. Priorities for research that can accelerate understanding in this area are highlighted.
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Affiliation(s)
- Sinead C Leahy
- New Zealand Agricultural Greenhouse Gas Research Centre (NZAGRC), Palmerston North, New Zealand.
| | - Peter H Janssen
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
| | - Graeme T Attwood
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
| | | | | | - William J Kelly
- New Zealand Agricultural Greenhouse Gas Research Centre (NZAGRC), Palmerston North, New Zealand
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Hagen LH, Brooke CG, Shaw CA, Norbeck AD, Piao H, Arntzen MØ, Olson HM, Copeland A, Isern N, Shukla A, Roux S, Lombard V, Henrissat B, O'Malley MA, Grigoriev IV, Tringe SG, Mackie RI, Pasa-Tolic L, Pope PB, Hess M. Proteome specialization of anaerobic fungi during ruminal degradation of recalcitrant plant fiber. ISME J 2020; 15:421-434. [PMID: 32929206 PMCID: PMC8026616 DOI: 10.1038/s41396-020-00769-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 08/21/2020] [Accepted: 09/02/2020] [Indexed: 12/17/2022]
Abstract
The rumen harbors a complex microbial mixture of archaea, bacteria, protozoa, and fungi that efficiently breakdown plant biomass and its complex dietary carbohydrates into soluble sugars that can be fermented and subsequently converted into metabolites and nutrients utilized by the host animal. While rumen bacterial populations have been well documented, only a fraction of the rumen eukarya are taxonomically and functionally characterized, despite the recognition that they contribute to the cellulolytic phenotype of the rumen microbiota. To investigate how anaerobic fungi actively engage in digestion of recalcitrant fiber that is resistant to degradation, we resolved genome-centric metaproteome and metatranscriptome datasets generated from switchgrass samples incubated for 48 h in nylon bags within the rumen of cannulated dairy cows. Across a gene catalog covering anaerobic rumen bacteria, fungi and viruses, a significant portion of the detected proteins originated from fungal populations. Intriguingly, the carbohydrate-active enzyme (CAZyme) profile suggested a domain-specific functional specialization, with bacterial populations primarily engaged in the degradation of hemicelluloses, whereas fungi were inferred to target recalcitrant cellulose structures via the detection of a number of endo- and exo-acting enzymes belonging to the glycoside hydrolase (GH) family 5, 6, 8, and 48. Notably, members of the GH48 family were amongst the highest abundant CAZymes and detected representatives from this family also included dockerin domains that are associated with fungal cellulosomes. A eukaryote-selected metatranscriptome further reinforced the contribution of uncultured fungi in the ruminal degradation of recalcitrant fibers. These findings elucidate the intricate networks of in situ recalcitrant fiber deconstruction, and importantly, suggest that the anaerobic rumen fungi contribute a specific set of CAZymes that complement the enzyme repertoire provided by the specialized plant cell wall degrading rumen bacteria.
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Affiliation(s)
- Live H Hagen
- Faculty of Biotechnology, Chemistry and Food Science, Norwegian University of Life Sciences, Aas, Norway.
| | | | | | | | - Hailan Piao
- Washington State University, Richland, WA, USA
| | - Magnus Ø Arntzen
- Faculty of Biotechnology, Chemistry and Food Science, Norwegian University of Life Sciences, Aas, Norway
| | - Heather M Olson
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, CA, USA
| | - Alex Copeland
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nancy Isern
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, CA, USA
| | - Anil Shukla
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Simon Roux
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Vincent Lombard
- CNRS, UMR 7257, Université Aix-Marseille, 13288, Marseille, France.,Institut National de la Recherche Agronomique, USC 1408 Architecture et Fonction des Macromolécules Biologiques, 13288, Marseille, France
| | - Bernard Henrissat
- CNRS, UMR 7257, Université Aix-Marseille, 13288, Marseille, France.,Institut National de la Recherche Agronomique, USC 1408 Architecture et Fonction des Macromolécules Biologiques, 13288, Marseille, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara, CA, USA
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Susannah G Tringe
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Roderick I Mackie
- Department of Animal Science, University of Illinois, Urbana-Champaign, IL, USA
| | - Ljiljana Pasa-Tolic
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, CA, USA
| | - Phillip B Pope
- Faculty of Biotechnology, Chemistry and Food Science, Norwegian University of Life Sciences, Aas, Norway.,Faculty of Biosciences, Norwegian University of Life Sciences, Aas, Norway
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10
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Oliveira BG, Mendes LW, Smyth EM, Tsai SM, Feigl BJ, Mackie RI. Assessment of microbial diversity associated with CH 4 emission from sugarcane vinasse storage and transportation systems. J Environ Manage 2020; 269:110748. [PMID: 32425165 DOI: 10.1016/j.jenvman.2020.110748] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 04/16/2020] [Accepted: 05/07/2020] [Indexed: 06/11/2023]
Abstract
Sugarcane bioethanol has favorable energy and greenhouse gas balance, although the production process generates several residues including vinasse, which deserves attention because of its significant methane (CH4) emission during storage and transportation stages. Considering that CH4 emissions are dependent on the structure and abundance of microbial communities, we hypothesized that different vinasse transportation systems would harbor different microbial community composition, resulting in distinct CH4 patterns. To test this hypothesis, we used high-throughput 16S rRNA sequencing with real-time PCR to evaluate the composition and abundance of microorganisms in the two main systems of vinasse storage and transportation (i.e. open channels and tanks systems) in Brazil. Our results showed higher microbial diversity and CH4 emissions in channel system, especially in the uncoated section. Significant differences in microbial community structure, diversity, and abundance between the uncoated/coated open channel and tanks indicated a clear selection at taxonomic and functional levels, especially in relation to CH4 production. These responses included higher methanogens diversity in the uncoated section of the channel and are in agreement with the methanogen abundance determined by mcrA and mba genes copy number (1.5 × 107 and 4.3 × 1010) and subsequent positive correlation with CH4 emissions (R2 = 0.8). The most representative methanogen genus across the samples was Methanobrevibacter. The results observed herein shows that the use of the coating in the bottom of channels and tanks prevent the growth and development of a methanogen-related community. We concluded that the improvements in vinasse storage and transportation systems would significantly change the microbial community and reduce CH4 emissions, thereby making bioethanol a greener biofuel.
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Affiliation(s)
- Bruna G Oliveira
- Agronomic Institute of Campinas, Soils and Environmental Resources Center, Barão de Itapura, 1481, Campinas, SP, 13001-970, Brazil; Center for Nuclear Energy in Agriculture, University of São Paulo, Av. Centenário 303, 13416-000, Piracicaba, SP, Brazil.
| | - Lucas W Mendes
- Center for Nuclear Energy in Agriculture, University of São Paulo, Av. Centenário 303, 13416-000, Piracicaba, SP, Brazil
| | - Eoghan M Smyth
- Energy Biosciences Institute, University of Illinois at Urbana-Champaign, 1206 W. Gregory Dr., Urbana, IL, 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 W. Gregory Dr., Urbana, IL, 61801, USA
| | - Siu M Tsai
- Center for Nuclear Energy in Agriculture, University of São Paulo, Av. Centenário 303, 13416-000, Piracicaba, SP, Brazil
| | - Brigitte J Feigl
- Center for Nuclear Energy in Agriculture, University of São Paulo, Av. Centenário 303, 13416-000, Piracicaba, SP, Brazil
| | - Roderick I Mackie
- Energy Biosciences Institute, University of Illinois at Urbana-Champaign, 1206 W. Gregory Dr., Urbana, IL, 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 W. Gregory Dr., Urbana, IL, 61801, USA; Department of Animal Sciences, University of Illinois at Urbana-Champaign, 1207 W. Gregory Dr., Urbana, IL, 61801, USA
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11
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Cann I, Pereira GV, Abdel-Hamid AM, Kim H, Wefers D, Kayang BB, Kanai T, Sato T, Bernardi RC, Atomi H, Mackie RI. Thermophilic Degradation of Hemicellulose, a Critical Feedstock in the Production of Bioenergy and Other Value-Added Products. Appl Environ Microbiol 2020; 86:e02296-19. [PMID: 31980431 PMCID: PMC7082577 DOI: 10.1128/aem.02296-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Renewable fuels have gained importance as the world moves toward diversifying its energy portfolio. A critical step in the biomass-to-bioenergy initiative is deconstruction of plant cell wall polysaccharides to their unit sugars for subsequent fermentation to fuels. To acquire carbon and energy for their metabolic processes, diverse microorganisms have evolved genes encoding enzymes that depolymerize polysaccharides to their carbon/energy-rich building blocks. The microbial enzymes mostly target the energy present in cellulose, hemicellulose, and pectin, three major forms of energy storage in plants. In the effort to develop bioenergy as an alternative to fossil fuel, a common strategy is to harness microbial enzymes to hydrolyze cellulose to glucose for fermentation to fuels. However, the conversion of plant biomass to renewable fuels will require both cellulose and hemicellulose, the two largest components of the plant cell wall, as feedstock to improve economic feasibility. Here, we explore the enzymes and strategies evolved by two well-studied bacteria to depolymerize the hemicelluloses xylan/arabinoxylan and mannan. The sets of enzymes, in addition to their applications in biofuels and value-added chemical production, have utility in animal feed enzymes, a rapidly developing industry with potential to minimize adverse impacts of animal agriculture on the environment.
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Affiliation(s)
- Isaac Cann
- Department of Animal Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Kyoto, Japan
| | - Gabriel V Pereira
- Department of Animal Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Ahmed M Abdel-Hamid
- Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Heejin Kim
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Daniel Wefers
- Karlsruhe Institute of Technology, Institute of Applied Biosciences, Department of Food Chemistry and Phytochemistry, Karlsruhe, Germany
| | - Boniface B Kayang
- Department of Animal Science, School of Agriculture, University of Ghana, Legon, Ghana
| | - Tamotsu Kanai
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Kyoto, Japan
| | - Takaaki Sato
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Kyoto, Japan
- JST, CREST, Tokyo, Japan
| | - Rafael C Bernardi
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Haruyuki Atomi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Kyoto, Japan
- JST, CREST, Tokyo, Japan
| | - Roderick I Mackie
- Department of Animal Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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12
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Oosterkamp MJ, Bauer S, Ibáñez AB, Méndez-García C, Hong PY, Cann I, Mackie RI. Identification of methanogenesis and syntrophy as important microbial metabolic processes for optimal thermophilic anaerobic digestion of energy cane thin stillage. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.biteb.2019.100254] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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13
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Mohamed ET, Mundhada H, Landberg J, Cann I, Mackie RI, Nielsen AT, Herrgård MJ, Feist AM. Generation of an E. coli platform strain for improved sucrose utilization using adaptive laboratory evolution. Microb Cell Fact 2019; 18:116. [PMID: 31255177 PMCID: PMC6599523 DOI: 10.1186/s12934-019-1165-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Accepted: 06/22/2019] [Indexed: 01/01/2023] Open
Abstract
Background Sucrose is an attractive industrial carbon source due to its abundance and the fact that it can be cheaply generated from sources such as sugarcane. However, only a few characterized Escherichia coli strains are able to metabolize sucrose, and those that can are typically slow growing or pathogenic strains. Methods To generate a platform strain capable of efficiently utilizing sucrose with a high growth rate, adaptive laboratory evolution (ALE) was utilized to evolve engineered E. coli K-12 MG1655 strains containing the sucrose utilizing csc genes (cscB, cscK, cscA) alongside the native sucrose consuming E. coli W. Results Evolved K-12 clones displayed an increase in growth and sucrose uptake rates of 1.72- and 1.40-fold on sugarcane juice as compared to the original engineered strains, respectively, while E. coli W clones showed a 1.4-fold increase in sucrose uptake rate without a significant increase in growth rate. Whole genome sequencing of evolved clones and populations revealed that two genetic regions were frequently mutated in the K-12 strains; the global transcription regulatory genes rpoB and rpoC, and the metabolic region related to a pyrimidine biosynthetic deficiency in K-12 attributed to pyrE expression. These two mutated regions have been characterized to confer a similar benefit when glucose is the main carbon source, and reverse engineering revealed the same causal advantages on M9 sucrose. Additionally, the most prevalent mutation found in the evolved E. coli W lineages was the inactivation of the cscR gene, the transcriptional repression of sucrose uptake genes. Conclusion The generated K-12 and W platform strains, and the specific sets of mutations that enable their phenotypes, are available as valuable tools for sucrose-based industrial bioproduction in the facile E. coli chassis. Electronic supplementary material The online version of this article (10.1186/s12934-019-1165-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elsayed T Mohamed
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, Lyngby, 2800 Kgs, Denmark
| | - Hemanshu Mundhada
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, Lyngby, 2800 Kgs, Denmark
| | - Jenny Landberg
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, Lyngby, 2800 Kgs, Denmark
| | - Isaac Cann
- Department of Animal Sciences, Institute for Genomic Biology and Energy Biosciences Institute, University of Illinois, Urbana, IL, 61801, USA
| | - Roderick I Mackie
- Department of Animal Sciences, Institute for Genomic Biology and Energy Biosciences Institute, University of Illinois, Urbana, IL, 61801, USA
| | - Alex Toftgaard Nielsen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, Lyngby, 2800 Kgs, Denmark
| | - Markus J Herrgård
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, Lyngby, 2800 Kgs, Denmark
| | - Adam M Feist
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, Lyngby, 2800 Kgs, Denmark. .,Department of Bioengineering, University of California, 9500 Gilman Drive La Jolla, San Diego, CA, 92093, USA.
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14
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Greening C, Geier R, Wang C, Woods LC, Morales SE, McDonald MJ, Rushton-Green R, Morgan XC, Koike S, Leahy SC, Kelly WJ, Cann I, Attwood GT, Cook GM, Mackie RI. Diverse hydrogen production and consumption pathways influence methane production in ruminants. ISME J 2019; 13:2617-2632. [PMID: 31243332 PMCID: PMC6776011 DOI: 10.1038/s41396-019-0464-2] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 06/03/2019] [Accepted: 06/07/2019] [Indexed: 01/17/2023]
Abstract
Farmed ruminants are the largest source of anthropogenic methane emissions globally. The methanogenic archaea responsible for these emissions use molecular hydrogen (H2), produced during bacterial and eukaryotic carbohydrate fermentation, as their primary energy source. In this work, we used comparative genomic, metatranscriptomic and co-culture-based approaches to gain a system-wide understanding of the organisms and pathways responsible for ruminal H2 metabolism. Two-thirds of sequenced rumen bacterial and archaeal genomes encode enzymes that catalyse H2 production or consumption, including 26 distinct hydrogenase subgroups. Metatranscriptomic analysis confirmed that these hydrogenases are differentially expressed in sheep rumen. Electron-bifurcating [FeFe]-hydrogenases from carbohydrate-fermenting Clostridia (e.g., Ruminococcus) accounted for half of all hydrogenase transcripts. Various H2 uptake pathways were also expressed, including methanogenesis (Methanobrevibacter), fumarate and nitrite reduction (Selenomonas), and acetogenesis (Blautia). Whereas methanogenesis-related transcripts predominated in high methane yield sheep, alternative uptake pathways were significantly upregulated in low methane yield sheep. Complementing these findings, we observed significant differential expression and activity of the hydrogenases of the hydrogenogenic cellulose fermenter Ruminococcus albus and the hydrogenotrophic fumarate reducer Wolinella succinogenes in co-culture compared with pure culture. We conclude that H2 metabolism is a more complex and widespread trait among rumen microorganisms than previously recognised. There is evidence that alternative hydrogenotrophs, including acetogenic and respiratory bacteria, can prosper in the rumen and effectively compete with methanogens for H2. These findings may help to inform ongoing strategies to mitigate methane emissions by increasing flux through alternative H2 uptake pathways, including through animal selection, dietary supplementation and methanogenesis inhibitors.
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Affiliation(s)
- Chris Greening
- School of Biological Sciences, Monash University, Clayton, VIC, 3800, Australia.
| | - Renae Geier
- Department of Animal Sciences and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Cecilia Wang
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | - Laura C Woods
- School of Biological Sciences, Monash University, Clayton, VIC, 3800, Australia
| | - Sergio E Morales
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | - Michael J McDonald
- School of Biological Sciences, Monash University, Clayton, VIC, 3800, Australia
| | - Rowena Rushton-Green
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | - Xochitl C Morgan
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | - Satoshi Koike
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Sinead C Leahy
- Grasslands Research Centre, AgResearch Ltd., Palmerston North, 4410, New Zealand
| | | | - Isaac Cann
- Department of Animal Sciences and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Graeme T Attwood
- Grasslands Research Centre, AgResearch Ltd., Palmerston North, 4410, New Zealand
| | - Gregory M Cook
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | - Roderick I Mackie
- Department of Animal Sciences and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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15
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Affiliation(s)
- Roderick I Mackie
- Department of Animal Sciences, University of Illinois, Urbana, IL, USA. .,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, USA.
| | - Isaac Cann
- Department of Animal Sciences, University of Illinois, Urbana, IL, USA. .,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, USA. .,Department of Microbiology, University of Illinois, Urbana, IL, USA.
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16
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Li Y, Li Y, Jin W, Sharpton TJ, Mackie RI, Cann I, Cheng Y, Zhu W. Combined Genomic, Transcriptomic, Proteomic, and Physiological Characterization of the Growth of Pecoramyces sp. F1 in Monoculture and Co-culture With a Syntrophic Methanogen. Front Microbiol 2019; 10:435. [PMID: 30894845 PMCID: PMC6414434 DOI: 10.3389/fmicb.2019.00435] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 02/19/2019] [Indexed: 11/13/2022] Open
Abstract
In this study, the effects of a syntrophic methanogen on the growth of Pecoramyces sp. F1 was investigated by characterizing fermentation profiles, as well as functional genomic, transcriptomic, and proteomic analysis. The estimated genome size, GC content, and protein coding regions of strain F1 are 106.83 Mb, 16.07%, and 23.54%, respectively. Comparison of the fungal monoculture with the methanogen co-culture demonstrated that during the fermentation of glucose, the co-culture initially expressed and then down-regulated a large number of genes encoding both enzymes involved in intermediate metabolism and plant cell wall degradation. However, the number of up-regulated proteins doubled at the late-growth stage in the co-culture. In addition, we provide a mechanistic understanding of the metabolism of this fungus in co-culture with a syntrophic methanogen. Further experiments are needed to explore this interaction during degradation of more complex plant cell wall substrates.
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Affiliation(s)
- Yuanfei Li
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China
| | - Yuqi Li
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China
| | - Wei Jin
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China.,Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agricultural University, Nanjing, China
| | - Thomas J Sharpton
- Department of Microbiology - Department of Statistics, Oregon State University, Corvallis, OR, United States
| | - Roderick I Mackie
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - Isaac Cann
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Champaign, IL, United States.,Department of Microbiology, University of Illinois at Urbana-Champaign, Champaign, IL, United States.,Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Champaign, IL, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - Yanfen Cheng
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China.,Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agricultural University, Nanjing, China
| | - Weiyun Zhu
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China.,Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agricultural University, Nanjing, China
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17
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D'Alessandro-Gabazza CN, Méndez-García C, Hataji O, Westergaard S, Watanabe F, Yasuma T, Toda M, Fujimoto H, Nishihama K, Fujiwara K, Taguchi O, Kobayashi T, Mackie RI, Cann I, Gabazza EC. Identification of Halophilic Microbes in Lung Fibrotic Tissue by Oligotyping. Front Microbiol 2018; 9:1892. [PMID: 30233503 PMCID: PMC6127444 DOI: 10.3389/fmicb.2018.01892] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Accepted: 07/27/2018] [Indexed: 12/19/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is an incurable disease with poor prognosis and unknown etiology. The poor clinical outcome is associated with enhanced microbial burden in bronchoalveolar lavage fluid from IPF patients. However, whether microbes from the respiratory tract fluid cause the disease remains uncertain. Tissue-associated microbes can influence host physiology in health and disease development. The aim of this study was to evaluate the existence of microbes in lung fibrotic tissues. We evaluated the microbial community in lung tissues from IPF and from human transforming growth factor-β1 (TGF-β1) transgenic mice with lung fibrosis by oligotyping. We also evaluated the microbial population in non-tumor-bearing tissues from surgical specimens of lung cancer patients. The phyla Firmicutes and the genus Clostridium tended to be predominant in the lung tissue from IPF and lung cancer patients. Oligotyping analysis revealed a predominance of bacteria belonging to the genera Halomonas, Shewanella, Christensenella, and Clostridium in lung tissue from IPF and lung cancer. Evaluation of the microbial community in the lung tissue from mice revealed abundance of Proteobacteria in both wild-type (WT) littermates and transgenic mice. However, the genus Halomonas tended to be more abundant in TGF-β1 transgenic mice compared to WT mice. In conclusion, this study describes tissue-associated microbes in lung fibrotic tissues from IPF patients and from aging TGF-β1 transgenic mice.
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Affiliation(s)
- Corina N D'Alessandro-Gabazza
- Department of Immunology, Mie University, Tsu, Japan.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Celia Méndez-García
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States.,Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Osamu Hataji
- Respiratory Center, Matsusaka Municipal Hospital, Matsusaka, Japan
| | - Sara Westergaard
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Fumiaki Watanabe
- Respiratory Center, Matsusaka Municipal Hospital, Matsusaka, Japan
| | - Taro Yasuma
- Department of Immunology, Mie University, Tsu, Japan.,Department of Diabetes and Endocrinology, Mie University, Tsu, Japan
| | - Masaaki Toda
- Department of Immunology, Mie University, Tsu, Japan
| | - Hajime Fujimoto
- Department of Pulmonary and Critical Care Medicine, Mie University, Tsu, Japan
| | - Kota Nishihama
- Department of Diabetes and Endocrinology, Mie University, Tsu, Japan
| | - Kentaro Fujiwara
- Department of Pulmonary and Critical Care Medicine, Mie University, Tsu, Japan
| | - Osamu Taguchi
- Center for Physical and Mental Health, Mie University, Tsu, Japan
| | - Tetsu Kobayashi
- Department of Pulmonary and Critical Care Medicine, Mie University, Tsu, Japan
| | - Roderick I Mackie
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States.,Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Isaac Cann
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States.,Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States.,Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Esteban C Gabazza
- Department of Immunology, Mie University, Tsu, Japan.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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18
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Naas AE, Solden LM, Norbeck AD, Brewer H, Hagen LH, Heggenes IM, McHardy AC, Mackie RI, Paša-Tolić L, Arntzen MØ, Eijsink VGH, Koropatkin NM, Hess M, Wrighton KC, Pope PB. "Candidatus Paraporphyromonas polyenzymogenes" encodes multi-modular cellulases linked to the type IX secretion system. Microbiome 2018; 6:44. [PMID: 29490697 PMCID: PMC5831590 DOI: 10.1186/s40168-018-0421-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 02/07/2018] [Indexed: 05/07/2023]
Abstract
BACKGROUND In nature, obligate herbivorous ruminants have a close symbiotic relationship with their gastrointestinal microbiome, which proficiently deconstructs plant biomass. Despite decades of research, lignocellulose degradation in the rumen has thus far been attributed to a limited number of culturable microorganisms. Here, we combine meta-omics and enzymology to identify and describe a novel Bacteroidetes family ("Candidatus MH11") composed entirely of uncultivated strains that are predominant in ruminants and only distantly related to previously characterized taxa. RESULTS The first metabolic reconstruction of Ca. MH11-affiliated genome bins, with a particular focus on the provisionally named "Candidatus Paraporphyromonas polyenzymogenes", illustrated their capacity to degrade various lignocellulosic substrates via comprehensive inventories of singular and multi-modular carbohydrate active enzymes (CAZymes). Closer examination revealed an absence of archetypical polysaccharide utilization loci found in human gut microbiota. Instead, we identified many multi-modular CAZymes putatively secreted via the Bacteroidetes-specific type IX secretion system (T9SS). This included cellulases with two or more catalytic domains, which are modular arrangements that are unique to Bacteroidetes species studied to date. Core metabolic proteins from Ca. P. polyenzymogenes were detected in metaproteomic data and were enriched in rumen-incubated plant biomass, indicating that active saccharification and fermentation of complex carbohydrates could be assigned to members of this novel family. Biochemical analysis of selected Ca. P. polyenzymogenes CAZymes further iterated the cellulolytic activity of this hitherto uncultured bacterium towards linear polymers, such as amorphous and crystalline cellulose as well as mixed linkage β-glucans. CONCLUSION We propose that Ca. P. polyenzymogene genotypes and other Ca. MH11 members actively degrade plant biomass in the rumen of cows, sheep and most likely other ruminants, utilizing singular and multi-domain catalytic CAZymes secreted through the T9SS. The discovery of a prominent role of multi-modular cellulases in the Gram-negative Bacteroidetes, together with similar findings for Gram-positive cellulosomal bacteria (Ruminococcus flavefaciens) and anaerobic fungi (Orpinomyces sp.), suggests that complex enzymes are essential and have evolved within all major cellulolytic dominions inherent to the rumen.
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Affiliation(s)
- A E Naas
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Post Office Box 5003, 1432, Ås, Norway
| | - L M Solden
- Department of Microbiology, The Ohio State University, Columbus, OH, 43201, USA
| | - A D Norbeck
- Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - H Brewer
- Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - L H Hagen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Post Office Box 5003, 1432, Ås, Norway
| | - I M Heggenes
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Post Office Box 5003, 1432, Ås, Norway
| | - A C McHardy
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Inhoffenstraβe 7, 38124, Braunschweig, Germany
| | - R I Mackie
- Institute for Genomic Biology and Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - L Paša-Tolić
- Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - M Ø Arntzen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Post Office Box 5003, 1432, Ås, Norway
| | - V G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Post Office Box 5003, 1432, Ås, Norway
| | - N M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - M Hess
- Department of Animal Science, University of California, Davis, CA, 95616, USA
| | - K C Wrighton
- Department of Microbiology, The Ohio State University, Columbus, OH, 43201, USA
| | - P B Pope
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Post Office Box 5003, 1432, Ås, Norway.
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19
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Wefers D, Cavalcante JJ, Schendel RR, Deveryshetty J, Wang K, Wawrzak Z, Mackie RI, Koropatkin NM, Cann I. Biochemical and Structural Analyses of Two Cryptic Esterases in Bacteroides intestinalis and their Synergistic Activities with Cognate Xylanases. J Mol Biol 2017; 429:2509-2527. [DOI: 10.1016/j.jmb.2017.06.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 06/25/2017] [Accepted: 06/26/2017] [Indexed: 11/17/2022]
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20
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Arntzen MØ, Várnai A, Mackie RI, Eijsink VGH, Pope PB. Outer membrane vesicles from Fibrobacter succinogenes S85 contain an array of carbohydrate-active enzymes with versatile polysaccharide-degrading capacity. Environ Microbiol 2017; 19:2701-2714. [PMID: 28447389 DOI: 10.1111/1462-2920.13770] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 04/18/2017] [Indexed: 11/30/2022]
Abstract
Fibrobacter succinogenes is an anaerobic bacterium naturally colonising the rumen and cecum of herbivores where it utilizes an enigmatic mechanism to deconstruct cellulose into cellobiose and glucose, which serve as carbon sources for growth. Here, we illustrate that outer membrane vesicles (OMVs) released by F. succinogenes are enriched with carbohydrate-active enzymes and that intact OMVs were able to depolymerize a broad range of linear and branched hemicelluloses and pectin, despite the inability of F. succinogenes to utilize non-cellulosic (pentose) sugars for growth. We hypothesize that the degradative versatility of F. succinogenes OMVs is used to prime hydrolysis by destabilising the tight networks of polysaccharides intertwining cellulose in the plant cell wall, thus increasing accessibility of the target substrate for the host cell. This is supported by observations that OMV-pretreatment of the natural complex substrate switchgrass increased the catalytic efficiency of a commercial cellulose-degrading enzyme cocktail by 2.4-fold. We also show that the OMVs contain a putative multiprotein complex, including the fibro-slime protein previously found to be important in binding to crystalline cellulose. We hypothesize that this complex has a function in plant cell wall degradation, either by catalysing polysaccharide degradation itself, or by targeting the vesicles to plant biomass.
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Affiliation(s)
- Magnus Ø Arntzen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Anikó Várnai
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Roderick I Mackie
- Institute for Genomic Biology, and Department of Animal Sciences, University of Illinois at Urbana-Champaign, IL, USA
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Phillip B Pope
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
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21
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Devendran S, Abdel-Hamid AM, Evans AF, Iakiviak M, Kwon IH, Mackie RI, Cann I. Multiple cellobiohydrolases and cellobiose phosphorylases cooperate in the ruminal bacterium Ruminococcus albus 8 to degrade cellooligosaccharides. Sci Rep 2016; 6:35342. [PMID: 27748409 PMCID: PMC5066209 DOI: 10.1038/srep35342] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 09/28/2016] [Indexed: 12/01/2022] Open
Abstract
Digestion of plant cell wall polysaccharides is important in energy capture in the gastrointestinal tract of many herbivorous and omnivorous mammals, including humans and ruminants. The members of the genus Ruminococcus are found in both the ruminant and human gastrointestinal tract, where they show versatility in degrading both hemicellulose and cellulose. The available genome sequence of Ruminococcus albus 8, a common inhabitant of the cow rumen, alludes to a bacterium well-endowed with genes that target degradation of various plant cell wall components. The mechanisms by which R. albus 8 employs to degrade these recalcitrant materials are, however, not clearly understood. In this report, we demonstrate that R. albus 8 elaborates multiple cellobiohydrolases with multi-modular architectures that overall enhance the catalytic activity and versatility of the enzymes. Furthermore, our analyses show that two cellobiose phosphorylases encoded by R. albus 8 can function synergistically with a cognate cellobiohydrolase and endoglucanase to completely release, from a cellulosic substrate, glucose which can then be fermented by the bacterium for production of energy and cellular building blocks. We further use transcriptomic analysis to confirm the over-expression of the biochemically characterized enzymes during growth of the bacterium on cellulosic substrates compared to cellobiose.
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Affiliation(s)
- Saravanan Devendran
- Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Ahmed M Abdel-Hamid
- Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Anton F Evans
- Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.,School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Michael Iakiviak
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - In Hyuk Kwon
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Roderick I Mackie
- Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.,Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Isaac Cann
- Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.,School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.,Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.,Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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22
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Oosterkamp MJ, Méndez-García C, Kim CH, Bauer S, Ibáñez AB, Zimmerman S, Hong PY, Cann IK, Mackie RI. Lignocellulose-derived thin stillage composition and efficient biological treatment with a high-rate hybrid anaerobic bioreactor system. Biotechnol Biofuels 2016; 9:120. [PMID: 27274357 PMCID: PMC4895995 DOI: 10.1186/s13068-016-0532-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 05/19/2016] [Indexed: 05/23/2023]
Abstract
BACKGROUND This study aims to chemically characterize thin stillage derived from lignocellulosic biomass distillation residues in terms of organic strength, nutrient, and mineral content. The feasibility of performing anaerobic digestion on these stillages at mesophilic (40 °C) and thermophilic (55 °C) temperatures to produce methane was demonstrated. The microbial communities involved were further characterized. RESULTS Energy and sugar cane stillage have a high chemical oxygen demand (COD of 43 and 30 g/L, respectively) and low pH (pH 4.3). Furthermore, the acetate concentration in sugar cane stillage was high (45 mM) but was not detected in energy cane stillage. There was also a high amount of lactate in both types of stillage (35-37 mM). The amount of sugars was 200 times higher in energy cane stillage compared to sugar cane stillage. Although there was a high concentration of sulfate (18 and 23 mM in sugar and energy cane stillage, respectively), both thin stillages were efficiently digested anaerobically with high COD removal under mesophilic and thermophilic temperature conditions and with an organic loading rate of 15-21 g COD/L/d. The methane production rate was 0.2 L/g COD, with a methane percentage of 60 and 64, and 92 and 94 % soluble COD removed, respectively, by the mesophilic and thermophilic reactors. Although both treatment processes were equally efficient, there were different microbial communities involved possibly arising from the differences in the composition of energy cane and sugar cane stillage. There was more acetic acid in sugar cane stillage which may have promoted the occurrence of aceticlastic methanogens to perform a direct conversion of acetate to methane in reactors treating sugar cane stillage. CONCLUSIONS Results showed that thin stillage contains easily degradable compounds suitable for anaerobic digestion and that hybrid reactors can efficiently convert thin stillage to methane under mesophilic and thermophilic conditions. Furthermore, we found that optimal conditions for biological treatment of thin stillage were similar for both mesophilic and thermophilic reactors. Bar-coded pyrosequencing of the 16S rRNA gene identified different microbial communities in mesophilic and thermophilic reactors and these differences in the microbial communities could be linked to the composition of the thin stillage.
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Affiliation(s)
- Margreet J. Oosterkamp
- />Institute for Genomic Biology, and Department of Animal Sciences, Energy Biosciences Institute, University of Illinois at Urbana-Champaign, 1207 W Gregory Dr, Urbana, IL 61801 USA
| | - Celia Méndez-García
- />Institute for Genomic Biology, and Department of Animal Sciences, Energy Biosciences Institute, University of Illinois at Urbana-Champaign, 1207 W Gregory Dr, Urbana, IL 61801 USA
| | - Chang-H. Kim
- />Institute for Genomic Biology, and Department of Animal Sciences, Energy Biosciences Institute, University of Illinois at Urbana-Champaign, 1207 W Gregory Dr, Urbana, IL 61801 USA
- />Department of Animal, Life and Environment Science, Biogas Research Center, Hankyong National University, 327 Jungang-ro, Anseong-si, Gyeonggi-do 456-749 South Korea
| | - Stefan Bauer
- />Energy Biosciences Institute, University of California at Berkeley, 120A Energy Biosciences Building, 2151 Berkeley Way, MC 5230, Berkeley, CA 94729, USA
| | - Ana B. Ibáñez
- />Energy Biosciences Institute, University of California at Berkeley, 120A Energy Biosciences Building, 2151 Berkeley Way, MC 5230, Berkeley, CA 94729, USA
| | - Sabrina Zimmerman
- />Energy Biosciences Institute, University of California at Berkeley, 120A Energy Biosciences Building, 2151 Berkeley Way, MC 5230, Berkeley, CA 94729, USA
- />BP Biofuels, University of California at Berkeley, 120A Energy Biosciences Building, 2151 Berkeley Way, MC 5230, Berkeley, CA 94729 USA
| | - Pei-Ying Hong
- />Biological and Environmental Sciences and Engineering Division (BESE), Water Desalination and Reuse Center (WDRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900 Saudi Arabia
| | - Isaac K. Cann
- />Institute for Genomic Biology, and Department of Animal Sciences, Energy Biosciences Institute, University of Illinois at Urbana-Champaign, 1207 W Gregory Dr, Urbana, IL 61801 USA
| | - Roderick I. Mackie
- />Institute for Genomic Biology, and Department of Animal Sciences, Energy Biosciences Institute, University of Illinois at Urbana-Champaign, 1207 W Gregory Dr, Urbana, IL 61801 USA
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23
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Abstract
Filamentous fungi are critical to production of many commercial enzymes and organic compounds. Fungal-based systems have several advantages over bacterial-based systems for protein production because high-level secretion of enzymes is a common trait of their decomposer lifestyle. Furthermore, in the large-scale production of recombinant proteins of eukaryotic origin, the filamentous fungi become the vehicle of choice due to critical processes shared in gene expression with other eukaryotic organisms. The complexity and relative dearth of understanding of the physiology of filamentous fungi, compared to bacteria, have hindered rapid development of these organisms as highly efficient factories for the production of heterologous proteins. In this review, we highlight several of the known benefits and challenges in using filamentous fungi (particularly Aspergillus spp., Trichoderma reesei, and Neurospora crassa) for the production of proteins, especially heterologous, nonfungal enzymes. We review various techniques commonly employed in recombinant protein production in the filamentous fungi, including transformation methods, selection of gene regulatory elements such as promoters, protein secretion factors such as the signal peptide, and optimization of coding sequence. We provide insights into current models of host genomic defenses such as repeat-induced point mutation and quelling. Furthermore, we examine the regulatory effects of transcript sequences, including introns and untranslated regions, pre-mRNA (messenger RNA) processing, transcript transport, and mRNA stability. We anticipate that this review will become a resource for researchers who aim at advancing the use of these fascinating organisms as protein production factories, for both academic and industrial purposes, and also for scientists with general interest in the biology of the filamentous fungi.
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Affiliation(s)
- Xiaoyun Su
- Energy Biosciences Institute, University of Illinois, Urbana, IL, USA; Institute for Genomic Biology, University of Illinois, Urbana, IL, USA; Equal contribution
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Geier RR, Kwon IH, Cann IK, Mackie RI. Interspecies Hydrogen Transfer and Its Effects on Global Transcript Abundance in
Ruminococcus albus
, a Predominant Fiber‐Degrading Species in the Rumen. FASEB J 2016. [DOI: 10.1096/fasebj.30.1_supplement.1102.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Renae R Geier
- Division of Nutritional SciencesUniversity of IllinoisUrbanaIL
- Institute for Genomic BiologyUniversity of IllinoisUrbanaIL
| | - In Hyuk Kwon
- Department of Animal SciencesUniversity of IllinoisUrbanaIL
| | - Isaac K Cann
- Department of Animal SciencesUniversity of IllinoisUrbanaIL
- Department of MicrobiologyUniversity of IllinoisUrbanaIL
- Institute for Genomic BiologyUniversity of IllinoisUrbanaIL
| | - Roderick I Mackie
- Division of Nutritional SciencesUniversity of IllinoisUrbanaIL
- Department of Animal SciencesUniversity of IllinoisUrbanaIL
- Institute for Genomic BiologyUniversity of IllinoisUrbanaIL
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Cann I, Bernardi RC, Mackie RI. Cellulose degradation in the human gut:Ruminococcus champanellensisexpands the cellulosome paradigm. Environ Microbiol 2016; 18:307-10. [DOI: 10.1111/1462-2920.13152] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Isaac Cann
- Department of Animal Science; University of Illinois at Urbana-Champaign; Urbana IL 61801 USA
- Department of Microbiology; University of Illinois at Urbana-Champaign; Urbana IL 61801 USA
- Carl R. Woese Institute for Genomic Biology; University of Illinois at Urbana-Champaign; Urbana IL 61801 USA
| | - Rafael C. Bernardi
- Beckman Institute; University of Illinois at Urbana-Champaign; Urbana IL 61801 USA
| | - Roderick I. Mackie
- Department of Animal Science; University of Illinois at Urbana-Champaign; Urbana IL 61801 USA
- Carl R. Woese Institute for Genomic Biology; University of Illinois at Urbana-Champaign; Urbana IL 61801 USA
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26
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Amato KR, Leigh SR, Kent A, Mackie RI, Yeoman CJ, Stumpf RM, Wilson BA, Nelson KE, White BA, Garber PA. The gut microbiota appears to compensate for seasonal diet variation in the wild black howler monkey (Alouatta pigra). Microb Ecol 2015; 69:434-43. [PMID: 25524570 DOI: 10.1007/s00248-014-0554-7] [Citation(s) in RCA: 182] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 12/03/2014] [Indexed: 05/04/2023]
Abstract
For most mammals, including nonhuman primates, diet composition varies temporally in response to differences in food availability. Because diet influences gut microbiota composition, it is likely that the gut microbiota of wild mammals varies in response to seasonal changes in feeding patterns. Such variation may affect host digestive efficiency and, ultimately, host nutrition. In this study, we investigate the temporal variation in diet and gut microbiota composition and function in two groups (N = 13 individuals) of wild Mexican black howler monkeys (Alouatta pigra) over a 10-month period in Palenque National Park, Mexico. Temporal changes in the relative abundances of individual bacterial taxa were strongly correlated with changes in host diet. For example, the relative abundance of Ruminococcaceae was highest during periods when energy intake was lowest, and the relative abundance of Butyricicoccus was highest when young leaves and unripe fruit accounted for 68 % of the diet. Additionally, the howlers exhibited increased microbial production of energy during periods of reduced energy intake from food sources. Because we observed few changes in howler activity and ranging patterns during the course of our study, we propose that shifts in the composition and activity of the gut microbiota provided additional energy and nutrients to compensate for changes in diet. Energy and nutrient production by the gut microbiota appears to provide an effective buffer against seasonal fluctuations in energy and nutrient intake for these primates and is likely to have a similar function in other mammal species.
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Affiliation(s)
- Katherine R Amato
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois, Urbana, IL, 61801, USA,
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27
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Hong PY, Mao Y, Ortiz-Kofoed S, Shah R, Cann I, Mackie RI. Metagenomic-based study of the phylogenetic and functional gene diversity in Galápagos land and marine iguanas. Microb Ecol 2015; 69:444-456. [PMID: 25524569 DOI: 10.1007/s00248-014-0547-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 11/27/2014] [Indexed: 06/04/2023]
Abstract
In this study, a metagenome-based analysis of the fecal samples from the macrophytic algae-consuming marine iguana (MI; Amblyrhynchus cristatus) and terrestrial biomass-consuming land iguanas (LI; Conolophus spp.) was conducted. Phylogenetic affiliations of the fecal microbiome were more similar between both iguanas than to other mammalian herbivorous hosts. However, functional gene diversities in both MI and LI iguana hosts differed in relation to the diet, where the MI fecal microbiota had a functional diversity that clustered apart from the other terrestrial-biomass consuming reptilian and mammalian hosts. A further examination of the carbohydrate-degrading genes revealed that several of the prevalent glycosyl hydrolases (GH), glycosyl transferases (GT), carbohydrate binding modules (CBM), and carbohydrate esterases (CE) gene classes were conserved among all examined herbivorous hosts, reiterating the important roles these genes play in the breakdown and metabolism of herbivorous diets. Genes encoding some classes of carbohydrate-degrading families, including GH2, GH13, GT2, GT4, CBM50, CBM48, CE4, and CE11, as well as genes associated with sulfur metabolism and dehalogenation, were highly enriched or unique to the MI. In contrast, gene sequences that relate to archaeal methanogenesis were detected only in LI fecal microbiome, and genes coding for GH13, GH66, GT2, GT4, CBM50, CBM13, CE4, and CE8 carbohydrate active enzymes were highly abundant in the LI. Bacterial populations were enriched on various carbohydrates substrates (e.g., glucose, arabinose, xylose). The majority of the enriched bacterial populations belong to genera Clostridium spp. and Enterococcus spp. that likely accounted for the high prevalence of GH13 and GH2, as well as the GT families (e.g., GT2, GT4, GT28, GT35, and GT51) that were ubiquitously present in the fecal microbiota of all herbivorous hosts.
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Affiliation(s)
- Pei-Ying Hong
- Department of Animal Sciences, University of Illinois at Urbana Champaign, Urbana, IL, 61801, USA
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28
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Chekan JR, Kwon IH, Agarwal V, Dodd D, Revindran V, Mackie RI, Cann I, Nair SK. Structural and biochemical basis for mannan utilization by Caldanaerobius polysaccharolyticus strain ATCC BAA-17. J Biol Chem 2014; 289:34965-77. [PMID: 25342756 DOI: 10.1074/jbc.m114.579904] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Hemicelluloses, the polysaccharide component of plant cell walls, represent one of the most abundant biopolymers in nature. The most common hemicellulosic constituents of softwoods, such as conifers and cycads, are mannans consisting of a 1,4-linked β-mannopyranosyl main chain with branch decorations. Efforts toward the utilization of hemicellulose for bioconversion into cellulosic biofuels have resulted in the identification of several families of glycoside hydrolases that can degrade mannan. However, effective biofermentation of manno-oligosaccharides is limited by a lack of appropriate uptake route in ethanologenic organisms. Here, we used transcriptome sequencing to gain insights into mannan degradation by the thermophilic anaerobic bacterium Caldanaerobius polysaccharolyticus. The most highly up-regulated genes during mannan fermentation occur in a cluster containing several genes encoding enzymes for efficient mannan hydrolysis as well as a solute-binding protein (CpMnBP1) that exhibits specificity for short mannose polymers but exhibited the flexibility to accommodate branched polysaccharide decorations. Co-crystal structures of CpMnBP1 in complex with mannobiose (1.4-Å resolution) and mannotriose (2.2-Å resolution) revealed the molecular rationale for chain length and oligosaccharide specificity. Calorimetric analysis of several active site variants confirmed the roles of residues critical to the function of CpMnBP1. This work represents the first biochemical characterization of a mannose-specific solute-binding protein and provides a framework for engineering mannan utilization capabilities for microbial fermentation.
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Affiliation(s)
| | | | | | - Dylan Dodd
- Institute for Genomic Biology, Energy Biosciences Institute, University of Illinois, Urbana, Illinois 61801 Microbiology
| | - Vanessa Revindran
- Institute for Genomic Biology, Energy Biosciences Institute, University of Illinois, Urbana, Illinois 61801
| | - Roderick I Mackie
- Institute for Genomic Biology, Animal Sciences, and Energy Biosciences Institute, University of Illinois, Urbana, Illinois 61801
| | - Isaac Cann
- Institute for Genomic Biology, Animal Sciences, and Energy Biosciences Institute, University of Illinois, Urbana, Illinois 61801 Microbiology,
| | - Satish K Nair
- From the Departments of Biochemistry, Institute for Genomic Biology, Center for Biophysics and Computational Biology, and
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29
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Dong Y, Sanford RA, Locke RA, Cann IK, Mackie RI, Fouke BW. Fe-oxide grain coatings support bacterial Fe-reducing metabolisms in 1.7-2.0 km-deep subsurface quartz arenite sandstone reservoirs of the Illinois Basin (USA). Front Microbiol 2014; 5:511. [PMID: 25324834 PMCID: PMC4179719 DOI: 10.3389/fmicb.2014.00511] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 09/11/2014] [Indexed: 02/01/2023] Open
Abstract
The Cambrian-age Mt. Simon Sandstone, deeply buried within the Illinois Basin of the midcontinent of North America, contains quartz sand grains ubiquitously encrusted with iron-oxide cements and dissolved ferrous iron in pore-water. Although microbial iron reduction has previously been documented in the deep terrestrial subsurface, the potential for diagenetic mineral cementation to drive microbial activity has not been well studied. In this study, two subsurface formation water samples were collected at 1.72 and 2.02 km, respectively, from the Mt. Simon Sandstone in Decatur, Illinois. Low-diversity microbial communities were detected from both horizons and were dominated by Halanaerobiales of Phylum Firmicutes. Iron-reducing enrichment cultures fed with ferric citrate were successfully established using the formation water. Phylogenetic classification identified the enriched species to be related to Vulcanibacillus from the 1.72 km depth sample, while Orenia dominated the communities at 2.02 km of burial depth. Species-specific quantitative analyses of the enriched organisms in the microbial communities suggest that they are indigenous to the Mt. Simon Sandstone. Optimal iron reduction by the 1.72 km enrichment culture occurred at a temperature of 40°C (range 20-60°C) and a salinity of 25 parts per thousand (range 25-75 ppt). This culture also mediated fermentation and nitrate reduction. In contrast, the 2.02 km enrichment culture exclusively utilized hydrogen and pyruvate as the electron donors for iron reduction, tolerated a wider range of salinities (25-200 ppt), and exhibited only minimal nitrate- and sulfate-reduction. In addition, the 2.02 km depth community actively reduces the more crystalline ferric iron minerals goethite and hematite. The results suggest evolutionary adaptation of the autochthonous microbial communities to the Mt. Simon Sandstone and carries potentially important implications for future utilization of this reservoir for CO2 injection.
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Affiliation(s)
- Yiran Dong
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign Urbana, IL, USA ; Department of Geology, University of Illinois at Urbana-Champaign Urbana, IL, USA ; Energy Biosciences Institute, University of Illinois at Urbana-Champaign Urbana, IL, USA
| | - Robert A Sanford
- Department of Geology, University of Illinois at Urbana-Champaign Urbana, IL, USA
| | - Randall A Locke
- Illinois State Geological Survey, Urbana-Champaign Urbana, IL, USA
| | - Isaac K Cann
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign Urbana, IL, USA ; Energy Biosciences Institute, University of Illinois at Urbana-Champaign Urbana, IL, USA ; Department of Animal Sciences, University of Illinois at Urbana-Champaign Urbana, IL, USA ; Department of Microbiology, University of Illinois at Urbana-Champaign Urbana, IL, USA
| | - Roderick I Mackie
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign Urbana, IL, USA ; Energy Biosciences Institute, University of Illinois at Urbana-Champaign Urbana, IL, USA ; Department of Animal Sciences, University of Illinois at Urbana-Champaign Urbana, IL, USA
| | - Bruce W Fouke
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign Urbana, IL, USA ; Department of Geology, University of Illinois at Urbana-Champaign Urbana, IL, USA ; Energy Biosciences Institute, University of Illinois at Urbana-Champaign Urbana, IL, USA ; Illinois State Geological Survey, Urbana-Champaign Urbana, IL, USA ; Department of Microbiology, University of Illinois at Urbana-Champaign Urbana, IL, USA
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30
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Amato KR, Leigh SR, Kent A, Mackie RI, Yeoman CJ, Stumpf RM, Wilson BA, Nelson KE, White BA, Garber PA. The role of gut microbes in satisfying the nutritional demands of adult and juvenile wild, black howler monkeys (Alouatta pigra). Am J Phys Anthropol 2014; 155:652-64. [DOI: 10.1002/ajpa.22621] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 09/09/2014] [Accepted: 09/10/2014] [Indexed: 01/22/2023]
Affiliation(s)
- Katherine R. Amato
- Program in Ecology, Evolution, and Conservation Biology; University of Illinois; Urbana IL 61801
- Department of Anthropology; University of Colorado; Boulder CO 80309
| | - Steven R. Leigh
- Department of Anthropology; University of Colorado; Boulder CO 80309
| | - Angela Kent
- Department of Natural Resources and Environmental Sciences; University of Illinois; Urbana IL 61801
| | - Roderick I. Mackie
- Department of Animal Sciences; University of Illinois; Urbana IL 61801
- Institute for Genomic Biology, University of Illinois; Urbana IL 61801
| | - Carl J. Yeoman
- Department of Animal and Range Sciences; Montana State University; Bozeman MT 59717
| | - Rebecca M. Stumpf
- Institute for Genomic Biology, University of Illinois; Urbana IL 61801
- Department of Anthropology; University of Illinois; Urbana IL 80301
| | - Brenda A. Wilson
- Institute for Genomic Biology, University of Illinois; Urbana IL 61801
- Department of Microbiology; University of Illinois; Urbana IL 61801
| | | | - Bryan A. White
- Department of Animal Sciences; University of Illinois; Urbana IL 61801
- Institute for Genomic Biology, University of Illinois; Urbana IL 61801
| | - Paul A. Garber
- Department of Anthropology; University of Illinois; Urbana IL 80301
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31
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Piao H, Lachman M, Malfatti S, Sczyrba A, Knierim B, Auer M, Tringe SG, Mackie RI, Yeoman CJ, Hess M. Temporal dynamics of fibrolytic and methanogenic rumen microorganisms during in situ incubation of switchgrass determined by 16S rRNA gene profiling. Front Microbiol 2014; 5:307. [PMID: 25101058 PMCID: PMC4106096 DOI: 10.3389/fmicb.2014.00307] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 06/03/2014] [Indexed: 01/08/2023] Open
Abstract
The rumen microbial ecosystem is known for its biomass-degrading and methane-producing phenotype. Fermentation of recalcitrant plant material, comprised of a multitude of interwoven fibers, necessitates the synergistic activity of diverse microbial taxonomic groups that inhabit the anaerobic rumen ecosystem. Although interspecies hydrogen (H2) transfer, a process during which bacterially generated H2 is transferred to methanogenic Archaea, has obtained significant attention over the last decades, the temporal variation of the different taxa involved in in situ biomass-degradation, H2 transfer and the methanogenesis process remains to be established. Here we investigated the temporal succession of microbial taxa and its effect on fiber composition during rumen incubation using 16S rRNA amplicon sequencing. Switchgrass filled nylon bags were placed in the rumen of a cannulated cow and collected at nine time points for DNA extraction and 16S pyrotag profiling. The microbial community colonizing the air-dried and non-incubated (0 h) switchgrass was dominated by members of the Bacilli (recruiting 63% of the pyrotag reads). During in situ incubation of the switchgrass, two major shifts in the community composition were observed: Bacilli were replaced within 30 min by members belonging to the Bacteroidia and Clostridia, which recruited 34 and 25% of the 16S rRNA reads generated, respectively. A second significant shift was observed after 16 h of rumen incubation, when members of the Spirochaetes and Fibrobacteria classes became more abundant in the fiber-adherent community. During the first 30 min of rumen incubation ~13% of the switchgrass dry matter was degraded, whereas little biomass degradation appeared to have occurred between 30 min and 4 h after the switchgrass was placed in the rumen. Interestingly, methanogenic members of the Euryarchaeota (i.e., Methanobacteria) increased up to 3-fold during this period of reduced biomass-degradation, with peak abundance just before rates of dry matter degradation increased again. We hypothesize that during this period microbial-mediated fibrolysis was temporarily inhibited until H2 was metabolized into CH4 by methanogens. Collectively, our results demonstrate the importance of inter-species interactions for the biomass-degrading and methane-producing phenotype of the rumen microbiome—both microbially facilitated processes with global significance.
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Affiliation(s)
- Hailan Piao
- Systems Microbiology and Biotechnology Group, School of Molecular Biosciences, Washington State University Richland, WA, USA
| | - Medora Lachman
- Department of Animal and Range Sciences, Montana State University Bozeman, MT, USA
| | - Stephanie Malfatti
- Lawrence Livermore National Laboratory, Biosciences and Biotechnology Division Livermore, CA, USA
| | - Alexander Sczyrba
- Faculty of Technology and Center for Biotechnology, Bielefeld University Bielefeld, Germany
| | - Bernhard Knierim
- Lawrence Berkeley National Laboratory, Life Sciences Division Berkeley, CA, USA
| | - Manfred Auer
- Lawrence Berkeley National Laboratory, Life Sciences Division Berkeley, CA, USA
| | - Susannah G Tringe
- Prokaryote Super Program, DOE Joint Genome Institute Walnut Creek, CA, USA
| | - Roderick I Mackie
- Department of Animal Sciences and Institute for Genomic Biology, University of Illinois, Urbana-Champaign IL, USA
| | - Carl J Yeoman
- Department of Animal and Range Sciences, Montana State University Bozeman, MT, USA
| | - Matthias Hess
- Systems Microbiology and Biotechnology Group, School of Molecular Biosciences, Washington State University Richland, WA, USA ; Prokaryote Super Program, DOE Joint Genome Institute Walnut Creek, CA, USA ; Energy and Efficiency Division, Chemical and Biological Process Development Group, Pacific Northwest National Laboratory Richland, WA, USA
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Mao Y, Li X, Smyth EM, Yannarell AC, Mackie RI. Enrichment of specific bacterial and eukaryotic microbes in the rhizosphere of switchgrass (Panicum virgatum L.) through root exudates. Environ Microbiol Rep 2014; 6:293-306. [PMID: 24983534 DOI: 10.1111/1758-2229.12152] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 01/30/2014] [Indexed: 05/09/2023]
Abstract
Identification of microbes that actively utilize root exudates is essential to understand plant-microbe interactions. To identify active root exudate-utilizing microorganisms associated with switchgrass - a potential bioenergy crop - plants were labelled in situ with (13) CO2 , and 16S and 18S rRNA genes in the (13) C-labelled rhizosphere DNA were pyrosequenced. Multi-pulse labelling for 5 days produced detectable (13) C-DNA, which was well separated from unlabelled DNA. Methylibium from the order Burkholderiales were the most heavily labelled bacteria. Pythium, Auricularia and Galerina were the most heavily labelled eukaryotic microbes. We also identified a Glomus intraradices-like species; Glomus members are arbuscular mycorrhizal fungi that are able to colonize the switchgrass root. All of these heavily labelled microorganisms were also among the most abundant species in the rhizosphere. Species belonging to Methylibium and Pythium were the most heavily labelled and the most abundant bacteria and eukaryotes in the rhizosphere of switchgrass. Our results revealed that nearly all of the dominant rhizosphere bacterial and eukaryotic microbes were able to utilize root exudates. The enrichment of microbial species in the rhizosphere is selective and mostly due to root exudation, which functions as a nutrition source, promoting the growth of these microbes.
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Affiliation(s)
- Yuejian Mao
- Energy Biosciences Institute, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA; Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
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Yi Z, Su X, Revindran V, Mackie RI, Cann I. Molecular and biochemical analyses of CbCel9A/Cel48A, a highly secreted multi-modular cellulase by Caldicellulosiruptor bescii during growth on crystalline cellulose. PLoS One 2013; 8:e84172. [PMID: 24358340 PMCID: PMC3865294 DOI: 10.1371/journal.pone.0084172] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 11/20/2013] [Indexed: 01/24/2023] Open
Abstract
During growth on crystalline cellulose, the thermophilic bacterium Caldicellulosiruptor bescii secretes several cellulose-degrading enzymes. Among these enzymes is CelA (CbCel9A/Cel48A), which is reported as the most highly secreted cellulolytic enzyme in this bacterium. CbCel9A/Cel48A is a large multi-modular polypeptide, composed of an N-terminal catalytic glycoside hydrolase family 9 (GH9) module and a C-terminal GH48 catalytic module that are separated by a family 3c carbohydrate-binding module (CBM3c) and two identical CBM3bs. The wild-type CbCel9A/Cel48A and its truncational mutants were expressed in Bacillus megaterium and Escherichia coli, respectively. The wild-type polypeptide released twice the amount of glucose equivalents from Avicel than its truncational mutant that lacks the GH48 catalytic module. The truncational mutant harboring the GH9 module and the CBM3c was more thermostable than the wild-type protein, likely due to its compact structure. The main hydrolytic activity was present in the GH9 catalytic module, while the truncational mutant containing the GH48 module and the three CBMs was ineffective in degradation of either crystalline or amorphous cellulose. Interestingly, the GH9 and/or GH48 catalytic modules containing the CBM3bs form low-density particles during hydrolysis of crystalline cellulose. Moreover, TM3 (GH9/CBM3c) and TM2 (GH48 with three CBM3 modules) synergistically hydrolyze crystalline cellulose. Deletion of the CBM3bs or mutations that compromised their binding activity suggested that these CBMs are important during hydrolysis of crystalline cellulose. In agreement with this observation, seven of nine genes in a C. bescii gene cluster predicted to encode cellulose-degrading enzymes harbor CBM3bs. Based on our results, we hypothesize that C. bescii uses the GH48 module and the CBM3bs in CbCel9A/Cel48A to destabilize certain regions of crystalline cellulose for attack by the highly active GH9 module and other endoglucanases produced by this hyperthermophilic bacterium.
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Affiliation(s)
- Zhuolin Yi
- Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Xiaoyun Su
- Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Vanessa Revindran
- Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Roderick I. Mackie
- Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Isaac Cann
- Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- * E-mail:
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Dong Y, Kumar CG, Chia N, Kim PJ, Miller PA, Price ND, Cann IKO, Flynn TM, Sanford RA, Krapac IG, Locke RA, Hong PY, Tamaki H, Liu WT, Mackie RI, Hernandez AG, Wright CL, Mikel MA, Walker JL, Sivaguru M, Fried G, Yannarell AC, Fouke BW. Halomonas sulfidaeris-dominated microbial community inhabits a 1.8 km-deep subsurface Cambrian Sandstone reservoir. Environ Microbiol 2013; 16:1695-708. [PMID: 24238218 DOI: 10.1111/1462-2920.12325] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2013] [Accepted: 10/31/2013] [Indexed: 01/12/2023]
Abstract
A low-diversity microbial community, dominated by the γ-proteobacterium Halomonas sulfidaeris, was detected in samples of warm saline formation porewater collected from the Cambrian Mt. Simon Sandstone in the Illinois Basin of the North American Midcontinent (1.8 km/5872 ft burial depth, 50°C, pH 8, 181 bars pressure). These highly porous and permeable quartz arenite sandstones are directly analogous to reservoirs around the world targeted for large-scale hydrocarbon extraction, as well as subsurface gas and carbon storage. A new downhole low-contamination subsurface sampling probe was used to collect in situ formation water samples for microbial environmental metagenomic analyses. Multiple lines of evidence suggest that this H. sulfidaeris-dominated subsurface microbial community is indigenous and not derived from drilling mud microbial contamination. Data to support this includes V1-V3 pyrosequencing of formation water and drilling mud, as well as comparison with previously published microbial analyses of drilling muds in other sites. Metabolic pathway reconstruction, constrained by the geology, geochemistry and present-day environmental conditions of the Mt. Simon Sandstone, implies that H. sulfidaeris-dominated subsurface microbial community may utilize iron and nitrogen metabolisms and extensively recycle indigenous nutrients and substrates. The presence of aromatic compound metabolic pathways suggests this microbial community can readily adapt to and survive subsurface hydrocarbon migration.
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Affiliation(s)
- Yiran Dong
- Energy Biosciences Institute, University of Illinois Urbana-Champaign, 1206 W. Gregory Drive, Urbana, IL, 61801, USA; Institute for Genomic Biology, University of Illinois Urbana-Champaign, 1206 W. Gregory Drive, Urbana, IL, 61801, USA; Department of Geology, University of Illinois Urbana-Champaign, 1301 W. Green Street, Urbana, IL, 61801, USA
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Oyama T, Schmitz GE, Dodd D, Han Y, Burnett A, Nagasawa N, Mackie RI, Nakamura H, Morikawa K, Cann I. Mutational and structural analyses of Caldanaerobius polysaccharolyticus Man5B reveal novel active site residues for family 5 glycoside hydrolases. PLoS One 2013; 8:e80448. [PMID: 24278284 PMCID: PMC3835425 DOI: 10.1371/journal.pone.0080448] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 10/03/2013] [Indexed: 11/30/2022] Open
Abstract
CpMan5B is a glycoside hydrolase (GH) family 5 enzyme exhibiting both β-1,4-mannosidic and β-1,4-glucosidic cleavage activities. To provide insight into the amino acid residues that contribute to catalysis and substrate specificity, we solved the structure of CpMan5B at 1.6 Å resolution. The structure revealed several active site residues (Y12, N92 and R196) in CpMan5B that are not present in the active sites of other structurally resolved GH5 enzymes. Residue R196 in GH5 enzymes is thought to be strictly conserved as a histidine that participates in an electron relay network with the catalytic glutamates, but we show that an arginine fulfills a functionally equivalent role and is found at this position in every enzyme in subfamily GH5_36, which includes CpMan5B. Residue N92 is required for full enzymatic activity and forms a novel bridge over the active site that is absent in other family 5 structures. Our data also reveal a role of Y12 in establishing the substrate preference for CpMan5B. Using these molecular determinants as a probe allowed us to identify Man5D from Caldicellulosiruptor bescii as a mannanase with minor endo-glucanase activity.
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Affiliation(s)
- Takuji Oyama
- Institute for Protein Research, Osaka University, Osaka, Japan
| | - George E. Schmitz
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
| | - Dylan Dodd
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
- Department of Microbiology, University of Illinois, Urbana, Illinois, United States of America
| | - Yejun Han
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
| | - Alanna Burnett
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
- Department of Microbiology, University of Illinois, Urbana, Illinois, United States of America
| | - Naoko Nagasawa
- Institute for Protein Research, Osaka University, Osaka, Japan
| | - Roderick I. Mackie
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
- Department of Animal Sciences, University of Illinois, Urbana, Illinois, United States of America
| | - Haruki Nakamura
- Institute for Protein Research, Osaka University, Osaka, Japan
| | - Kosuke Morikawa
- Institute for Protein Research, Osaka University, Osaka, Japan
| | - Isaac Cann
- Institute for Protein Research, Osaka University, Osaka, Japan
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
- Department of Microbiology, University of Illinois, Urbana, Illinois, United States of America
- Department of Animal Sciences, University of Illinois, Urbana, Illinois, United States of America
- * E-mail:
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Præsteng KE, Pope PB, Cann IKO, Mackie RI, Mathiesen SD, Folkow LP, Eijsink VGH, Sundset MA. Probiotic dosing of Ruminococcus flavefaciens affects rumen microbiome structure and function in reindeer. Microb Ecol 2013; 66:840-849. [PMID: 23959114 DOI: 10.1007/s00248-013-0279-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 08/06/2013] [Indexed: 06/02/2023]
Abstract
Highly cellulolytic bacterial species such as Ruminococcus flavefaciens are regarded essential for the microbial breakdown of cellulose in the rumen. We have investigated the effect of ruminal dosing of R. flavefaciens strain 8/94-32 during realimentation of starved reindeer (males, n = 3). Microbiome function measured as in situ digestion of cellulose and food pellets (percent DMD; dry matter disappearance) decreased after probiotic dosing. Microbial community analyses (>100,000 16S rDNA gene sequences for 27 samples) demonstrated that ruminal dosing influenced the microbiome structure; reflected by increased phylogenetic distances from background samples (unweighted UniFrac analysis) and reduced species diversity and evenness. Despite the inability to detect strain 8/94-32 post-dosing, the relative abundance of its affiliate family Ruminococcaceae remained consistent throughout the trial, whilst a dominant peak in the genus Prevotella and decline in uncharacterized Bacteroidetes (uBacNR) were observed in treatment samples. No clear relationships were observed between the relative abundance of Ruminococcaceae, Prevotella and uBacNR with cellulose DMD; however, Prevotella (negative) and uBacNR (positive) exhibited relationships with pellet DMD. These unexpected effects of ruminal dosing of a cellulolytic bacterium on digestibility are relevant for other studies on rumen manipulation.
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Abstract
All animals, including humans, are adapted to life in a microbial world. Anaerobic habitats have existed continuously throughout the history of the earth, the gastrointestinal tract being a contemporary microniche. Since microorganisms colonize and grow rapidly under the favorable conditions in the gut they could compete for nutrients with the host. This microbial challenge has modified the course of evolution in animals, resulting in selection of complex animal-microbe relationships that vary tremendously, ranging from competition to cooperation. The ecological and evolutionary interactions between herbivorous dinosaurs and the first mammalian herbivores and their food plants are reconstructed using knowledge gained during the study of modern living vertebrates, especially foregut and hindgut fermenting mammals. The ruminant is well adapted to achieve maximal digestion of roughage using the physiological mechanism at the reticulo-omasal orifice which selectively retains large particles in the reticulo-rumen. However, the most obvious feature of all ruminants is the regurgitation, rechewing and reswallowing of foregut digesta termed rumination. Foregut fermenting mammals also share interesting and unique features in two enzymes, stomach lysozyme and pancreatic ribonuclease which accompany and are adaptations to this mode of digestion. The microbial community inhabiting the gastrointestinal tract is represented by all major groups of microbes (bacteria, archaea, ciliate protozoa, anaerobic fungi and bacteriophage) and characterized by its high population density, wide diversity and complexity of interactions. The development and application of molecular ecology techniques promises to link distribution and identity of gastrointestinal microbes in their natural environment with their genetic potential and in situ activities.
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Affiliation(s)
- Roderick I Mackie
- Department of Animal Sciences and Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
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Su X, Zhang J, Mackie RI, Cann IKO. Supplementing with non-glycoside hydrolase proteins enhances enzymatic deconstruction of plant biomass. PLoS One 2012; 7:e43828. [PMID: 22952777 PMCID: PMC3428283 DOI: 10.1371/journal.pone.0043828] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2012] [Accepted: 07/30/2012] [Indexed: 11/19/2022] Open
Abstract
The glycoside hydrolases (GH) of Caldicellulosiruptor bescii are thermophilic enzymes, and therefore they can hydrolyze plant cell wall polysaccharides at high temperatures. Analyses of two C. bescii glycoside hydrolases, CbCelA-TM1 and CbXyn10A with cellulase and endoxylanase activity, respectively, demonstrated that each enzyme is highly thermostable under static incubation at 70°C. Both enzymes, however, rapidly lost their enzymatic activities when incubated at 70°C with end-over-end shaking. Since crowding conditions, even at low protein concentrations, seem to influence enzymatic properties, three non-glycoside hydrolase proteins were tested for their capacity to stabilize the thermophilic proteins at high temperatures. The three proteins investigated were a small heat shock protein CbHsp18 from C. bescii, a histone MkHistone1 from Methanopyrus kandleri, and bovine RNase A, from a commercial source. Fascinatingly, each of these proteins increased the thermostability of the glycoside hydrolases at 70°C during end-over-end shaking incubation, and this property translated into increases in hydrolysis of several substrates including the bioenergy feedstock Miscanthus. Furthermore, MkHistone1 and RNase A also altered the initial products released from the cello-oligosaccharide cellopentaose during hydrolysis with the cellodextrinase CbCdx1A, which further demonstrated the capacity of the three non-GH proteins to influence hydrolysis of substrates by the thermophilic glycoside hydrolases. The non-GH proteins used in the present report were small proteins derived from each of the three lineages of life, and therefore expand the space from which different polypeptides can be tested for their influence on plant cell wall hydrolysis, a critical step in the emerging biofuel industry.
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Affiliation(s)
- Xiaoyun Su
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
| | - Jing Zhang
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
- Department of Animal Sciences, University of Illinois, Urbana, Illinois, United States of America
| | - Roderick I. Mackie
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
- Department of Animal Sciences, University of Illinois, Urbana, Illinois, United States of America
| | - Isaac K. O. Cann
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
- Department of Animal Sciences, University of Illinois, Urbana, Illinois, United States of America
- Department of Microbiology, University of Illinois, Urbana, Illinois, United States of America
- * E-mail:
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Han Y, Agarwal V, Dodd D, Kim J, Bae B, Mackie RI, Nair SK, Cann IKO. Biochemical and structural insights into xylan utilization by the thermophilic bacterium Caldanaerobius polysaccharolyticus. J Biol Chem 2012; 287:34946-34960. [PMID: 22918832 DOI: 10.1074/jbc.m112.391532] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Hemicellulose is the next most abundant plant cell wall component after cellulose. The abundance of hemicellulose such as xylan suggests that their hydrolysis and conversion to biofuels can improve the economics of bioenergy production. In an effort to understand xylan hydrolysis at high temperatures, we sequenced the genome of the thermophilic bacterium Caldanaerobius polysaccharolyticus. Analysis of the partial genome sequence revealed a gene cluster that contained both hydrolytic enzymes and also enzymes key to the pentose-phosphate pathway. The hydrolytic enzymes in the gene cluster were demonstrated to convert products from a large endoxylanase (Xyn10A) predicted to anchor to the surface of the bacterium. We further use structural and calorimetric studies to demonstrate that the end products of Xyn10A hydrolysis of xylan are recognized and bound by XBP1, a putative solute-binding protein, likely for transport into the cell. The XBP1 protein showed preference for xylo-oligosaccharides as follows: xylotriose > xylobiose > xylotetraose. To elucidate the structural basis for the oligosaccharide preference, we solved the co-crystal structure of XBP1 complexed with xylotriose to a 1.8-Å resolution. Analysis of the biochemical data in the context of the co-crystal structure reveals the molecular underpinnings of oligosaccharide length specificity.
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Affiliation(s)
- Yejun Han
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois 61801; Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801
| | - Vinayak Agarwal
- Center for Biophysics and Computational Biology, University of Illinois, Urbana, Illinois 61801; Department of Biochemistry, University of Illinois, Urbana, Illinois 61801
| | - Dylan Dodd
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois 61801; Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801; Department of Microbiology, University of Illinois, Urbana, Illinois 61801
| | - Jason Kim
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois 61801; Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801; Department of Molecular and Cellular Biology, University of Illinois, Urbana, Illinois 61801
| | - Brian Bae
- Department of Biochemistry, University of Illinois, Urbana, Illinois 61801
| | - Roderick I Mackie
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois 61801; Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801; Department of Animal Sciences, University of Illinois, Urbana, Illinois 61801
| | - Satish K Nair
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801; Center for Biophysics and Computational Biology, University of Illinois, Urbana, Illinois 61801; Department of Biochemistry, University of Illinois, Urbana, Illinois 61801.
| | - Isaac K O Cann
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois 61801; Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801; Department of Microbiology, University of Illinois, Urbana, Illinois 61801; Department of Molecular and Cellular Biology, University of Illinois, Urbana, Illinois 61801; Department of Animal Sciences, University of Illinois, Urbana, Illinois 61801.
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Mao Y, Yannarell AC, Davis SC, Mackie RI. Impact of different bioenergy crops on N-cycling bacterial and archaeal communities in soil. Environ Microbiol 2012; 15:928-42. [DOI: 10.1111/j.1462-2920.2012.02844.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Kisiela DI, Chattopadhyay S, Libby SJ, Karlinsey JE, Fang FC, Tchesnokova V, Kramer JJ, Beskhlebnaya V, Samadpour M, Grzymajlo K, Ugorski M, Lankau EW, Mackie RI, Clegg S, Sokurenko EV. Evolution of Salmonella enterica virulence via point mutations in the fimbrial adhesin. PLoS Pathog 2012; 8:e1002733. [PMID: 22685400 PMCID: PMC3369946 DOI: 10.1371/journal.ppat.1002733] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Accepted: 04/20/2012] [Indexed: 11/18/2022] Open
Abstract
Whereas the majority of pathogenic Salmonella serovars are capable of infecting many different animal species, typically producing a self-limited gastroenteritis, serovars with narrow host-specificity exhibit increased virulence and their infections frequently result in fatal systemic diseases. In our study, a genetic and functional analysis of the mannose-specific type 1 fimbrial adhesin FimH from a variety of serovars of Salmonella enterica revealed that specific mutant variants of FimH are common in host-adapted (systemically invasive) serovars. We have found that while the low-binding shear-dependent phenotype of the adhesin is preserved in broad host-range (usually systemically non-invasive) Salmonella, the majority of host-adapted serovars express FimH variants with one of two alternative phenotypes: a significantly increased binding to mannose (as in S. Typhi, S. Paratyphi C, S. Dublin and some isolates of S. Choleraesuis), or complete loss of the mannose-binding activity (as in S. Paratyphi B, S. Choleraesuis and S. Gallinarum). The functional diversification of FimH in host-adapted Salmonella results from recently acquired structural mutations. Many of the mutations are of a convergent nature indicative of strong positive selection. The high-binding phenotype of FimH that leads to increased bacterial adhesiveness to and invasiveness of epithelial cells and macrophages usually precedes acquisition of the non-binding phenotype. Collectively these observations suggest that activation or inactivation of mannose-specific adhesive properties in different systemically invasive serovars of Salmonella reflects their dynamic trajectories of adaptation to a life style in specific hosts. In conclusion, our study demonstrates that point mutations are the target of positive selection and, in addition to horizontal gene transfer and genome degradation events, can contribute to the differential pathoadaptive evolution of Salmonella.
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Affiliation(s)
- Dagmara I. Kisiela
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Sujay Chattopadhyay
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Stephen J. Libby
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Joyce E. Karlinsey
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Ferric C. Fang
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Veronika Tchesnokova
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Jeremy J. Kramer
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Viktoriya Beskhlebnaya
- Institute for Environmental Health, Lake Forest Park, Washington, United States of America
| | - Mansour Samadpour
- Institute for Environmental Health, Lake Forest Park, Washington, United States of America
| | - Krzysztof Grzymajlo
- Department of Biochemistry, Pharmacology and Toxicology, Wroclaw University of Environmental and Life Sciences, Wroclaw, Poland
| | - Maciej Ugorski
- Department of Biochemistry, Pharmacology and Toxicology, Wroclaw University of Environmental and Life Sciences, Wroclaw, Poland
| | - Emily W. Lankau
- Department of Animal Sciences, University of Illinois, Urbana, Illinois, United States of America
| | - Roderick I. Mackie
- Department of Animal Sciences, University of Illinois, Urbana, Illinois, United States of America
| | - Steven Clegg
- Department of Microbiology, University of Iowa, Iowa City, Iowa, United States of America
| | - Evgeni V. Sokurenko
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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42
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Lankau EW, Cruz Bedon L, Mackie RI. Salmonella strains isolated from Galápagos iguanas show spatial structuring of serovar and genomic diversity. PLoS One 2012; 7:e37302. [PMID: 22615968 PMCID: PMC3353930 DOI: 10.1371/journal.pone.0037302] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Accepted: 04/19/2012] [Indexed: 01/31/2023] Open
Abstract
It is thought that dispersal limitation primarily structures host-associated bacterial populations because host distributions inherently limit transmission opportunities. However, enteric bacteria may disperse great distances during food-borne outbreaks. It is unclear if such rapid long-distance dispersal events happen regularly in natural systems or if these events represent an anthropogenic exception. We characterized Salmonella enterica isolates from the feces of free-living Galápagos land and marine iguanas from five sites on four islands using serotyping and genomic fingerprinting. Each site hosted unique and nearly exclusive serovar assemblages. Genomic fingerprint analysis offered a more complex model of S. enterica biogeography, with evidence of both unique strain pools and of spatial population structuring along a geographic gradient. These findings suggest that even relatively generalist enteric bacteria may be strongly dispersal limited in a natural system with strong barriers, such as oceanic divides. Yet, these differing results seen on two typing methods also suggests that genomic variation is less dispersal limited, allowing for different ecological processes to shape biogeographical patterns of the core and flexible portions of this bacterial species' genome.
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Affiliation(s)
- Emily W. Lankau
- Department of Animal Sciences and College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Lenin Cruz Bedon
- Armador del Pirata, Puerto Ayora, Isla Santa Cruz, Galápagos Islands, Ecuador
| | - Roderick I. Mackie
- Department of Animal Sciences and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
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Hong PY, Li X, Yang X, Shinkai T, Zhang Y, Wang X, Mackie RI. Monitoring airborne biotic contaminants in the indoor environment of pig and poultry confinement buildings. Environ Microbiol 2012; 14:1420-31. [PMID: 22414212 DOI: 10.1111/j.1462-2920.2012.02726.x] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Given the growing concerns over human and animal health issues related to confined animal feeding operations, an in-depth examination is required to monitor for airborne bacteria and associated antibiotic resistance genes. Our 16S rRNA-based pyrosequencing revealed that the airborne microbial community skewed towards a higher abundance of Firmicutes (> 59.2%) and Bacteroidetes (4.2-31.4%) within the confinement buildings, while the office environment was predominated by Proteobacteria (55.2%). Furthermore, bioaerosols in the confinement buildings were sporadically associated with genera of potential pathogens, and these genera were more frequently observed in the bioaerosols of pig and layer hen confinement than the turkey confinement buildings and office environment. High abundances of tetracycline resistance genes (9.55 × 10(2) to 1.69 × 10(6) copies ng(-1) DNA) were also detected in the bioaerosols sampled from confinement buildings. Bacterial lineages present in the poultry bioaerosols clustered apart from those present in the pig bioaerosols and among the different phases of pig production, suggesting that different livestock as well as production phase were associated with a distinct airborne microbial community. By understanding the diversity of biotic contaminants associated with the different confinement buildings, this study facilitates the implementation of better management strategies to minimize potential health impacts on both livestock and humans working in this environment.
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Affiliation(s)
- Pei-Ying Hong
- Departments of Animal Sciences Agricultural and Biological Engineering Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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Lankau EW, Hong PY, Mackie RI. Ecological drift and local exposures drive enteric bacterial community differences within species of Galápagos iguanas. Mol Ecol 2012; 21:1779-88. [PMID: 22369350 DOI: 10.1111/j.1365-294x.2012.05502.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Diet strongly influences the intestinal microbial communities through species sorting. Alternatively, these communicates may differ because of chance variation in local microbial exposures or species losses among allopatric host populations (i.e. ecological drift). We investigated how these forces shape enteric communities of Galápagos marine and land iguanas. Geographically proximate populations shared more similar communities within a host ecotype, suggesting a role for ecological drift during host colonization of the islands. Additionally, evidence of taxa sharing between proximate heterospecific host populations suggests that contemporary local exposures also influence the gut community assembly. While selective forces such as host-bacterial interactions or dietary differences are dominant drivers of intestinal community differences among hosts, historical and contemporary processes of ecological drift may lead to differences in bacterial composition within a host species. Whether such differences in community structure translate into geographic variation in benefits derived from these intimate microbial communities remains to be explored.
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Affiliation(s)
- Emily W Lankau
- Department of Animal Sciences and College of Veterinary Medicine, University of Illinois, Urbana, IL 61801, USA
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Præsteng KE, Mackie RI, Cann IKO, Mathiesen SD, Sundset MA. Development of a signature probe targeting the 16S-23S rRNA internal transcribed spacer of a ruminal Ruminococcus flavefaciens isolate from reindeer. Benef Microbes 2012; 2:47-55. [PMID: 21831789 DOI: 10.3920/bm2010.0044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The cellulolytic Ruminococcus flavefaciens has previously been introduced into the ruminant rumen to increase microbial degradation of plant cell wall carbohydrates. The functional effect of an introduced bacterium depends on its ability to establish in the digestive tract, and signature probes can be used as a tool to track and quantify introduced strains. The purpose of this current study was to develop an oligonucleotide signature probe targeting the 16S-23S rRNA internal transcribed spacer (ITS) of a putative probiotic cellulolytic isolate (R. flavefaciens strain 8/94-32) from the rumen of reindeer (Rangifer tarandus tarandus). The 16S-23S rRNA gene ITS of three Ruminococcus strains; R. flavefaciens strain 8/94-32, R. flavefaciens FD-1 and Ruminococcus albus Ra-8, was investigated. The ITS region has been reported to vary more between closely related bacteria compared to the widely used 16S rRNA gene, and a high degree of sequence polymorphism was indeed detected between the three Ruminococcus strains studied. Based on observed sequence differences, two oligonucloetide probes, ITSRumi1 and ITSRumi2, targeting the ITS region of the R. flavefaciens isolate 8/94-32 were developed. Probe specificity was evaluated in dot blot hybridisations with R. flavefaciens isolate 8/94-32 and four other Ruminococcus-strains tested. The probe ITSRumi1 gave positive signals for the R. flavefaciens isolate 8/94-32 only, while probe ITSRumi2 gave positive signals for R. flavefaciens isolate 8/94-32 as well as for R. albus Ra-8. The result of hybridisations with the probe ITSRumi1 indicates that the probe is specific for the R. flavefaciens strain 8/94-32 amongst the four Ruminococcus-strains tested, and is promising for further studies using it as a signature probe for tracking this strain when re-introduced to the reindeer rumen.
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Affiliation(s)
- K E Præsteng
- Department of Arctic and Marine Biology, University of Tromsø, Norway
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Nakamura N, Lin HC, McSweeney CS, Mackie RI, Gaskins HR. Mechanisms of microbial hydrogen disposal in the human colon and implications for health and disease. Annu Rev Food Sci Technol 2012; 1:363-95. [PMID: 22129341 DOI: 10.1146/annurev.food.102308.124101] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In the human gastrointestinal tract, dietary components, including fiber, that reach the colon are fermented principally to short-chain fatty acids, hydrogen, and carbon dioxide. Microbial disposal of the hydrogen generated during anaerobic fermentation in the human colon is critical to optimal functioning of this ecosystem. However, our understanding of microbial hydrogenotrophy is fragmented and, at least as it occurs in the colon, is mostly theoretical in nature. Thorough investigation and integration of knowledge on the diversity of hydrogenotrophic microbes, their metabolic variation and activities as a functional group, as well as the nature of their interactions with fermentative bacteria, are necessary to understand hydrogen metabolism in the human colon. Here, we review the limited data available on the three major groups of H(2)-consuming microorganisms found in the human colon [methanogens, sulfate-reducing bacteria (SRB), and acetogens] as well as evidence that end products of their metabolism have an important impact on colonic health.
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Affiliation(s)
- Noriko Nakamura
- Department of Animal Sciences and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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47
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Kim JN, Cann IKO, Mackie RI. Purification, characterization, and expression of multiple glutamine synthetases from Prevotella ruminicola 23. J Bacteriol 2012; 194:176-84. [PMID: 22020637 PMCID: PMC3256599 DOI: 10.1128/jb.05916-11] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Accepted: 10/14/2011] [Indexed: 11/20/2022] Open
Abstract
The Prevotella ruminicola 23 genome encodes three different glutamine synthetase (GS) enzymes: glutamine synthetase I (GSI) (ORF02151), GSIII-1 (ORF01459), and GSIII-2 (ORF02034). GSI, GSIII-1, and GSIII-2 have each been heterologously expressed in and purified from Escherichia coli. The subunit molecular mass of GSI was 56 kDa, while GSIII-1 and GSIII-2 were both 83 kDa. Optimal conditions for γ-glutamyl transferase activity were found to be 35°C at pH 5.6 with 0.25 mM Mn(2+) ions (GSI) or 37°C at pH 6.0 (GSIII-1 and GSIII-2) with 0.50 to 1.00 mM Mn(2+) ions. GSIII biosynthetic activity was found to be optimal at 50 to 60°C and pH 6.8 to 7.0 with 10 mM Mn(2+) ions, while GSI displayed no GS biosynthetic activity. Kinetic analysis revealed K(m) values for glutamate and ammonium as well as for hydrolysis of ATP to be 8.58, 0.48, and 1.91 mM, respectively, for GSIII-1 and 1.72, 0.43, and 2.65 mM, respectively, for GSIII-2. A quantitative reverse transcriptase PCR assay (qRT-PCR) revealed GSIII-2 to be significantly induced by high concentrations of ammonia, and this corresponded with increases in measured GS activity. Collectively, these results show that both GSIII enzymes in P. ruminicola 23 are functional and indicate that GSIII-2, flanked by GOGAT (gltB and gltD genes), plays an important role in the acquisition and metabolism of ammonia, particularly under nonlimiting ammonia growth conditions.
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Affiliation(s)
| | - Isaac K. O. Cann
- Department of Animal Sciences
- Department of Microbiology
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, USA
| | - Roderick I. Mackie
- Department of Animal Sciences
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, USA
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Mao Y, Yannarell AC, Mackie RI. Changes in N-transforming archaea and bacteria in soil during the establishment of bioenergy crops. PLoS One 2011; 6:e24750. [PMID: 21935454 PMCID: PMC3173469 DOI: 10.1371/journal.pone.0024750] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Accepted: 08/16/2011] [Indexed: 11/18/2022] Open
Abstract
Widespread adaptation of biomass production for bioenergy may influence important biogeochemical functions in the landscape, which are mainly carried out by soil microbes. Here we explore the impact of four potential bioenergy feedstock crops (maize, switchgrass, Miscanthus X giganteus, and mixed tallgrass prairie) on nitrogen cycling microorganisms in the soil by monitoring the changes in the quantity (real-time PCR) and diversity (barcoded pyrosequencing) of key functional genes (nifH, bacterial/archaeal amoA and nosZ) and 16S rRNA genes over two years after bioenergy crop establishment. The quantities of these N-cycling genes were relatively stable in all four crops, except maize (the only fertilized crop), in which the population size of AOB doubled in less than 3 months. The nitrification rate was significantly correlated with the quantity of ammonia-oxidizing archaea (AOA) not bacteria (AOB), indicating that archaea were the major ammonia oxidizers. Deep sequencing revealed high diversity of nifH, archaeal amoA, bacterial amoA, nosZ and 16S rRNA genes, with 229, 309, 330, 331 and 8989 OTUs observed, respectively. Rarefaction analysis revealed the diversity of archaeal amoA in maize markedly decreased in the second year. Ordination analysis of T-RFLP and pyrosequencing results showed that the N-transforming microbial community structures in the soil under these crops gradually differentiated. Thus far, our two-year study has shown that specific N-transforming microbial communities develop in the soil in response to planting different bioenergy crops, and each functional group responded in a different way. Our results also suggest that cultivation of maize with N-fertilization increases the abundance of AOB and denitrifiers, reduces the diversity of AOA, and results in significant changes in the structure of denitrification community.
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Affiliation(s)
- Yuejian Mao
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
| | - Anthony C. Yannarell
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
- Department of Natural Resources and Environmental Sciences, University of Illinois, Urbana, Illinois, United States of America
| | - Roderick I. Mackie
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
- Department of Animal Sciences, University of Illinois, Urbana, Illinois, United States of America
- * E-mail:
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Præsteng KE, Mackie RI, Cann IKO, Mathiesen SD, Sundset MA. Variations in the 16S-23S rRNA internal transcribed spacer of fibrolytic Butyrivibrio isolates from the reindeer rumen. Can J Microbiol 2011; 57:617-21. [PMID: 21774627 DOI: 10.1139/w11-038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Strains of Butyrivibrio are principal cellulytic bacteria in the rumen of the High Arctic Svalbard reindeer ( Rangifer tarandus platyrhynchus ). According to phylogenetic analysis based on 16S rRNA gene sequencing, Butyrivibrio can be divided into three subgroups within the Clostridia class of the phylum Firmicutes, but the current phenotypic and genotypic differentiation within the family Lachnospiraceae is insufficient. This current study describes the sequence diversity of the 16S-23S rRNA intergenic transcribed spacer (ITS) region of Butyrivibrio isolates from reindeer. A total of 17 different ITS sequences with sizes between 449 and 784 nt were obtained. Genes encoding tRNA(Ile) and tRNA(Ala) were identified in four of the sequences. Phylogenetic neighbor-joining trees were constructed based on the ITS sequence and compared with a phylogenetic neighbor-joining tree based on 16S rRNA gene sequences previously obtained for the same isolates. These comparisons indicated a better differentiation between strains in the ITS sequence than the 16S rRNA gene based tree. Through this study, a better means for identifying and tracking fibrolytic and potentially probiotic Butyrivibrio strains in reindeer and other ruminants has been provided.
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Affiliation(s)
- Kirsti E Præsteng
- Department of Arctic and Marine Biology, University of Tromsø, Norway
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50
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Grønvold AMR, Mao Y, L'Abée-Lund TM, Sørum H, Sivertsen T, Yannarell AC, Mackie RI. Fecal microbiota of calves in the clinical setting: effect of penicillin treatment. Vet Microbiol 2011; 153:354-60. [PMID: 21705160 DOI: 10.1016/j.vetmic.2011.05.040] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Revised: 05/03/2011] [Accepted: 05/25/2011] [Indexed: 10/18/2022]
Abstract
The effect of parenteral penicillin treatment on the intestinal microbiota was determined by monitoring the phenotypic antimicrobial resistance among Escherichia coli in 19 calves (15 calves received treatment and four calves were healthy controls) and by examining changes in the fecal microbial community structure using molecular fingerprinting techniques in a subset of eight calves (five treated calves and three control calves). After five days of penicillin treatment an increased resistance to multiple unrelated antimicrobial agents, including non-β-lactams, was seen in E. coli from treated calves, and this was not seen in the controls. Automated ribosomal intergenic spacer analysis (ARISA) and terminal restriction fragment length polymorphism (TRFLP) revealed that penicillin treatment causes a significant variation in the microbial structure within an individual calf. The study shows that parenteral administration of penicillin has an impact on the composition of the fecal microbiota in calves, and on the antimicrobial resistance pattern of their fecal E. coli.
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Affiliation(s)
- Anne-Mette R Grønvold
- Department of Food Safety and Infection Biology, Norwegian School of Veterinary Science (NSVS), Pb 8146 Dep, N-0033 Oslo, Norway
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