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Microbiome-based biotechnology for reducing food loss post harvest. Curr Opin Biotechnol 2022; 78:102808. [PMID: 36183451 DOI: 10.1016/j.copbio.2022.102808] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 08/21/2022] [Accepted: 08/29/2022] [Indexed: 12/14/2022]
Abstract
Microbiomes have an immense potential to enhance plant resilience to various biotic and abiotic stresses. However, intrinsic microbial communities respond to changes in their host's physiology and environment during plant's life cycle. The potential of the inherent plant microbiome has been neglected for a long time, especially for the postharvest period. Currently, close to 50% of all produced fruits and vegetables are lost either during production or storage. Biological control of spoilage and storage diseases is still lacking sufficiency. Today, novel multiomics technologies allow us to study the microbiome and its responses on a community level, which will help to advance current classic approaches and develop more effective and robust microbiome-based solutions for fruit and vegetable storability, quality, and safety.
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Tom LM, Aulitto M, Wu YW, Deng K, Gao Y, Xiao N, Rodriguez BG, Louime C, Northen TR, Eudes A, Mortimer JC, Adams PD, Scheller HV, Simmons BA, Ceja-Navarro JA, Singer SW. Low-abundance populations distinguish microbiome performance in plant cell wall deconstruction. MICROBIOME 2022; 10:183. [PMID: 36280858 PMCID: PMC9594917 DOI: 10.1186/s40168-022-01377-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 09/19/2022] [Indexed: 05/23/2023]
Abstract
BACKGROUND Plant cell walls are interwoven structures recalcitrant to degradation. Native and adapted microbiomes can be particularly effective at plant cell wall deconstruction. Although most understanding of biological cell wall deconstruction has been obtained from isolates, cultivated microbiomes that break down cell walls have emerged as new sources for biotechnologically relevant microbes and enzymes. These microbiomes provide a unique resource to identify key interacting functional microbial groups and to guide the design of specialized synthetic microbial communities. RESULTS To establish a system assessing comparative microbiome performance, parallel microbiomes were cultivated on sorghum (Sorghum bicolor L. Moench) from compost inocula. Biomass loss and biochemical assays indicated that these microbiomes diverged in their ability to deconstruct biomass. Network reconstructions from gene expression dynamics identified key groups and potential interactions within the adapted sorghum-degrading communities, including Actinotalea, Filomicrobium, and Gemmatimonadetes populations. Functional analysis demonstrated that the microbiomes proceeded through successive stages that are linked to enzymes that deconstruct plant cell wall polymers. The combination of network and functional analysis highlighted the importance of cellulose-degrading Actinobacteria in differentiating the performance of these microbiomes. CONCLUSIONS The two-tier cultivation of compost-derived microbiomes on sorghum led to the establishment of microbiomes for which community structure and performance could be assessed. The work reinforces the observation that subtle differences in community composition and the genomic content of strains may lead to significant differences in community performance. Video Abstract.
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Affiliation(s)
- Lauren M Tom
- Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Martina Aulitto
- Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yu-Wei Wu
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, 110, Taiwan
| | - Kai Deng
- Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yu Gao
- Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Systems and Genome Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Naijia Xiao
- Institute of Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | | | - Clifford Louime
- College of Natural Sciences, University of Puerto Rico, Rio Piedras, Puerto Rico
| | - Trent R Northen
- Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Systems and Genome Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Aymerick Eudes
- Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Systems and Genome Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jenny C Mortimer
- Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Systems and Genome Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- School of Agriculture, Food and Wine, & Waite Research Institute, University of Adelaide, Glen Osmond, SA, Australia
| | - Paul D Adams
- Joint BioEnergy Institute, Emeryville, CA, USA
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA
| | - Henrik V Scheller
- Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Systems and Genome Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, CA, USA
| | - Blake A Simmons
- Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Javier A Ceja-Navarro
- Joint BioEnergy Institute, Emeryville, CA, USA.
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA.
| | - Steven W Singer
- Joint BioEnergy Institute, Emeryville, CA, USA.
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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Conversion of Carbon Monoxide to Chemicals Using Microbial Consortia. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2021; 180:373-407. [PMID: 34811579 DOI: 10.1007/10_2021_180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Syngas, a gaseous mixture of CO, H2 and CO2, can be produced by gasification of carbon-containing materials, including organic waste materials or lignocellulosic biomass. The conversion of bio-based syngas to chemicals is foreseen as an important process in circular bioeconomy. Carbon monoxide is also produced as a waste gas in many industrial sectors (e.g., chemical, energy, steel). Often, the purity level of bio-based syngas and waste gases is low and/or the ratios of syngas components are not adequate for chemical conversion (e.g., by Fischer-Tropsch). Microbes are robust catalysts to transform impure syngas into a broad spectrum of products. Fermentation of CO-rich waste gases to ethanol has reached commercial scale (by axenic cultures of Clostridium species), but production of other chemical building blocks is underexplored. Currently, genetic engineering of carboxydotrophic acetogens is applied to increase the portfolio of products from syngas/CO, but the limited energy metabolism of these microbes limits product yields and applications (for example, only products requiring low levels of ATP for synthesis can be produced). An alternative approach is to explore microbial consortia, including open mixed cultures and synthetic co-cultures, to create a metabolic network based on CO conversion that can yield products such as medium-chain carboxylic acids, higher alcohols and other added-value chemicals.
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Kleerebezem R, Stouten G, Koehorst J, Langenhoff A, Schaap P, Smidt H. Experimental infrastructure requirements for quantitative research on microbial communities. Curr Opin Biotechnol 2021; 67:158-165. [PMID: 33596519 DOI: 10.1016/j.copbio.2021.01.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 01/21/2021] [Indexed: 01/27/2023]
Abstract
Natural microbial communities are composed of a large diversity of interacting microorganisms, each with a specific role in the functional properties of the ecosystem. The objectives in microbial ecology research are related to identifying, understanding and exploring the role of these different microorganisms. Because of the rapidly increasing power of DNA sequencing and the rapid increase of genomic data, main attention of microbial ecology research shifted from cultivation-oriented studies towards metagenomic studies. Despite these efforts, the direct link between the molecular properties and the measurable changes in the functional performance of the ecosystem is often poorly documented. A quantitative understanding of functional properties in relation to the molecular changes requires effective integration, standardization, and parallelization of experiments. High-resolution functional characterization is a prerequisite for interpretation of changes in metagenomic properties, and will improve our understanding of microbial communities and facilitate their exploration for health and circular economy related objectives.
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Affiliation(s)
- Robbert Kleerebezem
- Delft University of Technology, Department of Biotechnology, Delft, The Netherlands.
| | - Gerben Stouten
- Delft University of Technology, Department of Biotechnology, Delft, The Netherlands
| | - Jasper Koehorst
- Wageningen University and Research, Laboratory of Systems and Synthetic Biology, Wageningen, The Netherlands
| | - Alette Langenhoff
- Wageningen University and Research, Department of Environmental Technology, Wageningen, The Netherlands
| | - Peter Schaap
- Wageningen University and Research, Laboratory of Systems and Synthetic Biology, Wageningen, The Netherlands
| | - Hauke Smidt
- Wageningen University and Research, Laboratory of Microbiology, Wageningen, The Netherlands
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Schwan B, Abendroth C, Latorre-Pérez A, Porcar M, Vilanova C, Dornack C. Chemically Stressed Bacterial Communities in Anaerobic Digesters Exhibit Resilience and Ecological Flexibility. Front Microbiol 2020; 11:867. [PMID: 32477297 PMCID: PMC7235767 DOI: 10.3389/fmicb.2020.00867] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 04/14/2020] [Indexed: 12/02/2022] Open
Abstract
Anaerobic digestion is a technology known for its potential in terms of methane production. During the digestion process, multiple metabolites of high value are synthesized. However, recent works have demonstrated the high robustness and resilience of the involved microbiomes; these attributes make it difficult to manipulate them in such a way that a specific metabolite is predominantly produced. Therefore, an exact understanding of the manipulability of anaerobic microbiomes may open up a treasure box for bio-based industries. In the present work, the effect of nalidixic acid, γ-aminobutyric acid (GABA), and sodium phosphate on the microbiome of digested sewage sludge from a water treatment plant fed with glucose was investigated. Despite of the induced process perturbations, high stability was observed at the phylum level. However, strong variations were observed at the genus level, especially for the genera Trichococcus, Candidatus Caldatribacterium, and Phascolarctobacterium. Ecological interactions were analyzed based on the Lotka–Volterra model for Trichococcus, Rikenellaceae DMER64, Sedimentibacter, Candidatus Cloacimonas, Smithella, Cloacimonadaceae W5 and Longilinea. These genera dynamically shifted among positive, negative or no correlation, depending on the applied stressor, which indicates a surprisingly dynamic behavior. Globally, the presented work suggests a massive resilience and stability of the methanogenic communities coupled with a surprising flexibility of the particular microbial key players involved in the process.
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Affiliation(s)
- Benjamin Schwan
- Institute of Waste Management and Circular Economy, Technische Universität Dresden, Pirna, Germany
| | - Christian Abendroth
- Institute of Waste Management and Circular Economy, Technische Universität Dresden, Pirna, Germany.,Robert Boyle Institut e.V., Jena, Germany
| | - Adriel Latorre-Pérez
- Darwin Bioprospecting Excellence, S.L. Parc Cientific Universitat de València, Paterna, Spain
| | - Manuel Porcar
- Darwin Bioprospecting Excellence, S.L. Parc Cientific Universitat de València, Paterna, Spain.,Institute for Integrative Systems Biology, University of Valencia-CSIC, Paterna, Spain
| | - Cristina Vilanova
- Darwin Bioprospecting Excellence, S.L. Parc Cientific Universitat de València, Paterna, Spain
| | - Christina Dornack
- Institute of Waste Management and Circular Economy, Technische Universität Dresden, Pirna, Germany
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