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Castañeda-Barreto A, Olivera-Gonzales P, Tamariz-Angeles C. A natural consortium of thermophilic bacteria from Huancarhuaz hot spring (Ancash-Peru) for promising lignocellulose bioconversion. Heliyon 2024; 10:e27272. [PMID: 38486736 PMCID: PMC10937689 DOI: 10.1016/j.heliyon.2024.e27272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 02/14/2024] [Accepted: 02/27/2024] [Indexed: 03/17/2024] Open
Abstract
The lignocellulose bioconversion process is an eco-friendly and green-economy alternative technology that allows the reduction of pollution and global warming, so it is necessary for thermophilic and thermostable hydrolytic enzymes from natural sources. This research aimed to isolate cellulolytic and xylanolytic microbial consortia from Huancarhuaz hot spring (Peru) from sludge or in situ baiting cultured with or without sugarcane bagasse. According to the hydrolytic activities consortium T4 from in situ baiting was selected. It was cultivated in submerged fermentation at 65 °C, pH 6.5 for eight days using LB supplemented with sugar cane bagasse (SCB), pine wood sawdust (PWS), CMC, xylan of birchwood, or micro granular cellulose. Crude extract of culture supplemented with SCB (T4B) showed better endoglucanase and xylanase activities with higher activities at 75 °C and pH 6. In these conditions, cellulase activity was kept up to 57% after 1 h of incubation, while xylanase activity was up to 63% after 72 h. Furthermore, this crude extract released reduced sugars from pretreated SCB and PWS. According to metagenomic analysis of 16S rDNA, Geobacillus was the predominant genus. It was found thermostable genes: a type of endoglucanase (GH5), an endo-xylanase (GH10), and alkali xylanase (GH10) previously reported in Geobacillus sp. strains. Finally, Huancarhuaz hot spring harbors a genetic microbial diversity for lignocellulosic waste bioconversion in high temperatures, and the T4B consortium will be a promising source of novel extreme condition stable enzymes for the saccharification process.
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Affiliation(s)
- Alberto Castañeda-Barreto
- Facultad de Ciencias del Ambiente, Universidad Nacional Santiago Antúnez de Mayolo, Av. Centenario 200, 02002, Independencia, Huaraz, Ancash, Peru
| | - Percy Olivera-Gonzales
- Centro de Investigación de la Biodiversidad y Recursos Genéticos de Ancash, Facultad de Ciencias, Universidad Nacional Santiago Antúnez de Mayolo, Av. Centenario 200, 02002, Independencia, Huaraz, Ancash, Peru
| | - Carmen Tamariz-Angeles
- Centro de Investigación de la Biodiversidad y Recursos Genéticos de Ancash, Facultad de Ciencias, Universidad Nacional Santiago Antúnez de Mayolo, Av. Centenario 200, 02002, Independencia, Huaraz, Ancash, Peru
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Rajeswari G, Kumar V, Jacob S. A concerted enzymatic de-structuring of lignocellulosic materials using a compost-derived microbial consortia favoring the consolidated pretreatment and bio-saccharification. Enzyme Microb Technol 2024; 174:110393. [PMID: 38219439 DOI: 10.1016/j.enzmictec.2023.110393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 11/24/2023] [Accepted: 12/29/2023] [Indexed: 01/16/2024]
Abstract
The robustness of microbial consortia isolated from compost habitat encompasses the complementary metabolism that aids in consolidated bioprocessing (CBP) of lignocellulosic biomass (LCB) by division of labor across the symbionts. Composting of organic waste is deemed to be an efficient way of carbon recycling, where the syntrophic microbial population exerts a concerted action of lignin and polysaccharide (hemicellulose and cellulose) component of plant biomass. The potential of this interrelated microorganism could be enhanced through adaptive laboratory evolution (ALE) with LCB for its desired functional capabilities. Therefore, in this study, microbial symbionts derived from organic compost was enriched on saw dust (SD) (woody biomass), aloe vera leaf rind (AVLR) (agro-industrial waste) and commercial filter paper (FP) (pure cellulose) through ALE under different conditions. Later, the efficacy of enriched consortium (EC) on consolidated pretreatment and bio-saccharification was determined based on substrate degradation, endo-enzymes profiling and fermentable sugar yield. Among the treatment sets, AVLR biomass treated with EC-5 has resulted in the higher degradation rate of lignin (47.01 ± 0.66%, w/w) and polysaccharides (45.87 ± 1.82%, w/w) with a total sugar yield of about 60.01 ± 4.24 mg/g. In addition, the extent of structural disintegration of substrate after EC-treatment was clearly deciphered by FTIR and XRD analysis. And the factors of Pearson correlation matrix reinforces the potency of EC-5 by exhibiting a strong positive correlation between AVLR degradation and the sugar release. Thus, a consortium based CBP could promote the feasibility of establishing a sustainable second generation biorefinery framework.
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Affiliation(s)
- Gunasekaran Rajeswari
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, Faculty of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar, Chengalpattu District, Kattankulathur 603203, Tamil Nadu, India
| | - Vinod Kumar
- School of Water, Energy and Environment, Cranfield University, Cranfield MK43 0AL, UK.
| | - Samuel Jacob
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, Faculty of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar, Chengalpattu District, Kattankulathur 603203, Tamil Nadu, India.
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Wang Y, Chen Y, Gao X, Wang Q, Cui M, Zhang D, Guo P. Unveiling the driving role of pH on community stability and function during lignocellulose degradation in paddy soil. Front Microbiol 2024; 15:1338842. [PMID: 38468860 PMCID: PMC10925614 DOI: 10.3389/fmicb.2024.1338842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 01/25/2024] [Indexed: 03/13/2024] Open
Abstract
Introduction Crop straw, a major by-product of agricultural production, is pivotal in maintaining soil health and preserving the ecological environment. While straw incorporation is widely recognized as a sustainable practice, the incomplete decomposition of crop residues poses challenges to plant growth, increasing the risk of pests and diseases. This necessitates a comprehensive investigation. Methods The current study employs a 28-day pot experiment to simulate the degradation of rice straw in paddy soils. The impacts of bioaugmentation and biostimulation on lignocellulose degradation are systematically evaluated. Results Results indicate a high lignocellulose degradation ability in paddy soil, with over 80% straw weight loss within 28 days. Bioaugmentation with a lignocellulolytic microbial consortium enhances straw degradation during the initial stage (0-14 days). In contrast, biostimulation with readily available nutrients leads to soil acidification, hindering straw degradation and reducing microbial diversity. Furthermore, pH emerges as a critical factor influencing microbial community stability and function during lignocellulose degradation. Microbial co-occurrence network analysis reveals that microorganisms occupy ecological niches associated with different cellulose components. Notably, Module M2, comprising Proteobacteria, Firmicutes, Gemmatimonadota, Actinobacteriota, Bacteroidota, Myxococcota, Halobacterota, and Acidobacteriota, positively correlates with pH and weight loss. Discussion This study significantly advances our understanding of microbial mechanisms in soil decomposition, emphasizing the pivotal role of pH in community stability and function in paddy soil. These findings can inform future strategies for managing rice straw while safeguarding soil ecosystem health.
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Affiliation(s)
- Yi Wang
- Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Yonglun Chen
- Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research, Hubei Academy of Agricultural Sciences, Wuhan, China
- Sichuan Jiahuai Biotechnology Co., Ltd., Leshan, China
| | - Xiuqing Gao
- Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research, Hubei Academy of Agricultural Sciences, Wuhan, China
- College of Biological and Pharmaceutical Sciences, Three Gorges University, Yichang, China
| | - Qiong Wang
- Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Mingyu Cui
- Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research, Hubei Academy of Agricultural Sciences, Wuhan, China
- College of Biological and Pharmaceutical Sciences, Three Gorges University, Yichang, China
| | - Dongdong Zhang
- Institute of Marine Biology, Ocean College, Zhejiang University, Zhoushan, Zhejiang, China
| | - Peng Guo
- Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research, Hubei Academy of Agricultural Sciences, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
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Hoang DQ, Wilson LR, Scheftgen AJ, Suen G, Currie CR. Disturbance-diversity relationships of microbial communities change based on growth substrate. mSystems 2024; 9:e0088723. [PMID: 38259105 PMCID: PMC10878081 DOI: 10.1128/msystems.00887-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 12/18/2023] [Indexed: 01/24/2024] Open
Abstract
Disturbance events can impact ecological community dynamics. Understanding how communities respond to disturbances and how those responses can vary is a challenge in microbial ecology. In this study, we grew a previously enriched specialized microbial community on either cellulose or glucose as a sole carbon source and subjected them to one of five different disturbance regimes of varying frequencies ranging from low to high. Using 16S rRNA gene amplicon sequencing, we show that the community structure is largely driven by substrate, but disturbance frequency affects community composition and successional dynamics. When grown on cellulose, bacteria in the genera Cellvibrio, Lacunisphaera, and Asticcacaulis are the most abundant microbes. However, Lacunisphaera is only abundant in the lower disturbance frequency treatments, while Asticcacaulis is more abundant in the highest disturbance frequency treatment. When grown on glucose, the most abundant microbes are two Pseudomonas sequence variants and a Cohnella sequence variant that is only abundant in the highest disturbance frequency treatment. Communities grown on cellulose exhibited a greater range of diversity (1.95-7.33 Hill 1 diversity) that peaks at the intermediate disturbance frequency treatment or one disturbance every 3 days. Communities grown on glucose, however, ranged from 1.63 to 5.19 Hill 1 diversity with peak diversity at the greatest disturbance frequency treatment. These results demonstrate that the dynamics of a microbial community can vary depending on substrate and the disturbance frequency and may potentially explain the variety of diversity-disturbance relationships observed in microbial systems.IMPORTANCEA generalizable diversity-disturbance relationship (DDR) of microbial communities remains a contentious topic. Various microbial systems have different DDRs. Rather than finding support or refuting specific DDRs, we investigated the underlying factors that lead to different DDRs. In this study, we measured a cellulose-enriched microbial community's response to a range of disturbance frequencies from high to low, across two different substrates: cellulose and glucose. We demonstrate that the community displays a unimodal DDR when grown on cellulose and a monotonically increasing DDR when grown on glucose. Our findings suggest that the same community can display different DDRs. These results suggest that the range of DDRs we observe across different microbial systems may be due to the nutritional resources microbial communities can access and the interactions between bacteria and their environment.
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Affiliation(s)
- Don Q. Hoang
- Department of Bacteriology, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Lindsay R. Wilson
- Department of Bacteriology, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Department of Pediatrics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Andrew J. Scheftgen
- Department of Bacteriology, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Garret Suen
- Department of Bacteriology, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Cameron R. Currie
- Department of Bacteriology, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Department of Biochemistry & Biomedical Sciences, M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
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Díaz-García L, Chuvochina M, Feuerriegel G, Bunk B, Spröer C, Streit WR, Rodriguez-R LM, Overmann J, Jiménez DJ. Andean soil-derived lignocellulolytic bacterial consortium as a source of novel taxa and putative plastic-active enzymes. Syst Appl Microbiol 2024; 47:126485. [PMID: 38211536 DOI: 10.1016/j.syapm.2023.126485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 10/19/2023] [Accepted: 12/01/2023] [Indexed: 01/13/2024]
Abstract
An easy and straightforward way to engineer microbial environmental communities is by setting up liquid enrichment cultures containing a specific substrate as the sole source of carbon. Here, we analyzed twenty single-contig high-quality metagenome-assembled genomes (MAGs) retrieved from a microbial consortium (T6) that was selected by the dilution-to-stimulation approach using Andean soil as inoculum and lignocellulose as a selection pressure. Based on genomic metrics (e.g., average nucleotide and amino acid identities) and phylogenomic analyses, 15 out of 20 MAGs were found to represent novel bacterial species, with one of those (MAG_26) belonging to a novel genus closely related to Caenibius spp. (Sphingomonadaceae). Following the rules and requirements of the SeqCode, we propose the name Andeanibacterium colombiense gen. nov., sp. nov. for this taxon. A subsequent functional annotation of all MAGs revealed that MAG_7 (Pseudobacter hemicellulosilyticus sp. nov.) contains 20, 19 and 16 predicted genes from carbohydrate-active enzymes families GH43, GH2 and GH92, respectively. Its lignocellulolytic gene profile resembles that of MAG_2 (the most abundant member) and MAG_3858, both of which belong to the Sphingobacteriaceae family. Using a database that contains experimentally verified plastic-active enzymes (PAZymes), twenty-seven putative bacterial polyethylene terephthalate (PET)-active enzymes (i.e., alpha/beta-fold hydrolases) were detected in all MAGs. A maximum of five putative PETases were found in MAG_3858, and two PETases were found to be encoded by A. colombiense. In conclusion, we demonstrate that lignocellulose-enriched liquid cultures coupled with genome-resolved metagenomics are suitable approaches to unveil the hidden bacterial diversity and its polymer-degrading potential in Andean soil ecosystems.
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Affiliation(s)
- Laura Díaz-García
- Department of Chemical and Biological Engineering, Advanced Biomanufacturing Centre, University of Sheffield, UK
| | - Maria Chuvochina
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Brisbane, Queensland, Australia
| | - Golo Feuerriegel
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Wolfgang R Streit
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Luis M Rodriguez-R
- Department of Microbiology and Digital Science Center (DiSC), University of Innsbruck, Innsbruck, Austria
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany; Braunschweig University of Technology, Braunschweig, Germany
| | - Diego Javier Jiménez
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia; Microbiomes and Bioenergy Research Group, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia.
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Ma W, Lin L, Peng Q. Origin, Selection, and Succession of Coastal Intertidal Zone-Derived Bacterial Communities Associated with the Degradation of Various Lignocellulose Substrates. MICROBIAL ECOLOGY 2023; 86:1589-1603. [PMID: 36717391 DOI: 10.1007/s00248-023-02170-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 01/09/2023] [Indexed: 06/18/2023]
Abstract
Terrestrial microbial consortia were reported to play fundamental roles in the global carbon cycle and renewable energy production through the breakdown of complex organic carbon. However, we have a poor understanding of how biotic/abiotic factors combine to influence consortia assembly and lignocellulose degradation in aquatic ecosystems. In this study, we used 96 in situ lignocellulose enriched, coastal intertidal zone-derived bacterial consortia as the initial inoculating consortia and developed 384 cultured consortia under different lignocellulose substrates (aspen, pine, rice straw, and purified Norway spruce lignin) with gradients of salinity and temperature. As coastal consortia, salinity was the strongest driver for assembly, followed by Norway spruce lignin, temperature, and aspen. Moreover, a conceptual model was proposed to demonstrate different succession dynamics between consortia under herbaceous and woody lignocelluloses. The succession of consortium under Norway spruce lignin is greatly related with abiotic factors, while its substrate degradation is mostly correlated with biotic factors. A discrepant pattern was observed in the consortium under rice straw. Finally, we developed four groups of versatile, yet specific consortia. Our study not only reveals that coastal intertidal wetlands are important natural resources to enrich lignocellulolytic degrading consortia but also provides insights into the succession and ecological function of coastal consortium.
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Affiliation(s)
- Wenwen Ma
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, Shandong, China
| | - Lu Lin
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, Shandong, China.
| | - Qiannan Peng
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, Shandong, China
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7
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Hoang DQ, Wilson LR, Scheftgen AJ, Suen G, Currie CR. Disturbance-Diversity Relationships of Microbial Communities Change Based on Growth Substrate. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.25.554838. [PMID: 37662195 PMCID: PMC10473689 DOI: 10.1101/2023.08.25.554838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Disturbance events can impact ecological community dynamics. Understanding how communities respond to disturbances, and how those responses can vary, is a challenge in microbial ecology. In this study, we grew a previously enriched specialized microbial community on either cellulose or glucose as a sole carbon source, and subjected them to one of five different disturbance regimes of varying frequencies ranging from low to high. Using 16S rRNA gene amplicon sequencing, we show that community structure is largely driven by substrate, but disturbance frequency affects community composition and successional dynamics. When grown on cellulose, bacteria in the genera Cellvibrio, Lacunisphaera, and Asticaccacaulis are the most abundant microbes. However, Lacunisphaera is only abundant in the lower disturbance frequency treatments, while Asticaccaulis is more abundant in the highest disturbance frequency treatment. When grown on glucose, the most abundant microbes are two Pseudomonas sequence variants, and a Cohnella sequence variant that is only abundant in the highest disturbance frequency treatment. Communities grown on cellulose exhibited a greater range of diversity (0.67-1.99 Shannon diversity and 1.38-5.25 Inverse Simpson diversity) that peak at the intermediate disturbance frequency treatment, or 1 disturbance every 3 days. Communities grown on glucose, however, ranged from 0.49-1.43 Shannon diversity and 1.37- 3.52 Inverse Simpson with peak diversity at the greatest disturbance frequency treatment. These results demonstrate that the dynamics of a microbial community can vary depending on substrate and the disturbance frequency, and may potentially explain the variety of diversity-disturbance relationships observed in microbial ecosystems.
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Affiliation(s)
- Don Q Hoang
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Lindsay R Wilson
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Andrew J Scheftgen
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Garret Suen
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Cameron R Currie
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry & Biomedical Sciences, McMaster University, Hamilton, ON, Canada
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Wang Y, Jiménez DJ, Zhang Z, van Elsas JD. Functioning of a tripartite lignocellulolytic microbial consortium cultivated under two shaking conditions: a metatranscriptomic study. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:54. [PMID: 36991472 DOI: 10.1186/s13068-023-02289-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 02/25/2023] [Indexed: 03/30/2023]
Abstract
Abstract
Background
In a previous study, shaking speed was found to be an important factor affecting the population dynamics and lignocellulose-degrading activities of a synthetic lignocellulolytic microbial consortium composed of the bacteria Sphingobacterium paramultivorum w15, Citrobacter freundii so4, and the fungus Coniochaeta sp. 2T2.1. Here, the gene expression profiles of each strain in this consortium were examined after growth at two shaking speeds (180 and 60 rpm) at three time points (1, 5 and 13 days).
Results
The results indicated that, at 60 rpm, C. freundii so4 switched, to a large extent, from aerobic to flexible (aerobic/microaerophilic/anaerobic) metabolism, resulting in continued slow growth till late stage. In addition, Coniochaeta sp. 2T2.1 tended to occur to a larger extent in the hyphal form, with genes encoding adhesion proteins being highly expressed. Much like at 180 rpm, at 60 rpm, S. paramultivorum w15 and Coniochaeta sp. 2T2.1 were key players in hemicellulose degradation processes, as evidenced from the respective CAZy-specific transcripts. Coniochaeta sp. 2T2.1 exhibited expression of genes encoding arabinoxylan-degrading enzymes (i.e., of CAZy groups GH10, GH11, CE1, CE5 and GH43), whereas, at 180 rpm, some of these genes were suppressed at early stages of growth. Moreover, C. freundii so4 stably expressed genes that were predicted to encode proteins with (1) β-xylosidase/β-glucosidase and (2) peptidoglycan/chitinase activities, (3) stress response- and detoxification-related proteins. Finally, S. paramultivorum w15 showed involvement in vitamin B2 generation in the early stages across the two shaking speeds, while this role was taken over by C. freundii so4 at late stage at 60 rpm.
Conclusions
We provide evidence that S. paramultivorum w15 is involved in the degradation of mainly hemicellulose and in vitamin B2 production, and C. freundii so4 in the degradation of oligosaccharides or sugar dimers, next to detoxification processes. Coniochaeta sp. 2T2.1 was held to be strongly involved in cellulose and xylan (at early stages), next to lignin modification processes (at later stages). The synergism and alternative functional roles presented in this study enhance the eco-enzymological understanding of the degradation of lignocellulose in this tripartite microbial consortium.
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Kimeklis AK, Gladkov GV, Orlova OV, Afonin AM, Gribchenko ES, Aksenova TS, Kichko AA, Pinaev AG, Andronov EE. The Succession of the Cellulolytic Microbial Community from the Soil during Oat Straw Decomposition. Int J Mol Sci 2023; 24:ijms24076342. [PMID: 37047311 PMCID: PMC10094526 DOI: 10.3390/ijms24076342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 03/24/2023] [Accepted: 03/27/2023] [Indexed: 03/30/2023] Open
Abstract
The process of straw decomposition is dynamic and is accompanied by the succession of the microbial decomposing community, which is driven by poorly understood interactions between microorganisms. Soil is a complex ecological niche, and the soil microbiome can serve as a source of potentially active cellulolytic microorganisms. Here, we performed an experiment on the de novo colonization of oat straw by the soil microbial community by placing nylon bags with sterilized oat straw in the pots filled with chernozem soil and incubating them for 6 months. The aim was to investigate the changes in decomposer microbiota during this process using conventional sequencing techniques. The bacterial succession during straw decomposition occurred in three phases: the early phase (first month) was characterized by high microbial activity and low diversity, the middle phase (second to third month) was characterized by low activity and low diversity, and the late phase (fourth to sixth months) was characterized by low activity and high diversity. Analysis of amplicon sequencing data revealed three groups of co-changing phylotypes corresponding to these phases. The early active phase was abundant in the cellulolytic members from Pseudomonadota, Bacteroidota, Bacillota, and Actinobacteriota for bacteria and Ascomycota for fungi, and most of the primary phylotypes were gone by the end of the phase. The second intermediate phase was marked by the set of phylotypes from the same phyla persisting in the community. In the mature community of the late phase, apart from the core phylotypes, non-cellulolytic members from Bdellovibrionota, Myxococcota, Chloroflexota, and Thermoproteota appeared. Full metagenome sequencing of the microbial community from the end of the middle phase confirmed that major bacterial and fungal members of this consortium had genes of glycoside hydrolases (GH) connected to cellulose and chitin degradation. The real-time analysis of the selection of these genes showed that their representation varied between phases, and this occurred under the influence of the host, and not the GH family factor. Our findings demonstrate that soil microbial community may act as an efficient source of cellulolytic microorganisms and that colonization of the cellulolytic substrate occurs in several phases, each characterized by its own taxonomic and functional profile.
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Affiliation(s)
- Anastasiia K. Kimeklis
- All-Russian Research Institute of Agricultural Microbiology, 196608 Saint Petersburg, Russia
- Department of Applied Ecology, Saint-Petersburg State University, 199034 Saint Petersburg, Russia
- Correspondence: (A.K.K.); (E.E.A.)
| | - Grigory V. Gladkov
- All-Russian Research Institute of Agricultural Microbiology, 196608 Saint Petersburg, Russia
| | - Olga V. Orlova
- All-Russian Research Institute of Agricultural Microbiology, 196608 Saint Petersburg, Russia
| | - Alexey M. Afonin
- All-Russian Research Institute of Agricultural Microbiology, 196608 Saint Petersburg, Russia
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, FI-70211 Kuopio, Finland
| | - Emma S. Gribchenko
- All-Russian Research Institute of Agricultural Microbiology, 196608 Saint Petersburg, Russia
| | - Tatiana S. Aksenova
- All-Russian Research Institute of Agricultural Microbiology, 196608 Saint Petersburg, Russia
| | - Arina A. Kichko
- All-Russian Research Institute of Agricultural Microbiology, 196608 Saint Petersburg, Russia
| | - Alexander G. Pinaev
- All-Russian Research Institute of Agricultural Microbiology, 196608 Saint Petersburg, Russia
| | - Evgeny E. Andronov
- All-Russian Research Institute of Agricultural Microbiology, 196608 Saint Petersburg, Russia
- Dokuchaev Soil Science Institute, 119017 Moscow, Russia
- Correspondence: (A.K.K.); (E.E.A.)
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10
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Zhu J, Liu J, Li W, Ru Y, Sun D, Liu C, Li Z, Liu W. Dynamic changes in community structure and degradation performance of a bacterial consortium MMBC-1 during the subculturing revival reveal the potential decomposers of lignocellulose. BIORESOUR BIOPROCESS 2022; 9:110. [PMID: 38647799 PMCID: PMC10991580 DOI: 10.1186/s40643-022-00601-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 10/11/2022] [Indexed: 11/10/2022] Open
Abstract
Bacterial consortium is an important source of lignocellulolytic strains, but it is still a challenge to distinguish the direct decomposers of lignocellulose from other bacteria in such a complex community. This study aims at addressing this issue by focusing on the dynamic changes in community structure and degradation activity of MMBC-1, an established and stable lignocellulolytic bacterial consortium, during its subculturing revival. MMBC-1 was cryopreserved with glycerol as a protective agent and then inoculated for revival. Its enzyme activities for degradation recovered to the maximum level after two rounds of subculturing. Correspondingly, the cellulose and hemicellulose in lignocellulosic carbon source were gradually decomposed during the revival. Meanwhile, the initial dominant bacteria represented by genus Clostridium were replaced by the bacteria belonging to Lachnospira, Enterococcus, Bacillus, Haloimpatiens genera and family Lachnospiraceae. However, only three high-abundance (> 1%) operational taxonomic units (OTUs) (Lachnospira, Enterococcus and Haloimpatiens genera) were suggested to directly engage in lignocellulose degradation according to correlation analysis. By comparison, many low-abundance OTUs, such as the ones belonging to Flavonifractor and Anaerotruncus genera, may play an important role in degradation. These findings showed the dramatic changes in community structure that occurred during the subculturing revival, and paved the way for the discovery of direct decomposers in a stable consortium.
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Affiliation(s)
- Jingrong Zhu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, No.101, Shanghai Road, Tongshan New District, Xuzhou, 221116, Jiangsu Province, China
| | - Jiawen Liu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, No.101, Shanghai Road, Tongshan New District, Xuzhou, 221116, Jiangsu Province, China
| | - Weilin Li
- Institutional Center for Shared Technologies and Facilities, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yunrui Ru
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, No.101, Shanghai Road, Tongshan New District, Xuzhou, 221116, Jiangsu Province, China
| | - Di Sun
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, No.101, Shanghai Road, Tongshan New District, Xuzhou, 221116, Jiangsu Province, China
| | - Cong Liu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, No.101, Shanghai Road, Tongshan New District, Xuzhou, 221116, Jiangsu Province, China
| | - Zongyun Li
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, No.101, Shanghai Road, Tongshan New District, Xuzhou, 221116, Jiangsu Province, China.
| | - Weijie Liu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, No.101, Shanghai Road, Tongshan New District, Xuzhou, 221116, Jiangsu Province, China.
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11
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Díaz Rodríguez CA, Díaz-García L, Bunk B, Spröer C, Herrera K, Tarazona NA, Rodriguez-R LM, Overmann J, Jiménez DJ. Novel bacterial taxa in a minimal lignocellulolytic consortium and their potential for lignin and plastics transformation. ISME COMMUNICATIONS 2022; 2:89. [PMID: 37938754 PMCID: PMC9723784 DOI: 10.1038/s43705-022-00176-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/09/2022] [Accepted: 09/13/2022] [Indexed: 11/09/2023]
Abstract
The understanding and manipulation of microbial communities toward the conversion of lignocellulose and plastics are topics of interest in microbial ecology and biotechnology. In this study, the polymer-degrading capability of a minimal lignocellulolytic microbial consortium (MELMC) was explored by genome-resolved metagenomics. The MELMC was mostly composed (>90%) of three bacterial members (Pseudomonas protegens; Pristimantibacillus lignocellulolyticus gen. nov., sp. nov; and Ochrobactrum gambitense sp. nov) recognized by their high-quality metagenome-assembled genomes (MAGs). Functional annotation of these MAGs revealed that Pr. lignocellulolyticus could be involved in cellulose and xylan deconstruction, whereas Ps. protegens could catabolize lignin-derived chemical compounds. The capacity of the MELMC to transform synthetic plastics was assessed by two strategies: (i) annotation of MAGs against databases containing plastic-transforming enzymes; and (ii) predicting enzymatic activity based on chemical structural similarities between lignin- and plastics-derived chemical compounds, using Simplified Molecular-Input Line-Entry System and Tanimoto coefficients. Enzymes involved in the depolymerization of polyurethane and polybutylene adipate terephthalate were found to be encoded by Ps. protegens, which could catabolize phthalates and terephthalic acid. The axenic culture of Ps. protegens grew on polyhydroxyalkanoate (PHA) nanoparticles and might be a suitable species for the industrial production of PHAs in the context of lignin and plastic upcycling.
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Affiliation(s)
- Carlos Andrés Díaz Rodríguez
- Microbiomes and Bioenergy Research Group, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Laura Díaz-García
- Microbiomes and Bioenergy Research Group, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
- Department of Chemical and Biological Engineering, Advanced Biomanufacturing Centre, University of Sheffield, Sheffield, UK
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Katherine Herrera
- Department of Civil and Environmental Engineering, Universidad de los Andes, Bogotá, Colombia
| | | | - Luis M Rodriguez-R
- Department of Microbiology and Digital Science Center (DiSC), University of Innsbruck, Innsbruck, Austria
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- Braunschweig University of Technology, Braunschweig, Germany
| | - Diego Javier Jiménez
- Microbiomes and Bioenergy Research Group, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia.
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12
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Gladkov GV, Kimeklis AK, Afonin AM, Lisina TO, Orlova OV, Aksenova TS, Kichko AA, Pinaev AG, Andronov EE. The Structure of Stable Cellulolytic Consortia Isolated from Natural Lignocellulosic Substrates. Int J Mol Sci 2022; 23:ijms231810779. [PMID: 36142684 PMCID: PMC9501375 DOI: 10.3390/ijms231810779] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 08/31/2022] [Accepted: 09/04/2022] [Indexed: 10/27/2022] Open
Abstract
Recycling plant matter is one of the challenges facing humanity today and depends on efficient lignocellulose degradation. Although many bacterial strains from natural substrates demonstrate cellulolytic activities, the CAZymes (Carbohydrate-Active enZYmes) responsible for these activities are very diverse and usually distributed among different bacteria in one habitat. Thus, using microbial consortia can be a solution to rapid and effective decomposition of plant biomass. Four cellulolytic consortia were isolated from enrichment cultures from composting natural lignocellulosic substrates—oat straw, pine sawdust, and birch leaf litter. Enrichment cultures facilitated growth of similar, but not identical cellulose-decomposing bacteria from different substrates. Major components in all consortia were from Proteobacteria, Actinobacteriota and Bacteroidota, but some were specific for different substrates—Verrucomicrobiota and Myxococcota from straw, Planctomycetota from sawdust and Firmicutes from leaf litter. While most members of the consortia were involved in the lignocellulose degradation, some demonstrated additional metabolic activities. Consortia did not differ in the composition of CAZymes genes, but rather in axillary functions, such as ABC-transporters and two-component systems, usually taxon-specific and associated with CAZymes. Our findings show that enrichment cultures can provide reproducible cellulolytic consortia from various lignocellulosic substrates, the stability of which is ensured by tight microbial relations between its components.
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Affiliation(s)
- Grigory V. Gladkov
- All-Russian Research Institute of Agricultural Microbiology, 196608 Saint Petersburg, Russia
- Correspondence: ; Tel.: +7-921-402-65-16
| | - Anastasiia K. Kimeklis
- All-Russian Research Institute of Agricultural Microbiology, 196608 Saint Petersburg, Russia
- Department of Applied Ecology, Saint-Petersburg State University, 199034 Saint Petersburg, Russia
| | - Alexey M. Afonin
- All-Russian Research Institute of Agricultural Microbiology, 196608 Saint Petersburg, Russia
| | - Tatiana O. Lisina
- All-Russian Research Institute of Agricultural Microbiology, 196608 Saint Petersburg, Russia
| | - Olga V. Orlova
- All-Russian Research Institute of Agricultural Microbiology, 196608 Saint Petersburg, Russia
| | - Tatiana S. Aksenova
- All-Russian Research Institute of Agricultural Microbiology, 196608 Saint Petersburg, Russia
| | - Arina A. Kichko
- All-Russian Research Institute of Agricultural Microbiology, 196608 Saint Petersburg, Russia
| | - Alexander G. Pinaev
- All-Russian Research Institute of Agricultural Microbiology, 196608 Saint Petersburg, Russia
| | - Evgeny E. Andronov
- All-Russian Research Institute of Agricultural Microbiology, 196608 Saint Petersburg, Russia
- Dokuchaev Soil Science Institute, 119017 Moscow, Russia
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13
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Lewin GR, Davis NM, McDonald BR, Book AJ, Chevrette MG, Suh S, Boll A, Currie CR. Long-Term Cellulose Enrichment Selects for Highly Cellulolytic Consortia and Competition for Public Goods. mSystems 2022; 7:e0151921. [PMID: 35258341 PMCID: PMC9040578 DOI: 10.1128/msystems.01519-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 02/10/2022] [Indexed: 11/23/2022] Open
Abstract
The complexity of microbial communities hinders our understanding of how microbial diversity and microbe-microbe interactions impact community functions. Here, using six independent communities originating from the refuse dumps of leaf-cutter ants and enriched using the plant polymer cellulose as the sole source of carbon, we examine how changes in bacterial diversity and interactions impact plant biomass decomposition. Over up to 60 serial transfers (∼8 months) using Whatman cellulose filter paper, cellulolytic ability increased and then stabilized in four enrichment lines and was variable in two lines. Bacterial community characterization using 16S rRNA gene amplicon sequencing showed community succession differed between the highly cellulolytic enrichment lines and those that had slower and more variable cellulose degradation rates. Metagenomic and metatranscriptomic analyses revealed that Cellvibrio and/or Cellulomonas dominated each enrichment line and produced the majority of cellulase enzymes, while diverse taxa were retained within these communities over the duration of transfers. Interestingly, the less cellulolytic communities had a higher diversity of organisms competing for the cellulose breakdown product cellobiose, suggesting that cheating slowed cellulose degradation. In addition, we found competitive exclusion as an important factor shaping all of the communities, with a negative correlation of Cellvibrio and Cellulomonas abundance within individual enrichment lines and the expression of genes associated with the production of secondary metabolites, toxins, and other antagonistic compounds. Our results provide insights into how microbial diversity and competition affect the stability and function of cellulose-degrading communities. IMPORTANCE Microbial communities are a key driver of the carbon cycle through the breakdown of complex polysaccharides in diverse environments including soil, marine systems, and the mammalian gut. However, due to the complexity of these communities, the species-species interactions that impact community structure and ultimately shape the rate of decomposition are difficult to define. Here, we performed serial enrichment on cellulose using communities inoculated from leaf-cutter ant refuse dumps, a cellulose-rich environment. By concurrently tracking cellulolytic ability and community composition and through metagenomic and metatranscriptomic sequencing, we analyzed the ecological dynamics of the enrichment lines. Our data suggest that antagonism is prevalent in these communities and that competition for soluble sugars may slow degradation and lead to community instability. Together, these results help reveal the relationships between competition and polysaccharide decomposition, with implications in diverse areas ranging from microbial community ecology to cellulosic biofuels production.
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Affiliation(s)
- Gina R. Lewin
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Nicole M. Davis
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Bradon R. McDonald
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Adam J. Book
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Marc G. Chevrette
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Steven Suh
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Ardina Boll
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Cameron R. Currie
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
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14
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Borjigin Q, Zhang B, Yu X, Gao J, Zhang X, Qu J, Ma D, Hu S, Han S. Metagenomics study to compare the taxonomic composition and metabolism of a lignocellulolytic microbial consortium cultured in different carbon conditions. World J Microbiol Biotechnol 2022; 38:78. [PMID: 35325312 DOI: 10.1007/s11274-022-03260-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 03/02/2022] [Indexed: 11/28/2022]
Abstract
A lignocellulolytic microbial consortium holds promise for the in situ biodegradation of crop straw and the comprehensive and effective utilization of agricultural waste. In this study, we applied metagenomics technology to comprehensively explore the metabolic functional potential and taxonomic diversity of the microbial consortia CS (cultured on corn stover) and FP (cultured on filter paper). Analyses of the data on metagenomics taxonomic affiliations revealed considerable differences in the taxonomic composition and carbohydrate-active enzymes profile of the microbial consortia CS and FP. Pseudomonas, Dysgonomonas and Sphingobacterium in CS and Cellvibrio and Pseudomonas in FP had a much wider distribution of lignocellulose degradative ability. The genes for more lignocellulose degradative enzymes were detected when the relatively simple substrate filter paper was used as the carbon source. Clusters of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation analyses revealed considerable levels of similarity, and carbohydrate metabolic and amino acid metabolic pathways were the most enriched in CS and FP, respectively. The mechanism used by the two microbial consortia to degrade lignocellulose was similar, but the annotation of quantity of genes indicated that they are diverse and vary greatly. These data underlie the interactions between microorganisms and the synergism of enzymes during the degradative process of lignocellulose under different substrates and suggest the development of potential microbial resources.
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Affiliation(s)
- Qinggeer Borjigin
- Agricultural College, Inner Mongolia Agricultural University, No. 275, XinJian East Street, Hohhot, 010019, China.,Key Laboratory of Crop Cultivation and Genetic Improvement in Inner Mongolia Autonomous Region, No. 275, XinJian East Street, Hohhot, 010019, China
| | - Bizhou Zhang
- Special Crops Institute, Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, No.22, ZhaoJun Road, Hohhot, 010031, China
| | - Xiaofang Yu
- Agricultural College, Inner Mongolia Agricultural University, No. 275, XinJian East Street, Hohhot, 010019, China. .,Key Laboratory of Crop Cultivation and Genetic Improvement in Inner Mongolia Autonomous Region, No. 275, XinJian East Street, Hohhot, 010019, China.
| | - Julin Gao
- Agricultural College, Inner Mongolia Agricultural University, No. 275, XinJian East Street, Hohhot, 010019, China. .,Key Laboratory of Crop Cultivation and Genetic Improvement in Inner Mongolia Autonomous Region, No. 275, XinJian East Street, Hohhot, 010019, China.
| | - Xin Zhang
- Agricultural College, Inner Mongolia Agricultural University, No. 275, XinJian East Street, Hohhot, 010019, China
| | - Jiawei Qu
- Agricultural College, Inner Mongolia Agricultural University, No. 275, XinJian East Street, Hohhot, 010019, China.,Key Laboratory of Crop Cultivation and Genetic Improvement in Inner Mongolia Autonomous Region, No. 275, XinJian East Street, Hohhot, 010019, China
| | - Daling Ma
- Agricultural College, Inner Mongolia Agricultural University, No. 275, XinJian East Street, Hohhot, 010019, China.,Key Laboratory of Crop Cultivation and Genetic Improvement in Inner Mongolia Autonomous Region, No. 275, XinJian East Street, Hohhot, 010019, China
| | - Shuping Hu
- Key Laboratory of Crop Cultivation and Genetic Improvement in Inner Mongolia Autonomous Region, No. 275, XinJian East Street, Hohhot, 010019, China.,Vocational and Technical College, Inner Mongolia Agricultural University, Altan street, Baotou, 014109, China
| | - Shengcai Han
- Key Laboratory of Crop Cultivation and Genetic Improvement in Inner Mongolia Autonomous Region, No. 275, XinJian East Street, Hohhot, 010019, China.,Hortlculture and Plant Protection College, Inner Mongolia Agricultural University, No. 29, Eerduosi East Street, Hohhot, 010019, China
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15
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Lin L. Bottom-up synthetic ecology study of microbial consortia to enhance lignocellulose bioconversion. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:14. [PMID: 35418100 PMCID: PMC8822760 DOI: 10.1186/s13068-022-02113-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 01/28/2022] [Indexed: 01/21/2023]
Abstract
Lignocellulose is the most abundant organic carbon polymer on the earth. Its decomposition and conversion greatly impact the global carbon cycle. Furthermore, it provides feedstock for sustainable fuel and other value-added products. However, it continues to be underutilized, due to its highly recalcitrant and heterogeneric structure. Microorganisms, which have evolved versatile pathways to convert lignocellulose, undoubtedly are at the heart of lignocellulose conversion. Numerous studies that have reported successful metabolic engineering of individual strains to improve biological lignin valorization. Meanwhile, the bottleneck of single strain modification is becoming increasingly urgent in the conversion of complex substrates. Alternatively, increased attention has been paid to microbial consortia, as they show advantages over pure cultures, e.g., high efficiency and robustness. Here, we first review recent developments in microbial communities for lignocellulose bioconversion. Furthermore, the emerging area of synthetic ecology, which is an integration of synthetic biology, ecology, and computational biology, provides an opportunity for the bottom-up construction of microbial consortia. Then, we review different modes of microbial interaction and their molecular mechanisms, and discuss considerations of how to employ these interactions to construct synthetic consortia via synthetic ecology, as well as highlight emerging trends in engineering microbial communities for lignocellulose bioconversion.
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Affiliation(s)
- Lu Lin
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, Shandong, China.
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16
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Wei Z, Ahmed Mohamed T, Zhao L, Zhu Z, Zhao Y, Wu J. Microhabitat drive microbial anabolism to promote carbon sequestration during composting. BIORESOURCE TECHNOLOGY 2022; 346:126577. [PMID: 34923079 DOI: 10.1016/j.biortech.2021.126577] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/10/2021] [Accepted: 12/11/2021] [Indexed: 06/14/2023]
Abstract
Transforming organic waste into stable carbon by composting is an eco-friendly way. However, the complex environment, huge microbial community and complicated metabolic of composting have limited the directional transformation of organic carbon, which is also not conducive to the fixation of organic carbon. Therefore, this review is based on the formation of humus, a stable by-product of composting, to expound how to promote carbon fixation by increasing the yield of humus. Firstly, we have clarified the transformation regularity of organic matter during composting. Meanwhile, the microhabitat factors affecting microbial catabolism and anabolism were deeply analyzed, in order to provide a theoretical basis for the micro habitat regulation of directional transformation of organic matter during composting. Given that, a method to adjust the directional humification and stabilization of organic carbon has been proposed. Hoping the rapid reduction and efficient stabilization of organic waste can be realized according to this method.
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Affiliation(s)
- Zimin Wei
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Taha Ahmed Mohamed
- College of Life Science, Northeast Agricultural University, Harbin 150030, China; Soil, Water and Environment Research Institute, Agricultural Research Center, Giza, Egypt
| | - Li Zhao
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Zechen Zhu
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Yue Zhao
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Junqiu Wu
- College of Life Science, Northeast Agricultural University, Harbin 150030, China.
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17
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Vu V, Farkas C, Riyad O, Bujna E, Kilin A, Sipiczki G, Sharma M, Usmani Z, Gupta VK, Nguyen QD. Enhancement of the enzymatic hydrolysis efficiency of wheat bran using the Bacillus strains and their consortium. BIORESOURCE TECHNOLOGY 2022; 343:126092. [PMID: 34634465 DOI: 10.1016/j.biortech.2021.126092] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/30/2021] [Accepted: 10/01/2021] [Indexed: 06/13/2023]
Abstract
In the downstream process, the bioconversion of lignocellulosic biomass can be improved by applying a biological pretreatment procedure using microorganisms to produce hydrolytic enzymes to modify the recalcitrant structure of lignocellulose. In this study, various Bacillus strains (B. subtilis B.01162 and B.01212, B. coagulans B.01123 and B.01139, B. cereus B.00076 and B.01718, B. licheniformis B.01223 and B.01231) were evaluated for the degrading capacity of wheat bran in the submerged medium using enzymatic activities, reducing sugars and weight loss as indicators. The obtained results revealed that the B. subtilis B.01162, B. coagulans B.01123 and B. cereus B.00076 could be promising degraders for the wheat bran pretreatment. Besides, the application of their consortium (the combination of 2-3 Bacillus species) showed the positive effects on cellulose bioconversion compared with monocultures. Among them, the mixture of B. subtilis B.01162 and B. coagulans B.01123 increased significantly the cellulase, endo-glucanase, and xylanase enzyme activity resulting in accelerating the lignocellulose degradation. Our results served a very good base for the development of microbial consortium for biological pretreatment of lignocellulosic raw materials.
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Affiliation(s)
- Vi Vu
- Department of Bioengineering and Alcoholic Drink Technology, Institute of Food Science and Technology, Hungarian University of Agriculture and Life Sciences, 1118 Budapest, Ménesi út 45, Hungary
| | - Csilla Farkas
- Department of Bioengineering and Alcoholic Drink Technology, Institute of Food Science and Technology, Hungarian University of Agriculture and Life Sciences, 1118 Budapest, Ménesi út 45, Hungary
| | - Ouahab Riyad
- Department of Bioengineering and Alcoholic Drink Technology, Institute of Food Science and Technology, Hungarian University of Agriculture and Life Sciences, 1118 Budapest, Ménesi út 45, Hungary
| | - Erika Bujna
- Department of Bioengineering and Alcoholic Drink Technology, Institute of Food Science and Technology, Hungarian University of Agriculture and Life Sciences, 1118 Budapest, Ménesi út 45, Hungary
| | - Akos Kilin
- Department of Bioengineering and Alcoholic Drink Technology, Institute of Food Science and Technology, Hungarian University of Agriculture and Life Sciences, 1118 Budapest, Ménesi út 45, Hungary
| | - Gizella Sipiczki
- Department of Bioengineering and Alcoholic Drink Technology, Institute of Food Science and Technology, Hungarian University of Agriculture and Life Sciences, 1118 Budapest, Ménesi út 45, Hungary
| | - Minaxi Sharma
- Department of Applied Biology, University of Science and Technology, Meghalaya 793101, India
| | - Zeba Usmani
- Department of Applied Biology, University of Science and Technology, Meghalaya 793101, India
| | - Vijai Kumar Gupta
- Biorefining and Advanced Materials Research Center, Scotland's Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh EH9 3JG, UK
| | - Quang D Nguyen
- Department of Bioengineering and Alcoholic Drink Technology, Institute of Food Science and Technology, Hungarian University of Agriculture and Life Sciences, 1118 Budapest, Ménesi út 45, Hungary.
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18
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Blair EM, Dickson KL, O'Malley MA. Microbial communities and their enzymes facilitate degradation of recalcitrant polymers in anaerobic digestion. Curr Opin Microbiol 2021; 64:100-108. [PMID: 34700124 DOI: 10.1016/j.mib.2021.09.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 09/21/2021] [Indexed: 11/15/2022]
Abstract
Microbial consortia efficiently degrade complex biopolymers found in the organic fraction of municipal solid waste (OFMSW). Through enzyme production and division of labor during anaerobic digestion, microbial communities break down recalcitrant polymers and make fermentation products, including methane. However, microbial communities remain underutilized for waste degradation as it remains difficult to characterize and predict microbial interactions during waste breakdown, especially as cultivation conditions change drastically throughout anaerobic digestion. This review discusses recent progress and opportunities in cultivating natural and engineered consortia for OFMSW hydrolysis, including how recalcitrant substrates are degraded by enzymes as well as the critical factors that govern microbial interactions and culture stability. Methods to measure substrate degradation are also reviewed, and we demonstrate the need for increased standardization to enable comparisons across different environments.
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Affiliation(s)
- Elaina M Blair
- Department of Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA
| | - Katharine L Dickson
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, 93106, USA
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA; Joint BioEnergy Institute (JBEI), Emeryville, CA, 94608, USA.
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19
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Effect of culture conditions on the performance of lignocellulose-degrading synthetic microbial consortia. Appl Microbiol Biotechnol 2021; 105:7981-7995. [PMID: 34596724 PMCID: PMC8502130 DOI: 10.1007/s00253-021-11591-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 09/09/2021] [Accepted: 09/11/2021] [Indexed: 11/05/2022]
Abstract
In this study, we examined a synthetic microbial consortium, composed of two selected bacteria, i.e., Citrobacter freundii so4 and Sphingobacterium multivorum w15, next to the fungus Coniochaeta sp. 2T2.1, with respect to their fate and roles in the degradation of wheat straw (WS). A special focus was placed on the effects of pH (7.2, 6.2, or 5.2), temperature (25 versus 28 °C), and shaking speed (60 versus 180 rpm). Coniochaeta sp. 2T2.1 consistently had a key role in the degradation process, with the two bacteria having additional roles. Whereas temperature exerted only minor effects on the degradation, pH and shaking speed were key determinants of both organismal growth and WS degradation levels. In detail, the three-partner degrader consortium showed significantly higher WS degradation values at pH 6.2 and 5.2 than at pH 7.2. Moreover, the two bacteria revealed up to tenfold enhanced final cell densities (ranging from log8.0 to log9.0 colony forming unit (CFU)/mL) in the presence of Coniochaeta sp. 2T2.1 than when growing alone or in a bacterial bi-culture, regardless of pH range or shaking speed. Conversely, at 180 rpm, fungal growth was clearly suppressed by the presence of the bacteria at pH 5.2 and pH 6.2, but not at pH 7.2. In contrast, at 60 rpm, the presence of the bacteria fostered fungal growth. In these latter cultures, oxygen levels were significantly lowered as compared to the maximal levels found at 180 rpm (about 5.67 mg/L, ~ 62% of saturation). Conspicuous effects on biomass appearance pointed to a fungal biofilm–modulating role of the bacteria. Key points • Coniochaeta sp. 2T2.1 has a key role in wheat straw (WS) degradation. • Bacterial impact shifts when conditions change. • pH and shaking speed are key drivers of the growth dynamics and WS degradation.
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Considerations on the Identity and Diversity of Organisms Affiliated with Sphingobacterium multivorum-Proposal for a New Species, Sphingobacterium paramultivorum. Microorganisms 2021; 9:microorganisms9102057. [PMID: 34683378 PMCID: PMC8540502 DOI: 10.3390/microorganisms9102057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/21/2021] [Accepted: 09/24/2021] [Indexed: 11/16/2022] Open
Abstract
Plant biomass offers great potential as a sustainable resource, and microbial consortia are primordial in its bioconversion. The wheat-straw-biodegradative bacterial strain w15 has drawn much attention as a result of its biodegradative potential and superior degradation performance in bacterial-fungal consortia. Strain w15 was originally assigned to the species Sphingobacterium multivorum based on its 16S ribosomal RNA (rRNA) gene sequence. A closer examination of this taxonomic placement revealed that the sequence used has 98.9% identity with the ‘divergent’ 16S rRNA gene sequence of S. multivorum NCTC 11343T, yet lower relatedness with the canonical 16S rRNA sequence. A specific region of the gene, located between positions 186 and 210, was found to be highly variable and determinative for the divergence. To solve the identity of strain w15, genome metrics and analyses of ecophysiological niches were undertaken on a selection of strains assigned to S. multivorum and related species. These analyses separated all strains into three clusters, with strain w15, together with strain BIGb0170, constituting a separate radiation, next to S. multivorum and S. siyangense. Moreover, the strains denoted FDAARGOS 1141 and 1142 were placed inside S. siyangense. We propose the renaming of strains w15 and BIGb0170 as members of the novel species, coined Sphingobacterium paramultivorum.
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21
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Du P, He H, Wu X, Xu J, Dong F, Liu X, Zheng Y. Mesosulfuron-methyl influenced biodegradability potential and N transformation of soil. JOURNAL OF HAZARDOUS MATERIALS 2021; 416:125770. [PMID: 33838509 DOI: 10.1016/j.jhazmat.2021.125770] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 06/12/2023]
Abstract
The wide application of mesosulfuron-methyl (MS) in soil may affect soil microbial community, yet the information is limited. In this work, two distinct soil types from Anyang (AY) and Nanjing (NJ) were spiked with MS (0, 0.006, 0.06, or 0.6 mg kg-1) and incubated for 90 days. MS decreased bacterial and fungal (except the last sampling) abundance and altered their diversity and community. Five biomarkers of bacterial species may help MS degradation and more increased xenobiotics biodegradation pathways were also observed in 0.6 mg kg-1 treatment in AY soil. A co-occurrence network revealed the biomarkers grouped in one module in all AY soils, suggesting these biomarkers act in concert to degrade MS. MS impacted soil N transformation with increasing N2-fixing bacteria in both soils and ammonia-oxidising bacteria (AOB) in NJ and decreasing ammonia-oxidizing archaea (AOA) in AY. The contents of NO3--N and NH4+-N were increased by MS. Structural equation models revealed that the abundance of bacteria and fungi was responsible for the NO3--N and NH4+-N contents. In conclusion, this work aids safety assessments and degradation-related research of MS in soil.
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Affiliation(s)
- Pengqiang Du
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Beijing 100193, China; College of Plant Protection, Henan Agricultural University, No. 63, Agricultural Road, Zhengzhou 450002, China
| | - Hairong He
- College of Pharmacy, Henan University of Chinese Medicine, No. 156, Jinshui East Road, Zhengzhou 450046, China
| | - Xiaohu Wu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Beijing 100193, China.
| | - Jun Xu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Beijing 100193, China
| | - Fengshou Dong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Beijing 100193, China
| | - Xingang Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Beijing 100193, China
| | - Yongquan Zheng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Beijing 100193, China.
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Li W, Liu M, Siddique MS, Graham N, Yu W. Contribution of bacterial extracellular polymeric substances (EPS) in surface water purification. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 280:116998. [PMID: 33780840 DOI: 10.1016/j.envpol.2021.116998] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 03/10/2021] [Accepted: 03/18/2021] [Indexed: 06/12/2023]
Abstract
Naturally present aquatic microorganisms play an important role in water purification systems, such as the self-purification of surface waters. In this study, two water sources representing polluted surface water (Olympic Green; OG) and unpolluted surface water (Jingmi river; JM), were used to explore the self-purification of surface water by bacteria under different environmental conditions. The dominant bacterial community of OG and JM waters (both are Firmicutes and Proteobacteria) were isolated, cultured, and then used to carry out flocculation tests. Results showed that the flocculation ability of the dominant bacteria and extracellular polymeric substances (EPS) obtained from OG isolation was significantly greater than that from JM. Further examination illustrated that the main components of EPS were polysaccharides, which played an important role in improving the flocculation ability of bacteria. EPS from dominant cultural bacteria strains (OG1 and JM3) isolated from the two different sources lacked hydrophilic groups (e.g. COOH) and had a networked structure which are the main reasons to enhance the flocculation ability. The bacterial diversity and redundancy analysis (RDA) results also showed that microbial community composition is determined by water quality (SS, TOC, and NH4+), and different Bacteroidetes, Actinobacteria and Proteobacteria community structures can improve the water body's ability to remove environmental pollutants (such as SS, humic acid and fulvic acid). These findings provide new information showing how bacterial communities change with environmental factors while maintaining the purity of surface water.
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Affiliation(s)
- Weihua Li
- State Key Laboratory of Environmental Aquatic Chemistry, Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, People's Republic of China.
| | - Mengjie Liu
- State Key Laboratory of Environmental Aquatic Chemistry, Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, People's Republic of China
| | - Muhammad Saboor Siddique
- State Key Laboratory of Environmental Aquatic Chemistry, Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, People's Republic of China; University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Nigel Graham
- Department of Civil and Environmental Engineering, Imperial College London, South Kensington Campus, London, SW7 2AZ, United Kingdom.
| | - Wenzheng Yu
- State Key Laboratory of Environmental Aquatic Chemistry, Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, People's Republic of China.
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23
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Chang CY, Vila JCC, Bender M, Li R, Mankowski MC, Bassette M, Borden J, Golfier S, Sanchez PGL, Waymack R, Zhu X, Diaz-Colunga J, Estrela S, Rebolleda-Gomez M, Sanchez A. Engineering complex communities by directed evolution. Nat Ecol Evol 2021; 5:1011-1023. [PMID: 33986540 PMCID: PMC8263491 DOI: 10.1038/s41559-021-01457-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 03/28/2021] [Indexed: 02/03/2023]
Abstract
Directed evolution has been used for decades to engineer biological systems at or below the organismal level. Above the organismal level, a small number of studies have attempted to artificially select microbial ecosystems, with uneven and generally modest success. Our theoretical understanding of artificial ecosystem selection is limited, particularly for large assemblages of asexual organisms, and we know little about designing efficient methods to direct their evolution. Here, we have developed a flexible modelling framework that allows us to systematically probe any arbitrary selection strategy on any arbitrary set of communities and selected functions. By artificially selecting hundreds of in silico microbial metacommunities under identical conditions, we first show that the main breeding methods used to date, which do not necessarily let communities reach their ecological equilibrium, are outperformed by a simple screen of sufficiently mature communities. We then identify a range of alternative directed evolution strategies that, particularly when applied in combination, are well suited for the top-down engineering of large, diverse and stable microbial consortia. Our results emphasize that directed evolution allows an ecological structure-function landscape to be navigated in search of dynamically stable and ecologically resilient communities with desired quantitative attributes.
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Affiliation(s)
- Chang-Yu Chang
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Jean C C Vila
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Madeline Bender
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Richard Li
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Madeleine C Mankowski
- Department of Immunobiology and Department of Laboratory Medicine, Yale University, New Haven, CT, USA
| | - Molly Bassette
- Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Julia Borden
- Department of Molecular & Cellular Biology, University of California Berkeley, Berkeley, CA, USA
| | - Stefan Golfier
- Max Planck Institute of Molecular Cell Biology and Genetics, and Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Paul Gerald L Sanchez
- European Molecular Biology Laboratory (EMBL), Developmental Biology Unit, Heidelberg, Germany
| | - Rachel Waymack
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, CA, USA
| | - Xinwen Zhu
- Department of Biomedical Engineering and the Biological Design Center, Boston University, Boston, MA, USA
| | - Juan Diaz-Colunga
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Sylvie Estrela
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Maria Rebolleda-Gomez
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Alvaro Sanchez
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, USA.
- Microbial Sciences Institute, Yale University, New Haven, CT, USA.
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Tannery Wastewater Recalcitrant Compounds Foster the Selection of Fungi in Non-Sterile Conditions: A Pilot Scale Long-Term Test. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18126348. [PMID: 34208177 PMCID: PMC8296185 DOI: 10.3390/ijerph18126348] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/08/2021] [Accepted: 06/08/2021] [Indexed: 11/23/2022]
Abstract
This study demonstrated that a microbial community dominated by fungi can be selected and maintained in the long-term under non-sterile conditions, in a pilot-scale packed-bed reactor fed with tannery wastewater. During the start-up phase, the reactor, filled with 0.6 m3 of polyurethane foam cubes, was inoculated with a pure culture of Aspergillus tubingensis and Quebracho tannin, a recalcitrant compound widely used by tannery industry, was used as sole carbon source in the feeding. During the start-up, fungi grew attached as biofilm in carriers that filled the packed-bed reactor. Subsequently, the reactor was tested for the removal of chemical oxygen demand (COD) from an exhaust tanning bath collected from tanneries. The entire experiment lasted 121 days and average removals of 29% and 23% of COD and dissolved organic carbon (DOC) from the tannins bath were achieved, respectively. The evolution of the microbial consortium (bacteria and fungi) was described through biomolecular analyses along the experiment and also developed as a function of the size of the support media.
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25
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Sánchez Á, Vila JCC, Chang CY, Diaz-Colunga J, Estrela S, Rebolleda-Gomez M. Directed Evolution of Microbial Communities. Annu Rev Biophys 2021; 50:323-341. [PMID: 33646814 PMCID: PMC8105285 DOI: 10.1146/annurev-biophys-101220-072829] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Directed evolution is a form of artificial selection that has been used for decades to find biomolecules and organisms with new or enhanced functional traits. Directed evolution can be conceptualized as a guided exploration of the genotype-phenotype map, where genetic variants with desirable phenotypes are first selected and then mutagenized to search the genotype space for an even better mutant. In recent years, the idea of applying artificial selection to microbial communities has gained momentum. In this article, we review the main limitations of artificial selection when applied to large and diverse collectives of asexually dividing microbes and discuss how the tools of directed evolution may be deployed to engineer communities from the top down. We conceptualize directed evolution of microbial communities as a guided exploration of an ecological structure-function landscape and propose practical guidelines for navigating these ecological landscapes.
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Affiliation(s)
- Álvaro Sánchez
- Department of Ecology & Evolutionary Biology and Microbial Sciences Institute, Yale University, New Haven, Connecticut 06520, USA; , , , , ,
| | - Jean C C Vila
- Department of Ecology & Evolutionary Biology and Microbial Sciences Institute, Yale University, New Haven, Connecticut 06520, USA; , , , , ,
| | - Chang-Yu Chang
- Department of Ecology & Evolutionary Biology and Microbial Sciences Institute, Yale University, New Haven, Connecticut 06520, USA; , , , , ,
| | - Juan Diaz-Colunga
- Department of Ecology & Evolutionary Biology and Microbial Sciences Institute, Yale University, New Haven, Connecticut 06520, USA; , , , , ,
| | - Sylvie Estrela
- Department of Ecology & Evolutionary Biology and Microbial Sciences Institute, Yale University, New Haven, Connecticut 06520, USA; , , , , ,
| | - María Rebolleda-Gomez
- Department of Ecology & Evolutionary Biology and Microbial Sciences Institute, Yale University, New Haven, Connecticut 06520, USA; , , , , ,
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26
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Zhao ZQ, Wei XM, Shen XL, Abbas G, Fan R, Jin Y. Aerobic degradation of 4-fluoroaniline and 2,4-difluoroaniline: performance and microbial community in response to the inocula. Biodegradation 2021; 32:53-71. [PMID: 33428058 DOI: 10.1007/s10532-021-09925-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 01/02/2021] [Indexed: 11/27/2022]
Abstract
In this study, a distinct inoculum was investigated as an isolated variable within sequencing batch reactors via a comparison of the 4-fluoroaniline (4-FA) or 2,4-difluoroaniline (2,4-DFA) removal amounts. The inocula were derived from a treatment plant for treating pharmaceutical wastewater plus a small amount of municipal sewage (PMS), a treatment plant for treating fluoridated hydrocarbon wastewater (FHS), and a treatment plant for treating the comprehensive wastewater in an industrial park (CIS). There were slight differences among the degradation patterns of the 4-FA for the three inocula, whether during the enrichment period or the high concentration shock period. In contrast, it was observed that the degradation efficiency of 2,4-DFA initially varied with the inocula. The FHS-derived inoculum was determined to be optimal, exhibiting the earliest degradation reaction only after an acclimation of 7 days had the highest degradation rate constant of 0.519 h-1, and had the fastest recovery time of three weeks after high concentration shock. Additionally, compared with the PMS-derived inoculum, the CIS-derived inoculum exhibited an earlier degradation reaction within three weeks, and a higher microbial diversity, but a lower shock resistance and degradation rate constant of 0.257 h-1. High-throughput sequencing demonstrated that each final consortium was different in composition, and the microbial consortia developed well on the inoculum and substrate. In comparison of the similarity among the three 2,4-DFA enrichment cultures, the higher similarity (63.9-70.0%) among three final consortia enriching with 4-FA was observed. The results indicated that the inoculum played an important role in the degradation of FAs and the microbial bacterial communities of final consortia, and the effect extent might well depend on the fluorinated level of FAs.
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Affiliation(s)
- Zhi-Qing Zhao
- College of Chemical & Material Engineering, Quzhou University, Quzhou, 324000, People's Republic of China. .,College of Environment & Resource Sciences, Zhejiang University, Hangzhou, People's Republic of China.
| | - Xiao-Meng Wei
- Key Laboratory of Agro-Ecological Processes in Subtropical Region & Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, China
| | - Xiao-Li Shen
- College of Chemical & Material Engineering, Quzhou University, Quzhou, 324000, People's Republic of China
| | - Ghulam Abbas
- Department of Chemical Engineering, University of Gujrat, Gujrat, 50700, Pakistan
| | - Rui Fan
- College of Chemical & Material Engineering, Quzhou University, Quzhou, 324000, People's Republic of China
| | - Yi Jin
- College of Chemical & Material Engineering, Quzhou University, Quzhou, 324000, People's Republic of China
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Dilution-to-Stimulation/Extinction Method: a Combination Enrichment Strategy To Develop a Minimal and Versatile Lignocellulolytic Bacterial Consortium. Appl Environ Microbiol 2021; 87:AEM.02427-20. [PMID: 33127812 PMCID: PMC7783344 DOI: 10.1128/aem.02427-20] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 10/22/2020] [Indexed: 12/13/2022] Open
Abstract
The significance of our study mainly lies in the development of a combined top-down enrichment strategy (i.e., dilution to stimulation coupled to dilution to extinction) to build a minimal and versatile lignocellulolytic microbial consortium. We demonstrated that mainly two selectively enriched bacterial species (Pseudomonas sp. and Paenibacillus sp.) are required to drive the effective degradation of plant polymers. Our findings can guide the design of a synthetic bacterial consortium that could improve saccharification (i.e., the release of sugars from agricultural plant residues) processes in biorefineries. In addition, they can help to expand our ecological understanding of plant biomass degradation in enriched bacterial systems. The engineering of complex communities can be a successful path to understand the ecology of microbial systems and improve biotechnological processes. Here, we developed a strategy to assemble a minimal and effective lignocellulolytic microbial consortium (MELMC) using a sequential combination of dilution-to-stimulation and dilution-to-extinction approaches. The consortium was retrieved from Andean forest soil and selected through incubation in liquid medium with a mixture of three types of agricultural plant residues. After the dilution-to-stimulation phase, approximately 50 bacterial sequence types, mostly belonging to the Sphingobacteriaceae, Enterobacteriaceae, Pseudomonadaceae, and Paenibacillaceae, were significantly enriched. The dilution-to-extinction method demonstrated that only eight of the bacterial sequence types were necessary to maintain microbial growth and plant biomass consumption. After subsequent stabilization, only two bacterial species (Pseudomonas sp. and Paenibacillus sp.) became highly abundant (>99%) within the MELMC, indicating that these are the key players in degradation. Differences in the composition of bacterial communities between biological replicates indicated that selection, sampling, and/or priority effects could shape the consortium structure. The MELMC can degrade up to ∼13% of corn stover, consuming mostly its (hemi)cellulosic fraction. Tests with chromogenic substrates showed that the MELMC secretes an array of endoenzymes able to degrade xylan, arabinoxylan, carboxymethyl cellulose, and wheat straw. Additionally, the metagenomic profile inferred from the phylogenetic composition along with an analysis of carbohydrate-active enzymes of 20 bacterial genomes support the potential of the MELMC to deconstruct plant polysaccharides. This capacity was mainly attributed to the presence of Paenibacillus sp. IMPORTANCE The significance of our study mainly lies in the development of a combined top-down enrichment strategy (i.e., dilution to stimulation coupled to dilution to extinction) to build a minimal and versatile lignocellulolytic microbial consortium. We demonstrated that mainly two selectively enriched bacterial species (Pseudomonas sp. and Paenibacillus sp.) are required to drive the effective degradation of plant polymers. Our findings can guide the design of a synthetic bacterial consortium that could improve saccharification (i.e., the release of sugars from agricultural plant residues) processes in biorefineries. In addition, they can help to expand our ecological understanding of plant biomass degradation in enriched bacterial systems.
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28
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Díaz-García L, Bugg TDH, Jiménez DJ. Exploring the Lignin Catabolism Potential of Soil-Derived Lignocellulolytic Microbial Consortia by a Gene-Centric Metagenomic Approach. MICROBIAL ECOLOGY 2020; 80:885-896. [PMID: 32572536 DOI: 10.1007/s00248-020-01546-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 06/15/2020] [Indexed: 05/25/2023]
Abstract
An exploration of the ligninolytic potential of lignocellulolytic microbial consortia can improve our understanding of the eco-enzymology of lignin conversion in nature. In this study, we aimed to detect enriched lignin-transforming enzymes on metagenomes from three soil-derived microbial consortia that were cultivated on "pre-digested" plant biomass (wheat straw, WS1-M; switchgrass, SG-M; and corn stover, CS-M). Of 60 selected enzyme-encoding genes putatively involved in lignin catabolism, 20 genes were significantly abundant in WS1-M, CS-M, and/or SG-M consortia compared with the initial forest soil inoculum metagenome (FS1). These genes could be involved in lignin oxidation (e.g., superoxide dismutases), oxidative stress responses (e.g., catalase/peroxidases), generation of protocatechuate (e.g., vanAB genes), catabolism of gentisate, catechol and 3-phenylpropionic acid (e.g., gentisate 1,2-dioxygenases, muconate cycloisomerases, and hcaAB genes), the beta-ketoadipate pathway (e.g., pcaIJ genes), and tolerance to lignocellulose-derived inhibitors (e.g., thymidylate synthases). The taxonomic affiliation of 22 selected lignin-transforming enzymes from WS1-M and CS-M consortia metagenomes revealed that Pseudomonadaceae, Alcaligenaceae, Sphingomonadaceae, Caulobacteraceae, Comamonadaceae, and Xanthomonadaceae are the key bacterial families in the catabolism of lignin. A predictive "model" was sketched out, where each microbial population has the potential to metabolize an array of aromatic compounds through different pathways, suggesting that lignin catabolism can follow a "task division" strategy. Here, we have established an association between functions and taxonomy, allowing a better understanding of lignin transformations in soil-derived lignocellulolytic microbial consortia, and pinpointing some bacterial taxa and catabolic genes as ligninolytic trait-markers.
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Affiliation(s)
- Laura Díaz-García
- Microbiomes and Bioenergy Research Group, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | | | - Diego Javier Jiménez
- Microbiomes and Bioenergy Research Group, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia.
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Chang CY, Osborne ML, Bajic D, Sanchez A. Artificially selecting bacterial communities using propagule strategies. Evolution 2020; 74:2392-2403. [PMID: 32888315 PMCID: PMC7942404 DOI: 10.1111/evo.14092] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 08/21/2020] [Accepted: 08/29/2020] [Indexed: 02/06/2023]
Abstract
Artificial selection is a promising approach to manipulate microbial communities. Here, we report the outcome of two artificial selection experiments at the microbial community level. Both used "propagule" selection strategies, whereby the best-performing communities are used as the inocula to form a new generation of communities. Both experiments were contrasted to a random selection control. The first experiment used a defined set of strains as the starting inoculum, and the function under selection was the amylolytic activity of the consortia. The second experiment used multiple soil communities as the starting inocula, and the function under selection was the communities' cross-feeding potential. In both experiments, the selected communities reached a higher mean function than the control. In the first experiment, this was caused by a decline in function of the control, rather than an improvement of the selected line. In the second experiment, this response was fueled by the large initial variance in function across communities, and stopped when the top-performing community "fixed" in the metacommunity. Our results are in agreement with basic expectations from breeding theory, pointing to some of the limitations of community-level selection experiments that can inform the design of future studies.
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Affiliation(s)
- Chang-Yu Chang
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, USA.,Microbial Sciences Institute. Yale University, New Haven, CT, USA
| | - Melisa L. Osborne
- The Rowland Institute at Harvard, Harvard University, Cambridge, MA, USA.,Graduate Program in Bioinformatics and Biological Design Center, Boston University, Boston, Massachusetts, USA
| | - Djordje Bajic
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, USA.,Microbial Sciences Institute. Yale University, New Haven, CT, USA
| | - Alvaro Sanchez
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, USA.,Microbial Sciences Institute. Yale University, New Haven, CT, USA.,The Rowland Institute at Harvard, Harvard University, Cambridge, MA, USA.,Corresponding author:
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Jiménez DJ, Wang Y, Chaib de Mares M, Cortes-Tolalpa L, Mertens JA, Hector RE, Lin J, Johnson J, Lipzen A, Barry K, Mondo SJ, Grigoriev IV, Nichols NN, van Elsas JD. Defining the eco-enzymological role of the fungal strain Coniochaeta sp. 2T2.1 in a tripartite lignocellulolytic microbial consortium. FEMS Microbiol Ecol 2020; 96:5643886. [PMID: 31769802 DOI: 10.1093/femsec/fiz186] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 11/22/2019] [Indexed: 12/14/2022] Open
Abstract
Coniochaeta species are versatile ascomycetes that have great capacity to deconstruct lignocellulose. Here, we explore the transcriptome of Coniochaeta sp. strain 2T2.1 from wheat straw-driven cultures with the fungus growing alone or as a member of a synthetic microbial consortium with Sphingobacterium multivorum w15 and Citrobacter freundii so4. The differential expression profiles of carbohydrate-active enzymes indicated an onset of (hemi)cellulose degradation by 2T2.1 during the initial 24 hours of incubation. Within the tripartite consortium, 63 transcripts of strain 2T2.1 were differentially expressed at this time point. The presence of the two bacteria significantly upregulated the expression of one galactose oxidase, one GH79-like enzyme, one multidrug transporter, one laccase-like protein (AA1 family) and two bilirubin oxidases, suggesting that inter-kingdom interactions (e.g. amensalism) take place within this microbial consortium. Overexpression of multicopper oxidases indicated that strain 2T2.1 may be involved in lignin depolymerization (a trait of enzymatic synergism), while S. multivorum and C. freundii have the metabolic potential to deconstruct arabinoxylan. Under the conditions applied, 2T2.1 appears to be a better degrader of wheat straw when the two bacteria are absent. This conclusion is supported by the observed suppression of its (hemi)cellulolytic arsenal and lower degradation percentages within the microbial consortium.
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Affiliation(s)
- Diego Javier Jiménez
- Microbiomes and Bioenergy Research Group, Department of Biological Sciences, Universidad de los Andes, Carrera 1 No 18A-12, Bogotá, Colombia
| | - Yanfang Wang
- Cluster of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7 9747AG, Groningen, The Netherlands
| | - Maryam Chaib de Mares
- Cluster of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7 9747AG, Groningen, The Netherlands
| | - Larisa Cortes-Tolalpa
- Cluster of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7 9747AG, Groningen, The Netherlands
| | - Jeffrey A Mertens
- Bioenergy Research Unit, National Center for Agricultural Utilization Research, USDA-ARS, Peoria, Illinois 61604, USA
| | - Ronald E Hector
- Bioenergy Research Unit, National Center for Agricultural Utilization Research, USDA-ARS, Peoria, Illinois 61604, USA
| | - Junyan Lin
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Jenifer Johnson
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Anna Lipzen
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Kerrie Barry
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Stephen J Mondo
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.,Bioagricultural Science and Pest Management Department, Colorado State University, Fort Collins, Colorado 80521, USA
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California 94720-3102, USA
| | - Nancy N Nichols
- Bioenergy Research Unit, National Center for Agricultural Utilization Research, USDA-ARS, Peoria, Illinois 61604, USA
| | - Jan Dirk van Elsas
- Cluster of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7 9747AG, Groningen, The Netherlands
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Song N, Jiang HL. Coordinated photodegradation and biodegradation of organic matter from macrophyte litter in shallow lake water: Dual role of solar irradiation. WATER RESEARCH 2020; 172:115516. [PMID: 31986394 DOI: 10.1016/j.watres.2020.115516] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 12/31/2019] [Accepted: 01/15/2020] [Indexed: 05/20/2023]
Abstract
Eutrophication and climate warming cause macrophytes to spread rapidly in shallow lakes. The accumulation of excess decayed litter in lake water can improve the particulate organic matter content and lead to ecological deterioration. While decomposition of macrophyte litters in aquatic ecosystems is generally assumed to be biologically driven, photodegradation has been largely overlooked. In this study, the potential contribution of photodegradation to the decomposition of organic matter from macrophyte litter in a shallow lake was investigated under two types of light radiation: laboratory incubation light and natural solar radiation. Results showed that the combined photo- and biodegradation treatment removed more litter mass compared to solely photodegradation or biodegradation for over 108 days. More reactive oxygen species (ROS) were produced during litter degradation in lake water under the combined photo- and biodegradation treatments in comparison to other treatments. Removal efficiency of litter was doubled in the presence of ROS compared when ROS were captured. Additionally, NMR analysis revealed that lignin guaiacyl units were preferentially lost and the litter became more refractory under the combined photo oxidation and microbial degradation after 108 days. High-throughput sequencing analysis further indicated that solar irradiation stimulates the growth of bacteria (Treponema and Magnetospirillum) and fungi (Aspergillus) that have the ability to degrade aromatic compounds. Altogether, both ROS and specific microorganisms played important role in promoting litter degradation in lake water under light irradiation. Therefore, the role of solar radiation in particulate organic matter decomposition needs to be considered for a more accurate prediction of carbon dynamics in aquatic ecosystems.
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Affiliation(s)
- Na Song
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, PR China
| | - He-Long Jiang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, PR China.
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Cortes-Tolalpa L, Wang Y, Salles JF, van Elsas JD. Comparative Genome Analysis of the Lignocellulose Degrading Bacteria Citrobacter freundii so4 and Sphingobacterium multivorum w15. Front Microbiol 2020; 11:248. [PMID: 32194522 PMCID: PMC7065263 DOI: 10.3389/fmicb.2020.00248] [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: 11/10/2019] [Accepted: 02/03/2020] [Indexed: 01/19/2023] Open
Abstract
Two bacterial strains, denoted so4 and w15, isolated from wheat straw (WS)-degrading microbial consortia, were found to grow synergistically in media containing WS as the single carbon and energy source. They were identified as Citrobacter freundii so4 and Sphingobacterium multivorum w15 based on 16S rRNA gene sequencing and comparison to the respective C. freundii and S. multivorum type strains. In order to identify the mechanisms driving the synergistic interactions, we analyzed the draft genomes of the two strains and further characterized their metabolic potential. The latter analyses revealed that the strains had largely complementary substrate utilization patterns, with only 22 out of 190 compounds shared. The analyses further indicated C. freundii so4 to primarily consume amino acids and simple sugars, with laminarin as a key exception. In contrast, S. multivorum w15 showed ample capacity to transform complex polysaccharides, including intermediates of starch degradation. Sequence analyses revealed C. freundii so4 to have a genome of 4,883,214 bp, with a G + C content of 52.5%, 4,554 protein-encoding genes and 86 RNA genes. S. multivorum w15 has a genome of 6,678,278 bp, with a G + C content of 39.7%, 5,999 protein-encoding genes and 76 RNA genes. Genes for motility apparatuses (flagella, chemotaxis) were present in the genome of C. freundii so4, but absent from that of S. multivorum w15. In the genome of S. multivorum w15, 348 genes had regions matching CAZy family enzymes and/or carbohydrate-binding modules (CBMs), with 193 glycosyl hydrolase (GH) and 50 CBM domains. Remarkably, 22 domains matched enzymes of glycoside hydrolase family GH43, suggesting a strong investment in the degradation of arabinoxylan. In contrast, 130 CAZy family genes were found in C. freundii so4, with 61 GH and 12 CBM domains identified. Collectively, our results, based on both metabolic potential and genome analyses, revealed the two strains to harbor complementary catabolic armories, with S. multivorum w15 primarily attacking the WS hemicellulose and C. freundii so4 the cellobiose derived from cellulose, next to emerging oligo- or monosaccharides. Finally, C. freundii so4 may secrete secondary metabolites that S. multivorum w15 can consume, and detoxify the system by reducing the levels of (toxic) by-products.
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Affiliation(s)
- Larisa Cortes-Tolalpa
- Cluster of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Yanfang Wang
- Cluster of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Joana Falcao Salles
- Cluster of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Jan Dirk van Elsas
- Cluster of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
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Song N, Bai L, Xu H, Jiang HL. The composition difference of macrophyte litter-derived dissolved organic matter by photodegradation and biodegradation: Role of reactive oxygen species on refractory component. CHEMOSPHERE 2020; 242:125155. [PMID: 31669998 DOI: 10.1016/j.chemosphere.2019.125155] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 09/27/2019] [Accepted: 10/19/2019] [Indexed: 06/10/2023]
Abstract
The overgrowth of macrophytes has become serious due to increasing eutrophication in shallow lakes. The primary degradation processes of macrophytes litter, including photodegradation and biodegradation, induce considerable patchiness in the concentration and bioavailability of dissolved organic matter (DOM). In this study we investigated the composition evolution of DOM derived from emergent aquatic plant litter, Phragmites australis, in microbial degradation, photodegradation, and the combination of bio- and photo-degradation. Results revealed that the effects of photo- and biodegradation on the composition difference of macrophyte litter-derived DOM during short- and long-term degradation phase were different. Although large changes in DOM were observed after five days of incubation, the abundance and chemical composition were similar in the three treatments. However, more concentration of DOM was produced by combined photo- and biodegradation at the long-term degradation phase, and the composition of DOM showed less lignin-like formulae, as well as less condensed aromatic and aromatic compounds when compared to sole treatments. More reactive oxygen species (ROS) were found under the combined treatments, thus the contents of refractory components (condensed aromatic- and aromatic compound groups) were reduced. This study provide deeper insight into the fate of DOM and relevant biogeochemical processes in eutrophic lakes.
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Affiliation(s)
- Na Song
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Leilei Bai
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Huacheng Xu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - He-Long Jiang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China.
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Wang Y, Zhao C, Zhang D, Zhao M, Peng M, Guo P, Cui Z. Microbial Degradation of Zearalenone by a Novel Microbial Consortium, NZDC-6, and Its Application on Contaminated Corncob by Semisolid Fermentation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:1634-1644. [PMID: 31961687 DOI: 10.1021/acs.jafc.9b05343] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A novel microbial consortium (NZDC-6) was screened and characterized to detoxify the estrogenic mycotoxin zearalenone (ZEA), which commonly contaminates maize and is a major threat to food and health security. We found NZDC-6 to be thermophilic and highly effective, with a 90.3% ZEA degradation ratio at an optimum temperature of 60 °C. NZDC-6 was also effective at degrading the more estrogenic ZEA cognates, α-zearalenol (α-ZAL) and β-zearalenol (β-ZAL), with >90% degradation ratios. To evaluate a practical application, ZEA-contaminated corncobs were treated with NZDC-6 via semisolid fermentation. Measurements of physicochemical parameters and 16S microbial diversity and redundancy analysis (RDA) indicated that ZEA removal was most efficient at a low corncob solid content (< 5%), as a high solid content overwhelmed the microbial metabolic load, leading to increased dissolved oxygen and lowered pH. Our results demonstrate that the control of environmental variables is crucial for effective ZEA microbial removal in practical applications.
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Affiliation(s)
- Yi Wang
- Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research , Hubei Academy of Agricultural Sciences , Wuhan 430064 , China
| | - Chunxia Zhao
- Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research , Hubei Academy of Agricultural Sciences , Wuhan 430064 , China
| | - Dongdong Zhang
- Institute of Marine Biology, Ocean College , Zhejiang University , Zhoushan , Zhejiang 316021, China
| | - Mingming Zhao
- Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research , Hubei Academy of Agricultural Sciences , Wuhan 430064 , China
| | - Maomin Peng
- Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research , Hubei Academy of Agricultural Sciences , Wuhan 430064 , China
| | - Peng Guo
- Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research , Hubei Academy of Agricultural Sciences , Wuhan 430064 , China
| | - Zongjun Cui
- College of Agronomy and Biotechnology , China Agricultural University , Beijing 100193 , China
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Puentes-Téllez PE, Salles JF. Dynamics of Abundant and Rare Bacteria During Degradation of Lignocellulose from Sugarcane Biomass. MICROBIAL ECOLOGY 2020; 79:312-325. [PMID: 31286170 PMCID: PMC7033055 DOI: 10.1007/s00248-019-01403-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 06/19/2019] [Indexed: 06/02/2023]
Abstract
Microorganisms play a crucial role in lignocellulosic degradation. Many enriched microbial communities have demonstrated to reach functional and structural stability with effective degrading capacities of industrial interest. These microbial communities are typically composed by only few dominant species and a high number of usually overlooked rare species. Here, we used two sources of lignocellulose (sugarcane bagasse and straw) in order to obtain lignocellulose-degrading bacteria through an enriched process, followed the selective trajectory of both abundant and rare bacterial communities by 16S rRNA gene amplification and analyzed the outcomes of selection in terms of capacities and specialization. We verified the importance of pre-selection by using two sources of microbial inoculum: soil samples from a sugarcane field with history of straw addition (St15) and control samples, from the same field, without amendments (St0). We found similitudes in terms of stabilization between the abundant and rare fractions. We also found positive correlations of both abundant and rare taxa (like Caulobacteraceae and Alcaligenaceae) and the degradation of lignocellulosic fractions. Differences in the inocula's initial diversity rapidly decreased during the enrichment resulting in comparable richness levels at the end of the process; however, the legacy of the St15 inoculum and its specialization positively influenced the degradation capacities of the community. Analysis of specialization of the final communities revealed increased straw degradation capacity in the communities enriched in bagasse, which could be potentially used as a strategy for improving lignocellulose waste degradation on the sugarcane fields. This work highlights the importance of including the rare fraction of bacterial communities during investigations involving the screening and assessment of effective degrading communities.
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Affiliation(s)
- Pilar Eliana Puentes-Téllez
- Microbial Community Ecology, GELIFES, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
- Department of Biology, Institute of Environmental Biology, Ecology and Biodiversity Group, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Joana Falcao Salles
- Microbial Community Ecology, GELIFES, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
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36
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López-Mondéjar R, Algora C, Baldrian P. Lignocellulolytic systems of soil bacteria: A vast and diverse toolbox for biotechnological conversion processes. Biotechnol Adv 2019; 37:107374. [DOI: 10.1016/j.biotechadv.2019.03.013] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 03/06/2019] [Accepted: 03/21/2019] [Indexed: 12/12/2022]
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37
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Mondo SJ, Jiménez DJ, Hector RE, Lipzen A, Yan M, LaButti K, Barry K, van Elsas JD, Grigoriev IV, Nichols NN. Genome expansion by allopolyploidization in the fungal strain Coniochaeta 2T2.1 and its exceptional lignocellulolytic machinery. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:229. [PMID: 31572496 PMCID: PMC6757388 DOI: 10.1186/s13068-019-1569-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 09/13/2019] [Indexed: 05/03/2023]
Abstract
BACKGROUND Particular species of the genus Coniochaeta (Sordariomycetes) exhibit great potential for bioabatement of furanic compounds and have been identified as an underexplored source of novel lignocellulolytic enzymes, especially Coniochaeta ligniaria. However, there is a lack of information about their genomic features and metabolic capabilities. Here, we report the first in-depth genome/transcriptome survey of a Coniochaeta species (strain 2T2.1). RESULTS The genome of Coniochaeta sp. strain 2T2.1 has a size of 74.53 Mbp and contains 24,735 protein-encoding genes. Interestingly, we detected a genome expansion event, resulting ~ 98% of the assembly being duplicated with 91.9% average nucleotide identity between the duplicated regions. The lack of gene loss, as well as the high divergence and strong genome-wide signatures of purifying selection between copies indicates that this is likely a recent duplication, which arose through hybridization between two related Coniochaeta-like species (allopolyploidization). Phylogenomic analysis revealed that 2T2.1 is related Coniochaeta sp. PMI546 and Lecythophora sp. AK0013, which both occur endophytically. Based on carbohydrate-active enzyme (CAZy) annotation, we observed that even after in silico removal of its duplicated content, the 2T2.1 genome contains exceptional lignocellulolytic machinery. Moreover, transcriptomic data reveal the overexpression of proteins affiliated to CAZy families GH11, GH10 (endoxylanases), CE5, CE1 (xylan esterases), GH62, GH51 (α-l-arabinofuranosidases), GH12, GH7 (cellulases), and AA9 (lytic polysaccharide monoxygenases) when the fungus was grown on wheat straw compared with glucose as the sole carbon source. CONCLUSIONS We provide data that suggest that a recent hybridization between the genomes of related species may have given rise to Coniochaeta sp. 2T2.1. Moreover, our results reveal that the degradation of arabinoxylan, xyloglucan and cellulose are key metabolic processes in strain 2T2.1 growing on wheat straw. Different genes for key lignocellulolytic enzymes were identified, which can be starting points for production, characterization and/or supplementation of enzyme cocktails used in saccharification of agricultural residues. Our findings represent first steps that enable a better understanding of the reticulate evolution and "eco-enzymology" of lignocellulolytic Coniochaeta species.
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Affiliation(s)
- Stephen J. Mondo
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA
- Bioagricultural Science and Pest Management Department, Colorado State University, Fort Collins, CO 80521 USA
| | - Diego Javier Jiménez
- Microbiomes and Bioenergy Research Group, Department of Biological Sciences, Universidad de los Andes, Carrera 1 No 18A-12, Bogotá, Colombia
| | - Ronald E. Hector
- Bioenergy Research Unit, National Center for Agricultural Utilization Research, USDA-ARS, Peoria, IL 61604 USA
| | - Anna Lipzen
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Mi Yan
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Kurt LaButti
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Kerrie Barry
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Jan Dirk van Elsas
- Cluster of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Igor V. Grigoriev
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720-3102 USA
| | - Nancy N. Nichols
- Bioenergy Research Unit, National Center for Agricultural Utilization Research, USDA-ARS, Peoria, IL 61604 USA
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Herzog PL, Sützl L, Eisenhut B, Maresch D, Haltrich D, Obinger C, Peterbauer CK. Versatile Oxidase and Dehydrogenase Activities of Bacterial Pyranose 2-Oxidase Facilitate Redox Cycling with Manganese Peroxidase In Vitro. Appl Environ Microbiol 2019; 85:e00390-19. [PMID: 31028028 PMCID: PMC6581175 DOI: 10.1128/aem.00390-19] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 04/19/2019] [Indexed: 12/15/2022] Open
Abstract
Pyranose 2-oxidase (POx) has long been accredited a physiological role in lignin degradation, but evidence to provide insights into the biochemical mechanisms and interactions is insufficient. There are ample data in the literature on the oxidase and dehydrogenase activities of POx, yet the biological relevance of this duality could not be established conclusively. Here we present a comprehensive biochemical and phylogenetic characterization of a novel pyranose 2-oxidase from the actinomycetous bacterium Kitasatospora aureofaciens (KaPOx) as well as a possible biomolecular synergism of this enzyme with peroxidases using phenolic model substrates in vitro A phylogenetic analysis of both fungal and bacterial putative POx-encoding sequences revealed their close evolutionary relationship and supports a late horizontal gene transfer of ancestral POx sequences. We successfully expressed and characterized a novel bacterial POx gene from K. aureofaciens, one of the putative POx genes closely related to well-known fungal POx genes. Its biochemical characteristics comply with most of the classical hallmarks of known fungal pyranose 2-oxidases, i.e., reactivity with a range of different monosaccharides as electron donors as well as activity with oxygen, various quinones, and complexed metal ions as electron acceptors. Thus, KaPOx shows the pronounced duality of oxidase and dehydrogenase similar to that of fungal POx. We further performed efficient redox cycling of aromatic lignin model compounds between KaPOx and manganese peroxidase (MnP). In addition, we found a Mn(III) reduction activity in KaPOx, which, in combination with its ability to provide H2O2, implies this and potentially other POx as complementary enzymatic tools for oxidative lignin degradation by specialized peroxidases.IMPORTANCE Establishment of a mechanistic synergism between pyranose oxidase and (manganese) peroxidases represents a vital step in the course of elucidating microbial lignin degradation. Here, the comprehensive characterization of a bacterial pyranose 2-oxidase from Kitasatospora aureofaciens is of particular interest for several reasons. First, the phylogenetic analysis of putative pyranose oxidase genes reveals a widespread occurrence of highly similar enzymes in bacteria. Still, there is only a single report on a bacterial pyranose oxidase, stressing the need of closing this gap in the scientific literature. In addition, the relatively small K. aureofaciens proteome supposedly supplies a limited set of enzymatic functions to realize lignocellulosic biomass degradation. Both enzyme and organism therefore present a viable model to study the mechanisms of bacterial lignin decomposition, elucidate physiologically relevant interactions with specialized peroxidases, and potentially realize biotechnological applications.
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Affiliation(s)
- Peter L Herzog
- Department of Food Science and Technology, BOKU-University of Natural Resources and Life Sciences, Vienna, Austria
| | - Leander Sützl
- Department of Food Science and Technology, BOKU-University of Natural Resources and Life Sciences, Vienna, Austria
| | - Beate Eisenhut
- Department of Food Science and Technology, BOKU-University of Natural Resources and Life Sciences, Vienna, Austria
| | - Daniel Maresch
- Department of Chemistry, BOKU-University of Natural Resources and Life Sciences, Vienna, Austria
| | - Dietmar Haltrich
- Department of Food Science and Technology, BOKU-University of Natural Resources and Life Sciences, Vienna, Austria
| | - Christian Obinger
- Department of Chemistry, BOKU-University of Natural Resources and Life Sciences, Vienna, Austria
| | - Clemens K Peterbauer
- Department of Food Science and Technology, BOKU-University of Natural Resources and Life Sciences, Vienna, Austria
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Champreda V, Mhuantong W, Lekakarn H, Bunterngsook B, Kanokratana P, Zhao XQ, Zhang F, Inoue H, Fujii T, Eurwilaichitr L. Designing cellulolytic enzyme systems for biorefinery: From nature to application. J Biosci Bioeng 2019; 128:637-654. [PMID: 31204199 DOI: 10.1016/j.jbiosc.2019.05.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 05/06/2019] [Accepted: 05/11/2019] [Indexed: 12/14/2022]
Abstract
Cellulolytic enzymes play a key role on conversion of lignocellulosic plant biomass to biofuels and biochemicals in sugar platform biorefineries. In this review, we survey composite carbohydrate-active enzymes (CAZymes) among groups of cellulolytic fungi and bacteria that exist under aerobic and anaerobic conditions. Recent advances in designing effective cellulase mixtures are described, starting from the most complex microbial consortium-based enzyme preparations, to single-origin enzymes derived from intensively studied cellulase producers such as Trichoderma reesei, Talaromyces cellulolyticus, and Penicellium funiculosum, and the simplest minimal enzyme systems comprising selected sets of mono-component enzymes tailor-made for specific lignocellulosic substrates. We provide a comprehensive update on studies in developing high-performance cellulases for biorefineries.
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Affiliation(s)
- Verawat Champreda
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathumthani 12120, Thailand.
| | - Wuttichai Mhuantong
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathumthani 12120, Thailand
| | - Hataikarn Lekakarn
- Department of Biotechnology, Faculty of Science and Technology, Thammasat University, Rangsit Campus, Phahonyothin Road, Khlong Luang, Pathumthani 12120, Thailand
| | - Benjarat Bunterngsook
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathumthani 12120, Thailand
| | - Pattanop Kanokratana
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathumthani 12120, Thailand
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fei Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hiroyuki Inoue
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology, 3-11-32 Kagamiyama, Hiroshima 739-0046, Japan
| | - Tatsuya Fujii
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology, 3-11-32 Kagamiyama, Hiroshima 739-0046, Japan
| | - Lily Eurwilaichitr
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathumthani 12120, Thailand
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Lam MQ, Oates NC, Thevarajoo S, Tokiman L, Goh KM, McQueen-Mason SJ, Bruce NC, Chong CS. Genomic analysis of a lignocellulose degrading strain from the underexplored genus Meridianimaribacter. Genomics 2019; 112:952-960. [PMID: 31201854 DOI: 10.1016/j.ygeno.2019.06.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 05/13/2019] [Accepted: 06/11/2019] [Indexed: 02/06/2023]
Abstract
The genus Meridianimaribacter is one of the least-studied genera within Cytophaga-Flavobacteria. To date, no genomic analysis of Meridianimaribacter has been reported. In this study, Meridianimaribacter sp. strain CL38, a lignocellulose degrading halophile was isolated from mangrove soil. The genome of strain CL38 was sequenced and analyzed. The assembled genome contains 17 contigs with 3.33 Mbp, a GC content of 33.13% and a total of 2982 genes predicted. Lignocellulose degrading enzymes such as cellulases (GH3, 5, 9, 16, 74 and 144), xylanases (GH43 and CE4) and mannanases (GH5, 26, 27 and 130) are encoded in the genome. Furthermore, strain CL38 demonstrated its ability to decompose empty fruit bunch, a lignocellulosic waste residue arising from palm oil industry. The genome information coupled with experimental studies confirmed the ability of strain CL38 to degrade lignocellulosic biomass. Therefore, Meridianimaribacter sp. strain CL38, with its halotolerance, could be useful for seawater based lignocellulosic biorefining.
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Affiliation(s)
- Ming Quan Lam
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia
| | - Nicola C Oates
- Centre for Novel Agricultural Products, Department of Biology, University of York, Wentworth Way, York, YO10 5DD, United Kingdom
| | - Suganthi Thevarajoo
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia
| | - Lili Tokiman
- Johor National Parks Corporation, Kota Iskandar, 79575 Iskandar Puteri, Johor, Malaysia
| | - Kian Mau Goh
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia
| | - Simon J McQueen-Mason
- Centre for Novel Agricultural Products, Department of Biology, University of York, Wentworth Way, York, YO10 5DD, United Kingdom
| | - Neil C Bruce
- Centre for Novel Agricultural Products, Department of Biology, University of York, Wentworth Way, York, YO10 5DD, United Kingdom.
| | - Chun Shiong Chong
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia.
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Degradation profile of nixtamalized maize pericarp by the action of the microbial consortium PM-06. AMB Express 2019; 9:85. [PMID: 31197616 PMCID: PMC6565776 DOI: 10.1186/s13568-019-0812-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 06/08/2019] [Indexed: 11/25/2022] Open
Abstract
The nixtamalized maize pericarp (NMP) is a plentiful by-product of the tortilla industry and an important source of fermentable sugars. The aim of this study was to describe the degradation profile of NMP by the action of a consortium (PM-06) obtained from the native microbial community of this residue. The degradation was analyzed in terms of the changes in the community dynamics, production of enzymes (endo-xylanase and endo-cellulase), physicochemical parameters, and substrate chemical and microstructural characteristics, to understand the mechanisms behind the process. The consortium PM-06 degraded 86.8 ± 3.3% of NMP after 192 h of growth. Scanning electron microscopy images, and the composition and weight of the residual solids, showed that degradation was sequential starting with the consumption of hemicellulose. Xylanase was the highest enzyme activity produced, with a maximum value of 12.45 ± 0.03 U mL−1. There were fluctuations in the pH during the NMP degradation, starting with the acidification of the culture media and finishing with a pH close to 8.5. The most abundant species in the consortium, at the moment of maximum degradation activity, were Aneurinibacillus migulanus, Paenibacillus macerans, Bacillus coagulans, Microbacterium sp. LCT-H2, and Bacillus thuringiensis. The diversity of PM-06 provided metabolic abilities that in combination helped to produce an efficient process. The consortium PM-06 generated a set of different tools that worked coordinated to increase the substrate availability through the solubilization of components and elimination of structural diffusion barriers. This is the first report about the degradation of NMP using a microbial consortium.
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Silva MOD, Desmond P, Derlon N, Morgenroth E, Pernthaler J. Source Community and Assembly Processes Affect the Efficiency of Microbial Microcystin Degradation on Drinking Water Filtration Membranes. Front Microbiol 2019; 10:843. [PMID: 31057530 PMCID: PMC6482319 DOI: 10.3389/fmicb.2019.00843] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 04/02/2019] [Indexed: 01/14/2023] Open
Abstract
Microbial biofilms in gravity-driven membrane (GDM) filtration systems can efficiently degrade the cyanotoxin microcystin (MC), but it is unclear if this function depends on the presence of MC-producing cyanobacteria in the source water habitat. We assessed the removal of MC from added Microcystis aeruginosa biomass in GDMs fed with water from a lake with regular blooms of toxic cyanobacteria (ExpL) or from a stream without such background (ExpS). While initial MC removal was exclusively due to abiotic processes, significantly higher biological MC removal was observed in ExpL. By contrast, there was no difference in MC degradation capacity between lake and stream bacteria in separately conducted liquid enrichments on pure MC. Co-occurrence network analysis revealed a pronounced modularity of the biofilm communities, with a clear hierarchic distinction according to feed water origin and treatment type. Genotypes in the network modules associated with ExpS had significantly more links to each other, indicating that these biofilms had assembled from a more coherent source community. In turn, signals for stochastic community assembly were stronger in ExpL biofilms. We propose that the less "tightly knit" ExpL biofilm assemblages allowed for the better establishment of facultatively MC degrading bacteria, and thus for higher overall functional efficiency.
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Affiliation(s)
- Marisa O. D. Silva
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Peter Desmond
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Institute of Environmental Engineering, ETH Zurich, Institute of Environmental Engineering, Zurich, Switzerland
| | - Nicolas Derlon
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Eberhard Morgenroth
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Institute of Environmental Engineering, ETH Zurich, Institute of Environmental Engineering, Zurich, Switzerland
| | - Jakob Pernthaler
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
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43
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Ławniczak Ł, Marecik R. Comparison of metalworking fluids biodegradation efficiency by autochthonous and environmental communities. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 232:625-635. [PMID: 30530272 DOI: 10.1016/j.jenvman.2018.11.132] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 11/07/2018] [Accepted: 11/27/2018] [Indexed: 06/09/2023]
Abstract
The aim of this study was to evaluate the biodegradation potential of microbiota isolated from different environmental niches towards different types of metalworking fluids (MWF). The first experimental stage was focused on the assessment of biochemical oxygen demand reduction efficiency of autochthonous and environmental microbial communities. Based on the obtained results, the following order describing the biodegradation potential of communities from the studied niches was established: petroleum contaminated soil > waste repository ≥ waste MWF tanks > pesticide-treated field > activated sludge > municipal sewage effluents. For comparative purposes, the most efficient community originating from petroleum contaminated soil (PCS1) was selected for further studies along with the most efficient community originating from a waste MWF tank (WMT1). The studied communities achieved 100% biodegradation efficiency of decanedioic and dodecanedioic acids as well as glycerine and polyethoxylated dodecanol. However, the PCS1 community was more versatile and displayed significantly higher biodegradation efficiency of mineral oil (80% compared to 50% in case of WMT1). Similarly, experiments using pristine and spent MWF solutions confirmed that the PCS1 community outperformed the WMT1 community during the biodegradation of MWF containing oil as the main component (COD reduction of 80, 60 and 30% in case of semi-synthetic MWF, soluble oil and spent MWF, respectively). Results of community dynamics assessment using quantitative real-time PCR after the biodegradation of different types of MWF confirmed that the PCS1 community was characterized by high genetic stability and allowed to indicate the potential 'key players'.
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Affiliation(s)
- Łukasz Ławniczak
- Faculty of Chemical Technology, Poznan University of Technology, Berdychowo 4, 60-965, Poznań, Poland.
| | - Roman Marecik
- Department of Biotechnology and Food Microbiology, University of Life Sciences in Poznań, Wojska Polskiego 48, 60-627, Poznań, Poland
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Puentes-Téllez PE, Falcao Salles J. Construction of Effective Minimal Active Microbial Consortia for Lignocellulose Degradation. MICROBIAL ECOLOGY 2018; 76:419-429. [PMID: 29392382 PMCID: PMC6061470 DOI: 10.1007/s00248-017-1141-5] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 12/29/2017] [Indexed: 06/02/2023]
Abstract
Enriched microbial communities, obtained from environmental samples through selective processes, can effectively contribute to lignocellulose degradation. Unfortunately, fully controlled industrial degradation processes are difficult to reach given the intrinsically dynamic nature and complexity of the microbial communities, composed of a large number of culturable and unculturable species. The use of less complex but equally effective microbial consortia could improve their applications by allowing for more controlled industrial processes. Here, we combined ecological theory and enrichment principles to develop an effective lignocellulose-degrading minimal active microbial Consortia (MAMC). Following an enrichment of soil bacteria capable of degrading lignocellulose material from sugarcane origin, we applied a reductive-screening approach based on molecular phenotyping, identification, and metabolic characterization to obtain a selection of 18 lignocellulose-degrading strains representing four metabolic functional groups. We then generated 65 compositional replicates of MAMC containing five species each, which vary in the number of functional groups, metabolic potential, and degradation capacity. The characterization of the MAMC according to their degradation capacities and functional diversity measurements revealed that functional diversity positively correlated with the degradation of the most complex lignocellulosic fraction (lignin), indicating the importance of metabolic complementarity, whereas cellulose and hemicellulose degradation were either negatively or not affected by functional diversity. The screening method described here successfully led to the selection of effective MAMC, whose degradation potential reached up 96.5% of the degradation rates when all 18 species were present. A total of seven assembled synthetic communities were identified as the most effective MAMC. A consortium containing Stenotrophomonas maltophilia, Paenibacillus sp., Microbacterium sp., Chryseobacterium taiwanense, and Brevundimonas sp. was found to be the most effective degrading synthetic community.
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Affiliation(s)
- Pilar Eliana Puentes-Téllez
- Microbial Community Ecology, GELIFES - Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
- Department of Biology, Institute of Environmental Biology, Ecology and Biodiversity Group, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Joana Falcao Salles
- Microbial Community Ecology, GELIFES - Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
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45
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Alessi AM, Bird SM, Oates NC, Li Y, Dowle AA, Novotny EH, deAzevedo ER, Bennett JP, Polikarpov I, Young JPW, McQueen-Mason SJ, Bruce NC. Defining functional diversity for lignocellulose degradation in a microbial community using multi-omics studies. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:166. [PMID: 29946357 PMCID: PMC6004670 DOI: 10.1186/s13068-018-1164-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 06/05/2018] [Indexed: 05/24/2023]
Abstract
BACKGROUND Lignocellulose is one of the most abundant forms of fixed carbon in the biosphere. Current industrial approaches to the degradation of lignocellulose employ enzyme mixtures, usually from a single fungal species, which are only effective in hydrolyzing polysaccharides following biomass pre-treatments. While the enzymatic mechanisms of lignocellulose degradation have been characterized in detail in individual microbial species, the microbial communities that efficiently breakdown plant materials in nature are species rich and secrete a myriad of enzymes to perform "community-level" metabolism of lignocellulose. Single-species approaches are, therefore, likely to miss important aspects of lignocellulose degradation that will be central to optimizing commercial processes. RESULTS Here, we investigated the microbial degradation of wheat straw in liquid cultures that had been inoculated with wheat straw compost. Samples taken at selected time points were subjected to multi-omics analysis with the aim of identifying new microbial mechanisms for lignocellulose degradation that could be applied in industrial pre-treatment of feedstocks. Phylogenetic composition of the community, based on sequenced bacterial and eukaryotic ribosomal genes, showed a gradual decrease in complexity and diversity over time due to microbial enrichment. Taxonomic affiliation of bacterial species showed dominance of Bacteroidetes and Proteobacteria and high relative abundance of genera Asticcacaulis, Leadbetterella and Truepera. The eukaryotic members of the community were enriched in peritrich ciliates from genus Telotrochidium that thrived in the liquid cultures compared to fungal species that were present in low abundance. A targeted metasecretome approach combined with metatranscriptomics analysis, identified 1127 proteins and showed the presence of numerous carbohydrate-active enzymes extracted from the biomass-bound fractions and from the culture supernatant. This revealed a wide array of hydrolytic cellulases, hemicellulases and carbohydrate-binding modules involved in lignocellulose degradation. The expression of these activities correlated to the changes in the biomass composition observed by FTIR and ssNMR measurements. CONCLUSIONS A combination of mass spectrometry-based proteomics coupled with metatranscriptomics has enabled the identification of a large number of lignocellulose degrading enzymes that can now be further explored for the development of improved enzyme cocktails for the treatment of plant-based feedstocks. In addition to the expected carbohydrate-active enzymes, our studies reveal a large number of unknown proteins, some of which may play a crucial role in community-based lignocellulose degradation.
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Affiliation(s)
- Anna M. Alessi
- Department of Biology, Centre for Novel Agricultural Products, University of York, York, YO10 5DD UK
| | - Susannah M. Bird
- Department of Biology, Centre for Novel Agricultural Products, University of York, York, YO10 5DD UK
| | - Nicola C. Oates
- Department of Biology, Centre for Novel Agricultural Products, University of York, York, YO10 5DD UK
| | - Yi Li
- Department of Biology, Centre for Novel Agricultural Products, University of York, York, YO10 5DD UK
| | - Adam A. Dowle
- Department of Biology, Bioscience Technology Facility, University of York, York, YO10 5DD UK
| | | | - Eduardo R. deAzevedo
- Grupo de Biotecnologia Molecular, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP Brazil
| | - Joseph P. Bennett
- Department of Biology, Centre for Novel Agricultural Products, University of York, York, YO10 5DD UK
| | - Igor Polikarpov
- Grupo de Biotecnologia Molecular, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP Brazil
| | | | - Simon J. McQueen-Mason
- Department of Biology, Centre for Novel Agricultural Products, University of York, York, YO10 5DD UK
| | - Neil C. Bruce
- Department of Biology, Centre for Novel Agricultural Products, University of York, York, YO10 5DD UK
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46
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Carlos C, Fan H, Currie CR. Substrate Shift Reveals Roles for Members of Bacterial Consortia in Degradation of Plant Cell Wall Polymers. Front Microbiol 2018; 9:364. [PMID: 29545786 PMCID: PMC5839234 DOI: 10.3389/fmicb.2018.00364] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 02/15/2018] [Indexed: 01/05/2023] Open
Abstract
Deconstructing the intricate matrix of cellulose, hemicellulose, and lignin poses a major challenge in biofuel production. In diverse environments in nature, some microbial communities, are able to overcome plant biomass recalcitrance. Identifying key degraders of each component of plant cell wall can help improve biological degradation of plant feedstock. Here, we sequenced the metagenome of lignocellulose-adapted microbial consortia sub-cultured on xylan and alkali lignin media. We observed a drastic shift on community composition after sub-culturing, independently of the original consortia. Proteobacteria relative abundance increased after growth in alkali lignin medium, while Bacteroidetes abundance increased after growth in xylan medium. At the genus level, Pseudomonas was more abundant in the communities growing on alkali lignin, Sphingobacterium in the communities growing on xylan and Cellulomonas abundance was the highest in the original microbial consortia. We also observed functional convergence of microbial communities after incubation in alkali lignin, due to an enrichment of genes involved in benzoate degradation and catechol ortho-cleavage pathways. Our results represent an important step toward the elucidation of key members of microbial communities on lignocellulose degradation and may aide the design of novel lignocellulolytic microbial consortia that are able to efficiently degrade plant cell wall polymers.
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Affiliation(s)
- Camila Carlos
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States.,U.S. Department of Energy, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Huan Fan
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
| | - Cameron R Currie
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States.,U.S. Department of Energy, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States
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47
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Cortes-Tolalpa L, Norder J, van Elsas JD, Falcao Salles J. Halotolerant microbial consortia able to degrade highly recalcitrant plant biomass substrate. Appl Microbiol Biotechnol 2018; 102:2913-2927. [PMID: 29397428 PMCID: PMC5847192 DOI: 10.1007/s00253-017-8714-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 11/29/2017] [Accepted: 12/11/2017] [Indexed: 12/30/2022]
Abstract
The microbial degradation of plant-derived compounds under salinity stress remains largely underexplored. The pretreatment of lignocellulose material, which is often needed to improve the production of lignocellulose monomers, leads to high salt levels, generating a saline environment that raises technical considerations that influence subsequent downstream processes. Here, we constructed halotolerant lignocellulose degrading microbial consortia by enriching a salt marsh soil microbiome on a recalcitrant carbon and energy source, i.e., wheat straw. The consortia were obtained after six cycles of growth on fresh substrate (adaptation phase), which was followed by four cycles on pre-digested (highly-recalcitrant) substrate (stabilization phase). The data indicated that typical salt-tolerant bacteria made up a large part of the selected consortia. These were “trained” to progressively perform better on fresh substrate, but a shift was observed when highly recalcitrant substrate was used. The most dominant bacteria in the consortia were Joostella marina, Flavobacterium beibuense, Algoriphagus ratkowskyi, Pseudomonas putida, and Halomonas meridiana. Interestingly, fungi were sparsely present and negatively affected by the change in the substrate composition. Sarocladium strictum was the single fungal strain recovered at the end of the adaptation phase, whereas it was deselected by the presence of recalcitrant substrate. Consortia selected in the latter substrate presented higher cellulose and lignin degradation than consortia selected on fresh substrate, indicating a specialization in transforming the recalcitrant regions of the substrate. Moreover, our results indicate that bacteria have a prime role in the degradation of recalcitrant lignocellulose under saline conditions, as compared to fungi. The final consortia constitute an interesting source of lignocellulolytic haloenzymes that can be used to increase the efficiency of the degradation process, while decreasing the associated costs.
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Affiliation(s)
- Larisa Cortes-Tolalpa
- Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
| | - Justin Norder
- Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Jan Dirk van Elsas
- Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Joana Falcao Salles
- Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
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48
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Kanokratana P, Wongwilaiwalin S, Mhuantong W, Tangphatsornruang S, Eurwilaichitr L, Champreda V. Characterization of cellulolytic microbial consortium enriched on Napier grass using metagenomic approaches. J Biosci Bioeng 2017; 125:439-447. [PMID: 29169786 DOI: 10.1016/j.jbiosc.2017.10.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Revised: 09/11/2017] [Accepted: 10/25/2017] [Indexed: 11/17/2022]
Abstract
Energy grass is a promising substrate for production of biogas by anaerobic digestion. However, the conversion efficiency is limited by the enzymatically recalcitrant nature of cellulosic wastes. In this study, an active, structurally stable mesophilic lignocellulolytic degrading microbial consortium (Np-LMC) was constructed from forest compost soil microbiota by successive subcultivation on Napier grass under facultative anoxic conditions. According to tagged 16S rRNA gene amplicon sequencing, increasing abundance of facultative Proteobacteria was found in the middle of batch cycle which was then subsequently replaced by the cellulose degraders Firmicutes and Bacteroidetes along with decreasing CMCase, xylanase, and β-glucanase activity profiles in the supernatant after 5 days of incubation. Anaerobic/facultative bacteria Dysgonomonas and Sedimentibacter and aerobic bacteria Comamonas were the major genera found in Np-LMC. The consortium was active on degradation of the native and delignified grass. Direct shotgun sequencing of the consortium metagenome revealed relatively high abundance of genes encoding for various lignocellulose degrading enzymes in 23 glycosyl hydrolase (GH) families compared to previously reported cellulolytic microbial communities in mammalian digestive tracts. Enzymes attacking cellulose and hemicellulose were dominated by GH2, 3, 5, 9, 10, 26, 28 and 43 in addition to a variety of carbohydrate esterases (CE) and auxiliary activities (AA), reflecting adaptation of the enzyme systems to the native herbaceous substrate. The consortium identified here represents the microcosm specifically bred on energy grass, with potential for enhancing degradation of fibrous substrates in bioenergy industry.
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Affiliation(s)
- Pattanop Kanokratana
- Enzyme Technology Laboratory, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pahonyothin Road, Klong Luang, Pathum Thani 12120, Thailand.
| | - Sarunyou Wongwilaiwalin
- Enzyme Technology Laboratory, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pahonyothin Road, Klong Luang, Pathum Thani 12120, Thailand
| | - Wuttichai Mhuantong
- Enzyme Technology Laboratory, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pahonyothin Road, Klong Luang, Pathum Thani 12120, Thailand
| | - Sithichoke Tangphatsornruang
- Genomic Research Laboratory, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pahonyothin Road, Klong Luang, Pathum Thani 12120, Thailand
| | - Lily Eurwilaichitr
- Enzyme Technology Laboratory, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pahonyothin Road, Klong Luang, Pathum Thani 12120, Thailand
| | - Verawat Champreda
- Enzyme Technology Laboratory, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pahonyothin Road, Klong Luang, Pathum Thani 12120, Thailand
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49
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Cortes-Tolalpa L, Salles JF, van Elsas JD. Bacterial Synergism in Lignocellulose Biomass Degradation - Complementary Roles of Degraders As Influenced by Complexity of the Carbon Source. Front Microbiol 2017; 8:1628. [PMID: 29067002 PMCID: PMC5641323 DOI: 10.3389/fmicb.2017.01628] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 08/10/2017] [Indexed: 01/23/2023] Open
Abstract
Lignocellulosic biomass (LCB) is an attractive source of carbon for the production of sugars and other chemicals. Due to its inherent complexity and heterogeneity, efficient biodegradation requires the actions of different types of hydrolytic enzymes. In nature, complex microbial communities that work efficiently and often synergistically accomplish degradation. Studying such synergisms in LCB degradation is fundamental for the establishment of an optimal biological degradation process. Here, we examine the wheat straw degradation potential of synthetic microbial consortia composed of bacteria and fungi. Growth of, and enzyme secretion by, monocultures of degrader strains were studied in aerobic cultures using wheat straw as the sole carbon and energy source. To investigate synergism, co-cultures were constructed from selected strains and their performance was tested in comparison with the respective monocultures. In monoculture, each organism – with a typical enzymatic profile – was found to mainly consume the cellulose part of the substrate. One strain, Flavobacterium ginsengisoli so9, displayed an extremely high degradation capacity, as measured by its secreted enzymes. Among 13 different co-cultures, five presented synergisms. These included four bacterial bicultures and one bacterial–fungal triculture. The highest level of synergism was found in a Citrobacter freundii/Sphingobacterium multivorum biculture, which revealed an 18.2-fold increase of the produced biomass. As compared to both monocultures, this bacterial pair showed significantly increased enzymatic activities, in particular of cellobiohydrolases, mannosidases, and xylosidases. Moreover, the synergism was unique to growth on wheat straw, as it was completely absent in glucose-grown bicultures. Spent supernatants of either of the two partners were found to stimulate the growth on wheat straw of the counterpart organism, in a directional manner. Thus, the basis of the LCB-specific synergism might lie in the specific release of compounds or agents by S. multivorum w15 that promote the activity of C. freundii so4 and vice versa.
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Affiliation(s)
- Larisa Cortes-Tolalpa
- Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Joana F Salles
- Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Jan Dirk van Elsas
- Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
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50
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Jiménez DJ, Dini-Andreote F, DeAngelis KM, Singer SW, Salles JF, van Elsas JD. Ecological Insights into the Dynamics of Plant Biomass-Degrading Microbial Consortia. Trends Microbiol 2017. [PMID: 28648267 DOI: 10.1016/j.tim.2017.05.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Plant biomass (PB) is an important resource for biofuel production. However, the frequent lack of efficiency of PB saccharification is still an industrial bottleneck. The use of enzyme cocktails produced from PB-degrading microbial consortia (PB-dmc) is a promising approach to optimize this process. Nevertheless, the proper use and manipulation of PB-dmc depends on a sound understanding of the ecological processes and mechanisms that exist in these communities. This Opinion article provides an overview of arguments as to how spatiotemporal nutritional fluxes influence the successional dynamics and ecological interactions (synergism versus competition) between populations in PB-dmc. The themes of niche occupancy, 'sugar cheaters', minimal effective consortium, and the Black Queen Hypothesis are raised as key subjects that foster our appraisal of such systems. Here we provide a conceptual framework that describes the critical topics underpinning the ecological basis of PB-dmc, giving a solid foundation upon which further prospective experimentation can be developed.
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Affiliation(s)
- Diego Javier Jiménez
- Microbial Ecology Cluster, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747AG, Groningen, The Netherlands.
| | - Francisco Dini-Andreote
- Microbial Ecology Cluster, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747AG, Groningen, The Netherlands
| | - Kristen M DeAngelis
- Department of Microbiology, University of Massachusetts, 639 North Pleasant Street, Amherst, MA 01003-9298, USA
| | - Steven W Singer
- Joint BioEnergy Institute,5885 Hollis Street, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Joana Falcão Salles
- Microbial Ecology Cluster, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747AG, Groningen, The Netherlands
| | - Jan Dirk van Elsas
- Microbial Ecology Cluster, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747AG, Groningen, The Netherlands
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