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Cao Q, Liu C, Li Y, Qin Y, Wang C, Wang T. The underlying mechanisms of oxytetracycline degradation mediated by gut microbial proteins and metabolites in Hermetia illucens. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174224. [PMID: 38914334 DOI: 10.1016/j.scitotenv.2024.174224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 06/06/2024] [Accepted: 06/21/2024] [Indexed: 06/26/2024]
Abstract
Hermetia illucens larvae can enhance the degradation of oxytetracycline (OTC) through its biotransformation. However, the underlying mechanisms mediated by gut metabolites and proteins are unclear. To gain further insights, the kinetics of OTC degradation, the functional structures of gut bacterial communities, proteins, and metabolites were investigated. An availability-adjusted first-order model effectively evaluated OTC degradation kinetics, with degradation half-lives of 4.18 and 21.71 days for OTC degradation with and without larval biotransformation, respectively. Dominant bacteria in the larval guts were Enterococcus, Psychrobacter, Providencia, Myroides, Enterobacteriaceae, and Lactobacillales. OTC exposure led to significant differential expression of proteins, with functional classification revealing involvement in digestion, transformation, and adaptability to environmental stress. Upregulated proteins, such as aromatic ring hydroxylase, acted as oxidoreductases modifying the chemical structure of OTC. Unique metabolites, aclarubicin and sancycline identified were possible OTC metabolic intermediates. Correlation analysis revealed significant interdependence between gut bacteria, metabolites, and proteins. These findings reveal a synergistic mechanism involving gut microbial metabolism and enzyme structure that drives the rapid degradation of OTC and facilitates the engineering applications of bioremediation.
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Affiliation(s)
- Qingcheng Cao
- Key Laboratory of Green Chemical Process of Ministry of Education, Key Laboratory of Novel Reactor and Green Chemical Technology of Hubei Province, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, People's Republic of China
| | - Cuncheng Liu
- Key Laboratory of Green Chemical Process of Ministry of Education, Key Laboratory of Novel Reactor and Green Chemical Technology of Hubei Province, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, People's Republic of China; Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, People's Republic of China.
| | - Yun Li
- Key Laboratory of Green Chemical Process of Ministry of Education, Key Laboratory of Novel Reactor and Green Chemical Technology of Hubei Province, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, People's Republic of China
| | - Yuanhang Qin
- Key Laboratory of Green Chemical Process of Ministry of Education, Key Laboratory of Novel Reactor and Green Chemical Technology of Hubei Province, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, People's Republic of China
| | - Cunwen Wang
- Key Laboratory of Green Chemical Process of Ministry of Education, Key Laboratory of Novel Reactor and Green Chemical Technology of Hubei Province, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, People's Republic of China.
| | - Tielin Wang
- Key Laboratory of Green Chemical Process of Ministry of Education, Key Laboratory of Novel Reactor and Green Chemical Technology of Hubei Province, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, People's Republic of China
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Li Y, Xu T, Tu Y, Li T, Wei Y, Zhou Y. An aldolase-dependent phloroglucinol degradation pathway in Collinsella sp. zg1085. Appl Environ Microbiol 2024:e0104724. [PMID: 39028195 DOI: 10.1128/aem.01047-24] [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: 05/28/2024] [Accepted: 07/01/2024] [Indexed: 07/20/2024] Open
Abstract
Phloroglucinol (1,3,5-trihydroxybenzene) is a key intermediate in the degradation of polyphenols such as flavonoids and hydrolysable tannins and can be used by certain bacteria as a carbon and energy source for growth. The identification of enzymes that participate in the fermentation of phloroglucinol to acetate and butyrate in Clostridia was recently reported. In this study, we present the discovery and characterization of a novel metabolic pathway for phloroglucinol degradation in the bacterium Collinsella sp. zg1085, from marmot respiratory tract. In both the Clostridial and Collinsella pathways, phloroglucinol is first reduced to dihydrophoroglucinol by the NADPH-dependent phloroglucinol reductase (PGR), followed by ring opening to form (S)-3-hydroxy-5-oxohexanoate by a Mn2+-dependent dihydrophloroglucinol cyclohydrolase (DPGC). In the Collinsella pathway, (S)-3-hydroxy-5-oxohexanoate is then cleaved to form malonate semialdehyde and acetone by a newly identified aldolase (HOHA). Finally, a NADP+-dependent malonate-semialdehyde dehydrogenase converts malonate semialdehyde to CO2 and acetyl-CoA, an intermediate in carbon and energy metabolism. Recombinant expression of the Collinsella PGR, DPGC, and HOHA in E. coli enabled the conversion of phloroglucinol into acetone, providing support for the proposed pathway. Experiments with Olsenella profusa, another bacterium containing the gene cluster of interest, show that the PGR, DPGC, HOHA, and MSDH are induced by phloroglucinol. Our findings add to the variety of metabolic pathways for the degradation of phloroglucinol, a widely distributed phenolic compound, in the anaerobic microbiome.IMPORTANCEPhloroglucinol is an important intermediate in the bacterial degradation of polyphenols, a highly abundant class of plant natural products. Recent research has identified key enzymes of the phloroglucinol degradation pathway in butyrate-producing anaerobic bacteria, which involves cleavage of a linear triketide intermediate by a beta ketoacid cleavage enzyme, requiring acetyl-CoA as a co-substrate. This paper reports a variant of the pathway in the lactic acid bacterium Collinsella sp. zg1085, which involves cleavage of the triketide intermediate by a homolog of deoxyribose-5-phosphate aldolase, highlighting the variety of mechanisms for phloroglucinol degradation by different anaerobic bacterial taxa.
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Affiliation(s)
- Yating Li
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
| | - Tong Xu
- Department of Pharmacy, Northern Jiangsu People's Hospital, Clinical Medical School of Yangzhou University, Yangzhou, Jiangsu, China
| | - Yanqin Tu
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
| | - Tong Li
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
| | - Yifeng Wei
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Yan Zhou
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
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3
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Bouranis JA, Tfaily MM. Inside the microbial black box: a redox-centric framework for deciphering microbial metabolism. Trends Microbiol 2024:S0966-842X(24)00134-3. [PMID: 38825550 DOI: 10.1016/j.tim.2024.05.003] [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: 03/05/2024] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 06/04/2024]
Abstract
Microbial metabolism influences the global climate and human health and is governed by the balance between NADH and NAD+ through redox reactions. Historically, oxidative (i.e., catabolism) and reductive (i.e., fermentation) pathways have been studied in isolation, obscuring the complete metabolic picture. However, new omics technologies and biotechnological tools now allow an integrated system-level understanding of the drivers of microbial metabolism through observation and manipulation of redox reactions. Here we present perspectives on the importance of viewing microbial metabolism as the dynamic interplay between oxidative and reductive processes and apply this framework to diverse microbial systems. Additionally, we highlight novel biotechnologies to monitor and manipulate microbial redox status to control metabolism in unprecedented ways. This redox-focused systems biology framework enables a more mechanistic understanding of microbial metabolism.
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Affiliation(s)
- John A Bouranis
- Department of Environmental Science, The University of Arizona, Tucson, AZ, 85719, USA
| | - Malak M Tfaily
- Department of Environmental Science, The University of Arizona, Tucson, AZ, 85719, USA.
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Chaput G, Sogin M. Talented microbes unlatch peatland carbon. Nat Microbiol 2024; 9:1403-1405. [PMID: 38806672 DOI: 10.1038/s41564-024-01711-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Affiliation(s)
- Gina Chaput
- UC Davis Genome Center and Bioinformatics Program, College of Biological Sciences, University of California, Davis, Davis, CA, USA
| | - Maggie Sogin
- Department of Molecular and Cellular Biology, School of Natural Sciences, University of California, Merced, Merced, CA, USA.
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McGivern BB, Cronin DR, Ellenbogen JB, Borton MA, Knutson EL, Freire-Zapata V, Bouranis JA, Bernhardt L, Hernandez AI, Flynn RM, Woyda R, Cory AB, Wilson RM, Chanton JP, Woodcroft BJ, Ernakovich JG, Tfaily MM, Sullivan MB, Tyson GW, Rich VI, Hagerman AE, Wrighton KC. Microbial polyphenol metabolism is part of the thawing permafrost carbon cycle. Nat Microbiol 2024; 9:1454-1466. [PMID: 38806673 PMCID: PMC11153144 DOI: 10.1038/s41564-024-01691-0] [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: 12/08/2023] [Accepted: 04/02/2024] [Indexed: 05/30/2024]
Abstract
With rising global temperatures, permafrost carbon stores are vulnerable to microbial degradation. The enzyme latch theory states that polyphenols should accumulate in saturated peatlands due to diminished phenol oxidase activity, inhibiting resident microbes and promoting carbon stabilization. Pairing microbiome and geochemical measurements along a permafrost thaw-induced saturation gradient in Stordalen Mire, a model Arctic peatland, we confirmed a negative relationship between phenol oxidase expression and saturation but failed to support other trends predicted by the enzyme latch. To inventory alternative polyphenol removal strategies, we built CAMPER, a gene annotation tool leveraging polyphenol enzyme knowledge gleaned across microbial ecosystems. Applying CAMPER to genome-resolved metatranscriptomes, we identified genes for diverse polyphenol-active enzymes expressed by various microbial lineages under a range of redox conditions. This shifts the paradigm that polyphenols stabilize carbon in saturated soils and highlights the need to consider both oxic and anoxic polyphenol metabolisms to understand carbon cycling in changing ecosystems.
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Affiliation(s)
- Bridget B McGivern
- Department of Soil and Crop Science, Colorado State University, Fort Collins, CO, USA
| | - Dylan R Cronin
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
- Center of Microbiome Science, The Ohio State University, Columbus, OH, USA
| | - Jared B Ellenbogen
- Department of Soil and Crop Science, Colorado State University, Fort Collins, CO, USA
| | - Mikayla A Borton
- Department of Soil and Crop Science, Colorado State University, Fort Collins, CO, USA
| | - Eleanor L Knutson
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, USA
| | | | - John A Bouranis
- Department of Environmental Science; University of Arizona, Tucson, AZ, USA
| | - Lukas Bernhardt
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH, USA
| | - Alma I Hernandez
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH, USA
| | - Rory M Flynn
- Department of Soil and Crop Science, Colorado State University, Fort Collins, CO, USA
| | - Reed Woyda
- Department of Soil and Crop Science, Colorado State University, Fort Collins, CO, USA
| | - Alexandra B Cory
- Department of Environmental Sciences, Emory University, Atlanta, GA, USA
| | - Rachel M Wilson
- Department of Earth Ocean and Atmospheric Sciences, Florida State University, Tallahassee, FL, USA
| | - Jeffrey P Chanton
- Department of Earth Ocean and Atmospheric Sciences, Florida State University, Tallahassee, FL, USA
| | - Ben J Woodcroft
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Jessica G Ernakovich
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH, USA
| | - Malak M Tfaily
- Department of Environmental Science; University of Arizona, Tucson, AZ, USA
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
- Center of Microbiome Science, The Ohio State University, Columbus, OH, USA
| | - Gene W Tyson
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Virginia I Rich
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - Ann E Hagerman
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, USA
| | - Kelly C Wrighton
- Department of Soil and Crop Science, Colorado State University, Fort Collins, CO, USA.
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Qiao X, Li P, Zhao J, Li Z, Zhang C, Wu J. Gaining insight into the effect of laccase expression on humic substance formation during lignocellulosic biomass composting. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 923:171548. [PMID: 38458466 DOI: 10.1016/j.scitotenv.2024.171548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 02/19/2024] [Accepted: 03/04/2024] [Indexed: 03/10/2024]
Abstract
The aim is to enhance lignin humification by promoting laccase activities which can promote lignin depolymerization and reaggregation during composting. 1-Hydroxybenzotriazole (HBT) is employed to conduct laccase mediator system (LMS), application of oxidized graphene (GO) in combination to strengthen LMS. Compared with control, the addition of GO, HBT, and GH (GO coupled with HBT) significantly improved laccase expression and activities (P < 0.05), with lignin humification efficiency also increased by 68.6 %, 36.7 %, and 107.8 %. GH treatment induces microbial expression of laccase by increasing the abundance and synergy of core microbes. The unsupervised learning model, vector autoregressive model and Mantel test function were combined to elucidate the mechanism of action of exogenous materials. The results showed that GO stabilized the composting environment on the one hand, and acted as a support vector to stabilize the LMS and promote the function of laccase on the other. In GH treatment, degradation of macromolecules and humification of small molecules were promoted simultaneously by activating the dual function of laccase. Additionally, it also reveals the GH enhances the humification of lignocellulosic compost by converting phenolic pollutants into aggregates. These findings provide a new way to enhance the dual function of laccase and promote lignin humification during composting. It could effectively achieve the resource utilization of organic solid waste and reduce composting pollution.
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Affiliation(s)
- Xingyu Qiao
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Peiju Li
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Jinghan Zhao
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Zonglin Li
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Chunhao Zhang
- 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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Seitz VA, McGivem BB, Borton MA, Chaparro JM, Schipanski ME, Prenni JE, Wrighton KC. Cover Crop Root Exudates Impact Soil Microbiome Functional Trajectories in Agricultural Soils. RESEARCH SQUARE 2024:rs.3.rs-3956430. [PMID: 38410449 PMCID: PMC10896397 DOI: 10.21203/rs.3.rs-3956430/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Background Cover cropping is an agricultural practice that uses secondary crops to support the growth of primary crops through various mechanisms including erosion control, weed suppression, nutrient management, and enhanced biodiversity. Cover crops may elicit some of these ecosystem services through chemical interactions with the soil microbiome via root exudation, or the release of plant metabolites from roots. Phytohormones are one metabolite type exuded by plants that activate the rhizosphere microbiome, yet managing this chemical interaction remains an untapped mechanism for optimizing plant-soil microbiome interactions. Currently, there is limited understanding on the diversity of cover crop phytohormone root exudation patterns and how these chemical messages selectively enrich specific microbial taxa and functionalities in agricultural soils. Results Here, we link variability in cover crop root exudate composition to changes in soil microbiome functionality. Exudate chemical profiles from 4 cover crop species (Sorghum bicolor, Vicia villosa, Brassica napus, and Secale cereal) were used as the chemical inputs to decipher microbial responses. These distinct exudate profiles, along with a no exudate control, were amended to agricultural soil microcosms with microbial responses tracked over time using metabolomes and genome-resolved metatranscriptomes. Our findings illustrated microbial metabolic patterns were unique in response to cover crop exudate inputs over time, particularly by sorghum and cereal rye amended microcosms where we identify novel microbial members (at the genera and family level) who produced IAA and GA4 over time. We also identify broad changes in microbial nitrogen cycling in response chemical inputs. Conclusions We highlight that root exudate amendments alter microbial community function and phytohormone metabolisms, particularly in response to root exudates isolated from cereal rye and sorghum plants. Additionally, we constructed a soil microbial genomic catalog of microorganisms responding to commonly used cover crops, a public resource for agriculturally-relevant microbes. Many of our exudate-stimulated microorganisms are representatives from poorly characterized or novel taxa, highlighting the yet to be discovered metabolic reservoir harbored in agricultural soils. Our findings emphasize the tractability of high-resolution multiomics approaches to investigate processes relevant for agricultural soils, opening the possibility of targeting specific soil biogeochemical outcomes through biological precision agricultural practices that use cover crops and the microbiome as levers for enhanced crop production.
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Hájek T, Urbanová Z. Enzyme adaptation in Sphagnum peatlands questions the significance of dissolved organic matter in enzyme inhibition. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 911:168685. [PMID: 38000758 DOI: 10.1016/j.scitotenv.2023.168685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 11/16/2023] [Accepted: 11/16/2023] [Indexed: 11/26/2023]
Abstract
Peatlands store a large proportion of global soil carbon in the form of peat because decomposition of plant organic matter is slow. In Sphagnum-dominated peatlands, dissolved organic matter (DOM) is traditionally considered an important inhibitor of hydrolytic enzymes due to the polyphenolic polymers it contains. Interestingly, the acidic character of the polymers in such DOM has never been tested for its enzyme-inhibitory properties. We raised two principal hypotheses: (1) not only the polyphenolic but also the acidic character of DOM inhibits the activity of extracellular enzymes in Sphagnum-dominated peatlands; (2) environmental, peat-extracted enzymes will show adaptation to their environment. We tested the inhibition of commercial acid phosphatase and cellobiohydrolase, and environmental phosphatase and β-glucosidase by following dissolved substances: (1) polyphenol-free polycarboxylates from Sphagnum cell walls, i.e. sphagnan, (2) environmental DOM (peat-DOM) containing polymers of polyphenolic-polycarboxylate nature, (3) tannic acid (carboxyl-free polyphenolic oligomer) and (4) monomeric phenolic acids. Sphagnan strongly inhibited commercial acid phosphatase, to a similar extent as peat-DOM and more strongly than tannic acid and a polycarboxylate from another moss (Leucobryum glaucum). Monomeric phenolic acids were weak inhibitors. Commercial cellobiohydrolase was only partially inhibited by sphagnan or peat-DOM. Environmental phosphatase and β-glucosidase were consistently slightly inhibited by tannic acid, but not by sphagnan or peat-DOM. Inhibition of commercial phosphatase by sphagnan and peat-DOM was counteracted by a polycation chitosan, indicating the electrostatic nature of carboxylate-mediated inhibition. Our results question the polyphenol-mediated enzyme inhibition in Sphagnum-dominated peatlands as (1) the DOM had a strong inhibitory potential due to its polycarboxylates; nevertheless, (2) the peat microbial communities exhibited enzyme resistance to both polyphenol and polycarboxylate polymers in peat-DOM.
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Affiliation(s)
- Tomáš Hájek
- Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05 České Budějovice, Czechia.
| | - Zuzana Urbanová
- Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05 České Budějovice, Czechia
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Liu J, Xu Y, Si YJ, Li BQ, Chen P, Wu LL, Guo P, Ji RQ. The Diverse Mycorrizal Morphology of Rhododendron dauricum, the Fungal Communities Structure and Dynamics from the Mycorrhizosphere. J Fungi (Basel) 2024; 10:65. [PMID: 38248974 PMCID: PMC10817234 DOI: 10.3390/jof10010065] [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: 12/07/2023] [Revised: 01/10/2024] [Accepted: 01/11/2024] [Indexed: 01/23/2024] Open
Abstract
It is generally believed that mycorrhiza is a microecosystem composed of mycorrhizal fungi, host plants and other microscopic organisms. The mycorrhiza of Rhododendron dauricum is more complex and the diverse morphology of our investigated results displays both typical ericoid mycorrhizal characteristics and ectomycorrhizal traits. The characteristics of ectendoomycorrhiza, where mycelial invade from the outside into the root cells, have also been observed. In order to further clarify the mycorrhizal fungi members and other fungal communities of R. dauricum mycorrhiza, and explore the effects of vegetation and soil biological factors on their community structure, we selected two woodlands in the northeast of China as samples-one is a mixed forest of R. dauricum and Quercus mongolica, and the other a mixed forest of R. dauricum, Q. mongolica, and Pinus densiflor. The sampling time was during the local growing season, from June to September. High-throughput sequencing yielded a total of 3020 fungal amplicon sequence variants (ASVs), which were based on sequencing of the internal transcribed spacer ribosomal RNA (ITS rRNA) via the Illumina NovaSeq platform. In the different habitats of R. dauricum, there are differences in the diversity of fungi obtained from mycorrhizal niches, and specifically the mycorrhizal fungal community structure in the complex vegetation of mixed forests, where R. dauricum is found, exhibits greater stability, with relatively minor changes over time. Soil fungi are identified as the primary source of fungi within the mycorrhizal niche, and the abundance of mycorrhizal fungi from mycorrhizal niches in R. dauricum is significantly influenced by soil pH, organic matter, and available nitrogen. The relationship between soil fungi and mycorrhizal fungi from mycorrhizal niches is simultaneously found to be intricate, while the genus Hydnellum emerges as a central genus among mycorrhizal fungi from mycorrhizal niches. However, there is currently a substantial gap in the foundational research of this genus, including the fact that mycorrhizal fungi from mycorrhizal niches have, compared to fungi present in the soil, proven to be more sensitive to changes in soil moisture.
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Affiliation(s)
| | | | | | | | | | | | | | - Rui-Qing Ji
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun 130118, China; (J.L.); (Y.X.); (Y.-J.S.); (B.-Q.L.); (P.C.); (L.-L.W.); (P.G.)
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10
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Qin L, Tian W, Freeman C, Jia Z, Yin X, Gao C, Zou Y, Jiang M. Changes in bacterial communities during rice cultivation remove phenolic constraints on peatland carbon preservation. ISME COMMUNICATIONS 2024; 4:ycae022. [PMID: 38500699 PMCID: PMC10945358 DOI: 10.1093/ismeco/ycae022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/30/2023] [Accepted: 01/30/2024] [Indexed: 03/20/2024]
Abstract
Northern peatlands contain ~30% of terrestrial carbon (C) stores, but in recent decades, 14% to 20% of the stored C has been lost because of conversion of the peatland to cropland. Microorganisms are widely acknowledged as primary decomposers, but the keystone taxa within the bacterial community regulating C loss from cultivated peatlands remain largely unknown. In this study, we investigated the bacterial taxa driving peat C mineralization during rice cultivation. Cultivation significantly decreased concentrations of soil organic C, dissolved organic C (DOC), carbohydrates, and phenolics but increased C mineralization rate (CMR). Consistent with the classic theory that phenolic inhibition creates a "latch" that reduces peat C decomposition, phenolics were highly negatively correlated with CMR in cultivated peatlands, indicating that elimination of inhibitory phenolics can accelerate soil C mineralization. Bacterial communities were significantly different following peatland cultivation, and co-occurrence diagnosis analysis revealed substantial changes in network clusters of closely connected nodes (modules) and bacterial keystone taxa. Specifically, in cultivated peatlands, bacterial modules were significantly negatively correlated with phenolics, carbohydrates, and DOC. While keystone taxa Xanthomonadales, Arthrobacter, and Bacteroidetes_vadinHA17 can regulate bacterial modules and promote carbon mineralization. Those observations indicated that changes in bacterial modules can promote phenolic decomposition and eliminate phenolic inhibition of labile C decomposition, thus accelerating soil organic C loss during rice cultivation. Overall, the study provides deeper insights into microbe-driven peat C loss during rice cultivation and highlights the crucial role of keystone bacterial taxa in the removal of phenolic constraints on peat C preservation.
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Affiliation(s)
- Lei Qin
- State Key Laboratory of Black Soils Conservation and Utilization, Key Laboratory of Wetland Ecology and Environment, Heilongjiang Xingkai Lake Wetland Ecosystem National Observation and Research Station, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Wei Tian
- College of Forestry and Grassland, Jilin Agriculture University, Changchun 130118, China
| | - Chris Freeman
- School of Natural Sciences, Bangor University, Bangor LL57 2UW, United Kingdom
| | - Zhongjun Jia
- State Key Laboratory of Black Soils Conservation and Utilization, Key Laboratory of Wetland Ecology and Environment, Heilongjiang Xingkai Lake Wetland Ecosystem National Observation and Research Station, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Xiaolei Yin
- State Key Laboratory of Black Soils Conservation and Utilization, Key Laboratory of Wetland Ecology and Environment, Heilongjiang Xingkai Lake Wetland Ecosystem National Observation and Research Station, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Chuanyu Gao
- State Key Laboratory of Black Soils Conservation and Utilization, Key Laboratory of Wetland Ecology and Environment, Heilongjiang Xingkai Lake Wetland Ecosystem National Observation and Research Station, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Yuanchun Zou
- State Key Laboratory of Black Soils Conservation and Utilization, Key Laboratory of Wetland Ecology and Environment, Heilongjiang Xingkai Lake Wetland Ecosystem National Observation and Research Station, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Ming Jiang
- State Key Laboratory of Black Soils Conservation and Utilization, Key Laboratory of Wetland Ecology and Environment, Heilongjiang Xingkai Lake Wetland Ecosystem National Observation and Research Station, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
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11
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Likar M, Grašič M, Stres B, Regvar M, Gaberščik A. Metagenomics reveals effects of fluctuating water conditions on functional pathways in plant litter microbial community. Sci Rep 2023; 13:21741. [PMID: 38066117 PMCID: PMC10709317 DOI: 10.1038/s41598-023-49044-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 12/04/2023] [Indexed: 12/18/2023] Open
Abstract
Climate change modifies environmental conditions, resulting in altered precipitation patterns, moisture availability and nutrient distribution for microbial communities. Changes in water availability are projected to affect a range of ecological processes, including the decomposition of plant litter and carbon cycling. However, a detailed understanding of microbial stress response to drought/flooding is missing. In this study, an intermittent lake is taken up as a model for changes in water availability and how they affect the functional pathways in microbial communities of the decomposing Phragmites australis litter. The results show that most enriched functions in both habitats belonged to the classes of Carbohydrates and Clustering-based subsystems (terms with unknown function) from SEED subsystems classification. We confirmed that changes in water availability resulted in altered functional makeup of microbial communities. Our results indicate that microbial communities under more frequent water stress (due to fluctuating conditions) could sustain an additional metabolic cost due to the production or uptake of compatible solutes to maintain cellular osmotic balance. Nevertheless, although prolonged submergence seemed to have a negative impact on several functional traits in the fungal community, the decomposition rate was not affected.
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Affiliation(s)
- Matevž Likar
- Biotechnical Faculty, Department of Biology, University of Ljubljana, Večna Pot 111, 1000, Ljubljana, Slovenia.
| | - Mateja Grašič
- Biotechnical Faculty, Department of Biology, University of Ljubljana, Večna Pot 111, 1000, Ljubljana, Slovenia
| | - Blaž Stres
- Institute of Sanitary Engineering, Faculty of Civil and Geodetic Engineering, University of Ljubljana, Ljubljana, Slovenia
- Biocybernetics and Robotics, Department of Automation, Jožef Stefan Institute, Ljubljana, Slovenia
- Department of Catalysis and Chemical Reaction Engineering, National Institute of Chemistry, Ljubljana, Slovenia
| | - Marjana Regvar
- Biotechnical Faculty, Department of Biology, University of Ljubljana, Večna Pot 111, 1000, Ljubljana, Slovenia
| | - Alenka Gaberščik
- Biotechnical Faculty, Department of Biology, University of Ljubljana, Večna Pot 111, 1000, Ljubljana, Slovenia
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12
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Rogowska-van der Molen MA, Berasategui-Lopez A, Coolen S, Jansen RS, Welte CU. Microbial degradation of plant toxins. Environ Microbiol 2023; 25:2988-3010. [PMID: 37718389 DOI: 10.1111/1462-2920.16507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 09/05/2023] [Indexed: 09/19/2023]
Abstract
Plants produce a variety of secondary metabolites in response to biotic and abiotic stresses. Although they have many functions, a subclass of toxic secondary metabolites mainly serve plants as deterring agents against herbivores, insects, or pathogens. Microorganisms present in divergent ecological niches, such as soil, water, or insect and rumen gut systems have been found capable of detoxifying these metabolites. As a result of detoxification, microbes gain growth nutrients and benefit their herbivory host via detoxifying symbiosis. Here, we review current knowledge on microbial degradation of toxic alkaloids, glucosinolates, terpenes, and polyphenols with an emphasis on the genes and enzymes involved in breakdown pathways. We highlight that the insect-associated microbes might find application in biotechnology and become targets for an alternative microbial pest control strategy.
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Affiliation(s)
- Magda A Rogowska-van der Molen
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| | - Aileen Berasategui-Lopez
- Department of Microbiology and Biotechnology, University of Tübingen, Tübingen, Baden-Württemberg, Germany
- Amsterdam Institute for Life and Environment, Section Ecology and Evolution, Vrije Universiteit, Amsterdam, The Netherlands
| | - Silvia Coolen
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| | - Robert S Jansen
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| | - Cornelia U Welte
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
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13
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Ofiti NOE, Schmidt MWI, Abiven S, Hanson PJ, Iversen CM, Wilson RM, Kostka JE, Wiesenberg GLB, Malhotra A. Climate warming and elevated CO 2 alter peatland soil carbon sources and stability. Nat Commun 2023; 14:7533. [PMID: 37985767 PMCID: PMC10662476 DOI: 10.1038/s41467-023-43410-z] [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: 07/05/2023] [Accepted: 11/09/2023] [Indexed: 11/22/2023] Open
Abstract
Peatlands are an important carbon (C) reservoir storing one-third of global soil organic carbon (SOC), but little is known about the fate of these C stocks under climate change. Here, we examine the impact of warming and elevated atmospheric CO2 concentration (eCO2) on the molecular composition of SOC to infer SOC sources (microbe-, plant- and fire-derived) and stability in a boreal peatland. We show that while warming alone decreased plant- and microbe-derived SOC due to enhanced decomposition, warming combined with eCO2 increased plant-derived SOC compounds. We further observed increasing root-derived inputs (suberin) and declining leaf/needle-derived inputs (cutin) into SOC under warming and eCO2. The decline in SOC compounds with warming and gains from new root-derived C under eCO2, suggest that warming and eCO2 may shift peatland C budget towards pools with faster turnover. Together, our results indicate that climate change may increase inputs and enhance decomposition of SOC potentially destabilising C storage in peatlands.
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Affiliation(s)
- Nicholas O E Ofiti
- Department of Geography, University of Zurich, Zurich, Switzerland.
- CEREEP-Ecotron Ile De France, ENS, CNRS, PSL Research University, Saint-Pierre-lès-Nemours, France.
| | | | - Samuel Abiven
- CEREEP-Ecotron Ile De France, ENS, CNRS, PSL Research University, Saint-Pierre-lès-Nemours, France
- Laboratoire de Géologie, Département de Géosciences, Ecole normale supérieure (ENS), Paris, France
| | - Paul J Hanson
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Colleen M Iversen
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Rachel M Wilson
- Department of Earth, Ocean and Atmospheric Sciences, Florida State University, Tallahassee, FL, USA
| | - Joel E Kostka
- School of Biological Sciences and School of Earth and Atmospheric Sciences, Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
| | | | - Avni Malhotra
- Department of Geography, University of Zurich, Zurich, Switzerland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
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14
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Cui M, Wei Y, Tan J, Li T, Jiao X, Zhou Y. Biochemical investigations of polyphenol degradation enzymes in the phototrophic bacterium Rubrivivax gelatinosus. Biochem J 2023; 480:1753-1766. [PMID: 37903000 DOI: 10.1042/bcj20230387] [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: 09/13/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 11/01/2023]
Abstract
Phloroglucinol (1,3,5-trihydroxybenzene) is an important intermediate in the degradation of flavonoids and tannins by anaerobic bacteria. Recent studies have shed light on the enzymatic mechanism of phloroglucinol degradation in butyrate-forming anaerobic bacteria, including environmental and intestinal bacteria such as Clostridium and Flavonifractor sp. Phloroglucinol degradation gene clusters have also been identified in other metabolically diverse bacteria, although the polyphenol metabolism of these microorganisms remain largely unexplored. Here, we describe biochemical studies of polyphenol degradation enzymes found in the purple non-sulfur bacterium Rubrivivax gelatinosus IL144, an anaerobic photoheterotroph reported to utilize diverse organic compounds as carbon sources for growth. In addition to the phloroglucinol reductase and dihydrophloroglucinol cyclohydrolase that catalyze phloroglucinol degradation, we characterize a Mn2+-dependent phloretin hydrolase that catalyzes the cleavage of phloretin into phloroglucinol and phloretic acid. We also report a Mn2+-dependent decarboxylase (DeC) that catalyzes the reversible decarboxylation of 2,4,6-trihydroxybenzoate to form phloroglucinol. A bioinformatics search led to the identification of DeC homologs in diverse soil and gut bacteria, and biochemical studies of a DeC homolog from the human gut bacterium Flavonifractor plautii demonstrated that it is also a 2,4,6-trihydroxybenzoate decarboxylase. Our study expands the range of enzymatic mechanisms for phloroglucinol formation, and provides further biochemical insight into polyphenol metabolism in the anaerobic biosphere.
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Affiliation(s)
- Mengyu Cui
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, Jiangsu Province, China
| | - Yifeng Wei
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A*STAR), Singapore 138669, Singapore
| | - Jason Tan
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A*STAR), Singapore 138669, Singapore
| | - Tong Li
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, Jiangsu Province, China
| | - Xinan Jiao
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, Jiangsu Province, China
| | - Yan Zhou
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, Jiangsu Province, China
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15
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Borton MA, Shaffer M, Hoyt DW, Jiang R, Ellenbogen JB, Purvine S, Nicora CD, Eder EK, Wong AR, Smulian AG, Lipton MS, Krzycki JA, Wrighton KC. Targeted curation of the gut microbial gene content modulating human cardiovascular disease. mBio 2023; 14:e0151123. [PMID: 37695138 PMCID: PMC10653893 DOI: 10.1128/mbio.01511-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 07/17/2023] [Indexed: 09/12/2023] Open
Abstract
IMPORTANCE One of the most-cited examples of the gut microbiome modulating human disease is the microbial metabolism of quaternary amines from protein-rich foods. By-products of this microbial processing promote atherosclerotic heart disease, a leading cause of human mortality globally. Our research addresses current knowledge gaps in our understanding of this microbial metabolism by holistically inventorying the microorganisms and expressed genes catalyzing critical atherosclerosis-promoting and -ameliorating reactions in the human gut. This led to the creation of an open-access resource, the Methylated Amine Gene Inventory of Catabolism database, the first systematic inventory of gut methylated amine metabolism. More importantly, using this resource we deliver here, we show for the first time that these gut microbial genes can predict human disease, paving the way for microbiota-inspired diagnostics and interventions.
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Affiliation(s)
- Mikayla A. Borton
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Michael Shaffer
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - David W. Hoyt
- Environmental and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Ruisheng Jiang
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | | | - Samuel Purvine
- Environmental and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Carrie D. Nicora
- Environmental and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Elizabeth K. Eder
- Environmental and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Allison R. Wong
- Environmental and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - A. George Smulian
- Department of Internal Medicine, University of Cincinnati, Cincinnati, Ohio, USA
| | - Mary S. Lipton
- Environmental and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Joseph A. Krzycki
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Kelly C. Wrighton
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA
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16
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Panis F, Rompel A. Biochemical Investigations of Five Recombinantly Expressed Tyrosinases Reveal Two Novel Mechanisms Impacting Carbon Storage in Wetland Ecosystems. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:13863-13873. [PMID: 37656057 PMCID: PMC10515480 DOI: 10.1021/acs.est.3c02910] [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: 04/18/2023] [Revised: 07/23/2023] [Accepted: 07/24/2023] [Indexed: 09/02/2023]
Abstract
Wetlands are globally distributed ecosystems characterized by predominantly anoxic soils, resulting from water-logging. Over the past millennia, low decomposition rates of organic matter led to the accumulation of 20-30% of the world's soil carbon pool in wetlands. Phenolic compounds are critically involved in stabilizing wetland carbon stores as they act as broad-scale inhibitors of hydrolytic enzymes. Tyrosinases are oxidoreductases capable of removing phenolic compounds in the presence of O2 by oxidizing them to the corresponding o-quinones. Herein, kinetic investigations (kcat and Km values) reveal that low-molecular-weight phenolic compounds naturally present within wetland ecosystems (including monophenols, diphenols, triphenols, and flavonoids) are accepted by five recombinantly expressed wetland tyrosinases (TYRs) as substrates. Investigations of the interactions between TYRs and wetland phenolics reveal two novel mechanisms that describe the global impact of TYRs on the wetland carbon cycle. First, it is shown that o-quinones (produced by TYRs from low-molecular-weight phenolic substrates) are capable of directly inactivating hydrolytic enzymes. Second, it is reported that o-quinones can interact with high-molecular-weight phenolic polymers (which inhibit hydrolytic enzymes) and remove them through precipitation. The balance between these two mechanisms will profoundly affect the fate of wetland carbon stocks, particularly in the wake of climate change.
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Affiliation(s)
- Felix Panis
- Universität
Wien, Fakultät für Chemie, Institut für Biophysikalische
Chemie, Josef-Holaubek-Platz
2, 1090 Wien, Austria, https://www.bpc.univie.ac.at/en/
| | - Annette Rompel
- Universität
Wien, Fakultät für Chemie, Institut für Biophysikalische
Chemie, Josef-Holaubek-Platz
2, 1090 Wien, Austria, https://www.bpc.univie.ac.at/en/
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17
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Zhou Y, Wei Y, Jiang L, Jiao X, Zhang Y. Anaerobic phloroglucinol degradation by Clostridium scatologenes. mBio 2023; 14:e0109923. [PMID: 37341492 PMCID: PMC10470551 DOI: 10.1128/mbio.01099-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 05/05/2023] [Indexed: 06/22/2023] Open
Abstract
Polyphenols are abundant in nature, and their anaerobic biodegradation by gut and soil bacteria is a topic of great interest. The O2 requirement of phenol oxidases is thought to explain the microbial inertness of phenolic compounds in anoxic environments, such as peatlands, termed the enzyme latch hypothesis. A caveat of this model is that certain phenols are known to be degraded by strict anaerobic bacteria, although the biochemical basis for this process is incompletely understood. Here, we report the discovery and characterization of a gene cluster in the environmental bacterium Clostridium scatologenes for the degradation phloroglucinol (1,3,5-trihydroxybenzene), a key intermediate in the anaerobic degradation of flavonoids and tannins, which constitute the most abundant polyphenols in nature. The gene cluster encodes the key C-C cleavage enzyme dihydrophloroglucinol cyclohydrolase, as well as (S)-3-hydroxy-5-oxo-hexanoate dehydrogenase and triacetate acetoacetate-lyase, which enable phloroglucinol to be utilized as a carbon and energy source. Bioinformatics studies revealed the presence of this gene cluster in phylogenetically and metabolically diverse gut and environmental bacteria, with potential impacts on human health and carbon preservation in peat soils and other anaerobic environmental niches. IMPORTANCE This study provides novel insights into the microbiota's anaerobic metabolism of phloroglucinol, a critical intermediate in the degradation of polyphenols in plants. Elucidation of this anaerobic pathway reveals enzymatic mechanisms for the degradation of phloroglucinol into short-chain fatty acids and acetyl-CoA, which are used as a carbon and energy source for bacterium growth. Bioinformatics studies suggested the prevalence of this pathway in phylogenetically and metabolically diverse gut and environmental bacteria, with potential impacts on carbon preservation in peat soils and human gut health.
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Affiliation(s)
- Yan Zhou
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu Province, China
| | - Yifeng Wei
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Li Jiang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Xinan Jiao
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu Province, China
| | - Yan Zhang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
- Department of Chemistry, Tianjin University, Tianjin, China
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18
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Leleiwi I, Rodriguez-Ramos J, Shaffer M, Sabag-Daigle A, Kokkinias K, Flynn RM, Daly RA, Kop LFM, Solden LM, Ahmer BMM, Borton MA, Wrighton KC. Exposing new taxonomic variation with inflammation - a murine model-specific genome database for gut microbiome researchers. MICROBIOME 2023; 11:114. [PMID: 37210515 PMCID: PMC10199544 DOI: 10.1186/s40168-023-01529-7] [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: 11/04/2022] [Accepted: 03/21/2023] [Indexed: 05/22/2023]
Abstract
BACKGROUND The murine CBA/J mouse model widely supports immunology and enteric pathogen research. This model has illuminated Salmonella interactions with the gut microbiome since pathogen proliferation does not require disruptive pretreatment of the native microbiota, nor does it become systemic, thereby representing an analog to gastroenteritis disease progression in humans. Despite the value to broad research communities, microbiota in CBA/J mice are not represented in current murine microbiome genome catalogs. RESULTS Here we present the first microbial and viral genomic catalog of the CBA/J murine gut microbiome. Using fecal microbial communities from untreated and Salmonella-infected, highly inflamed mice, we performed genomic reconstruction to determine the impacts on gut microbiome membership and functional potential. From high depth whole community sequencing (~ 42.4 Gbps/sample), we reconstructed 2281 bacterial and 4516 viral draft genomes. Salmonella challenge significantly altered gut membership in CBA/J mice, revealing 30 genera and 98 species that were conditionally rare and unsampled in non-inflamed mice. Additionally, inflamed communities were depleted in microbial genes that modulate host anti-inflammatory pathways and enriched in genes for respiratory energy generation. Our findings suggest decreases in butyrate concentrations during Salmonella infection corresponded to reductions in the relative abundance in members of the Alistipes. Strain-level comparison of CBA/J microbial genomes to prominent murine gut microbiome databases identified newly sampled lineages in this resource, while comparisons to human gut microbiomes extended the host relevance of dominant CBA/J inflammation-resistant strains. CONCLUSIONS This CBA/J microbiome database provides the first genomic sampling of relevant, uncultivated microorganisms within the gut from this widely used laboratory model. Using this resource, we curated a functional, strain-resolved view on how Salmonella remodels intact murine gut communities, advancing pathobiome understanding beyond inferences from prior amplicon-based approaches. Salmonella-induced inflammation suppressed Alistipes and other dominant members, while rarer commensals like Lactobacillus and Enterococcus endure. The rare and novel species sampled across this inflammation gradient advance the utility of this microbiome resource to benefit the broad research needs of the CBA/J scientific community, and those using murine models for understanding the impact of inflammation on the gut microbiome more generally. Video Abstract.
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Affiliation(s)
- Ikaia Leleiwi
- Department of Cell and Molecular Biology, The Colorado State University, Fort Collins, CO USA
- Department of Soil and Crop Sciences, The Colorado State University, Fort Collins, CO USA
| | - Josué Rodriguez-Ramos
- Department of Soil and Crop Sciences, The Colorado State University, Fort Collins, CO USA
- Graduate Degree Program in Ecology, The Colorado State University, Fort Collins, CO USA
| | - Michael Shaffer
- Department of Soil and Crop Sciences, The Colorado State University, Fort Collins, CO USA
| | - Anice Sabag-Daigle
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH USA
| | - Katherine Kokkinias
- Department of Soil and Crop Sciences, The Colorado State University, Fort Collins, CO USA
- Department of Microbiology, Immunology, and Pathology, The Colorado State University, Fort Collins, CO USA
| | - Rory M. Flynn
- Department of Soil and Crop Sciences, The Colorado State University, Fort Collins, CO USA
| | - Rebecca A. Daly
- Department of Soil and Crop Sciences, The Colorado State University, Fort Collins, CO USA
| | - Linnea F. M. Kop
- Department of Microbiology, RIBES, Radbound University, Nijmegen, The Netherlands
- Department of Microbiology and Biophysics, The Ohio State University, Columbus, OH USA
| | - Lindsey M. Solden
- Department of Soil and Crop Sciences, The Colorado State University, Fort Collins, CO USA
| | - Brian M. M. Ahmer
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH USA
| | - Mikayla A. Borton
- Department of Soil and Crop Sciences, The Colorado State University, Fort Collins, CO USA
| | - Kelly C. Wrighton
- Department of Cell and Molecular Biology, The Colorado State University, Fort Collins, CO USA
- Department of Soil and Crop Sciences, The Colorado State University, Fort Collins, CO USA
- Graduate Degree Program in Ecology, The Colorado State University, Fort Collins, CO USA
- Department of Microbiology, Immunology, and Pathology, The Colorado State University, Fort Collins, CO USA
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19
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Chu N, Jiang Y, Liang Q, Liu P, Wang D, Chen X, Li D, Liang P, Zeng RJ, Zhang Y. Electricity-Driven Microbial Metabolism of Carbon and Nitrogen: A Waste-to-Resource Solution. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:4379-4395. [PMID: 36877891 DOI: 10.1021/acs.est.2c07588] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Electricity-driven microbial metabolism relies on the extracellular electron transfer (EET) process between microbes and electrodes and provides promise for resource recovery from wastewater and industrial discharges. Over the past decades, tremendous efforts have been dedicated to designing electrocatalysts and microbes, as well as hybrid systems to push this approach toward industrial adoption. This paper summarizes these advances in order to facilitate a better understanding of electricity-driven microbial metabolism as a sustainable waste-to-resource solution. Quantitative comparisons of microbial electrosynthesis and abiotic electrosynthesis are made, and the strategy of electrocatalyst-assisted microbial electrosynthesis is critically discussed. Nitrogen recovery processes including microbial electrochemical N2 fixation, electrocatalytic N2 reduction, dissimilatory nitrate reduction to ammonium (DNRA), and abiotic electrochemical nitrate reduction to ammonia (Abio-NRA) are systematically reviewed. Furthermore, the synchronous metabolism of carbon and nitrogen using hybrid inorganic-biological systems is discussed, including advanced physicochemical, microbial, and electrochemical characterizations involved in this field. Finally, perspectives for future trends are presented. The paper provides valuable insights on the potential contribution of electricity-driven microbial valorization of waste carbon and nitrogen toward a green and sustainable society.
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Affiliation(s)
- Na Chu
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yong Jiang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Qinjun Liang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Panpan Liu
- School of Ecology and Environment, Zhengzhou University, Zhengzhou 450001, China
| | - Donglin Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Xueming Chen
- Fujian Provincial Engineering Research Center of Rural Waste Recycling Technology, College of Environment and Safety Engineering, Fuzhou University, Fuzhou 350116, China
| | - Daping Li
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Peng Liang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Raymond Jianxiong Zeng
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yifeng Zhang
- Department of Environmental Engineering, Technical University of Denmark, DK-2800 Lyngby, Denmark
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20
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Li G, Sun L, Wang J, Dou X, Ji S, Hu T, Gao C. Effects of pyrogenic carbon addition after fire on soil carbon mineralization in the Great Khingan Mountains peatlands (Northeast China). THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 864:161102. [PMID: 36566854 DOI: 10.1016/j.scitotenv.2022.161102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 12/16/2022] [Accepted: 12/17/2022] [Indexed: 06/17/2023]
Abstract
Wildfires play a critical role in regulating soil carbon (C) budgets in peatland ecosystems, and their frequency and intensity are increasing owing to climate change and human activities. Wildfires not only emit CO2 during the combustion process but also produce pyrogenic carbon (PyC), which accumulates in the soil C pool and influences soil C decomposition. However, the role of PyC after a fire in peatland soil C mineralization has rarely been examined. This study investigated the effects of PyC addition on peatland soil C mineralization and its potential driving mechanisms using an anaerobic/aerobic incubation experiment with peat soils collected from typical peatlands in the Great Khingan Mountains, Northeast China. The effect of PyC was more pronounced under aerobic conditions than under anaerobic conditions. The mean C- mineralization rates of soil were significantly increased by 45.2 ± 15.5 % and 87.6 ± 14.3 % with 10 % PyC250°C addition after the initial stage (D7) of aerobic and anaerobic incubation, but PyC600°C addition caused a to decrease. Compared with PyC600°C, PyC250°C addition significantly increased the available N content and altered the soil microbial activities, which may be the primary reason for the increase in C mineralization rates. Furthermore, adding a high concentration of PyC (10 %) reduced the concentration of phenolics but increased phenol oxidase activity, which promoted C mineralization rates. Thus, PyC250°C addition to peat soils mainly influences the microbial biomass C content through the accumulation of available N and phenolics, which ultimately positively affects C mineralization rates.
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Affiliation(s)
- Guangxin Li
- Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, College of Forestry, Northeast Forestry University, Hexing Road 26, Harbin 150040, China; Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Shengbei Street 4888, 130102 Changchun, China
| | - Long Sun
- Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, College of Forestry, Northeast Forestry University, Hexing Road 26, Harbin 150040, China
| | - Jianyu Wang
- Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, College of Forestry, Northeast Forestry University, Hexing Road 26, Harbin 150040, China
| | - Xu Dou
- Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, College of Forestry, Northeast Forestry University, Hexing Road 26, Harbin 150040, China
| | - Shengzhen Ji
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Shengbei Street 4888, 130102 Changchun, China
| | - Tongxin Hu
- Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, College of Forestry, Northeast Forestry University, Hexing Road 26, Harbin 150040, China.
| | - Chuanyu Gao
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Shengbei Street 4888, 130102 Changchun, China.
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21
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Yu K, Song Y, Lin J, Dixon RA. The complexities of proanthocyanidin biosynthesis and its regulation in plants. PLANT COMMUNICATIONS 2023; 4:100498. [PMID: 36435967 PMCID: PMC10030370 DOI: 10.1016/j.xplc.2022.100498] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/07/2022] [Accepted: 11/23/2022] [Indexed: 05/04/2023]
Abstract
Proanthocyanidins (PAs) are natural flavan-3-ol polymers that contribute protection to plants under biotic and abiotic stress, benefits to human health, and bitterness and astringency to food products. They are also potential targets for carbon sequestration for climate mitigation. In recent years, from model species to commercial crops, research has moved closer to elucidating the flux control and channeling, subunit biosynthesis and polymerization, transport mechanisms, and regulatory networks involved in plant PA metabolism. This review extends the conventional understanding with recent findings that provide new insights to address lingering questions and focus strategies for manipulating PA traits in plants.
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Affiliation(s)
- Keji Yu
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing 100083, China; College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
| | - Yushuang Song
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing 100083, China; College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Jinxing Lin
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing 100083, China; College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China.
| | - Richard A Dixon
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA; Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China.
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22
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Tabaglio V, Fiorini A, Sterling TM, Schulz M. Abutilon theophrasti's Resilience against Allelochemical-Based Weed Management in Sustainable Agriculture - Due to Collection of Highly Advantageous Microorganisms? PLANTS (BASEL, SWITZERLAND) 2023; 12:700. [PMID: 36840048 PMCID: PMC9961861 DOI: 10.3390/plants12040700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
Abutilon theophrasti Medik. (velvetleaf) is a problematic annual weed in field crops which has invaded many temperate parts of the world. Since the loss of crop yields can be extensive, approaches to manage the weed include not only conventional methods, but also biological methods, for instance by microorganisms releasing phytotoxins and plant-derived allelochemicals. Additionally, benzoxazinoid-rich rye mulches effective in managing common weeds like Amaranthus retroflexus L. have been tested for this purpose. However, recent methods for biological control are still unreliable in terms of intensity and duration. Rye mulches were also ineffective in managing velvetleaf. In this review, we present the attempts to reduce velvetleaf infestation by biological methods and discuss possible reasons for the failure. The resilience of velvetleaf may be due to the extraordinary capacity of the plant to collect, for its own survival, the most suitable microorganisms from a given farming site, genetic and epigenetic adaptations, and a high stress memory. Such properties may have developed together with other advantageous abilities during selection by humans when the plant was used as a crop. Rewilding could be responsible for improving the microbiomes of A. theophrasti.
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Affiliation(s)
- Vincenzo Tabaglio
- Department of Sustainable Crop Production DI.PRO.VE.S., Section Agronomy and Plant Biotechnologies, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy
| | - Andrea Fiorini
- Department of Sustainable Crop Production DI.PRO.VE.S., Section Agronomy and Plant Biotechnologies, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy
| | - Tracy M. Sterling
- Department of Land Resources & Environmental Sciences, Montana State University, Bozeman, MT 59717, USA
| | - Margot Schulz
- IMBIO Institute of Molecular Physiology and Biotechnology of Plants, University of Bonn, Karlrobert-Kreiten Str. 13, 53115 Bonn, Germany
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Xu Y, You G, Yin J, Zhang M, Peng D, Xu J, Yang S, Hou J. Salt tolerance evolution facilitates antibiotic resistome in soil microbiota: Evidences from dissemination evaluation, hosts identification and co-occurrence exploration. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 317:120830. [PMID: 36481466 DOI: 10.1016/j.envpol.2022.120830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 11/26/2022] [Accepted: 12/04/2022] [Indexed: 06/17/2023]
Abstract
Salinity is considered as one of the vital factors affecting the profiles of antibiotic resistance genes (ARGs) in soils, whereby its roles in shaping the antibiotic resistome were still poorly understood. Here, metagenomic analysis was conducted to track the ARGs distributions and dissemination in soils during salt accumulation and desalinization processes. Neutral-salt accumulation for 45 and 90 days significantly increased the relative abundances of ARGs and mobile genetic elements (MGEs) carrying antibiotic resistance contigs (ARCs). The ARGs within antibiotic efflux and target protection families primarily carried by Streptomyces, Nocardioides, Rhodanobacter and Monashia were largely enriched by salinity. The ARGs subtypes of the resistance-nodulation-division (RND) family, ATP-binding cassette (ABC) family, rRNA methyltransferase and other efflux were closely associated with MGEs, contributing to the enrichment of ARGs. Moreover, the ARGs subtypes and transposons were genetically linked with the salt-tolerance mechanisms of organic osmolyte transporters and K+ uptake proteins on the same ARC, demonstrating the coselection of ARGs and halotolerant genes. Furthermore, the antibiotic resistome could recover to a normal state after the prolonged incubation by alleviating salt stress. Nevertheless, the acquisition of ARGs by opportunistic pathogens after salt treatment was increased, serving to prioritize further efforts on the health risks correlated with resistance propagation and human exposure in saline soils.
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Affiliation(s)
- Yi Xu
- College of Agricultural Science and Engineering, Hohai University, Nanjing, People's Republic of China, 210098.
| | - Guoxiang You
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing, People's Republic of China, 210098
| | - Jinbao Yin
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing, People's Republic of China, 210098
| | - Mairan Zhang
- College of Agricultural Science and Engineering, Hohai University, Nanjing, People's Republic of China, 210098
| | - Dengyun Peng
- College of Agricultural Science and Engineering, Hohai University, Nanjing, People's Republic of China, 210098
| | - Junzeng Xu
- College of Agricultural Science and Engineering, Hohai University, Nanjing, People's Republic of China, 210098; State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing 210098, PR China
| | - Shihong Yang
- College of Agricultural Science and Engineering, Hohai University, Nanjing, People's Republic of China, 210098; State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing 210098, PR China.
| | - Jun Hou
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing, People's Republic of China, 210098
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Zhang C, Li M, Sun J, Zhang S, Huang J. The mechanism of C-N-S interconnection degradation in organic-rich sediments by Ca(NO 3) 2 - CaO 2 synergistic remediation. ENVIRONMENTAL RESEARCH 2022; 214:113992. [PMID: 35921905 DOI: 10.1016/j.envres.2022.113992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 07/17/2022] [Accepted: 07/25/2022] [Indexed: 06/15/2023]
Abstract
The rebound of black-odorous occurred in organic-rich sediments has become a critical issue due to its great harm to the ecological environment. Elements such as S, C, and N play a crucial role in the biogeochemical cycle of black-odorous rivers. As electronic acceptors, Ca(NO3)2 and CaO2 can effectively remove acidified volatile sulfide (AVS) and organic matter to control the black-odorous rebound. However, the remediation mechanisms in organic-rich sediments by Ca(NO3)2 and CaO2 are unclear. The present study explored the mechanism of C-N-S interconnection degradation in organic-rich urban river sediments by adding different ratios and sequences of Ca(NO3)2 and CaO2. The results showed that Ca(NO3)2 remediation followed by CaO2 and the accepted electron ratio 1:1 of Ca(NO3)2 to CaO2 is an effective method for controlling the rebound of black-odorous and reducing the accumulation NO2--N. Mainly attributed to that, CaO2 enhanced the degradation of organic matter by stimulating enzymatic activities in the sediments, which is also the main reason for controlling the rebound of black-odorous. Since CaO2 releases O2 and •OH, which inhibit nosZgenes, NO2--N accumulates when remedied simultaneously with Ca(NO3)2 and CaO2. Co-occurrence network analysis illustrated that sulfur-driven autotrophic denitrification bacteria, heterotrophic denitrifying bacteria, and sulfate-reducing bacteria interact strongly inside one module, clarifying a solid interaction of C-N-S substances among these bacteria. Our results reveal the C-N-S interconnection degradation mechanism and provide a new perspective on applying biochemical remediation in organic-rich urban river sediments.
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Affiliation(s)
- Chao Zhang
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300350, PR China.
| | - Meng Li
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300350, PR China; North China Municipal Engineering Design & Research Institute Co, LTD, Tianjin, 300074, China
| | - Jingmei Sun
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300350, PR China
| | - Shiwei Zhang
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300350, PR China
| | - Jianjun Huang
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300350, PR China.
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Genome-Resolved Metagenomics Informs the Functional Ecology of Uncultured Acidobacteria in Redox Oscillated Sphagnum Peat. mSystems 2022; 7:e0005522. [PMID: 36036503 PMCID: PMC9599518 DOI: 10.1128/msystems.00055-22] [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] [Indexed: 12/24/2022] Open
Abstract
Understanding microbial niche differentiation along ecological and geochemical gradients is critical for assessing the mechanisms of ecosystem response to hydrologic variation and other aspects of global change. The lineage-specific biogeochemical roles of the widespread phylum Acidobacteria in hydrologically sensitive ecosystems, such as peatlands, are poorly understood. Here, we demonstrate that Acidobacteria sublineages in Sphagnum peat respond differentially to redox fluctuations due to variable oxygen (O2) availability, a typical feature of hydrologic variation. Our genome-centric approach disentangles the mechanisms of niche differentiation between the Acidobacteria genera Holophaga and Terracidiphilus in response to the transient O2 exposure of peat in laboratory incubations. Interlineage functional diversification explains the enrichment of the otherwise rare Holophaga in anoxic peat after transient O2 exposure in comparison to Terracidiphilus dominance in continuously anoxic peat. The observed niche differentiation of the two lineages is linked to differences in their carbon degradation potential. Holophaga appear to be primarily reliant on carbohydrate oligomers and amino acids, produced during the prior period of O2 exposure via the O2-stimulated breakdown of peat carbon, rich in complex aromatics and carbohydrate polymers. In contrast, Terracidiphilus genomes are enriched in diverse respiratory hydrogenases and carbohydrate active enzymes, enabling the degradation of complex plant polysaccharides into monomers and oligomers for fermentation. We also present the first evidence for the potential contribution of Acidobacteria in peat nitrogen fixation. In addition to canonical molybdenum-based diazotrophy, the Acidobacteria genomes harbor vanadium and iron-only alternative nitrogenases. Together, the results better inform the different functional roles of Acidobacteria in peat biogeochemistry under global change. IMPORTANCE Acidobacteria are among the most widespread and abundant members of the soil bacterial community, yet their ecophysiology remains largely underexplored. In acidic peat systems, Acidobacteria are thought to perform key biogeochemical functions, yet the mechanistic links between the phylogenetic and metabolic diversity within this phylum and peat carbon transformations remain unclear. Here, we employ genomic comparisons of Acidobacteria subgroups enriched in laboratory incubations of peat under variable O2 availability to disentangle the lineage-specific functional roles of these microorganisms in peat carbon transformations. Our genome-centric approach reveals that the diversification of Acidobacteria subpopulations across transient O2 exposure is linked to differences in their carbon substrate preferences. We also identify a previously unknown functional potential for biological nitrogen fixation in these organisms. This has important implications for carbon, nitrogen, and trace metal cycling in peat systems.
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Panis F, Rompel A. The Novel Role of Tyrosinase Enzymes in the Storage of Globally Significant Amounts of Carbon in Wetland Ecosystems. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:11952-11968. [PMID: 35944157 PMCID: PMC9454253 DOI: 10.1021/acs.est.2c03770] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/01/2022] [Accepted: 07/05/2022] [Indexed: 05/30/2023]
Abstract
Over the last millennia, wetlands have been sequestering carbon from the atmosphere via photosynthesis at a higher rate than releasing it and, therefore, have globally accumulated 550 × 1015 g of carbon, which is equivalent to 73% of the atmospheric carbon pool. The accumulation of organic carbon in wetlands is effectuated by phenolic compounds, which suppress the degradation of soil organic matter by inhibiting the activity of organic-matter-degrading enzymes. The enzymatic removal of phenolic compounds by bacterial tyrosinases has historically been blocked by anoxic conditions in wetland soils, resulting from waterlogging. Bacterial tyrosinases are a subgroup of oxidoreductases that oxidatively remove phenolic compounds, coupled to the reduction of molecular oxygen to water. The biochemical properties of bacterial tyrosinases have been investigated thoroughly in vitro within recent decades, while investigations focused on carbon fluxes in wetlands on a macroscopic level have remained a thriving yet separated research area so far. In the wake of climate change, however, anoxic conditions in wetland soils are threatened by reduced rainfall and prolonged summer drought. This potentially allows tyrosinase enzymes to reduce the concentration of phenolic compounds, which in turn will increase the release of stored carbon back into the atmosphere. To offer compelling evidence for the novel concept that bacterial tyrosinases are among the key enzymes influencing carbon cycling in wetland ecosystems first, bacterial organisms indigenous to wetland ecosystems that harbor a TYR gene within their respective genome (tyr+) have been identified, which revealed a phylogenetically diverse community of tyr+ bacteria indigenous to wetlands based on genomic sequencing data. Bacterial TYR host organisms covering seven phyla (Acidobacteria, Actinobacteria, Bacteroidetes, Firmicutes, Nitrospirae, Planctomycetes, and Proteobacteria) have been identified within various wetland ecosystems (peatlands, marshes, mangrove forests, bogs, and alkaline soda lakes) which cover a climatic continuum ranging from high arctic to tropic ecosystems. Second, it is demonstrated that (in vitro) bacterial TYR activity is commonly observed at pH values characteristic for wetland ecosystems (ranging from pH 3.5 in peatlands and freshwater swamps to pH 9.0 in soda lakes and freshwater marshes) and toward phenolic compounds naturally present within wetland environments (p-coumaric acid, gallic acid, protocatechuic acid, p-hydroxybenzoic acid, caffeic acid, catechin, and epicatechin). Third, analyzing the available data confirmed that bacterial host organisms tend to exhibit in vitro growth optima at pH values similar to their respective wetland habitats. Based on these findings, it is concluded that, following increased aeration of previously anoxic wetland soils due to climate change, TYRs are among the enzymes capable of reducing the concentration of phenolic compounds present within wetland ecosystems, which will potentially destabilize vast amounts of carbon stored in these ecosystems. Finally, promising approaches to mitigate the detrimental effects of increased TYR activity in wetland ecosystems and the requirement of future investigations of the abundance and activity of TYRs in an environmental setting are presented.
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27
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Genome-Resolved Metaproteomics Decodes the Microbial and Viral Contributions to Coupled Carbon and Nitrogen Cycling in River Sediments. mSystems 2022; 7:e0051622. [PMID: 35861508 PMCID: PMC9426555 DOI: 10.1128/msystems.00516-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Rivers have a significant role in global carbon and nitrogen cycles, serving as a nexus for nutrient transport between terrestrial and marine ecosystems. Although rivers have a small global surface area, they contribute substantially to worldwide greenhouse gas emissions through microbially mediated processes within the river hyporheic zone. Despite this importance, research linking microbial and viral communities to specific biogeochemical reactions is still nascent in these sediment environments. To survey the metabolic potential and gene expression underpinning carbon and nitrogen biogeochemical cycling in river sediments, we collected an integrated data set of 33 metagenomes, metaproteomes, and paired metabolomes. We reconstructed over 500 microbial metagenome-assembled genomes (MAGs), which we dereplicated into 55 unique, nearly complete medium- and high-quality MAGs spanning 12 bacterial and archaeal phyla. We also reconstructed 2,482 viral genomic contigs, which were dereplicated into 111 viral MAGs (vMAGs) of >10 kb in size. As a result of integrating gene expression data with geochemical and metabolite data, we created a conceptual model that uncovered new roles for microorganisms in organic matter decomposition, carbon sequestration, nitrogen mineralization, nitrification, and denitrification. We show how these metabolic pathways, integrated through shared resource pools of ammonium, carbon dioxide, and inorganic nitrogen, could ultimately contribute to carbon dioxide and nitrous oxide fluxes from hyporheic sediments. Further, by linking viral MAGs to these active microbial hosts, we provide some of the first insights into viral modulation of river sediment carbon and nitrogen cycling. IMPORTANCE Here we created HUM-V (hyporheic uncultured microbial and viral), an annotated microbial and viral MAG catalog that captures strain and functional diversity encoded in these Columbia River sediment samples. Demonstrating its utility, this genomic inventory encompasses multiple representatives of dominant microbial and archaeal phyla reported in other river sediments and provides novel viral MAGs that can putatively infect these. Furthermore, we used HUM-V to recruit gene expression data to decipher the functional activities of these MAGs and reconstruct their active roles in Columbia River sediment biogeochemical cycling. Ultimately, we show the power of MAG-resolved multi-omics to uncover interactions and chemical handoffs in river sediments that shape an intertwined carbon and nitrogen metabolic network. The accessible microbial and viral MAGs in HUM-V will serve as a community resource to further advance more untargeted, activity-based measurements in these, and related, freshwater terrestrial-aquatic ecosystems.
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Pu Q, Zhang K, Poulain AJ, Liu J, Zhang R, Abdelhafiz MA, Meng B, Feng X. Mercury drives microbial community assembly and ecosystem multifunctionality across a Hg contamination gradient in rice paddies. JOURNAL OF HAZARDOUS MATERIALS 2022; 435:129055. [PMID: 35650726 DOI: 10.1016/j.jhazmat.2022.129055] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 06/15/2023]
Abstract
Soil microbial communities are critical for maintaining terrestrial ecosystems and fundamental ecological processes. Mercury (Hg) is a heavy metal that is toxic to microorganisms, but its effects on microbial community assembly and ecosystem multifunctionality in rice paddy ecosystems remain largely unknown. In the current study, we analyzed the microbial community structure and ecosystem multifunctionality of paddy soils across a Hg contamination gradient. The results demonstrated that Hg contamination significantly altered the microbial community structure. The microbial communities were predominantly driven by deterministic selection rather than stochastic processes. The random forest model and variation partition analysis demonstrated that the Hg level was the most important predictor of microbial profiles. Ecosystem multifunctionality decreased across the Hg concentration gradient, and multifunctionality was significantly correlated with soil biodiversity, suggesting that Hg-induced reductions in soil biodiversity led to reduced ecosystem services. A structural equation model showed that Hg contamination directly and indirectly affected ecosystem multifunctionality. The present work broadens our knowledge of the assembly of the microbiome in rice paddies across a Hg contamination gradient and highlights the significance of soil biodiversity in regulating ecosystem functions, especially in Hg-polluted rice paddies.
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Affiliation(s)
- Qiang Pu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China
| | - Kun Zhang
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Alexandre J Poulain
- Biology Department, University of Ottawa, 30 Marie Curie, Ottawa, ON K1N 6N5, Canada
| | - Jiang Liu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China
| | - Rui Zhang
- Biology Department, University of Ottawa, 30 Marie Curie, Ottawa, ON K1N 6N5, Canada
| | - Mahmoud A Abdelhafiz
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China; University of Chinese Academy of Sciences, Beijing 100049, China; Geology Department, Faculty of Science, Al-Azhar University, Assiut 71524, Egypt
| | - Bo Meng
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China.
| | - Xinbin Feng
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China; Center for Excellence in Quaternary Science and Global Change, Chinese Academy of Sciences, Xi'an 710061, China
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29
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Kulshrestha S, Jibran R, van Klink JW, Zhou Y, Brummell DA, Albert NW, Schwinn KE, Chagné D, Landi M, Bowman JL, Davies KM. Stress, senescence, and specialized metabolites in bryophytes. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4396-4411. [PMID: 35259256 PMCID: PMC9291361 DOI: 10.1093/jxb/erac085] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 03/07/2022] [Indexed: 05/04/2023]
Abstract
Life on land exposes plants to varied abiotic and biotic environmental stresses. These environmental drivers contributed to a large expansion of metabolic capabilities during land plant evolution and species diversification. In this review we summarize knowledge on how the specialized metabolite pathways of bryophytes may contribute to stress tolerance capabilities. Bryophytes are the non-tracheophyte land plant group (comprising the hornworts, liverworts, and mosses) and rapidly diversified following the colonization of land. Mosses and liverworts have as wide a distribution as flowering plants with regard to available environments, able to grow in polar regions through to hot desert landscapes. Yet in contrast to flowering plants, for which the biosynthetic pathways, transcriptional regulation, and compound function of stress tolerance-related metabolite pathways have been extensively characterized, it is only recently that similar data have become available for bryophytes. The bryophyte data are compared with those available for angiosperms, including examining how the differing plant forms of bryophytes and angiosperms may influence specialized metabolite diversity and function. The involvement of stress-induced specialized metabolites in senescence and nutrient response pathways is also discussed.
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Affiliation(s)
- Samarth Kulshrestha
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand
| | - Rubina Jibran
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
| | - John W van Klink
- The New Zealand Institute for Plant and Food Research Limited, Department of Chemistry, Otago University, Dunedin, New Zealand
| | - Yanfei Zhou
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand
| | - David A Brummell
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand
| | - Nick W Albert
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand
| | - Kathy E Schwinn
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand
| | - David Chagné
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand
| | - Marco Landi
- Department of Agriculture, Food and Environment, University of Pisa, Italy
| | - John L Bowman
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia
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30
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Qi H, Wang J, Zhang L, Chen L, Zhao Y, Wei Z. Activation effect of catechol on biotic and abiotic factors of humus formation during chicken manure composting. WASTE MANAGEMENT (NEW YORK, N.Y.) 2022; 149:146-155. [PMID: 35728478 DOI: 10.1016/j.wasman.2022.06.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 06/11/2022] [Accepted: 06/13/2022] [Indexed: 06/15/2023]
Abstract
In this present study, catechol was added to promote humus formation in chicken manure composting using 12.5-L working volume lab-scale reactors. Chicken manure composting were carried out on two treatments, control (CK) and 0.5% (w/w) catechol treated group. Results showed that catechol addition reduced organic matter loss and improved the content of recalcitrant components. Humus and humic acid (HA) contents were, respectively, 69.2% and 82.3% higher in catechol treated-compost than in the control. With the addition of catechol, the bacterial community composition and richness was changed, e.g., the relative percentage of Bacillus and Sinibacillus were increased, which might contribute to humus and HA formation. Additionally, the activities of polyphenol oxidase and laccase (related to humus formation) were increased by the addition of catechol. Importantly, the catechol addition reduced the polyphenol content by 39.6% compared to control. Overall, the addition of catechol enhanced the biotic and abiotic factors to promote the humification process during composting, which might be a promising approach for accelerating the humification process and reducing contamination of phenolic compounds.
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Affiliation(s)
- Haishi Qi
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Jialin Wang
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Linyuan Zhang
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Lihua Chen
- Heilongjiang Province Intellectual Property Protection Center, Harbin 150030, China
| | - Yue Zhao
- College of Life Science, Northeast Agricultural University, Harbin 150030, China.
| | - Zimin Wei
- College of Life Science, Northeast Agricultural University, Harbin 150030, China.
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Metaproteomics reveals enzymatic strategies deployed by anaerobic microbiomes to maintain lignocellulose deconstruction at high solids. Nat Commun 2022; 13:3870. [PMID: 35790765 PMCID: PMC9256739 DOI: 10.1038/s41467-022-31433-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 06/16/2022] [Indexed: 11/08/2022] Open
Abstract
AbstractEconomically viable production of cellulosic biofuels requires operation at high solids loadings—on the order of 15 wt%. To this end we characterize Nature’s ability to deconstruct and utilize mid-season switchgrass at increasing solid loadings using an anaerobic methanogenic microbiome. This community exhibits undiminished fractional carbohydrate solubilization at loadings ranging from 30 g/L to 150 g/L. Metaproteomic interrogation reveals marked increases in the abundance of specific carbohydrate-active enzyme classes. Significant enrichment of auxiliary activity family 6 enzymes at higher solids suggests a role for Fenton chemistry. Stress-response proteins accompanying these reactions are similarly upregulated at higher solids, as are β-glucosidases, xylosidases, carbohydrate-debranching, and pectin-acting enzymes—all of which indicate that removal of deconstruction inhibitors is important for observed undiminished solubilization. Our work provides insights into the mechanisms by which natural microbiomes effectively deconstruct and utilize lignocellulose at high solids loadings, informing the future development of defined cultures for efficient bioconversion.
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Variation in Root Exudate Composition Influences Soil Microbiome Membership and Function. Appl Environ Microbiol 2022; 88:e0022622. [PMID: 35536051 DOI: 10.1128/aem.00226-22] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Root exudation is one of the primary processes that mediate interactions between plant roots, microorganisms, and the soil matrix, yet the mechanisms by which exudation alters microbial metabolism in soils have been challenging to unravel. Here, utilizing distinct sorghum genotypes, we characterized the chemical heterogeneity between root exudates and the effects of that variability on soil microbial membership and metabolism. Distinct exudate chemical profiles were quantified and used to formulate synthetic root exudate treatments: a high-organic-acid treatment (HOT) and a high-sugar treatment (HST). To parse the response of the soil microbiome to different exudate regimens, laboratory soil reactors were amended with these root exudate treatments as well as a nonexudate control. Amplicon sequencing of the 16S rRNA gene illustrated distinct microbial diversity patterns and membership in response to HST, HOT, or control amendments. Exometabolite changes reflected these microbial community changes, and we observed enrichment of organic and amino acids, as well as possible phytohormones in the HST relative to the HOT and control. Linking the metabolic capacity of metagenome-assembled genomes in the HST to the exometabolite patterns, we identified microorganisms that could produce these phytohormones. Our findings emphasize the tractability of high-resolution multiomics tools to investigate soil microbiomes, opening the possibility of manipulating native microbial communities to improve specific soil microbial functions and enhance crop production. IMPORTANCE Decrypting the chemical interactions between plant roots and the soil microbiome is a gateway for future manipulation and management of the rhizosphere, a soil compartment critical to promoting plant fitness and yields. Our experimental results demonstrate how soil microbial community and genomic diversity is influenced by root exudates of differing chemical compositions and how changes in this microbiome result in altered production of plant-relevant metabolites. Together, these findings demonstrate the tractability of high-resolution multiomics tools to investigate soil microbiomes and provide new information on plant-soil environments useful for the development of efficient and precise microbiota management strategies in agricultural systems.
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Omics-based ecosurveillance for the assessment of ecosystem function, health, and resilience. Emerg Top Life Sci 2022; 6:185-199. [PMID: 35403668 PMCID: PMC9023019 DOI: 10.1042/etls20210261] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/17/2022] [Accepted: 03/22/2022] [Indexed: 12/15/2022]
Abstract
Current environmental monitoring efforts often focus on known, regulated contaminants ignoring the potential effects of unmeasured compounds and/or environmental factors. These specific, targeted approaches lack broader environmental information and understanding, hindering effective environmental management and policy. Switching to comprehensive, untargeted monitoring of contaminants, organism health, and environmental factors, such as nutrients, temperature, and pH, would provide more effective monitoring with a likely concomitant increase in environmental health. However, even this method would not capture subtle biochemical changes in organisms induced by chronic toxicant exposure. Ecosurveillance is the systematic collection, analysis, and interpretation of ecosystem health-related data that can address this knowledge gap and provide much-needed additional lines of evidence to environmental monitoring programs. Its use would therefore be of great benefit to environmental management and assessment. Unfortunately, the science of ‘ecosurveillance’, especially omics-based ecosurveillance is not well known. Here, we give an overview of this emerging area and show how it has been beneficially applied in a range of systems. We anticipate this review to be a starting point for further efforts to improve environmental monitoring via the integration of comprehensive chemical assessments and molecular biology-based approaches. Bringing multiple levels of omics technology-based assessment together into a systems-wide ecosurveillance approach will bring a greater understanding of the environment, particularly the microbial communities upon which we ultimately rely to remediate perturbed ecosystems.
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Chen X, He X, Sun J, Wang Z. Phytochemical Composition, Antioxidant Activity, α-Glucosidase and Acetylcholinesterase Inhibitory Activity of Quinoa Extract and Its Fractions. Molecules 2022; 27:molecules27082420. [PMID: 35458616 PMCID: PMC9032577 DOI: 10.3390/molecules27082420] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/05/2022] [Accepted: 04/07/2022] [Indexed: 11/16/2022] Open
Abstract
This study is aimed to evaluate the chemical compositions and biological activities of quinoa, a novel and excellent food crop. Quinoa extract and its fractions were prepared by ethanol extraction and liquid-liquid extraction, including ethanol crude extract, and petroleum ether, chloroform, ethyl acetate (EAF), and n-butanol and water fractions. The total phenolic and flavonoid contents, antioxidant activities, α-glucosidase and acetylcholinesterase inhibitory abilities of the extract and fractions were further determined. Based on these foundations, the chemical composition of the EAF fraction exhibiting the strongest functional activity was analyzed by ultra-performance liquid chromatography-mass spectrometry. The results showed the EAF fraction had the highest phenolic and flavonoid contents, and the highest antioxidant activities, as well as the strongest α-glucosidase and acetylcholinesterase inhibitory abilities, which is even better than the positive control. The phytochemical composition of the EAF fraction indicated that 661 and 243 metabolites were identified in positive and negative ion modes, which were classified into superclass, class and subclass levels, respectively. Phenolic acids and flavonoids were the major bioactive compounds in the EAF fraction. This study found that quinoa, especially its ethyl acetate fraction, had the potential for the development of natural antioxidants, acetylcholinesterase inhibitors, and hypoglycemic agents.
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Affiliation(s)
- Xi Chen
- Agro-Food Science and Technology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (X.C.); (X.H.)
- College of Life Science, Southwest Forestry University, Kunming 650224, China
| | - Xuemei He
- Agro-Food Science and Technology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (X.C.); (X.H.)
- Guangxi Key Laboratory of Fruits and Vegetables Storage-Processing Technology, Nanning 530007, China
| | - Jian Sun
- Agro-Food Science and Technology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (X.C.); (X.H.)
- Guangxi Key Laboratory of Fruits and Vegetables Storage-Processing Technology, Nanning 530007, China
- Correspondence: (J.S.); (Z.W.)
| | - Zhenxing Wang
- College of Life Science, Southwest Forestry University, Kunming 650224, China
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China
- Correspondence: (J.S.); (Z.W.)
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Le CC, Bae M, Kiamehr S, Balskus EP. Emerging Chemical Diversity and Potential Applications of Enzymes in the DMSO Reductase Superfamily. Annu Rev Biochem 2022; 91:475-504. [PMID: 35320685 DOI: 10.1146/annurev-biochem-032620-110804] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Molybdenum- and tungsten-dependent proteins catalyze essential processes in living organisms and biogeochemical cycles. Among these enzymes, members of the dimethyl sulfoxide (DMSO) reductase superfamily are considered the most diverse, facilitating a wide range of chemical transformations that can be categorized as oxygen atom installation, removal, and transfer. Importantly, DMSO reductase enzymes provide high efficiency and excellent selectivity while operating under mild conditions without conventional oxidants such as oxygen or peroxides. Despite the potential utility of these enzymes as biocatalysts, such applications have not been fully explored. In addition, the vast majority of DMSO reductase enzymes still remain uncharacterized. In this review, we describe the reactivities, proposed mechanisms, and potential synthetic applications of selected enzymes in the DMSO reductase superfamily. We also highlight emerging opportunities to discover new chemical activity and current challenges in studying and engineering proteins in the DMSO reductase superfamily. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Chi Chip Le
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA;
| | - Minwoo Bae
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA;
| | - Sina Kiamehr
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA;
| | - Emily P Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA;
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Van Den Bossche T, Arntzen MØ, Becher D, Benndorf D, Eijsink VGH, Henry C, Jagtap PD, Jehmlich N, Juste C, Kunath BJ, Mesuere B, Muth T, Pope PB, Seifert J, Tanca A, Uzzau S, Wilmes P, Hettich RL, Armengaud J. The Metaproteomics Initiative: a coordinated approach for propelling the functional characterization of microbiomes. MICROBIOME 2021; 9:243. [PMID: 34930457 PMCID: PMC8690404 DOI: 10.1186/s40168-021-01176-w] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 10/10/2021] [Indexed: 05/04/2023]
Abstract
Through connecting genomic and metabolic information, metaproteomics is an essential approach for understanding how microbiomes function in space and time. The international metaproteomics community is delighted to announce the launch of the Metaproteomics Initiative (www.metaproteomics.org), the goal of which is to promote dissemination of metaproteomics fundamentals, advancements, and applications through collaborative networking in microbiome research. The Initiative aims to be the central information hub and open meeting place where newcomers and experts interact to communicate, standardize, and accelerate experimental and bioinformatic methodologies in this field. We invite the entire microbiome community to join and discuss potential synergies at the interfaces with other disciplines, and to collectively promote innovative approaches to gain deeper insights into microbiome functions and dynamics. Video Abstract.
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Affiliation(s)
- Tim Van Den Bossche
- VIB-UGent Center for Medical Biotechnology, VIB, 9000, Ghent, Belgium
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9000, Ghent, Belgium
| | - Magnus Ø Arntzen
- Faculty of Chemistry, Biotechnology and Food Science, NMBU-Norwegian University of Life Sciences, 1432, Ås, Norway
| | - Dörte Becher
- Institute for Microbiology, Department for Microbial Proteomics, University of Greifswald, 17498, Greifswald, Germany
| | - Dirk Benndorf
- Bioprocess Engineering, Otto von Guericke University, 39106, Magdeburg, Germany
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106, Magdeburg, Germany
- Microbiology, Anhalt University of Applied Sciences, 06354, Köthen, Germany
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, NMBU-Norwegian University of Life Sciences, 1432, Ås, Norway
| | - Céline Henry
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Pratik D Jagtap
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church Street SE, Minneapolis, MN, 55455, USA
| | - Nico Jehmlich
- Helmholtz-Centre for Environmental Research GmbH-UFZ, Department of Molecular Systems Biology, Permoserstrasse 15, 04318, Leipzig, Germany
| | - Catherine Juste
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Benoit J Kunath
- Luxembourg Centre for Systems Biomedicine and Department of Life Sciences and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Bart Mesuere
- VIB-UGent Center for Medical Biotechnology, VIB, 9000, Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Thilo Muth
- Section eScience (S.3), Federal Institute for Materials Research and Testing, Berlin, Germany
| | - Phillip B Pope
- Faculty of Chemistry, Biotechnology and Food Science, NMBU-Norwegian University of Life Sciences, 1432, Ås, Norway
- Faculty of Biosciences, NMBU - Norwegian University of Life Sciences, 1432, Ås, Norway
| | - Jana Seifert
- HoLMiR - Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Leonore-Blosser-Reisen-Weg 3, 70599, Stuttgart, Germany
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70599, Stuttgart, Germany
| | - Alessandro Tanca
- Center for Research and Education on the Microbiota, Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Sergio Uzzau
- Center for Research and Education on the Microbiota, Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine and Department of Life Sciences and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Robert L Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
| | - Jean Armengaud
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200, Bagnols-sur-Cèze, France
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Abstract
Dietary polyphenols can significantly benefit human health, but their bioavailability is metabolically controlled by human gut microbiota. To facilitate the study of polyphenol metabolism for human gut health, we have manually curated experimentally characterized polyphenol utilization proteins (PUPs) from published literature. This resulted in 60 experimentally characterized PUPs (named seeds) with various metadata, such as species and substrate. Further database search found 107,851 homologs of the seeds from UniProt and UHGP (Unified Human Gastrointestinal Protein) databases. All PUP seeds and homologs were classified into protein classes, families and subfamilies based on Enzyme Commission (EC) numbers, Pfam (protein family) domains and sequence similarity networks. By locating PUP homologs in the genomes of UHGP, we have identified 1,074 physically linked PUP gene clusters (PGCs), which are potentially involved in polyphenol metabolism in the human gut. The gut microbiome of Africans was consistently ranked the top in terms of the abundance and prevalence of PUP homologs and PGCs among all geographical continents. This reflects the fact that dietary polyphenols are more commonly consumed by African population than other populations such as Europeans and North Americans. A case study of the Hadza hunter-gatherer microbiome verified the feasibility of using dbPUP to profile metagenomic data for biologically meaningful discovery, suggesting an association between diet and PUP abundance. A Pfam domain enrichment analysis of PGCs identified a number of putatively novel PUP families. Lastly, a user-friendly web interface (https://bcb.unl.edu/dbpup/) provides all the data online to facilitate the research of polyphenol metabolism for improved human health. Importance Long-term consumption of polyphenol-rich foods have been shown to lower the risk of various human diseases such as cardiovascular diseases, cancers, and metabolic diseases. Raw polyphenols are often enzymatically processed by gut microbiome, which encode various polyphenol utilization proteins (PUPs) to produce metabolites with much higher bioaccessibility to gastrointestinal cells. This study delivered dbPUP as an online database for experimentally characterized PUPs and their homologs in human gut microbiome. This work also performed a systematic classification of PUPs into enzyme classes, families, and subfamilies. The signature Pfam domains were identified for PUP families, enabling conserved domain-based PUP annotation. This standardized sequence similarity-based PUP classification system offered a guideline for the future inclusion of new experimentally characterized PUPs and the creation of new PUP families. An in-depth data analysis was further conducted on PUP homologs and physically linked PUP gene clusters (PGCs) in gut microbiomes of different human populations.
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Wilmoth JL, Schaefer JK, Schlesinger DR, Roth SW, Hatcher PG, Shoemaker JK, Zhang X. The role of oxygen in stimulating methane production in wetlands. GLOBAL CHANGE BIOLOGY 2021; 27:5831-5847. [PMID: 34409684 PMCID: PMC9291790 DOI: 10.1111/gcb.15831] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 07/30/2021] [Indexed: 06/13/2023]
Abstract
Methane (CH4 ), a potent greenhouse gas, is the second most important greenhouse gas contributor to climate change after carbon dioxide (CO2 ). The biological emissions of CH4 from wetlands are a major uncertainty in CH4 budgets. Microbial methanogenesis by Archaea is an anaerobic process accounting for most biological CH4 production in nature, yet recent observations indicate that large emissions can originate from oxygenated or frequently oxygenated wetland soil layers. To determine how oxygen (O2 ) can stimulate CH4 emissions, we used incubations of Sphagnum peat to demonstrate that the temporary exposure of peat to O2 can increase CH4 yields up to 2000-fold during subsequent anoxic conditions relative to peat without O2 exposure. Geochemical (including ion cyclotron resonance mass spectrometry, X-ray absorbance spectroscopy) and microbiome (16S rDNA amplicons, metagenomics) analyses of peat showed that higher CH4 yields of redox-oscillated peat were due to functional shifts in the peat microbiome arising during redox oscillation that enhanced peat carbon (C) degradation. Novosphingobium species with O2 -dependent aromatic oxygenase genes increased greatly in relative abundance during the oxygenation period in redox-oscillated peat compared to anoxic controls. Acidobacteria species were particularly important for anaerobic processing of peat C, including in the production of methanogenic substrates H2 and CO2 . Higher CO2 production during the anoxic phase of redox-oscillated peat stimulated hydrogenotrophic CH4 production by Methanobacterium species. The persistence of reduced iron (Fe(II)) during prolonged oxygenation in redox-oscillated peat may further enhance C degradation through abiotic mechanisms (e.g., Fenton reactions). The results indicate that specific functional shifts in the peat microbiome underlie O2 enhancement of CH4 production in acidic, Sphagnum-rich wetland soils. They also imply that understanding microbial dynamics spanning temporal and spatial redox transitions in peatlands is critical for constraining CH4 budgets; predicting feedbacks between climate change, hydrologic variability, and wetland CH4 emissions; and guiding wetland C management strategies.
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Affiliation(s)
- Jared L. Wilmoth
- High Meadows Environmental InstitutePrinceton UniversityPrincetonNJUSA
| | - Jeffra K. Schaefer
- Department of Environmental SciencesRutgers UniversityNew BrunswickNJUSA
| | | | - Spencer W. Roth
- Department of Environmental SciencesRutgers UniversityNew BrunswickNJUSA
| | | | - Julie K. Shoemaker
- Department of Chemistry and BiochemistryOld Dominion UniversityNorfolkVAUSA
| | - Xinning Zhang
- High Meadows Environmental InstitutePrinceton UniversityPrincetonNJUSA
- Department of GeosciencesPrinceton UniversityPrincetonNJUSA
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