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Wang J, Appidi MR, Burdick LH, Abraham PE, Hettich RL, Pelletier DA, Doktycz MJ. Formation of a constructed microbial community in a nutrient-rich environment indicates bacterial interspecific competition. mSystems 2024; 9:e0000624. [PMID: 38470038 PMCID: PMC11019790 DOI: 10.1128/msystems.00006-24] [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: 01/10/2024] [Accepted: 02/14/2024] [Indexed: 03/13/2024] Open
Abstract
Understanding the organizational principles of microbial communities is essential for interpreting ecosystem stability. Previous studies have investigated the formation of bacterial communities under nutrient-poor conditions or obligate relationships to observe cooperative interactions among different species. How microorganisms form stabilized communities in nutrient-rich environments, without obligate metabolic interdependency for growth, is still not fully disclosed. In this study, three bacterial strains isolated from the Populus deltoides rhizosphere were co-cultured in complex medium, and their growth behavior was tracked. These strains co-exist in mixed culture over serial transfer for multiple growth-dilution cycles. Competition is proposed as an emergent interaction relationship among the three bacteria based on their significantly decreased growth levels. The effects of different initial inoculum ratios, up to three orders of magnitude, on community structure were investigated, and the final compositions of the mixed communities with various starting composition indicate that community structure is not dependent on the initial inoculum ratio. Furthermore, the competitive relationships within the community were not altered by different initial inoculum ratios. The community structure was simulated by generalized Lotka-Volterra and dynamic flux balance analysis to provide mechanistic predictions into emergence of community structure under a nutrient-rich environment. Metaproteomic analyses provide support for the metabolite exchanges predicted by computational modeling and for highly altered physiologies when microbes are grown in co-culture. These findings broaden our understanding of bacterial community dynamics and metabolic diversity in higher-order interactions and could be significant in the management of rhizospheric bacterial communities. IMPORTANCE Bacteria naturally co-exist in multispecies consortia, and the ability to engineer such systems can be useful in biotechnology. Despite this, few studies have been performed to understand how bacteria form a stable community and interact with each other under nutrient-rich conditions. In this study, we investigated the effects of initial inoculum ratios on bacterial community structure using a complex medium and found that the initial inoculum ratio has no significant impact on resultant community structure or on interaction patterns between community members. The microbial population profiles were simulated using computational tools in order to understand intermicrobial relationships and to identify potential metabolic exchanges that occur during stabilization of the bacterial community. Studying microbial community assembly processes is essential for understanding fundamental ecological principles in microbial ecosystems and can be critical in predicting microbial community structure and function.
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Affiliation(s)
- Jia Wang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Manasa R. Appidi
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, USA
| | - Leah H. Burdick
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Paul E. Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Robert L. Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Dale A. Pelletier
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Mitchel J. Doktycz
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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2
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Carnicero-Mayo Y, Sáenz de Miera LE, Ferrero MÁ, Navasa N, Casqueiro J. Modeling Dynamics of Human Gut Microbiota Derived from Gluten Metabolism: Obtention, Maintenance and Characterization of Complex Microbial Communities. Int J Mol Sci 2024; 25:4013. [PMID: 38612823 PMCID: PMC11012253 DOI: 10.3390/ijms25074013] [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: 02/28/2024] [Revised: 03/29/2024] [Accepted: 04/02/2024] [Indexed: 04/14/2024] Open
Abstract
Western diets are rich in gluten-containing products, which are frequently poorly digested. The human large intestine harbors microorganisms able to metabolize undigested gluten fragments that have escaped digestion by human enzymatic activities. The aim of this work was obtaining and culturing complex human gut microbial communities derived from gluten metabolism to model the dynamics of healthy human large intestine microbiota associated with different gluten forms. For this purpose, stool samples from six healthy volunteers were inoculated in media containing predigested gluten or predigested gluten plus non-digested gluten. Passages were carried out every 24 h for 15 days in the same medium and community composition along time was studied via V3-V4 16S rDNA sequencing. Diverse microbial communities were successfully obtained. Moreover, communities were shown to be maintained in culture with stable composition for 14 days. Under non-digested gluten presence, communities were enriched in members of Bacillota, such as Lachnospiraceae, Clostridiaceae, Streptococcaceae, Peptoniphilaceae, Selenomonadaceae or Erysipelotrichaceae, and members of Actinomycetota, such as Bifidobacteriaceae and Eggerthellaceae. Contrarily, communities exposed to digested gluten were enriched in Pseudomonadota. Hence, this study shows a method for culture and stable maintenance of gut communities derived from gluten metabolism. This method enables the analysis of microbial metabolism of gluten in the gut from a community perspective.
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Affiliation(s)
- Yaiza Carnicero-Mayo
- Área de Microbiología, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24007 León, Spain;
| | - Luis E. Sáenz de Miera
- Área de Genética, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24007 León, Spain;
| | - Miguel Ángel Ferrero
- Área de Bioquímica y Biología Molecular, Facultad de Veterinaria, Universidad de León, 24007 León, Spain; (M.Á.F.); (N.N.)
| | - Nicolás Navasa
- Área de Bioquímica y Biología Molecular, Facultad de Veterinaria, Universidad de León, 24007 León, Spain; (M.Á.F.); (N.N.)
| | - Javier Casqueiro
- Área de Microbiología, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24007 León, Spain;
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3
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Montoya-Giraldo M, Piper KR, Ikhimiukor OO, Park CJ, Caimi NA, Buecher DC, Valdez EW, Northup DE, Andam CP. Ecology shapes the genomic and biosynthetic diversification of Streptomyces bacteria from insectivorous bats. Microb Genom 2024; 10. [PMID: 38625724 DOI: 10.1099/mgen.0.001238] [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] [Indexed: 04/17/2024] Open
Abstract
Streptomyces are prolific producers of secondary metabolites from which many clinically useful compounds have been derived. They inhabit diverse habitats but have rarely been reported in vertebrates. Here, we aim to determine to what extent the ecological source (bat host species and cave sites) influence the genomic and biosynthetic diversity of Streptomyces bacteria. We analysed draft genomes of 132 Streptomyces isolates sampled from 11 species of insectivorous bats from six cave sites in Arizona and New Mexico, USA. We delineated 55 species based on the genome-wide average nucleotide identity and core genome phylogenetic tree. Streptomyces isolates that colonize the same bat species or inhabit the same site exhibit greater overall genomic similarity than they do with Streptomyces from other bat species or sites. However, when considering biosynthetic gene clusters (BGCs) alone, BGC distribution is not structured by the ecological or geographical source of the Streptomyces that carry them. Each genome carried between 19-65 BGCs (median=42.5) and varied even among members of the same Streptomyces species. Nine major classes of BGCs were detected in ten of the 11 bat species and in all sites: terpene, non-ribosomal peptide synthetase, polyketide synthase, siderophore, RiPP-like, butyrolactone, lanthipeptide, ectoine, melanin. Finally, Streptomyces genomes carry multiple hybrid BGCs consisting of signature domains from two to seven distinct BGC classes. Taken together, our results bring critical insights to understanding Streptomyces-bat ecology and BGC diversity that may contribute to bat health and in augmenting current efforts in natural product discovery, especially from underexplored or overlooked environments.
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Affiliation(s)
- Manuela Montoya-Giraldo
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, USA
| | - Kathryn R Piper
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, USA
| | - Odion O Ikhimiukor
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, USA
| | - Cooper J Park
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
| | - Nicole A Caimi
- Department of Biology, University of New Mexico, Albuquerque, New Mexico, USA
| | | | - Ernest W Valdez
- Department of Biology, University of New Mexico, Albuquerque, New Mexico, USA
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, USA
| | - Diana E Northup
- Department of Biology, University of New Mexico, Albuquerque, New Mexico, USA
| | - Cheryl P Andam
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, USA
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4
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Kumi M, Wang T, Ejeromedoghene O, Wang J, Li P, Huang W. Exploring the Potentials of Chitin and Chitosan-Based Bioinks for 3D-Printing of Flexible Electronics: The Future of Sustainable Bioelectronics. SMALL METHODS 2024:e2301341. [PMID: 38403854 DOI: 10.1002/smtd.202301341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Indexed: 02/27/2024]
Abstract
Chitin and chitosan-based bioink for 3D-printed flexible electronics have tremendous potential for innovation in healthcare, agriculture, the environment, and industry. This biomaterial is suitable for 3D printing because it is highly stretchable, super-flexible, affordable, ultrathin, and lightweight. Owing to its ease of use, on-demand manufacturing, accurate and regulated deposition, and versatility with flexible and soft functional materials, 3D printing has revolutionized free-form construction and end-user customization. This study examined the potential of employing chitin and chitosan-based bioinks to build 3D-printed flexible electronic devices and optimize bioink formulation, printing parameters, and postprocessing processes to improve mechanical and electrical properties. The exploration of 3D-printed chitin and chitosan-based flexible bioelectronics will open new avenues for new flexible materials for numerous industrial applications.
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Affiliation(s)
- Moses Kumi
- Frontiers Science Center for Flexible Electronics (FSCFE), Xi'an Institute of Flexible Electronics (IFE), Xi'an Institute of Biomedical Materials and Engineering (IBME), Northwestern Polytechnical University (NPU), 127 West Youyi Road, Xi'an, Shaanxi, 710072, P. R. China
| | - Tengjiao Wang
- Frontiers Science Center for Flexible Electronics (FSCFE), Xi'an Institute of Flexible Electronics (IFE), Xi'an Institute of Biomedical Materials and Engineering (IBME), Northwestern Polytechnical University (NPU), 127 West Youyi Road, Xi'an, Shaanxi, 710072, P. R. China
| | - Onome Ejeromedoghene
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou, Jiangsu, 215123, P. R. China
| | - Junjie Wang
- Frontiers Science Center for Flexible Electronics (FSCFE), Xi'an Institute of Flexible Electronics (IFE), Xi'an Institute of Biomedical Materials and Engineering (IBME), Northwestern Polytechnical University (NPU), 127 West Youyi Road, Xi'an, Shaanxi, 710072, P. R. China
| | - Peng Li
- Frontiers Science Center for Flexible Electronics (FSCFE), Xi'an Institute of Flexible Electronics (IFE), Xi'an Institute of Biomedical Materials and Engineering (IBME), Northwestern Polytechnical University (NPU), 127 West Youyi Road, Xi'an, Shaanxi, 710072, P. R. China
| | - Wei Huang
- Frontiers Science Center for Flexible Electronics (FSCFE), Xi'an Institute of Flexible Electronics (IFE), Xi'an Institute of Biomedical Materials and Engineering (IBME), Northwestern Polytechnical University (NPU), 127 West Youyi Road, Xi'an, Shaanxi, 710072, P. R. China
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5
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Yao T, Zhang J, Yates TB, Shrestha HK, Engle NL, Ployet R, John C, Feng K, Bewg WP, Chen MSS, Lu H, Harding SA, Qiao Z, Jawdy SS, Shu M, Yuan W, Mozaffari K, Harman-Ware AE, Happs RM, York LM, Binder BM, Yoshinaga Y, Daum C, Tschaplinski TJ, Abraham PE, Tsai CJ, Barry K, Lipzen A, Schmutz J, Tuskan GA, Chen JG, Muchero W. Expression quantitative trait loci mapping identified PtrXB38 as a key hub gene in adventitious root development in Populus. THE NEW PHYTOLOGIST 2023; 239:2248-2264. [PMID: 37488708 DOI: 10.1111/nph.19126] [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: 01/30/2023] [Accepted: 06/13/2023] [Indexed: 07/26/2023]
Abstract
Plant establishment requires the formation and development of an extensive root system with architecture modulated by complex genetic networks. Here, we report the identification of the PtrXB38 gene as an expression quantitative trait loci (eQTL) hotspot, mapped using 390 leaf and 444 xylem Populus trichocarpa transcriptomes. Among predicted targets of this trans-eQTL were genes involved in plant hormone responses and root development. Overexpression of PtrXB38 in Populus led to significant increases in callusing and formation of both stem-born roots and base-born adventitious roots. Omics studies revealed that genes and proteins controlling auxin transport and signaling were involved in PtrXB38-mediated adventitious root formation. Protein-protein interaction assays indicated that PtrXB38 interacts with components of endosomal sorting complexes required for transport machinery, implying that PtrXB38-regulated root development may be mediated by regulating endocytosis pathway. Taken together, this work identified a crucial root development regulator and sheds light on the discovery of other plant developmental regulators through combining eQTL mapping and omics approaches.
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Affiliation(s)
- Tao Yao
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Jin Zhang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, 311300, China
| | - Timothy B Yates
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Bredesen Center for Interdisciplinary Research, University of Tennessee, Knoxville, TN, 37996, USA
| | - Him K Shrestha
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Nancy L Engle
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Raphael Ployet
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Cai John
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Bredesen Center for Interdisciplinary Research, University of Tennessee, Knoxville, TN, 37996, USA
| | - Kai Feng
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - William Patrick Bewg
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA, 30602, USA
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Margot S S Chen
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA, 30602, USA
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Haiwei Lu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Department of Academic Education, Central Community College - Hastings, Hastings, NE, 68902, USA
| | - Scott A Harding
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA, 30602, USA
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Zhenzhen Qiao
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Sara S Jawdy
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Mengjun Shu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Wenya Yuan
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, 311300, China
| | - Khadijeh Mozaffari
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA, 30602, USA
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Anne E Harman-Ware
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Renee M Happs
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Larry M York
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Brad M Binder
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Yuko Yoshinaga
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Christopher Daum
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Timothy J Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Paul E Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Chung-Jui Tsai
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, 311300, China
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jeremy Schmutz
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
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6
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Lu Y, Fu Y, Chen L, Cui J, Huang M, Fu Y, Liu H. Combined effect of simulated microgravity and low-dose ionizing radiation on structure and antibiotic resistance of a synthetic community model of bacteria isolated from spacecraft assembly room. LIFE SCIENCES IN SPACE RESEARCH 2023; 38:29-38. [PMID: 37481305 DOI: 10.1016/j.lssr.2023.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 04/05/2023] [Accepted: 04/25/2023] [Indexed: 07/24/2023]
Abstract
Understanding the structural and antibiotic resistance changes of microbial communities in space environments is critical for identifying potential pathogens that may pose health risks to astronauts and for preventing and controlling microbial contamination. The research to date on microbes under simulated space factors has primarily been carried out on single bacterial species under the individual effects of microgravity or low-dose radiation. However, microgravity (MG) and low-dose ionizing radiation (LDIR) coexist in the actual spacecraft environment, and microorganisms coexist as communities in the spacecraft environment. Thus, the microbial response to the real changes present during space habitation has not been adequately explored. To address this knowledge gap, we compared the dynamics of community composition and antibiotic resistance of synthetic bacterial communities under simulated microgravit, low-dose ionizing radiation, and the conditions combined, as it occurs in spacecraft. To ensure representative bacteria were selected, we co-cultured of 12 bacterial strains isolated from spacecraft cleanrooms. We found that the weakened competition between communities increased the possibility of species coexistence, community diversity, and homogeneity. The number of Bacilli increased significantly, while different species under the combined conditions showed various changes in abundance compared to those under the individual conditions. The resistance of the synthetic community to penicillins increased significantly under low doses of ionizing radiation but did not change significantly under simulated microgravity or the combined conditions. The results of functional predictions revealed that antibiotic biosynthesis and resistance increased dramatically in the community under space environmental stress, which confirmed the results of the drug sensitivity assays. Our results show that combined space environmental factors exert different effects on the microbial community structure and antibiotic resistance, which provides new insights into our understanding of the mechanisms of evolution of microorganisms in spacecraft, and is relevant to effective microbial pollution prevention and control strategies.
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Affiliation(s)
- Yueying Lu
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, 37 Xueyuan Road, Haidian District, Beijing 100083, China; International Joint Research Center of Aerospace Biotechnology & Medical Engineering, Beihang University, Beijing 100083, China
| | - Yifan Fu
- School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China; 4+4 M D. Program, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Letian Chen
- School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Jingjing Cui
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, 37 Xueyuan Road, Haidian District, Beijing 100083, China; International Joint Research Center of Aerospace Biotechnology & Medical Engineering, Beihang University, Beijing 100083, China
| | - Min Huang
- School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Yuming Fu
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, 37 Xueyuan Road, Haidian District, Beijing 100083, China; International Joint Research Center of Aerospace Biotechnology & Medical Engineering, Beihang University, Beijing 100083, China; State Key Laboratory of Virtual Reality Technology and Systems, School of Computer Science and Engineering, Beihang University, Beijing 100083, China.
| | - Hong Liu
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, 37 Xueyuan Road, Haidian District, Beijing 100083, China; International Joint Research Center of Aerospace Biotechnology & Medical Engineering, Beihang University, Beijing 100083, China; State Key Laboratory of Virtual Reality Technology and Systems, School of Computer Science and Engineering, Beihang University, Beijing 100083, China
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7
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Pacheco AR, Vorholt JA. Resolving metabolic interaction mechanisms in plant microbiomes. Curr Opin Microbiol 2023; 74:102317. [PMID: 37062173 DOI: 10.1016/j.mib.2023.102317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 03/10/2023] [Accepted: 03/16/2023] [Indexed: 04/18/2023]
Abstract
Metabolic interactions are fundamental to the assembly and functioning of microbiomes, including those of plants. However, disentangling the molecular basis of these interactions and their specific roles remains a major challenge. Here, we review recent applications of experimental and computational methods toward the elucidation of metabolic interactions in plant-associated microbiomes. We highlight studies that span various scales of taxonomic and environmental complexity, including those that test interaction outcomes in vitro and in planta by deconstructing microbial communities. We also discuss how the continued integration of multiple methods can further reveal the general ecological characteristics of plant microbiomes, as well as provide strategies for applications in areas such as improved plant protection, bioremediation, and sustainable agriculture.
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Affiliation(s)
- Alan R Pacheco
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland.
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8
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Rush TA, Tannous J, Lane MJ, Gopalakrishnan Meena M, Carrell AA, Golan JJ, Drott MT, Cottaz S, Fort S, Ané JM, Keller NP, Pelletier DA, Jacobson DA, Kainer D, Abraham PE, Giannone RJ, Labbé JL. Lipo-Chitooligosaccharides Induce Specialized Fungal Metabolite Profiles That Modulate Bacterial Growth. mSystems 2022; 7:e0105222. [PMID: 36453934 PMCID: PMC9764981 DOI: 10.1128/msystems.01052-22] [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: 10/25/2022] [Accepted: 11/02/2022] [Indexed: 12/03/2022] Open
Abstract
Lipo-chitooligosaccharides (LCOs) are historically known for their role as microbial-derived signaling molecules that shape plant symbiosis with beneficial rhizobia or mycorrhizal fungi. Recent studies showing that LCOs are widespread across the fungal kingdom have raised questions about the ecological function of these compounds in organisms that do not form symbiotic relationships with plants. To elucidate the ecological function of these compounds, we investigate the metabolomic response of the ubiquitous human pathogen Aspergillus fumigatus to LCOs. Our metabolomics data revealed that exogenous application of various types of LCOs to A. fumigatus resulted in significant shifts in the fungal metabolic profile, with marked changes in the production of specialized metabolites known to mediate ecological interactions. Using network analyses, we identify specific types of LCOs with the most significant effect on the abundance of known metabolites. Extracts of several LCO-induced metabolic profiles significantly impact the growth rates of diverse bacterial species. These findings suggest that LCOs may play an important role in the competitive dynamics of non-plant-symbiotic fungi and bacteria. This study identifies specific metabolomic profiles induced by these ubiquitously produced chemicals and creates a foundation for future studies into the potential roles of LCOs as modulators of interkingdom competition. IMPORTANCE The activation of silent biosynthetic gene clusters (BGC) for the identification and characterization of novel fungal secondary metabolites is a perpetual motion in natural product discoveries. Here, we demonstrated that one of the best-studied symbiosis signaling compounds, lipo-chitooligosaccharides (LCOs), play a role in activating some of these BGCs, resulting in the production of known, putative, and unknown metabolites with biological activities. This collection of metabolites induced by LCOs differentially modulate bacterial growth, while the LCO standards do not convey the same effect. These findings create a paradigm shift showing that LCOs have a more prominent role outside of host recognition of symbiotic microbes. Importantly, our work demonstrates that fungi use LCOs to produce a variety of metabolites with biological activity, which can be a potential source of bio-stimulants, pesticides, or pharmaceuticals.
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Affiliation(s)
- Tomás A. Rush
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Joanna Tannous
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Matthew J. Lane
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee, USA
| | | | - Alyssa A. Carrell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Jacob J. Golan
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Milton T. Drott
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- USDA-ARS Cereal Disease Laboratory, St. Paul, Minnesota, USA
| | - Sylvain Cottaz
- Université Grenoble Alpes, CNRS, CERMAV, Grenoble, France
| | - Sébastien Fort
- Université Grenoble Alpes, CNRS, CERMAV, Grenoble, France
| | - Jean-Michel Ané
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Agronomy, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Nancy P. Keller
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Dale A. Pelletier
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Daniel A. Jacobson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - David Kainer
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Paul E. Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Richard J. Giannone
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Jesse L. Labbé
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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9
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Appidi MR, Bible AN, Carper DL, Jawdy SS, Giannone RJ, Hettich RL, Morrell-Falvey J, Abraham PE. Development of an Experimental Approach to Achieve Spatially Resolved Plant Root-Associated Metaproteomics Using an Agar-Plate System. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:639-649. [PMID: 35349304 DOI: 10.1094/mpmi-01-22-0011-ta] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Plant-microbe interactions in the rhizosphere play a vital role in plant health and productivity. The composition and function of root-associated microbiomes is strongly influenced by their surrounding environment, which is often customized by their host. How microbiomes change with respect to space and time across plant roots remains poorly understood, and methodologies that facilitate spatiotemporal metaproteomic studies of root-associated microbiomes are yet to be realized. Here, we developed a method that provides spatially resolved metaproteome measurements along plant roots embedded in agar-plate culture systems, which have long been used to study plants. Spatially defined agar "plugs" of interest were excised and subsequently processed using a novel peptide extraction method prior to metaproteomics, which was used to infer both microbial community composition and function. As a proof-of-principle, a previously studied 10-member community constructed from a Populus root system was grown in an agar plate with a 3-week-old Populus trichocarpa plant. Metaproteomics was performed across two time points (24 and 48 h) for three distinct locations (root base, root tip, and a region distant from the root). The spatial resolution of these measurements provides evidence that microbiome composition and expression changes across the plant root interface. Interrogation of the individual microbial proteomes revealed functional profiles related to their behavioral associations with the plant root, in which chemotaxis and augmented metabolism likely supported predominance of the most abundant member. This study demonstrated a novel peptide extraction method for studying plant agar-plate culture systems, which was previously unsuitable for (meta)proteomic measurements.
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Affiliation(s)
- Manasa R Appidi
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, U.S.A
- Department of Genome Science and Technology, University of Tennessee-Knoxville, Knoxville, TN 37996, U.S.A
| | - Amber N Bible
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, U.S.A
| | - Dana L Carper
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, U.S.A
| | - Sara S Jawdy
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, U.S.A
| | - Richard J Giannone
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, U.S.A
| | - Robert L Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, U.S.A
| | | | - Paul E Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, U.S.A
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10
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Pathania N, Kumar A, Sharma P, Kaur A, Sharma S, Jain R. Harnessing rhizobacteria to fulfil inter-linked nutrient dependency on soil and alleviate stresses in plants. J Appl Microbiol 2022; 133:2694-2716. [PMID: 35656999 DOI: 10.1111/jam.15649] [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: 03/09/2022] [Revised: 05/12/2022] [Accepted: 05/31/2022] [Indexed: 11/27/2022]
Abstract
Plant rhizo-microbiome comprises of complex microbial communities that colonizes at the interphase of plant roots and soil. Plant-growth-promoting rhizobacteria (PGPR) in the rhizosphere provides important ecosystem services ranging from release of essential nutrients for enhancing soil quality and improving plant health to imparting protection to plants against rising biotic and abiotic stresses. Hence, PGPR serve as restoring agents to rejuvenate soil health and mediate plant fitness in the facet of changing climate. Though, it is evident that nutrients availability in soil are managed through inter-linked mechanisms, how PGPR expediate these processes remain less recognized. Promising results of PGPR inoculation on plant growth are continually reported in controlled environmental conditions, however, their field application often fails due to competition with native microbiota and low colonization efficiency in roots. The development of highly efficient and smart bacterial synthetic communities by integrating bacterial ecological and genetic features provides better opportunities for successful inoculant formulations. This review provides an overview of the inter-play between nutrient availability and disease suppression governed by rhizobacteria in soil followed by the role of synthetic bacterial communities in developing efficient microbial inoculants. Moreover, an outlook on the beneficial activities of rhizobacteria in modifying soil characteristics to sustainably boost agroecosystem functioning is also provided.
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Affiliation(s)
- Neemisha Pathania
- Department of Soil Science, Punjab Agricultural University, Ludhiana, Punjab 141004, India
| | - Arun Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
| | - Poonam Sharma
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab 141004, India
| | - Avneet Kaur
- Department of Soil Science, Punjab Agricultural University, Ludhiana, Punjab 141004, India
| | - Sandeep Sharma
- Department of Soil Science, Punjab Agricultural University, Ludhiana, Punjab 141004, India
| | - Rahul Jain
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
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11
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Beck AE, Kleiner M, Garrell AK. Elucidating Plant-Microbe-Environment Interactions Through Omics-Enabled Metabolic Modelling Using Synthetic Communities. FRONTIERS IN PLANT SCIENCE 2022; 13:910377. [PMID: 35795346 PMCID: PMC9251461 DOI: 10.3389/fpls.2022.910377] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/16/2022] [Indexed: 05/10/2023]
Abstract
With a growing world population and increasing frequency of climate disturbance events, we are in dire need of methods to improve plant productivity, resilience, and resistance to both abiotic and biotic stressors, both for agriculture and conservation efforts. Microorganisms play an essential role in supporting plant growth, environmental response, and susceptibility to disease. However, understanding the specific mechanisms by which microbes interact with each other and with plants to influence plant phenotypes is a major challenge due to the complexity of natural communities, simultaneous competition and cooperation effects, signalling interactions, and environmental impacts. Synthetic communities are a major asset in reducing the complexity of these systems by simplifying to dominant components and isolating specific variables for controlled experiments, yet there still remains a large gap in our understanding of plant microbiome interactions. This perspectives article presents a brief review discussing ways in which metabolic modelling can be used in combination with synthetic communities to continue progress toward understanding the complexity of plant-microbe-environment interactions. We highlight the utility of metabolic models as applied to a community setting, identify different applications for both flux balance and elementary flux mode simulation approaches, emphasize the importance of ecological theory in guiding data interpretation, and provide ideas for how the integration of metabolic modelling techniques with big data may bridge the gap between simplified synthetic communities and the complexity of natural plant-microbe systems.
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Affiliation(s)
- Ashley E. Beck
- Department of Biological and Environmental Sciences, Carroll College, Helena, MT, United States
- *Correspondence: Ashley E. Beck,
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Anna-Katharina Garrell
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
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12
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Shrestha HK, Appidi MR, Villalobos Solis MI, Wang J, Carper DL, Burdick L, Pelletier DA, Doktycz MJ, Hettich RL, Abraham PE. Metaproteomics reveals insights into microbial structure, interactions, and dynamic regulation in defined communities as they respond to environmental disturbance. BMC Microbiol 2021; 21:308. [PMID: 34749649 PMCID: PMC8574000 DOI: 10.1186/s12866-021-02370-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 10/27/2021] [Indexed: 11/16/2022] Open
Abstract
Background Microbe-microbe interactions between members of the plant rhizosphere are important but remain poorly understood. A more comprehensive understanding of the molecular mechanisms used by microbes to cooperate, compete, and persist has been challenging because of the complexity of natural ecosystems and the limited control over environmental factors. One strategy to address this challenge relies on studying complexity in a progressive manner, by first building a detailed understanding of relatively simple subsets of the community and then achieving high predictive power through combining different building blocks (e.g., hosts, community members) for different environments. Herein, we coupled this reductionist approach with high-resolution mass spectrometry-based metaproteomics to study molecular mechanisms driving community assembly, adaptation, and functionality for a defined community of ten taxonomically diverse bacterial members of Populus deltoides rhizosphere co-cultured either in a complex or defined medium. Results Metaproteomics showed this defined community assembled into distinct microbiomes based on growth media that eventually exhibit composition and functional stability over time. The community grown in two different media showed variation in composition, yet both were dominated by only a few microbial strains. Proteome-wide interrogation provided detailed insights into the functional behavior of each dominant member as they adjust to changing community compositions and environments. The emergence and persistence of select microbes in these communities were driven by specialization in strategies including motility, antibiotic production, altered metabolism, and dormancy. Protein-level interrogation identified post-translational modifications that provided additional insights into regulatory mechanisms influencing microbial adaptation in the changing environments. Conclusions This study provides high-resolution proteome-level insights into our understanding of microbe-microbe interactions and highlights specialized biological processes carried out by specific members of assembled microbiomes to compete and persist in changing environmental conditions. Emergent properties observed in these lower complexity communities can then be re-evaluated as more complex systems are studied and, when a particular property becomes less relevant, higher-order interactions can be identified. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02370-4.
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Affiliation(s)
- Him K Shrestha
- Biosciences Division, Oak Ridge National Laboratory, 37831, Oak Ridge, Tennessee, United States.,Department of Genome Science and Technology, University of Tennessee-Knoxville, 37996, Knoxville, Tennessee, United States
| | - Manasa R Appidi
- Biosciences Division, Oak Ridge National Laboratory, 37831, Oak Ridge, Tennessee, United States.,Department of Genome Science and Technology, University of Tennessee-Knoxville, 37996, Knoxville, Tennessee, United States
| | | | - Jia Wang
- Biosciences Division, Oak Ridge National Laboratory, 37831, Oak Ridge, Tennessee, United States
| | - Dana L Carper
- Biosciences Division, Oak Ridge National Laboratory, 37831, Oak Ridge, Tennessee, United States
| | - Leah Burdick
- Biosciences Division, Oak Ridge National Laboratory, 37831, Oak Ridge, Tennessee, United States
| | - Dale A Pelletier
- Biosciences Division, Oak Ridge National Laboratory, 37831, Oak Ridge, Tennessee, United States
| | - Mitchel J Doktycz
- Biosciences Division, Oak Ridge National Laboratory, 37831, Oak Ridge, Tennessee, United States
| | - Robert L Hettich
- Biosciences Division, Oak Ridge National Laboratory, 37831, Oak Ridge, Tennessee, United States
| | - Paul E Abraham
- Biosciences Division, Oak Ridge National Laboratory, 37831, Oak Ridge, Tennessee, United States.
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