101
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Riu M, Kim MS, Choi SK, Oh SK, Ryu CM. Elicitation of Innate Immunity by a Bacterial Volatile 2-Nonanone at Levels below Detection Limit in Tomato Rhizosphere. Mol Cells 2022; 45:502-511. [PMID: 35791736 PMCID: PMC9260139 DOI: 10.14348/molcells.2022.2009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 02/24/2022] [Accepted: 02/24/2022] [Indexed: 11/27/2022] Open
Abstract
Bacterial volatile compounds (BVCs) exert beneficial effects on plant protection both directly and indirectly. Although BVCs have been detected in vitro, their detection in situ remains challenging. The purpose of this study was to investigate the possibility of BVCs detection under in situ condition and estimate the potentials of in situ BVC to plants at below detection limit. We developed a method for detecting BVCs released by the soil bacteria Bacillus velezensis strain GB03 and Streptomyces griseus strain S4-7 in situ using solid-phase microextraction coupled with gas chromatography-mass spectrometry (SPME-GC-MS). Additionally, we evaluated the BVC detection limit in the rhizosphere and induction of systemic immune response in tomato plants grown in the greenhouse. Two signature BVCs, 2-nonanone and caryolan-1-ol, of GB03 and S4-7 respectively were successfully detected using the soil-vial system. However, these BVCs could not be detected in the rhizosphere pretreated with strains GB03 and S4-7. The detection limit of 2-nonanone in the tomato rhizosphere was 1 µM. Unexpectedly, drench application of 2-nonanone at 10 nM concentration, which is below its detection limit, protected tomato seedlings against Pseudomonas syringae pv. tomato. Our finding highlights that BVCs, including 2-nonanone, released by a soil bacterium are functional even when present at a concentration below the detection limit of SPME-GC-MS.
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Affiliation(s)
- Myoungjoo Riu
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
- Department of Applied Biology, College of Agriculture & Life Sciences, Chungnam National University, Daejeon 34134, Korea
| | - Man Su Kim
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
- Department of Biosystems and Bioengineering Program, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon 34113, Korea
| | - Soo-Keun Choi
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
- Department of Biosystems and Bioengineering Program, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon 34113, Korea
| | - Sang-Keun Oh
- Department of Applied Biology, College of Agriculture & Life Sciences, Chungnam National University, Daejeon 34134, Korea
| | - Choong-Min Ryu
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
- Department of Biosystems and Bioengineering Program, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon 34113, Korea
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102
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Koza NA, Adedayo AA, Babalola OO, Kappo AP. Microorganisms in Plant Growth and Development: Roles in Abiotic Stress Tolerance and Secondary Metabolites Secretion. Microorganisms 2022; 10:microorganisms10081528. [PMID: 36013946 PMCID: PMC9415082 DOI: 10.3390/microorganisms10081528] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 07/19/2022] [Accepted: 07/25/2022] [Indexed: 11/23/2022] Open
Abstract
Crops aimed at feeding an exponentially growing population are often exposed to a variety of harsh environmental factors. Although plants have evolved ways of adjusting their metabolism and some have also been engineered to tolerate stressful environments, there is still a shortage of food supply. An alternative approach is to explore the possibility of using rhizosphere microorganisms in the mitigation of abiotic stress and hopefully improve food production. Several studies have shown that rhizobacteria and mycorrhizae organisms can help improve stress tolerance by enhancing plant growth; stimulating the production of phytohormones, siderophores, and solubilizing phosphates; lowering ethylene levels; and upregulating the expression of dehydration response and antioxidant genes. This article shows the secretion of secondary metabolites as an additional mechanism employed by microorganisms against abiotic stress. The understanding of these mechanisms will help improve the efficacy of plant-growth-promoting microorganisms.
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Affiliation(s)
- Ntombikhona Appear Koza
- Department of Biochemistry and Microbiology, University of Zululand, KwaDlangezwa 3886, South Africa
| | - Afeez Adesina Adedayo
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Science, North-West University, Mmabatho 2735, South Africa
| | - Olubukola Oluranti Babalola
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Science, North-West University, Mmabatho 2735, South Africa
- Correspondence: (O.O.B.); (A.P.K.); Tel.: +27-18-389-2568 (O.O.B.); +27-11-559-3182 (A.P.K.); Fax: +27-11-559-2605 (O.O.B.)
| | - Abidemi Paul Kappo
- Molecular Biophysics and Structural Biology Group, Department of Biochemistry, University of Johannesburg, Auckland Park 2006, South Africa
- Correspondence: (O.O.B.); (A.P.K.); Tel.: +27-18-389-2568 (O.O.B.); +27-11-559-3182 (A.P.K.); Fax: +27-11-559-2605 (O.O.B.)
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103
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Effects of Volatile Organic Compounds on Biofilms and Swimming Motility of Agrobacterium tumefaciens. Microorganisms 2022; 10:microorganisms10081512. [PMID: 35893570 PMCID: PMC9394263 DOI: 10.3390/microorganisms10081512] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/22/2022] [Accepted: 07/25/2022] [Indexed: 11/29/2022] Open
Abstract
Volatile organic compounds (VOCs) emitted by bacteria play an important role in the interaction between microorganisms and other organisms. They can inhibit the growth of phytopathogenic microorganisms, modulate plant growth, and serve as infochemicals. Here, we investigated the effects of ketones, alcohols, and terpenes on the colony biofilms of plant pathogenic Agrobacterium tumefaciens strains and swimming motility, which can play an important role in the formation of biofilms. It was shown that 2-octanone had the greatest inhibitory effect on biofilm formation, acting in a small amount (38.7 g/m3). Ketone 2-butanone and unsaturated ketone β-ionone reduced the formation of biofilms at higher doses (145.2–580.6 and 387.1–1548.3 g/m3, respectively, up to 2.5–5 times). Isoamyl alcohol and 2-phenylethanol decreased the formation of biofilms at doses of 88.7 and 122.9 g/m3 by 1.7 and 5 times, respectively, with an increased effect at 177.4 and 245.9 g/m3, respectively. The agrobacteria cells in mature biofilms were more resistant to the action of ketones and alcohols. These VOCs also suppressed the swimming motility of agrobacteria; the radius of swimming zones decreased ~from 2 to 5 times. Terpenes (−)-limonene and (+)-α-pinene had no significant influence on the colony biofilms and swimming motility at the doses used. The results obtained represent new information about the effect of VOCs on biofilms and the motility of bacteria.
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104
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Gfeller A, Fuchsmann P, De Vrieze M, Gindro K, Weisskopf L. Bacterial Volatiles Known to Inhibit Phytophthora infestans Are Emitted on Potato Leaves by Pseudomonas Strains. Microorganisms 2022; 10:microorganisms10081510. [PMID: 35893568 PMCID: PMC9394277 DOI: 10.3390/microorganisms10081510] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/24/2022] [Accepted: 07/05/2022] [Indexed: 11/29/2022] Open
Abstract
Bacterial volatiles play important roles in mediating beneficial interactions between plants and their associated microbiota. Despite their relevance, bacterial volatiles are mostly studied under laboratory conditions, although these strongly differ from the natural environment bacteria encounter when colonizing plant roots or shoots. In this work, we ask the question whether plant-associated bacteria also emit bioactive volatiles when growing on plant leaves rather than on artificial media. Using four potato-associated Pseudomonas, we demonstrate that potato leaves offer sufficient nutrients for the four strains to grow and emit volatiles, among which 1-undecene and Sulfur compounds have previously demonstrated the ability to inhibit the development of the oomycete Phytophthora infestans, the causative agent of potato late blight. Our results bring the proof of concept that bacterial volatiles with known plant health-promoting properties can be emitted on the surface of leaves and warrant further studies to test the bacterial emission of bioactive volatiles in greenhouse and field-grown plants.
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Affiliation(s)
- Aurélie Gfeller
- Changins School of Viticulture and Oenology, 1260 Nyon, Switzerland; (A.G.); (M.D.V.)
- Agroscope, Plant Protection, 1260 Nyon, Switzerland;
| | - Pascal Fuchsmann
- Agroscope, Nutrition, Sensory analysis and Flavour Group, 3003 Bern, Switzerland;
| | - Mout De Vrieze
- Changins School of Viticulture and Oenology, 1260 Nyon, Switzerland; (A.G.); (M.D.V.)
- Agroscope, Plant Protection, 1260 Nyon, Switzerland;
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Katia Gindro
- Agroscope, Plant Protection, 1260 Nyon, Switzerland;
| | - Laure Weisskopf
- Changins School of Viticulture and Oenology, 1260 Nyon, Switzerland; (A.G.); (M.D.V.)
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
- Correspondence:
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105
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Mengers HG, Zimmermann M, Blank LM. Using off-gas for insights through online monitoring of ethanol and baker's yeast volatilome using SESI-Orbitrap MS. Sci Rep 2022; 12:12462. [PMID: 35864195 PMCID: PMC9304407 DOI: 10.1038/s41598-022-16554-z] [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: 05/09/2022] [Accepted: 07/12/2022] [Indexed: 11/13/2022] Open
Abstract
Volatile organic compounds play an essential role in every domain of life, with diverse functions. In this study, we use novel secondary electrospray ionisation high-resolution Orbitrap mass spectrometry (SESI-Orbitrap MS) to monitor the complete yeast volatilome every 2.3 s. Over 200 metabolites were identified during growth in shake flasks and bioreactor cultivations, all with their unique intensity profile. Special attention was paid to ethanol as biotech largest product and to acetaldehyde as an example of a low-abundance but highly-volatile metabolite. While HPLC and Orbitrap measurements show a high agreement for ethanol, acetaldehyde could be measured five hours earlier in the SESI-Orbitrap MS. Volatilome shifts are visible, e.g. after glucose depletion, fatty acids are converted to ethyl esters in a detoxification mechanism after stopped fatty acid biosynthesis. This work showcases the SESI-Orbitrap MS system for tracking microbial physiology without the need for sampling and for time-resolved discoveries during metabolic transitions.
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Affiliation(s)
- Hendrik G Mengers
- Institute of Applied Microbiology - iAMB, Aachener Biology and Biotechnology - ABBt, RWTH Aachen University, Aachen, Germany
| | - Martin Zimmermann
- Institute of Applied Microbiology - iAMB, Aachener Biology and Biotechnology - ABBt, RWTH Aachen University, Aachen, Germany
| | - Lars M Blank
- Institute of Applied Microbiology - iAMB, Aachener Biology and Biotechnology - ABBt, RWTH Aachen University, Aachen, Germany.
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106
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Zinn MK, Flemming HC, Bockmühl D. A Comprehensive View of Microbial Communities in the Laundering Cycle Suggests a Preventive Effect of Soil Bacteria on Malodour Formation. Microorganisms 2022; 10:microorganisms10071465. [PMID: 35889184 PMCID: PMC9318688 DOI: 10.3390/microorganisms10071465] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/11/2022] [Accepted: 07/15/2022] [Indexed: 02/04/2023] Open
Abstract
Microorganisms are an important factor in the wash-and-use cycle of textiles since they can cause unwanted aesthetic effects, such as malodour formation, and even pose health risks. In this regard, a comprehensive view of the microbial communities in washing machines and consideration of the microbial contamination of used textiles is needed to understand the formation of malodour and evaluate the infection risk related to laundering. So far, neither the compositions of washing machine biofilms leading to the formation of or protection against malodour have been investigated intensively, nor have microbial communities on used towels been analysed after normal use. Our results link the qualitative and quantitative analysis of microbial communities in washing machines and on used towels with the occurrence of malodour and thus not only allow for a better risk evaluation but also suggest bacterial colonizers of washing machines that might prevent malodour formation. It was shown that soil bacteria such as Rhizobium, Agrobacterium, Bosea, and Microbacterium in particular are found in non-odourous machines, and that Rhizobium species are able to prevent malodour formation in an in vitro model.
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Affiliation(s)
- Marc-Kevin Zinn
- Faculty of Life Sciences, Rhine-Waal University of Applied Sciences, 47533 Kleve, Germany;
- Biofilm Centre, University of Duisburg-Essen, Universitätsstrasse 5, 45131 Essen, Germany;
| | - Hans-Curt Flemming
- Biofilm Centre, University of Duisburg-Essen, Universitätsstrasse 5, 45131 Essen, Germany;
| | - Dirk Bockmühl
- Faculty of Life Sciences, Rhine-Waal University of Applied Sciences, 47533 Kleve, Germany;
- Correspondence: ; Tel.: +49-2821-806-73-208
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107
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Sun J, Li S, Fan C, Cui K, Tan H, Qiao L, Lu L. N-Acetylglucosamine Promotes Tomato Plant Growth by Shaping the Community Structure and Metabolism of the Rhizosphere Microbiome. Microbiol Spectr 2022; 10:e0035822. [PMID: 35665438 PMCID: PMC9241905 DOI: 10.1128/spectrum.00358-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 05/20/2022] [Indexed: 11/20/2022] Open
Abstract
Communication between plants and microorganisms is vital because it influences their growth, development, defense, propagation, and metabolism in achieving maximal fitness. N-acetylglucosamine (N-GlcNAc), the building block of bacterial and fungal cell walls, was first reported to promote tomato plant growth via stimulation of microorganisms typically known to dominate the tomato root rhizosphere, such as members of Proteobacteria and Actinobacteria. Using KEGG pathway analysis of the rhizosphere microbial operational taxonomic units, the streptomycin biosynthesis pathway was enriched in the presence of N-GlcNAc. The biosynthesis of 3-hydroxy-2-butanone (acetoin) and 2,3-butanediol, two foremost types of plant growth promotion-related volatile organic compounds, were activated in both Bacillus subtilis and Streptomyces thermocarboxydus strains when they were cocultured with N-GlcNAc. In addition, the application of N-GlcNAc increased indole-3-acetic acid production in a dose-dependent manner in strains of Bacillus cereus, Proteus mirabilis, Pseudomonas putida, and S. thermocarboxydus that were isolated from an N-GlcNAc-treated tomato rhizosphere. Overall, this study found that N-GlcNAc could function as microbial signaling molecules to shape the community structure and metabolism of the rhizosphere microbiome, thereby regulating plant growth and development and preventing plant disease through complementary plant-microbe interactions. IMPORTANCE While the benefits of using plant growth-promoting rhizobacteria (PGPRs) to enhance crop production have been recognized and studied extensively under laboratory conditions, the success of their application in the field varies immensely. More fundamentally explicit processes of positive, plant-PGPRs interactions are needed. The utilization of organic amendments, such as chitin and its derivatives, is one of the most economical and practical options for improving soil and substrate quality as well as plant growth and resilience. In this study, we observed that the chitin monomer N-GlcNAc, a key microbial signaling molecule produced through interactions between chitin, soil microbes, and the plants, positively shaped the community structure and metabolism of the rhizosphere microbiome of tomatoes. Our findings also provide a new direction for enhancing the benefits and stability of PGPRs in the field.
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Affiliation(s)
- Jiuyun Sun
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, People’s Republic of China
| | - Shuhua Li
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, People’s Republic of China
| | - Chunyang Fan
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, People’s Republic of China
| | - Kangjia Cui
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, People’s Republic of China
| | - Hongxiao Tan
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, People’s Republic of China
| | - Liping Qiao
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, People’s Republic of China
| | - Laifeng Lu
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, People’s Republic of China
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108
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Microbiome engineering for sustainable agriculture: using synthetic biology to enhance nitrogen metabolism in plant-associated microbes. Curr Opin Microbiol 2022; 68:102172. [PMID: 35717707 DOI: 10.1016/j.mib.2022.102172] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 04/14/2022] [Accepted: 05/16/2022] [Indexed: 11/23/2022]
Abstract
Plants benefit from symbiotic relationships with their microbiomes. Modifying these microbiomes to further promote plant growth and improve stress tolerance in crops is a promising strategy. However, such efforts have had limited success, perhaps because the original microbiomes quickly re-establish. Since the complex biological networks involved are little understood, progress through conventional means is time-consuming. Synthetic biology, with its practical successes in multiple industries, could speed up this research considerably. Some fascinating candidates for production by synthetic microbiomes are organic nitrogen metabolites and related pyridoxal-5'-phosphate-dependent enzymes, which have pivotal roles in microbe-microbe and plant-microbe interactions. This review summarizes recent studies of these metabolites and enzymes and discusses prospective synthetic biology platforms for sustainable agriculture.
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109
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Biwer P, Neumann-Schaal M, Henke P, Jahn D, Schulz S. Thiol Metabolism and Volatile Metabolome of Clostridioides difficile. Front Microbiol 2022; 13:864587. [PMID: 35783419 PMCID: PMC9243749 DOI: 10.3389/fmicb.2022.864587] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 04/22/2022] [Indexed: 11/21/2022] Open
Abstract
Clostridioides difficile (previously Clostridium difficile) causes life-threatening gut infections. The central metabolism of the bacterium is strongly influencing toxin production and consequently the infection progress. In this context, the composition and potential origin of the volatile metabolome was investigated, showing a large number of sulfur-containing volatile metabolites. Gas chromatography/mass spectrometry (GC/MS)-based headspace analyses of growing C. difficile 630Δerm cultures identified 105 mainly sulfur-containing compounds responsible of the typical C. difficile odor. Major components were identified to be 2-methyl-1-propanol, 2-methyl-1-propanethiol, 2-methyl-1-butanethiol, 4-methyl-1-pentanethiol, and as well as their disulfides. Structurally identified were 64 sulfur containing volatiles. In order to determine their biosynthetic origin, the concentrations of the sulfur-containing amino acids methionine and cysteine were varied in the growth medium. The changes observed in the volatile metabolome profile indicated that cysteine plays an essential role in the formation of the sulfur-containing volatiles. We propose that disulfides are derived from cysteine via formation of cystathionine analogs, which lead to corresponding thiols. These thiols may then be oxidized to disulfides. Moreover, methionine may contribute to the formation of short-chain disulfides through integration of methanethiol into the disulfide biosynthesis. In summary, the causative agents of the typical C. difficile odor were identified and first hypotheses for their biosynthesis were proposed.
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Affiliation(s)
- Peter Biwer
- Institute of Organic Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Meina Neumann-Schaal
- Department of Metabolomics, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology, BRICS, Braunschweig, Germany
| | - Petra Henke
- Department of Metabolomics, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Dieter Jahn
- Braunschweig Integrated Centre of Systems Biology, BRICS, Braunschweig, Germany
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Stefan Schulz
- Institute of Organic Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
- *Correspondence: Stefan Schulz,
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110
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Yang Y, Chen S, Wu X, Peng L, Vílchez JI, Kaushal R, Liu X, Singh SK, He D, Yuan F, Lv S, Morcillo RJL, Wang W, Huang W, Lei M, Zhu JK, Paré PW, Zhang H. Plant latent defense response to microbial non-pathogenic factors antagonizes compatibility. Natl Sci Rev 2022; 9:nwac109. [PMID: 36072504 PMCID: PMC9440716 DOI: 10.1093/nsr/nwac109] [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: 11/17/2021] [Revised: 04/21/2022] [Accepted: 04/21/2022] [Indexed: 11/18/2022] Open
Abstract
Unlike microbe-associated molecular patterns (MAMPs) that are readily targeted by host immunity, microbial non-pathogenic factors (NPFs) appear negligible as they do not elicit defense. Little is known about whether and how NPFs may be monitored by hosts to control compatibility. Herein, a forward genetic screening isolated an Arabidopsis mutant with a loss of plant-rhizobacteria mutualism, leading to the disclosure of a plant latent defense response (LDR) to NPFs. The activation of LDR in the mutant, named rol1 for regulator of LDR 1, is triggered by several non-pathogenic volatile organic compounds and antagonizes plant compatibility with the beneficial bacterium Bacillus amyloliquefaciens GB03. The activation of LDR in rol1 is mediated through the prokaryotic pathway of chloroplastic lipid biosynthesis. The rol1 root microbiome showed a reduced proportion of the Bacillaceae family. We propose that, parallel to the forefront immunity to MAMPs, LDR to certain NPFs provides a hidden layer of defense for controlling compatibility with commensal or beneficial microbes.
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Affiliation(s)
- Yu Yang
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences , Shanghai 201602 , China
| | - Shenglan Chen
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences , Shanghai 201602 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Xiaoxuan Wu
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences , Shanghai 201602 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Li Peng
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences , Shanghai 201602 , China
| | - Juan I Vílchez
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences , Shanghai 201602 , China
| | - Richa Kaushal
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences , Shanghai 201602 , China
| | - Xiaomin Liu
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences , Shanghai 201602 , China
| | - Sunil K Singh
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences , Shanghai 201602 , China
| | - Danxia He
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences , Shanghai 201602 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Fengtong Yuan
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences , Shanghai 201602 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Suhui Lv
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences , Shanghai 201602 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Rafael J L Morcillo
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences , Shanghai 201602 , China
| | - Wei Wang
- Shanghai Chenshan Botanical Garden , Shanghai 201602 , China
| | - Weichang Huang
- Shanghai Chenshan Botanical Garden , Shanghai 201602 , China
| | - Mingguang Lei
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences , Shanghai 201602 , China
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences , Shanghai 201602 , China
| | - Paul W Paré
- Department of Chemistry & Biochemistry, Texas Tech University , Lubbock , TX 79409 , USA
| | - Huiming Zhang
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences , Shanghai 201602 , China
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111
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Doting EL, Davie-Martin CL, Johansen A, Benning LG, Tranter M, Rinnan R, Anesio AM. Greenland Ice Sheet Surfaces Colonized by Microbial Communities Emit Volatile Organic Compounds. Front Microbiol 2022; 13:886293. [PMID: 35747370 PMCID: PMC9211068 DOI: 10.3389/fmicb.2022.886293] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
Volatile organic compounds (VOCs) are emitted by organisms for a range of physiological and ecological reasons. They play an important role in biosphere–atmosphere interactions and contribute to the formation of atmospheric secondary aerosols. The Greenland ice sheet is home to a variety of microbial communities, including highly abundant glacier ice algae, yet nothing is known about the VOCs emitted by glacial communities. For the first time, we present VOC emissions from supraglacial habitats colonized by active microbial communities on the southern Greenland ice sheet during July 2020. Emissions of C5–C30 compounds from bare ice, cryoconite holes, and red snow were collected using a push–pull chamber active sampling system. A total of 92 compounds were detected, yielding mean total VOC emission rates of 3.97 ± 0.70 μg m–2 h–1 from bare ice surfaces (n = 31), 1.63 ± 0.13 μg m–2 h–1 from cryoconite holes (n = 4), and 0.92 ± 0.08 μg m–2 h–1 from red snow (n = 2). No correlations were found between VOC emissions and ice surface algal counts, but a weak positive correlation (r = 0.43, p = 0.015, n = 31) between VOC emission rates from bare ice surfaces and incoming shortwave radiation was found. We propose that this may be due to the stress that high solar irradiance causes in bare ice microbial communities. Acetophenone, benzaldehyde, and phenylmaleic anhydride, all of which have reported antifungal activity, accounted for 51.1 ± 11.7% of emissions from bare ice surfaces, indicating a potential defense strategy against fungal infections. Greenland ice sheet microbial habitats are, hence, potential sources of VOCs that may play a role in supraglacial microbial interactions, as well as local atmospheric chemistry, and merit future research efforts.
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Affiliation(s)
- Eva L. Doting
- Department of Environmental Science, iClimate, Aarhus University, Roskilde, Denmark
- *Correspondence: Eva L. Doting,
| | - Cleo L. Davie-Martin
- Terrestrial Ecology Section, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Anders Johansen
- Department of Environmental Science, iClimate, Aarhus University, Roskilde, Denmark
| | - Liane G. Benning
- Interface Geochemistry, German Research Centre for Geosciences, GFZ Potsdam, Potsdam, Germany
- Department of Earth Sciences, Freie Universität Berlin, Berlin, Germany
| | - Martyn Tranter
- Department of Environmental Science, iClimate, Aarhus University, Roskilde, Denmark
| | - Riikka Rinnan
- Terrestrial Ecology Section, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Alexandre M. Anesio
- Department of Environmental Science, iClimate, Aarhus University, Roskilde, Denmark
- Alexandre M. Anesio,
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112
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Koprivova A, Kopriva S. Plant secondary metabolites altering root microbiome composition and function. CURRENT OPINION IN PLANT BIOLOGY 2022; 67:102227. [PMID: 35525222 DOI: 10.1016/j.pbi.2022.102227] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/29/2022] [Accepted: 03/30/2022] [Indexed: 06/14/2023]
Abstract
Plants share their natural environment with numerous microorganisms, commensal as well as harmful. Plant fitness and performance are thus dependent on an efficient communication with such microbiota. The primary means of communication are metabolites exuded from roots, primarily diverse secondary metabolites. The exuded metabolites trigger changes in composition and function of plant associated microbiome. In the last few years, many metabolites were uncovered that are part of this communication network and modulate specific functions of the root microbiota. Here, we describe the progress in identification of such metabolites and their functions and outline the most significant knowledge gaps for future research.
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Affiliation(s)
- Anna Koprivova
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Stanislav Kopriva
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany.
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113
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Trivedi P, Batista BD, Bazany KE, Singh BK. Plant-microbiome interactions under a changing world: responses, consequences and perspectives. THE NEW PHYTOLOGIST 2022; 234:1951-1959. [PMID: 35118660 DOI: 10.1111/nph.18016] [Citation(s) in RCA: 112] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 01/19/2022] [Indexed: 05/07/2023]
Abstract
Climate change is increasing global temperatures and the frequency and severity of droughts in many regions. These anthropogenic stresses pose a significant threat to plant performance and crop production. The plant-associated microbiome modulates the impacts of biotic and abiotic stresses on plant fitness. However, climate change-induced alteration in composition and activities of plant microbiomes can affect host functions. Here, we highlight recent advancements in our understanding of the impact of climate change (warming and drought) on plant-microbiome interactions and on their ecological functions from genome to ecosystem scales. We identify knowledge gaps, propose new concepts and make recommendations for future research directions. It is proposed that in the short term (years to decades), the adaptation of plants to climate change is mainly driven by the plant microbiome, whereas in the long term (century to millennia), the adaptation of plants will be driven equally by eco-evolutionary interactions between the plant microbiome and its host. A better understanding of the response of the plant and its microbiome interactions to climate change and the ways in which microbiomes can mitigate the negative impacts will better inform predictions of climate change impacts on primary productivity and aid in developing management and policy tools to improve the resilience of plant systems.
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Affiliation(s)
- Pankaj Trivedi
- Microbiome Network and Department of Agricultural Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Bruna D Batista
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2751, Australia
| | - Kathryn E Bazany
- Microbiome Network and Department of Agricultural Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2751, Australia
- Global Centre for Land-Based Innovation, Western Sydney University, Richmond, NSW, 2751, Australia
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114
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Hall RD, D'Auria JC, Silva Ferreira AC, Gibon Y, Kruszka D, Mishra P, van de Zedde R. High-throughput plant phenotyping: a role for metabolomics? TRENDS IN PLANT SCIENCE 2022; 27:549-563. [PMID: 35248492 DOI: 10.1016/j.tplants.2022.02.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 01/18/2022] [Accepted: 02/02/2022] [Indexed: 05/17/2023]
Abstract
High-throughput (HTP) plant phenotyping approaches are developing rapidly and are already helping to bridge the genotype-phenotype gap. However, technologies should be developed beyond current physico-spectral evaluations to extend our analytical capacities to the subcellular level. Metabolites define and determine many key physiological and agronomic features in plants and an ability to integrate a metabolomics approach within current HTP phenotyping platforms has huge potential for added value. While key challenges remain on several fronts, novel technological innovations are upcoming yet under-exploited in a phenotyping context. In this review, we present an overview of the state of the art and how current limitations might be overcome to enable full integration of metabolomics approaches into a generic phenotyping pipeline in the near future.
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Affiliation(s)
- Robert D Hall
- BU Bioscience, Wageningen University & Research, 6700 AA, Wageningen, The Netherlands; Laboratory of Plant Physiology, Wageningen University, 6700 AA, Wageningen, The Netherlands; Netherlands Metabolomics Centre, Einsteinweg 55, Leiden, The Netherlands.
| | - John C D'Auria
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK Gatersleben), Gatersleben, Corrensstraße 3, 06466 Seeland, Germany
| | - Antonio C Silva Ferreira
- Universidade Católica Portuguesa, CBQF-Centro de Biotecnologia e Química Fina-Laboratório Associado, Escola Superior de Biotecnologia, Rua Arquiteto Lobão Vital, Apartado 2511, 4202-401 Porto, Portugal; Faculty of AgriSciences, University of Stellenbosch, Matieland 7602, South Africa; Cork Supply Portugal, S.A., Rua Nova do Fial, 4535, Portugal
| | - Yves Gibon
- UMR 1332 Biologie du Fruit et Pathologie, INRAE, Univ. Bordeaux, INRAE Nouvelle Aquitaine - Bordeaux, Avenue Edouard Bourlaux, Villenave d'Ornon, France; Bordeaux Metabolome, MetaboHUB, INRAE, Univ. Bordeaux, Avenue Edouard Bourlaux, Villenave d'Ornon, France PMB-Metabolome, INRAE, Centre INRAE de Nouvelle, Aquitaine-Bordeaux, Villenave d'Ornon, France
| | - Dariusz Kruszka
- Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznan, Poland
| | - Puneet Mishra
- Food and Biobased Research, Wageningen University & Research, 6708 WE, Wageningen, The Netherlands
| | - Rick van de Zedde
- Plant Sciences Group, Wageningen University & Research, 6700 AA, Wageningen, The Netherlands
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115
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Mycelial Growth-promoting Potential of Extracellular Metabolites of Paraburkholderia spp. Isolated from Rhizopogon roseolus Sporocarp. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2022. [DOI: 10.22207/jpam.16.2.43] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This study aimed to investigate the effect of potential metabolite(s) produced by Paraburkholderia spp. isolated from the Rhizopogon roseolus (shouro mushroom) sporocarp on the mycelial growth of R. roseolus. For this purpose, we selected two molecularly identified bacteria: P. fungorum GIB024 and P. caledonica KN1. Direct confrontation assay at three different distances, a pour plate method that sampled bacterial spent broth either with and without agitation at 25 °C, and an indirect confrontation assay was carried out in order to assess the R. roseolus growth-promoting ability of Paraburkholderia spp. These assessments were carried out in a 1:5 diluted Melin-Norkran-modified medium with glucose (hs-dMMN) and without glucose (ls-dMMN). GIB024 promoted the growth of R. roseolus in ls-dMMN in short distance, whereas KN1 inhibited the growth of the fungus in that condition. In hs-dMMN, both bacteria have neutral or slightly promotion effect toward R. roseolus. We determined from the spent broth analysis that Paraburkholderia spp. that grew axenically under static conditions had a more pronounced mycelial growth-promoting effect on R. roseolus than under agitation conditions. We also found that high concentration of spent broth resulted in a decrease in mycelial growth-promoting ability. Volatile metabolite(s) produced by both bacteria did not promote the mycelial growth of R. roseolus. In conclusion, Paraburkholderia spp. exhibited a species- and nutrient (sugar)-dependent ability to promote the mycelial growth of R. roseolus, and the bacterial soluble metabolite(s) play a crucial role in their growth-promoting ability.
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116
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Sadiq FA, Hansen MF, Burmølle M, Heyndrickx M, Flint S, Lu W, Chen W, Zhang H. Towards understanding mechanisms and functional consequences of bacterial interactions with members of various kingdoms in complex biofilms that abound in nature. FEMS Microbiol Rev 2022; 46:6595875. [PMID: 35640890 DOI: 10.1093/femsre/fuac024] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 04/11/2022] [Accepted: 05/27/2022] [Indexed: 11/12/2022] Open
Abstract
The microbial world represents a phenomenal diversity of microorganisms from different kingdoms of life which occupy an impressive set of ecological niches. Most, if not all, microorganisms once colonise a surface develop architecturally complex surface-adhered communities which we refer to as biofilms. They are embedded in polymeric structural scaffolds serve as a dynamic milieu for intercellular communication through physical and chemical signalling. Deciphering microbial ecology of biofilms in various natural or engineered settings has revealed co-existence of microorganisms from all domains of life, including Bacteria, Archaea and Eukarya. The coexistence of these dynamic microbes is not arbitrary, as a highly coordinated architectural setup and physiological complexity show ecological interdependence and myriads of underlying interactions. In this review, we describe how species from different kingdoms interact in biofilms and discuss the functional consequences of such interactions. We highlight metabolic advances of collaboration among species from different kingdoms, and advocate that these interactions are of great importance and need to be addressed in future research. Since trans-kingdom biofilms impact diverse contexts, ranging from complicated infections to efficient growth of plants, future knowledge within this field will be beneficial for medical microbiology, biotechnology, and our general understanding of microbial life in nature.
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Affiliation(s)
- Faizan Ahmed Sadiq
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Technology & Food Sciences Unit, Melle, Belgium
| | - Mads Frederik Hansen
- Section of Microbiology, Department of Biology, University of Copenhagen, Denmark
| | - Mette Burmølle
- Section of Microbiology, Department of Biology, University of Copenhagen, Denmark
| | - Marc Heyndrickx
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Technology & Food Sciences Unit, Melle, Belgium.,Department of Pathology, Bacteriology and Poultry Diseases, Ghent University, Merelbeke, Belgium
| | - Steve Flint
- School of Food and Advanced Technology, Massey University, Private Bag, 11222, Palmerston North, New Zealand
| | - Wenwei Lu
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Wei Chen
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
| | - Hao Zhang
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
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117
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Identification of Volatiles of the Dinoflagellate Prorocentrum cordatum. Mar Drugs 2022; 20:md20060371. [PMID: 35736174 PMCID: PMC9230497 DOI: 10.3390/md20060371] [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: 05/06/2022] [Revised: 05/17/2022] [Accepted: 05/25/2022] [Indexed: 11/21/2022] Open
Abstract
The dinoflagellate Prorocentrum cordatum, often called P. minimum, is a potentially toxic alga found in algal blooms. Volatile compounds released by the alga might carry important information, e.g., on its physiological state, and may act as chemical messengers. We report here the identification of volatile organic compounds emitted by two strains, xenic P. cordatum CCMP 1529 and axenic P. cordatum CCMP 1329. The volatiles released during culture were identified despite their low production rates, using sensitive methods such as open-system-stripping analysis (OSSA) on Tenax TA desorption tubes, thermodesorption, cryofocusing and GC/MS-analysis. The analyses revealed 16 compounds released from the xenic strain and 52 compounds from the axenic strain. The majority of compounds were apocarotenoids, aromatic compounds and small oxylipins, but new natural products such as 3,7-dimethyl-4-octanolide were also identified and synthesized. The large difference of compound composition between xenic and axenic algae will be discussed.
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118
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Chowdhury NN, Islam MN, Jafrin R, Rauf A, Khalil AA, Emran TB, Aljohani ASM, Alhumaydhi FA, Lorenzo JM, Shariati MA, Simal-Gandara J. Natural plant products as effective alternatives to synthetic chemicals for postharvest fruit storage management. Crit Rev Food Sci Nutr 2022; 63:10332-10350. [PMID: 35612470 DOI: 10.1080/10408398.2022.2079112] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Fruits contain enormous source of vitamins that provides energy to the human body. These are also affluent in essential and vital vitamins, minerals, fiber, and health-promoting components, which has led to an increase in fruit consumption in recent years. Though fruit consumption has expanded considerably in recent years, the use of synthetic chemicals to ripen or store fruits has been steadily increasing, resulting in postharvest deterioration. Alternatives to synthetic chemicals should be considered to control this problem. Instead of utilizing synthetic chemicals, this study suggests using natural plant products to control postharvest decay. The aim of this study indicates how natural plant products can be useful and effective to eliminate postharvest diseases rather than using synthetic chemicals. Several electronic databases were investigated as information sources, including Google Scholar, PubMed, Web of Science, Scopus, ScienceDirect, SpringerLink, Semantic Scholar, MEDLINE, and CNKI Scholar. The current review focused on the postharvest of fruits has become more and more necessary because of these vast demands of fruits. Pathogen-induced diseases are the main component and so the vast portion of fruits get wasted after harvest. Besides, it may occur harmful during harvesting and subsequent handling, storage, and marketing and after consumer purchasing and also causes for numerous endogenous and exogenous diseases via activating ROS, oxidative stress, lipid peroxidation, etc. However, pathogenicity can be halted by using postharvest originating natural fruits containing bioactive elements that may be responsible for the management of nutritional deficiency, inflammation, cancer, and so on. However, issues arising during the postharvest diseases must be controlled and resolved before releasing the horticultural commodities for commercialization. Therefore, the control of postharvest pathogens still depends on the use of synthetic fungicides; however, due to the problem of the development of the fungicide-resistant strains there is a good demand of public to eradicate the use of pesticides with the arrival of numerous diseases that are expanded in their intensity by the specific chemical product. By using of the organic or natural products for controlling postharvest diseases of fruits has become a mandatory step to take. In addition, antimicrobial packaging may have a greater impact on long-term food security by lowering the risk of pathogenicity and increasing the longevity of fruit shelf life. Taken together, natural chemicals as acetaldehyde, hexanal, eugenol, linalool, jasmonates, glucosinolates, essential oils, and many plant bioactive are reported for combating of the postharvest illnesses and guide to way of storage of fruits in this review.
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Affiliation(s)
- Nahidun Nesa Chowdhury
- Department of Pharmacy, International Islamic University Chittagong, Chittagong, Bangladesh
| | - Mohammad Nazmul Islam
- Department of Pharmacy, International Islamic University Chittagong, Chittagong, Bangladesh
| | - Rifat Jafrin
- Department of Pharmacy, International Islamic University Chittagong, Chittagong, Bangladesh
| | - Abdur Rauf
- Department of Chemistry, University of Swabi, Anbar, Khyber Pakhtunkhwa, Pakistan
| | - Anees Ahmed Khalil
- University Institute of Diet and Nutritional Sciences, Faculty of Allied Health Sciences, The University of Lahore, Pakistan
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, Bangladesh
| | - Abdullah S M Aljohani
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah, Saudi Arabia
| | - Fahad A Alhumaydhi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Jose M Lorenzo
- Centro Tecnológico de la Carne de Galicia, Ourense, Spain
- Área de Tecnología de los Alimentos, Facultad de Ciencias de Ourense, Universidad de Vigo, Ourense, Spain
| | - Mohammad Ali Shariati
- K.G. Razumovsky Moscow State University of Technologies and Management, The First Cossack University), Moscow, Russia
| | - Jesus Simal-Gandara
- Universidade de Vigo, Nutrition and Bromatology Group, Analytical Chemistry and Food Science Department, Faculty of Science, Ourense, Spain
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119
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Cabugao KGM, Gushgari-Doyle S, Chacon SS, Wu X, Bhattacharyya A, Bouskill N, Chakraborty R. Characterizing Natural Organic Matter Transformations by Microbial Communities in Terrestrial Subsurface Ecosystems: A Critical Review of Analytical Techniques and Challenges. Front Microbiol 2022; 13:864895. [PMID: 35602028 PMCID: PMC9114703 DOI: 10.3389/fmicb.2022.864895] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
Determining the mechanisms, traits, and pathways that regulate microbial transformation of natural organic matter (NOM) is critical to informing our understanding of the microbial impacts on the global carbon cycle. The capillary fringe of subsurface soils is a highly dynamic environment that remains poorly understood. Characterization of organo-mineral chemistry combined with a nuanced understanding of microbial community composition and function is necessary to understand microbial impacts on NOM speciation in the capillary fringe. We present a critical review of the popular analytical and omics techniques used for characterizing complex carbon transformation by microbial communities and focus on how complementary information obtained from the different techniques enable us to connect chemical signatures with microbial genes and pathways. This holistic approach offers a way forward for the comprehensive characterization of the formation, transformation, and mineralization of terrestrial NOM as influenced by microbial communities.
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Affiliation(s)
- Kristine Grace M Cabugao
- Department of Ecology, Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Sara Gushgari-Doyle
- Department of Ecology, Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Stephany S Chacon
- Department of Ecology, Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Xiaoqin Wu
- Department of Ecology, Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Amrita Bhattacharyya
- Department of Ecology, Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Nicholas Bouskill
- Department of Ecology, Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Romy Chakraborty
- Department of Ecology, Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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120
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Kuil SD, Hidad S, Schneeberger C, Singh P, Rhodes P, de Jong MD, Visser CE. Susceptibility Testing by Volatile Organic Compound Detection Direct from Positive Blood Cultures: A Proof-of-Principle Laboratory Study. Antibiotics (Basel) 2022; 11:antibiotics11060705. [PMID: 35740111 PMCID: PMC9220186 DOI: 10.3390/antibiotics11060705] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 12/23/2022] Open
Abstract
Background: Bacteria produce volatile organic compounds (VOCs) during growth, which can be detected by colorimetric sensor arrays (CSAs). The SpecifAST® system (Specific Diagnostics) employs this technique to enable antibiotic susceptibility testing (AST) directly from blood cultures without prior subculture of isolates. The aim of this study was to compare the SpecifAST® AST results and analysis time to the VITEK®2 (bioMérieux) system. Methods: In a 12-month single site prospective study, remnants of clinical positive monomicrobial blood cultures were combined with a series of antibiotic concentrations. Volatile emission was monitored at 37 °C via CSAs. Minimal Inhibitory Concentrations (MICs) of seven antimicrobial agents for Enterobacterales, Staphylococcus, and Enterococcus spp. were compared to VITEK®2 AST results. MICs were interpreted according to EUCAST clinical breakpoints. Performance was assessed by calculating agreement and discrepancy rates. Results: In total, 96 positive blood cultures containing Enterobacterales, Staphylococcus, and Enterococcus spp. were tested (269 bug–drug combinations). The categorical agreement of the SpecifAST® system compared to the VITEK®2 system was 100% and 91% for Gram-negatives and Gram-positives, respectively. Errors among Gram-positives were from coagulase-negative staphylococci. Overall results were available in 3.1 h (±0.9 h) after growth detection without the need for subculture steps. Conclusion: The AST results based on VOC detection are promising and warrant further evaluation in studies with a larger sample of bacterial species and antimicrobials.
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Affiliation(s)
- Sacha Daniëlle Kuil
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (S.H.); (C.S.); (M.D.d.J.); (C.E.V.)
- Correspondence: ; Tel.: +312-0566-7625
| | - Soemeja Hidad
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (S.H.); (C.S.); (M.D.d.J.); (C.E.V.)
| | - Caroline Schneeberger
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (S.H.); (C.S.); (M.D.d.J.); (C.E.V.)
| | - Pragya Singh
- Specific Diagnostics, San Jose, CA 95134, USA; (P.S.); (P.R.)
| | - Paul Rhodes
- Specific Diagnostics, San Jose, CA 95134, USA; (P.S.); (P.R.)
| | - Menno Douwe de Jong
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (S.H.); (C.S.); (M.D.d.J.); (C.E.V.)
| | - Caroline Elisabeth Visser
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (S.H.); (C.S.); (M.D.d.J.); (C.E.V.)
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121
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Multi-Strain and -Species Investigation of Volatile Metabolites Emitted from Planktonic and Biofilm Candida Cultures. Metabolites 2022; 12:metabo12050432. [PMID: 35629935 PMCID: PMC9146923 DOI: 10.3390/metabo12050432] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/02/2022] [Accepted: 05/06/2022] [Indexed: 02/04/2023] Open
Abstract
Candida parapsiliosis is a prevalent neonatal pathogen that attains its virulence through its strain-specific ability to form biofilms. The use of volatilomics, the profiling of volatile metabolites from microbes is a non-invasive, simple way to identify and classify microbes; it has shown great potential for pathogen identification. Although C. parapsiliosis is one of the most common clinical fungal pathogens, its volatilome has never been characterised. In this study, planktonic volatilomes of ten clinical strains of C. parapsilosis were analysed, along with a single strain of Candida albicans. Headspace-solid-phase microextraction coupled with gas chromatography-mass spectrometry were employed to analyse the samples. Species-, strain-, and media- influences on the fungal volatilomes were investigated. Twenty-four unique metabolites from the examined Candida spp. (22 from C. albicans; 18 from C. parapsilosis) were included in this study. Chemical classes detected across the samples included alcohols, fatty acid esters, acetates, thiols, sesquiterpenes, and nitrogen-containing compounds. C. albicans volatilomes were most clearly discriminated from C. parapsilosis based on the detection of unique sesquiterpene compounds. The effect of biofilm formation on the C. parapsilosis volatilomes was investigated for the first time by comparing volatilomes of a biofilm-positive strain and a biofilm-negative strain over time (0–48 h) using a novel sampling approach. Volatilomic shifts in the profiles of alcohols, ketones, acids, and acetates were observed specifically in the biofilm-forming samples and attributed to biofilm maturation. This study highlights species-specificity of Candida volatilomes, and also marks the clinical potential for volatilomics for non-invasively detecting fungal pathogens. Additionally, the range of biofilm-specificity across microbial volatilomes is potentially far-reaching, and therefore characterising these volatilomic changes in pathogenic fungal and bacterial biofilms could lead to novel opportunities for detecting severe infections early.
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122
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Lü F, Chen W, Duan H, Zhang H, Shao L, He P. Monitor process state of batch anaerobic digestion in reliance on volatile and semi-volatile metabolome. BIORESOURCE TECHNOLOGY 2022; 351:126953. [PMID: 35278621 DOI: 10.1016/j.biortech.2022.126953] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/02/2022] [Accepted: 03/03/2022] [Indexed: 06/14/2023]
Abstract
It has been a challenge to recognize appropriate compounds as indicators for monitoring and early-warning of the anaerobic digestion process. A strategy was initiated to explore the evolution of the panorama profile of volatile and semi-volatile metabolites. Non-target analysis using high-resolution gas chromatography coupled with Orbitrap mass spectrometry was applied to construct a time-series molecular fingerprint of 218 metabolites classified in 14 categories. Alkanes accounted for the main part in early and late stages of methanization and aromatic compounds were the major in middle stage. Spearman correlation analysis and partial least squares analysis unwind that Trichococcus (1.49%-83.96%) was positively related to most of metabolites at early and middle stages, while Brevundimonas (0%-24.04%) was positively related to acylamide at late stage. This indicated that microbial volatile organic compounds were possible to serve as biochemical indicators for anaerobic digestion performance and to build nexus of "what" (metabolites), "who" (microorganism), and "how" (kinetics).
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Affiliation(s)
- Fan Lü
- Institute of Waste Treatment and Reclamation, Tongji University, Shanghai 200092, PR China
| | - Wenwen Chen
- Institute of Waste Treatment and Reclamation, Tongji University, Shanghai 200092, PR China
| | - Haowen Duan
- Institute of Waste Treatment and Reclamation, Tongji University, Shanghai 200092, PR China
| | - Hua Zhang
- Institute of Waste Treatment and Reclamation, Tongji University, Shanghai 200092, PR China
| | - Liming Shao
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China
| | - Pinjing He
- Institute of Waste Treatment and Reclamation, Tongji University, Shanghai 200092, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China; Shanghai Engineering Research Center of Multi-source Solid Wastes Co-processing and Energy Utilization, Shanghai 200092, PR China.
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123
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Wang B, Allison SD. Climate-Driven Legacies in Simulated Microbial Communities Alter Litter Decomposition Rates. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.841824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The mechanisms underlying diversity-functioning relationships have been a consistent area of inquiry in biogeochemistry since the 1950s. Though these mechanisms remain unresolved in soil microbiomes, many approaches at varying scales have pointed to the same notion—composition matters. Confronting the methodological challenge arising from the complexity of microbiomes, this study used the model DEMENTpy, a trait-based modeling framework, to explore trait-based drivers of microbiome-dependent litter decomposition. We parameterized DEMENTpy for five sites along a climate gradient in Southern California, United States, and conducted reciprocal transplant simulations analogous to a prior empirical study. The simulations demonstrated climate-dependent legacy effects of microbial communities on plant litter decomposition across the gradient. This result is consistent with the previous empirical study across the same gradient. An analysis of community-level traits further suggests that a 3-way tradeoff among resource acquisition, stress tolerance, and yield strategies influences community assembly. Simulated litter decomposition was predictable with two community traits (indicative of two of the three strategies) plus local environment, regardless of the system state (transient vs. equilibrium). Although more empirical confirmation is still needed, community traits plus local environmental factors (e.g., environment and litter chemistry) may robustly predict litter decomposition across spatial-temporal scales. In conclusion, this study offers a potential trait-based explanation for climate-dependent community effects on litter decomposition with implications for improved understanding of whole-ecosystem functioning across scales.
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124
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Zambri MP, Williams MA, Elliot MA. How Streptomyces thrive: Advancing our understanding of classical development and uncovering new behaviors. Adv Microb Physiol 2022; 80:203-236. [PMID: 35489792 DOI: 10.1016/bs.ampbs.2022.01.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Streptomyces are soil- and marine-dwelling microbes that need to survive dramatic fluctuations in nutrient levels and environmental conditions. Here, we explore the advances made in understanding how Streptomyces bacteria can thrive in their natural environments. We examine their classical developmental cycle, and the intricate regulatory cascades that govern it. We discuss alternative growth strategies and behaviors, like the rapid expansion and colonization properties associated with exploratory growth, the release of membrane vesicles and S-cells from hyphal tips, and the acquisition of exogenous DNA along the lateral walls. We further investigate Streptomyces interactions with other organisms through the release of volatile compounds that impact nutrient levels, microbial growth, and insect behavior. Finally, we explore the increasingly diverse strategies employed by Streptomyces species in escaping and thwarting phage infections.
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Affiliation(s)
- Matthew P Zambri
- Department of Biology, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Michelle A Williams
- Department of Biology, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Marie A Elliot
- Department of Biology, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada.
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125
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Phosphorus and Zinc Are Strongly Associated with Belowground Fungal Communities in Wheat Field under Long-Term Fertilization. Microbiol Spectr 2022; 10:e0011022. [PMID: 35266812 PMCID: PMC9045391 DOI: 10.1128/spectrum.00110-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Belowground fungi are closely related to crop growth, and agricultural fertilization is widely known to affect soil fungal communities. Yet it remains unclear whether fungal communities in differing belowground habitats—root endosphere, rhizosphere soil, and bulk soil—respond differently to long-term fertilization. Here we investigated the variation in fungal communities of root endosphere, rhizosphere soil, and bulk soil under 35 years of fertilization in wheat fields. Specifically, the fertilization regimes were applied as five treatments: soils receiving NPK fertilizer, NPK and cow manure (NPK+CM), NPK and pig manure (NPK+PM), NPK and wheat straw (NPK+WS), and no fertilizer (Control). Long-term fertilization significantly impacted fungal community composition in all three habitats, and these effects were stronger in the rhizosphere and bulk soils than root endosphere. Mantel test results showed that fungal community composition was significantly correlated with phosphorus and zinc contents. Further, fungal alpha diversity was lowest in the NPK+PM treatment and was negatively correlated with both phosphorus and zinc contents. Moreover, NPK+PM treatment had the lowest complexity of fungal co-occurrence network, and in general network complexity was significantly negatively correlated with the zinc and phosphorus contents. Taken together, these results suggest that long-term fertilization can impact fungal communities not only in soils but in root endosphere, and this is strongly associated with the contents of phosphorus and zinc there, a finding important for guiding fertilization management practices and supporting sustainable agriculture. IMPORTANCE Fungi, an essential component in nutrient cycling and plant growth, are highly sensitive to fertilization. However, there are limited studies on fungi in root endosphere under long-term fertilization management. Our research extended the study on the endophytic fungal community of crop roots under agricultural management and found that its responses were similar to the communities in soil habitats. In addition, the type of organic materials was reported as the main driver affecting soil fungal community under long-term fertilization. Our research further revealed that the underlying mechanism of affecting the fungal communities in the soils and roots was the differences in phosphorus and zinc contents caused by the application of different organic materials. Therefore, our results highlight that except for phosphorus, zinc content of the organic materials should be considered in long-term organic fertilization systems.
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126
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Bauermeister A, Mannochio-Russo H, Costa-Lotufo LV, Jarmusch AK, Dorrestein PC. Mass spectrometry-based metabolomics in microbiome investigations. Nat Rev Microbiol 2022; 20:143-160. [PMID: 34552265 PMCID: PMC9578303 DOI: 10.1038/s41579-021-00621-9] [Citation(s) in RCA: 150] [Impact Index Per Article: 75.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2021] [Indexed: 02/08/2023]
Abstract
Microbiotas are a malleable part of ecosystems, including the human ecosystem. Microorganisms affect not only the chemistry of their specific niche, such as the human gut, but also the chemistry of distant environments, such as other parts of the body. Mass spectrometry-based metabolomics is one of the key technologies to detect and identify the small molecules produced by the human microbiota, and to understand the functional role of these microbial metabolites. This Review provides a foundational introduction to common forms of untargeted mass spectrometry and the types of data that can be obtained in the context of microbiome analysis. Data analysis remains an obstacle; therefore, the emphasis is placed on data analysis approaches and integrative analysis, including the integration of microbiome sequencing data.
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Affiliation(s)
- Anelize Bauermeister
- Institute of Biomedical Science, Universidade de São Paulo, São Paulo, SP, Brazil,Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, USA
| | - Helena Mannochio-Russo
- Department of Biochemistry and Organic Chemistry, Institute of Chemistry, São Paulo State University, Araraquara, SP, Brazil,Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, USA
| | | | - Alan K. Jarmusch
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, USA
| | - Pieter C. Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, USA.,Department of Pediatrics, University of California, San Diego, CA, USA.,Center for Microbiome Innovation, University of California, San Diego, CA, USA
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127
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Kodera SM, Das P, Gilbert JA, Lutz HL. Conceptual strategies for characterizing interactions in microbial communities. iScience 2022; 25:103775. [PMID: 35146390 PMCID: PMC8819398 DOI: 10.1016/j.isci.2022.103775] [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: 11/17/2022] Open
Abstract
Understanding the sets of inter- and intraspecies interactions in microbial communities is a fundamental goal of microbial ecology. However, the study and quantification of microbial interactions pose several challenges owing to their complexity, dynamic nature, and the sheer number of unique interactions within a typical community. To overcome such challenges, microbial ecologists must rely on various approaches to distill the system of study to a functional and conceptualizable level, allowing for a practical understanding of microbial interactions in both simplified and complex systems. This review broadly addresses the role of several conceptual approaches available for the microbial ecologist’s arsenal, examines specific tools used to accomplish such approaches, and describes how the assumptions, expectations, and philosophies underlying these tools change across scales of complexity.
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Affiliation(s)
- Sho M Kodera
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, USA
| | - Promi Das
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, USA.,Department of Pediatrics, University of California San Diego, La Jolla, CA 92161, USA
| | - Jack A Gilbert
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, USA.,Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, USA.,Department of Pediatrics, University of California San Diego, La Jolla, CA 92161, USA
| | - Holly L Lutz
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, USA.,Department of Pediatrics, University of California San Diego, La Jolla, CA 92161, USA.,Negaunee Integrative Collections Center, Field Museum of Natural History, Chicago, IL 60605, USA
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128
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Deshmukh SK, Dufossé L, Chhipa H, Saxena S, Mahajan GB, Gupta MK. Fungal Endophytes: A Potential Source of Antibacterial Compounds. J Fungi (Basel) 2022; 8:164. [PMID: 35205918 PMCID: PMC8877021 DOI: 10.3390/jof8020164] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/04/2022] [Accepted: 02/05/2022] [Indexed: 02/04/2023] Open
Abstract
Antibiotic resistance is becoming a burning issue due to the frequent use of antibiotics for curing common bacterial infections, indicating that we are running out of effective antibiotics. This has been more obvious during recent corona pandemics. Similarly, enhancement of antimicrobial resistance (AMR) is strengthening the pathogenicity and virulence of infectious microbes. Endophytes have shown expression of various new many bioactive compounds with significant biological activities. Specifically, in endophytic fungi, bioactive metabolites with unique skeletons have been identified which could be helpful in the prevention of increasing antimicrobial resistance. The major classes of metabolites reported include anthraquinone, sesquiterpenoid, chromone, xanthone, phenols, quinones, quinolone, piperazine, coumarins and cyclic peptides. In the present review, we reported 451 bioactive metabolites isolated from various groups of endophytic fungi from January 2015 to April 2021 along with their antibacterial profiling, chemical structures and mode of action. In addition, we also discussed various methods including epigenetic modifications, co-culture, and OSMAC to induce silent gene clusters for the production of noble bioactive compounds in endophytic fungi.
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Affiliation(s)
- Sunil K Deshmukh
- TERI-Deakin Nano Biotechnology Centre, The Energy and Resources Institute, Darbari Seth Block, IHC Complex, Lodhi Road, New Delhi 110003, Delhi, India
- Agpharm Bioinnovations LLP, Incubatee: Science and Technology Entrepreneurs Park (STEP), Thapar Institute of Engineering and Technology, Patiala 147004, Punjab, India
| | - Laurent Dufossé
- Chimie et Biotechnologie des Produits Naturels (CHEMBIOPRO Lab) & ESIROI Agroalimentaire, Université de la Réunion, 15 Avenue René Cassin, 97744 Saint-Denis, France
| | - Hemraj Chhipa
- College of Horticulture and Forestry, Agriculture University Kota, Jhalawar 322360, Rajasthan, India
| | - Sanjai Saxena
- Agpharm Bioinnovations LLP, Incubatee: Science and Technology Entrepreneurs Park (STEP), Thapar Institute of Engineering and Technology, Patiala 147004, Punjab, India
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala 147004, Punjab, India
| | - Girish B Mahajan
- HiMedia Laboratories Pvt. Ltd., Mumbai 400086, Maharashtra, India
| | - Manish Kumar Gupta
- SGT College of Pharmacy, SGT University, Gurugram 122505, Haryana, India
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129
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Antifungal volatile organic compounds from Streptomyces setonii WY228 control black spot disease of sweet potato. Appl Environ Microbiol 2022; 88:e0231721. [PMID: 35108080 DOI: 10.1128/aem.02317-21] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Volatile organic compounds (VOCs) produced by microorganisms are considered as promising environmental-safety fumigants for controlling postharvest diseases. Ceratocystis fimbriata, the pathogen of black spot disease, seriously affects the quality and yield of sweet potato in the field and postharvest. This study tested the effects of VOCs produced by Streptomyces setonii WY228 on the control of C. fimbriata in vitro and in vivo. The VOCs exhibited strong antifungal activity and significantly inhibited the growth of C. fimbriata. During the 20-days storage, VOCs fumigation significantly controlled the occurrence of pathogen, increased the content of antioxidant and defense-related enzymes and flavonoids, and boosted the starch content so as to maintain the quality of sweet potato. Headspace analysis showed that volatiles 2-ethyl-5-methylpyrazine and dimethyl disulfide significantly inhibited the mycelial growth and spore germination of C. fimbriata in a dose dependent manner. Fumigation with 100 μL/L 2-ethyl-5-methylpyrazine completely controlled the pathogen in vivo after 10-days storage. Transcriptome analysis showed that volatiles mainly downregulated the ribosomal synthesis genes and activated the proteasome system of pathogen in response to VOCs stress, while the genes related to spore development, cell membrane synthesis, mitochondrial function, as well as hydrolase and toxin synthesis were also downregulated, indicating that WY228-produced VOCs act diverse modes of action for pathogen control. Our study demonstrates that fumigation of sweet potato tuberous roots with S. setonii WY228 or use of formulations based on the VOCs is a promising new strategy to control sweet potato and other food and fruit pathogens during storage and shipment. Importance Black spot disease caused by Ceratocystis fimbriata has caused huge economic losses to worldwide sweet potato production. At present, the control of C. fimbriata mainly depends on toxic fungicides, and there is a lack of effective alternative strategies. The research on biological control of sweet potato black spot disease is also very limited. The development of efficient biocontrol technique against pathogens using microbial volatile organic compounds could be an alternative method to control this disease. Our study revealed the significant biological control effect of volatile organic compounds of Streptomyces setonii WY228 on black spot disease of postharvest sweet potato and the complex antifungal mechanism against C. fimbriata. Our data demonstrated that Streptomyces setonii WY228 and its volatile 2-ethyl-5-methylpyrazine could be candidate strain and compound for the creation of fumigants, and showed the important potential of biotechnology application in the field of food and agriculture.
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130
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Costa A, Corallo B, Amarelle V, Stewart S, Pan D, Tiscornia S, Fabiano E. Paenibacillus sp. Strain UY79, Isolated from a Root Nodule of Arachis villosa, Displays a Broad Spectrum of Antifungal Activity. Appl Environ Microbiol 2022; 88:e0164521. [PMID: 34757818 PMCID: PMC8788682 DOI: 10.1128/aem.01645-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 11/02/2021] [Indexed: 11/20/2022] Open
Abstract
A nodule-inhabiting Paenibacillus sp. strain (UY79) isolated from wild peanut (Arachis villosa) was screened for its antagonistic activity against diverse fungi and oomycetes (Botrytis cinerea, Fusarium verticillioides, Fusarium oxysporum, Fusarium graminearum, Fusarium semitectum, Macrophomina phaseolina, Phomopsis longicolla, Pythium ultimum, Phytophthora sojae, Rhizoctonia solani, Sclerotium rolfsii, and Trichoderma atroviride). The results obtained show that Paenibacillus sp. UY79 was able to antagonize these fungi/oomycetes and that agar-diffusible compounds and volatile compounds (different from HCN) participate in the antagonism exerted. Acetoin, 2,3-butanediol, and 2-methyl-1-butanol were identified among the volatile compounds produced by strain UY79 with possible antagonistic activity against fungi/oomycetes. Paenibacillus sp. strain UY79 did not affect symbiotic association or growth promotion of alfalfa plants when coinoculated with rhizobia. By whole-genome sequence analysis, we determined that strain UY79 is a new species of Paenibacillus within the Paenibacillus polymyxa complex. Diverse genes putatively involved in biocontrol activity were identified in the UY79 genome. Furthermore, according to genome mining and antibiosis assays, strain UY79 would have the capability to modulate the growth of bacteria commonly found in soil/plant communities. IMPORTANCE Phytopathogenic fungi and oomycetes are responsible for causing devastating losses in agricultural crops. Therefore, there is enormous interest in the development of effective and complementary strategies that allow the control of the phytopathogens, reducing the input of agrochemicals in croplands. The discovery of new strains with expanded antifungal activities and with a broad spectrum of action is challenging and of great future impact. Diverse strains belonging to the P. polymyxa complex have been reported to be effective biocontrol agents. Results presented here show that the novel discovered strain of Paenibacillus sp. presents diverse traits involved in antagonistic activity against a broad spectrum of pathogens and is a potential and valuable strain to be further assessed for the development of biofungicides.
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Affiliation(s)
- Andrés Costa
- Biochemistry and Microbial Genomics Department, Instituto de Investigaciones Biológicas Clemente Estable, Ministerio de Educación y Cultura, Montevideo, Uruguay
| | - Belén Corallo
- Sección Micología, Facultad de Ciencias-Universidad de la República, Montevideo, Uruguay
| | - Vanesa Amarelle
- Biochemistry and Microbial Genomics Department, Instituto de Investigaciones Biológicas Clemente Estable, Ministerio de Educación y Cultura, Montevideo, Uruguay
| | - Silvina Stewart
- Instituto Nacional de Investigación Agropecuaria (INIA), Programa Cultivos de Secano. Estación Experimental La Estanzuela, Colonia, Uruguay
| | - Dinorah Pan
- Sección Micología, Facultad de Ciencias-Universidad de la República, Montevideo, Uruguay
| | - Susana Tiscornia
- Sección Micología, Facultad de Ciencias-Universidad de la República, Montevideo, Uruguay
| | - Elena Fabiano
- Biochemistry and Microbial Genomics Department, Instituto de Investigaciones Biológicas Clemente Estable, Ministerio de Educación y Cultura, Montevideo, Uruguay
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131
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Cova CM, Rincón E, Espinosa E, Serrano L, Zuliani A. Paving the Way for a Green Transition in the Design of Sensors and Biosensors for the Detection of Volatile Organic Compounds (VOCs). BIOSENSORS 2022; 12:51. [PMID: 35200311 PMCID: PMC8869180 DOI: 10.3390/bios12020051] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/13/2022] [Accepted: 01/18/2022] [Indexed: 05/06/2023]
Abstract
The efficient and selective detection of volatile organic compounds (VOCs) provides key information for various purposes ranging from the toxicological analysis of indoor/outdoor environments to the diagnosis of diseases or to the investigation of biological processes. In the last decade, different sensors and biosensors providing reliable, rapid, and economic responses in the detection of VOCs have been successfully conceived and applied in numerous practical cases; however, the global necessity of a sustainable development, has driven the design of devices for the detection of VOCs to greener methods. In this review, the most recent and innovative VOC sensors and biosensors with sustainable features are presented. The sensors are grouped into three of the main industrial sectors of daily life, including environmental analysis, highly important for toxicity issues, food packaging tools, especially aimed at avoiding the spoilage of meat and fish, and the diagnosis of diseases, crucial for the early detection of relevant pathological conditions such as cancer and diabetes. The research outcomes presented in the review underly the necessity of preparing sensors with higher efficiency, lower detection limits, improved selectivity, and enhanced sustainable characteristics to fully address the sustainable manufacturing of VOC sensors and biosensors.
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Affiliation(s)
- Camilla Maria Cova
- Department of Chemistry, University of Florence and CSGI, Via della Lastruccia 3, 50019 Sesto Fiorentino, FI, Italy;
| | - Esther Rincón
- BioPren Group, Inorganic Chemistry and Chemical Engineering Department, Faculty of Sciences, University of Cordoba, 14014 Cordoba, Spain; (E.R.); (E.E.); (L.S.)
| | - Eduardo Espinosa
- BioPren Group, Inorganic Chemistry and Chemical Engineering Department, Faculty of Sciences, University of Cordoba, 14014 Cordoba, Spain; (E.R.); (E.E.); (L.S.)
| | - Luis Serrano
- BioPren Group, Inorganic Chemistry and Chemical Engineering Department, Faculty of Sciences, University of Cordoba, 14014 Cordoba, Spain; (E.R.); (E.E.); (L.S.)
| | - Alessio Zuliani
- Department of Chemistry, University of Florence and CSGI, Via della Lastruccia 3, 50019 Sesto Fiorentino, FI, Italy;
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132
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Meredith LK, Tfaily MM. Capturing the microbial volatilome: an oft overlooked 'ome'. Trends Microbiol 2022; 30:622-631. [PMID: 35039213 DOI: 10.1016/j.tim.2021.12.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 12/03/2021] [Accepted: 12/08/2021] [Indexed: 11/26/2022]
Abstract
Among the diverse metabolites produced by microbial communities, some are volatile. Volatile organic compounds (VOCs) are vigorously cycled by microbes as metabolic substrates and products and as signaling molecules. Yet, current microbial metabolomic studies predominantly focus on nonvolatile metabolites and overlook VOCs, which therefore represent a missing component of the metabolome. Advances in VOC detection now allow simultaneous observation of the numerous VOCs constituting the 'volatilome' of microbial systems. We present a roadmap for integrating and advancing VOC and other 'omics approaches and highlight the potential for realtime VOC measurements to help overcome limitations in discrete 'omics sampling. Including volatile metabolites in metabolomics, both conceptually and in practice, will build a more comprehensive understanding of microbial processes across ecological communities.
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Affiliation(s)
- Laura K Meredith
- School of Natural Resources and the Environment, University of Arizona, Tucson, AZ, USA; BIO5 Institute, University of Arizona, Tucson, AZ, USA.
| | - Malak M Tfaily
- BIO5 Institute, University of Arizona, Tucson, AZ, USA; Department of Environmental Science, University of Arizona, Tucson, AZ, USA.
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Lammers A, Lalk M, Garbeva P. Air Ambulance: Antimicrobial Power of Bacterial Volatiles. Antibiotics (Basel) 2022; 11:antibiotics11010109. [PMID: 35052986 PMCID: PMC8772769 DOI: 10.3390/antibiotics11010109] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 01/09/2022] [Accepted: 01/11/2022] [Indexed: 12/19/2022] Open
Abstract
We are currently facing an antimicrobial resistance crisis, which means that a lot of bacterial pathogens have developed resistance to common antibiotics. Hence, novel and innovative solutions are urgently needed to combat resistant human pathogens. A new source of antimicrobial compounds could be bacterial volatiles. Volatiles are ubiquitous produced, chemically divers and playing essential roles in intra- and interspecies interactions like communication and antimicrobial defense. In the last years, an increasing number of studies showed bioactivities of bacterial volatiles, including antibacterial, antifungal and anti-oomycete activities, indicating bacterial volatiles as an exciting source for novel antimicrobial compounds. In this review we introduce the chemical diversity of bacterial volatiles, their antimicrobial activities and methods for testing this activity. Concluding, we discuss the possibility of using antimicrobial volatiles to antagonize the antimicrobial resistance crisis.
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Affiliation(s)
- Alexander Lammers
- Department of Cellular Biochemistry and Metabolomics, University of Greifswald, 17487 Greifswald, Germany;
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands
- Correspondence: or (A.L.); (P.G.)
| | - Michael Lalk
- Department of Cellular Biochemistry and Metabolomics, University of Greifswald, 17487 Greifswald, Germany;
| | - Paolina Garbeva
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands
- Correspondence: or (A.L.); (P.G.)
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134
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Vlot AC, Rosenkranz M. Volatile compounds-the language of all kingdoms? JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:445-448. [PMID: 35024870 PMCID: PMC8757488 DOI: 10.1093/jxb/erab528] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Affiliation(s)
- A Corina Vlot
- Helmholtz Zentrum Muenchen, Institute of Biochemical Plant Pathology, Ingolstaedter Landstr. 1, D-85764 Neuherberg, Germany
| | - Maaria Rosenkranz
- Helmholtz Zentrum Muenchen, Institute of Biochemical Plant Pathology, Research Unit Environmental Simulation, Ingolstaedter Landstr. 1, D-85764 Neuherberg, Germany
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135
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Sharifi R, Jeon JS, Ryu CM. Belowground plant-microbe communications via volatile compounds. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:463-486. [PMID: 34727189 DOI: 10.1093/jxb/erab465] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 10/21/2021] [Indexed: 06/13/2023]
Abstract
Volatile compounds play important roles in rhizosphere biological communications and interactions. The emission of plant and microbial volatiles is a dynamic phenomenon that is affected by several endogenous and exogenous signals. Diffusion of volatiles can be limited by their adsorption, degradation, and dissolution under specific environmental conditions. Therefore, rhizosphere volatiles need to be investigated on a micro and spatiotemporal scale. Plant and microbial volatiles can expand and specialize the rhizobacterial niche not only by improving the root system architecture such that it serves as a nutrient-rich shelter, but also by inhibiting or promoting the growth, chemotaxis, survival, and robustness of neighboring organisms. Root volatiles play an important role in engineering the belowground microbiome by shaping the microbial community structure and recruiting beneficial microbes. Microbial volatiles are appropriate candidates for improving plant growth and health during environmental challenges and climate change. However, some technical and experimental challenges limit the non-destructive monitoring of volatile emissions in the rhizosphere in real-time. In this review, we attempt to clarify the volatile-mediated intra- and inter-kingdom communications in the rhizosphere, and propose improvements in experimental design for future research.
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Affiliation(s)
- Rouhallah Sharifi
- Department of Plant Protection, College of Agriculture and Natural Resources, Razi University, Kermanshah, Iran
| | - Je-Seung Jeon
- Molecular Phytobacteriology Laboratory, Infectious Disease Research Center, KRIBB, Daejeon 34141, South Korea
| | - Choong-Min Ryu
- Molecular Phytobacteriology Laboratory, Infectious Disease Research Center, KRIBB, Daejeon 34141, South Korea
- Biosystem and Bioengineering Program, University of Science and Technology (UST), Daejeon 34141, South Korea
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Song GC, Jeon JS, Sim HJ, Lee S, Jung J, Kim SG, Moon SY, Ryu CM. Dual functionality of natural mixtures of bacterial volatile compounds on plant growth. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:571-583. [PMID: 34679179 DOI: 10.1093/jxb/erab466] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 10/21/2021] [Indexed: 06/13/2023]
Abstract
Bacteria emit volatile compounds that modulate plant growth. Previous studies reported the impacts of bacterial volatile compounds on plant growth; however, the results varied depending on bacterial nutrient availability. We investigated whether the effects of plant growth-inhibiting volatiles (PGIVs) and plant growth-promoting volatiles (PGPVs) depended on the perceived dose by evaluating the growth of Arabidopsis thaliana seedlings placed at 7, 14, and 21 cm away from Bacillus amyloliquefaciens GB03 colonies growing in rich medium. A large bacterial colony (500 μl inoculum) inhibited plant growth at 7 cm and promoted growth at 21 cm, whereas a small bacterial colony (100 μl inoculum) induced the opposite pattern of response. We identified pyrazine and 2,5-dimethylpyrazine as candidate PGIVs that significantly reduced plant growth at a distance of 7 cm. PGIV effects were validated by exposing plants to synthetic 2,5-dimethylpyrazine and bacteria emitting PGPVs, which showed that PGIVs overwhelm PGPVs to rapidly increase salicylic acid content and related gene expression. This is referred to as the defence-growth trade-off. Our results indicate that high PGIV concentrations suppress plant growth and promote immunity, whereas low PGPV concentrations promote growth. This study provides novel insights into the complex effects of bacterial volatile mixtures and fine-tuning of bacteria-plant interactions.
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Affiliation(s)
- Geun Cheol Song
- Molecular Phytobacteriology Laboratory, KRIBB, Daejeon 34141, S. Korea
| | - Je-Seung Jeon
- Molecular Phytobacteriology Laboratory, KRIBB, Daejeon 34141, S. Korea
| | - Hee-Jung Sim
- Center for Genome Engineering, Institute for Basic Science (IBS), Daejeon 34126, S. Korea
- Environmental Safety Assessment Center, Korea Institute of Toxicology (KIT), 17 Jegok-gil, Munsan-eup, Jinju 52834, South Korea
| | - Soohyun Lee
- Molecular Phytobacteriology Laboratory, KRIBB, Daejeon 34141, S. Korea
| | - Jihye Jung
- Molecular Phytobacteriology Laboratory, KRIBB, Daejeon 34141, S. Korea
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Sang-Gyu Kim
- Center for Genome Engineering, Institute for Basic Science (IBS), Daejeon 34126, S. Korea
| | - Sun Young Moon
- Center for Genome Engineering, Institute for Basic Science (IBS), Daejeon 34126, S. Korea
| | - Choong-Min Ryu
- Molecular Phytobacteriology Laboratory, KRIBB, Daejeon 34141, S. Korea
- Biosystems and Bioengineering Program, University of Science and Technology (UST), Daejeon 34113, S. Korea
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137
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Pennerman KK, Yin G, Bennett JW. Eight-carbon volatiles: prominent fungal and plant interaction compounds. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:487-497. [PMID: 34727164 DOI: 10.1093/jxb/erab438] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 09/24/2021] [Indexed: 06/13/2023]
Abstract
Signaling via volatile organic compounds (VOCs) has historically been studied mostly by entomologists; however, botanists and mycologists are increasingly aware of the physiological potential of chemical communication in the gas phase. Most research to date focuses on the observed effects of VOCs on different organisms such as differential growth or metabolite production. However, with the increased interest in volatile signaling, more researchers are investigating the molecular mechanisms for these effects. Eight-carbon VOCs are among the most prevalent and best-studied fungal volatiles. Therefore, this review emphasizes examples of eight-carbon VOCs affecting plants and fungi. These compounds display different effects that include growth suppression in both plants and fungi, induction of defensive behaviors such as accumulation of mycotoxins, phytohormone signaling cascades, and the inhibition of spore and seed germination. Application of '-omics' and other next-generation sequencing techniques is poised to decipher the mechanistic basis of volatiles in plant-fungal communication.
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Affiliation(s)
- Kayla K Pennerman
- Joint Institute for Food Safety and Applied Nutrition, University of Maryland, College Park, MD 20742, USA
- United States Department of Agriculture, Toxicology and Mycotoxin Research Unit, Athens, GA 30605, USA
| | - Guohua Yin
- United States Department of Agriculture, Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Peoria, IL 61604, USA
- Department of Plant Biology, Rutgers University, The State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Joan W Bennett
- Department of Plant Biology, Rutgers University, The State University of New Jersey, New Brunswick, NJ 08901, USA
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138
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Djemiel C, Maron PA, Terrat S, Dequiedt S, Cottin A, Ranjard L. Inferring microbiota functions from taxonomic genes: a review. Gigascience 2022; 11:giab090. [PMID: 35022702 PMCID: PMC8756179 DOI: 10.1093/gigascience/giab090] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 12/02/2021] [Accepted: 12/02/2021] [Indexed: 12/13/2022] Open
Abstract
Deciphering microbiota functions is crucial to predict ecosystem sustainability in response to global change. High-throughput sequencing at the individual or community level has revolutionized our understanding of microbial ecology, leading to the big data era and improving our ability to link microbial diversity with microbial functions. Recent advances in bioinformatics have been key for developing functional prediction tools based on DNA metabarcoding data and using taxonomic gene information. This cheaper approach in every aspect serves as an alternative to shotgun sequencing. Although these tools are increasingly used by ecologists, an objective evaluation of their modularity, portability, and robustness is lacking. Here, we reviewed 100 scientific papers on functional inference and ecological trait assignment to rank the advantages, specificities, and drawbacks of these tools, using a scientific benchmarking. To date, inference tools have been mainly devoted to bacterial functions, and ecological trait assignment tools, to fungal functions. A major limitation is the lack of reference genomes-compared with the human microbiota-especially for complex ecosystems such as soils. Finally, we explore applied research prospects. These tools are promising and already provide relevant information on ecosystem functioning, but standardized indicators and corresponding repositories are still lacking that would enable them to be used for operational diagnosis.
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Affiliation(s)
- Christophe Djemiel
- Agroécologie, AgroSup Dijon, INRAE, Université de Bourgogne, Université de Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Pierre-Alain Maron
- Agroécologie, AgroSup Dijon, INRAE, Université de Bourgogne, Université de Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Sébastien Terrat
- Agroécologie, AgroSup Dijon, INRAE, Université de Bourgogne, Université de Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Samuel Dequiedt
- Agroécologie, AgroSup Dijon, INRAE, Université de Bourgogne, Université de Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Aurélien Cottin
- Agroécologie, AgroSup Dijon, INRAE, Université de Bourgogne, Université de Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Lionel Ranjard
- Agroécologie, AgroSup Dijon, INRAE, Université de Bourgogne, Université de Bourgogne Franche-Comté, F-21000 Dijon, France
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139
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Singh SK, Wu X, Shao C, Zhang H. Microbial enhancement of plant nutrient acquisition. STRESS BIOLOGY 2022; 2:3. [PMID: 37676341 PMCID: PMC10441942 DOI: 10.1007/s44154-021-00027-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 12/10/2021] [Indexed: 09/08/2023]
Abstract
Nutrient availability is a determining factor for crop yield and quality. While fertilization is a major approach for improving plant nutrition, its efficacy can be limited and the production and application of fertilizers frequently bring problems to the environment. A large number of soil microbes are capable of enhancing plant nutrient acquisition and thereby offer environmentally benign solutions to meet the requirements of plant nutrition. Herein we provide summations of how beneficial microbes enhance plant acquisition of macronutrients and micronutrients. We also review recent studies on nutrition-dependent plant-microbe interactions, which highlight the plant's initiative in establishing or deterring the plant-microbe association. By dissecting complex signaling interactions between microbes within the root microbiome, a greater understanding of microbe-enhanced plant nutrition under specific biotic and abiotic stresses will be possible.
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Affiliation(s)
- Sunil K Singh
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Xiaoxuan Wu
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chuyang Shao
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Huiming Zhang
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China.
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140
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Dai L, Li H, Zheng J, Chen H. Transcriptome analyses of the Chinese white pine beetle-fungal symbiont Leptographium qinlingensis under terpene stress or growth on host pine sawdust. Symbiosis 2022. [DOI: 10.1007/s13199-021-00822-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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141
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Freitas CSA, Maciel LF, Corrêa Dos Santos RA, Costa OMMM, Maia FCB, Rabelo RS, Franco HCJ, Alves E, Consonni SR, Freitas RO, Persinoti GF, Oliveira JVDC. Bacterial volatile organic compounds induce adverse ultrastructural changes and DNA damage to the sugarcane pathogenic fungus Thielaviopsis ethacetica. Environ Microbiol 2022; 24:1430-1453. [PMID: 34995419 DOI: 10.1111/1462-2920.15876] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 12/10/2021] [Accepted: 12/13/2021] [Indexed: 02/06/2023]
Abstract
Due to an increasing demand for sustainable agricultural practices, the adoption of microbial volatile organic compounds (VOCs) as antagonists against phytopathogens has emerged as an eco-friendly alternative to the use of agrochemicals. Here, we identified three Pseudomonas strains that were able to inhibit, in vitro, up to 80% of mycelial growth of the phytopathogenic fungus Thielaviopsis ethacetica, the causal agent of pineapple sett rot disease in sugarcane. Using GC/MS, we found that these bacteria produced 62 different VOCs, and further functional validation revealed compounds with high antagonistic activity to T. ethacetica. Transcriptomic analysis of the fungal response to VOCs indicated that these metabolites downregulated genes related to fungal central metabolism, such as those involved in carbohydrate metabolism. Interestingly, genes related to the DNA damage response were upregulated, and micro-FTIR analysis corroborated our hypothesis that VOCs triggered DNA damage. Electron microscopy analysis showed critical morphological changes in mycelia treated with VOCs. Altogether, these results indicated that VOCs hampered fungal growth and could lead to cell death. This study represents the first demonstration of the molecular mechanisms involved in the antagonism of sugarcane phytopathogens by VOCs and reinforces that VOCs can be a sustainable alternative for use in phytopathogen biocontrol.
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Affiliation(s)
- Carla Sant Anna Freitas
- Brazilian Biorenewable National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, Brazil.,Genetics and Molecular Biology Graduate Program, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Lucas Ferreira Maciel
- Brazilian Biorenewable National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, Brazil
| | - Renato Augusto Corrêa Dos Santos
- Genetics and Molecular Biology Graduate Program, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.,School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - Ohanna Maria Menezes Medeiro Costa
- Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, Brazil
| | - Francisco Carlos Barbosa Maia
- Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, Brazil
| | - Renata Santos Rabelo
- Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, Brazil
| | | | - Eduardo Alves
- Laboratory of Electron Microscopy and Ultrastructural Analysis, Plant Pathology Department, Federal University of Lavras (UFLA), Lavras, Minas Gerais, Brazil
| | - Sílvio Roberto Consonni
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Raul Oliveira Freitas
- Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, Brazil
| | - Gabriela Felix Persinoti
- Brazilian Biorenewable National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, Brazil
| | - Juliana Velasco de Castro Oliveira
- Brazilian Biorenewable National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, Brazil.,Genetics and Molecular Biology Graduate Program, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
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142
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Wei N, Whyle RL, Ashman TL, Jamieson MA. Genotypic variation in floral volatiles influences floral microbiome more strongly than interactions with herbivores and mycorrhizae in strawberriesd. HORTICULTURE RESEARCH 2022; 9:uhab005. [PMID: 35141759 PMCID: PMC8795819 DOI: 10.1093/hr/uhab005] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 01/18/2022] [Accepted: 10/15/2021] [Indexed: 06/14/2023]
Abstract
The floral microbiome is of significant relevance to plant reproduction and crop productivity. While plant genotype is key to floral microbiome assembly, whether and how genotypic variation in floral traits and plant-level mutualistic and antagonistic interactions at the rhizosphere and phyllosphere influence the microbiome in the anthosphere remain little known. Using a factorial field experiment that manipulated biotic interactions belowground (mycorrhizae treatments) and aboveground (herbivory treatments) in three strawberry genotypes, we assessed how genotypic variation in flower abundance and size and plant-level biotic interactions influence the bidirectional relationships between floral volatile organic compounds (VOCs) and the floral microbiome using structural equation modeling. We found that plant genotype played a stronger role, overall, in shaping the floral microbiome than biotic interactions with mycorrhizae and herbivores. Genotypic variation in flower abundance and size influenced the emission of floral VOCs, especially terpenes (e.g. α- and β-pinene, ocimene isomers) and benzenoids (e.g. p-anisaldehyde, benzaldehyde), which in turn affected floral bacterial and fungal communities. While the effects of biotic interactions on floral traits including VOCs were weak, mycorrhizae treatments (mycorrhizae and herbivory + mycorrhizae) affected the fungal community composition in flowers. These findings improve our understanding of the mechanisms by which plant genotype influences floral microbiome assembly and provide the first evidence that biotic interactions in the rhizosphere and phyllosphere can influence the floral microbiome, and offer important insights into agricultural microbiomes.
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Affiliation(s)
- Na Wei
- The Holden Arboretum, Kirtland, OH 44094, USA
- Department of Biological Sciences, University of Pittsburg, Pittsburg, PA 15260, USA
| | - Robert L Whyle
- Department of Biological Sciences, Oakland University, Rochester, MI 48309, USA
| | - Tia-Lynn Ashman
- Department of Biological Sciences, University of Pittsburg, Pittsburg, PA 15260, USA
| | - Mary A Jamieson
- Department of Biological Sciences, Oakland University, Rochester, MI 48309, USA
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143
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Tan Y, Luo Y, Wang J, Liu N. Effect of Dietary Tetramethylpyrazine on Egg Production, Nutrient Retention and Cecal Bacterial Diversity in Aged Laying Hens. BRAZILIAN JOURNAL OF POULTRY SCIENCE 2022. [DOI: 10.1590/1806-9061-2021-1524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Y Tan
- Henan University of Science and Technology, China
| | - Y Luo
- Henan University of Science and Technology, China
| | - J Wang
- Henan University of Science and Technology, China
| | - N Liu
- Henan University of Science and Technology, China; National Engineering Research Center of Biological Feed, China
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144
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Song GC, Jeon J, Choi HK, Sim H, Kim S, Ryu C. Bacterial type III effector-induced plant C8 volatiles elicit antibacterial immunity in heterospecific neighbouring plants via airborne signalling. PLANT, CELL & ENVIRONMENT 2022; 45:236-247. [PMID: 34708407 PMCID: PMC9298316 DOI: 10.1111/pce.14209] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 10/08/2021] [Accepted: 10/15/2021] [Indexed: 05/10/2023]
Abstract
Upon sensing attack by pathogens and insect herbivores, plants release complex mixtures of volatile compounds. Here, we show that the infection of lima bean (Phaseolus lunatus L.) plants with the non-host bacterial pathogen Pseudomonas syringae pv. tomato led to the production of microbe-induced plant volatiles (MIPVs). Surprisingly, the bacterial type III secretion system, which injects effector proteins directly into the plant cytosol to subvert host functions, was found to prime both intra- and inter-specific defense responses in neighbouring wild tobacco (Nicotiana benthamiana) plants. Screening of each of 16 effectors using the Pseudomonas fluorescens effector-to-host analyser revealed that an effector, HopP1, was responsible for immune activation in receiver tobacco plants. Further study demonstrated that 1-octen-3-ol, 3-octanone and 3-octanol are novel MIPVs emitted by the lima bean plant in a HopP1-dependent manner. Exposure to synthetic 1-octen-3-ol activated immunity in tobacco plants against a virulent pathogen Pseudomonas syringae pv. tabaci. Our results show for the first time that a bacterial type III effector can trigger the emission of C8 plant volatiles that mediate defense priming via plant-plant interactions. These results provide novel insights into the role of airborne chemicals in bacterial pathogen-induced inter-specific plant-plant interactions.
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Affiliation(s)
- Geun Cheol Song
- Molecular Phytobacteriology LaboratoryInfectious Disease Research Center, KRIBBDaejeonSouth Korea
| | - Je‐Seung Jeon
- Molecular Phytobacteriology LaboratoryInfectious Disease Research Center, KRIBBDaejeonSouth Korea
| | - Hye Kyung Choi
- Molecular Phytobacteriology LaboratoryInfectious Disease Research Center, KRIBBDaejeonSouth Korea
| | - Hee‐Jung Sim
- Environmental Chemistry Research GroupKorea Institute of Toxicology (KIT)JinjuSouth Korea
| | - Sang‐Gyu Kim
- Department of Biological SciencesKorea Advanced Institute of Science and TechnologyDaejeonSouth Korea
| | - Choong‐Min Ryu
- Molecular Phytobacteriology LaboratoryInfectious Disease Research Center, KRIBBDaejeonSouth Korea
- Biosystems and Bioengineering ProgramUniversity of Science and Technology (UST)DaejeonSouth Korea
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145
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Ehlers S, Schulz S. The scent chemistry of butterflies. Nat Prod Rep 2022; 40:794-818. [PMID: 36420976 DOI: 10.1039/d2np00067a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Butterflies use structurally highly diverse volatile compounds for communication, in addition to visual signals. These compounds originate from plants or a formed de novo especially by male butterflies that possess specific scent organs.
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Affiliation(s)
- Stephanie Ehlers
- Institute of Organic Chemistry, Technische Universität Braunschweig, Hagenring 30, 38106 Braunschweig, Germany
| | - Stefan Schulz
- Institute of Organic Chemistry, Technische Universität Braunschweig, Hagenring 30, 38106 Braunschweig, Germany
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146
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The Effect of Volatile Organic Compounds on Different Organisms: Agrobacteria, Plants and Insects. Microorganisms 2021; 10:microorganisms10010069. [PMID: 35056518 PMCID: PMC8781025 DOI: 10.3390/microorganisms10010069] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/22/2021] [Accepted: 12/27/2021] [Indexed: 01/29/2023] Open
Abstract
Bacteria and fungi emit a huge variety of volatile organic compounds (VOCs) that can provide a valuable arsenal for practical use. However, the biological activities and functions of the VOCs are poorly understood. This work aimed to study the action of individual VOCs on the bacteria Agrobacterium tumefaciens, Arabidopsis thaliana plants, and fruit flies Drosophila melanogaster. VOCs used in the work included ketones, alcohols, and terpenes. The potent inhibitory effect on the growth of A. tumefaciens was shown for 2-octanone and isoamyl alcohol. Terpenes (−)-limonene and (+)-α-pinene practically did not act on bacteria, even at high doses (up to 400 µmol). 2-Butanone and 2-pentanone increased the biomass of A. thaliana at doses of 200–400 μmol by 1.5–2 times; 2-octanone had the same effect at 10 μmol and decreased plant biomass at higher doses. Isoamyl alcohol and 2-phenylethanol suppressed plant biomass several times at doses of 50–100 μmol. Plant seed germination was most strongly suppressed by isoamyl alcohol and 2-phenylethanol. The substantial killing effect (at low doses) on D. melanogaster was exerted by the terpenes and the ketones 2-octanone and 2-pentanone. The obtained data showed new information about the biological activities of VOCs in relation to organisms belonging to different kingdoms.
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147
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Phylogeny of Leptographium qinlingensis cytochrome P450 genes and transcription levels of six CYPs in response to different nutrition media or terpenoids. Arch Microbiol 2021; 204:16. [DOI: 10.1007/s00203-021-02616-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 11/29/2021] [Accepted: 11/30/2021] [Indexed: 12/16/2022]
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148
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Barghi A, Esposti LD, Iafisco M, Adamiano A, Casado GE, Ivanchenko P, Mino L, Yoon HY, Joe EN, Jeon JR, Chang YS. Microbial Volatile Organic Compound (VOC)-Driven Dissolution and Surface Modification of Phosphorus-Containing Soil Minerals for Plant Nutrition: An Indirect Route for VOC-Based Plant-Microbe Communications. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:14478-14487. [PMID: 34813307 DOI: 10.1021/acs.jafc.1c05187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We investigated the ability of microbial volatile organic compounds (MVOCs) emitted by Bacillus megaterium (a well-known MVOC producer) to modify the dissolution kinetics and surface of hydroxyapatite, a natural soil mineral. Facilitated phosphate release was induced by the airborne MVOCs in a time-dependent manner. Use of each standard chemical of the MVOCs then revealed that acetic and oxalic acids are crucial for the phenomenon. In addition, the ability of such MVOCs to engineer the apatite surfaces was evidenced by FT-IR spectra showing the COO- band variation with incubation time and the prolonged acceleration of phosphate release during the negligible acidification of the hydroxyapatite-containing solutions. The formation of calcium oxalate was revealed through SEM-EDS and XRD analyses, suggesting that MVOC oxalic acid interacts with calcium ions, leading to the precipitation of calcium oxalate, thus preventing the recrystallization of calcium phosphates. Gel- and soil-based plant cultivation tests employing Arabidopsis thaliana and solid calcium phosphates (i.e., nano- and microsized hydroxyapatites and calcium phosphate dibasic) demonstrated that these MVOC mechanisms facilitate plant growth by ensuring the prolonged supply of plant-available phosphate. The relationship between the growth enhancement and the particle size of the calcium phosphates also substantiated the MVOC sorption onto soil minerals related to plant growth. Given that most previous studies have assumed that MVOCs are a molecular lexicon directly detected by the dedicated sensing machinery of plants, our approach provides a new mechanistic view of the presence of abiotic mediators in the interaction between plants and microbes via MVOCs.
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Affiliation(s)
- Anahita Barghi
- Division of Environmental Science and Engineering, Pohang University of Science and Technology (P.O.STECH), 77 Cheongam-ro, Pohang 37673, Republic of Korea
| | - Lorenzo Degli Esposti
- Institute of Science and Technology for Ceramics (ISTEC), National Research Council (CNR), Via Granarolo 64, Faenza (RA) 48018, Italy
| | - Michele Iafisco
- Institute of Science and Technology for Ceramics (ISTEC), National Research Council (CNR), Via Granarolo 64, Faenza (RA) 48018, Italy
| | - Alessio Adamiano
- Institute of Science and Technology for Ceramics (ISTEC), National Research Council (CNR), Via Granarolo 64, Faenza (RA) 48018, Italy
| | | | - Pavlo Ivanchenko
- Department of Chemistry and NIS Centre, University of Torino, Via Giuria 7, Torino 10125, Italy
- ETEC Department, MOBI Research Group, Belgium Flanders Make, Vrije Universiteit Brussel (VUB), Pleinlaan 2, 3001 Heverlee, Brussels 1050, Belgium
| | - Lorenzo Mino
- Department of Chemistry and NIS Centre, University of Torino, Via Giuria 7, Torino 10125, Italy
| | - Ho Young Yoon
- Division of Applied Life Science (BK21Plus), Department of Agricultural Chemistry and Food Science & Technology and IALS, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Eun-Nam Joe
- Division of Applied Life Science (BK21Plus), Department of Agricultural Chemistry and Food Science & Technology and IALS, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Jong-Rok Jeon
- Division of Applied Life Science (BK21Plus), Department of Agricultural Chemistry and Food Science & Technology and IALS, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Yoon-Seok Chang
- Division of Environmental Science and Engineering, Pohang University of Science and Technology (P.O.STECH), 77 Cheongam-ro, Pohang 37673, Republic of Korea
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149
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Naamala J, Smith DL. Microbial Derived Compounds Are a Promising Approach to Mitigating Salinity Stress in Agricultural Crops. Front Microbiol 2021; 12:765320. [PMID: 34867895 PMCID: PMC8640360 DOI: 10.3389/fmicb.2021.765320] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 10/26/2021] [Indexed: 11/23/2022] Open
Abstract
The use of microbial derived compounds is a technological approach currently gaining popularity among researchers, with hopes of complementing, supplementing and addressing key issues associated with use of microbial cells for enhancing plant growth. The new technology is a promising approach to mitigating effects of salinity stress in agricultural crops, given that these compounds could be less prone to effects of salt stress, are required in small quantities and are easier to store and handle than microbial cells. Microorganism derived compounds such as thuricin17, lipochitooligosaccharides, phytohormones and volatile organic compounds have been reported to mitigate the effects of salt stress in agricultural crops such as soybean and wheat. This mini-review compiles current knowledge regarding the use of microbe derived compounds in mitigating salinity stress in crops, the mechanisms they employ as well as future prospects.
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Affiliation(s)
- Judith Naamala
- Smith Laboratory, Department of Plant Science, McGill University, Montreal, QC, Canada
| | - Donald L Smith
- Smith Laboratory, Department of Plant Science, McGill University, Montreal, QC, Canada
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Loss and Gain of Gut Bacterial Phylotype Symbionts in Afrotropical Stingless Bee Species (Apidae: Meliponinae). Microorganisms 2021; 9:microorganisms9122420. [PMID: 34946022 PMCID: PMC8708602 DOI: 10.3390/microorganisms9122420] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/02/2021] [Accepted: 11/15/2021] [Indexed: 01/04/2023] Open
Abstract
Stingless bees (Apidae: Meliponini) are the most diverse group of corbiculate bees and are important managed and wild pollinators distributed in the tropical and subtropical regions of the globe. However, little is known about their associated beneficial microbes that play major roles in host nutrition, detoxification, growth, activation of immune responses, and protection against pathogens in their sister groups, honeybees and bumble bees. Here, we provide an initial characterization of the gut bacterial microbiota of eight stingless bee species from sub-Saharan Africa using 16S rRNA amplicon sequencing. Our findings revealed that Firmicutes, Actinobacteria, and Proteobacteria were the dominant and conserved phyla across the eight stingless bee species. Additionally, we found significant geographical and host intra-species-specific bacterial diversity. Notably, African strains showed significant phylogenetic clustering when compared with strains from other continents, and each stingless bee species has its own microbial composition with its own dominant bacterial genus. Our results suggest host selective mechanisms maintain distinct gut communities among sympatric species and thus constitute an important resource for future studies on bee health management and host-microbe co-evolution and adaptation.
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