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Schniete JK, Fernández-Martínez LT. Natural product discovery in soil actinomycetes: unlocking their potential within an ecological context. Curr Opin Microbiol 2024; 79:102487. [PMID: 38733791 DOI: 10.1016/j.mib.2024.102487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 02/23/2024] [Accepted: 04/25/2024] [Indexed: 05/13/2024]
Abstract
Natural products (NPs) produced by bacteria, particularly soil actinomycetes, often possess diverse bioactivities and play a crucial role in human health, agriculture, and biotechnology. Soil actinomycete genomes contain a vast number of predicted biosynthetic gene clusters (BGCs) yet to be exploited. Understanding the factors governing NP production in an ecological context and activating cryptic and silent BGCs in soil actinomycetes will provide researchers with a wealth of molecules with potential novel applications. Here, we highlight recent advances in NP discovery strategies employing ecology-inspired approaches and discuss the importance of understanding the environmental signals responsible for activation of NP production, particularly in a soil microbial community context, as well as the challenges that remain.
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Affiliation(s)
- Jana K Schniete
- Institute of Microbiology, Leibniz Universität Hannover, 30419 Hannover, Germany.
| | - Lorena T Fernández-Martínez
- School of Infection and Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK.
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2
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Pollock TY, Odom John AR. Thinking Small, Stinking Big: The World of Microbial Odors. J Infect Dis 2024; 229:1254-1255. [PMID: 37738417 PMCID: PMC11095540 DOI: 10.1093/infdis/jiad405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 09/19/2023] [Indexed: 09/24/2023] Open
Affiliation(s)
- Tzvi Y Pollock
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Audrey R Odom John
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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3
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Andreas MP, Giessen TW. The biosynthesis of the odorant 2-methylisoborneol is compartmentalized inside a protein shell. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.23.590730. [PMID: 38712110 PMCID: PMC11071394 DOI: 10.1101/2024.04.23.590730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Terpenoids are the largest class of natural products, found across all domains of life. One of the most abundant bacterial terpenoids is the volatile odorant 2-methylisoborneol (2-MIB), partially responsible for the earthy smell of soil and musty taste of contaminated water. Many bacterial 2-MIB biosynthetic gene clusters were thought to encode a conserved transcription factor, named EshA in the model soil bacterium Streptomyces griseus . Here, we revise the function of EshA, now referred to as Sg Enc, and show that it is a Family 2B encapsulin shell protein. Using cryo-electron microscopy, we find that Sg Enc forms an icosahedral protein shell and encapsulates 2-methylisoborneol synthase (2-MIBS) as a cargo protein. Sg Enc contains a cyclic adenosine monophosphate (cAMP) binding domain (CBD)-fold insertion and a unique metal-binding domain, both displayed on the shell exterior. We show that Sg Enc CBDs do not bind cAMP. We find that 2-MIBS cargo loading is mediated by an N-terminal disordered cargo-loading domain and that 2-MIBS activity and Sg Enc shell structure are not modulated by cAMP. Our work redefines the function of EshA and establishes Family 2B encapsulins as cargo-loaded protein nanocompartments involved in secondary metabolite biosynthesis.
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Suksaard P, Butdee W, Suriyachadkun C, Sirikesorn L, Duangmal K. Saccharopolyspora ipomoeae sp. nov., an Actinomycete Isolated from Sweet Potato Field Soils. Curr Microbiol 2024; 81:130. [PMID: 38589729 DOI: 10.1007/s00284-024-03661-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 03/03/2024] [Indexed: 04/10/2024]
Abstract
During the course of the isolation of actinobacteria from sweet potato field soils collected from Phra Nakhon Si Ayutthaya province of Thailand, strain TS4A08T was isolated and subjected to a polyphasic taxonomic approach. The 16S rRNA gene sequence analysis of strain TS4A08T revealed that it is closely related to the type strains of Saccharopolyspora aridisoli, and Saccharopolyspora endophytica with 98.7%, and 98.6% similarity, respectively. However, phylogenetic analyses using 16S rRNA gene and genome sequences indicated that strain TS4A08T clustered with Saccharopolyspora flava AS4.1520T (98.2% similarity), well-supported by bootstrap values, and formed distinct line from the two closest strains. The average nucleotide identity (ANI) values and digital DNA-DNA hybridization (dDDH) values between the genome sequences of strain TS4A08T and the closest type strains of S. aridisoli, S. endophytica, and S. flava, were 86.1-93.2% and 33.1-49.6%, respectively, which were less than the threshold for the species delineation. The genome size and the DNA G + C content of strain TS4A08T were 6.6 Mbp and 70.5%, respectively. The strain grew well at 25-37 °C, pH range of 7-9, and NaCl concentration of 0-5% (w/v). Whole-cell hydrolysates contained meso-diaminopimelic acid. The major fatty acids were iso-C16:0, anteiso-C17:0, and iso-C15:0. Strain TS4A08T exhibited phosphatidylcholine in its polar lipid profile, with MK-9(H4) being the predominant isoprenologue. The strain exhibits typical chemotaxonomic properties of the genus Saccharopolyspora, including arabinose, galactose, and ribose as whole-cell sugars. Strain TS4A08T represents a novel species within the genus Saccharopolyspora, for which the name Saccharopolyspora ipomoeae sp. nov. is proposed. The type strain is TS4A08T (= TBRC 17271T = NBRC 115967T).
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Affiliation(s)
- Paweena Suksaard
- Department of Science, Faculty of Science and Technology, Rajamangala University of Technology Suvarnabhumi, Huntra, Phra Nakhon Si Ayutthaya, 13000, Thailand.
| | - Waranya Butdee
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Chanwit Suriyachadkun
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Laongsri Sirikesorn
- Department of Plant Science, Faculty of Agricultural Technology and Agro-Industry, Rajamangala University of Technology Suvarnabhumi, Huntra, Phra Nakhon Si Ayutthaya, 13000, Thailand
| | - Kannika Duangmal
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
- Biodiversity Center, Kasetsart University (BDCKU), Bangkok, 10900, Thailand
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Lara AC, Kotrbová L, Keller M, Nouioui I, Neumann-Schaal M, Mast Y, Chroňáková A. Lentzea sokolovensis sp. nov., Lentzea kristufekii sp. nov. and Lentzea miocenica sp. nov., rare actinobacteria from Miocene lacustrine sediment of the Sokolov Coal Basin, Czech Republic. Int J Syst Evol Microbiol 2024; 74. [PMID: 38630118 DOI: 10.1099/ijsem.0.006335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024] Open
Abstract
The taxonomic position of three actinobacterial strains, BCCO 10_0061T, BCCO 10_0798T, and BCCO 10_0856T, recovered from bare soil in the Sokolov Coal Basin, Czech Republic, was established using a polyphasic approach. The multilocus sequence analysis based on 100 single-copy genes positioned BCCO 10_0061T in the same cluster as Lentzea waywayandensis, strain BCCO 10_0798T in the same cluster as Lentzea flaviverrucosa, Lentzea californiensis, Lentzea violacea, and Lentzea albidocapillata, and strain BCCO 10_0856T clustered together with Lentzea kentuckyensis and Lentzea alba. Morphological and chemotaxonomic characteristics of these strains support their assignment to the genus Lentzea. In all three strains, MK-9(H4) accounted for more than 80 % of the isoprenoid quinone. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The whole-cell sugars were rhamnose, ribose, mannose, glucose, and galactose. The major fatty acids (>10 %) were iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0, and C16 : 0. The polar lipids were diphosphatidylglycerol, methyl-phosphatidylethanolamine, phosphatidylethanolamine, hydroxy-phosphatidylethanolamine, phosphatidylglycerol, and phosphatidylinositol. The genomic DNA G+C content of strains (mol%) was 68.8 for BCCO 10_0061T, 69.2 for BCCO 10_0798T, and 68.5 for BCCO 10_0856T. The combination of digital DNA-DNA hybridization results, average nucleotide identity values and phenotypic characteristics of BCCO 10_0061T, BCCO 10_0798T, and BCCO 10_0856T distinguishes them from their closely related strains. Bioinformatic analysis of the genome sequences of the strains revealed several biosynthetic gene clusters (BGCs) with identities >50 % to already known clusters, including BGCs for geosmin, coelichelin, ε-poly-l-lysine, and erythromycin-like BGCs. Most of the identified BGCs showed low similarity to known BGCs (<50 %) suggesting their genetic potential for the biosynthesis of novel secondary metabolites. Based on the above results, each strain represents a novel species of the genus Lentzea, for which we propose the name Lentzea sokolovensis sp. nov. for BCCO 10_0061T (=DSM 116175T), Lentzea kristufekii sp. nov. for BCCO 10_0798T (=DSM 116176T), and Lentzea miocenica sp. nov. for BCCO 10_0856T (=DSM 116177T).
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Affiliation(s)
- Ana Catalina Lara
- Biology Centre Czech Academy of Sciences, Institute of Soil Biology and BiogeochemistryNaSádkách 7, 37005 České Budějovice, Czech Republic
- University of Chemistry, and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Technická 5, 16628 Prague, Czech Republic
| | - Lucie Kotrbová
- Biology Centre Czech Academy of Sciences, Institute of Soil Biology and BiogeochemistryNaSádkách 7, 37005 České Budějovice, Czech Republic
- University of South Bohemia, Faculty of Science, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Moritz Keller
- Biology Centre Czech Academy of Sciences, Institute of Soil Biology and BiogeochemistryNaSádkách 7, 37005 České Budějovice, Czech Republic
- University of South Bohemia, Faculty of Science, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Imen Nouioui
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Meina Neumann-Schaal
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Yvonne Mast
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Alica Chroňáková
- Biology Centre Czech Academy of Sciences, Institute of Soil Biology and BiogeochemistryNaSádkách 7, 37005 České Budějovice, Czech Republic
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Chagas FO, Garrido LM, Conti R, Borges RM, Bielinski VA, Padilla G, Pupo MT. Unusual Sesquiterpenes from Streptomyces olindensis DAUFPE 5622. JOURNAL OF NATURAL PRODUCTS 2024; 87:491-500. [PMID: 38422010 DOI: 10.1021/acs.jnatprod.3c00752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
In nature, the vast majority of sesquiterpenes are produced by type I mechanisms, and glycosylated sesquiterpenes are rare in actinobacteria. Streptomyces olindensis DAUFPE 5622 produces the sesquiterpenes olindenones A-G, a new class of rearranged drimane sesquiterpenes. Olindenones B-D are oxygenated derivatives of olindenone A, while olindenones E-G are analogs glycosylated with dideoxysugars. 13C-isotope labeling studies demonstrated olindenone A biosynthesis occurs via the methylerythritol phosphate (MEP) pathway and suggested the rearrangement is only partially concerted. Based on the structures, one potential mechanism of olindenone A formation proceeds by cyclization of the linear terpenoid precursor, likely occurring via a terpene cyclase-mediated type II mechanism whereby the terminal alkene of the precursor is protonated, triggering carbocation-driven cyclization followed by rearrangement. Diphosphate hydrolysis may occur either before or after cyclization. Although a biosynthetic route is proposed, the terpene cyclase gene responsible for producing olindenones currently remains unidentified.
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Affiliation(s)
- Fernanda O Chagas
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP 05508-070, Brazil
- Instituto de Pesquisas de Produtos Naturais Walter Mors, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-617, Brazil
| | - Leandro M Garrido
- Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP 05508-070, Brazil
| | - Raphael Conti
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP 05508-070, Brazil
| | - Ricardo M Borges
- Instituto de Pesquisas de Produtos Naturais Walter Mors, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-617, Brazil
| | - Vincent A Bielinski
- Synthetic Biology and Bioenergy Group, J. Craig Venter Institute, La Jolla, California 92037, United States
- Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-617, Brazil
| | - Gabriel Padilla
- Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP 05508-070, Brazil
| | - Mônica T Pupo
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP 05508-070, Brazil
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Li X, Yi S, Chen L, Hafeez M, Zhang Z, Zhang J, Zhou S, Dong W, Huang J, Lu Y. The application of entomopathogenic nematode modified microbial communities within nesting mounds of the red imported fire ants, Solenopsis invicta. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168748. [PMID: 38008315 DOI: 10.1016/j.scitotenv.2023.168748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 11/10/2023] [Accepted: 11/19/2023] [Indexed: 11/28/2023]
Abstract
Entomopathogenic microorganisms (e.g., fungi, bacteria, nematodes) have been widely used in biological control of soil-dwelling pests, including the red imported fire ant (RIFA), Solenopsis invicta, a notorious invasive pest worldwide. The application of large amounts of entomopathogenic microorganisms to soil may affect the indigenous soil microbial communities. However, reports about the effect of entomopathogenic nematodes (EPN) on soil microbial communities are very few. In this study, the effects of EPN on RIFA populations and microbial communities in mounds were investigated. Our results showed that the application of the EPN Steinernema carpocapsae. All strain on mounds efficaciously suppressed RIFA worker populations, without forming significantly more satellite mounds compared with the control treatment. The application of EPN did not impact the bacterial and fungal diversity in soils derived from the RIFA mounds. However, it slightly altered the taxonomic make-up of the bacterial communities, but significantly altered the taxonomic composition of fungal communities at the phylum, family, and genus levels. The abundances of some beneficial bacteria and fungi, such as Streptomyces, decreased, while those of plant and animal pathogenic bacteria and fungi, dramatically increased, after EPN treatment. On the other hand, the abundances of some entomopathogenic fungi, such as Fusicolla, Clonostachys, and Mortierella, increased. Redundancy analysis or canonical correspondence analysis revealed a positive correlation between the efficacious EPN control and the presence of the insect-resistant bacteria, Sinomonas, as well as entomopathogenic fungi Fusicolla and Mortierella. This suggests that the interactions between EPN and entomopathogenic fungi may play a role in the biological control of RIFA. Our discoveries shed light on the interactions among EPN, RIFA, and soil microbial communities, and emphasize a possible mutualistic relationship between EPN and entomopathogenic fungi in the biological control of RIFA.
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Affiliation(s)
- Xiaowei Li
- State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Songwang Yi
- State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou 311300, China
| | - Limin Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Muhammad Hafeez
- State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Zhijun Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jinming Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Shuxing Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Wanying Dong
- State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jun Huang
- State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| | - Yaobin Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; Institute of Bio-Interaction, Xianghu Laboratory, Hangzhou 311258, China.
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Zhong W, Aiosa N, Deutsch JM, Garg N, Agarwal V. Pseudobulbiferamides: Plasmid-Encoded Ureidopeptide Natural Products with Biosynthetic Gene Clusters Shared Among Marine Bacteria of Different Genera. JOURNAL OF NATURAL PRODUCTS 2023; 86:2414-2420. [PMID: 37713418 PMCID: PMC10616845 DOI: 10.1021/acs.jnatprod.3c00595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Indexed: 09/17/2023]
Abstract
Ureidopeptidic natural products possess a wide variety of favorable pharmacological properties. In addition, they have been shown to mediate core physiological functions in producer bacteria. Here, we report that similar ureidopeptidic natural products with conserved biosynthetic gene clusters are produced by different bacterial genera that coinhabit marine invertebrate microbiomes. We demonstrate that a Microbulbifer strain isolated from a marine sponge can produce two different classes of ureidopeptide natural products encoded by two different biosynthetic gene clusters that are positioned on the bacterial chromosome and on a plasmid. The plasmid encoded ureidopeptide natural products, which we term the pseudobulbiferamides (5-8), resemble the ureidopeptide natural products produced by Pseudovibrio, a different marine bacterial genus that is likewise present in marine sponge commensal microbiomes. Using imaging mass spectrometry, we find that the two classes of Microbulbifer-derived ureidopeptides occupy different physical spaces relative to the bacterial colony, perhaps implying different roles for these two compound classes in Microbulbifer physiology and environmental interactions.
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Affiliation(s)
- Weimao Zhong
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
| | - Nicole Aiosa
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
| | - Jessica M. Deutsch
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
| | - Neha Garg
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
- Center
for Microbial Dynamics and Infection, Georgia
Institute of Technology, Atlanta, Georgia 30332, United States
| | - Vinayak Agarwal
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
- School
of Biological Sciences, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
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Pereira ÉJMC, Amorim ÉADF, Aragão FMM, Câmara WDS, Araújo MC, Pereira CDDS, Dias LRL, Gomes WC, Aliança ASDS, Souza JCDS, da Silva LCN, de Miranda RDCM. Biocontrol Potential of Serratia Marcescens (B8) and Bacillus sp. (B13) Isolated from Urban Mangroves in Raposa, Brazil. Life (Basel) 2023; 13:2036. [PMID: 37895418 PMCID: PMC10607943 DOI: 10.3390/life13102036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 08/28/2023] [Accepted: 09/04/2023] [Indexed: 10/29/2023] Open
Abstract
This study analyzed the antifungal potential of 16 bacterial strains isolated from mangrove sediment. Bacterial selection was conducted in a solid medium. This was followed by the production and extraction of metabolites using ethyl acetate to evaluate chitinase production, antifungal activity, and toxicity toward Allium cepa and Tenebrio molitor. Bacterial strains B8, B11, and B13 produced the largest inhibition halos (>30 mm) toward Fusarium solani, Fusarium oxysporum, and Rhizoctonia solani fungi. Strains B1, B3, B6, B8, B11, B13, B14, and B16 produced chitinases. In assays using liquid media, B8 and B13 produced the largest inhibition halos. Exposing the fungal inocula to metabolic extracts of strains B6, B8, B11, B13, B14, B15, and B16 caused micromorphological alterations in the inocula, culminating in the inhibition of R. solani sporulation and spore germination. Toxicity tests using Allium cepa and Tenebrio molitor revealed that the metabolites showed low toxicity. Six of the bacterial strains were molecularly identified to species levels, and a further two to genus level. These included Serratia marcescens (B8), which exhibited activity in all tests. Mangroves provide a useful resource for the isolation of microorganisms for biocontrol. Among the isolates, Serratia marcescens and Bacillus spp. showed the greatest potential to produce metabolites for use as biocontrol agents in agriculture.
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Affiliation(s)
- Érima Jôyssielly Mendonça Castro Pereira
- Programa de Pós-Graduação em Biologia Microbiana, Universidade Ceuma, São Luís 65075-120, Brazil
- Programa de Pós-Graduação em Biodiversidade e Biotecnologia da Amazônia, Universidade CEUMA, São Luís 65075-120, Brazil; (É.A.d.F.A.)
| | - Érika Alves da Fonsêca Amorim
- Programa de Pós-Graduação em Biodiversidade e Biotecnologia da Amazônia, Universidade CEUMA, São Luís 65075-120, Brazil; (É.A.d.F.A.)
- Programa de Pós-Graduação em Odontologia, Universidade Ceuma, São Luís 65075-120, Brazil
| | - Felicia Maria Melo Aragão
- Programa de Pós-Graduação em Meio Ambiente, Universidade Ceuma, São Luís 65075-120, Brazil; (F.M.M.A.); (W.d.S.C.)
| | - Wallison de Souza Câmara
- Programa de Pós-Graduação em Meio Ambiente, Universidade Ceuma, São Luís 65075-120, Brazil; (F.M.M.A.); (W.d.S.C.)
| | - Maria Carvalho Araújo
- Programa de Pós-Graduação em Gestão de Programas e Serviços de Saúde, Universidade Ceuma, São Luís 65075-120, Brazil
| | - Carlos Drielson da Silva Pereira
- Programa de Pós-Graduação em Biologia Microbiana, Universidade Ceuma, São Luís 65075-120, Brazil
- Programa de Pós-Graduação em Biodiversidade e Biotecnologia da Amazônia, Universidade CEUMA, São Luís 65075-120, Brazil; (É.A.d.F.A.)
| | - Leo Ruben Lopes Dias
- Programa de Pós-Graduação em Biodiversidade e Biotecnologia da Amazônia, Universidade CEUMA, São Luís 65075-120, Brazil; (É.A.d.F.A.)
| | - Wolia Costa Gomes
- Programa de Pós-Graduação em Meio Ambiente, Universidade Ceuma, São Luís 65075-120, Brazil; (F.M.M.A.); (W.d.S.C.)
| | - Amanda Silva dos Santos Aliança
- Programa de Pós-Graduação em Biologia Microbiana, Universidade Ceuma, São Luís 65075-120, Brazil
- Programa de Pós-Graduação em Gestão de Programas e Serviços de Saúde, Universidade Ceuma, São Luís 65075-120, Brazil
| | - Joicy Cortez de Sá Souza
- Programa de Pós-Graduação em Biologia Microbiana, Universidade Ceuma, São Luís 65075-120, Brazil
| | - Luís Cláudio Nascimento da Silva
- Programa de Pós-Graduação em Biologia Microbiana, Universidade Ceuma, São Luís 65075-120, Brazil
- Programa de Pós-Graduação em Biodiversidade e Biotecnologia da Amazônia, Universidade CEUMA, São Luís 65075-120, Brazil; (É.A.d.F.A.)
- Programa de Pós-Graduação em Odontologia, Universidade Ceuma, São Luís 65075-120, Brazil
| | - Rita de Cássia Mendonça de Miranda
- Programa de Pós-Graduação em Biologia Microbiana, Universidade Ceuma, São Luís 65075-120, Brazil
- Programa de Pós-Graduação em Biodiversidade e Biotecnologia da Amazônia, Universidade CEUMA, São Luís 65075-120, Brazil; (É.A.d.F.A.)
- Programa de Pós-Graduação em Meio Ambiente, Universidade Ceuma, São Luís 65075-120, Brazil; (F.M.M.A.); (W.d.S.C.)
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10
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Bei Q, Reitz T, Schnabel B, Eisenhauer N, Schädler M, Buscot F, Heintz-Buschart A. Extreme summers impact cropland and grassland soil microbiomes. THE ISME JOURNAL 2023; 17:1589-1600. [PMID: 37419993 PMCID: PMC10504347 DOI: 10.1038/s41396-023-01470-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 06/20/2023] [Accepted: 06/23/2023] [Indexed: 07/09/2023]
Abstract
The increasing frequency of extreme weather events highlights the need to understand how soil microbiomes respond to such disturbances. Here, metagenomics was used to investigate the effects of future climate scenarios (+0.6 °C warming and altered precipitation) on soil microbiomes during the summers of 2014-2019. Unexpectedly, Central Europe experienced extreme heatwaves and droughts during 2018-2019, causing significant impacts on the structure, assembly, and function of soil microbiomes. Specifically, the relative abundance of Actinobacteria (bacteria), Eurotiales (fungi), and Vilmaviridae (viruses) was significantly increased in both cropland and grassland. The contribution of homogeneous selection to bacterial community assembly increased significantly from 40.0% in normal summers to 51.9% in extreme summers. Moreover, genes associated with microbial antioxidant (Ni-SOD), cell wall biosynthesis (glmSMU, murABCDEF), heat shock proteins (GroES/GroEL, Hsp40), and sporulation (spoIID, spoVK) were identified as potential contributors to drought-enriched taxa, and their expressions were confirmed by metatranscriptomics in 2022. The impact of extreme summers was further evident in the taxonomic profiles of 721 recovered metagenome-assembled genomes (MAGs). Annotation of contigs and MAGs suggested that Actinobacteria may have a competitive advantage in extreme summers due to the biosynthesis of geosmin and 2-methylisoborneol. Future climate scenarios caused a similar pattern of changes in microbial communities as extreme summers, but to a much lesser extent. Soil microbiomes in grassland showed greater resilience to climate change than those in cropland. Overall, this study provides a comprehensive framework for understanding the response of soil microbiomes to extreme summers.
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Affiliation(s)
- Qicheng Bei
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Halle (Saale), Germany.
| | - Thomas Reitz
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Halle (Saale), Germany
| | - Beatrix Schnabel
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Halle (Saale), Germany
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biology, Leipzig University, Leipzig, Germany
| | - Martin Schädler
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Department of Community Ecology, Helmholtz Centre for Environmental Research - UFZ, Halle (Saale), Germany
| | - François Buscot
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Halle (Saale), Germany
| | - Anna Heintz-Buschart
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands.
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11
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Garbeva P, Avalos M, Ulanova D, van Wezel GP, Dickschat JS. Volatile sensation: The chemical ecology of the earthy odorant geosmin. Environ Microbiol 2023; 25:1565-1574. [PMID: 36999338 DOI: 10.1111/1462-2920.16381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 03/21/2023] [Indexed: 04/01/2023]
Abstract
Geosmin may be the most familiar volatile compound, as it lends the earthy smell to soil. The compound is a member of the largest family of natural products, the terpenoids. The broad distribution of geosmin among bacteria in both terrestrial and aquatic environments suggests that this compound has an important ecological function, for example, as a signal (attractant or repellent) or as a protective specialized metabolite against biotic and abiotic stresses. While geosmin is part of our everyday life, scientists still do not understand the exact biological function of this omnipresent natural product. This minireview summarizes the current general observations regarding geosmin in prokaryotes and introduces new insights into its biosynthesis and regulation, as well as its biological roles in terrestrial and aquatic environments.
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Affiliation(s)
- Paolina Garbeva
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Mariana Avalos
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Dana Ulanova
- Faculty of Agriculture and Marine Science, Kochi University, 200 Otsu, Monobe, Nankoku, Kochi, 783-8502, Japan
| | - Gilles P van Wezel
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Jeroen S Dickschat
- University of Bonn, Kekulé-Institute of Organic Chemistry and Biochemistry, Gerhard-Domagk-Straße 1, 53121, Bonn, Germany
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12
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Schlimpert S, Elliot MA. The Best of Both Worlds-Streptomyces coelicolor and Streptomyces venezuelae as Model Species for Studying Antibiotic Production and Bacterial Multicellular Development. J Bacteriol 2023; 205:e0015323. [PMID: 37347176 PMCID: PMC10367585 DOI: 10.1128/jb.00153-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/23/2023] Open
Abstract
Streptomyces bacteria have been studied for more than 80 years thanks to their ability to produce an incredible array of antibiotics and other specialized metabolites and their unusual fungal-like development. Their antibiotic production capabilities have ensured continual interest from both academic and industrial sectors, while their developmental life cycle has provided investigators with unique opportunities to address fundamental questions relating to bacterial multicellular growth. Much of our understanding of the biology and metabolism of these fascinating bacteria, and many of the tools we use to manipulate these organisms, have stemmed from investigations using the model species Streptomyces coelicolor and Streptomyces venezuelae. Here, we explore the pioneering work in S. coelicolor that established foundational genetic principles relating to specialized metabolism and development, alongside the genomic and cell biology developments that led to the emergence of S. venezuelae as a new model system. We highlight key discoveries that have stemmed from studies of these two systems and discuss opportunities for future investigations that leverage the power and understanding provided by S. coelicolor and S. venezuelae.
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Affiliation(s)
- Susan Schlimpert
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Marie A. Elliot
- Department of Biology and M. G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
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13
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Zhang P, Yuan Y, Zhang J, Wen T, Wang H, Qu C, Tan W, Xi B, Hui K, Tang J. Specific response of soil properties to microplastics pollution: A review. ENVIRONMENTAL RESEARCH 2023; 232:116427. [PMID: 37327841 DOI: 10.1016/j.envres.2023.116427] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 06/06/2023] [Accepted: 06/13/2023] [Indexed: 06/18/2023]
Abstract
The soil environment is a critical component of the global ecosystem and is essential for nutrient cycling and energy flow. Various physical, chemical, and biological processes occur in the soil and are affected by environmental factors. Soil is vulnerable to pollutants, especially emerging pollutants, such as microplastics (MPs). MPs pollution has become a significant environmental problem, and its harm to human health and the environment cannot be underestimated. However, most studies on MPs pollution have focused on marine ecosystems, estuaries, lakes, rivers, and other aquatic environments, whereas few considered the effects and hazards of MPs pollution of the soil, especially the responses of different environmental factors to MPs. In addition, when many MPs pollutants produced by agricultural activities (mulching film, organic fertilizer) and atmospheric sedimentation enter the soil environment, it will cause changes in soil pH, organic matter composition, microbial community, enzyme activity, animals and plants and other environmental factors. However, due to the complex and changeable soil environment, the heterogeneity is very strong. The changes of environmental factors may react on the migration, transformation and degradation of MPs, and there are synergistic or antagonistic interactions among different factors. Therefore, it is very important to analyze the specific effects of MPs pollution on soil properties to clarify the environmental behavior and effects of MPs. This review focuses on the source, formation, and influencing factors of MPs pollution in soil and summarizes its effect and influence degree on various soil environmental factors. The results provide research suggestions and theoretical support for preventing or controlling MPs soil pollution.
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Affiliation(s)
- Panting Zhang
- State Key Laboratory of Environmental Criteria and Risk Assessment, and State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; College of Chemistry and Chemical Engineering, Xi'an Shiyou University, Xi'an, 710065, China
| | - Ying Yuan
- State Key Laboratory of Environmental Criteria and Risk Assessment, and State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Jia Zhang
- School of Chemistry and Chemical Engineering, Southwest Petroleum University, Chengdu, 610500, China
| | - Taoyi Wen
- School of Civil Engineering, Chang'an University, Xi'an, Shaanxi, 710061, China
| | - Hui Wang
- State Key Laboratory of Environmental Criteria and Risk Assessment, and State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Chengtun Qu
- College of Chemistry and Chemical Engineering, Xi'an Shiyou University, Xi'an, 710065, China
| | - Wenbing Tan
- State Key Laboratory of Environmental Criteria and Risk Assessment, and State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Beidou Xi
- State Key Laboratory of Environmental Criteria and Risk Assessment, and State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Kunlong Hui
- State Key Laboratory of Environmental Criteria and Risk Assessment, and State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China.
| | - Jun Tang
- State Key Laboratory of Environmental Criteria and Risk Assessment, and State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China.
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14
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Tarasova EV, Luchnikova NA, Grishko VV, Ivshina IB. Actinomycetes as Producers of Biologically Active Terpenoids: Current Trends and Patents. Pharmaceuticals (Basel) 2023; 16:872. [PMID: 37375819 DOI: 10.3390/ph16060872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 06/04/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Terpenes and their derivatives (terpenoids and meroterpenoids, in particular) constitute the largest class of natural compounds, which have valuable biological activities and are promising therapeutic agents. The present review assesses the biosynthetic capabilities of actinomycetes to produce various terpene derivatives; reports the main methodological approaches to searching for new terpenes and their derivatives; identifies the most active terpene producers among actinomycetes; and describes the chemical diversity and biological properties of the obtained compounds. Among terpene derivatives isolated from actinomycetes, compounds with pronounced antifungal, antiviral, antitumor, anti-inflammatory, and other effects were determined. Actinomycete-produced terpenoids and meroterpenoids with high antimicrobial activity are of interest as a source of novel antibiotics effective against drug-resistant pathogenic bacteria. Most of the discovered terpene derivatives are produced by the genus Streptomyces; however, recent publications have reported terpene biosynthesis by members of the genera Actinomadura, Allokutzneria, Amycolatopsis, Kitasatosporia, Micromonospora, Nocardiopsis, Salinispora, Verrucosispora, etc. It should be noted that the use of genetically modified actinomycetes is an effective tool for studying and regulating terpenes, as well as increasing productivity of terpene biosynthesis in comparison with native producers. The review includes research articles on terpene biosynthesis by Actinomycetes between 2000 and 2022, and a patent analysis in this area shows current trends and actual research directions in this field.
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Affiliation(s)
- Ekaterina V Tarasova
- Perm Federal Research Center, Ural Branch of the Russian Academy of Sciences, 13A Lenina Str., 614990 Perm, Russia
| | - Natalia A Luchnikova
- Perm Federal Research Center, Ural Branch of the Russian Academy of Sciences, 13A Lenina Str., 614990 Perm, Russia
- Department of Microbiology and Immunology, Perm State University, 15 Bukirev Str., 614990 Perm, Russia
| | - Victoria V Grishko
- Perm Federal Research Center, Ural Branch of the Russian Academy of Sciences, 13A Lenina Str., 614990 Perm, Russia
| | - Irina B Ivshina
- Perm Federal Research Center, Ural Branch of the Russian Academy of Sciences, 13A Lenina Str., 614990 Perm, Russia
- Department of Microbiology and Immunology, Perm State University, 15 Bukirev Str., 614990 Perm, Russia
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15
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Villa SM, Chen JZ, Kwong Z, Acosta A, Vega NM, Gerardo NM. Specialized acquisition behaviors maintain reliable environmental transmission in an insect-microbial mutualism. Curr Biol 2023:S0960-9822(23)00724-8. [PMID: 37385254 DOI: 10.1016/j.cub.2023.05.062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 04/07/2023] [Accepted: 05/25/2023] [Indexed: 07/01/2023]
Abstract
Understanding how horizontally transmitted mutualisms are maintained is a major focus of symbiosis research.1,2,3,4 Unlike vertical transmission, hosts that rely on horizontal transmission produce symbiont-free offspring that must find and acquire their beneficial microbes from the environment. This transmission strategy is inherently risky since hosts may not obtain the right symbiont every generation. Despite these potential costs, horizontal transmission underlies stable mutualisms involving a large diversity of both plants and animals.5,6,7,8,9 One largely unexplored way horizontal transmission is maintained is for hosts to evolve sophisticated mechanisms to consistently find and acquire specific symbionts from the environment. Here, we examine this possibility in the squash bug Anasa tristis, an insect pest that requires bacterial symbionts in the genus Caballeronia10 for survival and development.11 We conduct a series of behavioral and transmission experiments that track strain-level transmission in vivo among individuals in real-time. We demonstrate that nymphs can accurately find feces from adult bugs in both the presence and absence of those adults. Once nymphs locate the feces, they deploy feeding behavior that results in nearly perfect symbiont acquisition success. We further demonstrate that nymphs can locate and feed on isolated, cultured symbionts in the absence of feces. Finally, we show this acquisition behavior is highly host specific. Taken together, our data describe not only the evolution of a reliable horizontal transmission strategy, but also a potential mechanism that drives patterns of species-specific microbial communities among closely related, sympatric host species.
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Affiliation(s)
- Scott M Villa
- Department of Biology, Emory University, 1510 Clifton Rd., Atlanta, GA 30322, USA; Department of Biology, Davidson College, 209 Ridge Rd., Davidson, NC 28035, USA.
| | - Jason Z Chen
- Department of Biology, Emory University, 1510 Clifton Rd., Atlanta, GA 30322, USA
| | - Zeeyong Kwong
- Department of Biology, Emory University, 1510 Clifton Rd., Atlanta, GA 30322, USA
| | - Alice Acosta
- Department of Biology, Emory University, 1510 Clifton Rd., Atlanta, GA 30322, USA
| | - Nicole M Vega
- Department of Biology, Emory University, 1510 Clifton Rd., Atlanta, GA 30322, USA
| | - Nicole M Gerardo
- Department of Biology, Emory University, 1510 Clifton Rd., Atlanta, GA 30322, USA
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16
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Van Stan JT, Allen ST, Aubrey DP, Berry ZC, Biddick M, Coenders-Gerrits MAMJ, Giordani P, Gotsch SG, Gutmann ED, Kuzyakov Y, Magyar D, Mella VSA, Mueller KE, Ponette-González AG, Porada P, Rosenfeld CE, Simmons J, Sridhar KR, Stubbins A, Swanson T. Shower thoughts: why scientists should spend more time in the rain. Bioscience 2023; 73:441-452. [PMID: 37397836 PMCID: PMC10308363 DOI: 10.1093/biosci/biad044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/17/2023] [Accepted: 04/26/2023] [Indexed: 07/04/2023] Open
Abstract
Stormwater is a vital resource and dynamic driver of terrestrial ecosystem processes. However, processes controlling interactions during and shortly after storms are often poorly seen and poorly sensed when direct observations are substituted with technological ones. We discuss how human observations complement technological ones and the benefits of scientists spending more time in the storm. Human observation can reveal ephemeral storm-related phenomena such as biogeochemical hot moments, organismal responses, and sedimentary processes that can then be explored in greater resolution using sensors and virtual experiments. Storm-related phenomena trigger lasting, oversized impacts on hydrologic and biogeochemical processes, organismal traits or functions, and ecosystem services at all scales. We provide examples of phenomena in forests, across disciplines and scales, that have been overlooked in past research to inspire mindful, holistic observation of ecosystems during storms. We conclude that technological observations alone are insufficient to trace the process complexity and unpredictability of fleeting biogeochemical or ecological events without the shower thoughts produced by scientists' human sensory and cognitive systems during storms.
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Affiliation(s)
| | - Scott T Allen
- Department of Natural Resources and Environmental Science at the University of Nevada-Reno, Reno, Nevada, United States
| | - Douglas P Aubrey
- Savannah River Ecology Lab and with the Warnell School of Forestry at the University of Georgia, Athens, Georgia, United States
| | - Z Carter Berry
- Department of Biology at Wake Forest University, Winston-Salem, North Carolina, United States
| | - Matthew Biddick
- Terrestrial Ecology Research Group at the Technical University of Munich, Freising, Germany
| | | | - Paolo Giordani
- Dipartimento di Farmacia at the University of Genoa, Genoa, Italy
| | - Sybil G Gotsch
- Department of Forestry and Natural Resources at the University of Kentucky, Lexington, Kentucky, United States
| | - Ethan D Gutmann
- Research Applications Laboratory, at the National Center for Atmospheric Research, Boulder, Colorado, United States
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate Systems, Agricultural Soil Science, at Georg-August-Universität, Göttingen, Germany
- Peoples Friendship University of Russia, Moscow, Russia
| | - Donát Magyar
- National Public Health Center, Budapest, Hungary
| | - Valentina S A Mella
- Sydney School of Veterinary Science, at the University of Sydney, Sydney, New South Wales, Australia
| | - Kevin E Mueller
- Department of Biological, Geological, and Environmental Sciences at Cleveland State University, Cleveland, Ohio, United States
| | - Alexandra G Ponette-González
- Department of City and Metropolitan Planning and with the Natural History Museum of Utah at the University of Utah, Salt Lake City, Utah, United States
| | - Philipp Porada
- Department of Biology at Universität Hamburg, Hamburg, Germany
| | - Carla E Rosenfeld
- Department of Minerals and Earth Sciences at the Carnegie Museum of Natural History, Pittsburgh, Pennsylvania, United States
| | - Jack Simmons
- Department of Philosophy and Religious Studies at Georgia Southern University, Statesboro, Georgia, United States
| | - Kandikere R Sridhar
- Department of Biosciences at Mangalore University, Konaje, Mangaluru, Karnataka, India
| | - Aron Stubbins
- Departments of Marine and Environmental Science, Civil and Environmental Engineering, and Chemistry and Chemical Biology at Northeastern University, Boston, Massachusetts, United States
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17
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Nofiani R, Ardiningsih P, Zahra STA, Sukito A, Weisberg AJ, Chang JH, Mahmud T. Genome features and secondary metabolite potential of the marine symbiont Streptomyces sp. RS2. Arch Microbiol 2023; 205:244. [PMID: 37209150 DOI: 10.1007/s00203-023-03556-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 04/14/2023] [Accepted: 04/15/2023] [Indexed: 05/22/2023]
Abstract
Streptomyces sp. RS2 was isolated from an unidentified sponge collected around Randayan Island, Indonesia. The genome of Streptomyces sp. RS2 consists of a linear chromosome of 9,391,717 base pairs with 71.9% of G + C content, 8270 protein-coding genes, as well as 18 rRNA and 85 tRNA loci. Twenty-eight putative secondary metabolites biosynthetic gene clusters (BGCs) were identified in the genome sequence. Nine of them have 100% similarity to BGCs for albaflavenone, α-lipomycin, coelibactin, coelichelin, ectoine, geosmin, germicidin, hopene, and lanthionine (SapB). The remaining 19 BGCs have low (< 50%) or moderate (50-80%) similarity to other known secondary metabolite BGCs. Biological activity assays of extracts from 21 different cultures of the RS2 strain showed that SCB ASW was the best medium for the production of antimicrobial and cytotoxic compounds. Streptomyces sp. RS2 has great potential to be a producer of novel secondary metabolites, particularly those with antimicrobial and antitumor activities.
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Affiliation(s)
- Risa Nofiani
- Department of Chemistry, Universitas Tanjungpura, Pontianak, 78124, Indonesia.
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR, 97331, USA.
| | - Puji Ardiningsih
- Department of Chemistry, Universitas Tanjungpura, Pontianak, 78124, Indonesia
| | | | - Agus Sukito
- Research Center for Applied Microbiology, National Research and Innovation Agency, Bogor, 16458, Indonesia
| | - Alexandra J Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Taifo Mahmud
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR, 97331, USA
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18
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Alonso L, Pommier T, Simon L, Maucourt F, Doré J, Dubost A, Trân Van V, Minard G, Valiente Moro C, Douady CJ, Moënne‐Loccoz Y. Microbiome analysis in Lascaux Cave in relation to black stain alterations of rock surfaces and collembola. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:80-91. [PMID: 36424842 PMCID: PMC10103860 DOI: 10.1111/1758-2229.13133] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 10/25/2022] [Indexed: 05/20/2023]
Abstract
Anthropization of Palaeolithic caves open for tourism may favour collembola invasion and result in the formation of black stains attributed to pigmented fungi. However, ecological processes underpinning black stain formation are not fully understood. Here, we tested the hypotheses that black stains from the Apse room of Lascaux Cave display a specific microbiota enriched in pigmented fungi, and that collembola thriving on the stains have the potential to consume and disseminate these black fungi. Metabarcoding showed that the microbiota of black stains and neighbouring unstained parts strongly differed, with in black stains a higher prevalence of Ochroconis and other pigmented fungi and the strong regression of Pseudomonas bacteria (whose isolates inhibited in vitro the growth of pigmented fungi). Isotopic analyses indicated that Folsomia candida collembola thriving on stains could feed on black stain in situ and assimilate the pigmented fungi they were fed with in vitro. They could carry these fungi and disseminate them when tested with complex black stains from Lascaux. This shows that black stain formation is linked to the development of pigmented fungi, which coincides with the elimination of antagonistic pseudomonads, and points towards a key role of F. candida collembola in the dynamics of pigmented fungi.
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Affiliation(s)
- Lise Alonso
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie MicrobienneVilleurbanneFrance
| | - Thomas Pommier
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie MicrobienneVilleurbanneFrance
| | - Laurent Simon
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR5023 LEHNAVilleurbanneFrance
| | - Flavien Maucourt
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie MicrobienneVilleurbanneFrance
| | - Jeanne Doré
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie MicrobienneVilleurbanneFrance
| | - Audrey Dubost
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie MicrobienneVilleurbanneFrance
| | - Van Trân Van
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie MicrobienneVilleurbanneFrance
| | - Guillaume Minard
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie MicrobienneVilleurbanneFrance
| | - Claire Valiente Moro
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie MicrobienneVilleurbanneFrance
| | - Christophe J. Douady
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR5023 LEHNAVilleurbanneFrance
| | - Yvan Moënne‐Loccoz
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie MicrobienneVilleurbanneFrance
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19
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Manganelli M, Testai E, Tazart Z, Scardala S, Codd GA. Co-Occurrence of Taste and Odor Compounds and Cyanotoxins in Cyanobacterial Blooms: Emerging Risks to Human Health? Microorganisms 2023; 11:microorganisms11040872. [PMID: 37110295 PMCID: PMC10146173 DOI: 10.3390/microorganisms11040872] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/23/2023] [Accepted: 03/24/2023] [Indexed: 03/31/2023] Open
Abstract
Cyanobacteria commonly form large blooms in waterbodies; they can produce cyanotoxins, with toxic effects on humans and animals, and volatile compounds, causing bad tastes and odors (T&O) at naturally occurring low concentrations. Notwithstanding the large amount of literature on either cyanotoxins or T&O, no review has focused on them at the same time. The present review critically evaluates the recent literature on cyanotoxins and T&O compounds (geosmin, 2-methylisoborneol, β-ionone and β-cyclocitral) to identify research gaps on harmful exposure of humans and animals to both metabolite classes. T&O and cyanotoxins production can be due to the same or common to different cyanobacterial species/strains, with the additional possibility of T&O production by non-cyanobacterial species. The few environmental studies on the co-occurrence of these two groups of metabolites are not sufficient to understand if and how they can co-vary, or influence each other, perhaps stimulating cyanotoxin production. Therefore, T&Os cannot reliably serve as early warning surrogates for cyanotoxins. The scarce data on T&O toxicity seem to indicate a low health risk (but the inhalation of β-cyclocitral deserves more study). However, no data are available on the effects of combined exposure to mixtures of cyanotoxins and T&O compounds and to combinations of T&O compounds; therefore, whether the co-occurrence of cyanotoxins and T&O compounds is a health issue remains an open question.
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Affiliation(s)
- Maura Manganelli
- Istituto Superiore di Sanità, Department of Environment and Health, viale Regina Elena, 299, 00162 Rome, Italy; (E.T.); (S.S.)
- Correspondence:
| | - Emanuela Testai
- Istituto Superiore di Sanità, Department of Environment and Health, viale Regina Elena, 299, 00162 Rome, Italy; (E.T.); (S.S.)
| | - Zakaria Tazart
- Department of Food Sciences and Nutrition, University of Malta, 2080 Msida, Malta;
| | - Simona Scardala
- Istituto Superiore di Sanità, Department of Environment and Health, viale Regina Elena, 299, 00162 Rome, Italy; (E.T.); (S.S.)
| | - Geoffrey A. Codd
- School of Natural Sciences, University of Stirling, Stirling FK9 4LA, UK;
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
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20
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Scarano F, Deivarajan Suresh M, Tiraboschi E, Cabirol A, Nouvian M, Nowotny T, Haase A. Geosmin suppresses defensive behaviour and elicits unusual neural responses in honey bees. Sci Rep 2023; 13:3851. [PMID: 36890201 PMCID: PMC9995521 DOI: 10.1038/s41598-023-30796-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 03/01/2023] [Indexed: 03/10/2023] Open
Abstract
Geosmin is an odorant produced by bacteria in moist soil. It has been found to be extraordinarily relevant to some insects, but the reasons for this are not yet fully understood. Here we report the first tests of the effect of geosmin on honey bees. A stinging assay showed that the defensive behaviour elicited by the bee's alarm pheromone component isoamyl acetate (IAA) is strongly suppressed by geosmin. Surprisingly, the suppression is, however, only present at very low geosmin concentrations, and disappears at higher concentrations. We investigated the underlying mechanisms at the level of the olfactory receptor neurons by means of electroantennography, finding the responses to mixtures of geosmin and IAA to be lower than to pure IAA, suggesting an interaction of both compounds at the olfactory receptor level. Calcium imaging of the antennal lobe (AL) revealed that neuronal responses to geosmin decreased with increasing concentration, correlating well with the observed behaviour. Computational modelling of odour transduction and coding in the AL suggests that a broader activation of olfactory receptor types by geosmin in combination with lateral inhibition could lead to the observed non-monotonic increasing-decreasing responses to geosmin and thus underlie the specificity of the behavioural response to low geosmin concentrations.
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Affiliation(s)
- Florencia Scarano
- Department of Physics, University of Trento, 38120, Trento, Italy.,Center for Mind/Brain Sciences (CIMeC), University of Trento, 38068, Rovereto, Italy
| | | | - Ettore Tiraboschi
- Center for Mind/Brain Sciences (CIMeC), University of Trento, 38068, Rovereto, Italy
| | - Amélie Cabirol
- Center for Mind/Brain Sciences (CIMeC), University of Trento, 38068, Rovereto, Italy.,Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Morgane Nouvian
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany.,Zukunftskolleg, University of Konstanz, 78464, Konstanz, Germany
| | - Thomas Nowotny
- School of Engineering and Informatics, University of Sussex, Brighton, BN1 9QJ, UK.
| | - Albrecht Haase
- Department of Physics, University of Trento, 38120, Trento, Italy. .,Center for Mind/Brain Sciences (CIMeC), University of Trento, 38068, Rovereto, Italy.
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21
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Bioactive Metabolite Survey of Actinobacteria Showing Plant Growth Promoting Traits to Develop Novel Biofertilizers. Metabolites 2023; 13:metabo13030374. [PMID: 36984814 PMCID: PMC10052678 DOI: 10.3390/metabo13030374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 02/21/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
The use of chemical fertilizers and pesticides has caused harmful impacts on the environment with the increase in economic burden. Biofertilizers are biological products containing living microorganisms capable of improving plant growth through eco-friendly mechanisms. In this work, three actinobacterial strains Streptomyces violaceoruber, Streptomyces coelicolor, and Kocuria rhizophila were characterized for multiple plant growth promoting (PGP) traits such as indole acetic acid production, phosphate solubilization, N2-fixation, and drought and salt tolerance. Then, these strains were investigated for their secreted and cellular metabolome, revealing a rich arsenal of bioactive molecules, including antibiotics and siderophores, with S. violaceoruber being the most prolific strain. Furthermore, the in vivo assays, performed on tomato (Solanum lycopersicum L.), resulted in an improved germination index and the growth of seedlings from seeds treated with PGP actinobacteria, with a particular focus on S. violaceoruber cultures. In particular, this last strain, producing volatile organic compounds having antimicrobial activity, was able to modulate volatilome and exert control on the global DNA methylation of tomato seedlings. Thus, these results, confirming the efficacy of the selected actinobacteria strains in promoting plant growth and development by producing volatile and non-volatile bioactive molecules, can promote eco-friendly alternatives in sustainable agriculture.
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22
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Zhou W, Wang Y, Wang J, Peng C, Wang Z, Qin H, Li G, Li D. Geosmin disrupts energy metabolism and locomotor behavior of zebrafish in early life stages. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 859:160222. [PMID: 36400299 DOI: 10.1016/j.scitotenv.2022.160222] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 11/11/2022] [Accepted: 11/12/2022] [Indexed: 06/16/2023]
Abstract
Geosmin has been commonly detected both in various aquatic environments and biota, but its exact toxicological mechanisms to organisms need further experimentation. In the present study, zebrafish embryos were exposed to geosmin at nominal concentrations of 50, 500 and 5000 ng/L for 120 h post-fertilization (hpf), followed by locomotor activity and biochemical parameter examination, and multi-omics investigation of the transcriptome and metabolome. The results showed that geosmin exposure significantly reduced the mitochondrial electron transport chain (ETC) complexes I-V, ATP content and mitochondrial respiration and suppressed the locomotor behavior of zebrafish larvae. Transcriptomics analysis revealed that the transcripts of genes involved in oxidative phosphorylation, glycolysis, and lipid metabolism were significantly affected, indicating that geosmin disrupts energy metabolism. Furthermore, metabolomics results showed that 3 classes of lipids, namely glycerophospholipids (GPs), sphingolipids (SLs) and fatty acyls (FAs) were significantly decreased after geosmin exposure. This study provides novel insight into the underlying mechanisms of geosmin-induced energy metabolism and highlights the need for concern about geosmin exposure.
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Affiliation(s)
- Weicheng Zhou
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China; Hunan Provincial Key Laboratory of Xiangnan Rare-Precious Metals Compounds and Applications, School of Chemistry and Environmental Science, Xiangnan University, Chenzhou 423000, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Yuming Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Jinglong Wang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Chengrong Peng
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
| | - Zhicong Wang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
| | - Hongjie Qin
- Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Lab of Comprehensive Innovative Utilization of Ornamental Plant Germplasm, Guangzhou 510640, PR China
| | - Genbao Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
| | - Dunhai Li
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China.
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23
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Shepherdson EM, Baglio CR, Elliot MA. Streptomyces behavior and competition in the natural environment. Curr Opin Microbiol 2023; 71:102257. [PMID: 36565538 DOI: 10.1016/j.mib.2022.102257] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 12/24/2022]
Abstract
Streptomyces are ubiquitous terrestrial bacteria that are renowned for their robust metabolic capabilities and their behavioral flexibility. In competing for environmental niches, these bacteria can employ novel growth and dispersal behaviors. They also wield their diverse metabolic repertoire for everything from maximizing nutrient uptake, to preventing phage replication or inhibiting bacterial and fungal growth. Increasingly, they are found to live in association with plants and insects, often conferring protective benefits to their host courtesy of their ability to produce pathogen-inhibitory antimicrobial compounds. Here, we highlight recent advances in understanding the competitive and cooperative interactions between Streptomyces and phage, microbes, and higher organisms in their environment.
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Affiliation(s)
- Evan Mf Shepherdson
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada; M.G. DeGroote Institute for Infectious Disease Research, Canada
| | - Christine R Baglio
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada; M.G. DeGroote Institute for Infectious Disease Research, Canada
| | - Marie A Elliot
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada; M.G. DeGroote Institute for Infectious Disease Research, Canada.
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24
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Luo Y, Wang L, Cao T, Chen J, Lv M, Wei S, Lu S, Tian X. Microplastics are transferred by soil fauna and regulate soil function as material carriers. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 857:159690. [PMID: 36302410 DOI: 10.1016/j.scitotenv.2022.159690] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/15/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
The ecotoxicological effects of microplastics, a new and widespread ecosystem pollutant, have been extensively reported. However, it remains unclear whether soil fauna transfer microplastics and whether migration behaviours influence subsequent ecological functions in terrestrial ecosystems. We investigated the transfer patterns of microplastics and their adsorbed substances by soil animals (the springtail, Folsomia candida) and the effect of the transfer on the decomposition of soil organic matter through a standardized cotton strip assay. The results showed that springtails had a strong ability to transfer microplastics into the soil. The adsorbed nutrient (nitrogen; N), pollutant (cadmium; Cd), and green fluorescent Escherichia coli (GFP-E. coli) were also transferred with the microplastics. In addition, cotton strip decomposition was accelerated when the microplastics adsorbed N, but the adsorption of Cd decreased decomposition. These ecological effects were particularly strong for small microplastics. Microplastic transfer regulated soil bacterial communities, promoting the growth of Ascomycota fungi and inhibiting that of Basidiomycota, leading to cotton strip decomposition. Thus, microplastic pollution may occur at one site, but microplastics can be transferred anywhere in terrestrial ecosystems by soil animals and adsorb other substances, including nutrients and pollutants, that affect ecosystem function. Therefore, more studies on the migration behaviour of microplastics are necessary.
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Affiliation(s)
- Yunchao Luo
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, 210023, China
| | - Lin Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, 210023, China
| | - Tingting Cao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, 210023, China; State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Junxiu Chen
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Meiqi Lv
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, 210023, China
| | - Sijie Wei
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, 210023, China
| | - Shangxian Lu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, 210023, China
| | - Xingjun Tian
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, 210023, China; College of Eco-Environmental Engineering, Qinghai University, Xining, Qinghai 810016, China.
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25
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Zhang Z, Guo Q, Qian J, Ye C, Huang H. Construction and application of the genome-scale metabolic model of Streptomyces radiopugnans. Front Bioeng Biotechnol 2023; 11:1108412. [PMID: 36873364 PMCID: PMC9982006 DOI: 10.3389/fbioe.2023.1108412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 02/07/2023] [Indexed: 02/19/2023] Open
Abstract
Geosmin is one of the most common earthy-musty odor compounds, which is mainly produced by Streptomyces. Streptomyces radiopugnans was screened in radiation-polluted soil, which has the potential to overproduce geosmin. However, due to the complex cellular metabolism and regulation mechanism, the phenotypes of S. radiopugnans were hard to investigate. A genome-scale metabolic model of S. radiopugnans named iZDZ767 was constructed. Model iZDZ767 involved 1,411 reactions, 1,399 metabolites, and 767 genes; its gene coverage was 14.1%. Model iZDZ767 could grow on 23 carbon sources and five nitrogen sources, which achieved 82.1% and 83.3% prediction accuracy, respectively. For the essential gene prediction, the accuracy was 97.6%. According to the simulation of model iZDZ767, D-glucose and urea were the best for geosmin fermentation. The culture condition optimization experiments proved that with D-glucose as the carbon source and urea as the nitrogen source (4 g/L), geosmin production could reach 581.6 ng/L. Using the OptForce algorithm, 29 genes were identified as the targets of metabolic engineering modification. With the help of model iZDZ767, the phenotypes of S. radiopugnans could be well resolved. The key targets for geosmin overproduction could also be identified efficiently.
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Affiliation(s)
- Zhidong Zhang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Technology University, Nanjing, China.,Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Qi Guo
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Technology University, Nanjing, China
| | - Jinyi Qian
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Chao Ye
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - He Huang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Technology University, Nanjing, China.,School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
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26
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Chandrasekaran M, Paramasivan M, Sahayarayan JJ. Microbial Volatile Organic Compounds: An Alternative for Chemical Fertilizers in Sustainable Agriculture Development. Microorganisms 2022; 11:microorganisms11010042. [PMID: 36677334 PMCID: PMC9861404 DOI: 10.3390/microorganisms11010042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 12/12/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022] Open
Abstract
Microorganisms are exceptional at producing several volatile substances called microbial volatile organic compounds (mVOCs). The mVOCs allow the microorganism to communicate with other organisms via both inter and intracellular signaling pathways. Recent investigation has revealed that mVOCs are chemically very diverse and play vital roles in plant interactions and microbial communication. The mVOCs can also modify the plant's physiological and hormonal pathways to augment plant growth and production. Moreover, mVOCs have been affirmed for effective alleviation of stresses, and also act as an elicitor of plant immunity. Thus, mVOCs act as an effective alternative to various chemical fertilizers and pesticides. The present review summarizes the recent findings about mVOCs and their roles in inter and intra-kingdoms interactions. Prospects for improving soil fertility, food safety, and security are affirmed for mVOCs application for sustainable agriculture.
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Affiliation(s)
- Murugesan Chandrasekaran
- Department of Food Science and Biotechnology, Sejong University, Neungdong-ro 209, Gwangjin-gu, Seoul 05006, Republic of Korea
- Correspondence: ; Tel.: +82-2-3408-4026
| | - Manivannan Paramasivan
- Department of Microbiology, Bharathidasan University, Tiruchirappalli 620024, Tamilnadu, India
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27
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Ramírez-Ordorica A, Contreras-Cornejo HA, Orduño-Cruz N, Luna-Cruz A, Winkler R, Macías-Rodríguez L. Volatiles released by Beauveria bassiana induce oviposition behavior in the fall armyworm Spodoptera frugiperda (Lepidoptera: Noctuidae). FEMS Microbiol Ecol 2022; 98:6724240. [PMID: 36166365 DOI: 10.1093/femsec/fiac114] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/11/2022] [Accepted: 09/23/2022] [Indexed: 12/14/2022] Open
Abstract
Microbial volatile organic compounds may act as semiochemicals, inciting different behavioral responses in insects. Beauveria bassiana is an entomopathogenic fungus, and physiological and environmental factors are positively related to fungal virulence. In this study, we examined the volatile profiles produced by eight B. bassiana strains, isolated from soil plots and mycosed insect cadavers, with different speeds of kill and determined if these compounds induce oviposition behavior in Spodoptera frugiperda. Fungal volatilome analysis revealed differences between the isolates. Isolates from mycosed insects showed higher virulence, larger egg mass area and length, and a higher number of eggs by mass, than those obtained from soil. Furthermore, a dilution of the fungal odoriferous compounds increased the insect response, suggesting that S. frugiperda is highly susceptible to the fungal compound's fingerprint. Otherwise, the insect response to the natural blend of volatiles released by the fungus was different from that obtained with 3-methylbutanol, which was the most abundant compound in all isolates. The ability of an entomopathogen to produce volatiles that can induce olfactory stimulation of egg-laying behavior could represent an ecological adaptive advantage in which the entomopathogen stimulates the insect population growth.
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Affiliation(s)
- Arturo Ramírez-Ordorica
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, 58030, México
| | - Hexon Angel Contreras-Cornejo
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, 58030, México
| | - Nuvia Orduño-Cruz
- Facultad de Ciencias Agrotecnológicas, Universidad Autónoma de Chihuahua, Chihuahua, Chihuahua, 31350, México
| | - Alfonso Luna-Cruz
- CONACYT-Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, 58030, México
| | - Robert Winkler
- Department of Biotechnology and Biochemistry, CINVESTAV-Irapuato, Instituto Politécnico Nacional, Irapuato, Guanajuato, 36824, México
| | - Lourdes Macías-Rodríguez
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, 58030, México
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28
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Naundrup A, Bohman B, Kwadha CA, Jensen AB, Becher PG, De Fine Licht HH. Pathogenic fungus uses volatiles to entice male flies into fatal matings with infected female cadavers. THE ISME JOURNAL 2022; 16:2388-2397. [PMID: 35831484 PMCID: PMC9477817 DOI: 10.1038/s41396-022-01284-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 06/28/2022] [Accepted: 06/30/2022] [Indexed: 12/17/2022]
Abstract
To ensure dispersal, many parasites and pathogens behaviourally manipulate infected hosts. Other pathogens and certain insect-pollinated flowers use sexual mimicry and release deceptive mating signals. However, it is unusual for pathogens to rely on both behavioural host manipulation and sexual mimicry. Here, we show that the host-specific and behaviourally manipulating pathogenic fungus, Entomophthora muscae, generates a chemical blend of volatile sesquiterpenes and alters the profile of natural host cuticular hydrocarbons in infected female housefly (Musca domestica) cadavers. Healthy male houseflies respond to the fungal compounds and are enticed into mating with female cadavers. This is advantageous for the fungus as close proximity between host individuals leads to an increased probability of infection. The fungus exploits the willingness of male flies to mate and benefits from altering the behaviour of uninfected male host flies. The altered cuticular hydrocarbons and emitted volatiles thus underlie the evolution of an extended phenotypic trait.
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Affiliation(s)
- Andreas Naundrup
- Section for Organismal Biology, Department of Plant and Environmental Sciences, University of Copenhagen, København, Denmark.
| | - Björn Bohman
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Charles A Kwadha
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Annette B Jensen
- Section for Organismal Biology, Department of Plant and Environmental Sciences, University of Copenhagen, København, Denmark
| | - Paul G Becher
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Henrik H De Fine Licht
- Section for Organismal Biology, Department of Plant and Environmental Sciences, University of Copenhagen, København, Denmark.
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29
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Masteling R, de Boer W, Raaijmakers JM, Garbeva P, Dini-Andreote F. Microbial volatiles as mediators of eco-evolutionary dynamics. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.960198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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30
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Liu J, Clarke JA, McCann S, Hillier NK, Tahlan K. Analysis of Streptomyces Volatilomes Using Global Molecular Networking Reveals the Presence of Metabolites with Diverse Biological Activities. Microbiol Spectr 2022; 10:e0055222. [PMID: 35900081 PMCID: PMC9431705 DOI: 10.1128/spectrum.00552-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 07/09/2022] [Indexed: 12/20/2022] Open
Abstract
Streptomyces species produce a wide variety of specialized metabolites, some of which are used for communication or competition for resources in their natural environments. In addition, many natural products used in medicine and industry are derived from Streptomyces, and there has been interest in their capacity to produce volatile organic compounds (VOCs) for different industrial and agricultural applications. Recently, a machine-learning workflow called MSHub/GNPS was developed, which enables auto-deconvolution of gas chromatography-mass spectrometry (GC-MS) data, molecular networking, and library search capabilities, but it has not been applied to Streptomyces volatilomes. In this study, 131 Streptomyces isolates from the island of Newfoundland were phylogenetically typed, and 37 were selected based on their phylogeny and growth characteristics for VOC analysis using both a user-guided (conventional) and an MSHub/GNPS-based approach. More VOCs were annotated by MSHub/GNPS than by the conventional method. The number of unknown VOCs detected by the two methods was higher than those annotated, suggesting that many novel compounds remain to be identified. The molecular network generated by GNPS can be used to guide the annotation of such unknown VOCs in future studies. However, the number of overlapping VOCs annotated by the two methods is relatively small, suggesting that a combination of analysis methods might be required for robust volatilome analysis. More than half of the VOCs annotated with high confidence by the two approaches are plant-associated, many with reported bioactivities such as insect behavior modulation. Details regarding the properties and reported functions of such VOCs are described. IMPORTANCE This study represents the first detailed analysis of Streptomyces volatilomes using MSHub/GNPS, which in combination with a routinely used conventional method led to many annotations. More VOCs could be annotated using MSHub/GNPS as compared to the conventional method, many of which have known antimicrobial, anticancer, and insect behavior-modulating activities. The identification of numerous plant-associated VOCs by both approaches in the current study suggests that their production could be a more widespread phenomenon by members of the genus, highlighting opportunities for their large-scale production using Streptomyces. Plant-associated VOCs with antimicrobial activities, such as 1-octen-3-ol, octanol, and phenylethyl alcohol, have potential applications as fumigants. Furthermore, many of the annotated VOCs are reported to influence insect behavior, alluding to a possible explanation for their production based on the functions of other recently described Streptomyces VOCs in dispersal and nutrient acquisition.
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Affiliation(s)
- Jingyu Liu
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador, Canada
| | - Jody-Ann Clarke
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador, Canada
| | - Sean McCann
- Department of Biology, Acadia University, Wolfville, Nova Scotia, Canada
| | - N. Kirk Hillier
- Department of Biology, Acadia University, Wolfville, Nova Scotia, Canada
| | - Kapil Tahlan
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador, Canada
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31
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Pang F, Solanki MK, Wang Z. Streptomyces can be an excellent plant growth manager. World J Microbiol Biotechnol 2022; 38:193. [PMID: 35980475 DOI: 10.1007/s11274-022-03380-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 08/07/2022] [Indexed: 11/27/2022]
Abstract
Streptomyces, the most abundant and arguably the most important genus of actinomycetes, is an important source of biologically active compounds such as antibiotics, and extracellular hydrolytic enzymes. Since Streptomyces can have a beneficial symbiotic relationship with plants they can contribute to nutrition, health and fitness of the latter. This review article summarizes recent research contributions on the ability of Streptomyces to promote plant growth and improve plant tolerance to biotic and abiotic stress responses, as well as on the consequences, on plant health, of the enrichment of rhizospheric soils in Streptomyces species. This review summarizes the most recent reports of the contribution of Streptomyces to plant growth, health and fitness and suggests future research directions to promote the use of these bacteria for the development of a cleaner agriculture.
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Affiliation(s)
- Fei Pang
- Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology, College of Biology and Pharmacy, Yulin Normal University, Yulin, 537000, China
| | - Manoj Kumar Solanki
- Plant Cytogenetics and Molecular Biology Group, Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, 40-701, Katowice, Poland.
| | - Zhen Wang
- Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology, College of Biology and Pharmacy, Yulin Normal University, Yulin, 537000, China.
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32
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Pronk LJU, Bakker PAHM, Keel C, Maurhofer M, Flury P. The secret life of plant-beneficial rhizosphere bacteria: insects as alternative hosts. Environ Microbiol 2022; 24:3273-3289. [PMID: 35315557 PMCID: PMC9542179 DOI: 10.1111/1462-2920.15968] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 03/03/2022] [Accepted: 03/04/2022] [Indexed: 12/15/2022]
Abstract
Root-colonizing bacteria have been intensively investigated for their intimate relationship with plants and their manifold plant-beneficial activities. They can inhibit growth and activity of pathogens or induce defence responses. In recent years, evidence has emerged that several plant-beneficial rhizosphere bacteria do not only associate with plants but also with insects. Their relationships with insects range from pathogenic to mutualistic and some rhizobacteria can use insects as vectors for dispersal to new host plants. Thus, the interactions of these bacteria with their environment are even more complex than previously thought and can extend far beyond the rhizosphere. The discovery of this secret life of rhizobacteria represents an exciting new field of research that should link the fields of plant-microbe and insect-microbe interactions. In this review, we provide examples of plant-beneficial rhizosphere bacteria that use insects as alternative hosts, and of potentially rhizosphere-competent insect symbionts. We discuss the bacterial traits that may enable a host-switch between plants and insects and further set the multi-host lifestyle of rhizobacteria into an evolutionary and ecological context. Finally, we identify important open research questions and discuss perspectives on the use of these rhizobacteria in agriculture.
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Affiliation(s)
| | | | - Christoph Keel
- Department of Fundamental MicrobiologyUniversity of LausanneLausanneSwitzerland
| | - Monika Maurhofer
- Plant Pathology, Institute of Integrative BiologyETH ZürichZürichSwitzerland
| | - Pascale Flury
- Crop Protection – Phytopathology, Department of Crop SciencesResearch Institute of Organic Agriculture FiBLFrickSwitzerland
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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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Comparative Metagenomic Analysis of Biosynthetic Diversity across Sponge Microbiomes Highlights Metabolic Novelty, Conservation, and Diversification. mSystems 2022; 7:e0035722. [PMID: 35862823 PMCID: PMC9426513 DOI: 10.1128/msystems.00357-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Marine sponges and their microbial symbiotic communities are rich sources of diverse natural products (NPs) that often display biological activity, yet little is known about the global distribution of NPs and the symbionts that produce them. Since the majority of sponge symbionts remain uncultured, it is a challenge to characterize their NP biosynthetic pathways, assess their prevalence within the holobiont, and measure the diversity of NP biosynthetic gene clusters (BGCs) across sponge taxa and environments. Here, we explore the microbial biosynthetic landscapes of three high-microbial-abundance (HMA) sponges from the Atlantic Ocean and the Mediterranean Sea. This data set reveals striking novelty, with <1% of the recovered gene cluster families (GCFs) showing similarity to any characterized BGC. When zooming in on the microbial communities of each sponge, we observed higher variability of specialized metabolic and taxonomic profiles between sponge species than within species. Nonetheless, we identified conservation of GCFs, with 20% of sponge GCFs being shared between at least two sponge species and a GCF core comprised of 6% of GCFs shared across all species. Within this functional core, we identified a set of widespread and diverse GCFs encoding nonribosomal peptide synthetases that are potentially involved in the production of diversified ether lipids, as well as GCFs putatively encoding the production of highly modified proteusins. The present work contributes to the small, yet growing body of data characterizing NP landscapes of marine sponge symbionts and to the cryptic biosynthetic potential contained in this environmental niche. IMPORTANCE Marine sponges and their microbial symbiotic communities are a rich source of diverse natural products (NPs). However, little is known about the sponge NP global distribution landscape and the symbionts that produce them. Here, we make use of recently developed tools to perform untargeted mining and comparative analysis of sponge microbiome metagenomes of three sponge species in the first study considering replicate metagenomes of multiple sponge species. We present an overview of the biosynthetic diversity across these sponge holobionts, which displays extreme biosynthetic novelty. We report not only the conservation of biosynthetic and taxonomic diversity but also a core of conserved specialized metabolic pathways. Finally, we highlight several novel GCFs with unknown ecological function, and observe particularly high biosynthetic potential in Acidobacteriota and Latescibacteria symbionts. This study paves the way toward a better understanding of the marine sponge holobionts' biosynthetic potential and the functional and ecological role of sponge microbiomes.
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Gu B, Hou A, Dickschat JS. The stereochemical course of 2-methylisoborneol biosynthesis. Beilstein J Org Chem 2022; 18:818-824. [PMID: 35875708 PMCID: PMC9273983 DOI: 10.3762/bjoc.18.82] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 07/05/2022] [Indexed: 11/23/2022] Open
Abstract
Both enantiomers of 2-methyllinalyl diphosphate (2-Me-LPP) were synthesized enantioselectively using Sharpless epoxidation as a key step and purification of enantiomerically enriched intermediates through HPLC separation on a chiral stationary phase. Their enzymatic conversion with 2-methylisoborneol synthase (2MIBS) demonstrates that (R)-2-Me-LPP is the on-pathway intermediate, while a minor formation of 2-methylisoborneol from (S)-2-Me-LPP may be explained by isomerization to 2-Me-GPP and then to (R)-2-Me-LPP.
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Affiliation(s)
- Binbin Gu
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Anwei Hou
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Jeroen S Dickschat
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
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Li G, Zhang Z, Wu M, Chen X, Yin M, Jiang Y, Huang X, Jiang C, Han L. The discovery of germacradienol synthase: Construction of genetically-engineered strain, glycosylated modification, bioactive evaluation of germacradienol. Bioorg Chem 2022; 124:105819. [DOI: 10.1016/j.bioorg.2022.105819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 04/14/2022] [Accepted: 04/16/2022] [Indexed: 11/28/2022]
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Abdelrahman O, Yagi S, El Siddig M, El Hussein A, Germanier F, De Vrieze M, L’Haridon F, Weisskopf L. Evaluating the Antagonistic Potential of Actinomycete Strains Isolated From Sudan’s Soils Against Phytophthora infestans. Front Microbiol 2022; 13:827824. [PMID: 35847058 PMCID: PMC9277107 DOI: 10.3389/fmicb.2022.827824] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 06/08/2022] [Indexed: 11/16/2022] Open
Abstract
Soil microorganisms play crucial roles in soil fertility, e.g., through decomposing organic matter, cycling nutrients or through beneficial interactions with plants. Actinomycetes are a major component of soil inhabitants; they are prolific producers of specialized metabolites, among which many antibiotics. Here we report the isolation and characterization of 175 Actinomycetes from rhizosphere and bulk soil samples collected in 18 locations in Sudan. We evaluated the strains’ metabolic potential for plant protection by testing their ability to inhibit the mycelial growth of the oomycete Phytophthora infestans, which is one of the most devastating plant pathogens worldwide. Most strains significantly reduced the oomycete’s growth in direct confrontational in vitro assays. A significant proportion of the tested strains (15%) were able to inhibit P. infestans to more than 80%, 23% to 50%–80%, while the remaining 62% had inhibition percentages lesser than 50%. Different morphologies of P. infestans mycelial growth and sporangia formation were observed upon co-inoculation with some of the Actinomycetes isolates, such as the production of fewer, thinner hyphae without sporangia leading to a faint growth morphology, or on the contrary, of clusters of thick-walled hyphae leading to a bushy, or “frozen” morphology. These morphologies were caused by strains differing in activity levels but phylogenetically closely related with each other. To evaluate whether the isolated Actinomycetes could also inhibit the pathogen’s growth in planta, the most active strains were tested for their ability to restrict disease progress in leaf disc and full plant assays. Five of the active strains showed highly significant protection of potato leaves against the pathogen in leaf disc assays, as well as substantial reduction of disease progress in full plants assays. Using cell-free filtrates instead of the bacterial spores also led to full protection against disease on leaf discs, which highlights the strong crop protective potential of the secreted metabolites that could be applied as leaf spray. This study demonstrates the strong anti-oomycete activity of soil- and rhizosphere-borne Actinomycetes and highlights their significant potential for the development of sustainable solutions based on either cell suspensions or cell-free filtrates to safeguard potatoes from their most damaging pathogen.
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Affiliation(s)
- Ola Abdelrahman
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Department of Botany, University of Khartoum, Khartoum, Sudan
| | - Sakina Yagi
- Department of Botany, University of Khartoum, Khartoum, Sudan
| | | | - Adil El Hussein
- Department of Botany, University of Khartoum, Khartoum, Sudan
| | - Fanny Germanier
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Mout De Vrieze
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | | | - Laure Weisskopf
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- *Correspondence: Laure Weisskopf,
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Abstract
Bacteria have evolved numerous strategies to use resources efficiently. However, bacterial economies depend on both the physiological context of the organisms as well as their growth state - whether they are growing, non-growing or reinitiating growth. In this essay, we discuss some of the features that make bacteria efficient under these different conditions and during the transitions between them. We also highlight the many outstanding questions regarding the physiology of non-growing bacterial cells. Lastly, we examine how efficiency is apparent in both the mode and tempo of bacterial evolution.
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Affiliation(s)
- Roberto Kolter
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA.
| | - Nathalie Balaban
- Racah Institute of Physics, Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Thomas Julou
- Biozentrum and Swiss Institute of Bioinformatics, University of Basel, Basel, CH 4056, Switzerland
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Multikingdom interactions govern the microbiome in subterranean cultural heritage sites. Proc Natl Acad Sci U S A 2022; 119:e2121141119. [PMID: 35344401 PMCID: PMC9169738 DOI: 10.1073/pnas.2121141119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
SignificanceThe conservation of historical relics against microbial biodeterioration is critical to preserving cultural heritages. One major challenge is our limited understanding of microorganisms' dispersal, colonization, and persistence on relics after excavation and opening to external environments. Here, we investigate the ecological and physiological profiles of the microbiome within and outside the Dahuting Han Dynasty Tomb with a 1,800-y history. Actinobacteria dominate the microbiome in this tomb. Via interkingdom signaling mutualism, springtails carry Actinobacteria as one possible source into the tomb from surrounding environments. Subsequently, Actinobacteria produce cellulases combined with antimicrobial substances, which helps them to colonize and thrive in the tomb via intrakingdom competition. Our findings unravel the ecology of the microbiomes colonizing historical relics and provide help for conservation practices.
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Gu B, Dickschat JS. A non-natural biosynthesis pathway toward 2-methylisoborneol. Chem Commun (Camb) 2022; 58:4316-4319. [PMID: 35262160 DOI: 10.1039/d2cc00636g] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The biosynthesis of 2-methylisoborneol was reconstituted by elongation of dimethylallyl diphosphate (DMAPP) with (S)- and (R)-2-methylisopentenyl diphosphate (2-Me-IPP) using farnesyl diphosphate synthase (FPPS), followed by terpene cyclisation. The stereochemical course of the FPPS reaction was studied in detail using stereoselectively deuterated 2-Me-IPP isotopomers.
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Affiliation(s)
- Binbin Gu
- Research Center for Marine Drugs, State Key Laboratory of Oncogene and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.,Kekulé-Institute for Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany.
| | - Jeroen S Dickschat
- Kekulé-Institute for Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany.
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Abstract
Known as the smell of earth after rain, geosmin is an odorous terpene detectable by humans at picomolar concentrations. Geosmin production is heavily conserved in actinobacteria, myxobacteria, cyanobacteria, and some fungi, but its biological activity is poorly understood. We theorized that geosmin was an aposematic signal used to indicate the unpalatability of toxin-producing microbes, discouraging predation by eukaryotes. Consistent with this hypothesis, we found that geosmin altered the behavior of the bacteriophagous nematode Caenorhabditis elegans on agar plates in the absence of bacteria. Normal movement was restored in mutant worms lacking differentiated ASE (amphid neurons, single ciliated endings) neurons, suggesting that geosmin is a taste detected by the nematodal gustatory system. In a predation assay, geosmin and the related terpene 2-methylisoborneol reduced grazing on the bacterium Streptomyces coelicolor. Predation was restored by the removal of both terpene biosynthetic pathways or the introduction of C. elegans that lacked differentiated ASE taste neurons, leading to the apparent death of both bacteria and worms. While geosmin and 2-methylisoborneol appeared to be nontoxic, grazing triggered bacterial sporulation and the production of actinorhodin, a pigment coproduced with a number of toxic metabolites. In this system, geosmin thus appears to act as a warning signal indicating the unpalatability of its producers and reducing predation in a manner that benefits predator and prey. This suggests that molecular signaling may affect microbial predator-prey interactions in a manner similar to that of the well-studied visual markers of poisonous animal prey. IMPORTANCE One of the key chemicals that give soil its earthy aroma, geosmin is a frequent water contaminant produced by a range of unrelated microbes. Many animals, including humans, are able to detect geosmin at minute concentrations, but the benefit that this compound provides to its producing organisms is poorly understood. We found that geosmin repelled the bacterial predator Caenorhabditis elegans in the absence of bacteria and reduced contact between the worms and the geosmin-producing bacterium Streptomyces coelicolor in a predation assay. While geosmin itself appears to be nontoxic to C. elegans, these bacteria make a wide range of toxic metabolites, and grazing on them harmed the worms. In this system, geosmin thus appears to indicate unpalatable bacteria, reducing predation and benefiting both predator and prey. Aposematic signals are well known in animals, and this work suggests that metabolites may play a similar role in the microbial world.
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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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Exploratory Growth in Streptomyces venezuelae Involves a Unique Transcriptional Program, Enhanced Oxidative Stress Response, and Profound Acceleration in Response to Glycerol. J Bacteriol 2022; 204:e0062321. [PMID: 35254103 DOI: 10.1128/jb.00623-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Exploration is a recently discovered mode of growth and behavior exhibited by some Streptomyces species that is distinct from their classical sporulating life cycle. While much has been uncovered regarding initiating environmental conditions and phenotypic outcomes of exploratory growth, how this process is coordinated at a genetic level remains unclear. We used RNA sequencing to survey global changes in the transcriptional profile of exploring cultures over time in the model organism Streptomyces venezuelae. Transcriptomic analyses revealed widespread changes in gene expression impacting diverse cellular functions. Investigations into differentially expressed regulatory elements revealed specific groups of regulatory factors to be impacted, including the expression of several extracytoplasmic function (ECF) sigma factors, second messenger signaling pathways, and members of the whiB-like (wbl) family of transcription factors. Dramatic changes were observed among primary metabolic pathways, especially among respiration-associated genes and the oxidative stress response; enzyme assays confirmed that exploring cultures exhibit an enhanced oxidative stress response compared with classically growing cultures. Changes in the expression of the glycerol catabolic genes in S. venezuelae led to the discovery that glycerol supplementation of the growth medium promotes a dramatic acceleration of exploration. This effect appears to be unique to glycerol as an alternative carbon source, and this response is broadly conserved across other exploration-competent species. IMPORTANCE Exploration represents an alternative growth strategy for Streptomyces bacteria and is initiated in response to other microbes or specific environmental conditions. Here, we show that entry into exploration involves comprehensive transcriptional reprogramming, with an emphasis on changes in primary metabolism and regulatory/signaling functions. Intriguingly, a number of transcription factor classes were downregulated upon entry into exploration. In contrast, respiration-associated genes were strongly induced, and this was accompanied by an enhanced oxidative stress response. Notably, our transcriptional analyses suggested that glycerol may play a role in exploration, and we found that glycerol supplementation dramatically enhanced the exploration response in many streptomycetes. This work sheds new light on the regulatory and metabolic cues that influence a fascinating new microbial behavior.
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Choudoir MJ, DeAngelis KM. A framework for integrating microbial dispersal modes into soil ecosystem ecology. iScience 2022; 25:103887. [PMID: 35243247 PMCID: PMC8866892 DOI: 10.1016/j.isci.2022.103887] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Dispersal is a fundamental community assembly process that maintains soil microbial biodiversity across spatial and temporal scales, yet the impact of dispersal on ecosystem function is largely unpredictable. Dispersal is unique in that it contributes to both ecological and evolutionary processes and is shaped by both deterministic and stochastic forces. The ecosystem-level ramifications of dispersal outcomes are further compounded by microbial dormancy dynamics and environmental selection. Here we review the knowledge gaps and challenges that remain in defining how dispersal, environmental filtering, and microbial dormancy interact to influence the relationship between microbial community structure and function in soils. We propose the classification of microbial dispersal into three categories, through vegetative or active cells, through dormant cells, and through acellular dispersal, each with unique spatiotemporal dynamics and microbial trait associations. This conceptual framework should improve the integration of dispersal in defining soil microbial community structure-function relationships.
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Guo Z, Lv L, Liu D, He X, Wang W, Feng Y, Islam MS, Wang Q, Chen W, Liu Z, Wu S, Abied A. A global meta-analysis of animal manure application and soil microbial ecology based on random control treatments. PLoS One 2022; 17:e0262139. [PMID: 35061792 PMCID: PMC8782357 DOI: 10.1371/journal.pone.0262139] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 12/16/2021] [Indexed: 01/21/2023] Open
Abstract
The processes involved in soil domestication have altered the soil microbial ecology. We examined the question of whether animal manure application affects the soil microbial ecology of farmlands. The effects of global animal manure application on soil microorganisms were subjected to a meta-analysis based on randomized controlled treatments. A total of 2303 studies conducted in the last 30 years were incorporated into the analysis, and an additional 45 soil samples were collected and sequenced to obtain 16S rRNA and 18S rRNA data. The results revealed that manure application increased soil microbial biomass. Manure application alone increased bacterial diversity (M-Z: 7.546 and M-I: 8.68) and inhibited and reduced fungal diversity (M-Z: -1.15 and M-I: -1.03). Inorganic fertilizer replaced cattle and swine manure and provided nutrients to soil microorganisms. The soil samples of the experimental base were analyzed, and the relative abundances of bacteria and fungi were altered compared with no manure application. Manure increased bacterial diversity and reduced fungal diversity. Mrakia frigida and Betaproteobacteriales, which inhibit other microorganisms, increased significantly in the domesticated soil. Moreover, farm sewage treatments resulted in a bottleneck in the manure recovery rate that should be the focus of future research. Our results suggest that the potential risks of restructuring the microbial ecology of cultivated land must be considered.
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Affiliation(s)
- Zhenhua Guo
- Key Laboratory of Combining Farming and Animal Husbandry, Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Harbin, P. R. China
- * E-mail: , (ZG); (DL)
| | - Lei Lv
- Wood Science Research Institute of Heilongjiang Academy of Forestry, Harbin, P. R. China
| | - Di Liu
- Key Laboratory of Combining Farming and Animal Husbandry, Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Harbin, P. R. China
- * E-mail: , (ZG); (DL)
| | - Xinmiao He
- Key Laboratory of Combining Farming and Animal Husbandry, Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Harbin, P. R. China
| | - Wentao Wang
- Key Laboratory of Combining Farming and Animal Husbandry, Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Harbin, P. R. China
| | - Yanzhong Feng
- Key Laboratory of Combining Farming and Animal Husbandry, Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Harbin, P. R. China
| | - Md. Saiful Islam
- Department of Animal Production & Management, Sher-e-Bangla Agricultural University, Sher-e-Bangla Nagar, Dhaka, Bangladesh
| | - Qiuju Wang
- Key laboratory of Heilongjiang Soil Environment and Plant Nutrient, Institute of Soil Fertilizer and Environment Resources, Heilongjiang Academy of Agricultural Sciences, Harbin, P. R. China
| | - Wengui Chen
- Animal Science and Technology College, Northeast Agricultural University, Harbin, P. R. China
| | - Ziguang Liu
- Key Laboratory of Combining Farming and Animal Husbandry, Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Harbin, P. R. China
| | - Saihui Wu
- Key Laboratory of Combining Farming and Animal Husbandry, Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Harbin, P. R. China
| | - Adam Abied
- Key Laboratory of Combining Farming and Animal Husbandry, Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Harbin, P. R. China
- Dry Land Research Center (DLRC) and Animal Production, Agricultural Research Corporation (ARC), Khartoum, Sudan
- Projects and Programs Secretary of the Sudan Youth Organization on Climate Change, Khartoum, Sudan
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Hyphal compartmentalization and sporulation in Streptomyces require the conserved cell division protein SepX. Nat Commun 2022; 13:71. [PMID: 35013186 PMCID: PMC8748795 DOI: 10.1038/s41467-021-27638-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 11/03/2021] [Indexed: 11/25/2022] Open
Abstract
Filamentous actinobacteria such as Streptomyces undergo two distinct modes of cell division, leading to partitioning of growing hyphae into multicellular compartments via cross-walls, and to septation and release of unicellular spores. Specific determinants for cross-wall formation and the importance of hyphal compartmentalization for Streptomyces development are largely unknown. Here we show that SepX, an actinobacterial-specific protein, is crucial for both cell division modes in Streptomyces venezuelae. Importantly, we find that sepX-deficient mutants grow without cross-walls and that this substantially impairs the fitness of colonies and the coordinated progression through the developmental life cycle. Protein interaction studies and live-cell imaging suggest that SepX contributes to the stabilization of the divisome, a mechanism that also requires the dynamin-like protein DynB. Thus, our work identifies an important determinant for cell division in Streptomyces that is required for cellular development and sporulation. Streptomyces bacteria undergo two modes of cell division: formation of cross-walls in hyphae, leading to multicellular compartments, and septation for release of unicellular spores. Here, Bush et al. identify a protein that is important for both cell division modes in Streptomyces, likely by contributing to stabilization of the divisome.
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Drummond L, von Wallbrunn C, Buchhaupt M. Microbial Degradation of 2-Methylisoborneol in Forest Soil. Chem Biodivers 2021; 19:e202100734. [PMID: 34964253 DOI: 10.1002/cbdv.202100734] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/30/2021] [Indexed: 11/08/2022]
Abstract
Microorganisms use a complex array of chemical compounds to interact with their surroundings. They produce and process different molecules in response to changes in the environment or in their metabolism. One of the most well-known volatile organic compounds produced by microorganisms is the C11-terpenoid 2-methylisoborneol (2-MIB), which has received attention because of the off-flavor it confers to fresh and reservoir water as well as to cultured fish. Cleaning water supplies of the off-flavor 2-MIB has been of interest for the scientific community for years, with the use of techniques that are either expensive, e. g., activated carbon, or create toxic byproducts, e. g., ozonation. In the present study, soil samples from nature were collected from a forest and the volatile organic compounds produced by microbes were extracted and analyzed with focus on non-canonical terpenoid structures. HS-SPME-GC/MS analysis of soil samples revealed 1-methylcamphene (1-MC), 2-methylenebornane (2-MB) and 2-MIB as C11-terpenoids. Due to the high 1-MC/2-MIB ratio compared to previous reports, it was hypothesized that microbial degradation of 2-MIB was in place. Addition of synthetic 2-MIB to biologically active soil revealed complete degradation of the pollutant to 2-MB, 1-MC and 2-methyl-2-bornene (2-M2B). The results suggest the potential of using respective natural microorganisms for biodegradation of 2-MIB, with applications in water treatment, fishery and soil ecology.
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Affiliation(s)
- Laura Drummond
- Microbial Biotechnology, DECHEMA Research Institute, Theodor-Heuss-Allee 25, 60486, Frankfurt am Main, Germany.,Department of Microbiology and Biochemistry, Hochschule Geisenheim University, Von-Lade-Strasse 1, 65366, Geisenheim, Germany
| | - Christian von Wallbrunn
- Department of Microbiology and Biochemistry, Hochschule Geisenheim University, Von-Lade-Strasse 1, 65366, Geisenheim, Germany
| | - Markus Buchhaupt
- Microbial Biotechnology, DECHEMA Research Institute, Theodor-Heuss-Allee 25, 60486, Frankfurt am Main, Germany
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Re-classification of Streptomyces venezuelae strains and mining secondary metabolite biosynthetic gene clusters. iScience 2021; 24:103410. [PMID: 34877485 PMCID: PMC8627960 DOI: 10.1016/j.isci.2021.103410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 09/05/2021] [Accepted: 11/04/2021] [Indexed: 11/20/2022] Open
Abstract
Streptomyces species have attracted considerable interest as a reservoir of medically important secondary metabolites, which are even diverse and different between strains. Here, we reassess ten Streptomyces venezuelae strains by presenting the highly resolved classification, using 16S rRNA sequencing, MALDI-TOF MS protein profiling, and whole-genome sequencing. The results revealed that seven of the ten strains were misclassified as S. venezuelae species. Secondary metabolite biosynthetic gene cluster (smBGC) mining and targeted LC-MS/MS based metabolite screening of S. venezuelae and misclassified strains identified in total 59 secondary metabolites production. In addition, a comparison of pyrrolamide-type antibiotic BGCs of four misclassified strains, followed by functional genomics, revealed that athv28 is critical in the synthesis of the anthelvencin precursor, 5-amino-3,4-dihydro-2H-pyrrole-2-carboxylate (ADPC). Our findings illustrate the importance of the accurate classification and better utilization of misclassified Streptomyces strains to discover smBGCs and their secondary metabolite products.
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Connolly JA, Harcombe WR, Smanski MJ, Kinkel LL, Takano E, Breitling R. Harnessing intercellular signals to engineer the soil microbiome. Nat Prod Rep 2021; 39:311-324. [PMID: 34850800 DOI: 10.1039/d1np00034a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covering: Focus on 2015 to 2020Plant and soil microbiomes consist of diverse communities of organisms from across kingdoms and can profoundly affect plant growth and health. Natural product-based intercellular signals govern important interactions between microbiome members that ultimately regulate their beneficial or harmful impacts on the plant. Exploiting these evolved signalling circuits to engineer microbiomes towards beneficial interactions with crops is an attractive goal. There are few reports thus far of engineering the intercellular signalling of microbiomes, but this article argues that it represents a tremendous opportunity for advancing the field of microbiome engineering. This could be achieved through the selection of synergistic consortia in combination with genetic engineering of signal pathways to realise an optimised microbiome.
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Affiliation(s)
- Jack A Connolly
- Manchester Institute of Biotechnology, Manchester Synthetic Biology Research Centre SYNBIOCHEM, Faculty of Science and Engineering, School of Natural Sciences, Department of Chemistry, The University of Manchester, Manchester, M1 7DN, UK.
| | - William R Harcombe
- BioTechnology Institute, University of Minnesota, Twin-Cities, Saint Paul, MN55108, USA.,Department of Evolution, and Behaviour, University of Minnesota, Twin-Cities Saint Paul, MN55108, USA
| | - Michael J Smanski
- BioTechnology Institute, University of Minnesota, Twin-Cities, Saint Paul, MN55108, USA.,Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Twin-Cities, Saint Paul, MN55108, USA
| | - Linda L Kinkel
- BioTechnology Institute, University of Minnesota, Twin-Cities, Saint Paul, MN55108, USA.,Department of Plant Pathology, University of Minnesota, Twin-Cities, Saint Paul, MN 55108, USA
| | - Eriko Takano
- Manchester Institute of Biotechnology, Manchester Synthetic Biology Research Centre SYNBIOCHEM, Faculty of Science and Engineering, School of Natural Sciences, Department of Chemistry, The University of Manchester, Manchester, M1 7DN, UK.
| | - Rainer Breitling
- Manchester Institute of Biotechnology, Manchester Synthetic Biology Research Centre SYNBIOCHEM, Faculty of Science and Engineering, School of Natural Sciences, Department of Chemistry, The University of Manchester, Manchester, M1 7DN, UK.
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50
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Murphy T, Phan K, Irvine KN, Lean D. The Role of Micronutrients and Toxic Metals in the Management of Epidemics in Cambodia. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:11446. [PMID: 34769963 PMCID: PMC8582812 DOI: 10.3390/ijerph182111446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/11/2021] [Accepted: 10/28/2021] [Indexed: 11/16/2022]
Abstract
The illegal trade of wildlife in SE Asia has been identified as the likely cause of the COVID-19 pandemic. We reviewed 198 papers on the current COVID pandemic in Cambodia, diseases such as avian influenza and Nipah virus, most likely to develop into a new pandemic in Cambodia, and common features of disease that require mitigation. Artisanal goldmining uses pure mercury in the areas where wildlife is smuggled to China. Moreover, 30-40% of Cambodians are zinc deficient. High levels of arsenic in irrigation water (>1000 µg/L) are associated with very low levels of zinc in rice (5 µg/g) and rice is the primary staple food for the region. Brown rice from nine of 15 paddy fields in the arsenic zone of Cambodia had double the new guidelines of 100 µg/kg inorganic arsenic for children's food in the EU and USA. The combination of deficiencies of essential micronutrients like zinc and pervasive presence of arsenic and mercury has the potential to compromise the immunity of many Cambodians. Innovative solutions are suggested to improve micronutrient nutrition. Toxins that suppress the immune system must be better managed to reduce the virulence of pathogens. Cambodia was not likely the source of the COVID-19 but does have problems that could result in a new pandemic.
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Affiliation(s)
- Thomas Murphy
- Faculty of Science and Technology, International University, Phnom Penh 12000, Cambodia;
| | - Kongkea Phan
- Faculty of Science and Technology, International University, Phnom Penh 12000, Cambodia;
| | - Kim Neil Irvine
- Faculty of Architecture & Planning, Rangsit Campus, Thammasat University, Khlong Nueng 12121, Thailand;
| | - David Lean
- Lean Environmental, Apsley, ON K0L1A0, Canada;
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