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Tagele SB, Gachomo EW. A comparative study: impact of chemical and biological fungicides on soil bacterial communities. ENVIRONMENTAL MICROBIOME 2025; 20:44. [PMID: 40302004 PMCID: PMC12042651 DOI: 10.1186/s40793-025-00713-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2024] [Accepted: 04/21/2025] [Indexed: 05/01/2025]
Abstract
Soil microbial communities play key roles in agroecosystems, particularly in processes like organic matter decomposition and nutrient cycling. However, human activities can negatively impact their community structure and, consequently, soil function. SoilGard and Ridomil are effective methods for controlling carrot cavity spots caused by Pythium spp., but their effects on bacterial taxonomic and metabolic function shifts are not well understood. This study aims to investigate the comparative impact of the chemical fungicide Ridomil and the biological fungicide SoilGard on the bacterial communities in soils cultivated with carrots. Our results showed that both SoilGard and Ridomil significantly impacted soil bacterial diversity, but their effects were distinct and time-dependent. Ridomil had an immediate negative effect on soil bacterial diversity two weeks after treatment, whereas SoilGard was initially less disruptive but showed delayed negative consequences 12 weeks after treatment, particularly when combined with Pythium inoculation. Ridomil treatment led to an increase in Proteobacteria, especially the Pseudomonas population, as confirmed by both MiSeq and qPCR data. In contrast, SoilGard depleted the Mycobacterium population at 12 weeks after treatment. Furthermore, the results of community-level physiological profiling using Biolog Ecoplates showed significant differences in substrate-level diversity between Ridomil and SoilGard-treated samples, indicating a shift in the metabolic activity of bacterial communities. Ridomil-treated samples showed the lowest metabolic activity of bacterial communities, based on the diversity and richness of carbon source utilization, compared to control. Overall, this research highlights the distinct and time-dependent effects of biological and chemical fungicides on soil bacterial communities when applied at recommended doses.
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Affiliation(s)
- Setu Bazie Tagele
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, 92507, USA
| | - Emma W Gachomo
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, 92507, USA.
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2
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Meyer C, Jeanbille M, Breuil MC, Bru D, Höfer K, Screpanti C, Philippot L. Dynamic response of soil microbial communities and network to hymexazol exposure. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 957:177557. [PMID: 39557169 DOI: 10.1016/j.scitotenv.2024.177557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2024] [Revised: 11/08/2024] [Accepted: 11/12/2024] [Indexed: 11/20/2024]
Abstract
Fungicides are an essential component of current agricultural practices, but their extensive use has raised concerns about their effects on non-target soil microorganisms, which carry out essential ecosystem functions. However, despite the complexity of microbial communities, many studies investigating their response to fungicides focus only on bacteria or fungi at one point in time. In this study, we used amplicon sequencing to assess the effect of the fungicide hymexazol on the diversity, composition, and co-occurrence network of soil bacteria, fungi, and protists at 7, 21, and 60 days after application. We found that hymexazol had very little effect on microbial alpha-diversity, but that microbial community composition and OTU differential abundance were altered over the duration of the experiment, even after hymexazol concentrations were undetectable. The co-occurrence patterns within and between microbial kingdoms were affected by hymexazol dose, suggesting that indirect effects may play a role in the microbial community response. Nitrogen cycling was also affected, with a transient hymexazol-associated increase in the abundance of ammonia-oxidizing microorganisms and soil nitrate concentration. These findings highlight that the effects of fungicides on soil microorganisms are dynamic and extensive, spanning several taxonomic kingdoms.
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Affiliation(s)
- Cara Meyer
- Université Bourgogne, INRAE, Institut Agro Dijon, Agroécologie, 17 rue Sully, 21000 Dijon, France; Syngenta Crop Protection Research Stein, Schaffhauserstrasse 101, 4332 Stein, Switzerland
| | - Mathilde Jeanbille
- Université Bourgogne, INRAE, Institut Agro Dijon, Agroécologie, 17 rue Sully, 21000 Dijon, France
| | - Marie-Christine Breuil
- Université Bourgogne, INRAE, Institut Agro Dijon, Agroécologie, 17 rue Sully, 21000 Dijon, France
| | - David Bru
- Université Bourgogne, INRAE, Institut Agro Dijon, Agroécologie, 17 rue Sully, 21000 Dijon, France
| | - Kristin Höfer
- Syngenta Crop Protection Research Stein, Schaffhauserstrasse 101, 4332 Stein, Switzerland
| | - Claudio Screpanti
- Syngenta Crop Protection Research Stein, Schaffhauserstrasse 101, 4332 Stein, Switzerland
| | - Laurent Philippot
- Université Bourgogne, INRAE, Institut Agro Dijon, Agroécologie, 17 rue Sully, 21000 Dijon, France.
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Sellamuthu G, Chakraborty A, Vetukuri RR, Sarath S, Roy A. RNAi-biofungicides: a quantum leap for tree fungal pathogen management. Crit Rev Biotechnol 2024:1-28. [PMID: 39647992 DOI: 10.1080/07388551.2024.2430478] [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: 07/06/2024] [Revised: 10/03/2024] [Accepted: 10/27/2024] [Indexed: 12/10/2024]
Abstract
Fungal diseases threaten the forest ecosystem, impacting tree health, productivity, and biodiversity. Conventional approaches to combating diseases, such as biological control or fungicides, often reach limits regarding efficacy, resistance, non-target organisms, and environmental impact, enforcing alternative approaches. From an environmental and ecological standpoint, an RNA interference (RNAi) mediated double-stranded RNA (dsRNA)-based strategy can effectively manage forest fungal pathogens. The RNAi approach explicitly targets and suppresses gene expression through a conserved regulatory mechanism. Recently, it has evolved to be an effective tool in combating fungal diseases and promoting sustainable forest management approaches. RNAi bio-fungicides provide efficient and eco-friendly disease control alternatives using species-specific gene targeting, minimizing the off-target effects. With accessible data on fungal disease outbreaks, genomic resources, and effective delivery systems, RNAi-based biofungicides can be a promising tool for managing fungal pathogens in forests. However, concerns regarding the environmental fate of RNAi molecules and their potential impact on non-target organisms require an extensive investigation on a case-to-case basis. The current review critically evaluates the feasibility of RNAi bio-fungicides against forest pathogens by delving into the accessible delivery methods, environmental persistence, regulatory aspects, cost-effectiveness, community acceptance, and plausible future of RNAi-based forest protection products.
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Affiliation(s)
- Gothandapani Sellamuthu
- Faculty of Forestry & Wood Sciences, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Amrita Chakraborty
- Faculty of Forestry & Wood Sciences, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Ramesh R Vetukuri
- Department of Plant Breeding, Horticum, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Saravanasakthi Sarath
- Faculty of Forestry & Wood Sciences, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Amit Roy
- Faculty of Forestry & Wood Sciences, Czech University of Life Sciences Prague, Prague, Czech Republic
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He T, Yang M, Du H, Du R, He Y, Wang S, Deng W, Liu Y, He X, Zhu Y, Zhu S, Du F. Biocontrol agents transform the stability and functional characteristics of the grape phyllosphere microenvironment. FRONTIERS IN PLANT SCIENCE 2024; 15:1439776. [PMID: 39479547 PMCID: PMC11524152 DOI: 10.3389/fpls.2024.1439776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Accepted: 09/30/2024] [Indexed: 11/02/2024]
Abstract
The spread of grape leaf diseases has a negative impact on the sustainable development of agriculture. Diseases induced by Uncinula necator significantly affect the quality of grapes. Bacillus biocontrol agents have been proven effective in disease management. However, limited research has been conducted on the impact of biocontrol agents on the assembly and potential functions of plant phyllosphere microbial communities. This study used high-throughput sequencing combined with bioinformatics analysis and culture omics technology for analysis. The results showed that biocontrol bacteria B. subtilis utilized in this study can significantly reduce the disease index of powdery mildew (p<0.05); concurrently, it exhibits a lower disease index compared to traditional fungicides. A comprehensive analysis has revealed that biocontrol bacteria have no significant impact on the diversity of phyllosphere fungi and bacteria, while fungicides can significantly reduce bacterial diversity. Additionally, biocontrol agents can increase the complexity of fungal networks and enhance the degree of modularity and stability of the bacterial network. The results also showed that the biocontrol agents, which contained a high amount of B. subtilis, were able to effectively colonize the grapevine phyllosphere, creating a microenvironment that significantly inhibits pathogenic bacteria on grape leaves while enhancing leaf photosynthetic capacity. In conclusion, biocontrol agents significantly reduce the grape powdery mildew disease index, promote a microenvironment conducive to symbiotic microorganisms and beneficial bacteria, and enhance plant photosynthetic capacity. These findings provide a basis for promoting biocontrol agents and offer valuable insights into sustainable agriculture development.
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Affiliation(s)
- Tao He
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Meng Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Hongyan Du
- Institute of Ecological Agriculture in Hot Areas, Yunnan Academy of Agricultural Sciences, Yuanmou, Yunnan, China
| | - Ronghui Du
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Yueqiu He
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Sheng Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
| | - Weiping Deng
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Yixiang Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Xiahong He
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
| | - Youyong Zhu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Shusheng Zhu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Fei Du
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, China
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Pedrinho A, Karas PA, Kanellopoulos A, Feray E, Korman I, Wittenberg G, Ramot O, Karpouzas DG. The effect of natural products used as pesticides on the soil microbiota: OECD 216 nitrogen transformation test fails to identify effects that were detected via q-PCR microbial abundance measurement. PEST MANAGEMENT SCIENCE 2024; 80:2563-2576. [PMID: 38243771 DOI: 10.1002/ps.7961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 12/23/2023] [Accepted: 01/02/2024] [Indexed: 01/21/2024]
Abstract
BACKGROUND Natural products present an environmentally attractive alternative to synthetic pesticides which have been implicated in the off-target effect. Currently, the assessment of pesticide toxicity on soil microorganisms relies on the OECD 216 N transformation assay (OECD stands for the Organisation Economic Co-operation and Development, which is a key international standard-setting organisation). We tested the hypotheses that (i) the OECD 216 assay fails to identify unacceptable effects of pesticides on soil microbiota compared to more advanced molecular and standardized tests, and (ii) the natural products tested (dihydrochalcone, isoflavone, aliphatic phenol, and spinosad) are less toxic to soil microbiota compared to a synthetic pesticide compound (3,5-dichloraniline). We determined the following in three different soils: (i) ammonium (NH4 +) and nitrate (NO3 -) soil concentrations, as dictated by the OECD 216 test, and (ii) the abundance of phylogenetically (bacteria and fungi) and functionally distinct microbial groups [ammonia-oxidizing archaea (AOA) and bacteria (AOB)] using quantitative polymerase chain reaction (q-PCR). RESULTS All pesticides tested exhibited limited persistence, with spinosad demonstrating the highest persistence. None of the pesticides tested showed clear dose-dependent effects on NH4 + and NO3 - levels and the observed effects were <25% of the control, suggesting no unacceptable impacts on soil microorganisms. In contrast, q-PCR measurements revealed (i) distinct negative effects on the abundance of total bacteria and fungi, which were though limited to one of the studied soils, and (ii) a significant reduction in the abundance of both AOA and AOB across soils. This reduction was attributed to both natural products and 3,5-dichloraniline. CONCLUSION Our findings strongly advocate for a revision of the current regulatory framework regarding the toxicity of pesticides to soil microbiota, which should integrate advanced and well-standardized tools. © 2024 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Alexandre Pedrinho
- Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, University of Thessaly, Larissa, Greece
- Metabolic Insights Ltd, Ness Ziona, Israel
| | - Panagiotis A Karas
- Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, University of Thessaly, Larissa, Greece
| | - Alexandros Kanellopoulos
- Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, University of Thessaly, Larissa, Greece
| | - Emma Feray
- Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, University of Thessaly, Larissa, Greece
- National Museum of Natural History, Paris, France
| | - Ido Korman
- Metabolic Insights Ltd, Ness Ziona, Israel
| | | | - Ofir Ramot
- Metabolic Insights Ltd, Ness Ziona, Israel
| | - Dimitrios G Karpouzas
- Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, University of Thessaly, Larissa, Greece
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Meyer C, Jeanbille M, Breuil MC, Bru D, Höfer K, Screpanti C, Philippot L. Soil microbial community fragmentation reveals indirect effects of fungicide exposure mediated by biotic interactions between microorganisms. JOURNAL OF HAZARDOUS MATERIALS 2024; 470:134231. [PMID: 38598881 DOI: 10.1016/j.jhazmat.2024.134231] [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: 10/31/2023] [Revised: 03/22/2024] [Accepted: 04/04/2024] [Indexed: 04/12/2024]
Abstract
Fungicides are used worldwide to improve crop yields, but they can affect non-target soil microorganisms which are essential for ecosystem functioning. Microorganisms form complex communities characterized by a myriad of interspecies interactions, yet it remains unclear to what extent non-target microorganisms are indirectly affected by fungicides through biotic interactions with sensitive taxa. To quantify such indirect effects, we fragmented a soil microbial community by filtration to alter biotic interactions and compared the effect of the fungicide hymexazol between fractions in soil microcosms. We postulated that OTUs which are indirectly affected would exhibit a different response to the fungicide across the fragmented communities. We found that hymexazol primarily affected bacterial and fungal communities through indirect effects, which were responsible for more than 75% of the shifts in relative abundance of the dominant microbial OTUs after exposure to an agronomic dose of hymexazol. However, these indirect effects decreased for the bacterial community when hymexazol doses increased. Our results also suggest that N-cycling processes such as ammonia oxidation can be impacted indirectly by fungicide application. This work sheds light on the indirect impact of fungicide exposure on soil microorganisms through biotic interactions, which underscores the need for higher-tier risk assessment. ENVIRONMENTAL IMPLICATION: In this study, we used a novel approach based on the fragmentation of the soil microbial community to determine to which extent fungicide application could indirectly affect fungi and bacteria through biotic interactions. To assess off-target effects of fungicide on soil microorganisms, we selected hymexazol, which is used worldwide to control a variety of fungal plant pathogens, and exposed arable soil to the recommended field rate, as well as to higher rates. Our findings show that at least 75% of hymexazol-impacted microbial OTUs were indirectly affected, therefore emphasizing the importance of tiered risk assessment.
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Affiliation(s)
- Cara Meyer
- Université Bourgogne Franche-Comté, INRAE, AgroSup Dijon, Agroécologie, 17 rue Sully, 21000 Dijon, France; Syngenta Crop Protection Research Stein, Schaffhauserstrasse 101, 4332 Stein, Switzerland
| | - Mathilde Jeanbille
- Université Bourgogne Franche-Comté, INRAE, AgroSup Dijon, Agroécologie, 17 rue Sully, 21000 Dijon, France
| | - Marie-Christine Breuil
- Université Bourgogne Franche-Comté, INRAE, AgroSup Dijon, Agroécologie, 17 rue Sully, 21000 Dijon, France
| | - David Bru
- Université Bourgogne Franche-Comté, INRAE, AgroSup Dijon, Agroécologie, 17 rue Sully, 21000 Dijon, France
| | - Kristin Höfer
- Syngenta Crop Protection Research Stein, Schaffhauserstrasse 101, 4332 Stein, Switzerland
| | - Claudio Screpanti
- Syngenta Crop Protection Research Stein, Schaffhauserstrasse 101, 4332 Stein, Switzerland
| | - Laurent Philippot
- Université Bourgogne Franche-Comté, INRAE, AgroSup Dijon, Agroécologie, 17 rue Sully, 21000 Dijon, France.
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Jeyaseelan A, Murugesan K, Thayanithi S, Palanisamy SB. A review of the impact of herbicides and insecticides on the microbial communities. ENVIRONMENTAL RESEARCH 2024; 245:118020. [PMID: 38151149 DOI: 10.1016/j.envres.2023.118020] [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: 09/04/2023] [Revised: 11/23/2023] [Accepted: 12/21/2023] [Indexed: 12/29/2023]
Abstract
Enhancing crop yield to accommodate the ever-increasing world population has become critical, and diminishing arable land has pressured current agricultural practices. Intensive farming methods have been using more pesticides and insecticides (biocides), culminating in soil deposition, negatively impacting the microbiome. Hence, a deeper understanding of the interaction and impact of pesticides and insecticides on microbial communities is required for the scientific community. This review highlights the recent findings concerning the possible impacts of biocides on various soil microorganisms and their diversity. This review's bibliometric analysis emphasised the recent developments' statistics based on the Scopus document search. Pesticides and insecticides are reported to degrade microbes' structure, cellular processes, and distinct biochemical reactions at cellular and biochemical levels. Several biocides disrupt the relationship between plants and their microbial symbionts, hindering beneficial biological activities that are widely discussed. Most microbial target sites of or receptors are biomolecules, and biocides bind with the receptor through a ligand-based mechanism. The biomarker action mechanism in response to biocides relies on activating the receptor site by specific biochemical interactions. The production of electrophilic or nucleophilic species, free radicals, and redox-reactive agents are the significant factors of biocide's metabolic reaction. Most studies considered for the review reported the negative impact of biocides on the soil microbial community; hence, technological development is required regarding eco-friendly pesticide and insecticide, which has less or no impact on the soil microbial community.
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Affiliation(s)
- Aravind Jeyaseelan
- Department of Biotechnology, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS), Thandalam, Chennai, 602105, Tamil Nadu, India
| | - Kamaraj Murugesan
- Department of Biotechnology, Faculty of Science and Humanities, SRM Institute of Science and Technology-Ramapuram, Chennai, 600089, Tamil Nadu, India; Life Science Division, Faculty of Health and Life Sciences, INTI International University, Nilai, 71800, Malaysia.
| | - Saranya Thayanithi
- Department of Biotechnology, Rathinam Technical Campus, Coimbatore, 641021, Tamil Nadu, India
| | - Suresh Babu Palanisamy
- Department of Biotechnology, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS), Thandalam, Chennai, 602105, Tamil Nadu, India.
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Rangel LI, Leveau JHJ. Applied microbiology of the phyllosphere. Appl Microbiol Biotechnol 2024; 108:211. [PMID: 38358509 PMCID: PMC10869387 DOI: 10.1007/s00253-024-13042-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/24/2024] [Accepted: 01/29/2024] [Indexed: 02/16/2024]
Abstract
The phyllosphere, or plant leaf surface, represents a microbial ecosystem of considerable size, holding extraordinary biodiversity and enormous potential for the discovery of new products, tools, and applications in biotechnology, agriculture, medicine, and elsewhere. This mini-review highlights the applied microbiology of the phyllosphere as an original field of study concerning itself with the genes, gene products, natural compounds, and traits that underlie phyllosphere-specific adaptations and services that have commercial and economic value for current or future innovation. Examples include plant-growth-promoting and disease-suppressive phyllobacteria, probiotics and fermented foods that support human health, as well as microbials that remedy foliar contamination with airborne pollutants, residual pesticides, or plastics. Phyllosphere microbes promote plant biomass conversion into compost, renewable energy, animal feed, or fiber. They produce foodstuffs such as thickening agents and sugar substitutes, industrial-grade biosurfactants, novel antibiotics and cancer drugs, as well as enzymes used as food additives or freezing agents. Furthermore, new developments in DNA sequence-based profiling of leaf-associated microbial communities allow for surveillance approaches in the context of food safety and security, for example, to detect enteric human pathogens on leafy greens, predict plant disease outbreaks, and intercept plant pathogens and pests on internationally traded goods. KEY POINTS: • Applied phyllosphere microbiology concerns leaf-specific adaptations for economic value • Phyllobioprospecting searches the phyllosphere microbiome for product development • Phyllobiomonitoring tracks phyllosphere microbial profiles for early risk detection.
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Affiliation(s)
- Lorena I Rangel
- Cell & Molecular Sciences, The James Hutton Institute, Dundee, Scotland, UK.
- Department of Plant Pathology, University of California, Davis, CA, USA.
| | - Johan H J Leveau
- Department of Plant Pathology, University of California, Davis, CA, USA.
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Kalamaras SD, Christou ML, Tzenos CA, Vasileiadis S, Karpouzas DG, Kotsopoulos TA. Investigation of the Critical Biomass of Acclimated Microbial Communities to High Ammonia Concentrations for a Successful Bioaugmentation of Biogas Anaerobic Reactors with Ammonia Inhibition. Microorganisms 2023; 11:1710. [PMID: 37512885 PMCID: PMC10386354 DOI: 10.3390/microorganisms11071710] [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: 05/19/2023] [Revised: 06/19/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
This study aimed to investigate the role of the bioaugmented critical biomass that should be injected for successful bioaugmentation for addressing ammonia inhibition in anaerobic reactors used for biogas production. Cattle manure was used as a feedstock for anaerobic digestion (AD). A mixed microbial culture was acclimated to high concentrations of ammonia and used as a bioaugmented culture. Different volumes of bioaugmented culture were injected in batch anaerobic reactors under ammonia toxicity levels i.e., 4 g of NH4+-N L-1. The results showed that injecting a volume equal to 65.62% of the total working reactor volume yielded the best methane production. Specifically, this volume of bioaugmented culture resulted in methane production rates of 196.18 mL g-1 Volatile Solids (VS) and 245.88 mL g-1 VS after 30 and 60 days of AD, respectively. These rates were not significantly different from the control reactors (30d: 205.94 mL CH4 g-1 VS and 60d: 230.26 mL CH4 g-1 VS) operating without ammonia toxicity. Analysis of the microbial community using 16S rRNA gene sequencing revealed the dominance of acetoclastic methanogen members from the genus Methanosaeta in all reactors.
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Affiliation(s)
- Sotirios D Kalamaras
- Department of Hydraulics, Soil Science and Agricultural Engineering, School of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Maria Lida Christou
- Department of Hydraulics, Soil Science and Agricultural Engineering, School of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Christos A Tzenos
- Department of Hydraulics, Soil Science and Agricultural Engineering, School of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Sotirios Vasileiadis
- Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larissa, Greece
| | - Dimitrios G Karpouzas
- Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larissa, Greece
| | - Thomas A Kotsopoulos
- Department of Hydraulics, Soil Science and Agricultural Engineering, School of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
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Muñoz-Palazon B, Hurtado-Martinez M, Rosa-Masegosa A, Vilchez-Vargas R, Link A, Gorrasi S, Gonzalez-Lopez J, Gonzalez-Martinez A. Simultaneous removal of nitrate and pesticides from contaminated groundwater using aerobic granular biomass technology. JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING 2023; 11:109527. [DOI: 10.1016/j.jece.2023.109527] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2025]
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11
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Maria SB, Krystyna P, Monika L, Aleksandra J, Patrycja T, Kornelia K, Aleksandra BB, Joanna Ś, Piotr J, Katarzyna P, Agnieszka K. Natural compounds derived from Brassicaceae plants as an alternative to synthetic fungicides and their influence on soil fungus diversity. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2023; 103:317-327. [PMID: 35866526 DOI: 10.1002/jsfa.12143] [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: 03/22/2022] [Revised: 06/26/2022] [Accepted: 07/22/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND The study aimed to develop a new formulation based on active substances of natural origin to protect plant seedlings against fungal pathogens, and to evaluate the effect of this formulation on fungal communities in arable soil. RESULTS Coating seeds of common crop plants with a p-coumaric acid (p-CA)-based preparation resulted in a significant reduction in the growth of most of the tested pathogens. When applied to soil, both the p-CA-based formulation and Porter 250 EC had a similar overall effect on soil fungal communities and significantly altered the structure of fungal communities at all of the times examined. Shifts in the fungal community composition concerned less than 2% of the total number of amplicon sequence variants (ASVs). The strongest impact of the formulations on soil microbiota was recorded at the fourth week of treatment. Two ASVs assigned to Botrytis and Chromelosporium, known as plant pathogens, and an unidentified ASV from Diversisporales encompassing the arbuscular mycorrhizal fungi (AMF), were significantly depleted in soil samples treated with p-CA in comparison with Porter 250 EC. CONCLUSION The p-CA-based preparation has the potential to be used as an alternative to synthetic fungicides. It shows a similar effect to Porter 250 EC on the organization of soil communities, determining changes in the character of the communities of fungi in general, at any given time. Moreover, p-CA caused a reduction in ASVs belonging to Botrytis and Chromelosporium (plant pathogens) and ASVs of Diversisporales (containing arbuscular mycorrhizal fungi) in comparison with the commercial compound that was analyzed. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Swiontek Brzezinska Maria
- Department of Environmental Microbiology and Biotechnology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Torun, Torun, 87-100, Poland
| | - Pałubicka Krystyna
- Department of Environmental Microbiology and Biotechnology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Torun, Torun, 87-100, Poland
| | - Latos Monika
- Department of Environmental Microbiology and Biotechnology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Torun, Torun, 87-100, Poland
| | - Janik Aleksandra
- Department of Environmental Microbiology and Biotechnology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Torun, Torun, 87-100, Poland
| | - Tarnawska Patrycja
- Department of Environmental Microbiology and Biotechnology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Torun, Torun, 87-100, Poland
| | - Krajnik Kornelia
- Department of Environmental Microbiology and Biotechnology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Torun, Torun, 87-100, Poland
| | - Burkowska-But Aleksandra
- Department of Environmental Microbiology and Biotechnology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Torun, Torun, 87-100, Poland
| | - Świątczak Joanna
- Department of Environmental Microbiology and Biotechnology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Torun, Torun, 87-100, Poland
| | - Jedziniak Piotr
- Department of Pharmacology and Toxicology, National Veterinary Research Institute, Pulawy, Poland
| | - Pietruszka Katarzyna
- Department of Pharmacology and Toxicology, National Veterinary Research Institute, Pulawy, Poland
| | - Kalwasińska Agnieszka
- Department of Environmental Microbiology and Biotechnology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Torun, Torun, 87-100, Poland
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12
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Kakagianni M, Tsiknia M, Feka M, Vasileiadis S, Leontidou K, Kavroulakis N, Karamanoli K, Karpouzas DG, Ehaliotis C, Papadopoulou KK. Above- and below-ground microbiome in the annual developmental cycle of two olive tree varieties. FEMS MICROBES 2023; 4:xtad001. [PMID: 37333440 PMCID: PMC10117799 DOI: 10.1093/femsmc/xtad001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 12/18/2022] [Accepted: 01/05/2023] [Indexed: 10/22/2023] Open
Abstract
The olive tree is a hallmark crop in the Mediterranean region. Its cultivation is characterized by an enormous variability in existing genotypes and geographical areas. As regards the associated microbial communities of the olive tree, despite progress, we still lack comprehensive knowledge in the description of these key determinants of plant health and productivity. Here, we determined the prokaryotic, fungal and arbuscular mycorrhizal fungal (AMF) microbiome in below- (rhizospheric soil, roots) and above-ground (phyllosphere and carposphere) plant compartments of two olive varieties 'Koroneiki' and 'Chondrolia Chalkidikis' grown in Southern and Northern Greece respectively, in five developmental stages along a full fruit-bearing season. Distinct microbial communities were supported in above- and below-ground plant parts; while the former tended to be similar between the two varieties/locations, the latter were location specific. In both varieties/locations, a seasonally stable root microbiome was observed over time; in contrast the plant microbiome in the other compartments were prone to changes over time, which may be related to seasonal environmental change and/or to plant developmental stage. We noted that olive roots exhibited an AMF-specific filtering effect (not observed for bacteria and general fungi) onto the rhizosphere AMF communities of the two olive varieties/locations/, leading to the assemblage of homogenous intraradical AMF communities. Finally, shared microbiome members between the two olive varieties/locations include bacterial and fungal taxa with putative functional attributes that may contribute to olive tree tolerance to abiotic and biotic stress.
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Affiliation(s)
- Myrsini Kakagianni
- Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, University of Thessaly, Larissa 41500, Greece
- Department of Food Science and Nutrition, School of Agricultural Sciences, University of Thessaly, Temponera str, 43100 Karditsa, Greece
| | - Myrto Tsiknia
- Department of Natural Resources and Agricultural Engineering, Agricultural University of Athens, Athens 11855, Greece
| | - Maria Feka
- Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, University of Thessaly, Larissa 41500, Greece
| | - Sotirios Vasileiadis
- Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, University of Thessaly, Larissa 41500, Greece
| | - Kleopatra Leontidou
- Laboratory of Agricultural Chemistry, School of Agriculture, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
| | - Nektarios Kavroulakis
- Institute for Olive Tree, Subtropical Plants and Viticulture, Hellenic Agricultural Organization “ELGO-Dimitra”, Agrokipio-Souda, 73164 Chania, Greece
| | - Katerina Karamanoli
- Laboratory of Agricultural Chemistry, School of Agriculture, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
| | - Dimitrios G Karpouzas
- Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, University of Thessaly, Larissa 41500, Greece
| | - Constantinos Ehaliotis
- Department of Natural Resources and Agricultural Engineering, Agricultural University of Athens, Athens 11855, Greece
| | - Kalliope K Papadopoulou
- Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, University of Thessaly, Larissa 41500, Greece
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13
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Karpouzas DG, Vryzas Z, Martin-Laurent F. Pesticide soil microbial toxicity: setting the scene for a new pesticide risk assessment for soil microorganisms (IUPAC Technical Report). PURE APPL CHEM 2022. [DOI: 10.1515/pac-2022-0201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Pesticides constitute an integral part of modern agriculture. However, there are still concerns about their effects on non-target organisms. To address this the European Commission has imposed a stringent regulatory scheme for new pesticide compounds. Assessment of the aquatic toxicity of pesticides is based on a range of advanced tests. This does not apply to terrestrial ecosystems, where the toxicity of pesticides on soil microorganisms, is based on an outdated and crude test (N mineralization). This regulatory gap is reinforced by the recent methodological and standardization advances in soil microbial ecology. The inclusion of such standardized tools in a revised risk assessment scheme will enable the accurate estimation of the toxicity of pesticides on soil microorganisms and on associated ecosystem services. In this review we (i) summarize recent work in the assessment of the soil microbial toxicity of pesticides and point to ammonia-oxidizing microorganisms (AOM) and arbuscular mycorrhizal fungi (AMF) as most relevant bioindicator groups (ii) identify limitations in the experimental approaches used and propose mitigation solutions, (iii) identify scientific gaps and (iv) propose a new risk assessment procedure to assess the effects of pesticides on soil microorganisms.
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Affiliation(s)
- Dimitrios G. Karpouzas
- Department of Biochemistry and Biotechnology , Laboratory of Plant and Environmental Biotechnology, University of Thessaly , Viopolis 41500 , Larissa , Greece
| | - Zisis Vryzas
- Department of Agricultural Development , Democritus University of Thrace , Orestiada , Greece
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14
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Papazlatani CV, Karas PA, Lampronikou E, Karpouzas DG. Using biobeds for the treatment of fungicide-contaminated effluents from various agro-food processing industries: Microbiome responses and mobile genetic element dynamics. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 823:153744. [PMID: 35149062 DOI: 10.1016/j.scitotenv.2022.153744] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/03/2022] [Accepted: 02/04/2022] [Indexed: 06/14/2023]
Abstract
Agro-food processing industries generate large amounts of pesticide-contaminated effluents that pose a significant environmental threat if managed improperly. Biopurification systems like biobeds could be utilized for the depuration of these effluents although direct evidence for their efficiency are still lacking. We employed a column leaching experiment with pilot biobeds to (i) assess the depuration potential of biobeds against fungicide-contaminated effluents from seed-producing (carboxin, metalaxyl-M, fluxapyroxad), bulb-handling (thiabendazole, fludioxonil and chlorothalonil) and fruit-packaging (fludioxonil, imazalil) industries, (ii) to monitor microbial succession via amplicon sequencing and (iii) to determine the presence and dynamics of mobile genetic elements like intl1, IS1071, IncP-1 and IncP-1ε often associated with the transposition of pesticide-degrading genes. Biobeds could effectively retain (adsorbed but extractable with organic solvents) and dissipate (degraded and/or not extractable with organic solvents) the fungicides that were contained in the agro-industrial effluents with 93.1-99.98% removal efficiency in all cases. Lipophilic substances like fluxapyroxad were mostly retained in the biobed while more polar substances like metalaxyl-M and carboxin were mostly dissipated or showed higher leaching potential like metalaxyl-M. Biobeds supported a bacterial and fungal community that was not affected by fungicide application but showed clear temporal patterns in the different biobed horizons. This was most probably driven by the establishment of microaerophilic conditions upon water saturation of biobeds, as supported by the significant increase in the abundance of facultative or strict anaerobes like Chloroflexi/Anaerolinae, Acidibacter and Myxococcota. Wastewater application did not affect the dynamics of mobile genetic elements in biobeds whose abundance (intl1, IS1071, IncP-1ε) showed significant increases with time. Our findings suggest that biobeds could effectively decontaminate fungicide-contaminated effluents produced by agro-food industries and support a rather resilient microbial community.
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Affiliation(s)
- Christina V Papazlatani
- University of Thessaly, Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, Viopolis, 41500 Larissa, Greece
| | - Panagiotis A Karas
- University of Thessaly, Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, Viopolis, 41500 Larissa, Greece
| | - Eleni Lampronikou
- University of Thessaly, Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, Viopolis, 41500 Larissa, Greece
| | - Dimitrios G Karpouzas
- University of Thessaly, Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, Viopolis, 41500 Larissa, Greece.
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15
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Papazlatani CV, Kolovou M, Gkounou EE, Azis K, Mavriou Z, Testembasis S, Karaoglanidis GS, Ntougias S, Karpouzas DG. Isolation, characterization and industrial application of a Cladosporium herbarum fungal strain able to degrade the fungicide imazalil. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 301:119030. [PMID: 35189300 DOI: 10.1016/j.envpol.2022.119030] [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: 10/16/2021] [Revised: 02/11/2022] [Accepted: 02/17/2022] [Indexed: 06/14/2023]
Abstract
Imazalil (IMZ) is an imidazole fungicide commonly used by fruit-packaging plants (FPPs) to control fungal infections during storage. Its application leads to the production of pesticide-contaminated wastewaters, which, according to the European Commission, need to be treated on site. Considering the lack of efficient treatment methods, biodepuration systems inoculated with tailored-made inocula specialized on the removal of such persistent fungicides appear as an appropriate solution. However, nothing is known about the biodegradation of IMZ. We aimed to isolate and characterize microorganisms able to degrade the recalcitrant fungicide IMZ and eventually to test their removal efficiency under near practical bioengineering conditions. Enrichment cultures from a soil receiving regular discharges of effluents from a FPP, led to the isolation of a Cladosporium herbarum strain, which showed no pathogenicity on fruits, a trait essential for its biotechnological exploitation in FPPs. The fungus was able to degrade up to 100 mg L-1 of IMZ. However, its degrading capacity and growth was reduced at increasing IMZ concentrations in a dose-dependent manner, suggesting the involvement of a detoxification rather than an energy-gain mechanism in the dissipation of IMZ. The isolate could tolerate and gradually degrade the fungicides fludioxonil (FLD) and thiabendazole (TBZ), also used in FPPs and expected to coincide alongside IMZ in FPP effluents. The capacity of the isolate to remove IMZ in a practical context was evaluated in a benchtop immobilized-cell bioreactor fed with artificial IMZ-contaminated wastewater (200 mg L-1). The fungal strain established in the reactor, completely dominated the fungal community and effectively removed >96% of IMZ. The bioreactor also supported a diverse bacterial community composed of Sphingomonadales, Burkholderiales and Pseudomonadales. Our study reports the isolation of the first IMZ-degrading microorganism with high efficiency to remove IMZ from agro-industrial effluents under bioengineering conditions.
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Affiliation(s)
- Christina V Papazlatani
- University of Thessaly, Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, Viopolis, 41500, Larissa, Greece
| | - Maria Kolovou
- University of Thessaly, Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, Viopolis, 41500, Larissa, Greece
| | - Elisabeth E Gkounou
- University of Thessaly, Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, Viopolis, 41500, Larissa, Greece
| | - Konstantinos Azis
- Democritus University of Thrace, Department of Environmental Engineering, Laboratory of Wastewater Management and Treatment Technologies, Vas. Sofias 12, 67132, Xanthi, Greece
| | - Zografina Mavriou
- Democritus University of Thrace, Department of Environmental Engineering, Laboratory of Wastewater Management and Treatment Technologies, Vas. Sofias 12, 67132, Xanthi, Greece
| | - Stefanos Testembasis
- Aristotle University of Thessaloniki, Department of Agriculture, Plant Pathology Laboratory, University Campus, 54124, Thessaloniki, Greece
| | - George S Karaoglanidis
- Aristotle University of Thessaloniki, Department of Agriculture, Plant Pathology Laboratory, University Campus, 54124, Thessaloniki, Greece
| | - Spyridon Ntougias
- Democritus University of Thrace, Department of Environmental Engineering, Laboratory of Wastewater Management and Treatment Technologies, Vas. Sofias 12, 67132, Xanthi, Greece
| | - Dimitrios G Karpouzas
- University of Thessaly, Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, Viopolis, 41500, Larissa, Greece.
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16
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Zhang M, Jiang W, Gao S, Zhu Q, Ke Z, Jiang M, Qiu J, Hong Q. Degradation of dimethachlon by a newly isolated bacterium Paenarthrobacter sp. strain JH-1 relieves its toxicity against Chlorella ellipsoidea. ENVIRONMENTAL RESEARCH 2022; 208:112706. [PMID: 35031339 DOI: 10.1016/j.envres.2022.112706] [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: 11/21/2021] [Revised: 12/21/2021] [Accepted: 01/06/2022] [Indexed: 06/14/2023]
Abstract
Dimethachlon, a broad-spectrum dicarboximide fungicide, poses a hazard to the safety of human and ecosystem due to its residue in the environment. A high-efficient dimethachlon degrading bacteria JH-1 belonging to Paenarthrobacter sp. was isolated and characterized. Strain JH-1 can utilize high concentration of dimethachlon as sole carbon source for growth and degrade 98.53% of 300 mg·L-1 dimethachlon within 72 h. Crude enzyme of strain JH-1 could degrade 99.76% of 100 mg·L-1 dimethachlon within 2 h. The optimum degradation condition of dimethachlon by strain JH-1 was at 35 °C and pH 7.0. Dimethachlon was degraded in Paenarthrobacter sp. JH-1 as following: it was firstly converted to 4-(3,5-dichloroanilino)-4-oxobutanoic acid and then subjected to the hydrolysis to 3,5-dichloroaniline and succinic acid, the latter was further degraded. Dimethachlon inhibited the growth of Chlorella ellipsoidea, while Paenarthrobacter sp. JH-1 could degrade dimethachlon to relieve its toxicity. This work facilitates our knowledge of the degradation mechanism of dimethachlon and offers potential resource of microbial strains for the bioremediation of dimethachlon-contaminated environments in the future.
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Affiliation(s)
- Mingliang Zhang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China
| | - Wankui Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, 211800, Nanjing, PR China
| | - Siyuan Gao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China
| | - Qian Zhu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China
| | - Zhijian Ke
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China
| | - Mingli Jiang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China
| | - Jiguo Qiu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China
| | - Qing Hong
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China.
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17
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Sim JXF, Doolette CL, Vasileiadis S, Drigo B, Wyrsch ER, Djordjevic SP, Donner E, Karpouzas DG, Lombi E. Pesticide effects on nitrogen cycle related microbial functions and community composition. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 807:150734. [PMID: 34606862 DOI: 10.1016/j.scitotenv.2021.150734] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 09/20/2021] [Accepted: 09/28/2021] [Indexed: 06/13/2023]
Abstract
The extensive application of pesticides in agriculture raises concerns about their potential negative impact on soil microorganisms, being the key drivers of nutrient cycling. Most studies have investigated the effect of a single pesticide on a nutrient cycling in single soil type. We, for the first time, investigated the effect of 20 commercial pesticides with different mode of actions, applied at their recommended dose and five times their recommended dose, on nitrogen (N) microbial cycling in three different agricultural soils from southern Australian. Functional effects were determined by measuring soil enzymatic activities of β-1,4-N-acetyliglucosaminidase (NAG) and l-leucine aminopeptidase (LAP), potential nitrification (PN), and the abundance of functional genes involved in N cycling (amoA and nifH). Effects on nitrifiers diversity were determined with amplicon sequencing. Overall, the pesticides effect on N microbial cycling was dose-independent and soil specific. The fungicides flutriafol and azoxystrobin, the herbicide chlorsulfuron and the insecticide fipronil induced a significant reduction in PN and β-1,4-N-acetylglucosaminidase activity (P < 0.05) (NAG) in the alkaline loam soil with low organic carbon content i.e. a soil with properties which typically favors pesticide bioavailability and therefore potential toxicity. For the nitrifier community, the greatest pesticide effects were on the most dominant Nitrososphaeraceae (ammonia-oxidizing archaea; AOA) whose abundance increased significantly compared to the less dominant AOA and other nitrifiers. The inhibiting effects were more evident in the soil samples treated with fungicides. By testing multiple pesticides in a single study, our findings provide crucial information that can be used for pesticide hazard assessment.
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Affiliation(s)
- Jowenna X F Sim
- Future Industries Institute, University of South Australia, Mawson Lakes, SA 5095, Australia.
| | - Casey L Doolette
- Future Industries Institute, University of South Australia, Mawson Lakes, SA 5095, Australia
| | - Sotirios Vasileiadis
- University of Thessaly, Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, Larissa, Viopolis 41500, Greece
| | - Barbara Drigo
- Future Industries Institute, University of South Australia, Mawson Lakes, SA 5095, Australia
| | - Ethan R Wyrsch
- iThree Institute, University of Technology Sydney, City Campus, Ultimo, NSW 2007, Australia; The Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Steven P Djordjevic
- iThree Institute, University of Technology Sydney, City Campus, Ultimo, NSW 2007, Australia; The Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Erica Donner
- Future Industries Institute, University of South Australia, Mawson Lakes, SA 5095, Australia
| | - Dimitrios G Karpouzas
- University of Thessaly, Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, Larissa, Viopolis 41500, Greece
| | - Enzo Lombi
- Future Industries Institute, University of South Australia, Mawson Lakes, SA 5095, Australia; University of South Australia, UniSA STEM, Mawson Lakes, South Australia 5095, Australia
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18
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Aloo BN, Mbega ER, Makumba BA, Tumuhairwe JB. Effects of agrochemicals on the beneficial plant rhizobacteria in agricultural systems. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:60406-60424. [PMID: 34535866 DOI: 10.1007/s11356-021-16191-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 08/23/2021] [Indexed: 06/13/2023]
Abstract
Conventional agriculture relies heavily on chemical pesticides and fertilizers to control plant pests and diseases and improve production. Nevertheless, the intensive and prolonged use of agrochemicals may have undesirable consequences on the structure, diversity, and activities of soil microbiomes, including the beneficial plant rhizobacteria in agricultural systems. Although literature continues to mount regarding the effects of these chemicals on the beneficial plant rhizobacteria in agricultural systems, our understanding of them is still limited, and a proper account is required. With the renewed efforts and focus on agricultural and environmental sustainability, understanding the effects of different agrochemicals on the beneficial plant rhizobacteria in agricultural systems is both urgent and important to deduce practical solutions towards agricultural sustainability. This review critically evaluates the effects of various agrochemicals on the structure, diversity, and functions of the beneficial plant rhizobacteria in agricultural systems and propounds on the prospects and general solutions that can be considered to realize sustainable agricultural systems. This can be useful in understanding the anthropogenic effects of common and constantly applied agrochemicals on symbiotic systems in agricultural soils and shed light on the need for more environmentally friendly and sustainable agricultural practices.
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Affiliation(s)
- Becky Nancy Aloo
- Department of Biological Sciences, University of Eldoret, P.O. Box 1125-30100, Eldoret, Kenya.
| | - Ernest Rashid Mbega
- Department of Sustainable Agriculture and Biodiversity Conservation, Nelson Mandela African Institution of Science and Technology, P.O. Box 447, Arusha, Tanzania
| | - Billy Amendi Makumba
- Department of Biological Sciences, Moi University, P.O. Box 3900-30100, Eldoret, Kenya
| | - John Baptist Tumuhairwe
- Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, P.O. Box, 7062, Kampala, Uganda
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19
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Delitte M, Caulier S, Bragard C, Desoignies N. Plant Microbiota Beyond Farming Practices: A Review. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.624203] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Plants have always grown and evolved surrounded by numerous microorganisms that inhabit their environment, later termed microbiota. To enhance food production, humankind has relied on various farming practices such as irrigation, tilling, fertilization, and pest and disease management. Over the past few years, studies have highlighted the impacts of such practices, not only in terms of plant health or yields but also on the microbial communities associated with plants, which have been investigated through microbiome studies. Because some microorganisms exert beneficial traits that improve plant growth and health, understanding how to modulate microbial communities will help in developing smart farming and favor plant growth-promoting (PGP) microorganisms. With tremendous cost cuts in NGS technologies, metagenomic approaches are now affordable and have been widely used to investigate crop-associated microbiomes. Being able to engineer microbial communities in ways that benefit crop health and growth will help decrease the number of chemical inputs required. Against this background, this review explores the impacts of agricultural practices on soil- and plant-associated microbiomes, focusing on plant growth-promoting microorganisms from a metagenomic perspective.
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20
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Christou ML, Vasileiadis S, Kalamaras SD, Karpouzas DG, Angelidaki I, Kotsopoulos TA. Ammonia-induced inhibition of manure-based continuous biomethanation process under different organic loading rates and associated microbial community dynamics. BIORESOURCE TECHNOLOGY 2021; 320:124323. [PMID: 33157441 DOI: 10.1016/j.biortech.2020.124323] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/17/2020] [Accepted: 10/23/2020] [Indexed: 05/23/2023]
Abstract
Three Continuously Stirred Tank Reactors (CTSRs) were operating at steady state conditions with Organic Loading Rates (OLR) of 2.09, 3.024 and 4.0 g VS L-1 d-1. Glucose was used as the sole factor for increasing the OLR, linking the increase of the OLR with the C/N ratio increase. The reactors were stressed by increasing the ammonia concentration to 5 g L-1 from 1.862 g L-1. The results showed elevating inhibition of the anaerobic process by increasing the C/N ratio just by increasing the OLR, under the high ammonia concentration. A different response of the bacterial and archaeal community under ammonia stressed conditions was also observed. Under the high ammonia concentration, hydrogen-depended methylotrophic was the dominant methanogenesis route at OLR of 2.09 g VS L-1d-1, while the hydrogenotrophic route was the dominant at the high OLR of 4 g VS L-1d-1, which coincided with high acetate and propionate concentrations.
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Affiliation(s)
- M L Christou
- Department of Hydraulics, Soil Science and Agricultural Engineering, School of Agriculture, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece
| | - S Vasileiadis
- Department of Biochemistry and Biotechnology, University of Thessaly, GR-41500 Larissa, Greece
| | - S D Kalamaras
- Department of Hydraulics, Soil Science and Agricultural Engineering, School of Agriculture, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece
| | - D G Karpouzas
- Department of Biochemistry and Biotechnology, University of Thessaly, GR-41500 Larissa, Greece
| | - I Angelidaki
- Department of Environmental Engineering, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - T A Kotsopoulos
- Department of Hydraulics, Soil Science and Agricultural Engineering, School of Agriculture, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece.
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21
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Zhang M, Ren Y, Jiang W, Wu C, Zhou Y, Wang H, Ke Z, Gao Q, Liu X, Qiu J, Hong Q. Comparative genomic analysis of iprodione-degrading Paenarthrobacter strains reveals the iprodione catabolic molecular mechanism in Paenarthrobacter sp. strain YJN-5. Environ Microbiol 2020; 23:1079-1095. [PMID: 33169936 DOI: 10.1111/1462-2920.15308] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 11/05/2020] [Accepted: 11/06/2020] [Indexed: 12/16/2022]
Abstract
Degradation of the fungicide iprodione by the Paenarthrobacter sp. strain YJN-5 is initiated via hydrolysis of its N1 amide bond to form N-(3,5-dichlorophenyl)-2,4-dioxoimidazolidine. In this study, another iprodione-degrading strain, Paenarthrobacter sp. YJN-D, which harbours the same metabolic pathway as strain YJN-5 was isolated and characterized. The genes that encode the conserved iprodione catabolic pathway were identified based on comparative analysis of the genomes of the two iprodione-degrading Paenarthrobacter sp. and subsequent experimental validation. These genes include an amidase gene, ipaH (previously reported in AEM e01150-18); a deacetylase gene, ddaH, which is responsible for hydantoin ring cleavage of N-(3,5-dichlorophenyl)-2,4-dioxoimidazolidine, and a hydrolase gene, duaH, which is responsible for cleavage of the urea side chain of (3,5-dichlorophenylurea)acetic acid, thus yielding 3,5-dichloroaniline as the end product. These iprodione-catabolic genes are distributed on three plasmids in strain YJN-5 and are highly conserved between the two iprodione-degrading Paenarthrobacter strains. However, only the ipaH gene is flanked by a mobile genetic element. Two iprodione degradation cassettes bearing ipaH-ddaH-duaH were constructed and expressed in strains Pseudomonas putida KT2440 and Bacillus subtilis SCK6 respectively. Our findings enhance the current understanding of the microbial degradation mechanism of iprodione.
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Affiliation(s)
- Mingliang Zhang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Yijun Ren
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Wankui Jiang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Chenglong Wu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Yidong Zhou
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Hui Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Zhijian Ke
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Qinqin Gao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Xiaoan Liu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Jiguo Qiu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Qing Hong
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
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22
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Petrou M, Karas PA, Vasileiadis S, Zafiriadis I, Papadimitriou T, Levizou E, Kormas K, Karpouzas DG. Irrigation of radish (Raphanus sativus L.) with microcystin-enriched water holds low risk for plants and their associated rhizopheric and epiphytic microbiome. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 266:115208. [PMID: 32683235 DOI: 10.1016/j.envpol.2020.115208] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 07/01/2020] [Accepted: 07/06/2020] [Indexed: 06/11/2023]
Abstract
Microcystins (MCs) are toxins produced during cyanobacterial blooms. They reach soil and translocated to plants through irrigation of agricultural land with water from MC-impacted freshwater systems. To date we have good understanding of MC effects on plants, but not for their effects on plant-associated microbiota. We tested the hypothesis that MC-LR, either alone or with other stressors present in the water of the Karla reservoir (a low ecological quality and MC-impacted freshwater system), would affect radish plants and their rhizospheric and phyllospheric microbiome. In this context a pot experiment was employed where radish plants were irrigated with tap water without MC-LR (control) or with 2 or 12 μg L-1 of pure MC-LR (MC2 and MC12), or water from the Karla reservoir amended (12 μg L-1) or not with MC-LR. We measured MC levels in plants and rhizospheric soil and we determined effects on (i) plant growth and physiology (ii) the nitrifying microorganisms via q-PCR, (ii) the diversity of bacterial and fungal rhizospheric and epiphytic communities via amplicon sequencing. MC-LR and/or Karla water treatments resulted in the accumulation of MC in taproot at levels (480-700 ng g-1) entailing possible health risks. MC did not affect plant growth or physiology and it did not impose a consistent inhibitory effect on soil nitrifiers. Karla water rather than MC-LR was the stronger determinant of the rhizospheric and epiphytic microbial communities, suggesting the presence of biotic or abiotic stressors, other than MC-LR, in the water of the Karla reservoir which affect microorganisms with a potential role (i.e. pathogens inhibition, methylotrophy) in the homeostasis of the plant-soil system. Overall, our findings suggest that MC-LR, when applied at environmentally relevant concentrations, is not expected to adversely affect the radish-microbiota system but might still pose risk for consumers' health.
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Affiliation(s)
- M Petrou
- University of Thessaly, Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, Viopolis, 41500, Larissa, Greece
| | - P A Karas
- University of Thessaly, Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, Viopolis, 41500, Larissa, Greece
| | - S Vasileiadis
- University of Thessaly, Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, Viopolis, 41500, Larissa, Greece
| | - I Zafiriadis
- University of Thessaly, Department of Agriculture, Crop Production and Agricultural Environment, Fytokou, 38446, Nea Ionia, Volos, Greece
| | - T Papadimitriou
- University of Thessaly, Department of Agriculture, Ichthyology & Aquatic Environment, Fytokou, 38446, Nea Ionia, Volos, Greece
| | - E Levizou
- University of Thessaly, Department of Agriculture, Crop Production and Agricultural Environment, Fytokou, 38446, Nea Ionia, Volos, Greece
| | - K Kormas
- University of Thessaly, Department of Agriculture, Ichthyology & Aquatic Environment, Fytokou, 38446, Nea Ionia, Volos, Greece
| | - D G Karpouzas
- University of Thessaly, Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, Viopolis, 41500, Larissa, Greece.
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23
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Host Species Determines the Composition of the Prokaryotic Microbiota in Phlebotomus Sandflies. Pathogens 2020; 9:pathogens9060428. [PMID: 32485988 PMCID: PMC7350354 DOI: 10.3390/pathogens9060428] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 05/27/2020] [Accepted: 05/28/2020] [Indexed: 12/28/2022] Open
Abstract
Phlebotomine sandflies are vectors of the humans' and mammals' parasite Leishmania spp. Although the role of gut microbiome in the biological cycle of insects is acknowledged, we still know little about the factors modulating the composition of the gut microbiota of sandflies. We tested whether host species impose a strong structural effect on the gut microbiota of Phlebotomus spp. Sandflies were collected from the island of Leros, Greece, and classified to P. papatasi, P. neglectus, P. tobbi, and P. similis, all being negative to Leishmania spp. The prokaryotic gut microbiota was determined via 16S rRNA gene amplicon sequencing. Phlebotomus species supported distinct microbial communities (p < 0.001). P. papatasi microbiota was the most distinct over-dominated by three Spiroplasma, Wolbachia and Paenibacillus operational taxonomic units (OTUs), while another Wolbachia OTU prevailed in P. neglectus. Conversely, the microbiota of P. tobbi and P. similis was composed of several less dominant OTUs. Archaea showed low presence with the dominant OTUs belonging to methanogenic Euryarcheota, ammonia-oxidizing Thaumarcheota, and Nanoarchaeota. We provide first insights into the composition of the bacterial and archaeal community of Phlebotomus sandflies and showed that, in the absence of Leishmania, host genotype is the major modulator of Phlebotomus sandfly gut microbiota.
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