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Cruz FVDS, Barbosa da Costa N, Juneau P. Non-pathogenic microbiome associated to aquatic plants and anthropogenic impacts on this interaction. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 948:174663. [PMID: 38992379 DOI: 10.1016/j.scitotenv.2024.174663] [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: 03/29/2024] [Revised: 06/22/2024] [Accepted: 07/07/2024] [Indexed: 07/13/2024]
Abstract
The microbiota associated with aquatic plants plays a crucial role in promoting plant growth and development. The structure of the plant microbiome is shaped by intricate interactions among hosts, microbes, and environmental factors. Consequently, anthropogenic pressures that disrupt these interactions can indirectly impact the ecosystem services provided by aquatic plants, such as CO2 fixation, provision of food resources, shelter to animals, nutrient cycling, and water purification. Presently, studies on plant-microbiota interactions primarily focus on terrestrial hosts and overlook aquatic environments with their unique microbiomes. Therefore, there is a pressing need for a comprehensive understanding of plant microbiomes in aquatic ecosystems. This review delves into the overall composition of the microbiota associated with aquatic plant, with a particular emphasis on bacterial communities, which have been more extensively studied. Subsequently, the functions provided by the microbiota to their aquatic plants hosts are explored, including the acquisition and mobilization of nutrients, production of auxin and related compounds, enhancement of photosynthesis, and protection against biotic and abiotic stresses. Additionally, the influence of anthropogenic stressors, such as climate change and aquatic contamination, on the interaction between microbiota and aquatic plants is discussed. Finally, knowledge gaps are highlighted and future directions in this field are suggested.
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Affiliation(s)
- Fernanda Vieira da Silva Cruz
- Ecotoxicology of Aquatic Microorganisms Laboratory, GRIL, EcotoQ, TOXEN, Department of Biological Sciences, Université du Québec à Montréal, Montréal Succ. Centre-Ville, H3C 3P8 Montréal, QC, Canada
| | - Naíla Barbosa da Costa
- Institut national de la recherche scientifique - Centre Eau Terre Environnement, 490 Couronne St, Québec City, Québec G1K 9A9, Canada
| | - Philippe Juneau
- Ecotoxicology of Aquatic Microorganisms Laboratory, GRIL, EcotoQ, TOXEN, Department of Biological Sciences, Université du Québec à Montréal, Montréal Succ. Centre-Ville, H3C 3P8 Montréal, QC, Canada.
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Torres M, Paszti S, Eberl L. Shedding light on bacteria-host interactions with the aid of TnSeq approaches. mBio 2024; 15:e0039024. [PMID: 38722161 PMCID: PMC11237515 DOI: 10.1128/mbio.00390-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2024] Open
Abstract
Bacteria are highly adaptable and grow in diverse niches, where they often interact with eukaryotic organisms. These interactions with different hosts span the entire spectrum from symbiosis to pathogenicity and thus determine the lifestyle of the bacterium. Knowledge of the genetic determinants involved in animal and plant host colonization by pathogenic and mutualistic bacteria is not only crucial to discover new drug targets for disease management but also for developing novel biostimulant strategies. In the last decades, significant progress in genome-wide high-throughput technologies such as transposon insertion sequencing has led to the identification of pathways that enable efficient host colonization. However, the extent to which similar genes play a role in this process in different bacteria is yet unclear. This review highlights the commonalities and specificities of bacterial determinants important for bacteria-host interaction.
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Affiliation(s)
- Marta Torres
- Department of Plant and Microbial Biology, University of Zurich, Zürich, Switzerland
| | - Sarah Paszti
- Department of Plant and Microbial Biology, University of Zurich, Zürich, Switzerland
| | - Leo Eberl
- Department of Plant and Microbial Biology, University of Zurich, Zürich, Switzerland
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Wang Y, Duan S, Xu J, Long Y, Zhang S, Li S, Wu L, Zhang Y. Comparison of the colonization ability of Burkholderia strain B23 in the citrus rhizoplane and rhizosphere and assessment of the underlying mechanisms using full-length 16S rDNA amplicon and metatranscriptomic analyses. Microb Biotechnol 2023. [PMID: 36946260 PMCID: PMC10364312 DOI: 10.1111/1751-7915.14248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/05/2023] [Accepted: 03/07/2023] [Indexed: 03/23/2023] Open
Abstract
The characterization of bacterial strains with efficient root colonization ability and the mechanisms responsible for their efficient colonization is critical for the identification and application of beneficial bacteria. In this study, we found that Burkholderia strain B23 exhibited a strong niche differentiation between the rhizosphere and rhizoplane (a niche with more abundant easy-to-use nutrients but stronger selective pressures compared with the tightly adjacent rhizosphere) when inoculated into the field-grown citrus trees. Full-length 16S rDNA amplicon analysis demonstrated that the relative abundance of B23 in the rhizoplane microbiome at 3, 5, and 9 days post-inoculation (dpi) was always higher than that at 1 dpi, whereas its relative abundance in the rhizosphere microbiome was decreased continuously, as demonstrated by a 3.18-fold decrease at 9 dpi compared to 1 dpi. Time-series comparative expression profiling of B23 between the rhizoplane and rhizosphere was performed at representative time points (1, 3, and 9 dpi) through metatranscriptomic analysis, and the results demonstrated that multiple genes involved in the uptake and utilization of easy-to-use carbohydrates and amino acids and those involved in metabolism, energy production, replication, and translation were upregulated in the rhizoplane compared with the rhizosphere at 1 dpi and 3 dpi. Several genes involved in resistance to plant- and microbial competitor-derived stresses exhibited higher expression activities in the rhizoplane compared with the rhizosphere. Furthermore, gene loci responsible for the biosynthesis of the key antifungal and antibacterial metabolites occidiofungin and ornibactin were induced, and their expression levels remained relatively stable from 3 dpi to 9 dpi in the rhizoplane but not in the rhizosphere. Collectively, our findings provide novel lights into the mechanisms underlying the root colonization of the inoculated bacterial strains and serve as a basis for the identification of strains with efficient colonization ability, thus contributing to the development of beneficial bacteria applications.
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Affiliation(s)
- Yu Wang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Shuo Duan
- Citrus Huanglongbing Joint Laboratory, National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi, 341000, China
| | - Jin Xu
- Citrus Research and Education Center, Department of Plant Pathology, IFAS, University of Florida, Lake Alfred, Florida, 33850, USA
| | - Yunfei Long
- Citrus Huanglongbing Joint Laboratory, National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi, 341000, China
| | - Siyu Zhang
- Citrus Huanglongbing Joint Laboratory, National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi, 341000, China
| | - Shixin Li
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Lijuan Wu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Yunzeng Zhang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
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Rhizobial migration toward roots mediated by FadL-ExoFQP modulation of extracellular long-chain AHLs. THE ISME JOURNAL 2023; 17:417-431. [PMID: 36627434 PMCID: PMC9938287 DOI: 10.1038/s41396-023-01357-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 12/28/2022] [Accepted: 01/04/2023] [Indexed: 01/11/2023]
Abstract
Migration from rhizosphere to rhizoplane is a key selecting process in root microbiome assembly, but not fully understood. Rhizobiales members are overrepresented in the core root microbiome of terrestrial plants, and here we report a genome-wide transposon-sequencing of rhizoplane fitness genes of beneficial Sinorhizobium fredii on wild soybean, cultivated soybean, rice, and maize. There were few genes involved in broad-host-range rhizoplane colonization. The fadL mutant lacking a fatty acid transporter exhibited high colonization rates, while mutations in exoFQP (encoding membrane proteins directing exopolysaccharide polymerization and secretion), but not those in exo genes essential for exopolysaccharide biosynthesis, led to severely impaired colonization rates. This variation was not explainable by their rhizosphere and rhizoplane survivability, and associated biofilm and exopolysaccharide production, but consistent with their migration ability toward rhizoplane, and associated surface motility and the mixture of quorum-sensing AHLs (N-acylated-L-homoserine lactones). Genetics and physiology evidences suggested that FadL mediated long-chain AHL uptake while ExoF mediated the secretion of short-chain AHLs which negatively affected long-chain AHL biosynthesis. The fadL and exoF mutants had elevated and depleted extracellular long-chain AHLs, respectively. A synthetic mixture of long-chain AHLs mimicking that of the fadL mutant can improve rhizobial surface motility. When this AHL mixture was spotted into rhizosphere, the migration toward roots and rhizoplane colonization of S. fredii were enhanced in a diffusible way. This work adds novel parts managing extracellular AHLs, which modulate bacterial migration toward rhizoplane. The FadL-ExoFQP system is conserved in Alphaproteobacteria and may shape the "home life" of diverse keystone rhizobacteria.
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Acosta K, Sorrels S, Chrisler W, Huang W, Gilbert S, Brinkman T, Michael TP, Lebeis SL, Lam E. Optimization of Molecular Methods for Detecting Duckweed-Associated Bacteria. PLANTS (BASEL, SWITZERLAND) 2023; 12:872. [PMID: 36840219 PMCID: PMC9965182 DOI: 10.3390/plants12040872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/05/2023] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
The bacterial colonization dynamics of plants can differ between phylogenetically similar bacterial strains and in the context of complex bacterial communities. Quantitative methods that can resolve closely related bacteria within complex communities can lead to a better understanding of plant-microbe interactions. However, current methods often lack the specificity to differentiate phylogenetically similar bacterial strains. In this study, we describe molecular strategies to study duckweed-associated bacteria. We first systematically optimized a bead-beating protocol to co-isolate nucleic acids simultaneously from duckweed and bacteria. We then developed a generic fingerprinting assay to detect bacteria present in duckweed samples. To detect specific duckweed-bacterium associations, we developed a genomics-based computational pipeline to generate bacterial strain-specific primers. These strain-specific primers differentiated bacterial strains from the same genus and enabled the detection of specific duckweed-bacterium associations present in a community context. Moreover, we used these strain-specific primers to quantify the bacterial colonization of duckweed by normalization to a plant reference gene and revealed differences in colonization levels between strains from the same genus. Lastly, confocal microscopy of inoculated duckweed further supported our PCR results and showed bacterial colonization of the duckweed root-frond interface and root interior. The molecular methods introduced in this work should enable the tracking and quantification of specific plant-microbe associations within plant-microbial communities.
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Affiliation(s)
- Kenneth Acosta
- Department of Plant Biology, Rutgers the State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Shawn Sorrels
- Department of Plant Biology, Rutgers the State University of New Jersey, New Brunswick, NJ 08901, USA
| | - William Chrisler
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, WA 99354, USA
| | - Weijuan Huang
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou 510316, China
| | - Sarah Gilbert
- Department of Plant Biology, Rutgers the State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Thomas Brinkman
- Department of Plant Biology, Rutgers the State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Todd P. Michael
- The Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Sarah L. Lebeis
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
- Plant Resilience Institute, Michigan State University, East Lansing, MI 48824, USA
| | - Eric Lam
- Department of Plant Biology, Rutgers the State University of New Jersey, New Brunswick, NJ 08901, USA
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Bunyoo C, Roongsattham P, Khumwan S, Phonmakham J, Wonnapinij P, Thamchaipenet A. Dynamic Alteration of Microbial Communities of Duckweeds from Nature to Nutrient-Deficient Condition. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11212915. [PMID: 36365369 PMCID: PMC9658847 DOI: 10.3390/plants11212915] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 10/24/2022] [Accepted: 10/25/2022] [Indexed: 06/12/2023]
Abstract
Duckweeds live with complex assemblages of microbes as holobionts that play an important role in duckweed growth and phytoremediation ability. In this study, the structure and diversity of duckweed-associated bacteria (DAB) among four duckweed subtypes under natural and nutrient-deficient conditions were investigated using V3-V4 16S rRNA amplicon sequencing. High throughput sequencing analysis indicated that phylum Proteobacteria was predominant in across duckweed samples. A total of 24 microbial genera were identified as a core microbiome that presented in high abundance with consistent proportions across all duckweed subtypes. The most abundant microbes belonged to the genus Rhodobacter, followed by other common DAB, including Acinetobacter, Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, and Pseudomonas. After nutrient-deficient stress, diversity of microbial communities was significantly deceased. However, the relative abundance of Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Pelomonas, Roseateles and Novosphingobium were significantly enhanced in stressed duckweeds. Functional prediction of the metagenome data displayed the relative abundance of essential pathways involved in DAB colonization, such as bacterial motility and biofilm formation, as well as biodegradable ability, such as benzoate degradation and nitrogen metabolism, were significantly enriched under stress condition. The findings improve the understanding of the complexity of duckweed microbiomes and facilitate the establishment of a stable microbiome used for co-cultivation with duckweeds for enhancement of biomass and phytoremediation under environmental stress.
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Affiliation(s)
- Chakrit Bunyoo
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Duckweed Holobiont Resource & Research Center (DHbRC), Kasetsart University, Bangkok 10900, Thailand
| | - Peerapat Roongsattham
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Duckweed Holobiont Resource & Research Center (DHbRC), Kasetsart University, Bangkok 10900, Thailand
| | - Sirikorn Khumwan
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Duckweed Holobiont Resource & Research Center (DHbRC), Kasetsart University, Bangkok 10900, Thailand
| | - Juthaporn Phonmakham
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Duckweed Holobiont Resource & Research Center (DHbRC), Kasetsart University, Bangkok 10900, Thailand
| | - Passorn Wonnapinij
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Duckweed Holobiont Resource & Research Center (DHbRC), Kasetsart University, Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresource, Food and Health Kasetsart University (OmiKU), Bangkok 10900, Thailand
| | - Arinthip Thamchaipenet
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Duckweed Holobiont Resource & Research Center (DHbRC), Kasetsart University, Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresource, Food and Health Kasetsart University (OmiKU), Bangkok 10900, Thailand
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El-Sayed SM, Abdalla SS, Abdel-Khalek MA. Influence of Bacillus subtilis on the surface behavior and separation of talc and chlorite minerals. TENSIDE SURFACT DET 2022. [DOI: 10.1515/tsd-2022-2435] [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
Bacillus subtilis was used as a bio-surface modifier to improve the floatability of talc mineral (Mg3Si4O10(OH)2) in the talc ore. The surface behavior of chlorite mineral as the main associated gangue with talc mineral was studied in the presence of B. subtilis using zeta potential, scanning electron microscopy, and Fourier-transform infrared spectroscopy techniques. The floatability of both minerals was investigated as a function of pH, contact time, and concentration of B. subtilis. The results showed that the zeta potential of the talc mineral was strongly influenced by the treatment with B. subtilis. The maximum separation efficiency of talc from chlorite was achieved at pH 4. A talc concentrate with 98% quality and about 95% recovery was prepared from a binary talc-chlorite mixture containing 85% talc under optimum conditions of 8 × 105 cells/mL B. subtilis, pH 4, 35°C, and a contact time of 10 min.
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Affiliation(s)
- Samah M. El-Sayed
- Mineral Processing Department , Central Metallurgical R&D Institute , Cairo , Egypt
| | - Samah S. Abdalla
- Mineral Processing Department , Central Metallurgical R&D Institute , Cairo , Egypt
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