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Xie W, Xue J, Chen R, Su H, Fang X, Wu Q, Yang W, Jia L. Extraction of Genomic DNA from Soil Samples by Polyethylene Glycol-Modified Magnetic Particles via Isopropanol Promotion and Ca 2+ Mediation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:20550-20558. [PMID: 39288013 DOI: 10.1021/acs.langmuir.4c02198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/19/2024]
Abstract
Obtaining reliable and informative DNA data from soil samples is challenging due to the presence of interfering substances and typically low DNA yields. In this work, we prepared poly(ethylene glycol)-modified magnetic particles (PEG@Fe3O4) for DNA purification. The particles leverage the facilitative effect of calcium ions (Ca2+), which act as bridges between DNA and PEG@Fe3O4 by coordinating with the phosphate groups of DNA and the hydroxyl groups on the particles. The addition of 2-propanol further enhances this Ca2+-mediated DNA adsorption by inducing a conformational change from the B-form to the more compact A-form of DNA. PEG@Fe3O4 demonstrates a DNA adsorption capacity of 144.6 mg g-1. When applied to the extraction of genomic DNA from soil samples, PEG@Fe3O4 outperforms commercial kits and traditional phenol-chloroform extraction methods in terms of DNA yield and purity. Furthermore, we developed a 16-channel automated DNA extraction device to streamline the process and reduce the extraction time. The successful amplification of target bacterial and fungal amplicons underscores the potential of this automated, device-assisted method for studying soil microbial diversity.
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Affiliation(s)
- Wenting Xie
- Ministry of Education Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science & Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Jialiang Xue
- Ministry of Education Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science & Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Ruobo Chen
- Ministry of Education Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science & Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Huihui Su
- Ministry of Education Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science & Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Xun Fang
- Ministry of Education Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science & Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Qingxi Wu
- Ministry of Education Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science & Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Wenjuan Yang
- Ministry of Education Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science & Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Li Jia
- Ministry of Education Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science & Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou 510631, China
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Liang Y, Khanthaphixay B, Reynolds J, Leigh PJ, Lim ML, Yoon JY. A smartphone-based approach for comprehensive soil microbiome profiling. APPLIED PHYSICS REVIEWS 2024; 11:031412. [PMID: 39221035 PMCID: PMC11307194 DOI: 10.1063/5.0174176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 07/09/2024] [Indexed: 09/04/2024]
Abstract
The soil microbiome is crucial for nutrient cycling, health, and plant growth. This study presents a smartphone-based approach as a low-cost and portable alternative to traditional methods for classifying bacterial species and characterizing microbial communities in soil samples. By harnessing bacterial autofluorescence detection and machine learning algorithms, the platform achieved an average accuracy of 88% in distinguishing common soil-related bacterial species despite the lack of biomarkers, nucleic acid amplification, or gene sequencing. Furthermore, it successfully identified dominant species within various bacterial mixtures with an accuracy of 76% and three-level soil health identification at an accuracy of 80%-82%, providing insights into microbial community dynamics. The influence of other soil conditions (pH and moisture) was relatively minor, showcasing the platform's robustness. Various field soil samples were also tested with this platform at 80% accuracy compared with the laboratory analyses, demonstrating the practicality and usability of this approach for on-site soil analysis. This study highlights the potential of the smartphone-based system as a valuable tool for soil assessment, microbial monitoring, and environmental management.
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Affiliation(s)
- Yan Liang
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, USA
| | - Bradley Khanthaphixay
- Department of Biomedical Engineering, The University of Arizona, Tucson, Arizona 85721, USA
| | - Jocelyn Reynolds
- Department of Biomedical Engineering, The University of Arizona, Tucson, Arizona 85721, USA
| | - Preston J. Leigh
- Department of Biomedical Engineering, The University of Arizona, Tucson, Arizona 85721, USA
| | - Melissa L. Lim
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, USA
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Wang J, Deng Z, Gao X, Long J, Wang Y, Wang W, Li C, He Y, Wu Z. Combined control of plant diseases by Bacillus subtilis SL44 and Enterobacter hormaechei Wu15. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 934:173297. [PMID: 38761953 DOI: 10.1016/j.scitotenv.2024.173297] [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: 10/17/2023] [Revised: 04/12/2024] [Accepted: 05/14/2024] [Indexed: 05/20/2024]
Abstract
Co-incubation of plant growth promoting rhizobacteria (PGPRs) have been proposed as a potential alternative to pesticides for controlling fungal pathogens in crops, but their synergism mechanisms are not yet fully understood. In this study, combined use of Bacillus subtilis SL44 and Enterobacter hormaechei Wu15 could decrease the density of Colletotrichum gloeosporioides and Rhizoctonia solani and enhance the growth of beneficial bacteria on the mycelial surface, thereby mitigating disease severity. Meanwhile, PGPR application led to a reorganization of the rhizosphere microbial community through modulating its metabolites, such as extracellular polymeric substances and chitinase. These metabolites demonstrated positive effects on attracting and enhancing conventional periphery bacteria, inhibiting fungal pathogens and promoting soil health effectively. The improvement in the microbial community structure altered the trophic mode of soil fungal communities, effectively decreasing the proportion of saprotrophic soil and reducing fungal plant diseases. Certain combinations of PGPR have the potential to serve as precise instruments for managing plant pathogens.
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Affiliation(s)
- Jianwen Wang
- School of Chemistry and Chemical Engineering/Key Lab. for Green Processing of Chemical Engineering of Xinjiang Bingtuan, Shihezi University, Shihezi 832003, PR China; School of Environmental and Chemical Engineering, Xi'an Key Laboratory of Textile Chemical Engineering Auxiliaries, Engineering Research Center of Biological Resources Development and Pollution Control Universities of Shaanxi Province, Key Laboratory of Textile Dyeing Wastewater Treatment Universities of Shaanxi Province, Xi'an Polytechnic University, Xi'an 710048, PR China; Department of Chemical Engineering, Tsinghua University, Beijing 100084, PR China
| | - Zihe Deng
- School of Chemistry and Chemical Engineering/Key Lab. for Green Processing of Chemical Engineering of Xinjiang Bingtuan, Shihezi University, Shihezi 832003, PR China; School of Environmental and Chemical Engineering, Xi'an Key Laboratory of Textile Chemical Engineering Auxiliaries, Engineering Research Center of Biological Resources Development and Pollution Control Universities of Shaanxi Province, Key Laboratory of Textile Dyeing Wastewater Treatment Universities of Shaanxi Province, Xi'an Polytechnic University, Xi'an 710048, PR China
| | - Xizhuo Gao
- School of Environmental and Chemical Engineering, Xi'an Key Laboratory of Textile Chemical Engineering Auxiliaries, Engineering Research Center of Biological Resources Development and Pollution Control Universities of Shaanxi Province, Key Laboratory of Textile Dyeing Wastewater Treatment Universities of Shaanxi Province, Xi'an Polytechnic University, Xi'an 710048, PR China
| | - Jiajia Long
- School of Environmental and Chemical Engineering, Xi'an Key Laboratory of Textile Chemical Engineering Auxiliaries, Engineering Research Center of Biological Resources Development and Pollution Control Universities of Shaanxi Province, Key Laboratory of Textile Dyeing Wastewater Treatment Universities of Shaanxi Province, Xi'an Polytechnic University, Xi'an 710048, PR China
| | - Yiwei Wang
- School of Environmental and Chemical Engineering, Xi'an Key Laboratory of Textile Chemical Engineering Auxiliaries, Engineering Research Center of Biological Resources Development and Pollution Control Universities of Shaanxi Province, Key Laboratory of Textile Dyeing Wastewater Treatment Universities of Shaanxi Province, Xi'an Polytechnic University, Xi'an 710048, PR China
| | - Wanying Wang
- School of Environmental and Chemical Engineering, Xi'an Key Laboratory of Textile Chemical Engineering Auxiliaries, Engineering Research Center of Biological Resources Development and Pollution Control Universities of Shaanxi Province, Key Laboratory of Textile Dyeing Wastewater Treatment Universities of Shaanxi Province, Xi'an Polytechnic University, Xi'an 710048, PR China
| | - Chun Li
- School of Chemistry and Chemical Engineering/Key Lab. for Green Processing of Chemical Engineering of Xinjiang Bingtuan, Shihezi University, Shihezi 832003, PR China; Department of Chemical Engineering, Tsinghua University, Beijing 100084, PR China
| | - Yanhui He
- School of Environmental and Chemical Engineering, Xi'an Key Laboratory of Textile Chemical Engineering Auxiliaries, Engineering Research Center of Biological Resources Development and Pollution Control Universities of Shaanxi Province, Key Laboratory of Textile Dyeing Wastewater Treatment Universities of Shaanxi Province, Xi'an Polytechnic University, Xi'an 710048, PR China; Shanxi Qinfengkesheng Biotechnology Company Ltd., Xianyang 713700, PR China.
| | - Zhansheng Wu
- School of Environmental and Chemical Engineering, Xi'an Key Laboratory of Textile Chemical Engineering Auxiliaries, Engineering Research Center of Biological Resources Development and Pollution Control Universities of Shaanxi Province, Key Laboratory of Textile Dyeing Wastewater Treatment Universities of Shaanxi Province, Xi'an Polytechnic University, Xi'an 710048, PR China.
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4
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Galla G, Praeg N, Rzehak T, Sprecher E, Colla F, Seeber J, Illmer P, Hauffe HC. Comparison of DNA extraction methods on different sample matrices within the same terrestrial ecosystem. Sci Rep 2024; 14:8715. [PMID: 38622248 PMCID: PMC11018758 DOI: 10.1038/s41598-024-59086-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 04/07/2024] [Indexed: 04/17/2024] Open
Abstract
Metataxonomic studies of ecosystem microbiotas require the simultaneous processing of samples with contrasting physical and biochemical traits. However, there are no published studies of comparisons of different DNA extraction kits to characterize the microbiotas of the main components of terrestrial ecosystems. Here, and to our knowledge for the first time, five DNA extraction kits were used to investigate the composition and diversity of the microbiota of a subset of samples typically studied in terrestrial ecosystems such as bulk soil, rhizosphere soil, invertebrate taxa and mammalian feces. DNA extraction kit was associated with changes in the relative abundance of hundreds of ASVs, in the same samples, resulting in significant differences in alpha and beta diversity estimates of their microbiotas. Importantly, the impact of DNA extraction kit on sample diversity varies according to sample type, with mammalian feces and soil samples showing the most and least consistent diversity estimates across DNA extraction kits, respectively. We show that the MACHEREY-NAGEL NucleoSpin® Soil kit was associated with the highest alpha diversity estimates, providing the highest contribution to the overall sample diversity, as indicated by comparisons with computationally assembled reference communities, and is recommended to be used for any large-scale microbiota study of terrestrial ecosystems.
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Affiliation(s)
- Giulio Galla
- Conservation Genomics Research Unit, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige, Italy.
| | - Nadine Praeg
- Department of Microbiology, Universität Innsbruck, Innsbruck, Austria
| | - Theresa Rzehak
- Department of Microbiology, Universität Innsbruck, Innsbruck, Austria
| | - Else Sprecher
- Conservation Genomics Research Unit, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige, Italy
| | - Filippo Colla
- Institute for Alpine Environment, EURAC Research, Bolzano, Italy
- Department of Ecology, Universität Innsbruck, Innsbruck, Austria
| | - Julia Seeber
- Institute for Alpine Environment, EURAC Research, Bolzano, Italy
- Department of Ecology, Universität Innsbruck, Innsbruck, Austria
| | - Paul Illmer
- Department of Microbiology, Universität Innsbruck, Innsbruck, Austria
| | - Heidi C Hauffe
- Conservation Genomics Research Unit, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige, Italy
- National Biodiversity Future Center (NBFC), S.c.a.r.l., Palermo, Italy
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Jensen TBN, Dall SM, Knutsson S, Karst SM, Albertsen M. High-throughput DNA extraction and cost-effective miniaturized metagenome and amplicon library preparation of soil samples for DNA sequencing. PLoS One 2024; 19:e0301446. [PMID: 38573983 PMCID: PMC10994328 DOI: 10.1371/journal.pone.0301446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 03/13/2024] [Indexed: 04/06/2024] Open
Abstract
Reductions in sequencing costs have enabled widespread use of shotgun metagenomics and amplicon sequencing, which have drastically improved our understanding of the microbial world. However, large sequencing projects are now hampered by the cost of library preparation and low sample throughput, comparatively to the actual sequencing costs. Here, we benchmarked three high-throughput DNA extraction methods: ZymoBIOMICS™ 96 MagBead DNA Kit, MP BiomedicalsTM FastDNATM-96 Soil Microbe DNA Kit, and DNeasy® 96 PowerSoil® Pro QIAcube® HT Kit. The DNA extractions were evaluated based on length, quality, quantity, and the observed microbial community across five diverse soil types. DNA extraction of all soil types was successful for all kits, however DNeasy® 96 PowerSoil® Pro QIAcube® HT Kit excelled across all performance parameters. We further used the nanoliter dispensing system I.DOT One to miniaturize Illumina amplicon and metagenomic library preparation volumes by a factor of 5 and 10, respectively, with no significant impact on the observed microbial communities. With these protocols, DNA extraction, metagenomic, or amplicon library preparation for one 96-well plate are approx. 3, 5, and 6 hours, respectively. Furthermore, the miniaturization of amplicon and metagenome library preparation reduces the chemical and plastic costs from 5.0 to 3.6 and 59 to 7.3 USD pr. sample. This enhanced efficiency and cost-effectiveness will enable researchers to undertake studies with greater sample sizes and diversity, thereby providing a richer, more detailed view of microbial communities and their dynamics.
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Affiliation(s)
- Thomas Bygh Nymann Jensen
- Center for Microbial Communities, Dept. of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Sebastian Mølvang Dall
- Center for Microbial Communities, Dept. of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Simon Knutsson
- Center for Microbial Communities, Dept. of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Søren Michael Karst
- Center for Microbial Communities, Dept. of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Mads Albertsen
- Center for Microbial Communities, Dept. of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
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Pacheco-Moreno A, Bollmann-Giolai A, Chandra G, Brett P, Davies J, Thornton O, Poole P, Ramachandran V, Brown JKM, Nicholson P, Ridout C, DeVos S, Malone JG. The genotype of barley cultivars influences multiple aspects of their associated microbiota via differential root exudate secretion. PLoS Biol 2024; 22:e3002232. [PMID: 38662644 PMCID: PMC11045101 DOI: 10.1371/journal.pbio.3002232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 03/19/2024] [Indexed: 04/28/2024] Open
Abstract
Plant-associated microbes play vital roles in promoting plant growth and health, with plants secreting root exudates into the rhizosphere to attract beneficial microbes. Exudate composition defines the nature of microbial recruitment, with different plant species attracting distinct microbiota to enable optimal adaptation to the soil environment. To more closely examine the relationship between plant genotype and microbial recruitment, we analysed the rhizosphere microbiomes of landrace (Chevallier) and modern (NFC Tipple) barley (Hordeum vulgare) cultivars. Distinct differences were observed between the plant-associated microbiomes of the 2 cultivars, with the plant-growth promoting rhizobacterial genus Pseudomonas substantially more abundant in the Tipple rhizosphere. Striking differences were also observed between the phenotypes of recruited Pseudomonas populations, alongside distinct genotypic clustering by cultivar. Cultivar-driven Pseudomonas selection was driven by root exudate composition, with the greater abundance of hexose sugars secreted from Tipple roots attracting microbes better adapted to growth on these metabolites and vice versa. Cultivar-driven selection also operates at the molecular level, with both gene expression and the abundance of ecologically relevant loci differing between Tipple and Chevallier Pseudomonas isolates. Finally, cultivar-driven selection is important for plant health, with both cultivars showing a distinct preference for microbes selected by their genetic siblings in rhizosphere transplantation assays.
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Affiliation(s)
- Alba Pacheco-Moreno
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | | | - Govind Chandra
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | - Paul Brett
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | - Jack Davies
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | - Owen Thornton
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | - Philip Poole
- Department of Biology, University of Oxford, South Parks Road, Oxford, United Kingdom
| | - Vinoy Ramachandran
- Department of Biology, University of Oxford, South Parks Road, Oxford, United Kingdom
| | - James K. M. Brown
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | - Paul Nicholson
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | - Chris Ridout
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
- New Heritage Barley, Norwich Research Park, Norwich, United Kingdom
| | - Sarah DeVos
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
- New Heritage Barley, Norwich Research Park, Norwich, United Kingdom
| | - Jacob G. Malone
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
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Edwards JA, Saran UB, Bonnette J, MacQueen A, Yin J, Nguyen TU, Schmutz J, Grimwood J, Pennacchio LA, Daum C, Glavina Del Rio T, Fritschi FB, Lowry DB, Juenger TE. Genetic determinants of switchgrass-root-associated microbiota in field sites spanning its natural range. Curr Biol 2023; 33:1926-1938.e6. [PMID: 37080198 DOI: 10.1016/j.cub.2023.03.078] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 02/03/2023] [Accepted: 03/27/2023] [Indexed: 04/22/2023]
Abstract
A fundamental goal in plant microbiome research is to determine the relative impacts of host and environmental effects on root microbiota composition, particularly how host genotype impacts bacterial community composition. Most studies characterizing the effect of plant genotype on root microbiota undersample host genetic diversity and grow plants outside of their native ranges, making the associations between host and microbes difficult to interpret. Here, we characterized the root microbiota of a large diversity panel of switchgrass, a North American native C4 bioenergy crop, in three field locations spanning its native range. Our data, composed of 1,961 samples, suggest that field location is the primary determinant of microbiome composition; however, substantial heritable variation is widespread across bacterial taxa, especially those in the Sphingomonadaceae family. Despite diverse compositions, relatively few highly prevalent taxa make up the majority of the switchgrass root microbiota, a large fraction of which is shared across sites. Local genotypes preferentially recruit/filter for local microbes, supporting the idea of affinity between local plants and their microbiota. Using genome-wide association, we identified loci impacting the abundance of >400 microbial strains and found an enrichment of genes involved in immune responses, signaling pathways, and secondary metabolism. We found loci associated with over half of the core microbiota (i.e., microbes in >80% of samples), regardless of field location. Finally, we show a genetic relationship between a basal plant immunity pathway and relative abundances of root microbiota. This study brings us closer to harnessing and manipulating beneficial microbial associations via host genetics.
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Affiliation(s)
- Joseph A Edwards
- Department of Integrative Biology, University of Texas, Austin, 2415 Speedway, Austin, TX 78712, USA.
| | - Usha Bishnoi Saran
- Department of Integrative Biology, University of Texas, Austin, 2415 Speedway, Austin, TX 78712, USA
| | - Jason Bonnette
- Department of Integrative Biology, University of Texas, Austin, 2415 Speedway, Austin, TX 78712, USA
| | - Alice MacQueen
- Department of Integrative Biology, University of Texas, Austin, 2415 Speedway, Austin, TX 78712, USA
| | - Jun Yin
- Department of Integrative Biology, University of Texas, Austin, 2415 Speedway, Austin, TX 78712, USA
| | - Tu Uyen Nguyen
- Department of Integrative Biology, University of Texas, Austin, 2415 Speedway, Austin, TX 78712, USA
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, 601 Genome Way Northwest, Huntsville, AL 35806, USA; Joint Genome Institute, Lawrence Berkeley National Laboratory, 91R183 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Jane Grimwood
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, 601 Genome Way Northwest, Huntsville, AL 35806, USA
| | - Len A Pennacchio
- Joint Genome Institute, Lawrence Berkeley National Laboratory, 91R183 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Chris Daum
- Joint Genome Institute, Lawrence Berkeley National Laboratory, 91R183 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Tijana Glavina Del Rio
- Joint Genome Institute, Lawrence Berkeley National Laboratory, 91R183 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Felix B Fritschi
- Department of Plant Science and Technology, University of Missouri, Agriculture Bldg, 52, Columbia, MO 65201, USA
| | - David B Lowry
- Department of Plant Biology, Michigan State University, 612 Wilson Road, Rm 166, East Lansing, MI 48824, USA
| | - Thomas E Juenger
- Department of Integrative Biology, University of Texas, Austin, 2415 Speedway, Austin, TX 78712, USA.
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Sanchez-Cid C, Tignat-Perrier R, Franqueville L, Delaurière L, Schagat T, Vogel TM. Sequencing Depth Has a Stronger Effect than DNA Extraction on Soil Bacterial Richness Discovery. Biomolecules 2022; 12:biom12030364. [PMID: 35327556 PMCID: PMC8945597 DOI: 10.3390/biom12030364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/08/2022] [Accepted: 02/20/2022] [Indexed: 02/04/2023] Open
Abstract
Although Next-Generation Sequencing techniques have increased our access to the soil microbiome, each step of soil metagenomics presents inherent biases that prevent the accurate definition of the soil microbiome and its ecosystem function. In this study, we compared the effects of DNA extraction and sequencing depth on bacterial richness discovery from two soil samples. Four DNA extraction methods were used, and sequencing duplicates were generated for each DNA sample. The V3–V4 region of the 16S rRNA gene was sequenced to determine the taxonomical richness measured by each method at the amplicon sequence variant (ASV) level. Both the overall functional richness and antibiotic resistance gene (ARG) richness were evaluated by metagenomics sequencing. Despite variable DNA extraction methods, sequencing depth had a greater influence on bacterial richness discovery at both the taxonomical and functional levels. Sequencing duplicates from the same sample provided access to different portions of bacterial richness, and this was related to differences in the sequencing depth. Thus, the sequencing depth introduced biases in the comparison of DNA extraction methods. An optimisation of the soil metagenomics workflow is needed in order to sequence at a sufficient and equal depth. This would improve the accuracy of metagenomic comparisons and soil microbiome profiles.
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Affiliation(s)
- Concepcion Sanchez-Cid
- Environmental Microbial Genomics, Laboratoire Ampère, CNRS UMR 5005, Ecole Centrale de Lyon, Université de Lyon, 69134 Ecully, France; (R.T.-P.); (L.F.); (T.M.V.)
- Scientific Applications and Training, Promega France, 69100 Charbonnières-les-Bains, France;
- Correspondence:
| | - Romie Tignat-Perrier
- Environmental Microbial Genomics, Laboratoire Ampère, CNRS UMR 5005, Ecole Centrale de Lyon, Université de Lyon, 69134 Ecully, France; (R.T.-P.); (L.F.); (T.M.V.)
- Institut des Géosciences de l’Environnement, Université Grenoble Alpes, CNRS, IRD, Grenoble INP, Grenoble, 38400 Saint-Martin-d’Hères, France
| | - Laure Franqueville
- Environmental Microbial Genomics, Laboratoire Ampère, CNRS UMR 5005, Ecole Centrale de Lyon, Université de Lyon, 69134 Ecully, France; (R.T.-P.); (L.F.); (T.M.V.)
| | - Laurence Delaurière
- Scientific Applications and Training, Promega France, 69100 Charbonnières-les-Bains, France;
| | - Trista Schagat
- Scientific Applications and Training, Promega Corporation, Madison, WI 53711, USA;
| | - Timothy M. Vogel
- Environmental Microbial Genomics, Laboratoire Ampère, CNRS UMR 5005, Ecole Centrale de Lyon, Université de Lyon, 69134 Ecully, France; (R.T.-P.); (L.F.); (T.M.V.)
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9
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Forensic botany: time to embrace natural history collections, large scale environmental data and environmental DNA. Emerg Top Life Sci 2021; 5:475-485. [PMID: 33871012 DOI: 10.1042/etls20200329] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 03/23/2021] [Accepted: 03/30/2021] [Indexed: 01/01/2023]
Abstract
Forensic botany is a diverse discipline that spans many aspects of plant sciences, particularly taxonomy, field botany, anatomy, and ecology. Internationally, there is a significant opportunity to expand the application of forensic botany in criminal investigations, especially war crimes, genocide, homicide, sexual violence, serious physical assault, illegal trade in endangered species and wildlife crime. In civil proceedings, forensic botany may, for example, be called upon in trade disputes such as accidental contamination of commodities. Despite the potential, there are barriers to the wider application of forensic botany in criminal cases; there is a widespread need to improve the efficiency of botanical trace evidence identification. This could partly be addressed by embracing innovations in image recognition and by accessing the huge quantity of specimens and images housed in natural history collections worldwide. Additionally, the recent advances in DNA sequencing technologies and the expansion of environmental DNA (eDNA) and forensic ecogenomics, offers opportunities to more rapidly provide species-level identifications. The impact of taphonomic processes upon vegetation, and vice versa, remains poorly understood; improved understanding of these interactions and their ecological impacts may be invaluable in improving clandestine burial search protocols.
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