1
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Bomberg M, Miettinen H. Anionic nanocellulose as competing agent in microbial DNA extraction from mine process samples. J Microbiol Methods 2023; 215:106850. [PMID: 37907119 DOI: 10.1016/j.mimet.2023.106850] [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: 04/24/2023] [Revised: 09/04/2023] [Accepted: 10/25/2023] [Indexed: 11/02/2023]
Abstract
Microorganisms in flotation and minerals processing may significantly affect the grade and yield of metal concentrates. However, studying the phenomena requires working techniques to detach microorganisms and their DNA from mineral particles to which they strongly adhere. We developed a new method utilizing the competitive properties of anionic nanocellulose to block sorption of DNA to and detach microbial cells from mineral particles from ore processing. In general, up to one ng DNA mL-1 sample was obtained with the custom anionic nanocellulose method (CM) compared to DNA amounts below the Qubit assay's detection limit for extractions with a commercial kit (KIT). Similarly, 0.5-4 orders of magnitude more bacterial 16S and fungal 5.8S rRNA gene copies were detected by qPCR from CM treated samples compared to KIT extractions. A clear difference in the detected microbial community structure between CM and KIT extracted samples was also observed. Commercial kits optimized for mineral soils are easy to use and time efficient but may miss a considerable part of the microbial communities. A competing agent such as anionic nanocellulose may decrease the interaction between microorganisms or their DNA and minerals and provide a comprehensive view into the microbial communities in mineral processing environments.
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Affiliation(s)
- Malin Bomberg
- VTT Technical Research Centre of Finland, P.O. Box 1000, 02044 VTT, Finland.
| | - Hanna Miettinen
- VTT Technical Research Centre of Finland, P.O. Box 1000, 02044 VTT, Finland
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2
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Wei L, Zhao Q, Chen X, Sun Q, Zhang X, Chen Y. Seasonal variation in soil algal community structure in different forest plantations in subtropic China. FRONTIERS IN PLANT SCIENCE 2023; 14:1181184. [PMID: 37521936 PMCID: PMC10382206 DOI: 10.3389/fpls.2023.1181184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 06/28/2023] [Indexed: 08/01/2023]
Abstract
Algae exert great impact on soil formation and biogeochemical cycling. However, there is no full understanding of the response of soil algal community structure to the seasonal fluctuations in temperature and moisture and changes of soil physicochemical properties across different forests. Here, based on 23S rRNA gene sequencing, we analyzed soil algal community structure in four different forest plantations in two seasons and examined soil physiochemical properties. The results showed the significantly seasonal variation in soil algal community structure, with the higher overall diversity in summer than in winter. In addition, there existed significant correlations between soil algae (species composition, relative abundance, diversity index) and physicochemical properties (pH, total phosphorus, organic matter and nitrate nitrogen), suggesting that edaphic characteristics are also largely responsible for the variation in soil algal community. Nevertheless, the seasonal variation in algal community structure was greater than the variation across different forest plantations. This suggest temperature and moisture are more important than soil physicochemical properties in determining soil algal community structure. The findings of the present study enhance our understanding of the algal communities in forest ecosystems and are of great significance for the management and protection of algal ecosystem.
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Affiliation(s)
- Liman Wei
- School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui, China
- Agricultural Sensors and Intelligent Perception Technology Innovation Center of Anhui Province, Zhongke Hefei Institutes of Collaborative Research and Innovation for Intelligent Agriculture, Hefei, China
| | - Qiong Zhao
- School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui, China
| | - Xiangyu Chen
- Agricultural Sensors and Intelligent Perception Technology Innovation Center of Anhui Province, Zhongke Hefei Institutes of Collaborative Research and Innovation for Intelligent Agriculture, Hefei, China
- Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Qingye Sun
- School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui, China
| | - Xiang Zhang
- School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui, China
| | - Yongjing Chen
- School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui, China
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3
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Neidhöfer C, Bagniceva M, Wetzig N, Sieber MA, Thiele R, Parčina M. Pragmatic Considerations When Extracting DNA for Metagenomics Analyses of Clinical Samples. Int J Mol Sci 2023; 24:11262. [PMID: 37511022 PMCID: PMC10379426 DOI: 10.3390/ijms241411262] [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: 06/15/2023] [Revised: 07/01/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
Microbiome analyses are essential for understanding microorganism composition and diversity, but interpretation is often challenging due to biological and technical variables. DNA extraction is a critical step that can significantly bias results, particularly in samples containing a high abundance of challenging-to-lyse microorganisms. Taking into consideration the distinctive microenvironments observed in different bodily locations, our study sought to assess the extent of bias introduced by suboptimal bead-beating during DNA extraction across diverse clinical sample types. The question was whether complex targeted extraction methods are always necessary for reliable taxonomic abundance estimation through amplicon sequencing or if simpler alternatives are effective for some sample types. Hence, for four different clinical sample types (stool, cervical swab, skin swab, and hospital surface swab samples), we compared the results achieved from extracting targeted manual protocols routinely used in our research lab for each sample type with automated protocols specifically not designed for that purpose. Unsurprisingly, we found that for the stool samples, manual extraction protocols with vigorous bead-beating were necessary in order to avoid erroneous taxa proportions on all investigated taxonomic levels and, in particular, false under- or overrepresentation of important genera such as Blautia, Faecalibacterium, and Parabacteroides. However, interestingly, we found that the skin and cervical swab samples had similar results with all tested protocols. Our results suggest that the level of practical automation largely depends on the expected microenvironment, with skin and cervical swabs being much easier to process than stool samples. Prudent consideration is necessary when extending the conclusions of this study to applications beyond rough estimations of taxonomic abundance.
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Affiliation(s)
- Claudio Neidhöfer
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Venusberg Campus 1, 53127 Bonn, Germany
| | - Maria Bagniceva
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Venusberg Campus 1, 53127 Bonn, Germany
| | - Nina Wetzig
- Institute for Functional Gene Analytics, Bonn-Rhein-Sieg University of Applied Sciences, 53757 Sankt Augustin, Germany
| | - Martin A Sieber
- Institute for Functional Gene Analytics, Bonn-Rhein-Sieg University of Applied Sciences, 53757 Sankt Augustin, Germany
| | - Ralf Thiele
- Institute for Functional Gene Analytics, Bonn-Rhein-Sieg University of Applied Sciences, 53757 Sankt Augustin, Germany
| | - Marijo Parčina
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Venusberg Campus 1, 53127 Bonn, Germany
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4
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Bou Orm E, Sauvagère S, Rocher J, Benezet JC, Bayle S, Siatka C, Bergeret A, Malhautier L. Estimating the bias related to DNA recovery from hemp stems for retting microbial community investigation. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12582-5. [PMID: 37227475 DOI: 10.1007/s00253-023-12582-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 05/02/2023] [Accepted: 05/09/2023] [Indexed: 05/26/2023]
Abstract
The industrial hemp plant Cannabis sativa is a source of vegetable fiber for both textiles and biocomposite applications. After harvesting, the plant stems are laid out on the ground and colonized by microorganisms (bacteria and fungi) naturally present in the soil and on the stems. By producing hydrolytic enzymes that degrade the plant wall polymers, the natural cement that binds the fiber bundles together is removed, thus facilitating their dissociation (retting process) which is required for producing high-performant fibers. To investigate temporal dynamics of retting microbial communities (density levels, diversity, and structure), a reliable protocol for extracting genomic DNA from stems is mandatory. However, very little attention has been paid to the methodological aspects of nucleic acid extraction, although they are crucial for the significance of the final result. Three protocols were selected and tested: a commercial kit (FastDNA™ Spin Kit for soil), the Gns-GII procedure, and a custom procedure from the Genosol platform. A comparative analysis was carried out on soil and two different varieties of hemp stem. The efficiency of each method was measured by evaluating both the quantity and quality of the extracted DNA and the abundance and taxonomy of bacterial and fungal populations. The Genosol protocol provides interesting yields in terms of quantity and quality of genomic DNA compared to the other two protocols. However, no major difference was observed in microbial diversity between the two extraction procedures (FastDNA™ SPIN Kit and Genosol protocol). Based on these results, the FastDNA™ SPIN kit or the Genosol procedure seems to be suitable for studying bacterial and fungal communities of the retting process. It should be noted that this work has demonstrated the importance of evaluating biases associated with DNA recovery from hemp stems. KEY POINTS: • Metagenomic DNA was successfully extracted from hemp stem samples using three different protocols. • Further evaluation was performed in terms of DNA yield and purity, abundance level, and microbial community structure. • This work exhibited the crucial importance of DNA recovery bias evaluation.
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Affiliation(s)
- Eliane Bou Orm
- Polymers, Composites and Hybrids (PCH), IMT Mines Alès, 6 avenue de Clavières, 30319, Alès Cedex, France
- Laboratoire des Sciences des Risques (LSR), IMT Mines Alès, 6 avenue de Clavières, 30319, Alès Cedex, France
| | - Stéphane Sauvagère
- École de l'ADN, Université de Nîmes, 19 Grand Rue BP 81295, 30015, Nîmes cedex 1, France
| | - Janick Rocher
- Laboratoire des Sciences des Risques (LSR), IMT Mines Alès, 6 avenue de Clavières, 30319, Alès Cedex, France
| | - Jean-Charles Benezet
- Polymers, Composites and Hybrids (PCH), IMT Mines Alès, 6 avenue de Clavières, 30319, Alès Cedex, France
| | - Sandrine Bayle
- Laboratoire des Sciences des Risques (LSR), IMT Mines Alès, 6 avenue de Clavières, 30319, Alès Cedex, France
| | - Christian Siatka
- UPR CHROME, Université de Nîmes, Place Gabriel Péri, 30000, Nîmes cedex 1, France
| | - Anne Bergeret
- Polymers, Composites and Hybrids (PCH), IMT Mines Alès, 6 avenue de Clavières, 30319, Alès Cedex, France
| | - Luc Malhautier
- Laboratoire des Sciences des Risques (LSR), IMT Mines Alès, 6 avenue de Clavières, 30319, Alès Cedex, France.
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5
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Gall-David SL, Boudry G, Buffet-Bataillon S. Comparison of four DNA extraction kits efficiency for 16SrDNA microbiota profiling of diverse human samples. Future Sci OA 2023; 9:FSO837. [PMID: 37006230 PMCID: PMC10051199 DOI: 10.2144/fsoa-2022-0072] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 02/14/2023] [Indexed: 03/11/2023] Open
Abstract
Aim: The current study investigated the performance of 4 widely used DNA extraction kits using different types of high (stool) and low biomass samples (chyme, broncho alveolar lavage and sputum). Methods: Qiagen Powerfecal Pro DNA kit, Macherey Nucleospin Soil kit, Macherey Nucleospin Tissue Kit and MagnaPure LC DNA isolation kit III were evaluated in terms of DNA quantity, quality, diversity and composition profiles. Results: The quantity and quality of DNA varied among the four kits. The microbiota of the stool samples showed similar diversity and compositional profiles for the 4 kits. Conclusion: Despite differences in DNA quality and quantity, the 4 kits yielded similar results for stool samples, while all kits were not sensitive enough for low biomass samples.
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Affiliation(s)
| | - Gaëlle Boudry
- Institut Numecan, INSERM, INRAE, Univ Rennes, Rennes, France
| | - Sylvie Buffet-Bataillon
- Institut Numecan, INSERM, INRAE, Univ Rennes, Rennes, France
- Bacteriology, Pontchaillou University Hospital, Rennes, France
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6
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Yang S, Lee J, Mahmood M, Min D, Im J. Evaluation and optimization of lysis method for microbial DNA extraction from epiphytic phyllosphere samples. J Microbiol Methods 2023; 206:106677. [PMID: 36716930 DOI: 10.1016/j.mimet.2023.106677] [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: 11/28/2022] [Revised: 01/20/2023] [Accepted: 01/20/2023] [Indexed: 01/29/2023]
Abstract
Analysis of microbial communities in the epiphytic phyllosphere can be challenging, especially when applying sequencing-based techniques, owing to the interference of plant-derived biomolecules such as nucleic acids. A review of recent studies on the epiphytic microbiome revealed that both mechanical and enzymatic lysis methods are widely used. Here, we evaluated the effects of the two lysis methods on DNA extraction yield, purity, integrity, and microbial 16S rRNA gene copy number per ng of template genomic DNA under different extraction conditions. Furthermore, the effect on bacterial community composition, diversity, and reproducibility was examined using 16S rRNA gene amplicon sequencing. The enzymatic lysis method yielded one to two orders of magnitude more DNA, but the DNA quality was suboptimal. Conversely, the samples prepared using the mechanical method showed high DNA purity albeit lower yield. Unexpectedly, mechanical lysis showed a higher DNA integrity number (DIN) than enzymatic lysis. The 16S rRNA amplicon sequencing results demonstrated that the samples prepared via mechanical disruption exhibited reproducibly similar microbial community compositions regardless of the extraction conditions. In contrast, the enzymatic lysis method resulted in inconsistent taxonomic compositions under different extraction conditions. This study demonstrates that mechanical DNA disruption is more suitable for epiphytic phyllosphere samples than enzymatic disruption.
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Affiliation(s)
- Seongmin Yang
- Department of Civil Engineering, Kansas State University, Manhattan, KS 66506, USA
| | - Jaejin Lee
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA 50011, USA
| | - Maheen Mahmood
- Department of Civil Engineering, Kansas State University, Manhattan, KS 66506, USA
| | - Doohong Min
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA
| | - Jeongdae Im
- Department of Civil Engineering, Kansas State University, Manhattan, KS 66506, USA.
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7
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Hodgson LM, Cox BA, Lopez-Ruiz FJ, Gibberd MR, Thomas GJ, Zerihun A. Optimized Sample Processing Pipeline for PCR-Based Fungicide Resistance Quantification of Stubble-Borne Fungal Pathogens. PHYTOPATHOLOGY 2023; 113:321-333. [PMID: 36075052 DOI: 10.1094/phyto-07-22-0239-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Globally, yield losses associated with failed crop protection due to fungicide-resistant pathogens present an increasing problem. For stubble-borne pathogens, assessment of crop residues during the off-season could provide early fungicide resistance quantification for informed management decisions to mitigate yield losses. However, stubble assessment is hampered by assay inhibitors that are derived from decaying organic matter. To overcome assay inhibition from weathered stubble samples, we used a systems approach to quantify the frequency of resistance to demethylase inhibitor fungicides of the barley pathogen Pyrenophora teres f. teres. The system canvassed (i) 10 ball-milling conditions; (ii) four DNA extraction methodologies; and (iii) three column purification techniques for the provision of sufficient yield, quality, and purity of fungal DNA for a PCR-based fungicide resistance assay. Results show that DNA quantity and purity differed within each of the above three categories, with the optimized pipeline being (i) ball-milling samples in a 50-ml stainless steel canister for 5 min using a 20-mm ball at 30 revolutions s-1; (ii) a modified Brandfass method (extracted 64% more DNA than other methods assessed); and (iii) use of silica resin columns for the highest DNA concentration with optimal DNA purity. The chip-digital PCR assay, which quantified fungicide resistance from field samples, was unaffected by the DNA extraction method or purification technique, provided that thresholds of template quantity and purity were satisfied. In summary, this study has developed molecular pipeline options for pathogen fungicide resistance quantification from cereal stubbles, which can guide management for improved crop protection outcomes.
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Affiliation(s)
- Leon M Hodgson
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Belinda A Cox
- School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Francisco J Lopez-Ruiz
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Mark R Gibberd
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Geoff J Thomas
- Department of Primary Industries and Regional Development, South Perth, WA 6151, Australia
| | - Ayalsew Zerihun
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
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8
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Combrink L, Humphreys IR, Washburn Q, Arnold HK, Stagaman K, Kasschau KD, Jolles AE, Beechler BR, Sharpton TJ. Best practice for wildlife gut microbiome research: A comprehensive review of methodology for 16S rRNA gene investigations. Front Microbiol 2023; 14:1092216. [PMID: 36910202 PMCID: PMC9992432 DOI: 10.3389/fmicb.2023.1092216] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 01/18/2023] [Indexed: 02/24/2023] Open
Abstract
Extensive research in well-studied animal models underscores the importance of commensal gastrointestinal (gut) microbes to animal physiology. Gut microbes have been shown to impact dietary digestion, mediate infection, and even modify behavior and cognition. Given the large physiological and pathophysiological contribution microbes provide their host, it is reasonable to assume that the vertebrate gut microbiome may also impact the fitness, health and ecology of wildlife. In accordance with this expectation, an increasing number of investigations have considered the role of the gut microbiome in wildlife ecology, health, and conservation. To help promote the development of this nascent field, we need to dissolve the technical barriers prohibitive to performing wildlife microbiome research. The present review discusses the 16S rRNA gene microbiome research landscape, clarifying best practices in microbiome data generation and analysis, with particular emphasis on unique situations that arise during wildlife investigations. Special consideration is given to topics relevant for microbiome wildlife research from sample collection to molecular techniques for data generation, to data analysis strategies. Our hope is that this article not only calls for greater integration of microbiome analyses into wildlife ecology and health studies but provides researchers with the technical framework needed to successfully conduct such investigations.
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Affiliation(s)
- Leigh Combrink
- Department of Microbiology, Oregon State University, Corvallis, OR, United States.,Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States.,School of Natural Resources and the Environment, University of Arizona, Tucson, AZ, United States
| | - Ian R Humphreys
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Quinn Washburn
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Holly K Arnold
- Department of Microbiology, Oregon State University, Corvallis, OR, United States.,Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States
| | - Keaton Stagaman
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Kristin D Kasschau
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Anna E Jolles
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States.,Department of Integrative Biology, Oregon State University, Corvallis, OR, United States
| | - Brianna R Beechler
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States
| | - Thomas J Sharpton
- Department of Microbiology, Oregon State University, Corvallis, OR, United States.,Department of Statistics, Oregon State University, Corvallis, OR, United States
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9
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Grinding Beads Influence Microbial DNA Extraction from Organic-Rich Sub-Seafloor Sediment. Microorganisms 2022; 10:microorganisms10122505. [PMID: 36557758 PMCID: PMC9784657 DOI: 10.3390/microorganisms10122505] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022] Open
Abstract
Sub-seafloor sediment is the largest microbial habitat on Earth. The study of microbes in sub-seafloor sediment is largely limited by the technical challenge of acquiring ambient microbial DNA because of sediment heterogeneity. Changes in the extraction method, even just by one step, can affect the extraction yields for complicated sediment samples. In this work, sub-seafloor sediment samples from the Baltic Sea with high organic carbon content were used to evaluate the influence of different grinding beads on DNA extraction. We found that the grinding beads can affect the DNA extraction from the organic-matter- and biosiliceous-clay-rich samples. A mixture of 0.5-mm and 0.1-mm grinding beads exhibited higher DNA yields and recovered more unique taxa than other bead combinations, such as Stenotrophomonas from Gammaproteobacteria and Leptotrichia from Fusobacteria; therefore, these beads are more suitable than the others for DNA extraction from the samples used in this study. This advantage might be magnified in samples with high biomass. On the contrary, the use of only small beads might lead to underestimation for certain Gram-positive strains. Overall, the discovery of abundant widespread deep biosphere clades in our samples indicated that our optimized DNA extraction method successfully recovered the in situ microbial community.
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10
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Shi Z, Kong Q, Li X, Xu W, Mao C, Wang Y, Song W, Huang J. The Effects of DNA Extraction Kits and Primers on Prokaryotic and Eukaryotic Microbial Community in Freshwater Sediments. Microorganisms 2022; 10:1213. [PMID: 35744736 PMCID: PMC9230960 DOI: 10.3390/microorganisms10061213] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 05/24/2022] [Accepted: 06/08/2022] [Indexed: 02/01/2023] Open
Abstract
DNA based sequencing technology has revolutionized the field of microbial ecology and environmental studies. However, biases can be introduced at all experimental steps and, thus, affect the interpretation of microbial community. So far, previous studies on the biases introduced from the key steps of DNA extraction and primer sets mainly focused on the bacterial communities in soil or sediment samples, while little is known about the effect on the eukaryotic microbial communities. Here, we studied the effects of three different DNA extraction kits on both prokaryotic and micro-eukaryotic communities by 16S and 18S rRNA gene amplicon sequencing, and further disentangled the influence of primer choice on the micro-eukaryotic communities. Our results showed that the FastDNA SPIN Kit for Soil and DNeasy PowerSoil Kit produced much higher DNA yield with good reproducibility, and observed more eukaryotic OTUs compared to the MinkaGene DNA extraction kit, but all three kits exhibited comparable ability in recovering bacterial alpha diversity. Of the two primer sets, both targeting the V4 region of the 18S rRNA gene, the TAR primer set detected higher number of unique OTUs than the EK primer set, while the EK primer set resulted in longer amplicons and better reproducibility between replicates. Based on our findings, we recommend using the DNeasy PowerSoil Kit with the EK primer set to capture the abundant micro-eukaryotic taxa from freshwater sediment samples. If a more complete picture of the eukaryotic microbial community is desired, the TAR primer set in combination with the FastDNA SPIN Kit is more efficient in this study.
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Affiliation(s)
- Zihan Shi
- Institute of Evolution & Marine Biodiversity, College of Fisheries, Ocean University of China, Qingdao 266003, China; (Z.S.); (Y.W.); (W.S.)
- Donghu Experimental Station of Lake Ecosystems, Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (Q.K.); (W.X.); (C.M.)
| | - Qiaoyi Kong
- Donghu Experimental Station of Lake Ecosystems, Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (Q.K.); (W.X.); (C.M.)
| | - Xinghao Li
- Key Laboratory of Regional Development and Environmental Response, Hubei Engineering Research Center for Rural Drinking Water Security, Hubei University, Wuhan 430062, China;
| | - Wenxin Xu
- Donghu Experimental Station of Lake Ecosystems, Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (Q.K.); (W.X.); (C.M.)
| | - Chengzhi Mao
- Donghu Experimental Station of Lake Ecosystems, Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (Q.K.); (W.X.); (C.M.)
| | - Yunfeng Wang
- Institute of Evolution & Marine Biodiversity, College of Fisheries, Ocean University of China, Qingdao 266003, China; (Z.S.); (Y.W.); (W.S.)
- Donghu Experimental Station of Lake Ecosystems, Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (Q.K.); (W.X.); (C.M.)
| | - Weibo Song
- Institute of Evolution & Marine Biodiversity, College of Fisheries, Ocean University of China, Qingdao 266003, China; (Z.S.); (Y.W.); (W.S.)
| | - Jie Huang
- Donghu Experimental Station of Lake Ecosystems, Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (Q.K.); (W.X.); (C.M.)
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11
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Pawlowski J, Bruce K, Panksep K, Aguirre FI, Amalfitano S, Apothéloz-Perret-Gentil L, Baussant T, Bouchez A, Carugati L, Cermakova K, Cordier T, Corinaldesi C, Costa FO, Danovaro R, Dell'Anno A, Duarte S, Eisendle U, Ferrari BJD, Frontalini F, Frühe L, Haegerbaeumer A, Kisand V, Krolicka A, Lanzén A, Leese F, Lejzerowicz F, Lyautey E, Maček I, Sagova-Marečková M, Pearman JK, Pochon X, Stoeck T, Vivien R, Weigand A, Fazi S. Environmental DNA metabarcoding for benthic monitoring: A review of sediment sampling and DNA extraction methods. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 818:151783. [PMID: 34801504 DOI: 10.1016/j.scitotenv.2021.151783] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 11/06/2021] [Accepted: 11/14/2021] [Indexed: 06/13/2023]
Abstract
Environmental DNA (eDNA) metabarcoding (parallel sequencing of DNA/RNA for identification of whole communities within a targeted group) is revolutionizing the field of aquatic biomonitoring. To date, most metabarcoding studies aiming to assess the ecological status of aquatic ecosystems have focused on water eDNA and macroinvertebrate bulk samples. However, the eDNA metabarcoding has also been applied to soft sediment samples, mainly for assessing microbial or meiofaunal biota. Compared to classical methodologies based on manual sorting and morphological identification of benthic taxa, eDNA metabarcoding offers potentially important advantages for assessing the environmental quality of sediments. The methods and protocols utilized for sediment eDNA metabarcoding can vary considerably among studies, and standardization efforts are needed to improve their robustness, comparability and use within regulatory frameworks. Here, we review the available information on eDNA metabarcoding applied to sediment samples, with a focus on sampling, preservation, and DNA extraction steps. We discuss challenges specific to sediment eDNA analysis, including the variety of different sources and states of eDNA and its persistence in the sediment. This paper aims to identify good-practice strategies and facilitate method harmonization for routine use of sediment eDNA in future benthic monitoring.
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Affiliation(s)
- J Pawlowski
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland; Institute of Oceanology, Polish Academy of Sciences, 81-712 Sopot, Poland; ID-Gene Ecodiagnostics, 1202 Geneva, Switzerland
| | - K Bruce
- NatureMetrics Ltd, CABI Site, Bakeham Lane, Egham TW20 9TY, UK
| | - K Panksep
- Institute of Technology, University of Tartu, Tartu 50411, Estonia; Chair of Hydrobiology and Fishery, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia; Chair of Aquaculture, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Estonia
| | - F I Aguirre
- Water Research Institute, National Research Council of Italy (IRSA-CNR), Monterotondo, Rome, Italy
| | - S Amalfitano
- Water Research Institute, National Research Council of Italy (IRSA-CNR), Monterotondo, Rome, Italy
| | - L Apothéloz-Perret-Gentil
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland; ID-Gene Ecodiagnostics, 1202 Geneva, Switzerland
| | - T Baussant
- Norwegian Research Center AS, NORCE Environment, Marine Ecology Group, Mekjarvik 12, 4070 Randaberg, Norway
| | - A Bouchez
- INRAE, CARRTEL, 74200 Thonon-les-Bains, France
| | - L Carugati
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, Ancona 60131, Italy
| | - K Cermakova
- ID-Gene Ecodiagnostics, 1202 Geneva, Switzerland
| | - T Cordier
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland; NORCE Climate, NORCE Norwegian Research Centre AS, Bjerknes Centre for Climate Research, Jahnebakken 5, 5007 Bergen, Norway
| | - C Corinaldesi
- Department of Materials, Environmental Sciences and Urban Planning, Polytechnic University of Marche, Via Brecce Bianche, Ancona 60131, Italy
| | - F O Costa
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - R Danovaro
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, Ancona 60131, Italy
| | - A Dell'Anno
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, Ancona 60131, Italy
| | - S Duarte
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - U Eisendle
- University of Salzburg, Dept. of Biosciences, 5020 Salzburg, Austria
| | - B J D Ferrari
- Swiss Centre for Applied Ecotoxicology (Ecotox Centre), EPFL ENAC IIE-GE, 1015 Lausanne, Switzerland
| | - F Frontalini
- Department of Pure and Applied Sciences, Urbino University, Urbino, Italy
| | - L Frühe
- Technische Universität Kaiserslautern, Ecology Group, D-67663 Kaiserslautern, Germany
| | - A Haegerbaeumer
- Bielefeld University, Animal Ecology, 33615 Bielefeld, Germany
| | - V Kisand
- Institute of Technology, University of Tartu, Tartu 50411, Estonia
| | - A Krolicka
- Norwegian Research Center AS, NORCE Environment, Marine Ecology Group, Mekjarvik 12, 4070 Randaberg, Norway
| | - A Lanzén
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Pasaia, Gipuzkoa, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, Bizkaia, Spain
| | - F Leese
- University of Duisburg-Essen, Faculty of Biology, Aquatic Ecosystem Research, Germany
| | - F Lejzerowicz
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - E Lyautey
- Univ. Savoie Mont Blanc, INRAE, CARRTEL, 74200 Thonon-les-Bains, France
| | - I Maček
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia; Faculty of Mathematics, Natural Sciences and Information Technologies (FAMNIT), University of Primorska, Glagoljaška 8, 6000 Koper, Slovenia
| | - M Sagova-Marečková
- Czech University of Life Sciences, Dept. of Microbiology, Nutrition and Dietetics, Prague, Czech Republic
| | - J K Pearman
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | - X Pochon
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand; Institute of Marine Science, University of Auckland, Warkworth 0941, New Zealand
| | - T Stoeck
- Technische Universität Kaiserslautern, Ecology Group, D-67663 Kaiserslautern, Germany
| | - R Vivien
- Swiss Centre for Applied Ecotoxicology (Ecotox Centre), EPFL ENAC IIE-GE, 1015 Lausanne, Switzerland
| | - A Weigand
- National Museum of Natural History Luxembourg, 25 Rue Münster, L-2160 Luxembourg, Luxembourg
| | - S Fazi
- Water Research Institute, National Research Council of Italy (IRSA-CNR), Monterotondo, Rome, Italy.
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12
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Mahnkopp-Dirks F, Radl V, Kublik S, Gschwendtner S, Schloter M, Winkelmann T. Dynamics of Bacterial Root Endophytes of Malus domestica Plants Grown in Field Soils Affected by Apple Replant Disease. Front Microbiol 2022; 13:841558. [PMID: 35401446 PMCID: PMC8993231 DOI: 10.3389/fmicb.2022.841558] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 02/14/2022] [Indexed: 01/04/2023] Open
Abstract
Apple replant disease (ARD) is a worldwide problem for tree nurseries and orchards leading to reduced plant growth and fruit quality. The etiology of this complex phenomenon is poorly understood, but shifts of the bulk soil and rhizosphere microbiome seem to play an important role. Since roots are colonized by microbes from the rhizosphere, studies of the endophytic microbiome in relation to ARD are meaningful. In this study, culture-independent and culture-dependent approaches were used in order to unravel the endophytic root microbiome of apple plants 3, 7, and 12 months after planting in ARD-affected soil and ARD-unaffected control soil at two different field sites. Next to a high diversity of Pseudomonas in roots from all soils, molecular barcoding approaches revealed an increase in relative abundance of endophytic Actinobacteria over time in plants grown in ARD and control plots. Furthermore, several amplicon sequence variants (ASVs) linked to Streptomyces, which had been shown in a previous greenhouse ARD biotest to be negatively correlated to shoot length and fresh mass, were also detected in roots from both field sites. Especially in roots of apple plants from control soil, these Streptomyces ASVs increased in their relative abundance over time. The isolation of 150 bacterial strains in the culture-dependent approach revealed a high diversity of members of the genus Pseudomonas, confirming the data of the molecular barcoding approach. However, only partial overlaps were found between the two approaches, underlining the importance of combining these methods in order to better understand this complex disease and develop possible countermeasures. Overall, this study suggests a key role of Streptomyces in the etiology of ARD in the field.
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Affiliation(s)
- Felix Mahnkopp-Dirks
- Section Woody Plant and Propagation Physiology, Institute of Horticultural Production Systems, Leibniz Universität Hannover, Hanover, Germany
| | - Viviane Radl
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Munich, Germany
| | - Susanne Kublik
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Munich, Germany
| | - Silvia Gschwendtner
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Munich, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Munich, Germany
| | - Traud Winkelmann
- Section Woody Plant and Propagation Physiology, Institute of Horticultural Production Systems, Leibniz Universität Hannover, Hanover, Germany
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13
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Caron K, Craw P, Richardson MB, Bodrossy L, Voelcker NH, Thissen H, Sutherland TD. The Requirement of Genetic Diagnostic Technologies for Environmental Surveillance of Antimicrobial Resistance. SENSORS 2021; 21:s21196625. [PMID: 34640944 PMCID: PMC8513014 DOI: 10.3390/s21196625] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/28/2021] [Accepted: 09/28/2021] [Indexed: 12/11/2022]
Abstract
Antimicrobial resistance (AMR) is threatening modern medicine. While the primary cost of AMR is paid in the healthcare domain, the agricultural and environmental domains are also reservoirs of resistant microorganisms and hence perpetual sources of AMR infections in humans. Consequently, the World Health Organisation and other international agencies are calling for surveillance of AMR in all three domains to guide intervention and risk reduction strategies. Technologies for detecting AMR that have been developed for healthcare settings are not immediately transferable to environmental and agricultural settings, and limited dialogue between the domains has hampered opportunities for cross-fertilisation to develop modified or new technologies. In this feature, we discuss the limitations of currently available AMR sensing technologies used in the clinic for sensing in other environments, and what is required to overcome these limitations.
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Affiliation(s)
- Karine Caron
- CSIRO Health & Biosecurity, Canberra, ACT 2602, Australia;
| | - Pascal Craw
- CSIRO Oceans & Atmosphere, Hobart, TAS 7004, Australia; (P.C.); (L.B.)
| | - Mark B. Richardson
- CSIRO Manufacturing, Clayton, VIC 3168, Australia; (M.B.R.); (N.H.V.); (H.T.)
| | - Levente Bodrossy
- CSIRO Oceans & Atmosphere, Hobart, TAS 7004, Australia; (P.C.); (L.B.)
| | - Nicolas H. Voelcker
- CSIRO Manufacturing, Clayton, VIC 3168, Australia; (M.B.R.); (N.H.V.); (H.T.)
- Melbourne Centre for Nanofabrication, Victorian Node of the Australian National Fabrication Facility, Clayton, VIC 3168, Australia
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Helmut Thissen
- CSIRO Manufacturing, Clayton, VIC 3168, Australia; (M.B.R.); (N.H.V.); (H.T.)
| | - Tara D. Sutherland
- CSIRO Health & Biosecurity, Canberra, ACT 2602, Australia;
- Correspondence:
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14
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Nearing JT, Comeau AM, Langille MGI. Identifying biases and their potential solutions in human microbiome studies. MICROBIOME 2021; 9:113. [PMID: 34006335 PMCID: PMC8132403 DOI: 10.1186/s40168-021-01059-0] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 03/24/2021] [Indexed: 05/13/2023]
Abstract
Advances in DNA sequencing technology have vastly improved the ability of researchers to explore the microbial inhabitants of the human body. Unfortunately, while these studies have uncovered the importance of these microbial communities to our health, they often do not result in similar findings. One possible reason for the disagreement in these results is due to the multitude of systemic biases that are introduced during sequence-based microbiome studies. These biases begin with sample collection and continue to be introduced throughout the entire experiment leading to an observed community that is significantly altered from the true underlying microbial composition. In this review, we will highlight the various steps in typical sequence-based human microbiome studies where significant bias can be introduced, and we will review the current efforts within the field that aim to reduce the impact of these biases. Video abstract.
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Affiliation(s)
- Jacob T Nearing
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - André M Comeau
- Integrated Microbiome Resource, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Morgan G I Langille
- Integrated Microbiome Resource, Dalhousie University, Halifax, Nova Scotia, Canada.
- Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada.
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15
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Busi SB, Pramateftaki P, Brandani J, Fodelianakis S, Peter H, Halder R, Wilmes P, Battin TJ. Optimised biomolecular extraction for metagenomic analysis of microbial biofilms from high-mountain streams. PeerJ 2020; 8:e9973. [PMID: 33194372 PMCID: PMC7597623 DOI: 10.7717/peerj.9973] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 08/26/2020] [Indexed: 11/20/2022] Open
Abstract
Glacier-fed streams (GFS) are harsh ecosystems dominated by microbial life organized in benthic biofilms, yet the biodiversity and ecosystem functions provided by these communities remain under-appreciated. To better understand the microbial processes and communities contributing to GFS ecosystems, it is necessary to leverage high throughput sequencing. Low biomass and high inorganic particle load in GFS sediment samples may affect nucleic acid extraction efficiency using extraction methods tailored to other extreme environments such as deep-sea sediments. Here, we benchmarked the utility and efficacy of four extraction protocols, including an up-scaled phenol-chloroform protocol. We found that established protocols for comparable sample types consistently failed to yield sufficient high-quality DNA, delineating the extreme character of GFS. The methods differed in the success of downstream applications such as library preparation and sequencing. An adapted phenol-chloroform-based extraction method resulted in higher yields and better recovered the expected taxonomic profile and abundance of reconstructed genomes when compared to commercially-available methods. Affordable and straight-forward, this method consistently recapitulated the abundance and genomes of a mock community, including eukaryotes. Moreover, by increasing the amount of input sediment, the protocol is readily adjustable to the microbial load of the processed samples without compromising protocol efficiency. Our study provides a first systematic and extensive analysis of the different options for extraction of nucleic acids from glacier-fed streams for high-throughput sequencing applications, which may be applied to other extreme environments.
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Affiliation(s)
- Susheel Bhanu Busi
- Systems Ecology Research Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Paraskevi Pramateftaki
- Stream Biofilm and Ecosystems Research group, École Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | - Jade Brandani
- Stream Biofilm and Ecosystems Research group, École Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | - Stilianos Fodelianakis
- Stream Biofilm and Ecosystems Research group, École Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | - Hannes Peter
- Stream Biofilm and Ecosystems Research group, École Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | - Rashi Halder
- Systems Ecology Research Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Paul Wilmes
- Systems Ecology Research Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Tom J Battin
- Stream Biofilm and Ecosystems Research group, École Polytechnique Federale de Lausanne, Lausanne, Switzerland
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16
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Pearman JK, Keeley NB, Wood SA, Laroche O, Zaiko A, Thomson-Laing G, Biessy L, Atalah J, Pochon X. Comparing sediment DNA extraction methods for assessing organic enrichment associated with marine aquaculture. PeerJ 2020; 8:e10231. [PMID: 33194417 PMCID: PMC7597629 DOI: 10.7717/peerj.10231] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 10/02/2020] [Indexed: 12/21/2022] Open
Abstract
Marine sediments contain a high diversity of micro- and macro-organisms which are important in the functioning of biogeochemical cycles. Traditionally, anthropogenic perturbation has been investigated by identifying macro-organism responses along gradients. Environmental DNA (eDNA) analyses have recently been advocated as a rapid and cost-effective approach to measuring ecological impacts and efforts are underway to incorporate eDNA tools into monitoring. Before these methods can replace or complement existing methods, robustness and repeatability of each analytical step has to be demonstrated. One area that requires further investigation is the selection of sediment DNA extraction method. Environmental DNA sediment samples were obtained along a disturbance gradient adjacent to a Chinook (Oncorhynchus tshawytscha) salmon farm in Otanerau Bay, New Zealand. DNA was extracted using four extraction kits (Qiagen DNeasy PowerSoil, Qiagen DNeasy PowerSoil Pro, Qiagen RNeasy PowerSoil Total RNA/DNA extraction/elution and Favorgen FavorPrep Soil DNA Isolation Midi Kit) and three sediment volumes (0.25, 2, and 5 g). Prokaryotic and eukaryotic communities were amplified using primers targeting the 16S and 18S ribosomal RNA genes, respectively, and were sequenced on an Illumina MiSeq. Diversity and community composition estimates were obtained from each extraction kit, as well as their relative performance in established metabarcoding biotic indices. Differences were observed in the quality and quantity of the extracted DNA amongst kits with the two Qiagen DNeasy PowerSoil kits performing best. Significant differences were observed in both prokaryotes and eukaryotes (p < 0.001) richness among kits. A small proportion of amplicon sequence variants (ASVs) were shared amongst the kits (~3%) although these shared ASVs accounted for the majority of sequence reads (prokaryotes: 59.9%, eukaryotes: 67.2%). Differences were observed in the richness and relative abundance of taxonomic classes revealed with each kit. Multivariate analysis showed that there was a significant interaction between "distance" from the farm and "kit" in explaining the composition of the communities, with the distance from the farm being a stronger determinant of community composition. Comparison of the kits against the bacterial and eukaryotic metabarcoding biotic index suggested that all kits showed similar patterns along the environmental gradient. Overall, we advocate for the use of Qiagen DNeasy PowerSoil kits for use when characterizing prokaryotic and eukaryotic eDNA from marine farm sediments. We base this conclusion on the higher DNA quality values and richness achieved with these kits compared to the other kits/amounts investigated in this study. The additional advantage of the PowerSoil Kits is that DNA extractions can be performed using an extractor robot, offering additional standardization and reproducibility of results.
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Affiliation(s)
- John K. Pearman
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | | | - Susanna A. Wood
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | | | - Anastasija Zaiko
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
- Institute of Marine Science, University of Auckland, Auckland, New Zealand
| | | | - Laura Biessy
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Javier Atalah
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Xavier Pochon
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
- Institute of Marine Science, University of Auckland, Auckland, New Zealand
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17
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Hamilton A, Harper SJ, Critzer F. Optimization of a Method for the Concentration of Genetic Material in Bacterial and Fungal Communities on Fresh Apple Peel Surfaces. Microorganisms 2020; 8:microorganisms8101480. [PMID: 32993184 PMCID: PMC7601045 DOI: 10.3390/microorganisms8101480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/24/2020] [Accepted: 09/24/2020] [Indexed: 11/16/2022] Open
Abstract
Apples are the most consumed fruit in the United States and have recently been shown to exhibit some vulnerability to contamination across the supply chain. It is unclear what role a fruit microbiome analysis may serve in future food safety programs interested in understanding changes in the product and the processing environment. Ultimately, sample integrity is key if any of these approaches are to be employed; low microbial loads on apple surfaces, the inability to sample the entire surface, and inefficiency of removal may act as barriers to achieving high-quality DNA. As such, the objective of this study was to identify a reproducible method to concentrate and quantify bacterial and fungal DNA from fresh apple surfaces. Five methods were evaluated: two variations of wash solutions for bath sonication, wash filtration, epidermis excision, and surface swabbing. Epidermis excision returned the highest mean DNA quantities, followed by the sonicated washes and wash filtration. Surface swabbing was consistently below the limit of detection. Based on the quantity of host DNA contamination in surface excision, the sonicated wash solution containing a surfactant presents the greatest opportunity for consistent, high-yielding DNA recovery from the entire apple surface.
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Affiliation(s)
- Alexis Hamilton
- School of Food Science, Washington State University, Pullman, WA 99164, USA;
- Correspondence: ; Tel.:+1-509-786-9209
| | - Scott J. Harper
- Department of Plant Pathology, Washington State University, Pullman, WA 99164, USA;
| | - Faith Critzer
- School of Food Science, Washington State University, Pullman, WA 99164, USA;
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18
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Evaluation of a Highly Efficient DNA Extraction Method for Bacillus anthracis Endospores. Microorganisms 2020; 8:microorganisms8050763. [PMID: 32443768 PMCID: PMC7285266 DOI: 10.3390/microorganisms8050763] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/15/2020] [Accepted: 05/18/2020] [Indexed: 11/19/2022] Open
Abstract
A variety of methods have been established in order to optimize the accessibility of DNA originating from Bacillusanthracis cells and endospores to facilitate highly sensitive molecular diagnostics. However, most endospore lysis techniques have not been evaluated in respect to their quantitative proficiencies. Here, we started by systematically assessing the efficiencies of 20 DNA extraction kits for vegetative B.anthracis cells. Of these, the Epicentre MasterPure kit gave the best DNA yields and quality suitable for further genomic analysis. Yet, none of the kits tested were able to extract reasonable quantities of DNA from cores of the endospores. Thus, we developed a mechanical endospore lysis protocol, facilitating the extraction of high-quality DNA. Transmission electron microscopy or the labelling of spores with the indicator dye propidium monoazide was utilized to assess lysis efficiency. Finally, the yield and quality of genomic spore DNA were quantified by PCR and they were found to be dependent on lysis matrix composition, instrumental parameters, and the method used for subsequent DNA purification. Our final standardized lysis and DNA extraction protocol allows for the quantitative detection of low levels (<50 CFU/mL) of B. anthracis endospores and it is suitable for direct quantification, even under resource-limited field conditions, where culturing is not an option.
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19
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Venturini AM, Nakamura FM, Gontijo JB, da França AG, Yoshiura CA, Mandro JA, Tsai SM. Robust DNA protocols for tropical soils. Heliyon 2020; 6:e03830. [PMID: 32426533 PMCID: PMC7226647 DOI: 10.1016/j.heliyon.2020.e03830] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 09/06/2019] [Accepted: 04/21/2020] [Indexed: 12/14/2022] Open
Abstract
Studies in the Amazon are being intensified to evaluate the alterations in the microbial communities of soils and sediments in the face of increasing deforestation and land-use changes in the region. However, since these environments present highly heterogeneous physicochemical properties, including contaminants that hinder nucleic acids isolation and downstream techniques, the development of best molecular practices is crucial. This work aimed to optimize standard protocols for DNA extraction and gene quantification by quantitative real-time PCR (qPCR) based on natural and anthropogenic soils and sediments (primary forest, pasture, Amazonian Dark Earth, and várzea, a seasonally flooded area) of the Eastern Amazon. Our modified extraction protocol increased the fluorometric DNA concentration by 48%, reaching twice the original amount for most of the pasture and várzea samples, and the 260/280 purity ratio by 15% to values between 1.8 to 2.0, considered ideal for DNA. The addition of bovine serum albumin in the qPCR reaction improved the quantification of the 16S rRNA genes of Archaea and Bacteria and its precision among technical replicates, as well as allowed their detection in previously non-amplifiable samples. It is concluded that the changes made in the protocols improved the parameters of the DNA samples and their amplification, thus increasing the reliability of microbial communities' analysis and its ecological interpretations.
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Affiliation(s)
- Andressa Monteiro Venturini
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário, 303, Piracicaba, SP, 13416-000, Brazil
| | - Fernanda Mancini Nakamura
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário, 303, Piracicaba, SP, 13416-000, Brazil
| | - Júlia Brandão Gontijo
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário, 303, Piracicaba, SP, 13416-000, Brazil
| | - Aline Giovana da França
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário, 303, Piracicaba, SP, 13416-000, Brazil
| | - Caio Augusto Yoshiura
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário, 303, Piracicaba, SP, 13416-000, Brazil
| | - Jéssica Adriele Mandro
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário, 303, Piracicaba, SP, 13416-000, Brazil
| | - Siu Mui Tsai
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário, 303, Piracicaba, SP, 13416-000, Brazil
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20
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Tendentious effects of automated and manual metagenomic DNA purification protocols on broiler gut microbiome taxonomic profiling. Sci Rep 2020; 10:3419. [PMID: 32099013 PMCID: PMC7042355 DOI: 10.1038/s41598-020-60304-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 02/10/2020] [Indexed: 02/06/2023] Open
Abstract
Here, we developed protocols to improve sensitivity, rigor and comparability of 16S rRNA gene amplification-based next-generation sequencing (NGS) results. A thorough study was performed by evaluating extraction efficiency with respect to the yield, purity, fragmentation of the purified DNA, and sequencing metrics considering the number of quality reads, amplicon sequence variants (ASVs), community structure and biodiversity. We identified batch-effects that significantly bias broiler gastrointestinal tract (GIT) community compositions and made recommendations to improve sensitivity, consistency, and cross-study comparability. We found that the purity of the extracted nucleic acid had a strong effect on the success rate of downstream library preparations. The preparation of stool bacterial suspensions from feces showed a significant positive influence on community biodiversity by enriching Gram-negative bacteria and cataloguing low abundant taxa with greater success than direct processing of fecal material. Applications relying on the automated Roche MagNa Pure 24 magnetic-bead based method provided results with high consistency therefore it seems to be the optimal choice in large-scale studies for investigating broiler GIT microbiota.
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21
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de los Reyes AMM, Ocampo ETM, Manuel MCC, Mendoza BC. Analysis of the Bacterial and Fungal Community Profiles in Bulk Soil and Rhizospheres of Three Mungbean [<i>Vigna radiata</i> (L.) R. Wilczek] Genotypes through PCR-DGGE. INTERNATIONAL LETTERS OF NATURAL SCIENCES 2020. [DOI: 10.56431/p-9q7fup] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Each plant species is regarded to substantially influence and thus, select for specific rhizosphere microbial populations. This is considered in the exploitation of soil microbial diversity associated with important crops, which has been of interest in modern agricultural practices for sustainable productivity. This study used PCR-DGGE (polymerase chain reaction - denaturing gradient gel electrophoresis) in order to obtain an initial assessment of the bacterial and fungal communities associated in bulk soil and rhizospheres of different mungbean genotypes under natural field conditions. Integrated use of multivariate analysis and diversity index showed plant growth stage as the primary driver of community shifts in both microbial groups while rhizosphere effect was found to be less discrete in fungal communities. On the other hand, genotype effect was not discerned but not inferred to be absent due to possible lack of manifestations of differences among genotypes based on tolerance to drought under non-stressed environment, and due to detection limits of DGGE. Sequence analysis of prominent members further revealed that Bacillus and Arthrobacter species were dominant in bacterial communities whereas members of Ascomycota and Basidiomycota were common in fungal communities of mungbean. Overall, fungal communities had higher estimated diversity and composition heterogeneity, and were more dynamic under plant growth influence, rhizosphere effect and natural environmental conditions during mungbean growth in upland field. These primary evaluations are prerequisite to understanding the interactions between plant and rhizosphere microorganisms with the intention of employing their potential use for sustainable crop production.
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de los Reyes AMM, Ocampo ETM, Manuel MCC, Mendoza BC. Analysis of the Bacterial and Fungal Community Profiles in Bulk Soil and Rhizospheres of Three Mungbean [ Vigna radiata (L.) R. Wilczek] Genotypes through PCR-DGGE. INTERNATIONAL LETTERS OF NATURAL SCIENCES 2020. [DOI: 10.18052/www.scipress.com/ilns.77.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Each plant species is regarded to substantially influence and thus, select for specific rhizosphere microbial populations. This is considered in the exploitation of soil microbial diversity associated with important crops, which has been of interest in modern agricultural practices for sustainable productivity. This study used PCR-DGGE (polymerase chain reaction - denaturing gradient gel electrophoresis) in order to obtain an initial assessment of the bacterial and fungal communities associated in bulk soil and rhizospheres of different mungbean genotypes under natural field conditions. Integrated use of multivariate analysis and diversity index showed plant growth stage as the primary driver of community shifts in both microbial groups while rhizosphere effect was found to be less discrete in fungal communities. On the other hand, genotype effect was not discerned but not inferred to be absent due to possible lack of manifestations of differences among genotypes based on tolerance to drought under non-stressed environment, and due to detection limits of DGGE. Sequence analysis of prominent members further revealed that Bacillus and Arthrobacter species were dominant in bacterial communities whereas members of Ascomycota and Basidiomycota were common in fungal communities of mungbean. Overall, fungal communities had higher estimated diversity and composition heterogeneity, and were more dynamic under plant growth influence, rhizosphere effect and natural environmental conditions during mungbean growth in upland field. These primary evaluations are prerequisite to understanding the interactions between plant and rhizosphere microorganisms with the intention of employing their potential use for sustainable crop production.
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Spiking a Silty-Sand Reference Soil with Bacterial DNA: Limits and Pitfalls in the Discrimination of Live and Dead Cells When Applying Ethidium Monoazide (EMA) Treatment. Curr Microbiol 2019; 76:1425-1434. [PMID: 31552450 PMCID: PMC6817739 DOI: 10.1007/s00284-019-01772-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 08/30/2019] [Accepted: 09/11/2019] [Indexed: 10/28/2022]
Abstract
In the present study, EMA (ethidium monoazide) treatment was applied to a silty-sand reference soil prior to DNA extraction to enable a differentiation between dead and living cells. For this purpose, a reference soil was spiked with Listeria monocytogenes cells or cell equivalents, respectively. With the purpose of evaluating optimum treatment conditions, different EMA concentrations have been tested. However, the results remained largely inconclusive. Furthermore, varied dark incubation periods allowing EMA to penetrate dead cells did not allow the selective removal of DNA from membrane-compromised cells in downstream analyses. In contrast to undiluted soil, an effect of EMA treatment during DNA extraction could be observed when using a 1:10 dilution of the reference soil; however, the effect has not been sufficiently selective to act on heat-treated cells only. Although the application of EMA to soil requires further evaluation, the procedure harbors future potential for improving DNA-based approaches in microbial ecology studies.
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24
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Shahraki AH, Chaganti SR, Heath D. Assessing high-throughput environmental DNA extraction methods for meta-barcode characterization of aquatic microbial communities. JOURNAL OF WATER AND HEALTH 2019; 17:37-49. [PMID: 30758302 DOI: 10.2166/wh.2018.108] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The characterization of microbial community dynamics using genomic methods is rapidly expanding, impacting many fields including medical, ecological, and environmental research and applications. One of the biggest challenges for such studies is the isolation of environmental DNA (eDNA) from a variety of samples, diverse microbes, and widely variable community compositions. The current study developed environmentally friendly, user safe, economical, and high throughput eDNA extraction methods for mixed aquatic microbial communities and tested them using 16 s rRNA gene meta-barcoding. Five different lysis buffers including (1) cetyltrimethylammonium bromide (CTAB), (2) digestion buffer (DB), (3) guanidinium isothiocyanate (GITC), (4) sucrose lysis (SL), and (5) SL-CTAB, coupled with four different purification methods: (1) phenol-chloroform-isoamyl alcohol (PCI), (2) magnetic Bead-Robotic, (3) magnetic Bead-Manual, and (4) membrane-filtration were tested for their efficacy in extracting eDNA from recreational freshwater samples. Results indicated that the CTAB-PCI and SL-Bead-Robotic methods yielded the highest genomic eDNA concentrations and succeeded in detecting the core microbial community including the rare microbes. However, our study recommends the SL-Bead-Robotic eDNA extraction protocol because this method is safe, environmentally friendly, rapid, high-throughput and inexpensive.
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Affiliation(s)
- Abdolrazagh Hashemi Shahraki
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario N9B 3P4, Canada E-mail:
| | - Subba Rao Chaganti
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario N9B 3P4, Canada E-mail:
| | - Daniel Heath
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario N9B 3P4, Canada E-mail: ; Department of Biological Sciences, University of Windsor, Windsor, Ontario, Canada
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25
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Koziol A, Stat M, Simpson T, Jarman S, DiBattista JD, Harvey ES, Marnane M, McDonald J, Bunce M. Environmental DNA metabarcoding studies are critically affected by substrate selection. Mol Ecol Resour 2018; 19:366-376. [DOI: 10.1111/1755-0998.12971] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 11/08/2018] [Accepted: 11/14/2018] [Indexed: 01/24/2023]
Affiliation(s)
- Adam Koziol
- Trace and Environmental DNA (TrEnD) Laboratory, School Molecular and Life Sciences Curtin University Bentley Western Australia Australia
| | - Michael Stat
- Trace and Environmental DNA (TrEnD) Laboratory, School Molecular and Life Sciences Curtin University Bentley Western Australia Australia
- School of Biological Sciences Macquarie University North Ryde New South Wales Australia
| | - Tiffany Simpson
- Trace and Environmental DNA (TrEnD) Laboratory, School Molecular and Life Sciences Curtin University Bentley Western Australia Australia
| | - Simon Jarman
- Trace and Environmental DNA (TrEnD) Laboratory, School Molecular and Life Sciences Curtin University Bentley Western Australia Australia
- CSIRO Environomics Future Science Platform Indian Ocean Marine Research Centre The University of Western Australia Perth Western Australia Australia
| | - Joseph D. DiBattista
- Trace and Environmental DNA (TrEnD) Laboratory, School Molecular and Life Sciences Curtin University Bentley Western Australia Australia
- Australian Museum Research Institute, Australian Museum Sydney New South Wales Australia
| | - Euan S. Harvey
- Fish Ecology Laboratory, School Molecular and Life Sciences Curtin University Bentley Western Australia Australia
| | - Michael Marnane
- Chevron Energy Technology Company Perth Western Australia Australia
| | - Justin McDonald
- Sustainability and Biosecurity, Department of Primary Industries and Regional Development (DPIRD) Hillarys Western Australia Australia
| | - Michael Bunce
- Trace and Environmental DNA (TrEnD) Laboratory, School Molecular and Life Sciences Curtin University Bentley Western Australia Australia
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26
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Limited congruence exhibited across microbial, meiofaunal and macrofaunal benthic assemblages in a heterogeneous coastal environment. Sci Rep 2018; 8:15500. [PMID: 30341362 PMCID: PMC6195585 DOI: 10.1038/s41598-018-33799-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 10/04/2018] [Indexed: 02/01/2023] Open
Abstract
One of the most common approaches for investigating the ecology of spatially complex environments is to examine a single biotic assemblage present, such as macroinvertebrates. Underlying this approach are assumptions that sampled and unsampled taxa respond similarly to environmental gradients and exhibit congruence across different sites. These assumptions were tested for five benthic groups of various sizes (archaea, bacteria, microbial eukaryotes/protists, meiofauna and macrofauna) in Plymouth Sound, a harbour with many different pollution sources. Sediments varied in granulometry, hydrocarbon and trace metal concentrations. Following variable reduction, canonical correspondence analysis did not identify any associations between sediment characteristics and assemblage composition of archaea or macrofauna. In contrast, variation in bacteria was associated with granulometry, trace metal variations and bioturbation (e.g. community bioturbation potential). Protists varied with granulometry, hydrocarbon and trace metal predictors. Meiofaunal variation was associated with hydrocarbon and bioturbation predictors. Taxon turnover between sites varied with only three out of 10 group pairs showing congruence (meiofauna-protists, meiofauna-macrofauna and protists-macrofauna). While our results support using eukaryotic taxa as proxies for others, the lack of congruence suggests caution should be applied to inferring wider indicator or functional interpretations from studies of a single biotic assemblage.
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Xie K, Deng Y, Zhang X, Wang X, Kang G, Bai L, Huang H. Biases in Prokaryotic Community Amplicon Sequencing Affected by DNA Extraction Methods in Both Saline and Non-saline Soil. Front Microbiol 2018; 9:1796. [PMID: 30127778 PMCID: PMC6088177 DOI: 10.3389/fmicb.2018.01796] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 07/17/2018] [Indexed: 01/29/2023] Open
Abstract
High-throughput amplicon sequencing technology has been widely used in soil microbiome studies. Here, we estimated the bias of amplicon sequencing data affected by DNA extraction methods in a saline soil, and a non-saline normal soil was used as a control. Compared with the normal soil, several unique points were observed in the saline soil. The soil washing pretreatment can improve not only DNA quantity and quality but also microbial diversities in the saline soil; therefore, we recommend the soil washing pretreatment for saline soils especially hypersaline soils that cannot be achieved with detectable DNA amounts without the pretreatment. Also, evenness indices were more easily affected by DNA extraction methods than richness indices in the saline soil. Moreover, proportions of Gram-positive bacteria had significant positive correlations with the achieved microbial diversities within replicates of the saline soil. Though DNA extraction methods can bias the microbial diversity or community and relative abundances of some phyla/classes can vary by a factor of more than five, soil types were still the most important factor of the whole community. We confirmed good comparability in the whole community, but more attention should be paid when concentrating on an exact diversity value or the exact relative abundance of a certain taxon. Our study can provide references for the DNA extraction from saline and non-saline soils and comparing sequencing data across studies who may employ different DNA extraction methods.
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Affiliation(s)
- Kehui Xie
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, China
| | - Yong Deng
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, China
| | - Xuze Zhang
- School of Chemistry and Chemical Engineering, Qinghai University for Nationalities, Xining, China
| | - Xueting Wang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, China
| | - Guangbo Kang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, China
| | - Liang Bai
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, China
| | - He Huang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, China
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28
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Xue M, Wu L, He Y, Liang H, Wen C. Biases during DNA extraction affect characterization of the microbiota associated with larvae of the Pacific white shrimp, Litopenaeus vannamei. PeerJ 2018; 6:e5257. [PMID: 30038871 PMCID: PMC6052851 DOI: 10.7717/peerj.5257] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 06/27/2018] [Indexed: 11/20/2022] Open
Abstract
For in-depth characterization of the microbiota associated with shrimp larvae, careful selection of DNA isolation procedure is paramount for avoiding biases introduced in community profiling. Four E.Z.N.A.™ DNA extraction kits, i.e., Bacterial, Mollusc, Stool, and Tissue DNA Kits, abbreviated as Ba, Mo, St, and Ti, respectively, were initially evaluated with zoea 2 (Z2) larvae of the Pacific white shrimp (Litopenaeus vannamei) by 16S amplicon sequencing on a Illumina MiSeq platform. Further characterization of additional larval samples, specifically nauplii 5 (N5), mysis 1 (M1), and postlarvae 1 (P1), was performed with Ba and St kits to examine the changing microbiota profile during shrimp hatchery period. The results from the Z2 samples showed that DNA yields from the four kits varied significantly (P < 0.05), whereas no significant differences were detected in the α-diversity metrics of the microbiota. By contrast, the St kit, with the lowest DNA yield and quality, successfully recovered DNA from Gram-positive and gut-associated bacterial groups, whereas the Ba kit, which showed maximal microbiota similarity with the Mo kit, manifested the best reproducibility. Notably, significant differences were observed in relative abundances of most dominant taxa when comparing results from the Ba and St kits on Z2, M1, and P1 samples. In addition, the bacterial community identified shifted markedly with larval development regardless of the DNA extraction kits. The DNA recovery biases arising from the larval microbiota could be due to different protocols for cell lysis and purification. Therefore, combined application of different DNA extraction methods may facilitate identification of some biologically important groups owing to their complementary effects. This approach should receive adequate attention for a thorough understanding of the larvae-associated microbiota of the penaeid shrimp.
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Affiliation(s)
- Ming Xue
- Fisheries College, Guangdong Ocean University, Zhanjiang, Guangdong, China
| | - Liyou Wu
- Institute for Environmental Genomics, and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Yaoyao He
- Fisheries College, Guangdong Ocean University, Zhanjiang, Guangdong, China
| | - Huafang Liang
- Fisheries College, Guangdong Ocean University, Zhanjiang, Guangdong, China
| | - Chongqing Wen
- Fisheries College, Guangdong Ocean University, Zhanjiang, Guangdong, China
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29
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Scott M, Rani M, Samsatly J, Charron JB, Jabaji S. Endophytes of industrial hemp (Cannabis sativa L.) cultivars: identification of culturable bacteria and fungi in leaves, petioles, and seeds. Can J Microbiol 2018; 64:664-680. [PMID: 29911410 DOI: 10.1139/cjm-2018-0108] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Plant endophytes are a group of microorganisms that reside asymptomatically within the healthy living tissue. The diversity and molecular and biochemical characterization of industrial hemp-associated endophytes have not been previously studied. This study explored the abundance and diversity of culturable endophytes residing in petioles, leaves, and seeds of three industrial hemp cultivars, and examined their biochemical attributes and antifungal potential. A total of 134 bacterial and 53 fungal strains were isolated from cultivars Anka, CRS-1, and Yvonne. The number of bacterial isolates was similarly distributed among the cultivars, with the majority recovered from petiole tissue. Most fungal strains originated from leaf tissue of cultivar Anka. Molecular and phylogenetic analyses grouped the endophytes into 18 bacterial and 13 fungal taxa, respectively. The most abundant bacterial genera were Pseudomonas, Pantoea, and Bacillus, and the fungal genera were Aureobasidium, Alternaria, and Cochliobolus. The presence of siderophores, cellulase production, and phosphorus solubilization were the main biochemical traits. In proof-of-concept experiments, re-inoculation of tomato roots with some endophytes confirmed their migration to aerial tissues of the plant. Taken together, this study demonstrates that industrial hemp harbours a diversity of microbial endophytes, some of which could be used in growth promotion and (or) in biological control designed experiments.
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Affiliation(s)
- Maryanne Scott
- Plant Science Department, MacDonald Campus of McGill University, 21 111 Lakeshore, Ste. Anne-de-Bellevue, QC H9X 3V9, Canada.,Plant Science Department, MacDonald Campus of McGill University, 21 111 Lakeshore, Ste. Anne-de-Bellevue, QC H9X 3V9, Canada
| | - Mamta Rani
- Plant Science Department, MacDonald Campus of McGill University, 21 111 Lakeshore, Ste. Anne-de-Bellevue, QC H9X 3V9, Canada.,Plant Science Department, MacDonald Campus of McGill University, 21 111 Lakeshore, Ste. Anne-de-Bellevue, QC H9X 3V9, Canada
| | - Jamil Samsatly
- Plant Science Department, MacDonald Campus of McGill University, 21 111 Lakeshore, Ste. Anne-de-Bellevue, QC H9X 3V9, Canada.,Plant Science Department, MacDonald Campus of McGill University, 21 111 Lakeshore, Ste. Anne-de-Bellevue, QC H9X 3V9, Canada
| | - Jean-Benoit Charron
- Plant Science Department, MacDonald Campus of McGill University, 21 111 Lakeshore, Ste. Anne-de-Bellevue, QC H9X 3V9, Canada.,Plant Science Department, MacDonald Campus of McGill University, 21 111 Lakeshore, Ste. Anne-de-Bellevue, QC H9X 3V9, Canada
| | - Suha Jabaji
- Plant Science Department, MacDonald Campus of McGill University, 21 111 Lakeshore, Ste. Anne-de-Bellevue, QC H9X 3V9, Canada.,Plant Science Department, MacDonald Campus of McGill University, 21 111 Lakeshore, Ste. Anne-de-Bellevue, QC H9X 3V9, Canada
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30
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Sar A, Pal S, Dam B. Isolation of high molecular weight and humic acid-free metagenomic DNA from lignocellulose-rich samples compatible for direct fosmid cloning. Appl Microbiol Biotechnol 2018; 102:6207-6219. [PMID: 29846778 DOI: 10.1007/s00253-018-9102-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 05/06/2018] [Accepted: 05/08/2018] [Indexed: 11/28/2022]
Abstract
Activity-based screening of metagenomic DNA libraries is a promising approach to fish out genes encoding novel bioactive compounds/enzymes of industrial importance. The starting point of such functional screening in fosmid vectors is isolation of high molecular weight (HMW) DNA of sufficient purity from diverse environments. Metagenomic DNA isolation protocols mostly employ mechanical cell lysis that yields fragmented DNA. Those established for HMW DNA using enzymatic lysis have not considered samples with high lignocellulose or humic acid content. Enzymes from such environments are in great demand for bioenergy, paper, and related industries. Thus, an improved method was standardized that has three key features, i.e., use of harvested microbial biomass instead of raw samples, removal of humic substances prior to cell lysis by aluminum sulfate flocculation, and enzymatic/chemical lysis of cells with a lysozyme, mutanolysin, proteinase K, and SDS cocktail followed by phenol-chloroform extraction and precipitation of DNA by polyethylene glycol and NaCl. HMW DNA (~ 40 kb) was efficiently isolated from garden and forest soils, rice straw compost, and degrading wood from a hypersaline lake. The humic acid removal efficiency across samples was 96-98%. The isolated DNA was of high quality/purity and could be successfully used in downstream applications like PCR, ligation, and fosmid cloning. In fact, the DNA was directly used without any size selection, for fosmid library preparation with 70-90% efficiency as compared to the control insert. Thus, the method could suitably be used for HMW DNA isolation for the functional screening of enzymes from diverse humic acid-/lignocellulose-rich environments.
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Affiliation(s)
- Abhijit Sar
- Microbiology Laboratory, Department of Botany (DST-FIST & UGC-DRS Funded), Institute of Science, Visva-Bharati (A Central University), Santiniketan, West Bengal, 731235, India
| | - Srikanta Pal
- Microbiology Laboratory, Department of Botany (DST-FIST & UGC-DRS Funded), Institute of Science, Visva-Bharati (A Central University), Santiniketan, West Bengal, 731235, India
| | - Bomba Dam
- Microbiology Laboratory, Department of Botany (DST-FIST & UGC-DRS Funded), Institute of Science, Visva-Bharati (A Central University), Santiniketan, West Bengal, 731235, India.
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31
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De León-Lorenzana AS, Delgado-Balbuena L, Domínguez-Mendoza CA, Navarro-Noya YE, Luna-Guido M, Dendooven L. Soil Salinity Controls Relative Abundance of Specific Bacterial Groups Involved in the Decomposition of Maize Plant Residues. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00051] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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32
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Nnadozie CF, Lin J, Govinden R. Optimisation of protocol for effective detachment and selective recovery of the representative bacteria for extraction of metagenomic DNA from Eucalyptus spp. woodchips. J Microbiol Methods 2018; 148:155-160. [PMID: 29673787 DOI: 10.1016/j.mimet.2018.04.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 04/13/2018] [Accepted: 04/13/2018] [Indexed: 10/17/2022]
Abstract
For some environments such as planktonic/aqueous environments, the separation of bacteria cells from eukaryotic cells prior to DNA extraction using filtration is relatively straightforward. However, for woodchips, the bacteria are attached/embedded within the wood matrix, which prevents easy removal of bacterial cells. In this study, a method for the selective extraction of DNA from bacteria inhabiting Eucalyptus spp. woodchips has been developed. The objective was to compare milled and unmilled woodchips processed via three detachment methods, viz., sonication, vortexing and shaking followed by filtration using Teflon filters according to three relevant criteria: DNA yield, DNA purity and quality of DNA. Highest DNA yield was obtained by milling and vortexing for 10 min (77.50 ± 5.17 ng/μl), followed by milling and vortexing for 2 min (61.00 ± 6.56 ng/μl), unmilled and vortexing for 10 min (38.67 ± 5.17 ng/μl) and milled and shaking for 2 h (31.62 ± 5.17 ng/μl). The lowest DNA yield was obtained by using unmilled woodchips and 5 min of sonication treatment (7.00 ± 1.22 ng/μl). There was no significant difference in DNA purity for milled or unmilled woodchips processed via the three detachment methods. Duration of cell detachment treatment did not significantly influence DNA yield and purity. Following optimisation experiments, it was possible to extract bacterial DNA using milled woodchips and 10 minute vortexing devoid of DNA from the host background and other associated eukaryotes and of sufficient quality and quantity for metagenomic analysis.
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Affiliation(s)
- Chika F Nnadozie
- Biotechnology Cluster/Microbiology Discipline, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Private Bag X54001, Durban 4000, South Africa.
| | - Johnson Lin
- Biotechnology Cluster/Microbiology Discipline, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Private Bag X54001, Durban 4000, South Africa
| | - Roshini Govinden
- Biotechnology Cluster/Microbiology Discipline, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Private Bag X54001, Durban 4000, South Africa
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33
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Han Z, Sun J, Lv A, Wang A. Biases from different DNA extraction methods in intestine microbiome research based on 16S rDNA sequencing: a case in the koi carp, Cyprinus carpio var. Koi. Microbiologyopen 2018; 8:e00626. [PMID: 29667371 PMCID: PMC6341036 DOI: 10.1002/mbo3.626] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 12/31/2017] [Accepted: 01/29/2018] [Indexed: 11/26/2022] Open
Abstract
This study examined the technical bias associated with different DNA extraction methods used in microbiome research. Three methods were used to extract genomic DNA from the same intestinal microbiota sample that was taken from the koi carp Cyprinus carpio var. koi, after which their microbial diversity and community structure were investigated on the basis of a 16S rDNA high‐throughput sequencing analysis. Biased results were observed in relation to the number of reads, alpha diversity indexes and taxonomic composition among the three DNA extraction protocols. A total of 1,381 OTUs from the intestinal bacteria were obtained, with 852, 759, and 698 OTUs acquired, using the Lysozyme and Ultrasonic Lysis method, Zirmil‐beating Cell Disruption method, and a QIAamp Fast DNA Stool Mini Kit, respectively. Additionally, 336 OTUs were commonly acquired, using the three methods. The results showed that the alpha diversity indexes (Rarefaction, Shannon, and Chao1) of the community that were determined using the Lysozyme and Ultrasonic Lysis method were higher than those obtained with the Zirmil‐beating Cell Disruption method, while the Zirmil method results were higher than those measured, using the QIAamp Fast DNA Stool Mini Kit. Moreover, all the major phyla (ratio>1%) could be identified with all three DNA extraction methods, but the phyla present at a lower abundance (ratio <1%) could not. Similar findings were observed at the genus level. Taken together, these findings indicated that the bias observed in the results about the community structure occurred primarily in OTUs with a lower abundance. The results of this study demonstrate that possible bias exists in community analyses, and researchers should therefore be conservative when drawing conclusions about community structures based on the currently available DNA extraction methods.
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Affiliation(s)
- Zhuoran Han
- Key Laboratory of Ecology and Environment Science of Higher Education Institutes, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, College of Life Science, South China Normal University, Guangzhou, China.,Tianjin Key Lab of Aqua-ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin, China
| | - Jingfeng Sun
- Tianjin Key Lab of Aqua-ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin, China
| | - Aijun Lv
- Tianjin Key Lab of Aqua-ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin, China
| | - Anli Wang
- Key Laboratory of Ecology and Environment Science of Higher Education Institutes, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, College of Life Science, South China Normal University, Guangzhou, China
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Han Z, Sun J, Lv A, Sung Y, Sun X, Shi H, Hu X, Wang A, Xing K. A modified method for genomic DNA extraction from the fish intestinal microflora. AMB Express 2018; 8:52. [PMID: 29610998 PMCID: PMC5880796 DOI: 10.1186/s13568-018-0578-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 03/25/2018] [Indexed: 01/23/2023] Open
Abstract
A modified genomic DNA extraction method named the combination of lysozyme and ultrasonic lysis (CLU) method was used to analyze the fish intestinal microflora. In this method, the physical disruption and chemical lysis steps were combined, and some parameters in the key steps were adjusted. In addition, the results obtained by this method were compared with the results obtained by the Zirmil-beating cell disruption method and the QIAamp Fast DNA Stool Mini Kit. The OD260/OD280 ratio and concentration of the DNA extracted using the CLU method were 2.02 and 282.8 µg/µL, respectively; when the incubation temperatures for lysozyme and RNase were adjusted to 37 °C, those values were 2.08 and 309.8 µg/µL, respectively. On the agarose gel, a major high-intensity, discrete band of more than 10 kb was found for the CLU method. However, the smearing intensity of degraded DNA was lower when the incubation temperatures were 60 °C for lysozyme and 30 °C for RNase than when incubation temperatures of 37 °C for lysozyme and 37 °C for RNase were used. The V3 variable region of the prokaryotic 16S rDNA was amplified, and an approximately 600-bp fragment was observed when the DNA extracted using the CLU method was used as a template. The CLU method is simple and cost effective, and it yields high-quality, unsheared, high-molecular-weight DNA, which is comparable to that obtained with a commercially available kit. The extracted DNA has potential for applications in critical molecular biology techniques.
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35
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Biases during DNA extraction affect bacterial and archaeal community profile of anaerobic digestion samples. 3 Biotech 2017; 7:375. [PMID: 29071172 DOI: 10.1007/s13205-017-1009-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Accepted: 10/09/2017] [Indexed: 01/01/2023] Open
Abstract
The anaerobic digestion (AD) of organic waste for biogas production has received much attention in recent years due to the increasing need for renewable energy and environmentally friendly waste management systems. Identification of the microbial community involved in AD aids in better understanding and optimising of the process. The choice of DNA extraction method is an integral step in any molecular biodiversity study. In the present study, potential biases introduced by DNA extraction methods were examined by comparing quality, quantity and representability of DNA extracted from AD samples using various extraction methods. In spite of the non-kit based method (cetyltrimethylammonium bromide) yielding the largest quantity of DNA (approximately 44 µg DNA per gram dry weight), the extracted DNA contained PCR inhibitors. Furthermore, the quantity of extracted DNA was not proportional to species diversity. Diversity, determined using denaturing gradient gel electrophoresis (DGGE), was strongly linked to the type of extraction method used. The spin-column filter-based kit that incorporated mechanical and chemical lysis (Macherey-Nagel kit) gave the best results in terms of bacterial and archaeal diversity (Shannon-Wiener indices: average 2.5 and 2.6, respectively). Furthermore, this kit was the most effective at lysing hard-to-lyse bacterial and archaeal cells. The choice of DNA extraction method significantly influences the reliability and comparability of results obtained during AD microbial ecology investigations. Moreover, the careful selection of the DNA extraction method is of particular importance when analysing AD samples since these samples are rich in PCR inhibitors and hard-to-lyse cells such as archaea and gram-positive bacteria.
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Kuhn R, Böllmann J, Krahl K, Bryant IM, Martienssen M. Comparison of ten different DNA extraction procedures with respect to their suitability for environmental samples. J Microbiol Methods 2017; 143:78-86. [PMID: 29056447 DOI: 10.1016/j.mimet.2017.10.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 10/18/2017] [Accepted: 10/18/2017] [Indexed: 11/15/2022]
Abstract
DNA extraction for molecular biological applications usually requires target optimized extraction procedures depending on the origin of the samples. For environmental samples, a range of different procedures has been developed. We compared the applicability and efficiency of ten selected DNA extraction methods published in recent literature using four different environmental samples namely: activated sludge from a domestic wastewater treatment plant, river sediment, anaerobic digestion sludge and nitrifying enrichment culture. We assessed the suitability of the extraction procedures based on both DNA yield and quality. DNA quantification was performed by both ultra violet (UV) spectrophotometry and fluorescence spectrophotometry after staining with PicoGreen. In our study, DNA yields based on UV measurement were overestimated in most cases while DNA yields from fluorescence measurements correlated well with the sample load on agarose gels of crude DNA. The quality of the DNA extracts was determined by gel electrophoresis of crude DNA and PCR products from 16S rDNA with the universal primer set 27f/1525r. It was observed that gel electrophoresis of crude DNA was not always suitable to evaluate DNA integrity and purity since interfering background substances (e.g. humic substances) were not visible. Therefore, we strongly recommend examining the DNA quality of both crude DNA and 16S rDNA PCR products by gel electrophoresis when a new extraction method is established. Summarizing, we found four out of ten extraction procedures being applicable to all tested samples without noticeable restrictions. The procedure G (according to the standard method 432_10401 of the Lower Saxony State Office for Consumer Protection and Food Safety) had the broadest application range over procedure J (published by Wilson, 2001). These were followed by procedures F (Singka et al., 2012) and A (Bourrain et al., 1999). All four extraction procedures delivered reliable and reproducible crude DNA and PCR products. From an economical point of view, all procedures tested during this study were cheaper compared to commercial DNA extraction kits.
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Affiliation(s)
- Ramona Kuhn
- Brandenburg University of Technology Cottbus-Senftenberg, Institute of Environmental Technology, 03046 Cottbus, Germany.
| | - Jörg Böllmann
- Brandenburg University of Technology Cottbus-Senftenberg, Institute of Environmental Technology, 03046 Cottbus, Germany
| | - Kathrin Krahl
- Brandenburg University of Technology Cottbus-Senftenberg, Institute of Environmental Technology, 03046 Cottbus, Germany
| | - Isaac Mbir Bryant
- Brandenburg University of Technology Cottbus-Senftenberg, Institute of Environmental Technology, 03046 Cottbus, Germany
| | - Marion Martienssen
- Brandenburg University of Technology Cottbus-Senftenberg, Institute of Environmental Technology, 03046 Cottbus, Germany
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Comparison of two bacterial DNA extraction methods from non-polluted and polluted soils. Folia Microbiol (Praha) 2017; 63:85-92. [PMID: 28667598 DOI: 10.1007/s12223-017-0530-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 05/10/2017] [Indexed: 10/19/2022]
Abstract
DNA extraction from soil samples is a critical step for molecular biology analyses. The present study compared the efficiency of two DNA isolation methods from non-polluted and polluted soils with or without the presence of a plant. Both applied methods used chemical and physical lyses, but method 1 had an additional physical disruption. The main difference between these two methods was the humic acid purification technique as it was carried out during cell lysis for method 1 and after cell lysis for method 2. Samples were assessed on the basis of their yield and DNA purity as well as their bacterial quantity and diversity. Based on our results, method 1 proved to be more effective at removing protein and RNA, whereas method 2 proved to be more effective at removing humic acids. Although no differences were obtained in terms of the DNA yield, both the bacterial quantity and community structure were affected by the method used. Method 1 allowed for the recovery of more information than method 2, and polluted soil was more sensitive to the DNA extraction procedure. We recommend carefully selecting the DNA extraction method, especially when soil is disturbed.
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Santos SS, Nunes I, Nielsen TK, Jacquiod S, Hansen LH, Winding A. Soil DNA Extraction Procedure Influences Protist 18S rRNA Gene Community Profiling Outcome. Protist 2017; 168:283-293. [DOI: 10.1016/j.protis.2017.03.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 01/27/2017] [Accepted: 03/05/2017] [Indexed: 12/20/2022]
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Corcoll N, Österlund T, Sinclair L, Eiler A, Kristiansson E, Backhaus T, Eriksson KM. Comparison of four DNA extraction methods for comprehensive assessment of 16S rRNA bacterial diversity in marine biofilms using high-throughput sequencing. FEMS Microbiol Lett 2017; 364:3898816. [DOI: 10.1093/femsle/fnx139] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 06/27/2017] [Indexed: 01/07/2023] Open
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Zhao N, Cai J, Zhang C, Guo Z, Lu W, Yang B, Tian FW, Liu XM, Zhang H, Chen W. Suitability of various DNA extraction methods for a traditional Chinese paocai system. Bioengineered 2017; 8:642-650. [PMID: 28409998 DOI: 10.1080/21655979.2017.1300736] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Traditional paocai brine (PB), which is continuously propagated by back-slopping and contains various species of lactic acid bacteria (LAB), is critical for the flavor of paocai. Culture-independent approaches are commonly used to investigate the microbial communities of fermented food. To evaluate the influence of different DNA (DNA) extraction methods on estimates of bacterial community profiles from 4 PBs, the lysis efficiency, DNA yield, purity and denaturing gradient gel electrophoresis (DGGE) profiles of V3 region of a 16S ribosomal ribonucleic acid gene were acquired. The cell lysis pattern of SDS + beads and Lysing matrix E+ beads (methods 3 and 4) showed higher cell lysis efficiency than SDS and SDS + Lysozyme (methods 1 and 2) in all PBs. SDS + beads obtained the largest DNA yield of the 4 methods. Moreover, methods 3 and 4 resulted in higher H' values and generated more global bacteria profiles than other methods. Overall, our results demonstrate that the properties of PB significantly affect the efficiency of DNA extraction methods. Methods 3 and 4 were both suitable for DNA extraction from PB. Method 3 is more economic, simple and rapid than method 4 for large-scale studies of the bacterial profiles of PB.
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Affiliation(s)
- Nan Zhao
- a State Key Laboratory of Food Science and Technology, School of Food Science and Technology , Jiangnan University , Wuxi , P.R. China
| | - Jialiang Cai
- a State Key Laboratory of Food Science and Technology, School of Food Science and Technology , Jiangnan University , Wuxi , P.R. China
| | - Chuchu Zhang
- a State Key Laboratory of Food Science and Technology, School of Food Science and Technology , Jiangnan University , Wuxi , P.R. China
| | - Zhuang Guo
- d Northwest Hubei Research Institute of Traditional Fermented Food, College of Chemical Engineering and Food Science, Hu Bei University of Arts and Science , Xiangyang , China
| | - Wenwei Lu
- a State Key Laboratory of Food Science and Technology, School of Food Science and Technology , Jiangnan University , Wuxi , P.R. China.,c International Joint Research Laboratory for Probiotics at Jiangnan University
| | - Bo Yang
- a State Key Laboratory of Food Science and Technology, School of Food Science and Technology , Jiangnan University , Wuxi , P.R. China.,c International Joint Research Laboratory for Probiotics at Jiangnan University
| | - Feng-Wei Tian
- a State Key Laboratory of Food Science and Technology, School of Food Science and Technology , Jiangnan University , Wuxi , P.R. China.,c International Joint Research Laboratory for Probiotics at Jiangnan University
| | - Xiao-Ming Liu
- a State Key Laboratory of Food Science and Technology, School of Food Science and Technology , Jiangnan University , Wuxi , P.R. China.,c International Joint Research Laboratory for Probiotics at Jiangnan University
| | - Hao Zhang
- a State Key Laboratory of Food Science and Technology, School of Food Science and Technology , Jiangnan University , Wuxi , P.R. China.,c International Joint Research Laboratory for Probiotics at Jiangnan University
| | - Wei Chen
- a State Key Laboratory of Food Science and Technology, School of Food Science and Technology , Jiangnan University , Wuxi , P.R. China.,b Beijing Innovation Centre of Food Nutrition and Human Health , Beijing Technology & Business University , Beijing , P.R. China.,c International Joint Research Laboratory for Probiotics at Jiangnan University
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Zielińska S, Radkowski P, Blendowska A, Ludwig-Gałęzowska A, Łoś JM, Łoś M. The choice of the DNA extraction method may influence the outcome of the soil microbial community structure analysis. Microbiologyopen 2017; 6. [PMID: 28217901 PMCID: PMC5552907 DOI: 10.1002/mbo3.453] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 12/13/2016] [Accepted: 12/21/2016] [Indexed: 02/01/2023] Open
Abstract
Metagenomics approaches and recent improvements in the next‐generation sequencing methods, have become a method of choice in establishing a microbial population structure. Many commercial soil DNA extraction kits are available and due to their efficiency they are replacing traditional extraction protocols. However, differences in the physicochemical properties of soil samples require optimization of DNA extraction techniques for each sample separately. The aim of this study was to compare the efficiency, quality, and diversity of genetic material extracted with the use of commonly used kits. The comparative analysis of microbial community composition, displayed differences in microbial community structure depending on which kit was used. Statistical analysis indicated significant differences in recovery of the genetic material for 24 out of 32 analyzed phyla, and the most pronounced differences were seen for Actinobacteria. Also, diversity indexes and reproducibility of DNA extraction with the use of a given kit, varied among the tested methods. As the extraction protocol may influence the apparent structure of a microbial population, at the beginning of each project many extraction kits should be tested in order to choose one that would yield the most representative results and present the closest view to the actual structure of microbial population.
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Affiliation(s)
- Sylwia Zielińska
- Department of Molecular Biology, University of Gdansk, Gdansk, Poland
| | - Piotr Radkowski
- Center for Medical Genomics - OMICRON, Faculty of Medicine, Jagiellonian University Medical College, Kraków, Poland
| | | | - Agnieszka Ludwig-Gałęzowska
- Center for Medical Genomics - OMICRON, Faculty of Medicine, Jagiellonian University Medical College, Kraków, Poland
| | - Joanna M Łoś
- Department of Molecular Biology, University of Gdansk, Gdansk, Poland
| | - Marcin Łoś
- Department of Molecular Biology, University of Gdansk, Gdansk, Poland
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Shelton AO, O'Donnell JL, Samhouri JF, Lowell N, Williams GD, Kelly RP. A framework for inferring biological communities from environmental DNA. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2016; 26:1645-1659. [PMID: 27755698 DOI: 10.1890/15-1733.1] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 01/17/2016] [Accepted: 01/28/2016] [Indexed: 06/06/2023]
Abstract
Environmental DNA (eDNA), genetic material recovered from an environmental medium such as soil, water, or feces, reflects the membership of the ecological community present in the sampled environment. As such, eDNA is a potentially rich source of data for basic ecology, conservation, and management, because it offers the prospect of quantitatively reconstructing whole ecological communities from easily obtained samples. However, like all sampling methods, eDNA sequencing is subject to methodological limitations that can generate biased descriptions of ecological communities. Here, we demonstrate parallels between eDNA sampling and traditional sampling techniques, and use these parallels to offer a statistical structure for framing the challenges faced by eDNA and for illuminating the gaps in our current knowledge. Although the current state of knowledge on some of these steps precludes a full estimate of biomass for each taxon in a sampled eDNA community, we provide a map that illustrates potential methods for bridging these gaps. Additionally, we use an original data set to estimate the relative abundances of taxon-specific template DNA prior to PCR, given the abundance of DNA sequences recovered post-PCR-and-sequencing, a critical step in the chain of eDNA inference. While we focus on the use of eDNA samples to determine the relative abundance of taxa within a community, our approach also applies to single-taxon applications (including applications using qPCR), studies of diversity, and studies focused on occurrence. By grounding inferences about eDNA community composition in a rigorous statistical framework, and by making these inferences explicit, we hope to improve the inferential potential for the emerging field of community-level eDNA analysis.
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Affiliation(s)
- Andrew Olaf Shelton
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, 98112, USA.
| | - James Lawrence O'Donnell
- School of Marine and Environmental Affairs, University of Washington, 3707 Brooklyn Avenue NE, Seattle, Washington, 98105, USA
| | - Jameal F Samhouri
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, 98112, USA
| | - Natalie Lowell
- School of Marine and Environmental Affairs, University of Washington, 3707 Brooklyn Avenue NE, Seattle, Washington, 98105, USA
| | - Gregory D Williams
- Pacific States Marine Fisheries Commission, Under Contract to Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, 98112, USA
| | - Ryan P Kelly
- School of Marine and Environmental Affairs, University of Washington, 3707 Brooklyn Avenue NE, Seattle, Washington, 98105, USA
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de Bruin OM, Birnboim HC. A method for assessing efficiency of bacterial cell disruption and DNA release. BMC Microbiol 2016; 16:197. [PMID: 27566276 PMCID: PMC5002184 DOI: 10.1186/s12866-016-0815-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Accepted: 08/19/2016] [Indexed: 11/13/2022] Open
Abstract
Background DNA-based testing is becoming the preferred method both for identifying microorganisms and for characterizing microbial communities. However, no single DNA extraction method exists that is suitable for all types of microorganisms because bacteria are variable in their susceptibility to lysis by available extraction procedures. To develop and test new DNA extraction procedures, it would be helpful to determine their efficiencies. While the amount of extracted DNA can readily be measured by different methods, calculation of true efficiency requires knowledge of the initial amount of DNA in the starting bacterial sample, which cannot be done with precision by any existing method. In the process of developing a new extraction procedure, we developed a method that can be used to determine the total amount of both DNA and RNA in bacteria. The amount of DNA can be calculated from the amount of purines released after mild acid and alkali treatment. The amount of RNA in the same extract can also be calculated from the amount of ribonucleoside monophosphates. The released purines and ribonucleoside monophosphates can be quantified by absorbance using HPLC, with reference to appropriate standards. Results The acid/HPLC method was used to measure the efficiency of commonly used bead-beating and chemical protocols for releasing DNA from a particularly hardy organism, Mycobacterium smegmatis as well as several other species (Bacillus subtilis vegetative cells and spores; Francisella philomiragia; Pseudomonas aeruginosa; Moraxella catarrhalis; Bacillus thuringiensis; Staphylococcus aureus). Surprisingly large differences in efficiency between methods were found. Conclusions The acid/HPLC method is a new tool to determine DNA extraction efficiencies and should aid in the development of improved protocols for releasing DNA from a broad range of microorganisms. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0815-3) contains supplementary material, which is available to authorized users.
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Comparison of Boiling and Robotics Automation Method in DNA Extraction for Metagenomic Sequencing of Human Oral Microbes. PLoS One 2016; 11:e0154389. [PMID: 27104353 PMCID: PMC4841512 DOI: 10.1371/journal.pone.0154389] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 04/12/2016] [Indexed: 12/17/2022] Open
Abstract
The rapid improvement of next-generation sequencing performance now enables us to analyze huge sample sets with more than ten thousand specimens. However, DNA extraction can still be a limiting step in such metagenomic approaches. In this study, we analyzed human oral microbes to compare the performance of three DNA extraction methods: PowerSoil (a method widely used in this field), QIAsymphony (a robotics method), and a simple boiling method. Dental plaque was initially collected from three volunteers in the pilot study and then expanded to 12 volunteers in the follow-up study. Bacterial flora was estimated by sequencing the V4 region of 16S rRNA following species-level profiling. Our results indicate that the efficiency of PowerSoil and QIAsymphony was comparable to the boiling method. Therefore, the boiling method may be a promising alternative because of its simplicity, cost effectiveness, and short handling time. Moreover, this method was reliable for estimating bacterial species and could be used in the future to examine the correlation between oral flora and health status. Despite this, differences in the efficiency of DNA extraction for various bacterial species were observed among the three methods. Based on these findings, there is no "gold standard" for DNA extraction. In future, we suggest that the DNA extraction method should be selected on a case-by-case basis considering the aims and specimens of the study.
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Estimates of Soil Bacterial Ribosome Content and Diversity Are Significantly Affected by the Nucleic Acid Extraction Method Employed. Appl Environ Microbiol 2016; 82:2595-2607. [PMID: 26896137 DOI: 10.1128/aem.00019-16] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 02/13/2016] [Indexed: 12/18/2022] Open
Abstract
Modern sequencing technologies allow high-resolution analyses of total and potentially active soil microbial communities based on their DNA and RNA, respectively. In the present study, quantitative PCR and 454 pyrosequencing were used to evaluate the effects of different extraction methods on the abundance and diversity of 16S rRNA genes and transcripts recovered from three different types of soils (leptosol, stagnosol, and gleysol). The quality and yield of nucleic acids varied considerably with respect to both the applied extraction method and the analyzed type of soil. The bacterial ribosome content (calculated as the ratio of 16S rRNA transcripts to 16S rRNA genes) can serve as an indicator of the potential activity of bacterial cells and differed by 2 orders of magnitude between nucleic acid extracts obtained by the various extraction methods. Depending on the extraction method, the relative abundances of dominant soil taxa, in particular Actino bacteria and Proteobacteria, varied by a factor of up to 10. Through this systematic approach, the present study allows guidelines to be deduced for the selection of the appropriate extraction protocol according to the specific soil properties, the nucleic acid of interest, and the target organisms.
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Barrett M, Khalil MI, Jahangir MMR, Lee C, Cardenas LM, Collins G, Richards KG, O'Flaherty V. Carbon amendment and soil depth affect the distribution and abundance of denitrifiers in agricultural soils. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:7899-910. [PMID: 26762934 DOI: 10.1007/s11356-015-6030-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 12/28/2015] [Indexed: 05/22/2023]
Abstract
The nitrite reductase (nirS and nirK) and nitrous oxide reductase-encoding (nosZ) genes of denitrifying populations present in an agricultural grassland soil were quantified using real-time polymerase chain reaction (PCR) assays. Samples from three separate pedological depths at the chosen site were investigated: horizon A (0-10 cm), horizon B (45-55 cm), and horizon C (120-130 cm). The effect of carbon addition (treatment 1, control; treatment 2, glucose-C; treatment 3, dissolved organic carbon (DOC)) on denitrifier gene abundance and N2O and N2 fluxes was determined. In general, denitrifier abundance correlated well with flux measurements; nirS was positively correlated with N2O, and nosZ was positively correlated with N2 (P < 0.03). Denitrifier gene copy concentrations per gram of soil (GCC) varied in response to carbon type amendment (P < 0.01). Denitrifier GCCs were high (ca. 10(7)) and the bac:nirK, bac:nirS, bac:nir (T) , and bac:nosZ ratios were low (ca. 10(-1)/10) in horizon A in all three respective treatments. Glucose-C amendment favored partial denitrification, resulting in higher nir abundance and higher N2O fluxes compared to the control. DOC amendment, by contrast, resulted in relatively higher nosZ abundance and N2 emissions, thus favoring complete denitrification. We also noted soil depth directly affected bacterial, archaeal, and denitrifier abundance, possibly due to changes in soil carbon availability with depth.
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Affiliation(s)
- M Barrett
- Microbial Ecology Laboratory, Microbiology, School of Natural Sciences & Ryan Institute, National University of Ireland Galway, University Road, Galway, Ireland
| | - M I Khalil
- Crops, Environment and Land-Use Department, Teagasc, Johnstown Castle, Co., Wexford, Ireland
| | - M M R Jahangir
- Crops, Environment and Land-Use Department, Teagasc, Johnstown Castle, Co., Wexford, Ireland
| | - C Lee
- School of Civil & Environmental Engineering Nanyang Technological University, Singapore, 639798, Singapore
| | - L M Cardenas
- Rothamsted Research, North Wyke, Okehampton, Devon, EX20 2SB, UK
| | - G Collins
- Microbial EcoEngineering Laboratory, Microbiology, School of Natural Sciences & Ryan Institute, National University of Ireland Galway, University Road, Galway, Ireland
- Environmental Engineering Laboratory, School of Engineering, University of Glasgow, Rankine Building, Oakfield Avenue, Glasgow, G12 8LT, UK
| | - K G Richards
- Crops, Environment and Land-Use Department, Teagasc, Johnstown Castle, Co., Wexford, Ireland
| | - V O'Flaherty
- Microbial Ecology Laboratory, Microbiology, School of Natural Sciences & Ryan Institute, National University of Ireland Galway, University Road, Galway, Ireland.
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He X, So MJ, de los Reyes FL. Shifts in microbial communities in bioaugmented grease interceptors removing fat, oil, and grease (FOG). Appl Microbiol Biotechnol 2016; 100:7025-35. [DOI: 10.1007/s00253-016-7398-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 02/10/2016] [Accepted: 02/12/2016] [Indexed: 11/24/2022]
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The Host as the Driver of the Microbiota in the Gut and External Environment of Drosophila melanogaster. Appl Environ Microbiol 2015; 81:6232-40. [PMID: 26150460 DOI: 10.1128/aem.01442-15] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 06/26/2015] [Indexed: 12/16/2022] Open
Abstract
Most associations between animals and their gut microbiota are dynamic, involving sustained transfer of food-associated microbial cells into the gut and shedding of microorganisms into the external environment with feces, but the interacting effects of host and microbial factors on the composition of the internal and external microbial communities are poorly understood. This study on laboratory cultures of the fruit fly Drosophila melanogaster reared in continuous contact with their food revealed time-dependent changes of the microbial communities in the food that were strongly influenced by the presence and abundance of Drosophila. When germfree Drosophila eggs were aseptically added to nonsterile food, the microbiota in the food and flies converged to a composition dramatically different from that in fly-free food, showing that Drosophila has microbiota-independent effects on the food microbiota. The microbiota in both the flies that developed from unmanipulated eggs (bearing microorganisms) and the associated food was dominated by the bacteria most abundant on the eggs, demonstrating effective vertical transmission via surface contamination of eggs. Food coinoculated with a four-species defined bacterial community of Acetobacter and Lactobacillus species revealed the progressive elimination of Lactobacillus from the food bearing few or no Drosophila, indicating the presence of antagonistic interactions between Acetobacter and Lactobacillus. Drosophila at high densities ameliorated the Acetobacter/Lactobacillus antagonism, enabling Lactobacillus to persist. This study with Drosophila demonstrates how animals can have major, coordinated effects on the composition of microbial communities in the gut and immediate environment.
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Song Z, Schlatter D, Kennedy P, Kinkel LL, Kistler HC, Nguyen N, Bates ST. Effort versus Reward: Preparing Samples for Fungal Community Characterization in High-Throughput Sequencing Surveys of Soils. PLoS One 2015; 10:e0127234. [PMID: 25974078 PMCID: PMC4431839 DOI: 10.1371/journal.pone.0127234] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 04/12/2015] [Indexed: 11/29/2022] Open
Abstract
Next generation fungal amplicon sequencing is being used with increasing frequency to study fungal diversity in various ecosystems; however, the influence of sample preparation on the characterization of fungal community is poorly understood. We investigated the effects of four procedural modifications to library preparation for high-throughput sequencing (HTS). The following treatments were considered: 1) the amount of soil used in DNA extraction, 2) the inclusion of additional steps (freeze/thaw cycles, sonication, or hot water bath incubation) in the extraction procedure, 3) the amount of DNA template used in PCR, and 4) the effect of sample pooling, either physically or computationally. Soils from two different ecosystems in Minnesota, USA, one prairie and one forest site, were used to assess the generality of our results. The first three treatments did not significantly influence observed fungal OTU richness or community structure at either site. Physical pooling captured more OTU richness compared to individual samples, but total OTU richness at each site was highest when individual samples were computationally combined. We conclude that standard extraction kit protocols are well optimized for fungal HTS surveys, but because sample pooling can significantly influence OTU richness estimates, it is important to carefully consider the study aims when planning sampling procedures.
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Affiliation(s)
- Zewei Song
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN 55108, United States of America
- * E-mail:
| | - Dan Schlatter
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN 55108, United States of America
| | - Peter Kennedy
- Department of Plant Biology, University of Minnesota, Saint Paul, MN 55108, United States of America
| | - Linda L. Kinkel
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN 55108, United States of America
| | - H. Corby Kistler
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN 55108, United States of America
- USDA ARS Cereal Disease Laboratory, Saint Paul, MN 55108, United States of America
| | - Nhu Nguyen
- Department of Plant Biology, University of Minnesota, Saint Paul, MN 55108, United States of America
| | - Scott T. Bates
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN 55108, United States of America
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McCarthy A, Chiang E, Schmidt ML, Denef VJ. RNA preservation agents and nucleic acid extraction method bias perceived bacterial community composition. PLoS One 2015; 10:e0121659. [PMID: 25798612 PMCID: PMC4370824 DOI: 10.1371/journal.pone.0121659] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 02/11/2015] [Indexed: 01/08/2023] Open
Abstract
Bias is a pervasive problem when characterizing microbial communities. An important source is the difference in lysis efficiencies of different populations, which vary depending on the extraction protocol used. To avoid such biases impacting comparisons between gene and transcript abundances in the environment, the use of one protocol that simultaneously extracts both types of nucleic acids from microbial community samples has gained popularity. However, knowledge regarding tradeoffs to combined nucleic acid extraction protocols is limited, particularly regarding yield and biases in the observed community composition. Here, we evaluated a commercially available protocol for simultaneous extraction of DNA and RNA, which we adapted for freshwater microbial community samples that were collected on filters. DNA and RNA yields were comparable to other commonly used, but independent DNA and RNA extraction protocols. RNA protection agents benefited RNA quality, but decreased DNA yields significantly. Choice of extraction protocol influenced the perceived bacterial community composition, with strong method-dependent biases observed for specific phyla such as the Verrucomicrobia. The combined DNA/RNA extraction protocol detected significantly higher levels of Verrucomicrobia than the other protocols, and those higher numbers were confirmed by microscopic analysis. Use of RNA protection agents as well as independent sequencing runs caused a significant shift in community composition as well, albeit smaller than the shift caused by using different extraction protocols. Despite methodological biases, sample origin was the strongest determinant of community composition. However, when the abundance of specific phylogenetic groups is of interest, researchers need to be aware of the biases their methods introduce. This is particularly relevant if different methods are used for DNA and RNA extraction, in addition to using RNA protection agents only for RNA samples.
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Affiliation(s)
- Ann McCarthy
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States of America
| | - Edna Chiang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States of America
| | - Marian L. Schmidt
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States of America
| | - Vincent J. Denef
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States of America
- * E-mail:
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