1
|
Zhang X, Lou X, Zhang H, Ren W, Tang M. Effects of sodium sulfide application on the growth of Robinia pseudoacacia, heavy metal immobilization, and soil microbial activity in Pb-Zn polluted soil. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 197:110563. [PMID: 32278824 DOI: 10.1016/j.ecoenv.2020.110563] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/04/2020] [Accepted: 03/30/2020] [Indexed: 05/22/2023]
Abstract
Sodium sulfide (Na2S) is usually used as an amendment in industrial sewage treatment. To evaluate the effects of Na2S on the growth of Robinia pseudoacacia (black locust), heavy metal immobilization, and soil microbial activity, the R. pseudoacacia biomass and nutrient content and the soil heavy metal bioavailability, enzyme activity, and arbuscular mycorrhizal (AM) fungal community were measured by a single-factor pot experiment. The Pb-Zn-contaminated soil was collected from a Pb-Zn mine that had been remediated by R. pseudoacacia for five years. Three pollution levels (unpolluted, mildly polluted, and severely polluted) were evaluated by the pollution load index. Na2S application increased the shoot biomass under severe and mild contamination. In soil, Na2S application decreased the bioavailable Pb and Zn contents under severe and mild contamination, which resulted in a decrease in the Pb and Zn content in R. pseudoacacia. However, Na2S application did not affect the total Pb content per plant and enhanced the total Zn content per plant because of the higher biomass of the plants under Na2S application. Increased phosphatase activity and increased available phosphorous content may promote the uptake of phosphorus in R. pseudoacacia. Moreover, Na2S application is beneficial to the diversity of AM fungi under mild and severe pollution. Overall, Na2S application has great potential for enhancing soil heavy metal immobilization, enhancing soil microbial activity, and improving the growth of R. pseudoacacia in polluted soils. Therefore, Na2S is suitable for use in Pb-Zn remediation to ameliorate environmental heavy metal pollution.
Collapse
Affiliation(s)
- Xiangyu Zhang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Forestry, Northwest A&F University, Yangling, 712100, PR China
| | - Xiao Lou
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Forestry, Northwest A&F University, Yangling, 712100, PR China
| | - Haoqiang Zhang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Forestry, Northwest A&F University, Yangling, 712100, PR China.
| | - Wei Ren
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Forestry, Northwest A&F University, Yangling, 712100, PR China
| | - Ming Tang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Forestry, Northwest A&F University, Yangling, 712100, PR China; State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, PR China.
| |
Collapse
|
2
|
Puentes LA, Ramos YL, Inojosa YA, Rivera CE, De Sisto A. Isolation of PCR-quality Genomic DNA from Soils Impacted with Extra Heavy Crude Oil. Bio Protoc 2019; 9:e3265. [PMID: 33654785 DOI: 10.21769/bioprotoc.3265] [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: 04/02/2019] [Revised: 05/16/2019] [Accepted: 03/02/2019] [Indexed: 11/02/2022] Open
Abstract
For the study of microbial communities in samples of soils impacted with extra heavy crude oil, it is necessary to perform molecular analyses. Due to the difficulty of oil matrix handling, there are very few protocols reported in writing. Also, one can only observe a very low concentration of DNA. That's why it is required to have an effective protocol to conduct studies in this type of matrix. This protocol includes steps of cell lysis by saline buffer with ionic/non-ionic detergents, and enzymatic digestion with lysozyme and proteases, complemented with organic extraction and alcohol precipitation. Additionally, it requires purification to eliminate the inhibitory substances of the extract that cause PCR inhibition. The method of DNA extraction proposed in this study is easy to handle and low cost. It allows the extraction of DNA from different bacteria and fungi, associated with soil contaminated with extra heavy crude.
Collapse
Affiliation(s)
- Laynet A Puentes
- Department of Energy and the Environment, Institute for Advanced Studies Foundation, IDEA, Caracas, Venezuela
| | - Yusibeska L Ramos
- Department of Energy and the Environment, Institute for Advanced Studies Foundation, IDEA, Caracas, Venezuela
| | - Ysvic A Inojosa
- Department of Energy and the Environment, Institute for Advanced Studies Foundation, IDEA, Caracas, Venezuela
| | - César E Rivera
- Department of Energy and the Environment, Institute for Advanced Studies Foundation, IDEA, Caracas, Venezuela
| | - Angela De Sisto
- Department of Energy and the Environment, Institute for Advanced Studies Foundation, IDEA, Caracas, Venezuela
| |
Collapse
|
3
|
Jiang B, Sun J, Lv A, Hu X, Shi H, Sung Y, Wang Q, Wang Y. Impact of DNA extraction methods on the observed microbial communities from the intestinal flora of the penaeid shrimp Litopenaeus vannamei. FEMS Microbiol Lett 2019; 366:5487890. [PMID: 31074797 DOI: 10.1093/femsle/fnz099] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 05/09/2019] [Indexed: 12/25/2022] Open
Abstract
Two DNA extraction methods, the Zirmil-beating cell disruption method (ZBC) and the QIAamp fast DNA stool mini kit (QIA), were used to extract DNA from the intestinal flora of the penaeid shrimp Litopenaeus vannamei, and their microbial communities were analyzed using 16S rDNA high-throughput sequencing. Results were obtained in terms of the number of reads, alpha diversity indexes, beta diversity indexes and taxonomic composition. The alpha diversity indexes of the community, according to the ZBC method, were higher than those according to the QIA method. Furthermore, results from the three samples using the ZBC method were less consistent than those where the QIA method was used. Further, using the latter method led to substantive clustering. It is suggested that the QIA method is more stable and repeatable than the ZBC method. Although the two extraction methods shared the major abundant microflora based on 16S rDNA high-throughput sequencing, bias associated with diversity analysis indexes and certain species was observed.
Collapse
Affiliation(s)
- Boyun Jiang
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin 300384, China
| | - Jingfeng Sun
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin 300384, China
| | - Aijun Lv
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin 300384, China
| | - Xiucai Hu
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin 300384, China
| | - Hongyue Shi
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin 300384, China
| | - YeongYik Sung
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin 300384, China.,Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Terengganu 21030, Malaysia
| | - Qingkui Wang
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin 300384, China
| | - Yang Wang
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin 300384, China
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Hassan M, Essam T, Megahed S. Illumina sequencing and assessment of new cost-efficient protocol for metagenomic-DNA extraction from environmental water samples. Braz J Microbiol 2018; 49 Suppl 1:1-8. [PMID: 29631893 PMCID: PMC6328898 DOI: 10.1016/j.bjm.2018.03.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2017] [Accepted: 03/14/2018] [Indexed: 10/24/2022] Open
Abstract
In this study, the development and assessment of a modified, efficient, and cost-efficient protocol for mDNA (metagenomic DNA) extraction from contaminated water samples was attempted. The efficiency of the developed protocol was investigated in comparison to a well-established commercial kit (Epicentre, Metagenomic DNA Isolation Kit for Water). The comparison was in terms of degree of shearing, yield, purity, duration, suitability for polymerase chain reaction and next-generation sequencing in addition to the quality of next-generation sequencing data. The DNA yield obtained from the developed protocol was 2.6 folds higher than that of the commercial kit. No significant difference in the alpha (Observed species, Chao1, Simpson and PD whole tree) and beta diversity was found between the DNA samples extracted by the commercial kit and the developed protocol. The number of high-quality sequences of the samples extracted by the developed method was 20% higher than those obtained by the samples processed by the kit. The developed economic protocol successfully yielded high-quality pure mDNA compatible with complex molecular applications. Thus we propose the developed protocol as a gold standard for future metagenomic studies investigating a large number of samples.
Collapse
Affiliation(s)
- Mariam Hassan
- Cairo University, Faculty of Pharmacy, Department of Microbiology and Immunology, Cairo, Egypt.
| | - Tamer Essam
- Cairo University, Faculty of Pharmacy, Department of Microbiology and Immunology, Cairo, Egypt
| | - Salwa Megahed
- Cairo University, Faculty of Pharmacy, Department of Microbiology and Immunology, Cairo, Egypt; October University for Modern Sciences and Arts (MSA), Faculty of Pharmacy, Department of Microbiology and Immunology, Cairo, Egypt
| |
Collapse
|
6
|
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.
Collapse
|
7
|
Gorny AM, Hay FS, Wang X, Pethybridge SJ. Isolation of nematode DNA from 100 g of soil using Fe3O4 super paramagnetic nanoparticles. NEMATOLOGY 2018. [DOI: 10.1163/15685411-00003140] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
An economical method for extracting nematode DNA from 100 g of soil was developed to facilitate nematode detection and quantification, and tested using the Northern root-knot nematode,Meloidogyne hapla. The method utilised enzymatic laundry detergent lysis, Fe3O4super paramagnetic iron oxide nanoparticle (SPION) capture, and polyvinylpolypyrrolidone (PVPP) purification. Resultant DNA from this SPION capture method was approximately 100-fold less but of similar quality to DNA obtained from a standard phenol procedure and a commercial DNA extraction kit. An addition of 10 mg of nanoparticles to the extraction lysate was identified to maximise DNA yield while minimising co-capture of contaminants. The detection limit of the SPION capture method was approximately 100 nematodes (100 g soil)−1. The SPION capture method extracted nematode DNA from mineral soils but requires further optimisation for extraction from high organic matter (i.e., ‘muck’) soils. The benefits of this method compared to alternative techniques are discussed.
Collapse
Affiliation(s)
- Adrienne M. Gorny
- Plant Pathology & Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA
| | - Frank S. Hay
- Plant Pathology & Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA
| | - Xiaohong Wang
- Plant Pathology & Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA
- United States Department of Agriculture – Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
| | - Sarah J. Pethybridge
- Plant Pathology & Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA
| |
Collapse
|
8
|
Kim J, Wang HY, Kim S, Park SD, Yu K, Kim HY, Uh Y, Lee H. Evaluation of the Punch-it™ NA-Sample kit for detecting microbial DNA in blood culture bottles using PCR-reverse blot hybridization assay. J Microbiol Methods 2016; 128:24-30. [DOI: 10.1016/j.mimet.2016.06.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 06/01/2016] [Accepted: 06/02/2016] [Indexed: 11/25/2022]
|