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Kim YS, Yun HS, Lee JH, Lee KL, Choi JS, Won DH, Kim YJ, Kim HS, Yoon HS. Comparison of Metabarcoding and Microscopy Methodologies to Analyze Diatom Communities in Five Estuaries Along the Southern Coast of the Korean Peninsula. MICROBIAL ECOLOGY 2024; 87:95. [PMID: 39017940 PMCID: PMC11255046 DOI: 10.1007/s00248-024-02396-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 06/01/2024] [Indexed: 07/18/2024]
Abstract
The study of microalgal communities is critical for understanding aquatic ecosystems. These communities primarily comprise diatoms (Heterokontophyta), with two methods commonly used to study them: Microscopy and metabarcoding. However, these two methods often deliver different results; thus, their suitability for analyzing diatom communities is frequently debated and evaluated. This study used these two methods to analyze the diatom communities in identical water samples and compare the results. The taxonomy of the species constituting the diatom communities was confirmed, and both methods showed that species belonging to the orders Bacillariales and Naviculales (class Bacillariophyceae) are the most diverse. In the lower taxonomic levels (family, genus, and species), microscopy tended to show a bias toward detecting diatom species (Nitzschia frustulum, Nitzschia inconspicua, Nitzschia intermedia, Navicula gregaria, Navicula perminuta, Navicula recens, Navicula sp.) belonging to the Bacillariaceae and Naviculaceae families. The results of the two methods differed in identifying diatom species in the communities and analyzing their structural characteristics. These results are consistent with the fact that diatoms belonging to the genera Nitzschia and Navicula are abundant in the communities; furthermore, only the Illumina MiSeq data showed the abundance of the Melosira and Entomoneis genera. The results obtained from microscopy were superior to those of Illumina MiSeq regarding species-level identification. Based on the results obtained via microscopy and Illumina MiSeq, it was revealed that neither method is perfect and that each has clear strengths and weaknesses. Therefore, to analyze diatom communities effectively and accurately, these two methods should be combined.
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Affiliation(s)
- Young-Saeng Kim
- Research Institute of Ulleung-do & Dok-do, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Hyun-Sik Yun
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Jae-Hak Lee
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Kyung-Lak Lee
- Water Environmental Engineering Research Division, National Institute of Environmental Research, Incheon, 22689, Republic of Korea
| | - Jae-Sin Choi
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Doo Hee Won
- Doohee Institute of Ecological Research, Korea Ecosystem Service Inc., Ansan, 15426, Republic of Korea
| | - Yong Jae Kim
- Department of Biomedical Science, Daejin University, Pocheon, 11159, Republic of Korea
| | - Han-Soon Kim
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea.
- Research Institute of Ulleung-do & Dok-do, Kyungpook National University, Daegu, 41566, Republic of Korea.
| | - Ho-Sung Yoon
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea.
- School of Life Sciences and Biotechnology, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu, 41566, Republic of Korea.
- Advanced Bio-Resource Research Center, Kyungpook National University, Daegu, 41566, Republic of Korea.
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Badu IK, Asante D, Agyemang ED, Kwaku Duah K, Adokoh CK, Girela-Lopez E. Diatoms in maggots; a potential tool for drowning diagnosis - A preliminary study. MEDICINE, SCIENCE, AND THE LAW 2024:258024241241374. [PMID: 38557251 DOI: 10.1177/00258024241241374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Advanced putrefaction causes extensive loss of soft tissue, rendering it difficult to use the diatom test as a reliable diagnostic tool for drowning investigations. A positive diatom test in carrion insect larvae may provide significant assistance in overcoming the challenge of decomposition. The studies determined the utility of diatom test in carrion larvae on severely decomposed bodies. A modified acid digestion method involving nitric acid, K2Cr2O7 and HCl, was used to digest the blowfly larvae feeding on piglet carrion previously drowned in freshwater and sea water, respectively. Extracted diatom frustules were analysed and characterised using light microscopy coupled to a digital camera. Diatoms recovered from maggots on sea-drowned piglets were similar to diatoms from sea water (drowning medium). Centric diatoms recovered in maggots were higher (200 ± 60 diatoms/ mL) than pennate diatoms (80 ± 20 diatoms/mL). Isolated diatoms common to both maggots and water samples included Coscinodiscus sp. and Navicular spp. Albeit, there were no diatoms recovered from maggots on freshwater-drowned piglets. The findings of this study suggest that the diatom test is still a reliable diagnostic tool to determine if drowning was involved in the death of a fully decomposed body. This is the first study that isolated diatoms from maggots feeding on drowned bodies. It serves as the basis for further research into the utility of maggots for drowning investigations.
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Affiliation(s)
- I K Badu
- Department of Forensic Sciences, University of Cape Coast, Cape Coast, Ghana
| | - D Asante
- Department of Forensic Sciences, University of Cape Coast, Cape Coast, Ghana
| | - E D Agyemang
- Department of Forensic Sciences, University of Cape Coast, Cape Coast, Ghana
| | - K Kwaku Duah
- Department of Forensic Sciences, University of Cape Coast, Cape Coast, Ghana
| | - C K Adokoh
- Department of Forensic Sciences, University of Cape Coast, Cape Coast, Ghana
| | - E Girela-Lopez
- Section of Legal and Forensic Medicine, Faculty of Medicine and Nursing, University of Córdoba, Córdoba, Spain
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Wu Y, Luo L, Li Y, Sun Y, Huang X, Zhou Y, Wang Y, Wang Y, Zeng D, Yun L. A comparative assessment of time-consuming and laborious diatom analysis:Brief experimentation with suggestion of automatic identification. Forensic Sci Int 2024; 355:111939. [PMID: 38246065 DOI: 10.1016/j.forsciint.2024.111939] [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: 04/20/2022] [Revised: 11/02/2023] [Accepted: 01/14/2024] [Indexed: 01/23/2024]
Abstract
Diatom testing is considered a useful method for providing supportive evidence for the diagnosis of drowning in forensic pathology. However, various factors remain controversial for recognizing diatoms, such as being time-consuming and laborious and influencing the consistency of the results. Given the absence of precise and well-defined studies on this subject, this study aimed to determine the relationship between the ability to identify diatoms and researchers with different technical backgrounds. A total of 55 samples from 18 cases, including water, lungs, liver, and kidneys, were treated using the microwave digestion-vacuum filtration-automated scanning electron microscopy (MD-VF-Auto SEM), which was used to compare diatom analyses among three groups of well-trained forensic pathologists (FPs), trained junior employees (JEs), and new trainees (TEs). In addition to achieving similar accuracy of positive findings from drowning cases, counting efficiency was evaluated based on taxonomy records and counting time after viewing more than 5500 diatom images. In contrast to the higher counting efficiency of the JE group than that of the TE group, we observed a statistically significant difference (p < 0.05) in the diatom classification between these two groups. Based on our experiments, an efficient analysis for automatically identifying and classifying diatoms is urgently required.
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Affiliation(s)
- Yuhang Wu
- Department of Forensic Pathology, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, People' s Republic of China
| | - Lisiteng Luo
- Department of Forensic Pathology, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, People' s Republic of China
| | - Yuyang Li
- Department of Forensic Pathology, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, People' s Republic of China
| | - Yuntao Sun
- Department of Forensic Pathology, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, People' s Republic of China
| | - Xinyu Huang
- Department of Forensic Pathology, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, People' s Republic of China
| | - Yuchi Zhou
- Criminal Investigation Department of Sichuan Provincial Public Security Bureau, NO.36, Wenmiaohoujie Street, Qingyang district, Chengdu 610015, People's Republic of China
| | - Yi Wang
- Criminal Investigation Department of Sichuan Provincial Public Security Bureau, NO.36, Wenmiaohoujie Street, Qingyang district, Chengdu 610015, People's Republic of China
| | - Yongqing Wang
- Criminal Science and Technology Division, Criminal Investigation Bureau, Chengdu Public Security Bureau, Chengdu, Sichuan 610031, People's Republic of China
| | - Debing Zeng
- Criminal Science and Technology Division, Criminal Investigation Bureau, Chengdu Public Security Bureau, Chengdu, Sichuan 610031, People's Republic of China
| | - Libing Yun
- Department of Forensic Pathology, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, People' s Republic of China.
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Kasprzyk I. Forensic botany: who?, how?, where?, when? Sci Justice 2023; 63:258-275. [PMID: 36870705 DOI: 10.1016/j.scijus.2023.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 01/09/2023] [Accepted: 01/15/2023] [Indexed: 01/19/2023]
Abstract
Plants are a good source of biological forensic evidence; this is due to their ubiquity, their ability to collect reference material, and their sensitivity to environmental changes. However, in many countries, botanical evidence is recognised as being scientifically. Botanical evidence is not mostly used for perpertration, instead it tends to serve as circumstantial evidence. Plant materials constitute the basis, among others, for linking a suspect or object to a crime scene or a victim, confirming or not confirming an alibi, determining the post-mortem interval, and determining the origin of food/object. Forensic botany entails field work, knowledge of plants, understanding ecosystem processes, and a basis understaning of geoscience. In this study, experiments with mammal cadavers were conducted to determine the occurence of an event. The simplest criterion characterising botanical evidence is its size. Therefore, macroremains include whole plants or their larger fragments (e.g. tree bark, leaves, seeds, prickles, and thorns), whereas microscopic evidence includes palynomorphs (spores and pollen grains), diatoms, and tissues. Botanical methods allow for an analysis to be repeated multiple times and the test material is easy to collect in the field. Forensic botany can be supplemented with molecular analyses, which, although specific and sensitive, still require validation.
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Affiliation(s)
- Idalia Kasprzyk
- Institute of Biology and Biotechnology, College of Natural Sciences, University of Rzeszów, Al. Rejtana 16c, 35-959 Rzeszów, Poland.
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Epiphytic Diatom-Based Biomonitoring in Mediterranean Ponds: Traditional Microscopy versus Metabarcoding Approaches. WATER 2021. [DOI: 10.3390/w13101351] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Benthic diatoms have traditionally been used as bioindicators of aquatic ecosystems. Because diatom-based monitoring of water quality is required by European legislation, molecular-based methods had emerged as useful alternatives to classical methods based on morphological identification using light microscopy. The aim of this study was to test the reliability of DNA metabarcoding combined with High-Throughput Sequencing (HTS) techniques in the bioassessment of the trophic status of 22 Mediterranean shallow ponds in NW Spain. For each pond, the Trophic Diatom Index (TDI) was calculated from inventories obtained by identification using light microscopy (LM) followed by high-throughput sequencing (HTS) at the molecular level. Ponds were subsequently classified into five water quality classes. The results showed a good correspondence between both methods, especially after applying a correction factor that depended on the biovolume of the cells. This correspondence led to the assignment to the same quality class in 59% of the ponds. The determination and quantification of valves or DNA sequences was one of the main pitfalls, which mainly included those related to the variability in the relative abundances of some species. Accordingly, ponds with similar relative abundances for the dominant species were assigned to the same quality class. Moreover, other difficulties leading the discrepancies were the misidentification of some species due to the presence of semi-cryptic taxa, the incompleteness of the reference database and the bioinformatic protocol. Thus, the validation of DNA-based methods for the identification of freshwater diatoms represents an important goal, as an alternative to using traditional methods in Mediterranean shallow ponds.
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Liu Y, Xu C, Dong W, Yang X, Zhou S. Determination of a criminal suspect using environmental plant DNA metabarcoding technology. Forensic Sci Int 2021; 324:110828. [PMID: 34000616 DOI: 10.1016/j.forsciint.2021.110828] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/20/2021] [Accepted: 05/05/2021] [Indexed: 11/18/2022]
Abstract
There are criminal cases that no frequently used evidence, for example, human DNAs from the criminal, is available. Such cases usually are unresolvable. With the advent of DNA metabarcoding, evidences are mined from environmental DNA and such cases become resolvable. This study reports how a criminal suspect was determined by environmental plant DNA metabarcoding technology. A girl was killed in a rural wet area in China without a witness or video record. Pants with dried mud was found from one of her classmate's house. The mud was removed from the pants and 11 more mud or soil samples surrounding murder scene were collected. DNA was extracted from the soil. Chloroplast rbcL gene were amplified and sequenced on a next generation sequencing platform. After bioinformatics analysis, ZOTU composition of 12 samples demonstrated that the mud on the suspect's pants was from the criminal scene. The suspect finally made a clean breast of his crime. This case implies that plant DNA in the environment soil is a new source of evidence in determination of suspects using DNA metabarcoding technology and has high potentials of extensive applications in criminal cases.
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Affiliation(s)
- Yanlei Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Wenpan Dong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Xueying Yang
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China.
| | - Shiliang Zhou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
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MicroRNAs: An Update of Applications in Forensic Science. Diagnostics (Basel) 2020; 11:diagnostics11010032. [PMID: 33375374 PMCID: PMC7823886 DOI: 10.3390/diagnostics11010032] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/17/2020] [Accepted: 12/23/2020] [Indexed: 12/25/2022] Open
Abstract
MicroRNAs (miRNAs) are a class of non-coding RNAs containing 18–24 nucleotides that are involved in the regulation of many biochemical mechanisms in the human body. The level of miRNAs in body fluids and tissues increases because of altered pathophysiological mechanisms, thus they are employed as biomarkers for various diseases and conditions. In recent years, miRNAs obtained a great interest in many fields of forensic medicine given their stability and specificity. Several specific miRNAs have been studied in body fluid identification, in wound vitality in time of death determination, in drowning, in the anti-doping field, and other forensic fields. However, the major problems are (1) lack of universal protocols for diagnostic expression testing and (2) low reproducibility of independent studies. This review is an update on the application of these molecular markers in forensic biology.
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