Determination of diversity of actinomycete in forest soil subject to different blood groups; Classical approaches  before metagenomic

DOĞAN, Mazlum; ARSLAN AKVERAN, Gönül; KARASARTOVA, Djursun; ÖZKAN, Ayşegül Taylan; GÖKDEMİR, Fatma Şeyma; ŞENGÖZ, Sabiha

doi:10.5505/TurkHijyen.2023.76753

Determination of diversity of actinomycete in forest soil subject to different blood groups; Classical approaches before metagenomic

Fatma Şeyma GÖKDEMİR, (Michigan State University, Plant, Soil And Microbial Science, East Lansing/Michigan, USA)

Mazlum DOĞAN, (Hitit Üniversitesi, Lisansüstü Programlar Enstitüsü, Adli Bilimler Anabilim Dalı, Çorum, Türkiye)

Gönül ARSLAN AKVERAN, (Hitit Üniversitesi, Alaca Avni Çelik Meslek Yüksekokulu, Gıda İşleme Bölümü, Çorum, Türkiye)

Sabiha ŞENGÖZ, (Hitit Üniversitesi, Sağlık Bilimleri Fakültesi, Beslenme ve Diyetetik Bölümü, Çorum, Türkiye)

Djursun KARASARTOVA, (Hitit Üniversitesi, Tıbbi Mikrobiyoloji Anabilim Dalı, Çorum, Türkiye)

Ayşegül TAYLAN ÖZKAN (TOBB Ekonomi ve Teknoloji Üniversitesi, Tıp Fakültesi, Tıbbi Mikrobiyoloji Anabilim Dalı, Ankara, Türkiye)

Türk Hijyen ve Deneysel Biyoloji Dergisi

3 2

Yıl: 2023 Cilt: 80 Sayı: 3 Sayfa Aralığı: 285 - 308 Metin Dili: İngilizce DOI: 10.5505/TurkHijyen.2023.76753 İndeks Tarihi: 28-09-2023

Determination of diversity of actinomycete in forest soil subject to different blood groups; Classical approaches before metagenomic

Öz:

Objective: Forensic microbiology is the developing field of forensic science. Forensic microbiologist can use trace evidence to match people to crime scenes, to investigate bioterrorism incidents, and to determine cause and time of death. In recent years, important studies on the environmental microbiota have been carried out. These studies can be associated with many legally valuable data as well as being related to the microbiota of environmental events. Actinobacteria are gram-positive micelle bacteria with enormous diversity, common in soil, and have high economic value. So far 47 families and 711 species of Actinobacteria were isolated and identified in variety of habitats. Increasing forensic studies in recent years show that microbial profiles can be used as evidence. Methods: In this study, actinobacteria were isolated from forest soil samples exposed to eight different blood groups for two weeks and control group. Genomic DNA isolation from colonies selected by considering comparative colony morphology, PCR amplification targetted 16S rRNA and sequence analysis were carried. Results: A total of five Actinobacteria type bacteria (three Micromonospora sp., one is Streptomyces sp., and one Actinomadura sp.) were obtained from the soil samples mixed with the B Rh (+) blood group in the 7th day. No Actinobacteria growth was observed neither in the control group nor in the soils to which other blood groups were added. According to the p-distance values of all isolates, they were determined as subspecies rather than a new species. Conclusion: This is a preliminary study to identify bacterial communities that may be present and differ in soil exposed to blood. The inability to isolate Actinobacteria from most of the soil samples may be due to the chemical or enzymatical properties of the bloods that can degrade the bacterial spores. In the further studies, different media and genomic techniques should be tried in different types of soils.

Anahtar Kelime: Actinomycete forensic microbiology soil microbiome

Farklı kan gruplarına bağlı orman topraklarında aktinomiset çeşitliliğinin belirlenmesi; Metagenomik öncesi klasik yaklaşımlar

Öz:

Amaç: Adli mikrobiyoloji, adli bilimin gelişen alanıdır. Adli mikrobiyolog, insanları suç mahalli ile eşleştirmek, biyoterörizm olaylarını araştırmak ve ölüm nedenini ve zamanını belirlemek için iz kanıtları kullanabilir. Son yıllarda çevresel mikrobiyota ile ilgili önemli çalışmalar yapılmaktadır. Bu çalışmalar, çevresel olayların mikrobiyotası ile ilgili olabileceği gibi, yasal olarak değerli birçok veri ile ilişkilendirilebilir. Aktinobakteriler, toprakta yaygın olarak bulunan ve ekonomik değeri yüksek, muazzam çeşitliliğe sahip gram pozitif miselli bakterilerdir. Şimdiye kadar çeşitli habitatlarda 47 familya ve 711 Actinobacteria türü izole edilmiş ve tanımlanmıştır. Son yıllarda artan adli tıp çalışmaları mikrobiyal profillerin kanıt olarak kullanılabileceğini göstermektedir. Yöntem: Bu çalışmada, sekiz farklı kan grubuna iki hafta süreyle maruz bırakılan orman toprağı örneklerinden ve kontrol grubundan Aktinobakteriler izole edilmiştir. Karşılaştırmalı koloni morfolojisi dikkate alınarak seçilen kolonilerden genomik DNA izolasyonu, 16S rRNA hedefli PCR amplifikasyonu ve dizi analizi gerçekleştirilmiştir. Bulgular: 7. günde B Rh (+) kan grubu ile karıştırılan toprak örneklerinden toplam beş Actinobacteria türü bakteri (üç Micromonospora sp., bir Streptomyces sp. ve bir Actinomadura sp.) elde edildi. Ne kontrol grubunda ne de diğer kan gruplarının eklendiği topraklarda Actinobacteria üremesi gözlenmedi. Tüm izolatların p-distance değerlerine göre yeni bir tür olmadığı ancak var olan türlere ait alt tür oldukları belirlenmiştir. Sonuç: Bu çalışma, kana maruz kalan toprakta bulunabilecek ve farklılık gösterebilecek bakteri topluluklarını belirlemeye yönelik bir ön çalışmadır. Aktinobakterilerin toprak örneklerinin çoğundan izole edilememesi, bakteri sporlarını bozabilen kanların kimyasal veya enzimatik özelliklerinden kaynaklanabilir. Bundan sonraki çalışmalarda, farklı toprak türlerinde farklı ortam ve genomik teknikler denenmelidir.

Anahtar Kelime: Actinomycete adli mikrobiyoloji toprak mikrobiyomu

Belge Türü: Makale Makale Türü: Araştırma Makalesi Erişim Türü: Erişime Açık

1. Desmond AU, Nicholas O, Emmanuel OO. Microbial forensics: Forensic relevance of the individual person’s microbial signature. Int J Life Sci Scienti Res, eISSN, 2018:2455(1716), 1716.
2. Oliveira M, Amorim A. Microbial forensics: New breakthroughs and future prospects. App Microbiol Biotech, 102(24), 2018:10377-91.
3. MacCallum WG, Hastings TW. A case of acute endocarditis caused by Micrococcus zymogenes (nov. spec.), with a description of the microorganism. J Exp Med, 1899:4(5-6), 521-34.
4. Smith TF, Waterman MS. The continuing case of the Florida dentist. Science, 1992:256(5060), 1155-7.
5. Morgan RM, Levin EA. A crisis for the future of forensic science: lessons from the UK of the importance of epistemology for funding research and development. Forensic Sci Int Synerg, 2019:1, 243-52.
6. Richardson M, Gottel N, Gilbert JA, Lax S. Microbial similarity between students in a common dormitory environment reveals the forensic potential of individual microbial signatures. MBio, 2019:10(4), e01054-19.
7. Phan K, Barash M, Spindler X, Gunn P, Roux C. Retrieving forensic information about the donor through bacterial profiling. Int J Leg Med, 2020:134(1), 21-9.
8. Grantham NS, Reich BJ, Pacifici K, Laber EB, Menninger HL, Henley JB, et al. Fungi identify the geographic origin of dust samples. PloS one, 2015:10(4), e0122605.
9. Demanèche S, Schauser L, Dawson L, Franqueville L, Simonet P. Microbial soil community analyses for forensic science: application to a blind test. For Sci Int, 2017:270, 153-8.
10. Jose PA, Maharshi A, Jha B. Actinobacteria in natural products research: Progress and prospects. Microbiol Res, 2021, 126708.
11. Weyland Horst. Characteristics of actinomycetes isolated from marine sediments. Zentralblatt fur Bakteriologie, Mikrobiologie und Hygiene. I. Abt.: Supplemente. 1981.
12. William S, Feil H, Copeland A. Bacterial genomic DNA isolation using CTAB. Sigma, 2012, 50(6876).
13. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Sys Evol Mic, 2012, 62(Pt_3), 716-21.
14. Lane DJ. 16S/23S rRNA sequencing. In: Nucleic Acid Techniques in Bacterial Systematics, Edited by E. Stackebrandt and M. Goodfellow. John Wiley and Sons, Chichester. 1991. pp. 115-48.
15. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol, 2018:35, 1547-9.
16. Jukes TH, Cantor CR. Evolution of Protein Molecules. In Mammalian Protein Metabolism, pp. 21-132. Ed: HN Munro. Academic Press, New York. 1969. pp. 21-132.
17. Saitou N, Nei M. The neighbour-joining method: a new method for reconstructing phylogenetic trees, Mol Biol Evol, 1987:4, 406–25.
18. Van Belkum ALEX. DNA fingerprinting of medically important microorganisms by use of PCR. Clin Microbiol Rev, 1994:7(2), 174-84.
19. Bruce RG, Dettmann ME. Palynological analyses of Australian surface soils and their potential in forensic science. For Sci Int, 1996:81(2-3), 77-94.
20. Bryant VM, Mildenhall DC. (1998). Forensic palynology: A New Way to Catch Crooks. Contributions Series-American Association of Stratigraphic Palynologists, 1998:33, 145-55.
21. Budowle B, Schutzer SE, Einseln A, Kelley LC, Walsh AC, Smith JA, et al. Building microbial forensics as a response to bioterrorism. Science, 2003:301(5641):1852-53.
22. Budowle B, Wilson MR, Burans JP, Breeze RG, Chakraborty R. Microbial forensics. In: Microbial forensics. Academic Press. 2005;pp.1-25.
23. Carter DO, Metcalf JL, Bibat A, Knight R. Seasonal variation of postmortem microbial communities. Forensic Sci Med Pathol, 2015:11(2), 202-7.
24. Peters RP, van Agtmael MA, Danner SA, Savelkoul PH, Vandenbroucke-Grauls CM. New developments in the diagnosis of bloodstream infections. Lancet Infect Dis, 2004:4(12), 751-60.
25. Santos A, van Aerle R, Barrientos L, Martinez-Urtaza J. Computational methods for 16S metabarcoding studies using Nanopore sequencing data. Comp Struct Biotech J, 2020:18, 296-305.
26. Wróblewski F, Ladue JS. Lactic dehydrogenase activity in blood. Proc Soc Exp Biol Med, 1955:90(1), 210-3.
27. Finley SJ, Pechal JL, Benbow ME, Robertson BK, Javan GT. Microbial signatures of cadaver gravesoil during decomposition. Microbial ecology, 2016, 71(3), 524-9.
28. Delgado-Baquerizo M, Eldridge DJ, Hamonts K, Reich PB, Singh BK. Experimentally testing the species-habitat size relationship on soil bacteria: A proof of concept. Soil Bio Biochem, 2018:123, 200-6.
29. Trujillo ME, Riesco R, Benito P, Carro L. Endophytic actinobacteria and the interaction of Micromonospora and nitrogen fixing plants. Front Microbiol, 2015:6, 1341.
30. Kaltenpoth M. Actinobacteria as mutualists: general healthcare for insects? Trend Microbiol, 2009:17(12), 529-35.
31. Colquhoun JA, Heald SC, Li L, Tamaoka J, Kato C, Horikoshi K, et al. Taxonomy and biotransformation activities of some deep-sea actinomycetes. Extremophiles, 1998:2(3), 269-77.
32. Bull AT, Goodfellow M. Dark, rare and inspirational microbial matter in the extremobiosphere: 16 000 m of bioprospecting campaigns. Microbiology, 2019:165(12), 1252-64.
33. Sivakala KK, Gutiérrez-García K, Arul Jose P, Thinesh T, Anandham R, Barona-Gómez F, et al. Desert environments facilitate unique evolution of biosynthetic potential in Streptomyces. Molecules, 2021:26(3), 588.
34. Jose PA, Maharshi A, Jha B. Actinobacteria in natural products research: Progress and prospects. Microbiol Res, 2021:126708.
35. Sleator RD, Shortall C, Hill C. Metagenomics. Lett App Microbiol, 2008:47(5), 361-6.
36. Berglund EC, Kiialainen A, Syvänen AC. Next-generation sequencing technologies and applications for human genetic history and forensics. Invest Gen, 2011:2(1), 1-15.
37. Kuiper I. Microbial forensics: next generation sequencing as catalyst: The use of new sequencing technologies to analyze whole microbial communities could become a powerful tool for forensic and criminal investigations. EMBO reports, 2016:17(8), 1085-7.
38. Capasso L, Vento G, Loddo C, Tirone C, Iavarone F, Raimondi F, et al. Oxidative stress and bronchopulmonary dysplasia: evidences from microbiomics, metabolomics, and proteomics. Front Ped, 2019:7, 30.
39. Gokdemir FS, Aras S. Chemotaxonomy in bacterial systematics. Communications Faculty of Sciences University of Ankara Series C Biology, 2019:28(1), 78-90.
40. Vandamme P, Pot B, Gillis M, De Vos P, Kersters K, Swings J. Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol Rev, 1996:60(2), 407-38.
41. Colwell RR. Polyphasic taxonomy of the genus Vibrio: numerical taxonomy of Vibrio cholerae, Vibrio parahaemolyticus, and related Vibrio species. J Bacteriol, 1970:104(1), 410-33.
42. Rosselló-Móra R. DNA-DNA Reassociation Methods Applied to Microbial Taxonomy and Their Critical Evaluation. In: Molecular Identification, Systematics, and Population Structure of Prokaryotes. 2006:pp. 23-50. Springer, Berlin, Heidelberg.
43. Broekhuijsen M, Larsson P, Johansson A, Byström M, Eriksson U, Larsson E, et al. Genome-wide DNA microarray analysis of Francisella tularensis strains demonstrates extensive genetic conservation within the species but identifies regions that are unique to the highly virulent F. tularensis subsp. tularensis. J Clin Microbiol, 2003:41(7), 2924-31.
44. Stackebrandt E, Goebel BM. Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Evol Microbiol, 1994:44(4), 846-9.
45. Rossi-Tamisier M, Benamar S, Raoult D, Fournier, PE. Cautionary tale of using 16S rRNA gene sequence similarity values in identification of human-associated bacterial species. Int J Syst Evol Microbiol, 2015:65(Pt_6), 1929-34.

APA	GÖKDEMİR F, DOĞAN M, ARSLAN AKVERAN G, ŞENGÖZ S, KARASARTOVA D, ÖZKAN A (2023). Determination of diversity of actinomycete in forest soil subject to different blood groups; Classical approaches before metagenomic. , 285 - 308. 10.5505/TurkHijyen.2023.76753
Chicago	GÖKDEMİR Fatma Şeyma,DOĞAN Mazlum,ARSLAN AKVERAN Gönül,ŞENGÖZ Sabiha,KARASARTOVA Djursun,ÖZKAN Ayşegül Taylan Determination of diversity of actinomycete in forest soil subject to different blood groups; Classical approaches before metagenomic. (2023): 285 - 308. 10.5505/TurkHijyen.2023.76753
MLA	GÖKDEMİR Fatma Şeyma,DOĞAN Mazlum,ARSLAN AKVERAN Gönül,ŞENGÖZ Sabiha,KARASARTOVA Djursun,ÖZKAN Ayşegül Taylan Determination of diversity of actinomycete in forest soil subject to different blood groups; Classical approaches before metagenomic. , 2023, ss.285 - 308. 10.5505/TurkHijyen.2023.76753
AMA	GÖKDEMİR F,DOĞAN M,ARSLAN AKVERAN G,ŞENGÖZ S,KARASARTOVA D,ÖZKAN A Determination of diversity of actinomycete in forest soil subject to different blood groups; Classical approaches before metagenomic. . 2023; 285 - 308. 10.5505/TurkHijyen.2023.76753
Vancouver	GÖKDEMİR F,DOĞAN M,ARSLAN AKVERAN G,ŞENGÖZ S,KARASARTOVA D,ÖZKAN A Determination of diversity of actinomycete in forest soil subject to different blood groups; Classical approaches before metagenomic. . 2023; 285 - 308. 10.5505/TurkHijyen.2023.76753
IEEE	GÖKDEMİR F,DOĞAN M,ARSLAN AKVERAN G,ŞENGÖZ S,KARASARTOVA D,ÖZKAN A "Determination of diversity of actinomycete in forest soil subject to different blood groups; Classical approaches before metagenomic." , ss.285 - 308, 2023. 10.5505/TurkHijyen.2023.76753
ISNAD	GÖKDEMİR, Fatma Şeyma vd. "Determination of diversity of actinomycete in forest soil subject to different blood groups; Classical approaches before metagenomic". (2023), 285-308. https://doi.org/10.5505/TurkHijyen.2023.76753

APA	GÖKDEMİR F, DOĞAN M, ARSLAN AKVERAN G, ŞENGÖZ S, KARASARTOVA D, ÖZKAN A (2023). Determination of diversity of actinomycete in forest soil subject to different blood groups; Classical approaches before metagenomic. Türk Hijyen ve Deneysel Biyoloji Dergisi, 80(3), 285 - 308. 10.5505/TurkHijyen.2023.76753
Chicago	GÖKDEMİR Fatma Şeyma,DOĞAN Mazlum,ARSLAN AKVERAN Gönül,ŞENGÖZ Sabiha,KARASARTOVA Djursun,ÖZKAN Ayşegül Taylan Determination of diversity of actinomycete in forest soil subject to different blood groups; Classical approaches before metagenomic. Türk Hijyen ve Deneysel Biyoloji Dergisi 80, no.3 (2023): 285 - 308. 10.5505/TurkHijyen.2023.76753
MLA	GÖKDEMİR Fatma Şeyma,DOĞAN Mazlum,ARSLAN AKVERAN Gönül,ŞENGÖZ Sabiha,KARASARTOVA Djursun,ÖZKAN Ayşegül Taylan Determination of diversity of actinomycete in forest soil subject to different blood groups; Classical approaches before metagenomic. Türk Hijyen ve Deneysel Biyoloji Dergisi, vol.80, no.3, 2023, ss.285 - 308. 10.5505/TurkHijyen.2023.76753
AMA	GÖKDEMİR F,DOĞAN M,ARSLAN AKVERAN G,ŞENGÖZ S,KARASARTOVA D,ÖZKAN A Determination of diversity of actinomycete in forest soil subject to different blood groups; Classical approaches before metagenomic. Türk Hijyen ve Deneysel Biyoloji Dergisi. 2023; 80(3): 285 - 308. 10.5505/TurkHijyen.2023.76753
Vancouver	GÖKDEMİR F,DOĞAN M,ARSLAN AKVERAN G,ŞENGÖZ S,KARASARTOVA D,ÖZKAN A Determination of diversity of actinomycete in forest soil subject to different blood groups; Classical approaches before metagenomic. Türk Hijyen ve Deneysel Biyoloji Dergisi. 2023; 80(3): 285 - 308. 10.5505/TurkHijyen.2023.76753
IEEE	GÖKDEMİR F,DOĞAN M,ARSLAN AKVERAN G,ŞENGÖZ S,KARASARTOVA D,ÖZKAN A "Determination of diversity of actinomycete in forest soil subject to different blood groups; Classical approaches before metagenomic." Türk Hijyen ve Deneysel Biyoloji Dergisi, 80, ss.285 - 308, 2023. 10.5505/TurkHijyen.2023.76753
ISNAD	GÖKDEMİR, Fatma Şeyma vd. "Determination of diversity of actinomycete in forest soil subject to different blood groups; Classical approaches before metagenomic". Türk Hijyen ve Deneysel Biyoloji Dergisi 80/3 (2023), 285-308. https://doi.org/10.5505/TurkHijyen.2023.76753