Paper
Time Radically Alters Ex Situ Evidentiary Soil 16S Bacterial Profiles Produced Via Next-Generation Sequencing†,‡,§
Alyssa J. Badgley M.S.,
Ellen M. Jesmok M.S.,
David R. Foran Ph.D.,
Alyssa J. Badgley M.S.
Forensic Science Program, School of Criminal Justice, Michigan State University, 655 Auditorium Road, 560 Baker Hall, East Lansing, MI, 48824
Search for more papers by this authorEllen M. Jesmok M.S.
Forensic Science Program, School of Criminal Justice, Michigan State University, 655 Auditorium Road, 560 Baker Hall, East Lansing, MI, 48824
Search for more papers by this authorCorresponding Author
David R. Foran Ph.D.
Forensic Science Program, School of Criminal Justice and Department of Integrative Biology, Michigan State University, 655 Auditorium Road, 560 Baker Hall, East Lansing, MI, 48824
Additional information and reprint requests:
David Foran, Ph.D.
Michigan State University
560 Baker Hall
655 Auditorium Road
East Lansing
MI 48824
E-mail: [email protected]
Search for more papers by this authorAlyssa J. Badgley M.S.,
Ellen M. Jesmok M.S.,
David R. Foran Ph.D.,
Alyssa J. Badgley M.S.
Forensic Science Program, School of Criminal Justice, Michigan State University, 655 Auditorium Road, 560 Baker Hall, East Lansing, MI, 48824
Search for more papers by this authorEllen M. Jesmok M.S.
Forensic Science Program, School of Criminal Justice, Michigan State University, 655 Auditorium Road, 560 Baker Hall, East Lansing, MI, 48824
Search for more papers by this authorCorresponding Author
David R. Foran Ph.D.
Forensic Science Program, School of Criminal Justice and Department of Integrative Biology, Michigan State University, 655 Auditorium Road, 560 Baker Hall, East Lansing, MI, 48824
Additional information and reprint requests:
David Foran, Ph.D.
Michigan State University
560 Baker Hall
655 Auditorium Road
East Lansing
MI 48824
E-mail: [email protected]
Search for more papers by this author†
Presented in part at the Midwestern Association of Forensic Scientists Annual Meeting, September 20–25, 2015, in Mackinac Island, MI, and at the 69th Annual Scientific Meeting of the American Academy of Forensic Sciences, February 13–18, 2017, in New Orleans, LA.
‡
Supported by grant numbers 2013-R2-CX-K010 and 2015-DN-BX-K031, awarded by the National Institute of Justice, Office of Justice Programs, U.S. Department of Justice.
§
Points of view are those of the authors and do not necessarily represent the official position or policies of the U.S. Department of Justice.
¶
[This article was published online on 21 February 2018. Errors were subsequently identified in the caption for Table 2. The article was corrected on 1 March 2018.]
Abstract
Previous research has revealed the potential of soil bacterial profiling for forensic purposes; however, investigators have not thoroughly examined fluctuations in microbial profiles from soil aged on evidence. In this research, soils collected from multiple habitats were placed on evidence items and sampled over time, and then bacterial profiles were generated via next-generation sequencing of the 16S rRNA locus. Bacterial abundance charts and nonmetric multidimensional scaling plots provided visual representation of bacterial profiles temporally, while supervised classification was used to statistically associate evidence to a source. The ex situ evidence soils displayed specific, consistent taxonomic changes as they aged, resulting in their drift in multidimensional space, but never toward a different habitat. Ninety-five percent of the 364 evidentiary profiles statistically classified to the correct habitat, with misclassification generally stemming from evidence type and increased age. Ultimately, understanding bacterial changes that occur temporally in ex situ soils should enhance their use in forensic investigations.
References
- 1Sugita R, Marumo Y. Validity of color examination for forensic soil identification. Forensic Sci Int 1996; 83(3): 201–10.
- 2Murray RC, Solebello LP. Forensic examination of soil. In: R Saferstein, editor. Forensic science handbook. Vol. 1, 2nd edn. Boston, MA: Pearson Education Inc, 2002; 615–33.
- 3Kubic TA, Petraco N. Microanalysis and examination of trace evidence. In: SH James, JJ Nordby, S Bell, editors. Forensic science: an introduction to scientific and investigative techniques, 2nd edn. Boca Raton: FL; CRC Press, 2005; 315–39.
- 4 National Research Council. Strengthening forensic science in the United States: a path forward. Washington, DC: National Academies Press, 2009.
- 5Fitzpatrick RW. Section 7: geo- and biomaterials. In: MM Houck, editor. Materials analysis in forensic science. San Diego, CA: Academic Press, 2016; 371–8.
- 6Heath LE, Saunders VA. Assessing the potential of bacterial DNA Profiling for forensic soil comparisons. J Forensic Sci 2006; 51(5): 1062–8.
- 7Jesmok EM, Hopkins JM, Foran DR. Next-generation sequencing of the bacterial 16S rRNA gene for forensic soil comparison: a feasibility study. J Forensic Sci 2016; 61(3): 607–17.
- 8Sensabaugh GF. Microbial community profiling for the characterization of soil evidence: forensic considerations. In: K Ritz, L Dawson, D Miller, editors. Criminal and environmental soil forensics. New York, NY: Springer, 2009; 49–60.
10.1007/978-1-4020-9204-6_4 Google Scholar
- 9Horswell J, Cordiner SJ, Maas EW, Martin TM, Sutherland KB, Speir TW, et al. Forensic comparison of soils by bacterial community DNA profiling. J Forensic Sci 2002; 47(2): 350–3.
- 10Meyers MS, Foran DR. Spatial and temporal influences on bacterial profiling of forensic soil samples. J Forensic Sci 2008; 53(3): 652–60.
- 11Lenz EJ, Foran DR. Bacterial profiling of soil using genus-specific markers and multidimensional scaling. J Forensic Sci 2010; 55(6): 1437–42.
- 12Ranjard L, Poly F, Lata JC, Mougel C, Thioulouse J, Nazaret S. Characterization of bacterial and fungal soil communities by automated ribosomal intergenic spacer analysis fingerprints: biological and methodological variability. Appl Environ Microbiol 2001; 67(10): 4479–87.
- 13Habtom H, Demanèche S, Dawson L, Azulay C, Matan O, Robe P, et al. Soil characterisation by bacterial community analysis for forensic applications: a quantitative comparison of environmental technologies. Forensic Sci Int Genet 2017; 26: 21–9.
- 14Young JM, Weyrich LS, Breen J, Macdonald LM, Cooper A. Predicting the origin of soil evidence: high throughput eukaryote sequencing and MIR spectroscopy applied to a crime scene scenario. Forensic Sci Int 2015; 251: 22–31.
- 15Jesmok EM. Adoption of next-generation 16S bacterial sequencing practices for the forensic analysis of soil [thesis]. East Lansing, MI: Michigan State University, 2015.
- 16Magnabosco C, Tekere M, Lau MCY, Linage B, Kuloyo O, Erasmus M, et al. Comparisons of the composition and biogeographic distribution of the bacterial communities occupying South African thermal springs with those inhabiting deep subsurface fracture water. Front Microbiol 2014; 5: 679.
- 17Berg M, Stenuit B, Ho J, Wang A, Parke A, Knight M, et al. Assembly of the Caenorhabditis elegans gut microbiota from diverse soil microbial environments. ISME J 2016; 10(8): 1998–2009.
- 18Hopkins JM. Forensic soil bacterial profiling using 16S rRNA gene sequencing and diverse statistics [thesis]. East Lansing, MI: Michigan State University, 2014.
- 19Goltsman DSA, Comolli LR, Thomas BC, Banfield JF. Community transcriptomics reveals unexpected high microbial diversity in acidophilic biofilm communities. ISME J 2015; 9(4): 1014–23.
- 20Gibson MK, Forsberg KJ, Dantas G. Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology. ISME J 2015; 9(1): 207–16.
- 21Metcalf JL, Wegener Parfrey L, Gonzalez A, Lauber CL, Knights D, Ackermann G, et al. A microbial clock provides an accurate estimate of the postmortem interval in a mouse model system. eLife 2013; 2: 1–19.
- 22Knights D, Costello EK, Knight R. Supervised classification of human microbiota. FEMS Microbiol Rev 2011; 35(2): 343–59.
- 23Yang C, Mills D, Mathee K, Wang Y, Jayachandran K, Sikaroodi M, et al. An ecoinformatics tool for microbial community studies: supervised classification of amplicon length heterogeneity (ALH) profiles of 16S RNA. J Microbiol Methods 2006; 65(1): 49–62.
- 24Lauber CL, Ramirez KS, Aanderud Z, Lennon J, Fierer N. Temporal variability in soil microbial communities across land-use types. ISME J 2013; 7(8): 1641–50.
- 25Shade A, Caporaso JG, Handelsman J, Knight R, Fierer N. A meta-analysis of changes in bacterial and archaeal communities with time. ISME J 2013; 7(8): 1493–506.
- 26Pechal JL, Crippen TL, Benbow ME, Tarone AM, Dowd S, Tomberlin JK. The potential use of bacterial community succession in forensics as described by high throughput metagenomic sequencing. Int J Leg Med 2014; 128(1): 193–205.
- 27Finley SJ, Benbow ME, Javan GT. Microbial communities associated with human decomposition and their potential use as postmortem clocks. Int J Leg Med 2015; 129(3): 623–32.
- 28Breiman L. Random forests. Mach Learn 2001; 45(1): 5–32.
- 29Baker KL, Langenheder S, Nicol GW, Ricketts D, Killham K, Campbell CD, et al. Environmental and spatial characterization of bacterial community composition in soil to inform sampling strategies. Soil Biol Biochem 2009; 41: 2292–8.
- 30https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf (accessed Feb 6, 2018).
- 31Yarza P, Yilmaz P, Pruesse E, Glockner FO, Ludwig W, Schleifer KH, et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol 2014; 12(9): 635–45.
- 32Liu Z, Lozupone C, Hamady M, Bushman FD, Knight R. Short pyrosequencing reads suffice for accurate microbial community analysis. Nucleic Acids Res 2007; 35(18): 120.
- 33Caporaso GJ, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, et al. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci U S A 2011; 108(1 Suppl): 4516–22.
- 34Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N, et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J 2012; 6(8): 1621–4.
- 35Schloss PD, Westcott SI, Ryabin T, Hall JR, Hartmann M, Hollister EB. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 2009; 75(23): 7537–41.
- 36Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl Environ Microbiol 2013; 79(17): 5112–20.
- 37Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 2013; 41: D590–6.
- 38Dice LR. Measures of the amount of ecologic association between species. Ecology 1945; 26(3): 297–302.
- 39Sørensen T. A method of establishing groups of equal amplitude in plant sociology based on similarity of species and its application to analyses of the vegetation on Danish commons. Kongelige Danske Videnskabernes Selskab 1948; 5(4): 1–34.
- 40Kruskal JB. Nonmetric multidimensional scaling: a numerical method. Psychometrika 1964; 29(2): 115–29.
- 41Holland SM. Non-metric multidimensional scaling (MDS). Athens, GA: Department of Geology, University of Georgia, 2008.
- 42Hastie T, Tibshirani R, Friedman J. Ensemble learning. The elements of statistical learning: data mining, inference, and prediction, 2nd edn. New York, NY: Springer, 2009; 605–24.
10.1007/978-0-387-84858-7_16 Google Scholar
- 43Macdonald CA, Ang R, Cordiner SJ, Horswell J. Discrimination of soils at regional and local levels using bacterial and fungal T-RFLP profiling. J Forensic Sci 2011; 56(1): 61–9.
- 44Costello EK, Halloy SR, Reed SC, Sowell R, Schmidt SK. Fumarole-supported islands of biodiversity within a hyperarid high-elevation landscape on Socompa Volcano, Puna de Atacama, Andes. Appl Environ Microbiol 2009; 75(3): 735–47.
- 45Nicholson WL, Munakata N, Horneck G, Melosh HJ, Setlow P. Resistance of Bacillus endospores to extreme terrestrial and extraterrestrial environments. Microbiol Mol Biol Rev 2000; 64(3): 548–72.
- 46Janssen PH. Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl Environ Microbiol 2006; 72(3): 1719–28.
- 47Fierer N, Bradford MA, Jackson RB. Toward an ecological classification of soil bacteria. Ecology 2007; 86(6): 1354–64.
- 48Hobman JL, Crossman LC. Bacterial antimicrobial metal ion resistance. J Med Microbiol 2014; 64: 471–97.
- 49Schloss PD, Iverson KD, Petrosino JF, Schloss SJ. The dynamics of a family's gut microbiota reveal variations on a theme. Microbiome 2014; 2: 25. https://doi.org/10.1186/2049-2618-2-25.
- 50Badgley AJ. Influences of time, temperature, and quantity on next-generation 16S bacterial DNA profiles for forensic soil evidence analysis [thesis]. East Lansing, MI: Michigan State University, 2016.
- 51Mann RW, Bass WM, Meadows L. Time since death and decomposition of the human body: variables and observations in case and experimental field studies. J Forensic Sci 1990; 31(3): 103–11.
- 52Anderson GS. Insect succession on carrion and its relationship to determining time of death. In: JS Byrd, JL Castner, editors. Forensic entomology. New York, NY: CRC Press, 2001; 143–75.
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