Carcass mass has little influence on the structure of gravesoil microbial communities

International Journal of Legal Medicine

Volumn 130, Issue 1, 2016, Pages 253-263

  Weiss, Sophie ^a   Carter, David O ^b   Metcalf, Jessica L ^c   Knight, Rob ^d  

^a University of Colorado at Boulder   (United States)

^b CHAMINADE UNIVERSITY OF HONOLULU   (United States)

^c UNIVERSITY OF COLORADO   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Bacteria; Decomposition; Nematode; Pathology; Postmortem microbiology

Indexed keywords

BACTERIAL RNA; RNA 16S; RNA 18S;

ANIMAL; ANIMAL MODEL; BACTERIUM; BODY WEIGHT; FUNGUS; GENETICS; ISOLATION AND PURIFICATION; MICROBIOLOGY; PIG; POSTMORTEM CHANGE; SEQUENCE ANALYSIS;

ANIMALS; BACTERIA; BODY WEIGHT; FUNGI; MODELS, ANIMAL; POSTMORTEM CHANGES; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; RNA, RIBOSOMAL, 18S; SEQUENCE ANALYSIS, RNA; SOIL MICROBIOLOGY; SWINE;

EID: 84954365154     PISSN: 09379827     EISSN: 14371596     Source Type: Journal    
DOI: 10.1007/s00414-015-1206-2     Document Type: Article

References (56)

1. Gill-King H (1997) Chemical and ultra-structural aspects of decomposition. In: Haglund WD, Sorge MH (eds) Forensic taphonomy: the postmortem fate of human remains. CRC Press, Boca Raton
2. Correy JEL (1978) Possible sources of ethanol ante- and post-mortem: its relationships to the biochemistry and microbiology of decomposition. J Appl Bacteriol 44:1–56
3. Metcalf JL, Wegener Parfrey L, Gonzalez A, Lauber CL, Knights D, Ackermann G, Humphrey GC, Gebert MJ, Van Treuren W, Berg-Lyons D, Keepers K, Guo Y, Bullard J, Fierer N, Carter DO, Knight R (2013) A microbial clock provides an accurate estimate of the postmortem interval in a mouse model system. eLife 2:e01104. doi:10.7554/eLife.01104
4. Pechal JL, Crippen TL, Benbow ME, Tarone AM, Dowd S, Tomberlin JK (2014) The potential use of bacterial community succession in forensics as described by high throughput metagenomic sequencing. Int J Leg Med 128:193–205
5. Haskell NH, Catts EP (2008) Entomology and death: a procedural guide, 2nd edn. East Park Printing, Clemson
6. Putman RJ (1978) Patterns of carbon dioxide evolution from decaying carrion. 1. Decomposition of small mammal carrion in temperate systems. Oikos 31:47–57
7. Carter DO, Yellowlees D, Tibbett M (2008) Temperature affects microbial decomposition of cadavers (Rattus rattus) in contrasting soils. Appl Soil Ecol 40:129–137
8. Carter DO, Yellowlees D, Tibbett M (2010) Moisture can be the dominant environmental parameter governing cadaver decomposition in soil. Forensic Sci Int 200:60–66
9. Ibekwe AM, Kennedy AC, Frohne PS, Papiernik SK, Yang CH, Crowley DE (2002) Microbial diversity along a transect of agronomic zones. FEMS Microbiol Ecol 39(3):183–191. doi:10.1111/j.1574-6941.2002.tb00921.x
10. Kuske CR, Ticknor LO, Miller ME, Dunbar JM, Davis JA, Barns SM, Belnap J (2002) Comparison of soil bacterial communities in rhizospheres of three plant species and the interspaces in an arid grassland. Appl Environ Microbiol 68(4):1854–1863
11. Haslam TC, Tibbett M (2009) Soils of contrasting pH affect the decomposition of buried mammalian (Ovis aries) skeletal muscle tissue. J Forensic Sci 54(4):900–904. doi:10.1111/j.1556-4029.2009.01070.x
12. Lauber CL, Metcalf JL, Keepers K, Ackermann G, Carter DO, Knight R (2014) Vertebrate decomposition is accelerated by soil microbes. Appl Environ Microbiol 80:4920–4929
13. Tibbett M, Carter DO (2003) Mushrooms and taphonomy: the fungi that mark woodland graves. Mycologist 17:20–24
14. Sagara N, Yamanaka T, Tibbett M (2008) Soil fungi associated with graves and latrines: toward a forensic mycology. In: Tibbett M, Carter DO (eds) Soil analysis in forensic taphonomy: chemical and biological effects of buried human remains. CRC Press, Boca Raton, pp 67–108
15. Anderson GS (1995) The use of insects in death investigations: an analysis of cases in British Columbia over a 5-year period. J Can Soc Forensic Sci 28:277–292
16. Anderson GS, VanLaerhoven SL (1996) Initial studies on insect succession on carrion in southwestern British Columbia. J Forensic Sci 41:617–625
17. Campobasso CP, Introna F (2001) The forensic entomologist in the context of the forensic pathologist’s role. Forensic Sci Int 120(1-2):132–139
18. Hewadikaram KA, Goff ML (1991) Effect of carcass size on rate of decomposition and arthropod succession patterns. Am J Forensic Med Pathol 12:235–240
19. Komar D, Beattie O (1998) Effects of carcass size on decay rates of shade and sun exposed carrion. Can Soc Forensic Sci J 31:35–43
20. Simmons T, Adlam RE, Moffatt C (2010) Debugging decomposition data—comparative taphonomic studies and the influence of insects and carcass size on decomposition rate. J Forensic Sci 55(1):8–13. doi:10.1111/j.1556-4029.2009.01206.x
21. Spicka A, Johnson R, Bushing J, Higley LG, Carter DO (2011) Carcass mass can influence rate of decomposition and release of ninhydrin-reactive nitrogen. Forensic Sci Int 209:80–85
22. Sutherland A, Myburgh J, Steyn M, Becker PJ (2013) The effect of body size on the rate of decomposition in a temperate region of South Africa. Forensic Sci Int 231(1-3):257–262. doi:10.1016/j.forsciint.2013.05.035
23. Matuszewski S, Konwerski S, Fratczak K, Szafalowicz M (2014) Effect of body mass and clothing on decomposition of pig carcasses. Int J Legal Med 128(6):1039–1048. doi:10.1007/s00414-014-0965-5
24. Kuusela S, Hanski I (1982) The structure of carrion fly communities—the size and the type of carrion. Holarctic Ecol 5(4):337–348
25. Kneidel KA (1984) Influence of carcass taxon and size on species composition of carrion-breeding Diptera. Am Midl Nat 111(1):57–63. doi:10.2307/2425542
26. Arnold CY (1959) The determination and significance of the base temperature in a linear heat unit system. Proc Am Soc Hortic Sci 74:430–445
27. Vass AA, Bass WM, Wolt JD, Foss JE, Ammons JT (1992) Time since death determinations of human cadavers using soil solution. J Forensic Sci 37:1236–1253
28. Carter DO, Yellowlees D, Tibbett M (2007) Cadaver decomposition in terrestrial ecosystems. Die Naturwissenschaften 94(1):12–24. doi:10.1007/s00114-006-0159-1
29. McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, Probst A, Andersen GL, Knight R, Hugenholtz P (2012) An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J 6(3):610–618. doi:10.1038/ismej.2011.139
30. Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glockner FO (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 41(Database issue):D590–D596. doi:10.1093/nar/gks1219
31. Paulson JN, Stine OC, Bravo HC, Pop M (2013) Differential abundance analysis for microbial marker-gene surveys. Nat Methods 10(12):1200–1202. doi:10.1038/nmeth.2658
32. Lozupone CA, Hamady M, Kelley ST, Knight R (2007) Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities. Appl Environ Microbiol 73(5):1576–1585. doi:10.1128/AEM.01996-06
33. Lozupone C, Knight R (2005) UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71(12):8228–8235. doi:10.1128/AEM.71.12.8228-8235.2005
34. Pop M, Walker AW, Paulson J, Lindsay B, Antonio M, Hossain MA, Oundo J, Tamboura B, Mai V, Astrovskaya I, Corrada Bravo H, Rance R, Stares M, Levine MM, Panchalingam S, Kotloff K, Ikumapayi UN, Ebruke C, Adeyemi M, Ahmed D, Ahmed F, Alam MT, Amin R, Siddiqui S, Ochieng JB, Ouma E, Juma J, Mailu E, Omore R, Morris JG, Breiman RF, Saha D, Parkhill J, Nataro JP, Stine OC (2014) Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition. Genome Biol 15(6):R76. doi:10.1186/gb-2014-15-6-r76
35. Salter SJ, Cox MJ, Turek EM, Calus ST, Cookson WO, Moffatt MF, Turner P, Parkhill J, Loman NJ, Walker AW (2014) Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol 12:87. doi:10.1186/s12915-014-0087-z
36. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Gonzalez A, Goodrich JK, Gordon JL, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone C, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widman J, Yatsunenko T, Zaneveld J, Knight R (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7:335–336
37. Anderson MJ (2001) A new method for non-parametric multivariate analysis of variance. Austral Ecol 26:32–46
38. Jari Oksanen FGB, Roeland Kindt, Pierre Legendre, Peter R. Minchin, R. B. O’Hara, Gavin L. Simpson, Peter Solymos, M. Henry H. Stevens and Helene Wagner (2015) vegan: Community Ecology Package
39. Team RC (2014) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna
40. Meyer J, Anderson B, Carter DO (2013) Seasonal variation of carcass decomposition and gravesoil chemistry in a cold (Dfa) climate. J Forensic Sci 58(5):1175–1182. doi:10.1111/1556-4029.12169
41. Pechal JL, Crippen TL, Tarone AM, Lewis AJ, Tomberlin JK, Benbow ME (2013) Microbial community functional change during vertebrate carrion decomposition. PLoS One 8(11):e79035. doi:10.1371/journal.pone.0079035
42. LeBlanc HN, Logan JG (2010) Exploiting insect olfaction in forensic entomology. Curr Concepts Forensic Entomol:205-221. doi: 10.1007/978-1-4020-9684-6_11
43. Tomberlin JK, Benbow ME, Tarone AM, Mohr RM (2011) Basic research in evolution and ecology enhances forensics. Trends Ecol Evol 26(2):53–55. doi:10.1016/J.Tree.2010.12.001
44. Ma Q, Fonseca A, Liu WQ, Fields AT, Pimsler ML, Spindola AF, Tarone AM, Crippen TL, Tomberlin JK, Wood TK (2012) Proteus mirabilis interkingdom swarming signals attract blow flies. Isme J 6(7):1356–1366. doi:10.1038/Ismej.2011.210
45. Tomberlin JK, Crippen TL, Tarone AM, Singh B, Adams K, Rezenom YH, Benbow ME, Flores M, Longnecker M, Pechal JL, Russell DH, Beier RC, Wood TK (2012) Interkingdom responses of flies to bacteria mediated by fly physiology and bacterial quorum sensing. Anim Behav 84(6):1449–1456. doi:10.1016/J.Anbehav.2012.09.013
46. De Wit R, Bouvier T (2006) ‘Everything is everywhere, but the environment selects’; what did Baas Becking and Beijerinck really say? Environ Microbiol 8:755–758
47. Bongers T, Ferris H (1999) Nematode community structure as a bioindicator in environmental sampling. Trends Ecol Evol 14:224–228
48. Tibbett M, Carter DO (2008) Soil analysis in forensic taphonomy: chemical and biological effects of buried human remains. CRC Press, Boca Raton
49. Gunstone FD (1967) An introduction to the chemistry and biochemistry of fatty acids and their glycerides. Chapman Hall, London
50. Ridgway EJ, Harvey DJ (2010) Microbiology of the autopsy. In: Burton JL, Rutty G (eds) The hospital autopsy: a manual of fundamental autopsy practice. CRC Press, Boca Raton, pp 227–245
51. Caplan MJ, Koontz FP (2001) Cumitech 35 postmortem microbiology. ASM Press, Washington DC
52. Lauber CL, Metcalf JL, Keepers K, Ackermann G, Carter DO, Knight R (2014) Vertebrate decomposition is accelerated by soil microbes. Appl Environ Microbiol 80(16):4920–4929. doi:10.1128/AEM.00957-14
53. Hyde ER, Haarmann DP, Lynne AM, Bucheli SR, Petrosino JF (2013) The living dead: bacterial community structure of a cadaver at the onset and end of the bloat stage of decomposition. PLoS One 8(10):e77733. doi:10.1371/journal.pone.0077733
54. Maujean G, Guinet T, Fanton L, Malicier D (2013) The interest of postmortem bacteriology in putrefied bodies. J Forensic Sci 58(4):1069–1070. doi:10.1111/1556-4029.12155
55. Hyde ER, Haarmann DP, Lynne AM, Bucheli SR, Pertrosino JF (2013) The living dead: bacterial community structure of a cadaver at the onset and end of the bloat stage of decomposition. PLoS One 8:e77733
56. Fierer N, Lauber CL, Zhou N, McDonald D, Costello EK, Knight R (2010) Forensic identification using skin bacterial communities. Proc Natl Acad Sci U S A 107(14):6477–6481. doi:10.1073/pnas.1000162107