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Potential use of high-throughput sequencing of bacterial communities for postmortem submersion interval estimation

Brazilian Journal of Microbiology volume 50, pages 999–1010 (2019)Cite this article

Abstract

Microorganisms play vital roles in the natural decomposition of carcasses in aquatic systems. Using high-throughput sequencing techniques, we evaluated the composition and succession of microbial communities throughout the decomposition of rat carcasses in freshwater. A total of 4,428,781 high-quality 16S rRNA gene sequences and 2144 operational taxonomic units were obtained. Further analysis revealed that the microbial composition differed significantly between the epinecrotic (rat skins) and the epilithic (rocks) samples. During the carcass decomposition process, Proteobacteria became the dominant phylum in the epinecrotic, epilithic, and environmental (water) samples, followed by Firmicutes in the epinecrotic samples and Bacteroidetes in the epilithic and water samples. Microbial communities were influenced by numerous environmental factors, such as dissolved oxygen content and conductivity. Our study provides new insight about postmortem submersion interval (PMSI) estimation in aquatic environments.

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References

  1. Dickson GC, Poulter RT, Maas EW, Probert PK, Kieser JA (2011) Marine bacterial succession as a potential indicator of postmortem submersion interval. Forensic Sci Int 209:1–10

    PubMed  Google Scholar 

  2. Yang SH, Lim JS, Khan MA, Kim BS, Choi DY, Lee EY, Ahn HK (2015) High-throughput nucleotide sequence analysis of diverse bacterial communities in leachates of decomposing pig carcasses. Genet Mol Biol 38:373–380

    PubMed  PubMed Central  Google Scholar 

  3. Zimmerman KA, Wallace JR (2008) The potential to determine a postmortem submersion interval based on algal/diatom diversity on decomposing mammalian carcasses in brackish ponds in Delaware. J Forensic Sci 53:935–941

    PubMed  Google Scholar 

  4. Benbow ME, Pechal JL, Lang JM, Erb R, Wallace JR (2015) The potential of high-throughput metagenomic sequencing of aquatic bacterial communities to estimate the postmortem submersion interval. J Forensic Sci 60:1500–1510

    PubMed  Google Scholar 

  5. Lang JM, Erb R, Pechal JL, Wallace JR, McEwan RW, Benbow ME (2016) Microbial biofilm community variation in flowing habitats: potential utility as bioindicators of postmortem submersion intervals. Microorganisms. 4

  6. Reh H, Haarhoff K, Vogt CD (1977) The estimation of the time of death of corpses recovered from water [Die Scha¨tzung der Todeszeit bei Wasserleichen], Z. Rechtmedizin 79:261–266 (in German)

    CAS  Google Scholar 

  7. Heaton V, Lagden A, Moffatt C, Simmons T (2010) Predicting the postmortem submersion interval for human remains recovered from U.K. waterways. J Forensic Sci 55:302–307

    PubMed  Google Scholar 

  8. Humphreys MK, Panacek E, Green W, Albers E (2013) Comparison of protocols for measuring and calculating postmortem submersion intervals for human analogs in fresh water. J Forensic Sci 58:513–517

    PubMed  Google Scholar 

  9. Mateus M, Vieira V (2014) Study on the postmortem submersion interval and accumulated degree days for a multiple drowning accident. Forensic Sci Int 238:e15–e19

    CAS  PubMed  Google Scholar 

  10. Lee SY, Woo SK, Lee SM, Ha EJ, Lim KH, Choi KH, Roh YH, Eom YB (2017) Microbiota composition and pulmonary surfactant protein expression as markers of death by drowning. J Forensic Sci 62:1080–1088

    CAS  PubMed  Google Scholar 

  11. Metcalf JL, Xu ZZ, Weiss S, Lax S, Van Treuren W, Hyde ER, Song SJ, Amir A, Larsen P, Sangwan N, Haarmann D, Humphrey GC, Ackermann G, Thompson LR, Lauber C, Bibat A, Nicholas C, Gebert MJ1, Petrosino JF, Reed SC, Gilbert JA, Lynne AM, Bucheli SR Carter DO, Knight R. (2016). Microbial community assembly and metabolic function during mammalian corpse decomposition. Science. 351:158–162

    PubMed  Google Scholar 

  12. Guo J, Fu X, Liao H, Hu Z, Long L, Yan W, Ding Y, Zha L, Guo Y, Yan J, Chang Y, Cai J (2016) Potential use of bacterial community succession for estimating post-mortem interval as revealed by high-throughput sequencing. Sci Rep 6:24197

    CAS  PubMed  PubMed Central  Google Scholar 

  13. Kakizaki E, Ogura Y, Kozawa S, Nishida S, Uchiyama T, Hayashi T, Yukawa N (2012) Detection of diverse aquatic microbes in blood and organs of drowning victims: first metagenomic approach using high-throughput 454-pyrosequencing. Forensic Sci Int 220:135–146

    CAS  PubMed  Google Scholar 

  14. Juanita MG, Anna F, Núria P, Laura BF. (2016). Limits of the biofilm concept and types of aquatic biofilms. Anna M. Romaní, Helena Guasch, M. Dolors Balaguer, Eds.; Caister Academic Press Inc.: England

  15. Jakka Ravindran S, Kumar R, Srimany A, Philip L, Pradeep T (2018) Early detection of biofouling on water purification membranes by ambient ionization mass spectrometry imaging. Anal Chem 90:988–997

    CAS  PubMed  Google Scholar 

  16. Myrstener M, Rocher-Ros G, Burrows RM, Bergström AK, Giesler R, Sponseller RA (2018) Persistent nitrogen limitation of stream biofilm communities along climate gradients in the arctic. Glob Chang Biol 24:3680–3691

    PubMed  Google Scholar 

  17. Cai X, Yao L, Sheng Q, Jiang L, Dahlgren RA, Wang T (2018) Properties of bacterial communities attached to artificial substrates in a hypereutrophic urban river. AMB Express 8:22

    PubMed  PubMed Central  Google Scholar 

  18. Carrel M, Morales VL, Beltran MA, Derlon N, Kaufmann R, Morgenroth E, Holzner M (2018) Biofilms in 3D porous media: delineating the influence of the pore network geometry, flow and mass transfer on biofilm development. Water Res 134:280–291

    CAS  PubMed  Google Scholar 

  19. Yan L, Zhang S, Lin D, Guo C, Yan L, Wang S, He Z (2018) Nitrogen loading affects microbes, nitrifiers and denitrifiers attached to submerged macrophyte in constructed wetlands. Sci Total Environ 622-623:121–126

    CAS  PubMed  Google Scholar 

  20. Battin TJ, Besemer K, Bengtsson MM, Romani AM, Packmann AI (2016) The ecology and biogeochemistry of stream biofilms. Nat Rev Microbiol 14:251–263

    CAS  PubMed  Google Scholar 

  21. Battin TJ, Kaplan LA, Denis Newbold J, Hansen CM (2003) Contributions of microbial biofilms to ecosystem processes in stream mesocosms. Nature. 426:439–442

    CAS  PubMed  Google Scholar 

  22. 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 Legal Med 128:193–205

    PubMed  Google Scholar 

  23. Janetski DJ, Chaloner DT, Tiegs SD, Lamberti GA (2009) Pacific salmon effects on stream ecosystems: a quantitative synthesis. Oecologia. 159:583–595

    PubMed  Google Scholar 

  24. Gasol JM, Guerrero R, PedrosAlio C (1991) Seasonal variations in size structure and procaryotic dominance in sulfurous Lake Ciso. Limnol Oceanogr 36:588–592

    Google Scholar 

  25. Tomberlin JK, Adler PH (1998) Seasonal colonization and decomposition of rat carrion in water and on land in an open field in South Carolina. J Med Entomol 35:704–709

    CAS  PubMed  Google Scholar 

  26. Sinsabaugh RL, Golladay SW, Linkins AE (1991) Comparison of epilithic and epixylic biofilm development in a boreal river. Freshw Biol 25:179–187

    Google Scholar 

  27. Tank JL, Dodds WK (2003) Nutrient limitation of epilithic and epixylic biofilms in ten North American streams. Freshw Biol 48:1031–1049

    CAS  Google Scholar 

  28. Smucker NJ, Vis ML (2011) Acid mine drainage affects the development and function of epilithic biofilms in streams. J N Am Benthol Soc 30:728–738

    Google Scholar 

  29. Lang JM, McEwan RW, Benbow ME (2015) Abiotic autumnal organic matter deposition and grazing disturbance effects on epilithic biofilm succession. FEMS Microbiol Ecol 91

  30. Szelecz I, Lösch S, Seppey CVW, Lara E, Singer D, Sorge F, Tschui J, Perotti MA, Mitchell EAD (2018) Comparative analysis of bones, mites, soil chemistry, nematodes and soil micro-eukaryotes from a suspected homicide to estimate the post-mortem interval. Sci Rep 8:25

    PubMed  PubMed Central  Google Scholar 

  31. Corcoll N, Österlund T, Sinclair L, Eiler A, Kristiansson E, Backhaus T, Eriksson KM (2017) Comparison of four DNA extraction methods for comprehensive assessment of 16S rRNA bacterial diversity in marine biofilms using high-throughput sequencing. FEMS Microbiol Lett 364

  32. Maksimov P, Schares G, Press S, Fröhlich A, Basso W, Herzig M, Conraths FJ (2017) Comparison of different commercial DNA extraction kits and PCR protocols for the detection of Echinococcus multilocularis eggs in faecal samples from foxes. Vet Parasitol 237:83–93

    CAS  PubMed  Google Scholar 

  33. Li AD, Metch JW, Wang Y, Garner E, Zhang AN, Riquelme MV, Vikesland PJ, Pruden A, Zhang T (2018) Effects of sample preservation and DNA extraction on enumeration of antibiotic resistance genes in wastewater. FEMS Microbiol Ecol 94

  34. Xu N, Tan G, Wang H, Gai X (2016) Effect of biochar additions to soil on nitrogen leaching, microbial biomass and bacterial community structure. Eur J Soil Biol 74:1–8

    Google Scholar 

  35. Ye J, Joseph SD, Ji M, Nielsen S, Mitchell DRG, Donne S, Horvat J, Wang J, Munroe P, Thomas T (2017) Chemolithotrophic processes in the bacterial communities on the surface of mineral-enriched biochars [J]. The ISME journal 11:1087–1101

    CAS  PubMed  PubMed Central  Google Scholar 

  36. Fan X, Xing P (2016) The vertical distribution of sediment archaeal community in the “black bloom” disturbing Zhushan Bay of Lake Taihu. Archaea 8232135

  37. Wang JT, Zheng YM, Hu HW, Li J, Zhang LM, Chen BD, Chen WP, He JZ (2016) Coupling of soil prokaryotic diversity and plant diversity across latitudinal forest ecosystems. Sci Rep 6:19561

    CAS  PubMed  PubMed Central  Google Scholar 

  38. Haefner JN, Wallace JR, Merritt RW (2004) Pig decomposition in lotic aquatic systems: the potential use of algal growth in establishing a postmortem submersion interval (PMSI). J Forensic Sci 49:330–336

    PubMed  Google Scholar 

  39. Anderson GS, Hobischak NR (2004) Decomposition of carrion in the marine environment in British Columbia, Canada. Int J Legal Med 118:206–209

    CAS  PubMed  Google Scholar 

  40. van der Waaij D (1989) The ecology of the human intestine and its consequences for overgrowth by pathogens such as Clostridium difficile. Annu Rev Microbiol 43:69–87

    PubMed  Google Scholar 

  41. Gotkowska-Płachta A, Korzeniewska E (2015) Microbial evaluation of sandboxes located in urban area. Ecotoxicol Environ Saf 113:64–71

    PubMed  Google Scholar 

  42. Lalitha KV, Gopakumar K (2000) Distribution and ecology of Clostridium botulinum in fish and aquatic environments of a tropical region. Food Microbiol 17:535–541

    Google Scholar 

  43. Lee HW, Roh SW, Yim KJ, Shin NR, Lee J, Whon TW, Kim JY, Hyun DW, Kim D, Bae JW (2013) Paenibacillus marinisediminis sp. nov., a bacterium isolated from marine sediment. J Microbiol 51:312–317

    CAS  PubMed  Google Scholar 

  44. Berge O, Guinebretière MH, Achouak W, Normand P, Heulin T (2002) Paenibacillus graminis sp. nov. and Paenibacillus odorifer sp. nov., isolated from plant roots, soil and food. Int J Syst Evol Microbiol 52:607–616

    CAS  PubMed  Google Scholar 

  45. Huang Z, Zhao F, Li YH (2017) Isolation of Paenibacillus tumbae sp. nov., from the tomb of the emperor Yang of the Sui dynasty, and emended description of the genus Paenibacillus. Antonie Van Leeuwenhoek 110:357–364

    CAS  PubMed  Google Scholar 

  46. Zhou Y, Gao S, Wei DQ, Yang LL, Huang X, He J, Zhang YJ, Tang SK, Li WJ (2012) Paenibacillus thermophilus sp. nov., a novel bacterium isolated from a sediment of hot spring in Fujian province, China. Antonie Van Leeuwenhoek 102:601–609

    CAS  PubMed  Google Scholar 

  47. Kalmbach S, Manz W, Bendinger B, Szewzyk U (2000) In situ probing reveals Aquabacterium commune as a widespread and highly abundant bacterial species in drinking water biofilms. Water Res 34:575–581

    CAS  Google Scholar 

  48. Prichula J, Pereira RI, Wachholz GR, Cardoso LA, Tolfo NC, Santestevan NA, Medeiros AW, Tavares M, Frazzon J, d’Azevedo PA, Frazzon AP (2016) Resistance to antimicrobial agents among enterococci isolated from fecal samples of wild marine species in the southern coast of Brazil. Mar Pollut Bull 105:51–57

    CAS  PubMed  Google Scholar 

  49. Barros J, Igrejas G, Andrade M, Radhouani H, López M, Torres C, Poeta P (2011) Gilthead seabream (Sparus aurata) carrying antibiotic resistant enterococci. A potential bioindicator of marine contamination? Mar Pollut Bull 62:1245–1248

    CAS  PubMed  Google Scholar 

  50. Gilmore MS, Lebreton F, van Schaik W (2013) Genomic transition of enterococci from gut commensals to leading causes of multidrug-resistant hospital infection in the antibiotic era. Curr Opin Microbiol 16:10–16

    PubMed  PubMed Central  Google Scholar 

  51. Badgley BD, Thomas FI, Harwood VJ (2010) The effects of submerged aquatic vegetation on the persistence of environmental populations of Enterococcus spp. Environ Microbiol 12:1271–1281

    CAS  PubMed  Google Scholar 

  52. Docherty KM, Young KC, Maurice PA, Bridgham SD (2006) Dissolved organic matter concentration and quality influences upon structure and function of freshwater microbial communities. Microb Ecol 52:378–388

    CAS  PubMed  Google Scholar 

  53. Sabater S, Gregory SV, Sedell JR (2010) Community dynamics and metabolism of benthic algae colonizing wood and rock substrata in a forest stream. J Phycol 34:561–567

    Google Scholar 

  54. Cutler NA, Chaput DL, Oliver AE, Viles HA (2015) The spatial organization and microbial community structure of an epilithic biofilm. FEMS Microbiol Ecol 91

  55. Das M, Royer TV, Leff LG (2007) Diversity of fungi, bacteria, and actinomycetes on leaves decomposing in a stream. Appl Environ Microbiol 73:756–767

    CAS  PubMed  Google Scholar 

  56. Jiang XY, Wang JF, Zhu GH, Ma MY, Lai Y, Zhou H. (2016). Detection of metabolism function of microbial community of corpses by biolog-eco method. Fa Yi Xue Za Zhi 32(3):171–175. [in Chinese]

  57. Witt V, Wild C, Anthony KR, Diaz-Pulido G, Uthicke S (2011) Effects of ocean acidification on microbial community composition of, and oxygen fluxes through, biofilms from the Great Barrier Reef. Environ Microbiol 13:2976–2989

    CAS  Google Scholar 

  58. Witt V, Wild C, Uthicke S (2012) Terrestrial runoff controls the bacterial community composition of biofilms along a water quality gradient in the Great Barrier Reef. Appl Environ Microbiol 78:7786–7791

    CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgments

The authors are grateful for the technical support provided by the Majorbio Medical Technology Co., LTD. (Shanghai, China).

Funding

This work was funded by the National Natural Science Foundation of China (81571855).

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Affiliations

  1. Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, People’s Republic of China

    Jing He, Juanjuan Guo, Xiaoliang Fu & Jifeng Cai

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  1. Jing He
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  2. Juanjuan Guo
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  3. Xiaoliang Fu
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  4. Jifeng Cai
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Correspondence to Jifeng Cai.

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The study and all protocols were approved by the Medical Ethics Committee of Xiangya Hospital, Central South University (approval No: 201503465).

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He, J., Guo, J., Fu, X. et al. Potential use of high-throughput sequencing of bacterial communities for postmortem submersion interval estimation. Braz J Microbiol 50, 999–1010 (2019). https://doi.org/10.1007/s42770-019-00119-w

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  • DOI: https://doi.org/10.1007/s42770-019-00119-w

Keywords

  • PMSI
  • Epinecrotic
  • Epilithic
  • Forensic
  • Microorganism