Virus communities are associated with the degradation of recalcitrant carbon during the corpse decay of plateau pika (Ochoton curzoniae)

Abstract

Background: It has been reported that bacteria and fungi play a vital role in soil biogeochemical cycles during the decomposition of animal corpses. However, it is poorly understood how the viral composition and function of grassland soil change during the decay of wild mammal corpses.

Methods: Here, we tracked soil viral succession in the 94-day decomposition of mammalian (plateau pika) wildlife corpses through metagenomic analysis, 16S rRNA gene sequencing, and soil physicochemical assessment.

Results: A total of 2413 virus species were detected, and Podoviridae, Poxviridae, Mimiviridae, and Siphoviridae were abundant in the gravesoil (soil beneath the corpse). Viral diversity first followed a trend of decline and then increased in the gravesoil with succession time. Total carbon in the gravesoil had a significant negative correlation with viral diversity and Myoviridae. Stochastic processes dominated the assembly of viral communities and decreased with succession time in both control and gravesoil groups. The network interactions between viruses and bacteria became more complex and tighter, indicating a closer and mutualistic virus-host relationship during carrion decay. Notably, the major virus-associated carbon function involved the degradation of recalcitrant carbon (e.g., lignin, chitin, pectin, and cellulose).

Conclusions: Our study broadens the understanding of the functional role of viruses that participate in the biochemical cycle of grassland soil during the decay of animal remains.

Keywords

biochemical cycle / carbon decomposition / metagenomics / plateau pika / virus / wildlife carcass

References

[1] Abdallah, R. Z., Wegner, C.-E., & Liesack, W. (2019). Community transcriptomics reveals drainage effects on paddy soil microbiome across all three domains of life. Soil Biology and Biochemistry, 132, 131-142. https://doi.org/10.1016/j.soilbio.2019.01.023

[2] Albright, M. B. N., Gallegos-Graves, L. V., Feeser, K. L., Montoya, K., Emerson, J. B., Shakya, M., & Dunbar, J. (2022). Experimental evidence for the impact of soil viruses on carbon cycling during surface plant litter decomposition. ISME Communications, 2, 24. https://doi.org/10.1038/s43705-022-00109-4

[3] Andrew, S. (2010). FastQC: A quality control tool for high throughput sequence data. https://github.com/s-andrews/FastQC.

[4] Anderson, M. J. (2017). Permutational multivariate analysis of variance (PERMANOVA) (pp. 1-15). Wiley StatsRef: Statistics Reference Online. https://doi.org/10.1002/9781118445112.stat07841

[5] Bastian, M., Heymann, S., & Jacomy, M. (2009). Gephi: An open source software for exploring and manipulating networks. In Proceedings of the international AAAI conference on web and social media (Vol. 3, pp. 361-362). https://doi.org/10.1609/icwsm.v3i1.13937

[6] Besemer, J., & Borodovsky, M. (2005). GeneMark: Web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Research, 33(Suppl. 2), W451-W454. https://doi.org/10.1093/nar/gki487

[7] Blumer-Schuette, S. E., Giannone, R. J., Zurawski, J. V., Ozdemir, I., Ma, Q., Yin, Y., Xu, Y., Kataeva, I., Poole, F. L., Adams, M. W. W., Hamilton-Brehm, S. D., Elkins, J. G., Larimer, F. W., Land, M. L., Hauser, L. J., Cottingham, R. W., Hettich, R. L., & Kelly, R. M. (2012). Caldicellulosiruptor core and pangenomes reveal determinants for noncellulosomal thermophilic deconstruction of plant biomass. Journal of Bacteriology, 194(15), 4015-4028. https://doi.org/10.1128/JB.00266-12

[8] Boyd, E. F. (2012). Chapter 4 - Bacteriophage-encoded bacterial virulence factors and phage-pathogenicity island interactions. In M. Łobocka, & W. T. Szybalski (Eds.), Advances in virus research (Vol. 82, pp. 91-118). Academic Press.

[9] Breitbart, M. (2012). Marine viruses: Truth or dare. Annual Review of Marine Science, 4(1), 425-448. https://doi.org/10.1146/annurev-marine-120709-142805

[10] Breitbart, M., Bonnain, C., Malki, K., & Sawaya, N. A. (2018). Phage puppet masters of the marine microbial realm. Nature Microbiology, 3(7), 754-766. https://doi.org/10.1038/s41564-018-0166-y

[11] Breitbart, M., Salamon, P., Andresen, B., Mahaffy, J. M., Segall, A. M., Mead, D., Azam, F., & Rohwer, F. (2002). Genomic analysis of uncultured marine viral communities. Proceedings of the National Academy of Sciences of the United States of America, 99(22), 14250-14255. https://doi.org/10.1073/pnas.202488399

[12] Breitbart, M., Thompson, L., Suttle, C., & Sullivan, M. (2007). Exploring the vast diversity of marine viruses. Oceanography, 20(2), 135-139. https://doi.org/10.5670/oceanog.2007.58

[13] Brum, J. R., & Sullivan, M. B. (2015). Rising to the challenge: Accelerated pace of discovery transforms marine virology. Nature Reviews Microbiology, 13(3), 147-159. https://doi.org/10.1038/nrmicro3404

[14] Buchfink, B., Xie, C., & Huson, D. H. (2015). Fast and sensitive protein alignment using DIAMOND. Nature Methods, 12(1), 59-60. https://doi.org/10.1038/nmeth.3176

[15] Burcham, Z. M., Belk, A. D., McGivern, B. B., Bouslimani, A., Ghadermazi, P., Martino, C., Shenhav, L., Zhang, A. R., Shi, P., Emmons, A., Deel, H. L., Xu, Z. Z., Nieciecki, V., Zhu, Q., Shaffer, M., Panitchpakdi, M., Weldon, K. C., Cantrell, K., Ben-Hur, A., … Metcalf, J. L. (2024). A conserved interdomain microbial network underpins cadaver decomposition despite environmental variables. Nature Microbiology, 9(3), 595-613. https://doi.org/10.1038/s41564-023-01580-y

[16] Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., Fierer, N., Peña, A. G., Goodrich, J. K., Gordon, J. I., Huttley, G. A., Kelley, S. T., Knights, D., Koenig, J. E., Ley, R. E., Lozupone, C. A., McDonald, D., Muegge, B. D., Pirrung, M., … Knight, R. (2010). QIIME allows analysis of high-throughput community sequencing data. Nature Methods, 7(5), 335-336. https://doi.org/10.1038/nmeth.f.303

[17] Carter, D. O., Yellowlees, D., & Tibbett, M. (2006). Cadaver decomposition in terrestrial ecosystems. Naturwissenschaften, 94, 12-24. https://doi.org/10.1007/s00114-006-0159-1

[18] Chapman, M., & Underwood, A. (1999). Ecological patterns in multivariate assemblages: Information and interpretation of negative values in ANOSIM tests. Marine Ecology Progress Series, 180, 257-265. https://doi.org/10.3354/meps180257

[19] Chen, L., Wang, G., Wan, X., & Liu, W. (2015). Complex and nonlinear effects of weather and density on the demography of small herbivorous mammals. Basic and Applied Ecology, 16(2), 172-179. https://doi.org/10.1016/j.baae.2014.12.002

[20] Dai, Z., Zang, H., Chen, J., Fu, Y., Wang, X., Liu, H., Shen, C., Wang, J., Kuzyakov, Y., Becker, J. N., Hemp, A., Barberán, A., Gunina, A., Chen, H., Luo, Y., & Xu, J. (2021). Metagenomic insights into soil microbial communities involved in carbon cycling along an elevation climosequences. Environmental Microbiology, 23(8), 4631-4645. https://doi.org/10.1111/1462-2920.15655

[21] Daly, R. A., Roux, S., Borton, M. A., Morgan, D. M., Johnston, M. D., Booker, A. E., Hoyt, D. W., Meulia, T., Wolfe, R. A., Hanson, A. J., Mouser, P. J., Moore, J. D., Wunch, K., Sullivan, M. B., Wrighton, K. C., & Wilkins, M. J. (2019). Viruses control dominant bacteria colonizing the terrestrial deep biosphere after hydraulic fracturing. Nature Microbiology, 4(2), 352-361. https://doi.org/10.1038/s41564-018-0312-6

[22] Dedrick, R. M., Jacobs-Sera, D., Bustamante, C. A. G., Garlena, R. A., Mavrich, T. N., Pope, W. H., Reyes, J. C. C., Russell, D. A., Adair, T., Alvey, R., Bonilla, J. A., Bricker, J. S., Brown, B. R., Byrnes, D., Cresawn, S. G., Davis, W. B., Dickson, L. A., Edgington, N. P., Findley, A. M., … Hatfull, G. F. (2017). Prophage-mediated defence against viral attack and viral counter-defence. Nature Microbiology, 2, 16251. https://doi.org/10.1038/nmicrobiol.2016.251

[23] Drula, E., Garron, M.-L., Dogan, S., Lombard, V., Henrissat, B., & Terrapon, N. (2022). The carbohydrate-active enzyme database: Functions and literature. Nucleic Acids Research, 50(D1), D571-D577. https://doi.org/10.1093/nar/gkab1045

[24] Emerson, J. B., Roux, S., Brum, J. R., Bolduc, B., Woodcroft, B. J., Jang, H. B., Singleton, C. M., Solden, L. M., Naas, A. E., Boyd, J. A., Hodgkins, S. B., Wilson, R. M., Trubl, G., Li, C., Frolking, S., Pope, P. B., Wrighton, K. C., Crill, P. M., Chanton, J. P., … Sullivan, M. B. (2018). Host-linked soil viral ecology along a permafrost thaw gradient. Nature Microbiology, 3, 870-880. https://doi.org/10.1038/s41564-018-0190-y

[25] Gao, S.-M., Schippers, A., Chen, N., Yuan, Y., Zhang, M.-M., Li, Q., Liao, B., Shu, W.-S., & Huang, L.-N. (2020). Depth-related variability in viral communities in highly stratified sulfidic mine tailings. Microbiome, 8, 89. https://doi.org/10.1186/s40168-020-00848-3

[26] Hou, L., Mulla, S. I., Niño-Garcia, J. P., Ning, D., Rashid, A., Hu, A., & Yu, C. P. (2019). Deterministic and stochastic processes driving the shift in the prokaryotic community composition in wastewater treatment plants of a coastal Chinese city. Applied Microbiology and Biotechnology, 103(21-22), 9155-9168. https://doi.org/10.1007/s00253-019-10177-7

[27] Huang, D., Yu, P., Ye, M., Schwarz, C., Jiang, X., & Alvarez, P. J. J. (2021). Enhanced mutualistic symbiosis between soil phages and bacteria with elevated chromium-induced environmental stress. Microbiome, 9, 150. https://doi.org/10.1186/s40168-021-01074-1

[28] Hurwitz, B. L., U'Ren, J. M. (2016). Viral metabolic reprogramming in marine ecosystems. Current Opinion in Microbiology, 31, 161-168. https://doi.org/10.1016/j.mib.2016.04.002

[29] Jansson, J. K., & Wu, R. (2022). Soil viral diversity, ecology and climate change. Nature Reviews Microbiology, 21, 296-311. https://doi.org/10.1038/s41579-022-00811-z

[30] Jiao, X., Tan, C., Li, T., Li, X., & Qu, J. (2018). Efficacy of aerial application of rodenticide to control plateau pika (Ochotona curzoniae). Chinese Journal of Vector Biology and Control, 29(5), 488-490. https://doi.org/10.11853/j.issn.1003.8280.2018.05.017

[31] Kanehisa, M., & Goto, S. (2000). KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Research, 28(1), 27-30. https://doi.org/10.1093/nar/28.1.27

[32] Keenan, S. W., Schaeffer, S. M., Jin, V. L., & DeBruyn, J. M. (2018). Mortality hotspots: nitrogen cycling in forest soils during vertebrate decomposition. Soil Biology and Biochemistry, 121, 165-176. https://doi.org/10.1016/j.soilbio.2018.03.005

[33] Langmead, B., & Salzberg, S. L. (2012). Fast gapped-read alignment with Bowtie 2. Nature Methods, 9, 357-359. https://doi.org/10.1038/nmeth.1923

[34] Li, W., & Godzik, A. (2006). Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics, 22(13), 1658-1659. https://doi.org/10.1093/bioinformatics/btl158

[35] Li, Z., Pan, D., Wei, G., Pi, W., Zhang, C., Wang, J.-H., Peng, Y., Zhang, L., Wang, Y., Hubert, C. R. J., & Dong, X. (2021). Deep sea sediments associated with cold seeps are a subsurface reservoir of viral diversity. The ISME Journal, 15(8), 2366-2378. https://doi.org/10.1038/s41396-021-00932-y

[36] Liang, X., Radosevich, M., DeBruyn, J. M., Wilhelm, S. W., McDearis, R., & Zhuang, J. (2024). Incorporating viruses into soil ecology: A new dimension to understand biogeochemical cycling. Critical Reviews in Environmental Science Technology & Development of Chemical Industry, 54(2), 117-137. https://doi.org/10.1080/10643389.2023.2223123

[37] Liang, X., Wang, Y., Zhang, Y., Zhuang, J., & Radosevich, M. (2021). Viral abundance, community structure and correlation with bacterial community in soils of different cover plants. Appllied Soil Ecology, 168, 104138. https://doi.org/10.1016/j.apsoil.2021.104138

[38] López-Mondéjar, R., Zühlke, D., Becher, D., Riedel, K., & Baldrian, P. (2016). Cellulose and hemicellulose decomposition by forest soil bacteria proceeds by the action of structurally variable enzymatic systems. Scientific Reports, 6, 25279. https://doi.org/10.1038/srep25279

[39] López-Mondéjar, R., Zühlke, D., Větrovský, T., Becher, D., Riedel, K., & Baldrian, P. (2016). Decoding the complete arsenal for cellulose and hemicellulose deconstruction in the highly efficient cellulose decomposer Paenibacillus O199. Biotechnology for Biofuels, 9, 104. https://doi.org/10.1186/s13068-016-0518-x

[40] Luo, Y., Zang, H., Yu, Z., Chen, Z., Gunina, A., Kuzyakov, Y., Xu, J., Zhang, K., & Brookes, P. C. (2017). Priming effects in biochar enriched soils using a three-source-partitioning approach: ¹⁴C labelling and ¹³C natural abundance. Soil Biology and Biochemistry, 106, 28-35. https://doi.org/10.1016/j.soilbio.2016.12.006

[41] Malik, A. A., Puissant, J., Buckeridge, K. M., Goodall, T., Jehmlich, N., Chowdhury, S., Gweon, H. S., Peyton, J. M., Mason, K. E., van Agtmaal, M., Blaud, A., Clark, I. M., Whitaker, J., Pywell, R. F., Ostle, N., Gleixner, G., & Griffiths, R. I. (2018). Land use driven change in soil pH affects microbial carbon cycling processes. Nature Communications, 9, 3591. https://doi.org/10.1038/s41467-018-05980-1

[42] Martin, M. (2011). Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet Journal, 17(1), 10-12. https://doi.org/10.14806/ej.17.1.200

[43] Metcalf, J. L., Xu, Z. Z., Weiss, S., Lax, S., Van Treuren, W., Hyde, E. R., Song, S. J., Amir, A., Larsen, P., Sangwan, N., Haarmann, D., Humphrey, G. C., Ackermann, G., Thompson, L. R., Lauber, C., Bibat, A., Nicholas, C., Gebert, M. J., Petrosino, J. F., … Knight, R. (2016). Microbial community assembly and metabolic function during mammalian corpse decomposition. Science, 351, 158-162. https://doi.org/10.1126/science.aad2646

[44] Nobrega, F. L., Vlot, M., de Jonge, P. A., Dreesens, L. L., Beaumont, H. J. E., Lavigne, R., Dutilh, B. E., & Brouns, S. J. J. (2018). Targeting mechanisms of tailed bacteriophages. Nature Reviews Microbiology, 16(12), 760-773. https://doi.org/10.1038/s41579-018-0070-8

[45] Osiro, K. O., de Camargo, B. R., Satomi, R., Hamann, P. R. V., Silva, J. P., de Sousa, M. V., Quirino, B. F., Aquino, E. N., Felix, C. R., Murad, A. M., & Noronha, E. F. (2017). Characterization of Clostridium thermocellum (B8) secretome and purified cellulosomes for lignocellulosic biomass degradation. Enzyme and Microbial Technology, 97, 43-54. https://doi.org/10.1016/j.enzmictec.2016.11.002

[46] Paez-Espino, D., Eloe-Fadrosh, E. A., Pavlopoulos, G. A., Thomas, A. D., Huntemann, M., Mikhailova, N., Rubin, E., Ivanova, N. N., & Kyrpides, N. C. (2016). Uncovering earth's virome. Nature, 536, 425-430. https://doi.org/10.1038/nature19094

[47] Parmenter, R. R., & MacMahon, J. A. (2009). Carrion decomposition and nutrient cycling in a semiarid shrub-steppe ecosystem. Ecological Monographs, 79(4), 637-661. https://doi.org/10.1890/08-0972.1

[48] Peng, Y., Leung, H. C. M., Yiu, S. M., & Chin, F. Y. L. (2012). IDBA-UD: A de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics, 28(11), 1420-1428. https://doi.org/10.1093/bioinformatics/bts174

[49] Pertea, G. (2015). fqtrim: v0. 9.4 release. http://ccb.jhu.edu/software/fqtrim/index.shtml

[50] Pold, G., Billings, A. F., Blanchard, J. L., Burkhardt, D. B., Frey, S. D., Melillo, J. M., Schnabel, J., van Diepen, L. T. A., & DeAngelis, K. M. (2016). Long-term warming alters carbohydrate degradation potential in temperate forest soils. Applied and Environmental Microbiology, 82(22), 6518-6530. https://doi.org/10.1128/AEM.02012-16

[51] Qu, J., Russell, J. C., Ji, W., Yang, M., Chen, Q., Li, W., & Zhang, Y. (2017). Five-year population dynamics of plateau pikas (Ochotona curzoniae) on the east of Tibetan plateau. European Journal of Wildlife Research, 63(3), 51. https://doi.org/10.1007/s10344-017-1109-2

[52] Roossinck, M. J. (2011). The good viruses: Viral mutualistic symbioses. Nature Reviews Microbiology, 9(2), 99-108. https://doi.org/10.1038/nrmicro2491

[53] Sime-Ngando, T. (2014). Environmental bacteriophages: Viruses of microbes in aquatic ecosystems. Frontiers in Microbiology, 5, 355. https://doi.org/10.3389/fmicb.2014.00355

[54] Smith, A. T., & Foggin, J. M. (1999). The plateau pika (Ochotona curzoniae) is a keystone species for biodiversity on the Tibetan plateau. Animal Conservation, 2(4), 235-240. https://doi.org/10.1111/j.1469-1795.1999.tb00069.x

[55] Su, W., Wang, S., Yang, J., Yu, Q., Wirth, S., Huang, X., Qi, W., Zhang, X., & Li, H. (2022). Corpse decay of wild animals leads to the divergent succession of nrfA-type microbial communities. Applied Microbiology and Biotechnology, 106(13), 5287-5300. https://doi.org/10.1007/s00253-022-12065-z

[56] Suttle, C. A. (2005). Viruses in the sea. Nature, 437, 356-361. https://doi.org/10.1038/nature04160

[57] Tong, D., Wang, Y., Yu, H., Shen, H., Dahlgren, R. A., & Xu, J. (2023). Viral lysing can alleviate microbial nutrient limitations and accumulate recalcitrant dissolved organic matter components in soil. The ISME Journal, 17(8), 1247-1256. https://doi.org/10.1038/s41396-023-01438-5

[58] Vass, A. A., Smith, R. R., Thompson, C. V., Burnett, M. N., Dulgerian, N., & Eckenrode, B. A. (2008). Odor analysis of decomposing buried human remains. Journal of Forensic Sciences, 53(2), 384-391. https://doi.org/10.1111/j.1556-4029.2008.00680.x

[59] Wang, H., Liu, S., Zhang, X., Mao, Q., Li, X., You, Y., Wang, J., Zheng, M., Zhang, W., Lu, X., & Mo, J. (2018). Nitrogen addition reduces soil bacterial richness, while phosphorus addition alters community composition in an old-growth N-rich tropical forest in Southern China. Soil Biology and Biochemistry, 127, 22-30. https://doi.org/10.1016/j.soilbio.2018.08.022

[60] Warwick-Dugdale, J., Buchholz, H. H., Allen, M. J., & Temperton, B. (2019). Host-hijacking and planktonic piracy: How phages command the microbial high seas. Virology Journal, 16, 15. https://doi.org/10.1186/s12985-019-1120-1

[61] Williamson, K. E., Fuhrmann, J. J., Wommack, K. E., & Radosevich, M. (2017). Viruses in soil ecosystems: An unknown quantity within an unexplored territory. Annual Review of Virology, 4, 201-219. https://doi.org/10.1146/annurev-virology-101416-041639

[62] Wommack, K. E., & Colwell, R. R. (2000). Virioplankton: Viruses in aquatic ecosystems. Microbiology and Molecular Biology Reviews, 64(1), 69-114. https://doi.org/10.1128/mmbr.64.1.69-114.2000

[63] Yang, J., Su, W., Yu, Q., Shi, Z., Huang, X., Heděnec, P., Zhou, H., Qu, J., & Li, H. (2022). The long-term decomposition of wild animal corpses leads to carbon and phosphorus accumulation and disturbs the ecological succession of the denitrification community encoded by narG. Appllied Soil Ecology, 175, 104455. https://doi.org/10.1016/j.apsoil.2022.104455

[64] Ye, M., Sun, M., Huang, D., Zhang, Z., Zhang, H., Zhang, S., Hu, F., Jiang, X., & Jiao, W. (2019). A review of bacteriophage therapy for pathogenic bacteria inactivation in the soil environment. Environment International, 129, 488-496. https://doi.org/10.1016/j.envint.2019.05.062

[65] Yu, Q., Zhou, R., Wang, Y., Feng, T., & Li, H. (2020). Corpse decomposition increases nitrogen pollution and alters the succession of nirK-type denitrifying communities in different water types. Science of the Total Environment, 747, 141472. https://doi.org/10.1016/j.scitotenv.2020.141472

[66] Yu, Q., Zhou, R., Wang, Y., Su, W., Yang, J., Feng, T., Dou, Y., & Li, H. (2021). Carcass decay deteriorates water quality and modifies the nirS denitrifying communities in different degradation stages. Science of the Total Environment, 785, 147185. https://doi.org/10.1016/j.scitotenv.2021.147185

[67] Zeng, J., Liu, X., Song, L., Lin, X., Zhang, H., Shen, C., & Chu, H. (2016). Nitrogen fertilization directly affects soil bacterial diversity and indirectly affects bacterial community composition. Soil Biology and Biochemistry, 92, 41-49. https://doi.org/10.1016/j.soilbio.2015.09.018

[68] Zhang, J., Sayer, E. J., Zhou, J., Li, Y., Li, Y., Li, Z., & Wang, F. (2021). Long-term fertilization modifies the mineralization of soil organic matter in response to added substrate. Science of the Total Environment, 798, 149341. https://doi.org/10.1016/j.scitotenv.2021.149341

[69] Zhong, C., Han, M., Yu, S., Yang, P., Li, H., & Ning, K. (2018). Pan-genome analyses of 24 Shewanella strains re-emphasize the diversification of their functions yet evolutionary dynamics of metal-reducing pathway. Biotechnology for Biofuels, 11, 193. https://doi.org/10.1186/s13068-018-1201-1

[70] Zhou, R., Wang, Y., Hilal, M. G., Yu, Q., Feng, T., & Li, H. (2021). Temporal succession of water microbiomes and resistomes during carcass decomposition in a fish model. Journal of Hazardous Materials, 403, 123795. https://doi.org/10.1016/j.jhazmat.2020.123795

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