Using eDNA to determine the source of organic carbon in seagrass meadows

Limnology and Oceanography

Volumn 62, Issue 3, 2017, Pages 1254-1265

  Reef, Ruth ^a,b,c   Atwood, Trisha B ^a,d   Samper Villarreal, Jimena ^a,e   Adame, Maria Fernanda ^f   Sampayo, Eugenia M ^a   Lovelock, Catherine E ^a  

^a UNIVERSITY OF QUEENSLAND   (Australia)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^c MONASH UNIVERSITY   (Australia)

^d UTAH STATE UNIVERSITY   (United States)

^e UNIVERSIDAD DE COSTA RICA   (Costa Rica)

^f GRIFFITH UNIVERSITY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

CARBON BUDGET; CARBON FIXATION; CARBON ISOTOPE; MANGROVE; MEADOW; NITROGEN ISOTOPE; ORGANIC CARBON; SALTMARSH; SEAGRASS; SEDIMENT ANALYSIS;

AUSTRALIA; MORETON BAY; QUEENSLAND;

EID: 85016996327     PISSN: None     EISSN: 19395590     Source Type: Journal    
DOI: 10.1002/lno.10499     Document Type: Article

References (56)

1. Adame, M. F., S. F. Wright, A. Grinham, K. Lobb, C. E. Reymond, and C. E. Lovelock. 2012. Terrestrial–marine connectivity: Patterns of terrestrial soil carbon deposition in coastal sediments determined by analysis of glomalin related soil protein. Limnol. Oceanogr. 57: 1492–1502. doi:10.4319/lo.2012.57.5.1492
2. Anderson-Carpenter, L. L., J. S. McLachlan, S. T. Jackson, M. Kuch, C. Y. Lumibao, and H. N. Poinar. 2011. Ancient DNA from lake sediments: Bridging the gap between paleoecology and genetics. BMC Evol. Biol. 11: 1–15. doi:10.1186/1471-2148-11-30
3. Ball, M. C. 2009. Photosynthesis in mangroves. Wetlands (Australia) 6: 12–22.
4. Bauer, J. E., W. J. Cai, P. A. Raymond, T. S. Bianchi, C. S. Hopkinson, and P. A. Regnier. 2013. The changing carbon cycle of the coastal ocean. Nature 504: 61–70. doi:10.1038/nature12857
5. CBOL Plant Working Group. 2009. A DNA barcode for land plants. Proc. Natl. Acad. Sci. USA 106: 12794–12797. doi:10.1073/pnas.0905845106
6. Chen, S., and others. 2010. Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species. PLoS ONE 5: e8613. doi:10.1371/journal.pone.0008613
7. Connolly, R. M., and N. J. Waltham. 2015. Spatial analysis of carbon isotopes reveals seagrass contribution to fishery food web. Ecosphere 6: 1–12. doi:10.1890/ES14-00243.1
8. Coverdale, T. C., C. P. Brisson, E. W. Young, S. F. Yin, J. P. Donnelly, and M. D. Bertness. 2014. Indirect human impacts reverse centuries of carbon sequestration and salt marsh accretion. PLoS ONE 9: e93296. doi:10.1371/journal.pone.0093296
9. Deegan, L. A., D. S. Johnson, R. S. Warren, B. J. Peterson, J. W. Fleeger, S. Fagherazzi, and W. M. Wollheim. 2012. Coastal eutrophication as a driver of salt marsh loss. Nature 490: 388–392. doi:10.1038/nature11533
10. Deiner, K., and F. Altermatt. 2014. Transport distance of invertebrate environmental DNA in a natural river. PLoS ONE 9: e88786. doi:10.1371/journal.pone.0088786
11. Dejean, T., A. Valentini, A. Duparc, S. Pellier-Cuit, F. Pompanon, P. Taberlet, and C. Miaud. 2011. Persistence of environmental DNA in freshwater ecosystems. PLoS ONE 6: e23398. doi:10.1371/journal.pone.0023398
12. Dennison, W. C., and E. G. Abal. 1999. Moreton Bay study: A scientific basis for the healthy waterways campaign. South East Qld Regional Water Quality Management Strategy Team.
13. Donato, D. C., J. B. Kauffman, D. Murdiyarso, S. Kurnianto, M. Stidham, and M. Kanninen. 2011. Mangroves among the most carbon-rich forests in the tropics. Nat. Geosci. 4: 293–297. doi:10.1038/ngeo1123
14. Duarte, C. M., I. J. Losada, I. E. Hendriks, I. Mazarrasa, and N. Marba. 2013. The role of coastal plant communities for climate change mitigation and adaptation. Nat. Clim. Chang. 3: 961–968. doi:10.1038/nclimate1970
15. Emmett-Mattox, S., S. Crooks, and J. Findsen. 2010. Wetland grasses and gases: Are tidal wetlands ready for the carbon markets. National Wetlands Newslett. 32: 6–10. http://esassoc.com/sites/default/files/wetland-grasses-and-gases.pdf
16. Fourqurean, J. W., and others. 2012. Seagrass ecosystems as a globally significant carbon stock. Nat. Geosci. 5: 505–509. doi:10.1038/ngeo1477
17. Fry, B. 2013. Alternative approaches for solving underdetermined isotope mixing problems. Mar. Ecol. Prog. Ser. 472: 1–13. doi:10.3354/meps10168
18. Fry, B., M. Cieri, J. Hughes, C. Tobias, L. A. Deegan, and B. Peterson. 2008. Stable isotope monitoring of benthic–planktonic coupling using salt marsh fish. Mar. Ecol. Prog. Ser. 369: 193–204. doi:10.3354/meps07644
19. Galimberti, A., F. De Mattia, I. Bruni, D. Scaccabarozzi, A. Sandionigi, M. Barbuto, M. Casiraghi, and M. Labra. 2014. A DNA barcoding approach to characterize pollen collected by honeybees. PLoS ONE 9: e109363. doi:10.1371/journal.pone.0109363
20. Gonneea, M. E., A. Paytan, and J. Herrera-Silveira. 2004. Tracing organic matter sources and carbon burial in mangrove sediments over the past 160 years. Estuar. Coast. Shelf Sci. 61: 211–227. doi:10.1016/j.ecss.2004.04.015
21. Hemminga, M., and M. Mateo. 1996. Stable carbon isotopes in seagrasses: Variability in ratios and use in ecological studies. Mar. Ecol. Prog. Ser. 140: 285–298. doi:10.3354/meps140285
22. Holmer, M., and A. Olsen Bachmann. 2002. Role of decomposition of mangrove and seagrass detritus in sediment carbon and nitrogen cycling in a tropical mangrove forest. Mar. Ecol. Prog. Ser. 230: 87–101. doi:10.3354/meps230087
23. Kauffman, J. B., C. Heider, J. Norfolk, and F. Payton. 2014. Carbon stocks of intact mangroves and carbon emissions arising from their conversion in the Dominican Republic. Ecol. Appl. 24: 518–527. doi:10.1890/13-0640.1
24. Kennedy, H., J. Beggins, C. M. Duarte, J. W. Fourqurean, M. Holmer, N. Marbà, and J. J. Middelburg. 2010. Seagrass sediments as a global carbon sink: Isotopic constraints. Global Biogeochem. Cycles 24. doi:10.1029/2010GB003848
25. 13C and C/N ratios in organic material. Earth Sci. Rev. 75: 29–57. doi:10.1016/j.earscirev.2005.10.003
26. Leithold, E. L., and R. S. Hope. 1999. Deposition and modification of a flood layer on the northern California shelf: Lessons from and about the fate of terrestrial particulate organic carbon. Mar. Geol. 154: 183–195. doi:10.1016/S0025-3227(98)00112-1
27. Little, D. P. 2014. A DNA mini-barcode for land plants. Mol. Ecol. Resour. 14: 437–446. doi:10.1111/1755-0998.12194
28. Lucas, C., T. Thangaradjou, and J. Papenbrock. 2012. Development of a DNA barcoding system for seagrasses: Successful but not simple. PLoS ONE 7: e29987. doi:10.1371/journal.pone.0029987
29. Marbà, N., A. Arias-Ortiz, P. Masqué, G. A. Kendrick, I. Mazarrasa, G. R. Bastyan, J. Garcia-Orellana, and C. M. Duarte. 2015. Impact of seagrass loss and subsequent revegetation on carbon sequestration and stocks. J. Ecol. 103: 296–302. doi:10.1111/1365-2745.12370
30. Mateo, M. A., J. Romero, M. Pérez, M. M. Littler, and D. S. Littler. 1997. Dynamics of millenary organic deposits resulting from the growth of the Mediterranean seagrass Posidonia oceanica. Estuar. Coast. Shelf Sci. 44: 103–110. doi:10.1006/ecss.1996.0116
31. 2. Front. Ecol. Environ. 9: 552–560. doi:10.1890/110004
32. Monacci, N. M., U. Meier-Grünhagen, B. P. Finney, H. Behling, and M. J. Wooller. 2011. Paleoecology of mangroves along the Sibun River, Belize. Quat. Res. 76: 220–228. doi:10.1016/j.yqres.2011.06.001
33. Nguyen, X. V., S. Höfler, Y. Glasenapp, T. Thangaradjou, C. Lucas, and J. Papenbrock. 2015. New insights into DNA barcoding of seagrasses. Syst. Biodivers. 13: 496–508. doi:10.1080/14772000.2015.1046408
34. Oksanen, J., and others. 2015. vegan: Community Ecology Package.
35. Orth, R. J., and others. 2006. A Global crisis for seagrass ecosystems. BioScience 56: 987–996. doi:10.1641/0006-3568(2006)56[987:AGCFSE]2.0.CO;2
36. Parnell, A. C., R. Inger, S. Bearhop, and A. L. Jackson. 2010. Source partitioning using stable isotopes: Coping with too much variation. PLoS ONE 5: e9672. doi:10.1371/journal.pone.0009672
37. Pedersen, M. W., and others. 2015. Ancient and modern environmental DNA. Philos. Trans. R. Soc. B Biol. Sci. 370. doi:10.1098/rstb.2013.0383
38. Pendleton, L., and others. 2012. Estimating global “blue carbon” emissions from conversion and degradation of vegetated coastal ecosystems. PloS One 7: e43542. doi:10.1371/journal.pone.0029987 doi:10.1371/journal.pone.0043542
39. Prahl, F. G., J. R. Ertel, M. A. Goni, M. A. Sparrow, and B. Eversmeyer. 1994. Terrestrial organic carbon contributions to sediments on the Washington margin. Geochim. Cosmochim. Acta 58: 3035–3048. doi:10.1016/0016-7037(94)90177-5
40. Reef, R., S. Dunn, O. Levy, S. Dove, E. Shemesh, I. Brickner, W. Leggat, and O. Hoegh-Guldberg. 2009. Photoreactivation is the main repair pathway for UV-induced DNA damage in coral planulae. J. Exp. Biol. 212: 2760–2766. doi:10.1242/jeb.031286
41. Reef, R., I. C. Feller, and C. E. Lovelock. 2014. Mammalian herbivores in Australia transport nutrients from terrestrial to marine ecosystems via mangroves. J. Trop. Ecol. 30: 179–188. doi:10.1017/S0266467414000054
42. Rees, H. C., B. C. Maddison, D. J. Middleditch, J. R. Patmore, and K. C. Gough. 2014. REVIEW: The detection of aquatic animal species using environmental DNA–a review of eDNA as a survey tool in ecology. J. Appl. Ecol. 51: 1450–1459. doi: 10.1111/1365-2664.12306
43. Rodelli, M. R., J. N. Gearing, P. J. Gearing, N. Marshall, and A. Sasekumar. 1984. Stable isotope ratio as a tracer of mangrove carbon in Malaysian ecosystems. Oecologia 61: 326–333. doi:10.1007/BF00379629
44. Roelfsema, C., E. M. Kovacs, M. I. Saunders, S. Phinn, M. Lyons, and P. Maxwell. 2013. Challenges of remote sensing for quantifying changes in large complex seagrass environments. Estuar. Coast. Shelf Sci. 133: 161–171. doi:10.1016/j.ecss.2013.08.026
45. Romanowski, G., M. G. Lorenz, and W. Wackernagel. 1991. Adsorption of plasmid DNA to mineral surfaces and protection against DNase I. Appl. Environ. Microbiol. 57: 1057–1061.
46. Samper-Villarreal, J., C. E. Lovelock, M. I. Saunders, C. Roelfsema, and P. J. Mumby. 2016. Organic carbon in seagrass sediments is influenced by seagrass canopy complexity, turbidity, wave height, and water depth. Limnol. Oceanogr. 938–952. doi:10.1002/lno.10262
47. Saunders, M. I., and others. 2013. Coastal retreat and improved water quality mitigate losses of seagrass from sea level rise. Glob. Chang. Biol. 19: 2569–2583. doi:10.1111/gcb.12218
48. Simpson, G. L., and J. Oksanen. 2015. analogue: Analogue matching and Modern Analogue Technique transfer function models.
49. Thomsen, P. F., J. Kielgast, L. L. Iversen, P. R. Møller, M. Rasmussen, and E. Willerslev. 2012. Detection of a diverse marine fish fauna using environmental DNA from seawater samples. PLoS ONE 7: e41732. doi:10.1371/journal.pone.0041732
50. Thomsen, P. F., and E. Willerslev. 2015. Environmental DNA—An emerging tool in conservation for monitoring past and present biodiversity. Biol. Conserv. 183: 4–18. doi:10.1016/j.biocon.2014.11.019
51. Trevathan-Tackett, S. M., J. Kelleway, P. I. Macreadie, J. Beardall, P. Ralph, and A. Bellgrove. 2015. Comparison of marine macrophytes for their contributions to blue carbon sequestration. Ecology 96: 3043–3057. doi:10.1890/15-0149.1
52. Valiela, I., J. Bowen, and J. York. 2001. Mangrove forests: One of the world's threatened major tropical environments. Bioscience 51: 807–815. doi:10.1641/0006-3568(2001)051[0807:MFOOTW]2.0.CO;2
53. Watanabe, K., and T. Kuwae. 2015. How organic carbon derived from multiple sources contributes to carbon sequestration processes in a shallow coastal system? Glob. Chang. Biol. 21: 2612–2623. doi:10.1111/gcb.12924
54. Waycott, M., and others. 2009. Accelerating loss of seagrasses across the globe threatens coastal ecosystems. Proc. Natl. Acad. Sci. USA 106: 12377–12381. doi:10.1073/pnas.0905620106
55. Willerslev, E., and others. 2003. Diverse plant and animal DNA from Holocene and Pleistocene sedimentary records. Science 300. doi:10.1126/science.1084114
56. Yoccoz, N. G., and others. 2012. DNA from soil mirrors plant taxonomic and growth form diversity. Mol. Ecol. 21: 3647–3655. doi:10.1111/j.1365-294X.2012.05545.x