Research Article
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Assessment of microbial community diversity in lakes of İğneada floodplain forest by metabarcoding approach

Year 2021, Volume: 4 Issue: 4, 304 - 312, 01.10.2021

Emine Gözde Özbayram , İbrahim Halil Miraloğlu Bahar İnce

https://doi.org/10.3153/AR21025

Abstract

This paper aims to contribute to the understanding of bacterial community patterns of the lakes of İğneada Floodplain Forest by metabarcoding approach. Within this scope, surface water samples were collected from three lakes located in the area namely Mert Lake, Hamam Lake, and Saka Lake, and the bacterial diversity was assessed by a high throughput sequencing of the 16S rRNA gene. Chao1 richness and Shannon diversity were higher in Saka Lake indicated a more diverse bacterial community. Proteobacteria was by far the most abundant phyla in all lakes. Although Bacteroidetes and Actinobacteria also dominated the community, their abundances differed in each lake. While the family Burkholderiaceae represented 25% of the bacterial community in Saka Lake, the abundances were 9% and 4% in Hamam Lake and Mert Lake, respectively. This study is one of the first investigations specifically focused on the bacterial communities in three lakes of İğneada Floodplain by next-generation sequencing platform and gave a prescreening of the bacterial diversity. Further studies are required to determine the biotechnological potential of this unique habitat.

Keywords

Amplicon Sequencing Bacterial community İğneada Floodplain Forest

Supporting Institution

This study was supported by Boğaziçi University Research Fund

Project Number

19Y00D9

Thanks

The authors acknowledge MSc. Aslınur Çalışıyor for her kind help during sampling.

References

  • Altinsaçli, S. (2001). The Ostracoda (Crustacea) fauna of lakes Erikli, Hamam, Mert, Pedina and Saka (Iǧneada, Kirklareli, Turkey). Turkish Journal of Zoology, 25(4), 343-355.
  • Amir, A., Daniel, M., Navas-Molina, J., Kopylova, E., Morton, J., Xu, Z.Z., Eric, K., Thompson, L., Hyde, E., Gonzalez, A., Knight, R. (2017). Deblur Rapidly Resolves Single-. American Society for Microbiology, 2(2), 1-7. https://doi.org/10.1128/mSystems.00191-16
  • Arekhi, M., Goksel, C., Sanli, F.B., Senel, G. (2019). Comparative evaluation of the spectral and spatial consistency of Sentinel-2 and Landsat-8 OLI data for Igneada longos forest. ISPRS International Journal of Geo-Information, 8(2), 56. https://doi.org/10.3390/ijgi8020056
  • Bolyen, E., Rideout, J.R., Dillon, M.R., Bokulich, N.A., Abnet, C.C., Al-Ghalith, G.A., Alexander, H., Alm, E.J., Arumugam, M., Asnicar, F., Bai, Y., Bisanz, J.E., Bittinger, K., Brejnrod, A., Brislawn, C.J., Brown, C.T., Callahan, B.J., Caraballo-Rodríguez, A.M., Chase, J., Cope, E.K., Da Silva, R., Diener, C., Dorrestein, P.C., Douglas, G.M., Durall, D.M., Duvallet, C., Edwardson, C.F., Ernst, M., Estaki, M., Fouquier, J., Gauglitz, J.M., Gibbons, S.M., Gibson, D.L., Gonzalez, A., Gorlick, K., Guo, J., Hillmann, B., Holmes, S., Holste, H., Huttenhower, C., Huttley, G.A., Janssen, S., Jarmusch, A.K., Jiang, L., Kaehler, B.D., Kang, K. Bin, Keefe, C.R., Keim, P., Kelley, S.T., Knights, D., Koester, I., Kosciolek, T., Kreps, J., Langille, M.G.I., Lee, J., Ley, R., Liu, Y.X., Loftfield, E., Lozupone, C., Maher, M., Marotz, C., Martin, B.D., McDonald, D., McIver, L.J., Melnik, A. V., Metcalf, J.L., Morgan, S.C., Morton, J.T., Naimey, A.T., Navas-Molina, J.A., Nothias, L.F., Orchanian, S.B., Pearson, T., Peoples, S.L., Petras, D., Preuss, M.L., Pruesse, E., Rasmussen, L.B., Rivers, A., Robeson, M.S., Rosenthal, P., Segata, N., Shaffer, M., Shiffer, A., Sinha, R., Song, S.J., Spear, J.R., Swafford, A.D., Thompson, L.R., Torres, P.J., Trinh, P., Tripathi, A., Turnbaugh, P.J., Ul-Hasan, S., van der Hooft, J.J.J., Vargas, F., Vázquez-Baeza, Y., Vogtmann, E., von Hippel, M., Walters, W., Wan, Y., Wang, M., Warren, J., Weber, K.C., Williamson, C.H.D., Willis, A.D., Xu, Z.Z., Zaneveld, J.R., Zhang, Y., Zhu, Q., Knight, R., Caporaso, J.G. (2019). Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology, 37(8), 852-857. https://doi.org/10.1038/s41587-019-0209-9
  • Coenye, T. (2014). The Family Burkholderiaceae. In The Prokaryotes (pp. 759–776). Berlin, Heidelberg: Springer Berlin Heidelberg. https://doi.org/10.1007/978-3-642-30197-1_239
  • Comeau, A.M., Douglas, G.M., & Langille, M.G.I. (2017). Microbiome Helper: a Custom and Streamlined Workflow for Microbiome Research. MSystems, 2(1), 1-11. https://doi.org/10.1128/mSystems.00127-16
  • Diao, M., Sinnige, R., Kalbitz, K., Huisman, J., Muyzer, G. (2017). Succession of bacterial communities in a seasonally stratified lake with an anoxic and sulfidic hypolimnion. Frontiers in Microbiology, 8(DEC), 1–15. https://doi.org/10.3389/fmicb.2017.02511
  • Evtushenko, L.I., Takeuchi, M. (2006). The Family Microbacteriaceae. In The Prokaryotes (pp. 1020–1098). New York, NY: Springer New York. https://doi.org/10.1007/0-387-30743-5_43
  • Filippidou, S., Wunderlin, T., Junier, T., Jeanneret, N., Dorador, C., Molina, V., Johnson, D.R., Junier, P. (2016). A Combination of Extreme Environmental Conditions Favor the Prevalence of Endospore-Forming Firmicutes. 7, 1-11. https://doi.org/10.3389/fmicb.2016.01707
  • Güher, H. (1999). Mert, erikli, hamam, pedina gölleri’nin (i̇ǧneada/kirklareli) cladocera ve copepoda (crustacea) türleri üzerinde taksonomik bir çalişma. Turkish Journal of Zoology, 23(SUPPL. 1), 47-53.
  • Güher, H. (2003). Mert, Erikli, Hamam ve Pedina (İğ neada,Kırklareli) Göller’ inin Zooplanktonik Organizma-ların Kommunite Yap ı s ı. 20, 51-62.
  • Kambura, A.K., Mwirichia, R.K., Kasili, R.W., Karanja, E.N., Makonde, H.M., Boga, H.I. (2016). Bacteria and Archaea diversity within the hot springs of Lake Magadi and Little Magadi in Kenya. BMC Microbiology, 16(1), 1-12. https://doi.org/10.1186/s12866-016-0748-x
  • Kiersztyn, B., Chróst, R., Kaliński, T., Siuda, W., Bukowska, A., Kowalczyk, G., Grabowska, K. (2019). Structural and functional microbial diversity along a eutrophication gradient of interconnected lakes undergoing anthropopressure. Scientific Reports, 9(1), 11144. https://doi.org/10.1038/s41598-019-47577-8
  • Llorens-Marès, T., Catalan, J., Casamayor, E.O. (2020). Taxonomy and functional interactions in upper and bottom waters of an oligotrophic high-mountain deep lake (Redon, Pyrenees) unveiled by microbial metagenomics. Science of the Total Environment, 707, 135929. https://doi.org/10.1016/j.scitotenv.2019.135929
  • Lloyd, K.G., Ladau, J., Steen, A.D., Yin, J., Crosby, L. (2018). Phylogenetically novel uncultured microbial cells dominate Earth microbiomes. BioRxiv, 3(5), 1-12. https://doi.org/10.1101/303602
  • Martin, M. (2011). Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. Journal, 17(1), 10. https://doi.org/10.14806/ej.17.1.200
  • Michán, C., Blasco, J., Alhama, J. (2021). High‐throughput molecular analyses of microbiomes as a tool to monitor the wellbeing of aquatic environments. Microbial Biotechnology, 1751-7915.13763. https://doi.org/10.1111/1751-7915.13763
  • Nakatsu, C.H., Byappanahalli, M.N., Nevers, M.B. (2019). Bacterial Community 16S rRNA Gene Sequencing Characterizes Riverine Microbial Impact on Lake Michigan. 10, 1-12. https://doi.org/10.3389/fmicb.2019.00996
  • Newton, R.J., Jones, S.E., Eiler, A., McMahon, K.D., Bertilsson, S. (2011). A Guide to the Natural History of Freshwater Lake Bacteria. In Microbiology and Molecular Biology Reviews, 75, 14-49. https://doi.org/10.1128/MMBR.00028-10
  • Ondov, B.D., Bergman, N.H., Phillippy, A.M. (2011). Interactive metagenomic visualization in a Web browser. BMC Bioinformatics, 12(1), 385. https://doi.org/10.1186/1471-2105-12-385
  • Ozbayram, E.G., Koker, L., Akçaalan, R., Aydın, F., Ertürk, A., Ince, O., Albay, M. (2021). Contrasting the Water Quality and Bacterial Community Patterns in Shallow and Deep Lakes: Manyas vs. Iznik. Environmental Management, 67, 506-512. https://doi.org/10.1007/s00267-020-01357-7
  • Ozbayram, E.G., Koker, L., Akcaalan, R., Ince, O., Albay, M. (2020). Bacterial Community Composition of Sapanca Lake During a Cyanobacterial Bloom. Aquatic Sciences and Engineering, 35(2), 52-56. https://doi.org/10.26650/ASE2020652073
  • Riesenfeld, C.S., Schloss, P.D., Handelsman, J. (2004). Metagenomics: Genomic analysis of microbial communities. Annual Review of Genetics, 38, 525-552. https://doi.org/10.1146/annurev.genet.38.072902.091216
  • Sorokin, D.Y., van Pelt, S., Tourova, T.P., Evtushenko, L I. (2009). Nitriliruptor alkaliphilus gen. nov., sp. nov., a deep-lineage haloalkaliphilic actinobacterium from soda lakes capable of growth on aliphatic nitriles, and proposal of Nitriliruptoraceae fam. nov. and Nitriliruptorales ord. nov. International Journal of Systematic and Evolutionary Microbiology, 59, 248-253. https://doi.org/10.1002/9781118960608.fbm00051
  • Steen, A.D., Crits-Christoph, A., Carini, P., DeAngelis, K.M., Fierer, N., Lloyd, K.G., Cameron Thrash, J. (2019). High proportions of bacteria and archaea across most biomes remain uncultured. ISME Journal, 13(12), 3126-3130. https://doi.org/10.1038/s41396-019-0484-y
  • Tecimen, H.B., Kavgaci, A. (2010). Comparison of soil and forest floor properties of floodplain and surrounding forests in Igneada, Turkey. Journal of Environmental Biology, 31(1-2), 129-134.
  • Ung, P., Peng, C., Yuk, S., Tan, R., Ann, V., Miyanaga, K., Tanji, Y. (2019). Dynamics of bacterial community in Tonle Sap Lake, a large tropical flood-pulse system in Southeast Asia. Science of the Total Environment, 664, 414-423. https://doi.org/10.1016/j.scitotenv.2019.01.351
  • Yong, J.J.J.Y., Chew, K.W., Khoo, K.S., Show, P.L., Chang, J.S. (2021). Prospects and development of algal-bacterial biotechnology in environmental management and protection. Biotechnology Advances, 47, 107684. https://doi.org/10.1016/j.biotechadv.2020.107684
  • Zhang, L., Fang, W., Li, X., Gao, G., Jiang, J. (2020). Linking bacterial community shifts with changes in the dissolved organic matter pool in a eutrophic lake. Science of the Total Environment, 719, 137387. https://doi.org/10.1016/j.scitotenv.2020.137387
  • Zwirglmaier, K., Keiz, K., Engel, M., Geist, J., & Raeder, U. (2015). Seasonal and spatial patterns of microbial diversity along a trophic gradient in the interconnected lakes of the Osterseen Lake District, Bavaria. Frontiers in Microbiology, 6, 1-18. https://doi.org/10.3389/fmicb.2015.01168
  • URL 1. http://igneada.tabiat.gov.tr/ accessed 27/02/2021

Year 2021, Volume: 4 Issue: 4, 304 - 312, 01.10.2021

Emine Gözde Özbayram , İbrahim Halil Miraloğlu Bahar İnce

https://doi.org/10.3153/AR21025

Abstract

Project Number

19Y00D9

References

  • Altinsaçli, S. (2001). The Ostracoda (Crustacea) fauna of lakes Erikli, Hamam, Mert, Pedina and Saka (Iǧneada, Kirklareli, Turkey). Turkish Journal of Zoology, 25(4), 343-355.
  • Amir, A., Daniel, M., Navas-Molina, J., Kopylova, E., Morton, J., Xu, Z.Z., Eric, K., Thompson, L., Hyde, E., Gonzalez, A., Knight, R. (2017). Deblur Rapidly Resolves Single-. American Society for Microbiology, 2(2), 1-7. https://doi.org/10.1128/mSystems.00191-16
  • Arekhi, M., Goksel, C., Sanli, F.B., Senel, G. (2019). Comparative evaluation of the spectral and spatial consistency of Sentinel-2 and Landsat-8 OLI data for Igneada longos forest. ISPRS International Journal of Geo-Information, 8(2), 56. https://doi.org/10.3390/ijgi8020056
  • Bolyen, E., Rideout, J.R., Dillon, M.R., Bokulich, N.A., Abnet, C.C., Al-Ghalith, G.A., Alexander, H., Alm, E.J., Arumugam, M., Asnicar, F., Bai, Y., Bisanz, J.E., Bittinger, K., Brejnrod, A., Brislawn, C.J., Brown, C.T., Callahan, B.J., Caraballo-Rodríguez, A.M., Chase, J., Cope, E.K., Da Silva, R., Diener, C., Dorrestein, P.C., Douglas, G.M., Durall, D.M., Duvallet, C., Edwardson, C.F., Ernst, M., Estaki, M., Fouquier, J., Gauglitz, J.M., Gibbons, S.M., Gibson, D.L., Gonzalez, A., Gorlick, K., Guo, J., Hillmann, B., Holmes, S., Holste, H., Huttenhower, C., Huttley, G.A., Janssen, S., Jarmusch, A.K., Jiang, L., Kaehler, B.D., Kang, K. Bin, Keefe, C.R., Keim, P., Kelley, S.T., Knights, D., Koester, I., Kosciolek, T., Kreps, J., Langille, M.G.I., Lee, J., Ley, R., Liu, Y.X., Loftfield, E., Lozupone, C., Maher, M., Marotz, C., Martin, B.D., McDonald, D., McIver, L.J., Melnik, A. V., Metcalf, J.L., Morgan, S.C., Morton, J.T., Naimey, A.T., Navas-Molina, J.A., Nothias, L.F., Orchanian, S.B., Pearson, T., Peoples, S.L., Petras, D., Preuss, M.L., Pruesse, E., Rasmussen, L.B., Rivers, A., Robeson, M.S., Rosenthal, P., Segata, N., Shaffer, M., Shiffer, A., Sinha, R., Song, S.J., Spear, J.R., Swafford, A.D., Thompson, L.R., Torres, P.J., Trinh, P., Tripathi, A., Turnbaugh, P.J., Ul-Hasan, S., van der Hooft, J.J.J., Vargas, F., Vázquez-Baeza, Y., Vogtmann, E., von Hippel, M., Walters, W., Wan, Y., Wang, M., Warren, J., Weber, K.C., Williamson, C.H.D., Willis, A.D., Xu, Z.Z., Zaneveld, J.R., Zhang, Y., Zhu, Q., Knight, R., Caporaso, J.G. (2019). Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology, 37(8), 852-857. https://doi.org/10.1038/s41587-019-0209-9
  • Coenye, T. (2014). The Family Burkholderiaceae. In The Prokaryotes (pp. 759–776). Berlin, Heidelberg: Springer Berlin Heidelberg. https://doi.org/10.1007/978-3-642-30197-1_239
  • Comeau, A.M., Douglas, G.M., & Langille, M.G.I. (2017). Microbiome Helper: a Custom and Streamlined Workflow for Microbiome Research. MSystems, 2(1), 1-11. https://doi.org/10.1128/mSystems.00127-16
  • Diao, M., Sinnige, R., Kalbitz, K., Huisman, J., Muyzer, G. (2017). Succession of bacterial communities in a seasonally stratified lake with an anoxic and sulfidic hypolimnion. Frontiers in Microbiology, 8(DEC), 1–15. https://doi.org/10.3389/fmicb.2017.02511
  • Evtushenko, L.I., Takeuchi, M. (2006). The Family Microbacteriaceae. In The Prokaryotes (pp. 1020–1098). New York, NY: Springer New York. https://doi.org/10.1007/0-387-30743-5_43
  • Filippidou, S., Wunderlin, T., Junier, T., Jeanneret, N., Dorador, C., Molina, V., Johnson, D.R., Junier, P. (2016). A Combination of Extreme Environmental Conditions Favor the Prevalence of Endospore-Forming Firmicutes. 7, 1-11. https://doi.org/10.3389/fmicb.2016.01707
  • Güher, H. (1999). Mert, erikli, hamam, pedina gölleri’nin (i̇ǧneada/kirklareli) cladocera ve copepoda (crustacea) türleri üzerinde taksonomik bir çalişma. Turkish Journal of Zoology, 23(SUPPL. 1), 47-53.
  • Güher, H. (2003). Mert, Erikli, Hamam ve Pedina (İğ neada,Kırklareli) Göller’ inin Zooplanktonik Organizma-ların Kommunite Yap ı s ı. 20, 51-62.
  • Kambura, A.K., Mwirichia, R.K., Kasili, R.W., Karanja, E.N., Makonde, H.M., Boga, H.I. (2016). Bacteria and Archaea diversity within the hot springs of Lake Magadi and Little Magadi in Kenya. BMC Microbiology, 16(1), 1-12. https://doi.org/10.1186/s12866-016-0748-x
  • Kiersztyn, B., Chróst, R., Kaliński, T., Siuda, W., Bukowska, A., Kowalczyk, G., Grabowska, K. (2019). Structural and functional microbial diversity along a eutrophication gradient of interconnected lakes undergoing anthropopressure. Scientific Reports, 9(1), 11144. https://doi.org/10.1038/s41598-019-47577-8
  • Llorens-Marès, T., Catalan, J., Casamayor, E.O. (2020). Taxonomy and functional interactions in upper and bottom waters of an oligotrophic high-mountain deep lake (Redon, Pyrenees) unveiled by microbial metagenomics. Science of the Total Environment, 707, 135929. https://doi.org/10.1016/j.scitotenv.2019.135929
  • Lloyd, K.G., Ladau, J., Steen, A.D., Yin, J., Crosby, L. (2018). Phylogenetically novel uncultured microbial cells dominate Earth microbiomes. BioRxiv, 3(5), 1-12. https://doi.org/10.1101/303602
  • Martin, M. (2011). Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. Journal, 17(1), 10. https://doi.org/10.14806/ej.17.1.200
  • Michán, C., Blasco, J., Alhama, J. (2021). High‐throughput molecular analyses of microbiomes as a tool to monitor the wellbeing of aquatic environments. Microbial Biotechnology, 1751-7915.13763. https://doi.org/10.1111/1751-7915.13763
  • Nakatsu, C.H., Byappanahalli, M.N., Nevers, M.B. (2019). Bacterial Community 16S rRNA Gene Sequencing Characterizes Riverine Microbial Impact on Lake Michigan. 10, 1-12. https://doi.org/10.3389/fmicb.2019.00996
  • Newton, R.J., Jones, S.E., Eiler, A., McMahon, K.D., Bertilsson, S. (2011). A Guide to the Natural History of Freshwater Lake Bacteria. In Microbiology and Molecular Biology Reviews, 75, 14-49. https://doi.org/10.1128/MMBR.00028-10
  • Ondov, B.D., Bergman, N.H., Phillippy, A.M. (2011). Interactive metagenomic visualization in a Web browser. BMC Bioinformatics, 12(1), 385. https://doi.org/10.1186/1471-2105-12-385
  • Ozbayram, E.G., Koker, L., Akçaalan, R., Aydın, F., Ertürk, A., Ince, O., Albay, M. (2021). Contrasting the Water Quality and Bacterial Community Patterns in Shallow and Deep Lakes: Manyas vs. Iznik. Environmental Management, 67, 506-512. https://doi.org/10.1007/s00267-020-01357-7
  • Ozbayram, E.G., Koker, L., Akcaalan, R., Ince, O., Albay, M. (2020). Bacterial Community Composition of Sapanca Lake During a Cyanobacterial Bloom. Aquatic Sciences and Engineering, 35(2), 52-56. https://doi.org/10.26650/ASE2020652073
  • Riesenfeld, C.S., Schloss, P.D., Handelsman, J. (2004). Metagenomics: Genomic analysis of microbial communities. Annual Review of Genetics, 38, 525-552. https://doi.org/10.1146/annurev.genet.38.072902.091216
  • Sorokin, D.Y., van Pelt, S., Tourova, T.P., Evtushenko, L I. (2009). Nitriliruptor alkaliphilus gen. nov., sp. nov., a deep-lineage haloalkaliphilic actinobacterium from soda lakes capable of growth on aliphatic nitriles, and proposal of Nitriliruptoraceae fam. nov. and Nitriliruptorales ord. nov. International Journal of Systematic and Evolutionary Microbiology, 59, 248-253. https://doi.org/10.1002/9781118960608.fbm00051
  • Steen, A.D., Crits-Christoph, A., Carini, P., DeAngelis, K.M., Fierer, N., Lloyd, K.G., Cameron Thrash, J. (2019). High proportions of bacteria and archaea across most biomes remain uncultured. ISME Journal, 13(12), 3126-3130. https://doi.org/10.1038/s41396-019-0484-y
  • Tecimen, H.B., Kavgaci, A. (2010). Comparison of soil and forest floor properties of floodplain and surrounding forests in Igneada, Turkey. Journal of Environmental Biology, 31(1-2), 129-134.
  • Ung, P., Peng, C., Yuk, S., Tan, R., Ann, V., Miyanaga, K., Tanji, Y. (2019). Dynamics of bacterial community in Tonle Sap Lake, a large tropical flood-pulse system in Southeast Asia. Science of the Total Environment, 664, 414-423. https://doi.org/10.1016/j.scitotenv.2019.01.351
  • Yong, J.J.J.Y., Chew, K.W., Khoo, K.S., Show, P.L., Chang, J.S. (2021). Prospects and development of algal-bacterial biotechnology in environmental management and protection. Biotechnology Advances, 47, 107684. https://doi.org/10.1016/j.biotechadv.2020.107684
  • Zhang, L., Fang, W., Li, X., Gao, G., Jiang, J. (2020). Linking bacterial community shifts with changes in the dissolved organic matter pool in a eutrophic lake. Science of the Total Environment, 719, 137387. https://doi.org/10.1016/j.scitotenv.2020.137387
  • Zwirglmaier, K., Keiz, K., Engel, M., Geist, J., & Raeder, U. (2015). Seasonal and spatial patterns of microbial diversity along a trophic gradient in the interconnected lakes of the Osterseen Lake District, Bavaria. Frontiers in Microbiology, 6, 1-18. https://doi.org/10.3389/fmicb.2015.01168
  • URL 1. http://igneada.tabiat.gov.tr/ accessed 27/02/2021
There are 31 citations in total.

Details

Primary Language English
Subjects Hydrobiology
Journal Section Research Articles
Authors

Emine Gözde Özbayram 0000-0002-5416-0611

İbrahim Halil Miraloğlu 0000-0001-5291-8380

Bahar İnce 0000-0001-6205-2074

Project Number 19Y00D9
Publication Date October 1, 2021
Submission Date February 28, 2021
Published in Issue Year 2021Volume: 4 Issue: 4

Cite

APA Özbayram, E. G., Miraloğlu, İ. H., & İnce, B. (2021). Assessment of microbial community diversity in lakes of İğneada floodplain forest by metabarcoding approach. Aquatic Research, 4(4), 304-312. https://doi.org/10.3153/AR21025
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