FIGURE 1 Abundance of two marine microbes illustrated by three hypothetical scenarios. (a) equal relative abundance does not match cell abundance due to copy number variation of the target molecular marker (e.g., rRNA marker genes), (b) accurate relative abundance matches cell abundance when using single copy molecular marker genes (e.g.,psb0 gene) and (c) accurate absolute abundance when using single copy molecular marker and a DNA spike in.
References
Bik, H. M., Porazinska, D. L., Creer, S., Caporaso, J. G., Knight, R., & Thomas, W. K. (2012). Sequencing our way towards understanding global eukaryotic biodiversity. Trends in Ecology & Evolution ,27 (4), 233–243. doi: 10.1016/j.tree.2011.11.010
Creer, S., Deiner, K., Frey, S., Porazinksa, D., Taberlet, P., Kelley Thomas, W. K., … Bik, H. M. (2016). The ecologist’s field guide to sequence-based identification of biodiversity. Methods in Ecology and Evolution , 7 (9), 1008–1018. doi: 10.1111/2041-210X.12574
Delgado-Baquerizo, M., Oliverio, A. M., Brewer, T. E., Benavent-González, A., Eldridge, D. J., Bardgett, R. D., … Fierer, N. (2018). A global atlas of the dominant bacteria found in soil. Science , 359 (6373), 320–325. doi: 10.1126/science.aap9516
Di Pane, J., Wiltshire, K. H., McLean, M., Boersma, M., & Meunier, C. L. (2022). Environmentally induced functional shifts in phytoplankton and their potential consequences for ecosystem functioning. Global Change Biology , 28 (8), 2804–2819. doi: 10.1111/gcb.16098
Drautz-Moses, D. I., Luhung, I., Gusareva, E. S., Kee, C., Gaultier, N. E., Premkrishnan, B. N. V., … Schuster, S. C. (2022). Vertical stratification of the air microbiome in the lower troposphere.Proceedings of the National Academy of Sciences , 119 (7), e2117293119. doi: 10.1073/pnas.2117293119
Field, C. B., Behrenfeld, M. J., Randerson, J. T., & Falkowski, P. (1998). Primary production of the biosphere: Integrating terrestrial and oceanic components. Science , 281 (5374), 237–240. doi: 10.1126/science.281.5374.237
Giner, C. R., Forn, I., Romac, S., Logares, R., de Vargas, C., & Massana, R. (2016). Environmental Sequencing Provides Reasonable Estimates of the Relative Abundance of Specific Picoeukaryotes.Applied and Environmental Microbiology , 82 (15), 4757–4766. doi: 10.1128/AEM.00560-16
Jones, L., Brennan, G. L., Lowe, A., Creer, S., Ford, C. R., & de Vere, N. (2021). Shifts in honeybee foraging reveal historical changes in floral resources. Communications Biology , 4 (1), 37. doi: 10.1038/s42003-020-01562-4
Karlusich, J. J. P., Pelletier, E., Zinger, L., Lombard, F., Colin, S., Gasol, J., … Bowler, C. (2022). A robust approach to estimate relative phytoplankton cell abundances from metagenomes. Molecular Ecology Resources , XX (XX), XXX–XXX.
Lowe, A., Jones, L., Brennan, G., Creer, S., & de Vere, N. (2022). Seasonal progression and differences in major floral resource use by bees and hoverflies in a diverse horticultural and agricultural landscape revealed by DNA metabarcoding. Journal of Applied Ecology , 59 (6), 1484–1495. doi: 10.1111/1365-2664.14144
Makiola, A., Compson, Z. G., Baird, D. J., Barnes, M. A., Boerlijst, S. P., Bouchez, A., … Bohan, D. A. (2020). Key Questions for Next-Generation Biomonitoring. Frontiers in Environmental Science , 7 . Retrieved from https://www.frontiersin.org/articles/10.3389/fenvs.2019.00197
Rowney, F. M., Brennan, G. L., Skjøth, C. A., Griffith, G. W., McInnes, R. N., Clewlow, Y., … Creer, S. (2021). Environmental DNA reveals links between abundance and composition of airborne grass pollen and respiratory health. Current Biology , 31 (9), 1995-2003.e4. doi: 10.1016/j.cub.2021.02.019
Sunagawa, S., Acinas, S. G., Bork, P., Bowler, C., Eveillard, D., Gorsky, G., … de Vargas, C. (2020). Tara Oceans: Towards global ocean ecosystems biology. Nature Reviews Microbiology ,18 (8), 428–445. doi: 10.1038/s41579-020-0364-5
Tkacz, A., Hortala, M., & Poole, P. S. (2018). Absolute quantitation of microbiota abundance in environmental samples. Microbiome ,6 (1), 110. doi: 10.1186/s40168-018-0491-7