Bunse, C. & Pinhassi, J. Marine bacterioplankton seasonal succession dynamics. Trends Microbiol. 25, 494–505. https://doi.org/10.1016/j.tim.2016.12.013 (2017).
Google Scholar
Mestre, M., Höfer, J., Sala, M. M. & Gasol, J. M. Seasonal variation of bacterial diversity along the marine particulate matter continuum. Front. Microbiol. 11, 1590. https://doi.org/10.3389/fmicb.2020.01590 (2020).
Google Scholar
Teeling, H. et al. Substrate-controlled succession of marine bacterioplankton populations induced by a phytoplankton bloom. Science 336, 608–611. https://doi.org/10.1126/science.1218344 (2012).
Google Scholar
Gilbert, J. A. et al. The seasonal structure of microbial communities in the Western English Channel. Environ. Microbiol. 11, 3132–3139. https://doi.org/10.1111/j.1462-2920.2009.02017.x (2009).
Google Scholar
Sintes, E., Witte, H., Stodderegger, K., Steiner, P. & Herndl, G. J. Temporal dynamics in the free-living bacterial community composition in the coastal North Sea. FEMS Microbiol. Ecol. 83, 413–424. https://doi.org/10.1111/1574-6941.12003 (2013).
Google Scholar
Lindh, M. V. et al. Disentangling seasonal bacterioplankton population dynamics by high-frequency sampling. Environ. Microbiol. 17, 2459–2476. https://doi.org/10.1111/1462-2920.12720 (2015).
Google Scholar
El-Swais, H., Dunn, K. A., Bielawski, J. P., Li, W. K. W. & Walsh, D. A. Seasonal assemblages and short-lived blooms in coastal north-west Atlantic Ocean bacterioplankton. Environ. Microbiol. 17, 3642–3661. https://doi.org/10.1111/1462-2920.12629 (2015).
Google Scholar
Ward, C. S. et al. Annual community patterns are driven by seasonal switching between closely related marine bacteria. ISME J. 11, 1412–1422. https://doi.org/10.1038/ismej.2017.4 (2017).
Google Scholar
Teeling, H. et al. Recurring patterns in bacterioplankton dynamics during coastal spring algae blooms. Elife 5, e11888. https://doi.org/10.7554/eLife.11888 (2016).
Google Scholar
Tinta, T. et al. Bacterial community shift is induced by dynamic environmental parameters in a changing coastal ecosystem (northern Adriatic, northeastern Mediterranean Sea) – a 2-year time-series study. Environ. Microbiol. 17, 3581–3596. https://doi.org/10.1111/1462-2920.12519 (2015).
Google Scholar
Salter, I. et al. Seasonal dynamics of active SAR11 ecotypes in the oligotrophic Northwest Mediterranean Sea. ISME J. 9, 347–360. https://doi.org/10.1038/ismej.2014.129 (2015).
Google Scholar
Gilbert, J. A. et al. Defining seasonal marine microbial community dynamics. ISME J. 6, 298–308. https://doi.org/10.1038/ismej.2011.107 (2012).
Google Scholar
Alonso-Sáez, L. et al. Seasonality in bacterial diversity in north-west Mediterranean coastal waters: Assessment through clone libraries, fingerprinting and FISH. FEMS Microbiol. Ecol. 60, 98–112. https://doi.org/10.1111/j.1574-6941.2006.00276.x (2007).
Google Scholar
Alonso-Sáez, L., Díaz-Pérez, L. & Morán, X. A. G. The hidden seasonality of the rare biosphere in coastal marine bacterioplankton. Environ. Microbiol. 17, 3766–3780. https://doi.org/10.1111/1462-2920.12801 (2015).
Google Scholar
Needham, D. M. & Fuhrman, J. A. Pronounced daily succession of phytoplankton, archaea and bacteria following a spring bloom. Nat. Microbiol. 1, 1–7. https://doi.org/10.1038/nmicrobiol.2016.5 (2016).
Google Scholar
Fuhrman, J. A., Cram, J. A. & Needham, D. M. Marine microbial community dynamics and their ecological interpretation. Nat. Rev. Microbiol. 13, 133–146. https://doi.org/10.1038/nrmicro3417 (2015).
Google Scholar
Najdek, M. et al. Dynamics of environmental conditions during the decline of a Cymodocea nodosa meadow. Biogeosciences 17, 3299–3315. https://doi.org/10.5194/bg-17-3299-2020 (2020).
Google Scholar
Najdek, M. et al. Effects of the invasion of Caulerpa cylindracea in a Cymodocea nodosa meadow in the Northern Adriatic Sea. Front. Mar. Sci. 7, 602055. https://doi.org/10.3389/fmars.2020.602055 (2020).
Google Scholar
Ladau, J. et al. Global marine bacterial diversity peaks at high latitudes in winter. ISME J. 7, 1669–1677. https://doi.org/10.1038/ismej.2013.37 (2013).
Google Scholar
García, F. C., Alonso-Sáez, L., Morén, X. A. G. & López-Urrutia, Á. Seasonality in molecular and cytometric diversity of marine bacterioplankton: The re-shuffling of bacterial taxa by vertical mixing. Environ. Microbiol. 17, 4133–4142. https://doi.org/10.1111/1462-2920.12984 (2015).
Google Scholar
Reinthaler, T., Winter, C. & Herndl, G. J. Relationship between bacterioplankton richness, respiration, and production in the southern North Sea. Appl. Environ. Microbiol. 71, 2260–2266. https://doi.org/10.1128/AEM.71.5.2260-2266.2005 (2005).
Google Scholar
Mozetič, P. et al. Recent trends towards oligotrophication of the Northern Adriatic: Evidence from chlorophyll a time series. Estuaries Coast 33, 362–375. https://doi.org/10.1007/s12237-009-9191-7 (2010).
Google Scholar
Manna, V., De Vittor, C., Giani, M., Del Negro, P. & Celussi, M. Long-term patterns and drivers of microbial organic matter utilization in the northernmost basin of the Mediterranean Sea. Mar. Environ. Res. 164, 105245. https://doi.org/10.1016/j.marenvres.2020.105245 (2021).
Google Scholar
Ivančić, I. et al. Long-term changes in heterotrophic prokaryotes abundance and growth characteristics in the northern Adriatic Sea. J. Mar. Syst. 82, 206–216. https://doi.org/10.1016/j.jmarsys.2010.05.008 (2010).
Google Scholar
Bowman, J. P. The family Cryomorphaceae. In The Prokaryotes: Other Major Lineages of Bacteria and the Archaea (eds Rosenberg, E. et al.) (Springer, New York, 2014). https://doi.org/10.1007/978-3-642-38954-2_135.
Google Scholar
Ngugi, D. K. & Stingl, U. High-quality draft single-cell genome sequence of the NS5 marine group from the coastal Red Sea. Genome Announc. 6, e00565-18. https://doi.org/10.1128/genomeA.00565-18 (2018).
Google Scholar
Korlević, M., Pop Ristova, P., Garić, R., Amann, R. & Orlić, S. Bacterial diversity in the South Adriatic Sea during a strong, deep winter convection year. Appl. Environ. Microbiol. 81, 1715–1726; https://doi.org/10.1128/AEM.03410-14 (2015).
Korlević, M. et al. Bacterial diversity across a highly stratified ecosystem: A salt-wedge Mediterranean estuary. Syst. Appl. Microbiol. 39, 398–408. https://doi.org/10.1016/j.syapm.2016.06.006 (2016).
Google Scholar
Hoarfrost, A. et al. Global ecotypes in the ubiquitous marine clade SAR86. ISME J. 14, 178–188. https://doi.org/10.1038/s41396-019-0516-7 (2020).
Google Scholar
Šilović, T., Balagué, V., Orlić, S. & Pedrós-Alió, C. Picoplankton seasonal variation and community structure in the northeast Adriatic coastal zone. FEMS Microbiol. Ecol. 82, 678–691. https://doi.org/10.1111/j.1574-6941.2012.01438.x (2012).
Google Scholar
Palenik, B. et al. The genome of a motile marine Synechococcus. Nature 424, 1037–1042. https://doi.org/10.1038/nature01943 (2003).
Google Scholar
Spring, S. & Riedel, T. Mixotrophic growth of bacteriochlorophyll a-containing members of the OM60/NOR5 clade of marine gammaproteobacteria is carbon-starvation independent and correlates with the type of carbon source and oxygen availability. BMC Microbiol. 13, 117. https://doi.org/10.1186/1471-2180-13-117 (2013).
Google Scholar
Durham, B. P. et al. Draft genome sequence of marine alphaproteobacterial strain HIMB11, the first cultivated representative of a unique lineage within the Roseobacter clade possessing an unusually small genome. Stand. Genomic Sci. 9, 632–645. https://doi.org/10.4056/sigs.4998989 (2014).
Google Scholar
Carlson, C. A. et al. Seasonal dynamics of SAR11 populations in the euphotic and mesopelagic zones of the northwestern Sargasso Sea. ISME J. 3, 283–295. https://doi.org/10.1038/ismej.2008.117 (2009).
Google Scholar
Vergin, K. L. et al. High-resolution SAR11 ecotype dynamics at the Bermuda Atlantic Time-series study site by phylogenetic placement of pyrosequences. ISME J. 7, 1322–1332. https://doi.org/10.1038/ismej.2013.32 (2013).
Google Scholar
Kim, J.-G. et al. Distinct temporal dynamics of planktonic archaeal and bacterial assemblages in the bays of the Yellow Sea. PLoS One 14, e0221408. https://doi.org/10.1371/journal.pone.0221408 (2019).
Google Scholar
Bayer, B. et al. Nitrosopumilus adriaticus sp. nov. and Nitrosopumilus piranensis sp. nov., two ammonia-oxidizing archaea from the Adriatic Sea and members of the class Nitrososphaeria. Int. J. Syst. Evol. Microbiol. 69, 1892–1902. https://doi.org/10.1099/ijsem.0.003360 (2019).
Google Scholar
Strickland, J. D. H. & Parsons, T. R. A Practical Handbook of Seawater Analysis vol. 167 (Fisheries Research Board of Canada, 1972).
Holm-Hansen, O., Lorenzen, C. J., Holmes, R. W. & Strickland, J. D. H. Fluorometric determination of chlorophyll. ICES J. Mar. Sci. 30, 3–15. https://doi.org/10.1093/icesjms/30.1.3 (1965).
Google Scholar
Porter, K. G. & Feig, Y. S. The use of DAPI for identifying and counting aquatic microflora. Limnol. Oceanogr. 25, 943–948. https://doi.org/10.4319/lo.1980.25.5.0943 (1980).
Google Scholar
Massana, R., Murray, A. E., Preston, C. M. & DeLong, E. F. Vertical distribution and phylogenetic characterization of marine planktonic Archaea in the Santa Barbara Channel. Appl. Environ. Microbiol. 63, 50–56. https://doi.org/10.1128/aem.63.1.50-56.1997 (1997).
Google Scholar
Korlević, M., Markovski, M., Zhao, Z., Herndl, G. J. & Najdek, M. Selective DNA and protein isolation from marine macrophyte surfaces. Front. Microbiol. 12, 665999. https://doi.org/10.3389/fmicb.2021.665999 (2021).
Google Scholar
Caporaso, J. G. et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 6, 1621–1624. https://doi.org/10.1038/ismej.2012.8 (2012).
Google Scholar
Apprill, A., McNally, S., Parsons, R. & Weber, L. Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton. Aquat. Microb. Ecol. 75, 129–137. https://doi.org/10.3354/ame01753 (2015).
Google Scholar
Parada, A. E., Needham, D. M. & Fuhrman, J. A. Every base matters: Assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples. Environ. Microbiol. 18, 1403–1414. https://doi.org/10.1111/1462-2920.13023 (2016).
Google Scholar
Korlević, M., Markovski, M., Zhao, Z., Herndl, G. J. & Najdek, M. Seasonal dynamics of epiphytic microbial communities on marine macrophyte surfaces. Front. Microbiol. 12, 671342. https://doi.org/10.3389/fmicb.2021.671342 (2021).
Google Scholar
Schloss, P. D. et al. Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75, 7537–7541. https://doi.org/10.1128/AEM.01541-09 (2009).
Google Scholar
Kozich, J. J., Westcott, S. L., Baxter, N. T., Highlander, S. K. & Schloss, P. D. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl. Environ. Microbiol. 79, 5112–5120. https://doi.org/10.1128/AEM.01043-13 (2013).
Google Scholar
Quast, C. et al. The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acids Res. 41, D590–D596. https://doi.org/10.1093/nar/gks1219 (2013).
Google Scholar
Yilmaz, P. et al. The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks. Nucleic Acids Res. 42, D643–D648. https://doi.org/10.1093/nar/gkt1209 (2014).
Google Scholar
Schloss, P. D., Jenior, M. L., Koumpouras, C. C., Westcott, S. L. & Highlander, S. K. Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system. PeerJ 4, e1869. https://doi.org/10.7717/peerj.1869 (2016).
Google Scholar
R Core Team. R: A language and environment for statistical computing (R Foundation for Statistical Computing, 2021).
Oksanen, J. et al. vegan: Community ecology package (2020).
Wickham, H. et al. Welcome to the tidyverse. J. Open Source Softw. 4, 1686; https://doi.org/10.21105/joss.01686 (2019)
McKinnon Edwards, S. lemon: Freshing up your ’ggplot2’ plots (2020).
Wilke, C. O. cowplot: Streamlined plot theme and plot annotations for ’ggplot2’ (2020).
Neuwirth, E. RColorBrewer: ColorBrewer palettes (2014).
Zhu, H. kableExtra: Construct complex table with ’kable’ and pipe syntax (2021).
Allaire, J. et al. rmarkdown: Dynamic documents for R (2021).
Xie, Y., Allaire, J. J. & Grolemund, G. R Markdown: The Definitive Guide (Chapman and Hall/CRC, New York, 2018).
Google Scholar
Xie, Y., Dervieux, C. & Riederer, E. R Markdown Cookbook (Chapman and Hall/CRC, New York, 2020).
Google Scholar
Xie, Y. knitr: A general-purpose package for dynamic report generation in R (2021).
Xie, Y. & knitr, A comprehensive tool for reproducible research in R. In Implementing Reproducible Computational Research (eds Stodden, V. et al.) (Chapman and Hall/CRC, New York, 2014).
Xie, Y. Dynamic Documents with R and knitr (Chapman and Hall/CRC, New York, 2015).
Xie, Y. tinytex: Helper functions to install and maintain TeX Live, and compile LaTeX documents (2021).
Xie, Y. TinyTeX: A lightweight, cross-platform, and easy-to-maintain LaTeX distribution based on TeX Live. TUGboat 40, 30–32 (2019).
Google Scholar
Jost, L. Entropy and diversity. Oikos 113, 363–375. https://doi.org/10.1111/j.2006.0030-1299.14714.x (2006).
Google Scholar
Borcard, D., Gillet, F. & Legendre, P. Numerical Ecology with R (Springer, New York, 2018). https://doi.org/10.1007/978-3-319-71404-2.
Google Scholar
Legendre, P. & Legendre, L. Numerical Ecology (Elsevier, Amsterdam, 2012).
Google Scholar
Source: Ecology - nature.com