| Seasonal dynamics of selected taxa and nutrients. a-b., d-e., g-i. Numbers of rRNA

| Seasonal dynamics of selected taxa and nutrients. a-b., d-e., g-i. Numbers of rRNA

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Planktonic microorganisms in coastal waters form the foundation of food webs and biogeochemical cycles while exposed to pronounced environmental gradients, especially brackish salinities. Yet, commonplace ecological assessment overlooks most of their diversity. Here, we analyzed the protist and bacterial diversity from new and publicly available DN...

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... dissimilarities of bacterial and protist communities between the same pairs of 191 samples were roughly correlated (R 2 = 0.58). However, the protist communities were 192 generally less similar to each other than bacterial ones ( Supplementary Fig. S3a), as 193 has been reported for picoeukaryotes and bacteria in ocean surface waters 47 . 194 Principal Coordinate Analysis (PCoA) showed distinguishable geographic and 195 seasonal structuring of bacterial and protist communities ( Supplementary Fig. S4). ...
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... (Fig. 3a, Supplementary Fig. S6a). The rise in picocyanobacterial 242 abundance was followed by blooms of filamentous heterocyst-forming cyanobacteria 243 (Nostocacaea) in the Baltic Proper and the Bothnian Sea ( Fig. 3a-b). Expectedly, ...
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... (Fig. 3a, Supplementary Fig. S6a). The rise in picocyanobacterial 242 abundance was followed by blooms of filamentous heterocyst-forming cyanobacteria 243 (Nostocacaea) in the Baltic Proper and the Bothnian Sea ( Fig. 3a-b). Expectedly, ...
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... thrived in DIN-depleted conditions (Fig. 3b- and Chrysochromulinaceae were associated with high temperatures (Fig. 2f). However, 256 we could not connect any family to similar conditions across all the basins-not only 257 among haptophytes but among protists in general ( Supplementary Fig. S6b). This 258 suggests that despite stronger geographic structuring of bacterial ...
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... 258 suggests that despite stronger geographic structuring of bacterial communities along 259 the salinity gradient ( Fig. 2a-d), protist seasonal succession patterns differ more 260 between regions. The aforementioned haptophytes may best exemplify this 261 heterogeneity. Prymensiaceae were by far most abundant in summer in Baltic Proper 262 ( Fig. 3d), while Chrysochromulinaceae bloomed at a similar time in Bothnian Bay (Fig. 263 3e). These families also increased in abundance around June in Skagerrak, largely 264 explaining the increase in overall haptophyte counts (Fig. 1c). The same cannot be said 265 about Kattegat, where haptophytes were most abundant in May (Fig. 1c) . S7a, ...
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... along 259 the salinity gradient ( Fig. 2a-d), protist seasonal succession patterns differ more 260 between regions. The aforementioned haptophytes may best exemplify this 261 heterogeneity. Prymensiaceae were by far most abundant in summer in Baltic Proper 262 ( Fig. 3d), while Chrysochromulinaceae bloomed at a similar time in Bothnian Bay (Fig. 263 3e). These families also increased in abundance around June in Skagerrak, largely 264 explaining the increase in overall haptophyte counts (Fig. 1c). The same cannot be said 265 about Kattegat, where haptophytes were most abundant in May (Fig. 1c) . S7a, d). Still, it did not explain Kattegat's high abundance of haptophytes in May. 273 ...
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... to Cyanobiaceae, BACL11 thrived in cold waters (Fig. 2e, Supplementary Fig. 285 S6a). Our observations diverge from the previously suggested dinoflagellate-bloom 286 association of BACL11 20 . Complex seasonal patterns ( Fig. 3g) of BACL11 suggest 287 dependence on a combination of factors or a factor not investigated here. On the other ...
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... nitrite-oxidizing Nitrospinaceae 61 , a winter-associated family (Fig. 2e, 289 Supplementary Fig. S6a), was clearly influenced by DIN dynamics (Fig. 3c, h). Still, their 290 abundance usually decreased before DIN depletion, as well as during the summer in 291 the Bothnian Bay, where nitrogen availability remained relatively high throughout the 292 year. A better understanding of the growth-limiting factors of Nitrospinaceae is needed ...
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... family rose in abundance at the periods corresponding to a rapid decrease 297 in phosphate availability (Fig. 3f, i), as did total Bacteroidia abundance (Fig. 1c). 298 Recently, it has been suggested that Bacteroidia, and in particular Flavobacteria, gain a 299 competitive advantage under limited phosphate availability by efficiently mobilizing 300 organic phosphorus 61 62,63 . Our results further support this notion and suggest that 301 phosphorus ...
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... of nitrogen-depletion periods (Fig. 3c). Consistently, DIN was the environmental 320 factor by far best-explaining variation in bacterial richness using a linear model (Fig. 4c). 321 . CC-BY 4.0 International license available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is ...
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... that extra reads would not change alpha diversity much ( Supplementary Fig. 438 S9). Thus, another technical difference likely caused the dbOTU difference between 439 datasets. ...
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... comparability of results for protists and bacteria, we used only the samples 771 with data available from both 16S and 18S amplicon sequencing (excluding the under- were excluded from analyses in which spike-in normalization was used, except for 776 bacteria-only focused analyses in Fig. 1b and Fig. 3a-b, g-i. ...

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