Water column dynamics in Lake Nkuruba 1992–2010.

<p>a) annual means of depth to anoxia (squares) and transparency (diamonds), and inferred primary production (circles) expressed as sedimentary concentrations of β-carotene. b) 1992–2007 variations in the concentrations of four sedimentary pigments associated with diatoms (diamonds), cryptophytes (triangles), chlorophytes (squares *concentration values for sedimentary lutein were an order of magnitude higher than the others, and were divided by 10 to fit the graph) and cyanobacteria (circles).</p

Data_Sheet_3.ZIP

<p>Bacterial communities are composed of distinct groups of potentially interacting lineages, each thought to occupy a distinct ecological niche. It remains unclear, however, how quickly niche preference evolves and whether more closely related lineages are more likely to share ecological niches. We addressed these questions by following the dynamics of two bloom-forming cyanobacterial genera over an 8-year time-course in Lake Champlain, Canada, using 16S amplicon sequencing and measurements of several environmental parameters. The two genera, Microcystis (M) and Dolichospermum (D), are frequently observed simultaneously during bloom events and thus have partially overlapping niches. However, the extent of their niche overlap is debated, and it is also unclear to what extent niche partitioning occurs among strains within each genus. To identify strains within each genus, we applied minimum entropy decomposition (MED) to 16S rRNA gene sequences. We confirmed that at a genus level, M and D have different preferences for nitrogen and phosphorus concentrations. Within each genus, we also identified strains differentially associated with temperature, precipitation, and concentrations of nutrients and toxins. In general, niche similarity between strains (as measured by co-occurrence over time) declined with genetic distance. This pattern is consistent with habitat filtering – in which closely related taxa are ecologically similar, and therefore tend to co-occur under similar environmental conditions. In contrast with this general pattern, similarity in certain niche dimensions (notably particulate nitrogen and phosphorus) did not decline linearly with genetic distance, and instead showed a complex polynomial relationship. This observation suggests the importance of processes other than habitat filtering – such as competition between closely related taxa, or convergent trait evolution in distantly related taxa – in shaping particular traits in microbial communities.</p

Data_Sheet_2.FASTA

<p>Bacterial communities are composed of distinct groups of potentially interacting lineages, each thought to occupy a distinct ecological niche. It remains unclear, however, how quickly niche preference evolves and whether more closely related lineages are more likely to share ecological niches. We addressed these questions by following the dynamics of two bloom-forming cyanobacterial genera over an 8-year time-course in Lake Champlain, Canada, using 16S amplicon sequencing and measurements of several environmental parameters. The two genera, Microcystis (M) and Dolichospermum (D), are frequently observed simultaneously during bloom events and thus have partially overlapping niches. However, the extent of their niche overlap is debated, and it is also unclear to what extent niche partitioning occurs among strains within each genus. To identify strains within each genus, we applied minimum entropy decomposition (MED) to 16S rRNA gene sequences. We confirmed that at a genus level, M and D have different preferences for nitrogen and phosphorus concentrations. Within each genus, we also identified strains differentially associated with temperature, precipitation, and concentrations of nutrients and toxins. In general, niche similarity between strains (as measured by co-occurrence over time) declined with genetic distance. This pattern is consistent with habitat filtering – in which closely related taxa are ecologically similar, and therefore tend to co-occur under similar environmental conditions. In contrast with this general pattern, similarity in certain niche dimensions (notably particulate nitrogen and phosphorus) did not decline linearly with genetic distance, and instead showed a complex polynomial relationship. This observation suggests the importance of processes other than habitat filtering – such as competition between closely related taxa, or convergent trait evolution in distantly related taxa – in shaping particular traits in microbial communities.</p

Data_Sheet_1.pdf

<p>Bacterial communities are composed of distinct groups of potentially interacting lineages, each thought to occupy a distinct ecological niche. It remains unclear, however, how quickly niche preference evolves and whether more closely related lineages are more likely to share ecological niches. We addressed these questions by following the dynamics of two bloom-forming cyanobacterial genera over an 8-year time-course in Lake Champlain, Canada, using 16S amplicon sequencing and measurements of several environmental parameters. The two genera, Microcystis (M) and Dolichospermum (D), are frequently observed simultaneously during bloom events and thus have partially overlapping niches. However, the extent of their niche overlap is debated, and it is also unclear to what extent niche partitioning occurs among strains within each genus. To identify strains within each genus, we applied minimum entropy decomposition (MED) to 16S rRNA gene sequences. We confirmed that at a genus level, M and D have different preferences for nitrogen and phosphorus concentrations. Within each genus, we also identified strains differentially associated with temperature, precipitation, and concentrations of nutrients and toxins. In general, niche similarity between strains (as measured by co-occurrence over time) declined with genetic distance. This pattern is consistent with habitat filtering – in which closely related taxa are ecologically similar, and therefore tend to co-occur under similar environmental conditions. In contrast with this general pattern, similarity in certain niche dimensions (notably particulate nitrogen and phosphorus) did not decline linearly with genetic distance, and instead showed a complex polynomial relationship. This observation suggests the importance of processes other than habitat filtering – such as competition between closely related taxa, or convergent trait evolution in distantly related taxa – in shaping particular traits in microbial communities.</p

Water column data in Lake Nkuruba 1992–2012.

<p>Arrows indicate the timing of observed mixing events. a) thermal stability of the water column at the time of sampling expressed using the Schmidt Stability Index computed following <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0086561#pone.0086561-Taranu1" target="_blank">[27]</a>; line indicates trend; b) surface (black circles) and bottom (open diamonds) water temperatures; c) Secchi (black circles) and photic zone (open diamonds) depths (photic zone = Secchi×2.7 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0086561#pone.0086561-Margalef1" target="_blank">[28]</a>); d) depth to anoxia determined as the depth at which dissolved oxygen measurements drop below 1 mg L⁻¹; e) thermocline depth determined as the depth where the greatest inflection in the temperature curve occurs over a thickness of 1 m; f) annual occurrences of atelomixis events identified by thermocline depths greater than 15 m (black bar) or situated between 15 and 10 m (grey bar). For a–c) lines and grey bands indicate the nonlinear (GAM) response curves and the 95% confidence intervals, respectively. For d–e) lines indicate a 10-point running mean.</p

Sedimentary pigment variations (1910–2008) and core chronology.

<p>a) Historical variations in selected pigments and important 20^th century human interventions in the Lake Nkuruba catchment. The dotted horizontal line indicates that the uppermost data points (shown as empty circles) were not considered in our analyses due to differences in digenesis between these and older samples <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0086561#pone.0086561-Guillizzoni1" target="_blank">[29]</a>. b) Unsupported ²¹⁰Pb concentrations in 16 samples and constant rate of supply (CRS) model used to determine downcore ages (including error bars).</p

Map showing location of the study lake among other crater lakes of the Kabarole, Uganda region.

<p>The X marks the coring site and contour lines represent bathymetry (modified from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0086561#pone.0086561-Chapman2" target="_blank">[15]</a>).</p

Air (line) and surface water temperature (bars) anomalies for Lake Nkuruba over 20 years.

<p>Anomaly computed as the difference from the 1992–2011 mean air and surface water temperatures.</p

Sediment accumulation rate, minerogenic content, recent extreme rainfall events.

<p>a) Sediment accumulation rate (dashed line) in the Nkuruba core (in gr/cm⁻²/year; rates are comparable to other crater lakes from the region, Saulnier-Talbot unpublished) and minerogenic content (the unburnt fraction of the sediment after LOI) of the sediment; number of extreme rainfall events per year and total annual precipitation over the sampling period (data modified from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0086561#pone.0086561-Hartter1" target="_blank">[8]</a>).</p

Observed mixing events in Lake Nkuruba 1992–2012.

<p>Mixing events are defined as sampling days with either <0.2°C amplitude in water column and/or ≤1 mg L⁻¹ DO at surface. All temperatures are in °C.</p