Seasonality and environmental control of freshwater SAR11 (LD12) in a temperate lake (Lake Erken, Sweden)

Abstract

THE SAR11 clade is ubiquitous and abundant in planktonic environments. In freshwater lakes, the clade is represented by tribe LD12 which is phylogenetically distinct from the marine SAR11. We studied the ecology of LD12 in a temperate dimictic lake (Lake Erken, Sweden), by analyzing its seasonal dynamics with quantitative PCR, CARD-FISH and 454 pyrosequencing of the 16S rRNA gene. Results showed that LD12 can be as numerous in freshwater bacterioplankton as their marine SAR11 siblings. They exhibited strong seasonality and made up from 1.8 to 40% of the total bacterial 16S rRNA pool (mean 14%) with pronounced peaks in summer and late fall. Except in spring, LD12 was the dominant Alphaproteobacteria, contributing on average 72% of the 16S rRNA within this class. The LD12 population was dominated by a single persistent ribotype, suggesting low local divergence, at least at the phylogenetic resolution accessed with rRNA genes. The relative abundance of LD12 was positively correlated to nutrient concentrations (phosphate, ammonia, nitrate, and silica) and water transparency whereas the relative abundance was lower during periods characterized by high phytoplankton biomass. Based on these observations we propose that LD12 are poor competitors during periods of high phytoplankton productivity and associated release of labile organic compounds, but thrive when availability of inorganic nutrients is high. Similar to the marine SAR11 sibling group, local LD12 populations appear to respond in contrasting ways to nutrient availability in different lakes, pointing to either ecological divergence within the tribe or variations in the interplay between environmental driver variables.

Vertical partitioning of freshwater bacterioplankton community in a deep mesotrophic lake with a fully oxygenated hypolimnion (Lake Biwa, Japan)

“…B). Other well‐studied tribes of LD12 (Salcher et al ., ; Heinrich et al ., ), PnecB of the Polynucleobacter (Wu and Hahn, ; Salcher et al ., ; Hahn et al ., ) and LD28 (Salcher et al ., ) were less abundant but ranked as one of the representative groups of the epilimnetic community (Fig. B).…”

Phylogenetic Signals of Salinity and Season in Bacterial Community Composition Across the Salinity Gradient of the Baltic Sea

“…In contrast to investigations of the bacterial communities along the shoreline of the Gulf of Gdansk (Piwosz et al, 2013), we found no representative of the freshwater SAR11-IIIb clade (formerly “LD-12”) in the oligohaline samples of the Baltic Sea. However, the oligohaline areas of the Baltic Sea could not be sampled in February, and SAR11-IIIb may have been absent in our sampling campaign in July since SAR11-IIIb are poor competitors during phytoplankton blooms (Heinrich et al, 2013). The brackish and marine bacterial communities differed both in summer and in winter ( Figure 4 ), which is in line with the results of a previous metagenome study (Dupont et al, 2014; Hugerth et al, 2015).…”

Lake bacterioplankton dynamics over diurnal timescales

“…LD12, as well as its marine sister group SAR11, have repeatedly been observed in high abundances in surface waters during stratified or warm periods in marine and freshwater environments (Alonso‐Sáez et al ., ; Salcher, Pernthaler & Posh, ). In Lake Erken LD12 can contribute up to 40% of the bacterial community and annual maxima occurred during high zooplankton abundance (Heinrich et al ., ). In combination with data from the current study, we propose that this abundant tribe feeds on labile organic substances released during cell lysis.…”