Microbial communities of the Laurentian Great Lakes reflect connectivity and local biogeochemistry

The Laurentian Great Lakes are a vast, interconnected freshwater system spanning strong physicochemical gradients, thus constituting a powerful natural laboratory for addressing fundamental questions about microbial ecology and evolution. We present a comparative analysis of pelagic microbial communities across all five Laurentian Great Lakes, focusing on Bacterial and Archaeal picoplankton characterized via 16S rRNA amplicon sequencing. We collected samples throughout the water column from the major basins of each lake in spring and summer over 2 years. Two oligotypes, classified as LD12 (Alphaproteobacteria) and acI‐B1 (Actinobacteria), were among the most abundant in every sample. At the same time, microbial communities showed distinct patterns with depth during summer stratification. Deep hypolimnion samples were frequently dominated by a Chloroflexi oligotype that reached up to 19% relative abundance. Stratified surface communities differed between the colder, less productive upper lakes (Superior, Michigan, Huron) and warmer, more productive lower lakes (Erie, Ontario), in part due to an Actinobacteria oligotype (acI‐C2) that averaged 7.7% of sequences in the lower lakes but <0.2% in the upper lakes. Together, our findings suggest that both hydrologic connectivity and local selective pressures shape microbial communities in the Great Lakes and establish a framework for future investigations.

Reevaluating the Salty Divide: Phylogenetic Specificity of Transitions between Marine and Freshwater Systems

Marine and freshwater microbial communities are phylogenetically distinct, and transitions between habitat types are thought to be infrequent. We compared the phylogenetic diversity of marine and freshwater microorganisms and identified specific lineages exhibiting notably high or low similarity between marine and freshwater ecosystems using a meta-analysis of 16S rRNA gene tag-sequencing data sets. As expected, marine and freshwater microbial communities differed in the relative abundance of major phyla and contained habitat-specific lineages. At the same time, and contrary to expectations, many shared taxa were observed in both habitats. Based on several metrics, we found that Gammaproteobacteria, Alphaproteobacteria, Bacteroidetes, and Betaproteobacteria contained the highest number of closely related marine and freshwater sequences, suggesting comparatively recent habitat transitions in these groups. Using the abundant alphaproteobacterial group SAR11 as an example, we found evidence that new lineages, beyond the recognized LD12 clade, are detected in freshwater at low but reproducible abundances; this evidence extends beyond the 16S rRNA locus to core genes throughout the genome. Our results suggest that shared taxa are numerous, but tend to occur sporadically and at low relative abundance in one habitat type, leading to an underestimation of transition frequency between marine and freshwater habitats. Rare taxa with abundances near or below detection, including lineages that appear to have crossed the salty divide relatively recently, may possess adaptations enabling them to exploit opportunities for niche expansion when environments are disturbed or conditions change. IMPORTANCE The distribution of microbial diversity across environments yields insight into processes that create and maintain this diversity as well as potential to infer how communities will respond to future environmental changes. We integrated data sets from dozens of freshwater lake and marine samples to compare diversity across open water habitats differing in salinity. Our novel combination of sequence-based approaches revealed lineages that likely experienced a recent transition across habitat types. These taxa are promising targets for studying physiological constraints on salinity tolerance. Our findings contribute to understanding the ecological and evolutionary controls on microbial distributions, and open up new questions regarding the plasticity and adaptability of particular lineages.

Phytoplankton succession affects the composition of Polynucleobacter subtypes in humic lakes

Phytoplankton influence the composition of bacterial communities, but the taxonomic specificity of algal-bacterial interactions is unclear due to the aggregation of ecologically distinct bacterial populations by community characterization methods. Here we examine whether phytoplankton seasonal succession affects the composition of subtypes within the cosmopolitan freshwater bacterial genus Polynucleobacter. Changes in the composition of Polynucleobacter subtypes were characterized in samples collected weekly from May to August in 2003 and 2008 from three humic lakes using terminal restriction fragment length polymorphism fingerprinting of the protein-encoding cytochrome c oxidase ccoN gene. Changes in phytoplankton population abundances explained, on average, 30% of temporal variation in the composition of Polynucleobacter subtypes and the interaction between phytoplankton and the environment explained an additional 18% of temporal variation. The effect of phytoplankton on specific Polynucleobacter subtypes was experimentally confirmed by changes in Polynucleobacter subtype composition following incubation with different phytoplankton assemblages or a no-phytoplankton control. Phytoplankton-associated subtypes and differentiation in substrate use among subtypes likely contribute to the effects of phytoplankton on Polynucleobacter subtype composition. Interactions between unique Polynucleobacter populations and phytoplankton highlight the ecological significance and specificity of species interactions in freshwater communities.

Temporal patterns in glycolate-utilizing bacterial community composition correlate with phytoplankton population dynamics in humic lakes

Previous observations of correlated community dynamics between phytoplankton and bacteria in lakes indicate that phytoplankton populations may influence bacterial community structure. To investigate the possibility that bacterial use of phytoplankton exudates contributes to observed patterns of community change, we characterized the diversity and dynamics of heterotrophic bacterioplankton with genetic potential to use glycolate, a photorespiration-specific exudate, in five lakes over a 15-week period. Culture-independent approaches were used to track different bacterial phylotypes represented by DNA sequence variation in the functional gene glycolate oxidase subunit D (glcD). glcD gene sequences from freshwater bacteria exhibited broad phylogenetic diversity, including sequences representing the Alpha-, Beta-, and Gammaproteobacteria, Actinobacteria, Bacteroidetes, Firmicutes, and Verrucomicrobia. The majority of glcD gene sequences were betaproteobacterial, with 48% of the sequences clustering with the glcD gene from the cosmopolitan freshwater species Polynucleobacter necessarius. Terminal restriction fragment length polymorphism fingerprinting of the glcD gene revealed changes in glycolate-utilizing assemblages over time. An average of 39% of within-lake temporal variation in glycolate-utilizing assemblages across five lakes was explained by phytoplankton community composition and dynamics. The interaction between phytoplankton populations and the environment explained an additional 17% of variation on average. These observations offer new insight into the diversity and temporal dynamics of freshwater bacteria with genetic potential to use glycolate and support the hypothesis that algal exudates influence the structure of bacterial communities.