The study of freshwater microbial ecology has matured beyond the purely descriptive phase and now represents a compelling system in which to test explicit hypotheses addressing the physical, chemical, and biological forces that structure microbial communities. Results from our prior work suggest that various drivers are acting as a system of hierarchical constraints on freshwater microbes at different temporal and spatial scales. Therefore, we now seek to determine which factors contribute to structuring communities and populations, at regional and local spatial scales. Much of the work in this area is conducted in collaboration with the scientists working through the Center for Limnology and the North Temperate Lakes Long Term Ecological Research site. Below are descriptions of the main projects we currently have related to this area.




Disturbance as a driver of community composition and dynamics - We are currently studying the influence of disturbance on bacterial community assembly. The relationship between disturbance frequency and diversity is a longstanding area of classical ecological study. Disturbances cause habitat homogenization and initiate successional trajectories that are often (but not always) predictable in macroscale communities. In our previous work, we observed recurring seasonal succession in bacterial communities which seemed to be re-set by mixing events. We hypothesize that thermal stratification and mixing are major drivers of freshwater bacterial community composition and dynamics. To explore how lake mixing regime determines bacterial community assembly, we are conducting a survey of eight bog lakes during the summer of 2007. These lakes represent a gradient of water column stability because of differences in their morphometry and exposure to climatic drivers. We are also conducting enclosure experiments to tease apart the physical and chemical factors influencing bacterial communities in a dimictic humic lake.



Postdocs:

Todd Miller



Students:

Ashley Shade


Collaborators:

Timothy Kratz, University of Wisconsin-Madison

James Rusak, University of Wisconsin-Madison

Chin Wu, University of Wisconsin-Madison

Chih-Yu Chiu, Academia Sinica, Taiwan



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Polynucleobacter genome biology and ecology - The genome sequence of a free-living strain of Polynucleobacter, a cosmopolitan member of freshwater bacterial communities, was recently determined by the JGI. An endosymbiotic strain sharing 99.4% 16S rRNA sequence identity with the free-living strain is currently being sequenced also. Genome-enabled insights into the metabolism and ecological potential of the free-living strain will facilitate discovery of the ecological function of these numerically highly important freshwater bacteria. Comparison of genomes of the closely related free-living and endosymbiotic Polynucleobacter strains will provide unique insights in the evolutionary adaptations taking place during the early phase of endosymbiosis. Genome comparison with nonfreshwater Burkholderiaceae (Burkholderia spp., Ralstonia spp., Cupriavidus spp.) will provide first insights in evolutionary adaptations to planktonic life in freshwater.



Postdocs
:
Todd Miller



Students:

none currently



Collaborators:

Rachel Whitaker, University of Illinois at Urbana-Champaign

Martin Hahn, Austrian Academy of Sciences

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Freshwater Actinobacteria population ecology - The acI lineage of freshwater Actinobacteria is a cosmopolitan and often numerically dominant member of lake bacterial communities. We conducted a survey of acI 16S rRNA genes and 16S-23S rRNA internal transcribed spacer (ITS) regions from 18 Wisconsin, USA lakes; and used standard nonphylogenetic and phylogenetic statistical approaches to investigate the factors that determine acI community composition at the local (within lakes) and regional scales (across lakes). Phylogenetic reconstruction of more than 400 acI 16S rRNA genes revealed a well-defined and highly-resolved phylogeny. Eleven previously unrecognized monophyletic clades each with ≥97.9% within-clade 16S rRNA gene sequence identity were identified. Clade community similarity positively correlated with lake environmental similarity but not with geographic distance, implying that these lakes represent a single biotic region containing environmental filters for communities of similar composition. Relatively unrelated clades were the most abundant at the regional scale, but local communities were comprised of relatively related clades, with lake pH as a strong predictor of the community composition, but only when lakes with a pH below 6 were included in the dataset. In the remaining lakes (pH above 6) biogeographic patterns in the landscape were instead a predictor of the observed acI community structure. The non-random distribution of the newly defined acI clades suggests potential ecophysiological differences between the clades, with the clades acI-AI, BII, and BIII preferring acidic lakes and acI-AII, AVI, and BI preferring more alkaline lakes. We continue to study the population structure and ecology of this important freshwater group.



Former Students:

Ryan Newton

Stuart Jones



Collaborators:

Matthew Helmus, University of Wisconsin-Madison

Rachel Whitaker, University of Illinois at Urbana-Champaign



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Autonomous microbial geosensor - Microbial ecologists are currently limited in the scope of their research questions and monitoring capabilities by existing technologies for sample collection and analysis. Autonomous remote sensing devices capable of detecting bacteria at high frequency with adequate specificity are required to address these challenges. We are adapting a prototype autonomous microbial genosensor (AMG) developed at the University of South Florida Center for Ocean Technology, for use in freshwater lakes, to enable research on potentially toxic cyanobacteria and important groups of cosmopolitan heterotrophic bacteria.



Postdocs:

Todd Miller



Students:

Sheena Chaston



Collaborators:

David Fries, University of South Florida

Matthew Smith, University of South Florida

Juli Dyble, Great Lakes Environmental Research Laboratory, NOAA, Ann Arbor, MI

Stefan Bertilsson, Uppsala University



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Microbial contribution to phosphorus cycling in eutrophic lakes - Accelerated eutrophication of surface waters is a well-studied but extremely complex water quality problem. Despite the research efforts expended, widely applicable viable solutions remain elusive, partly because we do not fully understand the underlying mechanisms driving the process. Phosphorus (P) is of particular concern with respect to freshwater eutrophication, as it is often the limiting nutrient in these systems. Therefore, we are investigating the relationship between bacterial community structure, function, and phosphorus cycling. We are particularly interested in how variation in bacterial community structure across time and space relates to phosphorus dynamics. We have selected three contrasting eutrophic lakes to study: Lake Mendota, a large deep dimictic lake adjacent to Madison, WI; Lake Wingra, a small shallow polymictic lake in Madison; and Lake Taihu, a large shallow polymictic lake in China.

It is generally accepted that microbes (primarily algae and bacteria) control P-cycling in lakes, through their actions in both the water column and sediments. However, very little is known about the biochemical mechanisms involved in microbial P-cycling, or about the contribution of different taxonomic groups to specific P transformations. Recent studies of freshwater bacterial community dynamics in eutrophic lakes suggest that community composition varies significantly over time, and that this variation is correlated with changes in nutrient availability. A better understanding of the fundamental mechanisms involved, and how these may vary with community composition, will ultimately lead to an improved ability to predict the effects of lake management practices on water quality.



Students:
Emily Kara



Collaborators:

Chin Wu, University of Wisconsin-Madison



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