Ecology and Evolution of Thermophilic Synechococcus
Genetic modes of adaptation very across the microbial tree of life, but patterns of divergence and the environmental factors that lead to speciation remain elusive. In addition, it is not clear whether bacteria and archaea form species as we typically think of them. I have employed a variety of molecular techniques to examine the ecology and evolution of natural Cyanobacterial populations in model hot spring systems.
Published Work
Primary author
Editorial: Searching for the Boundaries of Microbial Speciation in a Rapidly Evolving World
December, 23, 2021
Whether bacteria and archaea form species-like populations has been a long-standing debate. In contrast to eukaryotic organisms, horizontal gene transfer in microorganisms can make observing vertical lineages of descent difficult. Microorganisms evolve very fast, most are difficult to culture, and the number of cells in a population and community can often be >109 cells/ml, all making studying the process of evolution and speciation difficult. There is evidence to support the idea that bacteria and archaea form cohesive sequence clusters (Jain et al., 2018; Cohan, 2019), that they form ecological species (Becraft et al., 2015; Cohan, 2017), that the rate of homologous recombination can be used as the defining species barrier (Vos and Didelot, 2009; Cadillo-Quiroz et al., 2012; Bobay and Ochman, 2017), and that microbial species simply do not exist due to speed of evolution and a high rate of horizontal gene transfer (Doolittle and Papke, 2006; Papke et al., 2007). Often the system or organisms analyzed effect how researchers subsequently define species, though until about 10 years ago sequencing technologies and techniques were not adequate to answer many of these questions in situ. The rapid increase in sequencing technologies, such as metagenomics and single cell genomics, is allowing researchers to once again approach this topic with higher genetic resolution.
Relationship between Microorganisms Inhabiting Alkaline Siliceous Hot Spring Mat Communities and Overflowing Water
December 1, 2020
The compositions of Octopus Spring and Mushroom Spring (Yellowstone National Park, Wyoming, USA) microbial mats have been thoroughly studied, but the compositions of the effluent waters that flow above the mats have not. In this study, cells in the mats and overflowing waters of both springs were investigated at multiple sites where Synechococcus spp. are the dominant cyanobacteria (ca. 72°C to ca. 50°C), and on several dates. In addition to microscopic analyses of stained and autofluorescent cells, 16S rRNA gene sequencing was used to characterize the major taxa present and a protein-encoding gene (psaA) was sequenced and analyzed by ecotype simulation to predict species of Synechococcus. The mats of both springs were similar in terms of the downstream distribution of predominant taxa detected previously. However, waters above these mats were predominated by taxa that reside in upstream mats or communities above the upper-temperature limit of the mat. A disturbance/recolonization study was performed at a site normally predominated by Synechococcus species adapted to low temperatures. After removing indigenous Synechococcus cells, Synechococcus species adapted to higher temperatures, which were predominant in the water overflowing this site, colonized the newly forming mat. Differences in recolonization under reduced and UV-screened irradiance suggested that, in addition to physical transport, environmental conditions likely select for species that are better adapted to these different conditions and can influence mat recovery. A transport model was developed and used to predict that, in Mushroom Spring, erosion predominates in the narrower and deeper upstream effluents and deposition predominates over erosion in wider and shallower downstream effluents.
Biogeography of American Northwest Hot Spring A/B′-Lineage Synechococcus Populations
February 24, 2020
Fone scale biogeography of Synechococcus species in Yellowstone and Oregon.
The molecular dimension of microbial species: 1. Ecological distinctions among, and homogeneity within, putative ecotypes of Synechococcus inhabiting the cyanobacterial mat of Mushroom Spring, Yellowstone National Park
2015
The first of three studies linking 1) fine-scale distribution of natural populations in the environment, 2) in vitro behavior of cultures representative of these natural populations in response to varying conditions, and 3) genomic analyses of genomes sequenced of individuals within these natural populations. We show that the ecology of these "ecotype" populations match their behavior in culture and genomic content.
Fine-Scale Distribution Patterns of Synechococcus Ecological Diversity in Microbial Mats of Mushroom Spring, Yellowstone National Park
2011
Denaturing gradient gel electrophoresis was used to track the distribution of dominant sequence variants of ecotype populations relative to temperature variation and to O2, pH, and spectral irradiance variation, as measured using microsensors. Different distributions along effluent channel flow and vertical gradients, where temperature, light, and O2Â concentrations are known to vary, confirmed the ecological distinctness of putative ecotypes.
Contributions in the Literature
Ecotype Simulation 2: An improved algorithm for efficiently demarcating microbial species from large sequence datasets
prepublication
Software that predicts microbial species from large data sets.
Recombination Does Not Hinder Formation or Detection of Ecological Species of Synechococcus Inhabiting a Hot Spring Cyanobacterial Mat
2016
Despite recombination within the A and B' lineages, there was evidence of ecological diversification within each lineage. We conclude that sexual isolation is more likely to follow ecological divergence than to precede it. Thus, an ecology-based model of speciation appears more appropriate than the biological species concept for bacterial and archaeal diversification.
The molecular dimension of microbial species: 2. Synechococcus strains representative of putative ecotypes inhabiting different depths in the Mushroom Spring microbial mat exhibit different adaptive and acclimative responses to light
2015
The results presented here are consistent with the hypothesis that closely related, but distinct, ecological species of Synechococcus occupy different light niches in the Mushroom Spring microbial mat and acclimate differently to changing light environments.
The molecular dimension of microbial species: 3. Comparative genomics of Synechococcus strains with different light responses and in situ diel transcription patterns of associated putative ecotypes in the Mushroom Spring microbial mat
2015
This study suggests that strains of closely related PEs have different genomic adaptations that enable them to inhabit distinct ecological niches while living in close proximity within a microbial community.
Diel metabolomics analysis of a hot spring chlorophototrophic microbial mat leads to new hypotheses of community member metabolismsng
2015
We have formulated the following new hypotheses: (1) the morning hours are a time of biosynthesis of amino acids, DNA, and RNA; (2) photo-inhibited cells may also produce lactate via fermentation as an alternate metabolism; (3) glycolate and lactate are exchanged among Synechococcus and Roseiflexus; and (4) fluctuations in many metabolite pools at different times of day result from species found at different depths within the mat responding to temporal differences in their niches.
Regulation of nif gene expression and the energetics of N2 fixation over the diel cycle in a hot spring microbial mat
2008
Transcripts for proteins associated with energy-producing metabolisms in the cell also followed diel patterns, with fermentation-related transcripts accumulating at night, photosynthesis- and respiration-related transcripts accumulating during the day and late afternoon, respectively. These results are discussed with respect to the energetics and regulation of N2Â fixation in hot spring mats and factors that can markedly influence the extent of N2Â fixation over the diel cycle.