Highlights of recent publications

Elucidating the Role of Chloroflexi That Bloom in the Depths of the World's Largest Lakes             > AEM

Relative to their global surface area, freshwater lakes are disproportionally active sites of carbon cycling. Few of the key bacterial populations involved in lake dissolved organic matter (DOM) mineralization have been characterized, particularly for bottom lake layers. Denef et al. (p. 1423–1432) focused on Chloroflexi clade CL500-11, which is the predominant organism in the hypolimnia of the world's largest lakes and likely contributes a significant proportion of the world's freshwater bacterial biomass. Through reconstruction of a nearly complete genome from metagenomic data and metatranscriptomic analysis of Lake Michigan samples, these authors show that CL500-11 plays an important role in the transformation of biologically derived organic matter, particularly nitrogen-rich DOM.

Microbial evolution in the wild             > Science

Microbial communities, Microbial evolution in the wild which drive Earth’s geochemical cycles, can rapidly respond to change, but the proportion of this response that can be attributed to evolutionary processes, rather than species composition or gene expression shifts, remains an unresolved question. Most evolutionary rate estimates are available for nucleotide substitution rates and derive from laboratory measurements. It is difficult to know how relevant these rates are for geochemical environments, because studies on natural populations have been restricted to pathogens and endosymbionts.

We analyzed biofilms collected from a well-defined acid mine drainage system over 9 years to investigate the processes and determine rates of bacterial evolution directly in the environment. Population metagenomic analyses of the dominant primary producer yielded the nucleotide substitution rate, which we used to show that proliferation of a series of recombinant bacterial strains occurred over the past few decades. The ecological success of hybrid bacterial types highlights the role of evolutionary processes in rapid adaptation within natural microbial communities.

Linking genotype to ecology in ecosystem context     > PNAS

Research highlights

The availability of genome sequences for closely related microorganisms has at the same time clarified and complicated our view of species delineation. While 16S rRNA gene based classification generally corresponds to genomic and ecological differences, organisms grouped as one species often display both significant gene content variation as well as resource partitioning.

In order to address the relationship between differences in gene content and sequence and ecological divergence in ecosystem context, I investigated links between genotype and ecology of two populations of Leptospirillum Group II bacteria in comprehensively characterized natural acidophilic biofilm communities. These populations share 99.7 % 16S rRNA gene sequence identity and 95 % average amino acid identity between their orthologs. One predominates during early colonization and the other typically proliferates in later successional stages. Absence of protein expression, measured via mass spectrometry-based community proteomics, of most population-specific gene content supports the argument that much of the laterally transferred gene pool found in closely related isolate genomes is of a transient, non-adaptive nature. Evolutionary signatures, and population-resolved expression patterns emphasize how sequence and expression variation of shared genes contributes to ecological divergence. This highlights an interesting parallel to higher organisms, where evolution of gene expression has been suggested as an important factor in species differentiation.

Ecological divergence between these two populations can be viewed as an example of r- vs. K-selection. The early colonizer proliferates optimally in the absence of competition from other organisms, thanks to adaptations that allow it to rapidly propagate in the AMD environment. Adaptations of the late colonizer allow its proliferation in conditions with high inter- and intra-specific competition for resources. Such distinct ecological strategies mediated by subtle genomic differences between closely related organisms, which are often found to co-exist in natural microbial systems, exemplify how fine-scale variation within ecological functional groups can have significant effects on community structure and functioning.