Description of the Earth’s microbiota has recently undergone a phenomenal expansion that has challenged basic assumptions in many areas of biology, including hominid evolution, human gastrointestinal and neurodevelopmental disorders, and plant adaptation to climate change. By using the classic model system of freshwater phytoplankton that has been drawn upon for numerous foundational theories in ecology, we show that microbiomes, by facilitating their host population, can also influence between-species interactions among their eukaryotic hosts. Between-species interactions, including competition for resources, have been a central tenet in the field of ecology because of their implications for the diversity and composition of communities and how this in turn shapes ecosystem functioning.

Cyanobacteria blooms in places like Lake Erie can persist for months, long after most of the available nutrients in the water have been depleted. How do these troublesome photosynthetic organisms, sometimes called blue-green algae, manage it? In a study published online July 25 in the journal Molecular Ecology, University of Michigan biologists and their colleagues report that different strains of the common cyanobacterium Microcystis aeruginosa appear to be adapted to different levels of the nutrient phosphorus in the water. As phosphorus is gradually depleted by high-nutrient-adapted cyanobacterial strains over the course of the summer, low-nutrient-adapted strains present in the same lake apparently take over. M. aeruginosa is the toxin-producing cyanobacterium blamed for the 2014 Toledo water crisis. The researchers did a genetic analysis of 46 M. aeruginosa isolates and their microbiomes, collected by collaborators at Michigan State University (Jeffrey White and Orlando Sarnelle), from 14 inland Michigan lakes with a wide range of phosphorus levels. Along the nutrient gradient, they found differences in Microcystis genome structure and function, in how the organisms form the multicellular colonies that make them so successful in the environment, and in the microbiomes that help them grow. (Image credit: John Megahan, UM EEB)

Species invasion is one of the primary forces modifying the diversity and functioning of life in Earth’s marine and freshwater systems. In the Great Lakes, it is well known that the most radical changes to community structure and the flow of energy and matter are mediated by invasive dreissenid mussels (IDM), the most impactful among its nearly 200 invaders. It is mostly unknown how IDM affect bacterial community composition and their crucial contributions to elemental cycling. We were the first to demonstrate that direct IDM effects reduced bacterial abundance and altered assemblage composition by preferentially removing particle-associated bacteria (Denef et al., 2017). In the current study, we showed that populations removed by IDM corresponded to the high-nucleic acid (HNA) flow cytometric functional group. This is important as HNA bacteria often are the largest contributors to carbon processing in aquatic systems. While focused on the biological question of IDM impacts on bacterioplankton communities, this study also contributed to the development of a novel flow cytometry-based method. This method allows tracking community diversity at high temporal resolution by calculating phenotypic diversity estimates from FCM data from minute amounts of sample. Through parallel FCM and 16S rRNA gene amplicon sequencing analysis of environments spanning a broad diversity range, we showed that the two approaches resulted in highly correlated diversity measures and captured the same community composition transitions.

Algal biofuels have the potential to curb greenhouse gas emissions from fossil fuels, but meeting the multiple standards necessary for industrial use has proven difficult. Jackrel et al. (e00953-18) showed that, relative to monocultures, species consortia can differentially regulate lipid metabolism genes that allow them to produce higher-quality biocrude while also growing to higher levels of biomass. This study further identified genes involved in lipid biosynthesis that are frequently upregulated in species consortia and are predictive of algal lipid content. These results suggest that it is possible to engineer consortia of algae that improve the production of bio-oil.

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 communities, 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.