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Intraspecific niche divergence is an important driver of species range, population abundance and impacts on ecosystem functions. Genetic changes are the primary focus when studying intraspecific divergence; however, the role of ecological interactions, particularly host‐microbiome symbioses, is receiving increased attention. The relative importance of these evolutionary and ecological mechanisms has seen only limited evaluation. To address this question, we used Microcystis aeruginosa, the globally distributed cyanobacterium that dominates freshwater harmful algal blooms. These blooms have been increasing in occurrence and intensity worldwide, causing major economic and ecological damages. We evaluated 46 isolates of M. aeruginosa and their microbiomes, collected from 14 lakes in Michigan, USA, that vary over 20‐fold in phosphorus levels, the primary limiting nutrient in freshwater systems. Genomes of M. aeruginosa diverged along this phosphorus gradient in genomic architecture and protein functions. Fitness in low‐phosphorus lakes corresponded with additional shifts within M. aeruginosa including genome‐wide reductions in nitrogen use, an expansion of phosphorus assimilation genes and an alternative life history strategy of nonclonal colony formation. In addition to host shifts, despite culturing in common‐garden conditions, host‐microbiomes diverged along the gradient in taxonomy, but converged in function with evidence of metabolic interdependence between the host and its microbiome. Divergence corresponded with a physiological trade‐off between fitness in low‐phosphorus environments and growth rate in phosphorus‐rich conditions. Co‐occurrence of genotypes adapted to different nutrient environments in phosphorus‐rich lakes may have critical implications for understanding how M. aeruginosa blooms persist after initial nutrient depletion. Ultimately, we demonstrate that the intertwined effects of genome evolution, host life history strategy and ecological interactions between a host and its microbiome correspond with an intraspecific niche shift with important implications for whole ecosystem function.

Metagenome-assembled genomes (MAGs) expand our understanding of microbial diversity, evolution, and ecology. Concerns have been raised on how sequencing, assembly, binning, and quality assessment tools may result in MAGs that do not reflect single populations in nature. Here, we reflect on another issue, i.e., how to handle highly similar MAGs assembled from independent data sets. Obtaining multiple genomic representatives for a species is highly valuable, as it allows for population genomic analyses; however, when retaining genomes of closely related populations, it complicates MAG quality assessment and abundance inferences. We show that (i) published data sets contain a large fraction of MAGs sharing >99% average nucleotide identity, (ii) different software packages and parameters used to resolve this redundancy remove very different numbers of MAGs, and (iii) the removal of closely related genomes leads to losses of population-specific auxiliary genes. Finally, we highlight some approaches that can infer strain-specific dynamics across a sample series without dereplication.

Our ability to reconstruct genomes from metagenomic datasets has rapidly evolved over the past decade, leading to publications presenting 1,000s, and even more than 100,000 metagenome-assembled genomes (MAGs) from 1,000s of samples. While this wealth of genomic data is critical to expand our understanding of microbial diversity, evolution, and ecology, various issues have been observed in some of these datasets that risk obfuscating scientific inquiry. In this perspective we focus on the issue of identical or highly similar genomes assembled from independent datasets. While obtaining multiple genomic representatives for a species is highly valuable, multiple copies of the same or highly similar genomes complicates downstream analysis. We analyzed data from recent studies to show the levels of redundancy within these datasets, the highly variable performance of commonly used dereplication tools, and to point to existing approaches to account and leverage repeated sampling of the same/similar populations.While initially, the reconstruction of MAGs was only achievable in lower-diversity or highly uneven communities (1), in the past five years reports on the reconstruction of hundreds to thousands of MAGs have become routine (2-5). In the past year, highly automated assembly and binning pipelines have accelerated this trend (6, 7). While these advances open up exciting prospects for addressing questions regarding the physiology, ecology, and evolution of microbial life, MAGs are inherently less reliable than isolate genomes due to their assembly and binning from DNA sequences originating from a mixed community. Various reports have highlighted issues associated with MAGs, including how misassemblies and/or incorrect binning can lead to composite genomes (8,9) and how fragmented assembly due to strain variation can lead to incomplete genomes that lead to wrong conclusions (10, 11). The latter is a reason why independent assembly of each individual sample is often preferable to avoid assembly fragmentation due to genomic variation between conspecific populations in different samples.However, this often leads to highly similar or identical MAGs being generated across the sample dataset. Multiple tools have been developed to remove redundant MAGs, mainly based on average nucleotide identity between MAGs after sequence alignment using blastn (e.g., pyANI (12)), or faster algorithms combining Mash (13) and gANI (14) or ANIm (15) (e.g., as implemented in dRep (16)).Why dereplicate? Dereplication is the reduction of a set of genomes, typically assembled from metagenomic data, based on high sequence similarity between these genomes. The main reason to do so is that when redundancy in a database of genomes is maintained, the subsequent step of mapping sequencing reads back to this database of genomes leads to sequencing reads having multiple high quality alignments which, depending on the software used and parameters chosen, leads to reads being randomly distributed across the redundant genomes with one random alignment report...

Cyanobacteria harmful algal blooms (cyanoHABs) dominated byMicrocystisspp. have significant public health and economic implications in freshwater bodies around the world. These blooms are capable of producing a variety of cyanotoxins, including microcystins, that affect fishing and tourism industries, human and environmental health, and access to drinking water. In this study, we isolated and sequenced the genomes of 21 unialgalMicrocystiscultures collected from western Lake Erie between 2017-2019. While some cultures isolated in different years have a high degree of genetic similarity (Average Nucleotide Identity >99%), genomic data shows that these cultures also represent much of the breadth of knownMicrocystisdiversity in natural populations. Only 5 isolates contained all the genes required for microcystin synthesis while 2 isolates contained a previously described partialmcyoperon. Microcystin production within cultures was also assessed using Enzyme-Linked Immunosorbent Assay (ELISA) and supported genomic results with high concentrations (up to 900 μg L-1) in cultures with completemcyoperons and no or low toxin detected otherwise. These xenic cultures also contained a substantial diversity of bacteria associated withMicrocystis, which has become increasingly recognized as an essential component of cyanoHAB community dynamics. These results highlight the genomic diversity amongMicrocystisstrains and associated bacteria in Lake Erie, and their potential impacts on bloom development, toxin production, and toxin degradation. This collection significantly increases the availability of environmentally relevantMicrocystisstrains from temperate North America, which is changing rapidly due to climate change.HighlightsTwenty one xenicMicrocystiscultures were isolated from western Lake Erie and capture the diversity ofMicrocystisstrains observed in natural populations as well as their associated bacteriaMicrocystisstrains show variability in core and accessory gene content, and genetically similar strains produce varying concentrations and congeners of microcystinsThis collection is a valuable resource for studying strain diversity and interactions betweenMicrocystisand associated bacteriaOur collection increases the availability of environmentally relevant strains from temperate North America, which is historically underrepresented in culture collections.