How Viruses Shape Microbial Plankton Microdiversity.

One major conundrum of modern microbiology is the large pangenome (gene pool) present in microbes, which is much larger than those found in complex organisms such as humans. Here, we argue that this diversity of gene pools carried by different strains is maintained largely due to the control exercised by viral predation. Viruses maintain a high strain diversity through time that we describe as constant-diversity equilibrium, preventing the hoarding of resources by specific clones. Thus, viruses facilitate the release and degradation of dissolved organic matter in the ocean, which may lead to better ecosystem functioning by linking top-down to bottom-up control. By maintaining this equilibrium, viruses act as a key element of the adaptation of marine microbes to their environment and likely evolve as a single evolutionary unit.

Microdiversity in marine pelagic ammonia-oxidizing archaeal populations in a Mediterranean long-read metagenome.

The knowledge of the different population-level processes operating within a species, and the genetic variability of the individual prokaryotic genomes, is key to understanding the adaptability of microbial populations. Here, we characterized the flexible genome of ammonia-oxidizing archaeal (AOA) populations using a metagenomic recruitment approach and long-read (PacBio HiFi) metagenomic sequencing. In the lower photic zone of the western Mediterranean Sea (75 m deep), the genomes Nitrosopelagicus brevis CN25 and Nitrosopumilus catalinensis SPOT1 had the highest recruitment values among available complete AOA genomes. They were used to analyse the diversity of flexible genes (variable from strain to strain) by examining the long-reads located within the flexible genomic islands (fGIs) identified by their under-recruitment. Both AOA genomes had a large fGI involved in the glycosylation of exposed structures, highly variable, and rich in glycosyltransferases. N. brevis had two fGIs related to the transport of phosphorus and ammonium respectively. N. catalinensis had fGIs involved in phosphorus transportation and metal uptake. A fGI5 previously reported as 'unassigned function' in N. brevis could be associated with defense. These findings demonstrate that the microdiversity of marine microbe populations, including AOA, can be effectively characterized using an approach that incorporates third-generation sequencing metagenomics.

The bacterial pan-genome: a new paradigm in microbiology

Bacterial strains belonging to the same species vary considerably in gene content. Thus, the genetic repertoire of a given species (its «pan-genome») is much larger than the gene content of individual strains. These variations in DNA material, together with differences in genomic structure and nucleotide polymorphisms among strains, confer upon prokaryotic species a phenomenal adaptability. Although the approach of sequencing multiple strains from a single species remains the main and often easiest way to study the pan-genome, feasible alternatives include those related to DNA hybridization. In other cases, the use of metagenomic sequences is already applicable by data mining from the growing metagenomic databases. Eventually, the single-cell genome approach might be the ideal solution. The pan-genome concept has important consequences for the way we understand bacterial evolution, adaptation, and population structure, as well as for more applied issues such as vaccine design or the identification of virulence genes (AU)

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