Phylogenetic clustering of soil microbial communities by 16S rRNA but not 16S rRNA genes

Understanding the evolutionary relationships among microorganisms is fundamental to microbial ecology and taxonomy. Phylogenetic trees are essential tools for inferring these relationships, relying primarily on comparative analyses of molecular sequences such as DNA, RNA, or proteins. In microbial studies, these trees typically depict the evolutionary paths of diverse bacterial and archaeal species by mapping genetic differences accumulated over time.Phylogenetic trees are composed of tips,...

The phylogenetic species concept (PSC) is a framework used to delineate species based on evolutionary relationships, emphasizing shared ancestry and diagnosable genetic traits. Unlike morphological or biological species concepts, the PSC is particularly advantageous for microbial taxonomy, where traditional reproductive or phenotypic criteria often fall short due to the prevalence of asexual reproduction, minimal morphological differentiation, and widespread horizontal gene transfer among...

Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...

Soil microbial ecology is defined by highly diverse, spatially structured communities that drive nutrient cycling, organic matter turnover, and overall ecosystem stability. Although a gram of soil can contain thousands of bacterial and archaeal taxa, the ecological processes they mediate are even more crucial for sustaining terrestrial life.Microhabitats and NichesSoil is a heterogeneous mixture of minerals, organic matter, water, and air. Microbes inhabit distinct microhabitats formed by...

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...