Evolution of Protein Superfamilies and Bacterial Genome Size

Prokaryotic organisms are exposed in the course of evolution to various impacts, resulting often in drastic changes of their genome size. Depending on circumstances, the same lineage may diverge into species having substantially reduced genomes, or such whose genomes have undergone considerable enlargement. Genome reduction is a consequence of obligate intracellular lifestyle rendering numerous genes expendable. Another consequence of intracellular lifestyle is reduction of effective population size and limited possibility of gene acquirement via lateral transfer. This causes a state of relaxed selection resulting in accumulation of mildly deleterious mutations that can not be corrected by recombination with the wild type copy. Thus, gene loss is usually irreversible. Additionally, constant environment of the eukaryotic cell renders that some bacterial genes involved in DNA repair are expandable. The loss of these genes is a probable cause of mutational bias resulting in a high A+T content. While causes of genome reduction are rather indisputable, those resulting in genome expansion seem to be less obvious. Presumably, the genome enlargement is an indirect consequence of adaptation to changing environmental conditions and requires the acquisition and integration of numerous genes. It seems that the need for a great number of capabilities is common among soil bacteria irrespective of their phylogenetic relationship. However, this would not be possible if soil bacteria lacked indigenous abilities to exchange and accumulate genetic information. The latter are considerably facilitated when housekeeping genes are physically separated from adaptive loci which are useful only in certain circumstances.

Download Full-text

Edaphic controls on genome size and GC content of bacteria in soil microbial communities

10.1101/2021.11.17.469016 ◽

2021 ◽

Author(s):

Peter Francis Chuckran ◽

Cody Flagg ◽

Jeffrey Propster ◽

William Austin Rutherford ◽

Ella T. Sieradzki ◽

...

Keyword(s):

Amino Acid ◽

Codon Usage ◽

Genome Size ◽

Acid Content ◽

Bacterial Genome ◽

Soil Microbial Communities ◽

Gc Content ◽

Amino Acid Content ◽

The United States ◽

Soil Bacterial

Genomic traits, such as genome size, GC content, codon usage, and amino acid content, shed insight into the evolutionary processes of bacteria and selective forces behind microbial community composition. Nutrient limitation has been shown to reduce bacterial genome size and influence nucleotide composition, yet little research has been conducted in the soil environment, and the factors which shape soil bacterial genomic traits remain largely unknown. Here we determined average genome size, GC content, codon usage, and amino acid content from 398 soil metagenomes across the United States from the National Ecological Observation Network (NEON) and observed the distribution of these traits across numerous environmental gradients. We found that genomic trait averages were most strongly related to pH, which we suggest results in both physiological constraints on growth as well as affects availability of nutrients in soil. Low pH soils had higher carbon to nitrogen ratios (C:N) and tended to have communities with larger genomes and lower GC-content, potentially a result of increased physiological stress and increased metabolic diversity. Conversely, smaller genomes with high GC content were associated with high pH and low soil carbon to nitrogen ratios, indicating potential resource driven selection against carbon-rich AT base pairs. We found that this relationship of nutrient conservation also applied to amino acid stoichiometry, where bacteria in soils with C:N ratios tended to code for amino acids with lower C:N. Together, these relationships point towards fundamental mechanisms which underpin nucleotide and amino acid selection in soil bacterial communities.

Download Full-text

Trophic Specialization Results in Genomic Reduction in Free-Living MarineIdiomarinaBacteria

mBio ◽

10.1128/mbio.02545-18 ◽

2019 ◽

Vol 10 (1) ◽

Cited By ~ 2

Author(s):

Qi-Long Qin ◽

Yi Li ◽

Lin-Lin Sun ◽

Zhi-Bin Wang ◽

Shi Wang ◽

...

Keyword(s):

Genome Size ◽

Bacterial Genome ◽

Substrate Utilization ◽

Comparative Genomic ◽

Metabolic Efficiency ◽

Trophic Specialization ◽

Free Living ◽

Carbohydrate Utilization ◽

New Hypothesis ◽

Living Bacteria

ABSTRACTThe streamlining hypothesis is generally used to explain the genomic reduction events related to the small genome size of free-living bacteria like marine bacteria SAR11. However, our current understanding of the correlation between bacterial genome size and environmental adaptation relies on too few species. It is still unclear whether there are other paths leading to genomic reduction in free-living bacteria. The genome size of marine free-living bacteria of the genusIdiomarinabelonging to the orderAlteromonadales(Gammaproteobacteria) is much smaller than the size of related genomes from bacteria in the same order. Comparative genomic and physiological analyses showed that the genomic reduction pattern in this genus is different from that of the classical SAR11 lineage. Genomic reduction reconstruction and substrate utilization profile showed thatIdiomarinaspp. lost a large number of genes related to carbohydrate utilization, and instead they specialized on using proteinaceous resources. Here we propose a new hypothesis to explain genomic reduction in this genus; we propose that trophic specialization increasing the metabolic efficiency for using one kind of substrate but reducing the substrate utilization spectrum could result in bacterial genomic reduction, which would be not uncommon in nature. This hypothesis was further tested in another free-living genus,Kangiella, which also shows dramatic genomic reduction. These findings highlight that trophic specialization is potentially an important path leading to genomic reduction in some marine free-living bacteria, which is distinct from the classical lineages like SAR11.IMPORTANCEThe streamlining hypothesis is usually used to explain the genomic reduction events in free-living bacteria like SAR11. However, we find that the genomic reduction phenomenon in the bacterial genusIdiomarinais different from that in SAR11. Therefore, we propose a new hypothesis to explain genomic reduction in this genus based on trophic specialization that could result in genomic reduction, which would be not uncommon in nature. Not only can the trophic specialization hypothesis explain the genomic reduction in the genusIdiomarina, but it also sheds new light on our understanding of the genomic reduction processes in other free-living bacterial lineages.

Download Full-text