Microbial Evolution from a Genomics Perspective

Grapes are a source of native yeasts and lactic acid bacteria (LAB); however, the microbial make up is dependent on the grape cultivar and the regional growth conditions. Therefore, the aim of this study was to characterize the yeast and LAB in seven grape cultivars cultivated in Chile. Grape juices were fermented at 25 °C for 7 days. Samples were collected to analyze sugar, organic acids, and ethanol. Microbial evolution was measured with culture-dependent and molecular approaches. Then, a native isolated Candida oleophila was selected for further sequential fermentations with Saccharomyces cerevisiae. The grape cultivars in the Maule showed a diversity of non-Saccharomyces yeasts, with a greater diversity observed at the beginning of the fermentation. However, species from the Hansenasporia, Metschnikowia, Torulaspora, Lachancea, and Candida genera were detected after 7 days, suggesting tolerance to environments rich in ethanol, capability may be associated to the terroir studied, which is characterized by torrid weather and antique and traditional vineyards. The alcoholic fermentation negatively impacted the LAB population, and after 7 days only Leuconostoc mesenteroides was isolated. In the sequential fermentations, C. oleophila was able to produce fermented grape juices with <1.5 g/L glucose, 12.5% (v/v) alcohol, and low concentrations of malic (<1.00 g/L) and succinic (2.05 g/L) acids, while acetic acid reached values >0.3 (g/L). To our knowledge this is the first time C. oleophila has been reported as a potential starter culture for wine production. However, more studies are necessary to fully characterize the potential of C. oleophila on wine attributes.

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Systematic Detection of Large-Scale Multi-Gene Horizontal Transfer in Prokaryotes

Molecular Biology and Evolution ◽

10.1093/molbev/msab043 ◽

2021 ◽

Author(s):

Lina Kloub ◽

Sean Gosselin ◽

Matthew Fullmer ◽

Joerg Graf ◽

J Peter Gogarten ◽

...

Keyword(s):

Gene Transfer ◽

Large Scale ◽

Single Gene ◽

Gene Families ◽

Microbial Evolution ◽

Phylogenetic Distance ◽

Secretion Systems ◽

Type Iii Secretion Systems ◽

A Genome ◽

Conserved Gene

Abstract Horizontal gene transfer (HGT) is central to prokaryotic evolution. However, little is known about the “scale” of individual HGT events. In this work, we introduce the first computational framework to help answer the following fundamental question: How often does more than one gene get horizontally transferred in a single HGT event? Our method, called HoMer, uses phylogenetic reconciliation to infer single-gene HGT events across a given set of species/strains, employs several techniques to account for inference error and uncertainty, combines that information with gene order information from extant genomes, and uses statistical analysis to identify candidate horizontal multi-gene transfers (HMGTs) in both extant and ancestral species/strains. HoMer is highly scalable and can be easily used to infer HMGTs across hundreds of genomes. We apply HoMer to a genome-scale dataset of over 22000 gene families from 103 Aeromonas genomes and identify a large number of plausible HMGTs of various scales at both small and large phylogenetic distances. Analysis of these HMGTs reveals interesting relationships between gene function, phylogenetic distance, and frequency of multi-gene transfer. Among other insights, we find that (i) the observed relative frequency of HMGT increases as divergence between genomes increases, (ii) HMGTs often have conserved gene functions, and (iii) rare genes are frequently acquired through HMGT. We also analyze in detail HMGTs involving the zonula occludens toxin and type III secretion systems. By enabling the systematic inference of HMGTs on a large scale, HoMer will facilitate a more accurate and more complete understanding of HGT and microbial evolution.

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Microbial evolution: Cholera gene swap

Nature ◽

10.1038/461148e ◽

2009 ◽

Vol 461 (7261) ◽

pp. 148-149

Keyword(s):

Microbial Evolution

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Genome Sequence of Lentisphaera araneosa HTCC2155T, the Type Species of the Order Lentisphaerales in the Phylum Lentisphaerae

Journal of Bacteriology ◽

10.1128/jb.00208-10 ◽

2010 ◽

Vol 192 (11) ◽

pp. 2938-2939 ◽

Cited By ~ 22

Author(s):

J. Cameron Thrash ◽

Jang-Cheon Cho ◽

Kevin L. Vergin ◽

Robert M. Morris ◽

Stephen J. Giovannoni

Keyword(s):

Genome Sequence ◽

Type Species ◽

Microbial Evolution ◽

Unusual Property ◽

Oregon Coast ◽

The Pacific ◽

Genome Content

ABSTRACT Information on the genome content of deeply branching phyla with very few cultured members is invaluable for expanding understanding of microbial evolution. Lentisphaera araneosa HTCC2155T was isolated from the Oregon coast using dilution-to-extinction culturing. It is a marine heterotroph found in surface and mesopelagic waters in both the Pacific and Atlantic oceans and has the unusual property of producing a net-like matrix of secreted exopolysaccharide. Here we present the genome sequence of L. araneosa HTCC2155T, importantly, one of only two sequenced members of the phylum Lentisphaerae.

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A holistic view of host-associated microbial evolution

Trends in Microbiology ◽

10.1016/j.tim.2021.09.003 ◽

2021 ◽

Author(s):

Or Shalev ◽

Christoph Ratzke

Keyword(s):

Microbial Evolution ◽

Holistic View

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Coupling Between Protein Level Selection and Codon Usage Optimization in the Evolution of Bacteria and Archaea

mBio ◽

10.1128/mbio.00956-14 ◽

2014 ◽

Vol 5 (2) ◽

Cited By ~ 25

Author(s):

Wenqi Ran ◽

David M. Kristensen ◽

Eugene V. Koonin

Keyword(s):

Codon Usage ◽

Protein Level ◽

Codon Usage Bias ◽

Protein Sequence ◽

Gc Content ◽

Protein Sequences ◽

Microbial Evolution ◽

Fine Tuning ◽

Selection For ◽

Genomic Gc Content

ABSTRACT The relationship between the selection affecting codon usage and selection on protein sequences of orthologous genes in diverse groups of bacteria and archaea was examined by using the Alignable Tight Genome Clusters database of prokaryote genomes. The codon usage bias is generally low, with 57.5% of the gene-specific optimal codon frequencies (F opt ) being below 0.55. This apparent weak selection on codon usage contrasts with the strong purifying selection on amino acid sequences, with 65.8% of the gene-specific dN/dS ratios being below 0.1. For most of the genomes compared, a limited but statistically significant negative correlation between F opt and dN/dS was observed, which is indicative of a link between selection on protein sequence and selection on codon usage. The strength of the coupling between the protein level selection and codon usage bias showed a strong positive correlation with the genomic GC content. Combined with previous observations on the selection for GC-rich codons in bacteria and archaea with GC-rich genomes, these findings suggest that selection for translational fine-tuning could be an important factor in microbial evolution that drives the evolution of genome GC content away from mutational equilibrium. This type of selection is particularly pronounced in slowly evolving, “high-status” genes. A significantly stronger link between the two aspects of selection is observed in free-living bacteria than in parasitic bacteria and in genes encoding metabolic enzymes and transporters than in informational genes. These differences might reflect the special importance of translational fine-tuning for the adaptability of gene expression to environmental changes. The results of this work establish the coupling between protein level selection and selection for translational optimization as a distinct and potentially important factor in microbial evolution. IMPORTANCE Selection affects the evolution of microbial genomes at many levels, including both the structure of proteins and the regulation of their production. Here we demonstrate the coupling between the selection on protein sequences and the optimization of codon usage in a broad range of bacteria and archaea. The strength of this coupling varies over a wide range and strongly and positively correlates with the genomic GC content. The cause(s) of the evolution of high GC content is a long-standing open question, given the universal mutational bias toward AT. We propose that optimization of codon usage could be one of the key factors that determine the evolution of GC-rich genomes. This work establishes the coupling between selection at the level of protein sequence and at the level of codon choice optimization as a distinct aspect of genome evolution.

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