scholarly journals Gene exchange networks define species-like units in marine prokaryotes

2020 ◽  
Author(s):  
R. Stepanauskas ◽  
J.M. Brown ◽  
U. Mai ◽  
O. Bezuidt ◽  
M. Pachiadaki ◽  
...  

SUMMARYAlthough horizontal gene transfer is recognized as a major evolutionary process in Bacteria and Archaea, its general patterns remain elusive, due to difficulties tracking genes at relevant resolution and scale within complex microbiomes. To circumvent these challenges, we analyzed a randomized sample of >12,000 genomes of individual cells of Bacteria and Archaea in the tropical and subtropical ocean - a well-mixed, global environment. We found that marine microorganisms form gene exchange networks (GENs) within which transfers of both flexible and core genes are frequent, including the rRNA operon that is commonly used as a conservative taxonomic marker. The data revealed efficient gene exchange among genomes with <28% nucleotide difference, indicating that GENs are much broader lineages than the nominal microbial species, which are currently delineated at 4-6% nucleotide difference. The 42 largest GENs accounted for 90% of cells in the tropical ocean microbiome. Frequent gene exchange within GENs helps explain how marine microorganisms maintain millions of rare genes and adapt to a dynamic environment despite extreme genome streamlining of their individual cells. Our study suggests that sharing of pangenomes through horizontal gene transfer is a defining feature of fundamental evolutionary units in marine planktonic microorganisms and, potentially, other microbiomes.

2017 ◽  
Vol 372 (1735) ◽  
pp. 20160424 ◽  
Author(s):  
James P. J. Hall ◽  
Michael A. Brockhurst ◽  
Ellie Harrison

In biological systems, evolutionary innovations can spread not only from parent to offspring (i.e. vertical transmission), but also ‘horizontally’ between individuals, who may or may not be related. Nowhere is this more apparent than in bacteria, where novel ecological traits can spread rapidly within and between species through horizontal gene transfer (HGT). This important evolutionary process is predominantly a by-product of the infectious spread of mobile genetic elements (MGEs). We will discuss the ecological conditions that favour the spread of traits by HGT, the evolutionary and social consequences of sharing traits, and how HGT is shaped by inherent conflicts between bacteria and MGEs.This article is part of the themed issue ‘Process and pattern in innovations from cells to societies’.


2019 ◽  
Vol 201 (7) ◽  
Author(s):  
Frances Tran ◽  
James Q. Boedicker

ABSTRACTHorizontal gene transfer is responsible for the exchange of many types of genetic elements, including plasmids. Properties of the exchanged genetic element are known to influence the efficiency of transfer via the mechanisms of conjugation, transduction, and transformation. Recently, an alternative general pathway of horizontal gene transfer has been identified, namely, gene exchange by extracellular vesicles. Although extracellular vesicles have been shown to facilitate the exchange of several types of plasmids, the influence of plasmid characteristics on genetic exchange within vesicles is unclear. Here, a set of different plasmids was constructed to systematically test the impact of plasmid properties, specifically, plasmid copy number, size, and origin of replication, on gene transfer in vesicles. The influence of each property on the production, packaging, and uptake of vesicles containing bacterial plasmids was quantified, revealing how plasmid properties modulate vesicle-mediated horizontal gene transfer. The loading of plasmids into vesicles correlates with the plasmid copy number and is influenced by characteristics that help set the number of plasmids within a cell, including size and origin of replication. Plasmid origin also has a separate impact on both vesicle loading and uptake, demonstrating that the origin of replication is a major determinant of the propensity of specific plasmids to transfer within extracellular vesicles.IMPORTANCEExtracellular vesicle formation and exchange are common within bacterial populations. Vesicles package multiple types of biomolecules, including genetic material. The exchange of extracellular vesicles containing genetic material facilitates interspecies DNA transfer and may be a promiscuous mechanism of horizontal gene transfer. Unlike other mechanisms of horizontal gene transfer, it is unclear whether characteristics of the exchanged DNA impact the likelihood of transfer in vesicles. Here, we systematically examine the influence of plasmid copy number, size, and origin of replication on the loading of DNA into vesicles and the uptake of DNA containing vesicles by recipient cells. These results reveal how each plasmid characteristic impacts gene transfer in vesicles and contribute to a greater understanding of the importance of vesicle-mediated gene exchange in the landscape of horizontal gene transfer.


1999 ◽  
Vol 15 (5) ◽  
pp. 173-175 ◽  
Author(s):  
Yuri I. Wolf ◽  
L. Aravind ◽  
Eugene V. Koonin

Microbiology ◽  
2004 ◽  
Vol 150 (6) ◽  
pp. 1707-1712 ◽  
Author(s):  
Elzbieta Krzywinska ◽  
Jaroslaw Krzywinski ◽  
Jeffrey S. Schorey

Acquisition of genetic information through horizontal gene transfer (HGT) is an important evolutionary process by which micro-organisms gain novel phenotypic characteristics. In pathogenic bacteria, for example, it facilitates maintenance and enhancement of virulence and spread of drug resistance. In the genus Mycobacterium, to which several primary human pathogens belong, HGT has not been clearly demonstrated. The few existing reports suggesting this process are based on circumstantial evidence of similarity of sequences found in distantly related species. Here, direct evidence of HGT between strains of Mycobacterium avium representing two different serotypes is presented. Conflicting evolutionary histories of genes encoding elements of the glycopeptidolipid (GPL) biosynthesis pathway led to an analysis of the GPL cluster genomic sequences from four Mycobacterium avium strains. The sequence of M. avium strain 2151 appeared to be a mosaic consisting of three regions having alternating identities to either M. avium strains 724 or 104. Maximum-likelihood estimation of two breakpoints allowed a ∼4100 bp region horizontally transferred into the strain 2151 genome to be pinpointed with confidence. The maintenance of sequence continuity at both breakpoints and the lack of insertional elements at these sites strongly suggest that the integration of foreign DNA occurred by homologous recombination. To our knowledge, this is the first report to demonstrate naturally occurring homologous recombination in Mycobacterium. This previously undiscovered mechanism of genetic exchange may have major implications for the understanding of Mycobacterium pathogenesis.


2015 ◽  
Author(s):  
Yoav Atsmon-Raz ◽  
Nathaniel Wagner ◽  
Emanuel David Tannenbaum

Antibiotic drug resistance spreads through horizontal gene transfer (HGT) via bacterial conjugation in unicellular populations of bacteria. Consequently, the efficiency of antibiotics is limited and the expected “grace period” of novel antibiotics is typically quite short. One of the mechanisms that allow the accelerated adaptation of bacteria to antibiotics is bacterial conjugation. However, bacterial conjugation is regulated by several biological factors, with one of the most important ones being repression and de-repression. In recent work, we have studied the effects that repression and de-repression on the mutation-selection balance of an HGT-enabled bacterial population in a static environment. Two of our main findings were that conjugation has a deleterious effect on the mean fitness of the population and that repression is expected to allow a restoration of the fitness cost due to plasmid hosting. Here, we consider the effect that conjugation-mediated HGT has on the speed of adaptation in a dynamic environment and the effect that repression will have on the dynamics of antibiotic drug resistance. We find that, the effect of repression is dynamic in its possible outcome, that a conjugators to non-conjugators phase transition exists in a dynamic landscape as we have previously found for a static landscape and we quantify the time required for a unicellular population to adapt to a new antibiotic in a periodically changing fitness landscape. Our results also confirmed that HGT accelerates adaptation for a population of prokaryotes which agrees with current knowledge, that HGT rates increase when a population is put under stress.


2020 ◽  
Author(s):  
José Darío Martínez-Ezquerro

Gene exchange between prokaryotes has long been recognized as an important biological process, to the extent that it has been proposed that a more suitable metaphor to describe the evolutionary process, at least in prokaryotes, should be that of "the web of life", where lines of descent not only diverge but also communicate and even fuse with each other, resulting in a reticulated pattern. This pattern partially describes and outlines the actual complexity because, with the exception of some ancestral horizontal gene transfer (HGT) events, it relegates most eukaryotes.In this work, I summarize the evidence on how such lines of descent diverge, communicate, and merge with each other, in both prokaryotes and eukaryotes, involving deep branches and recent divergences. In fact, both direct and indirect evidence shows the existence of active HGT mechanisms in eukaryotes, indicating that horizontal transfer of genetic material is an ongoing evolutionary process in these organisms, as important as it is in the case of prokaryotes. Some of the consequences in eukaryotic genomic evolution that this phenomenon implies include, as in prokaryotes, the acquisition of novel functions, reacquisition of lost genes, and incorporation of adaptive advantages.HGT involves not only phagocytic single-celled eukaryotes but all eukaryotes —protists, plants, fungi, and animals, including humans. This lateral transfer of genetic material occurs through homologous HGT mechanisms that also exist in bacteria: conjugation, transduction, endogenization, and transformation. Given the evidence, I suggest a global economy of genetic material among all current organisms: viruses, prokaryotes, and eukaryotes; fading the notion of barriers between species, as a result of the continuous horizontal circulation and use of available genetic material.Finally, I propose an ecological classification focused on the various interactions with which foreign genetic material is obtained, to facilitate the understanding of HGT as an ecological and evolutionary phenomenon, natural and global, that affects all organisms and involves all reservoirs of genetic material. **Resumen**Desde hace tiempo, se reconoce al intercambio de genes entre procariontes como un proceso biológico importante, al grado de que se ha propuesto que una metáfora más adecuada para describir el proceso evolutivo, al menos procarionte, debería ser la de “la red de la vida” en donde las líneas de la descendencia no sólo divergen sino también se comunican e incluso se fusionan unas con otras, dando como resultado un patrón reticulado. Este patrón describe y esquematiza parcialmente la complejidad real debido a que, con excepción de algunos eventos de transferencia horizontal de genes (THG) ancestrales, relega a la mayoría de los eucariontes.En este trabajo sintetizo la evidencia sobre cómo dichas líneas de descendencia divergen, se comunican y fusionan unas con otras, tanto en procariontes como en eucariontes, involucrando ramas profundas y divergencias recientes. De hecho, diversas evidencias tanto directas como indirectas, muestran la existencia de mecanismos de THG activos en los eucariontes, indicando que la transferencia horizontal de material genético es un proceso evolutivo actual en estos organismos, tan importante como lo es en el caso de los procariontes. Algunas de las consecuencias en la evolución genómica eucarionte que este fenómeno implica incluyen, al igual que en los procariontes, la adquisición de funciones novedosas, readquisición de genes perdidos e incorporación de ventajas adaptativas.La THG involucra no sólo a eucariontes unicelulares principalmente fagocíticos sino a todos los eucariontes —protistas, plantas, hongos y animales, incluyendo a los humanos. Esta transferencia lateral de material genético occure mediante mecanismos homólogos de THG que también existen en bacterias: conjugación, transducción, endogenización y transformación. Dada la evidencia, planteo una economía global del material genético entre todos los organismos actuales —virus, procariontes y eucariontes; desvaneciendo la noción de barreras entre las especies, resultado de la continua circulación horizontal y aprovechamiento del material genético disponible. Finalmente, propongo una clasificación ecológica centrada en las diversas interacciones con las que se obtiene el material genético foráneo, para facilitar el entendimiento de la THG como un fenómeno ecológico y evolutivo, natural y global, que afecta a todos los organismos e involucra a todos los reservorios de material genético.


2021 ◽  
Author(s):  
Michał Ciach ◽  
Julia Pawłowska ◽  
Anna Muszewska

AbstractNumerous studies have been devoted to individual cases of horizontally acquired genes in fungi. It has been shown that such genes expand their metabolic capabilities and contribute to their adaptations as parasites or symbionts. Some studies have provided a more extensive characterization of the horizontal gene transfer (HGT) in Dikarya. However, in the early diverging fungi (EDF), the overall influence of HGT on the ecological adaptation and evolution is largely unknown. In order to fill this gap, we have designed a computational pipeline to obtain a sample of over 600 phylogenetic trees with evidence for recent to moderately old HGT across multiple EDF genomes ranging from Chytridiomycota and Blastocladiomycota to Mucoromycota. Our pipeline is designed to obtain a small sample of reliable HGT events with a possibly minimal number of false detections that distort the overall statistical patterns. We show that transfer rates differ greatly between closely related species and strains, but the ancestrally aquatic fungi are generally more likely to acquire foreign genetic material than terrestrial ones. A close ecological relationship with another organism is a predisposing condition, but does not always result in an extensive gene exchange, with some fungal lineages showing a preference for HGT from loosely associated soil bacteria.ImportanceAlthough it is now recognized that horizontal gene exchange is a factor influencing the adaptation and evolution of eukaryotic organisms, the so far described cases in early diverging fungi (EDF) are fragmentary, and a large-scale comprehensive study is lacking. We have designed a methodology to obtain a reliable, statistical sample of inter-kingdom xenologs across the tree of life of EDF to give a preliminary characterization of their general properties and patterns. We study how different fungal lineages vary in terms of the number of xenologs, what are their ecological associations, and the molecular properties of proteins encoded by the acquired genes. Our results help to better understand to what extent and in what way the incorporation of foreign genetic material shaped the present biodiversity of fungi.


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