Horizontal Gene Transfer in Archaea—From Mechanisms to Genome Evolution

Gophna, Uri; Altman-Price, Neta

doi:10.1146/annurev-micro-040820-124627

Cited by 25 publications

(23 citation statements)

References 161 publications

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“…In these reservoirs, planktonic bacterial community structure is mainly affected by WT and pH, while planktonic archaeal community composition is mainly influenced by geological and geographical factors. Major geological events and horizontal gene transfer have been reported to be relevant to the evolution of archaea ( Yang et al, 2021 ; Gophna and Altman-Price, 2022 ). The composition of bacteria had tighter nexus with environmental factors than that of archaea ( Figure 6A ), implying that bacteria are easier to be affected by environmental variations.…”

Section: Discussionmentioning

confidence: 99%

River damming enhances ecological functional stability of planktonic microorganisms

Wang

Liu

et al. 2022

Front. Microbiol.

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Planktonic microorganisms play an important role in maintaining the ecological functions in aquatic ecosystems, but how their structure and function interrelate and respond to environmental changes is still not very clear. Damming interrupts the river continuum and alters river nutrient biogeochemical cycling and biological succession. Considering that river damming decreases the irregular hydrological fluctuation, we hypothesized that it can enhance the ecological functional stability (EFS) of planktonic microorganisms. Therefore, the community composition of planktonic bacteria and archaea, functional genes related to carbon, nitrogen, sulfur, and phosphorus cycling, and relevant environmental factors of four cascade reservoirs in the Pearl River, Southern China, were investigated to understand the impact of damming on microbial community structure and function and verify the above hypothesis. Here, the ratio of function to taxa (F:T) based on Euclidean distance matrix analysis was first proposed to characterize the microbial EFS; the smaller the ratio, the more stable the ecological functions. The results showed that the reservoirs created by river damming had seasonal thermal and chemical stratifications with an increasing hydraulic retention time, which significantly changed the microbial structure and function. The river microbial F:T was significantly higher than that of the reservoirs, indicating that river damming enhances the EFS of the planktonic microorganisms. Structural equation modeling demonstrated that water temperature was an important factor influencing the relationship between the microbial structure and function and thus affected their EFS. In addition, reservoir hydraulic load was found a main factor regulating the seasonal difference in microbial EFS among the reservoirs. This study will help to deepen the understanding of the relationship between microbial structure and function and provide a theoretical basis of assessing the ecological function change after the construction of river damming.

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Section: Discussionmentioning

confidence: 99%

River damming enhances ecological functional stability of planktonic microorganisms

Wang

Liu

et al. 2022

Front. Microbiol.

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“…Another key feature added to stdpopsim's simulation framework was the ability to model non-crossover recombination. In bacteria and archaea, recombination occurs through horizontal transfer of homologous DNA segments from one organism to another (Thomas and Nielsen, 2005;Didelot and Maiden, 2010;Gophna and Altman-Price, 2022). As a result, such species cannot be realistically simulated with a recombination model that considers only crossovers, as did the initial version of stdpopsim.…”

Section: Additions To Stdpopsimmentioning

confidence: 99%

Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations

Lauterbur

Cavassim

Gladstein³

et al. 2022

Preprint

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Simulation is a key tool in population genetics for both methods development and empirical research, but producing simulations that recapitulate the main features of genomic data sets remains a major obstacle. Today, more realistic simulations are possible thanks to large increases in the quantity and quality of available genetic data, and to the sophistication of inference and simulation software. However, implementing these simulations still requires substantial time and specialized knowledge. These challenges are especially pronounced for simulating genomes for species that are not well-studied, since it is not always clear what information is required to produce simulations with a level of realism sufficient to confidently answer a given question. The community-developed framework stdpopsim seeks to lower this barrier by facilitating the simulation of complex population genetic models using up-to-date information. The initial version of stdpopsim focused on establishing this framework using six well-characterized model species (Adrion et al., 2020). Here, we report on major improvements made in the new release of stdpopsim (version 0.2), which includes a significant expansion of the species catalog and substantial additions to simulation capabilities. Features added to improve the realism of the simulated genomes include non-crossover recombination and provision of species-specific genomic annotations. Through community-driven efforts, we expanded the number of species in the catalog more than three-fold and broadened coverage across the tree of life. During the process of expanding the catalog, we have identified common sticking points and developed best practices for setting up genome-scale simulations. We describe the input data required for generating a realistic simulation, suggest good practices for obtaining the relevant information from the literature, and discuss common pitfalls and major considerations. These improvements to stdpopsim aim to further promote the use of realistic whole-genome population genetic simulations, especially in non-model organisms, making them available, transparent, and accessible to everyone.

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“…Furthermore, HGT plays a major role during the adaptation of microbes to constantly changing environmental conditions by providing immediate access to beneficial traits and promoting cooperation within microbial communities 3 . Accordingly, bacteria and archaea have evolved dedicated mechanisms of HGT 4 , 5 . Traditionally, three major routes of HGT are recognized, namely, natural transformation, transduction, and conjugation.…”

Section: Introductionmentioning

confidence: 99%

Archaeal DNA-import apparatus is homologous to bacterial conjugation machinery

et al. 2023

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Conjugation is a major mechanism of horizontal gene transfer promoting the spread of antibiotic resistance among human pathogens. It involves establishing a junction between a donor and a recipient cell via an extracellular appendage known as the mating pilus. In bacteria, the conjugation machinery is encoded by plasmids or transposons and typically mediates the transfer of cognate mobile genetic elements. Much less is known about conjugation in archaea. Here, we determine atomic structures by cryo-electron microscopy of three conjugative pili, two from hyperthermophilic archaea (Aeropyrum pernix and Pyrobaculum calidifontis) and one encoded by the Ti plasmid of the bacterium Agrobacterium tumefaciens, and show that the archaeal pili are homologous to bacterial mating pili. However, the archaeal conjugation machinery, known as Ced, has been ‘domesticated’, that is, the genes for the conjugation machinery are encoded on the chromosome rather than on mobile genetic elements, and mediates the transfer of cellular DNA.

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Horizontal Gene Transfer in Archaea—From Mechanisms to Genome Evolution

Cited by 25 publications

References 161 publications

River damming enhances ecological functional stability of planktonic microorganisms

River damming enhances ecological functional stability of planktonic microorganisms

Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations

Archaeal DNA-import apparatus is homologous to bacterial conjugation machinery

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