Pangenome evolution in environmentally transmitted symbionts of deep-sea mussels is governed by vertical inheritance

Microbial pangenomes vary across species; their size and structure are determined by genetic diversity within the population and by gene loss and horizontal gene transfer (HGT). Many bacteria are associated with eukaryotic hosts where the host colonization dynamics may impact bacterial genome evolution. Host-associated lifestyle has been recognized as a barrier to HGT in parentally transmitted bacteria. However, pangenome evolution of environmentally acquired symbionts remains understudied, often due to limitations in symbiont cultivation. Using high-resolution metagenomics, here we study pangenome evolution of two co-occurring endosymbiont populations inhabiting individual Bathymodiolus brooksi mussels from a single cold seep. The symbionts, sulfur-oxidizing (SOX) and methane-oxidizing (MOX) gamma-proteobacteria, are environmentally acquired at an early developmental stage and individual mussels may harbor multiple strains of each species. We found differences in the accessory gene content of both symbionts across individual mussels, which are reflected by differences in symbiont strain composition. Compared to core genes, accessory genes are enriched in functions involved in genome integrity maintenance. We found no evidence for recent horizontal gene transfer between both symbionts. A comparison between the symbiont pangenomes revealed that the MOX population is less diverged and contains fewer accessory genes, supporting the view that the MOX association with B. brooksi is more recent than that of SOX. Our results show that the pangenomes of both symbionts evolved mainly by vertical inheritance. We conclude that association with individual hosts over their lifetime leads to genetically isolated symbiont subpopulations, constraining the frequency of HGT in the evolution of environmentally transmitted symbionts.

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Prediction of prophages and their host ranges in pathogenic and commensal Neisseria species

10.1101/2021.12.16.473053 ◽

2021 ◽

Author(s):

Giulia Orazi ◽

Alan J Collins ◽

Rachel J Whitaker

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Bacterial Genome ◽

Mobile Genetic Elements ◽

Pathogenic Species ◽

Chromosomal Dna ◽

Bacterial Physiology ◽

Neisseria Species ◽

Genetic Elements ◽

Commensal Neisseria

The genus Neisseria includes two pathogenic species, N. gonorrhoeae and N. meningitidis, and numerous commensal species. Neisseria species frequently exchange DNA with one other, primarily via transformation and homologous recombination, and via multiple types of mobile genetic elements (MGEs). Few Neisseria bacteriophages (phages) have been identified and their impact on bacterial physiology is poorly understood. Furthermore, little is known about the range of species that Neisseria phages can infect. In this study, we used three virus prediction tools to scan 248 genomes of 21 different Neisseria species and identified 1302 unique predicted prophages. Using comparative genomics, we found that many predictions are dissimilar from other prophages and MGEs previously described to infect Neisseria species. We also identified similar predicted prophages in genomes of different Neisseria species. Additionally, we examined CRISPR-Cas targeting of each Neisseria genome and predicted prophage. While CRISPR targeting of chromosomal DNA appears to be common among several Neisseria species, we found that 20% of the prophages we predicted are targeted significantly more than the rest of the bacterial genome in which they were identified (i.e., backbone). Furthermore, many predicted prophages are targeted by CRISPR spacers encoded by other species. We then used these results to infer additional host species of known Neisseria prophages and predictions that are highly targeted relative to the backbone. Together, our results suggest that we have identified novel Neisseria prophages, several of which may infect multiple Neisseria species. These findings have important implications for understanding horizontal gene transfer between members of this genus. IMPORTANCE: Drug-resistant N. gonorrhoeae is a major threat to human health. Commensal Neisseria species are thought to serve as reservoirs of antibiotic resistance and virulence genes for the pathogenic species N. gonorrhoeae and N. meningitidis. Therefore, it is important to understand both the diversity of mobile genetic elements (MGEs) that can mediate horizontal gene transfer within this genus, and the breadth of species these MGEs can infect. In particular, few bacteriophages (phages) have been identified and characterized in Neisseria species. In this study, we identified a large number of candidate phages integrated within the genomes of commensal and pathogenic Neisseria species, many of which appear to be novel phages. Importantly, we discovered extensive interspecies targeting of predicted phages by Neisseria CRISPR-Cas systems, which may reflect their movement between different species. Uncovering the diversity and host range of phages is essential for understanding how they influence the evolution of their microbial hosts.

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Nascent Genomic Evolution and Allopatric Speciation ofMyroides profundiD25 in Its Transition from Land to Ocean

mBio ◽

10.1128/mbio.01946-15 ◽

2016 ◽

Vol 7 (1) ◽

Cited By ~ 3

Author(s):

Yu-Zhong Zhang ◽

Yi Li ◽

Bin-Bin Xie ◽

Xiu-Lan Chen ◽

Qiong-Qiong Yao ◽

...

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Marine Environment ◽

High Salinity ◽

Genomic Sequence ◽

Bacterial Genome ◽

Comparative Genomic ◽

Human Pathogens ◽

Expression Levels ◽

Unique Genes

ABSTRACTA large amount of bacterial biomass is transferred from land to ocean annually. Most transferred bacteria should not survive, but undoubtedly some do. It is unclear what mechanisms these bacteria use in order to survive and even thrive in a new marine environment.Myroides profundiD25T, a member of theBacteroidetesphylum, was isolated from deep-sea sediment of the southern Okinawa Trough near the China mainland and had high genomic sequence identity to and synteny with the human opportunistic pathogenMyroides odoratimimus. Phylogenetic and physiological analyses suggested thatM. profundirecently transitioned from land to the ocean. This provided an opportunity to explore how a bacterial genome evolved to survive in a novel environment. Changes in the transcriptome were evaluated when both species were cultured under low-salinity conditions and then transferred to high-salinity conditions. Comparative genomic and transcriptomic analyses showed thatM. profundialtered transcription regulation in the early stages of survival. In these stages, vertically inherited genes played a key role in the survival ofM. profundi. The contribution ofM. profundiunique genes, some possibly acquired by horizontal gene transfer (HGT), appeared relatively small, and expression levels of unique genes were diminished under the high-salinity conditions. We postulate that HGT genes might play an important role in longer-term adaptation. These results suggested that some human pathogens might have the ability to survive in and adapt to the marine environment, which may have important implications for public health control in coastal regions.IMPORTANCEHorizontal gene transfer (HGT) is considered to be important for bacteria to adapt to a different microhabitat. However, our results showed that vertically inherited genes might play more important roles than HGT genes in the nascent adaptation to the marine environment in the bacteriumMyroides profundi, which has recently been transferred from land to ocean.M. profundiunique genes had low expression levels and were less regulated under high-salinity conditions, indicating that the contribution of HGT genes to survival of this bacterium under marine high-salinity conditions was limited. In the early adaptation stages,M. profundiapparently survived and adapted mainly by regulating the expression of inherited core genes. These results may explain in part why human pathogens can easily be detected in marine environments.

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The Enterococcus Cassette Chromosome, a Genomic Variation Enabler in Enterococci

mSphere ◽

10.1128/msphere.00402-18 ◽

2018 ◽

Vol 3 (6) ◽

Cited By ~ 1

Author(s):

A. Sivertsen ◽

J. Janice ◽

T. Pedersen ◽

T. M. Wagner ◽

J. Hegstad ◽

...

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Enterococcus Faecium ◽

Genomic Variation ◽

Conjugative Plasmid ◽

Natural Habitats ◽

Chloramphenicol Resistance ◽

Content Type ◽

Serine Recombinases ◽

Accessory Genes

ABSTRACT Enterococcus faecium has a highly variable genome prone to recombination and horizontal gene transfer. Here, we have identified a novel genetic island with an insertion locus and mobilization genes similar to those of staphylococcus cassette chromosome elements SCCmec. This novel element termed the enterococcus cassette chromosome (ECC) element was located in the 3′ region of rlmH and encoded large serine recombinases ccrAB similar to SCCmec. Horizontal transfer of an ECC element termed ECC::cat containing a knock-in cat chloramphenicol resistance determinant occurred in the presence of a conjugative reppLG1 plasmid. We determined the ECC::cat insertion site in the 3′ region of rlmH in the E. faecium recipient by long-read sequencing. ECC::cat also mobilized by homologous recombination through sequence identity between flanking insertion sequence (IS) elements in ECC::cat and the conjugative plasmid. The ccrABEnt genes were found in 69 of 516 E. faecium genomes in GenBank. Full-length ECC elements were retrieved from 32 of these genomes. ECCs were flanked by attR and attL sites of approximately 50 bp. The attECC sequences were found by PCR and sequencing of circularized ECCs in three strains. The genes in ECCs contained an amalgam of common and rare E. faecium genes. Taken together, our data imply that ECC elements act as hot spots for genetic exchange and contribute to the large variation of accessory genes found in E. faecium. IMPORTANCE Enterococcus faecium is a bacterium found in a great variety of environments, ranging from the clinic as a nosocomial pathogen to natural habitats such as mammalian intestines, water, and soil. They are known to exchange genetic material through horizontal gene transfer and recombination, leading to great variability of accessory genes and aiding environmental adaptation. Identifying mobile genetic elements causing sequence variation is important to understand how genetic content variation occurs. Here, a novel genetic island, the enterococcus cassette chromosome, is shown to contain a wealth of genes, which may aid E. faecium in adapting to new environments. The transmission mechanism involves the only two conserved genes within ECC, ccrABEnt, large serine recombinases that insert ECC into the host genome similarly to SCC elements found in staphylococci.

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TheblpLocus of Streptococcus pneumoniae Plays a Limited Role in the Selection of Strains That Can Cocolonize the Human Nasopharynx

Applied and Environmental Microbiology ◽

10.1128/aem.01048-16 ◽

2016 ◽

Vol 82 (17) ◽

pp. 5206-5215 ◽

Cited By ~ 5

Author(s):

Carina Valente ◽

Suzanne Dawid ◽

Francisco R. Pinto ◽

Jason Hinds ◽

Alexandra S. Simões ◽

...

Keyword(s):

Streptococcus Pneumoniae ◽

Gene Transfer ◽

Horizontal Gene Transfer ◽

Experimental Models ◽

Nasopharyngeal Colonization ◽

Content Type ◽

Limited Role ◽

Multiple Strains ◽

The Impact

ABSTRACTNasopharyngeal colonization is important forStreptococcus pneumoniaeevolution, providing the opportunity for horizontal gene transfer when multiple strains co-occur. Although colonization with more than one strain of pneumococcus is common, the factors that influence the ability of strains to coexist are not known. A highly variableblp(bacteriocin-like peptide) locus has been identified in all sequenced strains ofS. pneumoniae. This locus controls the regulation and secretion of bacteriocins, small peptides that target other bacteria. In this study, we analyzed a series of cocolonizing isolates to evaluate the impact of theblplocus on human colonization to determine whether competitive phenotypes of bacteriocin secretion restrict cocolonization. We identified a collection of 135 nasopharyngeal samples cocolonized with two or more strains, totaling 285 isolates. Theblplocus of all strains was characterized genetically with regard to pheromone type, bacteriocin/immunity content, and potential for locus functionality. Inhibitory phenotypes of bacteriocin secretion and locus activity were assessed through overlay assays. Isolates from single colonizations (n= 298) were characterized for comparison. Cocolonizing strains had a high diversity ofblpcassettes; approximately one-third displayed an inhibitory phenotypein vitro. Despitein vitroevidence of competition, pneumococci cocolonized the subjects independently ofblppheromone type (P= 0.577), bacteriocin/immunity content,blplocus activity (P= 0.798), and inhibitory phenotype (P= 0.716). In addition, no significant differences were observed when single and cocolonizing strains were compared. Despite clear evidence ofblp-mediated competition in experimental models, the results of our study suggest that theblplocus plays a limited role in restricting pneumococcal cocolonization in humans.IMPORTANCENasopharyngeal colonization withStreptococcus pneumoniae(pneumococcus) is important for pneumococcal evolution, as the nasopharynx represents the major site for horizontal gene transfer when multiple strains co-occur, a phenomenon known as cocolonization. Understanding how pneumococcal strains interact within the competitive environment of the nasopharynx is of chief importance in the context of pneumococcal ecology. In this study, we used an unbiased collection of naturally co-occurring pneumococcal strains and showed that a biological process frequently used by bacteria for competition—bacteriocin production—is not decisive in the coexistence of pneumococci in the host, in contrast to what has been shown in experimental models.

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Longitudinal study of vinyl chloride degrading Dehalococcoides mccartyi-containing cultures to promote horizontal gene transfer

10.1101/2020.12.18.423565 ◽

2020 ◽

Author(s):

Nadia Morson ◽

Olivia Molenda ◽

Katherine J. Picott ◽

Ruth E. Richardson ◽

Elizabeth A. Edwards

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Vinyl Chloride ◽

Nitrogen Sources ◽

Recipient Strain ◽

Gene Encoding ◽

Genetic Transfer ◽

Dehalococcoides Mccartyi ◽

Chlorinated Solvent ◽

Multiple Strains

ABSTRACTVinyl chloride (VC) is a human carcinogen that accumulates in soil and groundwater due to incomplete dechlorination of chlorinated ethenes. Some strains of obligate organohalide respiring Dehalococcoides mccartyi can synthesize the VC reductase that catalyzes the dechlorination of VC to ethene. The gene encoding the VC reductase, vcrA, is found on a mobile genetic element called the vcrA-Genomic Island (GI) that may participate in horizontal gene transfer. We designed an experiment to try to induce horizontal gene transfer of the vcrA-GI by mixing two enrichment cultures: one containing the donor D. mccartyi strain with the vcrA-GI that could not fix nitrogen and the second containing the recipient strain devoid of the vcrA-GI that could fix nitrogen. Therefore, mixing the two cultures in medium without ammonium while providing VC as the sole electron acceptor was hypothesized to select for a mutant strain of D. mccartyi that could both fix nitrogen and respire VC. However, after over 4 years of incubation, no evidence for horizontal gene transfer of the vcrA-GI was found. Rather, we observed VC-dechlorinating activity attributed to the TCE reductase, TceA, in the recipient strain. We also observed that D. mccartyi can grow by scavenging low concentrations of fixed nitrogen sources. During this experiment we identified two additional D. mccartyi strains in the KB-1 TCE-enriched culture that could fix nitrogen. The presence of multiple strains of D. mccartyi with distinct phenotypes may enhance bioaugmentation success, but here it may have undermined attempts to force horizontal gene transfer of the vcrA-GI.IMPORTANCEDehalococcoides mccartyi are a powerful bioremediation tool for the degradation of chlorinated solvent contamination in soil and groundwater. Only a few D. mccartyi strains have the ability to dechlorinate toxic chlorinated compounds like vinyl chloride. Interestingly, the genetic ability to dechlorinate vinyl chloride is theorized to be shared among D. mccartyi strains. In this study we attempted to promote the genetic transfer of vinyl chloride degrading ability from one D. mccartyi strain to another. Although we did not observe this exchange, our findings suggest there may be restrictions of genetic transfer between specific clades or sub-groups of D. mccartyi strains. Developing our understanding of genetic transfer among D. mccartyi strains could allow for enhanced degradation of chlorinated solvent contamination in situ.

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Extensive Horizontal Gene Transfer within and between Species of Coagulase-Negative Staphylococcus

Genome Biology and Evolution ◽

10.1093/gbe/evab206 ◽

2021 ◽

Vol 13 (9) ◽

Author(s):

Joshua T Smith ◽

Cheryl P Andam

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Methicillin Resistance ◽

Species Group ◽

Coagulase Negative Staphylococcus ◽

Accessory Gene ◽

Data Set ◽

Type Vii Secretion ◽

Staphylococcus Capitis ◽

Formation Type

Abstract Members of the gram-positive bacterial genus Staphylococcus have historically been classified into coagulase-positive Staphylococcus (CoPS) and coagulase-negative Staphylococcus (CoNS) based on the diagnostic presentation of the coagulase protein. Previous studies have noted the importance of horizontal gene transfer (HGT) and recombination in the more well-known CoPS species Staphylococcus aureus, yet little is known of the contributions of these processes in CoNS evolution. In this study, we aimed to elucidate the phylogenetic relationships, genomic characteristics, and frequencies of HGT in CoNS, which are now being recognized as major opportunistic pathogens of humans. We compiled a data set of 1,876 publicly available named CoNS genomes. These can be delineated into 55 species based on allele differences in 462 core genes and variation in accessory gene content. CoNS species are a reservoir of transferrable genes associated with resistance to diverse classes of antimicrobials. We also identified nine types of the mobile genetic element SCCmec, which carries the methicillin resistance determinant mecA. Other frequently transferred genes included those associated with resistance to heavy metals, surface-associated proteins related to virulence and biofilm formation, type VII secretion system, iron capture, recombination, and metabolic enzymes. The highest frequencies of receipt and donation of recombined DNA fragments were observed in Staphylococcus capitis, Staphylococcus caprae, Staphylococcus hominis, Staphylococcus haemolyticus, and members of the Saprophyticus species group. The variable rates of recombination and biases in transfer partners imply that certain CoNS species function as hubs of gene flow and major reservoir of genetic diversity for the entire genus.

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