Horizontal gene transfer of metal homeostasis genes and its role in microbial communities of the deep terrestrial subsurface

2010 ◽  
pp. 109-130 ◽  
Author(s):  
Jonna Coombs ◽  
Tamar Barkay ◽  
Hilary Lappin-Scott
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Microbial Communities ◽  
Metal Homeostasis ◽  
Terrestrial Subsurface

scholarly journals Molecular Evidence for the Evolution of Metal Homeostasis Genes by Lateral Gene Transfer in Bacteria from the Deep Terrestrial Subsurface

2004 ◽  
Vol 70 (3) ◽  
pp. 1698-1707 ◽  
Author(s):  
J. M. Coombs ◽  
T. Barkay
Keyword(s):  
Gene Transfer ◽  
Microbial Communities ◽  
Lateral Gene Transfer ◽  
Dna Sequences ◽  
Natural Waters ◽  
Gene Tree ◽  
Metal Homeostasis ◽  
Molecular Evidence ◽  
Rrna Gene ◽  
Terrestrial Subsurface

ABSTRACT Lateral gene transfer (LGT) plays a vital role in increasing the genetic diversity of microorganisms and promoting the spread of fitness-enhancing phenotypes throughout microbial communities. To date, LGT has been investigated in surface soils, natural waters, and biofilm communities but not in the deep terrestrial subsurface. Here we used a combination of molecular analyses to investigate the role of LGT in the evolution of metal homeostasis in lead-resistant subsurface bacteria. A nested PCR approach was employed to obtain DNA sequences encoding PIB-type ATPases, which are proteins that transport toxic or essential soft metals such as Zn(II), Cd(II), and Pb(II) through the cell wall. Phylogenetic incongruencies between a 16S rRNA gene tree and a tree based on 48 PIB-type ATPase amplicons and sequences available for complete bacterial genomes revealed an ancient transfer from a member of the β subclass of the Proteobacteria (β-proteobacterium) that may have predated the diversification of the genus Pseudomonas. Four additional phylogenetic incongruencies indicate that LGT has occurred among groups of β- and γ-proteobacteria. Two of these transfers appeared to be recent, as indicated by an unusual G+C content of the PIB-type ATPase amplicons. This finding provides evidence that LGT plays a distinct role in the evolution of metal homeostasis in deep subsurface bacteria, and it shows that molecular evolutionary approaches may be used for investigation of this process in microbial communities in specific environments.

scholarly journals Variability in Assembly of Degradation Operons for Naphthalene and its derivative, Carbaryl, Suggests Mobilization through Horizontal Gene Transfer

Genes ◽  
2019 ◽  
Vol 10 (8) ◽  
pp. 569 ◽  
Author(s):  
Phale ◽  
Shah ◽  
Malhotra
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Food Web ◽  
Microbial Communities ◽  
Metabolic Pathways ◽  
Anthropogenic Activities ◽  
Genetic Material ◽  
Genomic Islands ◽  
Biochemical Pathways ◽  
Integrative Conjugative Elements

In the biosphere, the largest biological laboratory, increased anthropogenic activities have led microbes to evolve and adapt to the changes occurring in the environment. Compounds, specifically xenobiotics, released due to such activities persist in nature and undergo bio-magnification in the food web. Some of these compounds act as potent endocrine disrupters, mutagens or carcinogens, and therefore their removal from the environment is essential. Due to their persistence, microbial communities have evolved to metabolize them partially or completely. Diverse biochemical pathways have evolved or been assembled by exchange of genetic material (horizontal gene transfer) through various mobile genetic elements like conjugative and non-conjugative plasmids, transposons, phages and prophages, genomic islands and integrative conjugative elements. These elements provide an unlimited opportunity for genetic material to be exchanged across various genera, thus accelerating the evolution of a new xenobiotic degrading phenotype. In this article, we illustrate examples of the assembly of metabolic pathways involved in the degradation of naphthalene and its derivative, Carbaryl, which are speculated to have evolved or adapted through the above-mentioned processes.

scholarly journals Horizontal Gene Transfer Can Help Maintain the Equilibrium of Microbial Communities

2017 ◽  
Author(s):  
Yuhang Fan ◽  
Yandong Xiao ◽  
Babak Momeni ◽  
Yang-Yu Liu
Keyword(s):  
Population Dynamics ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Microbial Communities ◽  
Transfer Rate ◽  
Species Coexistence ◽  
Focal Points ◽  
Dynamics Model ◽  
Population Dynamics Model ◽  
Evolutionary Advantage

Horizontal gene transfer and species coexistence are two focal points in the study of microbial communities. The evolutionary advantage of horizontal gene transfer has not been well-understood and is constantly being debated. Here we propose a simple population dynamics model based on the frequency-dependent interactions between different genotypes to evaluate the influence of horizontal gene transfer on microbial communities. We find that both structural stability and robustness of the microbial community are strongly affected by the gene transfer rate and direction. An optimal gene flux can stablize the ecosystem, helping it recover from disturbance and maintain the species coexistence.

scholarly journals Diverse Viruses in Deep-Sea Hydrothermal Vent Fluids Have Restricted Dispersal across Ocean Basins

mSystems ◽  
2021 ◽  
Author(s):  
Elaina Thomas ◽  
Rika E. Anderson ◽  
Viola Li ◽  
L. Jenni Rogan ◽  
Julie A. Huber
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Microbial Communities ◽  
Deep Sea ◽  
Hydrothermal Vent ◽  
Hydrothermal Vents ◽  
Viral Ecology ◽  
Unique Nature

Viruses play important roles in manipulating microbial communities and their evolution in the ocean, yet not much is known about viruses in deep-sea hydrothermal vents. However, viral ecology and evolution are of particular interest in hydrothermal vent habitats because of their unique nature: previous studies have indicated that most viruses in hydrothermal vents are temperate rather than lytic, and it has been established that rates of horizontal gene transfer (HGT) are particularly high among thermophilic vent microbes, and viruses are common vectors for HGT.

scholarly journals Horizontal gene transfer can help maintain the equilibrium of microbial communities

2018 ◽  
Vol 454 ◽  
pp. 53-59 ◽  
Author(s):  
Yuhang Fan ◽  
Yandong Xiao ◽  
Babak Momeni ◽  
Yang-Yu Liu
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Microbial Communities

scholarly journals Transductomics: sequencing-based detection and analysis of transduced DNA in pure cultures and microbial communities

Microbiome ◽  
2020 ◽  
Vol 8 (1) ◽  
Author(s):  
Manuel Kleiner ◽  
Brian Bushnell ◽  
Kenneth E. Sanderson ◽  
Lora V. Hooper ◽  
Breck A. Duerkop
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Microbial Communities ◽  
Microbial Evolution ◽  
Model Systems ◽  
Intestinal Microbiome ◽  
Mobile Dna ◽  
Pure Cultures ◽  
Taxonomic Range ◽  
Taxonomic Groups

Abstract Background Horizontal gene transfer (HGT) plays a central role in microbial evolution. Our understanding of the mechanisms, frequency, and taxonomic range of HGT in polymicrobial environments is limited, as we currently rely on historical HGT events inferred from genome sequencing and studies involving cultured microorganisms. We lack approaches to observe ongoing HGT in microbial communities. Results To address this knowledge gap, we developed a DNA sequencing-based “transductomics” approach that detects and characterizes microbial DNA transferred via transduction. We validated our approach using model systems representing a range of transduction modes and show that we can detect numerous classes of transducing DNA. Additionally, we show that we can use this methodology to obtain insights into DNA transduction among all major taxonomic groups of the intestinal microbiome. Conclusions The transductomics approach that we present here allows for the detection and characterization of genes that are potentially transferred between microbes in complex microbial communities at the time of measurement and thus provides insights into real-time ongoing horizontal gene transfer. This work extends the genomic toolkit for the broader study of mobile DNA within microbial communities and could be used to understand how phenotypes spread within microbiomes.

Sign in / Sign up

Export Citation Format

Share Document