ArticlePDF Available

Abstract and Figures

Horizontal gene transfer (HGT) has a crucial role in microbial evolution, in shaping the structure and function of microbial communities and in controlling a myriad of environmental and public-health problems. Here, Barth F. Smets and Tamar Barkay assess the importance of HGT and place the selection of articles in this Focus issue in context.
Content may be subject to copyright.
© 2005 Nature Publishing Group
*Institute of Environment &
Resources, Technical
University of Denmark,
Kongens Lyngby, DK 2800,
Denmark.
Department of
Biochemistry and
Microbiology, Rutgers
University, New Brunswick,
New Jersey 08901, USA.
Correspondence to B.F.S.
e-mail: bfs@er.dtu.dk
Recent years have witnessed an increased appreciation
for the role of microorganisms and their metabolism
in shaping and sustaining life on Earth. Most of life’s
fundamental processes were ‘invented’ during the first
2 billion years of life on Earth, prior to the appearance
of the first eukaryote. This achievement is especially
striking considering that it was accomplished by organ-
isms lacking sexual reproduction, the long-presumed
major mechanism of genetic innovation. Horizontal
gene transfer (HGT) is a process that can compensate
for the otherwise clonal mode of prokaryotic life,
affecting microbial adaptation, speciation and evolu-
tion. Microorganisms occupy — and adapt to occupy
— a plethora of ecological niches on earth, and their
activities in large part control global homeostasis.
Through its attendant effects on microbial adaptation,
HGT poses both challenges and opportunities in the
control of global human and environmental health.
For any gene to be horizontally transferred from
one genome to another, at least four (sometimes five)
distinct steps need to occur (FIG. 1). First, a nucleic-acid
molecule (DNA or RNA) in the donor organism is pre-
pared for transfer. This might entail the active packaging
of nucleic acids into phage particles, plasmid replication
from an origin that leads to conjugal transfer, integron
assembly or passive release of DNA into the environ-
ment upon cell death. Second, the transfer step, which
might or might not require physical contact between
the donor and recipient organism, takes place. Third,
the nucleic acid enters the recipient organisms through
specific or non-specific means. Fourth, the nucleic-acid
molecule is established in the recipient either as a self-
replicating element or through recombination with, or
transposition into, the recipient’s chromosome. This
existence can be transitory, as is the case with many
plasmids of which maintenance by the recipient genome
depends on selective pressure. Last, in step 5, stable
inheritance in the recipient genome might ensue.
Several scientific disciplines are addressing HGT,
each providing their unique perspective and each using
different approaches and methodologies. In general,
evolutionary biology considers HGT events that have
gone to completion (that is, through step 5). Molecular
ecology, on the other hand, tends to focus on HGT
events at the level of step 4. Finally, molecular biology
is most interested in the mechanisms controlling steps
1 through 4. With such distinct perspectives, conflicts
are bound to arise, but opportunities for synthesis are
certain to emerge. The goal of this Focus issue of Nature
Reviews Microbiology is to present HGT from the pers-
pective of these different disciplines and to provide a
path towards the construction of a holistic picture of
HGT and its effects on extant microbial communi-
ties. We argue that efforts towards such synthesis will
accelerate our understanding of the mechanisms and
factors that control HGT, the impacts of HGT on the
evolutionary history of prokaryotes, the effect of HGT
on microbial interactions with each other and their
environment, and the means by which HGT can be
controlled to affect human and environmental health.
HORIZONTAL GENE TRANSFER:
PERSPECTIVES AT A CROSSROADS
OF SCIENTIFIC DISCIPLINES
Barth F. Smets* and Tamar Barkay
Horizontal gene transfer (HGT) has a crucial role in microbial evolution, in shaping the structure
and function of microbial communities and in controlling a myriad of environmental and public-
health problems. Here, Barth F. Smets and Tamar Barkay assess the importance of HGT and
place the selection of articles in this Focus issue in context.
NATURE REVIEWS
|
MICROBIOLOGY VOLUME 3
|
SEPTEMBER 2005
|
675
FOREWORD
FOCUS ON HORIZONTAL GENE TRANSFER
© 2005 Nature Publishing Group
Bacteria Archaea Eukarya
Plastids
Mitochondria
Common ancestral community of primitive cells
12
3,4
5
Molecular evolution
Molecular evolution employs a retrospective approach
to infer HGT by examining the signatures left by HGT
in microbial genomes. This approach has benefited
enormously from the availability of complete microbial
genome sequences. As is described in this Focus issue
by Peter Gogarten and Jeffrey Townsend, HGT can be
inferred from phylogenetic dependent or independent
inspections of genes. In the first approach, the atypi-
cal distribution of genes, inferred from incongruence
between various gene phylogenies, is taken as evidence
of HGT. In the latter approach, genes that seem unu-
sual in their genomic context are considered to have
arrived in their current genome relatively recently
through horizontal transfer. In addition, experimental
approaches that specifically aim at the isolation and
identification of heterologous ‘gene islands’ in closely
related strains1 are also employed.
Molecular evolution examines HGT from a post-
step-5 position (FIG. 1), and whereas evidence of past
HGT in current genomes is pervasive, the ramification
of these observations to our understanding of lifes his-
tory is hotly contested. Certainly, HGT has challenged
our view of the evolutionary history of organisms and
genes from a tree-like paradigm2 to a network-like
paradigm3, and therefore its influence on microbial
speciation and diversification. This area of ongoing
controversy — the concept of the prokaryotic species
— is discussed in detail by Dirk Gevers and colleagues,
who also propose approaches to find a taxonomic
framework that can accommodate the vast differences
in biology presented by prokaryotes.
Understanding the way HGT has contributed
to microbial evolution can help identify intra- and
extracellular processes that affect the stable inherit-
ance of transferred genes in a new genome (step 5 in
FIG. 1). Crucial among them, according to Gogarten
and Townsend, is the question of selective pressure
for the inheritance of transferred genes in their
new host in light of their observation of selective
neutrality of transferred genes. There remain,
therefore, fundamental questions on the actual
(if any) ecological role of such transferred genes
and the mechanism that controls their mainte-
nance in a host genome. If harmful genes (for
example, antibiotic-resistance or virulence genes) are to
be prevented from spreading horizontally, or beneficial
genes (for example, biodegradative genes) are to be
stimulated to do so, information on the processes that
facilitate inheritance after HGT is essential, and bio-
informatic analyses should provide useful clues.
The traditional view that obligate intracellular
parasitic microorganisms have ‘fixed’ minimal
genomes with little influence of intra- and inter-
genomic genetic (ex)change is challenged by Seth
Bordenstein and William Reznikoff. These authors
argue that the extensive presence of mobile genetic
elements (MGEs) such as prophages, plasmids and
transposons in recently sequenced genomes of obli-
gate parasites suggests a more complex picture. As
the association of eukary otic organisms with obligate
intracellular parasites often leads to pathologies, the
issues raised by this review could have far-reaching
practical implications.
Molecular biology
Molecular biology has long been examining the
mechanisms that govern the first steps in the
gene-transfer process (steps 1–4 in FIG. 1), in part
because MGEs are at the core of much molecu-
lar biological experimentation. Diverse elements
and elegant mechanisms have been discovered
and elucidated. The molecular pro cesses that
govern, as well as those that serve as barriers for,
gene transfer have been thoroughly, yet incompletely,
characterized, as reviewed by Christopher Thomas
and Kaare Nielsen. The authors observe that any
identified explicit barrier to HGT (for example,
surface exclusion, restriction and so on) is subject
to genetic and/or physiological modulation, and is
therefore not impermeable. Remarkably little, how-
ever, is known about environmental and molecular
signals that control expression (or overexpression, if
such exists) of the HGT processes. Yet this question
is central to a correct assessment of HGT in microbial
communities. Is HGT an adaptive phenomenon that
is stimulated in challenging environments or is it a
random process of which the outcome is controlled
by natural selection?
Molecular biology has supplied microbial ecolo-
gists with the tools to interrogate the mobile gene pool
in microbial communities from diverse habitats. The
surprise and lesson from such studies is that the diver-
sity of mobile elements is much broader — and prob-
ably underestimated — than what has been gleaned
from the original molecular biological work that
focused primarily on pathogenic microorganisms.
The diversity of MGEs, and especially the challenges
and opportunities in annotation and cataloguing that
arise as their rate of discovery has accelerated with
Figure 1 | The 5 steps of horizontal gene flow. Horizontal gene transfer and how it has
impacted the evolution of life is presented through a web connecting bifurcating branches that
complicate, yet do not erase, the tree of life. The inset illustrates the continuum of 5 steps that
leads to the stable inheritance of a transferred gene in a new host.
676
|
SEPTEMBER 2005
|
VOLUME 3 www.nature.com/reviews/micro
FOREWORD
© 2005 Nature Publishing Group
the sequencing of microbial genomes, is addressed by
Anne Summers and colleagues. Together, these ele-
ments are in the process of being transferred (step 2)
and could be considered to be ‘genes in transit’.
Comparison of this gene pool — with the exclusion
of genes involved in the transfer processes themselves,
such as viral genes or plasmid maintenance genes
— with those that are identified in complete genome
sequences by bioinformatic approaches as laterally
transferred genes should generate new insights and
testable hypotheses on the processes that favour stable
inheritance of transferred genes in a new genomic
context (the transition from step 4 to 5 in FIG. 1).
Our expanded view on the diversity and distribu-
tion of MGEs has, to a large extent, been made possible
by the progression in microbial ecology from the
study of pure cultures (and the genetic elements
residing within them) to the direct isolation of nucleic
acids and mobile elements from microbial communi-
ties (for example, exogenous plasmid isolation, direct
sequencing of viral DNA). This newly found diversity
should be matched by an attempt at characterizing
these mobile elements beyond their sequence com-
position and understanding the manner in which
they might enhance microbial genome evolution.
An essential tool for progress towards this goal is
the establishment of curated and carefully annotated
databases and repositories of molecular information
specifically for the mobile gene pool, or ‘mobilome’,
which spans all kingdoms of life. Challenges associ-
ated with this effort are further discussed by Summers
and colleagues.
Microbial ecology
The role of HGT in adaptation of microbial com-
munities to changing environmental conditions has
intrigued microbial ecologists for at least three decades.
Although the advantage of spreading ‘ready made’
genes that enhance fitness under altered conditions
relative to their de novo evolution by the slow process
of mutations acted upon by natural selection is obvi-
ous, obtaining solid evidence of this occurrence in
extant microbial communities has been elusive. Most
evidence to date consists of observations that imply
HGT’s role in response to changing environments.
Chief among them is the frequent association of envi-
ronmentally beneficial genes, such as antibiotic- and
metal-resistance genes and xenobiotic-compound-deg-
radation genes, with MGEs, as described by Summer
and colleagues in this Focus issue. Observations of
such MGEs in man-impacted environments, and in
related but pristine environments, has led to the fas-
cinating hypothesis that the horizontal transfer events
that led to the dissemination of such genes are induced
by the introduction of substances such as antibiotics,
metals or organic contaminants into the environment.
However, the observation of HGT under apparently
selective conditions does not necessarily imply that
the environmental forces caused HGT; it could simply
mean that these elements were enriched to detectable
concentrations.
The documented incidence of HGT, as revealed
from comparative genome-sequence analysis, and
the discovery of an increased diversity of MGEs have
nevertheless given credence to the notion that HGT
could be an important determinant in shaping the
microbial community metagenome. Analytical and
experimental tools developed by molecular evolu-
tion and molecular biology are now routinely used to
examine strains and nucleic-acids pools from different
environments. For example, incongruence between gene
trees has been invoked to suggest horizontal transfer of
metal-homeostasis4 and 2,4-dichloro phenoxyacetic-
acid-degradation genes5 among micro organisms from
aquatic and terrestrial environments.
Perhaps most exciting are new experimental
approaches that facilitate the real-time demonstration
of HGT in undisturbed microbial communities. Søren
Sørensen and colleagues describe the issues, chal-
lenges and achievements in the study of HGT in extant
microbial communities. These methods are largely
driven by technological advances in optical detection
and biomarker construction to permit observations of
single-cell and single-MGE dynamics in undisturbed
microbial communities. Whereas achievements to
date have mostly focused on methods development,
future research employing these methods should place
HGT within the context of contemporary microbial
communities and their activities. The consequences
of such studies to enhance our ability to modulate
interactions with and among the microorganisms
around us might result in a better control of disease
processes and improved environmental management
(see below).
HGT: why care?
While the concept of HGT frequently engenders
joyful intellectual contemplation and lively philo-
sophical exchanges, it carries more than just ivory
tower relevance. The evidence indicates that HGT is a
central process in microbial activities that control our
health and the environment, and that it holds promise
as a tool for their improvement.
The increased global documentation of human
pathogenic bacteria (for example, Streptococcus
pneumoniae, Staphylococcus aureus and Pseudomonas
aeruginosa) that are resistant to multiple classes of
antibiotics — identified as one of the key challenges
to contemporary infectious-disease control — is one
example in which proficient HGT has resulted in
undesirable consequences6. The improper and exces-
sive administration of antibiotics (conferring selective
advantage), combined with the ready bacterial ability
to transfer antibiotic-resistance genes through plasmids
and transposons and the presence of large transfer
communities (for example, the gastrointestinal tract) in
places such as hospitals or animal husbandry facilities,
promotes the widespread dissemination of these genes.
An urgent need for a more prudent use of antibiotics,
combined with a better grasp of the ecology of HGT,
is essential to avoid a return to a pre-antibiotic area of
infectious-disease control7.
NATURE REVIEWS
|
MICROBIOLOGY VOLUME 3
|
SEPTEMBER 2005
|
677
FOCUS ON HORIZONTAL GENE TRANSFER
© 2005 Nature Publishing Group
Transgenic organisms hold great promise for
improved food production. Concerns about HGT from
these organisms have, however, shrouded and limited
their application. The appropriateness of current risk-
assessment models8 and monitoring protocols9 to depict
the potential for recombinant gene transfer through
HGT to unintended target organisms are issues that
are subject to fierce debate. A fuller understanding of
the mechanisms and constraints for HGT could ensure
development of effective gene-containment strategies
within target species and ultimately allow the full
realization of the promise of biotechnology.
On the other hand, the spread of genes by HGT
to microorganisms in contaminated environments is
a desired outcome of gene-augmentation strategies10.
In these strategies, donor cells carrying an MGE that
encodes essential genes for the biodegradation of a
target contaminant are introduced into the relevant
environment, and dissemination of the genes to indig-
enous bacteria, followed by expression of the degra-
dative genes in their new hosts, leads to accelerated
contaminant degradation. Although some promising
results have been obtained to date, more studies are
required to evaluate whether the concept of HGT-
based environmental management can be sustained.
The ability to control harmful effects and to enhance
desired attributes of HGT depends on the integrated
understanding of HGT as a continuum spanning
steps 1–5 of the gene-transfer paradigm (FIG. 1) and its
integra tion within an ecological framework.
Conclusions
Clearly, HGT has contributed to prokaryotic evolu-
tion and is an ongoing process in extant microbial
communities. The ‘mobilome’ is therefore receiving
unprecedented attention from a range of scientific
disciplines. The purpose of this themed issue is to
synthesize the state of our knowledge from these dif-
ferent perspectives. We believe that such a synthesis
will be mandatory to obtain a more precise appraisal
of HGT as a force in shaping prokaryotic evolution,
diversity and activity and, therefore, in modulating
the history of life on Earth.
1. Nesbo, C. L. & Doolittle, W. F. Targeting clusters of transferred genes
in Thermotoga maritima. Environ. Microbiol. 5, 1144–1154 (2003).
2. Woese, C. R. Interpreting the universal phylogenetic tree.
Proc. Natl Acad. Sci. USA 97, 8392–8396 (2000).
3. Bapteste, E. et al. Do orthologous gene phylogenies really support
tree-thinking? BMC Evol. Biol. 5, 33 (2005).
4. Coombs, J. M. & Barkay, T. Molecular evidence for the evolution of
metal homeostasis genes by lateral gene transfer in bacteria from the
deep terrestrial subsurface. Appl. Environ. Microbiol. 70, 1698–1707
(2004).
5. McGowan, C., Fulthorpe, R., Wright, A. & Tiedje. J. M.
Evidence for interspecies gene transfer in the evolution of
2, 4-dichlorophenoxyacetic acid degraders. Appl. Environ. Microbiol.
64, 4089–4092 (1998).
6. Monroe, S. & Polk, R. Antimicrobial use and bacterial resistance.
Curr. Opin. Microbiol. 3, 496–501 (2000).
7. Levy, S. B. & Marshall, B. Antibacterial resistance worldwide: causes,
challenges and responses. Nature Med. 10, S122–S129 (2004).
8. Heinemann, J. A. & Traavik, T. Problems in monitoring horizontal gene
transfer in field trials of transgenic plants. Nature Biotechnol. 22,
1105–1109 (2004).
9. Nielsen, K. M. & Townsend, J. P. Monitoring and modeling horizontal
gene transfer. Nature Biotechnol. 22, 1110–1114 (2004).
10. Springael, D. & Top, E. M. Horizontal gene transfer and microbial
adaptation to xenobiotics: new types of mobile genetic elements
and lessons from ecological studies. Trends Microbiol. 12, 53–58
(2004).
Acknowledgements
The authors would like to thank the US National Science Foundation (BES
pogramme) and the US Department of Energy (NABIR programme) for sup-
port of research on HGT in their laboratories. This article and special issue
were inspired by a workshop on ‘Horizontal Gene Flow in Microbial
Communities’ that was co-chaired by the authors in Warrenton, Virginia,
USA, in June 2004, and sponsored by the National Science Foundation
(MO/MIP programme) and the Department of Energy (NABIR programme).
These agencies, as well as the US National Aeronautics and Space Agency
(Astrobiology Programme) provided gracious support to the production of
this issue.
678
|
SEPTEMBER 2005
|
VOLUME 3 www.nature.com/reviews/micro
FOREWORD
... Significant evidence indicates that HGTs are the continuous and normal processes which perform critical role in prokaryotic organism adaptations in the natural environment particularly in soil system [91]. In this phase, the formation of bacterial genomes, the establishment of intra-species heterogeneity and the distribution of genetically modified functional modules between bacterial communities are essential. ...
... In this phase, the formation of bacterial genomes, the establishment of intra-species heterogeneity and the distribution of genetically modified functional modules between bacterial communities are essential. As a consequence, horizontal modules were widely used to adapt biotic interactions that are rapidly evolving within the natural systems [91]. Such kind of interactions basically include the development of antibiotics, antibiotic resistance dissemination, liberation of xenobiotic or novel secondary metabolites into the environment, dissemination of deteriorating genes as well as route assemblies [48] and lastly symbiotic or pathogenic interactions [33]. ...
Chapter
A crucial factor for soil fertility status and management of the health of the plant as well as plant stress acclimatization management is the sound ecological fitness of soil and root-related microbial communities present in the soil system. It preserves genetic diversity in microbial populations via genetic changes or mutation and transfer of genes in the soil microbes. In the in vitro condition and under the natural conditions, horizontal transfer of gene (HGT) is performed by the process of microbial conjugation, microbial transformation, and the process of rapid transduction. The genetic elements which are generally mobile in nature (MGE) also perform a critical part of gene distribution in the bacterial communities and improve their adaptation, rate of survival and colonization ability in various environmental conditions. The extra chromosomal DNA of bacteria, which are commonly known as plasmids, generally encode resistance genes for environmental stress tolerance and are of huge importance in the context of bioremediation process. Bacterial development and growth modes in biofilm further improves exchange of genes and enriches bacterial fitness and competitiveness. Given the value of transfer of genes horizontally, a better knowledge of rhizosphere genetic processes would further lead to the successful use of naturally engineered bacteria for sustainable use in agricultural research and development.
... Later, IncP-1 plasmids were reported from diverse environments, e.g., sewage, marine sediment, manure, biofilters, and rhizosphere that were affected by anthropogenic pollutants (Dahlberg et al., 1997;Schlüter et al., 2007;Binh et al., 2008;Bahl et al., 2009;Gomes et al., 2010;Brown et al., 2013;Jechalke et al., 2013;Dealtry et al., 2014;Wolters et al., 2015). A wide variety of adaptive traits conferring resistance to antibiotics, disinfectants, heavy metals, and/or degradation of xenobiotics was found as accessory genes in the insertion hot spots of IncP-1 plasmids (Hsu and Bartha, 1979;Top and Springael, 2003;Smets and Barkay, 2005). IncP-1 plasmids were so far mainly reported from polluted environments Tauch et al., 2003;Heuer et al., 2004;Tennstedt et al., 2005;Kamachi et al., 2006;Smalla et al., 2006). ...
... In contrast, the plasmids from the rhizosphere of plants grown in unpolluted soils showed higher diversity, and none of them carried previously known antibiotic resistance genes by searching in CARD. The presence of highly diverse IncP-1 plasmids suggested that the role of IncP-1 plasmids in unpolluted rhizosphere might be not only be conferring resistance to antibiotics, disinfectants, heavy metals, and/or degradation of xenobiotics (Hsu and Bartha, 1979;Top and Springael, 2003;Smets and Barkay, 2005) but also providing genetic flexibility of microbes in rhizosphere by a high rate of gene acquisition and loss via various IncP-1 plasmids. ...
Article
Full-text available
IncP-1 plasmids, first isolated from clinical specimens (R751, RP4), are recognized as important vectors spreading antibiotic resistance genes. The abundance of IncP-1 plasmids in the environment, previously reported, suggested a correlation with anthropogenic pollution. Unexpectedly, qPCR-based detection of IncP-1 plasmids revealed also an increased relative abundance of IncP-1 plasmids in total community DNA from the rhizosphere of lettuce and tomato plants grown in non-polluted soil along with plant age. Here we report the successful isolation of IncP-1 plasmids by exploiting their ability to mobilize plasmid pSM1890. IncP-1 plasmids were captured from the rhizosphere but not from bulk soil, and a high diversity was revealed by sequencing 14 different plasmids that were assigned to IncP-1β, δ, and ε subgroups. Although backbone genes were highly conserved and mobile elements or remnants as Tn 501 , IS 1071 , Tn 402 , or class 1 integron were carried by 13 of the sequenced IncP-1 plasmids, no antibiotic resistance genes were found. Instead, seven plasmids had a mer operon with Tn 501 -like transposon and five plasmids contained putative metabolic gene clusters linked to these mobile elements. In-depth sequence comparisons with previously known plasmids indicate that the IncP-1 plasmids captured from the rhizosphere are archetypes of those found in clinical isolates. Our findings that IncP-1 plasmids do not always carry accessory genes in unpolluted rhizospheres are important to understand the ecology and role of the IncP-1 plasmids in the natural environment.
... For the majority of effectors, this is corroborated by sequence identities of PAS-GAF-PHY core modules. Based on this observation, we conclude that the occurrence of multiple phytochrome-linked effector combinations is predominantly based on horizontal gene transfer, a well-established major player in microbial evolution [29], rather than recurring internal recombination events. This is further supported by the fact that relatively closely related sequences also occur in different phyla and classes of the bacterial kingdom. ...
Article
Understanding the relationship between protein sequence, structure and function is one of the fundamental challenges in biochemistry. A direct correlation, however, is often not trivial since protein dynamics also play an important functional role—especially in signal transduction processes. In a subfamily of bacterial light sensors, phytochrome-activated diguanylate cyclases (PadCs), a characteristic coiled-coil linker element connects photoreceptor and output module, playing an essential role in signal integration. Combining phylogenetic analyses with biochemical characterisations, we were able to show that length and composition of this linker determine sensor–effector function and as such are under considerable evolutionary pressure. The linker length, together with the upstream PHY-specific domain, influences the dynamic range of effector activation and can even cause light-induced enzyme inhibition. We demonstrate phylogenetic clustering according to linker length, and the development of new linker lengths as well as new protein function within linker families. The biochemical characterisation of PadC homologs revealed that the functional coupling of PHY dimer interface and linker element defines signal integration and regulation of output functionality. A small subfamily of PadCs, characterised by a linker length breaking the coiled-coil pattern, shows a markedly different behaviour from other homologs. The effect of the central helical spine on PadC function highlights its essential role in signal integration as well as direct regulation of diguanylate cyclase activity. Appreciation of sensor–effector linkers as integrator elements and their coevolution with sensory modules is a further step towards the use of functionally diverse homologs as building blocks for rationally designed optogenetic tools. Graphical abstract
... Selection, gene duplication, and horizontal gene transfer (HGT) have been considered the main mechanisms driving genomic adaptation to a changing environment (40,41). Although both positive selection and negative selection are pervasive in modern evolutionary genetics, negative selection has been proposed as a null model for explaining the genetic diversity (42). ...
Article
Full-text available
Despite the dominance of Rhodanobacter species in the subsurface of the contaminated Oak Ridge Reservation (ORR) site, very little is known about the mechanisms underlying their adaptions to the various stressors present at ORR. Recently, multiple Rhodanobacter strains have been isolated from the ORR groundwater samples from several wells with varying geochemical properties.
... Metagenome analysis via next-generation sequencing provides allows the extensive analysis of the environmental genomes where a metagenomic approach could investigate poorly characterized or unknown diverse degradation pathways that present in diverse microbes. Studies that investigated the microbial communities from diverse environments, such as sediments and marine water (DeLong et al., 2006;Yooseph et al., 2007), the human gut (Turnbaugh et al., 2007), soils (Smets and Barkay, 2005), and acid mine drainage (Tyson et al., 2005), provided novel insights into microbial systems and functions Metagenomic bioremediation offers more positive results and complete information to enhance degradation ratios compared with other approaches to bioremediation (Kosaric, 2001). With an increased understanding of the structural and functional attributes of microbes toward the degradation of xenobiotic compounds, information is generated about microbes from contaminated and undisturbed sites. ...
... The ability of MRSA to acquire vancomycin-resistance through horizontal gene transfer (HGT) is a looming health crisis (5,6). HGT is the process of acquisition of foreign DNA by bacteria through transduction, transformation or conjugation, and is a biological driver of bacterial evolution, ecology and pathogenicity (7,8). Restriction endonucleases (REases) that nucleolytically degrade foreign DNA are one of the main barriers to HGT in bacteria (9,10). ...
Article
Full-text available
Acquisition of foreign DNA by Staphylococcus aureus, including vancomycin resistance genes, is thwarted by the ATP-dependent endonuclease SauUSI. Deciphering the mechanism of action of SauUSI could unravel the reason how it singularly plays a major role in preventing horizontal gene transfer (HGT) in S. aureus. Here, we report a detailed biochemical and structural characterization of SauUSI, which reveals that in the presence of ATP, the enzyme can cleave DNA having a single or multiple target site/s. Remarkably, in the case of multiple target sites, the entire region of DNA flanked by two target sites is shred into smaller fragments by SauUSI. Crystal structure of SauUSI reveals a stable dimer held together by the nuclease domains, which are spatially arranged to hydrolyze the phosphodiester bonds of both strands of the duplex. Thus, the architecture of the dimeric SauUSI facilitates cleavage of either single-site or multi-site DNA. The structure also provides insights into the molecular basis of target recognition by SauUSI. We show that target recognition activates ATP hydrolysis by the helicase-like ATPase domain, which powers active directional movement (translocation) of SauUSI along the DNA. We propose that a pile-up of multiple translocating SauUSI molecules against a stationary SauUSI bound to a target site catalyzes random double-stranded breaks causing shredding of the DNA between two target sites. The extensive and irreparable damage of the foreign DNA by shredding makes SauUSI a potent barrier against HGT.
... Taken fromSmets and Barkay (2005). Horizontal gene transfer: Perspectives at a crossroads of scientific disciplines. ...
Article
Full-text available
Viruses are ubiquitous. They infect almost every species and are probably the most abundant biological entities on the planet, yet they are excluded from the Tree of Life (ToL). However, there can be no doubt that viruses play a significant role in evolution, the force that facilitates all life on Earth. Conceptually, viruses are regarded by many as non-living entities that hijack living cells in order to propagate. A strict separation between living and non-living entities places viruses far from the ToL, but this may be theoretically unsound. Advances in sequencing technology and comparative genomics have expanded our understanding of the evolutionary relationships between viruses and cellular organisms. Genomic and metagenomic data have revealed that co-evolution between viral and cellular genomes involves frequent horizontal gene transfer and the occasional co-option of novel functions over evolutionary time. From the giant, ameba-infecting marine viruses to the tiny Porcine circovirus harboring only two genes, viruses and their cellular hosts are ecologically and evolutionarily intertwined. When deciding how, if, and where viruses should be placed on the ToL, we should remember that the Tree functions best as a model of biological evolution on Earth, and it is important that models themselves evolve with our increasing understanding of biological systems.
... Metagenomics, along with other molecular techniques, has revolutionized the field of microbiology by focusing on microbial diversity, evolution, and adaption (Riesenfeld et al., 2004). Microbial communities studied in diverse environments (sediments, marine water, human gut, soils, and acid mine drainage) have unveiled the genetic makeup, evolutionary alterations, structural and functional diversity, and metabolic pathways of these communities (DeLong, 2005;Rusch et al., 2007;Smets and Barkay, 2005;Turnbaugh et al., 2007;Tyson et al., 2005). Metagenomics has increased our understanding about microbial degradation of xenobiotic compounds by differentiating native microbiota (having ability to degrade contaminant) and intensive ex situ treated or in situ bioaugmented contaminated sites. ...
Chapter
The quality of life on Earth is inevitably related to the quality of environment. Industrialization has led to the production of pollutants and contaminants especially inorganic contaminants such as mineral acids, metals, and inorganic salts. Numerous innovative and novel techniques have been designed to minimize the hazardous effects of these contaminants, and bioremediation is one of these approaches. In contrast to conventional remediation techniques, the key advantage of bioremediation is its low cost and environmentally friendly operation as compared with other typical approached. Researchers were previously focused on typical bioremediation approaches, but now advanced molecular techniques of bioremediation using multi omics approaches have been introduced to explore and comprehend the functional and structural characteristics of participating biotic factors. Several molecular techniques including 16S rRNA sequences analysis, denaturing gradient gel electrophoresis, ecological diversity, and omics approaches have been established and considered to be potent and vital tool for the degradation, eradication, and detoxification of contaminants from the nature.
Article
Full-text available
Acetic acid bacteria (AAB) are industrial microorganisms used for vinegar fermentation. Herein, we investigated the distribution and genome structures of mitomycin C-inducible temperate phages in AAB. Transmission electron microscopy analysis revealed phage-like particles in 15 out of a total 177 acetic acid bacterial strains, all of which showed morphology similar to myoviridae-type phage. The complete genome sequences of the six phages derived from three strains each of Acetobacter and Komagataeibacter strains were determined, harboring a genome size ranging from 34,100 to 53,798 bp. A phage AP1 from A. pasteurianus NBRC 109446 was predicted as an active phage based on the genomic information, and actually had the ability to infect its phiAP1-cured strain. The attachment sites for phiAP1 were located in the 3’-end region of the tRNAser gene. We also developed a chromosome-integrative vector, p2096int, based on the integrase function of phiAP1, and it was successfully integrated into the attachment site of the phiAP1-cured strain, which may be used as a valuable tool for the genetic engineering. Overall, this study showed the distribution of mitomycin C-inducible temperate phages in AAB, and identified the active temperate phage o f A. pasteurianus.
Chapter
Nature has the capability to maintain balance in environment. Rapid growth in industrialization has led to release of toxic chemicals into the environment. Microbial degradation is one of the economic methods for remediation of the polluted environment. Bioremediation/biodegradation and bioinformatics are the scientific areas in applied microbiology and biotechnology. Presently, several databases and prediction tools/approaches assist the development and application of bioremediation. The implementation of the in silico approach reduces time and basic laboratory experiments and is important in prediction of degradation pathways. Herein, we summarize the application of several bioinformatics tools, computational approaches, and omics approaches in analyzing the chemical and functional characteristics, toxicity prediction, and degradation pathways. In addition, detailed view of databases, web servers that may be implemented in the area of bioremediation and biodegradation are also mentioned.
Article
Full-text available
Transgenic crops are approved for release in some countries, while many more countries are wrestling with the issue of how to conduct risk assessments. Controls on field trials often include monitoring of horizontal gene transfer (HGT) from crops to surrounding soil microorganisms. Our analysis of antibiotic-resistant bacteria and of the sensitivity of current techniques for monitoring HGT from transgenic plants to soil microorganisms has two major implications for field trial assessments of transgenic crops: first, HGT from transgenic plants to microbes could still have an environmental impact at a frequency approximately a trillion times lower than the current risk assessment literature estimates the frequency to be; and second, current methods of environmental sampling to capture genes or traits in a recombinant are too insensitive for monitoring evolution by HGT. A model for HGT involving iterative short-patch events explains how HGT can occur at high frequencies but be detected at extremely low frequencies.
Article
Full-text available
Small-subunit ribosomal DNA (SSU rDNA) from 20 phenotypically distinct strains of 2,4-dichlorophenoxyacetic acid (2,4-D)-degrading bacteria was partially sequenced, yielding 18 unique strains belonging to members of the alpha, beta, and gamma subgroups of the class Proteobacteria. To understand the origin of 2,4-D degradation in this diverse collection, the first gene in the 2,4-D pathway, tfdA, was sequenced. The sequences fell into three unique classes found in various members of the beta and gamma subgroups of Proteobacteria. None of the alpha-Proteobacteria yielded tfdA PCR products. A comparison of the dendrogram of the tfdA genes with that of the SSU rDNA genes demonstrated incongruency in phylogenies, and hence 2,4-D degradation must have originated from gene transfer between species. Only those strains with tfdA sequences highly similar to the tfdA sequence of strain JMP134 (tfdA class I) transferred all the 2,4-D genes and conferred the 2,4-D degradation phenotype to a Burkholderia cepacia recipient.
Article
Full-text available
Monitoring efforts have failed to identify horizontal gene transfer (HGT) events occurring from transgenic plants into bacterial communities in soil or intestinal environments. The lack of such observations is frequently cited in biosafety literature and by regulatory risk assessment. Our analysis of the sensitivity of current monitoring efforts shows that studies to date have examined potential HGT events occurring in less than 2 g of sample material, when combined. Moreover, a population genetic model predicts that rare bacterial transformants acquiring transgenes require years of growth to out-compete wild-type bacteria. Time of sampling is there-fore crucial to the useful implementation of monitoring. A population genetic approach is advocated for elucidating the necessary sample sizes and times of sampling for monitoring HGT into large bacterial populations. Major changes in current monitoring approaches are needed, including explicit consideration of the population size of exposed bacteria, the bacterial generation time, the strength of selection acting on the transgene-carrying bacteria, and the sample size necessary to verify or falsify the HGT hypotheses tested.
Article
Full-text available
Transgenic crops are approved for release in some countries, while many more countries are wrestling with the issue of how to conduct risk assessments. Controls on field trials often include monitoring of horizontal gene transfer (HGT) from crops to surrounding soil microorganisms. Our analysis of antibiotic-resistant bacteria and of the sensitivity of current techniques for monitoring HGT from transgenic plants to soil microorganisms has two major implications for field trial assessments of transgenic crops: first, HGT from transgenic plants to microbes could still have an environmental impact at a frequency approximately a trillion times lower than the current risk assessment literature estimates the frequency to be; and second, current methods of environmental sampling to capture genes or traits in a recombinant are too insensitive for monitoring evolution by HGT. A model for HGT involving iterative short-patch events explains how HGT can occur at high frequencies but be detected at extremely low frequencies.
Article
Full-text available
The optimism of the early period of antimicrobial discovery has been tempered by the emergence of bacterial strains with resistance to these therapeutics. Today, clinically important bacteria are characterized not only by single drug resistance but also by multiple antibiotic resistance--the legacy of past decades of antimicrobial use and misuse. Drug resistance presents an ever-increasing global public health threat that involves all major microbial pathogens and antimicrobial drugs.
Article
Full-text available
Since Darwin's Origin of Species, reconstructing the Tree of Life has been a goal of evolutionists, and tree-thinking has become a major concept of evolutionary biology. Practically, building the Tree of Life has proven to be tedious. Too few morphological characters are useful for conducting conclusive phylogenetic analyses at the highest taxonomic level. Consequently, molecular sequences (genes, proteins, and genomes) likely constitute the only useful characters for constructing a phylogeny of all life. For this reason, tree-makers expect a lot from gene comparisons. The simultaneous study of the largest number of molecular markers possible is sometimes considered to be one of the best solutions in reconstructing the genealogy of organisms. This conclusion is a direct consequence of tree-thinking: if gene inheritance conforms to a tree-like model of evolution, sampling more of these molecules will provide enough phylogenetic signal to build the Tree of Life. The selection of congruent markers is thus a fundamental step in simultaneous analysis of many genes. Heat map analyses were used to investigate the congruence of orthologues in four datasets (archaeal, bacterial, eukaryotic and alpha-proteobacterial). We conclude that we simply cannot determine if a large portion of the genes have a common history. In addition, none of these datasets can be considered free of lateral gene transfer. Our phylogenetic analyses do not support tree-thinking. These results have important conceptual and practical implications. We argue that representations other than a tree should be investigated in this case because a non-critical concatenation of markers could be highly misleading.
Article
The universal phylogenetic tree not only spans all extant life, but its root and earliest branchings represent stages in the evolutionary process before modern cell types had come into being. The evolution of the cell is an interplay between vertically derived and horizontally acquired variation. Primitive cellular entities were necessarily simpler and more modular in design than are modern cells. Consequently, horizontal gene transfer early on was pervasive, dominating the evolutionary dynamic. The root of the universal phylogenetic tree represents the first stage in cellular evolution when the evolving cell became sufficiently integrated and stable to the erosive effects of horizontal gene transfer that true organismal lineages could exist.
Article
The current epidemic of bacterial resistance is attributed, in part, to the overuse of antibiotics. Recent studies have documented increases in resistance with over-use of particular antibiotics and improvements in susceptibility when antibiotic use is controlled. The most effective means of improving use of antibiotics is unknown. Comprehensive management programs directed by multi-disciplinary teams, computer-assisted decision-making, and antibiotic cycling have been beneficial in controlling antibiotic use, decreasing costs without impacting patient outcomes, and possibly decreasing resistance.
Article
We screened a Thermotoga sp. strain RQ2 lambda library for genes present in that strain but absent from the closely related completely sequenced relative Thermotoga maritima strain MSB8, by using probes generated in an earlier genomic subtraction study. Five lambda insert fragments were sequenced, containing, respectively, an archaeal type ATPase operon, rhamnose biosynthetic genes, ORFs with similarity to an arabinosidase, a Thermotoga sp. strain RQ2-specific alcohol dehydrogenase and a novel archaeal Mut-S homologue. All but one of these fragments contained additional Thermotoga sp. strain RQ2-specific sequences not screened for, suggesting that many such strain-specific genes will be found clustered in the genome. Moreover, phylogenetic analyses, phylogenetic distribution and/or G + C content suggests that all the Thermotoga sp. strain RQ2 specific sequences in the sequenced lambda clones have been acquired by lateral gene transfer. We suggest that the use of strain-specific small insert clones obtained by subtractive hybridization to target larger inserts for sequencing is an efficient, economical way to identify environmentally (or clinically) relevant interstrain differences and novel gene clusters, and will be invaluable in comparative genomics.
Article
The characterization of bacteria that degrade organic xenobiotics has revealed that they can adapt to these compounds by expressing 'novel' catabolic pathways. At least some of them appear to have evolved by patchwork assembly of horizontally transmitted genes and subsequent mutations and gene rearrangements. Recent studies have revealed the existence of new types of xenobiotic catabolic mobile genetic elements, such as catabolic genomic islands, which integrate into the chromosome after transfer. The significance of horizontal gene transfer and patchwork assembly for bacterial adaptation to pollutants under real environmental conditions remains uncertain, but recent publications suggest that these processes do occur in a polluted environment.