''Dehalogenimonas lykanthroporepellens'' is an
anaerobic
Anaerobic means "living, active, occurring, or existing in the absence of free oxygen", as opposed to aerobic which means "living, active, or occurring only in the presence of oxygen." Anaerobic may also refer to:
*Adhesive#Anaerobic, Anaerobic ad ...
,
Gram-negative bacteria
Gram-negative bacteria are bacteria that, unlike gram-positive bacteria, do not retain the Crystal violet, crystal violet stain used in the Gram staining method of bacterial differentiation. Their defining characteristic is that their cell envelo ...
in the phylum
Chloroflexota
The Chloroflexota are a phylum of bacteria containing isolates with a diversity of phenotypes, including members that are aerobic thermophiles, which use oxygen and grow well in high temperatures; anoxygenic phototrophs, which use light for ph ...
isolated from a
Superfund site
Superfund sites are Pollution, polluted locations in the United States requiring a long-term response to clean up hazardous material contaminations. Sites include landfills, mines, manufacturing facilities, processing plants where toxic waste h ...
in
Baton Rouge
Baton Rouge ( ; , ) is the List of capitals in the United States, capital city of the U.S. state of Louisiana. It had a population of 227,470 at the 2020 United States census, making it List of municipalities in Louisiana, Louisiana's second-m ...
,
Louisiana
Louisiana ( ; ; ) is a state in the Deep South and South Central regions of the United States. It borders Texas to the west, Arkansas to the north, and Mississippi to the east. Of the 50 U.S. states, it ranks 31st in area and 25 ...
.
It is useful in
bioremediation
Bioremediation broadly refers to any process wherein a biological system (typically bacteria, microalgae, fungi in mycoremediation, and plants in phytoremediation), living or dead, is employed for removing environmental pollutants from air, wate ...
for its ability to reductively
dehalogenate chlorinated
alkanes
In organic chemistry, an alkane, or paraffin (a historical trivial name that also has other meanings), is an acyclic saturated hydrocarbon. In other words, an alkane consists of hydrogen and carbon atoms arranged in a tree structure in whi ...
.
Discovery and description
''
Dehalogenimonas lykanthroporepellens'' cells are
Gram-negative
Gram-negative bacteria are bacteria that, unlike gram-positive bacteria, do not retain the crystal violet stain used in the Gram staining method of bacterial differentiation. Their defining characteristic is that their cell envelope consists ...
, non-
motile
Motility is the ability of an organism to move independently using metabolic energy. This biological concept encompasses movement at various levels, from whole organisms to cells and subcellular components.
Motility is observed in animals, mi ...
, irregular
cocci
Bacterial cellular morphologies are the shapes that are characteristic of various types of bacteria and often key to their identification. Their direct examination under a light microscope enables the classification of these bacteria (and archaea ...
that are 0.3–0.6 μm in diameter.
There is no evidence of
pathogenicity
In biology, a pathogen (, "suffering", "passion" and , "producer of"), in the oldest and broadest sense, is any organism or agent that can produce disease. A pathogen may also be referred to as an infectious agent, or simply a germ.
The term ...
.
They are
mesophiles that can grow in a temperature range of 20–34 °C with their optimum temperature range being 28–34 °C.
They grow best in
pH 7-7.5 (pH range 6–8, although it was isolated from groundwater of pH 5.1).
Growth has been observed in salt concentrations from 0.1–2% NaCl with optimum growth at ≤1%.
GC-content
In molecular biology and genetics, GC-content (or guanine-cytosine content) is the percentage of nitrogenous bases in a DNA or RNA molecule that are either guanine (G) or cytosine (C). This measure indicates the proportion of G and C bases out of ...
reported in characterization of ''D. lykanthroporellens'' is 53.8% as determined by
HPLC
High-performance liquid chromatography (HPLC), formerly referred to as high-pressure liquid chromatography, is a technique in analytical chemistry used to separate, identify, and quantify specific components in mixtures. The mixtures can origina ...
; however, as determined by genomic analysis, the GC-content is 55.04%.
''D. lyankanthroporepellens'' does not form
spores
In biology, a spore is a unit of sexual (in fungi) or asexual reproduction that may be adapted for dispersal and for survival, often for extended periods of time, in unfavourable conditions. Spores form part of the life cycles of many plant ...
.
Resistance to the antibiotics
ampicillin
Ampicillin is an antibiotic belonging to the aminopenicillin class of the penicillin family. The drug is used to prevent and treat several bacterial infections, such as respiratory tract infections, urinary tract infections, meningitis, s ...
and
vancomycin
Vancomycin is a glycopeptide antibiotic medication used to treat certain bacterial infections. It is administered intravenously ( injection into a vein) to treat complicated skin infections, bloodstream infections, endocarditis, bone an ...
has been observed.
''D. lykanthroporepellens'' is strictly
anaerobic
Anaerobic means "living, active, occurring, or existing in the absence of free oxygen", as opposed to aerobic which means "living, active, or occurring only in the presence of oxygen." Anaerobic may also refer to:
*Adhesive#Anaerobic, Anaerobic ad ...
and uses
hydrogen
Hydrogen is a chemical element; it has chemical symbol, symbol H and atomic number 1. It is the lightest and abundance of the chemical elements, most abundant chemical element in the universe, constituting about 75% of all baryon, normal matter ...
as an
electron donor
In chemistry, an electron donor is a chemical entity that transfers electrons to another compound. It is a reducing agent that, by virtue of its donating electrons, is itself oxidized in the process. An obsolete definition equated an electron dono ...
.
It has been cultured in an anaerobic basal medium at 30 °C in the dark.
It is able to reductively dehalogenate
aliphatic
In organic chemistry, hydrocarbons ( compounds composed solely of carbon and hydrogen) are divided into two classes: aromatic compounds and aliphatic compounds (; G. ''aleiphar'', fat, oil). Aliphatic compounds can be saturated (in which all ...
alkanes
In organic chemistry, an alkane, or paraffin (a historical trivial name that also has other meanings), is an acyclic saturated hydrocarbon. In other words, an alkane consists of hydrogen and carbon atoms arranged in a tree structure in whi ...
(non-aromatic alkanes) such as 1,2,3-trichloropropane (reduces it to
allyl chloride
Allyl chloride is the organic compound with the formula C H2=CHCH2 Cl. This colorless liquid is insoluble in water but soluble in common organic solvents. It is mainly converted to epichlorohydrin, used in the production of plastics. It is a c ...
which abiotically transforms in the presence of water to
allyl alcohol
Allyl alcohol (IUPAC name: prop-2-en-1-ol) is an organic compound with the structural formula . Like many alcohols, it is a water-soluble, colourless liquid. It is more toxic than typical small alcohols. Allyl alcohol is used as a precursor to ...
).
Two strains (BL-DC-9
T and BL-DC-8) were isolated from a
Superfund site
Superfund sites are Pollution, polluted locations in the United States requiring a long-term response to clean up hazardous material contaminations. Sites include landfills, mines, manufacturing facilities, processing plants where toxic waste h ...
in
Baton Rouge
Baton Rouge ( ; , ) is the List of capitals in the United States, capital city of the U.S. state of Louisiana. It had a population of 227,470 at the 2020 United States census, making it List of municipalities in Louisiana, Louisiana's second-m ...
,
Louisiana
Louisiana ( ; ; ) is a state in the Deep South and South Central regions of the United States. It borders Texas to the west, Arkansas to the north, and Mississippi to the east. Of the 50 U.S. states, it ranks 31st in area and 25 ...
in 2009 by Moe, Yan, Nobre, Costa, and Rainey—researchers at
Louisiana State University
Louisiana State University and Agricultural and Mechanical College, commonly referred to as Louisiana State University (LSU), is an American Public university, public Land-grant university, land-grant research university in Baton Rouge, Louis ...
and the
University of Coimbra
The University of Coimbra (UC; , ) is a Public university, public research university in Coimbra, Portugal. First established in Lisbon in 1290, it went through a number of relocations until moving permanently to Coimbra in 1537. The university ...
(
Coimbra
Coimbra (, also , , or ), officially the City of Coimbra (), is a city and a concelho, municipality in Portugal. The population of the municipality at the 2021 census was 140,796, in an area of .
The fourth-largest agglomerated urban area in Po ...
,
Portugal
Portugal, officially the Portuguese Republic, is a country on the Iberian Peninsula in Southwestern Europe. Featuring Cabo da Roca, the westernmost point in continental Europe, Portugal borders Spain to its north and east, with which it share ...
).
A Superfund site is an abandoned site that contains hazardous waste.
This site was contaminated with
chlorinated
In chemistry, halogenation is a chemical reaction which introduces one or more halogens into a chemical compound. Halide-containing compounds are pervasive, making this type of transformation important, e.g. in the production of polymers, drugs. ...
solvents
A solvent (from the Latin '' solvō'', "loosen, untie, solve") is a substance that dissolves a solute, resulting in a solution. A solvent is usually a liquid but can also be a solid, a gas, or a supercritical fluid. Water is a solvent for p ...
.
The genus name ''Dehalogenimonas'' reflects its ability to dehalogenate chlorinated alkanes.
The species name ''lykanthroporepellens'' comes from ''lykanthropos'' meaning werewolf and ''re-pellens'' meaning repelling.
The species name refers to the garlic smell of the bacteria when cultured.
Some folklore states that garlic can be used to repel creatures like werewolves and vampires.
Phylogeny
There are six classes within the phylum
Chloroflexota
The Chloroflexota are a phylum of bacteria containing isolates with a diversity of phenotypes, including members that are aerobic thermophiles, which use oxygen and grow well in high temperatures; anoxygenic phototrophs, which use light for ph ...
: Chloroflexia, Anaerolinea, Caldilinea,
Dehalococcoidia (previously known informally as
Dehalococcoidetes
''Dehalococcoidia'' is a class of Chloroflexota, a phylum of Bacteria. It is also known as the DHC group.
The name ''Dehalococcoidetes'' is a placeholder name given by Hugenholtz and Stackebrandt, 2004, after ''Dehalococcoides ethenogenes'', a ...
), Ktedonobacteria, and
Thermomicrobia.
''D. lykanthroporepellens'' is in the class Dehalococcoidia.
Chloroflexota consists of the green non-sulfur bacteria which are anoxygenic
phototrophs (do not produce oxygen during
photosynthesis
Photosynthesis ( ) is a system of biological processes by which photosynthetic organisms, such as most plants, algae, and cyanobacteria, convert light energy, typically from sunlight, into the chemical energy necessary to fuel their metabo ...
) that use either H
2 or H
2S as an electron donor.
However, ''D. lykanthroporepellens'' uses polychlorinated aliphatic alkanes as the electron acceptor.
Chloroflexota are the deepest branching (oldest) anoxygenic phototrophs on the
tree of life
The tree of life is a fundamental archetype in many of the world's mythology, mythological, religion, religious, and philosophy, philosophical traditions. It is closely related to the concept of the sacred tree.Giovino, Mariana (2007). ''The ...
.
Many of the species in Chloroflexota are
thermophilic
A thermophile is a type of extremophile that thrives at relatively high temperatures, between . Many thermophiles are archaea, though some of them are bacteria and fungi. Thermophilic eubacteria are suggested to have been among the earliest bact ...
however ''
Dehalogenimonas lykanthroporepellens'' is a mesophile.
The ''Oscillochloris'' (Class
Chloroflexia
The Chloroflexia are a class of bacteria in the phylum Chloroflexota. Chloroflexia are typically filamentous, and can move about through bacterial gliding. It is named after the order Chloroflexales.
Etymology
The name "Chloroflexi" is a Neo ...
) are also
mesophilic
A mesophile is an organism that grows best in moderate temperature, neither too hot nor too cold, with an optimum growth range from . The optimum growth temperature for these organisms is 37 °C (about 99 °F). The term is mainly applied ...
.
Despite this relationship, ''D. lykanthroporepellens'' is more closely related to the ''
Dehalococcoides
''Dehalococcoides'' is a genus of bacteria within class Dehalococcoidia that obtain energy via the oxidation of hydrogen and subsequent reductive dehalogenation of halocarbon, halogenated organic compounds in a mode of anaerobic respiration calle ...
'' (class Dehalococcoidia) with 90% 16S rRNA gene sequence similarity.
''D. lykanthroporepellens'' also differ from other species in the phylum Chloroflexota in that they are not
filamentous
The word filament, which is descended from Latin ''filum'' meaning "Thread (yarn), thread", is used in English for a variety of thread-like structures, including:
Astronomy
* Galaxy filament, the largest known cosmic structures in the universe
* ...
.
Metabolism
''Dehalogenimonas lykanthroporepellens'' is a
chemotroph
A chemotroph is an organism that obtains energy by the oxidation of electron donors in their environments. These molecules can be organic ( chemoorganotrophs) or inorganic ( chemolithotrophs). The chemotroph designation is in contrast to phot ...
ic organism that uses H
2 as an electron donor and polychlorinated aliphatic alkanes as an
electron acceptor
An electron acceptor is a chemical entity that accepts electrons transferred to it from another compound. Electron acceptors are oxidizing agents.
The electron accepting power of an electron acceptor is measured by its redox potential.
In the ...
.
These molecules include
1,2,3-trichloropropane,
1,2-dichloropropane,
1,1,2,2-tetrachloroethane 1,1,2,2-tetrachloroethane (TeCA), also known by the brand names Bonoform, Cellon and Westron, is an organic compound. It is colorless liquid and has a sweet odor. It is used as an industrial solvent and as a separation agent. TeCA is toxic and it ca ...
,
1,1,2-trichloroethane
1,1,2-Trichloroethane, vinyl trichloride or 1,1,2-TCA, is an organochloride solvent with the molecular formula and the structural formula . It is a colourless, sweet-smelling liquid that does not dissolve in water, but is soluble in most organic ...
, and
1,2-dichloroethane
The chemical compound 1,2-dichloroethane, commonly known as ethylene dichloride (EDC), is a chlorinated hydrocarbon. It is a colourless liquid with a chloroform-like odour. The most common use of 1,2-dichloroethane is in the production of vinyl ...
.
However, there are several chlorinated alkanes that it cannot reduce, such as
1-chloropropane and
2-chloropropane.
It uses these compounds as
electron acceptors in dihaloelimination reactions.
In dihaloelimination the electron donor (H
2 in this case) is used to remove two
halogens
The halogens () are a group (periodic table), group in the periodic table consisting of six chemically related chemical element, elements: fluorine (F), chlorine (Cl), bromine (Br), iodine (I), and the radioactive elements astatine (At) and ten ...
from adjacent carbons, forming a double bond between them. 1,2,3-trichloropropane is reduced to allyl chloride by ''D. lykanthroporepellens'', and further transformed abiotically to allyl alcohol in the presence of water (other abiotic reactions can occur).
The carbon source has not been determined for this species but other organisms within Chloroflexota use CO
2 as a carbon source.
Genome
Although two strains of ''D. lykanthroporepellens'' have been isolated and characterized, only the type strain BL-DC-9
T has had the genome sequenced. Therefore, when referring to ''D. lykanthroporepellens'' in this section, all information is only verified for BL-DC-9
T. ''D. lykanthroporepellens'' has a circular
chromosome
A chromosome is a package of DNA containing part or all of the genetic material of an organism. In most chromosomes, the very long thin DNA fibers are coated with nucleosome-forming packaging proteins; in eukaryotic cells, the most import ...
consisting of 1,686,510 bp and a
G-C content of 55.04%.
The
genome
A genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding genes, other functional regions of the genome such as ...
was
sequenced
In genetics and biochemistry, sequencing means to determine the primary structure (sometimes incorrectly called the primary sequence) of an unbranched biopolymer. Sequencing results in a symbolic linear depiction known as a sequence which succi ...
using both
Illumina and
454 sequencing.
Gene
In biology, the word gene has two meanings. The Mendelian gene is a basic unit of heredity. The molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protei ...
s were annotated using a combination of automated and manual curation.
1,771
gene
In biology, the word gene has two meanings. The Mendelian gene is a basic unit of heredity. The molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protei ...
s were predicted, in which 1,720 were protein-coding genes and 51 were RNAs.
Putative function was designated to nearly 70% of the protein-coding genes.
Interest in ''D. lykanthroporepellens'' stems from its ability to degrade polychlorinated aliphatic alkanes into nonhazardous products.
The catalysis of reductive dehalogenation of chlorinated compounds is dependent on the presence and expression of genes coding for reductive
dehalogenase enzymes.
These genes are organized in ''rdhAB'' operons, which encode the RdhA protein (reductive dehalogenase) and the RdhB protein (membrane anchor).
''D. lykanthroporepellens'' was shown to have several ''rdhA'' and ''rdhB'' genes in the chromosome.
Furthermore, ''D. lykanthroporepellens'' has a
prophage
A prophage is a bacteriophage (often shortened to "phage") genome that is integrated into the circular bacterial chromosome or exists as an extrachromosomal plasmid within the bacterial cell (biology), cell. Integration of prophages into the bacte ...
region containing 45 hypothetic proteins, which accounts for roughly 4% of the chromosome.
An additional ~4.3% of the genome of ''D. lykanthroporepellens'' is made up of
insertion sequence elements, which encode for 74 full or truncated
transposase
A transposase is any of a class of enzymes capable of binding to the end of a transposon and catalysing its movement to another part of a genome, typically by a cut-and-paste mechanism or a replicative mechanism, in a process known as transpositio ...
s.
Thus,
horizontal gene transfer
Horizontal gene transfer (HGT) or lateral gene transfer (LGT) is the movement of genetic material between organisms other than by the ("vertical") transmission of DNA from parent to offspring (reproduction). HGT is an important factor in the e ...
appears to be a potential mechanism for the adaptation of ''D. lykanthroporepellens'' to its
ecological niche
In ecology, a niche is the match of a species to a specific environmental condition.
Three variants of ecological niche are described by
It describes how an organism or population responds to the distribution of Resource (biology), resources an ...
.
Application in bioremediation
Polychlorinated aliphatic C2 and C3 alkanes are industrially important
chemical intermediates globally produced on a massive scale.
Due to spills and past inappropriate disposal methods, these chlorinated compounds are prevalent groundwater and soil contaminants throughout the US and around the world.
Bioremediation
Bioremediation broadly refers to any process wherein a biological system (typically bacteria, microalgae, fungi in mycoremediation, and plants in phytoremediation), living or dead, is employed for removing environmental pollutants from air, wate ...
approaches that rely on the action of anaerobic, reductively-dehalogenating bacteria, such as ''D. lykanthroporepellens'', have shown great promise for clean-up of chlorinated solvent-contaminated soil and
groundwater
Groundwater is the water present beneath Earth's surface in rock and Pore space in soil, soil pore spaces and in the fractures of stratum, rock formations. About 30 percent of all readily available fresh water in the world is groundwater. A unit ...
.
Using
qPCR, 16S rRNA gene sequences for ''Dehalogenimonas'' strains have been found to be at concentrations as high as 10
6 copies/ml of groundwater contaminated with high concentrations of chlorinated solvents and comprise up to nearly 19% of the total bacterial 16S rRNA gene copies.
The characterization of ''D. lykanthroporepellens'' has aided in remediation plans through better understanding of the overall process of reductive dehalogenation of chlorinated compounds present in groundwater and the diversity of organisms involved.
Due to its close relationship to ''
Dehalococcoides
''Dehalococcoides'' is a genus of bacteria within class Dehalococcoidia that obtain energy via the oxidation of hydrogen and subsequent reductive dehalogenation of halocarbon, halogenated organic compounds in a mode of anaerobic respiration calle ...
'' spp., ''D. lykanthroporepellens'' was found to be amplified by primers that at one time were believed to be specific to targeting ''Dehalococcoides'' spp.
Differentiation between the presence of ''Dehalococcoides'' spp. and ''D. lykanthroporepellens'' is important for remediation planning because ''D. lykanthroporepellens'' dehalogenates polychlorinated alkanes, but is unable to dehalogenate chlorinated ethenes like ''Dehalococcoides'' spp.
Furthermore, ''D. lykanthroporepellens'' was the first
pure culture
A microbiological culture, or microbial culture, is a method of multiplying microbial organisms by letting them reproduce in predetermined culture medium under controlled laboratory conditions. Microbial cultures are foundational and basic diag ...
isolated which could dehalogenate 1,2,3-trichloropropane (1,2,3-TCP) under anaerobic conditions.
''D. lykanthroporepellens'' has also been shown to dehalogenate 1,2-dichloroethane (1,2-DCA), 1,2-dichloropropane (1,2-DCP), and 1,1,2-trichloroethane (1,1,2-TCA) present in mixtures and at concentrations as high as 8.7, 4.0, and 3.8 mM respectively.
These findings are important because a large number of contaminated sites contain mixtures of various chlorinated solvents and/or high concentrations.
References
External links
Type strain of ''Dehalogenimonas lykanthroporepellens'' at Bac''Dive'' - the Bacterial Diversity Metadatabase
{{Taxonbar, from=Q16981240
Bioremediation
Gram-negative bacteria
Bacteria described in 2009
Dehalococcoidetes