Candidate division TM7
Encyclopedia
The candidate division TM7, is a major lineage of Bacteria, the existence of which is known solely through environmental 16S
rRNA sequences as to date no species has been grown in the lab, a requirement for taxonomy, making it a candidate phylum.
Along with Candidate divisions TM6, it was named after sequences obtained in 1994 in an environmental study of a soil sample of peat bog from near Gifhorn
, Lower Saxony
, Germany
(52°30′N 10°30′E), where 262 PCR amplified 16S rDNA fragments were cloned into a plasmid vector, named TM clones for 'Torf, Mittlere Schicht' (= peat, middle layer),.
It has been found in several environments since such as from activated sludges, water-treatment plant sludge rainforest soil, human salive , in association with sponges, cockroaches, gold mines and other environments (bar thermophilic), making it an abundant and widespread phylum. Recently, TM7 rDNA and whole-cells were detected in activated sludge with >99.7% identity to a human skin TM7 and 98.6% identity to the human oral TM7a , suggesting metabolically active TM7 in environmental sites may serve as model organisms to better understand the role TM7 play in human health.
cell envelopes and several morphotypes: a sheathed filament (abundant), a rod occurring in short chains, a thick filament and cocci; the former may be the cause of Eikelboom type 0041 (bulking problems of activated sludges).
The majority of bacterial phyla
are Gram-negative diderms, whereas only the Firmicutes
, the Actinobacteria
and Chloroflexi
are monoderms. Candidate phylum TM7 is in fact a close relative of the Chloroflexi
.
Using a polycarbonate membrane as a growth support and soil extract as the substrate, microcolonies of this clade were grown consisting of long filamentous rods up to 15 μm long with less than 50 cells or short rods with several hundred cells per colony, after 10 days incubation.
Thanks to a microfluidic chip allowing the isolation and amplification of the genome of a single cell, the genome of 3 long filament morphology cells with identical 16S rRNA were sequenced to create a draft sequence of the genome confirming some previously ascertained properties, elucidating some of its metabolic capabilities, revealing novel genes and hinting to potential pathogenic abilities.
Over 50 different phylotypes have been identified and it has a relatively modest intradivision 16S rDNA sequence divergence of 17%, which ranges from 13 to 33%. An interactive phylogenetic tree of TM7 , built using jsPhyloSVG , allows for quick access to GenBank sequences and distance matrix calculations between tree branches.
Stable isotope probing studies have found that some members of this phylum can degrade toluene.
16S ribosomal RNA
16S ribosomal RNA is a component of the 30S subunit of prokaryotic ribosomes. It is approximately 1.5kb in length...
rRNA sequences as to date no species has been grown in the lab, a requirement for taxonomy, making it a candidate phylum.
Along with Candidate divisions TM6, it was named after sequences obtained in 1994 in an environmental study of a soil sample of peat bog from near Gifhorn
Gifhorn
Gifhorn is a town and capital of the district Gifhorn in the east of Lower Saxony, Germany. It has a population of about 42,000 and is mainly influenced by the small distance to the industrial and commercially important cities nearby, Brunswick and Wolfsburg...
, Lower Saxony
Lower Saxony
Lower Saxony is a German state situated in north-western Germany and is second in area and fourth in population among the sixteen states of Germany...
, Germany
Germany
Germany , officially the Federal Republic of Germany , is a federal parliamentary republic in Europe. The country consists of 16 states while the capital and largest city is Berlin. Germany covers an area of 357,021 km2 and has a largely temperate seasonal climate...
(52°30′N 10°30′E), where 262 PCR amplified 16S rDNA fragments were cloned into a plasmid vector, named TM clones for 'Torf, Mittlere Schicht' (= peat, middle layer),.
It has been found in several environments since such as from activated sludges, water-treatment plant sludge rainforest soil, human salive , in association with sponges, cockroaches, gold mines and other environments (bar thermophilic), making it an abundant and widespread phylum. Recently, TM7 rDNA and whole-cells were detected in activated sludge with >99.7% identity to a human skin TM7 and 98.6% identity to the human oral TM7a , suggesting metabolically active TM7 in environmental sites may serve as model organisms to better understand the role TM7 play in human health.
Properties
Species singled out with TM7 specific FISH probes form a bioreactor sludge revealed the presence of a gram-positiveGram-positive
Gram-positive bacteria are those that are stained dark blue or violet by Gram staining. This is in contrast to Gram-negative bacteria, which cannot retain the crystal violet stain, instead taking up the counterstain and appearing red or pink...
cell envelopes and several morphotypes: a sheathed filament (abundant), a rod occurring in short chains, a thick filament and cocci; the former may be the cause of Eikelboom type 0041 (bulking problems of activated sludges).
The majority of bacterial phyla
Bacterial phyla
The bacterial phyla are the major lineages of the domain Bacteria.In the scientific classification established by Carl von Linné, each bacterial strain has to be assigned to a species , which is a lower level of a hierarchy of ranks...
are Gram-negative diderms, whereas only the Firmicutes
Firmicutes
The Firmicutes are a phylum of bacteria, most of which have Gram-positive cell wall structure. A few, however, such as Megasphaera, Pectinatus, Selenomonas and Zymophilus, have a porous pseudo-outer-membrane that causes them to stain Gram-negative...
, the Actinobacteria
Actinobacteria
Actinobacteria are a group of Gram-positive bacteria with high guanine and cytosine content. They can be terrestrial or aquatic. Actinobacteria is one of the dominant phyla of the bacteria....
and Chloroflexi
Chloroflexi
Chloroflexi is one of four classes of bacteria in the phylum Chloroflexi, known as filamentous green non-sulfur bacteria. They produce energy from light and are named for their green pigment, usually found in photosynthetic bodies called chlorosomes....
are monoderms. Candidate phylum TM7 is in fact a close relative of the Chloroflexi
Chloroflexi
Chloroflexi is one of four classes of bacteria in the phylum Chloroflexi, known as filamentous green non-sulfur bacteria. They produce energy from light and are named for their green pigment, usually found in photosynthetic bodies called chlorosomes....
.
Using a polycarbonate membrane as a growth support and soil extract as the substrate, microcolonies of this clade were grown consisting of long filamentous rods up to 15 μm long with less than 50 cells or short rods with several hundred cells per colony, after 10 days incubation.
Thanks to a microfluidic chip allowing the isolation and amplification of the genome of a single cell, the genome of 3 long filament morphology cells with identical 16S rRNA were sequenced to create a draft sequence of the genome confirming some previously ascertained properties, elucidating some of its metabolic capabilities, revealing novel genes and hinting to potential pathogenic abilities.
Over 50 different phylotypes have been identified and it has a relatively modest intradivision 16S rDNA sequence divergence of 17%, which ranges from 13 to 33%. An interactive phylogenetic tree of TM7 , built using jsPhyloSVG , allows for quick access to GenBank sequences and distance matrix calculations between tree branches.
Stable isotope probing studies have found that some members of this phylum can degrade toluene.