Pelodictyon phaeoclathratiforme BU-1

Gram-negativeBacilliNon-motileAnaerobic

Kingdom

Pseudomonadati

Phylum

Chlorobiota

Class

Chlorobiia

Order

Chlorobiales

Family

Chlorobiaceae

Genus

Pelodictyon

Description

Pelodictyon phaeoclathhratiforme is a green sulfur bacterium frequently observed in stratified freshwater lakes where light reaches sulfide-containing water layers; it frequently represents the dominant green sulfur bacterium in this habitat. BU 1, the type strain, was isolated from water samples of Buchensee, Germany in 1989. This lake is meromictic, that is the surface and deep waters do not mix; BU 1 was isolated from 9 m deep water. Like all green sulfur bacteria, this species is strictly anaerobic and obligately phototrophic. Photosynthetic pigments comprise mainly bacteriochlorophyll e and isorenieratene/b -isorenieratene plus small amounts of bacteriochlorophyll a. It is actually a brown color. P.phaeoclathratiforme forms net-like microcolonies and has intracellular gas vesicles. Ternary fission, which leads to the formation of ring-shaped and branched colonies, is observed at growth-limiting light intensities. Gas vesicles are proteinaceous hollow rigid structures which occur only in prokaryotic cells which are impermeable to liquid but permeable to gases. Because of their gas content, gas vesicles decrease the density of the cell and may provide neutral or even positive buoyancy if present in sufficient amounts. Like ternary fission, gas vesicles are exclusively observed in cells grown at light intensities below 5 umol photons m-2 s-1. Unlike some cyanobacteria, cells of P.phaeoclathratiforme do not attain positive buoyancy and thus are unlikely to rise to the lake surface and to leave their habitat. The capability of buoyant density regulation offers one explanation for the dominance of P.phaeoclathratiforme in many stratified lakes (modified from http://genome.jgi-psf.org/finished_microbes/pelph/pelph.home.html). (HAMAP: PELPB)

Taxonomy

KingdomPseudomonadati
PhylumChlorobiota
ClassChlorobiia
OrderChlorobiales
FamilyChlorobiaceae
GenusPelodictyon
SpeciesPelodictyon phaeoclathratiforme
StrainBU-1

Profile

Physiology
Gram staining propertiesNegative
ShapeBacilli
MobilityNo
Flagellar presenceYes
Number of membranes2
Image of Pelodictyon phaeoclathratiforme BU-1
AI-generated image based on bacteria physiology
Ecology, Host, and Life Cycle
Oxygen requirementsAnaerobic
Optimal temperature15
Temperature rangeMesophilic
HabitatMultiple
Biotic relationshipFree living
Host(s)Not Available
Cell arrangementSingles
SporulationNonsporulating
Energy sourcePhototroph- Photosynthetic
PathogenicityNot Available

Genome Summary

Pelodictyon phaeoclathratiforme BU-1


Gene Summary

Adenine Count

788810 bp

Thymine Count

778332 bp

Guanine Count

720469 bp

Cytosine Count

730627 bp

Genome Length

3018238 bp

Protein-coding Genes

2861 genes

Non-Coding Genes

61 genes

# of Chromosomes/Plasmids

1

Genes

NameLocus TagUniProtStrandCoordinatesMolecular Weight
chromosomal replication initiator protein dnaaPPHA_RS00005Not Available+1 - 146455084.1
dna polymerase iii subunit betaPPHA_RS00010Not Available+1746 - 287041979.6
dna replication/repair protein recfPPHA_RS00015Not Available+2931 - 399240413.7
duf721 domain-containing proteinPPHA_RS00020Not Available+3995 - 428811163.6
fpra family a-type flavoproteinPPHA_RS00025Not Available-4331 - 555445862.0
dna polymerase domain-containing proteinPPHA_RS00030Not Available-5681 - 807191527.9
trna uridine-5-carboxymethylaminomethyl(34) synthesis enzyme mnmgPPHA_RS00035Not Available-8136 - 1000168326.5
thiosulfate oxidation carrier protein soxyPPHA_RS00040Not Available+10466 - 1090316087.5
thiosulfate oxidation carrier complex protein soxzPPHA_RS00045Not Available+10928 - 1123611280.4
c-type cytochromePPHA_RS00050Not Available+11297 - 1167113045.7

Displaying genes 1 – 10 of 2922 in total

Pathways

0 pathways

No pathways found

No metabolic pathways have been associated with this bacterium yet.

Metabolites

1647 records
Metabolite IDMetabolite nameStructureCAS number
BASm0000217alpha-ribazoleC14H18N2O4Chemical structure of alpha-ribazoleNot available
Average278.3037Da
Monoisotopic278.126657074Da
BASm00002502,5-didehydro-D-gluconateC6H7O7Chemical structure of 2,5-didehydro-D-gluconate53736-12-2
Average191.1156Da
Monoisotopic191.019177578Da
BASm00002512-dehydropantoateC6H9O4Chemical structure of 2-dehydropantoateNot available
Average145.1333Da
Monoisotopic145.050083776Da
BASm00002532-oxopent-4-enoateC5H5O3Chemical structure of 2-oxopent-4-enoateNot available
Average113.093Da
Monoisotopic113.024417601Da
BASm00002603alpha,7alpha-dihydroxy-12-oxo-5beta-cholanateC24H37O5Chemical structure of 3alpha,7alpha-dihydroxy-12-oxo-5beta-cholanateNot available
Average405.556Da
Monoisotopic405.264647871Da
BASm0000377(S)-malateC4H4O5Chemical structure of (S)-malateNot available
Average132.0716Da
Monoisotopic132.005873238Da
BASm0000387(6R)-5,10-methylene-5,6,7,8-tetrahydrofolateC20H21N7O6Chemical structure of (6R)-5,10-methylene-5,6,7,8-tetrahydrofolateNot available
Average455.432Da
Monoisotopic455.1564286Da
BASm0000553biphenyl-2,3-diolC12H10O2Chemical structure of biphenyl-2,3-diolNot available
Average186.2066Da
Monoisotopic186.0680796Da
BASm0000592(S)-1-phenylethanolC8H10OChemical structure of (S)-1-phenylethanolNot available
Average122.1644Da
Monoisotopic122.0731649Da
BASm0000989GlycerolC3H8O3Chemical structure of Glycerol56-81-5
Average92.0938Da
Monoisotopic92.04734412Da

Displaying 1–10 of 1647 metabolites