Genome Sequences of Three Species in the Family Planctomycetaceae

Guo, Min; Han, Xifang; Jin, Tao; Zhou, Lisha; Yang, Jing; Li, Zihua; Chen, Jing; Geng, Bin; Zou, Yuanqiang; Wan, Daiwei; Li, Daocheng; Dai, Wenkui; Wang, Hui; Chen, Yanling; Ni, Peixiang; Fang, Chengxiang

doi:10.1128/jb.00639-12

Cited by 24 publications

(15 citation statements)

References 12 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Interestingly, 90% of the members of the phylum Firmicutes in SL3 were lost, while surprisingly, those of the phylum Planctomycetes were massively enriched in SL3 metagenome. The massive increase in the population of Planctomycetes may be attributed to the acidic pH observed in SL3 due to mercury contamination, heavy metal encrustation on the surface of the stalks of some members of Planctomycetes, and the detection of heavy metal resistance genes (Schmidt et al 1981;Schmidt et al 1982;Kulichevskaya et al 2008;Guo et al 2012). Though the massive reduction in the concentration of the added inorganic mercury may be connected to the sorption of Hg 2+ to iron oxides and organic matter in the soil (Selin 2009), the conversion of Hg 2+ to elemental mercury (Hg 0 ) via the activities of members of the microbial community possessing the mercury resistant mer gene may have also played a prominent role in the reduction (Gabriel and Williamson 2004).…”

Section: Discussionmentioning

confidence: 99%

“…The predominance of the genus Singulisphaera belonging to the phylum Planctomycetes in SL3 metagenome is interesting. Aside from the fact that the pH of SL3 microcosm (5.96 ± 0.25) falls within the range of optimum pH (5.1-6.2) of the species S. acidiphila (Kulichevskaya et al 2008), which perhaps contribute to the dominance of the genus and species in SL3 metagenome, the detection of heavy metal-translocating P-type ATPase in the draft genome of the species S. acidiphila (Guo et al 2012) may have played a prominent role in the predominance of these species in the mercuryamended SL3 metagenome.…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Mercury contamination imposes structural shift on the microbial community of an agricultural soil

Salam¹,

Shomope

Ummi

et al. 2019

Bull Natl Res Cent

View full text Add to dashboard Cite

Background: The purpose of this study is to use shotgun next-generation sequencing to unravel the microbial community structure of an agricultural soil, decipher the effects of mercury contamination on the structure of the microbial community and the soil physicochemistry and heavy metals content. Results: The soil physicochemistry after mercury contamination revealed a shift in soil pH from neutral (6.99 ± 0.001) to acidic (5.96 ± 0.25), a decline in moisture content to < 4 %, and a significant decrease in the concentrations of all the macronutrients and the total organic matter. Significant decrease in all the heavy metals detected in the agricultural soil was also observed in mercury inundated SL3 microcosm. Structural analysis of the metagenomes of SL1 (agricultural soil) and SL3 (mercury-contaminated agricultural soil) using Illumina shotgun next-generation sequencing revealed the loss due to mercury contamination of 54.75 % of the microbial community consisting of an archaeal domain, 11 phyla, 12 classes, 24 orders, 36 families, 59 genera, and 86 species. The dominant phylum, class, genus, and species in SL1 metagenome are Proteobacteria, Bacilli, Staphylococcus, and Sphingobacterium sp. 21; while in SL3 metagenome, Proteobacteria, Alphaproteobacteria, Singulisphaera, and Singulisphaera acidiphila were preponderant. Mercury contamination resulted in a massive upscale in the population of members of the phylum Planctomycetes and the genera Singulisphaera, Brevundimonas, Sanguibacter, Exiguobacterium, Desulfobacca, and Proteus in SL3 metagenome while it causes massive decline in the population of genera Staphylococcus and Brachybacterium. Conclusions: This study revealed that mercury contamination of the agricultural soil imposed selective pressure on the members of the microbial community, which negatively impact on their population, alter soil physicochemistry, and enriched sizable numbers of members of the community that are well adapted to mercury stress. It also reveals members of microbial community hitherto not reported to be important in mercury detoxification process.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Mercury contamination imposes structural shift on the microbial community of an agricultural soil

Salam¹,

Shomope

Ummi

et al. 2019

Bull Natl Res Cent

View full text Add to dashboard Cite

show abstract

“…The genomes of Schlesneria paludicola , Singulisphaera acidiphila , and Zavarzinella formosa were sequenced in our previously study [14].…”

Section: Methodsmentioning

confidence: 99%

Genomic Evolution of 11 Type Strains within Family Planctomycetaceae

Guo

Zhou

et al. 2014

PLoS ONE

Self Cite

View full text Add to dashboard Cite

The species in family Planctomycetaceae are ideal groups for investigating the origin of eukaryotes. Their cells are divided by a lipidic intracytoplasmic membrane and they share a number of eukaryote-like molecular characteristics. However, their genomic structures, potential abilities, and evolutionary status are still unknown. In this study, we searched for common protein families and a core genome/pan genome based on 11 sequenced species in family Planctomycetaceae. Then, we constructed phylogenetic tree based on their 832 common protein families. We also annotated the 11 genomes using the Clusters of Orthologous Groups database. Moreover, we predicted and reconstructed their core/pan metabolic pathways using the KEGG (Kyoto Encyclopedia of Genes and Genomes) orthology system. Subsequently, we identified genomic islands (GIs) and structural variations (SVs) among the five complete genomes and we specifically investigated the integration of two Planctomycetaceae plasmids in all 11 genomes. The results indicate that Planctomycetaceae species share diverse genomic variations and unique genomic characteristics, as well as have huge potential for human applications.

show abstract

“…6 and supplementary fig. S3 , Supplementary Material online) shows a progressive diversification of proteobacterial cytochrome b proteins fused with cytochrome c 1 from some of these Planctomycetes proteins that are fused with two c -type cytochromes, for example, Shlesneria cytochrome b / c subunit (accession: WP_010584211 or ZP11092181— Guo et al 2012 ), which has not been considered in recent surveys ( Dibrova et al 2013 ; ten Brink et al 2013 ). This finding supports previous structural deductions suggesting that mitochondrial cytochrome c 1 may derive from a collapsed di-heme cytochrome c ( Baymann et al 2004 ).…”

Section: The Bc 1 Complex Of Bacterimentioning

confidence: 99%

Bioenergetic Evolution in Proteobacteria and Mitochondria

Esposti

2014

Genome Biology and Evolution

View full text Add to dashboard Cite

Mitochondria are the energy-producing organelles of our cells and derive from bacterial ancestors that became endosymbionts of microorganisms from a different lineage, together with which they formed eukaryotic cells. For a long time it has remained unclear from which bacteria mitochondria actually evolved, even if these organisms in all likelihood originated from the α lineage of proteobacteria. A recent article (Degli Esposti M, et al. 2014. Evolution of mitochondria reconstructed from the energy metabolism of living bacteria. PLoS One 9:e96566) has presented novel evidence indicating that methylotrophic bacteria could be among the closest living relatives of mitochondrial ancestors. Methylotrophs are ubiquitous bacteria that live on single carbon sources such as methanol and methane; in the latter case they are called methanotrophs. In this review, I examine their possible ancestry to mitochondria within a survey of the common features that can be found in the central and terminal bioenergetic systems of proteobacteria and mitochondria. I also discuss previously overlooked information on methanotrophic bacteria, in particular their intracytoplasmic membranes resembling mitochondrial cristae and their capacity of establishing endosymbiotic relationships with invertebrate animals and archaic plants. This information appears to sustain the new idea that mitochondrial ancestors could be related to extant methanotrophic proteobacteria, a possibility that the genomes of methanotrophic endosymbionts will hopefully clarify.

show abstract

Genome Sequences of Three Species in the Family Planctomycetaceae

Cited by 24 publications

References 12 publications

Mercury contamination imposes structural shift on the microbial community of an agricultural soil

Mercury contamination imposes structural shift on the microbial community of an agricultural soil

Genomic Evolution of 11 Type Strains within Family Planctomycetaceae

Bioenergetic Evolution in Proteobacteria and Mitochondria

Contact Info

Product

Resources

About