scholarly journals Marseilleviruses: An Update in 2021

2021 ◽  
Vol 12 ◽  
Author(s):  
Dehia Sahmi-Bounsiar ◽  
Clara Rolland ◽  
Sarah Aherfi ◽  
Hadjer Boudjemaa ◽  
Anthony Levasseur ◽  
...  
Keyword(s):  
Deep Sea ◽  
Environmental Water ◽  
Comparative Genomic ◽  
Acanthamoeba Polyphaga ◽  
Deep Sea Sediment ◽  
Worldwide Distribution ◽  
The Family ◽  
Genomic Analyses ◽  
Giant Viruses ◽  
Rats And Mice

The family Marseilleviridae was the second family of giant viruses that was described in 2013, after the family Mimiviridae. Marseillevirus marseillevirus, isolated in 2007 by coculture on Acanthamoeba polyphaga, is the prototype member of this family. Afterward, the worldwide distribution of marseilleviruses was revealed through their isolation from samples of various types and sources. Thus, 62 were isolated from environmental water, one from soil, one from a dipteran, one from mussels, and two from asymptomatic humans, which led to the description of 67 marseillevirus isolates, including 21 by the IHU Méditerranée Infection in France. Recently, five marseillevirus genomes were assembled from deep sea sediment in Norway. Isolated marseilleviruses have ≈250 nm long icosahedral capsids and 348–404 kilobase long mosaic genomes that encode 386–545 predicted proteins. Comparative genomic analyses indicate that the family Marseilleviridae includes five lineages and possesses a pangenome composed of 3,082 clusters of genes. The detection of marseilleviruses in both symptomatic and asymptomatic humans in stool, blood, and lymph nodes, and an up-to-30-day persistence of marseillevirus in rats and mice, raise questions concerning their possible clinical significance that are still under investigation.

scholarly journals Marinithermofilum abyssi gen. nov., sp. nov. and Desmospora profundinema sp. nov., isolated from a deep-sea sediment, and emended description of the genus Desmospora Yassin et al. 2009

2015 ◽  
Vol 65 (Pt_8) ◽  
pp. 2622-2629 ◽  
Author(s):  
Yi Zhang ◽  
Jie Li ◽  
Xinpeng Tian ◽  
Si Zhang
Keyword(s):  
Fatty Acids ◽  
Deep Sea ◽  
Type Strain ◽  
Novel Species ◽  
Polar Lipids ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Deep Sea Sediment ◽  
The Family ◽  
Diamino Acid

Two novel filamentous bacteria, strains SCSIO 11157T and SCSIO 11154T, were isolated from a deep-sea sediment sample. Strain SCSIO 11157T grew optimally at 55–60 °C, while strain SCSIO 11154T grew optimally at 40 °C. Both strains produced aerial and substrate mycelia. Phylogenetic analysis of the 16S rRNA gene sequences of strains SCSIO 11157T and SCSIO 11154T showed that the isolates were affiliated to the family Thermoactinomycetaceae. The two isolates contained ll-diaminopimelic acid as the cell-wall diamino acid, and did not have diagnostic sugars. The major polar lipids of strain SCSIO 11157T were diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine and phosphatidylglycerol, and the major polar lipids of SCSIO 11154T were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The predominant menaquinone of both strains was MK-7. The major cellular fatty acids of strain SCSIO 11157T were iso-C15 : 0, C18 : 1ω9c and iso-C17 : 0, and strain SCSIO 11154T contained iso-C15 : 0 and iso-C17 : 0 as major fatty acids. The DNA G+C contents of strains SCSIO 11157T and SCSIO 11154T were 54.2 and 51.8 mol %, respectively. On the basis of its phenotypic and phylogenetic properties, strain SCSIO 11157T represents a novel species in the new genus, for which we propose the name Marinithermofilum abyssi gen. nov., sp. nov. The type strain of Marinithermofilum abyssi is SCSIO 11157T ( = CGMCC 1.15179T = NBRC 109939T). Strain SCSIO 11154T represents a novel species of the genus Desmospora, for which we propose the name Desmospora profundinema sp. nov. The type strain is SCSIO 11154T ( = DSM 45903T = NBRC 109626T).

Complete plastid genome sequences of three tropical Alseodaphne trees in the family Lauraceae

Holzforschung ◽  
2018 ◽  
Vol 72 (4) ◽  
pp. 337-345 ◽  
Author(s):  
Yu Song ◽  
Xin Yao ◽  
Bing Liu ◽  
Yunhong Tan ◽  
Richard T. Corlett
Keyword(s):  
Type Species ◽  
Phylogenetic Analyses ◽  
Comparative Genomic ◽  
Inverted Repeats ◽  
Genome Sequences ◽  
Complete Chloroplast Genome ◽  
Tropical Asia ◽  
Length Difference ◽  
The Family ◽  
Genomic Analyses

AbstractAlseodaphneis a genus of timber trees (ca. 40 spp.) belonging to thePerseagroup of the Lauraceae. It is widely distributed in tropical Asia, but is often confused withDehaasiaandNothaphoebe, and the systematics of the genus is unclear. Here, the complete chloroplast genome sequences ofA. semecarpifoliawill be reported, the type species ofAlseodaphne, and two China-endemic species,A. gracilisandA. huanglianshanensis. The three plastomes were 153 051 bp, 153 099 bp and 153 070 bp, respectively. Comparative genomic analyses indicate that the threeAlseodaphneplastomes have similar genome size and those are very different with previously published plastomes of Lauraceae in length. The length difference is directly caused by inverted repeats expansion/contraction. Four highly variable loci includingpsbD-trnM,ndhF-rpl32,rpl32-trnLandycf1among the threeAlseodaphnespecies were identified as useful plastid candidate barcodes forAlseodaphneand Lauraceae species. Phylogenetic analyses based on 12 complete plastomes of Lauraceae species confirm a monophyleticPerseagroup comprising species ofAlseodaphne,Phoebe,PerseaandMachilus.

scholarly journals Comparative genomics on cultivated and uncultivated, freshwater and marine Candidatus Manganitrophaceae species implies their worldwide reach in manganese chemolithoautotrophy

2021 ◽  
Author(s):  
Hang Yu ◽  
Grayson L Chadwick ◽  
Usha F Lingappa ◽  
Jared Renton Leadbetter
Keyword(s):  
South Africa ◽  
Carbon Fixation ◽  
Comparative Genomic ◽  
Santa Barbara ◽  
Manganese Oxidation ◽  
Species Phylogeny ◽  
Core Set ◽  
The Family ◽  
Genomic Analyses ◽  
A New Species

Chemolithoautotrophic manganese oxidation has long been theorized, but only recently demonstrated in a bacterial co-culture. The majority member of the co-culture, Candidatus Manganitrophus noduliformans, is a distinct but not yet isolated lineage in the phylum Nitrospirota (Nitrospirae). Here, we established two additional MnCO3-oxidizing cultures using inocula from Santa Barbara (USA) and Boetsap (South Africa). Both cultures were dominated by strains of a new species, designated Candidatus Manganitrophus morganii. The next abundant members differed in the available cultures, suggesting that while Ca. Manganitrophus species have not been isolated in pure culture, they may not require a specific syntrophic relationship with another species. Phylogeny of cultivated Ca. Manganitrophus and related metagenome-assembled genomes revealed a coherent taxonomic family, Candidatus Manganitrophaceae, from both freshwater and marine environments and distributed globally. Comparative genomic analyses support this family being Mn(II)-oxidizing chemolithoautotrophs. Among the 895 shared genes were a subset of those hypothesized for Mn(II) oxidation (Cyc2 and PCC_1) and oxygen reduction (TO_1 and TO_2) that could facilitate Mn(II) lithotrophy. An unusual, plausibly reverse Complex 1 containing 2 additional pumping subunits was also shared by the family, as were genes for the reverse TCA carbon fixation cycle, which could enable Mn(II) autotrophy. All members of the family lacked genes for nitrification found in Nitrospira species. The results suggest that Ca. Manganitrophaceae share a core set of candidate genes for the newly discovered manganese dependent chemolithoautotrophic lifestyle, and likely have a broad, global distribution.

scholarly journals Genome-based taxonomic framework for the class Negativicutes: division of the class Negativicutes into the orders Selenomonadales emend., Acidaminococcales ord. nov. and Veillonellales ord. nov.

2015 ◽  
Vol 65 (Pt_9) ◽  
pp. 3203-3215 ◽  
Author(s):  
Chantal Campbell ◽  
Mobolaji Adeolu ◽  
Radhey S. Gupta
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Trees ◽  
Core Protein ◽  
Phylogenetic Analyses ◽  
Comparative Genomic ◽  
Rrna Gene ◽  
Conserved Signature Indels ◽  
The Family ◽  
Genomic Analyses

The class Negativicutes is currently divided into one order and two families on the basis of 16S rRNA gene sequence phylogenies. We report here comprehensive comparative genomic analyses of the sequenced members of the class Negativicutes to demarcate its different evolutionary groups in molecular terms, independently of phylogenetic trees. Our comparative genomic analyses have identified 14 conserved signature indels (CSIs) and 48 conserved signature proteins (CSPs) that either are specific for the entire class or differentiate four main groups within the class. Two CSIs and nine CSPs are shared uniquely by all or most members of the class Negativicutes, distinguishing this class from all other sequenced members of the phylum Firmicutes. Four other CSIs and six CSPs were specific characteristics of the family Acidaminococcaceae, two CSIs and four CSPs were uniquely present in the family Veillonellaceae, six CSIs and eight CSPs were found only in Selenomonas and related genera, and 17 CSPs were identified uniquely in Sporomusa and related genera. Four additional CSPs support a pairing of the groups containing the genera Selenomonas and Sporomusa. We also report detailed phylogenetic analyses for the Negativicutes based on core protein sequences and 16S rRNA gene sequences, which strongly support the four main groups identified by CSIs and by CSPs. Based on the results from different lines of investigation, we propose a division of the class Negativicutes into an emended order Selenomonadales containing the new families Selenomonadaceae fam. nov. and Sporomusaceae fam. nov. and two new orders, Acidaminococcales ord. nov. and Veillonellales ord. nov., respectively containing the families Acidaminococcaceae and Veillonellaceae.

Verrucosispora sediminis sp. nov., a cyclodipeptide-producing actinomycete from deep-sea sediment

2010 ◽  
Vol 60 (8) ◽  
pp. 1807-1812 ◽  
Author(s):  
Huan-Qin Dai ◽  
Jian Wang ◽  
Yu-Hua Xin ◽  
Gang Pei ◽  
Shu-Kun Tang ◽  
...  
Keyword(s):  
Deep Sea ◽  
Phylogenetic Trees ◽  
Complete Sequence ◽  
Culture Broth ◽  
Rrna Gene ◽  
The Novel ◽  
Deep Sea Sediment ◽  
Phenotypic Differences ◽  
Distinct Cluster ◽  
The Family

An actinomycete, designated MS426T, the culture broth of which showed potent antimicrobial activity, was isolated from a deep-sea sediment sample of the South China Sea. An almost-complete sequence of the 16S rRNA gene of strain MS426T was determined and aligned with those of representatives of the family Micromonosporaceae available in public databases. Phylogenetic trees were inferred by using three algorithms. Strain MS426T formed a branch adjacent to Verrucosispora lutea YIM 013T in a distinct cluster occupied only by strains of the genus Verrucosispora. Strain MS426T was distinguishable from the type strains of the two described Verrucosispora species by using a combination of chemical and morphological markers and by DNA–DNA relatedness. On the basis of these genotypic and phenotypic differences, the novel antimicrobial strain with pharmaceutical potential represents a novel species, for which the name Verrucosispora sediminis sp. nov. is proposed. The type strain is MS426T (=CGMCC 4.3550T =JCM 15670T).

Chryseobacterium profundimaris sp. nov., a new member of the family Flavobacteriaceae isolated from deep-sea sediment

2015 ◽  
Vol 107 (4) ◽  
pp. 979-989 ◽  
Author(s):  
Lin Xu ◽  
Ying-Yi Huo ◽  
Zheng-Yang Li ◽  
Chun-Sheng Wang ◽  
Aharon Oren ◽  
...  
Keyword(s):  
Deep Sea ◽  
Deep Sea Sediment ◽  
The Family

scholarly journals Brevirhabdus pacifica gen. nov., sp. nov., isolated from deep-sea sediment in a hydrothermal vent field

2015 ◽  
Vol 65 (Pt_10) ◽  
pp. 3645-3651 ◽  
Author(s):  
Yue-Hong Wu ◽  
Lin Xu ◽  
Peng Zhou ◽  
Chun-Sheng Wang ◽  
Aharon Oren ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Deep Sea ◽  
Hydrothermal Vent ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Deep Sea Sediment ◽  
The Family ◽  
Hydrothermal Vent Field

A Gram-stain-negative, motile, aerobic bacterial strain, designated 22DY15T, was isolated from a deep-sea sediment sample collected from a hydrothermal vent field located in the East Pacific Rise. The isolate was a short rod with a single flagellum and was positive for catalase and oxidase activities. Q-10 was the predominant respiratory quinone. The major polar lipids consisted of phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphoglycolipid, one aminolipid and three unidentified phospholipids. The principal fatty acid (>70 %) was C18 : 1ω7c. The genomic DNA G+C content was 64.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 22DY15T represents a distinct lineage within the family Rhodobacteraceae. The closest relatives were species of the genera Aliiroseovarius (93.3–96.0 % 16S rRNA gene sequence similarity), Sulfitobacter (94.0–96.0 %) and Loktanella (92.0–95.9 %). Differential phenotypic properties, together with phylogenetic and genetic distinctiveness, revealed that strain 22DY15T could be differentiated from its most closely related genera. Therefore, it is proposed that strain 22DY15T represents a novel species in a new genus of the family Rhodobacteraceae, for which the name Brevirhabdus pacifica gen. nov., sp. nov. is proposed. The type strain of the type species is 22DY15T ( = JCM 19489T = DSM 27767T = CGMCC 1.12416T = MCCC 1K00276T).

scholarly journals Comparative Genomic Insights Into the Taxonomic Classification, Diversity, and Secondary Metabolic Potentials of Kitasatospora, a Genus Closely Related to Streptomyces

2021 ◽  
Vol 12 ◽  
Author(s):  
Yisong Li ◽  
Meng Wang ◽  
Zhong-Zhi Sun ◽  
Bin-Bin Xie
Keyword(s):  
Secondary Metabolism ◽  
Comparative Genomic ◽  
Metabolic Potential ◽  
Genomic Features ◽  
Separate Genus ◽  
The Family ◽  
Genomic Analyses ◽  
Genome Content ◽  
Phylogenomic Analyses ◽  
Close Relatives

While the genus Streptomyces (family Streptomycetaceae) has been studied as a model for bacterial secondary metabolism and genetics, its close relatives have been less studied. The genus Kitasatospora is the second largest genus in the family Streptomycetaceae. However, its taxonomic position within the family remains under debate and the secondary metabolic potential remains largely unclear. Here, we performed systematic comparative genomic and phylogenomic analyses of Kitasatospora. Firstly, the three genera within the family Streptomycetaceae (Kitasatospora, Streptomyces, and Streptacidiphilus) showed common genomic features, including high G + C contents, high secondary metabolic potentials, and high recombination frequencies. Secondly, phylogenomic and comparative genomic analyses revealed phylogenetic distinctions and genome content differences among these three genera, supporting Kitasatospora as a separate genus within the family. Lastly, the pan-genome analysis revealed extensive genetic diversity within the genus Kitasatospora, while functional annotation and genome content comparison suggested genomic differentiation among lineages. This study provided new insights into genomic characteristics of the genus Kitasatospora, and also uncovered its previously underestimated and complex secondary metabolism.

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