Genetics


Publications
355

Candidatus Alkanophaga archaea from Guaymas Basin hydrothermal vent sediment oxidize petroleum alkanes

Citation
Zehnle et al. (2023). Nature Microbiology 8 (7)
Names
Ca. Alkanophaga Ca. Syntrophoarchaeum Ca. Thermodesulfobacterium syntrophicum
Abstract
AbstractMethanogenic and methanotrophic archaea produce and consume the greenhouse gas methane, respectively, using the reversible enzyme methyl-coenzyme M reductase (Mcr). Recently, Mcr variants that can activate multicarbon alkanes have been recovered from archaeal enrichment cultures. These enzymes, called alkyl-coenzyme M reductase (Acrs), are widespread in the environment but remain poorly understood. Here we produced anoxic cultures degrading mid-chain petroleum n-alkanes between pentane (

Genome Sequence of a Clinical Isolate of the Human Pathogenic Strain “ Candidatus Borrelia fainii” Qtaro

Citation
Itokawa et al. (2023). Microbiology Resource Announcements 12 (5)
Names
“Borrelia fainii”
Abstract
We report sequences of the complete linear chromosome and five linear plasmids of the relapsing fever spirochete “ Candidatus Borrelia fainii” Qtaro. The chromosome sequence of 951,861 bp and the 243,291 bp of plasmid sequences were predicted to contain 852 and 239 protein-coding genes, respectively. The predicted total GC content was 28.4%.

Complete Genome of “ Candidatus Phytoplasma rubi” RS, a Phytopathogenic Bacterium Associated with Rubus Stunt Disease

Citation
Duckeck et al. (2023). Microbiology Resource Announcements 12 (5)
Names
Ca. Phytoplasma rubi
Abstract
The phytoplasma “ Candidatus Phytoplasma rubi” is associated with Rubus stunt disease. The complete genome was determined by assembling Oxford Nanopore Technologies system-derived long reads, with short-read polishing with Illumina reads. The genome of strain RS, from Germany, is organized in one circular chromosome with a length of 762 kb.

Metagenomic Discovery of “ Candidatus Parvarchaeales”-Related Lineages Sheds Light on Adaptation and Diversification from Neutral-Thermal to Acidic-Mesothermal Environments

Citation
Rao et al. (2023). mSystems 8 (2)
Names
“Jingweiarchaeaceae” “Rehaiarchaeum fermentans” “Parvarchaeales” “Haiyanarchaeum thermophilum” “Jingweiarchaeum tengchongense” “Parvarchaeum tengchongense” “Haiyanarchaeum” “Jingweiarchaeum” “Haiyanarchaeaceae” “Jingweiarchaeales” “Rehaiarchaeum”
Abstract
“ Candidatus Parvarchaeales” microbes may represent a lineage uniquely distributed in extreme environments such as AMD and hot springs. However, little is known about the strategies and processes of how they adapted to these extreme environments.

Metabolic Versatility of the FamilyHalieaceaeRevealed by the Genomics of Novel Cultured Isolates

Citation
Li et al. (2023). Microbiology Spectrum 11 (2)
Names
Litorirhabdus singularis Ts Marimicrobium litorale Litorirhabdus Seongchinamella marina Paraluminiphilus aquimaris Ts Paraluminiphilus
Abstract
Although the familyHalieaceae(OM60/NOR5 clade) is an abundant and cosmopolitan clade widely found in coastal seas and involved in interactions with phytoplankton, a limited number of cultured isolates are available. In this study, we isolated six pure culturedHalieaceaestrains from coastal seawaters and performed a comparative physiological and genomic analysis to give insights into the phylogeny and metabolic potential of this family.

Environmental Factors Affect the Bacterial Community in Diaphorina citri , an Important Vector of “ Candidatus Liberibacter asiaticus”

Citation
Jiang et al. (2023). Microbiology Spectrum 11 (2)
Names
Ca. Liberibacter asiaticus
Abstract
The Asian citrus psyllid (ACP) is an important vector of the HLB pathogen, which is a major threat to citrus production around the world. Bacterial communities harbored by insects could be affected by different environmental factors.

Candidatus Phytoplasma ziziphi encodes non-classically secreted proteins that suppress hypersensitive cell death response in Nicotiana benthamiana

Citation
Gao et al. (2023). Phytopathology Research 5 (1)
Names
Ca. Phytoplasma ziziphi
Abstract
AbstractIncreasing evidence is proving the biological significance of the phytoplasma-secreted proteins. However, besides a few Sec-dependent secretory proteins, no other phytoplasma-secreted proteins have been reported yet. Candidatus Phytoplasma ziziphi is a phytoplasma that causes witches’-broom, a devastating jujube disease prevalent in east Asia. In this study, using the SecretomeP server coupled with an Escherichia coli-based alkaline phosphatase assay, we identified 25 non-classically sec

Draft Genome Sequences of Three “ Candidatus Symbiopectobacterium” Isolates Collected from Potato Tubers Grown in New Zealand

Citation
Nunes Leite et al. (2023). Microbiology Resource Announcements 12 (3)
Names
Ca. Symbiopectobacterium
Abstract
The draft genome sequences of three “ Candidatus Symbiopectobacterium” isolates that were collected from New Zealand-grown potato tubers represent the first report of this proposed taxon in the Southern Hemisphere. Their symbiosis with insects and nematodes and their presence on plants may lead to new strategies for pest control and crop management.

Hyperactive nanobacteria with host-dependent traits pervade Omnitrophota

Citation
Seymour et al. (2023). Nature Microbiology 8 (4)
Names
“Multiplicimicrobium” “Fredricksoniimonas aquilentivivens” “Amyimicrobium” “Omnitrophia” “Omnitrophales” “Omnitrophaceae” “Pluralincolimonas frigidipaludosa” “Fontincolimonas calida” “Profunditerraquicola sanfordiae” “Fredricksoniimonas borealis” “Duberdicusella sinuisediminis” “Phelpsiimicrobium noxiivivens” “Velesiimonas alkalicola” “Aquitaenariimonas noxiae” “Aquincolibacterium aerophilum” “Aquincolibacterium lacustre” “Multiplicimicrobium inquinatum” “Pegaeibacterium caenilacustre” “Danuiimicrobium aquiferis” “Taenariivivens baikalensis” “Aquivivens invisus” “Abzuiibacterium crystallinum” “Makaraimicrobium” “Aquincolibacterium” “Pegaeibacterium” “Aquivivens” “Duberdicusellaceae” “Pluralincolimonadaceae” “Taenariiviventaceae” “Aquincolibacteriaceae” “Aquiviventaceae” “Duberdicusellales” “Ghiorseimicrobiales” “Aquitaenariimonadales” “Velesiimonadales” “Aquiviventales” “Undivivens” “Taenaricolales” “Undivivens industriae” “Sherwoodlollariibacterium unditelluris” “Sherwoodlollariibacterium” “Fontincolimonas” “Aquitaenariimonadaceae” “Profunditerraquicola” “Profunditerraquicolaceae” “Amyimicrobium silvilacustre” “Ghiorseimicrobiaceae” “Ghiorseimicrobium” “Ghiorseimicrobium undicola” “Fredricksoniimonadaceae” “Fredricksoniimonas” “Phelpsiimicrobium” “Pluralincolimonadales” “Duberdicusella” “Velesiimonadaceae” “Velesiimonas” “Taenaricolaceae” “Taenaricola” “Taenaricola geyseris” “Pluralincolimonas” “Aquitaenariimonas” “Makaraimicrobium thalassicum” “Taenariivivens” “Danuiimicrobiaceae” “Danuiimicrobium” “Aquiviventia” “Abzuiibacterium” “Abzuiibacteriaceae” Omnitrophus Omnitrophus fodinae Ts Omnitrophota
Abstract
AbstractCandidate bacterial phylum Omnitrophota has not been isolated and is poorly understood. We analysed 72 newly sequenced and 349 existing Omnitrophota genomes representing 6 classes and 276 species, along with Earth Microbiome Project data to evaluate habitat, metabolic traits and lifestyles. We applied fluorescence-activated cell sorting and differential size filtration, and showed that most Omnitrophota are ultra-small (~0.2 μm) cells that are found in water, sediments and soils. Omnitro

A novel and diverse group of Candidatus Patescibacteria from bathypelagic Lake Baikal revealed through long-read metagenomics

Citation
Haro-Moreno et al. (2023). Environmental Microbiome 18 (1)
Names
Ca. Patescibacteria
Abstract
Abstract Background Lake Baikal, the world’s deepest freshwater lake, contains important numbers of Candidatus Patescibacteria (formerly CPR) in its deepest reaches. However, previously obtained CPR metagenome-assembled genomes recruited very poorly indicating the potential of other groups being present. Here, we have applied for the first time a long-read (PacBio CCS) metagenomic approach to analyze in depth the Ca. Patescibacteria living in the bathypelagic wate