Description of the first marine-isolated member of the under-represented phylum Gemmatimonadota , and the environmental distribution and ecogenomics of Gaopeijiales ord. nov. DOI Creative Commons
Yu-Qi Ye,

Meng-Qi Ye,

Xinyue Zhang

et al.

mSystems, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 19, 2024

ABSTRACT The phylum Gemmatimonadota is widespread but rarely cultured and, in fact, there are only six described species isolated from soil, freshwater, and wastewater treatment. However, no isolates of marine environment have been described; thus, little known about the physiology metabolism members lineages. In this study, four novel facultatively anaerobic bacterial strains belonging to were sediments collected Xiaoshi Island Weihai, China, using an aerobic enrichment method. integrated results phylogenetic phenotypic characteristics supported that these represent one a genus, for which name Gaopeijia maritima gen. nov., sp. nov. proposed, as first representative taxa, Gaopeijiales ord. Gaopeijiaceae fam. class Longimicrobiia. was detected 22,884 out 95,549 amplicon data sets, mainly soil. highest mean relative abundances sponge (0.7%) sediment (0.35%), showing salt-related character. Most subgroups potentially belong rare biosphere. study could significantly increase abundance (from 0.37% 2.6%). Furthermore, metabolic capabilities inferred high-quality genomes/MAGs suggest group primarily performs chemoorganoheterotrophic with possesses various secondary metabolite biosynthesis gene clusters (BGCs), mirroring those observed strains. IMPORTANCE Despite rapid advances molecular sequencing technologies, obtaining pure cultures remains crucial research goal microbiology, it essential deeper understanding microbial metabolism. phylum. Currently, interesting group, all non-marine environments. Little Here we characterized strains, proposed new order within . global distribution, environmental preference, potential analyzed public data. Our work enriches resources available under-represented provides insights into physiological lineage ( ) through culturology omics.

Language: Английский

Erratic Calcareous Deposits: Biotic Formation Insights and Biomineralising Bacterial Strain Isolation DOI Creative Commons
Beatrice Farda,

Amedeo Mignini,

Rihab Djebaili

et al.

Acta Biomaterialia, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 1, 2025

Language: Английский

Citations

0
Updating the unnamed: over 20,000 new Candidatus names for unnamed taxa in GTDB release r214 DOI Creative Commons
Mark J. Pallen

Research Square (Research Square), Journal Year: 2024, Volume and Issue: unknown

Published: April 9, 2024

Abstract Here, an established approach to the generation of well-formed arbitrary Latinate names at a scale has been adopted and adapted name tens thousands new, but unnamed taxa within GTDB Release r214.1. New Candidatus have created assigned two new archaeal twelve bacterial phyla; six 48 classes; 13 158 orders; 60 597 families; 271 3,869 genera; 1,097 18,126 species. for phyla include Ca. Afuciota, Axiviota, Bobupiota, C a. Fitepiota, Hubebiota, Ibociota, Inuciota, Luxamiota, Megaciota, Nasexiota, Ca . Oviciota , Ucifiota, Uvuciota, while Acigarchota Omefarchota. These efforts show that creation prokaryotic remains sustainable, despite relentless progress discovery.

Language: Английский

Citations

2
The dynamic history of prokaryotic phyla: discovery, diversity and division DOI
Mark J. Pallen

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Journal Year: 2024, Volume and Issue: 74(9)

Published: Sept. 9, 2024

Here, I review the dynamic history of prokaryotic phyla. Following leads set by Darwin, Haeckel and Woese, concept phylum has evolved from a group sharing common phenotypes to organisms ancestry, with modern taxonomy based on phylogenetic classifications drawn macromolecular sequences. Phyla came as surprising latecomers formalities nomenclature in 2021. Since then names have been validly published for 46 phyla, replacing some established neologisms, prompting criticism debate within scientific community. Molecular barcoding enabled analysis microbial ecosystems without cultivation, leading identification candidate divisions (or phyla) diverse environments. The introduction metagenome-assembled genomes marked significant advance identifying classifying uncultured lumper–splitter dichotomy led disagreements, experts cautioning against pressure create profusion new phyla prominent databases adopting conservative stance. Candidatus designation widely used provide provisional status taxa, named under this convention now clearly surpassing those names. Genome Taxonomy Database (GTDB) offered stable, standardized normalized taxonomic ranks, which both lumping splitting pre-existing GTDB framework introduced unwieldy alphanumeric placeholder labels, recent publication over 100 user-friendly Latinate unnamed Most remain ‘known unknowns’, limited knowledge their genomic diversity, ecological roles, or Whether still reflect evolutionary partitions across life remains an area active debate. However, practical importance microbiome analyses, particularly clinical research. Despite potential diminishing returns discovery biodiversity, offer extensive research opportunities microbiologists foreseeable future.

Language: Английский

Citations

2
The interactive effects of shrub and aridity affect co-occurrence network complexity and stability of soil bacterial communities on the Qinghai–Tibet Plateau DOI

Wanyu Xia,

Hanwen Cui,

Jingwei Chen

et al.

CATENA, Journal Year: 2024, Volume and Issue: 249, P. 108634 - 108634

Published: Dec. 9, 2024

Language: Английский

Citations

1
The efficacy of bioretention systems amended with iron-modified biochar for the source-separated and component-specific treatment of rainwater runoff: A microbiome perspective DOI
Longfei Wang, Tian Yuan, Jie Sun

et al.

Journal of Environmental Management, Journal Year: 2024, Volume and Issue: 373, P. 123728 - 123728

Published: Dec. 18, 2024

Language: Английский

Citations

1
Deciphering the Effects of Phosphate Fertiliser on Rhizospheric Bacterial Community Structure and Potato Common Scab DOI Creative Commons
S. P. Chen, Jingjing Cao, Pan Zhao

et al.

Microorganisms, Journal Year: 2024, Volume and Issue: 12(11), P. 2322 - 2322

Published: Nov. 15, 2024

The prolonged practice of continuous potato cropping, coupled with inadequate field management, disrupts the soil bacterial community equilibrium. Such disturbances compromise resilience ecosystem, predisposing it to an increased incidence diseases. However, effects phosphorus fertiliser application rate on rhizosphere composition potatoes and occurrence common scab (CS) have not been adequately studied. Here, diseased soils from Dingxi Huidong Counties were collected for potting tests, tests conducted in County validation. An examination relationship between CS under different phosphate treatments was using 16S rRNA high-throughput sequencing. results show that a lower more conducive maintaining diversity habitats. In addition, relative abundance

Language: Английский

Citations

0
Description of the first marine-isolated member of the under-represented phylum Gemmatimonadota , and the environmental distribution and ecogenomics of Gaopeijiales ord. nov. DOI Creative Commons
Yu-Qi Ye,

Meng-Qi Ye,

Xinyue Zhang

et al.

mSystems, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 19, 2024

ABSTRACT The phylum Gemmatimonadota is widespread but rarely cultured and, in fact, there are only six described species isolated from soil, freshwater, and wastewater treatment. However, no isolates of marine environment have been described; thus, little known about the physiology metabolism members lineages. In this study, four novel facultatively anaerobic bacterial strains belonging to were sediments collected Xiaoshi Island Weihai, China, using an aerobic enrichment method. integrated results phylogenetic phenotypic characteristics supported that these represent one a genus, for which name Gaopeijia maritima gen. nov., sp. nov. proposed, as first representative taxa, Gaopeijiales ord. Gaopeijiaceae fam. class Longimicrobiia. was detected 22,884 out 95,549 amplicon data sets, mainly soil. highest mean relative abundances sponge (0.7%) sediment (0.35%), showing salt-related character. Most subgroups potentially belong rare biosphere. study could significantly increase abundance (from 0.37% 2.6%). Furthermore, metabolic capabilities inferred high-quality genomes/MAGs suggest group primarily performs chemoorganoheterotrophic with possesses various secondary metabolite biosynthesis gene clusters (BGCs), mirroring those observed strains. IMPORTANCE Despite rapid advances molecular sequencing technologies, obtaining pure cultures remains crucial research goal microbiology, it essential deeper understanding microbial metabolism. phylum. Currently, interesting group, all non-marine environments. Little Here we characterized strains, proposed new order within . global distribution, environmental preference, potential analyzed public data. Our work enriches resources available under-represented provides insights into physiological lineage ( ) through culturology omics.

Language: Английский

Citations

0