Advancement of DNA sequencing technology allows the routine use of genome sequences in the various fields of microbiology. The information held in genome sequences proved to provide objective and ...reliable means in the taxonomy of prokaryotes. Here, we describe the minimal standards for the quality of genome sequences and how they can be applied for taxonomic purposes.
The family
, belonging to the order
, class
, is globally distributed in various environments. Currently, this family consist of seven genera:
,
,
,
,
,
and
. As more species are identified, the ...taxonomic status of the family
should be revised at the genomic level because of its polyphyletic nature evident from 16S rRNA gene sequence analysis. Phylogenomic reconstruction based on 288 single-copy orthologous clusters led to the identification of three separate clades. Pairwise comparisons of average nucleotide identity, average amino acid identity (AAI), percentage of conserved protein and evolutionary distance indicated that AAI and evolutionary distance had the highest correlation. Thresholds for genera boundaries were proposed as 70 % and 0.4 for AAI and evolutionary distance, respectively. Based on the phylo-genomic and genomic similarity analysis, the three clades were classified into 16 genera, including 11 novel ones, for which the names
,
,
,
,
,
,
,
,
,
and
are proposed. We reclassified all species of
and
as species of
. This study is the first genomic-based study of the family
, and will contribute to further insights into the evolution of this family.
Cyanobacterial taxonomy developed in the botanical world because Cyanobacteria/Cyanophyta have traditionally been identified as algae. However, they possess a prokaryotic cell structure, and ...phylogenetically they belong to the Bacteria. This caused nomenclature problems as the provisions of the International Code of Nomenclature for algae, fungi, and plants (ICN; the “Botanical Code”) differ from those of the International Code of Nomenclature of Prokaryotes (ICNP; the “Prokaryotic Code”). While the ICN recognises names validly published under the ICNP, Article 45(1) of the ICN has not yet been reciprocated in the ICNP. Different solutions have been proposed to solve the current problems. In 2012 a Special Committee on the harmonisation of the nomenclature of Cyanobacteria was appointed, but its activity has been minimal. Two opposing proposals to regulate cyanobacterial nomenclature were recently submitted, one calling for deletion of the cyanobacteria from the groups of organisms whose nomenclature is regulated by the ICNP, the second to consistently apply the rules of the ICNP to all cyanobacteria. Following a general overview of the current status of cyanobacterial nomenclature under the two codes we present five case studies of genera for which nomenclatural aspects have been discussed in recent years:
Microcystis
,
Planktothrix
,
Halothece
,
Gloeobacter
and
Nostoc
.
Genomic information has already been applied to prokaryotic species definition and classification. However, the contribution of the genome sequence to prokaryotic genus delimitation has been less ...studied. To gain insights into genus definition for the prokaryotes, we attempted to reveal the genus-level genomic differences in the current prokaryotic classification system and to delineate the boundary of a genus on the basis of genomic information. The average nucleotide sequence identity between two genomes can be used for prokaryotic species delineation, but it is not suitable for genus demarcation. We used the percentage of conserved proteins (POCP) between two strains to estimate their evolutionary and phenotypic distance. A comprehensive genomic survey indicated that the POCP can serve as a robust genomic index for establishing the genus boundary for prokaryotic groups. Basically, two species belonging to the same genus would share at least half of their proteins. In a specific lineage, the genus and family/order ranks showed slight or no overlap in terms of POCP values. A prokaryotic genus can be defined as a group of species with all pairwise POCP values higher than 50%. Integration of whole-genome data into the current taxonomy system can provide comprehensive information for prokaryotic genus definition and delimitation.
Abstract
Mycosporines and mycosporine-like amino acids (MAAs) are low-molecular-weight water-soluble molecules absorbing UV radiation in the wavelength range 310–365 nm. They are accumulated by a ...wide range of microorganisms, prokaryotic (cyanobacteria) as well as eukaryotic (microalgae, yeasts, and fungi), and a variety of marine macroalgae, corals, and other marine life forms. The role that MAAs play as sunscreen compounds to protect against damage by harmful levels of UV radiation is well established. However, evidence is accumulating that MAAs may have additional functions: they may serve as antioxidant molecules scavenging toxic oxygen radicals, they can be accumulated as compatible solutes following salt stress, their formation is induced by desiccation or by thermal stress in certain organisms, they have been suggested to function as an accessory light-harvesting pigment in photosynthesis or as an intracellular nitrogen reservoir, and they are involved in fungal reproduction. Here, the evidence for these additional roles of MAAs as ‘multipurpose’ secondary metabolites is reviewed, with special emphasis on their functions in the microbial world.
In view of the finding of perchlorate among the salts detected by the Phoenix Lander on Mars, we investigated the relationships of halophilic heterotrophic microorganisms (archaea of the family
...Halobacteriaceae
and the bacterium
Halomonas elongata
) toward perchlorate. All strains tested grew well in NaCl-based media containing 0.4 M perchlorate, but at the highest perchlorate concentrations, tested cells were swollen or distorted. Some species (
Haloferax mediterranei
,
Haloferax denitrificans
,
Haloferax gibbonsii
,
Haloarcula marismortui
,
Haloarcula vallismortis
) could use perchlorate as an electron acceptor for anaerobic growth. Although perchlorate is highly oxidizing, its presence at a concentration of 0.2 M for up to 2 weeks did not negatively affect the ability of a yeast extract-based medium to support growth of the archaeon
Halobacterium salinarum
. These findings show that presence of perchlorate among the salts on Mars does not preclude the possibility of halophilic life. If indeed the liquid brines that may exist on Mars are inhabited by salt-requiring or salt-tolerant microorganisms similar to the halophiles on Earth, presence of perchlorate may even be stimulatory when it can serve as an electron acceptor for respiratory activity in the anaerobic Martian environment.
Raman spectroscopy of microbial pigments Jehlička, Jan; Edwards, Howell G M; Oren, Aharon
Applied and Environmental Microbiology,
06/2014, Letnik:
80, Številka:
11
Journal Article
Recenzirano
Odprti dostop
Raman spectroscopy is a rapid nondestructive technique providing spectroscopic and structural information on both organic and inorganic molecular compounds. Extensive applications for the method in ...the characterization of pigments have been found. Due to the high sensitivity of Raman spectroscopy for the detection of chlorophylls, carotenoids, scytonemin, and a range of other pigments found in the microbial world, it is an excellent technique to monitor the presence of such pigments, both in pure cultures and in environmental samples. Miniaturized portable handheld instruments are available; these instruments can be used to detect pigments in microbiological samples of different types and origins under field conditions.
Two bacterial strains, designated FR2A1
and MT2-5-38, were isolated from the surface sediments of an oyster farm on a tidal flat in Quanzhou Bay, China. Both strains were Gram-stain-negative, ...rod-shaped, aerobic, catalase-positive, and oxidase-positive. The 16S rRNA gene sequences of the two strains were 100% identical and had the highest similarity (97.1%) with
JA123
. The average nucleotide identity (ANI) value and digital DNA-DNA hybridization (DDH) value indicated that the two strains belonged to a single species. Gene annotation revealed that the two strains contained a gene cluster for nitrate reduction and a gene cluster for sulfur oxidation, indicating a possible role in N and S cycling in the tidal flat sediment. The phylogeny inferred from the 16S rRNA gene and 120 conserved proteins indicated that the two strains formed a distinct monophyletic clade within the family
. The respiratory quinone was Q-10. The major fatty acids consisted of summed feature 8 (C
7
and/or C
6
) and C
. The polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, and several unidentified phospholipids. Based on the above characteristics, strains FR2A1
and MT2-5-38 represent a novel genus and a novel species, for which we propose the name
gen. nov., sp. nov. The type strain is FR2A1
(=MCCC 1K08809
= KCTC 8317
). Phylogenomic analysis of 1,606 high-quality genomes of the family
, including type strains, non-type strains, and uncultivated bacteria, was performed using the Genome Taxonomic Database Toolkit (GTDB-Tk), and the average amino acid identity (AAI) value of the phylogenetic clade was estimated. We found that 35 species of the family
needed re-classification, and an AAI value of 70% was chosen as the genus boundary within the family
.
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