scholarly journals Taxonomy of Rhizobiaceae revisited: proposal of a new framework for genus delimitation

2021 ◽  
Author(s):  
Nemanja Kuzmanović ◽  
Camilla Fagorzi ◽  
Alessio Mengoni ◽  
Florent Lassalle ◽  
George C diCenzo
Keyword(s):  
New Genus ◽  
Core Genome ◽  
Amino Acid Identity ◽  
Phenotypic Data ◽  
Average Amino Acid Identity ◽  
The Family ◽  
Common Framework ◽  
Core Proteome ◽  
Genomic Relatedness ◽  
New Framework

The alphaproteobacterial family Rhizobiaceae is highly diverse, with 168 species with validly published names classified into 17 genera with validly published names. Most named genera in this family are delineated based on genomic relatedness and phylogenetic relationships, but some historically named genera show inconsistent distribution and phylogenetic breadth. Most problematic is Rhizobium, which is notorious for being highly paraphyletic, as most newly described species in the family being assigned to this genus without consideration for their proximity to existing genera, or the need to create novel genera. In addition, many Rhizobiaceae genera lack synapomorphic traits that would give them biological and ecological significance. We propose a common framework for genus delimitation within the family Rhizobiaceae. We propose that genera in this family should be defined as monophyletic groups in a core-genome gene phylogeny, that are separated from related species using a pairwise core-proteome average amino acid identity (cpAAI) threshold of approximately 86%. We further propose that the presence of additional genomic or phenotypic evidence can justify the division of species into separate genera even if they all share greater than 86% cpAAI. Applying this framework, we propose to reclassify Rhizobium rhizosphaerae and Rhizobium oryzae into the new genus Xaviernesmea gen. nov. Data is also provided to support the recently proposed genus "Peteryoungia", and the reclassifications of Rhizobium yantingense as Endobacterium yantingense comb. nov., Rhizobium petrolearium as Neorhizobium petrolearium comb. nov., Rhizobium arenae as Pararhizobium arenae comb. nov., Rhizobium tarimense as Pseudorhizobium tarimense comb. nov., and Rhizobium azooxidefex as Mycoplana azooxidifex comb. nov. Lastly, we present arguments that the unification of the genera Ensifer and Sinorhizobium in Opinion 84 of the Judicial Commission is no longer justified by current genomic and phenotypic data. We thus argue that the genus Sinorhizobium is not illegitimate and now encompasses 17 species.

scholarly journals Comparative genomics ofSynechococcusand proposal of the new genusParasynechococcus

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1522 ◽  
Author(s):  
Felipe Coutinho ◽  
Diogo Antonio Tschoeke ◽  
Fabiano Thompson ◽  
Cristiane Thompson
Keyword(s):  
Primary Productivity ◽  
New Genus ◽  
Core Genome ◽  
Amino Acid Identity ◽  
Average Nucleotide Identity ◽  
Acid Identity ◽  
Average Amino Acid Identity ◽  
Protein Encoding ◽  
Genomic Taxonomy ◽  
Encoding Genes

Synechococcusis among the most important contributors to global primary productivity. The genomes of several strains of this taxon have been previously sequenced in an effort to understand the physiology and ecology of these highly diverse microorganisms. Here we present a comparative study ofSynechococcusgenomes. For that end, we developed GenTaxo, a program written in Perl to perform genomic taxonomy based on average nucleotide identity, average amino acid identity and dinucleotide signatures, which revealed that the analyzed strains are drastically distinct regarding their genomic content. Phylogenomic reconstruction indicated a division ofSynechococcusin two clades (i.e. Synechococcus and the new genus Parasynechococcus), corroborating evidences that this is in fact a polyphyletic group. By clustering protein encoding genes into homologue groups we were able to trace the Pangenome and core genome of both marine and freshwaterSynechococcusand determine the genotypic traits that differentiate these lineages.

Reclassification of Haloactinobacterium glacieicola as Occultella glacieicola gen. nov., comb. nov., of Haloactinobacterium album as Ruania alba comb. nov, with an emended description of the genus Ruania, recognition that the genus names Haloactinobacterium and Ruania are heterotypic synonyms and description of Occultella aeris sp. nov., a halotolerant isolate from surface soil sampled at an ancient copper smelter

2021 ◽  
Vol 71 (4) ◽  
Author(s):  
Peter Schumann ◽  
Franziska Kalensee ◽  
Jialan Cao ◽  
Alexis Criscuolo ◽  
Dominique Clermont ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Type Species ◽  
Copper Smelter ◽  
Amino Acid Identity ◽  
Content Type ◽  
Link Type ◽  
Average Amino Acid Identity ◽  
The Family ◽  
Emended Description ◽  
Copper Mines

In the course of screening the surface soils of ancient copper mines and smelters (East Harz, Germany) an aerobic, non-motile and halotolerant actinobacterium forming small rods or cocci was isolated. The strain designated F300T developed creamy to yellow colonies on tryptone soy agar and grew optimally at 28 °C, pH 7–8 and with 0.5–2 % (m/v) NaCl. Its peptidoglycan was of type A4α l-Lys–l-Glu (A11.54). The menaquinone profile was dominated by MK-8(II, III-H4) and contained minor amounts of MK-8(H2), MK-8(H6) and MK-9(H4). The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, mono and diacylated phosphatidylinositol dimannosides, and components that were not fully characterized, including two phospholipids, two glycolipids and an uncharacterized lipid. Major whole-cell sugars were rhamnose and ribose. The fatty acid profile contained mainly iso and anteiso branched fatty acids (anteiso-C15 : 0, iso-C14 : 0) and aldehydes/dimethylacetals (i.e. not fatty acids). Sequence analysis of its genomic DNA and subsequent analysis of the data placed the isolate in the group currently defined by members of the genera Ruania and Haloactinobacterium (family Ruaniaceae , order Micrococcales ) as a sister taxon to the previously described species Haloactinobacterium glacieicola , sharing an average nucleotide identity and average amino acid identity values of 85.3 and 85.7 %, respectively. Genotypic and chemotaxonomic analyses support the view that strain F300T (=DSM 108350T=CIP 111667T) is the type strain of a new genus and new species for which the name Occultella aeris gen. nov., sp. nov. is proposed. Based on revised chemotaxonomic and additional genome based data, it is necessary to discuss and evaluate the results in the light of the classification and nomenclature of members of the family Ruaniaceae , i.e. the genera Haloactinobacterium and Ruania . Consequently, the reclassification of Haloactinobacterium glacieicola as Occultella glacieicola comb. nov. and Haloactinobacterium album as Ruania alba comb. nov., with an emended description of the genus Ruania are proposed.

Limnovirga soli gen. nov., sp. nov., isolated from river sediment

2021 ◽  
Vol 71 (10) ◽  
Author(s):  
Kyung June Yim ◽  
Dong-Hyun Jung ◽  
Seok Won Jang ◽  
Sanghwa Park
Keyword(s):  
Phylogenetic Trees ◽  
Amino Acid Identity ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Physiological Properties ◽  
Average Amino Acid Identity ◽  
The Family ◽  
Genome Analyses

A cream-coloured, Gram-stain-negative, rod-shaped bacterium, designated strain KSC-6T, was isolated from soil sampled at the Gapcheon River watershed in Daejeon, Republic of Korea. The organism does not require NaCl for growth and grows at pH 6.0–8.0 (optimum, pH 7.0) and 10–37 °C (optimum, 25 °C). Phylogenetic trees based on the 16S rRNA gene sequences reveal that strain KSC-6T belongs to the family Chitinophagaceae within the order Chitinophagales and is most closely related to Panacibacter ginsenosidivorans Gsoil 1550T (95.9% similarity). The genomic DNA G+C content was 38.9 mol%. The major cellular fatty acids (>8 %) of strain KCS-6T were iso-C15:0, iso-C15 : 1 G and iso-C17 : 0 3-OH. The predominant respiratory quinone was menaquinone 7 and the predominant polar lipids were phosphatidylethanolamine, five unidentified aminolipids and two unidentified lipids. Based on genome analyses, low digital DNA–DNA hybridization, average nucleotide identity and average amino acid identity values with closely related genera, and differential chemotaxonomic and physiological properties, we suggest that strain KCS-6T represents a novel species in a new genus in the family Chitinophagaceae , for which the name Limnovirga soli gen. nov., sp. nov. (type strain KCS-6T=KCCM 43337T=NBRC 114336T) is proposed.

scholarly journals Description of Three Novel Members in the Family Geobacteraceae, Oryzomonas japonicum gen. nov., sp. nov., Oryzomonas sagensis sp. nov., and Oryzomonas ruber sp. nov.

2020 ◽  
Vol 8 (5) ◽  
pp. 634 ◽  
Author(s):  
Zhenxing Xu ◽  
Yoko Masuda ◽  
Chie Hayakawa ◽  
Natsumi Ushijima ◽  
Keisuke Kawano ◽  
...  
Keyword(s):  
Housekeeping Genes ◽  
Amino Acid Identity ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Genomic Comparison ◽  
Novel Genus ◽  
Average Amino Acid Identity ◽  
The Family ◽  
Type Strains ◽  
Core Genes

Bacteria of the family Geobacteraceae are particularly common and deeply involved in many biogeochemical processes in terrestrial and freshwater environments. As part of a study to understand biogeochemical cycling in freshwater sediments, three iron-reducing isolates, designated as Red96T, Red100T, and Red88T, were isolated from the soils of two paddy fields and pond sediment located in Japan. The cells were Gram-negative, strictly anaerobic, rod-shaped, motile, and red-pigmented on agar plates. Growth of these three strains was coupled to the reduction of Fe(III)-NTA, Fe(III) citrate, and ferrihydrite with malate, methanol, pyruvate, and various organic acids and sugars serving as alternate electron donors. Phylogenetic analysis based on the housekeeping genes (16S rRNA gene, gyrB, rpoB, nifD, fusA, and recA) and 92 concatenated core genes indicated that all the isolates constituted a coherent cluster within the family Geobacteraceae. Genomic analyses, including average nucleotide identity and DNA–DNA hybridization, clearly differentiated the strains Red96T, Red100T, and Red88T from other species in the family Geobacteraceae, with values below the thresholds for species delineation. Along with the genomic comparison, the chemotaxonomic features further helped distinguish the three isolates from each other. In addition, the lower values of average amino acid identity and percentage of conserved protein, as well as biochemical differences with their relatives, indicated that the three strains represented a novel genus in the family Geobacteraceae. Hence, we concluded that strains Red96T, Red100T, and Red88T represented three novel species of a novel genus in the family Geobacteraceae, for which the names Oryzomonas japonicum gen. nov., sp. nov., Oryzomonas sagensis sp. nov., and Oryzomonas ruber sp. nov. are proposed, with type strains Red96T (= NBRC 114286T = MCCC 1K04376T), Red100T (= NBRC 114287T = MCCC 1K04377T), and Red88T (= MCCC 1K03694T = JCM 33033T), respectively.

scholarly journals Fibrivirga Algicola Gen. Nov., Sp. Nov., An Algicidal Bacterium Isolated from a Freshwater River

2021 ◽  
Author(s):  
Sanghwa Park ◽  
JaYoung Cho ◽  
Dong-Hyun Jung ◽  
SeokWon Jang ◽  
JungHye Eom ◽  
...  
Keyword(s):  
Genomic Dna ◽  
Sequence Similarity ◽  
Amino Acid Identity ◽  
Rrna Gene ◽  
The Novel ◽  
Respiratory Quinone ◽  
Algicidal Bacterium ◽  
Average Amino Acid Identity ◽  
The Family ◽  
Major Respiratory Quinone

Abstract An aerobic, gram-negative, pink-colored, non-motile, rod-shaped algicidal bacterium, designated JA-25T was isolated from the freshwater of the Geumgang River, Republic of Korea. It grew at 15–30°C, 6.0–9.0 pH, and in the presence of 0–1% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain JA-25T belongs to the Family ‘Spirosomaceae’ and is most closely related to Fibrella aestuarina BUZ 2T (93.6%). The strain JA-25T showed < 90% sequence similarity to other members of the Family ‘Spirosomaceae’. The average nucleotide identity(ANI), in silico DNA-DNA hybridization and the average amino acid identity(AAI) values based on the genomic sequences of JA-25T and F. aestuarina BUZ 2T were 74.4, 20.5 and 73.6 %, respectively. The genomic DNA G + C content was 52.5mol %. The major cellular fatty acids were Summed feature 3 (C16:1 ω6c/C16:1 ω7c), C16:1 ω5c, C16:0 (> 10%). The genomic DNA G + C content was 52.5 mol %. The major respiratory quinone was MK-7 and the polar lipids were phosphatidylethanolamine, two unidentified aminolipids, two phospholipids and five unidentified lipids. Considering the phylogenetic inference, phenotypic and chemotaxonomic data, strain JA-25T should be classified as a novel species of the novel genus Fibrivirga, with the proposed name Fibrivirga algicola sp. nov. The type strain is JA-25T (= KCCM 43334T = NBRC 114259T).

scholarly journals Genome-Based Taxonomic Rearrangement of the Order Geobacterales Including the Description of Geomonas azotofigens sp. nov. and Geomonas diazotrophica sp. nov.

2021 ◽  
Vol 12 ◽  
Author(s):  
Zhenxing Xu ◽  
Yoko Masuda ◽  
Xueding Wang ◽  
Natsumi Ushijima ◽  
Yutaka Shiratori ◽  
...  
Keyword(s):  
Taxonomic Status ◽  
Terrestrial Ecosystems ◽  
Single Copy ◽  
Amino Acid Identity ◽  
Taxonomic Structure ◽  
Phylogenomic Analysis ◽  
Genome Sequences ◽  
Average Amino Acid Identity ◽  
The Family ◽  
Genomic Similarity

Geobacterales is a recently proposed order comprising members who originally belonged to the well-known family Geobacteraceae, which is a key group in terrestrial ecosystems involved in biogeochemical cycles and has been widely investigated in bioelectrochemistry and bioenergy fields. Previous studies have illustrated the taxonomic structure of most members in this group based on genomic phylogeny; however, several members are still in a pendent or chaotic taxonomic status owing to the lack of genome sequences. To address this issue, we performed this taxonomic reassignment using currently available genome sequences, along with the description of two novel paddy soil-isolated strains, designated Red51T and Red69T, which are phylogenetically located within this order. Phylogenomic analysis based on 120 ubiquitous single-copy proteins robustly separated the species Geobacter luticola from other known genera and placed the genus Oryzomonas (fam. Geobacteraceae) into the family ‘Pseudopelobacteraceae’; thus, a novel genus Geomobilimonas is proposed, and the family ‘Pseudopelobacteraceae’ was emended. Moreover, genomic comparisons with similarity indexes, including average amino acid identity (AAI), percentage of conserved protein (POCP), and average nucleotide identity (ANI), showed proper thresholds as genera boundaries in this order with values of 70%, 65%, and 74% for AAI, POCP, and ANI, respectively. Based on this, the three species Geobacter argillaceus, Geobacter pelophilus, and Geobacter chapellei should be three novel genera, for which the names Geomobilibacter, Geoanaerobacter, and Pelotalea are proposed, respectively. In addition, the two novel isolated strains phylogenetically belonged to the genus Geomonas, family Geobacteraceae, and shared genomic similarity values higher than those of genera boundaries, but lower than those of species boundaries with each other and their neighbors. Taken together with phenotypic and chemotaxonomic characteristics similar to other Geomonas species, these two strains, Red51T and Red69T, represent two novel species in the genus Geomonas, for which the names Geomonas azotofigens sp. nov. and Geomonas diazotrophica sp. nov. are proposed, respectively.

scholarly journals Puniceibacterium antarcticum gen. nov., sp. nov., isolated from seawater

2014 ◽  
Vol 64 (Pt_5) ◽  
pp. 1566-1572 ◽  
Author(s):  
Chang Liu ◽  
Xi-Ying Zhang ◽  
Hai-Nan Su ◽  
Ming-Yang Zhou ◽  
Bo Chen ◽  
...  
Keyword(s):  
Type Strain ◽  
New Genus ◽  
Novel Species ◽  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type ◽  
The Family

A Gram-reaction-negative, aerobic, non-flagellated, rod-shaped bacterium, designated strain SM1211T, was isolated from Antarctic seawater. The isolate grew at 4–35 °C and with 0–10 % (w/v) NaCl. It could produce bacteriochlorophyll a, but did not reduce nitrate to nitrite or hydrolyse DNA. Phylogenetic analysis of 16S rRNA gene sequences revealed that strain SM1211T constituted a distinct phylogenetic line within the family Rhodobacteraceae and was closely related to species in the genera Litorimicrobium , Leisingera , Seohaeicola and Phaeobacter with 95.1–96.0 % similarities. The predominant cellular fatty acid was C18 : 1ω7c. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, an unidentified aminolipid and two unidentified phospholipids. The genomic DNA G+C content of strain SM1211T was 60.7 mol%. Based on the phylogenetic, chemotaxonomic and phenotypic data obtained in this study, strain SM1211T is considered to represent a novel species in a new genus within the family Rhodobacteraceae , for which the name Puniceibacterium antarcticum gen. nov., sp. nov. is proposed. The type strain of Puniceibacterium antarcticum is SM1211T ( = CCTCC AB 2013147T = KACC 16875T).

scholarly journals Marinibacterium profundimaris gen. nov., sp. nov., isolated from deep seawater

2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 4175-4179 ◽  
Author(s):  
Guizhen Li ◽  
Qiliang Lai ◽  
Yaping Du ◽  
Xiupian Liu ◽  
Fengqin Sun ◽  
...  
Keyword(s):  
New Genus ◽  
Novel Species ◽  
Sequence Similarity ◽  
Tween 80 ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Deep Seawater ◽  
Phenotypic Data ◽  
Respiratory Quinone ◽  
The Family

A taxonomic study was carried out on strain 22II1-22F33T, which was isolated from deep seawater of the Atlantic Ocean. The bacterium was Gram-stain-negative, oxidase-positive and weakly catalase-positive, oval in shape without flagellum. Growth was observed at salinities of 0–12 % and at temperatures of 4–41 °C. The isolate was capable of hydrolysing aesculin and Tween 80 and reduction of nitrate to nitrite, but unable to hydrolyse gelatin. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 22II1-22F33T belongs to the family Rhodobacteraceae, with highest sequence similarity to Pseudooceanicola marinus AZO-CT (96.5 %). The principal fatty acids (>10 %) were summed feature 8 (C18 : 1ω7c/ω6c) (73.8 %). The G+C content of the genomic DNA was 66.2 mol%. The respiratory quinone was Q-10 (100 %). Phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphatidylcholine (PC), two unidentified aminolipids (ALs), six unidentified phospholipids (PLs) and one unidentified lipid (L) were present. The combined genotypic and phenotypic data show that strain 22II1-22F33T represents a novel species within a new genus, for which the name Marinibacterium profundimaris gen. nov., sp. nov. is proposed. The type strain of Marinibacterium profundimaris is 22II1-22F33T ( = LMG 27151T = MCCC 1A09326T).

scholarly journals Phylogenetic relationships among haloalkaliphilic archaea of the family Natrialbaceae

2020 ◽  
Author(s):  
Shivakumara Siddaramappa
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Novel Species ◽  
Single Species ◽  
Amino Acid Identity ◽  
Average Nucleotide Identity ◽  
Acid Identity ◽  
Average Amino Acid Identity ◽  
The Family ◽  
Clade 1

ABSTRACTThe family Natrialbaceae is a member of the class Halobacteria of the archaeal phylum Euryarchaeota. Seventeen genera with validly or effectively published names are currently included within this family. In this study, using pairwise average nucleotide identity and average amino acid identity comparisons in conjunction with phylogenetic analysis, it has been shown that the family Natrialbaceae is highly diverse and contains several potentially novel species and genera that are yet to be fully characterized. The deduced proteome sequence-based phylogenetic tree, constructed using the alignment- and parameter-free method CVTree3, contained six major clades, with Salinarchaeum sp. Harcht-Bsk1 being the only representative within clade 1. Furthermore, Haloterrigena daqingensis was found to be closely related to Natronorubrum sediminis, and it is proposed that these archaea together represent a novel genus. Interestingly, Haloterrigena jeotgali, Haloterrigena thermotolerans, and Natrinema pellirubrum were found to be very closely related to each other, and it is proposed that they be merged into a single species. Notably, the type genus Natrialba itself appeared to be heterogenous and contains species that could be broadly classified among two genera. Likewise, the genus Natrinema is also heterogenous and contains species that could be classified among six genera. Altogether, 19 novel genera have been proposed to be created, and four haloalkaliphilic archaea hitherto recognized only using genus names are confirmed to represent novel species.

scholarly journals Phylogenetic study of thermophilic genera Anoxybacillus, Geobacillus, Parageobacillus, and proposal of a new classification Quasigeobacillus gen. nov.

2021 ◽  
Author(s):  
Berenice Talamantes-Becerra ◽  
Jason Carling ◽  
Jochen Blom ◽  
Arthur Georges
Keyword(s):  
New Genus ◽  
Gene Tree ◽  
Amino Acid Identity ◽  
Core Gene ◽  
Phylogenetic Study ◽  
Genome Sequences ◽  
New Classification ◽  
Maximum Likelihood Tree ◽  
Average Amino Acid Identity ◽  
Core Genes

A phylogenetic study of Anoxybacillus, Geobacillus and Parageobacillus was performed using publicly available whole genome sequences. A total of 113 genomes were selected for phylogenomic metrics including calculation of Average Nucleotide Identity (ANI) and Average Amino acid Identity (AAI), and a maximum likelihood tree was built from alignment of a set of 662 orthologous core genes. The combined results from the core gene tree and ANI and AAI dendrograms show that the genomes split into two main clades, clade I containing all Geobacillus, all Parageobacillus and some species of Anoxybacillus, and clade II, containing the majority of Anoxybacillus species. Clade I is further partitioned into three clades, consisting separately of Geobacillus, Parageobacillus, and a third clade which we suggest should be elevated to a new genus Quasigeobacillus gen. nov. Two species of Anoxybacillus showed inconsistent positioning among the trees produced by differing methods and could not be clearly resolved into any of the three existing genera or the new genus. This research shows the importance of considering closely related genera together when studying phylogeny or assigning genomic affinities.

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