Phylogenomic analyses and reclassification of the Mesorhizobium complex: proposal for 9 novel genera and reclassification of 15 species

BACKGROUD

The genus Mesorhizobium is shown by phylogenomics to be paraphyletic and forms part of a complex that includes the genera Aminobacter, Aquamicrobium, Pseudaminobacter and Tianweitania. The relationships for type strains belong to these genera need to be carefully re-evaluated.

RESULTS

The relationships of Mesorhizobium complex are evaluated based on phylogenomic analyses and overall genome relatedness indices (OGRIs) of 61 type strains. According to the maximum likelihood phylogenetic tree based on concatenated sequences of 539 core proteins and the tree constructed using the bac120 bacterial marker set from Genome Taxonomy Database, 65 type strains were grouped into 9 clusters. Moreover, 10 subclusters were identified based on the OGRIs including average nucleotide identity (ANI), average amino acid identity (AAI) and core-proteome average amino acid identity (cAAI), with AAI and cAAI showing a clear intra- and inter-(sub)cluster gaps of 77.40-80.91% and 83.98-86.16%, respectively. Combined with the phylogenetic trees and OGRIs, the type strains were reclassified into 15 genera. This list includes five defined genera Mesorhizobium, Aquamicrobium, Pseudaminobacter, Aminobacterand Tianweitania, among which 40/41 Mesorhizobium species and one Aminobacter species are canonical legume microsymbionts. The other nine (sub)clusters are classified as novel genera. Cluster III, comprising symbiotic M. alhagi and M. camelthorni, is classified as Allomesorhizobium gen. nov. Cluster VI harbored a single symbiotic species M. albiziae and is classified as Neomesorhizobium gen. nov. The remaining seven non-symbiotic members were proposed as: Neoaquamicrobium gen. nov., Manganibacter gen. nov., Ollibium gen. nov., Terribium gen. nov., Kumtagia gen. nov., Borborobacter gen. nov., Aerobium gen. nov.. Furthermore, the genus Corticibacterium is restored and two species in Subcluster IX-1 are reclassified as the member of this genus.

CONCLUSION

The Mesorhizobium complex are classified into 15 genera based on phylogenomic analyses and OGRIs of 65 type strains. This study resolved previously non-monophyletic genera in the Mesorhizobium complex.

Phyllobacteriaceae: a family of ecologically and metabolically diverse bacteria with the potential for different applications

The family Phyllobacteriaceae is a heterogeneous assemblage of more than 146 species of bacteria assigned to its existing 18 genera. Phylogenetic analyses have shown great phylogenetic diversity and also suggested about incorrect classification of several species that need to be reassessed for their proper phylogenetic classification. However, almost 50% of the family members belong to the genus Mesorhizobium only, of which the majority are symbiotic nitrogen fixers associated with different legumes. Other major genera are Phyllobacterium, Nitratireductor, Aquamicrobium, and Aminobacter. Nitrogen-fixing, legume nodulating members are present in Aminobacter and Phyllobacterium as well. Aquamicrobium spp. can degrade environmental pollutants, like 2,4-dichlorophenol, 4-chloro-2-methylphenol, and 4-chlorophenol. Chelativorans, Pseudaminobacter, Aquibium, and Oricola are the other genera that contain multiple species having diverse metabolic capacities, the rest being single-membered genera isolated from varied environments. In addition, heavy metal and antibiotic resistance, chemolithoautotrophy, poly-β-hydroxybutyrate storage, cellulase production, etc., are the other notable characteristics of some of the family members. In this report, we have comprehensively reviewed each of the species of the family Phyllobacteriaceae in their eco-physiological aspects and found that the family is rich with ecologically and metabolically highly diverse bacteria having great potential for human welfare and environmental clean-up.

Draft Genome Sequence of a Sulfur-Oxidizing Bacterium, Aquamicrobium lusatiense NLF2-7, Isolated from Livestock Wastewater

Here, we report the draft genome sequence of Aquamicrobium lusatiense NLF2-7, a Gram-negative, aerobic, non-flagellum-forming, rod-shaped bacterium that was isolated from livestock wastewater in South Korea. The assembled genome sequence is 5,201,486 bp, with 4,972 protein-coding sequences in 12 contigs, and possess the genes for the sulfur oxidation pathway.

Aquamicrobium zhengzhouense sp. nov., a Bacterium Isolated from Farmland Soil Applied with Amino Acid Fertilizer

A novel Gram-stain-negative, rod-shaped, strictly aerobic, non-motile bacterium, designated strain cd-1^T, was isolated from a farmland soil applied with amino acid fertilizer in Zhengzhou, Henan province, China. The optimum growth of strain cd-1^T occurred at 30 °C, pH 7.0 in Luria-Bertani (LB) broth without NaCl supplement. Phylogenetic analysis based on 16S rRNA gene sequences indicated that cd-1^T is member of the genus Aquamicrobium, and formed a separate branch with Aquamicrobium aerolatum DSM 21857^T (96.5%) and Aquamicrobium soli KCTC 52165^T (95.7%). The draft genome sequencing revealed a DNA G + C content of 59.2 mol% and Q-10 was the predominant respiratory quinone. The major cellular fatty acids were identified as C_18:1 ω7c (35.8%), C_19:0 cyclo ω8c (32.1%), and C_18:1 ω7c 11-methyl (5.2%). The polar lipids consisted of phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and phosphatidylmonomethylethanolamine. Average nucleotide identity (ANI) and the digital DNA-DNA hybridizations (dDDH) for draft genomes between strain cd-1^T and KCTC 52165^T were 71.0% and 19.9%, respectively, the values for strain cd-1^T and DSM 21857^T were 73.4% and 20.6%. Based on the physiological and biochemical characteristics, phylogenetic and chemotaxonomic analysis, strain cd-1^T is considered to represent a novel species of the genus Aquamicrobium, for which the name Aquamicrobium zhengzhouense sp. nov. is proposed. The type strain is cd-1^T (= KCTC 82182^T = CCTCC M 2018904^T).

Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria

The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.

Differential daptomycin resistance development in Staphylococcus aureus strains with active and mutated gra regulatory systems

The first-in-class lipopeptide antibiotic daptomycin (DAP) is highly active against Gram-positive pathogens including ß-lactam and glycopeptide resistant strains. Its molecular mode of action remains enigmatic, since a defined target has not been identified so far and multiple effects, primarily on the cell envelope have been observed. Reduced DAP susceptibility has been described in S. aureus and enterococci after prolonged treatment courses. In line with its pleiotropic antibiotic activities, a unique, defined molecular mechanism of resistance has not emerged, instead non-susceptibility appears often accompanied by alterations in membrane composition and changes in cell wall homeostasis. We compared S. aureus strains HG001 and SG511, which differ primarily in the functionality of the histidine kinase GraS, to evaluate the impact of the GraRS regulatory system on the development of DAP non-susceptibility. After extensive serial passing, both DAP^R variants reached a minimal inhibitory concentration of 31 μg/ml and shared some phenotypic characteristics (e.g. thicker cell wall, reduced autolysis). However, based on comprehensive analysis of the underlying genetic, transcriptomic and proteomic changes, we found that both strains took different routes to achieve DAP resistance. Our study highlights the impressive genetic and physiological capacity of S. aureus to counteract pleiotropic activities of cell wall- and membrane-active compounds even when a major cell wall regulatory system is dysfunctional.

Identification and characterization of a novel carboxylesterase (FpbH) that hydrolyzes aryloxyphenoxypropionate herbicides

OBJECTIVE

To identify and characterize a novel aryloxyphenoxypropionate (AOPP) herbicide-hydrolyzing carboxylesterase from Aquamicrobium sp. FPB-1.

RESULTS

A carboxylesterase gene, fpbH, was cloned from Aquamicrobium sp. FPB-1. The gene is 798 bp long and encodes a protein of 265 amino acids. FpbH is smaller than previously reported AOPP herbicide-hydrolyzing carboxylesterases and shares only 21-35% sequence identity with them. FpbH was expressed in Escherichia coli BL21(DE3) and the product was purified by Ni-NTA affinity chromatography. The purified FpbH hydrolyzed a wide range of AOPP herbicides with catalytic efficiency in the order: haloxyfop-P-methyl > diclofop-methyl > fenoxaprop-P-ethyl > quizalofop-P-ethyl > fluazifop-P-butyl > cyhalofop-butyl. The optimal temperature and pH for FpbH activity were 37 °C and 7, respectively.

CONCLUSIONS

FpbH is a novel AOPP herbicide-hydrolyzing carboxylesterase; it is a good candidate for mechanistic study of AOPP herbicide-hydrolyzing carboxylesterases and for bioremediation of AOPP herbicide-contaminated environments.

Aquamicrobium soli sp. nov., a bacterium isolated from a chlorobenzoate-contaminated soil

An aerobic, Gram-stain negative, short rod-shaped, asporogenous, non-motile bacterium designated strain NK8^T was isolated from a chlorobenzoate contaminated soil in China. Strain NK8^T was observed to grow optimally at pH 7.0, 30 °C and in the absence of NaCl in LB medium. The G + C content of the total DNA of strain NK8^T was found to be 65.5 mol%. The 16S rRNA gene sequence of strain NK8^T showed high similarity to that of Aquamicrobium aerolatum Sa14^T (97.3%), followed by Aquamicrobium lusatiense S1^T (96.7%) and Mesorhizobium sangali SCAU7^T (96.6%). The DNA-DNA relatedness between strain NK8^T and A. aerolatum Sa14^T was 35.5 ± 0.9%. The major fatty acids of strain NK8^T were determined to be C_19:0 cyclo ω8c (45.6%), C_18:1 ω7c (33.4%) and C_16:0 (8.4%). The respiratory quinone was found to be ubiquinone Q-10. The major polyamine was found to be spermidine. The polar lipid profile include the major compounds phosphatidylcholine and diphosphatidylglycerol, and moderate amounts of phosphatidylethanolamine, phosphatidylmonomethylethanolamine, aminolipid and phospholipid. Based on the differential biochemical and physiological characteristics, the geno-, chemo- and phenotypic characteristics, strain NK8^T is proposed to represent a novel species of the genus Aquamicrobium, Aquamicrobium soli sp. nov. The type strain is NK8^T (=KCTC 52165^T=CCTCC AB2016045^T).

Corticibacteriumpopuli gen. nov., sp. nov., a member of the family Phyllobacteriaceae, isolated from bark of Populus×euramericana

Two Gram-staining-negative, aerobic, motile, slimy, glossy bacterial strains were isolated from bark tissue of Populus×euramericana. The bacteria grew at 10-37 °C, pH 5-10, with optimal growth at 28-30 °C, pH 6.0-8.0. Both strains grew with 0-3 % (w/v) NaCl. In the maximum-likelihood phylogenetic tree, the two isolates formed a distinct branch within the family Phyllobacteriaceae, and they were not closely related to any of the genera within the family Phyllobacteriaceae. The two novel isolates werepositive for oxidase andcatalase activity. The polar lipids profile revealed diphosphatidylglycerol, phosphatidylcholine, phospholipid, phosphatidylethanolamine, phosphatidylglycerol and five unknown lipids. The major fatty acids were C18 : 1ω7c and C16 : 0. The DNA G+C content was 56.4 mol%. On the basis of phylogenetic, chemotaxonomic and phenotypic data, the two strains represent a novel species belonging to a novel genus of the family Phyllobacteriaceae, for which the name Corticibacterium populi gen. nov., sp. nov. is proposed. The type strain of the type species is 16B10-2-7^T (=CFCC 12884^T=KCTC 42249^T).

Aquamicrobium aestuarii sp. nov., a marine bacterium isolated from a tidal flat

A Gram-negative, strictly aerobic, motile bacterium with flagella, designated strain G210T, was isolated from a crude-oil-contaminated tidal flat of the Taean coast in South Korea. Cells were non-spore-forming, ovoid rods showing catalase- and oxidase-positive reactions. Growth of strain G210T was observed between 15 and 45 °C (optimum, 30–35 °C) and between pH 5.5 and 9.0 (optimum, pH 6.5–7.5). Strain G210T contained Q-10 as the sole isoprenoid quinone and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C19 : 0 cyclo ω8c as the major fatty acids. Putrescine and spermidine were identified as the major polyamines. Strain G210T contained phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylmonomethylethanolamine, an unidentified phospholipid and an unidentified aminolipid as polar lipids. The G+C content of the genomic DNA was 56.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain G210T formed a phyletic lineage with members of the genus Aquamicrobium . Strain G210T was most closely related to Aquamicrobium ahrensii 905/1T (97.9 % similarity). The DNA–DNA relatedness between strain G210T and the type strain of A. ahrensii was 24±0.5 %. On the basis of phenotypic, chemotaxonomic and molecular properties, strain G210T represents a novel species within the genus Aquamicrobium , for which the name Aquamicrobium aestuarii sp. nov. is proposed. The type strain is G210T ( = KACC 14931T = JCM 16876T).

Thermovum composti gen. nov., sp. nov., an alphaproteobacterium from compost

A Gram-stain-positive thermophilic bacterium, designated strain Nis3T, was isolated from compost. The strain grew at 23–57 °C (optimum, 50 °C); no growth was observed below 15 or above 60 °C. The pH range for growth was 5.9–8.8 (optimum, 7.0); no growth was observed below pH 5.4 or above pH 9.3. The DNA G+C content of strain Nis3T was 63.4 mol%. The dominant quinone type was ubiquinone Q-10. The major fatty acids were C18 : 1ω7c, C19 : 0ω8c cyclo and C18 : 0. The polar lipids comprised phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, hydroxyphosphatidylethanolamine, phosphatidylinositol, phosphatidylmonomethylethanolamine, an unknown glycolipid and a ninhydrin-positive phospholipid. 16S rRNA gene sequence analysis assigned this bacterium to the family Phyllobacteriaceae in the Alphaproteobacteria but it shared less than 95.2 % sequence similarity with other members of the family. The chemotaxonomic and phenotypic characteristics of strain Nis3T differed in some respects from those of members of the family Phyllobacteriaceae . Therefore, strain Nis3T is considered to represent a novel species of a new genus in the family Phyllobacteriaceae , for which the name Thermovum composti gen. nov., sp. nov. is proposed. The type strain is Nis3T ( = JCM 17863T = KCTC 23707T).