A long-awaited taxogenomic investigation of the family Halomonadaceae

The family Halomonadaceae is the largest family composed of halophilic bacteria, with more than 160 species with validly published names as of July 2023. Several classifications to circumscribe this family are available in major resources, such as those provided by the List of Prokaryotic names with Standing in Nomenclature (LPSN), NCBI Taxonomy, Genome Taxonomy Database (GTDB), and Bergey's Manual of Systematics of Archaea and Bacteria (BMSAB), with some degree of disagreement between them. Moreover, regardless of the classification adopted, the genus Halomonas is not phylogenetically consistent, likely because it has been used as a catch-all for newly described species within the family Halomonadaceae that could not be clearly accommodated in other Halomonadaceae genera. In the past decade, some taxonomic rearrangements have been conducted on the Halomonadaceae based on ribosomal and alternative single-copy housekeeping gene sequence analysis. High-throughput technologies have enabled access to the genome sequences of many type strains belonging to the family Halomonadaceae; however, genome-based studies specifically addressing its taxonomic status have not been performed to date. In this study, we accomplished the genome sequencing of 17 missing type strains of Halomonadaceae species that, together with other publicly available genome sequences, allowed us to re-evaluate the genetic relationship, phylogeny, and taxonomy of the species and genera within this family. The approach followed included the estimate of the Overall Genome Relatedness Indexes (OGRIs) such as the average amino acid identity (AAI), phylogenomic reconstructions using amino acid substitution matrices customized for the family Halomonadaceae, and the analysis of clade-specific signature genes. Based on our results, we conclude that the genus Halovibrio is obviously out of place within the family Halomonadaceae, and, on the other hand, we propose a division of the genus Halomonas into seven separate genera and the transfer of seven species from Halomonas to the genus Modicisalibacter, together with the emendation of the latter. Additionally, data from this study demonstrate the existence of various synonym species names in this family.

Aromatic compounds depurative and plant growth promotion rhizobacteria abilities of Allenrolfea vaginata (Amaranthaceae) rhizosphere microbial communities from a solar saltern hypersaline soil

Introduction

This work investigates whether rhizosphere microorganisms that colonize halophyte plants thriving in saline habitats can tolerate salinity and provide beneficial effects to their hosts, protecting them from environmental stresses, such as aromatic compound (AC) pollution.

Methods

To address this question, we conducted a series of experiments. First, we evaluated the effects of phenol, tyrosine, 4-hydroxybenzoic acid, and 2,4-dichlorophenoxyacetic (2,4-D) acids on the soil rhizosphere microbial community associated with the halophyte Allenrolfea vaginata. We then determined the ability of bacterial isolates from these microbial communities to utilize these ACs as carbon sources. Finally, we assessed their ability to promote plant growth under saline conditions.

Results

Our study revealed that each AC had a different impact on the structure and alpha and beta diversity of the halophyte bacterial (but not archaeal) communities. Notably, 2,4-D and phenol, to a lesser degree, had the most substantial decreasing effects. The removal of ACs by the rhizosphere community varied from 15% (2,4-D) to 100% (the other three ACs), depending on the concentration. Halomonas isolates were the most abundant and diverse strains capable of degrading the ACs, with strains of Marinobacter, Alkalihalobacillus, Thalassobacillus, Oceanobacillus, and the archaea Haladaptatus also exhibiting catabolic properties. Moreover, our study found that halophile strains Halomonas sp. LV-8T and Marinobacter sp. LV-48T enhanced the growth and protection of Arabidopsis thaliana plants by 30% to 55% under salt-stress conditions.

Discussion

These results suggest that moderate halophile microbial communities may protect halophytes from salinity and potential adverse effects of aromatic compounds through depurative processes.

Aliidiomarina quisquiliarum sp. nov., isolated from landfill leachate

Bacterial strain Y-6^T, isolated from a landfill site in Yiwu, PR China, was characterized using a polyphasic taxonomy approach. Cells were Gram-stain-negative, aerobic, rod-shaped, motile by means of a single polar flagellum and formed pale beige colonies. Strain Y-6^T grew at 4-40 °C (optimal at 30-37 °C), pH 6.5-9.5 (optimal at pH 7.2-8.5) and in the presence of 0.5-10.0 % (w/v) NaCl (optimal at 1.0-3.0 %). Phylogenetic analysis revealed that strain Y-6^T was a member of the genus Aliidiomarina and closely related to Aliidiomarina taiwanensis MCCC 1A06493^T with a 16S rRNA sequence similarity of 98.2 %. The major cellular fatty acids of the isolate were iso-C_15 : 0, C_16 : 0, iso-C_17 : 0 and summed feature 9 (iso-C_17 : 1  ω9c and/or 10-methyl-C_16 : 0). Q-8 was the predominant ubiquinone. The major polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, aminoglycophospholipid, aminophospholipid, phospholipid, three glycolipids and two unknown lipids. The genomic DNA G+C content was 46.6 mol%. The digital DNA-DNA hybridization value between Y-6^T and A. taiwanensis MCCC 1A06493^T was 18.3 %. Strain Y-6^T had an average nucleotide identity value of 74.09 % with A. taiwanensis MCCC 1A06493^T. Results from the polyphasic taxonomy study support the conclusion that strain Y-6^T represents a novel Aliidiomarina species, for which the name Aliidiomarina quisquiliarum sp.nov. is proposed. The type strain is Y-6^T (=MCCC 1K06228^T=KCTC 82676^T).

Complete genome sequencing and comparison of two nitrogen-metabolizing bacteria isolated from Antarctic deep-sea sediment

BACKGROUND

Bacteria are an essential component of the earth`s biota and affect circulation of matters through their metabolic activity. They also play an important role in the carbon and nitrogen cycle in the deep-sea environment. In this paper, two strains from deep-sea sediments were investigated in order to understand nitrogen cycling involved in the deep-sea environment.

RESULTS

In this paper, the basic genomic information of two strains was obtained by whole genome sequencing. The Cobetia amphilecti N-80 and Halomonas profundus 13 genome sizes are 4,160,095 bp with a GC content of 62.5% and 5,251,450 bp with a GC content of 54.84%. Through a comparison of functional analyses, we predicted the possible C and N metabolic pathways of the two strains and determined that Halomonas profundus 13 could use more carbon sources than Cobetia amphilecti N-80. The main genes associated with N metabolism in Halomonas profundus 13 are narG, narY, narI, nirS, norB, norC, nosZ, and nirD. On the contrast, nirD, using NH₄⁺ for energy, plays a main role in Cobetia amphilecti N-80. Both of them have the same genes for fixing inorganic carbon: icd, ppc, fdhA, accC, accB, accD, and accA.

CONCLUSION

In this study, the whole genomes of two strains were sequenced to clarify the basic characteristics of their genomes, laying the foundation for further studying nitrogen-metabolizing bacteria. Halomonas profundus 13 can utilize more carbon sources than Cobetia amphilecti N-80, as indicated by API as well as COG and KEGG prediction results. Finally, through the analysis of the nitrification and denitrification abilities as well as the inorganic carbon fixation ability of the two strains, the related genes were identified, and the possible metabolic pathways were predicted. Together, these results provide molecular markers and theoretical support for the mechanisms of inorganic carbon fixation by deep-sea microorganisms.

Halomonas alkalisoli sp. nov., a novel haloalkalophilic species from saline-alkaline soil, and reclassification of Halomonas daqingensis Wu et al. 2008 as a later heterotypic synonym of Halomonas desiderata Berendes et al. 1996

Two Gram-stain-negative, strictly aerobic, moderately halophilic, non-spore-forming and rod-shaped bacteria, designated M5N1S17T and M5N1S15, were isolated from saline soil in Baotou, China. A phylogenetic analysis based on 16S rRNA gene sequences showed that the two strains clustered closely with Halomonas montanilacus PYC7WT and shared 99.1 and 99.3% sequence similarities, respectively. The average nucleotide identity based on BLAST (ANIb) and MUMmer (ANIm) values of the two strains with each other were 95.5% and 96.7%, respectively, while the ANIb and ANIm values between the two strains and 15 closer Halomonas species were 74.8-91.3% and 84.1-92.6%, respectively. The major polar lipids of M5N1S17T are diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, and an unidentified phospholipid. The major polar lipids of M5N1S15 are diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, two unidentified phospholipids, and an unidentified lipid. The predominant ubiquinone in the two strains is Q-9. The major fatty acids of the two strains are C18:1ω6c and/or C18:1ω7c, C16:0, and C16:1ω7c and/or C16:1ω6c. Based on phylogenetic, phenotypic, and physiological results, strains M5N1S17T and M5N1S15 should be identified as a novel species of the genus Halomonas, for which Halomonas alkalisoli sp. nov. is proposed. The type strain is M5N1S17T (= CGMCC 1.19023T = KCTC 92130T). The phylogenetic trees showed that Halomonas daqingensis CGMCC 1.6443T clustered tightly with Halomonas desiderata FB2T, and the two strains shared >98.0% of ANI values with each other. Therefore, we propose the reclassification of H. daqingensis Wu et al. 2008 as a later heterotypic synonym of H. desiderata Berendes et al. 1996.

Halomonas salinarum sp. nov., a moderately halophilic bacterium isolated from saline soil in Yingkou, China

Strain G5-11^T, a Gram-negative, moderately halotolerant, facultatively aerobic, motile bacterium was isolated from saline soil collected from Yingkou, Liaoning, China. The cells of strain G5-11^T grew in the presence of 3–15% (w/v) NaCl (optimum 5%), at between 4 and 35 °C (optimum 30 °C), and at a pH of 6.0–9.0 (optimum 8.0). The major respiratory quinone was Q-9 and the dominant cellular fatty acids were summed feature 8 (C_18:1ω7c/C_18:1ω6c), C_16:0, and summed feature 3 (C_16:1ω7c/C_16:1ω6c). The major components of the polar lipid profile were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol and unidentified aminolipid. The G + C content of the strain G5-11^T genome was 61.0 mol%. The isolated strain G5-11^T showed the highest 16S rRNA gene similarity to Halomonas niordiana LMG 31227^T and Halomonas taeanensis DSM 16463^T, both reaching 98.3%, followed by Halomonas pacifica NBRC 102220^T. The results from phenotypic, chemotaxonomic, and phylogenetic analyses showed that strain G5-11^T represented a novel species of the genus Halomonas, for which the name Halomonas salinarum sp. nov. was proposed. The type strain of Halomonas salinarum is G5-11^T (= CGMCC 1.12051^T = LMG 31677^T).

Halomonas bachuensis sp. nov., Isolated from Gobi Soil

A novel aerobic bacterium designated DX6T was isolated from a Gobi soil sample collected in Bachu County, China. Cells are Gram-stain-negative and rod-shaped and colonies are creamy, circular and smooth. The growth range of NaCl concentration was 1-15% (optimum 2-10%, w/v). Growth occurs at 10-45 °C (optimum 37 °C) and pH 5.0-10.0 (optimum pH 7.0-9.0). Phylogenetic analysis of the 16S rRNA gene sequences indicated that strain DX6T formed a distinct lineage in the clade of genus Halomonas and is related to Halomonas desiderata DSM 9502T (98.3%), Halomonas kenyensis AIR-2T (97.7%), Halomonas daqingensis DQD2-30T (97.6%), Halomonas saliphila LCB169T (97.4%) and Halomonas endophytica MC28T (96.2%). Analysis of the housekeeping genes gryB and rpoD and calculation of the average nucleotide identities and the digital DNA-DNA hybridization values between strain DX6T and the related type Halomonas strains further revealed that strain DX6T represented a distinct species. The main respiratory quinones of strain DX6T were ubiquinone 9 (Q-9) and ubiquinone 8 (Q-8). The predominant cellular fatty acids were summed feature 8 (C18:1ω7c and/or C18:1ω6c), summed feature 3 (C16:1ω7c and/or C16:1ω6c) and C16:0. The major polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids, an unidentified phosphatidylglycolipid, and four unidentified lipids. Based on the phenotypic, phylogenetic, chemotaxonomic and genomic features, strain DX6T represents a novel species of the genus Halomonas. The name Halomonas bachuensis sp. nov. is proposed with strain DX6T (= CCTCC AB 2020094T = KCTC 82196T) designated as the type strain.

Nitratireductor mangrovi sp. nov., a Nitrate-Reducing Bacterium Isolated from Mangrove Soil

A Gram-stain-negative, non-motile and short-rod-shaped bacterium, designated as strain SY7^T, was isolated from rhizosphere soil of the mangrove Kandelia obovata of Fugong village, in Zhangzhou, China. The isolate grew at 10-45 °C (optimum 30 °C), pH 6.0-10.0 (optimum pH 7.0) and 0-8% NaCl (optimum 3%, w/v). The 16S rRNA gene sequence and phylogenetic analysis revealed that strain SY7^T located within the radiation of genus Nitratireductor and showed the highest sequence similarity of 97.23% to Nitratireductor pacificus MCCC 1A01024^T. The DNA G+C content was 64.9%. In silico DNA-DNA hybridization and average nucleotide identity values between strain SY7^T with reference strains of N. pacificus MCCC 1A01024^T, N. basaltis KCTC 22119^T and N. aquibiodomus DSM 15645^T were 16.7%, 14.3%, 14.7% and 75.2%, 72.6%, 73.5%, respectively. The major isoprenoid quinone was Q-10. The dominant fatty acids were 11-methyl C_18:1ω7c, iso-C_17:0, C_19:0ω8c cyclo and summed feature 8 (C_18:1ω6c/C_18:1ω7c), a profile that almost matched the other members of the genus Nitratireductor. The predominant polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol. On the basis of the phenotypic, phylogenetic and chemotaxonomic analysis, strain SY7^T represents a novel species of the genus Nitratireductor, for which the name Nitratireductor mangrovi sp. nov., is proposed. The type strain is SY7^T (= KCTC 72110^T = MCCC 1K03723^T).

Idiomarina mangrovi sp. nov., isolated from rhizosphere soil of a mangrove Avicennia marina forest

A Gram-staining negative, aerobic, motile and rod-shaped bacterium, designated ZQ330^T, was isolated from rhizosphere soil of a mangrove (Avicennia marina) forest of Zhangzhou, Fujian Province, China. The growth range of NaCl concentration was 0.5-10.0 % (w/v), with an optimum at 2.5-3.0 % (w/v), the temperature range for growth was 10-40 °C, with an optimum at 28-30 °C, the pH range for growth was pH 6.0-9.5, with an optimum at pH 7.5. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain ZQ330^T exhibited less than 97.0 % sequence similarity to all type strains with validly published names and revealed that strain ZQ330^T formed a distinct lineage in the genus Idiomarina. The average nucleotide identity, and in silico DNA-DNA hybridization values between strain ZQ330^T and the reference strains were 64.8-69.9 % and 27.5-28.4 %, respectively. Chemotaxonomic analysis indicated that the main respiratory quinone was Q-8, the predominant cellular fatty acids were iso-C15 : 0, iso-C17 : 0, summed feature 9 (C16 : 0 10-methyl and/or iso-C17 : 1ω9c), iso-C15 : 1F, C16 : 0, C18 : 0, summed feature 3 (C16 : 1ω8c and/or iso-C16 : 1 2-OH) and summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c). The polar lipid profile was composed of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unidentified glycolipid, an unidentified aminolipid, an unidentified phospholipid and two unidentified lipids. Based on the genotypic, phenotypic, chemotaxonomic and phylogenetic features, strain ZQ330^T is considered to represent a novel species, for which the name Idiomarina mangrovi sp. nov. is proposed. The type strain is ZQ330^T (=MCCC 1K03495^T=KCTC 62455^T).