Description and genomic characterization of Mesorhizobium marinum sp. nov., a bacterium isolated from sea sediment

Two Gram-stain-negative, aerobic strains, designed ZMM04-4T and ZMM04-5, were isolated from sea sediment collected from Qinzhou Bay, Guangxi Zhuang Automous Region, China. The predominant respiratory quinone was ubiquinone-10. The polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, aminophospholipid and phospholipid. The predominant fatty acids were C18:1ω7c, C19:0 cyclo ω8c and C16:0. Strain ZMM04-4T shared 99.7 % similarity of 16S rRNA gene sequence with ZMM04-5. The digital DNA-DNA hybridization and average nucleotide identity values between strain ZMM04-4T and ZMM04-5 were 92.9 % and 98.6 %, respectively, indicating that strains ZMM04-4T, ZMM04-5 belong to the same species. Phylogenetic and phylogenomic analysis indicated that strains ZMM04-4T and ZMM04-5 belong to the genus Mesorhizobium and showed the highest sequence similarity to Mesorhizobium qingshengii CGMCC 1.12097T (97.7 %-97.8 % sequence similarity) and Mesorhizobium shangrilense DSM 21850T (97.7 %-97.8 %). The average nucleotide identity and digital DNA-DNA hybridization values between strains ZMM04-4T, ZMM04-5 and their closely related species were within the ranges of 76.5 %-77.2 % and 20.9 %-21.8 %, respectively, indicating that strains ZMM04-4T, ZMM04-5 were novel species. In accordance with phylogenetic and genomic as well as phenotypic and chemotaxonomic characterizations, strains ZMM04-4T and ZMM04-5 should be assigned to the genus Mesorhizobium and indentified as a novel species, for which the name Mesorhizobium marinum sp. nov., is proposed. The type strain is ZMM04-4T (=MCCC 1K08883T = KCTC 8273T).

Mesorhizobium koreense sp. nov., Isolated from Soil

An aerobic, Gram-stain-negative, catalase-positive, rod-shaped, and motile bacteria, designated as a strain WR6T was isolated from soil in Republic of Korea. Strain WR6T grew at temperatures of 10-37°C, at pH of 5.0-9.0, and at NaCl concentrations of 0-3.0% (w/v). Phylogenetic and 16S rRNA gene nucleotide sequence analysis confirmed that strain WR6T affiliated to the genus Mesorhizobium, with the nearest relative being Mesorhizobium waimense ICMP 19557T (98.5%). The genome of strain WR6T was 5,035,462 bp with DNA G+C content of 62.6%. In strain WR6T, Q-10 was sole ubiquinone; summed feature 8 (C18:1ω7c and/or C18:1ω6c) and C19:0 cyclo ω8c were predominant fatty acids; and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylcholine, and phosphatidylethanolamine were major polar lipids. Based on these polyphasic taxonomic data, strain WR6T represents a novel species in the genus Mesorhizobium. Accordingly, we propose the name Mesorhizobium koreense sp. nov., with the type strain WR6T (=KCTC 92695T =NBRC 116021T).

New evidence supports the prophage origin of RcGTA

Gene transfer agents (GTAs) are phage-like entities that package and transfer random host genome fragments between prokaryotes. RcGTA, produced by Rhodobacter capsulatus, is hypothesized to originate from a prophage ancestor. Most of the evidence supporting this hypothesis came from the finding of RcGTA-like genes in phages. More than 75% of the RcGTA genes have a phage homolog. However, only a few RcGTA homologs have been identified in a (pro)phage genome, leaving the hypothesis that GTAs evolved from prophages through gene loss with only weak evidence. We herein report the discovery of an inducible prophage (vB_MseS-P1) from a Mesorhizobium sediminum strain that contains the largest number (12) of RcGTA homologs found in a phage genome to date. We also identified three putative prophages and two prophage remnants harboring 12-14 RcGTA homologs in a Methylobacterium nodulans strain. The protein remote homology detection also revealed more RcGTA homologs from other phages than we previously thought. Moreover, the head-tail gene architecture of these newly discovered prophage-related elements closely resembles that of RcGTA. Furthermore, vB_MseS-P1 virions have structural proteins similar to RcGTA particles. Close phylogenetic relationships between certain prophage genes and RcGTA-like genes in Alphaproteobacteria further support the shared ancestry between RcGTA and prophages. Our findings provide new relatively direct evidence of the origin of RcGTA from a prophage progenitor.IMPORTANCEGTAs are important genetic elements in certain groups of bacteria and contribute to the genetic diversification, evolution, and ecological adaptation of bacteria. RcGTA, a common type of GTA, is known to package and transfer random fragments of the bacterial genome to recipient cells. However, the origin of RcGTA is still elusive. It has been hypothesized that RcGTA evolved from a prophage ancestor through gene loss. However, the few RcGTA homologs identified in a (pro)phage genome leave the hypothesis lacking direct evidence. This study uncovers the presence of a large number of RcGTA homologs in an inducible prophage and several putative prophages. The similar head-tail gene architecture and structural protein compositions of these newly discovered prophage-related elements and RcGTA further demonstrate an unprecedentedly observed close evolutionary relationship between prophages and RcGTA. Together, our findings provide more direct evidence supporting the origin of RcGTA from prophage.

Aquibium pacificus sp. nov., a Novel Mixotrophic Bacterium from Bathypelagic Seawater in the Western Pacific Ocean

A novel Gram-stain-negative, facultatively anaerobic, and mixotrophic bacterium, designated as strain LZ166T, was isolated from the bathypelagic seawater in the western Pacific Ocean. The cells were short rod-shaped, oxidase- and catalase-positive, and motile by means of lateral flagella. The growth of strain LZ166T was observed at 10-45 °C (optimum 34-37 °C), at pH 5-10 (optimum 6-8), and in the presence of 0-5% NaCl (optimum 1-3%). A phylogenetic analysis based on the 16S rRNA gene showed that strain LZ166T shared the highest similarity (98.58%) with Aquibium oceanicum B7T and formed a distinct branch within the Aquibium genus. The genomic characterization, including average nucleotide identity (ANI, 90.73-76.79%), average amino identity (AAI, 88.50-79.03%), and digital DNA-DNA hybridization (dDDH, 36.1-22.2%) values between LZ166T and other species within the Aquibium genus, further substantiated its novelty. The genome of strain LZ166T was 6,119,659 bp in size with a 64.7 mol% DNA G+C content. The predominant fatty acid was summed feature 8 (C18:1ω7c and/or C18:1ω6c). The major polar lipids identified were diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), glycolipid (GL), and phosphatidylglycerol (PG), with ubiquinone-10 (Q-10) as the predominant respiratory quinone. The genomic annotation indicated the presence of genes for a diverse metabolic profile, including pathways for carbon fixation via the Calvin-Benson-Bassham cycle and inorganic sulfur oxidation. Based on the polyphasic taxonomic results, strain LZ166T represented a novel species of the genus Aquibium, for which the name Aquibium pacificus sp. nov. is proposed, with the type strain LZ166T (=MCCC M28807T = KACC 23148T = KCTC 82889T).

Lineage-specific evolution of Aquibium, a close relative of Mesorhizobium, during habitat adaptation

The novel genus Aquibium that lacks nitrogenase was recently reclassified from the Mesorhizobium genus. The genomes of Aquibium species isolated from water were smaller and had higher GC contents than those of Mesorhizobium species. Six Mesorhizobium species lacking nitrogenase were found to exhibit low similarity in the average nucleotide identity values to the other 24 Mesorhizobium species. Therefore, they were classified as the non-N2-fixing Mesorhizobium lineage (N-ML), an evolutionary intermediate species. The results of our phylogenomic analyses and the loss of Rhizobiales-specific fur/mur indicated that Mesorhizobium species may have evolved from Aquibium species through an ecological transition. Halotolerant and alkali-resistant Aquibium and Mesorhizobium microcysteis belonging to N-ML possessed many tripartite ATP-independent periplasmic transporter and sodium/proton antiporter subunits composed of seven genes (mrpABCDEFG). These genes were not present in the N2-fixing Mesorhizobium lineage (ML), suggesting that genes acquired for adaptation to highly saline and alkaline environments were lost during the evolution of ML as the habitat changed to soil. Land-to-water habitat changes in Aquibium species, close relatives of Mesorhizobium species, could have influenced their genomic evolution by the gain and loss of genes. Our study indicated that lineage-specific evolution could have played a significant role in shaping their genome architecture and conferring their ability to thrive in different habitats.IMPORTANCEPhylogenetic analyses revealed that the Aquibium lineage (AL) and non-N2-fixing Mesorhizobium lineage (N-ML) were monophyletically grouped into distinct clusters separate from the N2-fixing Mesorhizobium lineage (ML). The N-ML, an evolutionary intermediate species having characteristics of both ancestral and descendant species, could provide a genomic snapshot of the genetic changes that occur during adaptation. Genomic analyses of AL, N-ML, and ML revealed that changes in the levels of genes related to transporters, chemotaxis, and nitrogen fixation likely reflect adaptations to different environmental conditions. Our study sheds light on the complex and dynamic nature of the evolution of rhizobia in response to changes in their environment and highlights the crucial role of genomic analysis in understanding these processes.

Comparative Genome Analysis of Polar Mesorhizobium sp. PAMC28654 to Gain Insight into Tolerance to Salinity and Trace Element Stress

In this study, Mesorhizobium sp. PAMC28654 was isolated from a soil sample collected from the polar region of Uganda. Whole-genome sequencing and comparative genomics were performed to better understand the genomic features necessary for Mesorhizobium sp. PAMC28654 to survive and thrive in extreme conditions and stresses. Additionally, diverse sequence analysis tools were employed for genomic investigation. The results of the analysis were then validated using wet-lab experiments. Genome analysis showed trace elements' resistant proteins (CopC, CopD, CzcD, and Acr3), exopolysaccharide (EPS)-producing proteins (ExoF and ExoQ), and nitrogen metabolic proteins (NarG, NarH, and NarI). The strain was positive for nitrate reduction. It was tolerant to 100 mM NaCl at 15 °C and 25 °C temperatures and resistant to multiple trace elements (up to 1 mM CuSO4·5H2O, 2 mM CoCl2·6H2O, 1 mM ZnSO4·7H2O, 0.05 mM Cd(NO3)2·4H2O, and 100 mM Na2HAsO4·7H2O at 15 °C and 0.25 mM CuSO4·5H2O, 2 mM CoCl2·6H2O, 0.5 mM ZnSO4·7H2O, 0.01 mM Cd(NO3)2·4H2O, and 100 mM Na2HAsO4·7H2O at 25 °C). This research contributes to our understanding of bacteria's ability to survive abiotic stresses. The isolated strain can be a potential candidate for implementation for environmental and agricultural purposes.

Mesorhizobium liriopis sp. nov., isolated from the fermented fruit of Liriope platyphylla a medicinal plant

A facultative anaerobic and Gram-negative strain, designated RP14T, was isolated from the fruit of Liriope platyphylla fermented for 60 days at 25°C. Strain RP14T showed 98.0 % 16S rRNA similarity to Mesorhizobium huakuii IFO 15243T, but in the phylogenetic tree, Mesorhizobium terrae NIBRBAC000500504T was its closest neighbour. The average nucleotide identity and digital DNA-DNA hybridization values between strain RP14T and 15 genomes of type strains of Mesorhizobium, were 73.8-74.4% and 16.4-20.2 %, respectively, which were lower than the recommended thresholds for species delineation. The strain grew at 25-32°C (optimum, 28°C), at pH 7.0-12.0 (optimum, pH 9.0) and with 0-2% NaCl (optimum, 0 %; w/v). Cells of strain RP14T were catalase-positive, oxidase-negative, rod-shaped and formed yellow-coloured colonies. The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The major fatty acid were C16 : 0, C19 : 0 cyclo ω8c and summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c). The DNA G+C content was 62.8 mol%. Based on polyphasic evidence, we propose Mesorhizobium liriopis sp. nov as a novel species within the genus Mesorhizobium. The type strain is RP14T (=KACC 22720T=TBRC 16341T).

Aquibium microcysteis gen. nov., sp. nov., isolated from a Microcystis aeruginosa culture and reclassification of Mesorhizobium carbonis as Aquibium carbonis comb. nov. and Mesorhizobium oceanicum as Aquibium oceanicum comb. nov

A novel bacterial strain, NIBR3T, was isolated from a Microcystis aeruginosa culture. Strain NIBR3T was characterized as Gram-negative, rod-shaped, catalase- and oxidase-positive, and aerobic. The 16S rRNA gene sequence analysis showed that strain NIBR3T was most closely related to Mesorhizobium carbonis B2.3T (=KCTC 52461), Mesorhizobium oceanicum B7T (=KCTC 42783) and Mesorhizobium qingshengii CCBAU 33460T (=HAMBI 3277), at 98.7, 97.2 and 97.2% similarity, respectively. Our phylogenetic analyses revealed that three strains [strain NIBR3T with the previously reported two Mesorhizobium species ( M. carbonis B2.3T and M. oceanicum B7T)] formed a distinct cluster from other Mesorhizobium type strains. The average nucleotide identity of strain NIBR3T relative to M. carbonis B2.3T , M. oceanicum B7T, and M. qingshengii CCBAU 33460T was found to be 84.3, 79.4 and 75.8 %, with average amino-acid identities of 85.1, 74.8 and 64.3 %, and digital DNA–DNA hybridization values of 27.6, 22.6 and 20.7 %, respectively. The genome size and genomic DNA G+C content of NIBR3T were 6.1 Mbp and 67.9 mol%, respectively. Growth of strain NIBR3T was observed at 23–45 °C (optimum, 33 °C), at pH 6–11 (optimum, 8) and in the presence of 0–4 % (w/v) NaCl (optimum, 0 %). The major polar lipids in this novel strain were phosphatidylethanolamine, phosphatidylcholine and phosphatidylmethylethanolamine. The predominant respiratory quinone was Q-10. Summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) was the most abundant cellular fatty acid in strain NIBR3T. Based on genotypic characteristics using our genomic data, strain NIBR3T was identified as a member of new genus, Aquibium gen. nov., with the two aforementioned stains. The type strain f the novel species, Aquibium microcysteis sp. nov., is NIBR3T (=KACC 22092T=HAMBI 3738T). We also reclassified Mesorhizobium carbonis and M. oceanicum as Aquibium carbonis comb. nov. and A. oceanicum comb. nov., respectively.

Aquibium microcysteis gen. nov., sp. nov., isolated from a Microcystis aeruginosa culture and reclassification of Mesorhizobium carbonis as Aquibium carbonis comb. nov. and Mesorhizobium oceanicum as Aquibium oceanicum comb. nov

A novel bacterial strain, NIBR3T, was isolated from a Microcystis aeruginosa culture. Strain NIBR3T was characterized as Gram-negative, rod-shaped, catalase- and oxidase-positive, and aerobic. The 16S rRNA gene sequence analysis showed that strain NIBR3T was most closely related to Mesorhizobium carbonis B2.3T (=KCTC 52461), Mesorhizobium oceanicum B7T (=KCTC 42783) and Mesorhizobium qingshengii CCBAU 33460T (=HAMBI 3277), at 98.7, 97.2 and 97.2% similarity, respectively. Our phylogenetic analyses revealed that three strains [strain NIBR3T with the previously reported two Mesorhizobium species ( M. carbonis B2.3T and M. oceanicum B7T)] formed a distinct cluster from other Mesorhizobium type strains. The average nucleotide identity of strain NIBR3T relative to M. carbonis B2.3T , M. oceanicum B7T, and M. qingshengii CCBAU 33460T was found to be 84.3, 79.4 and 75.8 %, with average amino-acid identities of 85.1, 74.8 and 64.3 %, and digital DNA–DNA hybridization values of 27.6, 22.6 and 20.7 %, respectively. The genome size and genomic DNA G+C content of NIBR3T were 6.1 Mbp and 67.9 mol%, respectively. Growth of strain NIBR3T was observed at 23–45 °C (optimum, 33 °C), at pH 6–11 (optimum, 8) and in the presence of 0–4 % (w/v) NaCl (optimum, 0 %). The major polar lipids in this novel strain were phosphatidylethanolamine, phosphatidylcholine and phosphatidylmethylethanolamine. The predominant respiratory quinone was Q-10. Summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) was the most abundant cellular fatty acid in strain NIBR3T. Based on genotypic characteristics using our genomic data, strain NIBR3T was identified as a member of new genus, Aquibium gen. nov., with the two aforementioned stains. The type strain f the novel species, Aquibium microcysteis sp. nov., is NIBR3T (=KACC 22092T=HAMBI 3738T). We also reclassified Mesorhizobium carbonis and M. oceanicum as Aquibium carbonis comb. nov. and A. oceanicum comb. nov., respectively.

Mesorhizobium xinjiangense sp. nov., isolated from rhizosphere soil of Alhagi sparsifolia

A beige-pigmented, Gram-strain-negative, aerobic, rod-shaped, non-flagellated and non-gliding bacterium, designated strain lm94^T, was isolated from rhizosphere soil of Alhagi sparsifolia obtained from Alar city, located in Xinjiang province, China. Growth occurred at 20-45 °C (optimum, 37 °C), in the presence of 0-6% (w/v) NaCl (optimum, 0-1%) and at pH 6.0-9.5 (optimum, pH 7.0-7.5). Phylogenetic analysis based on 16S rRNA gene sequence showed that strain lm94^T belonged to the genus Mesorhizobium, with highest sequence similarity to Mesorhizobium wenxiniae WYCCWR 10195^T (96.6%). Genome sequencing revealed a genome size of 5 256 375 bp and a G + C content of 63.6 mol%. The average nucleotide identity value and the digital DNA-DNA hybridization value between strain lm94^T and M. wenxiniae LMG 30254^T were 75.0% and 20.0%, respectively. The major respiratory quinone was Q-10. The major fatty acids were C_19:0 cyclo ω8c and Summed Feature 8 (C_18:1 ω6c and/or C_18:1 ω7c) and its polar lipids consisted of phosphatidylethanolamine (PE), phosphatidylglycerol (PG), unidentified phospholipid (PL), phosphatidylcholine (PC), diphosphatidylglycerol (DPG), unidentified aminolipid (AL), unknown glycolipid (GL), unidentified aminophospholipid (APL2) and unidentified polar lipid (L1 and L2). On the basis of these data, strain lm94^T is considered to represent a novel species of the genus Mesorhizobium, for which the name Mesorhizobium xinjiangense sp. nov. is proposed. The type strain is lm94^T (=KCTC 72863^T=CCTCC AB2019377^T).

Mesorhizobium comanense sp. nov., isolated from groundwater

Strain 3P27G6^T was isolated from an artesian well connected to the thermal water basin of Comano Terme, Province of Trento, Italy. In phylogenetic analyses based on multilocus sequence analysis, strain 3P27G6^T clustered together with Mesorhizobium australicum WSM2073^T. Genome sequencing produced a 99.51 % complete genome, with a length of 7 363 057 bp and G+C content of 63.53 mol%, containing 6897 coding sequences, 55 tRNA and three rRNA. Average nucleotide identity analysis revealed that all distances calculated between strain 3P27G6^T and the other Mesorhizobium genomes were below 0.9, indicating that strain 3P27G6^T represents a new species. Therefore, we propose the name Mesorhizobium comanense sp. nov. with the type strain 3P27G6^T (=DSM 110654^T=CECT 30067^T). Strain 3P27G6^T is a Gram-negative, rod-shaped, aerobic bacterium. Growth condition, antibiotic susceptibility, metabolic and fatty acid-methyl esters profiles of the strain were determined. Only few nodulation and nitrogen fixation genes were found in the genome, suggesting that this strain may not be specialized in nodulation or in nitrogen fixation.

Mesorhizobium microcysteis sp. nov., isolated from a culture of Microcystis aeruginosa

Strain MaA-C15^T, a Gram-stain-negative, non-spore-forming and strictly aerobic bacterium, was isolated from a xenic culture of Microcystis aeruginosa in the Republic of Korea. Cells were motile rods showing positive reactions in catalase and oxidase tests. Growth was observed between 15 and 37 °C (optimum, 30 °C), between pH 6.0 and pH 11.0 (optimum, pH 7.5) and in the presence of 0-2.0 % (w/v) NaCl (optimum, 0 %). Strain MaA-C15^T contained C_16 : 0, 11-methyl-C_18 : 1  ω7c, cyclo-C_19 : 0  ω8c and summed feature 8 (C_18 : 1  ω6c and/or C_18 : 1  ω7c) as the major cellular fatty acids and ubiquinone-10 as the sole respiratory quinone. Phosphatidylethanolamine, phosphatidylmonomethylethanolamine, an unidentified aminophospholipid, an unidentified glycolipid and three unidentified phospholipids were detected as the major polar lipids. The G+C content of the genomic DNA was 64.1 mol%. Phylogenetic and phylogenomic analyses based on 16S rRNA gene and genome sequences revealed that strain MaA-C15^T formed a phyletic lineage with Mesorhizobium sediminum YIM M12096^T within the family Phyllobacteriaceae. Strain MaA-C15^T was most closely related to Mesorhizobium albiziae DSM 21822^T with a 98.2 % 16S rRNA sequence similarity. Average nucleotide identity and in silico DNA-DNA hybridization values between strain MaA-C15^T and M. albiziae DSM 21822^T were 75.4 and 20.1 %, respectively. Based on the results of phenotypic, chemotaxonomic and molecular analyses, strain MaA-C15^T represents a novel species of the genus Mesorhizobium, for which the name Mesorhizobium microcysteis sp. nov. is proposed. The type strain is MaA-C15^T (=KACC 21226^T=JCM 33503^T).

Investigating the Involvement of Cytoskeletal Proteins MreB and FtsZ in the Origin of Legume-Rhizobial Symbiosis

Rhizobia are rod-shaped bacteria that form nitrogen-fixing root nodules on leguminous plants; however, they don't carry MreB, a key determinant of rod-like cell shape. Here, we introduced an actin-like mreB homolog from a pseudomonad into Mesorhizobium huakuii 7653R (a microsymbiont of Astragalus sinicus L.) and examined the molecular, cellular, and symbiotic phenotypes of the resultant mutant. Exogenous mreB caused an enlarged cell size and slower growth in laboratory medium. However, the mutant formed small, ineffective nodules on A. sinicus (Nod⁺ Fix^-), and rhizobial cells in the infection zone were unable to differentiate into bacteroids. RNA sequencing analysis also revealed minor effects of mreB on global gene expression in free-living cells but larger effects for cells grown in planta. Differentially expressed nodule-specific genes include cell cycle regulators such as the tubulin-like ftsZ₁ and ftsZ₂. Unlike the ubiquitous FtsZ₁, an FtsZ₂ homolog was commonly found in Rhizobium, Sinorhizobium, and Mesorhizobium spp. but not in closely related nonsymbiotic species. Bacterial two-hybrid analysis revealed that MreB interacts with FtsZ₁ and FtsZ₂, which are targeted by the host-derived nodule-specific cysteine-rich peptides. Significantly, MreB mutation D283A disrupted the protein-protein interactions and restored the aforementioned phenotypic defects caused by MreB in M. huakuii. Together, our data indicate that MreB is detrimental for modern rhizobia and its interaction with FtsZ₁ and FtsZ₂ causes the symbiotic process to cease at the late stage of bacteroid differentiation. These findings led to a hypothesis that loss of mreB in the common ancestor of members of Rhizobiales and subsequent acquisition of ftsZ₂ are critical evolutionary steps leading to legume-rhizobial symbiosis.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Mesorhizobium rhizophilum sp. nov., a 1-aminocyclopropane-1-carboxylate deaminase producing bacterium isolated from rhizosphere of maize in Northeast China

A novel 1-aminocyclopropane-1-carboxylate deaminase producing bacterium, Gram- stain-negative, aerobic, motile, rod-shaped strain designated YM1C-6-2^T was isolated from rhizosphere of maize grown in Northeast China. The 16S rRNA gene sequence analysis indicated that strain YM1C-6-2^T belongs to the genus Mesorhizobium and is closely related to Mesorhizobium alhagi CCNWXJ12-2^T and M. camelthorni CCNWXJ40-4^T with sequence similarities of 98.4% and 97.9%, respectively. Multilocus sequence analysis of other housekeeping genes revealed that the new isolates YM1C-6-2^T forms a phylogenetically group with some species in the genus Mesorhizobium. The genome size of strain YM1C-6-2^T was 5.51 Mb, comprising 5378 predicted genes with a DNA G+C content of 64.5%. The average nucleotide identity and digital DNA-DNA hybridization comparisons between YM1C-6-2^T and the most related type strains showed values below the accepted threshold for species discrimination. The major fatty acids of strain YM1C-6-2^T were C_19:0 cyclo ω8c (47.5%), summed feature 8 (C_18:1ω7c and/or C_18:1ω6c) (19.5%) and C_16:0 (15.1%), which differed from the closely related reference strains in their relative abundance. The major polar lipids consist of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and an unidentified aminophospholipid. The predominant ubiquinone was identified as Quinone 10. Phenotypic and biochemical analysis results indicated that strain YM1C-6-2^T can be distinguished from closely related type strains. Based on the above results, strain YM1C-6-2^T represents a novel species of the genus Mesorhizobium, for which the name Mesorhizobium rhizophilum sp. nov. is proposed with YM1C-6-2^T (= CGMCC 1.15487^T = DSM 101712^T) as the type strain.

Mesorhizobium alexandrii sp. nov., isolated from phycosphere microbiota of PSTs-producing marine dinoflagellate Alexandrium minutum amtk4

An aerobic, Gram-stain-negative, motile and rod-shaped bacterial strain, designated as Z1-4^T, was isolated from the phycosphere microbiota of marine dinoflagellate Alexandrium minutum that produces paralytic shellfish poisoning toxins. Phylogenetic analysis based on 16S rRNA gene sequences showed that the new isolate belongs to the genus Mesorhizobium, and it was closely related to Mesorhizobium waimense LMG 28228^T and Mesorhizobium amorphae LMG 18977^T with both 16S rRNA gene sequence similarities of 97.3%. The values of average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) relatedness between strain Z1-4^T and its relatives are both well below the thresholds used for the delineation of a new species. A genome-based phylogenetic tree constructed by up-to-date bacterial core gene set (UBCG) indicates that strain Z1-4^T forms an independent branch within the genus Mesorhizobium. The respiratory quinone of strain Z1-4^T was Q-10. The major fatty acids were similar to other members of the genus Mesorhizobium containing the summed feature 8, C_16:0, C_19:0cycloω8c, C_17:0 and summed feature 3. The polar lipids are phosphatidylmonomethylethanolamine, diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminophospholipid, five glycolipids and seven unknown polar lipids. The DNA G + C content was determined to be 62.1 mol % based on its genomic sequence. Combined evidences based on the genotypic, chemotaxonomic and phenotypic characteristics clearly indicates that strain Z1-4^T represents a novel species of the genus Mesorhizobium, for which the name Mesorhizobium alexandrii sp. nov. is proposed. The type strain is Z1-4^T (= KCTC 72512^T = CCTCC AB 2019101^T).

Micromonospora zhangzhouensis sp. nov., a Novel Actinobacterium Isolated from Mangrove Soil, Exerts a Cytotoxic Activity in vitro

A new bacterial strain, designated HM134^T, was isolated from a sample of soil collected from a Chinese mangrove Avicennia marina forest. Assessed by a polyphasic approach, the taxonomy of strain HM134^T was found to be associated with a range of phylogenetic and chemotaxonomic properties consistent with the genus Micromonospora. Phylogenetic analysis based on the 16s rRNA gene sequence indicated that strain HM134^T formed a distinct lineage with the most closely related species, including M. rifamycinica AM105^T, M. wenchangensis CCTCC AA 2012002^T and M. mangrovi 2803GPT1-18^T. The ANI values between strain HM134^T and the reference strains ranged from 82.6% to 95.2%, which was below the standard criteria for classifying strains as the same species (96.5%). Strain HM134^T and related species shared in silico dDDH similarities values below the recommended 70% cut-off for the delineation of species (range from 25.7–62.6%). The DNA G+C content of strain HM134^T was 73.2 mol%. Analysis of phylogenetic, genomic, phenotypic and chemotaxonomic characteristics revealed that strain HM134^T is considered to represent a novel species of the genus Micromonospora, for which the name M. zhangzhouensis sp. nov. is proposed. The extract of strain HM134^T was demonstrated to exhibit cytotoxic activity against the human cancer cell lines HepG2, HCT-116 and A549. Active substance presented in the fermentation broth of strain HM134^T was isolated by bioassay-guided analysis and purified afterwards. A new derivative of diterpenoid was identified through electrospray ionizing mass spectrometry (MS) and nuclear magnetic resonance (NMR). The compound showed different cytotoxic activities against cancer cells, with the highest cytotoxicity against HCT-116, corresponding to IC₅₀ value of 38.4 μg/mL.

Pseudomonas mangrovi sp. nov., isolated from mangrove soil

A Gram-stain-negative, aerobic, non-motile, short-rod-shaped bacterium, designated as strain TC11^T, was isolated from rhizosphere soil of mangrove forest (Kandeliaobovata) in Fugong village, Zhangzhou, Fujian, China. Strain TC11^T grew at 15-45 °C (optimum, 35 °C), 0-8 % (w/v) NaCl (optimum, 1 %, w/v) and pH 5.5-9.5 (optimum, pH 7.5). Phylogenetic analyses revealed that strain TC11^T belonged to a clade of the genus Pseudomonas and showed the highest sequence similarity of 98.4 % to Pseudomonas fluvialis ASS-1^T, followed by Pseudomonas oleovorans subsp.oleovorans DSM 1045^T (97.9 %), Pseudomonas indoloxydans JCM 14246^T (97.7 %), Pseudomonas guguanensis JCM 18416^T(97.6 %) and Pseudomonas alcaliphila JCM 10630^T (97.5 %) on the basis of their 16S rRNA gene sequences. The DNA G+C content was 64.3 mol%. In silico DNA-DNA hybridization and average nucleotide identity values between strain TC11^T and the reference strains were 19-22 % and 72-78 %, respectively. Studies based on the three housekeeping genes, rpoB, gyrB and rpoD, further confirmed that strain TC11^T is a novel member of the genus Pseudomonas. The major fatty acids of strain TC11^Twere C16 : 0, summed feature 8 (C18 : 1ω6c/C18 : 1ω7c) and summed feature 3 (C16 : 1ω7c/C16 : 1ω6c). The sole isoprenoid quinone was Q-9. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Based on the phenotypic, chemotaxonomic and phylogenetic properties, strain TC11^T represents a novel species of the genus Pseudomonas, for which the name Pseudomonasmangrovi sp. nov., is proposed. The type strain is TC11^T (=KCTC 62159=MCCC 1K03499).