Genomic and Metabolomic Analyses of Nocardiopsis maritima YSL2 as the Mycorrhizosphere Bacterium of Suaeda maritima (L.) Dumort.

Nine bacteria were isolated from the episphere of Suaeda maritima (L.) Dumort. Among them, the bacterial strain YSL2 displayed the highest antimicrobial activity on agar plates and exhibited significant novelty compared with other bacteria based on 16S rRNA analysis. Consequently, Nocardiopsis maritima YSL2T was subjected to phenotypic characterization and whole-genome sequencing. Phylogenetic analysis revealed its close association with Nocardiopsis aegyptia SNG49T. Furthermore, genomic analysis of strain YSL2T revealed the presence of various gene clusters, indicating its potential for producing antimicrobial secondary metabolites. Upon cultivation on a large scale, maritiamides A and B (1 and 2) were isolated and characterized as cyclic hexapeptides based on nuclear magnetic resonance, ultraviolet, infrared, and mass spectrometric data. The absolute configurations of the amino acid residues in the maritiamides were determined through chiral derivatization, utilizing FDAA and GITC. Maritiamides 1 and 2 exhibited promising antibacterial activities against Staphylococcus epidermidis and weakly inhibited the growth of Escherichia coli and Pseudomonas fluorescens.

Pharmacological Properties of Four Plant Species of the Genus Anabasis, Amaranthaceae.

The genus Anabasis is a member of the family Amaranthaceae (former name: Chenopodiaceae) and includes approximately 102 genera and 1400 species. The genus Anabasis is one of the most significant families in salt marshes, semi-deserts, and other harsh environments. They are also renowned for their abundance in bioactive compounds, including sesquiterpenes, diterpenes, triterpenes, saponins, phenolic acids, flavonoids, and betalain pigments. Since ancient times, these plants have been used to treat various diseases of the gastrointestinal tract, diabetes, hypertension, and cardiovascular diseases and are used as an antirheumatic and diuretic. At the same time, the genus Anabasis is very rich in biologically active secondary metabolites that exhibit great pharmacological properties such as antioxidant, antibacterial, antiangiogenic, antiulcer, hypoglycemic, hepatoprotective, antidiabetic, etc. All of the listed pharmacological activities have been studied in practice by scientists from different countries and are presented in this review article to familiarize the entire scientific community with the results of these studies, as well as to explore the possibilities of using four plant species of the genus Anabasis as medicinal raw materials and developing medicines based on them.

Biostimulation of Salicornia europaea L. crops with plant growth-promoting bacteria in laboratory and field conditions: effects on growth and metabolite profile.

AIM: The objective of the work was to assess the effect of biostimulation with selected plant growth-promoting bacteria on growth and metabolite profile of Salicornia europaea. METHODS AND RESULTS: Salicornia europaea seeds were inoculated with different combinations of plant growth-promoting bacteria Brevibacterium casei EB3, Pseudomonas oryzihabitans RL18, and Bacillus aryabhattai SP20. Plants germinated from inoculated seeds were grown either in laboratory conditions or in a saline crop field. Fresh and dry weight were determined at the end of the experiment, for biomass quantification. The microbiological quality of fresh shoots for human consumption as salad greens was assessed, and the persistence of the inoculated strains in the plant rhizosphere was confirmed by next-generation sequencing (Illumina) of the 16S rDNA gene. The primary metabolite profile of biostimulated plants was characterized by GC-TOF-MS.In laboratory conditions, inoculation with the two strains Br. casei EB3 and Ps. oryzihabitans RL18 caused the most significant increase in biomass production (fresh and dry weight), and caused a shift in the central metabolic pathways of inoculated plants toward amino acid biosynthesis. In the field experiment, no significant biostimulation effect was detected with any of the tested inoculants. Seed inoculation had no significant effect on the microbiological quality of the edible parts. The persistence of inoculants was confirmed in both experiments. CONCLUSIONS: Manipulation of the plant microbiome can trigger primary metabolic reconfiguration and modulate the plant metabolism while promoting plant growth.

Acuticoccus kalidii sp. nov., a 1-aminocyclopropane-1-carboxylate (ACC) deaminase-producing endophyte from a root of Kalidium cuspidatum.

A 1-aminocyclopropane-1-carboxylate (ACC) deaminase-producing, Gram-stain-negative, strictly aerobic, non-motile, yellow-reddish, oval-shaped bacterial strain, designated M5D2P5T, was isolated from a root of Kalidium cuspidatum, in Tumd Right Banner, Inner Mongolia, PR China. M5D2P5T grew at 10-40 °C (optimum 30-35 °C), pH 5.0-10.0 (optimum pH 8.0) and with 0-7% NaCl (optimum 3.0 %). The strain was positive for catalase and oxidase. The phylogenetic trees based on 16S rRNA gene sequences indicated that M5D2P5T clustered with Acuticoccus yangtzensis JL1095T, and shared 98.0, 97.3, 97.2, 96.9 and less than 96.9 % 16S rRNA gene similarities to A. yangtzensis JL1095T, Acuticoccus mangrovi B2012T, Acuticoccus sediminis PTG4-2T, Acuticoccus kandeliae J103T, and all the other type strains, respectively. However, the phylogenomic tree showed it clustered with A. kandeliae J103T. M5D2P5T contained Q-10 as the major respiratory quinone, as well as two minor respiratory quinones, Q-7 and Q-8. Its major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unidentified phospholipid, an unidentified glycolipid, and four unidentified lipids. The genomic DNA G+C content was 66.5 %. The digital DNA-DNA hybridization score and the average nucleotide identity based on blast values of M5D2P5T to A. yangtzensis JL1095T, A. kandeliae J103T, A. mangrovi B2012T, and A. sediminis PTG4-2T, were 20.8, 23.7, 20.7, and 21.5 %, and 73.3, 79.5, 74.4, and 73.7 %, respectively. The phylogenetic and phenotypic characteristics allowed the discrimination of M5D2P5T from its phylogenetic relatives. The novel species Acuticoccus kalidii sp. nov. is therefore proposed, and the type strain is M5D2P5T (=CGMCC 1.19149T=KCTC 92132T).

The potential of mineral weathering of halophilic-endophytic bacteria isolated from Suaeda salsa and Spartina anglica.

Bacteria have the abilities of salt tolerant, mineral weathering and plant growth promoting can promote the growth of plants in saline lands. However, few reports of the mineral weathering capacity of halophilic-endophytic bacteria, raising the question of whether the halophilic-endophytic weathering bacteria are fundamentally distinct from those in plants communities. In this study, we isolated and characterized halophilic bacterial strains from the roots and leaves of Suaeda salsa and Spartina anglica with respect to their mineral weathering pattern, role in the promoting plant growth, community structure, and their changes in these two plants. Using improved Gibbson medium, we obtained 156 halophilic bacterial strains, among which 92 and 64 strains were isolated from the S. salsa and S. anglica samples, respectively. The rock weathering patterns of the isolates were characterized using batch cultures that measure the quantity of Si, Al, K, and Fe released from crystal biotite under aerobic conditions. Significantly, the biomass and capacity of the mineral weathering of the halophilic-endophytic bacteria were different in the plants. The abundance of the halophilic-endophytic bacterials in the Suaeda salsa was significantly greater than Spartina anglica, whereas the mineral weathering bacterial in the Suaeda salsa was similar to the Spartina anglica. Furthermore, the proportion of plant growth-promoting bacteria in the Suaeda salsa was higher than Spartina anglica. Phylogenetic analyses show that the weathered minerals were inhabited by specific functional groups of bacteria (Halomonas, Acinetobacter, Burkholderia, Alcaligenes, Sphingobium, Arthrobacter, Chryseobacterium, Paenibacillus, Microbacterium, Ensifer, Ralstonia and Enterobacter) that contribute to the mineral weathering. The changes in halophilic endophytes weathering communities between the two plants were attributable not only to major bacterial groups but also to a change in the minor population structure.

Description and characterization of three endophytic Bacillaceae from the halophyte Suaeda salsa: Paenalkalicoccus suaedae gen. nov., sp. nov., Cytobacillus suaedae sp. nov., and Bacillus suaedae sp. nov.

Three strains of members of the family Bacillaceae, which can inhibit the growth of some Gram-stain-positive strains, designated M4U3P1T, HD4P25T and RD4P76T, were isolated from Suaeda salsa halophytes in Baotou, Inner Mongolia, PR China. A phylogenetic analysis based on the 16S rRNA gene and the whole genome sequences revealed that HD4P25T clustered with Cytobacillus luteolus YIM 93174T with a similarity of 98.4 %, and RD4P76T shared the highest similarity of 16S rRNA gene with Bacillus mesophilus SA4T (97.5 %). M4U3P1T clustered with strains of genera Salipaludibacillus and Alkalicoccus based on whole-genome sequence analyses, but its 16S rRNA gene had the highest similarity to 'Evansella tamaricis' EGI 80668 (96.1 %). The average nucleotide's identity by blast (ANIb) and digital DNA-DNA hybridization (dDDH) values of the three isolated strains to their close relatives were well below the threshold value for identifying a novel species.On the basis of the phylogenetic, physiological and phenotypic results, Paenalkalicoccus suaedae gen. nov., sp. nov. [type strain M4U3P1T (=CGMCC 1.17076T=JCM 33851T)], Cytobacillus suaedae sp. nov. [type strain HD4P25T (=CGMCC 1.18651T =JCM 34524T)], and Bacillus suaedae sp. nov. [type strain RD4P76T (=CGMCC 1.18659T=JCM 34525T)] were proposed, respectively. All three species are ubiquitous in the bulk saline-alkaline soils, but only the species represented by strain RD4P76T was widely distributed in the rhizosphere soil, the above-ground part and the roots of S. salsa. The species represented by M4U3P1T can be detected in the roots of S. salsa, and rarely detected in the above-ground parts of S. salsa. The species represented by HD4P25T was rarely detected in the interior of S. salsa. The three strains could inhibit some of the Gram-stain-positive bacteria (i.e. members of the genera Planococcus, Zhihengliuella and Sanguibacter) in the saline-alkali soil. A genomic analysis of these three strains revealed that they can synthesize different antagonistic compounds, such as aminobenzoate and bacitracin or subtilisin.

Bacillus suaedae sp. nov., isolated from the stem of Suaeda aralocaspica in north-west China.

A bacterial strain, designated YZJH907-2T, was isolated from the stem of Suaeda aralocaspica, collected from the southern edge of the Gurbantunggut desert, Xinjiang, PR China. Cells of strain YZJH907-2T were Gram-stain-positive, aerobic and rod-shaped. They formed white or colourless circular colonies with smooth convex surfaces. Strain YZJH907-2T grew at 4-50 °C (optimum, 28-30 °C), pH 7.0-10.0 (optimum, pH 8.0-9.0) and with 0-10 % (w/v) NaCl (optimum, 3-7 %). The genomic DNA G+C content of strain YZJH907-2T was 38.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequence similarity showed that the strain was most closely related to Bacillus alcalophilus DSM 485T (97.37 %), Bacillus kiskunsagensis B16-24T (96.87 %) and Bacillus bogoriensis LBB3T (96.71 %). Average nucleotide identity values between YZJH907-2T and B. alcalophilus DSM 485Tand B. bogoriensis LBB3T were 69.2 and 69.0 %, respectively. Digital DNA-DNA hybridization values of YZJH907-2T with B. alcalophilus DSM 485T and B. bogoriensis LBB3T were 19.6 and 20.4 %, respectively. The cell wall of strain YZJH907-2T contained meso-diaminopimelic acid, and the major and secondary isoprenoid quinones were MK-7 and MK-5, respectively. Results of fatty acids showed that anteiso-C15 : 0, iso-C15 : 0 and C16 : 0 were the predominant cellular fatty acids. Two-dimensional thin-layer chromatography analysis indicated that the polar lipids included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, three unidentified phospholipids and two unidentified glycolipids. Based on the genomic, phylogenetic and phenotypic analyses, strain YZJH907-2T represented a novel species of the genus Bacillus, and thus the name Bacillus suaedae sp. nov. is proposed. The type strain is YZJH907-2T (=CGMCC 1.18763T=KCTC 43335T).

Marinilactibacillus kalidii sp. nov., an Indole Acetic Acid-Producing Endophyte Isolated from a Shoot of Halophyte Kalidium cuspidatum.

A Gram-stain-positive, facultatively anaerobic, non-sporulating, motile with single polar flagellum, rod-shaped, indole-3-acetic acid (IAA)-producing bacterium, named M4U5P12T, was isolated from a shoot of Kalidium cuspidatum, Inner Mongolia, China. Strain M4U5P12T grew at pH 6.0-11.0 (optimum 7.5), 4-40 °C (optimum 25 °C), and in the presence of 0-15% (w/v) NaCl (optimum 4%). Positive for catalase, urease, methyl red (M.R.) reaction, and hydrolysis of starch; and negative for oxidase, Voges-Proskauer (V-P) test, and hydrolysis of cellulose. The phylogenetic trees based on the 16S rRNA gene sequences and the whole genome sequences both revealed that it clustered with Marinilactibacillus piezotolerans JCM 12337T (99.3%) and Marinilactibacillus psychrotolerans M13-2T (99.1%). The dDDH and ANIb values of strain M4U5P12T to M. piezotolerans DSM 16108T and M. psychrotolerans M13-2T were 19.3 and 18.9%, and 74.3 and 74.0%, respectively. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid, and two unidentified lipids. The major fatty acids were C16:0, C18:1 ω9c, C16:1 ω9c, and C15:1 ω5c. The genomic DNA G + C content was 37.3%. On the basis of physiological, phenotypic, and phylogenetic characteristics, strain M4U5P12T should be classified as a novel species. Therefore, Marinilactibacillus kalidii sp. nov. is proposed, and the type strain is M4U5P12T (= CGMCC 1.17696T = KCTC 43247T).

Differences between the effects of plant species and compartments on microbiome composition in two halophyte Suaeda species.

Root-related or endophytic microbes in halophytes play an important role in adaptation to extreme saline environments. However, there have been few comparisons of microbial distribution patterns in different tissues associated with halophytes. Here, we analyzed the bacterial communities and distribution patterns of the rhizospheres and tissue endosphere in two Suaeda species (S. salsa and S. corniculata Bunge) using the 16S rRNA gene sequencing. The results showed that the bacterial abundance and diversity in the rhizosphere were significantly higher than that of endophytic, but lower than that of bulk soil. Microbial-diversity analysis showed that the dominant phyla of all samples were Proteobacteria, Actinobacteria, Bacteroidetes, Acidobacteria and Firmicutes, among which Proteobacteria were extremely abundant in all the tissue endosphere. Heatmap and Linear discriminant analysis Effect Size (LEfSe) results showed that there were notable differences in microbial community composition related to plant compartments. Different networks based on plant compartments exhibited distinct topological features. Additionally, the bulk soil and rhizosphere networks were more complex and showed higher centrality and connectedness than the three endosphere networks. These results strongly suggested that plant compartments, and not species, affect microbiome composition.

Rare ß-Resorcylic Acid Derivatives from a Halophyte-Associated Fungus Colletotrichum gloeosporioides JS0419 and Their Antifungal Activities.

Six new ß-resorcylic acid derivatives (1-5 and 7) were isolated from a halophyte-associated fungus, Colletotrichum gloeosporioides JS0419, together with four previously reported ß-resorcylic acid lactones (RALs). The relative and absolute stereochemistry of 1 was completely established by a combination of spectroscopic data and chemical reactions. The structures of the isolated compounds were elucidated by analysis of HRMS and NMR data. Notably, compounds 1-3 had a ß-resorcylic acid harboring a long unesterified aliphatic side chain, whereas the long aliphatic chains were esterified to form macrolactones in 4-9. Among the isolated compounds, monocillin I and radicicol showed potent antifungal activities against Cryptococcus neoformans, comparable to clinically available antifungal agents and radicicol showed weak antifungal activity against Candida albicans. These findings provide insight into the chemical diversity of fungal RAL-type compounds and their pharmacological potential.

Gracilibacillus suaedae sp. nov., an indole acetic acid-producing endophyte isolated from a root of Suaeda salsa.

A Gram-stain-positive, facultatively anaerobic, spore-forming, motile with unipolar biflagella, rod-shaped, indole acetic acid-producing bacterium, named LD4P30T, was isolated from a root of Suaeda salsa collected in Inner Mongolia, northern China. Strain LD4P30T grew at pH 6.0-11.0 (optimum, pH 7.0), 10-40 °C (35 °C) and in the presence of 1-15% (w/v) NaCl (5%). The strain was positive for oxidase and negative for catalase. The major cellular fatty acids of strain LD4P30T were iso-C15:0, C15:1 ω5c and anteiso-C15:0; the major polar lipids were diphosphatidylglycerol and phosphatidylglycerol; and menaquinone-7 was the only respiratory quinone. The genomic DNA G+C content was 36.7 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain LD4P30T clustered with Gracilibacillus thailandensis TP2-8T, Gracilibacillus saliphilus YIM 91119T and Gracilibacillus lacisalsi BH312T, and showed 99.0, 98.9, 98.0 and <97.7% 16S rRNA gene similarity to G. thailandensis TP2-8T, G. saliphilus YIM 91119T, G. lacisalsi BH312T and all other current type strains, respectively. The digital DNA-DNA hybridization and average nucleotide identity based on blast values between strain LD4P30T and G. saliphilus YIM 91119T, G. thailandensis TP2-8T and G. lacisalsi BH312T were 44.9, 44.7 and 44.4%, and 91.1, 91.0 and 90.8%, respectively. Based on its phenotypic, physiological and phylogenetic characteristics, strain LD4P30T represents a novel species, for which the name Gracilibacillus suaedae is proposed. The type strain is LD4P30T (=CGMCC 1.17697T=KCTC 82375T).

Sanguibacter suaedae sp. nov., isolated from the root of Suaeda aralocaspica in north-west PR China.

A bacterial strain, designated YZGR15T, was isolated from the root of an annual halophyte Suaeda aralocaspica, collected from the southern edge of the Gurbantunggut desert, north-west PR China. Cells of the isolate were Gram-stain-positive, facultatively anaerobic, irregular rods. Growth occurred at 4-42 °C (optimum, 30-37 °C), at pH 6.0-9.0 (optimum, pH 7.0-7.5) and in the presence of 0-9 % (w/v) NaCl (optimum, 2-5 %). Phylogenetic analysis using 16S rRNA gene sequences indicated that strain YZGR15T showed the highest sequence similarity to Sanguibacter keddieii (98.27 %), Sanguibacter antarcticus (98.20 %) and Sanguibacter inulinus (98.06 %). Results of genome analyses of strain YZGR15T indicated that the genome size was 3.16 Mb, with a genomic DNA G+C content of 71.9 mol%. Average nucleotide identity and digital DNA-DNA hybridization values between strain YZGR15Tand three type strains were in the range of 76.5-77.8 % and 20.0-22.2 %, respectively. Analysis of the cellular component of strain YZGR15T revealed that the primary fatty acids were anteiso-C15 : 0, C16 : 0, C14 : 0 and iso-C16 : 0 and the polar lipids included diphosphatidylglycerol, phosphatidylglycerol, three unidentified phospholipids and two unidentified glycolipids. The cell-wall characteristic amino acids were glutamic acid, alanine and an unknown amino acid. The whole-cell sugars for the strain were mannose, ribose, rhamnose, glucose and an unidentified sugar. The predominant respiratory quinone was MK-9(H4). Based on the results of genomic, phylogenetic, phenotypic and chemotaxonomic analyses, strain YZGR15T represents a novel species of the genus Sanguibacter, for which the name Sanguibacter suaedae sp. nov. is proposed. The type strain is YZGR15T (=CGMCC 1.18691T=KCTC 49659T).

Hoyosella suaedae sp. nov., a novel bacterium isolated from rhizosphere soil of Suaeda aralocaspica (Bunge) Freitag & Schütze.

A Gram-stain-positive, non-motile and coccus-shaped bacterium, designated strain LNNU 331112T, was isolated from the composite rhizosphere soil of the halophyte Suaeda aralocaspica (Bunge) Freitag and Schütze, which was collected in Xinjiang, north-west China. Growth occurred at 10-45 °C, pH 6.0-11.0 and in the presence of 0-10 % NaCl (w/v). Phylogenetic analysis based on the 16S rRNA gene sequence suggested that strain LNNU 331112T belonged to the genus Hoyosella and showed 95.6, 95.5 and 95.4 % sequence similarities to Hoyosella altamirensis DSM 45258T, Hoyosella subflava CGMCC 4.3532T and Hoyosella rhizosphaerae CGMCC 1.15478T, respectively. The estimated digital DNA-DNA hybridization relatedness values between strain LNNU 331112T and the type strains of H. altamirensis DSM 45258T, H. subflava CGMCC 4.3532T and H. rhizosphaerae CGMCC 1.15478T were 18.9, 19.3 and 18.3 %, respectively. The average nucleotide identity values between strain LNNU 331112T and H. altamirensis DSM 45258T, H. subflava CGMCC 4.3532T and H. rhizosphaerae CGMCC 1.15478T were 72.6, 72.7 and 72.3 %, respectively. The genome sequence of strain LNNU 331112T showed 69.0-72.3 % average amino acid identity values in comparison with the related genome sequences of three validly published Hoyosella species. The genome of strain LNNU 331112T was 3.47 Mb, with a DNA G+C content of 68.4 mol%. A total of 3182 genes were identified as protein-coding in strain LNNU 331112T. Genomic analysis revealed that a number of genes involved in osmotic pressure regulation, intracellular pH homeostasis and potassium (K+) uptake protein were found in strain LNNU 331112T. The predominant menaquinones were MK-8 (44.6 %) and MK-7 (55.4 %), which differentiated strain LNNU 331112T from other three recognized Hoyosella species. Major fatty acids (>10 %) were C17 : 1 ω8c (33.8 %), C16 : 0 (23.3 %), C17 : 0 (12.8 %) and summed feature 3 (12.9 %), which also clearly separated strain LNNU 331112T from three recognized Hoyosella species. The polar lipid profile of strain LNNU 331112T included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, one unidentified glycolipid, one unidentified phospholipid and two unidentified lipids. According to the results of phenotypic, chemotaxonomic and phylogenetic analyses, strain LNNU 331112T is considered to represent a novel species of the genus Hoyosella, for which the name Hoyosella suaedae sp. nov. is proposed. The type strain is LNNU 331112T (=KCTC 39808T=CGMCC 1.17107T=DSM 103463T).

Aquibacillus kalidii sp. nov., an indole acetic acid-producing endophyte from a shoot of Kalidium cuspidatum, and reclassification of Virgibacillus campisalis Lee et al. 2012 as a later heterotypic synonym of Virgibacillus alimentarius Kim et al. 2011.

A Gram-stain-positive, strictly aerobic, motile, endospore-forming, milk-white, indole acetic acid-producing, rod-shaped bacterial strain, designated as HU2P27T, was isolated from a shoot of Kalidium cuspidatum collected in Tumd Right Banner, Inner Mongolia, PR China. Strain grew at 10-40 °C (optimum, 30 °C), at pH 6.0-9.0 (optimum, pH 7.0) and with 0-14.0 % NaCl (optimum, 5.0-8.0 %). The strain tested positive for oxidase, catalase and nitrate reductase. The phylogenetic trees based on the 16S rRNA gene sequence and the core genome both showed that strain HU2P27T clustered with Aquibacillus koreensis BH30097T, sharing 97.7 % and <97.0 % of 16S rRNA gene similarity with A. koreensis BH30097T and any other type strain. Strain HU2P27T contained MK-7 as the major respiratory quinone. Its major fatty acids were anteiso-C15 : 0 and iso-C15 : 0, and the major polar lipids were phosphatidylglycerol, diphosphatidylglycerol and four unidentified phospholipids. The genomic DNA G+C content was 36.0 mol%. The average nucleotide identity, amino acid identity and digital DNA-DNA hybridization values of strain HU2P27T with A. koreensis BH30097T were 71.7, 69.2 and 19.4%, respectively. The phylogenetic, physiological and phenotypic results allowed the discrimination of strain HU2P27T from its phylogenetic relatives. The name Aquibacillus kalidii sp. nov. is therefore proposed. The type strain is strain HU2P27T (=CGMCC 1.18646T=KCTC 43248T). Based on the results of 16S rRNA gene and genome analyses, we propose the reclassification of Virgibacillus campisalis Lee et al. 2012 as a later heterotypic synonym of Virgibacillus alimentarius Kim et al. 2011.

Rossellomorea arthrocnemi sp. nov., a novel plant growth-promoting bacterium used in heavy metal polluted soils as a phytoremediation tool.

Strain EAR8T is a root endophyte isolated from Arthrocnemum macrostachyum plants collected from the Odiel marshes, Huelva (Spain). It presented in vitro plant growth-promoting properties and improved the plant growth and heavy metal accumulation in polluted soils playing an important role in phytoremediation strategies. Phenotypically, strain EAR8T cells were Gram-positive, aerobic and non-motile rods with terminal oval endospores and non-swollen sporangia which form beige, opaque, butyrous, raised and irregular colonies with undulate margins. The strain was able to grow between 15-45 °C, at pH 6.0-9.0 and tolerated 0-25 % NaCl (w/v) showing optimal growth conditions on trypticase soy agar plates supplemented with 2.5 % NaCl (w/v) at pH 7.0 and 37 °C for 24 h. Chemotaxonomic analyses showed that the isolate has meso-diaminopimelic acid as the peptidoglycan in the cell wall and MK-7 as the major respiratory quinone. The predominant fatty acids were anteiso-C15 : 0 and iso-C15 : 0 and the polar lipid profile was composed of diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Phylogenetic analyses based on the whole proteomes of closest sequenced relatives confirmed that strain EAR8T is affiliated to the genus Rossellomorea and forms a clade with Rossellomorea vietnamensis 15-1T with maximum support. Genome analyses showed that EAR8T has indole-3-acetic acid and siderophore biosynthesis and transporters genes and genes related to resistance against heavy metals. Phenotypic and phylogenomic comparative studies suggested that strain EAR8T is a new representative of the genus Rossellomorea and the name Rossellomorea arthrocnemi sp. nov. is proposed. Type strain is EAR8T (=CECT 9072T=DSM 103900T).

Profiles of Bacillus spp. Isolated from the Rhizosphere of Suaeda glauca and Their Potential to Promote Plant Growth and Suppress Fungal Phytopathogens.

Members of the genus Bacillus are known to play an important role in promoting plant growth and protecting plants against phytopathogenic microorganisms. In this study, 21 isolates of Bacillus spp. were obtained from the root micro-ecosystem of Suaeda glauca. Analysis of the 16S rRNA genes indicated that the isolates belong to the species Bacillus amyloliquefaciens, Bacillus velezensis, Bacillus subtilis, Bacillus pumilus, Bacillus aryabhattai and Brevibacterium frigoritolerans. One of the interesting findings of this study is that the four strains B1, B5, B16 and B21 are dominant in rhizosphere soil. Based on gyrA, gyrB, and rpoB gene analyses, B1, B5, and B21 were identified as B. amyloliquefaciens and B16 was identified as B. velezensis. Estimation of antifungal activity showed that the isolate B1 had a significant inhibitory effect on Fusarium verticillioides, B5 and B16 on Colletotrichum capsici (syd.) Butl, and B21 on Rhizoctonia cerealis van der Hoeven. The four strains grew well in medium with 1-10% NaCl, a pH value of 5-8, and promoted the growth of Arabidopsis thaliana. Our results indicate that these strains may be promising agents for the biocontrol and promotion of plant growth and further study of the relevant bacteria will provide a useful reference for the development of microbial resources.

Divergence of a genomic island leads to the evolution of melanization in a halophyte root fungus.

Understanding how organisms adapt to extreme living conditions is central to evolutionary biology. Dark septate endophytes (DSEs) constitute an important component of the root mycobiome and they are often able to alleviate host abiotic stresses. Here, we investigated the molecular mechanisms underlying the beneficial association between the DSE Laburnicola rhizohalophila and its host, the native halophyte Suaeda salsa, using population genomics. Based on genome-wide Fst (pairwise fixation index) and Vst analyses, which compared the variance in allele frequencies of single-nucleotide polymorphisms (SNPs) and copy number variants (CNVs), respectively, we found a high level of genetic differentiation between two populations. CNV patterns revealed population-specific expansions and contractions. Interestingly, we identified a ~20 kbp genomic island of high divergence with a strong sign of positive selection. This region contains a melanin-biosynthetic polyketide synthase gene cluster linked to six additional genes likely involved in biosynthesis, membrane trafficking, regulation, and localization of melanin. Differences in growth yield and melanin biosynthesis between the two populations grown under 2% NaCl stress suggested that this genomic island contributes to the observed differences in melanin accumulation. Our findings provide a better understanding of the genetic and evolutionary mechanisms underlying the adaptation to saline conditions of the L. rhizohalophila-S. salsa symbiosis.

Insights into the endophytic bacterial community comparison and their potential role in the dimorphic seeds of halophyte Suaeda glauca.

BACKGROUND: Seed dimorphism has been thought to be a bet-hedging strategy that helps plants survive in the disturbed environment and has been widely studied for its ecological adaptation mechanism. Many studies showed that seed-associated microorganisms play an important role in enhancing plant fitness, but information regarding endophytic bacteria associated with dimorphic seeds is limited. This study explores the influence of seed coat structure and seed phytochemical properties on the community composition and diversity of endophytic bacteria of dimorphic seeds of Suaeda glauca. In this study, we used 16S rRNA high-throughput gene sequencing method to compare the community composition and bacterial diversity between brown and black seeds of Suaeda glauca. RESULTS: A significant difference was observed in seed coat structure and phytochemical properties between brown and black seeds of S. glauca. Total 9 phyla, 13 classes, 31 orders, 53 families, 102 genera were identified in the dimorphic seeds. The dominant phyla were Proteobacteria, Firmicutes, and Actinobacteria. The results showed that seed dimorphism had little impact on the diversity and richness of endophytic bacterial communities but significantly differs in the relative abundance of the bacterial community between brown and black seeds. At the phylum level, Actinobacteria tend to be enriched significantly in brown seeds. At the genus level, Rhodococcus, Ralstonia, Pelomonas and Bradyrhizobium tend to be enriched significantly in brown seeds, while Marinilactibacillus was mainly found in black seeds. Besides, brown seeds harbored a large number of bacteria with plant-growth-promoting traits, whereas black seeds presented bacteria with enzyme activities (i.e., pectinase, cellulolytic and xylanolytic activities). CONCLUSION: The endophytic bacterial community compositions were significantly different between dimorphic seeds of Suaeda glauca, and play an important role in the ecological adaptation of dimorphic seeds by performing different biological function roles. The endophytic bacterial communities of the dimorphic seeds may be influenced mainly by the seed coat structureand partly by the seed phytochemical characteristics. These findings provide valuable information for better understanding of the ecological adaptation strategy of dimorphic seeds in the disturbed environment.

Effect of arbuscular mycorrhizal symbiosis on ion homeostasis and salt tolerance-related gene expression in halophyte Suaeda salsa under salt treatments.

Halophytes can remove large quantities of salts from saline soils, so their importance in ecology has received increasing attention. Preliminary studies have shown that arbuscular mycorrhizal (AM) fungi can improve the salt tolerance of halophytes. However, few studies have focused on the molecular mechanisms and effects of AM fungi in halophytes under different salt conditions. A pot experiment was carried out to investigate the effects of Funneliformis mosseae inoculation on growth, nutrient uptake, ion homeostasis and the expression of salt tolerance-related genes in Suaeda salsa under 0, 100, 200 and 400 mM NaCl. The results showed that F. mosseae promoted the growth of S. salsa and increased the shoot Ca2+ and Mg2+ concentrations under no-salt condition and high-salt condition. In addition, AM fungi increased the K+ concentration and maintained a high K+/Na+ ratio at 400 mM NaCl, while AM fungi decreased the K+ concentration and reduced the K+/Na+ ratio at 0 mM NaCl. AM fungi downregulated the expression of SsNHX1 in shoots and the expression of SsSOS1 in roots at 400 mM NaCl. These effects may decrease the compartmentation of Na+ into leaf vacuoles and restrict Na+ transport from roots to shoots, leading to an increase in root Na+ concentration. AM symbiosis upregulated the expression of SsSOS1 in shoots and downregulated the expression of SsSOS1 and SsNHX1 in roots at 100 mM NaCl. However, regulation of the genes (SsNHX1, SsSOS, SsVHA-B and SsPIP) was not significantly different with AM symbiosis at 0 mM or 200 mM NaCl. The results revealed that AM symbiosis might induce diverse modulation strategies in S. salsa, depending on external Na+ concentrations. These findings suggest that AM fungi may play significant ecological roles in the phytoremediation of salinized ecosystems.

Aurantiacibacter rhizosphaerae sp. nov., isolated from a rhizosphere mudflat of a halophyte and proposal to reclassify Erythrobacter suaedae Lee et al. 2019. and Erythrobacter flavus Yoon et al. 2003 as Aurantiacibacter suaedae comb. nov. and Qipengyuania flava comb. nov., respectively.

A marine alphaproteobacterium, designated as strain GH3-10T, was isolated from the rhizosphere mud of a halophyte (Suaeda japonica) collected at the seashore of Gangwha Island, Republic of Korea. The isolate was found to be Gram-stain-negative, strictly aerobic, catalase- and oxidase-positive, non-motile, short rods and produced orange-coloured colonies. The 16S rRNA gene- and whole genome-based phylogenetic analyses exhibited that strain GH3-10T belonged to the genus Aurantiacibacter and was most closely related to Aurantiacibacter atlanticus s21-N3T (98.7 % 16S rRNA gene sequence similarity) and Aurantiacibacter marinus KCTC 23554T (98.4 %). The major respiratory quinone was ubiquinone-10. The polar lipids consisted of phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid and an unidentified lipid. The major fatty acids were C18 : 1 ω7c, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and C18 : 1 ω7c 10-methyl. The DNA G+C content was 61.3 mol% (by genome). Average nucleotide identity and DNA-DNA relatedness values between the isolate and its phylogenetically closest relatives, together with phenotypic distinctness warranted the taxonomic description of a new species. On the basis of data obtained by a polyphasic approach, strain GH3-10T (=KCTC 62379T=JCM 32444T) represents a novel species of the genus Aurantiacibacter, for which the name Aurantiacibacter rhizosphaerae sp. nov. is proposed. According to phylogenetic coherence based on 16S rRNA genes and core genomes, it is also proposed that Erythrobacter suaedae Lee et al. 2019. and Erythrobacter flavus Yoon et al. 2003 be transferred to Aurantiacibacter suaedae comb. nov. and Qipengyuania flava comb. nov., respectively.