Commonalities between the Atacama Desert and Antarctica rhizosphere microbial communities

Plant-microbiota interactions have significant effects on plant growth, health, and productivity. Rhizosphere microorganisms are involved in processes that promote physiological responses to biotic and abiotic stresses in plants. In recent years, the interest in microorganisms to improve plant productivity has increased, mainly aiming to find promising strains to overcome the impact of climate change on crops. In this work, we hypothesize that given the desertic environment of the Antarctic and the Atacama Desert, different plant species inhabiting these areas might share microbial taxa with functions associated with desiccation and drought stress tolerance. Therefore, in this study, we described and compared the composition of the rhizobacterial community associated with Deschampsia antarctica (Da), Colobanthus quitensis (Cq) from Antarctic territories, and Croton chilensis (Cc), Eulychnia iquiquensis (Ei) and Nicotiana solanifolia (Ns) from coastal Atacama Desert environments by using 16S rRNA amplicon sequencing. In addition, we evaluated the putative functions of that rhizobacterial community that are likely involved in nutrient acquisition and stress tolerance of these plants. Even though each plant microbial rhizosphere presents a unique taxonomic pattern of 3,019 different sequences, the distribution at the genus level showed a core microbiome with a higher abundance of Haliangium, Bryobacter, Bacillus, MND1 from the Nitrosomonadaceae family, and unclassified taxa from Gemmatiamonadaceae and Chitinophagaceae families in the rhizosphere of all samples analyzed (781 unique sequences). In addition, species Gemmatirosa kalamazoonesis and Solibacter usitatus were shared by the core microbiome of both Antarctic and Desert plants. All the taxa mentioned above had been previously associated with beneficial effects in plants. Also, this microbial core composition converged with the functional prediction related to survival under harsh conditions, including chemoheterotrophy, ureolysis, phototrophy, nitrogen fixation, and chitinolysis. Therefore, this study provides relevant information for the exploration of rhizospheric microorganisms from plants in extreme conditions of the Atacama Desert and Antarctic as promising plant growth-promoting rhizobacteria.

Halomonas antri sp. nov., a carotenoid-producing bacterium isolated from surface seawater

A Gram-negative, moderately halophilic bacterium, designated as strain Y3S6T, was isolated from a surface seawater sample collected from Dongangyoeng cave, Udo-myeon, Jeju-si, Jeju-do, Repulic of Korea. Cells of strain Y3S6T were aerobic, rod-shaped, non-sporulated, yellow, catalase- negative, oxidase-negative and motile with one polar flagellum. Growth of strain Y3S6T occurred at 15–40 °C (optimum: 25–30 °C), at pH 6.0–9.0 (optimum: pH 7.0) and in the presence of 0–13% NaCl (optimum: 1–6 %, w/v). The novel strain was able to produce carotenoids. Its chemotaxonomic and morphological characteristics were consistent with those of members of the genus Halomonas . Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain Y3S6T formed a clade with Halomonas pellis L5T (98.97 %) and Halomonas saliphila LCB169T(98.90%). The average nucleotide identity and digital DNA–DNA hybridization values of strain Y3S6T with the most closely related strains for which whole genomes are publicly available were 82.3–85.2% and 62.8–66.1 %, respectively. The major fatty acids in strain Y3S6T were C16 : 0, C19 : 0 cyclo ω8c and summed feature 8 (composed of C18 : 1 ω7c and/or C18 : 1 ω6c), and the predominant quinone was Q-9. Its polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified phosphoglycolipid, one unidentified phosphoaminoglycolipid and one unidentified phospholipid. The genomic DNA G+C content based on the draft genome sequence was 64.2 mol%. The results of physiological and biochemical tests and 16S rRNA sequence analysis clearly revealed that strain Y3S6T represents a novel species in the genus Halomonas , for which the name Halomonas antri sp. nov. has been proposed. The type strain is Y3S6T (=KACC 21536T=NBRC 114315=TBRC 15164T).

Ilyomonas limi gen. nov., sp. nov., a new member of the family Chitinophagaceae isolated from mud

A Gram-strain negative, aerobic, catalase and oxidase positive, non-motile, short rod-shaped bacterium, designated 17mud1-8^T, was isolated from mud collected from Nowon-gu, Seoul, South Korea. The strain was found to be able to grow at 10-40 °C (optimum 28-30 °C), pH 5.0-8.0 (optimum 7.0), and in the absence of NaCl. The nearly full-length 16S rRNA gene of strain 17mud1-8^T exhibits sequence similarity of 94.1% with that of Panacibacter ginsenosidivorans Gsoil 1550^T, followed by 93.6% sequence similarity with Parafilimonas terrae DSM 28286^T. Phylogenetic analysis indicated that strain 17mud1-8^T belongs to the family Chitinophagaceae, sharing approximately 94.1-91.9% sequence similarity with members of closely related genera. The respiratory quinone was identified as MK-7. The predominant fatty acids were found to consist of iso-C_15:0, iso-C_17:1ω5c and iso-C_15:1 G. The polar lipids were identified as phosphatidylethanolamine, an unidentified aminophospholipid, an unidentified glycolipid, ten unidentified aminolipids and seven unidentified lipids. The draft genome of 17mud1-8^T has G+C content of 40.9 mol% and a 5.8 Mb chromosome. On the basis of the phenotypic and genotypic properties, and phylogenetic inference, strain 17mud1-8^T was found to represent a novel genus in the family Chitinophagaceae, for which the name Ilyomonas limi gen. nov., sp. nov. is proposed, with the type strain 17mud1-8^T(=KCTC 52874^T = NBRC 112826^T).

Distinct effects of short-term reconstructed topsoil on soya bean and corn rhizosphere bacterial abundance and communities in Chinese Mollisol

Eroded black soils (classified as Mollisols) lead to a thinner topsoil layer, reduced organic carbon storage and declined crop productivity. Understanding the changes in soil microbial communities owing to soil erosion is of vital importance as soil microbial communities are sensitive indicators of soil condition and are essential in soil nutrient cycling. This study used the reconstructed facility with 10, 20 and 30 cm topsoil thickness under no-till soya bean-corn rotation in black soil region of Northeast China. Illumina MiSeq sequencing targeting 16S rRNA, qPCR and soil respiration measurement were performed to assess the changes in soya bean and corn rhizosphere bacterial communities, as well as their abundance and activities due to the topsoil thickness. The results showed that soil bacterial communities from both soya bean and corn were more sensitive to topsoil removal than to soil biogeochemical characteristics. Topsoil depths significantly influenced both soya bean and corn bacterial communities, while they only significantly influenced the bacterial abundance and respiration in corn. We also found that the topsoil depths significantly induced the changes in phyla and genera from both soya bean and corn rhizosphere bacterial community, which aid further understandings on how topsoil layer influences the global nutrient cycling of Mollisols by influencing the change in microbial communities.

Microvirga rosea sp. nov.: a nanoparticle producing bacterium isolated from soil of rose garden

A Gram-stain negative, aerobic, non-motile, and rod-shaped novel bacterial strain, designated MAH-2^T, was isolated from a soil sample of rose garden and was characterized using a polyphasic approach. The colonies were light pink color, smooth, circular and 0.2-0.6 mm in diameter when grown on nutrient agar for 3 days. Strain MAH-2^T grows at 15-40 °C (optimum growth temperature 30 °C), at pH 5.0-7.0 (optimum growth pH 6.5) and at 0-2% NaCl (optimum 0-0.5%). Cell growth occurs on nutrient agar and R2A agar but not on tryptone soya agar, luria-bertani agar and MacConkey agar. The strain was positive for both catalase and oxidase tests. The strain was able to synthesis of silver nanoparticles. According to the 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus Microvirga and was most closely related to Microvirga soli R491^T (96.7% sequence similarity), Microvirga subterranea Fail4^T (96.4%), Microvirga guangxiensis 25B^T (96.0%) and Microvirga aerophila 5420S-12^T (95.9%). The genomic DNA G + C content of isolated strain was determined to be 62.5 mol% and the predominant isoprenoid quinone was Q-10. The major fatty acids were identified as summed feature 8 (comprising C_18:1 ω7c and/or C_18:1 ω6c) and C_19:0 cyclo ω8c. On the basis of these phenotypic, genotypic, and chemotaxonomic studies and DNA-DNA hybridization results, the isolated strain MAH-2^T represents a novel species, for which the name Microvirga rosea sp. nov. is proposed, with MAH-2^T as the type strain (= KACC 19290^T = CGMCC1.16488^T).

Flavobacterium ureilyticum sp. nov., a novel urea hydrolysing bacterium isolated from stream bank soil

A novel bacterium designated S-42^T was isolated from stream bank soil. Cells were found to be aerobic, Gram staining-negative, oxidase-positive, catalase-negative, non-motile, non-spore-forming, rod-shaped, and yellow-pigmented. The strain can grow at 15-35 °C, pH 6.0-10.0, and at 0.5% (w/v) NaCl concentration. Urea was hydrolysed. Flexirubin-type pigments were absent. Phylogenetic analysis based on its 16S rRNA gene sequence revealed that strain S-42^T formed a lineage within the family Flavobacteriaceae of the phylum Bacteroidetes that is distinct from various species of the genus Flavobacterium, including Flavobacterium maotaiense T9^T (97.6% sequence similarity), Flavobacterium hibernum ATCC 51468^T (97.4%), and Flavobacterium granuli Kw05^T (97.1%). The 16S rRNA gene sequences identity between strain S-42^T and other members of the genus Flavobacterium were < 97.0%. Strain S-42^T contains MK-6 as sole respiratory quinone. The major polar lipids were identified as phosphatidylethanolamine and an unidentified aminolipid. The major cellular fatty acids were identified as iso-C_15:0, summed feature 3 (C_16:1ω7c and/or C_{16: 1}ω6c), C_16:0, anteiso-C_15:0, iso-C_17:0 3-OH, iso-C_15:0 3-OH, and iso-C_15:1 G. The DNA G + C content of the strain was 35.8 mol%. The polyphasic characterization indicated that strain S-42^T represents a novel species of the genus Flavobacterium, for which the name Flavobacterium ureilyticum sp. nov. is proposed. The type strain is S-42^T (= KEMB 9005-537^T = KACC 19115^T = NBRC 112683^T).

Dyadobacter flavus sp. nov. and Dyadobacter terricola sp. nov., two novel members of the family Cytophagaceae isolated from forest soil

Two strains of bacteria designated strains S-53^T and A27^T were isolated from forest soil and subjected to polyphasic characterization. Cells were aerobic, Gram-staining-negative, catalase- and oxidase- positive, non-motile, non-spore-forming, rod-shaped, and yellow-pigmented. Flexirubin-type pigments were present. Both strains were positive for PNPG, hydrolysed casein, and tyrosine. A phylogenetic analysis based on its 16S rRNA gene sequence revealed that strains S-53^T and A27^T formed a lineage within the family Cytophagaceae that were distinct from various members of the genus Dyadobacter (98.9-93.2% sequence similarity). Closest member for strain S-53^T was Dyadobacter jejuensis AM1R11^T (95.7%) and for A27^T Dyadobacter endophyticus 65^T (98.9%). The predominant respiratory quinone was MK-7 for both strains. The major polar lipid for both strains was phosphatidylethanolamine. The major cellular fatty acids for both strains were summed feature 3 (C_16:1ω7c and/or C_16:1ω6c), iso-C_15:0, C_16:1ω5c, and C_16:0. The DNA G+C content of strains ranges from 46.5 to 48.7 mol%. On the basis of phenotypic, genotypic, chemotaxonomic, and phylogenetic analysis, both strains S-53^T and A27^T represent a novel member in the genus Dyadobacter, for which the name Dyadobacter flavus sp. nov. and Dyadobacter terricola sp. nov. are proposed, respectively. The type strain of D. flavus is S-53^T (= KEMB 9005-541^T = KACC 19149^T = NBRC 112681^T) and type strain of D. terricola is A27^T (= KEMB 9005-524^T = KACC 19147^T = NBRC 112680^T).