Dyadobacter endophyticus sp. nov., an endophytic bacterium isolated from maize root

Performance of a novel Built-in Static Magnetic Field - Biological Aerated Filter (BSMF-BAF) for treating high-salt textile dyeing wastewater

High-salt textile dyeing wastewater is difficult to treat. Magnetic fields can enhance the biodegradation capacity and extreme environmental adaptabilities of microorganisms. Thus, magnetically enhanced bioreactors are expected to improve the treatment efficiency and stability of high-salt textile dyeing wastewater. Accordingly, a novel Built-in Static Magnetic Field - Biological Aerated Filter (BSMF-BAF) was constructed and investigated for treating actual high-salt textile dyeing wastewater in this study. Two other BAFs packed with traditional and magnetic ceramsite carriers, respectively, were simultaneously operated for comparison. The removal of color, chemical oxygen demand (COD), suspended solid (SS) and acute toxicity were monitored. The activities of key enzymes and microbial community structure were analyzed to reveal possible mechanisms for improving the treatment efficiency of traditional BAF using the BSMF. The results showed that the BSMF-BAF possessed the highest removal efficiencies of color, COD, SS and acute toxicity among the three BAFs. The BSMF induced significant increases in the activities of azoreductase and lignin peroxidase, which were responsible for the degradation of azo compounds in the wastewater and the detoxification of toxic intermediates, respectively. Additionally, the BSMF induced the relative enrichment of potentially effective bacteria and fungi, and it maintained a relatively high abundance of fungi in the microbial community, resulting in a high treatment efficiency.

Dyadobacter chenhuakuii sp. nov., Dyadobacter chenwenxiniae sp. nov., and Dyadobacter fanqingshengii sp. nov., isolated from soil of the Qinghai-Tibetan Plateau

Six novel bacterial strains, designated CY22^T, CY357, LJ419^T, LJ53, CY399^T and CY107 were isolated from soil samples collected from the Qinghai-Tibetan Plateau, PR China. Cells were aerobic, rod-shaped, yellow-pigmented, catalase- and oxidase-positive, Gram-stain-negative, non-motile and non-spore-forming. All strains were psychrotolerant and could grow at 0 °C. The results of phylogenetic and phylogenomic analyses, based on 16S rRNA gene sequences and core genomic genes, indicated that the three strain pairs (CY22^T/CY357, LJ419^T/LJ53 and CY399^T/CY107) were closely related to members of the genus Dyadobacter and clustered tightly with two species with validly published names, Dyadobacter alkalitolerans 12116^T and Dyadobacter psychrophilus BZ26^T. Values of digital DNA-DNA hybridization between genome sequences of the isolates and other strains from the GenBank database in the genus Dyadobacter were far below the 70.0 % threshold. The genomic DNA G+C content of these six strains ranged from 45.2 to 45.8 %. The major cellular fatty acids of all six strains were iso-C_15 : 0 and summed feature 3 (comprising C_16 : 1 ω7c and/or C_16 : 1 ω6c). MK-7 was the only respiratory quinone, and phosphatidylethanolamine was the predominant polar lipid for strains CY22^T, LJ419^T and CY399^T. On the basis of the phenotypic, phylogenetic and genomic evidence presented, these six strains represent three novel members of the genus Dyadobacter, for which the names Dyadobacter chenhuakuii sp. nov., Dyadobacter chenwenxiniae sp. nov. and Dyadobacter fanqingshengii sp. nov. are proposed. The type strains are CY22^T (= GDMCC 1.3045^T = KCTC 92299^T), LJ419^T (= GDMCC 1.2872^T = JCM 33794^T) and CY399^T (= GDMCC 1.3052^T = KCTC 92306^T), respectively.

Dyadobacter diqingensis sp. nov., isolated from Baima snow mountain of Diqing Tibetan Autonomous Prefecture in Yunnan province, south-west China

A Gram-negative, aerobic, nonmotile, rod-shaped and yellow-pigment-producing bacteria was isolated from Baima snow mountain of Diqing Tibetan Autonomous Prefecture in Yunnan province, south-west China and characterized using a polyphasic approach. The results of 16S rRNA gene sequence similarity analysis showed that strain YIM B04101^T was closely related to the type strain of Dyadobacter koreensis DSM 19938^T (97.81%) and Dyadobacter frigoris AR-3-8^T (97.95%). The predominant respiratory quinone was menaquinone-7 (MK-7). The major polar lipid was phosphatidylethanolamine. The major fatty acids were summed feature 3 (C_16:1ω7c/C_16:1ω6c), C_18:1ω9c and C_16:0. The DNA G + C content was 43.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain YIM B04101^T belonged to a cluster comprising species of the genus Dyadobacter. However, it differed from its closest relative, Dyadobacter koreensis KCTC 12537^T and Dyadobacter frigoris AR-3-8^T, in many physiological properties. Based on these phenotypic characteristics and phylogenetic distinctiveness, strain YIM B04101^T is considered to be a novel species of the genus Dyadobacter, for which the name Dyadobacter diqingensis sp. nov. is proposed. The type strain is YIM B04101^T (= CGMCC 1.19249^T = CCTCC AB 2021270).

Dyadobacter sandarakinus sp. nov., isolated from Arctic tundra soil, and emended descriptions of Dyadobacter alkalitolerans, Dyadobacter koreensis and Dyadobacter psychrophilus

Strain Q3-56^T, isolated from Arctic tundra soil, was found to be a Gram-stain-negative, yellow-pigmented, oxidase- and catalase-positive, non-motile, non-spore-forming, rod-shaped and aerobic bacterium. Strain Q3-56^T grew optimally at pH 7.0 and 28 °C. The strain could tolerate up to 1 % (w/v) NaCl with optimum growth in the absence of NaCl. The strain was not sensitive to oxacillin and ceftazidime. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain Q3-56^T belonged to the genus Dyadobacter. Strain Q3-56^T showed the highest sequence similarities to Dyadobacter luticola T17^T (96.58 %), Dyadobacter ginsengisoli Gsoil 043^T (96.50 %), Dyadobacter flavalbus NS28^T (96.43 %) and Dyadobacter bucti QTA69^T (96.43 %). The predominant respiratory isoprenoid quinone was identified as MK-7, The polar lipid profile of strain Q3-56^T was found to contain one phosphatidylethanolamine, three unidentified aminolipids, three unidentified lipids and one unidentified phospholipid. The G+C content of the genomic DNA was determined to be 49.1 mol%. The main fatty acids were summed feature 3 (comprising C_16 : 1  ω7c/C_16 : 1  ω6c), iso-C_15 : 0, C_16 : 1  ω5c and iso-C_16 : 1 3-OH. On the basis of the evidence presented in this study, a novel species of the genus Dyadobacter, Dyadobacter sandarakinus sp. nov., is proposed, with the type strain Q3-56^T (=CCTCC AB 2019271^T=KCTC 72739^T). Emended descriptions of Dyadobacter alkalitolerans, Dyadobacter koreensis and Dyadobacter psychrophilus are also provided.

Distinct rhizomicrobiota assemblages and plant performance in lettuce grown in soils with different agricultural management histories

A better understanding of factors shaping the rhizosphere microbiota is important for sustainable crop production. We hypothesized that the effect of agricultural management on the soil microbiota is reflected in the assemblage of the rhizosphere microbiota with implications for plant performance. We designed a growth chamber experiment growing the model plant lettuce under controlled conditions in soils of a long-term field experiment with contrasting histories of tillage (mouldboard plough vs cultivator tillage), fertilization intensity (intensive standard nitrogen (N) + pesticides/growth regulators vs extensive reduced N without fungicides/growth regulators), and last standing field crop (rapeseed vs winter wheat). High-throughput sequencing of bacterial and archaeal 16S rRNA genes and fungal ITS2 regions amplified from total community DNA showed that these factors shaped the soil and rhizosphere microbiota of lettuce, however, to different extents among the microbial domains. Pseudomonas and Olpidium were identified as major indicators for agricultural management in the rhizosphere of lettuce. Long-term extensive fertilization history of soils resulted in higher lettuce growth and increased expression of genes involved in plant stress responses compared to intensive fertilization. Our work adds to the increasing knowledge on how soil microbiota can be manipulated by agricultural management practices which could be harnessed for sustainable crop production.

Endophytic microbes: biodiversity, plant growth-promoting mechanisms and potential applications for agricultural sustainability

Endophytic microbes are known to live asymptomatically inside their host throughout different stages of their life cycle and play crucial roles in the growth, development, fitness, and diversification of plants. The plant-endophyte association ranges from mutualism to pathogenicity. These microbes help the host to combat a diverse array of biotic and abiotic stressful conditions. Endophytic microbes play a major role in the growth promotion of their host by solubilizing of macronutrients such as phosphorous, potassium, and zinc; fixing of atmospheric nitrogen, synthesizing of phytohormones, siderophores, hydrogen cyanide, ammonia, and act as a biocontrol agent against wide array of phytopathogens. Endophytic microbes are beneficial to plants by directly promoting their growth or indirectly by inhibiting the growth of phytopathogens. Over a long period of co-evolution, endophytic microbes have attained the mechanism of synthesis of various hydrolytic enzymes such as pectinase, xylanases, cellulase, and proteinase which help in the penetration of endophytic microbes into tissues of plants. The effective usage of endophytic microbes in the form of bioinoculants reduce the usage of chemical fertilizers. Endophytic microbes belong to different phyla such as Actinobacteria, Acidobacteria, Bacteroidetes, Deinococcus-thermus, Firmicutes, Proteobacteria, and Verrucomicrobia. The most predominant and studied endophytic bacteria belonged to Proteobacteria followed by Firmicutes and then by Actinobacteria. The most dominant among reported genera in most of the leguminous and non-leguminous plants are Bacillus, Pseudomonas, Fusarium, Burkholderia, Rhizobium, and Klebsiella. In future, endophytic microbes have a wide range of potential for maintaining health of plant as well as environmental conditions for agricultural sustainability. The present review is focused on endophytic microbes, their diversity in leguminous as well as non-leguminous crops, biotechnological applications, and ability to promote the growth of plant for agro-environmental sustainability.

Dyadobacter bucti sp. nov., isolated from subsurface sediment

A Gram-reaction-negative, yellow-pigmented, rod-shaped, aerobic, non-motile, non-spore-forming bacterium, designated strain QTA69^T, was isolated from a subsurface sediment sample collected at the Qiangtang basin, Qinghai-Tibetan Plateau, PR China. Cells were catalase-positive and oxidase-negative. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain QTA69^T was a member of the genus Dyadobacter and was closely related to Dyadobacter sediminis, Dyadobacter ginsengisoli and Dyadobacter psychrophilus with sequence similarities from 97.90 % to 96.85 %. Strain QTA69^T grew at 4-35 °C, and the optimum temperature was 25-28 °C. It grew at the pH range of 6.0-9.0 (optimum, pH 7.0-8.0) and its NaCl tolerance was 0-2.0 % (optimum, 0-1.0 %). The major cellular fatty acids were summed feature 3 (iso-C_15 : 0 2-OH and C _16:1ω6c/C_16 : 1ω7c), iso-C_15 : 0 and C_16 : 1ω5c. The major respiratory quinone was MK-7 and the major polar lipid was phosphatidylethanolamine. Genome sequencing revealed a genome size of 8.41 Mbp and a G+C content of 46.87 mol%. Based on whole genome average nucleotide identity values, phenotypic data, phylogenetic data and genotypic data, strain QTA69^T represents a novel species of genus Dyadobacter, for which the name Dyadobacter bucti sp. nov is proposed. The type strain is QTA69^T (=CGMCC 1.13688^T=KCTC 72024^T).

Dyadobacter flavalbus sp. nov., isolated from lake sediment

A novel bacterial strain, designated NS28^T, was isolated from interfacial sediment sampled at Taihu Lake, PR China. Cells were rod-shaped, Gram-negative, aerobic and non-motile on Reasoner's 2A medium. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NS28^T was most closely related to species from the genus Dyadobacter, with 98.4 and 96.0 % 16S rRNA gene sequence similarity to its closest phylogenetic neighbours Dyadobacter sediminis CGMCC 1.12895^T and Dyadobacter luticola CCTCC AB 2017091^T, respectively. MK-7 was the only cellular menaquinone. The major fatty acids were summed feature 3 (C_16 : 1ω7c and/or C_16 : 1ω6c), iso-C_15 : 0 and C_16 : 1ω5c. The major polar lipids were phosphatidylethanolamine, one phospholipid, one aminolipid, one lipid and two unidentified lipids. Genomic analysis of strain NS28^T indicated that the total genome size was 6 477 094 bp with a G+C content of 44.8 mol%, 5380 protein-coding genes, 79 contigs and an N50 length of 299584 bp. On the basis of the genomic DNA sequence, the average nucleotide identity values were 90.5 and 74.1 % with D. sediminis CGMCC 1.12895^T and D. luticola CCTCC AB 2017091^T, respectively. Digital DNA-DNA hybridization results of strain NS28^T with D. sediminis CGMCC 1.12895^T and D. luticola CCTCC AB 2017091^T were 40.9 and 18.6 %, respectively. Based on the phenotypic, chemotaxonomic, phylogenetic and genome sequence data presented here, it is proposed that strain NS28^T represents a novel species of the genus Dyadobacter for which the name Dyadobacter flavalbus is proposed . The type strain is NS28^T (=NBRC 113854^T=MCCC 1K03764^T).

Dyadobacter luteus sp. nov., isolated from rose rhizosphere soil

A novel Gram-negative, aerobic, rod-shaped bacterium, RS19^T, was isolated from rose rhizosphere soil. The strain was psychrophilic and showed good growth over a temperature range of 1-37 ℃. Colonies on TSB agar were circular, smooth, mucoid, convex with clear edges and yellow. Phylogenetic analysis based on 16S rRNA gene sequences characterized RS19^T in the genus Dyadobacter and showed that strain RS19^T was most closely related to Dyadobacter psychrophilus CGMCC 1.8951^T (97.4%) and Dyadobacter alkalitolerans CGMCC 1.8973^T (97.1%). The average nucleotide identity values to the closest related species type strains were less than 84.0%. The DNA G + C content was 43.1 mol%, and the predominant respiratory menaquinone was MK-7. The major fatty acids were summed features 3 (C_16:1ω7c and/or C_16:1ω6c), iso-C_15:0, C_16:1ω5c and iso-C_17:0 3-OH. Based on genotypic, phenotypic and chemotaxonomic data, strain RS19^T is different from closely related species of the genus Dyadobacter. RS19^T represents a novel species within the genus Dyadobacter, for which the name Dyadobacter luteus sp. nov. is proposed. The type strain is RS19^T (= CGMCC 1.13719^T = ACCC 60381^T = JCM 32940^T).

Genomic Insights of Dyadobacter tibetensis Y620-1 Isolated from Ice Core Reveal Genomic Features for Succession in Glacier Environment

Glaciers have been recognized as biomes, dominated by microbial life. Many novel species have been isolated from glacier ecosystems, and their physiological features are well characterized. However, genomic features of bacteria isolated from the deep ice core are poorly understood. In this study, we performed a comparative genomic analysis to uncover the genomic features of strain Dyadobacter tibetensis Y620-1 isolated from a 59 m depth of the ice core drilled from a Tibetan Plateau glacier. Strain D. tibetensis Y620-1 had the smallest genome among the 12 cultured Dyadobacter strains, relatively low GC content, and was placed at the root position of the phylogenomic tree. The gene family based on a nonmetric multidimensional scaling (NMDS) plot revealed a clear separation of strain D. tibetensis Y620-1 from the reference strains. The genome of the deep ice core isolated strain contained the highest percentage of new genes. The definitive difference is that all genes required for the serine-glyoxylate cycle in one-carbon metabolism were only found in strain D. tibetensis Y620-1, but not in any of the reference strains. The placement of strain D. tibetensis Y620-1 in the root of the phylogenomic tree suggests that these new genes and functions are of ancient origin. All of these genomic features may contribute to the survival of D. tibetensis Y620-1 in the glacier.

Microbial diversity and soil physiochemical characteristic of higher altitude

Altitude is the major factor affecting both biodiversity and soil physiochemical properties of soil ecosystems. In order to understand the effect of altitude on soil physiochemical properties and bacterial diversity across the Himalayan cold desert, high altitude Gangotri soil ecosystem was studied and compared with the moderate altitude Kandakhal soil. Soil physiochemical analysis showed that altitude was positively correlated with soil pH, organic matter and total nitrogen content. However soil mineral nutrients and soil phosphorus were negatively correlated to the altitude. RT-PCR based analysis revealed the decreased bacterial and diazotrophic abundance at high altitude. Metagenomic study showed that Proteobacteria, Acidobacteria and Actinobacteria were dominant bacteria phyla at high altitude soil while Bacteroidetes and Fermicutes were found dominant at low altitude. High ratio of Gram-negative to Gram positive bacteria at Gangotri suggests the selective proliferation of Gram negative bacteria at high altitude with decrease in Gram positive bacteria. Moreover, Alphaproteobacteria was found more abundant at high altitude while the opposite was true for Betaproteobacteria. Abundance of Cytophaga, Flavobacterium and Bacteroides (CFB) were also found comparatively high at high altitude. Presence of many taxonomically unclassified sequences in Gangotri soil indicates the presence of novel bacterial diversity at high altitude. Further, isolation of bacteria through indigenously designed diffusion chamber revealed the existence of bacteria which has been documented in unculturable study of WIH (Western Indian Himalaya) but never been cultivated from WIH. Nevertheless, diverse functional free-living psychrotrophic diazotrophs were isolated only from the high altitude Gangotri soil. Molecular characterization revealed them as Arthrobacter humicola, Brevibacillus invocatus, Pseudomonas mandelii and Pseudomonas helmanticensis. Thus, this study documented the bacterial and psychrophilic diazotrophic diversity at high altitude and is an effort for exploration of low temperature bacteria in agricultural productivity with the target for sustainable hill agriculture.

Dyadobacter luticola sp. nov., isolated from a sewage sediment sample

A Gram-stain-negative, non-motile, aerobic bacterial strain, designated T17^T was isolated from a sample of sewage sediment from a Busan park (Republic of Korea). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain T17^T had the highest 16S rRNA gene sequence similarity to Dyadobacter soli KCTC 22481^T (97.3 %), D.yadobacter fermentans DSM 18053^T (97.1 %) and D.yadobacter sediminis CGMCC 1.12895^T (97.1 %). The isolate exhibited relatively low levels of DNA-DNA relatedness with respect to D. soli KCTC 22481^T (28.2±3.6 %). The DNA G+C content was 49.1 mol%. The unique respiratory quinone was MK-7 and the major polar lipids were phosphatidylethanolamine, five unidentified lipids, four aminolipids, two unidentified phospholipids and one glycophospholipid. The predominant cellular fatty acids (>5 % of total) were summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH; 44.3 %), iso-C15 : 0 (15.7 %), C16 : 1ω5c (9.6 %), iso-C17 : 0 3-OH (9.3 %) and C16 : 0 (5.6 %). Moreover, physiological and biochemical characteristics distinguished strain T17^T from its related species, including temperature and pH ranges for growth, being positive for acetate hydrolysis, and being negative for acid produced from melibiose and rhamnose. The genotypic, chemotaxonomic and phenotypic data revealed that strain T17^T represents a novel species of the genus Dyadobacter, for which the name Dyadobacter luticola sp. nov. is proposed. The type strain is T17^T (=KCTC 52981^T=CCTCC AB 2017091^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).