Complete genome sequence analysis of a biosurfactant-producing bacterium Bacillus velezensis L2D39.

Biosurfactants are amphipathic molecules with high industrial values owing to their chemical properties and stability under several environmental conditions. They have become attractive microbial products in the emerging biotechnology industry, offering a potential environmentally-friendly alternative to synthetic surfactants. Nowadays, several types of biosurfactants are commercially available for a wide range of applications in healthcare, agriculture, oil extraction and environmental remediation. In this study, a marine bacterium Bacillus velezensis L2D39 with the capability of producing biosurfactants was successfully isolated and characterized. The complete genome sequence of the bacterium B. velezensis L2D39 was obtained using PacBio Sequel HGAP.4, resulting in a sequence consisting of 4,140,042 base pairs with a 46.2 mol% G + C content and containing 4071 protein-coding genes. The presence of gene clusters associated with biosurfactants was confirmed through antiSMASH detection. The analysis of complete genome sequence will provide insight into the potential applications of this bacterium in biotechnological and natural product biosynthesis.

Isolation and Characterization of Paracoccus maritimus sp. nov., from Intertidal Sediment.

A novel Paracoccus-related strain, designated YLB-12T, was isolated from a sediment sample from the tidal zone of Shapowei Port, Xiamen, Fujian Province, PR China. The novel strain is a Gram-stain-negative, short, rod-shaped, nonmotile, catalase- and oxidase-positive strain that grows at 10-37 °C and pH 5.0-9.0 in the presence of 0-12.0% (w/v) NaCl. Phylogenetic analysis of the 16S rRNA gene sequences indicated that this strain belongs to the genus Paracoccus and that its highest sequence similarity was to Paracoccus homiensis DD-R11T (98.5%), followed by Paracoccus zeaxanthinifaciens ATCC 21588T (97.4%), Paracoccus rhizosphaerae LMG 26205T (97.2%), Paracoccus beibuensis CGMCC 1.7295T (97.1%) and Paracoccus halotolerans CFH 90064T (97.0%). The DNA‒DNA hybridization values between strain YLB-12T and the five closely related type strains ranged from 20.4 to 22.4%. The genomic G+C content of strain YLB-12T was 63.7%. In addition to diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and phosphatidylglycerol, the polar lipids of the strain YLB-12T also consisted of an unidentified glycolipid and four unidentified polar lipids. The cells contained summed feature 8 (C18: 1ω6c /C18: 1ω7c, 62.7%) as the major cellular fatty acid and ubiquinone-10 as the predominant menaquinone. On the basis of its phenotypic and genotypic characteristics, strain YLB-12T represents a novel species within the genus Paracoccus, for which the name Paracoccus maritimus sp. nov. is proposed. The type strain was YLB-12T (= MCCC 1A17213T = KCTC 82197T).

Microbacterium abyssi sp. nov. and Microbacterium limosum sp. nov., two new species of the genus Microbacterium, isolated from deep-sea sediment samples.

Two Gram-positive, non-motile, short rod-shaped actinomycete strains, designated as A18JL241T and Y20T, were isolated from deep-sea sediment samples collected from the Southwest Indian Ocean and Western Pacific Ocean, respectively. Both of the isolates were able to grow within the temperature range of 5-40 °C, NaCl concentration range of 0-7  % (w/v) and at pH 6.0-12.0. The two most abundant cellular fatty acids of both strains were anteiso-C15  :  0 and anteiso-C17  :  0. The major polar lipid contents of the two strains were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and one unidentified glycolipid. These two strains shared common chemotaxonomic features comprising MK-10 and MK-12 as the respiratory quinones. The genomic DNA G+C contents of the two strains were 68.1 and 70.4  mol%, respectively. The 16S rRNA gene phylogeny showed that the novel strains formed two distinct sublines within the genus Microbacterium. Strain A18JL241T was most closely related to the type strain of Microbacterium tenebrionis KCTC 49593T (98.8 % sequence similarity), whereas strain Y20T formed a tight cluster with the type strain of Microbacterium schleiferi NBRC 15075T (99.0 %). The orthologous average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values with the type strains of related Microbacterium species were in the range of 74.1-89.1  % and 19.4-36.9  %, respectively, which were below the recognized thresholds of 95-96 % ANI and 70 % dDDH for species definition. Based on the results obtained here, it can be concluded that strains A18JL241T and Y20T represent two novel species of the genus Microbacterium, for which the names Microbacterium abyssi sp. nov. (type strain A18JL241T=JCM 33956T=MCCC 1A16622T) and Microbacterium limosum sp. nov. (type strain Y20T=JCM 33960T=MCCC 1A16747T) are proposed.

Biological Oxidation of Manganese Mediated by the Fungus Neoroussoella solani MnF107.

Manganese oxides are highly reactive minerals and influence the geochemical cycling of carbon, nutrients, and numerous metals in natural environments. Natural Mn oxides are believed to be dominantly formed by biotic processes. A marine Mn-oxidizing fungus Neoroussoella solani MnF107 was isolated and characterized in this study. SEM observations show that the Mn oxides are formed on the fungal hyphal surfaces and parts of the hypha are enveloped by Mn oxides. TEM observations show that the Mn oxides have a filamentous morphology and are formed in a matrix of EPS enveloping the fungal cell wall. Mineral phase analysis of the fungal Mn oxides by XRD indicates that it is poorly crystalline. Chemical oxidation state analysis of the fungal Mn oxides confirms that it is predominantly composed of Mn(IV), indicating that Mn(II) has been oxidized to Mn (IV) by the fungus.

Sulfurovum mangrovi sp. nov., an obligately chemolithoautotrophic, hydrogen-oxidizing bacterium isolated from coastal marine sediments.

A novel mesophilic, chemolithoautotrophic, hydrogen-oxidizing bacterium, designated strain ST1-3T, was isolated from mud sediment samples collected from mangroves in Jiulong River estuary. The cells were Gram-stain-negative, non-motile and rod-shaped. The temperature, pH and salinity ranges for growth of strain ST1-3T were 4-45 °C (optimum, 35 °C), pH 5.0-8.5 (optimum, pH 7.0) and 0-8.0 % (w/v) NaCl (optimum, 4.0 %). The isolate was an obligate chemolithoautotroph capable of growth using hydrogen as the only energy source, and molecular oxygen, thiosulphate and elemental sulphur as electron acceptors. The major cellular fatty acids of strain ST1-3T were summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 0 and summed feature 8 (C18 : 1 ω7c). The major polar lipids were phosphatidylethanolamine, phosphatidyldimethyl ethanolamine and phosphatidylglycerol. The respiratory quinone was menaquinone-6. The genomic DNA G+C content was 43.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences and core genes showed that the novel isolate belonged to the genus Sulfurovum and was most closely related to Sulfurovum lithotrophicum 42BKTT (94.7 % sequence identity). The average nucleotide identity and digital DNA-DNA hybridization values between ST1-3T and S. lithotrophicum 42BKTT were 74.6 and 16.3 %, respectively. On the basis of the phenotypic, phylogenetic and genomic data presented here, strain ST1-3T represents a novel species of the genus Sulfurovum, for which the name Sulfurovum mangrovi sp. nov. is proposed, with the type strain ST1-3T (=MCCC M25234T=KCTC 25639T).

Nocardioides cremeus sp. nov., Nocardioides abyssi sp. nov. and Nocardioides oceani sp. nov., three actinobacteria isolated from Western Pacific Ocean sediment.

Three Gram-stain-positive, non-motile, short rod-shaped, catalase-positive and oxidase-negative actinomycete strains (SOB44T, SOB72T and SOB77T) were isolated from a deep-sea sediment sample collected from the Western Pacific Ocean. Cells of the three strains showed optimum growth at 30 °C and pH 7.0. Strains SOB44T, SOB72T and SOB77T could tolerate up to 10, 9 and 9 % (w/v) NaCl concentration and grow at pH 5.0-12.0, 5.0-11.0 and 5.0-11.0, respectively. Phylogenetic results based on 16S rRNA gene sequences showed that the three isolates belonged to the genus Nocardioides and were identified as representing three novel species based on 78.0-93.1 % average nucleotide identity and 21.3-50.0 % DNA-DNA hybridization values with closely related reference strains. Strains SOB44T, SOB72T and SOB77T showed highest 16S rRNA gene sequence similarity to Nocardioides salarius CL-Z59T (99.2 %), Nocardioides deserti SC8A-24T (99.2 %) and Nocardioides marmotae zg-579T (98.5 %), respectively. All three strains had MK-8(H4) as the respiratory quinone, iso-C16 : 0 as the major fatty acid, and phosphatidylglycerol, diphosphatidylglycerol and phosphatidylinositol as the major polar lipids. The diagnostic diamino acid in the cell-wall peptidoglycan of all three isolates was ll-diaminopimelic acid. The DNA G+C contents of strains SOB44T, SOB72T and SOB77T were 71.1, 72.9 and 72.9 mol%, respectively. Based on the phenotypic, phylogenetic and genotypic data, strains SOB44T, SOB72T and SOB77T clearly represent three novel taxa within the genus Nocardioides, for which the names Nocardioides cremeus sp. nov. (type strain SOB44T=JCM 35774T= MCCC M28400T), Nocardioides abyssi sp. nov. (type strain SOB72T=JCM 35775T=MCCC M28318T) and Nocardioides oceani sp. nov. (type strain SOB77T=JCM 35776T=MCCC M28544T) are proposed.

Physiological and Genomic Characterization of a Novel Obligately Chemolithoautotrophic, Sulfur-Oxidizing Bacterium of Genus Thiomicrorhabdus Isolated from a Coastal Sediment.

Thiomicrorhabdus species, belonging to the family Piscirickettsiaceae in the phylum Pseudomonadotav are usually detected in various sulfur-rich marine environments. However, only a few bacteria of Thiomicrorhabdus have been isolated, and their ecological roles and environmental adaptations still require further understanding. Here, we report a novel strain, XGS-01T, isolated from a coastal sediment, which belongs to genus Thiomicrorhabdus and is most closely related to Thiomicrorhabdus hydrogeniphila MAS2T, with a sequence similarity of 97.8%. Phenotypic characterization showed that XGS-01T is a mesophilic, sulfur-oxidizing, obligate chemolithoautotrophy, with carbon dioxide as its sole carbon source and oxygen as its sole electron acceptor. During thiosulfate oxidation, strain XGS-01T can produce extracellular sulfur of elemental α-S8, as confirmed via scanning electron microscopy and Raman spectromicroscopy. Polyphasic taxonomy results indicate that strain XGS-01T represents a novel species of the genus Thiomicrorhabdus, named Thiomicrorhabdus lithotrophica sp. nov. Genomic analysis confirmed that XGS-01T performed thiosulfate oxidation through a sox multienzyme complex, and harbored fcc and sqr genes for sulfide oxidation. Comparative genomics analysis among five available genomes from Thiomicrorhabdus species revealed that carbon fixation via the oxidation of reduced-sulfur compounds coupled with oxygen reduction is conserved metabolic pathways among members of genus Thiomicrorhabdus.

Vibrio intestinalis sp. nov., isolated from intestine of seahorse.

A novel Gram-stain-negative, catalase- and oxidase-positive, facultatively anaerobic, and rod-shaped motile bacterial strain, designated as YLB-11T, was isolated from seahorse intestine. The 16S rRNA gene sequencing analysis showed that YLB-11T was most closely related Vibrio mytili LMG 19157T (98.9 % nucleotide sequence identity). Phylogenetic analysis placed strain YLB-11T within the genus Vibrio. The major cellular fatty acids were summed feature 3 (C16: 1 ω6c/C16 : 1 ω7c, 36.4 %), C16 : 0 (19.1 %) and summed feature 8 (C18:1 ω6c/C18:1 ω7c, 12.3 %). The DNA G+C content of YLB-11T was 44.7 mol %. The in silico DNA-DNA hybridization and average nucleotide identity values for whole-genome sequence comparisons between YLB-11T and related species were clearly below the thresholds used for the delineation of a novel species. Therefore, YLB-11T is considered to represent novel species of the genus Vibrio, for which the name Vibrio intestinalis sp. nov. is proposed. The type strain is YLB-11T (=MCCC 1A17441T=KCTC 72604T).

Aerobic denitrifying bacterial-fungal consortium mediating nitrate removal: Dynamics, network patterns and interactions.

In recent years, nitrogen removal by mixed microbial cultures has received increasing attention owing to cooperative metabolism. A natural bacterial-fungal consortium was isolated from mariculture, which exhibited an excellent aerobic denitrification capacity. Under aerobic conditions, nitrate removal and denitrification efficiencies were up to 100% and 44.27%, respectively. High-throughput sequencing and network analysis suggested that aerobic denitrification was potentially driven by the co-occurrence of the following bacterial and fungal genera: Vibrio, Fusarium, Gibberella, Meyerozyma, Exophiala and Pseudoalteromonas, with the dominance of Vibrio and Fusarium in bacterial and fungal communities, respectively. In addition, the isolated consortium had a high steady aerobic denitrification performance in our sub-culturing experiments. Our results provide new insights on the dynamics, network patterns and interactions of aerobic denitrifying microbial consortia with a high potential for new biotechnology applications.

Response of methanogenic community and their activity to temperature rise in alpine swamp meadow at different water level of the permafrost wetland on Qinghai-Tibet Plateau.

Wetlands are an important source of atmospheric methane (CH4) and are sensitive to global climate change. Alpine swamp meadows, accounting for ~50% of the natural wetlands on the Qinghai-Tibet Plateau, were considered one of the most important ecosystems. Methanogens are important functional microbes that perform the methane producing process. However, the response of methanogenic community and the main pathways of CH4 production to temperature rise remains unknown in alpine swamp meadow at different water level in permafrost wetlands. In this study, we investigated the response of soil CH4 production and the shift of methanogenic community to temperature rise in the alpine swamp meadow soil samples with different water levels collected from the Qinghai-Tibet Plateau through anaerobic incubation at 5°C, 15°C and 25°C. The results showed that the CH4 contents increased with increasing incubation temperature, and were 5-10 times higher at the high water level sites (GHM1 and GHM2) than that at the low water level site (GHM3). For the high water level sites (GHM1 and GHM2), the change of incubation temperatures had little effect on the methanogenic community structure. Methanotrichaceae (32.44-65.46%), Methanobacteriaceae (19.30-58.86%) and Methanosarcinaceae (3.22-21.24%) were the dominant methanogen groups, with the abundance of Methanotrichaceae and Methanosarcinaceae having a significant positive correlation with CH4 production (p < 0.01). For the low water level site (GHM3), the methanogenic community structure changed greatly at 25°C. The Methanobacteriaceae (59.65-77.33%) was the dominant methanogen group at 5°C and 15°C; In contrast, the Methanosarcinaceae (69.29%) dominated at 25°C, and its abundance showed a significant positive correlation with CH4 production (p < 0.05). Collectively, these findings enhance the understanding of methanogenic community structures and CH4 production in permafrost wetlands with different water levels during the warming process.

A Novel Method Based on Hydrodynamic Cavitation for Improving Nitric Oxide Removal Performance of NaClO2.

In the removal of nitric oxide (NO) by sodium chlorite (NaClO2), the NaClO2 concentration is usually increased, and an alkaline absorbent is added to improve the NO removal efficiency. However, this increases the cost of denitrification. This study is the first to use hydrodynamic cavitation (HC) combined with NaClO2 for wet denitrification. Under optimal experimental conditions, when 3.0 L of NaClO2 with a concentration of 1.00 mmol/L was used to treat NO (concentration: 1000 ppmv and flow rate: 1.0 L/min), 100% of nitrogen oxides (NOx) could be removed in 8.22 min. Furthermore, the NO removal efficiency remained at 100% over the next 6.92 min. Furthermore, the formation of ClO2 by NaClO2 is affected by pH. The initial NOx removal efficiency was 84.8-54.8% for initial pH = 4.00-7.00. The initial NOx removal efficiency increases as the initial pH decreases. When the initial pH was 3.50, the initial NOx removal efficiency reached 100% under the synergistic effect of HC. Therefore, this method enhances the oxidation capacity of NaClO2 through HC, realizes high-efficiency denitrification with low NaClO2 concentration (1.00 mmol/L), and has better practicability for the treatment of NOx from ships.

Degradation of 2,4-Dichlorophenol by Nitrilotriacetic acid-modified photo-Fenton system: effects of organic and inorganic factors.

It has proved that the photo-Fenton system modified by polycarboxylic acid is effective against the degradation of organic pollutants. Still, its effect and impact on actual water bodies are not clear. Therefore, this study mainly discussed the effect of actual water elements on the degradation of 2,4-Dichlorophenol in photo-Fenton system modified by Nitrilotriacetic acid (NTA) and its mechanism in pure water. The specific research contents were: the effect of initial concentration of 2,4-Dichlorophenol on its degradation efficiency; the effect of organic matters on the degradation of 2,4-Dichlorophenol; the effect of cations and anions; the effect of different actual water bodies. And the main results were as follows: In the effect of initial concentration, when the concentration of 2,4-Dichlorophenol was 20 mg·L-1, the degradation efficiency was the best (reached 100%). But, with the increase of initial concentration, the degradation efficiency of the system became worse and worse; the coexistence of the same kind of organic compounds can inhibit each other's degradation, and the degradation rate of pollutants in the mixed system was slower than that in the single system; the addition of anions and cations inhibited the degradation of 2,4-Dichlorophenol, and the degradation efficiency varied with the concentration of ions, in which the effect of anions was more complex; the degradation efficiency of 2,4-Dichlorophenol in three kinds of actual water bodies was lower than in deionized water, especially in PPMW. However, the degradation rates of DSTP and NLW were the fastest in the first 20 min.

Photodegradation performance and mechanism of sulfadiazine in Fe(III)-EDDS-activated persulfate system.

In order to overcome the shortcomings in the traditional Fenton process, Fe(III)-EDDS-activated persulfate advanced oxidation process under irradiation is carried out as a promising technology. The photodegradation of sulfadiazine (SD) in Fe(III)-EDDS-activated persulfate system was investigated in this paper. The results showed that SD could be effectively degraded in Fe(III)-EDDS/S2O82-/hv system. The effects of Fe(III):EDDS molar ratio, the concentration of Fe(III)-EDDS, and the concentration of S2O82- on SD degradation were explored. At neutral pH, when Fe(III):EDDS = 1:1, Fe(III)-EDDS = 0.1 mM, S2O82- = 1.5 mM, the best SD degradation was achieved. The experiment of external influence factors showed that the degradation of SD could be obviously inhibited by the presence of CO32-, SO42-, whereas the degradation of SD was almost unaffected by the addition ofCl-. The degradation of SD could be slightly inhibited by the presence of humic acid and NO3-. The effect of pH on SD degradation was investigated, and SD could be degraded effectively in the pH range of 3-9. ESR proved that 1O2, ·OH, SO4-, and O2- were produced in the process. SO4- and ·OH were identified as the main radicals while O2·- also played non-ignorable role. Eleven intermediate products of SD were analysed. The C = N, S-N, and S-C bonds of SD were attacked by radicals firstly, leading to a series of reactions that eventually resulted in the destruction of SD molecules and the formation of small organic molecules.

Sulfurimonas marina sp. nov., an obligately chemolithoautotrophic, sulphur-oxidizing bacterium isolated from a deep-sea sediment sample from the South China Sea.

A novel marine bacterium, designated strain B2T, was isolated from a deep-sea sediment sample collected from the South China Sea. Cells were observed to be Gram-stain negative, motile and rod shaped with a single polar flagellum. B2T could grow at 10-45 °C (optimum, 35 °C), pH 4.5-9.0 (optimum, pH 7.0) and in the presence of 1.0-8.0 % (w/v) NaCl (optimum, 3.0%). The isolate grew chemolithoautotrophically with sulphide, elemental sulphur and thiosulphate as electron donors, carbon dioxide as the sole carbon source, and molecular oxygen as the sole electron acceptor. Molecular hydrogen did not support growth. The predominant fatty acids of B2T were C16 : 1ω7c, C16 : 0 and C18 : 1ω7c. The results of phylogenetic analysis based on 16S rRNA gene sequence indicated that B2T represented a member of the genus Sulfurimonas, with the highest similarity to the 16S rRNA gene sequences of Sulfurimonas indica NW8NT (95.9 %), Sulfurimonas crateris SN118T (95.7 %), Sulfurimonas xiamenensis 1-1NT (95.6 %) and Sulfurimonas paralvinellae GO25T (95.4 %). Sequence similarities to other members of the genus Sulfurimonas were less than 95.0 %. In addition, the average nucleotide identity (ANI) value and digital DNA-DNA hybridization (dDDH) estimate between B2T and S. indica NW8NT were 73.0 and 23.7 %, respectively. The size of the complete genome of B2T is 22 61 034 bp, with a DNA G+C content of 36.0 mol %. On the basis of the phenotypic, phylogenetic and genomic data presented here, strain B2T represent a novel species of the genus Sulfurimonas, for which the name Sulfurimonas marina sp. nov. is proposed, with the type strain B2T (=MCCC 1A14515T=KCTC 15852T).

Effects of alendronate sodium combined with InterTan on osteoporotic femoral intertrochanteric fractures and fracture recurrence.

BACKGROUND: Osteoporosis is a global disease affecting 6.6% of the total population. Osteoporosis complications include fractures, increased bone fragility, and reduced bone strength. The most commonly affected parts are the vertebral body, hip, and wrist. AIM: To examine the effect of alendronate sodium combined with InterTan for osteoporotic femoral intertrochanteric fractures on bone and fracture recurrence. METHODS: In total, 126 cases of osteoporotic femoral intertrochanteric fractures were selected and divided into two groups according to the 1:1 principle by the simple random method. They were admitted to the Department of Orthopedics, First Affiliated Hospital of Xingtai Medical College, from January 2018 to September 2020. The control group was treated with InterTan fixation combined with placebo, and the observation group with alendronate sodium based on InterTan fixation. Operation-related indicators, complications, and recurrent fractures were compared between the groups. Changes in bone metabolism markers, t value for hip bone mineral density, and Harris Hip Score were observed. RESULTS: Operation time, intraoperative blood loss, postoperative ambulation time, and complications were compared between the groups, and no significant difference was found. The fracture healing time was significantly shorter in the observation group than in the control group. ß-Collagen-specific sequence (ß-CTX) and total aminoterminal propeptide of type I procollagen (T-PINP) in the control group at 3 mo after operation were compared with those before operation, and the difference was not significant. Six months after the operation, the ß-CTX level decreased and T-PINP level increased. ß-CTX level at 3 and 6 mo in the observation group after operation was lower, and T-PINP level was higher, than that before operation. Compared with the control group, T-PINP level of the observation group was significantly higher and ß-CTX level was significantly lower at 3 and 6 mo after operation. The t value of hip bone mineral density was compared in the control group before and 1 mo after operation, and significant difference was not found. Compared with the control group, the t value of hip bone mineral density in the observation group was significantly higher at 1, 3, 6, and 12 mo after operation. Compared with the control group, the Harris score of the observation group was significantly higher at 1, 3, 6, and 12 mo after operation. The recurrence rate of fractures in the observation group within 12 mo was 0.00%, which was significantly lower than 6.35% in the control group. CONCLUSION: Alendronate sodium combined with InterTan in the treatment of osteoporotic femoral intertrochanteric fractures can increase bone mineral density, improve hip joint function, promote fracture healing, and reduce fracture recurrence.

Assessing the ecological risk of pesticides should not ignore the impact of their transformation byproducts - The case of chlorantraniliprole.

Risk assessments for pesticides typically focus on the compound itself ignoring the impact of its transformation byproducts. Challenges in isolating such byproducts (i.e. after application of pesticide in soil) often lead to underestimation of the real risk from such substances. The toxicological properties of these byproducts may differ from those of the parent pesticides; hence, special attention is required for these new emerging contaminants. In this study, two transformation byproducts of chlorantraniliprole were isolated from soil and identified, using nuclear magnetic resonance and high resolution mass spectrometry, as products of dechlorination (Z1) and bromination (Z2). Kinetic experiments revealed both byproducts degrade faster than chlorantraniliprole in soil (half-lives 38 & 43 d vs. 58 d). The ecological risk evaluation of chlorantraniliprole and its byproducts on soil bacterial community showed that they were all potentially harmful but they imposed different impacts on both alpha and beta diversities and co-occurrence networks of the bacterial community. Z2 had the biggest potential impact on soil bacteria and accounted as a high potential risk. By comparing their impacts on soil bacterial community, we confirm that ecological risk assessment necessitates the understanding of the environmental impacts of a substance as well as of its transformation byproducts.

Candicidin Isomer Production Is Essential for Biocontrol of Cucumber Rhizoctonia Rot by Streptomyces albidoflavus W68.

Diseases caused by soilborne fungal pathogens result in significant crop yield losses and quality reduction. Streptomyces albidoflavus strain W68 is effective in controlling several soilborne fungal diseases. To identify antifungal substances critical for biocontrol activity of W68, the genome of W68 was sequenced and a linear chromosome of 6.80 Mb was assembled. A total of 21 secondary metabolite biosynthesis gene clusters (BGCs), accounting for 12.27% of the genome, were identified. Core gene deletion mutants for each of all 8 BGCs for nonribosomal peptide synthetases and polyketide synthases were created. Among them, only the mutant lacking ctg1-5755 (the gene was renamed as fscDW68) in BGC 19, which shares 100% sequence similarity with the BGC for candicidin synthesis, showed obvious reduction in antifungal activity. A pot experiment revealed that biocontrol effects of the ΔfscDW68 mutant in Rhizoctonia rot of cucumber were also significantly compromised relative to W68. Liquid chromatography-mass spectrometry (LC-MS) analysis revealed that W68 but not the ΔfscDW68 mutant can produce candicidin isomers, indicating that the production of candicidin isomers is key for antifungal activity and biocontrol activity of S. albidoflavus W68.IMPORTANCE This study reports that candicidin-like secondary metabolites produced by microbial cells in natural soil environments can effectively control soilborne fungal diseases, revealing a novel mechanism of microbial biocontrol agents. We demonstrated that the main antifungal activity and biocontrol activity of Streptomyces albidoflavus strain W68 are attributable to the production of candicidin isomers, suggesting that gene clusters for candicidin-like compound biosynthesis might be used as molecular markers to screen and breed microbial strains for biocontrol agent development.

Bacterial synthesis of PbS nanocrystallites in one-step with L-cysteine serving as both sulfur source and capping ligand.

The green bacterial biosynthesis of lead sulfide nanocrystallites by L-cysteine-desulfurizing bacterium Lysinibacillus sphaericus SH72 was demonstrated in this work. Nanocrystals formed by this bacterial method were characterized using the mineralogical and morphological approaches. The results revealed that the microbially synthesized PbS nanocrystals assume a cubic structure, and are often aggregated as spheroids of about 105 nm in size. These spheroids are composed of numerous nanoparticles with diameter 5-10 nm. Surface characterization of the bacterial nanoparticles with FTIR spectroscopy shows that the L-cysteine coats the surface of PbS nanoparticle as a stabilizing ligand. The optical features of the PbS nanocrystallites were assessed by UV-Vis spectroscopy and PL spectroscopy. The maximum absorption wavelength of the bacterial PbS particles occurs at 240 nm, and the photoluminescence emission band ranges from 375 to 550 nm. The band gap energy is calculated to be 4.36 eV, compared to 0.41 eV for the naturally occurring bulk PbS, with this clear blue shift attributable to the quantum size effect.

Molecular level changes during suppression of Rhizoctonia solani growth by humic substances and relationships with chemical structure.

Elucidation of the inhibitory effects of humic substances (HSs) on phytopathogenic fungi and the underlying molecular mechanisms are highly important for improved biocontrol. In this study, we investigated the growth suppression, morphological characteristics, transcriptomic sequence, and radical signals of Rhizoctonia solani following HS addition (50 mg/L). Through mycelial cultured experiment, mycelia growth of R. solani had been suppressed with HS addition, and the inhibition rate was 24.88 ± 0.11% compared to the control. Field emission-scanning electron microscopy showed increased and superimposed branching mycelial growth, with a shriveled appearance. RNA samples of R. solani cultured with or without HSs were both extracted to examine the sequence on molecular level by Illumina HiSeq sequencing platform. RNA sequencing analysis revealed 175 differentially expressed genes (DEGs; 111 upregulated and 64 downregulated) between the HSs treatment and control. The upregulated unigenes were annotated and significantly enriched to three molecular processes: vitamin B6 metabolism, ABC transporters, and glutathione metabolism, while the downregulated unigenes were annotated to carbohydrate metabolism, but not significantly enriched. Real time-quantitative polymerase chain reaction analysis showed that the unigenes related to hexokinase, glucose-6-phosphate isomerase, glutathione synthase, and glutathione reductase were significantly decreased (by 60.03%, 70.70%, 60.33%, and 57.59%, respectively), while those related to glutathione S-transferase were significantly increased (2.66-fold). The electron paramagnetic resonance spectra showed that HSs induced increased the intensity of radical signals of R. solani in a cultured system increased by 59.56% compared to CK (without HSs addition). Network analysis based on DEGs expression and the chemical structure of HSs revealed that the carbonyl moiety in HSs formed the most links with nodes of the DEGs (sum of the links of positive and negative effects = 70), implicating this structure as the active fraction responsible for the inhibitory effect. This study provides molecular and chemical evidence of the biofungicidal activity of HSs with the potential for practical application.

Diversity and Distribution of Methanogenic Community Between Two Typical Alpine Ecosystems on the Qinghai-Tibetan Plateau.

Alpine permafrost regions are important sources of biogenic CH4 and methanogens play an important role in the methane-producing process. The alpine permafrost on the Qinghai-Tibetan plateau comprises about one-sixth of China's land area, and there are various types of alpine ecosystems. However, the methanogenic communities in the typical alpine ecosystems are poorly understood. In this study, the active layers and permafrost layers of the natural ecosystem of alpine grassland (DZ2-1) and alpine swamp meadow (DZ2-5) were selected to investigate the diversity and abundance of methanogenic communities. Methanobacterium (63.65%) are overwhelmingly dominant in the active layer of the alpine grassland (DZ2-1A). ZC-I cluster (26.13%), RC-I cluster (19.56%), and Methanobacterium (15.02%) are the dominant groups in the permafrost layer of the alpine grassland (DZ2-1P). Methanosaeta (32.92%), Fen cluster (29.59%), Methanosarcina (16.33%), and Methanobacterium (13.95%) are the dominant groups in the active layer of the alpine swamp meadow (DZ2-5A), whereas the Fen cluster (50.85%), ZC-I cluster (27.63%), and RC-I cluster (14.15%) are relatively abundant in the permafrost layer of the alpine swamp meadow (DZ2-5P). qPCR data showed that the abundance of methanogens was higher in the natural ecosystem of alpine swamp meadow than in alpine grassland. We found that the community characteristics of methanogens were related to environmental factors. Pearson correlation analyses indicated that the relative abundance of Methanobacterium had a significantly positive correlation with hydrogen concentration (P < 0.01), while the relative abundances of Methanosaeta and Methanosarcina were positively correlated with acetate concentration (P < 0.05). This study will help us to understand the methanogenic communities and their surrounding environments in alpine ecosystems.