B. subtilis CNBG-PGPR-1 induces methionine to regulate ethylene pathway and ROS scavenging for improving salt tolerance of tomato.

Soil salinity severely threatens plant growth and crop yields. The utilization of PGPR is an effective strategy for enhancing plant salt tolerance, but the mechanisms involved in this process have rarely been reported. In this study, we investigated the effects of Bacillus subtilis CNBG-PGPR-1 on improving plant salt tolerance and elucidated the molecular pathways involved. The results showed that CNBG-PGPR-1 significantly improved the cellular homeostasis and photosynthetic efficiency of leaves and reduced ion toxicity and osmotic stress caused by salt in tomato. Transcriptome analysis uncovered that CNBG-PGPR-1 enhanced plant salt tolerance through the activation of complex molecular pathways, with plant hormone signal transduction playing an important role. Comparative analysis and pharmacological experiments confirmed that the ethylene pathway was closely related to the beneficial effect of CNBG-PGPR-1 on improving plant salt tolerance. Furthermore, we found that methionine, a precursor of ethylene synthesis, significantly accumulated in response to CNBG-PGPR-1 in tomato. Exogenous L-methionine largely mimicked the beneficial effects of CNBG-PGPR-1 and activated the expression of ethylene pathway-related genes, indicating CNBG-PGPR-1 induces methionine accumulation to regulate the ethylene pathway in tomato. Finally, CNBG-PGPR-1 reduced salt-induced ROS by activating ROS scavenger-encoding genes, mainly involved in GSH metabolism and POD-related genes, which were also closely linked to methionine metabolism. Overall, our studies demonstrate that CNBG-PGPR-1-induced methionine is a key regulator in enhancing plant salt tolerance through the ethylene pathway and ROS scavenging, providing a novel understanding of the mechanism by which beneficial microbes improve plant salt tolerance.

G-quadruplex structures in FGFR3 promoter negatively regulate its gene expression and DNA replication.

FGFR3 activating mutations and abnormal expression are linked to tumor development. However, the current state of research on FGFR3 gene expression regulation is relatively insufficient. In this study, we have reported that the FGFR3 promoter's positive strand contains several G-tracts and most likely forms a G-quadruplex (G4) structure. Circular dichroism investigations revealed that oligonucleotides from this region exhibit G-quadruplex-like molar ellipticity. We further validated the G4 structure of the FGFR3 promoter using biochemical and cellular molecular biology techniques. The G-quadruplex mutation enhanced the transcriptional activity of the FGFR3 promoter and DNA replication, suggesting that the G4 structure inhibits its expression. Furthermore, we conducted a preliminary screen for helicases associated with FGFR3 expression and explored their regulatory effects on FGFR3 gene transcription. Subsequently, we investigated the effect of curcumin on the stability of the G4 structure of the FGFR3 promoter and its regulatory effect on FGFR3 expression.

Antifungal Activity and Possible Mechanism of Bacillus amyloliquefaciens FX2 Against the Postharvest Apple Ring Rot Pathogen.

Botryosphaeria dothidea-induced apple ring rot is one of the most serious postharvest diseases in apple production. In our preliminary work, we isolated a bacterial strain (FX2) from an infested apple orchard. Here, we confirmed the strong antifungal activity of FX2 on B. dothidea. Through phylogenetic analysis and morphological observations, we identified FX2 as a Bacillus amyloliquefaciens strain. We also found that 10% cell-free supernatant (CFS) of FX2 significantly affected mycelial growth and morphology and almost completely inhibited spore germination and germ tube elongation in B. dothidea. Furthermore, 10% CFS damaged the cell ultrastructure, resulting in a remarkable increase in cellular leakage in B. dothidea mycelia. Thus, CFS has the potential to effectively reduce in vivo B. dothidea infection, reduced lesion diameters to 64.7% compared with the control group, and reduced disease incidence by 15%. Finally, ultrafiltration, desalting chromatography, and anion exchange chromatography showed that the antifungal constituents in CFS are composed mainly of antifungal proteins. We further characterized these potential antifungal proteins via liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. Herein, we provide novel insights into the antifungal mechanisms of B. amyloliquefaciens FX2, and we highlight its potential as a novel biocontrol agent for controlling postharvest apple ring rot.

Schwertmannite formation at cell junctions by a new filament-forming Fe(II)-oxidizing isolate affiliated with the novel genus Acidithrix.

A new acidophilic iron-oxidizing strain (C25) belonging to the novel genus Acidithrix was isolated from pelagic iron-rich aggregates ('iron snow') collected below the redoxcline of an acidic lignite mine lake. Strain C25 catalysed the oxidation of ferrous iron [Fe(II)] under oxic conditions at 25 °C at a rate of 3.8 mM Fe(II) day(-1) in synthetic medium and 3.0 mM Fe(II) day(-1) in sterilized lake water in the presence of yeast extract, producing the rust-coloured, poorly crystalline mineral schwertmannite [Fe(III) oxyhydroxylsulfate]. During growth, rod-shaped cells of strain C25 formed long filaments, and then aggregated and degraded into shorter fragments, building large cell-mineral aggregates in the late stationary phase. Scanning electron microscopy analysis of cells during the early growth phase revealed that Fe(III)-minerals were formed as single needles on the cell surface, whereas the typical pincushion-like schwertmannite was observed during later growth phases at junctions between the cells, leaving major parts of the cell not encrusted. This directed mechanism of biomineralization at specific locations on the cell surface has not been reported from other acidophilic iron-oxidizing bacteria. Strain C25 was also capable of reducing Fe(III) under micro-oxic conditions which led to a dissolution of the Fe(III)-minerals. Thus, strain C25 appeared to have ecological relevance for both the formation and transformation of the pelagic iron-rich aggregates at oxic/anoxic transition zones in the acidic lignite mine lake.

Insights into the structure and metabolic function of microbes that shape pelagic iron-rich aggregates ("iron snow").

Microbial ferrous iron [Fe(II)] oxidation leads to the formation of iron-rich macroscopic aggregates ("iron snow") at the redoxcline in a stratified lignite mine lake in east-central Germany. We aimed to identify the abundant Fe-oxidizing and Fe-reducing microorganisms likely to be involved in the formation and transformation of iron snow present in the redoxcline in two basins of the lake that differ in their pH values. Nucleic acid- and lipid-stained microbial cells of various morphologies detected by confocal laser scanning microscopy were homogeneously distributed in all iron snow samples. The dominant iron mineral appeared to be schwertmannite, with shorter needles in the northern than in the central basin samples. Total bacterial 16S rRNA gene copies ranged from 5.0 × 10(8) copies g (dry weight)(-1) in the acidic central lake basin (pH 3.3) to 4.0 × 10(10) copies g (dry weight)(-1) in the less acidic (pH 5.9) northern basin. Total RNA-based quantitative PCR assigned up to 61% of metabolically active microbial communities to Fe-oxidizing- and Fe-reducing-related bacteria, indicating that iron metabolism was an important metabolic strategy. Molecular identification of abundant groups suggested that iron snow surfaces were formed by chemoautotrophic iron oxidizers, such as Acidimicrobium, Ferrovum, Acidithiobacillus, Thiobacillus, and Chlorobium, in the redoxcline and were rapidly colonized by heterotrophic iron reducers, such as Acidiphilium, Albidiferax-like, and Geobacter-like groups. Metaproteomics yielded 283 different proteins from northern basin iron snow samples, and protein identification provided a glimpse into some of their in situ metabolic processes, such as primary production (CO2 fixation), respiration, motility, and survival strategies.

Primer selection impacts the evaluation of microecological patterns in environmental microbiomes.

This study revealed that primer selection substantially influences the taxonomic and predicted functional composition and the characterization of microecological patterns, which was not alleviated by close-reference clustering. Biases were relatively consistent across different habitats in community profiling but not in microecological patterns. These primer biases could be attributed to multiple aspects, including taxa specificity, regional hypervariability, and amplification efficiency.

Bile acids and their receptors: Potential therapeutic targets in inflammatory bowel disease.

Chronic and recurrent inflammatory disorders of the gastrointestinal tract caused by a complex interplay between genetics and intestinal dysbiosis are called inflammatory bowel disease. As a result of the interaction between the liver and the gut microbiota, bile acids are an atypical class of steroids produced in mammals and traditionally known for their function in food absorption. With the development of genomics and metabolomics, more and more data suggest that the pathophysiological mechanisms of inflammatory bowel disease are regulated by bile acids and their receptors. Bile acids operate as signalling molecules by activating a variety of bile acid receptors that impact intestinal flora, epithelial barrier function, and intestinal immunology. Inflammatory bowel disease can be treated in new ways by using these potential molecules. This paper mainly discusses the increasing function of bile acids and their receptors in inflammatory bowel disease and their prospective therapeutic applications. In addition, we explore bile acid metabolism and the interaction of bile acids and the gut microbiota.

Interactions of Vallisneria natans and Iron-Oxidizing Bacteria Enhance Iron-Bound Phosphorus Formation in Eutrophic Lake Sediments.

Submerged macrophyte restoration and in situ phosphorus (P) passivation are effective methods for the control of internal P loading from sediments. This study explored the synergistic effects of Vallisneria natans and iron (Fe)-oxidizing bacteria (IOB) on internal P loading from eutrophic freshwater lake sediments by taking into account Fe-bound P (FeP) formation and associated bacterial community structures. Sediment samples were prepared in glass tanks under four treatments, namely no V. natans planting or IOB inoculation (control), planting V. natans without IOB inoculation (Va), planting V. natans with IOB inoculation (Va-IOB), and planting V. natans with autoclaved IOB inoculation (Va-IOB[A]). Compared with the control, all three treatments with V. natans (Va, Va-IOB, and Va-IOB[A]) had significantly decreased organic matter contents and increased redox potential in sediments (p < 0.05), at the rapid growth and mature stages of V. natans. Planting V. natans with and without IOB inoculation also decreased the total P (TP) and Fe-P concentrations in sediments. Conversely, Fe3+ concentrations, Fe3+/Fe2+ ratios, and the proportions of Fe-P in TP all increased in sediments planted with V. natans, especially under the Va-IOB treatment (p < 0.05). Furthermore, bacterial community diversity increased in sediments due to the presence of V. natans. The relative abundances of IOB (including Acidovorax and Chlorobium) increased from the transplanting to the rapid growth stage of V. natans and then decreased afterwards. In the later stages, the relative abundances of IOB and their ratios to Fe-reducing bacteria were the highest under the Va-IOB treatment. Accordingly, synergistic interactions between V. natans and IOB could enhance Fe-P formation and reduce TP concentrations in eutrophic lake sediments by altering sediment physicochemical properties and Fe oxidation-related bacterial community structures.

A plant growth-promoting bacteria Priestia megaterium JR48 induces plant resistance to the crucifer black rot via a salicylic acid-dependent signaling pathway.

Xanthomonas campestris pv. campestris (Xcc)-induced black rot is one of the most serious diseases in cruciferous plants. Using beneficial microbes to control this disease is promising. In our preliminary work, we isolated a bacterial strain (JR48) from a vegetable field. Here, we confirmed the plant-growth-promoting (PGP) effects of JR48 in planta, and identified JR48 as a Priestia megaterium strain. We found that JR48 was able to induce plant resistance to Xcc and prime plant defense responses including hydrogen peroxide (H2O2) accumulation and callose deposition with elevated expression of defense-related genes. Further, JR48 promoted lignin biosynthesis and raised accumulation of frees salicylic acid (SA) as well as expression of pathogenesis-related (PR) genes. Finally, we confirmed that JR48-induced plant resistance and defense responses requires SA signaling pathway. Together, our results revealed that JR48 promotes plant growth and induces plant resistance to the crucifer black rot probably through reinforcing SA accumulation and response, highlighting its potential as a novel biocontrol agent in the future.

Draft Genome Sequences of Acidithrix sp. Strain C25 and Acidocella sp. Strain C78, Acidophiles Isolated from Iron-Rich Pelagic Aggregates (Iron Snow).

We report the draft genome sequences of two acidophiles, the Fe-oxidizing bacterium Acidithrix sp. strain C25 and the putative Fe-reducing Acidocella sp. strain C78. Both strains were isolated from iron-rich pelagic aggregates (iron snow) collected below the redoxcline at a 5-m depth in an acidic pit lake located in Germany (51°31'8.2″N, 13°41'34.7″E).

Ecophysiology of Fe-cycling bacteria in acidic sediments.

Using a combination of cultivation-dependent and -independent methods, this study aimed to elucidate the diversity of microorganisms involved in iron cycling and to resolve their in situ functional links in sediments of an acidic lignite mine lake. Using six different media with pH values ranging from 2.5 to 4.3, 117 isolates were obtained that grouped into 38 different strains, including 27 putative new species with respect to the closest characterized strains. Among the isolated strains, 22 strains were able to oxidize Fe(II), 34 were able to reduce Fe(III) in schwertmannite, the dominant iron oxide in this lake, and 21 could do both. All isolates falling into the Gammaproteobacteria (an unknown Dyella-like genus and Acidithiobacillus-related strains) were obtained from the top acidic sediment zones (pH 2.8). Firmicutes strains (related to Bacillus and Alicyclobacillus) were only isolated from deep, moderately acidic sediment zones (pH 4 to 5). Of the Alphaproteobacteria, Acidocella-related strains were only isolated from acidic zones, whereas Acidiphilium-related strains were isolated from all sediment depths. Bacterial clone libraries generally supported and complemented these patterns. Geobacter-related clone sequences were only obtained from deep sediment zones, and Geobacter-specific quantitative PCR yielded 8 × 10(5) gene copy numbers. Isolates related to the Acidobacterium, Acidocella, and Alicyclobacillus genera and to the unknown Dyella-like genus showed a broad pH tolerance, ranging from 2.5 to 5.0, and preferred schwertmannite to goethite for Fe(III) reduction. This study highlighted the variety of acidophilic microorganisms that are responsible for iron cycling in acidic environments, extending the results of recent laboratory-based studies that showed this trait to be widespread among acidophiles.

The complete chloroplast genome sequence of Michelia compressa.

Michelia compressa is an evergreen ornamental tree species. The high-throughput sequencing technology was used to sequence and assemble the chloroplast genome of Michelia compressa. Results showed that the chloroplast genome is 160,061 bp in length, of which the inverted repeats sequence (IRs) is 26,581 bp, the large single-copy region (LSC) and the small single copy region (SSC) are 88,097 bp and 18,802 bp, respectively. The GC content of the plastome was 39.2%, with 43.2%, 37.9% and 34.2% in IRs, LSC and SSC, respectively. A total of 132 genes are annotated, 86 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. This study enriched the Michelia compressa genomic information which provides the basis for rational exploitation and utilization of germplasm resources.

Biological treatment of selenium-laden wastewater containing nitrate and sulfate in an upflow anaerobic sludge bed reactor at pH 5.0.

This study investigated the removal of selenate (SeO42-), sulfate (SO42-) and nitrate (NO3-) at different influent pH values ranging from 7.0 to 5.0 and 20 °C in an upflow anaerobic sludge blanket (UASB) reactor using lactate as an electron donor. At pH 5.0, the UASB reactor showed a 20-30% decrease in reactor performance compared to operation at pH 5.5 to 7.0, reaching removal efficiencies of 79%, 15%, 43% and 61% for NO3-, SO42-, Setotal and Sediss, respectively. However, the reactor stability was an issue upon lowering the pH to 5.0 and further experiments are recommended. The sludge formed during low pH operation had a fluffy, floc-like appearance with filamentous structure, possibly due to the low polysaccharide (PS) to protein (PN) ratio (0.01 PS/PN) in the soluble extracellular polymeric substances (EPS) matrix of the biomass. Scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM-EDX) analysis of the sludge confirmed Se oxyanion reduction and deposition of Se0 particles inside the biomass. Microbial community analysis using Illumina MiSeq sequencing revealed that the families of Campylobacteraceae and Desulfomicrobiaceae were the dominant phylotypes throughout the reactor operation at approximately 23% and 10% relative abundance, respectively. Furthermore, approximately 10% relative abundance of both Geobacteraceae and Spirochaetaceae was observed in the granular sludge during the pH 5.0 operation. Overall, this study demonstrated the feasibility of UASB operation at pH values ranging from 7.0 to 5.0 for removing Se and other oxyanions from wastewaters.

Sticking together: inter-species aggregation of bacteria isolated from iron snow is controlled by chemical signaling.

Marine and lake snow is a continuous shower of mixed organic and inorganic aggregates falling from the upper water where primary production is substantial. These pelagic aggregates provide a niche for microbes that can exploit these physical structures and resources for growth, thus are local hot spots for microbial activity. However, processes underlying their formation remain unknown. Here, we investigated the role of chemical signaling between two co-occurring bacteria that each make up more than 10% of the community in iron-rich lakes aggregates (iron snow). The filamentous iron-oxidizing Acidithrix strain showed increased rates of Fe(II) oxidation when incubated with cell-free supernatant of the heterotrophic iron-reducing Acidiphilium strain. Amendment of Acidithrix supernatant to motile cells of Acidiphilium triggered formation of cell aggregates displaying similar morphology to those of iron snow. Comparative metabolomics enabled the identification of the aggregation-inducing signal, 2-phenethylamine, which also induced faster growth of Acidiphilium. We propose a model that shows rapid iron snow formation, and ultimately energy transfer from the photic zone to deeper water layers, is controlled via a chemically mediated interplay.

Analysis of microbial communities using culture-dependent and culture-independent approaches in an anaerobic/aerobic SBR reactor.

Comparative analysis of microbial communities in a sequencing batch reactor which performed enhanced biological phosphorus removal (EBPR) was carried out using a cultivation-based technique and 16S rRNA gene clone libraries. A standard PCR protocol and a modified PCR protocol with low PCR cycle was applied to the two clone libraries of the 16S rRNA gene sequences obtained from EBPR sludge, respectively, and the resulting 424 clones were analyzed using restriction fragment length polymorphisms (RFLPs) on 16S rRNA gene inserts. Comparison of two clone libraries showed that the modified PCR protocol decreased the incidence of distinct fragment patterns from about 63% (137 of 217) in the standard PCR method to about 34% (70 of 207) under the modified protocol, suggesting that just a low level of PCR cycling (5 cycles after 15 cycles) can significantly reduce the formation of chimeric DNA in the final PCR products. Phylogenetic analysis of 81 groups with distinct RFLP patterns that were obtained using the modified PCR method revealed that the clones were affiliated with at least 11 phyla or classes of the domain Bacteria. However, the analyses of 327 colonies, which were grouped into just 41 distinct types by RFLP analysis, showed that they could be classified into five major bacterial lineages: alpha, beta, gamma- Proteobacteria, Actinobacteria, and the phylum Bacteroidetes, which indicated that the microbial community yielded from the cultivation-based method was still much simpler than that yielded from the PCR-based molecular method. In this study, the discrepancy observed between the communities obtained from PCR-based and cultivation-based methods seems to result from low culturabilities of bacteria or PCR bias even though modified culture and PCR methods were used. Therefore, continuous development of PCR protocol and cultivation techniques is needed to reduce this discrepancy.

Extremophile microbiomes in acidic and hypersaline river sediments of Western Australia.

We investigated the microbial community compositions in two sediment samples from the acidic (pH ∼3) and hypersaline (>4.5% NaCl) surface waters, which are widespread in Western Australia. In West Dalyup River, large amounts of NaCl, Fe(II) and sulfate are brought by the groundwater into the surface run-off. The presence of K-jarosite and schwertmannite minerals in the river sediments suggested the occurrence of microbial Fe(II) oxidation because chemical oxidation is greatly reduced at low pH. 16S rRNA gene diversity analyses revealed that sequences affiliated with an uncultured archaeal lineage named Aplasma, which has the genomic potential for Fe(II) oxidation, were dominant in both sediment samples. The acidophilic heterotrophs Acidiphilium and Acidocella were identified as the dominant bacterial groups. Acidiphilium strain AusYE3-1 obtained from the river sediment tolerated up to 6% NaCl at pH 3 under oxic conditions and cells of strain AusYE3-1 reduced the effects of high salt content by forming filamentous structure clumping as aggregates. Neither growth nor Fe(III) reduction by strain AusYE3-1 was observed in anoxic salt-containing medium. The detection of Aplasma group as potential Fe(II) oxidizers and the inhibited Fe(III)-reducing capacity of Acidiphilium contributes to our understanding of the microbial ecology of acidic hypersaline environments.

Effect of nano-TiO(2) on strength of naturally aged seeds and growth of spinach.

The effects of nano-TiO(2) (rutile) and non-nano-TiO(2) on the germination and growth of naturally aged spinach seeds were studied by measuring the germination rate and the germination and vigor indexes of aged spinach seeds. An increase of these factors was observed at 0.25-4% nano-TiO(2) treatment. During the growth stage, the plant dry weight was increased, as was the chlorophyll formation, the ribulosebisphosphate carboxylase/oxygenase activity, and the photosynthetic rate. The best results were found at 2.5% nano-TiO(2). The effects of non-nano-TiO(2) are not significant. It is shown that the physiological effects are related to the nanometer-size particles, but the mechanism by which nano-TiO(2) improves the growth of spinach seeds still needs further study.

Simplicispira limi sp. nov., isolated from activated sludge.

A Gram-negative, motile, rod-shaped bacterium, designated strain EMB325(T), was isolated from activated sludge that performed enhanced biological phosphorus removal in a sequencing batch reactor. The predominant fatty acids of strain EMB325(T) were summed feature 3 (C(16 : 1)omega7c and/or iso-C(15 : 0) 2-OH), C(16 : 0), C(18 : 1)omega7c and C(18 : 1)omega7c 11-methyl. The strain contained phosphatidylethanolamine and diphosphatidylglycerol as polar lipids. The G+C content of the genomic DNA was 63.3 mol%. The major quinone was Q-8. Phylogenetic analysis of 16S rRNA gene sequences showed that strain EMB325(T) formed a phyletic lineage with members of the genus Simplicispira and was most closely related to Simplicispira psychrophila LMG 5408(T) and Simplicispira metamorpha DSM 1837(T) with similarities of 98.1 and 97.9 %, respectively. Levels of DNA-DNA relatedness between strain EMB325(T) and S. psychrophila LMG 5408(T) and S. metamorpha DSM 1837(T) were 28 and 23 %, respectively. On the basis of chemotaxonomic data and molecular characteristics, strain EMB325(T) is considered to represent a novel species within the genus Simplicispira, for which the name Simplicispira limi sp. nov. is proposed. The type strain is EMB325(T) (=KCTC 12608(T)=DSM 17964(T)).

Runella defluvii sp. nov., isolated from a domestic wastewater treatment plant.

A long, Gram-negative, rod-shaped bacterium, designated strain EMB13T, was isolated from a wastewater treatment plant in Korea. The isolate was strictly aerobic and non-motile. The strain grew optimally at 30-35 degrees C and pH 7.5-8.0, and the predominant fatty acids were iso-C15:0, summed feature 3 (C16:1omega7c and/or iso-C15:0 2-OH), C16:1omega5c and iso-C17:0 3-OH. The strain contained a large amount of phosphatidylethanolamine and small amounts of phosphatidylcholine and an unknown phospholipid as the polar lipids. The G+C content of the genomic DNA was 40.1 mol% and the major isoprenoid quinone was menaquinone-7. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain EMB13T belonged to the genus Runella and was most closely related to Runella limosa EMB111T, with a 16S rRNA gene sequence similarity of 97.1%. DNA-DNA relatedness between strain EMB13T and R. limosa EMB111T was approximately 25%. On the basis of phenotypic, chemotaxonomic and molecular data, it is clear that strain EMB13T represents a novel species within the genus Runella, for which the name Runella defluvii sp. nov. is proposed. The type strain is EMB13T (=KCTC 12614T=DSM 17976T).