Synthesis,spectral analysis,antibacterial and antifungal activities of some 4,6-diaryl-4,5-dihydro-3-hydroxy-2[H]-indazole—a novel fused indazole derivative

A novel class of 4,6-diaryl-4,5-dihydro-3-hydroxy-2[H]-indazoles 25-32 were synthesized and evaluated for their in vitro antibacterial and antifungal activities. Four Compounds, which all possessed electron withdrawing functional groups (–Cl, –NO₂, –Br) 27, 28, 30 and 32 were more potent against the tested bacterial/fungal strains than the standard bacterial and fungal drugs ciprofloxacin and fluconazole respectively.     

Design, synthesis, characterization and in vitro antimicrobial evaluation of 4,6-diaryl-4,5-dihydro-2-phenyl-2H-indazol-3-ols

New 4,6-diaryl-4,5-dihydro-2-phenyl-2H-indazol-3-ols 25-32 were designed, synthesized and in vitro microbially evaluated using clinically isolated bacterial strains viz Staphylococcus aureus, beta-Heamolytic streptococcus, Vibreo cholerae, Salmonella typhii, Shigella felxneri and fungal strains viz Aspergillus flavus, Mucor, Rhizopus and Microsporum gypsuem. Results of this study showed that the nature of the substituents on the phenyl rings viz., methyl, methoxy, chloro, nitro as well as the bromo functions at the meta and para positions of the aryl moieties determined the nature and extent of the activity of the fused indazolonol compounds 25-32.     

Microbial Community Diversity of Moonmilk Deposits at Ballynamintra Cave, Co. Waterford, Ireland

Caves are extreme and specialised habitats for terrestrial life that sometimes contain moonmilk, a fine-grained paste-like secondary mineral deposit that is found in subterranean systems worldwide. While previous studies have investigated the possible role of microorganisms in moonmilk precipitation, the microbial community ecology of moonmilk deposits is poorly understood. Bacterial and fungal community structure associated with four spatially isolated microcrystalline, acicular calcite moonmilk deposits at Ballynamintra Cave (S. Ireland) was investigated during this study. Statistical analyses revealed significant differences in microbial activity, number of bacterial species, bacterial richness and diversity, and fungal diversity (Shannon's diversity) among the moonmilk sites over an area of approximately 2.5 m². However, the number of fungal species and fungal community richness were unaffected by sampling location. SIMPER analysis revealed significant differences in bacterial and fungal community composition among the sampling sites. These data suggest that a rich assemblage of microorganisms exists associated with moonmilk, with some spatial diversity, which may reflect small-scale spatial differences in cave biogeochemistry.     

A statistical analysis of the relationships among viable microbial populations,vegetation, and environment in a subantarctic tundra

Parametric and nonparametric analyses were used to investigate the relationships between the populations of viable microbes and 4 edaphic variables — soil moisture, rainfall, temperature, and pH. Microbial populations were sampled over a 2-year period in contrasting grass and moss stands on the subantarctic island of South Georgia. Moisture was found to be the most significant edaphic variable, but there were highly significant correlations between bacterial and fungal populations at both sites. Individual plant species showed clear correlations with both bacterial and fungal populations.     

Parasitic Bacteria and Fungi on Common Mistletoe (Viscum album L.) and Their Potential Application in Biocontrol

This study was carried out to identify pathogenic bacteria and fungi on mistletoe (Viscum album L.) and investigate their potential use in biological control of this parasitic plant. For this purpose, a total of 48 fungal isolate and 193 bacterial strains were isolated from contaminated V. album during the summers 2005–2006. The isolated bacterial strains and fungal isolates were identified by using the Sherlock Microbial Identification System (MIS; Microbial ID, Newark) and microscopic methods, respectively. The bacterial strains that induced hypersensitive reaction (HR) on tobacco (Nicotiana tabacum L.) and fungal isolates were tested for pathogenicity on young shoots of mistletoe by using injection methods. The pathogenic bacterial strains and fungal isolates were also tested for their activity against mistletoe using spray methods. Five bacterial strains (two Burkholderia cepacia, one each of Bacillus megaterium, Bacillus pumilus and Pandoraea pulminicola) were HR and pathogenicity positive when injected but none of them when sprayed on mistletoe. When fungi were injected, 32 isolates were pathogenic but only thirteen when sprayed on mistletoe. Alternaria alternata VA?‐202, VA?‐205, VA?‐217 and Acremonium kiliense VA‐11 fungal isolates were the most effective ones and caused strong disease symptoms on mistletoe. The present study is the first report on the efficiency of potential biocontrol agents against mistletoe in Turkey.     

Fungal and Bacterial Diversity of Airway Microbiota in Adults with Cystic Fibrosis: Concordance Between Conventional Methods and Ultra-Deep Sequencing,and Their Practical use in the Clinical Laboratory

Given the complexity of the airway microbiota in the respiratory tract of cystic fibrosis (CF) patients, it seems crucial to compile the most exhaustive and exact list of the microbial communities inhabiting CF airways. The aim of the present study was to compare the bacterial and fungal diversity of sputa from adult CF patients during non-exacerbation period by culture-based and molecular methods, and ultra-deep-sequencing (UDS). Sputum samples from four CF patients were cultured and analysed by DNA extractions followed by terminal restriction fragment length polymorphism analysis through resolution of bacterial ribosomal gene (rDNA) fragments, and cloning plus sequencing of part of fungal rRNA genes. These approaches were compared with UDS method targeting 16S rDNA gene and the internal transcribed spacer (ITS) 2 region of rDNA. A total of 27 bacterial and 18 fungal genera were detected from the four patients. Five (18%) and 3 (16%) genera were detected by culture for bacteria and fungi, respectively, 9 (33%) and 3 (16%) by first generation sequencing (FGS) methods, and 26 (96%) and 18 (100%) by UDS. The mean number of genera detected by UDS per patient was statistically higher than by culture or FGS methods. Patients with severe airway disease as assessed by standard spirometry exhibited a reduced fungal and bacterial diversity. UDS approach evaluates more extensively the diversity of fungal and bacterial flora compared with cultures. However, it currently remains difficult to routinely use UDS mainly because of the lack of standardization, and the current cost of this method.     

Responses of soil bacterial and fungal communities to reciprocal transfers of soil between adjacent coniferous forest and meadow vegetation in the Cascade Mountains of Oregon

Little information exists on the responses of soil fungal and bacterial communities in high elevation coniferous forest/open meadow ecosystems of the northwest United States of America to treatments that impact vegetation and soil conditions. An experiment was conducted in which soil cores were reciprocally transplanted between immediately adjacent forests and meadows at two high elevation (∼1,600 m) sites (Carpenter and Lookout) in the H.J. Andrews Experimental Forest located in the Cascade Mountains of Oregon. Half of the cores were placed in PVC pipe (closed) to prevent new root colonization, whereas the other cores were placed in mesh bags (open) to allow recolonization by fine roots. A duplicate set of open and closed soil cores was not transferred between sites and was incubated in place. After 2 year, soil cores were removed and changes in fungal and bacterial biomasses determined using light microscopy, and changes in microbial community composition determined by PLFA analysis, and by length heterogeneity PCR of the internal transcribed spacer region of fungal ribosomal DNA. At both sites soil microbial community structures had responded to treatments after 2 year of incubation. At Carpenter, both fungal and bacterial community structures of forest soil changed significantly in response to transfer from forest to meadow, with the shift in fungal community structure being accompanied by a significant decrease in the PLFA biomarker of fungal biomass,18:2ω6,9. At Lookout, both fungal and bacterial community structures of forest soil changed significantly in response to open versus closed core treatments, with the shift in the fungal community being accompanied by a significant decrease in the 18:2ω6,9 content of closed cores, and the shift in the bacterial community structure being accompanied by a significant increase in bacterial biomass of closed cores. At both sites, fungal community structures of meadow soils changed differently between open and closed cores in response to transfer to forest, and were accompanied by increases in the18:2ω6,9 content of open cores. Although there were no significant treatment effects on the bacterial community structure of meadow soil at either site, bacterial biomass was significantly higher in closed versus open cores regardless of transfer.     

Design,synthesis, characterization and in vitro antimicrobial evaluation of 4,6-diaryl-4,5-dihydro-2-phenyl-2H-indazol-3-ols

New 4,6-diaryl-4,5-dihydro-2-phenyl-2H-indazol-3-ols 25-32 were designed, synthesized and in vitro microbially evaluated using clinically isolated bacterial strains viz Staphylococcus aureus, β-Heamolytic streptococcus, Vibreo cholerae, Salmonella typhii, Shigella felxneri and fungal strains viz Aspergillus flavus, Mucor, Rhizopus and Microsporum gypsuem. Results of this study showed that the nature of the substituents on the phenyl rings viz., methyl, methoxy, chloro, nitro as well as the bromo functions at the meta and para positions of the aryl moieties determined the nature and extent of the activity of the fused indazolonol compounds 25-32.     

Seeking clarity within cloudy effluents: differentiating fungal from bacterial peritonitis in peritoneal dialysis patients

Background

Fungal peritonitis is a serious complication of peritoneal dialysis (PD) therapy with the majority of patients ceasing PD permanently. The aims of this study were to identify risk factors and clinical associations that may discriminate between fungal from bacterial peritonitis.

Methods

We retrospectively identified episodes of fungal peritonitis from 2001–2010 in PD patients at Liverpool and Westmead Hospitals (Australia). Fungal peritonitis cases were matched in a 1∶2 ratio with patients with bacterial peritonitis from each institution''s dialysis registry, occurring closest in time to the fungal episode. Patient demographic, clinical and outcome data were obtained from the medical records.

Results

Thirty-nine episodes of fungal peritonitis (rate of 0.02 episodes per patient-year of dialysis) were matched with 78 episodes of bacterial peritonitis. Candida species were the commonest pathogens (35/39; 90% episodes) with Candida albicans (37%), Candida parapsilosis (32%) and Candida glabrata (13%) the most frequently isolated species. Compared to bacterial peritonitis, fungal peritonitis patients had received PD for significantly longer (1133 vs. 775 catheter-days; p = 0.016), were more likely to have had previous episodes of bacterial peritonitis (51% vs. 10%; p = 0.01), and to have received prior antibacterial therapy (51% vs. 10%; p = 0.01). Patients with fungal peritonitis were less likely to have fever and abdominal pain on presentation, but had higher rates of PD catheter removal (79% vs. 22%; p<0.005), and permanent transfer to haemodialysis (87% vs. 24%; p<0.005). Hospital length of stay was significantly longer in patients with fungal peritonitis (26.1 days vs. 12.6 days; p = 0.017), but the all-cause 30-day mortality rate was similar in both groups. Fluconazole was a suitable empiric antifungal agent; with no Candida resistance detected.

Conclusion

Prompt recognition of clinical risk factors, initiation of antifungal therapy and removal of PD catheters are key considerations in optimising outcomes.     

Co-Occurring Anammox,Denitrification, and Codenitrification in Agricultural Soils

Anammox and denitrification mediated by bacteria are known to be the major microbial processes converting fixed N to N₂ gas in various ecosystems. Codenitrification and denitrification by fungi are additional pathways producing N₂ in soils. However, fungal codenitrification and denitrification have not been well investigated in agricultural soils. To evaluate bacterial and fungal processes contributing to N₂ production, molecular and ¹⁵N isotope analyses were conducted with soil samples collected at six different agricultural fields in the United States. Denitrifying and anammox bacterial abundances were measured based on quantitative PCR (qPCR) of nitrous oxide reductase (nosZ) and hydrazine oxidase (hzo) genes, respectively, while the internal transcribed spacer (ITS) of Fusarium oxysporum was quantified to estimate the abundance of codenitrifying and denitrifying fungi. ¹⁵N tracer incubation experiments with ¹⁵NO₃⁻ or ¹⁵NH₄⁺ addition were conducted to measure the N₂ production rates from anammox, denitrification, and codenitrification. Soil incubation experiments with antibiotic treatments were also used to differentiate between fungal and bacterial N₂ production rates in soil samples. Denitrifying bacteria were found to be the most abundant, followed by F. oxysporum based on the qPCR assays. The potential denitrification rates by bacteria and fungi ranged from 4.118 to 42.121 nmol N₂-N g⁻¹ day⁻¹, while the combined potential rates of anammox and codenitrification ranged from 2.796 to 147.711 nmol N₂-N g⁻¹ day⁻¹. Soil incubation experiments with antibiotics indicated that fungal codenitrification was the primary process contributing to N₂ production in the North Carolina soil. This study clearly demonstrates the importance of fungal processes in the agricultural N cycle.     

CRAMP analogues having potent antibiotic activity against bacterial, fungal, and tumor cells without hemolytic activity

CRAMP-18 (GEKLKKIGQKIKNFFQKL) is the antibacterial sequence derived from CRMAP, a member of cathelicidin-derived antimicrobial peptides. To develop the novel antibiotic peptides useful as therapeutic drugs requires strong antibiotic activity against bacterial and fungal cells without hemolytic effect. To this goal, the analogues were designed to increase only net positively charge by Lys-substitution of positions 2, 9, 13, or 16 at the hydrophilic helix face of CRAMP-18 without any change at the hydrophobic helix face. In particular, Lys-substitution (K(2)-CRAMP-18) of position 2 in CRAMP-18 induced the enhanced antibiotic activity without any increase in hemolysis. Thus, this peptide may provide a useful template for the design novel antibiotic peptides for the treatment of infectious diseases. Additional CD spectra studies suggested that the alpha-helical structure of the peptides plays an important role in killing bacterial and fungal cells, but the increase of alpha-helical content is less connected with the enhanced antibiotic activity.     

Spatial and Temporal Variation of Archaeal,Bacterial and Fungal Communities in Agricultural Soils

Background

Soil microbial communities are in constant change at many different temporal and spatial scales. However, the importance of these changes to the turnover of the soil microbial communities has been rarely studied simultaneously in space and time.

Methodology/Principal Findings

In this study, we explored the temporal and spatial responses of soil bacterial, archaeal and fungal β-diversities to abiotic parameters. Taking into account data from a 3-year sampling period, we analyzed the abundances and community structures of Archaea, Bacteria and Fungi along with key soil chemical parameters. We questioned how these abiotic variables influence the turnover of bacterial, archaeal and fungal communities and how they impact the long-term patterns of changes of the aforementioned soil communities. Interestingly, we found that the bacterial and fungal β-diversities are quite stable over time, whereas archaeal diversity showed significantly higher fluctuations. These fluctuations were reflected in temporal turnover caused by soil management through addition of N-fertilizers.

Conclusions

Our study showed that management practices applied to agricultural soils might not significantly affect the bacterial and fungal communities, but cause slow and long-term changes in the abundance and structure of the archaeal community. Moreover, the results suggest that, to different extents, abiotic and biotic factors determine the community assembly of archaeal, bacterial and fungal communities.     

Copper and zinc mixtures induce shifts in microbial communities and reduce leaf litter decomposition in streams

1. To assess the impact of metal mixtures on microbial decomposition of leaf litter, we exposed leaves previously immersed in a stream to environmentally realistic concentrations of copper (Cu) and zinc (Zn) (three levels), alone and in all possible combinations. The response of the microbial community was monitored after 10, 25 and 40 days of metal exposure by examining leaf mass loss, fungal and bacterial biomass, fungal reproduction and fungal and bacterial diversity.
2. Analysis of microbial diversity, assessed by denaturing gradient gel electrophoresis and identification of fungal spores, indicated that metal exposure altered the structure of fungal and bacterial communities on decomposing leaves.
3. Exposure to metal mixtures or to the highest Cu concentration significantly reduced leaf decomposition rates and fungal reproduction, but not fungal biomass. Bacterial biomass was strongly inhibited by all metal treatments.
4. The effects of Cu and Zn mixtures on microbial decomposition of leaf litter were mostly additive, because observed effects did not differ from those expected as the sum of single metal effects. However, antagonistic effects on bacterial biomass were found in all metal combinations and on fungal reproduction in metal combinations with the highest Cu concentrations, particularly at longer exposure times.     

Incorporation of fungal cellulases in bacterial minicellulosomes yields viable, synergistically acting cellulolytic complexes

Artificial designer minicellulosomes comprise a chimeric scaffoldin that displays an optional cellulose-binding module (CBM) and bacterial cohesins from divergent species which bind strongly to enzymes engineered to bear complementary dockerins. Incorporation of cellulosomal cellulases from Clostridium cellulolyticum into minicellulosomes leads to artificial complexes with enhanced activity on crystalline cellulose, due to enzyme proximity and substrate targeting induced by the scaffoldin-borne CBM. In the present study, a bacterial dockerin was appended to the family 6 fungal cellulase Cel6A, produced by Neocallimastix patriciarum, for subsequent incorporation into minicellulosomes in combination with various cellulosomal cellulases from C. cellulolyticum. The binding of the fungal Cel6A with a bacterial family 5 endoglucanase onto chimeric miniscaffoldins had no impact on their activity toward crystalline cellulose. Replacement of the bacterial family 5 enzyme with homologous endoglucanase Cel5D from N. patriciarum bearing a clostridial dockerin gave similar results. In contrast, enzyme pairs comprising the fungal Cel6A and bacterial family 9 endoglucanases were substantially stimulated (up to 2.6-fold) by complexation on chimeric scaffoldins, compared to the free-enzyme system. Incorporation of enzyme pairs including Cel6A and a processive bacterial cellulase generally induced lower stimulation levels. Enhanced activity on crystalline cellulose appeared to result from either proximity or CBM effects alone but never from both simultaneously, unlike minicellulosomes composed exclusively of bacterial cellulases. The present study is the first demonstration that viable designer minicellulosomes can be produced that include (i) free (noncellulosomal) enzymes, (ii) fungal enzymes combined with bacterial enzymes, and (iii) a type (family 6) of cellulase never known to occur in natural cellulosomes.     

施肥和土壤管理对土壤微生物生物量碳、氮和群落结构的影响

以中国科学院沈阳生态试验站的长期定位试验为平台,研究了不同施肥和土壤管理对潮棕壤微生物生物量碳、氮和群落结构的影响。结果表明,裸地和农田处理的微生物生物量碳、氮较低,但是农田处理下施肥增加了微生物生物量,其中NPK+M效果最明显。DGGE图谱显示,处理间细菌条带分布较相似,其中裸地的细菌多样性最高;长期施肥和土壤管理改变了土壤真菌群落结构,施肥增加了真菌多样性,且有机肥的影响大于化肥;不同处理间氨氧化细菌群落结构差异显著,NPK+M显著增加了氨氧化细菌多样性,且无机肥和有机肥对氨氧化细菌群落影响不同。施肥和土壤管理对细菌影响较小,但显著改变了真菌和氨氧化细菌的群落结构。聚类分析结果显示,土壤管理措施较施肥对细菌、真菌和氨氧化细菌群落的影响更为显著。     

Nitrogen sources of Oligoporus placenta and Trametes versicolor evaluated in a 2(3) experimental plan

Four full-factorial 2(3) experimental plans were applied to evaluate the nitrogen (N) sources of Oligoporus placenta and Trametes versicolor and their interaction with the atmospheric N(2)-assimilating bacterium Beijerinckia acida. The effects of N from peptone, of sapwood and of N from gaseous N(2) on fungal, bacterial and fungal-bacterial activity were investigated. The activities were determined by quantification of biomass, formation of CO(2), consumption of O(2) and laccase activity. The significance of each effect was tested according to t-test recommendation. The activity of both fungi was enhanced by peptone rather than sapwood or gaseous N(2). Nevertheless, comparative studies under an N(2)-free gas mixture as well as under air revealed that the presence of N(2) affected bacterial growth and bacterial-fungal cocultivations. Elemental analysis isotope ratio mass spectrometry (IRMS) of the bacterial and fungal biomass enabled estimation of N transfer and underlined gaseous N(2) as requisite for fungal-bacterial interactions. Combining full-factorial experimental plans with an analytical set-up comprising gas chromatography, IRMS and enzymatic activity allowed synergistic effects to be revealed, fungal N sources to be traced, and symbiotic fungal-bacterial interactions to be investigated.     

Pyrosequencing-derived bacterial, archaeal, and fungal diversity of spacecraft hardware destined for Mars

Spacecraft hardware and assembly cleanroom surfaces (233 m(2) in total) were sampled, total genomic DNA was extracted, hypervariable regions of the 16S rRNA gene (bacteria and archaea) and ribosomal internal transcribed spacer (ITS) region (fungi) were subjected to 454 tag-encoded pyrosequencing PCR amplification, and 203,852 resulting high-quality sequences were analyzed. Bioinformatic analyses revealed correlations between operational taxonomic unit (OTU) abundance and certain sample characteristics, such as source (cleanroom floor, ground support equipment [GSE], or spacecraft hardware), cleaning regimen applied, and location about the facility or spacecraft. National Aeronautics and Space Administration (NASA) cleanroom floor and GSE surfaces gave rise to a larger number of diverse bacterial communities (619 OTU; 20 m(2)) than colocated spacecraft hardware (187 OTU; 162 m(2)). In contrast to the results of bacterial pyrosequencing, where at least some sequences were generated from each of the 31 sample sets examined, only 13 and 18 of these sample sets gave rise to archaeal and fungal sequences, respectively. As was the case for bacteria, the abundance of fungal OTU in the GSE surface samples dramatically diminished (9× less) once cleaning protocols had been applied. The presence of OTU representative of actinobacteria, deinococci, acidobacteria, firmicutes, and proteobacteria on spacecraft surfaces suggests that certain bacterial lineages persist even following rigorous quality control and cleaning practices. The majority of bacterial OTU observed as being recurrent belonged to actinobacteria and alphaproteobacteria, supporting the hypothesis that the measures of cleanliness exerted in spacecraft assembly cleanrooms (SAC) inadvertently select for the organisms which are the most fit to survive long journeys in space.     

Regulation of Microbial Community Composition and Activity by Soil Nutrient Availability, Soil pH, and Herbivory in the Tundra

Soil nitrogen (N) availability and pH constitute major abiotic controls over microbial community composition and activity in tundra ecosystems. On the other hand, mammalian grazers form an important biotic factor influencing resource coupling between plants and soil microorganisms. To investigate individual effects and interactions among soil nutrients, pH, and grazing on tundra soils, we performed factorial treatments of fertilization, liming, and grazer exclusion in the field for 3 years at 2 contrasting tundra habitats, acidic (N-poor) and non-acidic (N-rich) tundra heaths. The effects of all treatments were small in the non-acidic tundra heaths. In the acidic tundra heaths, fertilization decreased the fungal:bacterial ratio as analyzed by soil PLFAs, but there were no effects of liming. Fertilization increased soil N concentrations more drastically in ungrazed than grazed plots, and in parallel, fertilization decreased the fungal:bacterial ratio to a greater extent in the ungrazed plots. Liming, on the other hand, partly negated the effects of fertilization on both soil N concentrations and PLFAs. Fertilization drastically increased the activity of phenol oxidase, a microbial enzyme synthesized for degradation of soil phenols, in grazed plots, but had no effect in ungrazed plots. Taken together, our results demonstrate that grazers have the potential to regulate the fungal:bacterial ratio in soils through influencing N availability for the soil microorganisms.     

Effect of bacterial antagonists on lettuce: active biocontrol of Rhizoctonia solani and negligible, short-term effects on nontarget microorganisms

The aim of this study was to assess the biocontrol efficacy against Rhizoctonia solani of three bacterial antagonists introduced into naturally Rhizoctonia-infested lettuce fields and to analyse their impact on the indigenous plant-associated bacteria and fungi. Lettuce seedlings were inoculated with bacterial suspensions of two endophytic strains, Serratia plymuthica 3Re4-18 and Pseudomonas trivialis 3Re2-7, and with the rhizobacterium Pseudomonas fluorescens L13-6-12 7 days before and 5 days after planting in the field. Similar statistically significant biocontrol effects were observed for all applied bacterial antagonists compared with the uninoculated control. Single-strand conformation polymorphism analysis of 16S rRNA gene or ITS1 fragments revealed a highly diverse rhizosphere and a less diverse endophytic microbial community for lettuce. Representatives of several bacterial (Alpha-, Beta- and Gammaproteobacteria, Firmicutes, Bacteriodetes), fungal (Ascomycetes, Basidiomycetes) and protist (Oomycetes) groups were present inside or on lettuce plants. Surprisingly, given that lettuce is a vegetable that is eaten raw, species of genera such as Flavobacterium, Burkholderia, Staphylococcus, Cladosporium and Aspergillus, which contain potentially human pathogenic strains, were identified. Analysis of the indigenous bacterial and endophytic fungal populations revealed only negligible, short-term effects resulting from the bacterial treatments, and that they were more influenced by field site, plant growth stage and microenvironment.