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The second messenger cyclic diguanylate monophosphate (c‐di‐GMP) regulates a wide range of bacterial behaviours through diverse mechanisms and binding receptors. Single‐domain PilZ proteins, the most widespread and abundant known c‐di‐GMP receptors in bacteria, act as trans‐acting adaptor proteins that enable c‐di‐GMP to control signalling pathways with high specificity. This study identifies a single‐domain PilZ protein, XAC3402 (renamed N5MapZ), from the phytopathogen Xanthomonas citri subsp. citri (Xcc), which modulates Xcc virulence by directly interacting with the methyltransferase HemK. Through yeast two‐hybrid, co‐immunoprecipitation and immunofluorescent staining, we demonstrated that N5MapZ and HemK interact directly under both in vitro and in vivo conditions, with the strength of the protein–protein interaction decreasing at high c‐di‐GMP concentrations. This finding distinguishes N5MapZ from other characterized single‐domain PilZ proteins, as it was previously known that c‐di‐GMP enhances the interaction between those single‐domain PilZs and their protein partners. This observation is further supported by the fact that the c‐di‐GMP binding‐defective mutant N5MapZR10A can interact with HemK to inhibit the methylation of the class 1 translation termination release factor PrfA. Additionally, we found that HemK plays an important role in Xcc pathogenesis, as the deletion of hemK leads to extensive phenotypic changes, including reduced virulence in citrus plants, decreased motility, production of extracellular enzymes and stress tolerance. Gene expression analysis has revealed that c‐di‐GMP and the HemK‐mediated pathway regulate the expression of multiple virulence effector proteins, uncovering a novel regulatory mechanism through which c‐di‐GMP regulates Xcc virulence by mediating PrfA methylation via the single‐domain PilZ adaptor protein N5MapZ. [ABSTRACT FROM AUTHOR]

Ear infections are a common health problem, the most common microorganism which cause of infection is Pseudomonas aeruginosa. The study aimed to detection for bacterium ability of virulence factors production, molecular detection on that Exoenzyme effectors. The results of P. aeruginosa is the most type at18.62%. This bacterium was had a high level of resistance to the Ticarcillin antibiotic at 73.69%, were 10% of isolates (MDR), 42% (XDR) and 5% (PDR), production was each of the biofilm at 89.47%, protease enzyme at 79.94%, and Metallo betalactamase at 47.36%. Presence of exoenzyme genes (exoS:57.89%, exoT: 84.21%, exoU: 73.68% and exoY: 89.47%). [ABSTRACT FROM AUTHOR]

Priming of soil organic matter (SOM) decomposition by microorganisms is a key phenomenon of global carbon (C) cycling. Soil pH is a main factor defining priming effects (PEs) because it (i) controls microbial community composition and activities, including enzyme activities, (ii) defines SOM stabilization and destabilization mechanisms, and (iii) regulates intensities of many biogeochemical processes. In this critical review, we focus on prerequisites and mechanisms of PE depending on pH and assess the global change consequences for PE. The highest PEs were common in soils with pH between 5.5 and 7.5, whereas low molecular weight organic compounds triggered PE mainly in slightly acidic soils. Positive PEs up to 20 times of SOM decomposition before C input were common at pH around 6.5. Negative PEs were common at soil pH below 4.5 or above 7 reflecting a suboptimal environment for microorganisms and specific SOM stabilization mechanisms at low and high pH. Short‐term soil acidification (in rhizosphere, after fertilizer application) affects PE by: mineral‐SOM complexation, SOM oxidation by iron reduction, enzymatic depolymerization, and pH‐dependent changes in nutrient availability. Biological processes of microbial metabolism shift over the short‐term, whereas long‐term microbial community adaptations to slow acidification are common. The nitrogen fertilization induced soil acidification and land use intensification strongly decrease pH and thus boost the PE. Concluding, soil pH is one of the strongest but up to now disregarded factors of PE, defining SOM decomposition through short‐term metabolic adaptation of microbial groups and long‐term shift of microbial communities. [ABSTRACT FROM AUTHOR]

Decomposition of organic matters in volcanic soils (ando soils) is generally slowed by sorption onto short-range-order minerals, while decomposition of non-charged substrates such as cellulose and glucose is hypothesized to be promoted by high microbial biomass and nitrogen availability, irrespective of short-range-order minerals. To analyze factors regulating decomposition activities of cellulose and glucose, we measured the decomposition rates of cellulose filter papers and the mineralization rates of 14C-labeled glucose in five volcanic soils in Japan. Glucose mineralization activities increased with increasing microbial biomass C and N, while cellulose decomposition activities (standardized with cumulative temperature) were not related to microbial biomass C or N. Cellulose decomposition activities increased with increasing ratio of soil available N relative to microbial biomass N (microbial N availability), while they decreased with decreasing soil pH and with increasing fungal activities. Soils with relatively high soil pH and microbial N availability exhibit the relatively high potentials of cellulose decomposition. Because cellulose decomposition, rather than glucose mineralization, is a rate-limiting step, soil pH and microbial N availability, rather than microbial biomass, could primarily regulate decomposition rates of cellulose and glucose in volcanic soils. [ABSTRACT FROM AUTHOR]

Background and aim. Pseudomonas aeruginosa is considered as a notorious pathogen due to its multidrug resistance and life threatening infections. We investigated the relationship between type III secretion toxins, biofilm formation, and antibiotic resistance among clinical P. aeruginosa isolates. Methods. A total of 70 genetically distinct clinical P. aeruginosa isolates were characterized for antibiotic resistance by disk diffusion assay. Biofilm formation was evaluated by microtiter plate method and presence of four exo genes (exoS, exoU, exoT and exoY) was investigated by PCR. A p-value < 0.05 was regarded statistically significant. Results. The most effective antibiotics were Meropenem and Piperacillin. Multidrug resistance was more prevalent in the ciprofloxacin-resistant isolates than in the susceptible isolates. The most frequently identified exo was exoS (37.1%). Genotype exoS/exoT was found in 4 isolates, while genotype exoU/exoT was not found. Prevalence of exoS was generally higher in the susceptible isolates than in the resistant isolates. A significant association was found between the formation of strong biofilm and resistance to antibiotics (p < 0.05). Prevalence of exoY and exoU was higher in the non-strong biofilm producers compared to the strong biofilm producers. Conclusion. Our study revealed formation of strong biofilm along with antibiotic resistance and the presence of exo genes in P. aeruginosa isolates. Knowledge of virulence gene profiles and biofilm formation may be useful in deciding appropriate treatment.

Most of Earth's biomass is composed of polysaccharides. During biomass decomposition, polysaccharides are degraded by heterotrophic bacteria as a nutrient and energy source and are thereby partly remineralized into CO 2 . As polysaccharides are heterogeneously distributed in nature, following the colonization and degradation of a polysaccharide hotspot the cells need to reach new polysaccharide hotspots. Even though many studies indicate that these degradation-dispersal cycles contribute to the carbon flow in marine systems, we know little about how cells alternate between polysaccharide degradation and motility, and which environmental factors trigger this behavioral switch. Here, we studied the growth of the marine bacterium Vibrio cyclitrophicus ZF270 on the abundant marine polysaccharide alginate, both in its soluble polymeric form as well as on its breakdown products. We used microfluidics coupled to time-lapse microscopy to analyze motility and growth of individual cells, and RNA sequencing to study associated changes in gene expression. We found that single cells grow at reduced rate on alginate until they form large groups that cooperatively break down the polymer. Exposing cell groups to digested alginate accelerates cell growth and changes the expression of genes involved in alginate degradation and catabolism, central metabolism, ribosomal biosynthesis, and transport. However, exposure to digested alginate also triggers cells to become motile and disperse from cell groups, proportionally increasing with the group size before the nutrient switch, and this is accompanied by high expression of genes involved in flagellar assembly, chemotaxis, and quorum sensing. The motile cells chemotax toward polymeric but not digested alginate, likely enabling them to find new polysaccharide hotspots. Overall, our findings reveal cellular mechanisms that might also underlie bacterial degradation-dispersal cycles, which influence the remineralization of biomass in marine environments., Competing Interests: AS, JK, JS, SP, EC, SC, RS, CM, OS, MA, GD No competing interests declared, (© 2024, Stubbusch et al.)

Paenibacillus konkukensis sp. nov., SK3146 is a novel strain isolated from a pig feed. Here, we present complete genome sequence of SK3146. The genome consists of a single circular genome measuring 7,968,964 bp in size with an average guanine + cytosine (G+C) content of 53.4%. Genomic annotation revealed that the strain encodes 151 proteins related to hydrolases (EC3), which was higher than those in Bacillus subtilis and Escherichia coli. Diverse kinds of hydrolases including galactosidase, glucosidase, cellulase, lipase, xylanase, and protease were found in the genome of SK3146, coupled with one bacteriocin encoding gene. The complete genome sequence of P. konkukensis SK3146 indicates the immense probiotic potential of the strain with nutrient digestibility and antimicrobial activity functions.

Citrus canker, caused by the bacterium Xanthomonas citri subsp. citri (Xcc), seriously affects fruit quality and yield, leading to significant economic losses around the world. Understanding the mechanism of Xcc virulence is important for the effective control of Xcc infection. In this report, we investigate the role of a protein named HemK in the regulation of the virulence traits of Xcc. The hemK gene was deleted in the Xcc jx-6 background, and the ΔhemK mutant phenotypically displayed significantly decreased motility, biofilm formation, extracellular enzymes, and polysaccharides production, as well as increased sensitivity to oxidative stress and high temperatures. In accordance with the role of HemK in the regulation of a variety of virulence-associated phenotypes, the deletion of hemK resulted in reduced virulence on citrus plants as well as a compromised hypersensitive response on a non-host plant, Nicotiana benthamiana. These results indicated that HemK is required for the virulence of Xcc. To characterize the regulatory effect of hemK deletion on gene expression, RNA sequencing analysis was conducted using the wild-type Xcc jx-6 strain and its isogenic ΔhemK mutant strain, grown in XVM2 medium. Comparative transcriptome analysis of these two strains revealed that hemK deletion specifically changed the expression of several virulence-related genes associated with the bacterial secretion system, chemotaxis, and quorum sensing, and the expression of various genes related to nutrient utilization including amino acid metabolism, carbohydrate metabolism, and energy metabolism. In conclusion, our results indicate that HemK plays an essential role in virulence, the regulation of virulence factor synthesis, and the nutrient utilization of Xcc. [ABSTRACT FROM AUTHOR]

Herbicide application in farm soil invariably impacts non-target biota including the microbes. Herbicides inhibit microbial exoenzyme activities, crucial for the decomposition of organics and release of nutrients. It was hypothesised that increasing the antioxidant level in soil through organic amendments could reduce the toxicity of the herbicide pretilachlor on soil microbial activity. This study reports the effects of organic amendments with farmyard manure (FYM-T1), poultry manure (PM-T2) and vermimanure (VM-T3) at recommended doses on the activities of the exoenzymes, invertase, amylase and cellulase in farm soils pre-treated with the herbicide pretilachlor. Significant spikes in percent organic carbon (OC), total antioxidant capacity (TAC) and activities of the exoenzymes were observed in amended soils relative to control. The percent soil OC was maximum in T1 (2.63) followed by T3 (2.28) at 120 h. T3 indicated the maximum amylase (0.27 mg glucose/gsoil/h), cellulase (0.26 mg glucose/gsoil/h), invertase (0.39 mg glucose/gsoil/h) activities and soil TAC (1.03 Mm Trolox/cm3/g soil) at 168 h. A significant positive correlation between % OC, TAC and exoenzyme activities was observed. TAC and invertase proved to be the most responsive markers. It was concluded that selective organic amendments of soil could significantly enhance soil antioxidant level, and reduce herbicide induced stress on soil microbiota with an increase in exoenzyme secretion. [ABSTRACT FROM AUTHOR]

Soils of mountain ecosystems are one of the most vulnerable ecosystems to climate change, while the ecosystem services they produce are significant and currently at risk. High altitude soils contain high C stocks, but due to difficult access to sites these areas are understudied. Moreover, how the C and N cycling is changing in response to climate change in these ecosystems, is still unclear. Microbial carbon use efficiency (CUE) and its dependency on the environmental constraints along the altitudinal gradients is one important unknown factor. Here we present results from an altitudinal gradient study (3500 to 4500 m a.s.l.) from a Polylepis forest in the Peruvian Andes. We measured the soil organic carbon (SOC) stocks and microbial metabolic CUE by 13C glucose tracing and microbial resource use efficiency (CUE C:N) based on enzyme activity measurements. We expected to find an increase in SOC stock, microbial nutrient limitations, and lower CUE with elevation. SOC stocks depended on soil development and followed a unimodal curve that peaks at 4000 m in two of the three studied valleys. Neither 13CUE nor CUE C:N changed significantly with altitude. Soil C:N ratio, β-glucosidase, chitinase, and phosphatase enzyme activities increased with elevation, but peroxidase activity decreased with elevation. We suggest that more labile organic matter left at high elevation could compensate for the increasing nutrient limitation at high elevation, resulting in no noticeable change in CUE with elevation. [Display omitted] [ABSTRACT FROM AUTHOR]

The increasing demand for sugarcane residue to produce industrial biofuels competes with organic-matter inputs to tropical soils for increasing fertility. Soil nitrogen (N) availability to plants and carbon (C) storage can be optimized by the selection of substrate types and quantities. We tested whether substrate-induced microbial growth increases soil N mineralization and C stabilization as substrate inputs increase. The effects of substrate additions (cane sugar, leaf litter, and humic acid extracted from filter cake) on microbial growth and N availability were studied using C3/C4 plant C isotopic signatures in a sandy soil of northeast Thailand. The initial growth of microbial biomass in cane sugar-amended soil caused a short-term flush of N derived from the native soil organic matter within 3 days, whereas in the soils amended with leaf litter or humic acid, N was retained in microbial biomass or dissolved organic matter, respectively. Net mineralization of the native soil organic N was maximized by sugar addition at a dosage corresponding to 10 folds of microbial biomass-C. The efficacy of substrates stabilized in the heavy density fraction (>1.6 g cm−3) followed the order: leaf litter > humic acid > sugar. Soil net N mineralization can be promoted by sugar inputs (e.g., bud node) at an early growth stage, while leaf litter and humic acid inputs can increase C storage efficiently in the sandy soil without increasing risks of N starvation and loss when they are applied at several tons of C per hectare at least 3 weeks before planting. [ABSTRACT FROM AUTHOR]

Citrus canker, caused by the bacterium Xanthomonas citri subsp. citri (Xcc), seriously affects fruit quality and yield, leading to significant economic losses around the world. Understanding the mechanism of Xcc virulence is important for the effective control of Xcc infection. In this report, we investigate the role of a protein named HemK in the regulation of the virulence traits of Xcc. The hemK gene was deleted in the Xcc jx-6 background, and the ΔhemK mutant phenotypically displayed significantly decreased motility, biofilm formation, extracellular enzymes, and polysaccharides production, as well as increased sensitivity to oxidative stress and high temperatures. In accordance with the role of HemK in the regulation of a variety of virulence-associated phenotypes, the deletion of hemK resulted in reduced virulence on citrus plants as well as a compromised hypersensitive response on a non-host plant, Nicotiana benthamiana. These results indicated that HemK is required for the virulence of Xcc. To characterize the regulatory effect of hemK deletion on gene expression, RNA sequencing analysis was conducted using the wild-type Xcc jx-6 strain and its isogenic ΔhemK mutant strain, grown in XVM2 medium. Comparative transcriptome analysis of these two strains revealed that hemK deletion specifically changed the expression of several virulence-related genes associated with the bacterial secretion system, chemotaxis, and quorum sensing, and the expression of various genes related to nutrient utilization including amino acid metabolism, carbohydrate metabolism, and energy metabolism. In conclusion, our results indicate that HemK plays an essential role in virulence, the regulation of virulence factor synthesis, and the nutrient utilization of Xcc.

Bacteria producing hydrolytic exoenzymes are of great importance considering their contribution to the host metabolism as well as for their various applications in industrial bioprocesses. In this work hydrolytic capacity of bacteria isolated from the gastrointestinal tract of Bombay duck (Harpadon nehereus) was analyzed and the enzyme-producing bacteria were genetically characterized. A total of twenty gut-associated bacteria, classified into seventeen different species, were isolated and screened for the production of protease, lipase, pectinase, cellulase and amylase enzymes. It was found that thirteen of the isolates could produce at least one of these hydrolytic enzymes among which protease was the most common enzyme detected in ten isolates; lipase in nine, pectinase in four, and cellulase and amylase in one isolate each. This enzymatic array strongly correlated to the previously reported eating behavior of Bombay duck. 16S rRNA gene sequence-based taxonomic classification of the enzyme-producing isolates revealed that the thirteen isolates were grouped into three different classes of bacteria consisting of eight different genera. Staphylococcus, representing ∼46% of the isolates, was the most dominant genus. Measurement of enzyme-production via agar diffusion technique revealed that one of the isolates which belonged to the genus Exiguobacterium, secreted the highest amount of lipolytic and pectinolytic enzymes, whereas a Staphylococcus species produced highest proteolytic activity. The Exiguobacterium sp. expressing a maximum of four hydrolases, appeared to be the most promising isolate of all.

Reduction in moisture in the top soil and decomposing organic substrate is likely to influence the epigeic earthworms along with the microbial population and exoenzyme secretions. This study reports the results of the effects of consistent moisture reduction in semidecomposed organic substrate on the tissue protein, lipid peroxidation and catalase activity of the earthworm Eudrilus eugeniae along with pH, organic carbon reduction, bacterial-fungal population, activities of exoenzymes, amylase, cellulase, invertase over an experimental period of 22 days. Consistent depletion in tissue protein, increase in lipid peroxidation level and catalase activity was observed in the earthworm with moisture depletion. Catalase activity indicated significant negative correlation with substrate moisture. Significant differences in the carbon reduction, microbial population, exoenzyme activities in the substrate was observed with reduction of moisture and with respect to control. Significant positive correlation was observed between percent substrate moisture with microbial population and activities cellulase. It was concluded that desiccation of decomposing organics could enhance physiological stress on the earthworm and adversely impact the microbial population, exoenzyme secretions, consequently impairing mineralization.

Reduction in moisture in the top soil and decomposing organic substrate is likely to influence the epigeic earthworms along with the microbial population and exoenzyme secretions. This study reports the results of the effects of consistent moisture reduction in semidecomposed organic substrate on the tissue protein, lipid peroxidation and catalase activity of the earthworm Eudrilus eugeniae along with pH, organic carbon reduction, bacterial-fungal population, activities of exoenzymes, amylase, cellulase, invertase over an experimental period of 22 days. Consistent depletion in tissue protein, increase in lipid peroxidation level and catalase activity was observed in the earthworm with moisture depletion. Catalase activity indicated significant negative correlation with substrate moisture. Significant differences in the carbon reduction, microbial population, exoenzyme activities in the substrate was observed with reduction of moisture and with respect to control. Significant positive correlation was observed between percent substrate moisture with microbial population and activities cellulase. It was concluded that desiccation of decomposing organics could enhance physiological stress on the earthworm and adversely impact the microbial population, exoenzyme secretions, consequently impairing mineralization. [ABSTRACT FROM AUTHOR]

In recent years, numerous outbreaks of multidrug‐resistant Pseudomonas aeruginosa have been reported across the world. Once an outbreak occurs, besides routinely testing isolates for susceptibility to antimicrobials, it is required to check their virulence genotypes and clonality profiles. Replacing pulsed‐field gel electrophoresis DNA fingerprinting are faster, easier‐to‐use, and less expensive polymerase chain reaction (PCR)‐based methods for characterizing hospital isolates. P. aeruginosa possesses a mosaic genome structure and a highly conserved core genome displaying low sequence diversity and a highly variable accessory genome that communicates with other Pseudomonas species via horizontal gene transfer. Multiple‐locus variable‐number tandem‐repeat analysis and multilocus sequence typing methods allow for phylogenetic analysis of isolates by PCR amplification of target genes with the support of Internet‐based services. The target genes located in the core genome regions usually contain low‐frequency mutations, allowing the resulting phylogenetic trees to infer evolutionary processes. The multiplex PCR‐based open reading frame typing (POT) method, integron PCR, and exoenzyme genotyping can determine a genotype by PCR amplifying a specific insertion gene in the accessory genome region using a single or a multiple primer set. Thus, analyzing P. aeruginosa isolates for their clonality, virulence factors, and resistance characteristics is achievable by combining the clonality evaluation of the core genome based on multiple‐locus targeting methods with other methods that can identify specific virulence and antimicrobial genes. Software packages such as eBURST, R, and Dendroscope, which are powerful tools for phylogenetic analyses, enable researchers and clinicians to visualize clonality associations in clinical isolates. [ABSTRACT FROM AUTHOR]

The aim of this study is to restore the nutrient status of iron ore mine spoil through suitable organic interventions. This paper reports the effects of different organic manure and bio-fertilizer amendments with inoculation of the earthworm Eisenia fetida in iron mine spoil on certain chemical parameters, microbial load and soil exoenzyme activities. The mine spoil samples were collected at random from five years old spoil dump and amended with farmyard manure (FYM), poultry manure (PM) and vermimanure (VM) along with biofertilizer in different combinations. The pH, conductivity, % organic carbon, N,P,K, bacterial and fungal population with activities of soil exoenzymes amylase, cellulase and invertase were studied in organically amended mine spoil. Significant variations (p<0.05) in the chemical and biological parameters were observed between treatments and days of incubation. Higher values were obtained with PM followed by FYM and VM. Earthworm inoculation enhanced the values of all the chemical parameters except % organic carbon. Bacterial population and exoenzyme activities increased significantly (p<0.05) with earthworm. PM with biofertilizer was found to be the most suitable combination followed by FYM. Inoculation of Eisenia fetida could facilitate mineralization of organics resulting in higher nutrient availability, higher microbial load and exoenzyme activities required to facilitate spoil reclamation. [ABSTRACT FROM AUTHOR]

Manganese bio-mineralization is a widespread process among bacteria and fungi. To date there is no conclusive experimental evidence for, how and if this process impacts microbial fitness in the environment. Here we show how a model organism for manganese oxidation is growth-inhibited by nitrite, and that this inhibition is mitigated in presence of manganese. We show that such manganese-mediated mitigation of nitrite-inhibition is dependent on the culture inoculum size and that manganese oxide (MnOX) forms granular precipitates in the culture, rather than sheaths around individual cells. We provide evidence that MnOX protection involves both its ability to catalyze nitrite oxidation into (non-toxic) nitrate under physiological conditions, and its potential role in influencing processes involving reactive oxygen species (ROS). Taken together, these results demonstrate improved microbial fitness through MnOX deposition in an ecological setting, i.e. mitigation of nitrite toxicity, and point to a key role of MnOX in handling stresses arising from ROS. [ABSTRACT FROM AUTHOR]

Zinc oxide nanoparticles (ZnO NPs) have been used as additives in a variety of consumer products. While these particles may enter the environment, only a limited number of studies have investigated the effects of ZnO NPs on soil exoenzymes. Here, we investigate the long-term effects of ZnO NPs at concentrations of 50 and 500 mg/kg on the activities of six soil exoenzymes in planted soils: Dehydrogenase, fluorescein diacetate (FDA) hydrolase, urease, acid phosphatase, arylsulfatase, and ß-glucosidase. Significant effects were observed at one or more time points for all enzymes except for FDA hydrolase. These effects included both decreases and increases in enzyme activity. Our results suggest that ZnO NP treatments of 50 and 500 mg/kg can adversely affect soil enzymes, particularly acid phosphatase and urease, and thus, these data may have implications for phosphorous and nitrogen cycles in the soil. [ABSTRACT FROM AUTHOR]

ABSTRACT Zoocin A is a Zn-metallopeptidase secreted by Streptococcus zooepidemicus strain 4881. Its catalytic domain is responsible for cleaving the D-alanyl-L-alanine peptide bond in streptococcal peptidoglycan. The solution NMR structure of the Cys74 to Ala74 mutant of the recombinant catalytic domain (rCAT C74A) has been determined. With a previous structure determination for the recombinant target recognition domain (rTRD), this completes the 3D structure of zoocin A. While the structure of rCAT C74A resembles those of the catalytic domains of lysostaphin and LytM, the substrate binding groove is wider and no tyrosine residue was observed in the active site. Proteins 2016; 85:177-181. © 2016 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Extracellular enzymes are the proximate drivers of biogeochemical cycling in ecosystems. In terrestrial environments, studies of extracellular enzyme activities (EEAs) in soils far outpace studies in substrates such as leaf litter. Despite recent methodological advances that have made EEA assays feasible for researchers conducting large-scale studies, there are still a number of methodological uncertainties that exist, particularly when working with less studied substrates ( i.e. grassland leaf litter). These uncertainties are of particular importance when considering the logistics of sample processing after collecting samples in large numbers and/or from distant field sites. Studies of soil handling suggest that while assaying biochemical and molecular markers in fresh samples is ideal, that freezing samples is often a viable solution if the former is not feasible. Due to the inherent differences of litter and soil materials and associated microenvironments, we can draw only limited conclusions from the results of studies on sample handling using soil. As a result, we investigated the effect of two typical freezing temperatures (−20° and −80 °C) on subsequent EEAs in decomposing leaf litter material. We incubated litter material from six grassland plant communities for 12 weeks at 25 °C, then measured the EEA of five hydrolytic and two oxidative enzymes in fresh litter, and in litter that was frozen for four weeks at either −20° or −80 °C. Results indicate that freezing only affected the activity of N -acetyl-β glucosaminidase (NAG), an enzyme that was affected by freezing in prior soil studies. We observed an approximate 35% increase in NAG activity with freezing. The remaining six EEAs measured were not observed to be affected by freezing, and the level of freezing ( i.e. temperature) did not influence any of the seven EEAs measured, suggesting that freezing is a suitable alternative when laboratory analyses on fresh litter samples are not logistically possible. [ABSTRACT FROM AUTHOR]

The incidence of coagulase-negative staphylococci (CoNS) may render food unsafe, as the clinical isolates have been reported to exude virulent traits. A total of 255 CoNS isolates from 6 traditional fermented foods ( nono, kunu, wara, iru, ogi, and kindirmo) from North Central Nigeria, identified as Staphylococcus epidermidis, Staphylococcus simulans, Staphylococcus xylosus, Staphylococcus kloosii, and Staphylococcus caprae, were investigated for virulence traits. The strains were examined for biofilm formation and production of hyaluronidase, DNase, TNase, haemolysins, and superantigenic toxins (SEA, SEB, SEC, SED, and TSST-1) using standard and genotypic methods. The analysis of virulence factors revealed the production of slime in 200 isolates (78.4%); α-haemolysin in 136 (53.3%); β-haemolysin in 43 (16.9%); DNase in 199 (78.0%); TNase in 29 (11.4%); hyaluronidase in 125 (49.0%); TSST-1 in 119 (46.7%); and enterotoxin-producing isolates SEA, SEB, SEC, and SED in 61 (23.9%), 19 (7.5%), 9 (3.5%), and 8 (3.1%), respectively. PCR analysis detected tsst- 1, sea, seb, and sec genes. The ability of these microorganisms to exhibit virulence evokes the potential to cause disease especially under determinate conditions or in immune-compromised patients. The occurrence of CoNS in food should not be ignored nor their pathogenic potential considered as insignificant, rather safety measures should be taken to reduce or totally eliminate their occurrence in foods. [ABSTRACT FROM AUTHOR]

The colonization by Candida species is one of the most important factors related to the development of oral candidiasis in HIV-infected individuals. The aim of the study was to evaluate and discuss the phospholipase, proteinase, DNAse and haemolytic activities of Candida albicans isolated from the oral cavity of HIV individuals with high efficiency antiretroviral therapy. Seventy-five isolates of C. albicans obtained from saliva samples of patients with HIV and 41 isolates from HIV-negative individuals were studied. Haemolytic activity was determined in Sabouraud dextrose agar plates containing 3% glucose and 7% sheep red cells. Culture medium containing DNA base-agar, egg yolk, and bovine albumin were used to determine DNase, phospholipase and proteinase activities, respectively. All isolates from the HIV patients group had haemolytic activity, 98% showed phospholipase activity, 92% were positive for proteinase and 32% DNAse activity. Regarding the group of indivídios HIV negative, all 41 isolates presented hemolytic activity, 90.2% showed phospholipase and proteinase activity and 12.2% were positive for DNAse. The phospholipase activity was more intense for the group of HIV positive individuals. DNase production was more frequently observed in the group of HIV-positive individuals. The percentage of isolates having DNAse activity was also significantly different between the groups of patients not using any antiretroviral therapy, those using transcriptase inhibitors and those using transcriptase inhibitor and protease inhibitor in combination. [ABSTRACT FROM AUTHOR]

Given that analytical precision affects the number of biological replicates required to achieve adequate statistical power, and analytical variation is often high for soil assays, we investigated ways to reduce variation of soil hydrolase assays. For two mineral soils (sandy and loamy) and one organic soil (peat), we compared variation of fluorescence for acid phosphatase, β-glucosidase, and N-acetyl-glucosaminidase using incubation methods that differed in assay volume and the ability of reagents to mix. For fluorescence of β-glucosidase and N-acetyl-glucosaminidase from the mineral soils, which had coefficients of variation that exceeded 10% on average, well-mixed, larger volumes significantly reduced variation. This reduction was not observed for fluorescence of acid phosphatase from peat, which had consistently low variation. For all soils tested, thorough mixing of NaOH also reduced variation. Because the goal of enzyme assays is to estimate the total enzyme pool in a sample of soil, modifications to reduce analytical variation, such as those proposed here, should be considered. These modifications can potentially increase our ability to detect treatment differences within the heterogeneous soil matrix. [ABSTRACT FROM AUTHOR]

In this study, 342 bacterial strains were isolated from the gut of channel catfish Ictalurus punctatus. Two different screening strategies, including the production of antagonistic effects against pathogens and the capacity of secreting exoenzyme, were used to select potential probiotics from the bacterial strains. Among them, 6 isolates showed antagonism against the pathogens, 15 isolates could produce high amylase and protease, and 3 isolates (BHI344, BH0142 and BH03124) had both the two characteristics . Then, BHI344, BH0142, and BH03124 were tested for survival rate in channel catfish bile and at low pH, antimicrobial susceptibilities, and pathogenicity in channel catfish. The results of the obtained assays showed that BHI344 possessed the broadest inhibitory potential, a strong ability of secreting extra-cellular amylase and protease, high viability in simulated gastrointestinal conditions, and sensitivity to most of the used antibiotics and non-pathogenic to channel catfish. Therefore, it could be selected as the most promising probiotics candidate. BHI344 was identified as Bacillus subtilis based on the phenotypic characterization and 16S rRNA gene sequencing. [ABSTRACT FROM AUTHOR]

How carbon partitions between microbial biomass and CO 2 (carbon use efficiency, CUE) is key in all soil carbon cycling models. Traditional methods to estimate CUE focus on the physiological partitioning of specific substrates, typically labeled with isotopes. However, an alternative approach (Sinsabaugh et al., 2016) is based on community-level resource capture using assays of extracellular enzymes; although this uses the same name (CUE), it measures something distinctly different from the isotopic methods. Rather, it assesses how microbes shift resource use in response to substrate stoichiometry. [Display omitted] • Carbon partitioning between reuse and respiration (carbon use efficiency) is central to C cycling. • CUE is regularly measured using isotopic tracer methods. • CUE can also be estimated from stoichiometric theory: excess C is respired to balance cell C/N. • These are distinctly different concepts and measurements. [ABSTRACT FROM AUTHOR]