Phylogenetic position of Gluconobacter species as a coherent cluster separated from all Acetobacter species on the basis of 16S ribosomal RNA sequences

Abstract The 16S rRNA sequences from the Gluconobacter species G. asaii G. cerinus and G. frateurii were determined and compared with homologous sequences from published databases and sequences of G. oxydans and Acetobacter species previously described [Sievers M., Ludwig W. and Teuber M. (1994) System. Appl. Microbiol. 17, 189–196]. The Gluconobacter species have unique 16S rRNA sequences and exhibit sequence similarity values of 97.4 to 99.1%, corresponding to 36 to 14 base differences. The phylogenetic tree inferring methods (distance matrix, maximum parsimony and maximum likelihood) show that the species of Gluconobacter form a coherent, closely related cluster. Based on the distance matrix method including Rhodopila globiformis as an outgroup reference organism, Gluconobacter is well separated from Acetobacter .     

Nickel resistance in Escherichia coli V38 is dependent on the concentration used for induction

Strain Escherichia coli V38 resistant to 4 mM NiCl₂ was isolated from the city sewage sludge. It showed low nickel accumulation by cells and nickel ion efflux. Cells were pregrown (induced) overnight in the presence of Ni²⁺, then the culture was kept on ice for 20–30 min and transferred to 37°C for further incubation. When the Ni²⁺ concentration during growth was the same as during incubation, there was no noticeable accumulation of Ni²⁺. When the Ni²⁺ concentration during incubation was higher than that used for induction, uptake of ⁶³Ni²⁺ and delayed efflux were seen. The uptake and delay of both efflux and growth were directly proportional to the difference between the concentrations used for induction and incubation. Active nickel ion uptake was seen in cells taken from cultures in the delayed efflux period.     

Conversion of two distinct Rhodopseudomonas capsulata isolates to the glycerol-utilizing phenotype

Abstract Previous studies employing a single strain of the photosynthetic bacterium Rhodopseudomonas capsulata have demonstrated that this organism, which normally is not capable of growth on glycerol, can gain glycerol-utilizing ability through mutational events. We have examined other strains of R. capsulata of divergent geographic origin, and have found that they could also be converted to a glycerol-catabolic phenotype. Mutant derivatives were found to express high constitutive levels of glycerophosphate dehydrogenase (GPD) and glycerokinase (GK) which were barely detectable in the parental strains. These results suggest that the ability to utilize glycerol after undergoing a gain of function mutation is a widespread property of R. capsulata .     

A Novel Electrochemically Active and Fe(III)-reducing Bacterium Phylogenetically Related to Clostridium butyricum Isolated from a Microbial Fuel Cell

An obligatory anaerobic bacterium was isolated from a mediator-less microbial fuel cell using starch processing wastewater as the fuel and designated as EG3. The isolate was Gram-positive, motile and rod (2.8–3.0 μm long, 0.5–0.6 μm wide). The partial 16S rRNA gene sequence and analysis of the cellular fatty acids profile suggested that EG3 clusters with Clostridium sub-phylum and exhibited the highest similarity (98%) with Clostridium butyricum. The temperature and pH optimum for growth were 37°C and 7.0, respectively. The major products of glucose and glucose/Fe(O)OH metabolism were lactate, formate, butyrate, acetate, CO₂and H₂. Growth was faster at the initial phase and the cell yield was higher when the medium was supplemented with Fe(O)OH than without Fe(O)OH. These results suggest that Fe(III) ion is utilised as an electron sink. Cyclic voltammetry showed that Clostridium butyricum EG3 cells were electrochemically active. It is a novel characteristic of strict anaerobic Gram-positive bacteria.     

The use of disposable gaas generating kits for the growth of hydrogen-oxidizing bacteria and the determination of hydrogen autotrophy

A simplified procedure for the determination of autotropic growth of hydrogen-oxidizing bacteria has been developed. The method uses commercially available disposable hydrogen and carbon dioxide kits, commonly used in anaerobic bacteriology, to produce a gaseous atmosphre containing by volume approximately 41% hydrogen, 6% carbon dioxide, 11% oxygen and 42% nitrogen. The atmosphere was suitable for the growth of strains assigned to the species Alcaligenes eutrophus, Alcaligenes paradoxus, Paracoccus denitrificans, Pseudomonas facilis, Pseudomonas flava, Pseudomonas palleronii, Pseudomonas saccahrophilia and Rhodococcus sp. (‘Nocardia opaca’). The method can also be used for the screening of hydrogen-oxidizing ability in bacterial isolates, thus eliminating the need for complex gas mixing devices or expensive gas mixtures.     

Use of milk electrical conductivity for the differentiation of mastitis causing pathogens in Holstein cows

Mastitis is one of the most prevalent and costly diseases in dairy cattle. Key components for adequate mastitis control are the detection of early stages of infection, as well as the selection of appropriate management interventions and therapies based on the causal pathogens associated with the infection. The objective was to characterize the pattern of electrical conductivity (EC) in milk during intramammary infection, considering specific mastitis-causing pathogen groups involvement. Cows (n = 200) identified by an in-line mastitis detection system with a positive deviation ≥15% in the manufacturer’s proprietary algorithm for EC (high electrical conductivity (HEC)) were considered cases and enrolled in the study at the subsequent milking. One control (CON) cow, within normal ranges for EC, was matched to each case. A composite milk sample was collected aseptically from each cow for bacteriological culture. Milk yield (MY) and EC were recorded for each milking during ±7 days relative to enrollment. Milk cultures were categorized into gram positive (GP), gram negative (GN), other (OTH) and no growth (NOG). Data were submitted for repeated-measures analysis with EC as the dependent variable and EC status at day −1, bacteriological culture category, parity number, stage of lactation and days relative to sampling as main independent variables. Average (± standard error (SE)) EC was greater in HEC than in CON cows (12.5 ± 0.5 v. 10.8 ± 0.5 mS/cm) on the day of identification (day −1). Milk yield on day −1 was greater in CON than in HEC (37.6 ± 5.1 v. 33.5 ± 5.2 kg). For practical management purposes, average EC on day −1 was similar for the different bacteriological culture categories: 11.4 ± 0.6, 11.7 ± 0.5, 12.3 ± 0.8 and 11.7 ± 0.5 mS/cm in GN, GP, OTH and NOG, respectively. Parity number was only associated with day −1 EC in HEC group, with the greatest EC values in parity 3 (12.3 ± 0.3 mS/cm), followed by parity 2 (11.9 ± 0.2 mS/cm), parity >3 (11.6 ± 0.5 mS/cm) and primiparous cows (11.2 ± 0.2 mS/cm). An effect on EC for the interaction of day relative to identification by pathogen gram category was observed. The same interaction effect was observed on daily MY. Overall, the level of variation for MY and EC between- and within-cows was substantial, and as indicated by the model diagnostic procedures, the magnitude of the variance in the cows in the CON group resulted in deviations from normality in the residuals. We concluded that characteristic temporal patterns in EC and MY in particular pathogen groups may provide indications for differentiation of groups of mastitis-causing pathogens. Further research to build detection models including EC, MY and cow-level factors is required for accurate differentiation.     

Plant community composition steers grassland vegetation via soil legacy effects

Soil legacy effects are commonly highlighted as drivers of plant community dynamics and species co‐existence. However, experimental evidence for soil legacy effects of conditioning plant communities on responding plant communities under natural conditions is lacking. We conditioned 192 grassland plots using six different plant communities with different ratios of grasses and forbs and for different durations. Soil microbial legacies were evident for soil fungi, but not for soil bacteria, while soil abiotic parameters did not significantly change in response to conditioning. The soil legacies affected the composition of the succeeding vegetation. Plant communities with different ratios of grasses and forbs left soil legacies that negatively affected succeeding plants of the same functional type. We conclude that fungal‐mediated soil legacy effects play a significant role in vegetation assembly of natural plant communities.     

Isolation of ultrasmall (filterable) bacteria from patients suffering from ME,and patients and staff of a paediatric hospital

A total of 108 blood samples obtained from 28 male and 80 female patients diagnosed with ME were diluted in sterile, Ringer’s Solution and forced (by suction) through 0.2 µm filters. Of the 28 male samples, 4 yielded filterable bacteria and of the 80 female samples, 18 gave filterable bacteria; as a result, of the total of 124 samples, 22 yielded FB. Filterable (0.4 and 0.2, but not 0.1micron filterable) bacteria were also isolated from the nose throat and skin of paediatric patients and from the throat and skin of staff at an emergency paediatric hospital. The highest percentage of bacterial passage occurred through the largest (0.4 µm) pores. The results show that ultrasmall bacteria occur in ME patients and in paediatric patients and nurses. The potential pathogenic role of such filterable bacteria is briefly discussed.     

MALDI-TOF-MS and 16S rRNA characterization of lead tolerant metallophile bacteria isolated from saffron soils of Kashmir for their sequestration potential

Toxic metal contamination in soils due industrialization is nowadays a concern to the scientists worldwide. The current study deals with the evaluation of response and tolerance by isolated metallophilic bacteria in different lead concentrations (100 ppm to 1000 ppm). By taking optical densities of the isolates, the minimum inhibitory concentration (MIC) of Pb²⁺ were determined.16S rRNA and MALDI-TOF MS were used for the identification of the bacteria. Total of 37 isolates were observed, among them 04 (Staphylococcus equorum, Staphylococcus warneri, Bacillus safensis and Bacillus thuringiensis), isolated were detected having efficacy of Pb²⁺tolerance and sequestration at varying MIC. Furthermore, B. thuringiensis was observed to have highest (900 ppm) tolerance for lead and lowest (500 ppm) for Staphylococcus warneri. Moreover, the highest (65.3%) sequestration potential has been observed for B. thuringiensis and least (52.8%) for S. warneri. The tolerance and sequestration potential properties of these isolated species can be utilised to exterminate heavy metals and reduce their toxicity from the contaminated environment.     

Keeping it cool: Soil sample cold pack storage and DNA shipment up to 1 month does not impact metabarcoding results

With the advances of sequencing tools, the fields of environmental microbiology and soil ecology have been transformed. Today, the unculturable majority of soil microbes can be sequenced. Although these tools give us tremendous power and open many doors to answer important questions, we must understand how sample processing may impact our results and interpretations. Here, we test the impacts of four soil storage methods on downstream amplicon metabarcoding and qPCR analyses for fungi and bacteria. We further investigate the impact of thaw time on extracted DNA to determine a safe length of time during which this can occur with minimal impact on study results. Overall, we find that storage using standard cold packs with subsequent storage at ?20°C is little different than immediate storage in liquid nitrogen, suggesting that the historical and current method is adequate. We further find evidence that storage at room temperature or with aid of RNAlater can lead to changes in community composition and in the case of RNAlater, lower gene copies. We therefore advise against these storage methods for metabarcoding analyses. Finally, we show that over 1 month, DNA extract thaw time does not impact diversity or qPCR metrics. We hope that this work will help researchers working with soil bacteria and fungi make informed decisions about soil storage and transport to ensure repeatability and accuracy of results and interpretations.