Search

Abstract Background Approximately 500 Tg of isoprene are emitted to the atmosphere annually, an amount similar to that of methane, and despite its significant effects on the climate, very little is known about the biological degradation of isoprene in the environment. Isolation and characterisation of isoprene degraders at the molecular level has allowed the development of probes targeting isoA encoding the α-subunit of the isoprene monooxygenase. This enzyme belongs to the soluble diiron centre monooxygenase family and catalyses the first step in the isoprene degradation pathway. The use of probes targeting key metabolic genes is a successful approach in molecular ecology to study specific groups of bacteria in complex environments. Here, we developed and tested a novel isoA PCR primer set to study the distribution, abundance, and diversity of isoprene degraders in a wide range of environments. Results The new isoA probes specifically amplified isoA genes from taxonomically diverse isoprene-degrading bacteria including members of the genera Rhodococcus, Variovorax, and Sphingopyxis. There was no cross-reactivity with genes encoding related oxygenases from non-isoprene degraders. Sequencing of isoA amplicons from DNA extracted from environmental samples enriched with isoprene revealed that most environments tested harboured a considerable variety of isoA sequences, with poplar leaf enrichments containing more phylogenetically diverse isoA genes. Quantification by qPCR using these isoA probes revealed that isoprene degraders are widespread in the phyllosphere, terrestrial, freshwater and marine environments. Specifically, soils in the vicinity of high isoprene-emitting trees contained the highest number of isoprene-degrading bacteria. Conclusion This study provides the molecular ecology tools to broaden our knowledge of the distribution, abundance and diversity of isoprene degraders in the environment, which is a fundamental step necessary to assess the impact that microbes have in mitigating the effects of this important climate-active gas.

Lymphocytic choriomeningitis mammarenavirus (LCMV) is an enveloped, negative-strand RNA virus that causes serious disease in humans but establishes an asymptomatic, lifelong infection in reservoir rodents. Different models have been proposed to describe how arenaviruses regulate the replication and transcription of their bisegmented, single-stranded RNA genomes, particularly during persistent infection. However, these models were based largely on viral RNA profiling data derived from entire populations of cells. To better understand LCMV replication and transcription at the single-cell level, we established a high-throughput, single-molecule fluorescence in situ hybridization (smFISH) image acquisition and analysis pipeline and examined viral RNA species at discrete time points from virus entry through the late stages of persistent infection in vitro. We observed the transcription of viral nucleoprotein and polymerase mRNAs from the incoming S and L segment genomic RNAs, respectively, within 1 h of infection, whereas the transcription of glycoprotein mRNA from the S segment antigenome required ~4 to 6 h. This confirms the temporal separation of viral gene expression expected due to the ambisense coding strategy of arenaviruses and also suggests that antigenomic RNA contained in virions is not transcriptionally active upon entry. Viral replication and transcription peaked at 36 h postinfection, followed by a progressive loss of viral RNAs over the next several days. During persistence, the majority of cells showed repeating cyclical waves of viral transcription and replication followed by the clearance of viral RNA. Thus, our data support a model of LCMV persistence whereby infected cells can spontaneously clear infection and become reinfected by viral reservoir cells that remain in the population. IMPORTANCE Arenaviruses are human pathogens that can establish asymptomatic, lifelong infections in their rodent reservoirs. Several models have been proposed to explain how arenavirus spread is restricted within host rodents, including the periodic accumulation and loss of replication-competent, but transcriptionally incompetent, viral genomes. A limitation of previous studies was the inability to enumerate viral RNA species at the single-cell level. We developed a high-throughput, smFISH assay and used it to quantitate lymphocytic choriomeningitis mammarenavirus (LCMV) replicative and transcriptional RNA species in individual cells at distinct time points following infection. Our findings support a model whereby productively infected cells can clear infection, including viral RNAs and antigen, and later be reinfected. This information improves our understanding of the timing and possible reg- ulation of LCMV genome replication and transcription during infection. Importantly, the smFISH assay and data analysis pipeline developed here is easily adaptable to other RNA viruses. [ABSTRACT FROM AUTHOR]

Aims: To compare the standard culture method with a new, rapid test (ScanVIT-Legionella™) using fluorescently labelled gene probes for the detection and enumeration of Legionella spp. The new technique was validated through experiments conducted on both artificially and naturally contaminated water and through an inter-laboratory comparison. Methods and Results: All samples were processed by the ScanVIT test according to the manufacturer's instructions and by a culture method (ISO 11731). ScanVIT detected significantly more positive samples, although concentrations were similar and a strong positive correlation between the two methods was observed ( r = 0·888, P < 0·001). The new test was more accurate in identifying the co-presence of Legionella pneumophila and Leg. non- pneumophila. ScanVIT showed a slightly higher Legionella recovery from water samples artificially contaminated with Leg. pneumophila alone or together with Pseudomonas aeruginosa. Lastly, the inter-laboratory comparison revealed that the ScanVIT test exhibits a lower variability than the traditional culture test (mean coefficient of variation 8·7 vs 16·1%). Conclusions: The results confirmed that the ScanVIT largely overlaps the reference method and offers advantages in terms of sensitivity, quantitative reliability and reduced assay time. Significance and Impact of the Study: The proposed method may represent a useful validated alternative to traditional culture for the rapid detection and quantification of Legionella spp. in water. [ABSTRACT FROM AUTHOR]

Conventional, morphological identification of ciliates and other protozoa needs considerable experience and often is difficult as various staining methods must be applied. New molecular techniques, such as fluorescence in situ hybridization (FISH) with gene probes, are powerful means to overcome this problem. As a test case, the morphology of two very similar, and thus difficult to differentiate ciliate morphospecies, Glaucoma scintillans and Glaucomides bromelicola, were compared. They were then distinguished by applying the Ciliate-FISH technique with a set of eight 18S rRNA targeted oligonucleotide probes, four of which have been developed for specific detection of G. scintillans. The remaining four probes were designed to detect G. bromelicola in order to prove probe specificities by binding to the homologous target region of the probes mentioned before. The tests resulted in a clear and easy differentiation of the two species by fluorescence signals of three of the four tested probe pairs. Thus, FISH techniques are very useful for the identification and detection of protozoa and might be of great help studying geographical distributions of known taxa. [ABSTRACT FROM AUTHOR]

Based on morphological and morphogenetic characters alone, the sibling species Stylonychia lemnae and Stylonychia mytilus, members of the Stylonychia mytilus complex, can hardly be distinguished. However, biochemical investigations of the isoenzyme pattern of different enzymes showed a distinct differentiation between these two species. In the last few years, fluorescence in situ hybridization (FISH) techniques have become a suitable and reliable tool for identification and differentiation of closely related species of protozoa, such as ciliates. To distinguish the sibling species, a set of specific oligonucleotide probes were developed. In the present study, the SSU rDNA of 7 clones of Stylonychia lemnae and 13 clones of Stylonychia mytilus, isolated from different geographic regions, were sequenced. Comparing all SSU rDNA sequences of both species, only one single difference within the whole gene was detected. Based on this difference, a set of two oligonucleotide probes, targeting the SSU rRNA of each species (Stylonychia mytilus and Stylonychia lemnae) was designed. These probes were successfully tested by applying the FISH techniques on preserved cells of different clones of both species. [Copyright &y& Elsevier]

Degenerate primers to detect nrfA were designed by aligning six nrfA sequences including Escherichia coli K-12, Sulfurospirillum deleyianum and Wolinella succinogenes. These primers amplified a 490 bp fragment of nrfA. The ability of these primers to detect nrfA was tested with chromosomal DNA isolated from a variety of bacteria: they could distinguish between bacteria in which the gene is known to be present or absent. The positive reference organisms spanned the various classes of Proteobacteria, suggesting that these primers are probably generic. The primer pair F1 and R1 was also used successfully to analyse nrfA diversity from community DNA isolated from a sulphate reducing bioreactor, and from two established Anammox reactors (for anaerobic ammonia oxidation, in which nitrite is reduced by ammonia to dinitrogen gas). The nrfA clones isolated from these three sources grouped with the Bacteroidetes phylum. The nrfA primers also amplified 570 bp fragments from the Anammox community DNA. These fragments encoded a protein with four haem-binding motifs typical of a c-type cytochrome, but were unrelated to the NrfA nitrite reductase. A BLAST search failed to reveal similarity to any known proteins. However, similarity was found to one sequence, which was annotated as rapC (response regulator aspartate phosphatase), in the genome of the planctomycete Rhodopirellula baltica. These sequences possibly belong to a new class of c-type cytochrome that might be specific to members of the order Planctomycetales. The data are consistent with the proposal that cytochrome c nitrite reductases, present in the periplasm of Gram-negative bacteria, are widely distributed in many different environments where they provide a short circuit in the biological nitrogen cycle by reducing nitrite directly to ammonia. [Copyright &y& Elsevier]

Plastids in phytoplankton retain prokaryote-like DNA sequences that may generate false-positive signals from eubacterial small subunit (ssu) rRNA oligonucleotide probes, resulting in the overestimation of bacterial activity in aquatic microbial communities. To assess the extent of possible plastid-associated binding to eubacterial signals, we performed an extensive database search, flask experiments using algal and cyanobacterial pure cultures, and field trials on five common eubacterial probes: S-D-Bact-008-a-A-19, S-D-Bact-338-a-A-18, S-D-Bact-785-a-A-19, S-D-Bact-927-a-A-17, and S-D-Bact-1088-a-A-20. The database search and laboratory tests showed significant potential for binding among most bacterial probes and organelle ssu-rRNA. However, we propose two probing strategies to overcome this problem. First, one could use Bact-785 and Bact-338 in tandem, with the plastid component being estimated as the difference between the two signals (Bact-338 has ~70% overlap with known plastid sequences). Alternately, one might use Bact-338 as the primary eubacterial probe, but then use Cyan-785-a-A-19 (a probe that binds significantly to plastid rRNA) to correct for the plastid-associated false-positive signal. Both strategies would use a eukaryotic probe (S-D-Euca-1379-a-A-16) and Cyan-785-b-A-19 (a probe for most cyanobacteria) to further segregate rRNA signals. Trials were successfully performed using the strategies on samples from a recent field study. [Copyright &y& Elsevier]

The prebiotic effects of lactulose were monitored in a human feeding study. Prebiotics are dietary carbohydrates that have a selective microbial metabolism in the gut, directed towards bacteria seen as beneficial, examples being bifidobacteria and/or lactobacilli. The study was conducted in a double blind, placebo controlled manner. A dose of 10 g per day, half the pharmacological dose, was fed to 10 healthy adult volunteers. In parallel, 10 persons were fed a placebo (glucose/lactose). Both culture based methodologies and genetic probing, based around fluorescent in situ hybridization were used to determine bacterial populations. Faecal water genotoxicity was assessed using the Comet assay to investigate the ability of lactulose to protect against DNA damage. Bifidobacteria showed a statistically significant increase during lactulose intake, whilst genetic probing showed a concomitant decrease in clostridia. Viable plate counts of lactobacilli increased when lactulose was fed, but this was not replicated by the genetic probing. During the trial, none of the recruits experienced any significant adverse gastrointestinal symptoms. Single-cell gel electrophoresis, used to assess faecal water genotoxicity, did not reveal that lactulose intervention reduced genotoxicity. The prebiotic nature of 10 g/day lactulose towards the human gut microbiota has been clearly demonstrated in this study. Lactulose is shown to be an effective food-grade prebiotic for healthy adults particularly in sections of the community with low bifidobacterial populations. The value of the more direct, culture independent FISH technique in the microbial ecology of the gut has been demonstrated in this study. [ABSTRACT FROM AUTHOR]

Prebiotics are non-digestible food ingredients that target selected groups of the human colonic microflora, thus having the ability to alter the composition towards a more ???beneficial??? community, i.e. selectively increasing populations of bifidobacteria and/or lactobacilli. In the present study the prebiotic potential of partially hydrolysed guar gum (PHGG) and fructo-oligosaccharides (FOS) in a biscuit was assessed in human volunteers. Fluorescent in situ hybridization using oligonucleotide probes targeting Bacteroides spp., Bifidobacterium spp., Clostridium spp. and Lactobacillus???Enterococcus spp. were used for the bacteriology and total bacteria were enumerated using the fluorescent stain 4???,6-diamidino-2-phenylindole. Thirty-one volunteers consumed daily either three experimental biscuits (providing a total (g/d) of 6??6 FOS and 3??4 PHGG) or three placebo biscuits for two 21-d crossover periods. Bifidobacteria significantly increased in number on ingestion of the experimental biscuits compared with pre-treatment and placebo population levels. Bifidobacterial numbers returned to pretreatment levels within 7 d of the cessation of intake of experimental biscuits. A correlation was observed between the initial faecal bifidobacterial numbers and the magnitude of bifidogenesis, with volunteers who possessed low initial population levels of bifidobacteria experiencing the greatest increase in bifidogenesis. No changes were observed in the other bacterial groups monitored during the trial. Thus, the prebiotic nature of FOS and PHGG was maintained in a final food product as evidenced from the selective increase in bifidobacterial numbers. [ABSTRACT FROM PUBLISHER]

The Maillard reaction produces coloured, macromolecular materials (melanoidins) in a variety of foods, on heating. Significant quantities may enter the human gut on a daily basis, but there is little information on their metabolism in the human colon. As the large bowel contains a diverse population of bacteria involved in normal bowel function, it is possible that melanoidins are metabolized therein. Depending on the bacteria involved, there may be disease or health implications. The aim of the present study was to use in vitro models to determine the digestibility of melanoidins and the effect of melanoidins on colonic bacteria in the gastrointestinal tract. Melanoidins were prepared and the effects of simulated upper-gut secretions on their stability determined in a model system. The effects of faecal bacteria were also determined, in batch culture, with a combination of phenotypic and genotypic (probes) criteria being used to identify the microbial diversity involved. Simulation of peptic and pancreatic digestion showed that the melanoidins did not produce detectable amounts of low-molecular-mass degradation products. However, melanoidins affected the growth of gut bacteria during mixed culture growth. The effect was to cause a non-specific increase in the anaerobic bacteria enumerated. This in vitro study indicates that melanoidins can affect the growth of human large-bowel bacteria and serves to demonstrate possible effects that may occur in vivo. Given the large and varied number of food items that contain Maillard reaction products, this may have relevance for lower-gut health. [ABSTRACT FROM PUBLISHER]

The widespread problem of contaminated water by enteric microorganisms necessitates the need to develop a rapid protocol to detect pathogens in water bodies. Usual methods like plating, biochemical tests and use of DNA probes are time consuming which is a limiting factor especially in epidemic situations. Moreover, some cells can exist in a virulent viable but non-culturable state making detection very difficult by plating method. This paper describes a rapid method to detect the enteropathogens, E.coli, Salmonella and Vibrio and enteric viruses from water samples by Polymerase Chain Reaction. E.coli was specially chosen as it is an indicator of fecal contamination. The sensitivity of E.coli detection was improved to 10 cells to keep in tune with the WHO guidelines. The presence of E.coli would also indicate the probable presence of other pathogens. [ABSTRACT FROM AUTHOR]

The emergence and acceptance of the concept of sustainable development warrants that the scope of environmental biotechnology be enlarged to address issues like environmental monitoring, restoration of environmental quality, resource/residue/waste-recovery/utilization/treatment, and substitution of the non-renewable resource base with renewable resources. This paper delineates the current and prospective applications in these sub-areas of environmental biotechnology, and documents case studies on environmental monitoring (enteric viruses), restoration of environmental quality (oil spill remediation), resource recovery (hydrocarbon recovery from oily sludges, biosurfactants from distillery spentwash, desulphurization of coal & sour gases), and substitution of non-renewable resources with renewables (conversion of lignocellulisics into value added chemicals). [ABSTRACT FROM AUTHOR]

Mercury-resistance genes were detected by in situ hybridization using new synthetic oligonucleotide probes specific for merA and merB genes according to the published sequences of the corresponding enzymes. These DNA probes were used for the detection of specific mercury-resistant microorganisms isolated from the Rhine River which had been polluted 3 years previously in 1986. Mercuric reductase and organomercurial lyase genes persist in the bacterial genome even after the disappearance of the pollutant but are absent in axenic amoebae. A total of 49 bacterial isolates showed DNA homologies with theP-labelled DNA probes and 15 free-living amoebae were selected due to their harboured symbiotic mercury-resistant bacteria. [ABSTRACT FROM AUTHOR]

A bench scale experimental system was developed for the analysis of polycyclic aromatic hydrocarbon (PAH) degradation by mixed microbial cultures in PAH contaminated Manufactured Gas Plant (MGP) soils and on sand. The reactor system was chosen in order to provide a fundamental protocol capable for evaluating the performance of specific mixed microbial cultures on specific soil systems by elucidating the important system variables and their interactions. The reactor design and peripherals are described. A plug flow differential volume reactor (DVR) was used in order to remove performance effects related to reactor type, as opposed to system structure. This reactor system could be well represented mathematically. Methods were developed for on-line quantitative determination of PAH liquid phase concentrations. The mathematical models and experimental data are presented for the biodegradation of naphthalene on artificial and MGP soils. [ABSTRACT FROM AUTHOR]

An experimental and mathematical method is developed for the microbial systems analysis of polyaromatic hydrocarbon (PAH)-degrading mixed cultures in PAH-contaminated 'town gas' soil systems. Frequency response is the primary experimental and data analysis tool used to probe the structure of these complicated systems. The objective is to provide a fundamental protocol for evaluating the performance of specific mixed microbial cultures on specific soil systems by elucidating the salient system variables and their interactions. Two well-described reactor systems, a constant volume stirred tank reactor (CSTR) and a plug flow differential volume reactor, are used in order to remove performance effects that are related to reactor type as opposed to system structure. These two reactor systems are well-defined systems that can be described mathematically and represent the two extremes of one potentially important system variable, macroscopic mass transfer. The experimental and mathematical structure of the protocol is described, experimental data is presented, and data analysis is demonstrated for the stripping, sorption, and biodegradation of napththalene. [ABSTRACT FROM AUTHOR]

The SARS-CoV-2 pandemic has strained manufacturing capacity worldwide, resulting in significant shortages of laboratory supplies both directly and indirectly. Such shortages include probe-based kits for detection of the Mycobacterium tuberculosis complex from positive liquid broth cultures. These shortages and possible loss of this particular assay have consequences for laboratory testing algorithms and public health in the United States. As there are no FDA-approved, commercially available options that currently exist which could immediately fill this gap, laboratories must identify alternatives and plan for modifying current testing algorithms to accommodate this change.