Effect of integration of a GFP reporter gene on fitness of Ralstonia eutropha during growth with 2,4-dichlorophenoxyacetic acid

Microbial competition among anammox bacteria in nitrite-limited bioreactors

Phylogenetically diverse anammox bacteria have been detected in most of anoxic natural and engineered ecosystems and thus regarded as key players in the global nitrogen cycle. However, ecological niche differentiation of anammox bacteria remains unresolved despite its ecological and practical importance. In this study, the microbial competitions for a common substrate (nitrite) among three anammox species (i.e. "Candidatus Brocadia sinica", "Candidatus Jettenia caeni" and "Candidatus Kuenenia stuttgartiensis") were systematically investigated in nitrite-limited gel-immobilized column reactors (GICR) and membrane bioreactors (MBRs) under different nitrogen loading rates (NLRs). 16 S rRNA gene-based population dynamics revealed that "Ca. J. caeni" could proliferate only at low NLRs, whereas "Ca. B. sinica" outcompeted other two species at higher NLRs in both types of reactors. Furthermore, FISH analysis revealed that "Ca. J. caeni" was mainly present as spherical microclusters at the inner part (low NO₂^- environment), whereas "Ca. B. sinica" was present throughout the gel beads and granules. This spatial distribution supports the outcomes of the competition experiments. However, the successful competition of "Ca. J. caeni" at low NLR could not be explained with the Monod model probably due to inaccuracy of kinetic parameters such as half saturation constant (K_s) for nitrite and a difference in the maintenance rate (m). In addition, the growth of "Ca. K. stuttgartiensis" could not be observed in any experimental conditions, suggesting possible unknown factor(s) is missing. Taken together, NLR was one of factors determining ecological niche differentiation of "Ca. B. sinica" and "Ca. J. caeni".

Construction and use of a Cupriavidus necator H16 soluble hydrogenase promoter (PSH) fusion to gfp (green fluorescent protein)

Hydrogenases are metalloenzymes that reversibly catalyse the oxidation or production of molecular hydrogen (H₂). Amongst a number of promising candidates for application in the oxidation of H₂ is a soluble [Ni–Fe] uptake hydrogenase (SH) produced by Cupriavidus necator H16. In the present study, molecular characterisation of the SH operon, responsible for functional SH synthesis, was investigated by developing a green fluorescent protein (GFP) reporter system to characterise P_SH promoter activity using several gene cloning approaches. A P_SH promoter-gfp fusion was successfully constructed and inducible GFP expression driven by the P_SH promoter under de-repressing conditions in heterotrophic growth media was demonstrated in the recombinant C. necator H16 cells. Here we report the first successful fluorescent reporter system to study P_SH promoter activity in C. necator H16. The fusion construct allowed for the design of a simple screening assay to evaluate P_SH activity. Furthermore, the constructed reporter system can serve as a model to develop a rapid fluorescent based reporter for subsequent small-scale process optimisation experiments for SH expression.

Variation in Growth, Colonization of Maize, and Metabolic Parameters of GFP- and DsRed-Labeled Fusarium verticillioides Strains

Autofluorescent proteins are frequently applied as visual markers in the labeling of filamentous fungi. Genes gfp and DsRed were transformed into the genome of Fusarium verticillioides via the Agrobacterium tumefaciens-mediated transformation method. The selected transformants displayed a bright green or red fluorescence in all the organelles of the growing fungal mycelia and spores (except for the vacuoles) both in cultures and in the maize (Zea mays) roots they colonized. The results of gene-specific polymerase chain reaction (PCR) analysis and the thermal asymmetrical interlaced (TAIL)-PCR analysis demonstrated that gfp and DsRed were integrated on different chromosomes of the fungus. Reductions in the colony growth on the plates at pH 4.0 and 5.5 was observed for the green fluorescent protein (GFP)-transformant G3 and the DsRed-transformant R4, but transformants G4 and R1 grew as well as the wild-type strain at pH 4.0. The speed of growth of all the transformants was similar to the wild-type strain at pH ≥ 7. The insertion of gfp and DsRed did not alter the production of extracellular enzymes and fumonisin B by F. verticillioides. The transformants expressing GFP and DsRed proteins were able to colonize maize roots. However, the four transformants examined produced fewer CFU in the root samples than the wild-type strain during a sampling period of 7 to 28 days after inoculation.

Survival of GFP-tagged Rhodococcus sp. D310-1 in chlorimuron-ethyl-contaminated soil and its effects on the indigenous microbial community

The recently isolated bacterial strain Rhodococcus sp. D310-1 can degrade high concentrations of chlorimuron-ethyl (up to 1000 mg L(-1)), indicating its potential for the bioremediation of soil contaminated with high levels of chlorimuron-ethyl. In this study, Rhodococcus sp. D310-1 was tagged with green fluorescent protein gene (gfp) to track its survival in soil. Subsequently, degradation activity of the gfp-tagged strain and its effects on indigenous microbial community were analyzed. Results showed the cell numbers of Rhodococcus sp. D310-1::gfp in non-sterilized soil maintained at 8.5 × 10(4) cells g(-1) dry soil 45 days after inoculation of 7.74 × 10(6) cells g(-1) dry soil and approximately 49% of chlorimuron-ethyl was removed. However, The cell numbers of Rhodococcus sp. D310-1::gfp in sterilized samples increased gradually to 7.85 × 10(7) cells g(-1) dry soil and approximately 78% of chlorimuron-ethyl was removed. PCR-DGGE demonstrated that inoculation of this gfp-tagged strain in chlorimuron-ethyl-contaminated soil has negligible impact on the community structure of bacteria, actinomycetes and fungi. These results indicate that Rhodococcus sp. D310-1 is effective for the remediation of chlorimuron-ethyl-contaminated soil and also provides valuable information about the behavior of the inoculant population during bioremediation, which could be directly used in the risk assessment of inoculant population and optimization of bioremediation process.

In glucose-limited continuous culture the minimum substrate concentration for growth, Smin, is crucial in the competition between the enterobacterium Escherichia coli and Chelatobacter heintzii, an environmentally abundant bacterium

The competition for glucose between Escherichia coli ML30, a typical copiotrophic enterobacterium and Chelatobacter heintzii ATCC29600, an environmentally successful strain, was studied in a carbon-limited culture at low dilution rates. First, as a base for modelling, the kinetic parameters μ(max) and K(s) were determined for growth with glucose. For both strains, μ(max) was determined in batch culture after different precultivation conditions. In the case of C. heintzii, μ(max) was virtually independent of precultivation conditions. When inoculated into a glucose-excess batch culture medium from a glucose-limited chemostat run at a dilution rate of 0.075 h(-1) C. heintzii grew immediately with a μ(max) of 0.17 ± 0.03 h(-1). After five transfers in batch culture, μ(max) had increased only slightly to 0.18 ± 0.03 h(-1). A different pattern was observed in the case of E. coli. Inoculated from a glucose-limited chemostat at D = 0.075 h(-1) into glucose-excess batch medium E. coli grew only after an acceleration phase of ~3.5 h with a μ(max) of 0.52 h(-1). After 120 generations and several transfers into fresh medium, μ(max) had increased to 0.80 ± 0.03 h(-1). For long-term adapted chemostat-cultivated cells, a K(s) for glucose of 15 μg l(-1) for C. heintzii, and of 35 μg l(-1) for E. coli, respectively, was determined in (14)C-labelled glucose uptake experiments. In competition experiments, the population dynamics of the mixed culture was determined using specific surface antibodies against C. heintzii and a specific 16S rRNA probe for E. coli. C. heintzii outcompeted E. coli in glucose-limited continuous culture at the low dilution rates of 0.05 and 0.075 h(-1). Using the determined pure culture parameter values for K(s) and μ(max), it was only possible to simulate the population dynamics during competition with an extended form of the Monod model, which includes a finite substrate concentration at zero growth rate (s(min)). The values estimated for s(min) were dependent on growth rate; at D = 0.05 h(-1), it was 12.6 and 0 μg l(-1) for E. coli and C. heintzii, respectively. To fit the data at D=0.075 h(-1), s(min) for E. coli had to be raised to 34.9 μg l(-1) whereas s(min) for C. heintzii remained zero. The results of the mathematical simulation suggest that it is not so much the higher K(s) value, which is responsible for the unsuccessful competition of E. coli at low residual glucose concentration, but rather the existence of a significant s(min).

Whole-cell fluorescent biosensors for bioavailability and biodegradation of polychlorinated biphenyls

Whole-cell microbial biosensors are one of the newest molecular tools used in environmental monitoring. Such biosensors are constructed through fusing a reporter gene such as lux, gfp or lacZ, to a responsive promoter. There have been many reports of the applications of biosensors, particularly their use in assaying pollutant toxicity and bioavailability. This paper reviews the basic concepts behind the construction of whole-cell microbial biosensors for pollutant monitoring, and describes the applications of two such biosensors for detecting the bioavailability and biodegradation of Polychlorinated Biphenyls (PCBs).

Development of an autofluorescent organophosphates-degrading Stenotrophomonas sp. with dehalogenase activity for the biodegradation of hexachlorocyclohexane (HCH)

Simultaneous biodegradation of hexachlorocyclohexane (HCH) and organophosphates (OPs) by a recombinant Stenotrophomonas sp. was studied in the study. The broad-host-range plasmid pVGAB, harboring enhanced green fluorescent protein gene (egfp) and dehalogenase genes (linA and linB), was constructed and transformed into the OP-degrading strain Stenotrophomonas YC-1 to get the recombinant strain YC-H. Over-expression of dehalogenase (LinA and LinB) and enhanced green fluorescent protein (EGFP) was obtained in YC-H by determining their enzymatic activities and fluorescence intensity. YC-H was capable of rapidly and simultaneously degrading 10mg/l gamma-HCH and 100mg/l methyl parathion (MP) determined by GC-ECD analysis. A bioremediation assay with YC-H inoculated into fumigated and nonfumigated soil showed that both 10mg/kg gamma-HCH and 100mg/kg MP could be completely degraded within 32 days. The novel EGFP-marked bacterium could be potentially applied in the field-scale decontamination of HCH and OPs residues in the environment.

Correlation between transcript profiles and fitness of deletion mutants in anaerobic chemostat cultures of Saccharomyces cerevisiae

The applicability of transcriptomics for functional genome analysis rests on the assumption that global information on gene function can be inferred from transcriptional regulation patterns. This study investigated whether Saccharomyces cerevisiae genes that show a consistently higher transcript level under anaerobic than aerobic conditions do indeed contribute to fitness in the absence of oxygen. Tagged deletion mutants were constructed in 27 S. cerevisiae genes that showed a strong and consistent transcriptional upregulation under anaerobic conditions, irrespective of the nature of the growth-limiting nutrient (glucose, ammonia, sulfate or phosphate). Competitive anaerobic chemostat cultivation showed that only five out of the 27 mutants (eug1Δ, izh2Δ, plb2Δ, ylr413wΔ and yor012wΔ) conferred a significant disadvantage relative to a tagged reference strain. The implications of this study are that: (i) transcriptome analysis has a very limited predictive value for the contribution of individual genes to fitness under specific environmental conditions, and (ii) competitive chemostat cultivation of tagged deletion strains offers an efficient approach to select relevant leads for functional analysis studies.

Design and evaluation of 16S rRNA sequence based oligonucleotide probes for the detection and quantification of Comamonas testosteroni in mixed microbial communities

Background

The β-proteobacterial species Comamonas testosteroni is capable of biotransformation and also biodegradation of a range of chemical compounds and thus potentially useful in chemical manufacturing and bioremediation. The ability to detect and quantify members of this species in mixed microbial communities thus may be desirable.

Results

We have designed an oligonucleotide probe for use in fluorescent in situ hybridization (FISH) and two pairs of PCR primers targeting a C. testosteroni subgroup. The FISH probe and one of the PCR primer pairs are suitable for quantification of C. testosteroni in mixed microbial communities using FISH followed by quantitative image analysis or real-time quantitative PCR, respectively. This has been shown by analysis of samples from an enrichment of activated sludge on testosterone resulting in an increase in abundance and finally isolation of C. testosteroni. Additionally, we have successfully used quantitative PCR to follow the C. testosteroni abundance during a laboratory scale wastewater bioaugmentation experiment.

Conclusion

The oligonucleotides presented here provide a useful tool to study C. testosteroni population dynamics in mixed microbial communities.

Information from single-cell bacterial biosensors: what is it good for?

Bacterial reporter cells (i.e. strains engineered to produce easily measurable signals in response to one or more chemical targets) can principally be used to quantify chemical signals and analytes, physicochemical conditions and gradients on a microscale (i.e. micrometer to submillimeter distances), when the reporter signal is determined in individual cells. This makes sense, as bacterial life essentially thrives in microheterogenic environments and single-cell reporter information can help us to understand the microphysiology of bacterial cells and its importance for macroscale processes like pollutant biodegradation, beneficial bacteria-eukaryote interactions, and infection. Recent findings, however, showed that clonal bacterial populations are essentially always physiologically, phenotypically and genotypically heterogeneous, thus emphasizing the need for sound statistical approaches for the interpretation of reporter response in individual bacterial cells. Serious attempts have been made to measure and interpret single-cell reporter gene expression and to understand variability in reporter expression among individuals in a population.