Quantitation and Comparison of Phenotypic Heterogeneity Among Single Cells of Monoclonal Microbial Populations

Phenotypic heterogeneity within microbial populations arises even when the cells are exposed to putatively constant and homogeneous conditions. The outcome of this phenomenon can affect the whole function of the population, resulting in, for example, new "adapted" metabolic strategies and impacting its fitness at given environmental conditions. Accounting for phenotypic heterogeneity becomes thus necessary, due to its relevance in medical and applied microbiology as well as in environmental processes. Still, a comprehensive evaluation of this phenomenon requires a common and unique method of quantitation, which allows for the comparison between different studies carried out with different approaches. Consequently, in this study, two widely applicable indices for quantitation of heterogeneity were developed. The heterogeneity coefficient (HC) is valid when the population follows unimodal activity, while the differentiation tendency index (DTI) accounts for heterogeneity implying outbreak of subpopulations and multimodal activity. We demonstrated the applicability of HC and DTI for heterogeneity quantitation on stable isotope probing with nanoscale secondary ion mass spectrometry (SIP-nanoSIMS), flow cytometry, and optical microscopy datasets. The HC was found to provide a more accurate and precise measure of heterogeneity, being at the same time consistent with the coefficient of variation (CV) applied so far. The DTI is able to describe the differentiation in single-cell activity within monoclonal populations resolving subpopulations with low cell abundance, individual cells with similar phenotypic features (e.g., isotopic content close to natural abundance, as detected with nanoSIMS). The developed quantitation approach allows for a better understanding on the impact and the implications of phenotypic heterogeneity in environmental, medical and applied microbiology, microbial ecology, cell biology, and biotechnology.

Key sub-community dynamics of medium-chain carboxylate production

BACKGROUND

The carboxylate platform is a promising technology for substituting petrochemicals in the provision of specific platform chemicals and liquid fuels. It includes the chain elongation process that exploits reverse β-oxidation to elongate short-chain fatty acids and forms the more valuable medium-chain variants. The pH value influences this process through multiple mechanisms and is central to effective product formation. Its influence on the microbiome dynamics was investigated during anaerobic fermentation of maize silage by combining flow cytometric short interval monitoring, cell sorting and 16S rRNA gene amplicon sequencing.

RESULTS

Caproate and caprylate titres of up to 6.12 g L-1 and 1.83 g L-1, respectively, were achieved in a continuous stirred-tank reactor operated for 241 days. Caproate production was optimal at pH 5.5 and connected to lactate-based chain elongation, while caprylate production was optimal at pH 6.25 and linked to ethanol utilisation. Flow cytometry recorded 31 sub-communities with cell abundances varying over 89 time points. It revealed a highly dynamic community, whereas the sequencing analysis displayed a mostly unchanged core community. Eight key sub-communities were linked to caproate or caprylate production (rS > | ± 0.7|). Amongst other insights, sorting and subsequently sequencing these sub-communities revealed the central role of Bifidobacterium and Olsenella, two genera of lactic acid bacteria that drove chain elongation by providing additional lactate, serving as electron donor.

CONCLUSIONS

High-titre medium-chain fatty acid production in a well-established reactor design is possible using complex substrate without the addition of external electron donors. This will greatly ease scaling and profitable implementation of the process. The pH value influenced the substrate utilisation and product spectrum by shaping the microbial community. Flow cytometric single cell analysis enabled fast, short interval analysis of this community and was coupled with 16S rRNA gene amplicon sequencing to reveal the major role of lactate-producing bacteria.

Characterizing Microbiome Dynamics - Flow Cytometry Based Workflows from Pure Cultures to Natural Communities

The investigation of pure cultures and monitoring of microbial community dynamics is vital to understand and control natural ecosystems and technical applications driven by microorganisms. Next generation sequencing methods are widely utilized to resolve microbiomes, but they are generally resource and time intensive and deliver mostly qualitative information. Flow cytometric microbiome analysis does not suffer from those disadvantages and can provide relative subcommunity abundances and absolute cell numbers at-line. Although it does not deliver direct phylogenetic information, it can enhance the analysis depth and resolution of sequencing approaches. In sharp contrast to medical applications in both research and routine settings, flow cytometry is still not widely used for microbiome analysis. Missing information on sample preparation and data analysis pipelines may create an entry barrier for the researchers facing microbiome analysis challenges that would often be textbook flow cytometry applications. Here, we present three comprehensive workflows for pure cultures, complex communities in clear medium and complex communities in challenging matrices, respectively. We describe individual sampling and fixation procedures and optimized staining protocols for the respective sample sets. We elaborate the cytometric analysis with a complex research centered and an application focused bench top device, describe the cell sorting procedure and suggest data analysis packages. We furthermore propose important experimental controls and apply the presented workflows to the respective sample sets.

Flow cytometric quantification, sorting and sequencing of methanogenic archaea based on F420 autofluorescence

Background

The widely established production of CH₄ from renewable biomass in industrial scale anaerobic reactors may play a major role in the future energy supply. It relies on methanogenic archaea as key organisms which represent the bottleneck in the process. The quantitative analysis of these organisms can help to maximize process performance, uncover disturbances before failure, and may ultimately lead to community-based process control schemes. Existing qPCR and fluorescence microscopy-based methods are very attractive but can be cost-intensive and laborious.

Results

In this study we present an autofluorescence-based, flow cytometric method for the fast low-cost quantification of methanogenic archaea in complex microbial communities and crude substrates. The method was applied to a methanogenic enrichment culture (MEC) and digester samples (DS). The methanogenic archaea were quantified using the distinct fluorescence of their cofactor F₄₂₀ in a range from 3.7 × 10⁸ (± 3.3 × 10⁶) cells mL⁻¹ and 1.8 x 10⁹ (± 1.1 × 10⁸) cells mL⁻¹. We evaluated different fixation methods and tested the sample stability. Stable abundance and fluorescence intensity were recorded up to 26 days during aerobic storage in PBS at 6 °C. The discrimination of the whole microbial community from the ubiquitous particle noise was facilitated by SYBR Green I staining and enabled calculation of relative abundances of methanogenic archaea of up to 9.64 ± 0.23% in the MEC and up to 4.43 ± 0.74% in the DS. The metaprofiling of the mcrA gene reinforced the results.

Conclusions

The presented method allows for fast and reliable quantification of methanogenic archaea in microbial communities under authentic digester conditions and can thus be useful for process monitoring and control in biogas digesters.

Electronic supplementary material

The online version of this article (10.1186/s12934-017-0793-7) contains supplementary material, which is available to authorized users.

Short-term cardiorespiratory adaptation to high altitude in children compared with adults

As short-term cardiorespiratory adaptation to high altitude (HA) exposure has not yet been studied in children, we assessed acute mountain sickness (AMS), hypoxic ventilatory response (HVR) at rest and maximal exercise capacity (CPET) at low altitude (LA) and HA in pre-pubertal children and their fathers. Twenty father-child pairs (11 ± 1 years and 44 ± 4 years) were tested at LA (450 m) and HA (3450 m) at days 1, 2, and 3 after fast ascent (HA1/2/3). HVR was measured at rest and CPET was performed on a cycle ergometer. AMS severity was mild to moderate with no differences between generations. HVR was higher in children than adults at LA and increased at HA similarly in both groups. Peak oxygen uptake (VO2 peak) relative to body weight was similar in children and adults at LA and decreased significantly by 20% in both groups at HA; maximal heart rate did not change at HA in children while it decreased by 16% in adults (P < 0.001). Changes in HVR and VO2 peak from LA to HA were correlated among the biological child-father pairs. In conclusion, cardiorespiratory adaptation to altitude seems to be at least partly hereditary. Even though children and their fathers lose similar fractions of aerobic capacity going to high altitude, the mechanisms might be different.

Continuous neuronal ensemble control of simulated arm reaching by a human with tetraplegia

Functional electrical stimulation (FES), the coordinated electrical activation of multiple muscles, has been used to restore arm and hand function in people with paralysis. User interfaces for such systems typically derive commands from mechanically unrelated parts of the body with retained volitional control, and are unnatural and unable to simultaneously command the various joints of the arm. Neural interface systems, based on spiking intracortical signals recorded from the arm area of motor cortex, have shown the ability to control computer cursors, robotic arms and individual muscles in intact non-human primates. Such neural interface systems may thus offer a more natural source of commands for restoring dexterous movements via FES. However, the ability to use decoded neural signals to control the complex mechanical dynamics of a reanimated human limb, rather than the kinematics of a computer mouse, has not been demonstrated. This study demonstrates the ability of an individual with long-standing tetraplegia to use cortical neuron recordings to command the real-time movements of a simulated dynamic arm. This virtual arm replicates the dynamics associated with arm mass and muscle contractile properties, as well as those of an FES feedback controller that converts user commands into the required muscle activation patterns. An individual with long-standing tetraplegia was thus able to control a virtual, two-joint, dynamic arm in real time using commands derived from an existing human intracortical interface technology. These results show the feasibility of combining such an intracortical interface with existing FES systems to provide a high-performance, natural system for restoring arm and hand function in individuals with extensive paralysis.

Varikose der V. saphena accessoria lateralis: Darstellung des Rezirkulationskreislaufs durch präoperative Phlebographie

Background: The incidence of varicosis of the anterior side branch of the long saphenous vein clinically ranges about 8 to 10% of descending venous decompensation, originating at the level of the thigh. Its incidence in women showing significant overweight is clearly pronounced. Mostly torturous and enlarged varicosed segments of the accessorial lateral saphenous vein can be seen clinically crossing the anterior middle of the thigh. The indications for surgical radical extirpation of the entire varicosed side branch depends from pain, phlebitic complications, peripheral venous dysfunction including cosmetic aspects. Patients: In a clientel of 138 patients (females: 114, males: 24) the phlebographic demonstration of the entire recirculation pathways was performed prior to surgery. Results: Ascending leg phlebography was found sufficient in 7.7% of cases only. Combined with varicography however, in further 90,7% of patients a clear demonstration of the upper and lower points of venous insufficiency was possible. The extent of functional disorders was calculated by additional peripheral venous pressure measurements. Conclusions: This clientel clearly shows that long-term reflux via the varicosed side branch increases the tendency of peripheral functional decompensation along the lower leg. Adequate surgical therapy depends from a clear demonstration of the varicosed veins beeing involved, and this can be realized by combined phlebography and varicography.

Varicosis of the accessorial lateral saphenous vein: evidence of recirculation shown by pre-operative phlebography

BACKGROUND

The incidence of varicosis of the anterior side branch of the long saphenous vein clinically ranges about 8 to 10% of descending venous decompensation, originating at the level of the thigh. Its incidence in women showing significant overweight is clearly pronounced. Mostly torturous and enlarged varicosed segments of the accessorial lateral saphenous vein can be seen clinically crossing the anterior middle of the thigh. The indications for surgical radical extirpation of the entire varicosed side branch depends from pain, phlebitic complications, peripheral venous dysfunction including cosmetic aspects.

PATIENTS

In a clientele of 138 patients (females: 114, males: 24) the phlebographic demonstration of the entire recirculation pathways was performed prior to surgery.

RESULTS

Ascending leg phlebography was found sufficient in 7.7% of cases only. Combined with varicography however, in further 90.7% of patients a clear demonstration of the upper and lower points of venous insufficiency was possible. The extent of functional disorders was calculated by additional peripheral venous pressure measurements.

CONCLUSIONS

This clientele clearly shows that long-term reflux via the varicosed side branch increases the tendency of peripheral functional decompensation along the lower leg. Adequate surgical therapy depends from a clear demonstration of the varicosed veins being involved, and this can be realized by combined phlebography and varicography.