Thermodynamic modelling of synthetic communities predicts minimum free energy requirements for sulfate reduction and methanogenesis

Microbial communities are complex dynamical systems harbouring many species interacting together to implement higher-level functions. Among these higher-level functions, conversion of organic matter into simpler building blocks by microbial communities underpins biogeochemical cycles and animal and plant nutrition, and is exploited in biotechnology. A prerequisite to predicting the dynamics and stability of community-mediated metabolic conversions is the development and calibration of appropriate mathematical models. Here, we present a generic, extendable thermodynamic model for community dynamics and calibrate a key parameter of this thermodynamic model, the minimum energy requirement associated with growth-supporting metabolic pathways, using experimental population dynamics data from synthetic communities composed of a sulfate reducer and two methanogens. Our findings show that accounting for thermodynamics is necessary in capturing the experimental population dynamics of these synthetic communities that feature relevant species using low energy growth pathways. Furthermore, they provide the first estimates for minimum energy requirements of methanogenesis (in the range of −30 kJ mol−1) and elaborate on previous estimates of lactate fermentation by sulfate reducers (in the range of −30 to −17 kJ mol−1 depending on the culture conditions). The open-source nature of the developed model and demonstration of its use for estimating a key thermodynamic parameter should facilitate further thermodynamic modelling of microbial communities

Duplicate retention in signalling proteins and constraints from network dynamics

Both single-gene and whole-genome duplications (WGD) are well documented in various organisms (Brenner et al., 1995; Zhang, 2003; Vogel & Chothia, 2006), and it is estimated that single-gene duplication

Increasing sulfate levels show a differential impact on synthetic communities comprising different methanogens and a sulfate reducer

Methane producing microbial communities are of ecological and biotechnological interest. Syntrophic interactions among sulphate reducers and aceto/hydrogenotrophic and obligate hydrogenotrophic methanogens form a key component of these communities, yet, the impact of these different syntrophic routes on methane production and their stability against sulphate availability are not well understood. Here, we construct model synthetic communities using a sulphate reducer and two types of methanogens representing different methanogenesis routes. We find that tri-cultures with both routes increase methane production by almost two-fold compared to co-cultures, and are stable in the absence of sulphate. With increasing sulphate, system stability and productivity decreases, and does so faster in communities with aceto/hydrogenotrophic methanogens despite the continued presence of acetate. We show that this is due to a shift in these methanogens’ metabolism towards co-utilisation of hydrogen with acetate. These findings indicate the important role of hydrogen dynamics in the stability and productivity of syntrophic communities

Response dynamics of phosphorelays suggest their potential utility in cell signalling

Phosphorelays are extended two-component signalling systems found in diverse bacteria, lower eukaryotes and plants. Only few of these systems are characterized, and we still lack a full understanding of their signalling abilities. Here, we aim to achieve a global understanding of phosphorelay signalling and its dynamical properties. We develop a generic model, allowing us to systematically analyse response dynamics under different assumptions. Using this model, we find that the steady-state concentration of phosphorylated protein at the final layer of a phosphorelay is a linearly increasing, but eventually saturating function of the input. In contrast, the intermediate layers can display ultrasensitivity. We find that such ultrasensitivity is a direct result of the phosphorelay biochemistry; shuttling of a single phosphate group from the first to the last layer. The response dynamics of the phosphorelay results in tolerance of cross-talk, especially when it occurs as cross-deactivation. Further, it leads to a high signal-to-noise ratio for the final layer. We find that a relay length of four, which is most commonly observed, acts as a saturating point for these dynamic properties. These findings suggest that phosphorelays could act as a mechanism to reduce noise and effects of cross-talk on the final layer of the relay and enforce its input–response relation to be linear. In addition, our analysis suggests that middle layers of phosphorelays could embed thresholds. We discuss the consequence of these findings in relation to why cells might use phosphorelays along with enzymatic kinase cascades

Effects of nitrogen supply on must quality and anthocyanin accumulation in berries of cv. Merlot

Nitrogen supply to Merlot vines (Vitis vinifera L.), grown under controlled conditions, affected must quality and the anthocyanin content in berry skins irrespective of vegetative growth. High N supply delayed fruit maturation; berries had a higher arginine and a lower anthocyanin content with relatively more abundant acylated anthocyanins compared to berries of vines supplied with low N. During maturation the anthocyanin content in the skin of berries decreased; this was more significant in high-N vines. It is concluded that high nitrogen supply affects the metabolic pathway of anthocyanins in different ways, e.g. it delays the quantitative and qualitative biosynthesis and enhances their degradation during the final steps of berry maturation.

Consumer acceptance of patient-performed mobile teledermoscopy for the early detection of melanoma

Background Mobile teledermoscopy allows consumers to send images of skin lesions to a teledermatologist for remote diagnosis. Currently, technology acceptance of mobile teledermoscopy by people at high risk of melanoma is unknown. Objectives We aimed to determine the acceptance of mobile teledermoscopy by consumers based on perceived usefulness, ease of use, compatibility, attitude/intention, subjective norms, facilitators and trust before use. Consumer satisfaction was explored after use

What do Australian dermatologists expect to be paid for store-and-forward teledermoscopy? A preliminary investigation

Introduction: Determining appropriate remuneration for teledermoscopy service is important because inadequate remuneration can be a barrier to practitioner uptake and participation. This study explores dermatologist remuneration expectations for a single lesion store-and-forward teledermoscopy consultation. Methods: Fourteen dermatologists participated in telephone interviews during May–June 2017. Questions regarding remuneration focused on a clinical scenario involving teledermoscopy of a single lesion suspected to be skin cancer. The initial scenario was an existing patient, with a provisional diagnosis of benign neoplasm from the images, to be followed-up with routine skin checks, taking three minutes to review. Participants indicated their remuneration expectation by selecting from an ascending array of pre-determined remuneration ranges. The question was repeated a further four times with one aspect of the scenario changed each time; consultation length, source (patient or general practitioner), required follow-up, and a new rather than existing patient. Participants were also asked how appropriate they thought teledermoscopy was for the scenario, and whether they would choose to undertake the consultation presented. Results: Nine dermatologists selected the AU$61–90 or AU$91–120 remuneration ranges for the initial scenario. When given the opportunity to comment on teledermoscopy service provision in Australia, respondents reflected that it was a valuable, advanced dermatology service, but they would prefer face-to-face consultation with patients where possible to allow for a full body examination. Discussion: Dermatologists expect to be remunerated in the range of AU$61–120 for a single lesion store-and-forward teledermoscopy consultation when face-to-face examination is not possible

Challenges in microbial ecology: building predictive understanding of community function and dynamics

he importance of microbial communities (MCs) cannot be overstated. MCs underpin the biogeochemical cycles of the earth’s soil, oceans and the atmosphere, and perform ecosystem functions that impact plants, animals and humans. Yet our ability to predict and manage the function of these highly complex, dynamically changing communities is limited. Building predictive models that link MC composition to function is a key emerging challenge in microbial ecology. Here, we argue that addressing this challenge requires close coordination of experimental data collection and method development with mathematical model building. We discuss specific examples where model–experiment integration has already resulted in important insights into MC function and structure. We also highlight key research questions that still demand better integration of experiments and models. We argue that such integration is needed to achieve significant progress in our understanding of MC dynamics and function, and we make specific practical suggestions as to how this could be achieved