Spatial scaling of forest soil microbial communities across a temperature gradient.

Temperature is an important correlate of global patterns of biodiversity, yet the mechanisms driving these relationships are not well understood. Taxa-area relationships (TARs) have been intensively examined, but the effects of temperature on TARs, particularly for microbial communities, are largely undocumented. Here we present a continental-scale description of temperature-dependent nested TARs of microbial communities (bacteria and archaea) from soils of six forest sites spanning a temperature gradient from subalpine Colorado to tropical Panama. Our results revealed that spatial scaling rates (z-values) of microbial communities varied with both taxonomic resolutions and phylogenetic groups. Additionally, microbial TAR z-values increased with temperature (r = 0.739, P < 0.05), but were not correlated with other environmental variables tested (P > 0.05), indicating that microbial spatial scaling rate is temperature-dependent. Understanding how temperature affects the spatial scaling of microbial biodiversity is of fundamental importance for preservation of soil biodiversity and management of ecosystems

Effects of glucose and lactate on <em>Streptococcus </em><em>mutans </em>abundance in a novel multispecies oral biofilm model

The oral microbiome plays an important role in protecting oral health. Here, we established a controlled mixed-species in vitro biofilm model and used it to assess the impact of glucose and lactate on the ability of Streptococcus mutans, an acidogenic and aciduric species, to compete with commensal oral bacteria. A chemically defined medium was developed that supported the growth of S. mutans and four common early colonizers of dental plaque: Streptococcus gordonii, Actinomyces oris, Neisseria subflava, and Veillonella parvula. Biofilms containing the early colonizers were developed in a continuous flow bioreactor, exposed to S. mutans, and incubated for up to 7 days. The abundance of bacteria was estimated by quantitative polymerase chain reaction (qPCR). At high glucose and high lactate, the pH in bulk fluid rapidly decreased to approximately 5.2, and S. mutans outgrew other species in biofilms. In low glucose and high lactate, the pH remained above 5.5, and V. parvula was the most abundant species in biofilms. By contrast, in low glucose and low lactate, the pH remained above 6.0 throughout the experiment, and the microbial community in biofilms was relatively balanced. Fluorescence in situ hybridization confirmed that all species were present in the biofilm and the majority of cells were viable using live/dead staining. These data demonstrate that carbon source concentration is critical for microbial homeostasis in model oral biofilms. Furthermore, we established an experimental system that can support the development of computational models to predict transitions to microbial dysbiosis based on metabolic interactions. 38376204</strong

Advancing dental biofilm models: the integral role of pH in predicting S. mutans colonization

Mathematical models can provide insights into complex interactions and dynamics within microbial communities to complement and extend experimental laboratory approaches. For dental biofilms, they can give a basis for evaluating biofilm growth or the transition from health to disease. We have developed mathematical models to simulate the transition toward a cariogenic microbial biofilm, modeled as the overgrowth of Streptococcus mutans within a five-species dental community. This work builds on experimental data from a continuous flow reactor with hydroxyapatite coupons for biofilm growth, in a chemically defined medium with varying concentrations of glucose and lactic acid. The biofilms formed on the coupons were simulated using individual-based models (IbMs), with bacterial growth modeled using experimentally measured kinetic parameters. The IbM assumes that the maximum theoretical growth yield for biomass is dependent on the local concentration of reactants and products, while the growth rates were described using traditional Monod equations. We have simulated all the conditions studied experimentally, considering different initial relative abundance of the five species, and also different initial clustering in the biofilm. The simulation results only reproduced the experimental dominance of S. mutans at high glucose concentration after we considered the species-specific effect of pH on growth rates. This highlights the significance of the aciduric property of S. mutans in the development of caries. Our study demonstrates the potential of combining in vitro and in silico studies to gain a new understanding of the factors that influence dental biofilm dynamics

Hypolithic and soil microbial community assembly along an aridity gradient in the Namib Desert

The Namib Dessert is considered the oldest desert in the world and hyperarid for the last 5 million years. However, the environmental buffering provided by quartz and other translucent rocks supports extensive hypolithic microbial communities. In this study, open soil and hypolithic microbial communities have been investigated along an East–West transect characterized by an inverse fog-rainfall gradient. Multivariate analysis showed that structurally different microbial communities occur in soil and in hypolithic zones. Using variation partitioning, we found that hypolithic communities exhibited a fog-related distribution as indicated by the significant East– West clustering. Sodium content was also an important environmental factor affecting the composition of both soil and hypolithic microbial communities. Finally, although null models for patterns in microbial communities were not supported by experimental data, the amount of unexplained variation (68–97 %) suggests that stochastic processes also play a role in the assembly of such communities in the Namib Desert.Web of Scienc

Individual based model links thermodynamics, chemical speciation and environmental conditions to microbial growth

Individual based Models (IbM) must transition from research tools to engineering tools. To make the transition we must aspire to develop large, three dimensional and physically and biologically credible models. Biological credibility can be promoted by grounding, as far as possible, the biology in thermodynamics. Thermodynamic principles are known to have predictive power in microbial ecology. However, this in turn requires a model that incorporates pH and chemical speciation. Physical credibility implies plausible mechanics and a connection with the wider environment. Here, we propose a step toward that ideal by presenting an individual based model connecting thermodynamics, pH and chemical speciation and environmental conditions to microbial growth for 5·105 individuals. We have showcased the model in two scenarios: a two functional group nitrification model and a three functional group anaerobic community. In the former, pH and connection to the environment had an important effect on the outcomes simulated. Whilst in the latter pH was less important but the spatial arrangements and community productivity (that is, methane production) were highly dependent on thermodynamic and reactor coupling. We conclude that if IbM are to attain their potential as tools to evaluate the emergent properties of engineered biological systems it will be necessary to combine the chemical, physical, mechanical and biological along the lines we have proposed. We have still fallen short of our ideals because we cannot (yet) calculate specific uptake rates and must develop the capacity for longer runs in larger models. However, we believe such advances are attainable. Ideally in a common, fast and modular platform. For future innovations in IbM will only be of use if they can be coupled with all the previous advances

Capturing Multicellular System Designs Using Synthetic Biology Open Language (SBOL)

8 Pág.Synthetic biology aims to develop novel biological systems and increase their reproducibility using engineering principles such as standardization and modularization. It is important that these systems can be represented and shared in a standard way to ensure they can be easily understood, reproduced, and utilized by other researchers. The Synthetic Biology Open Language (SBOL) is a data standard for sharing biological designs and information about their implementation and characterization. Previously, this standard has only been used to represent designs in systems where the same design is implemented in every cell; however, there is also much interest in multicellular systems, in which designs involve a mixture of different types of cells with differing genotype and phenotype. Here, we show how the SBOL standard can be used to represent multicellular systems, and, hence, how researchers can better share designs with the community and reliably document intended system functionality.This work was supported in part by NSF Expeditions in Computing Program Award No. 1522074 as part of the Living Computing Project and by the Defense Advanced Research Projects Agency under Contract No. W911NF-17-2-0098. The views, opinions, and/or findings expressed are of the author(s) and should not be interpreted as representing official views or policies of the Department of Defense or the U.S. Government. A.G.-M. was supported by the SynBio3D project of the UK Engineering and Physical Sciences Research Council (No.EP/R019002/1) and the European CSA on biological standardization BIOROBOOST (EU Grant No. 820699)Peer reviewe

Diversity and metabolic energy in bacteria

Why are some groups of bacteria more diverse than others? We hypothesise that the metabolic energy available to a bacterial functional group (a biogeochemical group or ‘guild’) has a role in such a group's taxonomic diversity. We tested this hypothesis by looking at the metacommunity diversity of functional groups in multiple biomes. We observed a positive correlation between estimates of a functional group's diversity and their metabolic energy yield. Moreover, the slope of that relationship was similar in all biomes. These findings could imply the existence of a universal mechanism controlling the diversity of all functional groups in all biomes in the same way. We consider a variety of possible explanations from the classical (environmental variation) to the ‘non-Darwinian’ (a drift barrier effect). Unfortunately, these explanations are not mutually exclusive, and a deeper understanding of the ultimate cause(s) of bacterial diversity will require us to determine if, and how, the key parameters in population genetics (effective population size, mutation rate and selective gradients) vary between functional groups and with environmental conditions: this is a difficult task

SynBioHub: A Standards-Enabled Design Repository for Synthetic Biology.

The SynBioHub repository (synbiohub.org) is an open-source software project which facilitates the sharing of information about engineered biological systems. SynBioHub provides computational access for software and data integration, and a graphical user interface that enables users to search for and share designs in a Web browser. By connecting to relevant repositories (e.g. the iGEM repository, JBEI ICE, and other instances of SynBioHub), the software allows users to browse, upload, and download data in various standard formats, regardless of their location or representation. SynBioHub also provides a central reference point for other resources to link to, delivering design information in a standardized format using the Synthetic Biology Open Language (SBOL). The adoption and use of SynBioHub, a community-driven effort, has the potential to overcome the reproducibility challenge across laboratories by helping to address the current lack of information about published designs

Evaluation of the Benefit of Ropeginterferon Treatment in Patients with Polycythemia Vera

Results: Twenty-three patients (15 men and 8 women) with a median age of 57 years were enrolled, with 87.5% having the JAK617F mutation. Six patients had a history of thrombosis. Besremi was used as a first-line treatment in 11 patients and as a second-line treatment in 12 patients after Hydroxyurea administration. Complete hematologic response, defined by normalized blood counts and symptom resolution, was achieved in 3.46 ± 2.53 months in more than 50% of patients. One patient discontinued treatment, two did not achieve complete response, and four had less than 3 months of follow-up. After 6 months, the mean hematocrit was 44.17 ± 7.76 (p = 0.01), WBC 7.6 ± 3.92 x 1000/mmc (p = 0.02), and thrombocytosis significantly decreased in the first month (p = 0.02). Conclusions: Ropeginterferon treatment improved the quality of life for all patients, eliminating symptoms of cardiovascular and thrombotic complications. Approximately 60% of patients achieved complete hematologic response within the first 3 months