Signatures of arithmetic simplicity in metabolic network architecture

Metabolic networks perform some of the most fundamental functions in living cells, including energy transduction and building block biosynthesis. While these are the best characterized networks in living systems, understanding their evolutionary history and complex wiring constitutes one of the most fascinating open questions in biology, intimately related to the enigma of life's origin itself. Is the evolution of metabolism subject to general principles, beyond the unpredictable accumulation of multiple historical accidents? Here we search for such principles by applying to an artificial chemical universe some of the methodologies developed for the study of genome scale models of cellular metabolism. In particular, we use metabolic flux constraint-based models to exhaustively search for artificial chemistry pathways that can optimally perform an array of elementary metabolic functions. Despite the simplicity of the model employed, we find that the ensuing pathways display a surprisingly rich set of properties, including the existence of autocatalytic cycles and hierarchical modules, the appearance of universally preferable metabolites and reactions, and a logarithmic trend of pathway length as a function of input/output molecule size. Some of these properties can be derived analytically, borrowing methods previously used in cryptography. In addition, by mapping biochemical networks onto a simplified carbon atom reaction backbone, we find that several of the properties predicted by the artificial chemistry model hold for real metabolic networks. These findings suggest that optimality principles and arithmetic simplicity might lie beneath some aspects of biochemical complexity

A stochastic model of Escherichia coli AI-2 quorum signal circuit reveals alternative synthesis pathways

Quorum sensing (QS) is an important determinant of bacterial phenotype. Many cell functions are regulated by intricate and multimodal QS signal transduction processes. The LuxS/AI-2 QS system is highly conserved among Eubacteria and AI-2 is reported as a ‘universal' signal molecule. To understand the hierarchical organization of AI-2 circuitry, a comprehensive approach incorporating stochastic simulations was developed. We investigated the synthesis, uptake, and regulation of AI-2, developed testable hypotheses, and made several discoveries: (1) the mRNA transcript and protein levels of AI-2 synthases, Pfs and LuxS, do not contribute to the dramatically increased level of AI-2 found when cells are grown in the presence of glucose; (2) a concomitant increase in metabolic flux through this synthesis pathway in the presence of glucose only partially accounts for this difference. We predict that ‘high-flux' alternative pathways or additional biological steps are involved in AI-2 synthesis; and (3) experimental results validate this hypothesis. This work demonstrates the utility of linking cell physiology with systems-based stochastic models that can be assembled de novo with partial knowledge of biochemical pathways

Bacterial Communities in the Sediments of Dianchi Lake, a Partitioned Eutrophic Waterbody in China

Bacteria play an important role in the decomposition and cycling of a variety of compounds in freshwater aquatic environments, particularly nutrient-rich eutrophic lakes. A unique Chinese eutrophic lake - Dianchi - was selected for study because it has two separate and distinct basins, Caohai with higher organic carbon levels and Waihai with lower organic carbon levels. Sediment bacterial communities were studied in the two basins using samples collected in each season from June 2010 to March 2011. Barcoded pyrosequencing based on the 16 S rRNA gene found that certain common phyla, Proteobacteria, Bacteroidetes, Firmicutes and Chloroflexi, were dominant in the sediments from both basins. However, from the class to genus level, the dominant bacterial groups found in the sediments were distinct between the two basins. Correlation analysis revealed that, among the environmental parameters examined, total organic carbon (TOC) accounted for the greatest proportion of variability in bacterial community. Interestingly, study results suggest that increasing allochthonous organic carbon could enhance bacterial diversity and biomass in the sediment. In addition, analysis of function genes (amoA and nosZ) demonstrated that ammonia-oxidizing bacteria (AOB) were dominant in sediments, with 99% belonging to Nitrosomonas. Denitrifying bacteria were comparatively diverse and were associated with some cultivatable bacteria

Microbial Fuel Cells and Microbial Ecology: Applications in Ruminant Health and Production Research

Microbial fuel cell (MFC) systems employ the catalytic activity of microbes to produce electricity from the oxidation of organic, and in some cases inorganic, substrates. MFC systems have been primarily explored for their use in bioremediation and bioenergy applications; however, these systems also offer a unique strategy for the cultivation of synergistic microbial communities. It has been hypothesized that the mechanism(s) of microbial electron transfer that enable electricity production in MFCs may be a cooperative strategy within mixed microbial consortia that is associated with, or is an alternative to, interspecies hydrogen (H2) transfer. Microbial fermentation processes and methanogenesis in ruminant animals are highly dependent on the consumption and production of H2in the rumen. Given the crucial role that H2 plays in ruminant digestion, it is desirable to understand the microbial relationships that control H2 partial pressures within the rumen; MFCs may serve as unique tools for studying this complex ecological system. Further, MFC systems offer a novel approach to studying biofilms that form under different redox conditions and may be applied to achieve a greater understanding of how microbial biofilms impact animal health. Here, we present a brief summary of the efforts made towards understanding rumen microbial ecology, microbial biofilms related to animal health, and how MFCs may be further applied in ruminant research

Metal Oxide Surfaces and Their Interactions with Aqueous Solutions and Microbial Organisms

During the past decade, interest in chemical reactions occurring at metal oxide-aqueous solution interfaces has increased significantly because of their importance in a variety of fields, including atmospheric chemistry, heterogeneous catalysis and photocatalysis, chemical sensing, corrosion science, environmental chemistry and geochemistry, metallurgy and ore beneficiation, metal oxide crystal growth, soil science, semiconductor manufacturing and cleaning, and tribology. The metal oxide-aqueous solution interface is reactive due to acid-base, ligand-exchange, and/or redox chemistry involving protons (hydronium ions), hydroxyl groups, aqueous metal ions, and aqueous organic species and also complexes among these species. Interfacial localization of those species (adsorption) may result from electrostatic, chemical complexation, and hydrophobic interactions chemistry and geochemistry. Indeed, hydrous oxides of Al, Fe, Mn, and aluminosilicates such as clays are ubiquitous in the natural environment, and their surface chemical properties control such important phenomena as nutrient and contaminant element release and uptake, pH buffering, water quality, and soil rheological properties. These surfaces function as templates for the growth of other solid phases and as a matrix for microflora. Polyvalent metal ions [e.g., Fe(III) and Mn(IV)] in the metal (hydr)oxide-aqueous solution interfacial region serve as terminal electron acceptors in the respiratory cycle of microorganisms common to soil, aquatic and marine sediments, and groundwater, a process of central importance to the global biogeochemical cycling of C, N, P, and other elements. Given the importance of metal oxide surfaces in these processes, surprisingly little is known about their atomic-scale structure and chemical reactivity, particularly in aqueous environments

Label-Free Bacterial Imaging with Deep-UV-Laser-Induced Native Fluorescence ▿ †

We introduce a near-real-time optical imaging method that works via the detection of the intrinsic fluorescence of life forms upon excitation by deep-UV (DUV) illumination. A DUV (<250-nm) source enables the detection of microbes in their native state on natural materials, avoiding background autofluorescence and without the need for fluorescent dyes or tags. We demonstrate that DUV-laser-induced native fluorescence can detect bacteria on opaque surfaces at spatial scales ranging from tens of centimeters to micrometers and from communities to single cells. Given exposure times of 100 μs and low excitation intensities, this technique enables rapid imaging of bacterial communities and cells without irreversible sample alteration or destruction. We also demonstrate the first noninvasive detection of bacteria on in situ-incubated environmental experimental samples from the deep ocean (Lo'ihi Seamount), showing the use of DUV native fluorescence for in situ detection in the deep biosphere and other nutrient-limited environments

Redox sensing within the genus Shewanella

A novel bacterial behavior called congregation was recently described in Shewanella oneidensis MR-1 as the accumulation of cells around insoluble electron acceptors (IEA). It is the result of a series of "run-and-reversal" events enabled by modulation of swimming speed and direction. The model proposed that the swimming cells constantly sense their surroundings with specialized outer membrane cytochromes capable of extracellular electron transport (EET). Up to this point, neither the congregation nor attachment behavior have been studied in any other strains. In this study, the wild type of S. oneidensis MR-1 and several deletion mutants as well as eight other Shewanella strains (Shewanella putrefaciens CN32, S. sp. ANA-3, S. sp. W3-18-1, Shewanella amazonensis SB2B, Shewanella loihica PV-4, Shewanella denitrificans OS217, Shewanella baltica OS155, and Shewanella frigidimarina NCIMB400) were screened for the ability to congregate. To monitor congregation and attachment, specialized cell-tracking techniques, as well as a novel cell accumulation after photo-bleaching (CAAP) confocal microscopy technique were utilized in this study. We found a strong correlation between the ability of strain MR-1 to accumulate on mineral surface and the presence of key EET genes such as mtrBC/omcA (SO_1778, SO_1776, and SO_1779) and gene coding for methyl-accepting protein (MCPs) with Ca+ channel chemotaxis receptor (Cache) domain (SO_2240). These EET and taxis genes were previously identified as essential for characteristic run and reversal swimming around IEA surfaces. CN32, ANA-3, and PV-4 congregated around both Fe(OH)3 and MnO2. Two other Shewanella spp. showed preferences for one oxide over the other: preferences that correlated with the metal content of the environments from which the strains were isolated: e.g., W3-18-1, which was isolated from an iron-rich habitat congregated and attached preferentially to Fe(OH)3, while SB2B, which was isolated from a MnO2-rich environment, preferred MnO2