Microbial functional diversity: From concepts to applications

Functional diversity is increasingly recognized by microbial ecologists as the essential link between biodiversity patterns and ecosystem functioning, determining the trophic relationships and interactions between microorganisms, their participation in biogeochemical cycles, and their responses to environmental changes. Consequently, its definition and quantification have practical and theoretical implications. In this opinion paper, we present a synthesis on the concept of microbial functional diversity from its definition to its application. Initially, we revisit to the original definition of functional diversity, highlighting two fundamental aspects, the ecological unit under study and the functional traits used to characterize it. Then, we discuss how the particularities of the microbial world disallow the direct application of the concepts and tools developed for macroorganisms. Next, we provide a synthesis of the literature on the types of ecological units and functional traits available in microbial functional ecology. We also provide a list of more than 400 traits covering a wide array of environmentally relevant functions. Lastly, we provide examples of the use of functional diversity in microbial systems based on the different units and traits discussed herein. It is our hope that this paper will stimulate discussions and help the growing field of microbial functional ecology to realize a potential that thus far has only been attained in macrobial ecology.     

Microbial production of cyanophycin: From enzymes to biopolymers

Cyanophycin is an attractive biopolymer with chemical and material properties that are suitable for industrial applications in the fields of food, medicine, cosmetics, nutrition, and agriculture. For efficient production of cyanophycin, considerable efforts have been exerted to characterize cyanophycin synthetases (CphAs) and optimize fermentations and downstream processes. In this paper, we review the characteristics of diverse CphAs from cyanobacteria and non-cyanobacteria. Furthermore, strategies for cyanophycin production in microbial strains, including Escherichia coli, Pseudomonas putida, Ralstonia eutropha, Rhizopus oryzae, and Saccharomyces cerevisiae, heterologously expressing different cphA genes are reviewed. Additionally, chemical and material properties of cyanophycin and its derivatives produced through biological or chemical modifications are reviewed in the context of their industrial applications. Finally, future perspectives on microbial production of cyanophycin are provided to improve its cost-effectiveness.     

Growth Kinetics of Yaba Tumor Poxvirus After In Vitro Adaptation to Cercopithecus Kidney Cells

Yaba tumor poxvirus has been adapted to continuous in vitro cultivation in monolayers of cercopithecus kidney cells. At 35 C, the minimum replicative cycle, after synchronous infection of CV-1 cells with multiplicity of infection of 135 focusforming units per cell, was 35 hr; however, maximum virus yields were not obtained until 75 hr postinfection (PI). Cytoplasmic incorporation of (3)H-thymidine [viral deoxyribonucleic acid (DNA) synthesis] was detected 3 hr PI and was preceded by synthesis of nonstructural associated antigens (YS). Synthesis of YS antigens was not inhibited by the DNA inhibitor, arabinofuranosyl cytosine (ARA-C). Synthesis of at least two virion structural antigens, although not detected by immunofluorescence until 2 hr after the onset of DNA synthesis, occurred in the presence of ARA-C, indicating potential translation of these structural antigens from parental DNA. The first progeny DNA was completed by 20 hr PI but was not detected in infectious form until 35 hr PI. The maximum rate of progeny DNA completion occurred between 20 and 30 hr PI. DNA synthesis continued 45 to 50 hr PI. The adapted virus retained its oncogenicity and, like the wild type, replicated better at 35 C than at 37 C. A synthetic step associated with viral DNA synthesis appears to be temperature-sensitive.     

Substrate Degradation Kinetics, Microbial Diversity, and Current Efficiency of Microbial Fuel Cells Supplied with Marine Plankton

The decomposition of marine plankton in two-chamber, seawater-filled microbial fuel cells (MFCs) has been investigated and related to resulting chemical changes, electrode potentials, current efficiencies, and microbial diversity. Six experiments were run at various discharge potentials, and a seventh served as an open-circuit control. The plankton consisted of a mixture of freshly captured phytoplankton and zooplankton (0.21 to 1 mm) added at an initial batch concentration of 27.5 mmol liter⁻¹ particulate organic carbon (OC). After 56.7 days, between 19.6 and 22.2% of the initial OC remained, sulfate reduction coupled to OC oxidation accounted for the majority of the OC that was degraded, and current efficiencies (of the active MFCs) were between 11.3 and 15.5%. In the open-circuit control cell, anaerobic plankton decomposition (as quantified by the decrease in total OC) could be modeled by three terms: two first-order reaction rate expressions (0.79 day⁻¹ and 0.037 day⁻¹, at 15°C) and one constant, no-reaction term (representing 10.6% of the initial OC). However, in each active MFC, decomposition rates increased during the third week, lagging just behind periods of peak electricity generation. We interpret these decomposition rate changes to have been due primarily to the metabolic activity of sulfur-reducing microorganisms at the anode, a finding consistent with the electrochemical oxidization of sulfide to elemental sulfur and the elimination of inhibitory effects of dissolved sulfide. Representative phylotypes, found to be associated with anodes, were allied with Delta-, Epsilon-, and Gammaproteobacteria as well as the Flavobacterium-Cytophaga-Bacteroides and Fusobacteria. Based upon these results, we posit that higher current efficiencies can be achieved by optimizing plankton-fed MFCs for direct electron transfer from organic matter to electrodes, including microbial precolonization of high-surface-area electrodes and pulsed flowthrough additions of biomass.     

Growth of Mouse L Cells in Shaken Culture and Mengovirus Plaque Formation on L Cells Suspended in Agar

Procedures are described that require a minimum of equipment and maintenance for growing mouse L cells suspended in liquid medium and for plaquing mengovirus on L cells suspended in agar. Viability of L cells during storage for 1 to 2 hr at relatively high concentrations was better in media at 30 C than at 0 C, as measured by viable counts after growth for 24 hr at 35 C. The number and size of plaques increased with increasing concentration of NaHCO(3) in the agar layers, but the relative difference in plaque size was maintained. Large- and small-plaque-size variants had similar virulence as determined by the rates of viability loss of L cells in liquid suspension cultures.     

Kinetics of Growth of Individual Cells of Escherichia coli and Azotobacter agilis

Escherichia coli and Azotobacter agilis were grown in minimal media until a steady state was established. The distribution of cell size was determined electronically. From the equation of Collins and Richmond, the growth rate of individual cells was computed as a function of size. The main features of the growth of individual E. coli and A. agilis cells revealed by this work were: the specific growth rate decreased at the time of division, and both the absolute and specific growth rates increased between divisions. The frequency function of interdivision times was computed and was found to be positively skewed with a coefficient of variation of approximately 0.3. The results supported the hypothesis of Koch and Schaechter that the size of an individual cell at division is highly regulated.     

Mechanical Fluidity of Fully Suspended Biological Cells

Mechanical characteristics of single biological cells are used to identify and possibly leverage interesting differences among cells or cell populations. Fluidity—hysteresivity normalized to the extremes of an elastic solid or a viscous liquid—can be extracted from, and compared among, multiple rheological measurements of cells: creep compliance versus time, complex modulus versus frequency, and phase lag versus frequency. With multiple strategies available for acquisition of this nondimensional property, fluidity may serve as a useful and robust parameter for distinguishing cell populations, and for understanding the physical origins of deformability in soft matter. Here, for three disparate eukaryotic cell types deformed in the suspended state via optical stretching, we examine the dependence of fluidity on chemical and environmental influences at a timescale of ∼1 s. We find that fluidity estimates are consistent in the time and frequency domains under a structural damping (power-law or fractional-derivative) model, but not under an equivalent-complexity, lumped-component (spring-dashpot) model; the latter predicts spurious time constants. Although fluidity is suppressed by chemical cross-linking, we find that ATP depletion in the cell does not measurably alter the parameter, and we thus conclude that active ATP-driven events are not a crucial enabler of fluidity during linear viscoelastic deformation of a suspended cell. Finally, by using the capacity of optical stretching to produce near-instantaneous increases in cell temperature, we establish that fluidity increases with temperature—now measured in a fully suspended, sortable cell without the complicating factor of cell-substratum adhesion.     

Mechanical Fluidity of Fully Suspended Biological Cells

Mechanical characteristics of single biological cells are used to identify and possibly leverage interesting differences among cells or cell populations. Fluidity—hysteresivity normalized to the extremes of an elastic solid or a viscous liquid—can be extracted from, and compared among, multiple rheological measurements of cells: creep compliance versus time, complex modulus versus frequency, and phase lag versus frequency. With multiple strategies available for acquisition of this nondimensional property, fluidity may serve as a useful and robust parameter for distinguishing cell populations, and for understanding the physical origins of deformability in soft matter. Here, for three disparate eukaryotic cell types deformed in the suspended state via optical stretching, we examine the dependence of fluidity on chemical and environmental influences at a timescale of ∼1 s. We find that fluidity estimates are consistent in the time and frequency domains under a structural damping (power-law or fractional-derivative) model, but not under an equivalent-complexity, lumped-component (spring-dashpot) model; the latter predicts spurious time constants. Although fluidity is suppressed by chemical cross-linking, we find that ATP depletion in the cell does not measurably alter the parameter, and we thus conclude that active ATP-driven events are not a crucial enabler of fluidity during linear viscoelastic deformation of a suspended cell. Finally, by using the capacity of optical stretching to produce near-instantaneous increases in cell temperature, we establish that fluidity increases with temperature—now measured in a fully suspended, sortable cell without the complicating factor of cell-substratum adhesion.     

Single-Molecule Light-Sheet Imaging of Suspended T Cells

Adaptive immune responses are initiated by triggering of the T cell receptor. Single-molecule imaging based on total internal reflection fluorescence microscopy at coverslip/basal cell interfaces is commonly used to study this process. These experiments have suggested, unexpectedly, that the diffusional behavior and organization of signaling proteins and receptors may be constrained before activation. However, it is unclear to what extent the molecular behavior and cell state is affected by the imaging conditions, i.e., by the presence of a supporting surface. In this study, we implemented single-molecule light-sheet microscopy, which enables single receptors to be directly visualized at any plane in a cell to study protein dynamics and organization in live, resting T cells. The light sheet enabled the acquisition of high-quality single-molecule fluorescence images that were comparable to those of total internal reflection fluorescence microscopy. By comparing the apical and basal surfaces of surface-contacting T cells using single-molecule light-sheet microscopy, we found that most coated-glass surfaces and supported lipid bilayers profoundly affected the diffusion of membrane proteins (T cell receptor and CD45) and that all the surfaces induced calcium influx to various degrees. Our results suggest that, when studying resting T cells, surfaces are best avoided, which we achieve here by suspending cells in agarose.     

Branching Morphogenesis: From Cells to Organs and Back

Many animal organs, such as the lung, the kidney, the mammary gland, and the vasculature, consist of branched tubular structures that arise through a process known as “branching morphogenesis” that results from the remodeling of epithelial or endothelial sheaths into multicellular tubular networks. In recent years, the combination of molecular biology, forward and reverse genetic approaches, and their complementation by live imaging has started to unravel rules and mechanisms controlling branching processes in animals. Common patterns of branch formation spanning diverse model systems are beginning to emerge that might reflect unifying principles of tubular organ formation.     

生物学因子对紫苏悬浮培养细胞生长和花色素形成的影响

应用摇瓶培养研究了生物学因子,即：细胞聚集体大小、继代周期和接种量,对紫苏悬浮细胞生长和次生代谢物花色素产生的影响。结果表明：与未经筛选的或细胞聚集体小于250μm的细胞团块相比,大于250μm的细胞团块作为接种细胞时,培养所得的花色素含量较低。7一10天为合适的继代周期,在长时期的继代过程中,细胞生长良好、并且色素含量也高。实验还表明,每升接种50克湿细胞最适合于细胞增殖与色素积累。     

Kin Discrimination in Protists: From Many Cells to Single Cells and Backwards

During four decades (1960–1990s), the conceptualization and experimental design of studies in kin recognition relied on work with multicellular eukaryotes, particularly Unikonta (including invertebrates and vertebrates) and some Bikonta (including plants). This pioneering research had an animal behavior approach. During the 2000s, work on taxa‐, clone‐ and kin‐discrimination and recognition in protists produced genetic and molecular evidence that unicellular organisms (e.g. Saccharomyces, Dictyostelium, Polysphondylium, Tetrahymena, Entamoeba and Plasmodium) could distinguish between same (self or clone) and different (diverse clones), as well as among conspecifics of close or distant genetic relatedness. Here, we discuss some of the research on the genetics of kin discrimination/recognition and highlight the scientific progress made by switching emphasis from investigating multicellular to unicellular systems (and backwards). We document how studies with protists are helping us to understand the microscopic, cellular origins and evolution of the mechanisms of kin discrimination/recognition and their significance for the advent of multicellularity. We emphasize that because protists are among the most ancient organisms on Earth, belong to multiple taxonomic groups and occupy all environments, they can be central to reexamining traditional hypotheses in the field of kin recognition, reformulating concepts, and generating new knowledge.     

Effects of Above-Optimum Growth Temperature and Cell Morphology on Thermotolerance of Listeria monocytogenes Cells Suspended in Bovine Milk

The thermotolerances of two different cell forms of Listeria monocytogenes (serotype 4b) grown at 37 and 42.8°C in commercially pasteurized and laboratory-tyndallized whole milk (WM) were investigated. Test strains, after growth at 37 or 42.8°C, were suspended in WM at concentrations of approximately 1.5 × 10⁸ to 3.0 × 10⁸ cells/ml and were then heated at 56, 60, and 63°C for various exposure times. Survival was determined by enumeration on tryptone-soya-yeast extract agar and Listeria selective agar, and D values (decimal reduction times) and Z values (numbers of degrees Celsius required to cause a 10-fold change in the D value) were calculated. Higher average recovery and higher D values (i.e., seen as a 2.5- to 3-fold increase in thermotolerance) were obtained when cells were grown at 42.8°C prior to heat treatment. A relationship was observed between thermotolerance and cell morphology of L. monocytogenes. Atypical Listeria cell types (consisting predominantly of long cell chains measuring up to 60 μm in length) associated with rough (R) culture variants were shown to be 1.2-fold more thermotolerant than the typical dispersed cell form associated with normal smooth (S) cultures (P ≤ 0.001). The thermal death-time (TDT) curves of R-cell forms contained a tail section in addition to the shoulder section characteristic of TDT curves of normal single to paired cells (i.e., S form). The factors shown to influence the thermoresistance of suspended Listeria cells (P ≤ 0.001) were as follows: growth and heating temperatures, type of plating medium, recovery method, and cell morphology. Regression analysis of nonlinear data can underestimate survival of L. monocytogenes; the end point recovery method was shown to be a better method for determining thermotolerance because it takes both shoulders and tails into consideration. Despite their enhanced heat resistance, atypical R-cell forms of L. monocytogenes were unable to survive the low-temperature, long-time pasteurization process when freely suspended and heated in WM.     

From Atoms to Cells: Using Mesoscale Landscapes to Construct Visual Narratives

Modeling and visualization of the cellular mesoscale, bridging the nanometer scale of molecules to the micrometer scale of cells, is being studied by an integrative approach. Data from structural biology, proteomics, and microscopy are combined to simulate the molecular structure of living cells. These cellular landscapes are used as research tools for hypothesis generation and testing, and to present visual narratives of the cellular context of molecular biology for dissemination, education, and outreach.     

红豆杉悬浮细胞放大培养的细胞生长与紫杉醇合成动力学

研究了在Murashige&skoog s(MS)和 6 2号两种不同的培养基中 ,红豆杉细胞悬浮细胞从摇瓶到 1 0L机械通气搅拌式反应器放大培养过程中细胞生长与紫杉醇合成动力学 .结果表明 :尽管在不同的培养条件下 ,细胞生长曲线均呈现“S”型 .紫杉醇在延迟期与指数生长期中基本上没有积累 ,而且随着培养规模的增大 ,紫杉醇的含量逐渐降低 .进一步对各级放大培养的细胞生长 ,比生长率与胞内外紫杉醇合成量进行分析 ,发现MS利于细胞生长但不利于紫杉醇合成 ,而 6 2号则相反 .根据此文的结果 ,提出了红豆杉细胞培养条件的优化和大规模细胞培养生产紫杉醇应采取的策略     

Microbial production of small medicinal molecules and biologics: From nature to synthetic pathways

Natural products are promising chemicals due to their structural diversity and bioactivities. Over the decades, a vast variety of gene clusters encoding natural products have been identified and overexpressed in microbes. Recently, the development of metabolic engineering, synthetic biology and bioinformatics strategies have facilitated target discovery and design. Microbial cells have been therefore constantly engineered for product accumulation. This review summarizes approaches of domesticating microbial hosts in producing major classes of natural products, with an emphasis on recent advances.