Fewer invited talks by women in evolutionary biology symposia.

Lower visibility of female scientists, compared to male scientists, is a potential reason for the under-representation of women among senior academic ranks. Visibility in the scientific community stems partly from presenting research as an invited speaker at organized meetings. We analysed the sex ratio of presenters at the European Society for Evolutionary Biology (ESEB) Congress 2011, where all abstract submissions were accepted for presentation. Women were under-represented among invited speakers at symposia (15% women) compared to all presenters (46%), regular oral presenters (41%) and plenary speakers (25%). At the ESEB congresses in 2001-2011, 9-23% of invited speakers were women. This under-representation of women is partly attributable to a larger proportion of women, than men, declining invitations: in 2011, 50% of women declined an invitation to speak compared to 26% of men. We expect invited speakers to be scientists from top ranked institutions or authors of recent papers in high-impact journals. Considering all invited speakers (including declined invitations), 23% were women. This was lower than the baseline sex ratios of early-mid career stage scientists, but was similar to senior scientists and authors that have published in high-impact journals. High-quality science by women therefore has low exposure at international meetings, which will constrain Evolutionary Biology from reaching its full potential. We wish to highlight the wider implications of turning down invitations to speak, and encourage conference organizers to implement steps to increase acceptance rates of invited talks.

Bacterial community structure, compartmentalization and activity in a microbial fuel cell.

AIMS: To characterize bacterial populations and their activities within a microbial fuel cell (MFC), using cultivation-independent and cultivation approaches. METHODS AND RESULTS: Electron microscopic observations showed that the fuel cell electrode had a microbial biofilm attached to its surface with loosely associated microbial clumps. Bacterial 16S rRNA gene libraries were constructed and analysed from each of four compartments within the fuel cell: the planktonic community; the membrane biofilm; bacterial clumps (BC) and the anode biofilm. Results showed that the bacterial community structure varied significantly between these compartments. It was observed that Gammaproteobacteria phylotypes were present at higher numbers within libraries from the BC and electrode biofilm compared with other parts of the fuel cell. Community structure of the MFC determined by analyses of bacterial 16S rRNA gene libraries and anaerobic cultivation showed excellent agreement with community profiles from denaturing gradient gel electrophoresis (DGGE) analysis. CONCLUSIONS: Members of the family Enterobacteriaceae, such as Klebsiella sp. and Enterobacter sp. and other Gammaproteobacteria with Fe(III)-reducing and electrochemical activity had a significant potential for energy generation in this system. SIGNIFICANCE AND IMPACT OF THE STUDY: This study has shown that electrochemically active bacteria can be enriched using an electrochemical fuel cell.

Dissimilatory Fe(III) reduction by an electrochemically active lactic acid bacterium phylogenetically related to Enterococcus gallinarum isolated from submerged soil.

AIMS: The isolation and identification of a glucose-oxidizing Fe(III)-reducing bacteria (FRB) with electrochemical activity from an anoxic environment, and characterization of the role of Fe(III) in its metabolism. METHODS AND RESULTS: A Gram-positive (Firmicutes), nonmotile, coccoid and facultative anaerobic FRB was isolated based on its ability to reduce Fe(III). Using the Vitek Gram-positive identification card kit and 16S rRNA gene sequence analysis, the isolate was identified as Enterococcus gallinarum, designated strain MG25. On glucose this isolate produced lactate plus small amounts of acetate, formate and CO2 and its growth rates were similar in the presence and absence of Fe(O)OH. These results suggest that MG25 can couple glucose oxidation to Fe(III) reduction, but without conservation of energy to support growth. Cyclic voltammetry showed that strain MG25 was electrochemically active. CONCLUSIONS: An electrochemically active and FRB, E. gallinarum MG25, was isolated from submerged soil. Fe(III) is used in the bacterial metabolism as an electron sink. SIGNIFICANCE AND IMPACT OF THE STUDY: This is the first report concerning the electrochemical activity of glucose-oxidizing FRB, E. gallinarum. This organism and others like it could be used as new biocatalysts to improve the performance of a mediator-less microbial fuel cell.

Modelling microbial growth in structured foods: towards a unified approach.

Historically, the ability of foods to support the growth of spoilage organisms and food-borne pathogens has been assessed by inoculating a food with an organism of interest, and following its growth over a period of time. Information gained from such challenge tests, together with knowledge of the organoleptic stability of the product, can then be used to determine an appropriate shelf-life for the food. Whilst this approach may be seen as the "gold-standard" of microbiological assessment of food, it is both time-consuming and costly. A major advance to complement challenge testing was the development of predictive modelling, when it was demonstrated that the growth of a wide range of organisms of interest could be quite accurately modelled as a function of only a few environmental parameters-primarily temperature, pH and water activity (a(w)), with perhaps other factors such as nitrite, organic acids and oxygen. This approach to predictive microbiology is embodied in software tools such as the UK Food MicroModel and the Pathogen Modeling Program from the USA. Whilst modelling of this form yields accurate predictions of the growth of organisms in the majority of foods, there are occasions when there are discrepancies between the model and the observed growth. These discrepancies are most often described as "fail-safe", i.e. the observed growth is slower than predicted by the model. This paper examines the role of food structure in the development of microbial populations and communities, and describes the methodologies we propose to begin to tackle some of these complex and interlinked issues.

Individual-based modelling of biofilms.

Understanding the emergence of the complex organization of biofilms from the interactions of its parts, individual cells and their environment, is the aim of the individual-based modelling (IbM) approach. This IbM is version 2 of BacSim, a model of Escherichia coli colony growth, which was developed into a two-dimensional multi-substrate, multi-species model of nitrifying biofilms. It was compared with the established biomass-based model (BbM) of Picioreanu and others. Both models assume that biofilm growth is due to the processes of diffusion, reaction and growth (including biomass growth, division and spreading). In the IbM, each bacterium was a spherical cell in continuous space and had variable growth parameters. Spreading of biomass occurred by shoving of cells to minimize overlap between cells. In the BbM, biomass was distributed in a discrete grid and each species had uniform growth parameters. Spreading of biomass occurred by cellular automata rules. In the IbM, the effect of random variation of growth parameters of individual bacteria was negligible in contrast to the E. coli colony model, because the heterogeneity of substrate concentrations in the biofilm was more important. The growth of a single cell into a clone, and therefore also the growth of the less abundant species, depended on the randomly chosen site of attachment, owing to the heterogeneity of substrate concentrations in the biofilm. The IbM agreed with the BbM regarding the overall growth of the biofilm, due to the same diffusion-reaction processes. However, the biofilm shape was different due to the different biomass spreading mechanisms. The IbM biofilm was more confluent and rounded due to the steady, deterministic and directionally unconstrained spreading of the bacteria. Since the biofilm shape is influenced by the spreading mechanism, it is partially independent of growth, which is driven by diffusion-reaction. Chance in initial attachment events modifies the biofilm shape and the growth of single cells because of the high heterogeneity of substrate concentrations in the biofilm, which again results from the interaction of diffusion-reaction with spreading. This stresses the primary importance of spreading and chance in addition to diffusion-reaction in the emergence of the complexity of the biofilm community.

Effect of EPS on biofilm structure and function as revealed by an individual-based model of biofilm growth.

We have simulated a nitrifying biofilm with one ammonia and one nitrite oxidising species in order to elucidate the effect of various extracellular polymeric substance (EPS) production scenarios on biofilm structure and function. The individual-based model (IbM) BacSim simulates diffusion of all substrates on a two-dimensional lattice. Each bacterium is individually simulated as a sphere of given size in a continuous, three-dimensional space. EPS production kinetics was described by a growth rate dependent and an independent term (Leudeking-Piret equation). The structure of the biofilm was dramatically influenced by EPS production or capsule formation. EPS production decreased growth of producers and stimulated growth of non-producers because of the energy cost involved. For the same reason, EPS accumulation can fall as its rate of production increases. The patchiness and roughness of the biofilm decreased and the porosity increased due to EPS production. EPS density was maximal in the middle of the vertical profile. Introduction of binding forces between like cells increased clustering.

Heterogeneity in biofilms.

Biofilms, accumulations of microorganisms at interfaces, have been described for every aqueous system supporting life. The structure of these microbial communities ranges from monolayers of scattered single cells to thick, mucous structures of macroscopic dimensions (microbial mats; algal-microbial associations; trickling filter biofilms). During recent years the structure of biofilms from many different environments has been documented and evaluated by use of a broad variety of microscopic, physico-chemical and molecular biological techniques, revealing a generally complex 3D structure. Parallel to these investigations more and more complex mathematical models and simulations were developed to explain the development, structures, and interactions of biofilms. The forces determining the spatial structure of biofilms, including microcolonies, extracellular polymeric substances (EPS), and channels, are still the subject of controversy. To achieve conclusive explanations for the structures observed in biofilms the cooperation of both fields of investigation, modelling and experimental research, is necessary. The expanding field of molecular techniques not only allows more and more detailed documentation of the spatial distribution of species, but also of functional activities of single cells in their biofilm environment. These new methods will certainly reveal new insights in the mechanisms involved in the developmental processes involved in the formation and behavior of biofilms.

Adenylates and adenylate-energy charge in submerged and planktonic cultures of Salmonella enteritidis and Salmonella typhimurium.

Adenine nucleotide values and adenylate energy charge (AEC) were measured during the growth of Salmonella enteritidis and Salmonella typhimurium as submerged colonies in agarose gel and gelatin gel, and as planktonic cells in broth. Growth in all three systems showed similar trends with a ten-fold decrease in total adenylate pool during exponential growth, before attaining a fairly stable value throughout stationary phase. AEC values were generally low, (approximately 0.66), but did rise slightly during stationary phase. The large proportion of dead cells during early exponential phase may have contributed to the adenosine diphosphate and adenosine monophosphate pools, through cell lysis or excretion, and it is suggested that this was likely to account for the low values of AEC. In agarose and gelatin gelled cultures the percentage of adenosine triphosphate (ATP) in relation to the total adenylates showed random fluctuations. This was contrary to the broth culture where percentage ATP was highest after 12 h and the data formed a smooth curve. These data demonstrated that considerable physiological heterogeneity exists within a colony of bacteria growing in a gel matrix and by analogy a food material also, and that AEC is a poor indicator of cell viability in such systems.

Synergist effect of sucrose fatty acid esters on nisin inhibition of gram-positive bacteria.

Nisin in combination with the sucrose fatty acid esters, sucrose palmitate (P-1570 and P-1670) or sucrose stearate (S-1570 and S-1670) was tested against a range of Gram-negative and Gram-positive bacteria. Initial liquid culture investigation showed that the sugar ester P-1670 resulted in a synergist enhancement of the bacteriostatic activity of nisin against Gram-positive bacteria and not Gram-negative bacteria. Some enhancement of the bactericidal activity of nisin against Listeria monocytogenes was also observed. This increased nisin inhibitory effect was confirmed on solid media using plates with gradients of pH and NaCl. Synergism was observed with all four sucrose fatty acid esters, which enhanced the antimicrobial activity of nisin against several strains of L. monocytogenes, Bacillus cereus (both cells and spores), Lactobacillus plantarum and Staphylococcus aureus. The combination of nisin and the sucrose fatty acid esters showed no inhibition of Gram-negative bacteria (Salmonella enteritidis, Salm. typhimurium and Pseudomonas aeruginosa).

The effects of agar concentration on the growth and morphology of submerged colonies of motile and non-motile bacteria.

The growth and morphology of submerged bacterial colonies was investigated. Five separate colonial forms were recognized depending both on species and on agar concentration. These were (i) branched, dendritic structures seen only with Bacillus cereus; (ii) lenticular colonies for all other species at high agar concentrations; (iii) small lobed to spherical colonies for non-motile organisms at low agar concentrations; (iv) and (v) large diffuse spherical colonies which can be further subdivided into 'snowball' or 'wispy' types for motile bacteria growing at agar concentrations below about 0.65% w/v. Viable count determinations suggested that agar concentration had little effect in the early stages of growth but that motile cells at low agar concentrations achieved higher cell numbers than did those in concentrations greater than 0.65% w/v. Transmission electron microscopy indicated that bacteria in lenticular colonies were tightly packed within lens-shaped splits in the agar whilst at low agar concentrations motile cells were well separated and appeared to move through the agar matrix.

The effects of growth dynamics upon pH gradient formation within and around subsurface colonies of Salmonella typhimurium.

pH measurements made in and around submerged colonies of Salmonella typhimurium grown within a model gelatin gel system using pH-sensitive micro- and macroelectrodes indicated some pH heterogeneity occurring in and around the bacterial colony. Inoculation density, initial pH and glucose concentration were all found to influence colony diameter and metabolism of Salmonella colonies. Colony growth in the presence of glucose, at pH 7.0 with an inoculation density of 1 cell ml-1 led to a pH fall of 1-2 pH units after 2 d. At pH 5.0, with glucose, colony growth rates were much slower than at pH 7.0, and the pH change varied by less than one pH unit often becoming alkaline. In the absence of glucose, only small pH changes were observed within the medium, although growth rates were similar to those in glucose-containing media. At the higher inoculation density (ca 1000 cells ml-1), isolated pH changes were not observed. Morphological changes, such as the production of annular rings, were noted in stationary phase colonies as was alkali production in colonies. These results are discussed in relation to observations with surface colonies.

The validity of models.

The ubiquity of biofilm and its classification as a microbial aggregate is discussed. Investigations into any microbial ecological problem operate at four levels: (i) in situ investigations, (ii) the use of microcosms, (iii) experimental model systems, and (iv) mathematical models. Each of these is defined and their use in biofilm research illustrated. It is concluded that all these approaches are valid and that scientific research in general and biofilm research in particular must profit by the use widely different methods if a complete understanding of a system is to be achieved.

The effect of chlorhexidine on defined, mixed culture oral biofilms grown in a novel model system.

In order to develop an improved method to evaluate antimicrobial agents for use in clinical dentistry, a constant-depth film fermenter (CDFF) has been used to generate biofilms of fixed depth comprising nine species of bacteria commonly found in dental plaque in health and disease. These bacteria were grown together initially in a conventional chemostat which was used to inoculate the CDFF over an 8 h period. Medium was then supplied directly to the CDFF and biofilms allowed to develop. The biofilms were then challenged with eight short pulses of two concentrations of chlorhexidine (0.0125 and 0.125% w/v). The lower concentration had a limited effect on the composition of the biofilms while a differential and substantial inhibition was obtained with a higher concentration. Actinomyces naeslundii was lost from the biofilm, and the viable counts of streptococci, Fusobacterium nucleatum and Porphyromonas gingivalis were inhibited by over three orders of magnitude by 0.125% chlorhexidine, whereas Veillonella dispar was only transiently affected. The findings were consistent with those from clinical studies of dental plaque, suggesting that this model would have a predictive value when evaluating novel antiplaque or antimicrobial inhibitors.

Investigation of the effect of combined variations in temperature, pH, and NaCl concentration on nisin inhibition of Listeria monocytogenes and Staphylococcus aureus.

Gradient plates were used to investigate the effects of varying temperature, pH, and sodium chloride (NaCl) concentration on nisin inhibition of Staphylococcus aureus and Listeria monocytogenes, Nisin was incorporated into the plates of 0, 50, 100, 250, and 500 IU ml -1. Gradients of pH (3.7 to 7.92) at right angles to NaCl concentration (2.1 to 7% [wt/vol]) were used for the plates, which were incubated at 20, 25, 30 and 35 degrees C. Growth on the plates were recorded by eye and by image analysis. The presence of viable but nongrowing cells was revealed by transfer to nongradient plates. Lower temperatures and greater NaCl concentrations increased the nisin inhibition of S. aureus synergistically. Increasing the NaCl concentration potentiated the nisin action against L. monocytogenes; the effect of temperature difference was not so apparent. Between pH 7.92 and ca. pH 5, a fall pH appeared to increase nisin's effectiveness against both organisms. At more acid pH values (ca. pH 4.5 to 5), the organisms showed resistance to both nisin and NaCl at 20 and 25 degrees C. Similar results were obtained with one-dimensional liquid cultures.

Competition between Salmonella and Pseudomonas species growing in and on agar, as affected by pH, sodium chloride concentration and temperature.

pH/sodium chloride (NaCl) gradient plates were used to investigate competition between Pseudomonas and Salmonella species. At 30 degrees C and at particular NaCl/pH conditions the salmonellae inhibited growth of P. fluorescens and not P. putida. At 20 degrees C P. putida and not P. fluorescens inhibited the salmonellae. The growth of the pure and mixed strains in agar plates with the pH/NaCl conditions was compared by viable counts. Competition in pour plates at 30 degrees C was confirmed. At 20 degrees C, sub-surface growth of the salmonellae inhibited the P. putida. With surface growth this did not occur; the salmonellae was slightly inhibited by the P. putida.

Ecological determinants of biofilm formation.

Biofilm formation is discussed in terms of the ecological processes involved in their formation. It is emphasised that any cell responds to its environment i.e. to the composition of a liquid layer a few microns thick adjacent to the cell surface. The concept of multidimensional habitat domains defining the growth limits to every species is introduced, and put into the context of competition between different organisms. Activity domains of organisms are discussed and a definition for the niche of an organism introduced. The development of a biofilm on a clean surface is described. The constant depth film fermenter is introduced as an appropriate tool for investigating spatial and temporal sequence in biofilm formation. Finally, nutrient concentration is considered and the effects of diffusion limitation on film structure explored with the aid of a cellular automaton model.

The use of two-dimensional gradient plates to investigate the range of conditions under which conjugal plasmid transfer occurs.

Gel-stabilized two-dimensional gradient plates were used to study the effects of pH, salt concentration and temperature on the conjugal transfer of plasmid RP4 between strains of Escherichia coli and Pseudomonas putida. The combinations of pH and salt concentration that permitted conjugation were mapped as a two-dimensional growth area occupied by transconjugants following conjugation. This conjugation domain was less extensive than the areas that supported growth of the parental strains, and showed evidence for the interactive effects of pH and salt concentration in determination of conditions that permitted conjugation. The size and shape of the conjugation domain was influenced by time, temperature, the identities of the donor and recipient bacteria, and the combination of donor and recipient bacteria.

Method for Investigation of Competition between Bacteria as a Function of Three Environmental Factors Varied Simultaneously.

Competition between microorganisms as affected by temperature, pH, and the sodium chloride (NaCl) concentration was investigated by selective replication from gradient plates. Salmonella typhimurium was inhibited by Pseudomonas putida at 20 and 23 degrees C but not 30 and 35 degrees C. P. putida no longer grew at the extremes of pH and NaCl concentration, particularly at 30 and 35 degrees C.