Essay - The role of ecological theory in microbial ecology

Microbial ecology is currently undergoing a revolution, with repercussions spreading throughout microbiology, ecology and ecosystem science. The rapid accumulation of molecular data is uncovering vast diversity, abundant uncultivated microbial groups and novel microbial functions. This accumulation of data requires the application of theory to provide organization, structure, mechanistic insight and, ultimately, predictive power that is of practical value, but the application of theory in microbial ecology is currently very limited. Here we argue that the full potential of the ongoing revolution will not be realized if research is not directed and driven by theory, and that the generality of established ecological theory must be tested using microbial systems.

Self-potential and spectral induced polarization signals associated with microbial sulphate reduction

Self-potential and spectral induced polarization responses associated with microbial processes involved in sulphate reduction have been monitored in a Perspex Winogradsky column filled with glass beads and growth medium. Salt-bridge is utilized as an electrolytic contact between experiment and control column. Equally spaced SP electrodes are used in combination of Ag-AgCl electrodes to compare electrodic and SP signals associated with the microbial processes involved in sulphate reduction. This study reveals that magnitude of SP varies from 5 to -2 mV and Electrodic potential 0 to -20 mV at the time of domination (day 39) of sulphate reducing bacteria which are very small in comparison to those measured by fixing both measuring and reference Ag-AgCl electrodes in experiment column. We observed that real and imaginary parts of complex conductivities increase with increase in production of H2S and CO in the experiment column. Both real and imaginary parts of surface complex conductivity vary at low frequencies similar to typical growth curve of bacterial population. Sodium lactate as a carbon source, dissolved in Lagan River water was flushed into the column for biostimulation on 144th day. The dissolved oxygen in flushed fluid might have killed the anaerobes in the column and decrease in complex conductivities similar to death phase of bacteria is observed for one week. The results obtained from this experiment should contribute to further understanding the biogeophysical responses involved in complex environments.


Read More: http://library.seg.org/doi/abs/10.1190/segj092009-001.57

Stable isotope probing analysis of the influence of liming on root exudate utilization by soil microorganisms

Rhizosphere microorganisms play an important role in soil carbon flow, through turnover of root exudates, but there is little information on which organisms are actively involved or on the influence of environmental conditions on active communities. In this study, a (CO2)-C-13 pulse labelling field experiment was performed in an upland grassland soil, followed by RNA-stable isotope probing (SIP) analysis, to determine the effect of liming on the structure of the rhizosphere microbial community metabolizing root exudates. The lower limit of detection for SIP was determined in soil samples inoculated with a range of concentrations of C-13-labelled Pseudomonas fluorescens and was found to lie between 10(5) and 10(6) cells per gram of soil. The technique was capable of detecting microbial communities actively assimilating root exudates derived from recent photo-assimilate in the field. Denaturing gradient gel electrophoresis (DGGE) profiles of bacteria, archaea and fungi derived from fractions obtained from caesium trifluoroacetate (CsTFA) density gradient ultracentrifugation indicated that active communities in limed soils were more complex than those in unlimed soils and were more active in utilization of recently exuded C-13 compounds. In limed soils, the majority of the community detected by standard RNA-DGGE analysis appeared to be utilizing root exudates. In unlimed soils, DGGE profiles from C-12 and C-13 RNA fractions differed, suggesting that a proportion of the active community was utilizing other sources of organic carbon. These differences may reflect differences in the amount of root exudation under the different conditions.

IQ-motif peptides as novel anti-microbial agents

The IQ-motif is an amphipathic, often positively charged, a-helical, calmodulin binding sequence found in a number of eukaryote signalling, transport and cytoskeletal proteins. They share common biophysical characteristics with established, cationic a-helical antimicrobial peptides, such as the human cathelicidin LL-37. Therefore, we tested eight peptides encoding the sequences of IQ-motifs derived from the human cytoskeletal scaffolding proteins IQGAP2 and IQGAP3. Some of these peptides were able to inhibit the growth of Escherichia coli and Staphylococcus aureus with minimal inhibitory concentrations (MIC) comparable to LL-37. In addition some IQ-motifs had activity against the fungus Candida albicans. This antimicrobial activity is combined with low haemolytic activity (comparable to, or lower than, that of LL-37). Those IQ-motifs with anti-microbial activity tended to be able to bind to lipopolysaccharide. Some of these were also able to permeabilise the cell membranes of both Gram positive and Gram negative bacteria. These results demonstrate that IQ-motifs are viable lead sequences for the identification and optimisation of novel anti-microbial peptides. Thus, further investigation of the anti-microbial properties of this diverse group of sequences is merited.

Stochastic and deterministic processes interact in the assembly of desert microbial communities on a global scale

Extreme arid regions in the worlds' major deserts are typified by quartz pavement terrain. Cryptic hypolithic communities colonize the ventral surface of quartz rocks and this habitat is characterized by a relative lack of environmental and trophic complexity. Combined with readily identifiable major environmental stressors this provides a tractable model system for determining the relative role of stochastic and deterministic drivers in community assembly. Through analyzing an original, worldwide data set of 16S rRNA-gene defined bacterial communities from the most extreme deserts on the Earth, we show that functional assemblages within the communities were subject to different assembly influences. Null models applied to the photosynthetic assemblage revealed that stochastic processes exerted most effect on the assemblage, although the level of community dissimilarity varied between continents in a manner not always consistent with neutral models. The heterotrophic assemblages displayed signatures of niche processes across four continents, whereas in other cases they conformed to neutral predictions. Importantly, for continents where neutrality was either rejected or accepted, assembly drivers differed between the two functional groups. This study demonstrates that multi-trophic microbial systems may not be fully described by a single set of niche or neutral assembly rules and that stochasticity is likely a major determinant of such systems, with significant variation in the influence of these determinants on a global scale.

A Trip from a Tube to a Chip Applied Micro and Nanotechnology in Biotechnology, Veterinary and Life Sciences

More than 200 known diseases are transmitted via foods or food products. In the United States, food-borne diseases are responsible for 76 million cases of illness, 32,500 cases of hospitalisation and 5000 cases of death yearly. The ongoing increase in worldwide trade in livestock, food, and food products in combination with increase in human mobility (business- and leisure travel, emigration etc.) will increase the risk of emergence and spreading of such pathogens. There is therefore an urgent need for development of rapid, efficient and reliable methods for detection and identification of such pathogens.

Microchipfabrication has had a major impact on electronics and is expected to have an equally pronounced effect on life sciences. By combining micro-fluidics with micromechanics, micro-optics, and microelectronics, systems can be realized to perform complete chemical or biochemical analyses. These socalled ’Lab-on-a-Chip’ will completely change the face of laboratories in the future where smaller, fully automated devices will be able to perform assays faster, more accurately, and at a lower cost than equipment of today. A general introduction of food safety and applied micro-nanotechnology in life sciences will be given. In addition, examples of DNA micro arrays, micro fabricated integrated PCR chips and total integrated lab-on-achip systems from different National and EU research projects being carried out at the Laboratory of Applied Micro- Nanotechnology (LAMINATE) group at the National Veterinary Institute (DTU-Vet) Technical University of Denmark and the BioLabchip group at the Department of Micro and Nanotechnology (DTU-Nanotech), Technical University of Denmark (DTU), Ikerlan-IK4 (Spain) and other 16 partners from different European countries will be presented.

Water-hydrophobic compound interactions with the microbial cell

The structural interactions of biological macromolecules, their biochemical activities and, ultimately, the metabolic function of cellular systems are dependent upon weak inter- and intra-molecular forces such as hydrogen bonds, Van der Waals forces, and the hydrophobic effect. Water molecules, and those of hydrophobic substances such as hydrocarbons, can take part in and/or modify these interactions and thereby determine the operational and structural stability of the microbial cell and its macromolecular systems. We explain how the cytosol, plasma membrane and the extracellular solution form a material and energetic continuum; and discuss the behavior of hydrophobic substances of extracellular origin as they migrate into the plasma membrane and into the cell's interior. The adverse effects of substances with a log P octanol-water =2, that partition into the hydrophobic domains of biological macromolecules, are discussed in relation to microbial cell function; and we speculate whether the cellular stress that they induce is symmetrical or asymmetrical in nature. In the context of the microbial environment, we take a situational-functional approach to consider how hydrophobic stressors interact with the microbial cell, and what types of evasion tactics microbes can employ to minimize their inhibitory activities. Finally, we discuss the ecological implications of hydrocarbon-induced cellular stress for microbial systems.

Cathelicidin-like Helminth Defence Molecules (HDMs):Absence of Cytotoxic, Anti-microbial and Anti-protozoan Activities Imply a Specific Adaptation to Immune Modulation

Host defence peptides (HDPs) are expressed throughout the animal and plant kingdoms. They have multifunctional roles in the defence against infectious agents of mammals, possessing both bactericidal and immune-modulatory activities. We have identified a novel family of molecules secreted by helminth parasites (helminth defence molecules; HDMs) that exhibit similar structural and biochemical characteristics to the HDPs. Here, we have analyzed the functional activities of four HDMs derived from Schistosoma mansoni and Fasciola hepatica and compared them to human, mouse, bovine and sheep HDPs. Unlike the mammalian HDPs the helminth-derived HDMs show no antimicrobial activity and are non-cytotoxic to mammalian cells (macrophages and red blood cells). However, both the mammalian- and helminth-derived peptides suppress the activation of macrophages by microbial stimuli and alter the response of B cells to cytokine stimulation. Therefore, we hypothesise that HDMs represent a novel family of HDPs that evolved to regulate the immune responses of their mammalian hosts by retaining potent immune modulatory properties without causing deleterious cytotoxic effects.

Microbial weeds in hypersaline habitats: the enigma of the weed-like Haloferax mediterranei

Heterotrophic prokaryotic communities that inhabit saltern crystallizer ponds are typically dominated by two species, the archaeon Haloquadratum walsbyi and the bacterium Salinibacter ruber, regardless of location. These organisms behave as ‘microbial weeds’ as defined by Cray et al. (Microb Biotechnol 6: 453–492, 2013) that possess the biological traits required to dominate the microbiology of these open habitats. Here, we discuss the enigma of the less abundant Haloferax mediterranei, an archaeon that grows faster than any other, comparable extreme halophile. It has a wide window for salt tolerance, can grow on simple as well as on complex substrates and degrade polymeric substances, has different modes of anaerobic growth, can accumulate storage polymers, produces gas vesicles, and excretes halocins capable of killing other Archaea. Therefore, Hfx. mediterranei is apparently more qualified as a ‘microbial weed’ than Haloquadratum and Salinibacter. However, the former differs because it produces carotenoid pigments only in the lower salinity range and lacks energy-generating retinal-based, light-driven ion pumps such as bacteriorhodopsin and halorhodopsin. We discuss these observations in relation to microbial weed biology in, and the open-habitat ecology of, hypersaline systems.

Plant extract: A promising biomatrix for ecofriendly, controlled synthesis of silver nanoparticles

Uses of plants extracts are found to be more advantageous over chemical, physical and microbial (bacterial, fungal, algal) methods for silver nanoparticles (AgNPs) synthesis. In phytonanosynthesis, biochemical diversity of plant extract, non-pathogenicity, low cost and flexibility in reaction parameters are accounted for high rate of AgNPs production with different shape, size and applications. At the same time, care has to be taken to select suitable phytofactory for AgNPs synthesis based on certain parameters such as easy availability, large-scale nanosynthesis potential and non-toxic nature of plant extract. This review focuses on synthesis of AgNPs with particular emphasis on biological synthesis using plant extracts. Some points have been given on selection of plant extract for AgNPs synthesis and case studies on AgNPs synthesis using different plant extracts. Reaction parameters contributing to higher yield of nanoparticles are presented here. Synthesis mechanisms and overview of present and future applications of plant-extract-synthesized AgNPs are also discussed here. Limitations associated with use of AgNPs are summarised in the present review.