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Soil properties, the chemical composition of cementation solution, injection technique, and environmental conditions have all been extensively studied as variables influencing microbially induced carbonate precipitation performance. However, despite the fact that different researchers have used different bacterial suspensions, the influence of bacterial suspension type, more specifically some organic matters in bacterial suspensions, which can play a key role in the morphology and mechanical properties of CaC[O.sub.3], has often been overlooked. In this study, the harvested bacterial solutions were centrifuged to separate bacterial cells and supernatant. The precipitated cells were then diluted with three distinct solutions: supernatant (RB), fresh culture medium (FB), and 0.9% NaCl solution (NB), which were subsequently utilized to stabilize the sand. The results indicated that the bacterial suspension type could greatly impact the strength of biocemented sand, particularly coarse and medium sand. Differences in unconfined compressive strength can be related to differences in precipitated CaC[O.sub.3] microstructures, morphologies, and compositions, which were examined using scanning electron microscopy, X-ray diffraction analysis, and Fourier transform infrared spectroscopy. Key words: microbially induced calcite precipitation (MICP), unconfined compressive strength (UCS), bacterial suspension type, microstructure Les proprietes du sol, la composition chimique de la solution de cimentation, la technique d'injection et les conditions environnementales ont toutes ete largement etudiees comme variables influencant les performances du MICP. Cependant, malgre le fait que differents chercheurs aient utilise differentes suspensions bacteriennes, l'influence du type de suspension bacterienne, plus precisement de certaines matieres organiques dans les suspensions bacteriennes, qui peuvent jouer un role cle dans la morphologie et les proprietes mecaniques du CaC[O.sub.3], a souvent ete negligee. Dans cette etude, les solutions bacteriennes recoltees ont ete centrifugees pour separer les cellules bacteriennes et le surnageant. Les cellules precipitees ont ensuite ete diluees dans trois solutions distinctes : surnageant (RB), milieu de culture frais (FB) et solution de NaCl a 0,9% (NB), qui ont ensuite ete utilises pour stabiliser le sable. Les resultats ont indique que le type de suspension bacterienne pouvait avoir un impact important sur la resistance du sable biocimente, en particulier le sable grossier et moyen. Les differences de NGC peuvent etre liees aux differences de microstructures, de morphologies et de compositions du CaC[O.sub.3] precipite, qui ont ete examinees a l'aide de la microscopie electronique a balayage (MEB), de l'analyse par diffraction des rayons X (DRX) et de la spectroscopie infrarouge transformee de Fourier (IRTF). [Traduit par la Redaction] Mots-cles : precipitation de calcite induite par les microbes (MICP), resistance a la compression non confinee (UCS), type de suspension bacterienne, microstructure, Introduction The microbially induced carbonate precipitation (MICP)-based soil improvement approach has been introduced to geotechnical engineering for decades. Several studies have been conducted to investigate the performance of MICP in [...]

Soils provide the substrate for important microbial mechanisms that moderate a variety of processes in both managed and natural terrestrial ecosystems. Australian soils are particularly 'stressed' and are considered to be highly weathered and nutrient deficient. This places increased pressure on the Australian cotton industry to sustainably increase productivity to support the fibre demands of a growing global population. We explored Vertosol subsoils (>30 cm) under rotational cotton crops, measuring the distribution of soil microbial activity (SMA) and biomass (SMB) to 100 cm depth, as influenced by crop system and time, using respiration-based experiments. Seasonal SMA fluctuations were considered by capturing the long-term SMA between systems using stable oxygen isotope methodology. Our results indicate that subsoils contributed 47% of SMA, regardless of system, but subsoil SMB (26%) was constrained by resource availability. Long-term SMA was not significantly influenced by depth and system, presumably as a consequence of the shrink-swell nature of Vertosols facilitating organic matter movement down the profile. The impact of this organic matter on the activity of indigenous microorganisms below the top 30 cm of the profile highlights a need to consider deeper soil when unravelling the potential microbial benefits to our cropping systems. Additional keywords: agronomy, isotope techniques, soil microbiology, soil organic matter, Vertisol., Introduction The terrestrial biosphere is facing increasing pressures to meet the food and fibre demands of a growing world population (Fedoroff et al. 2010; Godfray el at. 2010). A prominent [...]

Genomics studies are helping to reveal how bacteria and archaea influence one of Earth's largest carbon stores as it begins to thaw. Genomics studies are helping to reveal how bacteria and archaea influence one of Earth's largest carbon stores as it begins to thaw., Author(s): Monique Brouillette Author Affiliations: A boardwalk for traversing Sweden's Stordalen Mire sinks in the thawing landscape. Credit: Moira Hough In a boggy landscape a line of boardwalk stretches into [...]

Abstract: Patterns that maintain and generate biodiversity of macro‐organisms in the Neotropics are widely discussed in the scientific literature, yet the spatial ecology of micro‐organisms is largely unknown. The unique character of the tropical Andes and adjacent Amazon lowlands generates a wide gradient of environmental conditions to advance our understanding of what drives community assembly and diversity processes. We analysed the distribution patterns of benthic diatoms (unicellular siliceous algae) as a model group of microbial passive dispersers, including predictors that describe limnological and geo‐climatic gradients for a total of 113 waterbodies (0–28°S and 58–80°W), including lakes and streams. Complementary multivariate statistical analyses were performed to correlate (1) community composition and (2) diatom species richness with environmental and spatial factors to infer niche‐based and dispersal‐based assembly processes, respectively. Results showed that two gradients structured both diatom assemblages and waterbodies, namely climate and landscape configuration. Variance partitioning revealed that broadscale spatial variables (distance‐based Moran's Eigenvectors) outperformed the two environmental components (limnological and geo‐climatic), suggesting dispersal‐assembled communities. However, diatom assemblages were structured by geo‐climatic (regional) factors in certain lakes in the northern and central Andes, although their effects were partially manifested via local variables after the geographical distances were factored out. In a similar way, climatic and topographic structuring homogenized lake and stream communities within ecoregions, as indicated by the strong overlap between the two community types and the weak correlation between biota and limnological variables. Notably, a significant increase in diatom species richness was related to increased water connectivity, interpreted to indicate that a decrease in the remoteness of the system increase species number. Synthesis. We emphasize the strength of macroecological gradients (landscape configuration and climatic factors) in affecting both diatom diversity and community composition in the South American tropics. In this context, our results and the commonalities of ecoregion patterning with groups of macro‐organisms (vegetation) suggest the need to integrate microbial ecology into a macroecology framework to unravel mechanisms behind diversity gradients. [ABSTRACT FROM AUTHOR]

Medical researchers are increasingly interested in knowing how the complex community of micro-organisms living on human body impacts human health. Key to this is to understand how the microbes interact with each other. Time-course studies on human microbiome indicate that the composition of microbiome changes over short time periods, primarily as a consequence of synergistic and antagonistic interactions of the members of the microbiome with each other and with the environment. Knowledge of the abundance of bacteria—which are the predominant members of the human microbiome—in such time-course studies along with appropriate mathematical models will allow us to identify key dynamic interaction networks within the microbiome. However, the high-dimensional nature of these data poses significant challenges to the development of such mathematical models. We propose a high-dimensional linear State Space Model (SSM) with a new Expectation-Regularization-Maximization (ERM) algorithm to construct a dynamic icrobial nteraction etwork (MIN). System noise and measurement noise can be separately specified through SSMs. In order to deal with the problem of high-dimensional parameter space in the SSMs, the proposed new ERM algorithm employs the idea of the adaptive LASSO-based variable selection method so that the sparsity property of MINs can be preserved. We performed simulation studies to evaluate the proposed ERM algorithm for variable selection. The proposed method is applied to identify the dynamic MIN from a time-course vaginal microbiome study of women. This method is amenable to future developments, which may include interactions between microbes and the environment. [ABSTRACT FROM AUTHOR]

The degree of polycyclic aromatic hydrocarbon contamination of environmental matrices has increased over the last several years due to increase in industrial activities. Interest has surrounded the occurrence and distribution of polycyclic aromatic hydrocarbons for many decades because they pose a serious threat to the health of humans and ecosystems. The importance of the need for sustainable abatement strategies to alleviate contamination therefore cannot be overemphasised, as daily human activities continue to create pollution from polycyclic aromatic hydrocarbons and impact the natural environment. Globally, attempts have been made to design treatment schemes for the remediation and restoration of contaminated sites. Several techniques and technologies have been proposed and tested over time, the majority of which have significant limitations. This has necessitated research into environmentally friendly and cost-effective clean-up techniques. Bioremediation is an appealing option that has been extensively researched and adopted as it has been proven to be relatively cost-effective, environmentally friendly and is publicly accepted. In this review, the physicochemical properties of some priority polycyclic aromatic hydrocarbons, as well as the pathways and mechanisms through which they enter the soil, river systems, drinking water, groundwater and food are succinctly examined. Their effects on human health, other living organisms, the aquatic ecosystem, as well as soil microbiota are also elucidated. The persistence and bioavailability of polycyclic aromatic hydrocarbons are discussed as well, as they are important factors that influence the rate, efficiency and overall success of remediation. Bioremediation (aerobic and anaerobic), use of biosurfactants and bioreactors, as well as the roles of biofilms in the biological treatment of polycyclic aromatic hydrocarbons are also explored. [ABSTRACT FROM AUTHOR]

Growing evidence points out that the capacity of organisms to acclimate or adapt to new habitat conditions basically depends on their phenomic plasticity attributes, of which their gut commensal microbiota might be an essential impact factor. Especially in aquatic organisms, which are in direct and continual contact with the aquatic environment, the complex and dynamic microbiota have significant effects on health and development. However, an understanding of the relative contribution of internal sorting (host genetic) and colonization (environmental) processes is still unclear. To understand how microbial communities differ in response to rapid environmental change, we surveyed and studied the environmental and gut microbiota of native and habitat-exchanged shrimp (Macrobrachium nipponense) using 16S rRNA amplicon sequencing on the Illumina MiSeq platform. Corresponding with microbial diversity of their living water areas, the divergence in gut microbes of lake-to-river shrimp (CK) increased, while that of river-to-lake shrimp (KC) decreased. Importantly, among the candidate environment specific gut microbes in habitat-exchanged shrimp, over half of reads were associated with the indigenous bacteria in native shrimp gut, yet more candidates presented in CK may reflect the complexity of new environment. Our results suggest that shrimp gut microbiota has high plasticity when its host faces environmental changes, even over short timescales. Further, the changes in external environment might influence the gut microbiome not just by providing environment-associated microbes directly, but also by interfering with the composition of indigenous gut bacteria indirectly. [ABSTRACT FROM AUTHOR]

The mass-ratio and niche complementarity mechanisms drive the influence of litter trait diversity on decomposition. However, the implications of these mechanisms remain poorly understood, as few studies have evaluated their importance relative to environmental conditions and soil decomposers when assessing different processes during decomposition (e.g. C dynamics and N transformations)., We measured litter C and N losses during decomposition in 10 litter mixtures and calculated community-weighted means ( CWM) and dissimilarity (Rao's Q) of 13 litter traits as metrics of the mass-ratio and niche complementarity mechanisms respectively. The 10 litter mixtures were incubated along a regional gradient (10 sites) in southern France over a year, where local environmental conditions (climate and soil parameters), and soil decomposers (microbes, nematodes, and macrofauna) were considered as drivers of decomposition., Sites and litter mixtures represented a wide range of environmental conditions, decomposers, and litter diversity. Litter mixture was the major factor affecting litter C and N loss. N was immobilized during the early decomposition stages (up to c. 40% mass loss), especially in mixtures of low N concentrations. Litter CWM traits were the key drivers of litter C and N loss, but litter trait dissimilarity emerged as a major driver of litter N loss. Macrofauna played a significant role on C and N loss, but environmental conditions exerted a minor influence., Our results highlight that distinct aspects of trait diversity in mixed species litter can play a more important role than environmental conditions and decomposers, which can affect the cycling of litter C and N at regional scales. Rather than opposing mass-ratio and niche complementarity mechanisms, our study shows that both can play a critical role simultaneously in litter decomposition., Synthesis. Our study emphasizes that, in the current context of global biodiversity decline, the mass-ratio and niche complementarity mechanisms should be considered to assess litter decomposition dynamics under global change. As litter diversity mechanisms distinctly affected the cycling of C and N, we recommend taking into account such element-specific effects to improve the prediction of the impacts of biodiversity change on biogeochemical cycles. [ABSTRACT FROM AUTHOR]

Background: Despite the important role that microorganisms play in environmental processes, the low percentage of cultured microbes (5%) has limited, until now, our knowledge of their ecological strategies. However, the development of high-throughput sequencing has generated a huge amount of genomic and metagenomic data without the need of culturing that can be used to study ecological questions. This study aims to estimate the functional capabilities, genomic sizes and 16S copy number of different taxa in relation to their ubiquity and their environmental preferences. Results: To achieve this goal, we compiled data regarding the presence of each prokaryotic genera in diverse environments. Then, genomic characteristics such as genome size, 16S rRNA gene copy number, and functional content of the genomes were related to their ubiquity and different environmental preferences of the corresponding taxa. The results showed clear correlations between genomic characteristics and environmental conditions. Conclusions: Ubiquity and adaptation were linked to genome size, while 16S copy number was not directly related to ubiquity. We observed that different combinations of these two characteristics delineate the different environments. Besides, the analysis of functional classes showed some clear signatures linked to particular environments. [ABSTRACT FROM AUTHOR]

Among all known microbes capable of thriving under extreme and, therefore, potentially extraterrestrial environmental conditions, methanogens from the domain Archaea are intriguing organisms. This is due to their broad metabolic versatility, enormous diversity, and ability to grow under extreme environmental conditions. Several studies revealed that growth conditions of methanogens are compatible with environmental conditions on extraterrestrial bodies throughout the Solar System. Hence, life in the Solar System might not be limited to the classical habitable zone. In this contribution we assess the main ecophysiological characteristics of methanogens and compare these to the environmental conditions of putative habitats in the Solar System, in particular Mars and icy moons. Eventually, we give an outlook on the feasibility and the necessity of future astrobiological studies concerning methanogens. [ABSTRACT FROM AUTHOR]

Environmental organoarsenicals are produced by microorganisms and are introduced anthropogenically as herbicides and antimicrobial growth promoters for poultry and swine. Nearly every prokaryote has an ars (arsenic resistance) operon, and some have an arsH gene encoding an atypical flavodoxin. The role of ArsH in arsenic resistance has been unclear. Here we demonstrate that ArsH is an organoarsenical oxidase that detoxifies trivalent methylated and aromatic arsenicals by oxidation to pentavalent species. E scherichia coli, which does not have an arsH gene, is very sensitive to the trivalent forms of the herbicide monosodium methylarsenate [ MSMA or MAs( V)] and antimicrobial growth promoter roxarsone [ Rox( V)], as well as to phenylarsenite [ PhAs( III), also called phenylarsine oxide or PAO]. P seudomonas putida has two chromosomally encoded arsH genes and is highly resistant to the trivalent forms of these organoarsenicals. A derivative of P . putida with both arsH genes deleted is sensitive to MAs( III), PhAs( III) or Rox( III). P . putida arsH expressed in E. coli conferred resistance to each trivalent organoarsenical. Cells expressing PpArsH oxidized the trivalent organoarsenicals. PpArsH was purified, and the enzyme in vitro similarly oxidized the trivalent organoarsenicals. These results suggest that ArsH catalyzes a novel biotransformation that confers resistance to environmental methylated and aromatic arsenicals. [ABSTRACT FROM AUTHOR]

Atmospheric methane (C[H.sub.4]) increased through much of the twentieth century, but this trend gradually weakened until a stable state was temporarily reached around the turn of the millennium (1,2), after which levels increased once more (3). The reasons for the slowdown are incompletely understood, with past work identifying changes in fossil fuel, wetland and agricultural sources and hydroxyl (OH) sinks as important causal factors (1,4-8). Here we show that the late-twentieth-century changes in the C[H.sub.4] growth rates are best explained by reduced microbial sources in the Northern Hemisphere. Our results, based on synchronous time series of atmospheric C[H.sub.4] mixing and [sup.13]C/[sup.12]C ratios and a two-box atmospheric model, indicate that the evolution of the mixing ratio requires no significant change in Southern Hemisphere sources between 1984 and 2005. Observed changes in the interhemispheric difference of [sup.13]C effectively exclude reduced fossil fuel emissions as the primary cause of the slowdown. The [sup.13]C observations are consistent with long-term reductions in agricultural emissions or another microbial source within the Northern Hemisphere. Approximately half (51 ± 18%) of the decrease in Northern Hemisphere C[H.sub.4] emissions can be explained by reduced emissions from rice agriculture in Asia over the past three decades associated with increases in fertilizer application (9) and reductions in water use (10,11)., Several mechanisms have been proposed to explain the long-term slowdown of atmospheric C[H.sub.4], including decreases in source emissions (4,5,8,10,12), changes in sink processes (7), and a stabilization of C[H.sub.4] with [...]

The global decline in biodiversity has generated concern over the consequences for ecosystem functioning and services. Although ecosystem functions driven by soil microorganisms such as plant productivity, decomposition, and nutrient cycling are of particular importance, interrelationships between plant diversity and soil microorganisms are poorly understood. We analyzed the response of soil microorganisms to variations in plant species richness (1-60) and plant functional group richness (1-4) in an experimental grassland system over a period of six years. Major abiotic and biotic factors were considered for exploring the mechanisms responsible for diversity effects. Further, microbial growth characteristics were assessed following the addition of macronutrients. Effects of plant diversity on soil microorganisms were most pronounced in the most diverse plant communities though differences only became established after a time lag of four years. Differences in microbial growth characteristics indicate successional changes from a disturbed (zymogeneous) to an established (autochthonous) microbial community four years after establishment of the experiment. Supporting the singular hypothesis for plant diversity, the results suggest that plant species are unique, each contributing to the functioning of the belowground system. The results reinforce the need for long-term biodiversity experiments to fully appreciate consequences of current biodiversity loss for ecosystem functioning. Key words: above- and belowground interrelationships; biodiversity ecosystem functioning relationship; Jena Experiment; microbial biomass; microbial nutrient limitation; microbial respiration; redundancy hypothesis.

Large-scale industrial use of ehromium(Vl) has resulted in widespread contamination with carcinogenic chromium(VI). The abilities of microorganisms to survive in these environments and to detoxify chromate require the presence of specific resistance systems. Here we report identification of the transposon-located (TnOtChr) chromate resistance genes from the highly tolerant strain Ochrobactrum tritici 5bvll surviving chromate concentrations of >50 raM. The 7,189-bp-long TnOtChr of the mixed Tn21/Tn3 transposon subfamily contains a group of chrB, chrA, chrC, and chrF genes situated between divergently transcribed resolvase and transposase genes. The chrB and chrA genes, but not chrF or chrC, were essential for establishment of high resistance in chromium-sensitive O. tritici. The chr promoter was strongly induced by chromate or dichromate, but it was completely unresponsive to Cr(III), oxidants, sulfate, or other oxyanions. Plasmid reporter experiments identified ChrB as a chromate-sensing regulator of chr expression. Induction of the chr operon suppressed accumulation of cellular Cr through the activity of a chromate efflux pump encoded by chrA. Expression of chrB, chrC, or chrF in an Escherichia coli soda sodB double mutant restored its aerobic growth in minimal medium and conferred resistance to superoxide-generating agents menadione and paraquat. Nitroblue tetrazolium staining on native gels showed that ChrC protein had superoxide dismutase activity. TnOtChr appears to represent a mobile genetic system for the distribution of the chromate-regulated resistance operon. The presence of three genes protecting against superoxide toxicity should provide an additional survival advantage to TnOtChr-containing cells in the environments with multiple redox-active contaminants.

The Earth possesses a number of regulatory feedback mechanisms involving life. In the absence of a population of competing biospheres, it has proved hard to find a robust evolutionary mechanism that would generate environmental regulation. It has been suggested that regulation must require altruistic environmental alterations by organisms and, therefore, would be evolutionarily unstable. This need not be the case if organisms alter the environment as a selectively neutral by-product of their metabolism, as in the majority of biogeochemical reactions, but a question then arises: Why should the combined by-product effects of the biota have a stabilizing, rather than destabilizing, influence on the environment? Under certain conditions, selection acting above the level of the individual can be an effective adaptive force. Here we present an evolutionary simulation model in which environmental regulation involving higher-level selection robustly emerges in a network of interconnected microbial ecosystems. Spatial structure creates conditions for a limited form of higher-level selection to act on the collective environment-altering properties of local communities. Local communities that improve their environmental conditions achieve larger populations and are better colonizers of available space, whereas local communities that degrade their environment shrink and become susceptible to invasion. The spread of environment-improving communities alters the global environment toward the optimal conditions for growth and tends to regulate against external perturbations. This work suggests a mechanism for environmental regulation that is consistent with evolutionary theory. evolution | Gaia theory | microbial ecology | multilevel selection

Streptococcus mutans (S. mutans) bacteria were killed using a low-power millimeter-size atmospheric-pressure glow-discharge plasma or plasma needle. The plasma was applied to a culture of S. mutans that was plated onto the surface of an agar nutrient in a Petri dish. S. mutans is the most important microorganism for causing dental caries. A spatially resolved biological diagnostic of the plasma is introduced, where the spatial pattern of bacterial colonies in the sample was imaged after plasma treatment and incubation. For low-power conditions that would be attractive for dentistry, images from this biological diagnostic reveal that S. mutans was killed within a solid circle with a 5-mm diameter, demonstrating that site-specific treatment is possible. For other conditions, which are of interest for understanding plasma transport, images show that bacteria were killed with a ring-shaped spatial pattern. This ring pattern coincides with a similar ring in the spatial distribution of energetic electrons, as revealed by Abel-inverted images of the glow. The presence of the radicals OH and O was verified using optical-emission spectroscopy. Index Terms--Atmospheric glow discharge, disinfection, microorganisms, microplasma, nonthermal plasma, plasma applications, sterilization.

We determine the physicochemical habitat for microorganisms in subsurface terrestrial ice by quantitatively constraining the partitioning of bacteria and fluorescent beads (1-10 [micro]m) between the solid ice crystals and the water-filled veins and boundaries around individual ice crystals. We demonstrate experimentally that the partitioning of spherical particles within subsurface ice depends strongly on size but is largely independent of source particle concentration. Although bacteria are shown consistently to partition to the veins, larger particles, which would include eukaryotic cells, become trapped in the crystals with little potential for continued metabolism. We also calculate the expected concentrations of soluble impurities in the veins for typical bulk concentrations found in natural ice. These calculations and scanning electron microscope observations demonstrate a concentrated chemical environment (3.5 M total ions at -10 [degrees]C) in the veins, where bacteria were found to reside, with a mixture of impurities that could sustain metabolism. Our calculations show that typical bacterial cells in glacial ice would fit within the narrow veins, which are a few micrometers across. These calculations are confirmed by microscopic images of spherical, 1.9-[micro]m-diameter, fluorescent beads and stained bacteria in subsurface veins. Typical bacterial concentrations in clean ice ([10.sup.2]-[10.sup.3] cells/mL) would result in concentrations of [10.sup.6]-[10.sup.8] cells/mL of vein fluid, but occupy only a small fraction of the total available vein volume ( Keywords: ice, glacier, water veins, bacteria, eukaryote, bacterial habitat.

An integrated multidisciplinary study utilizing geochemical and microbial ecological approaches was conducted to characterize the origins, chemical nature, and quantities of dissolved and particulate organic matter (OM) utilized by heterotrophic bacteria in a temperate estuary. C : N, stable isotope ([[sigma].sup.13]C), and lipid biomarker analyses revealed differences in the inferred reactivity of autochthonous versus allochthonous OM sources. Isotopic comparison of OM size fractions and bacterial nucleic acids suggests that high- molecular-weight dissolved OM (DOM) is consistently linked to bacterial biomass synthesis along the estuarine salinity gradient. Polyunsaturated fatty acids (as percent of total fatty acids, FA) were a reliable predictor of DOM decomposition in bioassays, thus providing an indicator directly linking DOM reactivity to its composition. Significant positive correlations between FA diagnostic of bacterial sources and lipid biomarker compounds diagnostic of planktonic origin indicate a systematic bacterial response to autochthonous DOM sources along the estuarine continuum. These findings further suggest that, although the geochemical signature of algal-derived OM in the dissolved phase may appear quantitatively insignificant, this fraction may nevertheless represent a principal source of bioreactive OM to heterotrophic bacteria in estuarine waters.

Environmental ethics has almost exclusively been focused on multicellular organisms. However, because microorganisms form the base of the world's food chains, allowing for the existence of all higher organisms, the complexities of the moral considerability of microorganisms deserve attention. Despite the impossible task of protecting individual microorganisms--the paradigmatic example of the limitations to a Schweitzerian 'reverence for life'--microorganisms can be considered to have intrinsic value on the basis of conation, along with their enormous instrumental value. This intrinsic value even manifests itself at the individual level, although in this case the ethic can only be regulative (an ethical principle). Biocentrism is the most appropriate ethical framework for microorganisms, and the most useful normative framework for implementing the preservation and conservation of microorganisms. This ethic has implications for how we deal with disease-causing microorganisms.

Active containment systems based on the controlled expression of a lethal gene are designed to increase containment of recombinant micro-organisms used for environmental applications. A major drawback in containment is the existence of mutations that generate surviving cells that cease to respond to the toxic effect of the lethal function. In this work the authors have developed for the first time a strategy to reduce the problem of mutations and increase the efficiency of containment based on the combination of two lethal functions acting on different cellular targets of major concern in containment, DNA and RNA, and whose expression is under control of different regulatory signals. To engineer the dual gene containment circuit, two toxin--antitoxin pairs, i.e. the colicin E3--immunity E3 and the EcoRI restriction--modification systems, were combined. The genes encoding the immunity E3 and the EcoRI methyltransferase proteins (antitoxins) were stably inserted into the chromosome of the host cell, whereas the broad-host-range lethal genes encoding the colicin E3 RNase and the EcoRI restriction endonuclease (toxins) were flanking the contained trait in a plasmid. This dual lethal cassette decreased gene transfer frequencies, through killing of the recipient cells, by eight orders of magnitude, which provides experimental evidence that the anticipated containment level due to the combination of single containment systems is generally achieved. Survivors that escaped killing were analysed and the mutational events involved were characterized.

Archaea are best known in their capacities as extremophiles, i.e. micro-organisms able to thrive in some of the most drastic environments on Earth. The protein-based surface layer that envelopes many archaeal strains must thus correctly assemble and maintain its structural integrity in the face of the physical challenges associated with, for instance, life in high salinity, at elevated temperatures or in acidic surroundings. Study of archaeal surface-layer (glyco) proteins has thus offered insight into the strategies employed by these proteins to survive direct contact with extreme environments, yet has also served to elucidate other aspects of archaeal protein biosynthesis, including glycosylation, lipid modification and protein export. In this mini-review, recent advances in the study of archaeal surface-layer (glyco)proteins are discussed.

Research has been conducted on the ecology of several bacterial species. The study has been carried out in determining whether the species abundance could be related to seasonality, and the results are reported.

Research has been conducted on the fecal bacteria regrowth in the costal environments. The distribution and factors affecting Escherichia coli, entericocci and Clostridium perfringens in the water and sediments have been investigated and the results are reported.

An effective antimicrobial packaging or food contact surface should be able to kill or inhibit micro-organisms that cause food-borne illnesses. Setting up such systems, by nisin adsorption on hydrophilic and hydrophobic surfaces, is still a matter of debate. For this purpose, nisin was adsorbed on two types of low-density polyethylene: the hydrophobic native film and the hydrophilic acrylic acid-treated surface. The antibacterial activity was compared for those two films and it was highly dependent on the nature of the surface and the nisin-adsorbed amount. The hydrophilic surfaces presented higher antibacterial activity and higher amount of nisin than the hydrophobic surfaces. The effectiveness of the activated surfaces was assessed against Listeria innocua and the food pathogens Listeria monocytogenes, Bacillus cereus, and Staphylococcus aureus. S. aureus was more sensitive than the three other test bacteria toward both nisin-functionalized films. Simulation tests to mimic refrigerated temperature showed that the films were effective at 20 and 4 °C with no significant difference between the two temperatures after 30 min of exposure to culture media. [ABSTRACT FROM AUTHOR]

We have previously reported that disruption of a maize root-expressed 9-lipoxygenase (9-LOX) gene, ZmLOX3, results in dramatic increase in resistance to diverse leaf and stalk pathogens. Despite evident economic significance of these findings, the mechanism behind this increased resistance remained elusive. In this study, we found that increased resistance of the lox3-4 mutants is due to constitutive activation of induced systemic resistance (ISR) signaling. We showed that ZmLOX3lacked expression in leaves in response to anthracnose leaf blight pathogen Colletotrichum graminicola, but was expressed constitutively in the roots, thus, prompting our hypothesis: the roots of lox3-4 mutants are the source of increased resistance in leaves. Supporting this hypothesis, treatment of wild-type plants (WT) with xylem sap of lox3-4 mutant induced resistance to C. graminicola to the levels comparable to those observed in lox3-4 mutant. Moreover, treating mutants with the sap collected from WT plants partially restored the susceptibility to C. graminicola.lox3-4 mutants showed primed defense responses upon infection, which included earlier and greater induction of defense-related PAL and GST genes compared to WT. In addition to the greater expression of the octadecanoid pathway genes, lox3-4 mutant responded earlier and with a greater accumulation of H2O2 in response to C. graminicola infection or treatment with alamethicin. These findings suggest that lox3-4 mutants display constitutive ISR-like signaling. In support of this idea, root colonization by Trichoderma virens strain GV29-8 induced the same level of disease resistance in WT as the treatment with the mutant sap, but had no additional resistance effect in lox3-4 mutant. While treatment with T. virens GV29 strongly and rapidly suppressed ZmLOX3 expression in hydroponically grown WT roots, T. virens Δsml mutant, which is deficient in ISR induction, was unable to suppress expression of ZmLOX3, thus, providing genetic evidence that SM1 function in ISR, at least in part, by suppressing host ZmLOX3 gene. This study and the genetic tools generated herein will allow the identification of the signals regulating the induction of resistance to aboveground attackers by beneficial soil microorganisms in the future. [ABSTRACT FROM AUTHOR]

This review discusses major classes of chemical sensors among microorganisms and elaborates on the recent findings on alternative strategies used by microorganisms to monitor their chemical surroundings. Discussions on transmembrane chemoreceptors, PTS taxis receptors, and energy taxis receptors are presented.

An evaluation is presented on the micronization of compost and whether such fine-gauge crushing will kill off living organisms within compost materials. While some organic matter can be rejuvenated with the addition of water, findings suggest that micronized compost should be analyzed for organism content prior to application.

The article focuses on collaborations between microbiologists with experts who studies bowels of earth. It says that Jillian Banfield works in a mine pumping toxics of earth metals to analyze and sequence its DNA wherein Michael Morowitz who studies necrotizing enterocolitis (NEC) and David Relman has collaborated with her to understand the relation of microbial mass to the disease. It also mentions that similar collaborations have been made to explore human microbiota in microbial environment.

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Microorganisms can restructure their transcriptional output to adapt to environmental conditions by sensing endogenous metabolite pools. In this paper, an Agilent customized microarray representing 4,106 genes was used to study temporal transcript profiles of Bacillus subtilis in response to valine, glutamate and glutamine pulses over 24 h. A total of 673, 835, and 1135 amino-acid-regulated genes were identified having significantly changed expression at one or more time points in response to valine, glutamate, and glutamine, respectively, including genes involved in cell wall, cellular import, metabolism of amino-acids and nucleotides, transcriptional regulation, flagellar motility, chemotaxis, phage proteins, sporulation, and many genes of unknown function. Different amino acid treatments were compared in terms of both the global temporal profiles and the 5-minute quick regulations, and between-experiment differential genes were identified. The highlighted genes were analyzed based on diverse sources of gene functions using a variety of computational tools, including T-profiler analysis, and hierarchical clustering. The results revealed the common and distinct modes of action of these three amino acids, and should help to elucidate the specific signaling mechanism of each amino acid as an effector. [ABSTRACT FROM AUTHOR]

Some applications of products of alkaliphiles, microorganisms that grow best or very well at pH values above 9 but that cannot grow or do not grow well near neutral, are discussed. Biological detergents contain alkaline enzymes from alkaliphiles and industrial production of cyclodextrin by alkaline cyclomaltodextrin glucanotransferase is an important application related to foods, chemicals and pharmaceuticals. Much of enzyme production is for the laundry detergent market. are alkaliphiles. Alkali-treated wood pulp might be biologically bleached by xylanases from alkaliphiles.

The article discusses a study on effects of free-air carbon dioxide (CO2) enrichment (FACE) on an underground processes of forest of loblolly pine, or Pinus taeda. It states that the co2 level was increased above ambient levels using a FACE apparatus, and mentions role of CO2 in plant production. It cites that the CO2 in soil increase after the first year of FACE treatment, and notes changes associated with the plant like microbial biomass.

There is a lack of empirical data concerning genetically modified microorganisms (GMMs) and their environmental fitness. In an effort to address this problem, a Pseudomonas fluorescens isolate was genetically modified for application in various environmental conditions. Upon analysis, fitness of the recombinant organism was found to be dependent on the environment. Metabolic load was also found to affect fitness. On the other hand, site of chromosomal insertion of marker genes had little effect on the fitness of the recombinant organisms.

The summit of Mount Rainier is attempted by up to 10,000 climbers per year. During their two-day ascents, they use either a pit or solar-assisted toilet at Camp Muir, or the snowfields for disposal of their feces and urine. Mount Rainier National Park personnel know neither the flow path directions nor the concentrations of microorganisms or chemicals from these wastes during annual runoff. This initial study attempted to determine the concentration of fecal coliforms, fecal streptococci, enterococci, E. coli, Pseudomonas aeruginosa, chloride ion, conductivity and total dissolved solids (TDS) in runoff along the most frequently used ascent route to the summit, the Muir Snowfield. During the five-week sampling period, no fecal microorganisms were found in the runoff. Although conductivity and TDS values approached those of distilled water, samples from the margins of the snowfield had values nearly twice as high as runoff sampled from fell fields within the snowfield. Computer modeling of the predicted flow paths of runoff completed after field work indicated that the main areas of runoff may be hydrogeologically different from those areas sampled. Further studies need to be completed to study the fate of feces and fecal organisms, and the flow paths of runoff contaminated by human wastes., Introduction As is typical of many of our national parks, Mount Rainier National Park has experienced a consistent increase in visitors since it was established in 1899 (1). Located in [...]

Microorganisms have a significant influence on the environmental fate of radionuclides in aquatic and terrestrial ecosystems with a multiplicity of physico-chemical and biological mechanisms effecting changes in mobility and speciation. Physico-chemical mechanisms of removal include association with extracellular materials, metabolites and cell walls which are features of living and dead organisms. In living cells, some physico-chemical processes are reversible, influenced by metabolism and changing environmental conditions. Metabolism-dependent mechanisms of radionuclide immobilization include sulphide precipitation, transport and intracellular compartmentation and/or sequestration by proteins and peptides. In addition, chemical reduction to less soluble forms can result in immobilization. Microbial processes involved in radionuclide solubilization include autotrophic and heterotrophic leaching, and complexation by siderophores and other metabolites. Such mechanisms are important components of biogeochemical cycles for radionuclides and should be considered in any analyses of environmental radionuclide contamination. In addition, several microorganism-based biotechnologies are receiving interest as potential treatment methods.

Fermentative anaerobic and aerobic bacteria and polymer-degrading micro-organisms were enumerated in refuse excavated from municipal solid waste landfills in New York, Florida and Arizona. Anaerobic bacteria ranged from 10(super 5) to 10(super 8) colony forming unit (c.f.u.) (g dry wt of refuse)(super -1); aerobic bacteria ranged from 10(super 4) and 10(super 7) c.f.u. (g dry wt)(super -1). Only a small proportion (0-15 percent) of the fermentative population produced extracellular enzymes capable of hydrolyzing protein and starch.

Modelling of the interactions between antibiotic production and antibiotic degradation reveals that these opposing activities are key to maintaining diversity in microbial communities. See Letter p.516 Microbial community structure Understanding how stability in multispecies communities is maintained in the face of negative interactions via antibiotic production is a key goal in microbial ecology. Most ecological models for antibiotic interactions assume pairwise relationships between species that result in rock-scissor-paper type cycling and spatial separation. This doesn't reflect the in situ observations though, where communities are far more intermixed. Instead, Eric Kelsic and colleagues propose a three-species interaction assay, in which one species is capable of antibiotic degradation. Using a mixture of modelling and experimental validation, the authors show that including antibiotic degraders allows the system to robustly move towards an intermixed stable state., Author(s): Carl T. Bergstrom [sup.1] , Benjamin Kerr [sup.1] Author Affiliations: (1) Carl T. Bergstrom and Benjamin Kerr are in the Department of Biology, University of Washington, Seattle, Washington 98195-1800, [...]

Bacteria could have a larger role than previously thought in generating uranium ores. Bacteria could have a larger role than previously thought in generating uranium ores., Author Affiliations: A sediment core from uranium deposits in Wyoming reveals a form of the element that's made by microbes. Amrita Bhattacharyya New Content Item Uranium deposits made by microbes [...]