Microbial community

The kinetics of abiotic oxidation in the dark and the kinetics of biological mineralization in soil and in a compost environment of thermally oxidized LDPE were studied. It was demonstrated that different activation energies are obtained for the thermal oxidation, depending on the composition of the materials. Significantly higher levels of biodegradability have been obtained in a soil environment at 23 C compared with the compost environment at 58 C. After two years of mineralization, 91% conversion to carbon dioxide was obtained in the soil test, compared with 43% in the compost test. The differences between fungal, archaeal and bacterial community structures in soil and compost after 607 days of biodegradability assay were mapped out. It was found that the most dominant bacterial and fungal terminal restriction fragments (TRFs) in the compost containing the test material are significantly different from the TRFs in the other environments.

Gut microbial communities represent one source of human genetic and metabolic diversity. To examine how gut microbiomes differ among human populations, here we characterize bacterial species in fecal samples from 531 individuals, plus the gene content of 110 of them. The cohort encompassed healthy children and adults from the Amazonas of Venezuela, rural Malawi and US metropolitan areas and included mono-and dizygotic twins. Shared features of the functional maturation of the gut microbiome were identified during the first three years of life in all three populations, including age-associated changes in the genes involved in vitamin biosynthesis and metabolism. Pronounced differences in bacterial assemblages and functional gene repertoires were noted between US residents and those in the other two countries. These distinctive features are evident in early infancy as well as adulthood. Our findings underscore the need to consider the microbiome when evaluating human development, nutritional needs, physiological variations and the impact of westernization.

Dynamic, multicompartment in vitro gastrointestinal simulators are often used to monitor gut microbial dynamics and activity. These reactors need to harbor a microbial community that is stable upon inoculation, colon region specific, and relevant to in vivo conditions. Together with the reproducibility of the colonization process, these criteria are often overlooked when the modulatory properties from different treatments are compared. We therefore investigated the microbial colonization process in two identical simulators of the human intestinal microbial ecosystem (SHIME), simultaneously inoculated with the same human fecal microbiota with a high-resolution phylogenetic microarray: the human intestinal tract chip (HITChip). Following inoculation of the in vitro colon compartments, microbial community composition reached steady state after 2 weeks, whereas 3 weeks were required to reach functional stability. This dynamic colonization process was reproducible in both SHIME units and resulted in highly diverse microbial communities which were colon region specific, with the proximal regions harboring saccharolytic microbes (e.g., Bacteroides spp. and Eubacterium spp.) and the distal regions harboring mucindegrading microbes (e.g., Akkermansia spp.). Importantly, the shift from an in vivo to an in vitro environment resulted in an increased Bacteroidetes/Firmicutes ratio, whereas Clostridium cluster IX (propionate producers) was enriched compared to clusters IV and XIVa (butyrate producers). This was supported by proportionally higher in vitro propionate concentrations. In conclusion, high-resolution analysis of in vitro-cultured gut microbiota offers new insight on the microbial colonization process and indicates the importance of digestive parameters that may be crucial in the development of new in vitro models.

and total counts) correlated negatively. The overall assessment of soil activity, the soil respiration, did not correlate with either. Significant correlations were found between the principal components of pH, CLPP, EAA, and culturable and total number of bacteria, while no correlations were found to soil respiration, loss on ignition and soil moisture content. The pH in the test system might make differences between bacterial communities more detectable. The functional characterization of the bacterial communities by the growth based CLPP correlated positively to the bacterial community function assayed by the EAA, which is independent of growth and, hence, more closely reflects the in situ activities.

The extracellular and intracellular metabolites formed upon exposure of activated sludge microorganisms to a sublethal concentration of N-ethylmaleimide were monitored by liquid chromatography with ion trap mass spectrometry. The metabolite N-ethylsuccinimido-S-glutathione (m/z 433) was converted rapidly to N-(2-oxoethyl)-2,2-(propionylamino)propanamide (m/z 187) and N-ethylmaleamic acid (m/z 144).

Hybridization probes produced from DNA sequences have proven to be a powerful tool in the rapid and sensitive analysis of natural microbial communities. By using function-specific probes, such as those identifying genes coding for photosynthesis, the potential a microbial community has for performing a given function may be rapidly determined. Gene probes have also been used in the idelatification and isolation of a specific catabolic genotype in less than one-fourth the time required for the conventional culture enrichment technique. Species-specific probes constructed from portions of genes coding for ribosomal RNA have been used for the rapid identification and enumeration of bacterial species in environmental samples. The use of reassociation kinetics as a measure of community diversity and complexity is also discussed. The successful application of this technique to community analysis may reduce the time required from 1 year, for conventional analysis, to 2 weeks.

Phospholipid fatty acid (PLFA) analysis of a soil microbial community was coupled with 13C isotope tracer analysis to measure the community’s response to addition of 35 μg of [13C]toluene ml of soil solution−1. After 119 h of incubation with toluene, 96% of the incorporated 13C was detected in only 16 of the total 59 PLFAs (27%) extracted from the soil. Of the total 13C-enriched PLFAs, 85% were identical to the PLFAs contained in a toluene-metabolizing bacterium isolated from the same soil. In contrast, the majority of the soil PLFAs (91%) became labeled when the same soil was incubated with [13C]glucose. Our study showed that coupling 13C tracer analysis with PLFA analysis is an effective technique for distinguishing a specific microbial population involved in metabolism of a labeled substrate in complex environments such as soil.

For most marine aquaculture species, one of the main bottlenecks is the stable production of high quality juveniles. The high and unpredictable mortality in the first weeks after hatching of marine fish larvae remains a challenging problem that needs to be solved. The severity of the problem differs between species, but cannot be considered adequately solved for any species. Both scientific evidence and experience in hatcheries for a variety of fish, shrimp and shellfish species are accumulating as support for the hypothesis that detrimental fishmicrobe interactions are the cause of these problems. Host-microbe interactions in reared fish are still poorly understood, except for a few pathogens, and empirical data of the quality required to test this hypothesis, are lacking. This article provides an overview on the current knowledge of the microbial environment of fish larvae, including methodological aspects to characterize the microbial community (both using culture-dependent and culture-independent methods). Further, the current knowledge of the immunology of fish larvae is reviewed, including recent advances in the understanding of toll-like receptors, inflammatory cytokines, mast cells and piscidins, and the ontogeny of the adaptive immune system. Finally, we provide an overview of the state of the art with respect to steering of microbial communities associated with fish larvae-both steering of community composition and of its activity (e.g. by quorum sensing interference).

Paddy soils make up the largest anthropogenic wetlands on earth. They may originate from any type of soil in pedological terms, but are highly modified by anthropogenic activities. The formation of these Anthrosols is induced by tilling the wet soil (puddling), and the flooding and drainage regime associated with the development of a plough pan and specific redoximorphic features. Redox potential oscillations due to paddy management control microbial community structure and function and thus short-term biogeochemical processes. After flooding, microbial reduction processes sequentially use NO 3 -, Mn 4+ , Fe 3+ , SO 4 2-as electron acceptors, accompanied by the emission of the trace gases N 2 O, N 2 , H 2 S, CH 4 anddue to reduction-induced increasing pH -NH 3 . This results in N losses and low N fertilizer use efficiency. However, transport of atmospheric O 2 to the roots via the rice plant's aerenchyma modifies conditions in the rhizosphere, leading to nitrification and methane oxidation, and precipitation of Mn and Fe oxides. High concentrations and fluxes of dissolved organic matter (DOM) in paddy soils from plant debris trigger microbial activity and thus the emission of greenhouse gases. Retention of DOM by soil minerals and its subsequent stabilisation against microbial decay depend on the redox state (e.g. DOM precipitation by Fe 2+ under anaerobic conditions). Oscillation in redox conditions may enhance retention and stabilisation of DOM by Fe oxyhydroxides. Induced by the periodic short-term redox cycles, paddy management over long periods has strong effects on long-term biogeochemical processes. Frequent irrigation intensifies mineral weathering and leaching processes. High concentrations of DOM during flooding seasons enhance the changes and the release of structural iron in clay minerals, and support the formation of ferrihydrite. Repeated redox alternations lead to a translocation of iron in various directions, and particularly increase the crystallinity of iron oxides. This results also in higher total iron oxide contents in paddy compared to non-paddy soils. The large accumulation of soil organic matter (SOM) observed in some, but not all paddy soils, is considered to be due to high input of plant residues and charred material associated with retarded decomposition under anaerobic conditions. There is also evidence of SOM stabilisation via occlusion into aggregates and phytoliths as well as interactions with clay minerals and iron oxides. SOM accumulation in paddy subsoils can be explained by downward movement of DOM and its stabilisation by interaction with iron oxides. A specific feature of paddy soils is the coupling of organic matter turnover with mineral transformations and fluxes, which seem to be intensified by the alternating redox conditions with increasing age of paddy soil development. Bioavailability of soil organic N is strongly coupled to SOM cycling and is a crucial parameter determining crop yield. Anaerobic conditions inhibit N mineralization, with a high risk of gaseous N losses. In paddy soils the management-induced, microbially mediated redox processes control the dynamics of soil minerals and soil organic matter, which are strongly related to the microbial accessibility of C and N, but also of Fe.

A study of 25 paper mill slime deposits and one additive revealed nine pink-pigmented bacterial isolates, eight of which were different from pink-pigmented bacteria identified in the paper industry in the middle 1900s. The pinkpigmented bacteria described previously in pulp and paper included Micrococcus agilis, Bacillus subtilis, Serratia sp. and Alcaligenes viscosus. With the exception of one isolate, Micrococcus sp., these isolates possessed many cultural, biochemical and chemical properties which were different from the ones previously reported for paper mills. Eight of these bacteria were Gram-negative rods or filamentous, aerobic and positive for catalase production. Two isolates were methylotrophic, oxidizing methanol and identified as Methylobacterium zatmanii. Cellular fatty acid analysis and other characteristics showed one isolate to be Roseomonas sp. Using 16S rRNA gene sequencing, one isolate which was a Gram-negative rod was identified as Deionococcus grandis. Four bacteria had cells that were long or filamentous and these were isolated from mills with pink slime problems. The identity of one of the filamentous bacteria was determined by 16S rRNA gene sequencing to be close to Flectobacillus sp. strain MWH38. Most of the isolates were susceptible to 11 industrial biocides.

We compared the abilities of Biolog’s GN and ECO plates to distinguish among aerobic and heterotrophic bacterial communities in samples from six aquatic environments. The Biolog system is based on interpreting patterns of sole-carbon substrate utilization indicated by color development in a 96-well microtiter plate. Whether of fresh or saltwater origin, bacterial communities utilized >95% of substrates in both types of plates. Samples from any one environment exhibited similar time courses of average well color development (AWCD) in both GN and ECO plates. Principal component analysis was performed on data sets resulting from combinations of algorithms (AWCD and curve-integration methods) and levels of color development (end-point and set-point approaches). In all cases, the two types of plates demonstrated an equal capacity to discriminate among the heterotrophic expressions of the six microbial communities. Substantial deviation from an anticipated 1:1 correspondence occurred when color development of 25 substrates common to both types of plates was compared. The discrepancies likely are related to the different formulations of low-nutrient media in GN and ECO plates.

We compared the microbial community composition in soils from the Brazilian Amazon with two contrasting histories; anthrosols and their adjacent nonanthrosol soils of the same mineralogy. The anthrosols, also known as the Amazonian Dark Earths or terra preta, were managed by the indigenous pre-Colombian Indians between 500 and 8,700 years before present and are characterized by unusually high cation exchange capacity, phosphorus (P), and calcium (Ca) contents, and soil carbon pools that contain a high proportion of incompletely combusted biomass as biochar or black carbon (BC). We

Le septembre 2008 Titre : Caractérisation moléculaire et physiologique des Facteurs de Réponse à l'Ethylène (ERF) chez la tomate (Solanum lycopersicon) JURY Mr. Jean-Claude PECH Président (INP-ENSAT) Mr. Christophe ROTHAN Rapporteur (INRA Bordeaux) Mr. Guy ALBAGNAC Rapporteur (INRA Montpellier) Mme. Mathilde CAUSSE Examinatrice (INRA Avignon) Mr. Masaru OHME-TAKAGI Examinateur (AIST Tsukuba) Mr. Farid REGAD Examinateur (INP-ENSAT) Mr. Mondher BOUZAYEN Directeur de thèse (INP-ENSAT) Mr. Xavier BERTHET Membre invité (NINSAR Barcelone) Ecole doctorale : Biologie Santé et Biotechnologie Unité de recherche : UMR990 INP-ENSAT/INRA Génomique et Biotechnologie des Fruits Directeur de Thèse : Pr. Mondher BOUZAYEN Je remercie Mondher BOUZ AYEN et Masaru OHME-T AKAGI pour m'avoir acceuilli, encadré et fait confiance pendant ce travail de thèse. Je remercie Farid REGAD pour les discussions scientifiques ainsi que son soutien jusqu'à très tard dans la nuit. Je remercie Jean-Claude PECH et Alain LATCHE pour avoir échangé scientifiquement avec moi. Un merci tout spéciale à Corinne, Isabelle, Simone, Marie, Salma et Benoît pour tous les moments de sciences (ou pas) partagés. Merci à Prassad, Ravi, Wangshu et Lanlan d'avoir participé à cette aventure. Un grand merci à Hélène, Carole, Lydie, Olivie r et Dominique pour la transformation et le suivi des plantes transgéniques (et ce n'est pas peu dire). Un grand merci à l'ensemble des membres du laboratoire pour tous les moments partagés, de sciences, et de convivialité : Christian, Je tiens également à remercier tous les membres du Research Institute of Genome-based Biofactory Miho Ikeda, Akira Iwase, Yoshimi Umemura, Tomotsugu Koyama, Masahito Shikata, Kyoko Matsui, Nobut aka Mitsuda, Naoko Kaneta , sans qui cette thèse n'aurait pas eu le même parfum. ありがとう. Merci aussi à Toshi et Hiroshi Ez ura de m'avoir acceuilli. Merci à mes proches qui m'ont soutenu pendant ces années, mes parents et mon frère. Enfin, je tiens à remercier tout particulièrement Laëtitia qui m'a suivi au bout du monde (au sens propre et au sens figuré), pour son soutien permanent et sans qui ce travail aurait été un peu différent. (2007): Isolation and characterization of a Vitis vinifera transcription factor, VvWRKY1, and its effect on responses to fungal pathogens in transgenic tobacco plants J Exp Bot.;58 (8):

Wildfi re-produced charcoal is a common component of soils, affecting a range of important abiotic and biotic soil processes. Our ability to predict the effects of charcoal addition to soil is currently limited, however, by our understanding of how charcoal affects the soil microbial community mediating many of these processes. This study sought to improve our understanding of the relationship between charcoal addition and soil microbial biomass and activity among temperate soils. Charcoal was added to four distinct temperate soils, a Mollisol, an Alfi sol, an Entisol, and a Spodosol, at fi ve application levels ranging from 0 to 0.1 kg charcoal kg −1 soil, and incubated at 25°C with measurements at approximately 0, 1.5, and 3 mo. We hypothesized that microbial biomass and activity would increase with increasing charcoal application in all soils, but the relative magnitude of the response would depend on the texture and fertility of each soil. As hypothesized, microbial biomass and activity and Bray P increased signifi cantly with increasing charcoal application, while extractable N decreased. The coniferous forest soil provided a notable exception to the general patterns of N availability, having the highest total extractable N at the highest charcoal application level. Our results suggest that charcoal additions affected microbial biomass, microbial activity, and nutrient availability in relatively similar ways in all four soils that we studied, suggesting considerable predictability in response to charcoal application. Differences in the magnitude of the microbial response, however, appeared dependent on differences in nutrient availability among soils.

Microbial life predominates in the ocean, yet little is known about its genomic variability, especially along the depth continuum. We report here genomic analyses of planktonic microbial communities in the North Pacific Subtropical Gyre, from the ocean's surface to near-sea floor depths. Sequence variation in microbial community genes reflected vertical zonation of taxonomic groups, functional gene repertoires, and metabolic potential. The distributional patterns of microbial genes suggested depth-variable community trends in carbon and energy metabolism, attachment and motility, gene mobility, and host-viral interactions. Comparative genomic analyses of stratified microbial communities have the potential to provide significant insight into higher-order community organization and dynamics.

The discovery of gullies and debris aprons raises the question of the existence of aqueous environments on Mars in recent geological times and its astrobiological implications. Three cases of such environments are surveyed at MOC high resolution in the E-Gorgonum chaos and Newton and Hale craters. The regional setting of these craters suggests that the mechanisms of aquifer destabilization, flow discharge, and gully formation in these three cases result from local geological triggers that can include impact cratering, and tectonic processes, rather than climate or insolation factor. We take as a working hypothesis that microbial life appeared on Mars in ancient geological times, probably in a geothermal environment but potentially evolving via infrared detection systems to give photosynthetic communities under the selective pressure of energetic solar radiation. We hypothesize that some microbial communities could have survived underground in either dormant or active state, or that their biomolecules could be preserved either frozen or desiccated in the subsurface beneath the upper oxidized zone. We assess the known environmental constraints for life and what type of potential habitats are provided in these three craters by aquifer discharges using comparison with terrestrial analogues and their associated microbial communities. These environments include: (1) the release of water on a dry crater floor in E-Gorgonum and the possibility for microorganisms and preserved biomolecules to be flushed out and mixed in with the sediment exposed at the surface; (2) the evidence of a recent lacustrine episode in the Newton crater with analogy to Antarctic Dry Valley lakes; (3) the exposure on the floor of Hale crater of material from a regional subsurface that is likely to have retained traces of one of the oldest martian bodies of water recognized to date in the Argyre basin. We show how the water in Argyre (∼3.8 billion years ago (Gya) was likely to have been alterated by hydrothermal processes and how the subsequent formation of the 150-km Hale crater on the northern ring of Argyre generated hydrothermal pumping. This accounts for the anomalously high location of the springs on the crater crests today with respect to the rest of the regional subsurface distribution. Finally, we envision current impact cratering as a factor for destabilizing aquifers on Mars today, thus creating new environments. We analyze the implications of impacts for two geological types of rock units that could harbor traces of life. As a result, we compare the potential of astrobiological exploration of crater floors, rims, and ejecta on future missions to Mars. c 2001 Elsevier Science

Sponges of the Aplysinidae family contain large amounts of bacteria that are embedded within the sponge tissue matrix. In order to determine the stability and specificity of the Aplysina^microbe association, sponges were maintained in recirculating seawater aquariums for 11 days. One aquarium was left untreated, a second one contained 0.45 Wm filtered seawater (starvation conditions) and the third one contained 0.45 Wm filtered seawater plus antibiotics (antibiotics exposure). Changes in the microbial community were monitored using group-specific, 16S rRNA targeted oligonucleotide probes, by denaturing gradient gel electrophoresis and by electron microscopic observations. Furthermore, the changes in the natural product profile were monitored using high-performance liquid chromatography. The measured parameters showed that a large fraction of the sponge-associated microbial community could not be cleared under the given experimental conditions. Based on these cumulative results we postulate that a large fraction of sponge-associated bacteria resides permanently in the Aplysina aerophoba mesohyl pointing to a highly integrated interaction between the host sponge and associated microorganisms. ß

The application of soil solarization (SS), one of the most promising techniques for the control of soilborne pathogens, is seriously limited by the drawback regarding the disposal of the used plastic materials. A possible solution to this problem is the use of biodegradable plastics. The aim of this study was to make comparisons between the impact of SS performed with biodegradable materials and that of SS with plastic films and other pest management techniques (i.e. organic matter amendment, calcium cyanamide and Dazomet fungicide application) on crop productivity, soilborne disease incidence, weed suppression, and soil chemical (total N, NH 4 -N, nitrate, available phosphorus, organic matter, hydrolysis of fluorescein diacetate) and microbial (cultivable Pseudomonas, DGGE fingerprinting of bacterial 16S-and fungal 28S rRNA gene fragments from total soil community DNA) parameters. We carried out field experiments in two types of soil with different textures (clay and sand) artificially inoculated with Fusarium oxysporum f.sp. lycopersici (vs. tomato) and Sclerotinia minor (vs. lettuce). The temperature of soils covered with solarizing materials was always higher than that of bare soils, but plastic cover was more effective and consistent in rising soil temperature compared to biodegradable materials. Plant growth promotion by SS was limited, especially compared to Dazomet and organic matter applications, and a positive effect was observed only for lettuce in the clay soil. Differently, both plastic and biodegradable solarizing materials were effective in reducing lettuce drop caused by S. minor. Weed development was significantly suppressed by Dazomet application and SS with plastic film, while control with biodegradable materials was limited. SS had a variable and limited effect on chemical and microbial parameters, with a general tendency to reduce richness of bacteria and fungi. Dazomet caused the most pronounced reduction of the microbial community diversity in both soil types and a significant stimulation of the fluorescent Pseudomonas group. Organic amendment significantly enhanced the organic matter content, the hydrolysis of fluorescein diacetate and the Pseudomonas population. Among all measured soil parameters, the size of the fluorescent Pseudomonas population emerged as the most important factor affecting crop productivity. The results of this experimentation show the potential of using biodegradable solarizing materials in place of plastic films, but also indicate the need for improving their properties to obtain performances comparable to those of other pest management techniques.

The occurrence of microbial colonisation on artificial surfaces in urban areas (building facades, roof tiles) and interiors (damp rooms: silicone sealings, wallpaper) causes not only an aesthetically unacceptable discolouration of the surface, it also represents a conspicuous problem in terms of biodeterioration, accelerated weathering and a potential health risk for humans by fungal mycotoxines. The most conspicuous organisms responsible for biofouling terrestrial surfaces are fungi and green microalgae as well as cyanobacteria. Microorganisms are often estimated by cultivating, but the biomass can be misjudged because of contaminations or the existence of nonculturable cells and spores. By using ergosterol as a specific biomarker for living fungi and yeasts in combination with chlorophyll a for aeroterrestrial microalgae it is possible to quantify fungal and algal infection independent from cultivation and undisturbed by surface (dis)colouration. Using HPLC and photometric methods, conversion factors for microbial biomass were determined in representative fungal and algal species: 5 mg ergosterol g À1 fungal dry biomass and 23 mg chlorophyll a g À1 algal dry biomass. The applied wipe technique allowed a non-invasive sampling and evaluating of infections per square meter. Very low detection limits for ergosterol and chlorophyll a permitted determining fungi and algae before they become macroscopically visible. Up to 36 mg ergosterol m À2 and 180 mg chlorophyll a m À2 were detected on outdoor artificial surfaces, equivalent to approximately 7 g m À2 fungal dry biomass and 8 g m À2 algal dry biomass. The distribution and the composition of the microbial communities varied strongly between the sampling locations. Fungi were observed above windows of damp rooms or at more sun-exposed locations, whereas algae covered more wet and shadowed surfaces. The established methods are well suited for the precise joint determination of fungal and algal biomass in microbial communities of natural biofilms on artificial surfaces as a pre-condition for the development of prevention strategies against microbial colonisation. r

Community level physiological profile Mesocosms BIOLOG ecoplate a b s t r a c t A novel experiment design based on the axial simplex design was used to study the effects of earthworm functional diversity on microbial biomass and microbial community level physiological profiles in soils. This mesocosm experiment was carried out at two densities of earthworm and at two levels of food supply. Soil mesocosms were maintained for 7 months and watered each week with 300 ml of distilled water. At the end of this period the soil columns were divided into upper and lower halves and microbial biomass carbon and functional diversity assessed. Greater microbial biomass and activity was found in the upper layer of soil. Food supply was the major driver leading to increased microbial activity and biomass. Increased earthworm biomass had the opposite effect. In the lower soil layer, the presence of anecic worms had the greatest effect on microbial biomass and activity.

by in situ X-ray observations based on the same pressure scale in the previous study . The overpressure was calculated using these boundaries. We observed the pressure to drop during the transformation by 1-2 GPa, but this would not affect the transformation rate significantly because the overpressure is very large in the present study. This has been confirmed in the post-spinel transformation 7 .

Over the last decade, important advances in molecular biology led to the development of culture-independent approaches to describing bacterial communities. These new strategies, based on the analysis of DNA directly extracted from environmental samples, circumvent the steps of isolation and culturing of bacteria, which are known for their selectivity leading to a non-representative view of the extent of bacterial diversity. This review provides an overview of the potentials and limitations of some molecular approaches currently used in microbial ecology. Examples of applications to the study of indigenous soil microbial community illustrate the feasibility and the power of such approaches. © 2000 Éditions scientifiques et médicales Elsevier SAS bacterial community / soil / molecular biology / DNA / genetic diversity / genetic structure

Reed canary grass (Phalaris arundinacea, L.) invasion of wetlands is an ecological issue that has received attention, but its impact on soil microbial diversity is not well documented. The present study assessed the size (substrate-induced respiration), catabolic diversity (CLPP, community level physiological profiles) and composition (selective inhibition) of the soil microbial community in invaded (>95% P. arundinacea cover) and in non-invaded areas of a wetland occupied by native species grown either as a mixed assemblage (22 species) or as quasi-monotypic stands of Scirpus cyperinus (74% cover). The study also tested the hypothesis that decomposition of ligninand phenolics-rich plant tissues would be fastest in soils exhibiting high catabolic diversity. Results showed that soil respiration, microbial biomass and diversity were significantly higher (P<0.03; 1.5 to 3 fold) in P. arundinacea-invaded soils than in soils supporting native plant species. Fungal to bacterial ratios were also higher in invaded (0.6) than in noninvaded (0.4) plots. Further, canonical discriminant analysis of CLPP data showed distinct communities of soil decomposers associated with each plant community. However, these differences in microbial attributes had no effect on decomposition of plant biomass which was primarily controlled by its chemical composition. While P. arundinacea invasion has substantially reduced plant diversity, this study found no parallel decline in the size and diversity of the soil microbial community in the invaded areas.

Soil microbial biomass plays important roles in nutrient cycling, plant-pathogen suppression, decomposition of residues and degradation of pollutants; therefore, it is often regarded as a good indicator of soil quality. We reviewed more than a hundred studies in which microbial biomass-C (MB-C), microbial quotient (MB-C/TSOC, total soil organic carbon) and metabolic quotient (qCO 2 ) were evaluated with the objective of understanding MB-C responses to various soil-management practices in Brazilian ecosystems. These practices included tillage systems, crop rotations, pastures, organic farming, inputs of industrial residues and urban sewage sludge, applications of agrochemicals and burning. With a metaanalysis of 233 data points, we confirmed the benefits of no-tillage in preserving MB-C and reducing qCO 2 in comparison to conventional tillage. A large number of studies described increases in MB-C and MB-C/TSOC due to permanent organic farming, also benefits from crop rotations particularly with several species involved, whereas application of agrochemicals and burning severely disturbed soil microbial communities. The MB-C decreased in overgrazed pastures, but increased in pastures rotated with wellmanaged crops. Responses of MB-C, MB-C/TSOC and qCO 2 to amendment with organic industrial residues varied with residue type, dose applied and soil texture. In conclusion, MB-C and related parameters were, indeed, useful indicators of soil quality in various Brazilian ecosystems. However, direct relationships between MB-C and nutrient-cycling dynamics, microbial diversity and functionality are still unclear. Further studies are needed to develop strategies to maximize beneficial effects of microbial communities on soil fertility and crop productivity.

Hydrogen (H 2) production from simulated cheese processing wastewater via anaerobic fermentation was conducted using mixed microbial communities under mesophilic conditions. In batch H 2 fermentation experiments H 2 yields of 8 and 10 mM/g COD fed were achieved at foodto-microorganism (F /M) ratios of 1.0 and 1.5, respectively. Butyric, acetic, propionic, and valeric acids were the major volatile fatty acids (VFA) produced in the fermentation process. Continuous H 2 fermentation experiments were also performed using a completely mixed reactor (CSTR). The pH of the bioreactor was controlled in a range of 4.0-5.0 by addition of carbonate in the feed material. Maximum H 2 yields were between 1.8 and 2.3 mM/g COD fed for the loading rates (LRs) tested with a hydraulic retention time (HRT) of 24 h. Occasionally CH 4 was produced in the biogas with concurrent reductions in H 2 production; however, continuous H 2 production was achieved for over 3 weeks at each LR. The 16S rDNA analysis of DNA extracted from the bioreactors during periods of high H 2 production revealed that more than 50% of the bacteria present were members of the genus Lactobacillus and about 5% were Clostridia. When H 2 production in the bioreactors decreased concurrent reductions in the genus Lactobacillus were also observed. Therefore, the microbial populations in the bioreactors were closely related to the conditions and performance of the bioreactors.

Methanogenesis provides a means of H 2 disposal and a mechanism to maintain low partial H 2 pressure in the rumen, a prerequisite for efficient ruminal fermentation. As methanogens possess stringent requirements for cultivation, only a few species have been successfully isolated from the rumen and cultured. Culture independent molecular based approaches have provided new insight into the diversity, prevalence and role of methanogens within the overall rumen microbial community. In addition, recent developments in next generation sequencing technology have enabled the ruminal microbial community to be investigated at a metagenomic level, providing information to explore the structure, function and metabolic diversity of microbial communities. This review summarizes existing molecular technologies utilized in studies of ruminal methanogens by outlining their advantages and limitations, and introduces future applications of next generation sequencing approaches for studying the ecology of ruminal methanogens. These approaches could provide new understanding of the mechanisms of methanogenesis, as well as interactions of methanogens with other members of the rumen microbial community. An understanding of the fundamental role of methanogens in ruminal CH 4 production would provide insight into methods of curtailing emissions of this greenhouse gas from ruminants.

Little information is currently available about water column microbial processes or mortality during Arctic winter. To address this paucity, we used epifluorescence microscopy and dilution experiments to determine the abundance of flagellates, bacteria and virus-like particles (VLP) and the rates of bacterial growth, bacterivory and virus-induced mortality in subzero-temperature bottom waters (≤ 230 m) of Franklin Bay during February and March 2004, when ice-covered surface waters were highly oligotrophic (maximum chlorophyll a value of 0.09 µg l -1 ). We focused on bottom waters due to the possible importance of sediment resuspension as a source of organic matter. While flagellates were present at low densities (1.5 to 3.1 × 10 2 ml -1 ), bacterial concentrations resembled those from other seasons in the region and increased over the 5 wk sampling period, from 1.4 × 10 5 to 3.0 × 10 5 ml -1 . VLPs were typically an order of magnitude more abundant than bacteria (range of 1.4 to 4.5 × 10 6 VLP ml -1 ) and, like the fraction of particle-associated bacteria (but not total bacteria), correlated with particulate organic carbon concentration (r s = 0.82, p < 0.04, n = 7). Grazing rates, whether measured in dilution experiments or calculated from flagellate abundance, were low or undetectable (maximum of -0.004 h -1 ). Of 3 parallel experiments, 2 yielded substantial virus-induced mortality (-0.006 to -0.015 h -1 ), comparable to or exceeding the intrinsic bacterial growth rate (0.010 h -1 in both experiments) and suggesting viruses were the more important agents of bacterial mortality under these conditions. Using a viral reduction approach, VLP production measured in the water column or ice-moored sediment traps was commonly low (0.3 to 7.7 × 10 4 VLP ml -1 h -1 ) or undetectable, highly variable among replicates and, when measurable, implied viral turnover times between 0.9 and 12 d. In general, our results show that, despite the oligotrophy of Arctic winter, bottom water bacterial communities can remain active and subject to viral predation.

Microcalorimetry was applied to assess and compare the toxic effect of heavy metals, such as As, Cu, Cd, Cr, Co, Pb and Zn, on the soil microbial activities and community. About 1.0 g soil spiked 5.0 mg glucose and 5.0 mg ammonium sulfate, the microbial activities were recorded as power-time curves, and their indices, microbial growth rate constant k, total heat evolution Q T , metabolic enthalpy H met and mass specific heat rate J Q/S , were calculated. Comparing these thermodynamic parameters associated with growth yield, a general order of toxicity to the soil was found to be Cr > Pb > As > Co > Zn > Cd > Cu. When soil was exposed to heavy metals, the amount of bacteria and fungi decreased with the incubation time, and the bacterial number diminished sharply. It illustrates that fungi are more tolerant, and bacteria-fungi ratio would be altered under metal stress. To determine the status of the glucose consumed, a glucose biosensor with eggshell membrane was used to measure the remaining glucose in soil sample. Results showed that the time at which glucose was consumed completely was agreed with the microcalorimetric time to a large extent, and depended on the toxicity of heavy metals as well.

Effluent organic matter Managed aquifer recharge Riverbank filtration Biotransformation Co-metabolism Primary substrate a b s t r a c t This study explored the effect of different bulk organic carbon matrices on the fate of trace organic chemicals (TOrC) during managed aquifer recharge (MAR). Infiltration through porous media was simulated in biologically active column experiments under aerobic and anoxic recharge conditions. Wastewater effluent derived organic carbon types, differing in hydrophobicity and biodegradability (i. e., hydrophobic acids, hydrophilic carbon, organic colloids), were used as feed substrates in the column experiments. These carbon substrates while fed at the same concentration differed in their ability to support soil biomass growth during porous media infiltration. Removal of degradable TOrC (with the exception of diclofenac and propyphenazone) was equal or better under aerobic versus anoxic porous media infiltration conditions. During the initial phase of infiltration, the presence of biodegradable organic carbon (BDOC) enhanced the decay of degradable TOrC by promoting soil biomass growth, suggesting that BDOC served as a co-substrate in a cometabolic transformation of these contaminants. However, unexpected high removal efficiencies were observed for all degradable TOrC in the presence of low BDOC concentrations under well adopted oligotrophic conditions. It is hypothesized that removal under these conditions is caused by a specialized microbial community growing on refractory carbon substrates such as hydrophobic acids. Findings of this study reveal that the concentration and character of bulk organic carbon present in effluents affect the degradation efficiency for TOrC during recharge operation. Specifically aerobic, oligotrophic microbiological soil environments present favorable conditions for the transformation of TOrC, including rather recalcitrant compounds such as chlorinated flame retardants. (J.E. Drewes). A v a i l a b l e a t w w w . s c i e n c e d i r e c t . c o m j o u r n a l h o m e p a g e : w w w . e l s e v i e r . c o m / l o c a t e / w a t r e s 0043-1354/$ -see front matter ª w a t e r r e s e a r c h 4 4 ( 2 0 1 0 ) 4 4 9 -4 6 0

In this chapter, we review empirical evidence for stronger allelopathic effects of exotic European invaders on North American natives than on other European species. We argue that this evidence provides critical insights into the impor- tance of coevolutionary relationships within plant communities. We discuss how the disruption of these and other biochemical coevolutionary relation- ships may lead to the success

This study investigates an arable field soil with long-term (27 and 28 years) mineral (NPK) and organic (cattle manure, cattle manure with biodynamic preparations) fertilizer amendments at low, medium and high amounts. Arbuscular mycorrhizal (AM) fungi host plant wheat was cultivated in the first vegetation period and non-host amaranth in the second. Phospholipid fatty acids (PLFA) were used to assess soil microbial biomass and community structure. AM fungi were quantified using the marker fatty acid 16:15, with its occurrence in soil PLFAs representing hyphae and in neutral lipid fatty acid (NLFA) spores. Soil microbial biomass was enhanced by the addition of manure and at higher amounts for both fertilizers. AM fungal hyphae and spore biomass responded positively to manure application. The soil microbial community under both crops was dominated by bacteria. The ratio of fungal to bacterial (f/b) PLFAs increased with higher fertilizer amounts but decreased in amaranth plots with the application of manure. Meanwhile the ratio of Gram+/Gram− bacteria indicating environmental conditions (e.g. pH, temperature) was higher in amaranth plots with the addition of manure as compared to wheat plots. Soil PLFA revealed distinct effect of crop type displayed by changes in the occurrence of saturated fatty acids and biomarkers for Gram-negative bacteria and saprotrophic fungi. The latter additionally accounted for the dissimilarity between fertilizer treatments. In sum, the soil PLFA pattern distinctively separated wheat from amaranth plots at 0-5 cm soil depth, indicating a stronger effect of crop rotation and crop identity on soil microorganisms than long-term fertilizer practice.

The Gaia hypothesis originally proposed by James E. Lovelock states that the composition, oxidation-reduction state and temperature of the troposphere are actively regulated by the activities of the biota. The gaian concept has been extrapolated to include the composition of surface sediments through the process of biomlneralization. The stratified microbial community dominated by the cyanobacterium Microcoleus chthonopZustes is actively involved in the deposition of laminated sediments at Laguna Figueroa, Baja California, Mexico. Unusually heavy rains in the winters of 1979 and 1980 flooded the evaporite flat with up to 3 meters of meteoric water and deposited 5 -10 cm of allocthonous sediment. The composition of the microbial community changed as a succession of dominating microbial species ensued, ultimately leading to the recolonization of the surface sediment by the original Microcoleusdominated community. The resiliency of bacterial communities is suggested to be an important mechanism of gaian control systems.

Electron microscopy and biomolecular methods have been used to describe and identify microbial communities inhabiting the glassy margins of ocean floor basalts. The investigated samples were collected from a neovolcanic ridge and from older, sediment-covered lava flows in the rift valley of the Knipovich Ridge at a water depth around 3500 m and an ambient seawater temperature of 30.7³C. Successive stages from incipient microbial colonisation, to welldeveloped biofilms occur on fracture surfaces in the glassy margins. Observed microbial morphologies are various filamentous, coccoidal, oval, rod-shaped and stalked forms. Etch marks in the fresh glass, with form and size resembling the attached microbes, are common. Precipitation of alteration products around microbes has developed hollow subspherical and filamentous structures. These precipitates are often enriched in Fe and Mn. The presence of branching and twisted stalks that resemble those of the iron-oxidising Gallionella, indicate that reduced iron may be utilised in an energy metabolic process. Analysis of 16S-rRNA gene sequences from microbes present in the rock samples, show that the bacterial population inhabiting these samples cluster within the Q-and O-Proteobacteria and the Cytophaga/Flexibacter/Bacteroides subdivision of the Bacteria, while the Archaea all belong to the Crenarchaeota kingdom. This microbial population appears to be characteristic for the rock and their closest relatives have previously been reported from cold marine waters in the Arctic and Antarctic, deep-sea sediments and hydrothermal environments. ß

Microbial community structure of a lab scale thermophilic aerobic wastewater treatment reactor was analyzed by a combination of culture-independent methods. Quinone profile method provides for chemical analysis of respiratory quinone molecular species, which corresponds to bacterial groups. Denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rDNA partial sequences (PCR-DGGE) clarifies community changes at species level, as DGGE can separate DNA fragments of different sequences. Certain phylogenetic groups of bacterial cells can be labeled by fluorescence in situ hybridization (FISH). Quinone profile showed a predominant presence of MK-7. PCR-DGGE revealed that constituents of the community were unchanged during the stable phase. FISH demonstrated the existence of the relatives of Bacillus lentus and B. thermocloacae in considerable proportions. The community was mainly composed of Bacillaceae, and obligate thermophilic and mesophilic Bacillus appeared in spite of the temperature fluctuation from 351C to 601C. The combination of these culture-independent methods revealed the community precisely enough to evaluate the reactor performance.

Legume-based green manures are important nitrogen sources in organic crop production. Direct incorporation of a green manure crop before sowing or planting of the subsequent cash crops is the most common practice. However, growing green manure crops on fields suitable for cash crop production might be economically suboptimal for the producer and it is difficult to synchronize nutrient release from the green manure with crop demand. Therefore, in this study direct incorporation of green manure was compared with other ways of using green manure where the green manure crop can be grown on fields a p p l i e d s o i l e c o l o g y 3 6 (2 0 0 7

Research during the last decade has revealed that glacier beds are inhabited by microbes . This short article reviews and expands on the current literature, with the aim of establishing that hydrological flowpaths and the connectivity of chemical weathering environments with sources of oxygen are key controls on the redox potential (Eh) of the environments that microbes colonize. The converse is that these factors are also key controls on the types of microbe that colonize subglacial chemical weathering environments.

Fresh pig/cattle slaughterhouse waste mixtures, with different lipid-protein ratios, were characterized and their anaerobic biodegradability assessed in batch tests. The resultant methane potentials were high (270-300 L CH 4 kg À1 COD ) making them interesting substrates for the anaerobic digestion process. However, when increasing substrate concentrations in consecutive batch tests, up to 15 g COD kg À1 , a clear inhibitory process was monitored. Despite the reported severe inhibition, related to lipid content, the system was able to recover activity and successfully degrade the substrate. Furthermore, 16S rRNA gene-based DGGE results showed an enrichment of specialized microbial populations, such as b-oxidizing/proteolitic bacteria (Syntrophomonas sp., Coprothermobacter sp. and Anaerobaculum sp.), and syntrophic methanogens (Methanosarcina sp.). Consequently, the lipid concentration of substrate and the structure of the microbial community are the main limiting factors for a successful anaerobic treatment of fresh slaughterhouse waste.

TM Sole carbon source tests (Biolog), designed to identify microbial isolates can be used to metabolically fingerprint soil microbial communities, although the carbon source profiles were not selected for this purpose. This paper reports on the use TM of alternative carbon sources not available in the Biolog GN plates to characterize soil microbial communities. The carbon sources used are compounds commonly found in plant root exudates and are, therefore, ecologically more relevant and representative of the types of substrates available to microorganisms in rhizosphere soil. The additional carbon sources tested included various phenolic acids, amino acids, carboxylic acids, long chain aliphatics and carbohydrates. In total, 125 different carbon sources were used to discriminate between soil samples from 9 different sites each with three types of grassland vegetation. The growth curves for different groups of carbon sources were all sigmoidal, but the maximum rate of utilization was faster for carbohydrates, amino acids and carboxylic acids than for amides, phenolic and long chain aliphatic acids. Significant discrimination of soil microbial communities between sites, but not grassland types, was shown and was more distinct using the exudate carbon sources than those in the Biolog GN plate. The use of fewer carbon sources which are more ecologically meaningful constitutes a more efficient and economical technique.

The Neogene basins of Southern Cyprus provide a good opportunity to improve the knowledge of the paleoenvironmental changes involved in the triggering of the Messinian evaporite deposition in the Mediterranean, and of their chronology, which is still questionable with regards to the parameters responsible for the triggering of the salinity crisis. It is still difficult to discriminate the individual effects of tectonics, climate, global sea-level changes. In Cyprus, considerable progress has been made on the events leading to the MSC, since the 70's, in highresolution microfossil biostratigraphy, astrochronology, cyclostratigraphy and magnetostratigraphy. A study of the Tochni section, in the Psematismemos Basin, correlated with previously studied sections in the western Polemi and Pissouri basins, allows these regional paleoenvironmental changes to be correlated with the major events identified in other Mediterranean basins. The depth of the basins, in which evaporites were deposited, and the increase of salinity leading to the formation of evaporites are better constrained and studies confirm that restriction proceeded by steps throughout the Mediterranean. The very short time involved in the triggering of the onset of evaporite deposition in Cyprus basins is marked by tectonic instability, and development of very shallow water fauna and microbial communities indicating the water level lowered significantly just before the beginning of the massive gypsum precipitation. Correlation with other peri-Mediterranean basins, where similar changes have been observed, confirms that the period preceding the deposition of evaporites may correspond to the final closure of connections between the Atlantic Ocean and the Mediterranean Basin, leading to a sea-level drop and important hydrologic changes.