Structure et biogéographie des communautés de pico- et de nanoeurcaryotes pélagiques autour de l'archipel du Svalbard

L’Arctique s’est réchauffé rapidement et il y a urgence d’anticiper les effets que cela pourrait avoir sur les protistes à la base de la chaîne alimentaire. Le phytoplancton de l’Océan Arctique inclut les pico- et nano-eucaryotes (0.45-10 μm diamètre de la cellule) et plusieurs de ceux-ci sont des écotypes retrouvés seulement dans l’Arctique alors que d’autres sont introduits des océans plus méridionaux. Alors que les océans tempérés pénètrent dans l’Arctique, il devient pertinent de savoir si ces communautés microbiennes pourraient être modifiées. L’archipel du Svalbard est une région idéale pour observer la biogéographie des communautés microbiennes sous l’influence de processus polaires et tempérés. Bien qu’ils soient géographiquement proches, les régions côtières entourant le Svalbard sont sujettes à des intrusions alternantes de masses d’eau de l’Arctique et de l’Atlantique en plus des conditions locales. Huit sites ont été échantillonnés en juillet 2013 pour identifier les protistes selon un gradient de profondeur et de masses d’eau autour de l’archipel. En plus des variables océanographiques standards, l’eau a été échantillonnée pour synthétiser des banques d’amplicons ciblant le 18S SSU ARNr et son gène pour ensuite être séquencées à haut débit. Cinq des sites d’étude avaient de faibles concentrations de chlorophylle avec des compositions de communauté post-efflorescence dominée par les dinoflagellés, ciliés, des alvéolés parasites putatifs, chlorophycées et prymnesiophytées. L’intrusion des masses d’eau et les conditions environnementales locales étaient corrélées avec la structure des communautés ; l’origine de la masse d’eau contribuant le plus à la distance phylogénétique des communautés microbiennes. Au sein de trois fjords, de fortes concentrations de chlorophylle sous-entendaient des activités d’efflorescence. Un fjord était dominé par Phaeocystis, un deuxième par un clade arctique identifié comme un Pelagophyceae et un troisième par un assemblage mixte. En général, un signal fort d’écotypes liés à l’Arctique prédominait autour du Svalbard.

Tracking changes to a microplankton community in a North Atlantic sea loch using the microplankton index PI(mp).

Microplankton plays a vital part in marine ecosystems and its importance has been recognised by the inclusion of microplankton community composition in regulatory frameworks such as the European Water Framework Directive and the Marine Strategy Framework Directive as an indicator of ecological status. Quantitative techniques are therefore required to assess the environmental status of the microplankton in a water body. Here we demonstrate the use of a method known as the Microplankton Index PI(mp) to evaluate changes in the microplankton community of the West coast Scottish Sea Loch Creran. Microplankton in this fjord has been studied since the 1970’s providing a data set spanning four decades. Our analysis compares an arbitrarily chosen reference period between 1979 and 1981 with a period between 2011 and 2013 and demonstrates that between these two periods community structure has changed considerably with a substantial drop in the numbers of observed diatoms accompanied by a rise in the number of autotrophic/mixotrophic dinoflagellates as well as an increase in the potentially toxin producing genus Pseudo-nitzschia and that these are related to changes in both the intensity and timing of local patterns of precipitation. The PI(mp) is shown to be a useful and robust method to visualise and quantify changes in the underlying structure of the microplankton community and is a powerful addition to the toolbox of techniques needed to determine the health of our seas.

Abrupt shifts in the Gironde fish community: an indicator of ecological changes in an estuarine ecosystem

For decades, global climate change has directly and indirectly affected the structure and function of ecosystems. Abrupt changes in biodiversity have been observed in response to linear or sudden modifications to the environment. These abrupt shifts can cause long-term reorganizations within ecosystems, with communities exhibiting new functional responses to environmental factors. Over the last 3 decades, the Gironde estuary in southwest France has experienced 2 abrupt shifts in both the physical and chemical environments and the pelagic community. Rather than describing these shifts and their origins, we focused on the 3 inter-shift periods, describing the structure of the fish community and its relationship with the environment during these periods. We described fish biodiversity using a limited set of descriptors, taking into account both species composition and relative species abundances. Inter-shift ecosystem states were defined based on the relationship between this description and the hydro-physico-chemical variables and climatic indices defining the main features of the environment. This relationship was described using generalized linear mixed models on the entire time series and for each inter-shift period. Our results indicate that (1) the fish community structure has been significantly modified, (2) environmental drivers influencing fish diversity have changed during these 3 periods, and (3) the fish-environment relationships have been modified over time. From this, we conclude a regime shift has occurred in the Gironde estuary. We also highlight that anthropogenic influences have increased, which re-emphasizes the importance of local management in maintaining fish diversity and associated goods and services within the context of climate change.

La face cachée de la dune : communautés fongiques du sol: dynamique, succession et interactions avec la végétation d’un écosystème dunaire côtier aux Îles de la Madeleine, Qc

Les écosystèmes dunaires remplissent plusieurs fonctions écologiques essentielles comme celle de protéger le littoral grâce à leur capacité d’amortissement face aux vents et vagues des tempêtes. Les dunes jouent aussi un rôle dans la filtration de l’eau, la recharge de la nappe phréatique, le maintien de la biodiversité, en plus de présenter un attrait culturel, récréatif et touristique. Les milieux dunaires sont très dynamiques et incluent plusieurs stades de succession végétale, passant de la plage de sable nu à la dune bordière stabilisée par l’ammophile à ligule courte, laquelle permet aussi l’établissement d’autres herbacées, d’arbustes et, éventuellement, d’arbres. Or, la survie de ces végétaux est intimement liée aux microorganismes du sol. Les champignons du sol interagissent intimement avec les racines des plantes, modifient la structure des sols, et contribuent à la décomposition de la matière organique et à la disponibilité des nutriments. Ils sont donc des acteurs clés de l’écologie des sols et contribuent à la stabilisation des dunes. Malgré cela, la diversité et la structure des communautés fongiques, ainsi que les mécanismes influençant leur dynamique écologique, demeurent relativement méconnus. Le travail présenté dans cette thèse explore la diversité des communautés fongiques à travers le gradient de succession et de conditions édaphiques d’un écosystème dunaire côtier afin d’améliorer la compréhension de la dynamique des sols en milieux dunaires. Une vaste collecte de données sur le terrain a été réalisée sur une plaine de dunes reliques se trouvant aux Îles de la Madeleine, Qc. J’ai échantillonné plus de 80 sites répartis sur l’ensemble de ce système dunaire et caractérisé les champignons du sol grâce au séquençage à haut débit. Dans un premier temps, j’ai dressé un portait d’ensemble des communautés fongiques du sol à travers les différentes zones des dunes. En plus d’une description taxonomique, les modes de vie fongiques ont été prédits afin de mieux comprendre comment les variations au niveau des communautés de champignons du sol peuvent se traduire en changements fonctionnels. J’ai observé un niveau de diversité fongique élevé (plus de 3400 unités taxonomiques opérationnelles au total) et des communautés taxonomiquement et fonctionnellement distinctes à travers un gradient de succession et de conditions édaphiques. Ces résultats ont aussi indiqué que toutes les zones des dunes, incluant la zone pionière, supportent des communautés fongiques diversifiées. Ensuite, le lien entre les communautés végétales et fongiques a été étudié à travers l’ensemble de la séquence dunaire. Ces résultats ont montré une augmentation claire de la richesse spécifique végétale, ainsi qu’une augmentation de la diversité des stratégies d’acquisition de nutriments (traits souterrains lié à la nutrition des plantes, soit mycorhizien à arbuscule, ectomycorhizien, mycorhizien éricoide, fixateur d’azote ou non spécialisé). J’ai aussi pu établir une forte corrélation entre les champignons du sol et la végétation, qui semblent tous deux réagir de façon similaire aux conditions physicochimiques du sol. Le pH du sol influençait fortement les communautés végétales et fongiques. Le lien observé entre les communautés végétales et fongiques met l’emphase sur l’importance des interactions biotiques positives au fil de la succession dans les environnements pauvres en nutriments. Finalement, j’ai comparé les communautés de champignons ectomycorhiziens associées aux principales espèces arborescentes dans les forêts dunaires. J’ai observé une richesse importante, avec un total de 200 unités taxonomiques opérationnelles ectomycorhiziennes, appartenant principalement aux Agaricomycètes. Une analyse de réseaux n’a pas permis de détecter de modules (c'est-à-dire des sous-groupes d’espèces en interaction), ce qui indique un faible niveau de spécificité des associations ectomycorhiziennes. De plus, je n’ai pas observé de différences en termes de richesse ou de structure des communautés entre les quatre espèces hôtes. En conclusion, j’ai pu observer à travers la succession dunaire des communautés diversifiées et des structures distinctes selon la zone de la dune, tant chez les champignons que chez les plantes. La succession semble toutefois moins marquée au niveau des communautés fongiques, par rapport aux patrons observés chez les plantes. Ces résultats ont alimenté une réflexion sur le potentiel et les perspectives, mais aussi sur les limitations des approches reposant sur le séquençage à haut-débit en écologie microbienne.

Chronic Polyaromatic Hydrocarbon (PAH) Contamination Is a Marginal Driver for Community Diversity and Prokaryotic Predicted Functioning in Coastal Sediments

Benthic microorganisms are key players in the recycling of organic matter and recalcitrant compounds such as polyaromatic hydrocarbons (PAHs) in coastal sediments. Despite their ecological importance, the response of microbial communities to chronic PAH pollution, one of the major threats to coastal ecosystems, has received very little attention. In one of the largest surveys performed so far on coastal sediments, the diversity and composition of microbial communities inhabiting both chronically contaminated and non-contaminated coastal sediments were investigated using high-throughput sequencing on the 18S and 16S rRNA genes. Prokaryotic alpha-diversity showed significant association with salinity, temperature, and organic carbon content. The effect of particle size distribution was strong on eukaryotic diversity. Similarly to alpha-diversity, beta-diversity patterns were strongly influenced by the environmental filter, while PAHs had no influence on the prokaryotic community structure and a weak impact on the eukaryotic community structure at the continental scale. However, at the regional scale, PAHs became the main driver shaping the structure of bacterial and eukaryotic communities. These patterns were not found for PICRUSt predicted prokaryotic functions, thus indicating some degree of functional redundancy. Eukaryotes presented a greater potential for their use as PAH contamination biomarkers, owing to their stronger response at both regional and continental scales.

Bacterial communities of the specialty crop phyllosphere: response to biological soil amendment use, rainfall, and insect visitation

Microorganisms in the plant rhizosphere, the zone under the influence of roots, and phyllosphere, the aboveground plant habitat, exert a strong influence on plant growth, health, and protection. Tomatoes and cucumbers are important players in produce safety, and the microbial life on their surfaces may contribute to their fitness as hosts for foodborne pathogens such as Salmonella enterica and Listeria monocytogenes. External factors such as agricultural inputs and environmental conditions likely also play a major role. However, the relative contributions of the various factors at play concerning the plant surface microbiome remain obscure, although this knowledge could be applied to crop protection from plant and human pathogens. Recent advances in genomic technology have made investigations into the diversity and structure of microbial communities possible in many systems and at multiple scales. Using Illumina sequencing to profile particular regions of the 16S rRNA gene, this study investigates the influences of climate and crop management practices on the field-grown tomato and cucumber microbiome. The first research chapter (Chapter 3) involved application of 4 different soil amendments to a tomato field and profiling of harvest-time phyllosphere and rhizosphere microbial communities. Factors such as water activity, soil texture, and field location influenced microbial community structure more than soil amendment use, indicating that field conditions may exert more influence on the tomato microbiome than certain agricultural inputs. In Chapter 4, the impact of rain on tomato and cucumber-associated microbial community structures was evaluated. Shifts in bacterial community composition and structure were recorded immediately following rain events, an effect which was partially reversed after 4 days and was strongest on cucumber fruit surfaces. Chapter 5 focused on the contribution of insect visitors to the tomato microbiota, finding that insects introduced diverse bacterial taxa to the blossom and green tomato fruit microbiome. This study advances our understanding of the factors that influence the microbiomes of tomato and cucumber. Farms are complex environments, and untangling the interactions between farming practices, the environment, and microbial diversity will help us develop a comprehensive understanding of how microbial life, including foodborne pathogens, may be influenced by agricultural conditions.

Ichthyofauna in an estuary of the Mataripe area, Todos os Santos Bay, Bahia, Brazil

The community structure and dynamics as well as some biological parameters of selected species of the ichthyofauna of the Mataripe estuarine region affected by the Landulfo Alves Oil Refinery (RLAM) were analyzed. Twenty stations were sampled with a gillnet in five different periods: August and December 2003, March and July/August 2004 and January 2005. Thirty-five actinopterygian species and one elasmobranch species were recorded, Oligoplites saurus, Diapterus rhombeus, Lutjanus synagris and Scomberomorus brasiliensis among them, on all the campaigns. A total of 1368 specimens, weighing 36.10 kg, were caught. The ichthyofauna total biomass was greater, in weight, on the eastern side of the study region, especially at the stations close to the shoals/reefs and the rocky bottom. A similar pattern was also observed for the diversity values. In general, low evenness and diversity were observed in the area studied, possibly as a result of the fishing gear used. D. rhombeus juveniles dominated in all but one of the samplings (July 2004), in which latter Cyclichthys spinosus was dominant. Carangids and species associated with consolidated bottoms were observed, although in small numbers, throughout the study period. In spite of the limitations imposed by the gear used for sampling, the estuarine area influenced by the RLAM was seen to play a role as a growth area for the great majority of species, especially the mojarra (D. rhombeus), but it offers no fishing potential due to the prevalence of young and small individuals. Evidence of imminent spawning was recorded for Pomadasys corvinaeformis in August 2003, and recent spawning in March 2004 for Oligoplites saurus. Further, mature individuals occurred in insufficient numbers to permit population level evaluation.

A reliable measure of similarity based on dependency for short time series: an application to gene expression networks

Background: Microarray techniques have become an important tool to the investigation of genetic relationships and the assignment of different phenotypes. Since microarrays are still very expensive, most of the experiments are performed with small samples. This paper introduces a method to quantify dependency between data series composed of few sample points. The method is used to construct gene co-expression subnetworks of highly significant edges. Results: The results shown here are for an adapted subset of a Saccharomyces cerevisiae gene expression data set with low temporal resolution and poor statistics. The method reveals common transcription factors with a high confidence level and allows the construction of subnetworks with high biological relevance that reveals characteristic features of the processes driving the organism adaptations to specific environmental conditions. Conclusion: Our method allows a reliable and sophisticated analysis of microarray data even under severe constraints. The utilization of systems biology improves the biologists ability to elucidate the mechanisms underlying celular processes and to formulate new hypotheses.

Generalized connectivity between any two nodes in a complex network

This article focuses on the identification of the number of paths with different lengths between pairs of nodes in complex networks and how these paths can be used for characterization of topological properties of theoretical and real-world complex networks. This analysis revealed that the number of paths can provide a better discrimination of network models than traditional network measurements. In addition, the analysis of real-world networks suggests that the long-range connectivity tends to be limited in these networks and may be strongly related to network growth and organization.

Effects of drill cuttings discharge on meiofauna communities of a shelf break site in the southwest Atlantic

The present study investigates the effects of drill cutting discharges on the structure of meiofauna communities in an area of the shelf break at Campos Basin, Southeast Brazil. Drilling activities were operated, in a first phase, with water-based fluid and, in a second phase, with synthetic fluid paraffin-based (NAF-III). A total of 135 samples taken at a pre-drilling situation (MS1) and two post-drilling moments (MS2 and MS3-3 and 22 months post-drilling, respectively) were analyzed. Effects on meiofauna were dependent on two main factors: 1-the impact received during drilling operation, if water-based or synthetic/water-based drilling fluid and 2-the background state, if it already presented signs of previous drilling activities or not. Based on univariate and multivariate analysis, there were evidences that the most affected area after drilling was those under the influence of synthetic-based fluid and that already had signs of previous drillings activities. The region impacted only by water-based fluid was less affected and the only one that completely recovered after 22 months. Nematodes and copepods had different responses to the impact. While copepods flourish in the impacted area and recovered 22 months after drilling, nematodes were adversely affected shortly after drilling and the community structure only recovered where hydrocarbons had been depleted.

Anaerobic degradation of linear alkylbenzene sulfonate (LAS) in fluidized bed reactor by microbial consortia in different support materials

Four anaerobic fluidized bed reactors filled with activated carbon (R1), expanded clay (R2), glass beads (R3) and sand (R4) were tested for anaerobic degradation of LAS. All reactors were inoculated with sludge from a UASB reactor treating swine wastewater and were fed with a synthetic substrate supplemented with approximately 20 mg l(-1) of LAS, on average. To 560 mg l(-1) COD influent, the maximum COD and LAS removal efficiencies were mean values of 97 +/- 2% and 99 +/- 2%, respectively, to all reactors demonstrating the potential applicability of this reactor configuration for treating LAS. The reactors were kept at 30 degrees C and operated with a hydraulic retention time (HRT) of 18 h. The use of glass beads and sand appear attractive because they favor the development of biofilms capable of supporting LAS degradation. Subsequent 16S rRNA gene sequencing and phylogenetic analysis of samples from reactors R3 and R4 revealed that these reactors gave rise to broad microbial diversity, with microorganisms belonging to the phyla Bacteroidetes, Firmicutes, Actinobacteria and Proteobacteria, indicating the role of microbial consortia in degrading the surfactant LAS. (C) 2010 Elsevier Ltd. All rights reserved.

Application of molecular techniques to evaluate the methanogenic archaea and anaerobic bacteria in the presence of oxygen with different COD : sulfate ratios in a UASB reactor

In this paper, the microbial characteristics of the granular sludge in the presence of oxygen (3.0 +/- 0.7 mg O-2 1(-1)) were analyzed using molecular biology techniques. The granules were provided by an upflow anaerobic sludge blanket (UASB) operated over 469 days and fed with synthetic substrate. Ethanol and sulfate were added to obtain different COD/SO42- ratios (3.0, 2.0, and 1.6). The results of fluorescent in situ hybridization (FISH) analyses showed that archaeal cells, detected by the ARC915 probe, accounted for 77%, 84%, and 75% in the COD/SO42- ratios (3.0, 2.0, and 1.6, respectively). Methanosaeta sp. was the predominant acetoclastic archaea observed by optical microscopy and FISH analyses, and confirmed by sequencing of the excised bands of the DGGE gel with a similarity of 96%. The sulfate-reducing bacterium Desulfovibrio vulgaris subsp. vulgaris (similarity of 99%) was verified by sequencing of the DGGE band. Others identified microorganism were similar to Shewanella sp. and Desulfitobacterium hafniense, with similarities of 95% and 99%, respectively. These results confirmed that the presence of oxygen did not severely affect the metabolism of microorganisms that are commonly considered strictly anaerobic. We obtained mean efficiencies of organic matter conversion and sulfate reducing higher than 74%. (C) 2008 Elsevier Ltd. All rights reserved.

Cultivation of hitherto-uncultured bacteria belonging to the Verrucomicrobia subdivision 1 from the potato (Solanum tuberosum L.) rhizosphere

The role of dominant bacterial groups in the plant rhizosphere, e.g., those belonging to the phyla Acidobacteria and Verrucomicrobia, has, so far, not been elucidated, and this is mainly due to the lack of culturable representatives. This study aimed to isolate hitherto-uncultured bacteria from the potato rhizosphere by a combination of cultivation approaches. An agar medium low in carbon availability (oligotrophic agar medium) and either amended with potato root exudates or catalase or left unamended was used with the aim to improve the culturability of bacteria from the potato rhizosphere. The colony forming unit numbers based on colonies and microcolonies were compared with microscopically determined fluorescence-stained cell numbers. Taxonomical diversity of the colonies was compared with that of library clones made from rhizosphere DNA, on the basis of 16S rRNA gene comparisons. The oligotrophic media amended or not with catalase or rhizosphere extract recovered up to 33.6% of the total bacterial numbers, at least seven times more than the recovery observed on R2A. Four hitherto-uncultured Verrucomicrobia subdivision 1 representatives were recovered on agar, but representatives of this group were not found in the clone library. The use of oligotrophic medium and its modifications enabled the growth of colony numbers, exceeding those on classical agar media. Also, it led to the isolation of hitherto-uncultured bacteria from the potato rhizosphere. Further improvement in cultivation will certainly result in the recovery of other as-yet-unexplored bacteria from the rhizosphere, making these groups accessible for further investigation, e.g., with respect to their possible interactions with plants.

Microbial Metabolic Potential Affected by Surplus Wastewater Irrigation in Tropical Soil Cultivated with Tifton 85 Bermuda Grass (Cynodon dactylon Pers. X C. niemfuensis Vanderyst)

Agricultural reuse of treated sewage effluent (TSE) is an environmental and economic practice; however, little is known about its effects on the characteristics and microbial function in tropical soils. The effect of surplus irrigation of a pasture with TSE, in a period of 18 months, was investigated, considering the effect of 0% surplus irrigation with TSE as a control. In addition, the experiment consisted of three surplus treatments (25%, 50%, and 100% excess) and a nonirrigated pasture area (SE) to compare the soil microbial community level physiological profiles, using the Biolog method. The TSE application increased the average substrate consumption of the soil microbial community, based on the kinetic parameters of the average well color development curve fitting. There were no significant differences between the levels of surplus irrigation treatments. Surplus TSE pasture irrigation caused minor increases in the physiological status of the soil microbial community but no detectable damage to the pasture or soil.

Transgenic tobacco revealing altered bacterial diversity in the rhizosphere during early plant development

The rhizosphere constitutes a complex niche that may be exploited by a wide variety of bacteria. Bacterium-plant interactions in this niche can be influenced by factors such as the expression of heterologous genes in the plant. The objective of this work was to describe the bacterial communities associated with the rhizosphere and rhizoplane regions of tobacco plants, and to compare communities from transgenic tobacco lines (CAB1, CAB2 and TRP) with those found in wild-type (WT) plants. Samples were collected at two stages of plant development, the vegetative and flowering stages (1 and 3 months after germination). The diversity of the culturable microbial community was assessed by isolation and further characterization of isolates by amplified ribosomal RNA gene restriction analysis (ARDRA) and 16S rRNA sequencing. These analyses revealed the presence of fairly common rhizosphere organisms with the main groups Alphaproteobacteria, Betaproteobacteria, Actinobacteria and Bacilli. Analysis of the total bacterial communities using PCR-DGGE (denaturing gradient gel electrophoresis) revealed that shifts in bacterial communities occurred during early plant development, but the reestablishment of original community structure was observed over time. The effects were smaller in rhizosphere than in rhizoplane samples, where selection of specific bacterial groups by the different plant lines was demonstrated. Clustering patterns and principal components analysis (PCA) were used to distinguish the plant lines according to the fingerprint of their associated bacterial communities. Bands differentially detected in plant lines were found to be affiliated with the genera Pantoea, Bacillus and Burkholderia in WT, CAB and TRP plants, respectively. The data revealed that, although rhizosphere/rhizoplane microbial communities can be affected by the cultivation of transgenic plants, soil resilience may be able to restore the original bacterial diversity after one cycle of plant cultivation.