Méthode de sélection de lacs de référence dans le cadre d'une étude Before-After Control-Impact (BACI) évaluant les effets des coupes forestières sur le zooplancton des lacs de la forêt boréale

Plusieurs approches tentent de mesurer l'impact des perturbations anthropiques sur les écosystèmes. L'approche BACI (Before-After Control-Impact) consiste à suivre deux groupes de sites (contrôle et impact), avant et après une perturbation, afin de mesurer l'effet de cette dernière sur les écosystèmes. Les études BACI permettent de contrôler la variabilité naturelle entre les groupes de sites, par le suivi des mêmes sites d'impact avant et après la perturbation, tout en minimisant la variabilité naturelle entre les années grâce au suivi de sites de contrôle échantillonnés également avant et après la perturbation. Puisque la variation naturelle entre les années dans les sites d'impact est estimée à partir de celle des sites de contrôle, il est nécessaire de sélectionner des sites de contrôle dont les caractéristiques limnologiques sont semblables à celles des sites d'impact. Ceci est essentiel pour une bonne application de l'approche BACI, afin de s'assurer que les sites naturels et perturbés répondent de la même façon aux variations naturelles interannuelles dans l'environnement et que les différences observées dans les sites d'impact avant et après la perturbation soient attribuables à celle-ci.Cet article propose une méthode de sélection des sites de contrôle dans le cadre d'une étude BACI portant sur l'impact des coupes forestières sur le zooplancton des lacs de la forêt boréale au Québec. Le zooplancton de 16 lacs de la forêt boréale a été échantillonné un an avant (2000) et deux ans après (2001-2002) des coupes forestières sur le bassin versant de certains lacs. Six lacs ont subi des coupes importantes sur 44 à 77 % du bassin versant (lacs de coupe: DA2, DF2, DF7, DF9, K4, K8) et 10 lacs sont restés à l'état naturel ou n'ont subi que des coupes négligeables sur moins de 2 % du bassin versant (lacs de référence: K2, AB34, AB35, AB40, CSL5, DA4, DF4, N35, N89, N43). Parmi ces dix lacs de référence, nous avons sélectionné les six lacs les plus semblables aux lacs de coupe, à l'aide d'analyses en composantes principales (ACP) basées sur la similarité des variables morphométriques, de la qualité de l'eau et du zooplancton avant la coupe (2000). De plus, les variables ayant la plus grande contribution à la variation totale au niveau de ces trois groupes de variables ont été déterminées. Quatre lacs ont été exclus (K2, N89, AB35, AB40) et six lakes (AB34, CSL5, DA4, DF4, N35, N43) ont été sélectionnés comme référence. Finalement, la validité du choix des six lacs de référence a été testée par des analyses de redondance (RDA) avec une variable binaire qui permettait de distinguer les lacs de coupe des lacs de référence sélectionnés. Les analyses de redondance ont montré que les variables de la morphométrie, de la qualité de l'eau et du zooplancton des lacs de référence sélectionnés ne différaient pas significativement de celles des lacs de coupe avant la perturbation. En conséquence, les différences observées après la perturbation dans les six lacs de coupe, relativement aux variations naturelles dans les six lacs de référence sélectionnés, devraient être attribuables à l'effet de la coupe forestière. La méthode de sélection développée dans le cadre de cette étude peut être utilisée pour évaluer à l'aide d'une approche BACI les effets de toute perturbation anthropique sur les écosystèmesSeveral designs can be used to assess the effects of human perturbations on ecosystems. However, the main difficulty is to isolate natural sources of variation from the variation induced by the perturbation. Several studies have shown that the natural differences between the reference and the impacted sites may influence their responses to the perturbation. In a comparative design comparing the conditions at the reference sites and the impacted sites after the perturbation, it is not possible to control for the natural sources of variation between these two groups of sites that occurred before the perturbation. This natural variation among sites is taken into account in a Before-After design in which the same sites are monitored before and after perturbation, but the natural sources of variation among years cannot be separated from the variation induced by the perturbation. In this study, we used a BACI (Before-After Control-Impact) design to measure the effect of a perturbation on an ecosystem by following two groups of sites (control and impacted) before and after the perturbation. A BACI design is the only one that allows controlling for the natural variability among sites by following the same impacted sites before and after the perturbation. This approach also takes into account the natural variability among years by monitoring concomitantly the control sites before and after the perturbation. Since the natural variability among years at the impacted sites is estimated by the variability measured at the control sites, it is essential to select control sites that are the most similar to the impacted sites with respect to their limnological characteristics. This is a requirement for the good use of the BACI design, to make sure that control and impacted sites have the same responses towards year-to-year natural variations in their environment and to ensure that the differences observed at the impacted sites before-after the perturbation are caused by it.This paper proposes a method for the selection of control sites in a BACI design to study the impact of forest harvesting on zooplankton communities in lakes of the boreal forest in Québec. Zooplankton in 16 lakes was sampled one year before (2000) and two years after (2001-2002) forest harvesting in the watersheds of some lakes. Six lakes were impacted by important harvesting on 44 to 77% of their watershed (cut lakes: DA2, DF2, DF7, DF9, K4, K8) and ten lakes were considered as natural lakes with forest harvesting on less than 2% of their watershed (reference lakes: K2, AB34, AB35, AB40, CSL5, DA4, DF4, N35, N89, N43). Among these ten natural lakes, we selected the six reference lakes that had limnological features most similar to the cut lakes, based on the morphometry, water quality and zooplankton variables before forest harvesting (2000). We used principal component analyses (PCA) to compare the lakes (10 natural lakes and six lakes to be impacted by watershed harvesting) using ordination biplots. A PCA was done for each group of variables. Lake volume, maximal depth, and area and the slope of the watershed were the variables having the most important contributions to the total variation in morphometry. Positive correlations were found between the slope of the watershed and the maximal depth of the lake and between the lake area and the lake volume. This PCA allowed us to eliminate two reference lakes that had higher values in lake volume and area for one lake (K2) and in lake volume and maximal depth for the other one (AB35), compared to the cut lakes. When comparing water quality variables, total phosphorus (TP), total nitrogen (TN), dissolved organic carbon (DOC), Secchi depth, Ca2+, Mg2+, alkalinity (ALK) and pH contributed more to the total variation than other variables. Among these variables, DOC, TP and TN were positively correlated together whereas they were negatively correlated to water transparency (Secchi). Two reference lakes (AB35, N89) had higher transparency and lower values in DOC, TP and TN and one reference lake (AB40) had lower values in pH, ALK, Ca2+ and Mg2+ compared to cut lakes. Since one of these three lakes had previously been eliminated on the basis of its morphometric variables, we had a total of four reference lakes excluded from the study. The PCA on zooplankton variables revealed that only the largest class of zooplankton (>500 µm) contributed significantly to zooplankton total variation. In general, reference lakes and cut lakes had a similar distribution on the ordination biplot so no lake was eliminated with respect to zooplankton variables. Finally, four reference lakes were excluded (K2, N89, AB35, AB40) and six reference lakes were selected (AB34, CSL5, DA4, DF4, N35, N43).The validation of the selection of the six reference lakes was made using redundancy analyses (RDA) with a binary variable discriminating between the six cut lakes and the six reference lakes selected in the PCAs. Multivariate methods such as RDA have the advantage of testing if the two groups of lakes are different with respect to many variables and not just one, as would be the case when using a univariate method. Redundancy analyses showed that the morphometric, water quality and zooplankton variables in the six selected reference lakes were not significantly different from those in the six cut lakes before harvesting. The RDA results supported the selection of the six reference lakes based on the ordination biplots from the three PCA made on the three groups of variables. We could then presume that any difference observed after the perturbation in the cut lakes, relative to the natural variation among years in the six reference lakes, could be attributed to the effect of forest harvesting. Finally, this method of selection of control sites could be used for any BACI study testing the effects of human perturbation on ecosystems

Microbes on a bottle: substrate, season and geography influence community composition of microbes colonizing marine plastic debris

Plastic debris pervades in our oceans and freshwater systems and the potential ecosystem-level impacts of this anthropogenic litter require urgent evaluation. Microbes readily colonize aquatic plastic debris and members of these biofilm communities are speculated to include pathogenic, toxic, invasive or plastic degrading-species. The influence of plastic-colonizing microorganisms on the fate of plastic debris is largely unknown, as is the role of plastic in selecting for unique microbial communities. This work aimed to characterize microbial biofilm communities colonizing single-use poly(ethylene terephthalate) (PET) drinking bottles, determine their plastic-specificity in contrast with seawater and glass-colonizing communities, and identify seasonal and geographical influences on the communities. A substrate recruitment experiment was established in which PET bottles were deployed for 5–6 weeks at three stations in the North Sea in three different seasons. The structure and composition of the PET-colonizing bacterial/archaeal and eukaryotic communities varied with season and station. Abundant PET-colonizing taxa belonged to the phylum Bacteroidetes (e.g. Flavobacteriaceae, Cryomorphaceae, Saprospiraceae—all known to degrade complex carbon substrates) and diatoms (e.g. Coscinodiscophytina, Bacillariophytina). The PET-colonizing microbial communities differed significantly from free-living communities, but from particle-associated (>3 μm) communities or those inhabiting glass substrates. These data suggest that microbial community assembly on plastics is driven by conventional marine biofilm processes, with the plastic surface serving as raft for attachment, rather than selecting for recruitment of plastic-specific microbial colonizers. A small proportion of taxa, notably, members of the Cryomorphaceae and Alcanivoraceae, were significantly discriminant of PET but not glass surfaces, conjuring the possibility that these groups may directly interact with the PET substrate. Future research is required to investigate microscale functional interactions at the plastic surface

Single‐cell and population level viral infection dynamics revealed by phage FISH , a method to visualize intracellular and free viruses

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/99658/1/emi12100.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/99658/2/emi12100-sup-0001-suppl.pd

Sulfur oxidation genes in diverse deep-sea viruses

Author Posting. © The Author(s), 2014. This is the author's version of the work. It is posted here by permission of AAAS for personal use, not for redistribution. The definitive version was published in Science 344 (2014): 757-760, doi:10.1126/science.1252229.Viruses are the most abundant biological entities in the oceans and a pervasive cause of mortality of microorganisms that drive biogeochemical cycles. Although the ecological and evolutionary impacts of viruses on marine phototrophs are well-recognized, little is known about their impact on ubiquitous marine lithotrophs. Here we report 18 genome sequences of double-stranded DNA viruses that putatively infect widespread sulfur-oxidizing bacteria. Fifteen of these viral genomes contain auxiliary metabolic genes for the alpha and gamma subunits of reverse dissimilatory sulfite reductase (rdsr). This enzyme oxidizes elemental sulfur, which is abundant in the hydrothermal plumes studied here. Our findings implicate viruses as a key agent in the sulfur cycle and as a reservoir of genetic diversity for bacterial enzymes that underpin chemosynthesis in the deep oceans.This project is funded in part by the Gordon and Betty Moore Foundation Grant GBMF2609 and National Science Foundation Grant OCE1038006

Thirty Years After Michael E. Porter: What Do We Know About Business Exit?

Although a business exit is an important corporate change initiative, the buyer’s side seems to be more appealing to management researchers than the seller’s because acquisitions imply growth, i.e., success. Yet from an optimistic viewpoint, business exit can effectively create value for the selling company. In this paper we attempt to bring the relevance of the seller’s side back into our consciousness by asking: What do we know about business exit? We start our exploration with Porter (1976), focusing on literature that investigates the antecedents of, barriers to, and outcomes of business exit. We also include studies from related fields such as finance and economics.1 Through this research we determine three clusters of findings: factors promoting business exit, exit barriers, and exit outcomes. Overall, it is the intention of this paper to highlight the importance of business exit for research and practice. Knowing what we know about business exits and their high financial value we should bear in mind that exit need not mean failure but a new beginning for a corporation

Widespread movement of invasive cattle fever ticks (Rhipicephalus microplus) in southern Texas leads to shared local infestations on cattle and deer

Background: Rhipicephalus (Boophilus) microplus is a highly-invasive tick that transmits the cattle parasites (Babesia bovis and B. bigemina) that cause cattle fever. R. microplus and Babesia are endemic in Mexico and ticks persist in the United States inside a narrow tick eradication quarantine area (TEQA) along the Rio Grande. This containment area is threatened by unregulated movements of illegal cattle and wildlife like white-tailed deer (WTD; Odocoileus virginianus). Methods: Using 11 microsatellite loci we genotyped 1,247 R. microplus from 63 Texas collections, including outbreak infestations from outside the TEQA. We used population genetic analyses to test hypotheses about ecological persistence, tick movement, and impacts of the eradication program in southern Texas. We tested acaricide resistance with larval packet tests (LPTs) on 47 collections. Results: LPTs revealed acaricide resistance in 15/47 collections (32%); 11 were outside the TEQA and three were resistant to multiple acaricides. Some collections highly resistant to permethrin were found on cattle and WTD. Analysis of genetic differentiation over time at seven properties revealed local gene pools with very low levels of differentiation (F-ST 0.00-0.05), indicating persistence over timespans of up to 29 months. However, in one neighborhood differentiation varied greatly over a 12-month period (F-ST 0.03-0.13), suggesting recurring immigration from distinct sources as another persistence mechanism. Ticks collected from cattle and WTD at the same location are not differentiated (F-ST = 0), implicating ticks from WTD as a source of ticks on cattle (and vice versa) and emphasizing the importance of WTD to tick control strategies. We identified four major genetic groups (K = 4) using Bayesian population assignment, suggesting multiple introductions to Texas. Conclusions: Two dispersal mechanisms give rise to new tick infestations: 1) frequent short-distance dispersal from the TEQA; and 2) rare long-distance, human-mediated dispersal from populations outside our study area, probably Mexico. The threat of cattle fever tick transport into Texas is increased by acaricide resistance and the ability of R. microplus to utilize WTD as an alternate host. Population genetic analyses may provide a powerful tool for tracking invasions in other parts of the world where these ticks are established

A Multilevel Measurement Model of Social Cohesion

In spite of its currency both in academic research and political rhetoric, there are numerous attempts to define and conceptualize the social cohesion concept but there has been paid little attention to provide a rigorous and empirically tested definition. There are even fewer studies that address social cohesion in a framework of cross-cultural validation of the indicators testing the equivalence of the factorial structure across countries. Finally, as far as we know there is no study that attempt to provide an empirically tested multilevel definition of social cohesion specifying a Multilevel Structural Equation Model. This study aims to cover this gap. First, we provide a theoretical construct of social cohesion taking into account not only its multidimensionality but also its multilevel structure. In the second step, to test the validity of this theoretical construct, we perform a multilevel confirmatory factor analysis in order to verify if the conceptual structure suggested in first step holds. In addition, we test the cross-level structural equivalence and the measurement invariance of the model in order to verify if the same multilevel model of social cohesion holds across the 29 countries analysed. In the final step, we specify a second-order multilevel CFA model in order to identify the existence of a general factor that can be called “social cohesion” operating in society that accounts for the surface phenomena that we observe

Validation of a social cohesion theoretical framework: a multiple group SEM strategy

Social cohesion dates back to the end of the nineteenth century. Back then, society experienced epochal transformations, as are also happening nowadays. Whenever there are epochal changes, a social order (cohesion) matter arises. The paper provides a conceptual scheme of social cohesion identifying its constituent dimensions subdivided by three spheres (macro, meso, micro) and two perspectives (objective and subjective). The overarching aim is to test the validity of the operationalization of the social cohesion model provided. Firstly, we conducted an exploratory factor analysis introducing an approach implemented in Mplus named exploratory structural equation modeling that shows several useful characteristics. Afterward, through a structural equation modeling approach, we performed several confirmatory factor analyses adopting a multiple group SEM strategy in order to cross-validate the social cohesion model

Showing our seams: a reply to Eric Funkhouser

In a recent paper published in this journal, Eric Funkhouser argues that some of our beliefs have the primary function of signaling to others, rather than allowing us to navigate the world. Funkhouser’s case is persuasive. However, his account of beliefs as signals is underinclusive, omitting both beliefs that are signals to the self and less than full-fledged beliefs as signals. The latter set of beliefs, moreover, has a better claim to being considered as constituting a psychological kind in its own right than the set of beliefs Funkhouser identifies

Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition

A unique collection of oceanic samples was gathered by the Tara Oceans expeditions (2009-2013), targeting plankton organisms ranging from viruses to metazoans, and providing rich environmental context measurements. Thanks to recent advances in the field of genomics, extensive sequencing has been performed for a deep genomic analysis of this huge collection of samples. A strategy based on different approaches, such as metabarcoding, metagenomics, single-cell genomics and metatranscriptomics, has been chosen for analysis of size-fractionated plankton communities. Here, we provide detailed procedures applied for genomic data generation, from nucleic acids extraction to sequence production, and we describe registries of genomics datasets available at the European Nucleotide Archive (ENA, www.ebi.ac.uk/ena). The association of these metadata to the experimental procedures applied for their generation will help the scientific community to access these data and facilitate their analysis. This paper complements other efforts to provide a full description of experiments and open science resources generated from the Tara Oceans project, further extending their value for the study of the world's planktonic ecosystems