Search results for "ecosystem"
showing 10 items of 1752 documents
Finding the missing link between diversity and activity using denitrifying bacteria as a model functional community
2005
The recent development and application of numerous methods mainly based on 16S rDNA analyses have brought insights into the questions of which and how many bacterial populations can be found in a given ecosystem. A new and challenging question for microbial ecologists has emerged from the exploration of this diversity: what is its significance for ecosystem functioning? We propose the denitrifying bacteria as a model microbial community for understanding the relationship between community structure and activity, and have summarized the recent progress in studies of this functional community.
Contrasting Effects of Environmental Concentrations of Sulfonamides on Microbial Heterotrophic Activities in Freshwater Sediments
2021
The sulfonamide antibiotics sulfamethoxazole (SMX) and sulfamethazine (SMZ) are regularly detected in surface sediments of contaminated hydrosystems, with maximum concentrations that can reach tens of μg kg–1 in stream and river sediments. Little is known about the resulting effects on the exposed benthic organisms. Here we investigated the functional response of stream sediment microbial communities exposed for 4 weeks to two levels of environmentally relevant concentrations of SMX and SMZ, tested individually. To this end, we developed a laboratory channel experiment where natural stream sediments were immersed in water contaminated with nominal environmental concentrations of 500 and 5,0…
Perspectives on the Impact of Sampling Design and Intensity on Soil Microbial Diversity Estimates
2019
Soil bacterial communities have long been recognized as important ecosystem components, and have been the focus of many local and regional studies. However, there is a lack of data at large spatial scales, on the biodiversity of soil microorganisms; national or more extensive studies to date have typically consisted of low replication of haphazardly collected samples. This has led to large spatial gaps in soil microbial biodiversity data. Using a pre-existing dataset of bacterial community composition across a 16-km regular sampling grid in France, we show that the number of detected OTUs changes little under different sampling designs (grid, random, or representative), but increases with t…
Spatial segregation of the biological soil crust microbiome around its foundational cyanobacterium, Microcoleus vaginatus, and the formation of a nit…
2019
12 pages; International audience; Background Biological soil crusts (biocrusts) are a key component of arid land ecosystems, where they render critical services such as soil surface stabilization and nutrient fertilization. The bundle-forming, filamentous, non-nitrogen-fixing cyanobacterium Microcoleus vaginatus is a pioneer primary producer, often the dominant member of the biocrust microbiome, and the main source of leaked organic carbon. We hypothesized that, by analogy to the rhizosphere of plant roots, M. vaginatus may shape the microbial populations of heterotrophs around it, forming a specialized cyanosphere. Results By physically isolating bundles of M. vaginatus from biocrusts, we …
The use of multiplex PCR to detect and differentiate food- and beverage-associated microorganisms: a review.
2007
Regarding food safety, rapid detection of microbial species is crucial to develop effective preventive and/or adjustment measures. Classical methods for determining the presence of certain species are time-consuming and labor-intensive, hence, molecular methods, which offer speed, sensitivity and specificity, have been developed to address this problem. Multiplex PCR (MPCR) is widely applied in the various fields of microbiology for the rapid differentiation of microbial species without compromising accuracy. This paper describes the method and reports on the state-of-the-art application of this technique to the identification of microorganisms vehiculated with foods and beverages. The iden…
A molecular method to assess Phytophthora diversity in environmental samples
2012
Current molecular detection methods for the genus Phytophthora are specific to a few key species rather than the whole genus and this is a recognized weakness of protocols for ecological studies and international plant health legislation. In the present study a molecular approach was developed to detect Phytophthora species in soil and water samples using novel sets of genus-specific primers designed against the internal transcribed spacer (ITS) regions. Two different rDNA primer sets were tested: one assay amplified a long product including the ITS1, 5.8S and ITS2 regions (LP) and the other a shorter product including the ITS1 only (SP). Both assays specifically amplified products from Phy…
Dissemination of CTX-M-Producing Escherichia coli in Freshwater Fishes From a French Watershed (Burgundy)
2019
International audience; The burden of extended-spectrum beta-lactamases producing Escherichia coli (ESBL-Ec), has increased over several decades. Freshwater ecosystems are suspected to play an important ecological and evolutionary role in driving the dissemination of antimicrobial resistance. The aim of our study was to decipher the occurrence of ESBL-Ec in a small watershed (Ouche river, Burgundy, France), targeting environmental matrices and fishes. Among cefotaxime resistant E. coli (ctxR Ec) isolates, we detected and characterized 36 ESBL-Ec from water, biofilm and fish guts. ctxR Ec and ESBL-Ec were found in samples from sites near the first small town, located downstream from the wate…
Functional gene pyrosequencing reveals core proteobacterial denitrifiers in boreal lakes
2015
Denitrification is an important microbial process in aquatic ecosystems that can reduce the effects of eutrophication. Here, quantification and pyrosequencing of nirS, nirK, and nosZ genes encoding for nitrite and nitrous oxide reductases was performed in sediment samples from four boreal lakes to determine the structure and seasonal stability of denitrifying microbial populations. Sediment quality and nitrate concentrations were linked to the quantity and diversity of denitrification genes, the abundance of denitrifying populations (nirS and nosZ genes) correlated with coupled nitrificationdenitrification (Dn), and the denitrification of the overlying water NO3 − (Dw) correlated with the n…
Impervious Surfaces Alter Soil Bacterial Communities in Urban Areas: A Case Study in Beijing, China
2018
The rapid expansion of urbanization has caused land cover change, especially the increasing area of impervious surfaces. Such alterations have significant effects on the soil ecosystem by impeding the exchange of gasses, water, and materials between soil and the atmosphere. It is unclear whether impervious surfaces have any effects on soil bacterial diversity and community composition. In the present study, we conducted an investigation of bacterial communities across five typical land cover types, including impervious surfaces (concrete), permeable pavement (bricks with round holes), shrub coverage (Buxus megistophylla Levl.), lawns (Festuca elata Keng ex E. Alexeev), and roadside trees (S…
Hybridization of mouse lemurs: different patterns under different ecological conditions
2011
Abstract Background Several mechanistic models aim to explain the diversification of the multitude of endemic species on Madagascar. The island's biogeographic history probably offered numerous opportunities for secondary contact and subsequent hybridization. Existing diversification models do not consider a possible role of these processes. One key question for a better understanding of their potential importance is how they are influenced by different environmental settings. Here, we characterized a contact zone between two species of mouse lemurs, Microcebus griseorufus and M. murinus, in dry spiny bush and mesic gallery forest that border each other sharply without intermediate habitats…