报告题目：
1， NO, a signal molecule and an air pollutant
报 告 人：Lars Bakken, Professor
Dept of Plant and Environmental Sciences
Norwegian University of life Sciences

报告题目：
2， Regulatory biology and ecology of denitrifying bacteria; why do we need pure culture studies?
报 告 人：Asa Frostegard, Professor
Dep. of Chemistry, Biotechnology and Food Science
Norwegian University of Life Sciences

报告题目：
3， Identification of active players by high-throughput amplicon sequencing of functional genes and transcripts
报 告 人：Binbin Liu（刘彬彬）, 博士
Dep. of Chemistry, Biotechnology and Food Science
Norwegian University of Life Sciences

报告题目：
4, characterization of the diversity and prevalence of antibiotic resistance gene determinants in the environment using a metagenomic approach
报 告 人：Joseph Nesme
Equipe «Génomique Microbienne Environnementale» (Environ. Microb.  Genom. Group)
UMR CNRS 5005, Laboratoire Ampère, Ecole Centrale de Lyon, France (里昂中央理工大学)

报告时间：2011年11月18日(周五) 上午9:00
报告地点：上海交通大学闵行校区生物药学楼树华多功能厅
组织单位：赵立平实验室
上海交通大学生命科学技术学院
上海市微生物学会

报告摘要：

NO, a signal molecule and an air pollutant
Lars Bakken
Dept of Plant and Environmental Sciences, Norwegian University of life Sciences

Abstract
NO is an important signal molecule for denitrifying organisms by exerting a positive feedback on the expression of some but not all the genes for denitrification. On the other hand, a careful control of the NO concentrations at nanomolar concentrations has long been considered an essential fitness character for denitrifying organisms, since micromolar concentrations of NO is toxic. For the same reason, organisms lacking the gene coding for NO reductase enzyme (NOR) have been considered unfit for denitrification. This view is challenged by isolation of organisms whose primary product of denitrification is NO, either because they lack the gene for NO reductase, or because their expression of the denitrification proteome is extremely unbalanced, resulting in transient NO accumulation to micromolar concentrations when grown in pure culture. Such paralyzing NO concentrations are probably never reached in natural environments, however, due to diffusion and NO-absorption by adjacent organisms, be it by NOR or other NO scavenging enzymes. Hypothetically, the production of NO by denitrifying organisms may be an advantage by fending off nearby competitors. Soils emit significant amounts of NO to the atmosphere; the emission is possibly "gunsmoke" from a battle down under.



Regulatory biology and ecology of denitrifying bacteria; why do we need pure culture studies?
Åsa Frostegård,
Norwegian University of Life Sciences

Abstract
Emissions of N2O from agricultural soils are largely caused by denitrifying bacteria. Field measurements of N2O fluxes show large variations and depend on several environmental factors, as well as on the composition and activity of the denitrifying microbial community. As this data is gathering, the need to understand the mechanisms underlying the emissions of N2O to the atmosphere becomes evident, in order to find appropriate mitigation options. Analyses of denitrification genes and transcripts extracted from soils are important for describing the system, but have limited value for prediction of N2O emissions. In contrast, phenotypic analyses are direct measures of the organisms´ responses to changing environmental conditions. Our approach is to combine phenotypic characterizations using high-resolution gas kinetics, with gene transcription analyses to study denitrification regulatory phenotypes (DRP) of bacterial strains or complex microbial communities. The rich data sets obtained provide a basis for refinement of biochemical and physiological research on this key process in the nitrogen cycle and may also serve as a platform for mechanistic and predictive models (systems biology/systems ecology). Most of the current knowledge on denitrification is based on detailed studies of a few paradigm strains and there is a need to extend this knowledge to a wider range of denitrifiers, with the practical, long-term goal to provide improved parameters for mathematical models that predict NOx emissions. The talk will present a diversity of DRPs represented by a range of recently isolated Gram-negative and Gram- positive denitrifiers, including the genera Thauera, Bradyrhizobium and Bacillus, and compare them with selected paradigm strains.

Identification of active players by high-throughput amplicon sequencing of functional genes and transcripts
Binbin Liu1  Xiaojun Zhang2  Åsa Frostegård1  Las Bakken3
1Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Ås, Norway.
2 Shanhai Jiaotong University Shanghai China
3 Department of Plant and Environmental Sciences, Norwegian University of Life Sciences, Ås, Norway.

Abstract:
Our earlier studies of denitrification gene expression in soil show that transcription occurs only during a few hours after oxygen depletion. DGGE analysis indicated sequential triggering of gene expression by different populations. We used a robotized incubation system, and guided by the gas kinetics we sampled soil for mRNA isolation at time intervals (1, 3 and 6h after O2 depletion). Functional genes (narG, napA, nirS, nirK, qnorB, nosZ) were amplified from both DNA and cDNA using ID tagged primers. A total of 210,000 sequences were analyzed, mostly representing Proteobacteria. The cDNA libraries confirmed that some groups initiated transcription earlier than others. The same groups were detected both in cDNA and DNA libraries, but in different proportions; those dominating the DNA library were often less abundant in the cDNA and vice versa. For example, Dechloromonassequences constituted 4 and 6% of the total sequences in nirS and napA DNA and 56% and 22% in the corresponding cDNA,  Cupriavidusconstituted 5% innirSDNA and 22% in the cDNAlibraries andPseudomonas increased from 15% in nosZ DNA to >50% in cDNA while, in contrast, Herbaspirillum decreased from58% in DNA to 16% in cDNA. The findings reveal key-player denitrifiers and will be used to for targeted isolation of these groups.
CHARACTERIZATION OF THE DIVERSITY AND PREVALENCE OF ANTIBIOTIC RESISTANCE GENE DETERMINANTS IN THE ENVIRONMENT USING A METAGENOMIC APPROACH

J.-M. Monier1, S. Cecillon1, T.O. Delmont1, T.M. Vogel1, P. Simonet1, J. Nesme2
1Environmental Microbial Genomics Group, Laboratoire AMPERE, Ecole Centrale de Lyon,
Université de Lyon, Ecully, 2Environmental Microbial Genomics Group, Laboratoire AMPERE,
Ecole Centrale de Lyon, Université de Lyon, Lyon, France


Abstract
Recent work has revealed that the vast majority of antibiotics currently used for treating infections and the antibiotic resistance gene determinants (ARGD) acquired by human pathogens have an environmental origin. A better understanding of the diversity, prevalence and ecological significance of ARGD may help predict the emergence and spreading of newly acquired resistances and assess the impact of the release of large amounts of antibiotics on microbial communities and the disruption of natural ecosystems. The number of available environmental metagenomic sequence datasets is rapidly expanding and therefore offer the ability to gain a more comprehensive understanding of antibiotic resistance at the global scale.
The objective of our work was to characterize the diversity and prevalence of ARGD in natural and anthropogenic environments. A total of 65 metagenome datasets were used, 58 publically available on the MG-RAST server (metagenomics.nmpdr.org) and 7 obtained from the Rothamsted Park Grass soil were screened for ARGD. Datasets from the different environments (oceans, deep oceans, Antarctic lakes, sediments, sludges, soils…) were compiled into a unique dataset (1.68 x 106 sequences; 7.66 x 109 base pairs) and a local blast was performed using over 23,000 amino-acid sequences obtained from the ARDB Database (ardb.cbcb.umd.edu). Results show that about a third of these sequences were detected and unevenly distributed among the different metagenomes, and corresponded to ca 0.3% of the sequences. The approach used in this study is currently being completed with the screening of metagenomic DNA libraries. Results obtained will be presented and discussed during the symposium.