Meeting Report: Molecular Ecology Workshop. Detection of Microbial Biodiversity in Environmental Samples, Camerino, Italy, September 19–21, 2005

Environmental DNA, i.e., DNA directly extracted from environmental samples, has been applied to understand microbial communities in the environments and to monitor contemporary biodiversity in the conservation context. Environmental DNA often contains both intracellular DNA (iDNA) and extracellular DNA (eDNA). eDNA can persist in the environment and complicate environmental DNA sequencing-based analyses of microbial communities and biodiversity. Although several studies acknowledged the impact of eDNA on DNA-based profiling of environmental communities, eDNA is still being neglected or ignored in most studies dealing with environmental samples. In this article, we summarize key findings on eDNA in environmental samples and discuss the methods used to extract and quantify eDNA as well as the importance of eDNA on the interpretation of experimental results. We then suggest several factors to consider when designing experiments and analyzing data to negate or determine the contribution of eDNA to environmental DNA-based community analyses. This field of research will be driven forward by: (i) carefully designing environmental DNA extraction pipelines by taking into consideration technical details in methods for eDNA extraction/removal and membrane-based filtration and concentration; (ii) quantifying eDNA in extracted environmental DNA using multiple methods including qPCR and fluorescent DNA binding dyes; (iii) carefully interpretating effect of eDNA on DNA-based community analyses at different taxonomic levels; and (iv) when possible, removing eDNA from environmental samples for DNA-based community analyses.

Download Full-text

Meeting Report: The Institute for Genomic Research/Wellcome Trust Conference: Genomes 2004 14–17 April 2004, the Wellcome Trust Conference Centre, The Wellcome Trust Genome Campus, Hinxton, Cambridge, Uk

Comparative and Functional Genomics ◽

10.1002/cfg.431 ◽

2004 ◽

Vol 5 (6-7) ◽

pp. 491-496

Author(s):

Jo Wixon

Keyword(s):

Comparative Genomics ◽

Functional Genomics ◽

Cross Section ◽

Genome Analysis ◽

Environmental Samples ◽

Pathogenic Bacteria ◽

Computational Genomics ◽

Genomic Research ◽

Meeting Report ◽

Conference Centre

This conference brought the microbial genomics community together to share their most up-to-the-minute achievements, so much so that several talks cannot be covered here, as the work discussed has not yet been published. This meeting report has details of a cross-section of the talks from the sessions on ‘Genome analysis and comparative genomics’, ‘Computational genomics’ and ‘Functional genomics’, ranging from studies on complex environmental samples, to specific pathogenic bacteria, to yeasts.

Download Full-text

Molecular Ecology of Listeria monocytogenes and Other Listeria Species in Small and Very Small Ready-to-Eat Meat Processing Plants

Journal of Food Protection ◽

10.4315/0362-028x.jfp-10-097 ◽

2011 ◽

Vol 74 (1) ◽

pp. 63-77 ◽

Cited By ~ 28

Author(s):

SHANNA K. WILLIAMS ◽

SHERRY ROOF ◽

ELIZABETH A. BOYLE ◽

DENNIS BURSON ◽

HARSHAVARDHAN THIPPAREDDI ◽

...

Keyword(s):

Gel Electrophoresis ◽

Environmental Samples ◽

Molecular Ecology ◽

Meat Products ◽

Positive Sample ◽

Pulsed Field Gel Electrophoresis ◽

Meat Processing ◽

Molecular Serotyping ◽

Processing Plants ◽

Allelic Type

A longitudinal study was conducted to track Listeria contamination patterns in ready-to-eat meats from six small or very small meat processing plants located in three states over 1 year. A total of 688 environmental sponge samples were collected from nonfood contact surfaces during bimonthly visits to each plant. Overall, L. monocytogenes was isolated from 42 (6.1%) environmental samples, and its prevalence ranged from 1.7 to 10.8% across different plants. Listeria spp., other than L. monocytogenes, were isolated from 9.5% of samples overall, with the prevalence ranging from 1.5 to 18.3% across different plants. The prevalence of L. monocytogenes correlated well with that of other Listeria spp. for some but not all plants. One L. monocytogenes isolate representing each positive sample was characterized by molecular serotyping, EcoRI ribotyping, and pulsed-field gel electrophoresis typing. Seven sample sites tested positive for L. monocytogenes on more than one occasion, and the same ribotype was detected more than once at five of these sites. Partial sigB sequencing was used to speciate other Listeria spp. isolates and assign an allelic type to each isolate. Other Listeria spp. were isolated more than once from 14 sample sites, and the same sigB allelic type was recovered at least twice from seven of these sites. One plant was colonized by an atypical hemolytic L. innocua strain. Our findings indicate that small and very small meat processing plants that produce ready-to-eat meat products are characterized by a varied prevalence of Listeria, inconsistent correlation between contamination by L. monocytogenes and other Listeria spp., and a unique Listeria molecular ecology.

Download Full-text

Molecular Ecology of Listeria monocytogenes: Evidence for a Reservoir in Milking Equipment on a Dairy Farm

Applied and Environmental Microbiology ◽

10.1128/aem.01826-08 ◽

2008 ◽

Vol 75 (5) ◽

pp. 1315-1323 ◽

Cited By ~ 60

Author(s):

Alejandra A. Latorre ◽

Jo Ann S. Van Kessel ◽

Jeffrey S. Karns ◽

Michael J. Zurakowski ◽

Abani K. Pradhan ◽

...

Keyword(s):

New York ◽

Listeria Monocytogenes ◽

Environmental Samples ◽

Molecular Ecology ◽

New York State ◽

Dairy Farm ◽

Bulk Tank Milk ◽

Fecal Samples ◽

Milk Samples ◽

Bulk Tank

ABSTRACT A longitudinal study aimed to detect Listeria monocytogenes on a New York State dairy farm was conducted between February 2004 and July 2007. Fecal samples were collected every 6 months from all lactating cows. Approximately 20 environmental samples were obtained every 3 months. Bulk tank milk samples and in-line milk filter samples were obtained weekly. Samples from milking equipment and the milking parlor environment were obtained in May 2007. Fifty-one of 715 fecal samples (7.1%) and 22 of 303 environmental samples (7.3%) were positive for L. monocytogenes. A total of 73 of 108 in-line milk filter samples (67.6%) and 34 of 172 bulk tank milk samples (19.7%) were positive for L. monocytogenes. Listeria monocytogenes was isolated from 6 of 40 (15%) sampling sites in the milking parlor and milking equipment. In-line milk filter samples had a greater proportion of L. monocytogenes than did bulk tank milk samples (P < 0.05) and samples from other sources (P < 0.05). The proportion of L. monocytogenes-positive samples was greater among bulk tank milk samples than among fecal or environmental samples (P < 0.05). Analysis of 60 isolates by pulsed-field gel electrophoresis (PFGE) yielded 23 PFGE types after digestion with AscI and ApaI endonucleases. Three PFGE types of L. monocytogenes were repeatedly found in longitudinally collected samples from bulk tank milk and in-line milk filters.

Download Full-text

Pollutant Identification by Selected Area Electron Diffraction

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100052675 ◽

1974 ◽

Vol 32 ◽

pp. 532-533

Author(s):

R. E. Ferrell ◽

G. G. Paulson ◽

C. W. Walker

Keyword(s):

Thermal Treatment ◽

Electron Diffraction ◽

Sample Preparation ◽

Crystal Structures ◽

Water Samples ◽

Environmental Samples ◽

Short Review ◽

Selected Area Electron Diffraction ◽

Multiple Component

Selected area electron diffraction (SAD) has been used successfully to determine crystal structures, identify traces of minerals in rocks, and characterize the phases formed during thermal treatment of micron-sized particles. There is an increased interest in the method because it has the potential capability of identifying micron-sized pollutants in air and water samples. This paper is a short review of the theory behind SAD and a discussion of the sample preparation employed for the analysis of multiple component environmental samples.

Download Full-text