Direct analysis of ribosomal DNA in denaturing gradients: application on the effects of Phlebiopsis gigantea treatment on fungal communities of conifer stumps

Vainio, Eeva J.; Hallaksela, Anna‐Maija; Lipponen, K.; Hantula, Jarkko

doi:10.1017/s0953756204001406

Cited by 16 publications

(9 citation statements)

References 24 publications

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“…The evenness of the bacterial communities in the holes was described using Pareto-Lorenz distribution curves (De Schryver et al, 2008;Marzorati et al, 2008) and the corrected Gini coefficients (G corr ) (Vainio et al, 2005;Halet et al, 2006;Wittebolle et al, 2008) derived for each hole. The Pareto-Lorenz distribution curves obtained by plotting the cumulative relative abundance of each T-RF against its cumulative proportion of the number of T-RFs for each cryoconite hole are shown in Figure 2.…”

Section: T-rflp Analysesmentioning

confidence: 99%

Possible interactions between bacterial diversity, microbial activity and supraglacial hydrology of cryoconite holes in Svalbard

et al. 2010

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The diversity of highly active bacterial communities in cryoconite holes on three Arctic glaciers in Svalbard was investigated using terminal restriction fragment length polymorphism (T-RFLP) of the 16S rRNA locus. Construction and sequencing of clone libraries allowed several members of these communities to be identified, with Proteobacteria being the dominant one, followed by Cyanobacteria and Bacteroidetes. T-RFLP data revealed significantly different communities in holes on the (cold) valley glacier Austre Brøggerbreen relative to two adjacent (polythermal) valley glaciers, Midtre Lové nbreen and Vestre Brøggerbreen. These population compositions correlate with differences in organic matter content, temperature and the metabolic activity of microbial communities concerned. No within-glacier spatial patterns were observed in the communities identified over the 2-year period and with the 1 km-spaced sampling. We infer that surface hydrology is an important factor in the development of cryoconite bacterial communities.

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Section: T-rflp Analysesmentioning

confidence: 99%

Possible interactions between bacterial diversity, microbial activity and supraglacial hydrology of cryoconite holes in Svalbard

et al. 2010

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“…This technique was applied to compare species composition between plots treated with Phlebiopsis gigantea (Fr.) Jülich and untreated plots (Vainio et al 2005).…”

Section: Molecular Community Profilingmentioning

confidence: 99%

Molecular epidemiology of forest pathogens: from genes to landscape

Hamelin

2006

Canadian Journal of Plant Pathology

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In the last two decades, important developments in molecular biology have significantly improved our capacity to address questions in population biology, which could have an impact on our understanding of the epidemiology of plant pathogens. In turn, some of the molecular tools that are now available, in particular those based on the polymerase chain reaction, have made it possible to detect and monitor pathogens directly from the environment, by-passing the need for culturing. This has had a large impact in forest pathology, where hosts and pathogens often cover large ranges of latitude, longitude, and altitude. Genomics data as well are being generated in forest pathology, with fungal and tree genomes being completely sequenced. The integration of genomic and environmental data is a promising area of forest pathology, and this review will address some of the issues and potential future directions in this field.Résumé : Au cours des deux dernières décennies, d'importants développements en biologie moléculaire ont grandement amélioré notre capacité à aborder les questions de biologie des populations qui pourraient influer sur notre compréhension de l'épidémiologie des agents pathogènes des plantes. Pour leur part, certains des outils moléculaires maintenant disponibles, en particulier ceux basés sur l'amplification en chaîne de la polymérase, ont permis de détecter et surveiller des agents pathogènes directement dans l'environnement, éliminant la nécessité de les cultiver. Ceci a eu un impact considérable en pathologie forestière, où les hôtes et les agents pathogènes couvrent souvent de grands intervalles de latitude, de longitude et d'altitude. De plus, des données génomiques sont générées en pathologie forestière, des génomes de champignons et d'arbres étant complètement séquencés. L'intégration des données génomiques et environnementales est un domaine prometteur de la pathologie forestière, et la présente synthèse abordera quelques-unes des problématiques et des avenues dans ce domaine.Mots clés : génétique des populations, diagnostic, amplification en chaîne de la polymérase, génomique fongique, éta-blissement de profils de communautés, pathologie forestière.Hamelin: forest pathogens / molecular epidemiology / genomics 181

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“…Microbiota are for the most part responsible for the decay of organic matter and recycling of nutrients from plant inaccessible forms (i.e., N 2 gas, complex organic polymers) to plant accessible ones (i.e., NH 4 + , NO 3 - , PO 4 + and organic monomers; Prescott et al, 1993 ; Elsas et al, 2007 ; Finlay, 2007 ; Prosser, 2007 ). In this study we used polymerase chain reaction (PCR) and denaturing gradient gel electrophoresis (DGGE) as an inexpensive, replicable technique to efficiently screen the principal constituents of nutrient-cycling microbial communities ( Nicolaisen and Ramsing, 2002 ; Vainio et al, 2005 ; Fierer and Jackson, 2006 ; Oros-Sichler et al, 2007 ; Hoshino and Morimoto, 2010 ) accross climatic gradients within the same forest ecosystem.…”

Section: Introductionmentioning

confidence: 99%

Nutrient-cycling microbes in coastal Douglas-fir forests: regional-scale correlation between communities, in situ climate, and other factors

2015

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Microbes such as fungi and bacteria play fundamental roles in litter-decay and nutrient-cycling; however, their communities may respond differently than plants to climate change. The structure (diversity, richness, and evenness) and composition of microbial communities in climate transects of mature Douglas-fir stands of coastal British Columbia rainshadow forests was analyzed, in order to assess in situ variability due to different temperature and moisture regimes. We compared denaturing gradient gel electrophoresis profiles of fungi (18S-FF390/FR1), nitrogen-fixing bacteria (NifH-universal) and ammonia-oxidizing bacteria (AmoA) polymerase chain reaction amplicons in forest floor and mineral soil samples from three transects located at different latitudes, each transect spanning the Coastal Western Hemlock and Douglas-fir biogeoclimatic zones. Composition of microbial communities in both soil layers was related to degree days above 0°C (2725–3489), while pH (3.8–5.5) best explained shifts in community structure. At this spatial scale, climatic conditions were likely to directly or indirectly select for different microbial species while local site heterogeneity influenced community structure. Significant changes in microbial community composition and structure were related to differences as small as 2.47% and 2.55°C in mean annual moisture and temperature variables, respectively. The climatic variables best describing microbial composition changed from one functional group to the next; in general they did not alter community structure. Spatial distance, especially associated with latitude, was also important in accounting for community variability (4–23%); but to a lesser extent than the combined influence of climate and soil characteristics (14–25%). Results suggest that in situ climate can independently account for some patterns of microbial biogeography in coastal Douglas-fir forests. The distribution of up to 43% of nutrient-cycling microorganisms detected in forest soils responded to smaller abiotic gradients than host trees.

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Direct analysis of ribosomal DNA in denaturing gradients: application on the effects of Phlebiopsis gigantea treatment on fungal communities of conifer stumps

Cited by 16 publications

References 24 publications

Possible interactions between bacterial diversity, microbial activity and supraglacial hydrology of cryoconite holes in Svalbard

Possible interactions between bacterial diversity, microbial activity and supraglacial hydrology of cryoconite holes in Svalbard

Molecular epidemiology of forest pathogens: from genes to landscape

Nutrient-cycling microbes in coastal Douglas-fir forests: regional-scale correlation between communities, in situ climate, and other factors

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