Microalgae community structure analysis based on 18S rDNA amplification from DNA extracted directly from soil as a potential soil bioindicator

Bérard, Annette; Dorigo, Ursula; Humbert, Jean‐François; Martin-Laurent, Fabrice

doi:10.1051/agro:2005004

Cited by 29 publications

(25 citation statements)

References 44 publications

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“…The 18S rRNA genes were amplified using the primer pairs P73 (5'-AAT CAG TTA TAG TTT ATT TGR TGG TAC C-3') and P47 (5'-TCT CAG GCT CCC TCT CCG GA-3') (Berard et al 2005) and EukA (5'-AAC CTG GTT GAT CCT GCC AGT-3') and EukB (5'-TGA TCC TTC TGC AGG TTC ACC TAC-3') (dieZ et al 2001). PCRs were carried out in 25 µl aliquots containing approximately 100 ng DNA, a deoxynucleoside triphosphate mixture (0.2 mM each), buffer (1/10 volume of the supplied 10x buffer) supplemented to give a final concentration of 3 mM MgCl 2 , 1 U of Taq polymerase (Promega), and 0.5 pmol of each primer.…”

Section: Methodsmentioning

confidence: 99%

The biodiversity of subaerophytic phototrophic biofilms from Maltese hypogea.

Zammit¹,

Billi²,

Shubert³

et al. 2011

Fottea

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Abstract:The present study focuses on a description of the biodiversity of subaerial phototrophic biofilms occurring on archaeological surfaces in Maltese hypogean environments, namely St Paul's, St Agatha's and Abbatija tad-Dejr Catacombs, all situated in Rabat and the ancient Ħal Saflieni Hypogeum at Paola, Malta. Direct observation of the biofilms, carried out using light (LM), epifluorescent and confocal laser scanning microscopy (CLSM), allowed the description of the major cyanobacterial and microalgal taxa, and also the associated heterotrophic microorganisms, mainly actinobacteria. Some biofilm microorganisms were able to grow in culture and this allowed the isolation of cyanobacterial, microalgal and chemoorganotrophic bacterial strains. Thylakoid arrangement and cell division were examined using transmission electron microscopy (TEM). The cytomorphology of isolated microorganisms was described. The undisputed phototrophic protagonists in these subaerial biofilms of Maltese hypogean environments were the non-heterocytous (Oscillatorialean) cyanobacteria. In order to increase the limited data available for Leptolyngbya spp. from aerophytic epilithic biofilms in catacombs, the 16S rRNA genes of isolated Leptolyngbya strains were sequenced and compared with those obtained for related strains. Phylogenetic trees of cyanobacterial 16S rRNA sequences were constructed using parsimony and Bayesian analyses. Microorganisms forming biofilms in Maltese hypogea were found to be similar, both cytomorphologically and genetically, to those colonising lithic surfaces of caves and catacombs in other Mediterranean countries.

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Section: Methodsmentioning

confidence: 99%

The biodiversity of subaerophytic phototrophic biofilms from Maltese hypogea.

Zammit¹,

Billi²,

Shubert³

et al. 2011

Fottea

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“…Due to their metabolic pathway close to higher plants, microalgae and cyanobacteria are major targets of herbicides molecules compared to the often studied bacteria and fungi, in microbial ecotoxicology studies. Acquisition of knowledge on the diversity and the functioning of soil phototrophic communities and their responses to herbicides contaminations represents therefor a major issue in order to identify good pollution indicators in soil (Bérard et al , 2005Zancan et al 2006). In this purpose, the analysis of pigment composition to characterize phototrophic microbial structure is already a recognized tool to study this specific community in comparison with microscopic and culture methods (Dorigo et al 2004;Kirkwood and Henley 2006).…”

Section: Introductionmentioning

confidence: 99%

Soil surface colonization by phototrophic indigenous organisms, in two contrasted soils treated by formulated maize herbicide mixtures

et al. 2014

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Soil phototrophic microorganisms, contributors to soil health and food webs, share their particular metabolism with plants. Current agricultural practices employ mixtures of pesticides to ensure the crops yields and can potentially impair these non-target organisms. However despite this environmental reality, studies dealing the susceptibility of phototrophic microorganisms to pesticide mixtures are scarce. We designed a 3 months microcosm study to assess the ecotoxicity of realistic herbicide mixtures of formulated S-metolachlor (Dual Gold Safeneur(®)), mesotrione (Callisto(®)) and nicosulfuron (Milagro(®)) on phototrophic communities of two soils (Limagne vertisol and Versailles luvisol). The soils presented different colonizing communities, with diatoms and chlorophyceae dominating communities in Limagne soil and cyanobacteria and bryophyta communities in Versailles soil. The results highlighted the strong impairment of Dual Gold Safeneur(®) treated microcosms on the biomass and the composition of both soil phototrophic communities, with no resilience after a delay of 3 months. This study also excluded any significant mixture effect on these organisms for Callisto(®) and Milagro(®) herbicides. We strongly recommend carrying on extensive soil studies on S-metolachlor and its commercial formulations, in order to reconsider its use from an ecotoxicological point of view.

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“…In addition, the lysis of Bacillariophyceae cells is difficult, hampering DNA extraction, probably because of the presence of the robust silicate valves (Bérard et al. ). In this study, our data set showed that DGGE diversity was more closely related to generic diversity, but it did not enable us to unequivocally determine whether diversity with lower resolution power at the species level could also be reliable.…”

Section: Resultsmentioning

confidence: 99%

Characterization of Freshwater Diatom Communities: Comparing Taxonomic and Genetic‐Fingerprinting Approaches

Morin

Roubeix

Batisson

et al. 2012

Journal of Phycology

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Benthic diatom assemblages from five sampling sites located on two rivers were characterized simultaneously by means of traditional microscopic observations and PCR-DGGE fingerprinting with primers specifically designed for Bacillariophyceae. Community structure, richness, and diversity assessed by both methods were compared. Diatom lists obtained from morphological identification were separated into subsets, depending on (i) the taxonomic level considered (genus, species, variety) and, for each of them, (ii) the relative abundance (RA) of each component (the whole data set, RA > 1%, RA > 2%). These data were then compared to genetic fingerprinting data. Clusters based on taxonomic composition and DGGE banding patterns were very similar, showing good correspondence of community structure between the two methods. Data were compared by linear regressions between indices (richness, diversity) and by Mantel tests on dissimilarity matrices generated for each community composition data set. Statistical analysis indicated that the most reliable correlations with fingerprinting were obtained for genera representing more than 1% RA or species representing more than 2% RA. The results reveal that the PCR-DGGE protocol described here offers a satisfactory alternative for performing preliminary screening of coarse differences in diatom global community structure between samples. It can be regarded as a good complement to taxonomic analyses, which still remain necessary to detect precise changes in richness and diversity, especially when considering species with low abundance in natural assemblages.

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Microalgae community structure analysis based on 18S rDNA amplification from DNA extracted directly from soil as a potential soil bioindicator

Cited by 29 publications

References 44 publications

The biodiversity of subaerophytic phototrophic biofilms from Maltese hypogea.

The biodiversity of subaerophytic phototrophic biofilms from Maltese hypogea.

Soil surface colonization by phototrophic indigenous organisms, in two contrasted soils treated by formulated maize herbicide mixtures

Characterization of Freshwater Diatom Communities: Comparing Taxonomic and Genetic‐Fingerprinting Approaches

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