Molecular approaches to the assessment of biodiversity in aquatic microbial communities

Dorigo, Ursula; Volatier, Laurence; Humbert, Jean‐François

doi:10.1016/j.watres.2005.04.007

Cited by 95 publications

(55 citation statements)

References 132 publications

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“…Because microbes have lived on Earth for more than 3 billion years, they are ubiquitous and play important roles in the Earth's ecosystems (Kowalchuk et al 2008). In particular, they participate in essential biogeochemical processes such as the carbon, nitrogen and sulphur cycles in terrestrial and aquatic ecosystems, are producers and decomposers in food webs (Dorigo et al 2005;Kisand et al 2012;Zehr 2010), and are primarily responsible for degradation of a large variety of natural organic compounds (Ogawa et al 2001).…”

Section: Introductionmentioning

confidence: 99%

The influence of invasive jellyfish blooms on the aquatic microbiome in a coastal lagoon (Varano, SE Italy) detected by an Illumina-based deep sequencing strategy

et al. 2014

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The rapid expansion of multicellular native and alien species outbreaks in aquatic and terrestrial ecosystems (bioinvasions) may produce significant impacts on bacterial community dynamics and nutrient pathways with major ecological implications. In aquatic ecosystems, bioinvasions may cause adverse effects on the water quality resulting from changes in biological, chemical and physical properties linked to significant transformations of the microbial taxonomic and functional diversity. Here we used an effective and highly sensitive experimental strategy, bypassing the efficiency bottleneck of the traditional bacterial isolation and culturing method, to identify changes of the planktonic microbial community inhabiting a marine coastal lagoon (Varano, Adriatic Sea) under the influence of an outbreakforming alien jellyfish species. Water samples were collected from two areas that differed in their level of confinement inside in the lagoon and jellyfish densities (W, up to 12.4 medusae m -3 ; E, up to 0.03 medusae m -3 ) to conduct a snapshot microbiome analysis by a metagenomic approach. After extraction of the genetic material in the environmental water samples, we deepsequenced metagenomic amplicons of the V5-V6 region of the 16S rRNA bacterial gene by an Illumina MiSeq platform. Experiments were carried out in Caterina Manzari, Bruno Fosso and Marinella Marzano have contributed equally to this work.Stefano Piraino and Graziano Pesole are senior authors.Electronic supplementary material The online version of this article (doi:10.1007/s10530-014-0810-2) contains supplementary material, which is available to authorized users. triplicates, so six libraries of dual indexed amplicons of 420 bp were successfully sequenced on the MiSeq platform using a 2 9 250 bp paired-end sequencing strategy. Approximately 7.5 million paired-end reads (i.e. 15 million total reads) were generated, with an average of 2.5 million reads (1.25 M pairs) per sample replicate. The sequence data, analyzed through a novel bioinformatics pipeline (BioMaS), showed that the structure of the resident bacterial community was significantly affected by the occurrence of jellyfish outbreaks. Clear qualitative and quantitative differences were found between the western and eastern areas (characterized by many or few jellyfish), with 84 families, 153 genera and 324 species in the W samples, and 104 families, 199 genera and 331 species in the E samples. Significant differences between the two sampling areas were particularly detected in the occurrence of 16 families, 22 genera and 61 species of microbial taxa. This is the first time that a NGS platform has been used to screen the impact of jellyfish bioinvasions on the aquatic microbiome, providing a preliminary assessment of jellyfish-driven changes of the functional and structural microbial biodiversity.

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Section: Introductionmentioning

confidence: 99%

The influence of invasive jellyfish blooms on the aquatic microbiome in a coastal lagoon (Varano, SE Italy) detected by an Illumina-based deep sequencing strategy

et al. 2014

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“…Methodological advances during the last three decades have greatly increased our understanding of diversity and turnover of natural bacterial communities (Ovreas, 2000;Dorigo et al, 2005) and also, more recently, about the underlying assembly mechanisms (Lindström and Langenheder, 2011). It has been shown that bacterial communities can be assembled by species sorting (Beisner et al, 2006;Van der Gucht et al, 2007;Logue and Lindströ m, 2010) as well as mass effects (Lindströ m et al, 2006;Crump et al, 2007).…”

Section: Introductionmentioning

confidence: 99%

Temporal variation of β-diversity and assembly mechanisms in a bacterial metacommunity

et al. 2011

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The turnover of community composition across space, b-diversity, is influenced by different assembly mechanisms, which place varying weight on local habitat factors, such as environmental conditions and species interactions, and regional factors such as dispersal and history. Several assembly mechanisms may function simultaneously; however, little is known about how their importance changes over time and why. Here, we implemented a field survey where we sampled a bacterial metacommunity consisting of 17 rock pools located at the Swedish Baltic Sea coast at 11 occasions during 1 year. We determined to which extent communities were structured by different assembly mechanisms using variation partitioning and studied changes in b-diversity across environmental gradients over time. b-Diversity was highest at times of high overall productivity and environmental heterogeneity in the metacommunity, at least partly due to species sorting, that is, selection of taxa by the prevailing environmental conditions. In contrast, dispersal-driven assembly mechanisms were primarily detected at times when b-diversity was relatively low. There were no indications for strong and persistent differences in community composition or b-diversity between permanent and temporary pools, indicating that the physical disturbance regime is of relatively minor importance. In summary, our study clearly suggests that there are temporal differences in the relative importance of different assembly mechanisms related to abiotic factors and shows that the temporal variability of those factors is important for a more complete understanding of bacterial metacommunity dynamics.

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“…If comparable samples collected from different locations harbor similar communities in the same area, the fingerprinting patterns are theoretically expected to be similar. To date, the fingerprinting techniques commonly used in aquatic habitats include denaturing/temperature gradient gel electrophoresis (DGGE/TGGE), single strand conformation polymorphism (SSCP), randomly amplified polymorphic DNA (RAPD), terminal-restriction fragment length polymorphism (T-RFLP), amplified ribosomal DNA restriction analysis (ARDRA), ribosomal intergenic spacer analysis (RISA) and automated ribosomal intergenic spacer analysis (ARISA) (see [31] for details). These methods provide a rapid means for screening microbial communities from different environments or for comparing community dynamics at different spatial/temporal scales.…”

Section: Community Fingerprinting Analysismentioning

confidence: 99%

Metagenome-based analysis: A promising direction for plankton ecological studies

Yan

2010

Sci. China Life Sci.

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The plankton community plays an especially important role in the functioning of aquatic ecosystems and also in biogeochemical cycles. Since the beginning of marine research expeditions in the 1870s, an enormous number of planktonic organisms have been described and studied. Plankton investigation has become one of the most important areas of aquatic ecological study, as well as a crucial component of aquatic environmental evaluation. Nonetheless, traditional investigations have mainly focused on morphospecies composition, abundances and dynamics, which primarily depend on morphological identification and counting under microscopes. However, for many species/groups, with few readily observable characteristics, morphological identification and counting have historically been a difficult task. Over the past decades, microbiologists have endeavored to apply and extend molecular techniques to address questions in microbial ecology. These culture-independent studies have generated new insights into microbial ecology. One such strategy, metagenome-based analysis, has also proved to be a powerful tool for plankton research. This mini-review presents a brief history of plankton research using morphological and metagenome-based approaches and the potential applications and further directions of metagenomic analyses in plankton ecological studies are discussed. The use of metagenome-based approaches for plankton ecological study in aquatic ecosystems is encouraged. metagenome, plankton community, morphospecies, molecular microbial ecology Citation:Yan Q Y, Yu Y H. Metagenome-based analysis: A promising direction for plankton ecological studies. Sci China Life Sci, 2011, 54: 75-81,

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Molecular approaches to the assessment of biodiversity in aquatic microbial communities

Cited by 95 publications

References 132 publications

The influence of invasive jellyfish blooms on the aquatic microbiome in a coastal lagoon (Varano, SE Italy) detected by an Illumina-based deep sequencing strategy

The influence of invasive jellyfish blooms on the aquatic microbiome in a coastal lagoon (Varano, SE Italy) detected by an Illumina-based deep sequencing strategy

Temporal variation of β-diversity and assembly mechanisms in a bacterial metacommunity

Metagenome-based analysis: A promising direction for plankton ecological studies

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