Dataset Information

Diversity, Dynamics, and Distribution of Bdellovibrio and Like Organisms in Perialpine Lakes.

ABSTRACT: Microbes drive a variety of ecosystem processes and services, but many of them remain largely unexplored because of a lack of knowledge on both the diversity and functionality of some potentially crucial microbiological compartments. This is the case with and within the group of bacterial predators collectively known as Bdellovibrio and like organisms (BALOs). Here, we report the abundance, distribution, and diversity of three families of these obligate predatory Gram-negative bacteria in three perialpine lakes (Lakes Annecy, Bourget, and Geneva). The study was conducted at different depths (near-surface versus 45 or 50?m) from August 2015 to January 2016. Using PCR-denaturing gradient gel electrophoresis (PCR-DGGE) and cloning-sequencing approaches, we show that the diversity of BALOs is relatively low and very specific to freshwaters or even the lakes themselves. While the Peredibacteraceae family was represented mainly by a single species (Peredibacter starrii), it could represent up to 7% of the total bacterial cell abundances. Comparatively, the abundances of the two other families (Bdellovibrionaceae and Bacteriovoracaceae) were significantly lower. In addition, the distributions in the water column were very different between the three groups, suggesting various life strategies/niches, as follows: Peredibacteraceae dominated near the surface, while Bdellovibrionaceae and Bacteriovoracaceae were more abundant at greater depths. Statistical analyses revealed that BALOs seem mainly to be driven by depth and temperature. Finally, this original study was also the opportunity to design new quantitative PCR (qPCR) primers for Peredibacteraceae quantification.IMPORTANCE This study highlights the abundance, distribution, and diversity of a poorly known microbial compartment in natural aquatic ecosystems, the Bdellovibrio and like organisms (BALOs). These obligate bacterial predators of other bacteria may have an important functional role. This study shows the relative quantitative importance of the three main families of this group, with the design of a new primer pair, and their diversity. While both the diversity and the abundances of these BALOs were globally low, it is noteworthy that the abundance of the Peredibacteraceae could reach important values.

SUBMITTER: Paix B

PROVIDER: S-EPMC6414362 | biostudies-literature | 2019 Mar

REPOSITORIES: biostudies-literature

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Diversity, Dynamics, and Distribution of <i>Bdellovibrio</i> and Like Organisms in Perialpine Lakes.

Paix Benoit B Ezzedine Jade A JA Jacquet Stéphan S

Applied and environmental microbiology 20190306 6

Microbes drive a variety of ecosystem processes and services, but many of them remain largely unexplored because of a lack of knowledge on both the diversity and functionality of some potentially crucial microbiological compartments. This is the case with and within the group of bacterial predators collectively known as <i>Bdellovibrio</i> and like organisms (BALOs). Here, we report the abundance, distribution, and diversity of three families of these obligate predatory Gram-negative bacteria in ...[more]

PMID: 30635378

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Project description:We reconstructed cyanobacterial community structure and phylogeny using DNA that was isolated from layers of stratified sediments spanning 200 years of lake history in the perialpine lakes Greifensee and Lake Zurich (Switzerland). Community analysis based on amplification and sequencing of a 400-nucleotide (nt)-long 16S rRNA fragment specific to Cyanobacteria revealed operational taxonomic units (OTUs) capturing the whole phylum, including representatives of a newly characterized clade termed Melainabacteria, which shares common ancestry with Cyanobacteria and has not been previously described in lakes. The reconstruction of cyanobacterial richness and phylogenetic structure was validated using a data set consisting of 40 years of pelagic microscopic counts from each lake. We identified the OTUs assigned to common taxa known to be present in Greifensee and Lake Zurich and found a strong and significant relationship (adjusted R2 = 0.89; P < 0.001) between pelagic species richness in water and OTU richness in the sediments. The water-sediment richness relationship varied between cyanobacterial orders, indicating that the richness of Chroococcales and Synechococcales may be underestimated by microscopy. PCR detection of the microcystin synthetase gene mcyA confirmed the presence of potentially toxic cyanobacterial taxa over recent years in Greifensee and throughout the last century in Lake Zurich. The approach presented in this study demonstrates that it is possible to reconstruct past pelagic cyanobacterial communities in lakes where the integrity of the sedimentary archive is well preserved and to explore changes in phylogenetic and functional diversity over decade-to-century timescales.ImportanceCyanobacterial blooms can produce toxins that affect water quality, especially under eutrophic conditions, which are a consequence of human-induced climate warming and increased nutrient availability. Lakes worldwide have suffered from regular cyanobacterial blooms over the last century. The lack of long-term data limits our understanding of how these blooms form. We successfully reconstructed the past diversity of whole cyanobacterial communities over two hundred years by sequencing genes preserved in the sediments of two perialpine lakes in Switzerland. We identified changes in diversity over time and validated our results using existing data collected in the same two lakes over the past 40 years. This work shows the potential of our approach for addressing important ecological questions about the effects of a changing environment on lake ecology.

Project description:The impact of key environmental factors, salinity, prey, and temperature, on the survival and ecology of Bdellovibrio and like bacteria (BALOs), including the freshwater/terrestrial, non-halotolerant group and the halophilic Halobacteriovorax strains, has been assessed based on a review of data in the literature. These topics have been studied by numerous investigators for nearly six decades now, and much valuable information has been amassed and reported. The collective data shows that salinity, prey, and temperature play a major role in, not only the growth and survival of BALOs, but also the structure and composition of BALO communities and the distribution of the predators. Salinity is a major determinant in the selection of BALO habitats, distribution, prey bacteria, and systematics. Halophilic BALOs require salt for cellular functions and are found only in saltwater habitats, and prey primarily on saltwater bacteria. To the contrary, freshwater/terrestrial BALOs are non-halotolerant and inhibited by salt concentrations greater than 0.5%, and are restricted to freshwater, soils, and other low salt environments. They prey preferentially on bacteria in the same habitats. The halophilic BALOs are further separated on the basis of their tolerance to various salt concentrations. Some strains are found in low salt environments and others in high salt regions. In situ studies have demonstrated that salinity gradients in estuarine systems govern the type of BALO communities that will persist within a specific gradient. Bacterial prey for BALOs functions more than just being a substrate for the predators and include the potential for different prey species to structure the BALO community at the phylotype level. The pattern of susceptibility or resistance of various bacteria species has been used almost universally to differentiate strains of new BALO isolates. However, the method suffers from a lack of uniformity among different laboratories. The use of molecular methods such as comparative analysis of the 16S rDNA gene and metagenomics have provided more specific approaches to distinguished between isolates. Differences in temperature growth range among different BALO groups and strains have been demonstrated in many laboratory experiments. The temperature optima and growth range for the saltwater BALOs is typically lower than that of the freshwater/terrestrial BALOs. The collective data shows not only that environmental factors have a great impact on BALO ecology, but also how the various factors affect BALO populations in nature.

Dataset Information

Diversity, Dynamics, and Distribution of Bdellovibrio and Like Organisms in Perialpine Lakes.

Publications

Diversity, Dynamics, and Distribution of <i>Bdellovibrio</i> and Like Organisms in Perialpine Lakes.

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