The α-proteobacteria: the Darwin finches of the bacterial world

Ettema, Thijs J. G.; Andersson, Siv G. E.

doi:10.1098/rsbl.2008.0793

Cited by 88 publications

(75 citation statements)

References 21 publications

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“…This can be expected as the physiological diversity within the phylum Proteobacteria is well known. Alphaproteobacteria, which also comprises orders displaying a diverse niche specialization (Ettema and Andersson, 2009), displayed patterns that could not be explained by any environmental parameter measured. Distinct response to contamination by Alphaproteobacteria could be noticed only upon further analysis at order and family level.…”

Section: Discussionmentioning

confidence: 99%

Spatial patterns of microbial diversity and activity in an aged creosote-contaminated site

et al. 2014

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Restoration of polluted sites via in situ bioremediation relies heavily on the indigenous microbes and their activities. Spatial heterogeneity of microbial populations, contaminants and soil chemical parameters on such sites is a major hurdle in optimizing and implementing an appropriate bioremediation regime. We performed a grid-based sampling of an aged creosote-contaminated site followed by geostatistical modelling to illustrate the spatial patterns of microbial diversity and activity and to relate these patterns to the distribution of pollutants. Spatial distribution of bacterial groups unveiled patterns of niche differentiation regulated by patchy distribution of pollutants and an east-to-west pH gradient at the studied site. Proteobacteria clearly dominated in the hot spots of creosote pollution, whereas the abundance of Actinobacteria, TM7 and Planctomycetes was considerably reduced from the hot spots. The pH preferences of proteobacterial groups dominating in pollution could be recognized by examining the order and family-level responses. Acidobacterial classes came across as generalists in hydrocarbon pollution whose spatial distribution seemed to be regulated solely by the pH gradient. Although the community evenness decreased in the heavily polluted zones, basal respiration and fluorescein diacetate hydrolysis rates were higher, indicating the adaptation of specific indigenous microbial populations to hydrocarbon pollution. Combining the information from the kriged maps of microbial and soil chemistry data provided a comprehensive understanding of the long-term impacts of creosote pollution on the subsurface microbial communities. This study also highlighted the prospect of interpreting taxa-specific spatial patterns and applying them as indicators or proxies for monitoring polluted sites.

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Section: Discussionmentioning

confidence: 99%

Spatial patterns of microbial diversity and activity in an aged creosote-contaminated site

et al. 2014

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“…By contrast, more complex traits such as oxygenic photosynthesis or sulfate reduction involve many more genes and show phylogenetic conservation at much deeper taxonomic levels (80% and 92.2% mean 16S rRNA sequence identity, respectively; Martiny et al, 2012). Other traits not directly related to resource use, such as rRNA operon copy number (Rastogi et al, 2009) and host adaptation (Ettema and Andersson, 2009), may also be conserved at deeper taxonomic levels.…”

Section: Discussionmentioning

confidence: 99%

Microdiversity of extracellular enzyme genes among sequenced prokaryotic genomes

2013

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Understanding the relationship between prokaryotic traits and phylogeny is important for predicting and modeling ecological processes. Microbial extracellular enzymes have a pivotal role in nutrient cycling and the decomposition of organic matter, yet little is known about the phylogenetic distribution of genes encoding these enzymes. In this study, we analyzed 3058 annotated prokaryotic genomes to determine which taxa have the genetic potential to produce alkaline phosphatase, chitinase and b-N-acetyl-glucosaminidase enzymes. We then evaluated the relationship between the genetic potential for enzyme production and 16S rRNA phylogeny using the consenTRAIT algorithm, which calculated the phylogenetic depth and corresponding 16S rRNA sequence identity of clades of potential enzyme producers. Nearly half (49.2%) of the genomes analyzed were found to be capable of extracellular enzyme production, and these were non-randomly distributed across most prokaryotic phyla. On average, clades of potential enzymeproducing organisms had a maximum phylogenetic depth of 0.008004-0.009780, though individual clades varied broadly in both size and depth. These values correspond to a minimum 16S rRNA sequence identity of 98.04-98.40%. The distribution pattern we found is an indication of microdiversity, the occurrence of ecologically or physiologically distinct populations within phylogenetically related groups. Additionally, we found positive correlations among the genes encoding different extracellular enzymes. Our results suggest that the capacity to produce extracellular enzymes varies at relatively fine-scale phylogenetic resolution. This variation is consistent with other traits that require a small number of genes and provides insight into the relationship between taxonomy and traits that may be useful for predicting ecological function.

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“…It is of note that T. saltatorassociated bacterial communities contained taxa both known to include members of animal associated species (e.g. Gammaproteobacteria and Firmicutes of Bacillales and Clostridiales classes), but also other classes, such as Alphaproteobacteria, which include marine (Morris et al, 2002) and plant-associated species (Ettema and Andersson, 2009). The assignment of TRFs to members of Clostridiales may also suggest an involvement of this group of bacteria in cellulose degradation within the gut, as previously reported (Nuti et al, 1971;Martineti et al, 1995), similarly to other herbivores (Zhu et al, 2011).…”

Section: Discussionmentioning

confidence: 99%

High genetic diversity and variability of bacterial communities associated with the sandhopper Talitrus saltator (Montagu) (Crustacea, Amphipoda)

Mengoni

Focardi

Bacci

et al. 2013

Estuarine, Coastal and Shelf Science

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a b s t r a c tThe microbiome present in individuals of Talitrus saltator belonging to seven populations distributed along the Tuscan coast (Italy) was assessed by using Terminal-Restriction Fragment Length Polymorphism (T-RFLP) analysis of amplified 16S rRNA genes. Talitrus saltator is one of the key species of the damp band of European sandy beaches and despite of the large interest on animal-associated bacteria, only a few and preliminary data were present. Results showed a high diversity of the microbiome, composed mainly by members of Alphaproteobacteria, Gammaproteobacteria, Bacillales and Clostridiales classes. The microbiome fingerprints were highly variable among individuals, even from the same populations, the inter-individual differences accounting for 88.7% of total fingerprint variance. However, statistically significant population-specific microbiome signatures were detected, and accounted for the remaining 11.3% of total fingerprint variance. These population-specific differences were mainly attributed to sequences from members of known host-associated bacteria such as Gammaproteobacteria and Betaproteobacteria, Cytophagia and Spirochaetia. This study showed the high complexity of the microbiome associated with an amphipod species and on the inter-individual microbiome variation with potential importance for understanding amphipod trophic and ecologic processes.

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The α-proteobacteria: the Darwin finches of the bacterial world

Cited by 88 publications

References 21 publications

Spatial patterns of microbial diversity and activity in an aged creosote-contaminated site

Spatial patterns of microbial diversity and activity in an aged creosote-contaminated site

Microdiversity of extracellular enzyme genes among sequenced prokaryotic genomes

High genetic diversity and variability of bacterial communities associated with the sandhopper Talitrus saltator (Montagu) (Crustacea, Amphipoda)

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