‘Rare biosphere’ bacteria as key phenanthrene degraders in coastal seawaters

Sauret, Caroline; Séverin, Tatiana; Vétion, Gilles; Guigue, Catherine; Goutx, Madeleine; Pujo‐Pay, Mireille; Conan, Pascal; Fagervold, Sonja K.; Ghiglione, Jean-François

doi:10.1016/j.envpol.2014.07.024

Cited by 76 publications

(49 citation statements)

References 50 publications

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“…PAH-degrading bacteria were close to this detection limit (between 1 and 5 %). A recent paper using new pyrosequencing technology with detection limit of less than 0.1 % (the socalled Brare biosphere,^Sogin et al 2006) coupled with DNA-stable isotope probing confirmed that PAH degraders originated from the same stations used in this study (Port-deBouc and SOFCOM) were close to the detection limit of pyrosequencing (Sauret et al 2014). More generally, previous papers found also no difference in bacterial community structure between SML and SSW in the NW Mediterranean Sea (Agogué et al 2005), whereas others found distinct SML and SSW communities in the North Sea (Franklin et al 2005) and Pacific Ocean (Cunliffe et al 2009).…”

Section: Discussionsupporting

confidence: 78%

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Influence of PAHs among other coastal environmental variables on total and PAH-degrading bacterial communities

Sauret

Tedetti

Guigue

et al. 2015

Environ Sci Pollut Res

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We evaluated the relative impact of anthropogenic polycyclic aromatic hydrocarbons (PAHs) among biogeochemical variables on total, metabolically active, and PAH bacterial communities in summer and winter in surface microlayer (SML) and subsurface seawaters (SSW) across short transects along the NW Mediterranean coast from three harbors, one wastewater effluent, and one nearshore observatory reference site. At both seasons, significant correlations were found between dissolved total PAH concentrations and PAH-degrading bacteria that formed a gradient from the shore to nearshore waters. Accumulation of PAH degraders was particularly high in the SML, where PAHs accumulated. Harbors and wastewater outfalls influenced drastically and in a different way the total and active bacterial community structure, but they only impacted the communities from the nearshore zone (<2 km from the shore). By using direct multivariate statistical analysis, we confirmed the significant effect of PAH concentrations on the spatial and temporal dynamic of total and active communities in this area, but this effect was putted in perspective by the importance of other biogeochemical variables.

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Section: Discussionsupporting

confidence: 78%

“…Further studies are needed to identify PAH-degrader communities living in the SML and to evaluate if they possess original metabolic capacities for the PAH degradation. A recent paper proposed the use of DNA-stable isotope probing to answer these questions in SSW marine ecosystems (Sauret et al 2014).…”

Section: Discussionmentioning

confidence: 99%

Influence of PAHs among other coastal environmental variables on total and PAH-degrading bacterial communities

Sauret

Tedetti

Guigue

et al. 2015

Environ Sci Pollut Res

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“…The genera Alcanivorax and Thalassolituus are main alkane degraders, whereas Cycloclasticus has mainly been associated with PAH degradation. Cycloclasticus strains have been reported in seawater as part of the rare members that bloomed after phenanthrene addition and have become key hydrocarbon degraders (49). Therefore, OHCB are examples of conditionally rare taxa, a concept proposed based on the dynamics of rare taxa in other environments but not in soil (18).…”

Section: Fig 2 Effect Of Diesel Pollution and Bioremediation Treatmenmentioning

confidence: 99%

“…Most environments are dominated by low-abundance taxa (i.e., the rare biosphere), in which rare is usually defined as members present in Յ0.1% of a microbial community (16,49). It is well known that the microbial community structure can rapidly change across space and time, reflecting a fast growth or dispersal of rare or dormant taxa.…”

Section: Fig 2 Effect Of Diesel Pollution and Bioremediation Treatmenmentioning

confidence: 99%

From Rare to Dominant: a Fine-Tuned Soil Bacterial Bloom during Petroleum Hydrocarbon Bioremediation

Fuentes

Barra

Caporaso

et al. 2016

Appl Environ Microbiol

116

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Hydrocarbons are worldwide-distributed pollutants that disturb various ecosystems. The aim of this study was to characterize the short-lapse dynamics of soil microbial communities in response to hydrocarbon pollution and different bioremediation treatments. Replicate diesel-spiked soil microcosms were inoculated with either a defined bacterial consortium or a hydrocarbonoclastic bacterial enrichment and incubated for 12 weeks. The microbial community dynamics was followed weekly in microcosms using Illumina 16S rRNA gene sequencing. Both the bacterial consortium and enrichment enhanced hydrocarbon degradation in diesel-polluted soils. A pronounced and rapid bloom of a native gammaproteobacterium was observed in all dieselpolluted soils. A unique operational taxonomic unit (OTU) related to the Alkanindiges genus represented ϳ0.1% of the sequences in the original community but surprisingly reached >60% after 6 weeks. Despite this Alkanindiges-related bloom, inoculated strains were maintained in the community and may explain the differences in hydrocarbon degradation. This study shows the detailed dynamics of a soil bacterial bloom in response to hydrocarbon pollution, resembling microbial blooms observed in marine environments. Rare community members presumably act as a reservoir of ecological functions in high-diversity environments, such as soils. This rare-to-dominant bacterial shift illustrates the potential role of a rare biosphere facing drastic environmental disturbances. Additionally, it supports the concept of "conditionally rare taxa," in which rareness is a temporary state conditioned by environmental constraints.

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“…There is evidence that rare taxa are or can become active in their communities (Hunt et al 2013, Wilhelm et al 2014, Aanderud et al 2015, sometimes providing key functions (Pester et al 2010, Sauret et al 2014. Additionally, some rare taxa are sensitive to disturbances (Sjöstedt et al 2012, Coveley et al 2015, Vuono et al 2016, notably after the recent Deepwater Horizon oil spill (Newton et al 2013).…”

Section: Raritymentioning

confidence: 99%

Lifestyles of rarity: understanding heterotrophic strategies to inform the ecology of the microbial rare biosphere

Newton¹,

Shade²

2016

Aquat. Microb. Ecol.

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There are patterns in the dynamics of rare taxa that lead to hypotheses about their lifestyles. For example, persistently rare taxa may be oligotrophs that are adapted for efficiency in resource-limiting environments, while conditionally rare or blooming taxa may be copiotrophs that are adapted to rapid growth when resources are available. Of course, the trophic strategies of microorganisms have direct ecological implications for their abundances, contributions to community structure, and role in nutrient turnover. We summarize general frameworks for separately considering rarity and heterotrophy, pulling examples from a variety of ecosystems. We then integrate these 2 topics to discuss the technical and conceptual challenges to understanding their precise linkages. Because much has been investigated especially in marine aquatic environments, we finally extend the discussion to lifestyles of rarity for freshwater lakes by offering case studies of Lake Michigan lineages that have rare and prevalent patterns hypothesized to be characteristic of oligotrophs and copiotrophs. To conclude, we suggest moving forward from assigning dichotomies of rarity/prevalence and oligotrophs/copiotrophs towards their more nuanced continua, which can be linked via genomic information and coupled to quantifications of microbial physiologies during cell maintenance and growth.

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‘Rare biosphere’ bacteria as key phenanthrene degraders in coastal seawaters

Cited by 76 publications

References 50 publications

Influence of PAHs among other coastal environmental variables on total and PAH-degrading bacterial communities

Influence of PAHs among other coastal environmental variables on total and PAH-degrading bacterial communities

From Rare to Dominant: a Fine-Tuned Soil Bacterial Bloom during Petroleum Hydrocarbon Bioremediation

Lifestyles of rarity: understanding heterotrophic strategies to inform the ecology of the microbial rare biosphere

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