The sequence capture by hybridization: a new approach for revealing the potential of mono‐aromatic hydrocarbons bioattenuation in a deep oligotrophic aquifer

Abstract

SummaryThe formation water of a deep aquifer (853 m of depth) used for geological storage of natural gas was sampled to assess the mono‐aromatic hydrocarbons attenuation potential of the indigenous microbiota. The study of bacterial diversity suggests that Firmicutes and, in particular, sulphate‐reducing bacteria (Peptococcaceae) predominate in this microbial community. The capacity of the microbial community to biodegrade toluene and m‐ and p‐xylenes was demonstrated using a culture‐based approach after several hundred days of incubation. In order to reveal the potential for biodegradation of these compounds within a shorter time frame, an innovative approach named the solution hybrid selection method, which combines sequence capture by hybridization and next‐generation sequencing, was applied to the same original water sample. The bssA and bssA‐like genes were investigated as they are considered good biomarkers for the potential of toluene and xylene biodegradation. Unlike a PCR approach which failed to detect these genes directly from formation water, this innovative strategy demonstrated the presence of the bssA and bssA‐like genes in this oligotrophic ecosystem, probably harboured by Peptococcaceae. The sequence capture by hybridization shows significant potential to reveal the presence of genes of functional interest which have low‐level representation in the biosphere.

Geological gas‐storage shapes deep life

“…The various studies that we have done in the past (Basso et al, 2009;Berlendis et al, 2010;Aüllo et al, 2016;Ranchou-Peyruse et al, 2017), lead us to suggest that the functioning of these communities would be most likely based on heterotrophy and fermentation of organic molecules trapped in the aquifer rock-forming minerals, such as clays (Katayama et al, 2015). Their metabolic byproducts therefore favour hydrogenotrophic, acetoclastic or methylotrophic methanogenic archaea.…”

“…They also allow study of the functioning of microbial communities populating these subsurface anoxic environments. Ad hoc studies have been carried out on the microbial ecology of gas storage aquifers in France for almost two decades (Basso et al ., ; Berlendis et al ., ; Aüllo et al ., ; Ranchou‐Peyruse et al ., ). While various microbial metabolisms have been highlighted in these ecosystems, some seem to play key roles in the functioning of the microbial communities, particularly sulfate‐reducing microorganisms (SRM) and methanogenic archaea, as already demonstrated for other subsurface environments (Itävaara et al ., ; Schrenk et al ., ; Purkamo et al ., ).…”

¬Estimating Microbial Hydrogen Consumption in Hydrogen Storage in Porous Media as a Basis for Site Selection

“…Oxygen and nitrate are scarce in the subsurface [11,24,55,56] and aerobic hydrogen oxidation, denitrification and ammonification hence only become significant when contamination of the aquifer occurs, e.g. by drilling fluid [57][58][59].…”

Sequence capture by hybridization reveals elusive hydrocarbon degradation potential

“…The incubation experiment of Ranchou‐Peyruse et al . (), patiently performed with biomass gained from filtrated formation water over several years, showed reproducible degradation of toluene and o , m ‐xylene under sulphate‐reducing conditions, but the authors were not able to detect the involved functional genes with the aforementioned PCR methods. The authors then turned to a sequence capture hybridization method (established by Denonfoux et al .…”

“…The paper of Ranchou-Peyruse et al (2016) presents evidence of hydrocarbon degraders present in formation water from a depth of 853 m in the Paris Basin in France. Such deep formation waters are used for storing natural gas.…”