Biology subjects

Gittins, D. A.

Publications and source records attributed to Gittins, D. A..

2 recordsLinked to original sources

bioRxiv2022

Environmental selection influences the microbiome of subsurface petroleum reservoirs

Petroleum reservoirs within the deep biosphere are extreme environments inhabited by diverse microbial communities creating biogeochemical hotspots in the subsurface. Despite their ecological and industrial importance, systematic studies of core microbial taxa and associated genomic attributes of the oil reservoir microbiome are limited. This study compiles and compares 343 16S rRNA gene amplicon libraries and 25 shotgun metagenomic libraries from oil reservoirs in different parts of the world. Taxonomic composition varies among reservoirs with different physicochemical characteristics, and with geographic distance. Despite oil reservoirs lacking a taxonomic core microbiome in these datasets, gene-centric metagenomic analysis reveals a functional core featuring carbon acquisition and energy conservation strategies consistent with other deep biosphere environments. Genes for anaerobic hydrocarbon degradation are observed in a subset of the samples and are therefore not considered to represent core biogeochemical functions in oil reservoirs. Metabolic redundancy within the petroleum reservoir microbiome reveals these to be deep biosphere systems poised to respond to changes in redox biogeochemistry. This highlights the potential to use microbial genomics for predicting microbial responses to (bio)engineering perturbations to these subsurface habitats.

microbiology↗

bioRxiv2021

CANT-HYD: A curated database of phylogeny-derived Hidden Markov Models for annotation of marker genes involved in hydrocarbon degradation

Discovery of microbial hydrocarbon degradation pathways has traditionally relied on laboratory isolation and characterization of microorganisms. Although many metabolic pathways for hydrocarbon degradation have been discovered, the absence of tools dedicated to their annotation makes it difficult to identify the relevant genes and predict the hydrocarbon degradation potential of microbial genomes and metagenomes. Furthermore, sequence homology between hydrocarbon degradation genes and genes with other functions often results in misannotation. A tool that systematically identifies hydrocarbon metabolic potential is therefore needed. We present the Calgary approach to ANnoTating HYDrocarbon degradation genes (CANT-HYD), a database containing HMMs of 37 marker genes involved in anaerobic and aerobic degradation pathways of aliphatic and aromatic hydrocarbons. Using this database, we show that hydrocarbon metabolic potential is widespread in the tree of life and identify understudied or overlooked hydrocarbon degradation potential in many phyla. We also demonstrate scalability by analyzing large metagenomic datasets for the prediction of hydrocarbon utilization in diverse environments. To the best of our knowledge, CANT-HYD is the first comprehensive tool for robust and accurate identification of marker genes associated with aerobic and anaerobic hydrocarbon degradation.

bioinformatics↗