TABLE 1.
Recent studies using omics approaches to characterize anaerobic hydrocarbon biodegrading microbial communities.
| Omics approaches | Major findings | Citation |
| Genomics | Novel genomic features associated with the energy metabolism of Geobacter ferrireducens IRF9 strain. | Jung et al., 2018 |
| Proteomics and gene expression study (by qPCR) | The regulation of benzylsuccinate synthase expression in Magnetospirillum sp. strain 15-1 has an extra layer on the post-transcriptional level to better cope with the redox dynamics of the environment. Various sensory inputs play an important role in regulation. | Meyer-Cifuentes et al., 2020 |
| 16S rDNA profiling and whole metagenome sequencing and metabolomics | Enrichment cultures derived from seafloor sediments are capable of anaerobic degradation of hexadecane and phenanthrene. Sulfate-reducing bacteria were identified as the main actors of the microbial community, along with syntrophic partners. | Shin et al., 2019 |
| 16S rDNA profiling | An anaerobic phenanthrene degrading consortium was successfully used for producing electricity in a microbial fuel cell. | Sharma et al., 2020 |
| 16S rDNA profiling and whole metagenomics was combined with qPCR studies | Novel fumarate adding enzyme was discovered from metagenomic data which is hypothesized participating in o-xylene activation. | Rossmassler et al., 2019 |
| 16S rDNA profiling | Four keystone microbial taxa SAR202 clade, Thermoanaerobaculum, Nitrospira, and Xanthomonadales were identified in PAH-contaminated soil samples with co-occurrence analysis. | Geng et al., 2020 |
| 16S rDNA and bamA gene profiling | Anaerolineaceae, Dechloromonas, Bacteroidetes Vadin HA17 and Geobacter were found as keystone microorganisms in PAH biodegradation under nitrate-reducing conditions. | Han et al., 2021 |
| Whole metagenomics | The presence of methane metabolism and sulfur reduction genes were detected in Korarchaeota. Methane metabolism was suggested as an early energy conservation strategy in Archaea. Furthermore, the authors proposed the new archaeal species Methanodesulfokores washburnensis. | McKay et al., 2019 |
| 16S profile, whole metagenomics, comparative genomics, metatranscriptomics | Manganese reducing Candidatus Methanoperedens spp. are capable of reverse methanogenesis. | Leu et al., 2020 |
| Reanalysis of metagenomes | Putative multi-carbon oxidizing mcr genes were found in many archaeal phyla. | Wang et al., 2019 |
| Whole metagenome analysis | Horizontal gene transfer of mcr genes into Asgard group archaea was demonstrated. The oxidation of short-chain alkanes via alkyl-CoM was also suggested. | Seitz et al., 2019 |
| Whole metagenomics combined with metabolomics | Acetate and hydrogen are the central metabolites on which the biochemical interactions between community members rely in deep-sea sediments. Acetate consumption is strongly connected to sulfate reduction, organohalide respiration and acetoclastic methanogenesis while hydrogen consumption can promote carbon fixation. Upstream actors of the biochemical pathways will degrade necromass and hydrocarbon compounds in the sediment on an acetogenic and hydrogenogenic manner. | Dong et al., 2019 |
| Whole metagenome sequencing | The full sett of fumarate addition genes was found in the members of the candidate phylum Atribacteria. The metabolic capabilities of the phylum members suggest their importance in the carbon cycle of hydrocarbon-rich environments. | Liu et al., 2019 |
| Whole metagenome sequencing | Assimilatory sulfate and dissimilatory nitrate reduction are dominant in a petroleum-contaminated aquifer. While the environment is anaerobic, many genes were found in the metagenomic data corresponding to aerobic biodegradation. | Cai et al., 2019 |
| 16S rDNA profile and metatranscriptomics | RNA seq data revealed that a group of nitrifiers insignificant in number has a rather significant impact on the metabolic pathways by supplying nitrate to the nitrate reducers in activated sludge bioreactors. | Sato et al., 2019 |
| Metatranscriptomics | Nitrate and sulfate metabolism is connected to aerobic hydrocarbon biodegradation and methane production/oxidation in freshwater sediments. | Reid et al., 2018 |
| Metatranscriptomics | Versatile metabolic pathways were found active in the hydrocarbon contaminated Detroit River sediment. Transcriptomics data showed that aerobic hydrocarbon biodegradation was closely connected to nitrate reduction, acetogenesis, methanogenesis, polyester synthesis and gluconeogenesis. | Falk et al., 2019 |
| Metatranscriptomics | A nitrate-reducing consortium degrades benzene mainly via carboxylation. The involvement of a facultative anaerobe pathway during downstream bioconversion of benzene and the evolution of oxygen from nitrate was also suggested. | Atashgahi et al., 2018 |
| Whole metagenomics and metaproteomics | A metabolic model for G. metallireducens which suggests that the catabolic pathways for the favored substrates -like toluene- are expressed continuously even if the substrate is not present. | Marozava et al., 2020 |
| 16S rDNA profile, whole metagenomics, metabolomics | Metagenomic data showed that sulfate-reducing bacteria responsible for oil pipe corrosion are able to thrive in the pipes despite nitrate treatment. | Bonifay et al., 2017 |