Marine sediments harbor diverse archaea and bacteria with the potential for anaerobic hydrocarbon degradation via fumarate addition

Abstract

Marine sediments can contain large amounts of alkanes and methylated aromatic hydrocarbons that are introduced by natural processes or anthropogenic activities. These compounds can be biodegraded by anaerobic microorganisms via enzymatic addition of fumarate. However, the identity and ecological roles of a significant fraction of hydrocarbon degraders containing fumarate-adding enzymes (FAE) in various marine sediments remains unknown. By combining phylogenetic reconstructions, protein homolog modelling, and functional profiling of publicly available metagenomes and genomes, 61 draft bacterial and archaeal genomes encoding anaerobic hydrocarbon degradation via fumarate addition were obtained. Besides Desulfobacterota (previously known as Deltaproteobacteria) that are well-known to catalyze these reactions, Chloroflexi are dominant FAE-encoding bacteria in hydrocarbon-impacted sediments, potentially coupling sulfate reduction or fermentation to anaerobic hydrocarbon degradation. Among Archaea, besides Archaeoglobi previously shown to have this capability, genomes of Heimdallarchaeota, Lokiarchaeota, Thorarchaeota and Thermoplasmata also suggest fermentative hydrocarbon degradation using archaea-type FAE. These bacterial and archaeal hydrocarbon degraders occur in a wide range of marine sediments, including high abundances of FAE-encoding Asgard archaea associated with natural seeps and subseafloor ecosystems. Our results expand the knowledge of diverse archaeal and bacterial lineages engaged in anaerobic degradation of alkanes and methylated aromatic hydrocarbons.

Unexpected genetic and microbial diversity for arsenic cycling in deep sea cold seep sediments

“…In addition, five arrA -carrying MAGs possessed genes for AssA ( Figure 5c ), which mediate the first step of anaerobic activation of alkanes via fumarate addition. Phylogenetic analyses revealed that identified AssA sequences were phylogenetically close to archaea-type and Group V AssA 51 ( Figure S5 ). These potential hydrocarbon degraders were classified as Chloroflexota (n=2), Deferribacterota (n=1), Desulfobacterota (n=1), and Bacteroidota (n=1).…”

“…The identification of arsenic-related genes in MAGs was performed by searching against As-related HMM profiles from Lavy et al (2020) 67 as reported above. Genes involved in anaerobic hydrocarbon degradation were screened using BLASTp (identity >30%, coverage >90%, e < 1 × 10 −20 ) against local protein databases 51 .…”

“…Reference protein sequences for As-based respiratory cycle were obtained from Saunders et al (2019) 34 . Reference protein sequences for fumarate addition were derived from Zhang et al (2021) 51 . All the tree files were uploaded to Interactive tree of life (iTOL; v6) 75 for visualization and annotation.…”

Optimization of indigenous hydrocarbon Degrading-microbial niche for effective bioremediation of petroleum contaminated soil

“…According to Olowomofe et al [12], 9ml of already prepared MSM broth was dispensed into each of the test tubes and 1ml of the respective hydrocarbon products (petrol, engine oil and gear oil) was dispensed into each test tube (this was done in duplicates) and further sterilized at 121°C for 15 minutes and allowed to cool. The medium was adjusted to a neutral pH (7). 0.1ml of each inoculum was introduced into the prepared MSM broth and incubated at 37°C for 28 days.…”

“…Soil pollution with hydrocarbons causes extensive damage to local systems, since the accumulation of pollutants in animals and plant tissues may cause death or mutations [6]. The maintenance of soil quality is a major concern of agronomists and soil scientists as hydrocarbon pollutions are dangerous to both animals and plants, due to their carcinogenic and mutagenic effects [7] The problems of pollutions have resulted in the exploration of various remedial approaches to aid the cleanup of polluted soils [8]. A variety of technologies are currently available to treat soil contaminated with hazardous materials, including excavation and containment in secured landfills, vapour extraction, stabilization and solidification, soil flushing, soil washing, solvent extraction, etc.…”