Novel insights into freshwater hydrocarbon-rich sediments using metatranscriptomics: Opening the black box

Reid, Thomas; Chaganti, Subba Rao; Droppo, Ian G.; Weisener, Christopher G.

doi:10.1016/j.watres.2018.02.039

Cited by 33 publications

(10 citation statements)

References 48 publications

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“…Coupled metagenomics and metatranscriptomics provide useful perspectives on microbial activity and microbial responses to changing environmental conditions (44), revealing metabolic niches (45), metabolic pathways, and potential syntrophic interactions in complex microbial communities (46,47). Despite extensive analysis of cold seep microbial communities (8, 9, 37, 48-50), there have been comparatively few reports of gene expression profiling of these environments, and these have been based largely on single-gene analyses (51) or enrichments (11,25,(27)(28)(29)(30)38).…”

Section: Discussionmentioning

confidence: 99%

Contrasting Pathways for Anaerobic Methane Oxidation in Gulf of Mexico Cold Seep Sediments

et al. 2019

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Gulf of Mexico sediments harbor numerous hydrocarbon seeps associated with high sedimentation rates and thermal maturation of organic matter. These ecosystems host abundant and diverse microbial communities that directly or indirectly metabolize components of the emitted fluid. To investigate microbial function and activities in these ecosystems, metabolic potential (metagenomic) and gene expression (metatranscriptomic) analyses of two cold seep areas of the Gulf of Mexico were carried out. Seeps emitting biogenic methane harbored microbial communities dominated by archaeal anaerobic methane oxidizers of phylogenetic group 1 (ANME-1), whereas seeps producing fluids containing a complex mixture of thermogenic hydrocarbons were dominated by ANME-2 lineages. Metatranscriptome measurements in both communities indicated high levels of expression of genes for methane metabolism despite their distinct microbial communities and hydrocarbon composition. In contrast, the transcription level of sulfur cycle genes was quite different. In the thermogenic seep community, high levels of transcripts indicative of syntrophic anaerobic oxidation of methane (AOM) coupled to sulfate reduction were detected. This syntrophic partnership between the dominant ANME-2 and sulfate reducers potentially involves direct electron transfer through multiheme cytochromes. In the biogenic methane seep, genes from an ANME-1 lineage that are potentially involved in polysulfide reduction were highly expressed, suggesting a novel bacterium-independent anaerobic methane oxidation pathway coupled to polysulfide reduction. The observed divergence in AOM activities provides a new model for bacterium-independent AOM and emphasizes the variation that exists in AOM pathways between different ANME lineages.IMPORTANCECold seep sediments are complex and widespread marine ecosystems emitting large amounts of methane, a potent greenhouse gas, and other hydrocarbons. Within these sediments, microbial communities play crucial roles in production and degradation of hydrocarbons, modulating oil and gas emissions to seawater. Despite this ecological importance, our understanding of microbial functions and methane oxidation pathways in cold seep ecosystems is poor. Based on gene expression profiling of environmental seep sediment samples, the present work showed that (i) the composition of the emitted fluids shapes the microbial community in general and the anaerobic methanotroph community specifically and (ii) AOM by ANME-2 in this seep may be coupled to sulfate reduction byDeltaproteobacteriaby electron transfer through multiheme cytochromes, whereas AOM by ANME-1 lineages in this seep may involve a different, bacterium-independent pathway, coupling methane oxidation to elemental sulfur/polysulfide reduction.

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Section: Discussionmentioning

confidence: 99%

Contrasting Pathways for Anaerobic Methane Oxidation in Gulf of Mexico Cold Seep Sediments

et al. 2019

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“…(Gonzalez et al 2015) found Bacillus and Klebsiella in greater abundance in trees cultivated on hydrocarbon contaminated soil. (Reid et al 2018) observed abundance of alkane-degrading and RHO gene expression that suggest considerable natural degradation in hydrocarbon rich sediments. Although most of the dominant species were unclassified, which revealed novel lineages of microbes potentially involved in hydrocarbon degradation.…”

Section: Metatranscriptomicsmentioning

confidence: 90%

“…Metagenomics coupled with metatranscriptomics allows elucidation of the active metabolic processes by quantification of gene expression in an existing microbial community. Only a few metatranscriptomics studies have been applied in hydrocarbon degradation in soils and sediments so far (Gonzalez et al 2015;de Menezes et al 2012;Reid et al 2018). The studies show increases in RHO gene expression and widespread changes in the microbial community structure of soils contaminated with phenanthrene.…”

Section: Metatranscriptomicsmentioning

confidence: 99%

From Functional Potential of Soil Bacterial Communities Towards Petroleum Hydrocarbons Bioremediation

2019

JBAH

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Molecular ecology researches are rapidly advancing the knowledge of microorganisms associated with petroleum hydrocarbon degradation, one of the major large-scale pollutants in terrestrial ecosystems. The design and monitoring of bioremediation techniques for hydrocarbons rely on a thorough understanding of the diversity of enzymes involved in the processes of hydrocarbon degradation and the microbes that harbor their allocated genes. This review describes the impact of hydrocarbon pollution on soil microbial communities, the state of the art of detecting functional genes, and functional groups. We will focus on i) the structure, function and succession behavior of microbial communities exposed to hydrocarbons, ii) key genes and pathways, iii) future prospect into bioremediation of petroleum hydrocarbons in aerobic environments. The aim is to get a fundamental insight in these issues to ultimately improve petroleum hydrocarbons bioremediation.

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“…In a recent study, Sato and colleagues showed that, contrary to their low abundance, nitrifiers play an important role in heavy oil biodegradation by providing nitrate to denitrifying hydrocarbon degraders in activated sludge reactors (Sato et al, 2019). Another study showed both nitrogen and sulfur cycles are active alongside methanogenesis and methane oxidation in hydrocarbon-containing freshwater sediments (Reid et al, 2018). Falk and colleagues reported that nitrate reduction and methanogenesis are the most abundant pathways in the hydrocarbon-contaminated Detroit River (Falk et al, 2019).…”

Section: Metatranscriptomicsmentioning

confidence: 99%

New Frontiers of Anaerobic Hydrocarbon Biodegradation in the Multi-Omics Era

et al. 2020

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The accumulation of petroleum hydrocarbons in the environment substantially endangers terrestrial and aquatic ecosystems. Many microbial strains have been recognized to utilize aliphatic and aromatic hydrocarbons under aerobic conditions. Nevertheless, most of these pollutants are transferred by natural processes, including rain, into the underground anaerobic zones where their degradation is much more problematic. In oxic zones, anaerobic microenvironments can be formed as a consequence of the intensive respiratory activities of (facultative) aerobic microbes. Even though aerobic bioremediation has been well-characterized over the past few decades, ample research is yet to be done in the field of anaerobic hydrocarbon biodegradation. With the emergence of high-throughput techniques, known as omics (e.g., genomics and metagenomics), the individual biodegraders, hydrocarbon-degrading microbial communities and metabolic pathways, interactions can be described at a contaminated site. Omics approaches provide the opportunity to examine single microorganisms or microbial communities at the system level and elucidate the metabolic networks, interspecies interactions during hydrocarbon mineralization. Metatranscriptomics and metaproteomics, for example, can shed light on the active genes and proteins and functional importance of the less abundant species. Moreover, novel unculturable hydrocarbon-degrading strains and enzymes can be discovered and fit into the metabolic networks of the community. Our objective is to review the anaerobic hydrocarbon biodegradation processes, the most important hydrocarbon degraders and their diverse metabolic pathways, including the use of various terminal electron acceptors and various electron transfer processes. The review primarily focuses on the achievements obtained by the current high-throughput (multi-omics) techniques which opened new perspectives in understanding the processes at the system level including the metabolic routes of individual strains, metabolic/electric interaction of the members of microbial communities. Based on the multi-omics techniques, novel metabolic blocks can be designed and used for the construction of microbial strains/consortia for efficient removal of hydrocarbons in anaerobic zones.

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Novel insights into freshwater hydrocarbon-rich sediments using metatranscriptomics: Opening the black box

Cited by 33 publications

References 48 publications

Contrasting Pathways for Anaerobic Methane Oxidation in Gulf of Mexico Cold Seep Sediments

Contrasting Pathways for Anaerobic Methane Oxidation in Gulf of Mexico Cold Seep Sediments

From Functional Potential of Soil Bacterial Communities Towards Petroleum Hydrocarbons Bioremediation

New Frontiers of Anaerobic Hydrocarbon Biodegradation in the Multi-Omics Era

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