Iron Compounds in Anaerobic Degradation of Petroleum Hydrocarbons: A Review

Waste and wastewater containing hydrocarbons are produced worldwide by various oil-based industries, whose activities also contribute to the occurrence of oil spills throughout the globe, causing severe environmental contamination. Anaerobic microorganisms with the ability to biodegrade petroleum hydrocarbons are important in the treatment of contaminated matrices, both in situ in deep subsurfaces, or ex situ in bioreactors. In the latter, part of the energetic value of these compounds can be recovered in the form of biogas. Anaerobic degradation of petroleum hydrocarbons can be improved by various iron compounds, but different iron species exert distinct effects. For example, Fe(III) can be used as an electron acceptor in microbial hydrocarbon degradation, zero-valent iron can donate electrons for enhanced methanogenesis, and conductive iron oxides may facilitate electron transfers in methanogenic processes. Iron compounds can also act as hydrocarbon adsorbents, or be involved in secondary abiotic reactions, overall promoting hydrocarbon biodegradation. These multiple roles of iron are comprehensively reviewed in this paper and linked to key functional microorganisms involved in these processes, to the underlying mechanisms, and to the main influential factors. Recent research progress, future perspectives, and remaining challenges on the application of iron-assisted anaerobic hydrocarbon degradation are highlighted.

Taxonomic and functional trait-based approaches suggest that aerobic and anaerobic soil microorganisms allow the natural attenuation of oil from natural seeps

Natural attenuation, involving microbial adaptation, helps mitigating the effect of oil contamination of surface soils. We hypothesized that in soils under fluctuating conditions and receiving oil from seeps, aerobic and anaerobic bacteria as well as fungi could coexist to efficiently degrade hydrocarbons and prevent the spread of pollution. Microbial community diversity was studied in soil longitudinal and depth gradients contaminated with petroleum seeps for at least a century. Hydrocarbon contamination was high just next to the petroleum seeps but this level drastically lowered from 2 m distance and beyond. Fungal abundance and alpha-diversity indices were constant along the gradients. Bacterial abundance was constant but alpha-diversity indices were lower next to the oil seeps. Hydrocarbon contamination was the main driver of microbial community assemblage. 281 bacterial OTUs were identified as indicator taxa, tolerant to hydrocarbon, potentially involved in hydrocarbon-degradation or benefiting from the degradation by-products. These taxa belonging to lineages of aerobic and anaerobic bacteria, have specific functional traits indicating the development of a complex community adapted to the biodegradation of petroleum hydrocarbons and to fluctuating conditions. Fungi are less impacted by oil contamination but few taxa should contribute to the metabolic complementary within the microbial consortia forming an efficient barrier against petroleum dissemination.

Using Stable Isotope Probing and Raman Microspectroscopy To Measure Growth Rates of Heterotrophic Bacteria

The suitability of stable isotope probing (SIP) and Raman microspectroscopy to measure growth rates of heterotrophic bacteria at the single-cell level was evaluated. Label assimilation into Escherichia coli biomass during growth on a complex ¹³C-labeled carbon source was monitored in time course experiments. ¹³C incorporation into various biomolecules was measured by spectral "red shifts" of Raman-scattered emissions. The ¹³C- and ¹²C-isotopologues of the amino acid phenylalanine (Phe) proved to be quantitatively accurate reporter molecules of cellular isotopic fractional abundances (f_cell). Values of f_cell determined by Raman microspectroscopy and independently by isotope ratio mass spectrometry (IRMS) over a range of isotopic enrichments were statistically indistinguishable. Progressive labeling of Phe in E. coli cells among a range of ¹³C/¹²C organic substrate admixtures occurred predictably through time. The relative isotopologue abundances of Phe determined by Raman spectral analysis enabled the accurate calculation of bacterial growth rates as confirmed independently by optical density (OD) measurements. The results demonstrate that combining SIP and Raman microspectroscopy can be a powerful tool for studying bacterial growth at the single-cell level on defined or complex organic ¹³C carbon sources, even in mixed microbial assemblages. IMPORTANCE Population growth dynamics and individual cell growth rates are the ultimate expressions of a microorganism's fitness under its environmental conditions, whether natural or engineered. Natural habitats and many industrial settings harbor complex microbial assemblages. Their heterogeneity in growth responses to existing and changing conditions is often difficult to grasp by standard methodologies. In this proof-of-concept study, we tested whether Raman microspectroscopy can reliably quantify the assimilation of isotopically labeled nutrients into E. coli cells and enable the determination of individual growth rates among heterotrophic bacteria. Raman-derived growth rate estimates were statistically indistinguishable from those derived by standard optical density measurements of the same cultures. Raman microspectroscopy can also be combined with methods for phylogenetic identification. We report the development of Raman-based techniques that enable researchers to directly link genetic identity to functional traits and rate measurements of single cells within mixed microbial assemblages, currently a major technical challenge in microbiological research.

Availability of Nitrite and Nitrate as Electron Acceptors Modulates Anaerobic Toluene-Degrading Communities in Aquifer Sediments

Microorganisms are essential in the degradation of environmental pollutants. Aromatic hydrocarbons, e.g., benzene, toluene, ethylbenzene, and xylene (BTEX), are common aquifer contaminants, whose degradation in situ is often limited by the availability of electron acceptors. It is clear that different electron acceptors such as nitrate, iron, or sulfate support the activity of distinct degraders. However, this has not been demonstrated for the availability of nitrate vs. nitrite, both of which can be respired in reductive nitrogen cycling. Here via DNA-stable isotope probing, we report that nitrate and nitrite provided as electron acceptors in different concentrations and ratios not only modulated the microbial communities responsible for toluene degradation but also influenced how nitrate reduction proceeded. Zoogloeaceae members, mainly Azoarcus spp., were the key toluene degraders with nitrate-only, or both nitrate and nitrite as electron acceptors. In addition, a shift within Azoarcus degrader populations was observed on the amplicon sequence variant (ASV) level depending on electron acceptor ratios. In contrast, members of the Sphingomonadales were likely the most active toluene degraders when only nitrite was provided. Nitrate reduction did not proceed beyond nitrite in the nitrate-only treatment, while it continued when nitrite was initially also present in the microcosms. Likely, this was attributed to the fact that different microbial communities were stimulated and active in different microcosms. Together, these findings demonstrate that the availability of nitrate and nitrite can define degrader community selection and N-reduction outcomes. It also implies that nitrate usage efficiency in bioremediation could possibly be enhanced by an initial co-supply of nitrite, via modulating the active degrader communities.

Anammox co-fungi accompanying denitrifying bacteria are the thieves of the nitrogen cycle in paddy-wheat crop rotated soils

Anammox bacteria are the key microbes after denitrifiers in the anaerobic environment. Nitrogen gap cannot be satisfied till date even with the advanced techniques, due to complex microbial network and different pathways. Recently, anaerobic fungi are the concerning point to investigate, which was previously ignored for a long time. Study was conducted with the aim of assessment of an individual and combined contribution of anammox, co-denitrification, and denitrification processes for N losses, under different organic-chemical fertilizers, i.e. 1) control _CK; 2) chemical fertilization _CF; 3) pig manure plus chemical fertilization _PMCF; and 4) straw returned plus chemical fertilization _SRCF). Hybrid techniques of ¹³C-DNA-Stable isotope and ¹⁵N isotopic tracer were used to discriminate the contribution of anammox-co-fungi using antibacterial and antifungal inhibitors. Results showed that fungi are the major culprit in N losses; the overall contribution rate by anammox-co-denitrification was 14.82-29.74%. While in case of individual N losses, fungi were dominating the N losses (3.51-25.60%, AB) than bacteria (7.50-21.80%, AF). The anammox and fungi have a positive correlation with each other's (r = 0.67), principal component analysis (PCA) and correlation analysis validate each other (anammox and fungi), and both showed the same type of attraction to the soil physicochemical properties. However, fungi did not show a significant relationship with NH⁺₄-N (r = 0.38). A clone library of ¹³C-DNA-SIP was constructed, and results showed that denitrifying fungi were very likely belonges to the genera Agaricus, Aspergillus, Phycomyces, Saitoella, and Trichoderma. Conclusively, we propose that fertilization pattern can change anammox activity and abundance, but fungal activity and community structure undergo changes with organic amendments rather than inorganic fertilizers.

Stable Isotope and Metagenomic Profiling of a Methanogenic Naphthalene-Degrading Enrichment Culture

Polycyclic aromatic hydrocarbons (PAH) such as naphthalene are widespread, recalcitrant pollutants in anoxic and methanogenic environments. A mechanism catalyzing PAH activation under methanogenic conditions has yet to be discovered, and the microbial communities coordinating their metabolism are largely unknown. This is primarily due to the difficulty of cultivating PAH degraders, requiring lengthy incubations to yield sufficient biomass for biochemical analysis. Here, we sought to characterize a new methanogenic naphthalene-degrading enrichment culture using DNA-based stable isotope probing (SIP) and metagenomic analyses. 16S rRNA gene sequencing of fractionated DNA pinpointed an unclassified Clostridiaceae species as a putative naphthalene degrader after two months of SIP incubation. This finding was supported by metabolite and metagenomic evidence of genes predicted to encode for enzymes facilitating naphthalene carboxylic acid CoA-thioesterification and degradation of an unknown arylcarboxyl-CoA structure. Our findings also suggest a possible but unknown role for Desulfuromonadales in naphthalene degradation. This is the first reported functional evidence of PAH biodegradation by a methanogenic consortium, and we envision that this approach could be used to assess carbon flow through other slow growing enrichment cultures and environmental samples.

Stable isotope compounds - production, detection, and application

Stable isotopes are used in wide fields of application from natural tracers in biology, geology and archeology through studies of metabolic fluxes to their application as tracers in quantitative proteomics and structural biology. We review the use of stable isotopes of biogenic elements (H, C, N, O, S, Mg, Se) with the emphasis on hydrogen and its heavy isotope deuterium. We will discuss the limitations of enriching various compounds in stable isotopes when produced in living organisms. Finally, we overview methods for measuring stable isotopes, focusing on methods for detection in single cells in situ and their exploitation in modern biotechnologies.

The ecology of anaerobic degraders of BTEX hydrocarbons in aquifers

The degradation of benzene, toluene, ethylbenzene and xylene (BTEX) contaminants in groundwater relies largely on anaerobic processes. While the physiology and biochemistry of selected relevant microbes have been intensively studied, research has now started to take the generated knowledge back to the field, in order to trace the populations truly responsible for the anaerobic degradation of BTEX hydrocarbons in situ and to unravel their ecology in contaminated aquifers. Here, recent advances in our knowledge of the identity, diversity and ecology of microbes involved in these important ecosystem services are discussed. At several sites, distinct lineages within the Desulfobulbaceae, the Rhodocyclaceae and the Gram-positive Peptococcaceae have been shown to dominate the degradation of different BTEX hydrocarbons. Especially for the functional guild of anaerobic toluene degraders, specific molecular detection systems have been developed, allowing researchers to trace their diversity and distribution in contaminated aquifers. Their populations appear enriched in hot spots of biodegradation in situ. ¹³C-labelling experiments have revealed unexpected pathways of carbon sharing and obligate syntrophic interactions to be relevant in degradation. Together with feedback mechanisms between abiotic and biotic habitat components, this promotes an enhanced ecological perspective of the anaerobic degradation of BTEX hydrocarbons, as well as its incorporation into updated concepts for site monitoring and bioremediation.

RNA-stable isotope probing: from carbon flow within key microbiota to targeted transcriptomes

Stable isotope probing of RNA has enthused researchers right from its first introduction in 2002. The concept of a labelling-based detection of process-targeted microbes independent of cellular replication or growth has allowed for a much more direct handle on functionally relevant microbiota than by labelling of other biomarkers. This has led to a widespread application of the technology, and breakthroughs in our understanding of carbon flow in natural microbiomes, autotrophic and heterotrophic physiologies, microbial food webs, host-microbe interactions and environmental biotechnology. Recent studies detecting labelled mRNA demonstrate that RNA-SIP is not limited to the analysis of rRNA, but is currently developing towards an approach for accessing targeted transcriptomes. In combination with next-generation sequencing and other methodological advances, RNA-SIP will continue to deliver invaluable insights into the functioning of microbial communities.

Protein-SIP in environmental studies

Metaproteomics coupled to stable isotope probing (SIP) was established to detect metabolically active key players in microbial communities. Here, we discuss the current state of protein-based stable isotope probing (protein-SIP) and the perspectives of using different stable isotope atoms (i.e. ¹³C, ¹⁵N, ¹⁸O, ^34/36S), multiple isotope labelling, the utilisation of substrates of major abundance and micro-pollutants [pesticides, herbicides and pharmaceuticals present in the environment at very low concentrations (ngμg/L)], and applications in complex model systems and in situ studies in the environment.

Anaerobic Microbial Degradation of Hydrocarbons: From Enzymatic Reactions to the Environment

Hydrocarbons are abundant in anoxic environments and pose biochemical challenges to their anaerobic degradation by microorganisms. Within the framework of the Priority Program 1319, investigations funded by the Deutsche Forschungsgemeinschaft on the anaerobic microbial degradation of hydrocarbons ranged from isolation and enrichment of hitherto unknown hydrocarbon-degrading anaerobic microorganisms, discovery of novel reactions, detailed studies of enzyme mechanisms and structures to process-oriented in situ studies. Selected highlights from this program are collected in this synopsis, with more detailed information provided by theme-focused reviews of the special topic issue on 'Anaerobic biodegradation of hydrocarbons' [this issue, pp. 1-244]. The interdisciplinary character of the program, involving microbiologists, biochemists, organic chemists and environmental scientists, is best exemplified by the studies on alkyl-/arylalkylsuccinate synthases. Here, research topics ranged from in-depth mechanistic studies of archetypical toluene-activating benzylsuccinate synthase, substrate-specific phylogenetic clustering of alkyl-/arylalkylsuccinate synthases (toluene plus xylenes, p-cymene, p-cresol, 2-methylnaphthalene, n-alkanes), stereochemical and co-metabolic insights into n-alkane-activating (methylalkyl)succinate synthases to the discovery of bacterial groups previously unknown to possess alkyl-/arylalkylsuccinate synthases by means of functional gene markers and in situ field studies enabled by state-of-the-art stable isotope probing and fractionation approaches. Other topics are Mo-cofactor-dependent dehydrogenases performing O2-independent hydroxylation of hydrocarbons and alkyl side chains (ethylbenzene, p-cymene, cholesterol, n-hexadecane), degradation of p-alkylated benzoates and toluenes, glycyl radical-bearing 4-hydroxyphenylacetate decarboxylase, novel types of carboxylation reactions (for acetophenone, acetone, and potentially also benzene and naphthalene), W-cofactor-containing enzymes for reductive dearomatization of benzoyl-CoA (class II benzoyl-CoA reductase) in obligate anaerobes and addition of water to acetylene, fermentative formation of cyclohexanecarboxylate from benzoate, and methanogenic degradation of hydrocarbons.