Anaerobic hydrocarbon degradation in candidate phylum 'Atribacteria' (JS1) inferred from genomics

Composition and metabolic flexibility of hydrocarbon-degrading consortia in oil reservoirs

Hydrocarbon-degrading consortia (HDC) play an important role in petroleum exploitation. However, the real composition and metabolic mechanism of HDC in the microbial enhanced oil recovery (MEOR) process remain unclear. By combining 13C-DNA stable isotope probing microcosms with metagenomics, some newly reported phyla, including Chloroflexi, Synergistetes, Thermotogae, and Planctomycetes, dominated the HDC in the oil reservoirs. In the field trials, the HDC in the aerobic-facultative-anaerobic stage of oilfields jointly promoted the MEOR process, with monthly oil increments of up to 189 tons. Pseudomonas can improve oil recovery by producing rhamnolipid in the facultative condition. Roseovarius was the novel taxa potentially oxidizing alkane and producing acetate to improve oil porosity and permeability in the aerobic condition. Ca. Bacteroidia were the new members potentially degrading hydrocarbons by fumarate addition in the anaerobic environment. Comprehensive identification of the active HDC in oil reservoirs provides a novel theoretical basis for oilfield regulatory scheme.

Long-term evaluating the strengthening effects of iron-carbon mediator for coking wastewater treatment in EGSB reactor

Coking wastewater (CWW) treatment is difficult due to its complex composition and high biological toxicity. Iron-carbon mediators was used to enhance the treatment of CWW through iron-carbon microelectrolysis (ICME). The results indicated that the removal rate of COD and phenolic compounds were enhanced by 24.1 % and 23.5 %, while biogas production and methane content were promoted by 50 % and 7 %. Microbial community analysis indicated that iron-carbon mediators had a transformative impact on the reactor's performance and dependability by enriching microorganisms involved in direct and indirect electron transfer, such as Anaerolineae and Methanothrix. The mediator also produced noteworthy gains in LB-EPS and TB-EPS, increasing by roughly 109.3 % and 211.6 %, respectively. PICRISt analysis demonstrated that iron-carbon mediators effectively augment the abundance of functional genes associated with metabolism, Citrate cycle, and EET pathway. This study provides a new approach for CWW treatment.

Cultivation of novel Atribacterota from oil well provides new insight into their diversity, ecology, and evolution in anoxic, carbon-rich environments

BACKGROUND

The Atribacterota are widely distributed in the subsurface biosphere. Recently, the first Atribacterota isolate was described and the number of Atribacterota genome sequences retrieved from environmental samples has increased significantly; however, their diversity, physiology, ecology, and evolution remain poorly understood.

RESULTS

We report the isolation of the second member of Atribacterota, Thermatribacter velox gen. nov., sp. nov., within a new family Thermatribacteraceae fam. nov., and the short-term laboratory cultivation of a member of the JS1 lineage, Phoenicimicrobium oleiphilum HX-OS.bin.34TS, both from a terrestrial oil reservoir. Physiological and metatranscriptomics analyses showed that Thermatribacter velox B11T and Phoenicimicrobium oleiphilum HX-OS.bin.34TS ferment sugars and n-alkanes, respectively, producing H2, CO2, and acetate as common products. Comparative genomics showed that all members of the Atribacterota lack a complete Wood-Ljungdahl Pathway (WLP), but that the Reductive Glycine Pathway (RGP) is widespread, indicating that the RGP, rather than WLP, is a central hub in Atribacterota metabolism. Ancestral character state reconstructions and phylogenetic analyses showed that key genes encoding the RGP (fdhA, fhs, folD, glyA, gcvT, gcvPAB, pdhD) and other central functions were gained independently in the two classes, Atribacteria (OP9) and Phoenicimicrobiia (JS1), after which they were inherited vertically; these genes included fumarate-adding enzymes (faeA; Phoenicimicrobiia only), the CODH/ACS complex (acsABCDE), and diverse hydrogenases (NiFe group 3b, 4b and FeFe group A3, C). Finally, we present genome-resolved community metabolic models showing the central roles of Atribacteria (OP9) and Phoenicimicrobiia (JS1) in acetate- and hydrocarbon-rich environments.

CONCLUSION

Our findings expand the knowledge of the diversity, physiology, ecology, and evolution of the phylum Atribacterota. This study is a starting point for promoting more incisive studies of their syntrophic biology and may guide the rational design of strategies to cultivate them in the laboratory. Video Abstract.

Active microbial communities facilitate carbon turnover in brine pools found in the deep Southeastern Mediterranean Sea

Discharge of gas-rich brines fuels productive chemosynthetic ecosystems in the deep sea. In these salty, methanic and sulfidic brines, microbial communities adapt to specific niches along the physicochemical gradients. However, the molecular mechanisms that underpin these adaptations are not fully known. Using metagenomics, we investigated the dense (∼106 cell ml-1) microbial communities that occupy small deep-sea brine pools found in the Southeastern Mediterranean Sea (1150 m water depth, ∼22 °C, ∼60 PSU salinity, sulfide, methane, ammonia reaching millimolar levels, and oxygen usually depleted), reaching high productivity rates of 685 μg C L-1 d-1 ex-situ. We curated 266 metagenome-assembled genomes of bacteria and archaea from the several pools and adjacent sediment-water interface, highlighting the dominance of a single Sulfurimonas, which likely fuels its autotrophy using sulfide oxidation or inorganic sulfur disproportionation. This lineage may be dominant in its niche due to genome streamlining, limiting its metabolic repertoire, particularly by using a single variant of sulfide: quinone oxidoreductase. These primary producers co-exist with ANME-2c archaea that catalyze the anaerobic oxidation of methane. Other lineages can degrade the necromass aerobically (Halomonas and Alcanivorax), or anaerobically through fermentation of macromolecules (e.g., Caldatribacteriota, Bipolaricaulia, Chloroflexota, etc). These low-abundance organisms likely support the autotrophs, providing energy-rich H2, and vital organics such as vitamin B12.

Ecological indicators and biological resources for hydrocarbon rhizoremediation in a protected area

Spillage from oil refineries, pipelines, and service stations consistently leads to soil, food and groundwater contamination. Bacterial-assisted phytoremediation is a non-invasive and sustainable solution to eliminate or decrease the concentration of xenobiotic contaminants in the environment. In the present study, a protected area interested by a fuel discharge was considered to assess a bioremediation intervention. From the spill point, a plume of contamination flowed South-West into the aquifer, eventually reaching a wetland area. Soils, groundwaters and plants belonging to the species Scirpus sylvaticus (L.) were sampled. In the majority of the soil samples, concentrations of total petroleum hydrocarbons, both C ≤ 12 and C > 12, exceeded legal limits set forth in Directive 2000/60/EC. The analysis of diatom populations, used as ecological indicators, evidenced morphology alterations and the presence of Ulnaria ulna and Ulnaria biceps species, previously detected in hydrocarbon-polluted waters. Tests for phytotoxicity and phytodegradation, carried out in soil mesocosms, planted with Zea mays and Helianthus annuus, demonstrated that both species significantly contributed to the removal of total petroleum hydrocarbons. Removal of C ≤ 12 and C > 12 petroleum hydrocarbons was in the range of 80%-82% for Z. mays and 71%-72% for H. annuus. Microbial communities inhabiting high organic carbon and vegetated soils were more active in hydrocarbon degradation than those inhabiting subsoils, as evidenced by soil slurry experiments. The abundance of functional genes encoding toluene-benzene monooxygenase (tbmD) and alkane hydroxylase (alkB), quantified in environmental samples, confirmed that the plant rhizosphere recruited a microbial community with higher biodegradation capacity. Bacterial strains isolated from the sampling site were able to grow on model hydrocarbons (hexane, hexadecane and o-, m-, p-xylene) as sole carbon and energy sources, indicating that a natural bio-attenuation process was on-going at the site. The bacterial strains isolated from rhizosphere soil, rhizoplane and endosphere showed plant growth promoting traits according to in vitro and in vivo tests on Z. mays and Oryza sativa, allowing to forecast a possible application of bacterial assisted rhizoremediation to recover the protected area.

Comparative single-cell genomics of Atribacterota JS1 in the Japan Trench hadal sedimentary biosphere

Deep-sea and subseafloor sedimentary environments host heterotrophic microbial communities that contribute to Earth's carbon cycling. However, the potential metabolic functions of individual microorganisms and their biogeographical distributions in hadal ocean sediments remain largely unexplored. In this study, we conducted single-cell genome sequencing on sediment samples collected from six sites (7,445-8,023 m water depth) along an approximately 500 km transect of the Japan Trench during the International Ocean Discovery Program Expedition 386. A total of 1,886 single-cell amplified genomes (SAGs) were obtained, offering comprehensive genetic insights into sedimentary microbial communities in surface sediments (<1 m depth) above the sulfate-methane transition zone along the Japan Trench. Our genome data set included 269 SAGs from Atribacterota JS1, the predominant bacterial clade in these hadal environments. Phylogenetic analysis classified SAGs into nine distinct phylotypes, whereas metagenome-assembled genomes were categorized into only two phylotypes, advancing JS1 diversity coverage through a single cell-based approach. Comparative genomic analysis of JS1 lineages from different habitats revealed frequent detection of genes related to organic carbon utilization, such as extracellular enzymes like clostripain and α-amylase, and ABC transporters of oligopeptide from Japan Trench members. Furthermore, specific JS1 phylotypes exhibited a strong correlation with in situ methane concentrations and contained genes involved in glycine betaine metabolism. These findings suggest that the phylogenomically diverse and novel Atribacterota JS1 is widely distributed in Japan Trench sediment, playing crucial roles in carbon cycling within the hadal sedimentary biosphere.IMPORTANCEThe Japan Trench represents tectonically active hadal environments associated with Pacific plate subduction beneath the northeastern Japan arc. This study, for the first time, documented a large-scale single-cell and metagenomic survey along an approximately 500 km transect of the Japan Trench, obtaining high-quality genomic information on hadal sedimentary microbial communities. Single-cell genomics revealed the predominance of diverse JS1 lineages not recoverable through conventional metagenomic binning. Their metabolic potential includes genes related to the degradation of organic matter, which contributes to methanogenesis in the deeper layers. Our findings enhance understanding of sedimentary microbial communities at water depths exceeding 7,000 m and provide new insights into the ecological role of biogeochemical carbon cycling in the hadal sedimentary biosphere.

Flexible catabolism of monoaromatic hydrocarbons by anaerobic microbiota adapting to oxygen exposure

Microbe-mediated anaerobic degradation is a practical method for remediation of the hazardous monoaromatic hydrocarbons (BTEX, including benzene, toluene, ethylbenzene and xylenes) under electron-deficient contaminated sites. However, how do the anaerobic functional microbes adapt to oxygen exposure and flexibly catabolize BTEX remain poorly understood. We investigated the switches of substrate spectrum and bacterial community upon oxygen perturbation in a nitrate-amended anaerobic toluene-degrading microbiota which was dominated by Aromatoleum species. DNA-stable isotope probing demonstrated that Aromatoleum species was involved in anaerobic mineralization of toluene. Metagenome-assembled genome of Aromatoleum species harbored both the nirBD-type genes for nitrate reduction to ammonium coupled with toluene oxidation and the additional meta-cleavage pathway for aerobic benzene catabolism. Once the anaerobic microbiota was fully exposed to oxygen and benzene, 1.05 ± 0.06% of Diaphorobacter species rapidly replaced Aromatoleum species and flourished to 96.72 ± 0.01%. Diaphorobacter sp. ZM was isolated, which was not only able to utilize benzene as the sole carbon source for aerobic growth and but also innovatively reduce nitrate to ammonium with citrate/lactate/glucose as the carbon source under anaerobic conditions. This study expands our understanding of the adaptive mechanism of microbiota for environmental redox disturbance and provides theoretical guidance for the bioremediation of BTEX-contaminated sites.

Effects of microplastics on cold seep sediment prokaryotic communities

Cold seep sediments are an important reservoir of microplastics (MPs) whose impact on the structure and function of prokaryotic community is not well understood. In this study, the impact of 0.2% and 1% (w/w) polyethylene (PE), polystyrene (PS), and polypropylene (PP) MPs on the cold seep sediment prokaryotic community was investigated in a 120-day laboratory incubation experiment. The results revealed that exposure to MPs altered sedimentary chemical properties in a type- and concentration-dependent manner. Furthermore, MPs significantly altered the structure of bacterial community, with some MPs degradation-associated bacterial phyla significantly increasing (p < 0.05). However, in the case of archaea, the changes in the structure of microbial community were less pronounced (p > 0.05). Co-occurrence network analysis revealed that the addition of MPs reduced the network complexity, while PICRUSt2 and FAPROTAX analyses suggested that 0.2% PP and 1% PS MPs had the most significant effects on the nitrogen and carbon cycles (p < 0.05). Overall, this study provides new insights into the effects of MPs on the structure and function of microbial communities in cold seep sediments.

An Arctic natural oil seep investigated from space to the seafloor

Due to climate change, decreasing ice cover and increasing industrial activities, Arctic marine ecosystems are expected to face higher levels of anthropogenic stress. To sustain healthy and productive ocean ecosystems, it is imperative to build baseline data to assess future climatic and environmental changes. Herein, a natural oil seep site offshore western Svalbard (Prins Karls Forland, PKF, 80-100 m water depth), discovered using satellite radar images, was investigated using an extensive multiscale and multisource geospatial dataset collected by satellite, aerial, floating, and underwater platforms. The investigated PKF seep area covers roughly a seafloor area of 30,000 m2 and discharges oil from Tertiary or younger source rocks. Biomarker analyses confirm that the oil in the slicks on the sea surface and from the seep on the seafloor have the same origin. Uranium/Thorium dating of authigenic carbonate crusts indicated that the seep had emanated since the Late Pleistocene when ice sheet melting unlocked the hydrocarbons trapped beneath the ice. The faunal communities at the PKF seep are a mix of typical high latitude fauna and taxa adapted to reducing environments. Remarkably, the inhospitable oil-impregnated sediments were also colonized by abundant infaunal organisms. Altogether, in situ observations obtained at the site provide essential insights into the characteristics of high-latitude oil seeps and can be used as a natural laboratory for understanding the potential impacts of human oil discharge into the ocean.

Anaerobic hydrocarbon biodegradation by alkylotrophic methanogens in deep oil reservoirs

In subsurface biodegraded oil reservoirs, methanogenic biodegradation of crude oil is a common process. This process was previously assigned to the syntrophy of hydrocarbon-degrading bacteria and methanogenic archaea. Recent studies showed that archaea of the Candidatus Methanoliparum named as alkylotrophic methanogens couple hydrocarbon degradation and methane production in a single archaeon. To assess the geochemical role of Ca. Methanoliparum, we analyzed the chemical and microbial composition and metabolites of 209 samples from 15 subsurface oil reservoirs across China. Gas chromatography-mass spectrometry analysis revealed that 92% of the tested samples were substantially degraded. Molecular analysis showed that 85% of the tested samples contained Ca. Methanoliparum, and 52% of the tested samples harbored multiple alkyl-coenzyme M derivatives, the intercellular metabolites of alkylotrophic archaea. According to metagenomic and metatranscriptomic analyses, Ca. Methanoliparum dominates hydrocarbon degradation in biodegraded samples from the Changqing, Jiangsu, and Shengli (SL) oilfields, and it is persistently present as shown in a 15-year-long sampling effort at the Shengli oilfield. Together, these findings demonstrate that Ca. Methanoliparum is a widely distributed oil degrader in reservoirs of China, suggesting that alkylotrophic methanogenesis by archaea plays a key role in the alteration of oil reservoirs, thereby expanding our understanding of biogeochemical process in the deep biosphere.

Unveiling the hidden role of aquatic viruses in hydrocarbon pollution bioremediation

Hydrocarbon pollution poses substantial environmental risks to water and soil. Bioremediation, which utilizes microorganisms to manage pollutants, offers a cost-effective solution. However, the role of viruses, particularly bacteriophages (phages), in bioremediation remains unexplored. This study examines the diversity and activity of hydrocarbon-degradation genes encoded by environmental viruses, focusing on phages, within public databases. We identified 57 high-quality phage-encoded auxiliary metabolic genes (AMGs) related to hydrocarbon degradation, which we refer to as virus-encoded hydrocarbon degradation genes (vHYDEGs). These genes are encoded by taxonomically diverse aquatic phages and highlight the under-characterized global virosphere. Six protein families involved in the initial alkane hydroxylation steps were identified. Phylogenetic analyses revealed the diverse evolutionary trajectories of vHYDEGs across habitats, revealing previously unknown biodegraders linked evolutionarily with vHYDEGs. Our findings suggest phage AMGs may contribute to alkane and aromatic hydrocarbon degradation, participating in the initial, rate-limiting hydroxylation steps, thereby aiding hydrocarbon pollution bioremediation and promoting their propagation. To support future research, we developed vHyDeg, a database containing identified vHYDEGs with comprehensive annotations, facilitating the screening of hydrocarbon degradation AMGs and encouraging their bioremediation applications.

Environmental heterogeneity shapes the C and S cycling-associated microbial community in Haima's cold seeps

Environmental heterogeneity in cold seeps is usually reflected by different faunal aggregates. The sediment microbiome, especially the geochemical cycling-associated communities, sustains the ecosystem through chemosynthesis. To date, few studies have paid attention to the structuring and functioning of geochemical cycling-associated communities relating to environmental heterogeneity in different faunal aggregates of cold seeps. In this study, we profiled the microbial community of four faunal aggregates in the Haima cold seep, South China Sea. Through a combination of geochemical and meta-omics approaches, we have found that geochemical variables, such as sulfate and calcium, exhibited a significant variation between different aggregates, indicating changes in the methane flux. Anaerobic methanotrophic archaea (ANME), sulfate-reducing, and sulfide-oxidizing bacteria (SRB and SOB) dominated the microbial community but varied in composition among the four aggregates. The diversity of archaea and bacteria exhibited a strong correlation between sulfate, calcium, and silicate. Interspecies co-exclusion inferred by molecular ecological network analysis increased from non-seep to clam aggregates and peaked at the mussel aggregate. The networked geochemical cycling-associated species showed an obvious aggregate-specific distribution pattern. Notably, hydrocarbon oxidation and sulfate reduction by ANME and SRB produced carbonate and sulfide, driving the alkalization of the sediment environment, which may impact the microbial communities. Collectively, these results highlighted that geofluid and microbial metabolism together resulted in environmental heterogeneity, which shaped the C and S cycling-associated microbial community.

Utilization of-Omic technologies in cold climate hydrocarbon bioremediation: a text-mining approach

Hydrocarbon spills in cold climates are a prominent and enduring form of anthropogenic contamination. Bioremediation is one of a suite of remediation tools that has emerged as a cost-effective strategy for transforming these contaminants in soil, ideally into less harmful products. However, little is understood about the molecular mechanisms driving these complex, microbially mediated processes. The emergence of -omic technologies has led to a revolution within the sphere of environmental microbiology allowing for the identification and study of so called 'unculturable' organisms. In the last decade, -omic technologies have emerged as a powerful tool in filling this gap in our knowledge on the interactions between these organisms and their environment in vivo. Here, we utilize the text mining software Vosviewer to process meta-data and visualize key trends relating to cold climate bioremediation projects. The results of text mining of the literature revealed a shift over time from optimizing bioremediation experiments on the macro/community level to, in more recent years focusing on individual organisms of interest, interactions within the microbiome and the investigation of novel metabolic degradation pathways. This shift in research focus was made possible in large part by the rise of omics studies allowing research to focus not only what organisms/metabolic pathways are present but those which are functional. However, all is not harmonious, as the development of downstream analytical methods and associated processing tools have outpaced sample preparation methods, especially when dealing with the unique challenges posed when analyzing soil-based samples.

Anaerobic degradation of organic carbon supports uncultured microbial populations in estuarine sediments

BACKGROUND

A large proportion of prokaryotic microbes in marine sediments remains uncultured, hindering our understanding of their ecological functions and metabolic features. Recent environmental metagenomic studies suggested that many of these uncultured microbes contribute to the degradation of organic matter, accompanied by acetogenesis, but the supporting experimental evidence is limited.

RESULTS

Estuarine sediments were incubated with different types of organic matters under anaerobic conditions, and the increase of uncultured bacterial populations was monitored. We found that (1) lignin stimulated the increase of uncultured bacteria within the class Dehalococcoidia. Their ability to metabolize lignin was further supported by the presence of genes associated with a nearly complete degradation pathway of phenolic monomers in the Dehalococcoidia metagenome-assembled genomes (MAGs). (2) The addition of cellulose stimulated the increase of bacteria in the phylum Ca. Fermentibacterota and family Fibrobacterales, a high copy number of genes encoding extracellular endoglucanase or/and 1,4-beta-cellobiosidase for cellulose decomposition and multiple sugar transporters were present in their MAGs. (3) Uncultured lineages in the order Bacteroidales and the family Leptospiraceae were enriched by the addition of casein and oleic acid, respectively, a high copy number of genes encoding extracellular peptidases, and the complete β-oxidation pathway were found in those MAGs of Bacteroidales and Leptospiraceae, respectively. (4) The growth of unclassified bacteria of the order Clostridiales was found after the addition of both casein and cellulose. Their MAGs contained multiple copies of genes for extracellular peptidases and endoglucanase. Additionally, ¹³C-labeled acetate was produced in the incubations when ¹³C-labeled dissolved inorganic carbon was provided.

CONCLUSIONS

Our results provide new insights into the roles of microorganisms during organic carbon degradation in anaerobic estuarine sediments and suggest that these macro and single molecular organic carbons support the persistence and increase of uncultivated bacteria. Acetogenesis is an additional important microbial process alongside organic carbon degradation. Video Abstract.

Revealing the response of microbial communities to polyethylene micro(nano)plastics exposure in cold seep sediment

To date, multiple studies have shown that the accumulation of microplastics (MPs)/nanoplastics (NPs) in the environment may lead to various problems. However, the effects of MPs/NPs on microbial communities and biogeochemical processes, particularly methane metabolism in cold seep sediments, have not been well elucidated. In this study, an indoor microcosm experiment for a period of 120 days exposure of MPs/NPs was conducted. The results showed that MPs/NPs addition did not significantly influence bacterial and archaeal richness in comparison with the control (p > 0.05), whereas higher levels of NPs (1 %, w/w) had a significant adverse effect on bacterial diversity (p < 0.05). Moreover, the bacterial community was more sensitive to the addition of MPs/NPs than the archaea, and Epsilonbacteraeota replaced Proteobacteria as the dominant phylum in the MPs/NPs treatments (except 0.2 % NPs). With respect to the co-occurrence relationships, network analysis showed that the presence of NPs, in comparison with MPs, reduced microbial network complexity. Finally, the presence of MPs/NPs decreased the abundance of mcrA, while promoting the abundance of pmoA. This study will help elucidate the responses of microbial communities to MPs/NPs and evaluate their effects on methane metabolism in cold seep ecosystems.

Tracing the Century-Long Evolution of Microplastics Deposition in a Cold Seep

Microplastic (MP) pollution is one of the greatest threats to marine ecosystems. Cold seeps are characterized by methane-rich fluid seepage fueling one of the richest ecosystems on the seafloor, and there are approximately more than 900 cold seeps globally. While the long-term evolution of MPs in cold seeps remains unclear. Here, how MPs have been deposited in the Haima cold seep since the invention of plastics is demonstrated. It is found that the burial rates of MPs in the non-seepage areas significantly increased since the massive global use of plastics in the 1930s, nevertheless, the burial rates and abundance of MPs in the methane seepage areas are much lower than the non-seepage area of the cold seep, suggesting the degradation potential of MPs in cold seeps. More MP-degrading microorganism populations and functional genes are discovered in methane seepage areas to support this discovery. It is further investigated that the upwelling fluid seepage facilitated the fragmentation and degradation behaviors of MPs. Risk assessment indicated that long-term transport and transformation of MPs in the deeper sediments can reduce the potential environmental and ecological risks. The findings illuminated the need to determine fundamental strategies for sustainable marine plastic pollution mitigation in the natural deep-sea environments.

Thermal Selection of Microbial Communities and Preservation of Microbial Function in Guaymas Basin Hydrothermal Sediments

The Guaymas Basin in the Gulf of California is characterized by active seafloor spreading, hydrothermal activity, and organic matter accumulation on the seafloor due to high sedimentation rates. In the hydrothermal sediments of Guaymas Basin, microbial community compositions and coexistence patterns change across steep gradients of temperature, potential carbon sources, and electron acceptors. Nonmetric multidimensional scaling and guanine-cytosine percentage analyses reveal that the bacterial and archaeal communities adjust compositionally to their local temperature regime. Functional inference using PICRUSt shows that microbial communities consistently maintain their predicted biogeochemical functions in different sediments. Phylogenetic profiling shows that microbial communities retain distinct sulfate-reducing, methane-oxidizing, or heterotrophic lineages within specific temperature windows. The preservation of similar biogeochemical functions across microbial lineages with different temperature adaptations stabilizes the hydrothermal microbial community in a highly dynamic environment. IMPORTANCE Hydrothermal vent sites have been widely studied to investigate novel bacteria and archaea that are adapted to these extreme environments. However, community-level analyses of hydrothermal microbial ecosystems look beyond the presence and activity of particular types of microbes and examine to what extent the entire community of bacteria and archaea is adapted to hydrothermal conditions; these include elevated temperatures, hydrothermally generated carbon sources, and inorganic electron donors and acceptors that are characteristic for hydrothermal environments. In our case study of bacterial and archaeal communities in hydrothermal sediments of Guaymas Basin, we found that sequence-inferred microbial function was maintained in differently structured bacterial and archaeal communities across different samples and thermal regimes. The resulting preservation of biogeochemical functions across thermal gradients is an important factor in explaining the consistency of the microbial core community in the dynamic sedimentary environment of Guaymas Basin.

The majority of microorganisms in gas hydrate-bearing subseafloor sediments ferment macromolecules

BACKGROUND

Gas hydrate-bearing subseafloor sediments harbor a large number of microorganisms. Within these sediments, organic matter and upward-migrating methane are important carbon and energy sources fueling a light-independent biosphere. However, the type of metabolism that dominates the deep subseafloor of the gas hydrate zone is poorly constrained. Here we studied the microbial communities in gas hydrate-rich sediments up to 49 m below the seafloor recovered by drilling in the South China Sea. We focused on distinct geochemical conditions and performed metagenomic and metatranscriptomic analyses to characterize microbial communities and their role in carbon mineralization.

RESULTS

Comparative microbial community analysis revealed that samples above and in sulfate-methane interface (SMI) zones were clearly distinguished from those below the SMI. Chloroflexota were most abundant above the SMI, whereas Caldatribacteriota dominated below the SMI. Verrucomicrobiota, Bathyarchaeia, and Hadarchaeota were similarly present in both types of sediment. The genomic inventory and transcriptional activity suggest an important role in the fermentation of macromolecules. In contrast, sulfate reducers and methanogens that catalyze the consumption or production of commonly observed chemical compounds in sediments are rare. Methanotrophs and alkanotrophs that anaerobically grow on alkanes were also identified to be at low abundances. The ANME-1 group actively thrived in or slightly below the current SMI. Members from Heimdallarchaeia were found to encode the potential for anaerobic oxidation of short-chain hydrocarbons.

CONCLUSIONS

These findings indicate that the fermentation of macromolecules is the predominant energy source for microorganisms in deep subseafloor sediments that are experiencing upward methane fluxes. Video Abstract.

Riddles of Lost City: Chemotrophic Prokaryotes Drives Carbon, Sulfur, and Nitrogen Cycling at an Extinct Cold Seep, South China Sea

Deep-sea cold seeps are one of the most productive ecosystems that sustained by hydrocarbons carried by the fluid. Once the seep fluid ceases, the thriving autotrophic communities die out, terming as the extinct seep. But heterotrophic fauna can still survive even for thousands of years. The critical role of prokaryotes in active seeps are well defined, but their functions in extinct seeps are poorly understood to date. Here, we clarified the diversity, taxonomic specificity, interspecies correlation, and metabolic profiles of sediment prokaryotes at an extinct seep site of Haima cold seep, South China Sea. Alpha diversity of archaea significantly increased, while that of bacteria remained unchanged in extinct seep compared to active seep. However, archaea composition did not differ significantly at extinct seep from active or nonseep sites based on weighted-unifrac dissimilarity, while bacteria composition exhibited significant difference. Distribution of archaea and bacteria showed clear specificity to extinct seeps, indicating the unique life strategies here. Prokaryotes might live chemolithoautotrophically on cycling of inorganic carbon, sulfur, and nitrogen, or chemoorganotrophically on recycling of hydrocarbons. Notably, many of the extinct seep specific species and networked keystone lineages are classified as Proteobacteria. Regarding the functional diversity and metabolic flexibility of this clade, Proteobacteria is supposed to integrate the geochemical cycles and play a critical role in energy and resource supplement for microbiome in extinct seep. Collectively, our findings shed lights on the microbial ecology and functional diversity in extinct seeps, providing new understanding of biogeochemical cycling after fluid cessation. IMPORTANCE This research paper uncovered the potential mechanisms for microbiota mediated geochemical cycling in extinct cold seep, advancing our understanding in deep sea microbiology ecology.

Anaerobic oxidation of propane coupled to nitrate reduction by a lineage within the class Symbiobacteriia

Anaerobic microorganisms are thought to play a critical role in regulating the flux of short-chain gaseous alkanes (SCGAs; including ethane, propane and butane) from terrestrial and aquatic ecosystems to the atmosphere. Sulfate has been confirmed to act as electron acceptor supporting microbial anaerobic oxidation of SCGAs, yet several other energetically more favourable acceptors co-exist with these gases in anaerobic environments. Here, we show that a bioreactor seeded with biomass from a wastewater treatment facility can perform anaerobic propane oxidation coupled to nitrate reduction to dinitrogen gas and ammonium. The bioreactor was operated for more than 1000 days, and we used ¹³C- and ¹⁵N-labelling experiments, metagenomic, metatranscriptomic, metaproteomic and metabolite analyses to characterize the microbial community and the metabolic processes. The data collectively suggest that a species representing a novel order within the bacterial class Symbiobacteriia is responsible for the observed nitrate-dependent propane oxidation. The closed genome of this organism, which we designate as 'Candidatus Alkanivorans nitratireducens', encodes pathways for oxidation of propane to CO₂ via fumarate addition, and for nitrate reduction, with all the key genes expressed during nitrate-dependent propane oxidation. Our results suggest that nitrate is a relevant electron sink for SCGA oxidation in anaerobic environments, constituting a new microbially-mediated link between the carbon and nitrogen cycles.

Genome-resolved analyses show an extensive diversification in key aerobic hydrocarbon-degrading enzymes across bacteria and archaea

Background

Hydrocarbons (HCs) are organic compounds composed solely of carbon and hydrogen that are mainly accumulated in oil reservoirs. As the introduction of all classes of hydrocarbons including crude oil and oil products into the environment has increased significantly, oil pollution has become a global ecological problem. However, our perception of pathways for biotic degradation of major HCs and key enzymes in these bioconversion processes has mainly been based on cultured microbes and is biased by uneven taxonomic representation. Here we used Annotree to provide a gene-centric view of the aerobic degradation ability of aliphatic and aromatic HCs in 23,446 genomes from 123 bacterial and 14 archaeal phyla. 

Results

Apart from the widespread genetic potential for HC degradation in Proteobacteria, Actinobacteriota, Bacteroidota, and Firmicutes, genomes from an additional 18 bacterial and 3 archaeal phyla also hosted key HC degrading enzymes. Among these, such degradation potential has not been previously reported for representatives in the phyla UBA8248, Tectomicrobia, SAR324, and Eremiobacterota. Genomes containing whole pathways for complete degradation of HCs were only detected in Proteobacteria and Actinobacteriota. Except for several members of Crenarchaeota, Halobacterota, and Nanoarchaeota that have tmoA, ladA, and alkB/M key genes, respectively, representatives of archaeal genomes made a small contribution to HC degradation. None of the screened archaeal genomes coded for complete HC degradation pathways studied here; however, they contribute significantly to peripheral routes of HC degradation with bacteria.

Conclusion

Phylogeny reconstruction showed that the reservoir of key aerobic hydrocarbon-degrading enzymes in Bacteria and Archaea undergoes extensive diversification via gene duplication and horizontal gene transfer. This diversification could potentially enable microbes to rapidly adapt to novel and manufactured HCs that reach the environment.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08906-w.

Microbial communities in crude oil phase and filter-graded aqueous phase from a Daqing oilfield after polymer flooding

AIMS

The aim was to characterize indigenous microorganisms in oil reservoirs after polymer flooding (RAPF).

METHODS

The microbial communities in the crude oil phase (Oil) and in the filter-graded aqueous phases Aqu0.22 (>0.22 μm) and Aqu0.1 (0.1~0.22 μm) were investigated by 16S rRNA gene high-throughput sequencing.

RESULTS

Indigenous microorganisms related to hydrocarbon degradation prevailed in the three phases of each well. However, obvious differences of bacterial compositions were observed among the three phases of the same well and among the same phase of different wells. The crude oil and Aqu0.22 shared many dominant bacteria. Aqu0.1 contained a unique bacterial community in each well. Most bacteria in Aqu0.1 were affiliated to culturable genera, suggesting that they may adapt to the oil reservoir environment by reduction of cell size. Contrary to the bacterial genera, archaeal genera were similar in the three phases but varied in relative abundances. The observed microbial differences may be driven by specific environmental factors in each oil well.

CONCLUSIONS

The results suggest an application potential of microbial enhanced oil recovery (MEOR) technology in RAPF. The crude oil and Aqu0.1 contain many different functional microorganisms related to hydrocarbon degradation. Both should not be overlooked when investing and exploring the indigenous microorganisms for MEOR.

SIGNIFICANCE AND IMPACT OF THE STUDY

This work facilitates the understanding of microbial community structures in RAPF and provides information for microbial control in oil fields.

Diversity of Anaerobic Methane Oxidizers in the Cold Seep Sediments of the Okinawa Trough

Active cold seeps in the Okinawa Trough (OT) have been widely identified, but the sediment microbial communities associated with these sites are still poorly understood. Here, we investigated the distribution and biomass of the microbial communities, particularly those associated with the anaerobic oxidation of methane (AOM), in sediments from an active cold seep in the mid-Okinawa Trough. Methane-oxidizing archaea, including ANME-1a, ANME-1b, ANME-2a/b, ANME-2c, and ANME-3, were detected in the OT cold seep sediments. Vertical stratification of anaerobic methanotrophic archaea (ANME) communities was observed in the following order: ANME-3, ANME-1a, and ANME-1b. In addition, the abundance of methyl coenzyme M reductase A (mcrA) genes corresponded to high levels of dissolved iron, suggesting that methane-metabolizing archaea might participate in iron reduction coupled to methane oxidation (Fe-AOM) in the OT cold seep. Furthermore, the relative abundance of ANME-1a was strongly related to the concentration of dissolved iron, indicating that ANME-1a is a key microbial player for Fe-AOM in the OT cold seep sediments. Co-occurrence analysis revealed that methane-metabolizing microbial communities were mainly associated with heterotrophic microorganisms, such as JS1, Bathy-1, and Bathy-15.

Physiological and Genomic Characterization of Actinotalea subterranea sp. nov. from Oil-Degrading Methanogenic Enrichment and Reclassification of the Family Actinotaleaceae

The goal of the present work was to determine the diversity of prokaryotes involved in anaerobic oil degradation in oil fields. The composition of the anaerobic oil-degrading methanogenic enrichment obtained from an oil reservoir was determined by 16S rRNA-based survey, and the facultatively anaerobic chemoorganotrophic bacterial strain HO-Ch2^T was isolated and studied using polyphasic taxonomy approach and genome sequencing. The strain HO-Ch2^T grew optimally at 28 °C, pH 8.0, and 1–2% (w/v) NaCl. The 16S rRNA gene sequence of the strain HO-Ch2^T had 98.8% similarity with the sequence of Actinotalea ferrariae CF5-4^T. The genomic DNA G + C content of strain HO-Ch2^T was 73.4%. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between the genome of strain HO-Ch2^T and Actinotalea genomes were 79.8–82.0% and 20.5–22.2%, respectively, i.e., below the thresholds for species delineation. Based on the phylogenomic, phenotypic, and chemotaxonomic characterization, we propose strain HO-Ch2^T (= VKM Ac-2850^T = KCTC 49656^T) as the type strain of a new species within the genus Actinotalea, with the name Actinotalea subterranea sp. nov. Based on the phylogenomic analysis of 187 genomes of Actinobacteria we propose the taxonomic revision of the genera Actinotalea and Pseudactinotalea and of the family Actinotaleaceae. We also propose the reclassification of Cellulomonas carbonis as Actinotalea carbonis comb. nov., Cellulomonas bogoriensis as Actinotalea bogoriensis comb. nov., Actinotalea caeni as Pseudactinotalea caeni comb. nov., and the transfer of the genus Pseudactinotalea to the family Ruaniaceae of the order Ruaniales.

CANT-HYD: A Curated Database of Phylogeny-Derived Hidden Markov Models for Annotation of Marker Genes Involved in Hydrocarbon Degradation

Many pathways for hydrocarbon degradation have been discovered, yet there are no dedicated tools to identify and predict the hydrocarbon degradation potential of microbial genomes and metagenomes. Here we present the Calgary approach to ANnoTating HYDrocarbon degradation genes (CANT-HYD), a database of 37 HMMs of marker genes involved in anaerobic and aerobic degradation pathways of aliphatic and aromatic hydrocarbons. Using this database, we identify understudied or overlooked hydrocarbon degradation potential in many phyla. We also demonstrate its application in analyzing high-throughput sequence data by predicting hydrocarbon utilization in large metagenomic datasets from diverse environments. CANT-HYD is available at https://github.com/dgittins/CANT-HYD-HydrocarbonBiodegradation.

Non-syntrophic methanogenic hydrocarbon degradation by an archaeal species

The methanogenic degradation of oil hydrocarbons can proceed through syntrophic partnerships of hydrocarbon-degrading bacteria and methanogenic archaea^1-3. However, recent culture-independent studies have suggested that the archaeon 'Candidatus Methanoliparum' alone can combine the degradation of long-chain alkanes with methanogenesis^4,5. Here we cultured Ca. Methanoliparum from a subsurface oil reservoir. Molecular analyses revealed that Ca. Methanoliparum contains and overexpresses genes encoding alkyl-coenzyme M reductases and methyl-coenzyme M reductases, the marker genes for archaeal multicarbon alkane and methane metabolism. Incubation experiments with different substrates and mass spectrometric detection of coenzyme-M-bound intermediates confirm that Ca. Methanoliparum thrives not only on a variety of long-chain alkanes, but also on n-alkylcyclohexanes and n-alkylbenzenes with long n-alkyl (C_≥13) moieties. By contrast, short-chain alkanes (such as ethane to octane) or aromatics with short alkyl chains (C_≤12) were not consumed. The wide distribution of Ca. Methanoliparum^4-6 in oil-rich environments indicates that this alkylotrophic methanogen may have a crucial role in the transformation of hydrocarbons into methane.

Indigenous microbial communities in heavy oil show a threshold response to salinity

Microbial degradation influences the quality of oil resources. The environmental factors that shape the composition of oil microbial communities are largely unknown because most samples from oil fields are impacted by anthropogenic oil production, perturbing the native ecosystem with exogenous fluids and microorganisms. We investigated the relationship between formation water geochemistry and microbial community composition in undisturbed oil samples. We isolated 43 microliter-sized water droplets naturally enclosed in the heavy oil of the Pitch Lake, Trinidad and Tobago. The water chemistry and microbial community composition within the same water droplet were determined by ion chromatography and 16S rRNA gene amplicon sequencing, respectively. The results revealed a high variability in ion concentrations and community composition between water droplets. Microbial community composition was mostly affected by the chloride concentration, which ranged from freshwater to brackish-sea water. Remarkably, microbial communities did not respond gradually to increasing chloride concentration but showed a sudden change to less diverse and uneven communities when exceeding a chloride concentration of 57.3 mM. The results reveal a threshold-regulated response of microbial communities to salinity, offering new insights into the microbial ecology of oil reservoirs.

Stochastic assembly process dominates bacterial succession during a long-term microbial enhanced oil recovery

Microbial enhanced oil recovery (MEOR) has been successfully used in oil exploitation to increase oil production. However, the mechanisms of microbial interactions and community assembly related to oil production performance along MEOR process are poorly understood. Here, we investigated the microbiome of an oil reservoir for a period of 5 years under three phases of different treatments with the injection of a mixture of microbes, nutrients, and air at different intensity. During the MEOR process, amplification of functional genes revealed an increase of genes related to hydrocarbon degradation linked to methanogenesis, supported by stable isotope analysis for confirmation of the methanogenesis activity. Meanwhile, a lower contribution of the ubiquitous/common taxa, closer and more positive associations, and lower modularity were observed in bacterial co-occurrence networks, with the rare taxa being the keystone taxa. The null model analysis and structural equation modeling revealed that the contribution of stochastic processes affected by functional groups and co-occurrence patterns to bacterial community increased significantly with the increase of oil production. This provides new insight that stochastic assembly in bacterial community increased along with MEOR process, and it is worthwhile paying attention to the uncertain consequences caused by random evolution since the treatment effect of MEOR is closely related to the in-situ community in oil reservoir.

Microbial metabolism and adaptations in Atribacteria-dominated methane hydrate sediments

Gas hydrates harbour gigatons of natural gas, yet their microbiomes remain understudied. We bioprospected 16S rRNA amplicons, metagenomes, and metaproteomes from methane hydrate-bearing sediments under Hydrate Ridge (offshore Oregon, USA, ODP Site 1244, 2-69 mbsf) for novel microbial metabolic and biosynthetic potential. Atribacteria sequences generally increased in relative sequence abundance with increasing sediment depth. Most Atribacteria ASVs belonged to JS-1-Genus 1 and clustered with other sequences from gas hydrate-bearing sediments. We recovered 21 metagenome-assembled genomic bins spanning three geochemical zones in the sediment core: the sulfate-methane transition zone, the metal (iron/manganese) reduction zone, and the gas hydrate stability zone. We found evidence for bacterial fermentation as a source of acetate for aceticlastic methanogenesis and as a driver of iron reduction in the metal reduction zone. In multiple zones, we identified a Ni-Fe hydrogenase-Na⁺ /H⁺ antiporter supercomplex (Hun) in Atribacteria and Firmicutes bins and in other deep subsurface bacteria and cultured hyperthermophiles from the Thermotogae phylum. Atribacteria expressed tripartite ATP-independent transporters downstream from a novel regulator (AtiR). Atribacteria also possessed adaptations to survive extreme conditions (e.g. high salt brines, high pressure and cold temperatures) including the ability to synthesize the osmolyte di-myo-inositol-phosphate as well as expression of K⁺ -stimulated pyrophosphatase and capsule proteins.

Organic Electron Donors and Terminal Electron Acceptors Structure Anaerobic Microbial Communities and Interactions in a Permanently Stratified Sulfidic Lake

The extent to which nutrients structure microbial communities in permanently stratified lakes is not well understood. This study characterized microbial communities from the anoxic layers of the meromictic and sulfidic Fayetteville Green Lake (FGL), NY, United States, and investigated the roles of organic electron donors and terminal electron acceptors in shaping microbial community structure and interactions. Bacterial communities from the permanently stratified layer below the chemocline (monimolimnion) and from enrichment cultures inoculated by lake sediments were analyzed using 16S rRNA gene sequencing. Results showed that anoxygenic phototrophs dominated microbial communities in the upper monimolimnion (21 m), which harbored little diversity, whereas the most diverse communities resided at the bottom of the lake (∼52 m). Organic electron donors explained 54% of the variation in the microbial community structure in aphotic cultures enriched on an array of organic electron donors and different inorganic electron acceptors. Electron acceptors only explained 10% of the variation, but were stronger drivers of community assembly in enrichment cultures supplemented with acetate or butyrate compared to the cultures amended by chitin, lignin or cellulose. We identified a range of habitat generalists and habitat specialists in both the water column and enrichment samples using Levin's index. Network analyses of interactions among microbial groups revealed Chlorobi and sulfate reducers as central to microbial interactions in the upper monimolimnion, while Syntrophaceae and other fermenting organisms were more important in the lower monimolimnion. The presence of photosynthetic microbes and communities that degrade chitin and cellulose far below the chemocline supported the downward transport of microbes, organic matter and oxidants from the surface and the chemocline. Collectively, our data suggest niche partitioning of bacterial communities via interactions that depend on the availability of different organic electron donors and terminal electron acceptors. Thus, light, as well as the diversity and availability of chemical resources drive community structure and function in FGL, and likely in other stratified, meromictic lakes.

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

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.

Innovations to culturing the uncultured microbial majority

Despite the surge of microbial genome data, experimental testing is important to confirm inferences about the cell biology, ecological roles and evolution of microorganisms. As the majority of archaeal and bacterial diversity remains uncultured and poorly characterized, culturing is a priority. The growing interest in and need for efficient cultivation strategies has led to many rapid methodological and technological advances. In this Review, we discuss common barriers that can hamper the isolation and culturing of novel microorganisms and review emerging, innovative methods for targeted or high-throughput cultivation. We also highlight recent examples of successful cultivation of novel archaea and bacteria, and suggest key microorganisms for future cultivation attempts.

Cultivation of elusive microbes unearthed exciting biology

Many newly-discovered microbial phyla have been studied solely by cultivation-independent techniques such as metagenomics. Much of their biology thus remains elusive, because the organisms have not yet been isolated and grown in the lab. Katayama et al. lift the curtain on some intriguing biology by cultivating and studying bacteria from the elusive OP9 phylum (Atribacterota).

New Microbial Biodiversity in Marine Sediments

Microbes in marine sediments represent a large portion of the biosphere, and resolving their ecology is crucial for understanding global ocean processes. Single-gene diversity surveys have revealed several uncultured lineages that are widespread in ocean sediments and whose ecological roles are unknown, and advancements in the computational analysis of increasingly large genomic data sets have made it possible to reconstruct individual genomes from complex microbial communities. Using these metagenomic approaches to characterize sediments is transforming our view of microbial communities on the ocean floor and the biodiversity of the planet. In recent years, marine sediments have been a prominent source of new lineages in the tree of life. The incorporation of these lineages into existing phylogenies has revealed that many belong to distinct phyla, including archaeal phyla that are advancing our understanding of the origins of cellular complexity and eukaryotes. Detailed comparisons of the metabolic potentials of these new lineages have made it clear that uncultured bacteria and archaea are capable of mediating key previously undescribed steps in carbon and nutrient cycling.

Halomonas plays a central role in the syntrophic community of an alkaline oil reservoir with alkali-surfactant-polymer (ASP) flooding

Little is known about the microbial characteristics in oil reservoirs under alkali-surfactant-polymer (ASP)-flooding. In the present study, we collected two ASP-flooding samples and two nearby water-flooding samples from the Daqing oil field and performed 16S rRNA gene sequencing and metagenomic sequencing to fill this knowledge gap. The results indicated that the highly elevated pH resulted in a simple Euryarchaeotal community and a Halomonas &Nitrincola-dominated bacterial community in the production water of the alkaline oil reservoir. In addition, we hypothesized that multiple copies of genes encoding monovalent cation/proton antiporters in Halomonas and Nitrincola, and their facultative anaerobic and movable traits, were the adaptive mechanisms responsible for their competitive growth in the alkaline oil reservoir. We also revealed a unique syntrophic community in the alkaline oil reservoir and identified the central role of Halomonas within it. The present study revealed the microbial characteristics in an alkaline oil reservoir environment formed by ASP-flooding and indicated the application potential of Halomonas in AMP-flooding and microbial enhanced oil recovery (MEOR) technology to elevate the oil recovery rate from ASP-flooded oil reservoirs.

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

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.

Atribacteria Reproducing over Millions of Years in the Atlantic Abyssal Subseafloor

How microbial metabolism is translated into cellular reproduction under energy-limited settings below the seafloor over long timescales is poorly understood. Here, we show that microbial abundance increases an order of magnitude over a 5 million-year-long sequence in anoxic subseafloor clay of the abyssal North Atlantic Ocean. This increase in biomass correlated with an increased number of transcribed protein-encoding genes that included those involved in cytokinesis, demonstrating that active microbial reproduction outpaces cell death in these ancient sediments. Metagenomes, metatranscriptomes, and 16S rRNA gene sequencing all show that the actively reproducing community was dominated by the candidate phylum "Candidatus Atribacteria," which exhibited patterns of gene expression consistent with fermentative, and potentially acetogenic, metabolism. "Ca. Atribacteria" dominated throughout the 8 million-year-old cored sequence, despite the detection limit for gene expression being reached in 5 million-year-old sediments. The subseafloor reproducing "Ca. Atribacteria" also expressed genes encoding a bacterial microcompartment that has potential to assist in secondary fermentation by recycling aldehydes and, thereby, harness additional power to reduce ferredoxin and NAD⁺ Expression of genes encoding the Rnf complex for generation of chemiosmotic ATP synthesis were also detected from the subseafloor "Ca Atribacteria," as well as the Wood-Ljungdahl pathway that could potentially have an anabolic or catabolic function. The correlation of this metabolism with cytokinesis gene expression and a net increase in biomass over the million-year-old sampled interval indicates that the "Ca Atribacteria" can perform the necessary catabolic and anabolic functions necessary for cellular reproduction, even under energy limitation in millions-of-years-old anoxic sediments.IMPORTANCE The deep subseafloor sedimentary biosphere is one of the largest ecosystems on Earth, where microbes subsist under energy-limited conditions over long timescales. It remains poorly understood how mechanisms of microbial metabolism promote increased fitness in these settings. We discovered that the candidate bacterial phylum "Candidatus Atribacteria" dominated a deep-sea subseafloor ecosystem, where it exhibited increased transcription of genes associated with acetogenic fermentation and reproduction in million-year-old sediment. We attribute its improved fitness after burial in the seabed to its capabilities to derive energy from increasingly oxidized metabolites via a bacterial microcompartment and utilize a potentially reversible Wood-Ljungdahl pathway to help meet anabolic and catabolic requirements for growth. Our findings show that "Ca Atribacteria" can perform all the necessary catabolic and anabolic functions necessary for cellular reproduction, even under energy limitation in anoxic sediments that are millions of years old.

Anaerobic Degradation of Paraffins by Thermophilic Actinobacteria under Methanogenic Conditions

Microbial anaerobic alkane degradation is a key process in subsurface oil reservoirs and anoxic environments contaminated with petroleum, with a major impact on global carbon cycling. However, the thermophiles capable of water-insoluble paraffins (>C₁₇) degradation under methanogenic conditions has remained understudied. Here, we established thermophilic (55 °C) n-paraffins-degrading (C₂₁-C₃₀) cultures from an oil reservoir. After over 900 days of incubation, the even-numbered n-paraffins were biodegraded to methane. The bacterial communities are dominated by a novel class-level lineage of actinobacteria, 'Candidatus Syntraliphaticia'. These 'Ca. Syntraliphaticia'-like metagenome-assembled genomes (MAGs) encode a complete alkylsuccinate synthases (ASS) gene operon, as well as hydrogenases and formate dehydrogenase, and several enzymes potentially involved in alkyl-CoA oxidation and the Wood-Ljungdahl pathway. Metatranscriptomic analysis suggests that n-paraffins are activated via fumarate addition reaction, and oxidized into carbon dioxide, hydrogen/formate and acetate by 'Ca. Syntraliphaticia', that could be further converted to methane by the abundant hydrogenotrophic and acetoclastic methanogens. We also found a divergent methyl-CoM reductase-like complex (MCR) and a canonical MCR in two MAGs representing 'Ca. Methanosuratus' (within candidate phylum Verstraetearchaeota), indicating the capability of methane and short-chain alkane metabolism in the oil reservoir. Ultimately, this result offers new insights into the degradability and the mechanisms of n-paraffins under methanogenic conditions at high temperatures.

Long-chain n-alkane biodegradation coupling to methane production in an enriched culture from production water of a high-temperature oil reservoir

Paraffinic n-alkanes (C22–C30), crucial portions of residual oil, are generally considered to be difficult to be biodegraded owing to their general solidity at ambient temperatures and low water solubility, rendering relatively little known about metabolic processes in different methanogenic hydrocarbon-contaminated environments. Here, we established a methanogenic C22–C30 n-alkane-degrading enrichment culture derived from a high-temperature oil reservoir production water. During two-year incubation (736 days), unexpectedly significant methane production was observed. The measured maximum methane yield rate (164.40 μmol L⁻¹ d⁻¹) occurred during the incubation period from day 351 to 513. The nearly complete consumption (> 97%) of paraffinic n-alkanes and the detection of dicarboxylic acids in n-alkane-amended cultures indicated the biotransformation of paraffin to methane under anoxic condition. 16S rRNA gene analysis suggested that the dominant methanogen in n-alkane-degrading cultures shifted from Methanothermobacter on day 322 to Thermoplasmatales on day 736. Bacterial community analysis based on high-throughput sequencing revealed that members of Proteobacteria and Firmicutes exhibiting predominant in control cultures, while microorganisms affiliated with Actinobacteria turned into the most dominant phylum in n-alkane-dependent cultures. Additionally, the relative abundance of mcrA gene based on genomic DNA significantly increased over the incubation time, suggesting an important role of methanogens in these consortia. This work extends our understanding of methanogenic paraffinic n-alkanes conversion and has biotechnological implications for microbial enhanced recovery of residual hydrocarbons and effective bioremediation of hydrocarbon-containing biospheres.

Metabolic potentials of archaeal lineages resolved from metagenomes of deep Costa Rica sediments

Numerous archaeal lineages are known to inhabit marine subsurface sediments, although their distributions, metabolic capacities, and interspecies interactions are still not well understood. Abundant and diverse archaea were recently reported in Costa Rica (CR) margin subseafloor sediments recovered during IODP Expedition 334. Here, we recover metagenome-assembled genomes (MAGs) of archaea from the CR margin and compare them to their relatives from shallower settings. We describe 31 MAGs of six different archaeal lineages (Lokiarchaeota, Thorarchaeota, Heimdallarchaeota, Bathyarcheota, Thermoplasmatales, and Hadesarchaea) and thoroughly analyze representative MAGs from the phyla Lokiarchaeota and Bathyarchaeota. Our analysis suggests the potential capability of Lokiarchaeota members to anaerobically degrade aliphatic and aromatic hydrocarbons. We show it is genetically possible and energetically feasible for Lokiarchaeota to degrade benzoate if they associate with organisms using nitrate, nitrite, and sulfite as electron acceptors, which suggests a possibility of syntrophic relationships between Lokiarchaeota and nitrite and sulfite reducing bacteria. The novel Bathyarchaeota lineage possesses an incomplete methanogenesis pathway lacking the methyl coenzyme M reductase complex and encodes a noncanonical acetogenic pathway potentially coupling methylotrophy to acetogenesis via the methyl branch of Wood-Ljungdahl pathway. These metabolic characteristics suggest the potential of this Bathyarchaeota lineage to be a transition between methanogenic and acetogenic Bathyarchaeota lineages. This work expands our knowledge about the metabolic functional repertoire of marine benthic archaea.

Odor emission and microbial community succession during biogas residue composting covered with a molecular membrane

A membrane-covered composting system was used to investigate the odor emission and microbial community succession during biogas residue composting. Results showed that in comparison with the control (CK) group, the NH₃ and H₂S emissions outside the membrane of the membrane-covered (CT) group decreased by 58.64% and 38.13%, respectively. The nitrogen preservation rate of the CT group was increased by 17.27% in comparison with the CK group. Moreover, the ammonium nitrogen and nitrate nitrogen contents of the CT group were 37.68% and 11.77% higher than those of the CK group, respectively. Microbial analysis showed that the average abundance and co-occurrence rate of ammonification bacteria dominated by Pseudomonas and Bacillus in the CT group were lower than those in the CK group, and the abundance of anaerobic sulfate-reducing bacteria (SRB) dominated by Desulfovibrio in the CT group was higher than that in the CK group.