Comparative genomic analysis of Geosporobacter ferrireducens and its versatility of anaerobic energy metabolism

Co-exposure of microplastics and polychlorinated biphenyls strongly influenced the cycling processes of typical biogenic elements in anoxic soil

The co-exposure of microplastics (MPs) and polychlorinated biphenyls (PCBs) in soil is inevitable, but their combined effect on cycles of typical biogenic elements (e.g. C, N, Fe, S) is still unclear. And the co-exposure of MPs and PCBs caused more severe effects than single exposure to pollution. Therefore, in this study, a 255-day anaerobic incubation experiment was conducted by adding polyethylene microplastics (PE MPs, including 30 ± 10 μm and 500 μm) and PCB138. The presence of PE MPs inhibited the PCB138 degradation. Also, PE MPs addition (1%, w/w) enhanced the methanogenesis, Fe(Ⅲ) reduction, and sulfate reduction while inhibited nitrate reduction and the biodegradation of PCB138. And PCB138 addition (10 mg·kg-1) promoted the methanogenesis and Fe(Ⅲ) reduction, but inhibited sulfate reduction and nitrate reduction. Strikingly, the presence of PE MPs significantly reduced the impact of PCB138 on the soil redox processes. The abundance changes of special microbial communities, including Anaeromyxobate, Geobacter, Bacillus, Desulfitobacterium, Thermodesulfovibrio, Metanobacterium, etc., were consistent with the changes in soil redox processes, revealing that the effect of PE MPs and/or PCB138 on the cycle of typical biogenic elements was mainly achieved by altering the functional microorganisms. This study improves the knowledge of studies on the impact of MPs and combined organic pollutants to soil redox processes, which is greatly important to the stabilization and balance of biogeochemical cycling in ecology.

Iron and total organic carbon shape the spatial distribution pattern of sediment Fe(III) reducing bacteria in a volcanic lake, NE China

Fe(III) reducing bacteria (FeRB) play a vital role in the biogeochemical cycle of Fe, C and N in nature. The volcanic lake can be considered as an ideal habitat for FeRB. Here, we investigated the diversity and spatial distribution of FeRB in sediments of Wenbo lake in Wudalianchi volcano based on culture-dependent and independent methods. A total of 28 isolates affiliated with the genera of Enterobacter, Bacillus, Pseudomonas and Clostridium were obtained from 18 sediment samples. We detected 783 operational taxonomic units (OTUs) belonged to FeRB using high high-throughput sequencing, and the dominant phyla were Proteobacteria (3.65%), Acidobacteria (0.29%), Firmicutes (10.78%). The representative FeRB genera such as Geobacter, Pseudomonas, Thiobacillus and Acinetobacter distributed widely in Wenbo lake. Results showed that the diversity and abundance of FeRB declined along the water-flow direction from Libo to Jingbo. In contrast, the FeRB diversity decreased and the FeRB abundance increased along with depth transect of sediments. It was found that the dominant phylum changed from Firmicutes to Proteobacteria along the water-flow direction, while changed from Proteobacteria to Firmicutes along with the depth of sediments. RDA indicated that the FeRB distribution were driven by soluble total iron, total organic carbon, Fe(II) and Fe(III). These will provide information for understanding the role of FeRB in the elements geochemical cycles in the volcanic environment.

A review on microbial diversity and genetic markers involved in methanogenic degradation of hydrocarbons: futuristic prospects of biofuel recovery from contaminated regions

Microbial activities within oil reservoirs have adversely impacted the world's majority of oil by lowering its quality, thereby increasing its recovery and refining cost. Moreover, conventional method of extraction leaves behind nearly two-thirds of the fossil fuels in the oil fields. This huge potential can be extracted if engineered methanogenic consortium is adapted to convert the hydrocarbons into natural gas. This process involves conversion of crude oil hydrocarbons into methanogenic substrates by syntrophic and fermentative bacteria, which are subsequently utilized by methanogens to produce methane. Microbial diversity of such environments supports the viability of this process. This review illuminates the potentials of abundant microbial groups such as Syntrophaceae, Anaerolineaceae, Clostridiales and Euryarchaeota in petroleum hydrocarbon-related environment, their genetic markers, biochemical process and omics-based bioengineering methods involved in methane generation. Increase in the copy numbers of catabolic genes during methanogenesis highlights the prospect of developing engineered biofuel recovery technology. Several lab-based methanogenic consortia from depleted petroleum reservoirs and microcosm studies so far would not be enough for field application without the advent of multi-omics-based technologies to trawl out the bottleneck parameters of the enhanced fuel recovery process. The adaptability of efficient consortium of versatile hydrocarbonoclastic and methanogenic microorganisms under environmental stress conditions is further needed to be investigated. The improved process might hold the potential of methane extraction from petroleum waste like oil tank and refinery sludge, oil field deposits, etc. What sounds as biodegradation could be a beginning of converting waste into wealth by recovery of stranded energy assets.

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.

Maize straw biochar addition inhibited pentachlorophenol dechlorination by strengthening the predominant soil reduction processes in flooded soil

Biochar has received increasing attention for its multifunctional applications as a soil amendment. The dual effect of biochar on reductive organic pollutants and soil biogeochemical processes under anaerobic environments in parallel has yet to be fully explored. In this study, anaerobic batch experiments were conducted to examine the effect of biochar on both reductive transformation of pentachlorophenol (PCP) and soil redox processes in flooded soil. Compared to biochar-free controls, the reductive dechlorination of PCP was significantly inhibited following biochar addition, with the inhibition degree increased with increasing amount of biochar. Dissimilatory iron and sulfate reduction, as well as the production of methane, were significantly enhanced following biochar addition. The bacterial and archaeal communities showed a functional selection responded to the addition of biochar and PCP, with the core functional groups at the genus level including Dethiobacter, Clostridium, Geosporobacter, Desulfuromonas, Desulfatitalea, and Methanosarcina. These findings indicated that biochar could affect soil microbial redox processes and may act as an electron mediator altering electron distribution from PCP dechlorination to the predominant soil reduction processes, and increase understanding regarding biochar's comprehensive effects on the remediation of natural flooded soil polluted by chlorinated organic pollutants that can be degraded reductively.

Enrichment of Marinobacter sp. and Halophilic Homoacetogens at the Biocathode of Microbial Electrosynthesis System Inoculated With Red Sea Brine Pool

Homoacetogens are efficient CO₂ fixing bacteria using H₂ as electron donor to produce acetate. These organisms can be enriched at the biocathode of microbial electrosynthesis (MES) for electricity-driven CO₂ reduction to acetate. Studies exploring homoacetogens in MES are mainly conducted using pure or mix-culture anaerobic inocula from samples with standard environmental conditions. Extreme marine environments host unique microbial communities including homoacetogens that may have unique capabilities due to their adaptation to harsh environmental conditions. Anaerobic deep-sea brine pools are hypersaline and metalliferous environments and homoacetogens can be expected to live in these environments due to their remarkable metabolic flexibility and energy-efficient biosynthesis. However, brine pools have never been explored as inocula for the enrichment of homacetogens in MES. Here we used the saline water from a Red Sea brine pool as inoculum for the enrichment of halophilic homoacetogens at the biocathode (-1 V vs. Ag/AgCl) of MES. Volatile fatty acids, especially acetate, along with hydrogen gas were produced in MES systems operated at 25 and 10% salinity. Acetate concentration increased when MES was operated at a lower salinity ∼3.5%, representing typical seawater salinity. Amplicon sequencing and genome-centric metagenomics of matured cathodic biofilm showed dominance of the genus Marinobacter and phylum Firmicutes at all tested salinities. Seventeen high-quality draft metagenome-assembled genomes (MAGs) were extracted from the biocathode samples. The recovered MAGs accounted for 87 ± 4% of the quality filtered sequence reads. Genome analysis of the MAGs suggested CO₂ fixation via Wood-Ljundahl pathway by members of the phylum Firmicutes and the fixed CO₂ was possibly utilized by Marinobacter sp. for growth by consuming O₂ escaping from the anode to the cathode for respiration. The enrichment of Marinobacter sp. with homoacetogens was only possible because of the specific cathodic environment in MES. These findings suggest that in organic carbon-limited saline environments, Marinobacter spp. can live in consortia with CO₂ fixing bacteria such as homoacetogens, which can provide them with fixed carbon as a source of carbon and energy.