Identification and Characterization of a Dominant Sulfolane-Degrading Rhodoferax sp. via Stable Isotope Probing Combined with Metagenomics

A biodegradable chitosan-based polymer for sustained nutrient release to stimulate groundwater hydrocarbon-degrading microflora

Petroleum hydrocarbon-contaminated groundwater often has a low indigenous microorganism population and lacks the necessary nutrient substrates for biodegradation reaction, resulting in a weak natural remediation ability within the groundwater ecosystem. In this paper, we utilized the principle of petroleum hydrocarbon degradation by microorganisms to identify effective nutrients (NaH2PO4, K2HPO4, NH4NO3, CaCl2, MgSO4·7H2O, FeSO4·7H2O, and VB12) and optimize nutrient substrate allocation through a combination of actual surveys of petroleum hydrocarbon-contaminated sites and microcosm experiments. Building on this, combining biostimulation and controlled-release technology, we developed a biodegradable chitosan-based encapsulated targeted biostimulant (i.e., YZ-1) characterized by easy uptake, good stability, controllable slow-release migration, and longevity to stimulate indigenous microflora in groundwater to efficiently degrade petroleum hydrocarbon. Results showed that YZ-1 extended the active duration of nutrient components by 5-6 times, with a sustainable release time exceeding 2 months. Under YZ-1 stimulation, microorganisms grew rapidly, increasing the degradation rate of petroleum hydrocarbon (10 mg L-1) by indigenous microorganisms from 43.03% to 79.80% within 7 d. YZ-1 can easily adapt to varying concentrations of petroleum hydrocarbon-contaminated groundwater. Specifically, in the range of 2-20 mg L-1 of petroleum hydrocarbon, the indigenous microflora was able to degrade 71.73-80.54% of the petroleum hydrocarbon within a mere 7 d. YZ-1 injection facilitated the delivery of nutrient components into the underground environment, improved the conversion ability of inorganic electron donors/receptors in the indigenous microbial community system, and strengthened the co-metabolism mechanism among microorganisms, achieving the goal of efficient petroleum hydrocarbon degradation.

Advances and perspectives of using stable isotope probing (SIP)-based technologies in contaminant biodegradation

Stable isotope probing (SIP) is a powerful tool to study microbial community structure and function in both nature and engineered environments. Coupling with advanced genomics and other techniques, SIP studies have generated substantial information to allow researchers to draw a clearer picture of what is occurring in complex microbial ecosystems. This review provides an overview of the advances of SIP-based technologies over time, summarizes the status of SIP applications to contaminant biodegradation, provides critical perspectives on ecological interactions within the community, and important factors (controllable and non-controllable) to be considered in SIP experimental designs and data interpretation. Current trend and perspectives of adapting SIP techniques for environmental applications are also discussed.

Lower Compositional Variation and Higher Network Complexity of Rhizosphere Bacterial Community in Constructed Wetland Compared to Natural Wetland

Macrophyte rhizosphere microbes, as crucial components of the wetland ecosystem, play an important role in maintaining the function and stability of natural and constructed wetlands. Distinct environmental conditions and management practices between natural and constructed wetlands would affect macrophytes rhizosphere microbial communities and their associated functions. Nevertheless, the understanding of the diversity, composition, and co-occurrence patterns of the rhizosphere bacterial communities in natural and constructed wetlands remains unclear. Here, we used 16S rRNA gene high-throughput sequencing to characterize the bacterial community of the rhizosphere and bulk sediments of macrophyte Phragmites australis in representative natural and constructed wetlands. We observed higher alpha diversity of the bacterial community in the constructed wetland than that of the natural wetland. Additionally, the similarity of bacterial community composition between rhizosphere and bulk sediments in the constructed wetland was increased compared to that of the natural wetland. We also found that plants recruit specific taxa with adaptive functions in the rhizosphere of different wetland types. Rhizosphere samples of the natural wetland significantly enriched the functional bacterial groups that mainly related to nutrient cycling and plant-growth-promoting, while those of the constructed wetland-enriched bacterial taxa with potentials for biodegradation. Co-occurrence network analysis showed that the interactions among rhizosphere bacterial taxa in the constructed wetland were more complex than those of the natural wetland. This study broadens our understanding of the distinct selection processes of the macrophytes rhizosphere-associated microbes and the co-occurrence network patterns in different wetland types. Furthermore, our findings emphasize the importance of plant-microbe interactions in wetlands and further suggest P. australis rhizosphere enriched diverse functional bacteria that might enhance the wetland performance through biodegradation, nutrient cycling, and supporting plant growth.

Comparing the indigenous microorganism system in typical petroleum-contaminated groundwater

The environmental conditions at a contaminated site will impact on the indigenous microbial communities, with implications for the removal of pollutants. An analysis of the characteristics of microbial communities in petroleum-contaminated groundwater can give insights into the relationships between microbial community and environmental factors, and provide guidance about how microbes can be used to remediate and regulate petroleum-contaminated groundwater. This study focuses on two petroleum-contaminated sites in northeast China, the physico-chemical-biological changes in petroleum-contaminated groundwater were analyzed, the response relationship between hydro-chemical indicators and microbial communities was characterized, and the bioindicator that can reflect the petroleum contamination status were established for environmental monitoring and management. The results showed that Proteobacteria was the dominant bacteria in petroleum-contaminated groundwater, with a relative abundance of 42.45%-91.19%. pH, TDS, DO, NO3-, NO2-, SO42-, NH4+, Al, and Mn have significant effects on microbial community. The effect of petroleum pollutants on microbial communities is not only related to the concentration and composition of the pollutants themselves, but also could indirectly affect microbial communities by changing the content of inorganic electron acceptor components such as iron, manganese, sulfate and nitrate in groundwater, and this indirect effect is significantly greater than the direct impact of pollutants on microbial communities. In petroleum-contaminated groundwater, the dominant genera (Polaromonas, Caulobacter) and microbial metabolic functions (methanol oxidation, methylotrophy, ureolysis, and reductive biosynthesis) of the indigenous microbial community can be used as bioindicators to indicate petroleum contamination status. The higher abundance of these bioindicators in petroleum-contaminated groundwater, the more serious petroleum pollution in groundwater.

Microaerobic enrichment of benzene-degrading bacteria and description of Ideonella benzenivorans sp. nov., capable of degrading benzene, toluene and ethylbenzene under microaerobic conditions

In the present study, the bacterial community structure of enrichment cultures degrading benzene under microaerobic conditions was investigated through culturing and 16S rRNA gene Illumina amplicon sequencing. Enrichments were dominated by members of the genus Rhodoferax followed by Pseudomonas and Acidovorax. Additionally, a pale amber-coloured, motile, Gram-stain-negative bacterium, designated B7^T was isolated from the microaerobic benzene-degrading enrichment cultures and characterized using a polyphasic approach to determine its taxonomic position. The 16S rRNA gene and whole genome-based phylogenetic analyses revealed that strain B7^T formed a lineage within the family Comamonadaceae, clustered as a member of the genus Ideonella and most closely related to Ideonella dechloratans CCUG 30977^T. The sole respiratory quinone is ubiquinone-8. The major fatty acids are C_16:0 and summed feature 3 (C_16:1ω7c/iso-C_15:0 2-OH). The DNA G + C content of the type strain is 68.8 mol%. The orthologous average nucleotide identity (OrthoANI) and in silico DNA–DNA hybridization (dDDH) relatedness values between strain B7^T and closest relatives were below the threshold values for species demarcation. The genome of strain B7^T, which is approximately 4.5 Mb, contains a phenol degradation gene cluster, encoding a multicomponent phenol hydroxylase (mPH) together with a complete meta-cleavage pathway including a I.2.C-type catechol 2,3-dioxygenase (C23O) gene. As predicted by the genome, the type strain is involved in aromatic hydrocarbon-degradation: benzene, toluene and ethylbenzene are degraded aerobically and also microaerobically as sole source of carbon and energy. Based on phenotypic characteristics and phylogenetic analysis, strain B7^T is a member of the genus Ideonella and represents a novel species for which the name Ideonella benzenivorans sp. nov. is proposed. The type strain of the species is strain B7^T (= LMG 32,345^T = NCAIM B.02664^T).

Remediation of soil polluted with petroleum hydrocarbons and its reuse for agriculture: Recent progress, challenges, and perspectives

Petroleum hydrocarbons (PHs) are used as raw materials in many industries and primary energy sources. However, excessive PHs act as soil pollutants, posing serious threats to living organisms. Various ex-situ or in-situ chemical and biological methods are applied to restore polluted soil. However, most of the chemical treatment methods are expensive, environmentally unfriendly, and sometimes inefficient. That attracts scientists and researchers to develop and select new strategists to remediate polluted soil through risk-based analysis and eco-friendly manner. This review discusses the sources of PHs, properties, distribution, transport, and fate in the environment, internal and external factors affecting the soil remediation and restoration process, and its effective re-utilization for agriculture. Bioremediation is an eco-friendly method for degrading PHs, specifically by using microorganisms. Next-generation sequencing (NGS) technologies are being used to monitor contaminated sites. Currently, these new technologies have caused a paradigm shift by giving new insights into the microbially mediated biodegradation processes by targeting rRNA are discussed concisely. The recent development of risk-based management for soil contamination and its challenges and future perspectives are also discussed. Furthermore, nanotechnology seems very promising for effective soil remediation, but its success depends on its cost-effectiveness. This review paper suggests using bio-electrochemical systems that utilize electro-chemically active microorganisms to remediate and restore polluted soil with PHs that would be eco-friendlier and help tailor-made effective and sustainable remediation technologies.

Distribution of a Sulfolane-Metabolizing Rhodoferax sp. Throughout a Contaminated Subarctic Aquifer and Two Groundwater Treatment Systems

An extensive plume of the emerging contaminant sulfolane has been found emanating from a refinery in Interior Alaska, raising questions about the microbial potential for natural attenuation and bioremediation in this subarctic aquifer. Previously, an aerobic sulfolane-assimilating Rhodoferax sp. was identified from the aquifer using stable isotope probing. Here, we assessed the distribution of known sulfolane-assimilating bacteria throughout the contaminated subarctic aquifer using 16S-rRNA-amplicon analyses of ~100 samples collected from groundwater monitoring wells and two groundwater treatment systems. One treatment system was an in situ air sparging system where air was injected directly into the aquifer. The other was an ex situ granular activated carbon (GAC) filtration system for the treatment of private well water. We found that the sulfolane-assimilating Rhodoferax sp. was present throughout the aquifer but was significantly more abundant in groundwater associated with the air sparge system. The reduction of sulfolane concentrations combined with the apparent enrichment of sulfolane degraders in the air sparging zone suggests that the addition of oxygen facilitated sulfolane biodegradation. To investigate other environmental controls on Rhodoferax populations, we also examined correlations between groundwater geochemical parameters and the relative abundance of the Rhodoferax sp. and found only manganese to be significantly positively correlated. The sulfolane-assimilating Rhodoferax sp. was not a major component of the GAC filtration system, suggesting that biodegradation is not an important contributor to sulfolane removal in these systems. We conclude that air sparging is a promising approach for enhancing the abundance and activity of aerobic sulfolane-degraders like Rhodoferax to locally stimulate sulfolane biodegradation in situ.

Impact of microecological agents on water environment restoration and microbial community structures of trench system in a Baiyangdian wetland ecosystem

AIMS

To evaluate effect of periodic application of effective microorganisms (EM) bacteria and calcium peroxide on water environment restoration of a trench wetland ecosystem and its impact on microbiota in water and sediment.

METHODS AND RESULTS

The EM bacteria and calcium peroxide were alternately sprayed into the trench water and changes in the physicochemical indices of water and sediment, and in microbiota structure were subsequently investigated. Alternately spraying of calcium peroxide and EM bacteria improved the water quality, especially in terms of the dissolved oxygen and transparency of water body, and could further reduce the levels of total nitrogen, total phosphorus, and ammonia nitrogen. At the same time, the microbiota structure of the water body was significantly changed by spraying with calcium peroxide and EM bacteria, and the relative abundances of Pseudanabaena, Legionellaceae, Planktothrix, Planctomyces, Phenylobacterium, Rhodobacter, Rhodoferax, and Aquirestis were significantly increased. However, there was no significant effect on the physicochemical indexes and microbiota composition of the sediment.

CONCLUSIONS

The water quality of the Baiyangdian trench could be significantly restored by regular sprinkling of calcium peroxide and EM bacteria.

SIGNIFICANCE AND IMPACT OF STUDY

The results provide an effective technical method for the restoration of trench wetland water.

Beneficial microbiomes for bioremediation of diverse contaminated environments for environmental sustainability: present status and future challenges

Over the past few decades, the rapid development of agriculture and industries has resulted in contamination of the environment by diverse pollutants, including heavy metals, polychlorinated biphenyls, plastics, and various agrochemicals. Their presence in the environment is of great concern due to their toxicity and non-biodegradable nature. Their interaction with each other and coexistence in the environment greatly influence and threaten the ecological environment and human health. Furthermore, the presence of these pollutants affects the soil quality and fertility. Physicochemical techniques are used to remediate such environments, but they are less effective and demand high costs of operation. Bioremediation is an efficient, widespread, cost-effective, and eco-friendly cleanup tool. The use of microorganisms has received significant attention as an efficient biotechnological strategy to decontaminate the environment. Bioremediation through microorganisms appears to be an economically viable and efficient approach because it poses the lowest risk to the environment. This technique utilizes the metabolic potential of microorganisms to clean up contaminated environments. Many microbial genera have been known to be involved in bioremediation, including Alcaligenes, Arthrobacter, Aspergillus, Bacillus, Burkholderia, Mucor, Penicillium, Pseudomonas, Stenotrophomonas, Talaromyces, and Trichoderma. Archaea, including Natrialba and Haloferax, from extreme environments have also been reported as potent bioresources for biological remediation. Thus, utilizing microbes for managing environmental pollution is promising technology, and, in fact, the microbes provide a useful podium that can be used for an enhanced bioremediation model of diverse environmental pollutants.

The key active degrader, metabolic pathway and microbial ecology of triclosan biodegradation in an anoxic/oxic system

A lab-scale anoxic/oxic (A/O) system was used to reveal the key active triclosan-degrading bacteria (TCS-DB) in this study. The results showed that TCS was mainly removed by metabolism of heterotrophic bacteria (accounting for about 62%), and the potential metabolic pathway was the break of ether bond in TCS formed 2,4-dichlorophenol, and further dechlorination formed phenol or other metabolic end products. DNA-based stable isotope probing (DNA-SIP) assay further revealed that Methylobacillus accounting for 20.75% in ¹³C sample was the key active TCS-DB. Furthermore, methylotrophy and methanol oxidation were found to be the potential metabolic routes of TCS degradation by functional annotation of prokaryotic taxa analysis. Interestingly, TCS accelerated the propagation of antibiotic resistance genes (fabI) and intI1 which positively correlated with several functional microorganisms (p < 0.05). This study contributes to comprehend the potential mechanism, metabolic pathway and microbial ecology of TCS biodegradation in A/O system.

Genome analysis provides insights into microaerobic toluene-degradation pathway of Zoogloea oleivorans BucT

Zoogloea oleivorans, capable of using toluene as a sole source of carbon and energy, was earlier found to be an active degrader under microaerobic conditions in aquifer samples. To uncover the genetic background of the ability of microaerobic toluene degradation in Z. oleivorans, the whole-genome sequence of the type strain Buc^T was revealed. Metatranscriptomic sequence reads, originated from a previous SIP study on microaerobic toluene degradation, were mapped on the genome. The genome (5.68 Mb) had a mean G + C content of 62.5%, 5005 protein coding gene sequences and 80 RNA genes. Annotation predicted that 66 genes were involved in the metabolism of aromatic compounds. Genome analysis revealed the presence of a cluster with genes coding for a multicomponent phenol-hydroxylase system and a complete catechol meta-cleavage pathway. Another cluster flanked by mobile-element protein coding genes coded a partial catechol meta-cleavage pathway including a subfamily I.2.C-type extradiol dioxygenase. Analysis of metatranscriptomic data of a microaerobic toluene-degrading enrichment, containing Z .  oleivorans as an active-toluene degrader revealed that a toluene dioxygenase-like enzyme was responsible for the ring-hydroxylation, while enzymes of the partial catechol meta-cleavage pathway coding cluster were responsible for further degradation of the aromatic ring under microaerobic conditions. This further advances our understanding of aromatic hydrocarbon degradation between fully oxic and strictly anoxic conditions.

Current Status and Potential Applications of Underexplored Prokaryotes

Thousands of prokaryotic genera have been published, but methodological bias in the study of prokaryotes is noted. Prokaryotes that are relatively easy to isolate have been well-studied from multiple aspects. Massive quantities of experimental findings and knowledge generated from the well-known prokaryotic strains are inundating scientific publications. However, researchers may neglect or pay little attention to the uncommon prokaryotes and hard-to-cultivate microorganisms. In this review, we provide a systematic update on the discovery of underexplored culturable and unculturable prokaryotes and discuss the insights accumulated from various research efforts. Examining these neglected prokaryotes may elucidate their novelties and functions and pave the way for their industrial applications. In addition, we hope that this review will prompt the scientific community to reconsider these untapped pragmatic resources.