Microbial diversity and co-occurrence patterns in deep soils contaminated by polycyclic aromatic hydrocarbons (PAHs)

Geng, Shuying; Cao, Wei; Yuan, Jing; Wang, Yingying; Guo, Yanqing; Ding, Aizhong; Zhu, Yi; Dou, Junfeng

doi:10.1016/j.ecoenv.2020.110931

Cited by 73 publications

(30 citation statements)

References 72 publications

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“…4(b)). The results suggested that pH could drive the variation and assembly of microbial communities, which was also demonstrated in previous studies where it was found that pH could be the main factor affecting the structure of bacterial communities in PAH‐contaminated soils 33,34 …”

Section: Resultssupporting

confidence: 82%

“…The results suggested that pH could drive the variation and assembly of microbial communities, which was also demonstrated in previous studies where it was found that pH could be the main factor affecting the structure of bacterial communities in PAH-contaminated soils. 33,34 To further analyze the community composition and structure of the consortia, RDP classifier was used to perform the taxonomic assignments of sequencing tags to different levels. At the phylum level, Proteobacteria was extremely predominant in the microbial consortia, accounting for 97.26% to 99.97% of the total classified sequences (Fig.…”

Section: Community Profiles Of Microbial Consortiamentioning

confidence: 99%

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Bioremediation of petroleum hydrocarbons by alkali–salt‐tolerant microbial consortia and their community profiles

Zhang

Bao

et al. 2020

J of Chemical Tech & Biotech

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BACKGROUND Petroleum hydrocarbon pollution has become a global concern, and seeking an appropriate strategy for treatment of petroleum hydrocarbons is necessary, especially under saline–alkaline conditions. In this study, microbial consortia capable of utilizing low‐molecular‐weight aliphatic petroleum hydrocarbons (n‐decane, n‐dodecane and n‐hexadecane) as the sole carbon source were enriched from crude‐oil‐contaminated soils, and their community profiles were evaluated using high‐throughput sequencing of 16S rRNA gene. RESULTS The microbial consortia were able to degrade 5–100 mL L−1 n‐decane, n‐dodecane and n‐hexadecane by approximately 37.6–97.3%, 52.1–93.2% and 72.4–96.5%, respectively. The consortia also exhibited alkali‐tolerant and moderately salt‐resistant capability, which enabled them to retain high degradation efficiencies of hydrocarbons within a pH range of 7.0–11.0 and salinities of 5–20 g L−1 NaCl. High‐throughput sequencing analysis demonstrated that Pseudomonas, Stenotrophomonas, Achromobacter, Mesorhizobium and Brucella were the core genera (average > 1%) in the consortia, which were more enriched under alkaline condition (pH 11.0). PICRUSt (phylogenetic investigation of communities by reconstruction of unobserved states) prediction revealed a rich set of metabolic functions involved in degradation of hydrocarbons and aromatics, and the critical functional gene, alkane 1‐monooxygenase, was more abundant in the microbial consortia under alkaline condition. CONCLUSIONS The results suggested that these alkali–salt‐tolerant microbial consortia could be a promising candidate for bioremediation of petroleum hydrocarbons. © 2020 Society of Chemical Industry (SCI)

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Section: Resultssupporting

confidence: 82%

Section: Community Profiles Of Microbial Consortiamentioning

confidence: 99%

Bioremediation of petroleum hydrocarbons by alkali–salt‐tolerant microbial consortia and their community profiles

Zhang

Bao

et al. 2020

J of Chemical Tech & Biotech

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“…[70] indicated proficient bioremediation activities. However, the functioning of bacterial community structures and diversity for the complete bioremediation/biodegradation is influenced by hydrocarbon components, nutrients limitation upon competition (TC, TN, TP, and TOM), metabolites produced, soil physicochemical properties, and the compatibility of the mixture during bioremediation [73]. erefore, using the consortium of potential microbes with overall broad catabolic enzymes and genes, biodegradation may become faster, efficient, and complete.…”

Section: Bacterial Community Structure and Diversity/microbialmentioning

confidence: 99%

“…e soil is the most multifaceted environment to harbor various kinds and populations of microorganisms. Its environmental factors (physicochemical properties) are the determinant stimuli for the nature of indigenous microbes, bacterial community, and the composition of functional genes [73]. e soil physicochemical characteristics that show such effect include soil type, region, texture, particle size, maximum water holding capacity (moisture), temperature, nutrient content, oxygen content, and pH [6,91].…”

Section: Soil Characteristicsmentioning

confidence: 99%

Factors Influencing the Bacterial Bioremediation of Hydrocarbon Contaminants in the Soil: Mechanisms and Impacts

Kebede

Tafese

Abda

et al. 2021

Journal of Chemistry

123

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The discharge of hydrocarbons and their derivatives to environments due to human and/or natural activities cause environmental pollution (soil, water, and air) and affect the natural functioning of an ecosystem. To minimize or eradicate environmental pollution by hydrocarbon contaminants, studies showed strategies including physical, chemical, and biological approaches. Among those strategies, the use of biological techniques (especially bacterial biodegradation) is critically important to remove hydrocarbon contaminants. The current review discusses the insights of major factors that enhance or hinder the bacterial bioremediation of hydrocarbon contaminants (aliphatic, aromatic, and polyaromatic hydrocarbons) in the soil. The key factors limiting the overall hydrocarbon biodegradation are generally categorized as biotic factors and abiotic factors. Among various environmental factors, temperature range from 30 to 40°C, pH range from 5 to 8, moisture availability range from 30 to 90%, carbon/nitrogen/phosphorous (C/N/P; 100:20:1) ratio, and 10–40% of oxygen for aerobic degradation are the key factors that show positive correlation for greatest hydrocarbon biodegradation rate by altering the activities of the microbial and degradative enzymes in soil. In addition, the formation of biofilm and production of biosurfactants in hydrocarbon-polluted soil environments increase microbial adaptation to low bioavailability of hydrophobic compounds, and genes that encode for hydrocarbon degradative enzymes are critical for the potential of microbes to bioremediate soils contaminated with hydrocarbon pollutants. Therefore, this review works on the identification of factors for effective hydrocarbon biodegradation, understanding, and optimization of those factors that are essential and critical.

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“…Besides the taxonomic classification, the richness and diversity of the samples can also be estimated (Potts et al, 2019). Co-occurrence of microorganisms in multiple hydrocarbon-contaminated samples suggests their association and microbial networks can be built from co-occurrence studies (Geng et al, 2020;Tikariha and Purohit, 2020;Han et al, 2021). Genes of selected function are also utilized in targeted metagenomics, which narrows the analysis to particular group of microbes and/or a function in the community.…”

Section: Bonifay Et Al 2017mentioning

confidence: 99%

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

et al. 2020

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

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Microbial diversity and co-occurrence patterns in deep soils contaminated by polycyclic aromatic hydrocarbons (PAHs)

Cited by 73 publications

References 72 publications

Bioremediation of petroleum hydrocarbons by alkali–salt‐tolerant microbial consortia and their community profiles

Bioremediation of petroleum hydrocarbons by alkali–salt‐tolerant microbial consortia and their community profiles

Factors Influencing the Bacterial Bioremediation of Hydrocarbon Contaminants in the Soil: Mechanisms and Impacts

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

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