Widespread pollution of terrestrial ecosystems with petroleum hydrocarbons (PHCs) has generated a need for remediation and, given that many PHCs are biodegradable, bio- and phyto-remediation are often viable approaches for active and passive remediation. This review focuses on phytoremediation with particular interest on the interactions between and use of plant-associated bacteria to restore PHC polluted sites. Plant-associated bacteria include endophytic, phyllospheric, and rhizospheric bacteria, and cooperation between these bacteria and their host plants allows for greater plant survivability and treatment outcomes in contaminated sites. Bacterially driven PHC bioremediation is attributed to the presence of diverse suites of metabolic genes for aliphatic and aromatic hydrocarbons, along with a broader suite of physiological properties including biosurfactant production, biofilm formation, chemotaxis to hydrocarbons, and flexibility in cell-surface hydrophobicity. In soils impacted by PHC contamination, microbial bioremediation generally relies on the addition of high-energy electron acceptors (e.g., oxygen) and fertilization to supply limiting nutrients (e.g., nitrogen, phosphorous, potassium) in the face of excess PHC carbon. As an alternative, the addition of plants can greatly improve bioremediation rates and outcomes as plants provide microbial habitats, improve soil porosity (thereby increasing mass transfer of substrates and electron acceptors), and exchange limiting nutrients with their microbial counterparts. In return, plant-associated microorganisms improve plant growth by reducing soil toxicity through contaminant removal, producing plant growth promoting metabolites, liberating sequestered plant nutrients from soil, fixing nitrogen, and more generally establishing the foundations of soil nutrient cycling. In a practical and applied sense, the collective action of plants and their associated microorganisms is advantageous for remediation of PHC contaminated soil in terms of overall cost and success rates for in situ implementation in a diversity of environments. Mechanistically, there remain biological unknowns that present challenges for applying bio- and phyto-remediation technologies without having a deep prior understanding of individual target sites. In this review, evidence from traditional and modern omics technologies is discussed to provide a framework for plant-microbe interactions during PHC remediation. The potential for integrating multiple molecular and computational techniques to evaluate linkages between microbial communities, plant communities and ecosystem processes is explored with an eye on improving phytoremediation of PHC contaminated sites.

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The Interaction between Plants and Bacteria in the Remediation of Petroleum Hydrocarbons: An Environmental Perspective

Biotransformation of Sulfluramid (N-ethyl perfluorooctane sulfonamide) and dynamics of associated rhizospheric microbial community in microcosms of wetland plants.

Biotransformation of polyfluoroalkyl substances by microbial consortia from constructed wetlands under aerobic and anoxic conditions

The wide application of 6:2 fluorotelomer sulfonate (6:2 FTS) and its precursors results in their ubiquitous occurrence in the environment. This study investigated the biotransformation of 6:2 FTS using fresh slurries collected from constructed wetland under aerobic and anoxic conditions. Biotransformation rates of 6:2 FTS was extremely slow under both aerobic and anoxic conditions. The analysis of transformation products showed that less than 0.7 mol% of initial concentration of 6:2 FTS was biotransformed under anoxic conditions. Effects of 6:2 FTS on the shifts in microbial community in wetland slurry during aerobic and anoxic transformation were evaluated using 16S rRNA gene amplicon sequencing. Under aerobic conditions, 6:2 FTS altered the microbial community structure, in which Methylocaldum (Gamma-proteobacteria) became the predominant genus after being exposed to 6:2 FTS. This means that Methylocaldum appears to have higher tolerance to 6:2 FTS and seems to be potential 6:2 FTS-degrading bacteria. Under anoxic transformation, only the genus Methanomethylovorans (Euryarchaeota) was increased remarkably in wetland slurry exposed to 6:2 FTS.

ABSTRACT Crenothrix polyspora Cohn 1870 and Clonothrix fusca Roze 1896 are two filamentous, sheathed microorganisms exhibiting complex morphological differentiation, whose phylogeny and physiology have been obscure for a long time due to the inability to cultivate them. Very recently, DNA sequencing data from uncultured C. polyspora-enriched material have suggested that Crenothrix is a methane-oxidizing γ-proteobacterium (39). In contrast, the possible ecological function of C. fusca, originally considered a developmental stage of C. polyspora, is unknown. In this study, temporal succession of two filamentous, sheathed microorganisms resembling Cohn's Crenothrix and Roze's Clonothrix was observed by analyzing the microbial community of an artesian well by optical microscopy. Combined culture-based and culture-independent approaches enabled us to assign C. fusca to a novel subgroup of methane-oxidizing γ-proteobacteria distinct from that of C. polyspora. This assignment was supported by (i) methane uptake and assimilation experiments, (ii) ultrastructural data showing the presence in C. fusca cytoplasm of an elaborate membrane system resembling that of methanotrophic γ-proteobacteria, and (iii) sequencing data demonstrating the presence in its genome of a methanol dehydrogenase α subunit-encoding gene (mxaF) and a conventional particulate methane mono-oxygenase α subunit-encoding gene (pmoA) that is different from the unusual pmoA (u-pmoA) of C. polyspora.

Clonothrix fusca (Roze, 1896), a filamentous, sheathed, methanotrophic γ-Proteobacterium

Methane is an important greenhouse gas which is produced from many natural and anthropogenic sources. It plays an important role in overall global warming. A significant amount of methane is removed through microbiological oxidation by methanotrophic bacteria, which are widespread in the environment, including many extreme environments. The key enzyme of these microorganisms, methane monooxygenase (MMO), especially the soluble MMO, is remarkable in its broad substrate specificity. This unique capability, that is, catalyzing reactions of environmental importance, has attracted great attention for applied microbiologists and biochemical engineers. In this article, recent advances in the application of methanotrophs to environmental bioengineering are summarized, including biodiversity, catalytic properties and cultivation, etc. We have focused on two aspects of the application and potential value of methanotrophs in environmental bioengineering, namely methane removal and biodegradation of toxic compounds. The removal of methane produced from landfills has been widely studied, and much of this work can be used as a source of reference for coal mine gas removal. Many bioreactors using methanotrophs in bioremediation have been developed in recent years. These reactors have two forms of configuration, single-stage and multi-stage. Current limitations which may affect the engineering applications of methanotrophs are discussed, such as the lack of suitable methanotrophic isolate, gas transfer limitation, competitive inhibition of MMO, regeneration of reducing equivalents for MMO, and product toxicity.

H. Jiang

Papers

6.22 – Methanotrophs: Multifunctional Bacteria with Promising Applications in Environmental Bioengineering