1. Sphingomonads in Microbe-Assisted Phytoremediation: Tackling Soil Pollution 
Michael Gatheru Waigi, Kai Sun, Yanzheng Gao 
Trends in Biotechnology 
Volume 35, Issue 9, Pages (September 2017)
DOI: /j.tibtech
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2. Figure 1
Taxonomic and Autecological Features and Processes Involved in Intra- and Intercellular (Extracellular) Reactions in Sphingomonad–Plant Interactions During Phytoremediation. Sphingomonads are highly adapted to microbe-assisted phytoremediation. Their flagella can be polar, lateral subpolar, or non-motile to allow movement in the uptake system. They have a chromosome and either one or two plasmids (i.e., a mega plasmid and one or more plasmids) critical to the encoding of genes that show a flexible organization, producing enzymes such as 1-aminocyclopropane-1-carboxylate (ACC) synthase and 1-aminocyclopropane-1-carboxylate deaminase (ACCD), as well as antioxidant enzymes, such as glutathione synthase [62], to induce heavy metal tolerance, as well as for biodegrading genes for the bioremediation of organics in plants. For more details on sphingomonad adaptations in organic bioremediation, refer to [11]. The versatility of sphingomonads allows for various detoxification and containment strategies. For instance, induction of indole-3-acetic acid (IAA) production has a greater impact on the growth of host plants in metal-contaminated soils, because these plants do not have a direct efflux system for heavy metal disposal. IAA production may represent further evidence of plant–sphingomonad interactions in heavy metal-polluted environments, according to two main perspectives. First, the control of 1-aminocyclopropane-1-carboxylic acid oxidase gene expression and the stimulation of ACC synthase gene expression prevent ethylene from acting immediately after IAA production by the plant cells that sphingomonads inhabit, thereby accelerating plant growth and development under metal stress. Second, ACCD enzyme production has no function in bacteria but controls ethylene levels in developing plants, which is a key factor in plant growth.
Trends in Biotechnology  , DOI: ( /j.tibtech )
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3. Figure 2
Plant–Bacterial Associations Found in Soils Involving Sphingomonads. In plant–microbe partnerships involving sphingomonads, the main types of bacterium at the rhizospheric and endospheric levels are free-living [84], rhizospheric [9], and associative [9,39] bacteria, in addition to those involved in endophytic and/or symbiotic interactions [9]. Free-living bacteria (A) aid in the release of extracellular enzymes and exopolysaccharides (EPS) required for the removal of contaminants from soil, which is critical to uptake processes at the root level. Rhizospheric sphingomonads (B) fulfill the dual function of degrading organics and releasing and/or containing inorganics, while being dependent on the extensive root system and uptake mechanism, as well as on root exudates and other rhizodeposits that aid their rhizospheric effect; together, this constitutes an extensive and/or proliferated phytoremediation strategy. Regarding the associative approach (C), the bacteria inhabit intercellular spaces between the internal plant cortex tissue cells. This allows the release of EPS from bacterial cells, which aids the bacteria in phytosiderophore production because they can induce chelation and complexation in the endosphere. Finally, endophytic interactions (D) among sphingomonads facilitate heavy metal disposal within the plant tissue cells, via expulsion from plant and bacterial cells (for both inorganics and organics using EPS, and plant organic acids functioning as attachers in the rhizodeposition removal process) or bioaccumulation into bacterial cells (e.g., microbial chelators, bacterial siderophores, and active efflux transport for inorganics, and enzymatic detoxification for both inorganics and organics). Abbreviations: HMW, high-molecular-weight; LMW, low-molecular-weight; PGPR, plant growth-promoting rhizobacteria.
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4. Figure 3
Phytoremediation Strategies Used by Sphingomonads. Sphingomonads involved in microbe–plant interactions use different phytoremediation strategies in the endosphere and rhizosphere parts of the phytosphere (see Table 1 in the main text). In the rhizosphere [83], the main processes are rhizodegradation and/or phytodegradation and rhizofiltration for organics, and phytostabilization and/or rhizostabilization for inorganics. In the endosphere, the main strategies are phytodegradation for organics and phytoextraction and/or hyperaccumulation for inorganics. Regarding the phyllosphere, although not proven, phytovolatilization of organics may be a viable strategy for bacteria such as sphingomonads, because some of these have been isolated from this part of the phytosphere [81,82]. Questions remain regarding the potential for phytovolatilization and rhizovolatilization using this versatile group. The following points describe the stages of phytoremediation: (i) rhizofiltration and uptake of organic compounds (parent compounds) from the soil before rhizodegradation in the root endosphere by associative and endophytic microbes, such as sphingomonads. This could enable complete mineralization of organics, inducing rhizovolatilization (step v), or incomplete mineralization, leading to step iv; (ii) free-living or rhizospheric bacteria, such as sphingomonads, biodegrade organics (parent compounds) at the soil or rhizoplane level, before uptake of remediated metabolites occurs via symplastic or apoplastic pathways, followed by final endospheric (root and shoot) deposition; (iii) bioavailable metals from the soil undergo uptake via xylem transport or cortex tissue cells, before hyperaccumulation at the root or shoot endosphere level; (iv) for translocated metals, final phytoextraction occurs via storage of excess metals, either in their oxidized forms or attached to plant or bacterial siderophores. For organics, total phytodegradation, enhanced by microbes such as sphingomonads, occurs for rhizofiltrated parent compounds. Meanwhile, final metabolites from the root endosphere and rhizosphere are used by both bacterial and plant cells, entering the tricarboxylic acid cycle and Calvin cycle, respectively (as carbon and energy sources); and (v) although unproven, phytovolatilization may occur at the leaf and phyllosphere levels for organics and volatilized heavy metals capable of translocation to these parts of the plant. For organics, phytovolatilization may occur, allowing evapotranspiration into the atmosphere. Abbreviations: HMW, high-molecular-weight; LMW, low-molecular-weight; PAH, polycyclic aromatic hydrocarbons; PCB, polychlorinated biphenyls; PGPR, plant growth-promoting rhizobacteria; POP, persistent organic pollutants.
Trends in Biotechnology  , DOI: ( /j.tibtech )
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