Adaptive Evolution of Sphingobium hydrophobicum C1T in Electronic Waste Contaminated River Sediment

Abstract

Electronic waste (e-waste) has caused a severe worldwide pollution problem. Despite increasing isolation of degradative microorganisms from e-waste contaminated environments, the mechanisms underlying their adaptive evolution in such habitats remain unclear. Sphingomonads generally have xenobiotic-degrading ability and may play important roles in bioremediation. Sphingobium hydrophobicum C1T, characterized with superior cell surface hydrophobicity, was recently isolated from e-waste contaminated river sediment. To dissect the mechanisms driving its adaptive evolution, we evaluated its stress resistance, sequenced its genome and performed comparative genomic analysis with 19 other Sphingobium strains. Strain C1T can feed on several kinds of e-waste-derived xenobiotics, exhibits a great resistance to heavy metals and possesses a high colonization ability. It harbors abundant genes involved in environmental adaptation, some of which are intrinsic prior to experiencing e-waste contamination. The extensive genomic variations between strain C1T and other Sphingobium strains, numerous C1T-unique genes, massive mobile elements and frequent genome rearrangements reflect a high genome plasticity. Positive selection, gene duplication, and especially horizontal gene transfer drive the adaptive evolution of strain C1T. Moreover, presence of type IV secretion systems may allow strain C1T to be a source of beneficial genes for surrounding microorganisms. This study provides new insights into the adaptive evolution of sphingomonads, and potentially guides bioremediation strategies.

Comparative genomics of the plant-growth promoting bacterium Sphingobium sp. strain AEW4 isolated from the rhizosphere of the beachgrass Ammophila breviligulata

“…Additionally, this strain contains multiple RND efflux outer membrane lipoproteins including CmeA (PSO11242, PSO11927), CmeB (PSO11243, PSO11837), CmeC (PSO13250, PSO09623, PSO11244, PSO11836), as well as a tripartite multidrug resistance operon (PSO13749, PSO13511, PSO13510). The presence of these genes is in line with other species within the Sphingobium genus, which have been isolated from sites with high levels of heavy metal contamination, including strains of S. xenophagum [ 38 ] and S. hydrophobicum [ 49 ].…”

First Study Case of Microbial Biocontrol Agents Isolated from Aquaponics Through the Mining of High-Throughput Sequencing Data to Control Pythium aphanidermatum on Lettuce

“…S. xenophagum and M. fortuitum had never been described as root disease biocontrol agents. The bacterium S. xenophagum can degrade xenobiotic aromatic compounds and is studied for bioremediation of contaminated environments [47,48]. This species was already identified in the lettuce root zone and notably in aquaponics where the genus is among the most abundant ones [49][50][51].…”

The variations of native plasmids greatly affect the cell surface hydrophobicity of sphingomonads

“…Microbial cell surface hydrophobicity (CSH), an important cell surface property, mainly reflects nonspecific adhesion ability and is related to ecological functions and adaptation. Generally, high CSH can enhance adhesion to the surfaces of biological tissues, mineral particles, and artificial materials and increase adsorption capacity for hydrophobic substrates, which therefore promote cell-cell interaction, aggregation, biofilm formation, and substrate utilization ( 1 – 3 ). On the contrary, hydrophilic microbes are likely to disperse and may have high tolerance to hydrophobic chemicals due to little affinity ( 4 , 5 ).…”

“…Sphingobium xenophagum C1 (formerly Sphingobium hydrophobicum ), isolated from the electronic waste (e-waste) contaminated sediment, is the most hydrophobic sphingomonad ever known ( 19 ). It exhibits great resistance to multiple heavy metals and can degrade common organic pollutants, such as phthalate esters, diphenyl ether, biphenyl, and chlorobenzene ( 3 ). Compared with its hydrophilic variant C2 obtained by continuous subculture, it has a higher colonization ability and more adsorption capacity for hydrophobic pollutants ( 3 , 20 ).…”

“…It exhibits great resistance to multiple heavy metals and can degrade common organic pollutants, such as phthalate esters, diphenyl ether, biphenyl, and chlorobenzene ( 3 ). Compared with its hydrophilic variant C2 obtained by continuous subculture, it has a higher colonization ability and more adsorption capacity for hydrophobic pollutants ( 3 , 20 ). The upregulated expression of some outer membrane proteins in strain C1 detected by comparative proteome analysis may be a key hydrophobic factor ( 20 ).…”