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Lignin‐modifying processes in the rhizosphere of arid land grasses

Hudson, Corey M., Kirton, Edward, Hutchinson, Miriam I., Redfern, Joanna L., Simmons, Blake, Ackerman, Eric, Singh, Seema, Williams, Kelly P., Natvig, Donald O., Powell, Amy J.
Environmental microbiology 2015 v.17 no.12 pp. 4965-4978
Glomeromycota, arid lands, bacteria, carbon, chemistry, deserts, enzyme activity, gene expression, genes, grasses, lignin, messenger RNA, microbial communities, microbiome, mycorrhizal fungi, open reading frames, peroxidases, polymerase chain reaction, polysaccharides, rhizosphere, ribosomal RNA, root systems, surveys
Genes associated with elevated oxidative enzyme activities in arid systems have not been well characterized. To link measured oxidative activities with specific enzymes, we assembled protein‐coding reads from the rhizospheres (RHZ) of two arid land grasses. Targeted gene scans for open reading frames, encoding genes potentially involved in lignin modification, resulted in 127 distinct assembly products. The putative genes included those significantly similar to Class II secretory fungal peroxidases. These genes are expressed at sufficiently high levels for assembly, annotation and differentiation across experimental conditions, and they demonstrate the interplay of root systems, environment and plant microbiomes. The genes assembled also included copper‐dependent lytic polysaccharide monooxygenases. We detail the enzymes in the host grass RHZs and present a preliminary taxonomic microhabitat characterization. Our findings provide support for biologically mediated Fenton chemistry in the root zones of desert grasses, and provide insight into arid land carbon flow. These results also demonstrate a hyperdiverse microbial community. Both ribosomal RNA and messenger RNA sequences were dominated by bacteria, followed by fungal sequence abundance. Among the notable fungal sequences were those from the members of the arbuscular mycorrhizal fungi (Glomeromycota), which though abundant in this study, we rarely observed in previous PCR‐based surveys.