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Spalted heartwood is valued for its vibrant colors, patterns, and decay-free appearance. Using microscopy, scanning electron microscopy with energy-dispersive spectroscopy, transmission electron microscopy, and non-targeted metabolomics, we aimed to study some distinctive features of black patterning. The results showed that cocci might be associated with the production of spalted heartwood. There was an absence of decay in the spalted heartwood because the cocci had not aggressively attacked the cell walls. 4-pyridoxine, often associated with the bacterial stimulation of organisms, was identified as an upregulated metabolite in the black-patterned wood compared to non-colored areas. We identified four primary metabolic pathways related to bacterial activity associated with the black patterning: pentose and glucuronate interconversions, ATP-binding cassette transporters, histidine metabolism, and plant hormone signal transduction. These results suggest that microbes might play a significant role in the development of the heartwood’s distinctive black pattern in  Diospyros  spp.

Microscopic features and untargeted metabolomics reveal special features of the black-patterning in spalted heartwood of Diospyros spp.