Metagenomics of African Empogona and Tricalysia (Rubiaceae) reveals the presence of leaf endophytes

Abstract

Background Leaf symbiosis is a phenomenon in which host plants of Rubiaceae interact with bacterial endophytes within their leaves. To date, it has been found in around 650 species belonging to eight genera in four tribes; however, the true extent in Rubiaceae remains unknown. Our aim is to investigate the possible occurrence of leaf endophytes in the African plant genera Empogona and Tricalysia and, if present, to establish their identity. Methods Total DNA was extracted from the leaves of four species of the Coffeeae tribe (Empogona congesta, Tricalysia hensii, T. lasiodelphys, and T. semidecidua) and sequenced. Bacterial reads were filtered out and assembled. Phylogenetic analysis of the endophytes was used to reveal their identity and their relationship with known symbionts. Results All four species have non-nodulated leaf endophytes, which are identified as Caballeronia. The endophytes are distinct from each other but related to other nodulated and non-nodulated endophytes. An apparent phylogenetic or geographic pattern appears to be absent in endophytes or host plants. Caballeronia endophytes are present in the leaves of Empogona and Tricalysia, two genera not previously implicated in leaf symbiosis. This interaction is likely to be more widespread, and future discoveries are inevitable.

Keetia nodulosasp. nov. (Rubiaceae - Vanguerieae) of West - Central Africa: bacterial leaf nodulation discovered in a fourth genus and tribe of Rubiaceae

“…2017). Such endophytic non BLN bacteria occur more widely in genera of Rubiaceae than do BLN and have been reported from two non BLN genera of Coffeeae (Verstraete et al . 2023) and five non BLN genera of the Vanguerieae, but were not found in Keetia species sampled (Verstraete et al .…”

“…Bacterial colonization of leaves without the bacteria being organized into visible leaf structures also occurs, with the bacteria thinly scattered inside the leaf (endophytic) between the mesophyll cells (Verstraete et al 2017). Such endophytic non BLN bacteria occur more widely in genera of Rubiaceae than do BLN and have been reported from two non BLN genera of Coffeeae (Verstraete et al 2023) and five non BLN genera of the Vanguerieae, but were not found in Keetia species sampled (Verstraete et al 2013). Transmission of bacteria between plants is known to be mainly vertical (Pinto-Carbó et al 2018).…”

Keetia nodulosa sp. nov. (Rubiaceae - Vanguerieae) of West-Central Africa: bacterial leaf nodulation discovered in a fourth genus and tribe of Rubiaceae

“…Bacterial colonization of leaves without the bacteria being organized into visible leaf structures also occurs, with the bacteria thinly scattered inside the leaf (endophytic) between the mesophyll cells (Verstraete et al 2017). Such endophytic non BLN bacteria occur more widely in genera of Rubiaceae than do BLN and have been reported from two non BLN genera of Coffeeae (Empogona and Tricalysia) (Verstraete et al 2023) and five non BLN genera of the Vanguerieae, but were not found in Keetia species sampled (Verstraete et al 2013).…”