The Greenhouse Phyllosphere Microbiome and Associations with Introduced Bumblebees and Predatory Mites

Abstract

Greenhouses, though highly effective agricultural environments, are characterized by reduced sources of bacterial diversity and means of dispersal compared to more natural settings. As it is known that plant health and productivity are affected by associated bacteria, improving our knowledge on the bacterial communities on greenhouse crops is key to further innovate in horticulture.

Bacterial community structure analysis onListeria monocytogenesinoculated spinach leaves is affected by PCR based methods to exclude chloroplast co-amplification

“…While low bacterial read numbers were no an issue in the current study, the use of pPNA clamps by Legein and colleagues (2022) did not resolve the issue of low bacterial read numbers i.e., 4,394 and 1,282 for strawberry and tomato leaf phyllospheres, respectively. The same authors revealed that bacterial densities were low at approximately 2 to 3 logs cfu g -1 .…”

“…However, similar to the observations of Kim and colleagues (2020), utilisation of PNA clamps did increase recovery of usable bacterial sequences by 5,395 reads belonging to the apple flower phytobiome (Steven et al, 2018). In contrast to Legein and colleagues (2022), nearly all non-bacterial reads belonged to plastid DNA whereas very little were mitochondria. Moreover, the most abundant bacterial OTUs were present in both the PNA clamp and control samples, suggesting utilisation of PNA clamps did not result in bias in reads recovered.…”

“…In the present study, the use of the same pPNA clamp (BLOCK) was highly effective in reducing chloroplast content from 10.93 to 0.26 % (40-fold). An additional study assessing the phyllosphere of tomato and strawberry leaves revealed the total percentage of non-bacterial reads were 96.6% (Legein et al, 2022). Utilising together pPNA and mPNA clamps reduced the percentage of non-bacterial reads to 39.6% while using pPNA alone only reduced the percentage to 81%.…”

“…Thus, due to the specifity of pPNA’s sequence (ggctcaaccctggacag) it has high binding affinity to chloroplast DNA of the selected target hypervariable region and blocks their amplification. pPNA clamps have been previously employed in research on plant based products such as strawberrry and tomato leaves, apple flower phytobiome and the root communities of 32 plant species (Fitzpatrick et al, 2018, Legein et al, 2022, Steven et al, 2018). Although, to our knowledge pPNA clamps have not been used to block the co-amplififcation of chloroplast DNA from the spinach phyllosphere.…”