Biological Control of the Noxious Weed Angled Onion (Allium triquetrum) Thwarted by Endophytic Bacteria in Victoria, Australia

The noxious weed Allium triquetrum (Alliaceae) has invaded widespread areas in southern Australia, forming dense monocultures that threaten indigenous ground flora. Two soilborne biocontrol agents, the fungus Stromatinia cepivora and the bacterium Pectobacterium carotovorum subsp. carotovorum (Pcc) have previously been reported as killing A. triquetrum in gnotobiotic controlled conditions. This study aimed to find why glasshouse pot trials in complex potting media and field trials showed no effect of inoculation with either agent. Bacteria were consistently isolated from inside surface-sterilised bases and bulbs of A. triquetrum. Most bacteria from actively growing plants were closely related to Bacillus but one from dormant bulbs (RPTAtOch1) belonged to Ochrobactrum. Most bacteria reduced soft rot caused by Pcc in vitro by up to 100% when inoculated the day before Pcc. Co-cultivation with Pcc reduced its extracellular pectin lyase and polygalacturonase, which target plant cell walls. RPTAtOch1 was identified as O. quorumnocens by traditional physiological, biochemical and molecular tests, whole genome sequencing and Average Nucleotide Identity comparisons. Its draft genome consisted of 76 contigs, 70% of which were closest to isolate A44 of O. quorumnocens, which antagonises soft rotting of potato by Pcc by destroying its quorum-sensing lactones but, like RPTAtOch1, does not inhibit growth of Pcc. Also, endophytic bacteria inhibited germination of S. cepivora sclerotia and so prevented white rot. Thus, the failure in biocontrol of A. triquetrum by both S. cepivora and Pcc may be due, ironically, to biocontrol of the intended pathogens by endophytic bacteria inside the target weed.