Land plants are engaged in intricate communities with soil bacteria and fungi indispensable for plant survival and growth. The plant-microbial interactions are largely governed by specific metabolites. We employed a combination of lipid-fingerprinting, enzyme activity assays, high-throughput DNA sequencing and isolation of cultivable microorganisms to uncover the dynamics of the bacterial and fungal community structures in the soil after exposure to isothiocyanates (ITC) obtained from rapeseed glucosinolates. Rapeseed-derived ITCs, including the cyclic, stable goitrin, are secondary metabolites with strong allelopathic affects against other plants, fungi and nematodes, and in addition can represent a health risk for human and animals. However, the effects of ITC application on the different bacterial and fungal organisms in soil are not known in detail. ITCs diminished the diversity of bacteria and fungi. After exposure, only few bacterial taxa of the Gammaproteobacteria, Bacteriodetes and Acidobacteria proliferated while Trichosporon (Zygomycota) dominated the fungal soil community. Many surviving microorganisms in ITC-treated soil where previously shown to harbor plant growth promoting properties. Cultivable fungi and bacteria were isolated from treated soils. A large number of cultivable microbial strains was capable of mobilizing soluble phosphate from insoluble calcium phosphate, and their application to Arabidopsis plants resulted in increased biomass production, thus revealing growth promoting activities. Therefore, inclusion of rapeseed-derived glucosinolates during biofumigation causes losses of microbiota, but also results in enrichment with ITC-tolerant plant microorganisms, a number of which show growth promoting activities, suggesting that Brassicaceae plants can shape soil microbiota community structure favoring bacteria and fungi beneficial for Brassica plants.

Plant metabolites can shape the microbial community composition in the soil. Two indole metabolites, benzoxazolinone (BOA) and gramine, produced by different Gramineae species, and quercetin, a flavonoid synthesized by many dicot species, were studied for their impacts on the community structure of field soil bacteria. The three plant metabolites were directly added to agricultural soil over a period of 28 days. Alterations in bacterial composition were monitored by next generation sequencing of 16S rRNA gene PCR products and phospholipid fatty acid analysis. Treatment of the soil with the plant metabolites altered the community composition from phylum to amplicon sequence variant (ASV) level. Alpha diversity was significantly reduced by BOA or quercetin, but not by gramine. BOA treatment caused a decrease of the relative abundance of 11 ASVs, while only 10 ASVs were increased. Gramine or quercetin treatment resulted in the increase in relative abundance of many more ASVs (33 or 38, respectively), most of them belonging to the Proteobacteria. Isolation and characterization of cultivable bacteria indicated an enrichment in Pseudarthrobacter or Pseudomonas strains under BOA/quercetin or BOA/gramine treatments, respectively. Therefore, the effects of the treatments on soil bacteria were characteristic for each metabolite, with BOA exerting a predominantly inhibitory effect, with only few genera being able to proliferate, while gramine and quercetin caused the proliferation of many potentially beneficial strains. As a consequence, BOA or gramine biosynthesis, which have evolved in different barley species, is accompanied with the association of distinct bacterial communities in the soil, presumably after mutual adaptation during evolution.

Benzoxazinoids, secondary metabolites of several Poaceae, and some benzoxazinoid downstream metabolites are bioactive compounds that act as allelochemicals and natural pesticides. Since a short lifetime of the substances is crucial to avoid long-term environmental effects, total degradation by microorganisms is of exceptional importance. We performed a screening with cultivable microorganisms (Species names and strain numbers: Mycobacterium fortuitum, 7; Bacillus aryabhattai, 34; Bacillus cereus, 59; Bacillus megaterium, 21, 48; Bacillus methylotrophicus, 58; Lysinibacillus xylanilyticus, 56; Paenibacillus polymyxa, 51; Aminobacter aminovorans, 49; the fungi Papulaspora sepedonioides, 12 and Trichoderma viride, 47) isolated from soil previously used for wheat and Persian clover mixed-culture systems to assess their behavior in the presence of the compounds. The microorganisms were exposed to glucosylated benzoxazinones, the benzoxazinones HBOA, DIBOA, and DIMBOA, the benzoxazolinones BOA, BOA-6-OH, and MBOA, and to several downstream products (AP, AAP, oHPMA, glucoside carbamate) in liquid culture to avoid interferences with soil minerals and other organisms. The microorganisms differed strongly in their metabolic activities in terms of growth, compound modification, and degradation. We observed degradation with DIBOA and GDIMBOA but rarely with DIMBOA, whereas BOA and MBOA showed almost no degradation when directly applied. Hydroxylation of BOA and demethylation of MBOA by the plant, resulting in BOA-6-OH, activated the benzoxazolinones for bacterial nitration. The resulting NBOA-6-OH was short-lived but could function temporarily as an allelochemical by inhibiting photosynthesis, e.g., in young seedlings of cress and kohlrabi. The BOA downstream products AP and oHPMA were converted to AAP, which can be nitrated to N-(2-OH-5-nitrophenyl)-acetamide and then degraded by A. aminovorans (49) and P. polymyxa (51). Only P. sepedonioides (12) and P. polymyxa (51) failed in the conversion of HBOA into AAP. While DIBOA, DIMBOA, MBOA, NBOA-6-OH, AP, AAP, and oHPMA reduced the growth of most microorganisms, glucoside carbamate promoted their growth. GDIMBOA had a stimulatory effect toward the fungi and three bacterial species. These findings lead to the hypothesis that in a natural habitat, such as the root surface, microorganisms may cooperate, perhaps by involving the plant, for the successful elimination of benzoxazinoids and their downstream metabolites.

6-Methoxy-benzoxazolin-2(3H)-one (MBOA) is a degradation product derived from 2,4-Dihydroxy-7-methoxy-2H-1,4-benzoxazin-3(4H)-one (DIMBOA), one of the bioactive compounds found e.g., in maize. Here we present hitherto unknown 6-methoxy-4-nitro-benzoxazolin-2(3H)-one (NMBOA) produced in Czapek medium by Pantoea ananatis (Enterobacteriaceae). P. ananatis is a member of a microbial consortium dominated by the zygomycete Actinomucor elegans, which was isolated from roots of Abutilon theophrasti. NMBOA was identified by NMR spectra and HR-ESI-MS analyses, revealing an unusual position of the nitro group at C-4. Nitration of MBOA initiates the degradation of the compound that is almost completed within three days by the entire consortium and isolated P. ananatis. The yeast Papiliotrema baii, another member of the consortium, is unable to degrade NMBOA but stored it at the surface of its polysacchararide capsule. NMBOA has negative effects on microbial growth in liquid medium whereas seedlings of Brassica oleracea var. gongylodes L. (kohlrabi) or Lepidium sativum (cress) are not impaired up to 500 µM. Degradation via nitration may be important to understand the behavior of microbial species and effects of microbiomes when exposed to MBOA.

Numerous allelopathic plant secondary metabolites impact plant-microorganism interactions by injuring plant-associated beneficial bacteria and fungi. Fungi belonging to the genus Trichoderma positively influence crops, including benzoxazinonecontaining maize. However, benzoxazinones and their downstream metabolites such as benzoxazolinone and phenoxazinones are often fungitoxic. Specimen Trichoderma viride F-00612 was found to be insensitive to 100-µM phenoxazinone and 500-µM benzoxazolinone. Screening of 46 additional specimens of ascomycetes revealed insensitivity to phenoxazinones among fungi that cause disease in benzoxazinone-producing cereal crops, whereas many other ascomycetes were highly sensitive. In contrast, most of the screened fungi were insensitive to benzoxazolinone. T. viride F-00612 was associated with bacteria and, thus, existed as a consortium. By contrast, Enterobacter species and Acinetobacter calcoaceticus were prominent in the original specimen, and Bacillus species predominated after antibiotic application. Prolonged cultivation of T. viride F-00612 in liquid medium and on Czapek agar in the presence of < 100 µM phenoxazinone and < 500 µM benzoxazolinone resulted in a massive loss of bacteria accompanied by impacted fungal growth in the presence of phenoxazinone. The original consortium was actively involved in implementing metabolic sequences for the degradation and detoxification of nitrated benzoxazolinone derivatives. The 2-aminophenol was rapidly converted into acetamidophenol, but benzoxazolinone, methoxylated benzoxazolinone, and picolinic acid remained unchanged. Excluding phenoxazinone, none of the tested compounds markedly impaired fungal growth in liquid culture. In conclusion, members of the T. viride F-00612 consortium may contribute to the ability to manage benzoxazinone downstream products and facilitate BOA-6-OH degradation via nitration.