Factors Structuring the Epiphytic Archaeal and Fungal Communities in a Semi-arid Mediterranean Ecosystem

The phyllosphere microbiome exerts a strong effect on plants' productivity, and its composition is determined by various factors. To date, most phyllosphere studies have focused on bacteria, while fungi and especially archaea have been overlooked. We studied the effects of plant host and season on the abundance and diversity of the epiphytic archaeal and fungal communities in a typical semi-arid Mediterranean ecosystem. We collected leaves in two largely contrasting seasons (summer and winter) from eight perennial species of varying attributes which could be grouped into the following: (i) high-canopy, evergreen sclerophyllοus shrubs with leathery leaves, and low-canopy, either semi-deciduous shrubs or non-woody perennials with non-leathery leaves, and (ii) aromatic and non-aromatic plants. We determined the abundance of epiphytic Crenarchaea, total fungi, Alternaria and Cladosporium (main airborne fungi) via q-PCR and the structure of the epiphytic archaeal and fungal communities via amplicon sequencing. We observed a strong seasonal effect with all microbial groups examined showing higher abundance in summer. Plant host and season were equally important determinants of the composition of the fungal community consisted mostly of Ascomycota, with Hypocreales dominating in winter and Capnodiales and Pleosporales in summer. In contrast, the archaeal community showed plant host driven patterns dominated by the Soil Crenarchaeotic Group (SCG) and Aenigmarchaeota. Plant habit and aromatic nature exhibited filtering effects only on the epiphytic fungal communities. Our study provides a first in-depth analysis of the key determinants shaping the phyllosphere archaeal and fungal communities of a semi-arid Mediterranean ecosystem.

The response of soil and phyllosphere microbial communities to repeated application of the fungicide iprodione: accelerated biodegradation or toxicity?

Pesticides interact with microorganisms in various ways with the outcome being negative or positive for the soil microbiota. Pesticides' effects on soil microorganisms have been studied extensively in soil but not in other pesticides-exposed microbial habitats like the phyllosphere. We tested the hypothesis that soil and phyllosphere support distinct microbial communities, but exhibit a similar response (accelerated biodegradation or toxicity) to repeated exposure to the fungicide iprodione. Pepper plants received four repeated foliage or soil applications of iprodione, which accelerated its degradation in soil (DT50_1st = 1.23 and DT50_4th = 0.48 days) and on plant leaves (DT50_1st > 365 and DT50_4th = 5.95 days). The composition of the epiphytic and soil bacterial and fungal communities, determined by amplicon sequencing, was significantly altered by iprodione. The archaeal epiphytic and soil communities responded differently; the former showed no response to iprodione. Three iprodione-degrading Paenarthrobacter strains were isolated from soil and phyllosphere. They hydrolyzed iprodione to 3,5-dichloraniline via the formation of 3,5-dichlorophenyl-carboxiamide and 3,5-dichlorophenylurea-acetate, a pathway shared by other soil-derived arthrobacters implying a phylogenetic specialization in iprodione biotransformation. Our results suggest that iprodione-repeated application could affect soil and epiphytic microbial communities with implications for the homeostasis of the plant-soil system and agricultural production.

Isolation and characterization of soil bacteria able to rapidly degrade the organophosphorus nematicide fosthiazate

Foshtiazate is an organophosphorus nematicide commonly used in protected crops and potato plantations. It is toxic to mammals, birds and honeybees, it is persistent in certain soils and can be transported to water resources. Recent studies by our group demonstrated, for the first time, the development of enhanced biodegradation of fosthiazate in agricultural soils. However, the micro-organisms driving this process are still unknown. We aimed to isolate soil bacteria responsible for the enhanced biodegradation of fosthiazate and assess their degradation potential against high concentrations of the nematicide. Enrichment cultures led to the isolation of two bacterial cultures actively degrading fosthiazate. Denaturating Gradient Gel Electrophoresis analysis revealed that they were composed of a single phylotype, identified via 16S rRNA cloning and phylogenetic analysis as Variovorax boronicumulans. This strain showed high degradation potential against fosthiazate. It degraded up to 100 mg l^-1 in liquid cultures (DT₅₀  = 11·2 days), whereas its degrading capacity was reduced at higher concentration levels (500 mg l^-1 , DT₅₀  = 20 days). This is the first report for the isolation of a fosthiazate-degrading bacterium, which showed high potential for use in future biodepuration and bioremediation applications. SIGNIFICANCE AND IMPACT OF THE STUDY: This study reported for the first time the isolation and molecular identification of bacteria able to rapidly degrade the organophosphorus nematicide fosthiazate; one of the few synthetic nematicides still available on the global market. Further tests demonstrated the high capacity of the isolated strain to degrade high concentrations of fosthiazate suggesting its high potential for future bioremediation applications in contaminated environmental sites, considering high acute toxicity and high persistence and mobility of fosthiazate in acidic and low in organic matter content soils.