Resumen de Influence of agricultural practices on the microbiome and the antibiotic resistance gene complement in soils, plants, and crops
Francisco Diogo De Almeida Cerqueira
Antibiotic (AB) Resistance is an increasing global problem for public health, with multi-resistant bacteria persisting and spreading not only in clinical settings but also in the environment. One of the possible vectors of this spread is the use and re-use of waste water (WW) and of manure and sludge from WW treatment plants (WWTPs) in different agriculture practices (irrigation, soil amendment). These practices are becoming widespread in regions with scarcity of water. WWTPs are known as AB resistance hotspots, whereas soil amendment by organic fertilization is known to increase AB resistance in the soil microbiomes. Hence, there is a growing concern about the possible transmission of AB resistance from agricultural soils to crops and, ultimately, to the microbiomes of consumers' guts. In this Thesis, this issue was assessed in commercial fields producing vegetable crops. This strategy allowed us to analyze AB resistance elements in foodstuffs actually reaching the consumers, and to understand the risk their consumption poses. Moreover, this Thesis tackles the alterations in soil, plant and crops bacterial communities due to these agricultural practices. To achieve this, five agricultural fields located in the area of Barcelona (NE Spain) were selected, under different irrigation regimes and soil amendment. The selected crops were lettuce, tomatoes, and broad beans as they represent vegetables with different edible parts, commonly eaten either raw or beans, as cooked. The Thesis is divided into five chapters. Chapter I describes the state of the art of the studies of ABR in food and agricultural fields and presents the objectives of the PhD project. Chapter II and III assess the distribution of ARGs and microbiomes along the soil-plant continuum in Lycopersicum esculentum and, grown in peri-urban and rural agricultural fields under different irrigation regimes and soil amendment. Our data show that field practices influenced the distribution of ARGs and intI1 along the soil-plant continuum in both cases, although the impact on soil and plant microbiomes differed between the two crops. In tomatoes, few abundant bacterial families discriminated the different agricultural fields, including Pseudomonadaceae and Enterobacteriaceae. The predominance of Pseudomonadacea correlated positively with the levels of intI1, blaTEM, blaOXA-58 and sul1 detected in the fruits. In contrast, microbiomes from broad bean plant parts (beans, leaves, roots) were dominated by Rhizobiales, whose predominance inversely correlated with intl1 and ARGs abundances. We concluded that Rhizobiales limits the translocation of ARGs into the crops, as well as the colonization of roots and plant parts by other bacteria. Chapter IV integrates the data from the distribution and abundance of the ARGs in different model crops. The results obtained from the different soils and crops showed that ARGs were detected in all plant compartments, with highest loads in roots and lowest in fruits or beans. ARGs profiles within the crops reflect the soil ARG composition. The analyses also showed positive correlations between certain soil taxa and ARG profiles. The crop type revealed to be determinant for both ARG distribution and microbiome composition. Irrigation water appeared to have a limited influence, suggesting that the soil amendment practices were determinants on ARG distribution and on their abundance in edible crop parts. Chapter V presents a general discussion of the results showed previously, followed in Chapter VI including the main conclusions of the Thesis.
