Antibiotics have been intensively used over the last decades in human and animal therapy and livestock, resulting in serious environmental and public health problems, namely due to the antibiotic residues concentration in wastewaters and to the development of antibiotic-resistant bacteria. This study aimed to access the contribution of some anthropological activities, namely urban household, hospital and a wastewater treatment plant, to the spread of antibiotic resistances in the treated wastewater released into the Mondego River, Coimbra, Portugal. Six sampling sites were selected in the wastewater network and in the river. The ampicillin-resistant Enterobacteriaceae of the water samples were enumerated, isolated and phenotypically characterized in relation to their resistance profile to 13 antibiotics. Some isolates were identified into species level and investigated for the presence of class A and class C -lactamases. Results revealed high frequency of resistance to the -lactam group, cefoxitin (53.5%), amoxicillin/clavulanic acid combination (43.5%), cefotaxime (22.7%), aztreonam (21.3) cefpirome (19.2%), ceftazidime (16.2%) and to the non--lactam group, trimethoprim/sulfamethoxazol (21.1%), tetracycline (18.2%), followed by ciprofloxacin (14.1%). The hospital effluent showed the higher rates of resistance to all antibiotic, except two (chloramphenicol and gentamicin). Similarly, higher resistance rates were detected in the wastewater treatment plant (WWTP) effluent compared with the untreated affluent. Regarding the multidrug resistance, the highest incidence was recorded in the hospital sewage and the lowest in the urban waste. The majority of the isolates altogether are potentially extended-spectrum -lactamases positive (ESBL⁺) (51.9%), followed by AmpC⁺ (44.4%) and ESBL⁺/AmpC⁺ (35.2%). The most prevalent genes among the potential ESBL producers were bla_OXA (33.3%), bla_TEM (24.1%) and bla_CTX-M (5.6%) and among the AmpC producers were bla_EBC (38.9%), bla_FOX (1.9%) and bla_CIT (1.9%). In conclusion, the hospital and the WWTP activities revealed to have the highest contribution to the spread of multidrug resistant bacteria in the study area. Such data is important for future management of the environmental and public health risk of these contaminants. This is the first embracing study in the water network of Coimbra region on the dissemination of antibiotic resistance determinants. Moreover, it is also the first report with the simultaneous detection of multiresistant bacteria producers of AmpC and ESBLs -lactamases in aquatic systems in Portugal.

The exposure of both crop fields and humans to antibiotic-resistant bacteria in animal excreta is an emergent concern of the One Health initiative. This study assessed the contamination of livestock manure from poultry, pig, dairy farms and slaughterhouses in Portugal with resistance determinants. The resistance profiles of 331 Enterobacteriaceae isolates to eight β-lactam (amoxicillin, cefoxitin, cefotaxime, cefpirome, aztreonam, ceftazidime, imipenem and meropenem) and to five non-β-lactam antibiotics (tetracycline (TET), trimethoprim/sulfamethoxazole (SXT), ciprofloxacin (CIP), chloramphenicol (CHL) and gentamicin) was investigated. Forty-nine integron and non-β-lactam resistance genes were also screened for. Rates of resistance to the 13 antibiotics ranged from 80.8% to 0.6%. Multidrug resistance (MDR) rates were highest in pig farm samples (79%). Thirty different integron and resistance genes were identified. These were mainly associated with resistance to CHL (catI and catII), CIP (mainly, qnrS, qnrB and oqx), TET (mainly tet(A) and tet(M)) and SXT (mostly dfrIa group and sul3). In MDR isolates, integron presence and non-β-lactam resistance to TET, SXT and CHL were positively correlated. Overall, a high prevalence of MDR Enterobacteriaceae was found in livestock manure. The high gene diversity for antibiotic resistance identified in this study highlights the risk of MDR spread within the environment through manure use.

During a survey for Trichodoridae in cultivated and natural environments, mainly from southern Spain, 7 new Trichodorus species were found. Four of them, T. andalusicus n. sp., T. asturanus n. sp., T. silvestris n. sp. and T. parasilvestris n. sp., belong to the T. lusitanicus morpho-species group characterised in the male by the slightly ventrally curved spicules with a mid-blade constriction with bristles, and in the female by well developed, rounded triangular to quadrangular, vaginal sclerotised pieces. They were mainly differentiated based upon differences in body length, onchiostyle length, spicule shape and number of ventromedian cervical papillae in the male, and size and shape of the vaginal sclerotised pieces in the female. The presence of the T. lusitanicus morpho-species group with 8 species, apparently endemic to the Iberian Peninsula, could point to a recent speciation event. Additionally, 3 new species, T. onubensis n. sp., T. iliplaensis n. sp. and T. paragiennensis n. sp., more closely resembling the morpho-species group of T. sparsus, to which the Spanish species T. giennensis also belongs, were identified. They were differentiated based on body length, length of onchiostyle and position of the secretory-excretory pore and, in the male, by length and shape of the spicules and number of ventromedian cervical papillae and in the female by the vaginal sclerotised pieces. Molecular support to differentiate the new species using the D2-D3 expansion segments of 28S rDNA is also provided. In addition, a new population of T. variabilis from Greece was studied as well as T. lusitanicus type specimens, and a population of T. giennensis and T. lusitanicus were also sequenced.

Irrigation districts play a decisive role in Portuguese agriculture and require the adaptation to the new water management paradigm through a change in technology and practices compatible with farmers’ technical know-how and economic sustainability. Therefore, improvement of water management, focusing on water savings and increasing farmers’ income, is a priority. In this perspective, an applied research study is being carried out on the gravity-fed Lis Valley Irrigation District to assess the performance of collective water supply, effectiveness of water pumping, and safety of crop production due to the practice of reuse of drainage water. The water balance method was applied at irrigation supply sectors, including gravity and Pumping Irrigation Allocation. The average 2018 irrigation water allocated was 7400 m³/ha, being 9.3% by pumping recharge, with a global efficiency of about 67%. The water quality analysis allowed identifying some risk situations regarding salinization and microbiological issues, justifying action to solve or mitigate the problems, especially at the level of the farmers’ fields, according to the crops and the irrigation systems. Results point to priority actions to consolidate improved water management: better maintenance and conservation of infrastructure of hydraulic infrastructures to reduce water losses and better flow control; implementation of optimal operational plans, to adjust the water demand with distribution; improvement of the on-farm systems with better water application control and maintenance procedures; and improvement of the control of water quality on the water reuse from drainage ditches. The technological innovation is an element of the modernization of irrigation districts that justifies the development of multiple efforts and synergies among stakeholders, namely farmers, water users association, and researchers.

Rice irrigation by continuous flooding is highly water demanding in comparison with most methods applied in the irrigation of other crops, due to a significant deep percolation and surface drainage of paddies. The pollution of water resources and methane emissions are other environmental problems of rice agroecosystems, which require effective agronomic changes to safeguard its sustainable production. To contribute to this solution, an experimental study of alternate wetting and drying flooding (AWD) was carried out in the Center of Portugal in farmer’s paddies, using the methodology of field irrigation evaluation. The AWD results showed that there is a relevant potential to save about 10% of irrigation water with a reduced yield impact, allowing an additional period of about 10 to 29 days of dry soil. The guidelines to promote the on-farm scale AWD automation were outlined, integrating multiple data sources, to get a safe control of soil water and crop productivity. The conclusions point out the advantages of a significant change in the irrigation procedures, the use of water level sensors to assess the right irrigation scheduling to manage the soil deficit and the mild crop stress during the dry periods, and the development of paddy irrigation supplies, to allow a safe and smart AWD.