Volume 29, Issue 8 pp. 2472-2484
RESEARCH ARTICLE
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Antibiotics and microbial resistance in Brazilian soils under manure application

Marilia Camotti Bastos

Corresponding Author

Marilia Camotti Bastos

Universidade Federal de Santa Maria, Cidade Universitária, Prédio 42, sala 3308, Av. Roraima no. 1000, Bairro Camobi, Santa Maria, RS CEP 97105-900 Brazil

Université de Poitiers, IC2MP UMR 7285 ENSI Poitiers Bâtiment B16 7, rue Marcel Doré TSA 41105 86073 Poitiers Cedex 9, France

Correspondence

M. C. Bastos, Universidade Federal de Santa Maria, Prédio 42, sala 3308, Av. Roraima no. 1000, Cidade Universitária, Bairro Camobi, Santa Maria, RS CEP 97105-900, Brazil.

Email: [email protected]

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Danilo Rheinheimer dos Santos

Danilo Rheinheimer dos Santos

Universidade Federal de Santa Maria, Cidade Universitária, Prédio 42, sala 3308, Av. Roraima no. 1000, Bairro Camobi, Santa Maria, RS CEP 97105-900 Brazil

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Élodie Aubertheau

Élodie Aubertheau

Université de Poitiers, IC2MP UMR 7285 ENSI Poitiers Bâtiment B16 7, rue Marcel Doré TSA 41105 86073 Poitiers Cedex 9, France

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José Augusto Monteiro de Castro Lima

José Augusto Monteiro de Castro Lima

Instituto Federal de Educação Ciência e Tecnologia - Alagoas, Câmpus Maragogi, Rodovia Arnon de Melo, AL 101 Norte, S/N Atemar de Barros 56304205 - Maragogi, AL, Brasil

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Thibaut Le Guet

Thibaut Le Guet

Université de Poitiers, IC2MP UMR 7285 ENSI Poitiers Bâtiment B16 7, rue Marcel Doré TSA 41105 86073 Poitiers Cedex 9, France

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Laurent Caner

Laurent Caner

Université de Poitiers, IC2MP UMR 7285 ENSI Poitiers Bâtiment B16 7, rue Marcel Doré TSA 41105 86073 Poitiers Cedex 9, France

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Leslie Mondamert

Leslie Mondamert

Université de Poitiers, IC2MP UMR 7285 ENSI Poitiers Bâtiment B16 7, rue Marcel Doré TSA 41105 86073 Poitiers Cedex 9, France

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Jérôme Labanowski

Jérôme Labanowski

Université de Poitiers, IC2MP UMR 7285 ENSI Poitiers Bâtiment B16 7, rue Marcel Doré TSA 41105 86073 Poitiers Cedex 9, France

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First published: 14 April 2018
Citations: 45

Abstract

Animal manure is commonly used in agriculture as fertiliser. This practice could represent, however, a risk of soil degradation through the accumulation of pharmaceutical residues or resistant microorganisms. Thus, 12 pharmaceuticals (11 antibiotics and 1 nonsteroidal anti-inflammatory drug) were quantified in soil samples from 15 sites regularly fertilised with different animal manures (dairy cow, pig or poultry litter manure) and from forest sites in southern Brazil. This study (a) investigated the impacts of Brazilian animal waste application on antibiotic levels and induced bacterial resistance of soils and (b) determined whether one type of waste is more polluting than others. Three bacterial resistance genes, namely, sul1, qnr A, and erm, were also quantified to determine the impacts of manure application on the resistance of soil microbial communities. The effect of manure application was confirmed by the presence of antibiotic residues (up to 38.3 μg kg−1) and bacterial resistance modifications of the bacterial community (up to 8.97 × 10−3 copies of genes per bacteria) in the studied soils. Soils amended with pig manure presented the highest antibiotic concentrations. However, soils subjected to dairy cow grazing over long periods of time presented the highest concentrations of sulfonamide resistance gene (sul1). Our results lead us to infer that the type of manure can induce a “specific pollution fingerprint.”

1 INTRODUCTION

Veterinary pharmaceuticals with specific chemical and physical properties are available on the market (Thiele-Bruhn, 2003). These products are administered to animals around the world for the prevention, diagnosis, cure, or treatment of different diseases (Aitken, Dilworth, Heil, Pharm, & Nailor, 2016). In Brazil, the Ministry of Agriculture is in charge of the inspection and regularisation of 6,652 veterinary pharmaceuticals authorised for commercialisation. The most consumed products are antibiotics and drugs against ectoparasites (Regitano & Leal, 2010). In 2010 and 2011, cattle, pig and poultry farms contributed more than 90% to the Brazilian national meat production, and in the southern region of Brazil, more than 80% of the medicines marketed in the Country were applied. Thus, the intensive use of pharmaceuticals in the south of Brazil is linked to a high animal production (Sidan, 2017).

Via metabolic processes, 30% to 90% of the ingested dose is eliminated in urine and faeces (Rang, Dale, Ritter, & Flower, 2007). Therefore, manure application represents an important gateway of pharmaceuticals into the environment. The various treatments and husbandry methods influence the quantities and the forms of pharmaceuticals (metabolites and unchanged active molecules) brought into soils (Boxall, Kolpin, Holling-Sørensen, & Tolls, 2003; Veterinary International Conference on Harmonization, 2011). About 70% to 80% of administered compounds are released into the environment via the application of animal manure (Halling-Sørensen, 2001).

Manure application is an important source of nutrients, improving soil fertility and maintaining or increasing soil organic matter levels. It also represents an important way of valorisation of animal wastes (Davis, Sloan, Kidder, & Jacobs, 2003; Kumar, Gupta, Chander, & Singh, 2005; Shappell, Billey, & Shipitalo, 2016). In Brazil and also in many other agricultural countries, manure represents one of the main nutrient resources for agriculture. Despite the potential retention by soils through sorption processes, large amounts of pharmaceuticals are transported to water bodies through runoff or erosion (Koschorreck, Koch, & Rönnefahrt, 2002) or via infiltration in groundwater (Avisar, Lester, & Ronen, 2009).

In 2015, the Brazilian chicken meat production reached 13.14 million megatons and was largely concentrated in the southern states. Paraná, Santa Catarina, and Rio Grande do Sul, respectively, contributed 32.5%, 16.2%, and 14.1% to the national production (Associação Brasileira de Proteína Animal, 2016). Brazil also produces around 10 billion megatons of cattle each year. Considering a daily dry waste production of 2.4 kg for pig and of 10 to 15 kg for cattle (Salomon & Lora, 2005), the potential manure production is approximately 28.3 million t yr−1 and 1.1 billion t yr−1, respectively.

The nutrient status of soils and the crop needs (Sociedade Brasileira de Ciência do Solo, 2016), as well as the soil phosphorus status (Gatiboni, Smyth, Schmitt, Cassol, & Oliveira, 2014), dictates manure application management. Due to the low fertility of soils in southern Brazil, the Committee on Soil Chemistry and Fertility (Sociedade Brasileira de Ciência do Solo, 2016) recommended high application rates of manure. However, manure application represents a potential source of pollution because of the presence of potentially toxic chemicals such as metals and organic compounds (e.g., veterinary drugs; Davis et al., 2003; Kumar et al., 2005). The retention, transfer, and mobility of these veterinary drugs in the environment are governed by sorption effects in the soil, depending on the chemical property (hydrophobicity, pKa, and solubility) and the soil characteristics (such as mineralogy, organic matter, and inorganic content, pH; Thiele-Bruhn, 2003).

A larger number of studies have shown that manure application is a major source of agricultural soil contamination with veterinary pharmaceuticals (Christian et al., 2003; Karcı & Balcıoğlu, 2009; Wang et al., 2014). Such findings are necessary for an evidence-based risk assessment of the effects of veterinary pharmaceuticals in the environment and subsequent policies and regulatory measures aiming to monitor and minimise these effects (Kaczala & Blum, 2016). The development of antibiotic-resistant microorganisms could be associated with manure application to soils. The emergence of antibiotic resistance among pathogenic bacteria could become a major public health concern due to ineffective treatment of a number of diseases (Igbinosa & Odjadjare, 2015). Antibiotic resistance is defined as the skill of certain bacteria to annihilate the action of the antibiotic or to eliminate it from their cells. Horizontal gene transfers (e.g., DNA exchange) are the result of resistance development in living organisms, and antibiotic resistance can be transmitted to following generations (Aubertheau et al., 2017). Several studies have highlighted the risks of the migration of genes or resistant bacteria from soils, air, and water to animals and humans (Halling-Sørensen, 2001; Hirsch, Ternes, Haberer, & Kratz, 1999; Nwosu, 2001). Manure represents a reservoir of plasmids, and its application to soil for extended periods could favour the development and/or the spread of bacterial resistance (Binh, Heuer, Kaupenjohann, & Smalla, 2008). Horizontal gene transfer could efficiently be enhanced by different factors (e.g., wind and water), resulting in the transport of aerosols or soil particles to urban environments. Resistant bacteria present in croplands can be endophytic or attached to the surface of crops, resulting in human exposure through food consumption (Dolliver, Kumar, & Gupta, 2007; Heuer, Schmitt, & Smalla, 2011). If these resistant organisms are present in human food, the treatment of infections could be compromised (Greenson, Suliman, Sami, Alowaimer, & Koohmaraie, 2013).

On a global level, antibiotics and antibiotic resistance in various aspects of life are monitored by health organisations (e.g., the World Health Organization). However, the amounts of antibiotics in soil microhabitats may be largely underestimated, especially in developing countries such as Brazil, where data on in situ bioavailability are still missing (Heuer et al., 2011). Agriculture in southern Brazil combines animal and grain production. Family farming practices are intensive, with confined animal production (e.g., chickens or pigs) and a high use of antibiotics. On these farms, fertilisation by manure application is one of the most important ways to increase soil fertility and to discard high volumes of manure. The intensive application of animal waste could, however, result in soil degradation through the accumulation of pharmaceutical residues or resistant microorganisms. In this context, we tried to answer the following questions: Which are the impacts of the application of animal waste on antibiotic levels and induced bacterial resistance of soils? Is there a type of waste more polluting than others? Is the contamination larger in Brazil than in other countries? To answer these questions, we sampled 15 soils, with and without manure application, in a typical region of southern Brazil and investigated the contents of antibiotics and three antibiotic resistance genes.

2 MATERIALS AND METHODS

2.1 Study area

Soils sampling was performed in the Guaporé watershed (Rio Grande do Sul, Brazil), which extends over 2,030 km2 of rivers, streams, and lakes, representing 0.57% of its surface. The climate of the catchment area is subtropical superhumid mesothermal with an average precipitation of 1,401 to 2,005 mm yr−1 and an average temperature of 18.3 °C; there is no distinct dry season (Bastos, 2017).

The region is mainly rural, with agriculture as the main human activity. Crop fields and grasslands cover about 32.5% (small cultivated areas) and 9.7%, respectively, of the area. The remaining area is occupied by forests (56.7%; Bastos, 2017). Pastures are mainly cultivated for animal feeding (poultry, pig and dairy cattle farming) and grain crop production (wheat, soybean, and maize). Urban areas cover less than 1% of the total surface area of the watershed.

In the upper part of the watershed, no-tillage systems are commonly used on large farms for soy and maize cultivation, with low livestock numbers. The middle and lower parts of the watershed are characterised by a sloping relief, with a large number of small tobacco farms. Farmers also raise poultry or pigs. This region is characterised by severe soil erosion, mainly in the hilly areas, along with high sediment loss (Tiecher, Caner, Minella, & dos Santos, 2015).

Soil vulnerability is rarely considered in cropping systems (without crop rotation or winter cover crops), resulting in more favourable conditions for erosion.

2.2 Soil collection

In the four subwatersheds Lajeado-Carazinho, Marau, Capingui, and Arvorezinha, we sampled 15 sites (Figure 1). At all sites, soils are regularly amended with the application of animal manure (except the forest sites) or are subject to grazing. Manure application methods differed between sites (Tables 1 and 2).

Details are in the caption following the image
Sites sampled in four subwatershed areas of the Guaporé watershed [Colour figure can be viewed at wileyonlinelibrary.com]
Table 1. Land use types and geographical locations of the sampling sites
Manure application Abbreviation Exposure time to manure (years) Land use Time of manure application GPS coordinates Subwatershed
Without application Ft1 Forest 28°51′21.50″S 52°13′29.44″W Arvorezinha
Ft2 Forest 28°26′40.91″S 52° 7′13.27″W Marau
FLONA National forest 28°19′12.14″S 52°11′4.61″W Capingui
Rf1 Restored forest 28°44′42.04″S 52° 6′40.10″W Lajeado-Carazinho
Rf2 Restored forest 28°43′13.16″S 52° 5′11.89″W Lajeado-Carazinho
Poultry litter PoL1 5 Conventional yield ≥30 days 28°25′51.95″S 52° 8′50.58″W Marau
PoL2 6 Annual pasture 28°26′29.26″S 52°10′30.55″W Marau
PoL3 8 Tobacco ≥30 days 28°51′37.90″S 52°13′35.29″W Arvorezinha
Swine SWI1 8 Conventional yield ≥30 days 28°44′35.51″S 52° 6′37.69″W Lajeado-Carazinho
SWI2 11 Annual pasture 28°44′40.21″S 52° 6′41.13″W Lajeado-Carazinho
SWI3 12 Conventional yield ≥30 days 28°51′37.90″S 52°13′35.29″W Arvorezinha
SWI4 >20 Conventional yield ≥30 days 28°51′12.29″S 52°12′46.37″W Arvorezinha
Dairy cow DaC1 15 Annual pasture 28°43′42.51″S 52° 4′42.63″W Lajeado-Carazinho
DaC2 >15 Annual pasture 28°25′52.45″S 52° 9′11.33″W Marau
DaC3 40 Annual pasture 28°26′7.99″S 28°26′7.99″W Marau
  • a The application of manure is undertaken every year, and the area is used for grazing.
  • b The application of manure is undertaken every 2 years, and the area is used for maize and soybeans.
Table 2. Proprieties of the studied soils
Soils Sand Silt Clay SSA pHwater C N K Ca Mg Na P Ecx. Al
% cm2·ml g kg−1 μg/g cmolc/dm3
Ft1 21.5 57.6 20.8 23,450 4.4 39.2 0.40 1.54 0.74 1.82 0.22 4.42 4.66
Ft2 19.4 58.2 22.4 23,925 4.6 35.5 0.29 0.88 1.18 1.70 0.27 17.80 3.41
FLONA 41.6 47.9 10.5 15,976 5.0 46.0 0.18 1.32 0.97 2.04 0.70 2.54 2.15
Rf1 43.3 46.7 9.9 16,186 6.4 80.3 0.84 1.98 6.41 3.42 0.23 9.27 0.16
Rf2 29.9 51.9 18.2 20,912 5.7 99.8 0.98 3.36 4.64 3.24 0.83 9.63 0.27
PoL1 26.8 55.3 17.8 22,005 6.2 24.3 0.26 1.32 2.74 4.25 0.75 32.45 0.09
PoL2 15.6 51.3 33.1 33,297 5.3 19.3 0.19 3.78 0.87 1.67 0.52 33.01 0.36
PoL3 21.1 60.2 18.8 20,311 4.8 14.5 0.16 3.08 1.37 2.73 0.66 61.07 3.59
SWI1 29.2 50.8 20.0 23,840 5.4 26.3 0.28 1.54 3.13 5.18 0.44 18.45 0.18
SWI2 28.5 53.9 17.6 21,215 6.1 24.4 0.25 4.20 2.74 3.29 0.29 30.20 0.00
SWI3 20.3 61.9 17.7 19,722 4.7 19.5 0.17 1.76 0.82 2.02 0.69 28.51 2.33
SWI4 36.1 47.5 16.4 22,091 6.0 14.0 0.15 1.54 1.42 2.42 0.43 67.83 0.00
DaC1 34.4 48.6 17.0 21,561 5.4 16.6 0.18 3.36 1.25 2.08 0.59 13.38 0.45
DaC2 19.9 61.1 19.1 21,083 5.8 23.4 0.28 5.04 1.71 2.91 0.67 13.30 0.18
DaC3 31.1 51.4 17.4 22,101 6.3 21.3 0.24 7.98 1.80 2.39 0.70 57.24 0.09
  • Note. Ecx. Al = exchangeable aluminium; SSA = specific surface area.

Pig manure is applied in the subwatersheds of Arvorezinha and Lajeado-Carazinho (SWI1 to SWI4). These sites are cultivated under conventional tillage, with two to three grain crops annually, which may be interrupted by animal grazing periods.

Site SWI1 is reserved for tobacco growth and has been amended with pig manure for 8 years. Site SWI2 is also used for tobacco growth in summer and serves as a pasture in winter; it has been receiving manure for 11 years.

Sites SWI3 and SWI4 are used for grain and silage maize production in summer and for forage production in winter. Site SWI3 has been amended with manure every 2 years for 12 years, whereas SWI4 has been amended for 20 years.

Poultry litter is largely used in the Marau subwatershed (PoL1 and PoL2). These two sites are subject to cropping management with conventional tillage and to annual animal grazing. Sites PoL1 and PoL2 have been amended with poultry litter application for 5 and 6 years, respectively.

Site PoL3, located in the Arvorezinha subwatershed, has also been receiving poultry litter for 8 years.

Sites DaC1, DaC2, and DaC3 correspond to sites used for dairy cattle over periods of 5, 15, and 40 years, respectively, and are continuously fertilised.

As reference soils, several forest soils were sampled. Forest Site Ft1 is situated in the southeastern part of the Arvorezinha subwatershed catchment, whereas Forest Site Ft2 is situated in the eastern part of the Marau subwatershed. FLONA corresponds to the national forest (FLONA—Federal Conservation Unit), situated in the Capingui subwatershed. In the 1940s, the FLONA site was demarcated, resulting in 1,300 ha of forest, including 450 ha of native Atlantic Forest.

The restored forest (Rf) sites are sites in which ecological processes have been re-established, resulting in increased biodiversity levels and functioning. These areas have previously been used for agricultural activities but have not been fertilised for the last 50 years.

Sampling was performed at a depth of 0- to 20-cm layer with an auger. The samples were dried and subsequently prepared for chemical analyses.

2.3 Analysis of pharmaceuticals

Twelve pharmaceuticals (11 antibiotics and diclofenac [DFC]) were measured via liquid chromatography–tandem mass spectrometry (Table 3). The antibiotics belonged to the most commonly used ones on family farms in Rio Grande do Sul: macrolide (erythromycin, roxithromycin [ROXY], and tylosin [TYL]), quinolone (norfloxacin [NORFL], ciprofloxacin [CIPRO], enrofloxacin [ENRO], and levofloxacin [LEVO]), sulfonamide (sulfamethazine [SMTZ], sulfaquinoxaline, and sulfamethoxazole [SMX]), and tetracycline (oxytetracycline [OXYT]).

Table 3. Proprieties of the studied pharmaceuticals
Therapeutic class Family Pharmaceuticals Abbreviation Chemical formula Molar mass (g/mol) Provider Purity (%) Parent ion (m/z) Product ion (m/z) Collision energy (V)
Anti-inflammatory Diclofenac DFC C14H11Cl2NO2 296.14 Sigma-Aldrich NI 318.00591 261.1040 13
Antibiotic Sulfonamide Sulfamethazine SMTZ C12H14N4O2S 278.33 Sigma-Aldrich ≥99.7 279.08962 204.03990 35
Sulfamethoxazole SMX C10H11N3O3S 253.28 Sigma-Aldrich PS Standard 254.05972 156.01137 30
Sulfaquinoxaline SQXL C14H12N4O2S 300.33 Sigma-Aldrich ≥96.0 301.06751

156.01138

275.8543

25
Quinolones Norfloxacin NORFL C16H18FN3O3 319.33 Sigma-Aldrich ≥99.8 342.12244 312.92000 85
Ciprofloxacin CIPRO C17H18FN3O3 331.34 Sigma-Aldrich PS Standard 332.14000 231.05600 60
Enrofloxacin ENRO C19H22FN3O3 359.39 Sigma-Aldrich ≥99.0 360.17000 296.09900 65
Levofloxacin LEVO C18H20N3FO4 361.37 Sigma-Aldrich ≥99.0 362.15000 318.16100 30
Macrolides Erythromycin ERTM C37H67NO13 733.93 Sigma-Aldrich PS Standard 734.46800 576.37000 14
Roxithromycin ROXY C41H76N2O15 837.05 Sigma-Aldrich ≥90.0 837.52766 679.43600 13
Tylosin TYL C46H77NO17 916.10 Sigma-Aldrich ≥89.7 916.52399 174.11276 21
Tetracycline Oxytetracycline OXYT C22H24N2O9 460.43 Sigma-Aldrich ≥97.0 483.13740 443.14426 15
426.12000
  • Note. NI = not identified; PS Standard = Pharmaceutical Secondary Standard.

For analysis, 500 mg of soil was extracted by pressurised solvent extraction (ASE™350, Thermo Fisher Scientific, Waltham, USA) at 80 °C, using methanol/water (1:2; vol/vol) as extraction solvent. The extracted volume (approx. 30 ml) was then adjusted to 500 ml with deionised water. The final solution contained <5% of methanol. The extracts were purified by solid-phase extraction (Autotrace™ 150, Thermo Scientific, Waltham, USA) using Oasis® HLB cartridges (6 cc, 200 mg of sorbent; Waters, Milford, USA), with methanol as eluent. The final extracts were evaporated under mild nitrogen steam until they reached a volume of 100 μl for posterior restitution to 500 μl with methanol/water (10:90; vol/vol). Each soil studied was analysed twice with triplicate measurements.

The samples were finally separated by high-pressure liquid chromatography in an Acquity UPLC®BEH C18 column (2.1 × 100 mm, 1.7 μm; water) with methanol/water acidified with 0.3% formic acid. Liquid chromatography was coupled to a Q-Exactive Orbitrap™ mass spectrometer (Thermo Fisher Scientific), combining high-performance quadrupole precursor selection with high-resolution/accurate-mass detection. All pharmaceuticals were detected using an electrospray ion source operating in positive mode. Data acquisition and processing were performed using Xcalibur 2.2 software (Thermo Fisher Scientific). Quantification was performed according to the external standard methods. Separation and mass parameters are provided in the Supporting Information.

The identity of each molecule was confirmed by the correspondence of three criteria between the mass spectrum of the analysed compound and the mass spectrum of a certified standard solution of this compound: the exact mass of the compounds (nb. measured in high resolution, R = 20,000 with the Q-exactive mass detector), the retention time (nb. determined with the liquid chromatography system in the given condition of the analytical run), and the isotope pattern of the mass spectra.

Detection limits were calculated on the basis of the results obtained for “matrix samples” calibration (quantity and confidence range) and blanks. The calculation is based on a standard method (Neuilly, 1998). Corrected variance (Sc) is needed to apply this method. The detection limit (LD) can be calculated as follows:
urn:x-wiley:10853278:media:ldr2964:ldr2964-math-0001
where k is the slope of the calibration curve, and
urn:x-wiley:10853278:media:ldr2964:ldr2964-math-0002
where urn:x-wiley:10853278:media:ldr2964:ldr2964-math-0003; xi is the standard concentration; urn:x-wiley:10853278:media:ldr2964:ldr2964-math-0004is the standard mean; n is the number of standards; nb is the number of blanks; Q is the calibration residue; and Qb is the residue in blanks.

It was possible to obtain the most accurate detection limit with four calibrations. The standard curve method was used, with concentrations ranging from 5 to 20 μg/L and with three replicates of injections per point. Ten blanks were analysed.

Recovery experiments were performed only with deuterated standards of sulfamethazine (13C6) and sulfamethoxazole (D4). In the literature, values between 80% and 120% are considered as satisfying for the quantification method. Recovery values of 89% for sulfamethazine and 77% for sulfamethoxazole are acceptable.

2.4 Quantification of resistance genes

We extracted soil DNA by using a Fast DNA® SPIN kit for faeces, which efficiently isolates PCR-ready genomic DNA from the samples. Extraction was performed according to the manufacturer's instructions, using FastPrep®135 (MP Biomedicals, California, USA). Extracted DNA was quantified with a Nanodrop spectrophotometer (Thermo Scientific, Waltham, USA) and stored at −80 °C until analysis. Three antibiotic resistance genes, frequently observed in the environment (Zhang, Zhang, & Fang, 2009), were quantified from the soil DNA extracts: sul1 (sulphonamide resistance), qnrA (quinolone resistance), and erm (erythromycin resistance). Genes were detected by quantitative polymerase chain reaction (qPCR; Realplex Eppendorf) and realised by INRA Transfert Environment (Narbonne, France). We used the kit Mix Express qPCR Super Mix, with premixed Rox Invitrogen. Complementary data about qPCR analyses were not furnished by INRA Transfert Environment.

The 16S rRNA-encoding gene was quantified by the SYBR Green assay, using the universal primers 338F and 518R (Might Cycler® FastStart DNA Master plus SYBR Green I, Roche Life Science). Subsequently, the 16S rRNA-encoding gene quantities were divided by 4.1 (Hardwick, Stokes, Findlay, Taylor, & Gillings, 2008, Klappenbach, Saxman, Cole, & Schmidt, 2001, Stalder, 2012).

3 RESULTS AND DISCUSSION

3.1 Impacts of manure type on soil contamination

The highest diversity of antibiotics was found in the soils receiving pig manure (Table 3). Several macrolides (minimum, TYL: 1.6 μg kg−1 maximum, ROXY: 11.50 μg kg−1) and several sulfonamides (maximum, SMTZ: 20.9 μg kg−1 minimum, SMX: 1.1 μg kg−1) were found in the Sites SWI1, SWI2, and SWI3. ROXY and TYL were up to 100 times higher than the values typically observed in Chinese soils receiving pig manure (Hou et al., 2015). Significant concentrations of quinolones were also found in the Sites SWI2, SWI3, and SWI4 (maximum, LEVO: 22.2 μg kg−1 minimum, ENRO: 1.90 μg kg−1). These values are similar to those found in a previous study (Zhou et al., 2013). The concentration of OXYT, which was only found in Site SWI2 (5.90 μg kg−1), was about 20 times higher than that found in a study in the United States (0.30 μg kg−1 Boxall et al., 2003). Diclofenac was detected in all SWI soils (maximum: 15.90 μg kg−1 minimum: 2.80 μg kg−1). The presence of this compound is consistent with its wide use as an anti-inflammatory drug and a painkiller in pigs (Cevc & Blume, 2001) and cattle (Sawaguchi et al., 2016).

The lowest concentrations of pharmaceutical substances were observed for soils receiving poultry litter. Soils receiving pig and dairy cow manure were more highly contaminated. However, Wei et al. (2016) stated that poultry litters are significant sources of pharmaceutical compounds. Poultry manure is of high interest for farmers because of its low water content and high nutrient concentration, enabling a reduction of the application frequency compared with other manures (Bastos, 2017). In the present work, soils receiving poultry litter presented several quinolones (Table 3). In particular, LEVO was found in Site PoL2 and CIPRO in Site PoL1, at concentrations of 4.20 and 1.23 μg kg−1, respectively. Nevertheless, CIPRO was found in lower amounts in these soils than in French soils treated with livestock manure (30 μg kg−1 Pourcher et al., 2014) or in soils in China (53.40 μg kg−1 Hou et al., 2015). Site PoL3 contained a DFC level of 1.30 μg kg−1 which is lower than the levels found in other studies (Hou et al., 2015; Zhou et al., 2013).

In the DaC sites, we found high levels of OXYT and DFC. Site DaC1 also presented SMTZ (1.11 μg kg−1), ENRO (1.20 μg kg−1), SMX (2.40 μg kg−1), sulfaquinoxaline (3.41 μg kg−1), OXYT (9.80 μg kg−1), and DFC (38.3 μg kg−1). The substance LEVO was detected in Sites DaC2 (3.90 μg kg−1) and DaC3 (1.60 μg kg−1). Li et al. (2013) also found OXYT (5.10 μg kg−1), SMTZ (0.46 μg kg−1), NORFL (0.85 μg kg−1), CIPRO (0.53 μg kg−1), ENRO (1.18 μg kg−1), and TYL (0.25 μg kg−1) in Chinese soils receiving concentrated dairy cow manure.

The forest soils (i.e., regenerated and natural forests) were characterised by the presence of several antibiotics. This finding gives cause for serious concern, because it suggests that soils not fertilised with manure could still contain pharmaceuticals (Table 3). Only sulfonamides were not found in these soils. In the FLONA sites, only DFC was found, at a concentration of 1.40 μg kg−1. The Forest Sites Ft1 and Ft2 were marked by high concentrations of LEVO (8.10 μg kg−1) and NORFL (27.80 μg kg−1), respectively. The substances OXYT (2.10 μg kg−1), DFC (2.50 μg kg−1), and ROXY (3.10 μg kg−1) were also found in the Forest Site RFt1. Several quinolones, namely, ENRO (1.10 μg kg−1), NORFL (7.20 μg kg−1), and LEVO (17.30 μg kg−1) were also found in the Forest Site Rf2.

The presence of pharmaceutical compounds, in particular synthetic antibiotics such as norfloxacin, in several of the studied forest sites (FLONA, Ft 1, and Ft2) was surprising at first. However, this presence was validated by the analytical method used in this work, which is supported by various controls to avoid ‘false-positive’ detections. Thus, the identity of each molecule was confirmed by the correspondence of three criteria between the mass spectrum of the analysed compound and the mass spectrum of a certified standard solution of this compound: the exact mass of the compound, its retention time, and the isotope pattern of its mass spectra.

Therefore, the presence of these compounds in the forest soils, which have never received manure fertilisation, suggests a contamination by the surrounding agricultural soils. Three putative ways of contamination can be considered.

The first hypothesis considers the possible transport of the antibiotics through aerosols or dusts generated during manure spreading. The forest canopy would act as a trap for contaminated drops or particles, which finally reach the soil surface during rainfall events. Indeed, aerial transport of antibiotics associated with particulate matter has been reported from cattle feed yards by McEachran et al. (2015). This transport could occur up to 2.2 km. A recent study also shows that dry or wet deposition of atmospheric particles contributes to the dissemination of pharmaceuticals and other contaminants (Ferrey, Hamilton, Backe, & Anderson, 2018). This way of contamination is possible in the studied forest sites soils due to the large presence of soils amended with animal wastes in Rio Grande do Sul.

Another hypothesis considers the transport of antibiotics by runoff during extreme rainfall/storm events, especially in the days following manure application (annual rainfall is 1,695 and 1,765 mm for Ft1 FLONA and Ft2 soils, respectively). Dolliver and Gupta (2008), in a 3-year field study in southwestern Wisconsin, compared runoff losses of antibiotics from the application of liquid hog and solid beef manures under chisel ploughing and no-tillage systems. Their work shows that antibiotics could be transported through runoff, especially during the nongrowing season, and antibiotic levels were generally higher in the no-tillage compared with the chisel plough treatment. Field observations suggest that this way of contamination seems to be possible for the FLONA soil, because this soil is located below a large agricultural field (slope ~5%) For the Sites Rf1 and Rf2 (slope ~5%), which represent small fragmented forest stands surrounded by agricultural fields, this contamination pathway is also possible (Appendix).

Rainfall events favour also soil erosion, which in turn may favour the transport of pharmaceutical compounds attached to soils particles. Bailey, Spielmeyer, Frings, Hamscher, and Schüttrumpf (2015) highlight the displacement of 15 veterinary antibiotics (introduced to German agricultural fields via fertilisation) by runoff and soil erosion. The authors argue that this transport pathway should be studied more intensely to investigate the contamination of river sediments, because some veterinary antibiotics tend to be strongly sorbed to soil particles (Pereira Leal, Ferracciu Alleoni, Tornisielo, & Regitano, 2013). For the three forest soils studied, erosion was observed in the surrounding agricultural soils or next to the road. Tiecher (2017) highlighted that unpaved roads (such as those near the FLONA site) are a major source of eroded soils. Figure 2 shows the roads surrounding the FLONA sampling point. Consequently, erosion of agricultural soils might also contribute to an input of contaminated soil particles into forest soils, especially at the forest edge.

Details are in the caption following the image
Roads surrounding the national forest (FLONA) sampling point [Colour figure can be viewed at wileyonlinelibrary.com]

Soils can also be a natural reservoir of antibiotic-producing microorganisms (Madigan, Martinko, Dunlap, & Clark, 2009; Popowska et al., 2012). Nearly 50% of soil actinomycetes species can synthesise natural antibiotics (Topp, 1981). Consequently, the absence of erythromycin and TYL in the forest soils shows no contribution of the natural soil biomass. Nevertheless, antibiotics of natural origin cannot be ruled out to explain the presence of ROXY and OXYT in these soils.

However, it should be noted that this finding is a case-specific result, because the contamination of manure can greatly vary between different farms. In particular, the contamination of animal excreta depends on the use of pharmaceuticals. However, NORFL, which is an antibacterial compound frequently used in pig production in Brazil, was not found in the SW soils. It should be noted that the metabolism of pharmaceuticals in pigs is not that different from the metabolism in cattle; we can therefore not explain why norfloxacin occurred in soil fertilised with cattle manure but not in soil fertilised with pig manure.

The pollution induced by pig manure application could be related to several factors, such as the maintenance of animals in confinement, the technological conditions for pork production (with the use of more pharmaceuticals than in dairy production), the application of manure with a high content of humidity, allowing its mobility in the soil, and the maturation period of manure, which is often neglected.

3.2 Potential transfer of pharmaceuticals by erosion

Particles carrying pharmaceuticals may be transported to rivers during storm events and in soil runoff. The Guaporé watershed presents an erosion rate of 394.6 Mg·km−2·yr−1 (Tiecher et al., 2015). Regardless of the soil potential soil particle export, there is a significant risk of transporting these chemicals into water systems and higher trophic levels. Bailey et al. (2015) found the substances SMX (30–37 μg kg−1), SMTZ (>20 μg kg−1), and tetracyclines (<750 μg kg−1) in river sediments adjacent to agricultural fields in Germany. Considering a concentration of 1 μg kg−1 of compound (e.g., SMX), the erosion rate in the Guaporé catchment may lead to a potential export of 394.6 mg of compound per km2 per year (assuming that the compound concentration in soil remains stable throughout 1 year, i.e., not considering biodegradation or additional contamination). Considering a concentration of 38.3 μg kg−1 of compound (e.g., DFC), the erosion rate can lead to a potential export of 15.1 g of compound per year. These findings suggest that even if pollutants are retained by the soil and not leached by runoff, erosion may constitute a significant route to bring them into the aquatic environment.

3.3 Resistance genes in soil

All soils receiving poultry litter residue showed a similar number of resistance genes (sul1: 10−7 genes per bacteria, qnr A: 10−4 genes per bacteria, and erm: 10−7 genes per bacteria). The erm gene was not found in the Site PoL2. Thus, compared with slurry from pig and cattle farms, the application of poultry litter seems to limit the transfer of antibiotic resistance. Wei et al. (2016) suggested that the specific composition and the particularities of poultry manure may influence its pollution potential. Furthermore, PoL soils were characterised by low amounts of antibiotics, impeding the presence of resistance genes in bacteria.

Long-term dairy cow grazing (with the application of manure for more than 15 and for 40 years) leads to high concentrations of sul1 genes (10−6–10−5 genes per bacteria) in soils. On the contrary, practices involving grazing shorter periods lead to low concentrations (10−8 genes per bacteria). Significant differences in sul1 contents between these soils were confirmed by Student's t test (p < .05).

Similarly, differences were also found between the different DaC soils, depending on their location and their land use, although these differences were not confirmed by statistical testing. Pastures from the Marau region had higher qnr A and erm gene amounts (DaC2: 10−3 and 10−6 genes per bacteria, respectively; DaC3: 10−4 and 10−7 genes per bacteria, respectively) compared with the pastures from the Lajeado-Carazinho region (DaC1: 10−5 and 10−8 genes per bacteria, respectively). Some DaC soils are used for animal grazing but with a large dispersion of the manure. Consequently, the amount of resistance genes is limited, although these repeated inputs seem to maintain these resistances in microbial communities.

Sites SWI1 and SWI4 were characterised by low amount of sul1 gene (~10−7 genes per bacteria). They also presented similar values of quinolone and macrolide resistance genes when compared with Site SWI3. It should be noted that on Site SWI3, manure is only applied every 2 years. Such nonintensive practices are probably related to the low resistance observed. Heuer and Smalla (2007) reported that the presence of antibiotic-resistant bacteria was especially high for pigs compared with other animals. Furthermore, the resistance is linked to the doses of antibiotics applied.

The sul1 gene was not observed in the forest soils, except in the Ft1 site (10−8 genes per bacteria; Table 4). This gene is widely found in environments exposed to anthropic activities (Wellington et al., 2013). For example, a typical baseline for sul1 genes below 1.5 × 10−2 genes per bacteria was defined for 21 lake sediments (Czekalski, Sigdel, Birtel, Matthews, & Bürgmann, 2015). Thus, the absence of sul1 genes may be linked to the absence of sulfonamides in the studied forest soils. The Sites FLONA, Ft1, and Ft2 presented lower values of erm (10−7 genes per bacteria) and qnrA genes (10−4 genes per bacteria) than the Sites Rf1 and Rf2 (10−6 and 10−3 genes per bacteria, respectively; Table 5). The two restored forests have been cultivated in the past (~50 years ago); our results suggest that manure application in the surrounding fields could have contaminated these sites via aerosol deposition or runoff. Indeed, the Lajeado-Carazinho region produces (with frequent manure application) different crops on hilly areas. Heuer and Smalla (2007) showed that antibiotic resistance conferred by plasmid exchange was more pronounced in microbial communities of preserved soils exposed to manure.

Table 4. Concentrations of pharmaceuticals in each soil
Soil DCF SMTZ SMX SQXL NORFL CIPRO ENRO LEVO ERTM ROXY TYL OXYT
μg kg−1
Ft1 <LD <LD <LD <LD 27.80 ± 25.1 <LD <LD <LD <LD <LD <LD <LD
Ft2 <LD <LD <LD <LD <LD <LD <LD 8.10±3.2 <LD <LD <LD <LD
FLONA 1.42 ± 1.4 <LD <LD <LD <LD <LD <LD <LD <LD <LD <LD <LD
Rf1 2.53 ± 1.1 <LD <LD <LD <LD <LD <LD <LD <LD 3.10 ± 3.0 <LD 2.10 ± 1.4
Rf2 <LD <LD <LD <LD 7.20 ± 6.7 <LD 1.10 ± 0.9 17.30 ± 7.3 <LD <LD <LD <LD
SWI1 15.93 ± 5.1 5.80 ± 5.0 2.20 ± 1.9 9.50 ± 5.3 <LD <LD <LD <LD 3.00 ± 1.8 <LD <LD <LD
SWI2 6.72 ± 1.8 6.00 ± 3.2 1.10 ± 0.9 4.00 ± 3.2 3.40 ± 3.2 4.50 ± 3.8 12.90 ± 7.0 11.40 ± 10.2 <LD 11.50 ± 9.9 1.60 ± 1.4 5.90 ± 4.3
SWI3 2.83 ± 1.5 <LD <LD <LD <LD 3.00 ± 2.7 1.90 ± 1.3 <LD <LD <LD <LD <LD
SWI4 12.09 ± 9.4 20.90 ± 11.9 <LD <LD <LD <LD <LD 22.20 ± 15.7 <LD <LD <LD <LD
PoL1 <LD <LD <LD <LD <LD 1.20 ± 0.9 <LD <LD <LD <LD <LD <LD
PoL2 <LD <LD <LD <LD <LD <LD <LD 4.20 ± 2.7 <LD <LD <LD <LD
PoL3 1.33 ± 0.4 <LD <LD <LD <LD <LD <LD <LD <LD <LD <LD <LD
DaC1 38.30 ± 25.3 1.10 ± 0.9 2.40 ± 1.2 3.40 ± 2.1 <LD <LD 1.20 ± 0.9 <LD <LD <LD <LD 9.80 ± 7.9
DaC2 <LD <LD <LD <LD <LD <LD <LD 3.90 ± 2.3 <LD <LD <LD <LD
DaC3 <LD <LD <LD <LD <LD <LD <LD 1.60 ± 1.1 <LD <LD <LD <LD
  • Note. Sites without manure application: Ft = forest; Flona = national forest; Rf = reforest; sites with manure application: PoL = poultry litter; SWI = swine; DaC = dairy cow; and pharmaceuticals: DFC = diclofenac; OXYT = oxytetracycline; SMTZ = sulfamethazine; SMX = sulfamethoxazole; SQXL = sulfaquinoxaline; NORFL = norfloxacin; CIPRO = ciprofloxacin; ENRO = enrofloxacin; LEVO = levofloxacin; ERTM = erythromycin; ROXY = roxithromycin; TYL = tylosin. LD = detection limit.
Table 5. Quantification of the gene classes sul1, qnr A, and erm in soils sampled in the Guapore watershed
Sample sul1 qnr A erm
genes per bacteria
Ft1 6.2 × 10−8 5.4 × 10−4 2.2 × 10−7
Ft2 n.d. 4.2 × 10−4 8.9 × 10−7
Flona n.d. 2.8 × 10−4 4.4 × 10−7
RF1 n.d. 9.0 × 10−3 5.7 × 10−6
RF2 n.d. 2.5 × 10−3 1.7 × 10−6
SWI1 1.8 × 10−6 2.7 × 10−4 1.1 × 10−7
SWI2 7.8 × 10−7 1.2 × 10−4 7.3 × 10−8
SWI3 1.4 × 10−7 1.2 × 10−5 6.0 × 10−7
SWI4 1.5 × 10−6 3.50 × 10−4 4.0 × 10−7
PoL1 2.4 × 10−7 1.7 × 10−4 1.2 × 10−7
PoL2 8.6 × 10−7 1.1 × 10−4 n.d.
PoL3 1.50 × 10−7 2.1 × 10−4 3.1 × 10−7
DaC1 9.6 × 10−8 3.9 × 10−5 8.1 × 10−8
DaC2 2.7 × 10−6 9.1 × 10−4 6.1 × 10−7
DaC3 1.9 × 10−5 1.2 × 10−3 1.5 × 10−6

3.4 Specific manure impact

The concentrations of antibiotics and resistance genes were used to discriminate the different soil samples according to their type of management (without application, DaC, SWI, and PoL). The graphical representation of the discriminant analysis displays only a partial differentiation between the management types. Thus, the results show an overlap of the ellipse of confidence for dairy cow and poultry litter soils, for poultry litter and nonfertilised soils, and for soils without pig manure fertilisation. However, this approach also shows that some types of management are different. Hence, the type of management can induce a ‘specific pollution fingerprint,’ but some of these fingerprints can present similitudes. Nevertheless, discriminant analysis points out that soils fertilised with dairy cow manure seem to present specific contents of in sul1 gene and tetracyclines. Soils with or without fertilisation with poultry litter seem to be impacted by the presence of the resistance genes erm and qnr A. Soils treated with pig manure tend to be more impacted by the presence of antibiotics (Figure 3).

Details are in the caption following the image
Discriminant analyses (DA) between the different kinds of manure application and the resulting antibiotic contamination and antibiotic-resistant genes (erm, qnr A, and sul1) of soils (the significance of the DA is confirmed by Pillai's trace = 1.93 and Fisher's statistic F = 1.808 at p value .092; sum sulfonamides: [sulfamethazine + sulfamethoxazole + sulfaquinoxaline]; sum macrolides: [erythromycin + roxithromycin + tylosin]; sum quinolones: [norfloxacin + ciprofloxacin + enrofloxacin + levofloxacin]; and tetracicline: oxytetracicline) [Colour figure can be viewed at wileyonlinelibrary.com]

Studies agree that the chronic exposure to antibiotics favours the presence of resistance genes in microbial communities (Balcázar, Subirats, & Borrego, 2015; Martinez, 2012). Thus, some correlations are frequently observed between the abundance in resistance genes and the concentration of antibiotics (Gao, Munir, & Xagoraraki, 2012). According to the results of Pearson's correlation test, no correlation was found between the gene contents (sul1, erm, or qnr A) and the antibiotic contents, suggesting that the abundance of resistance genes may be associated with the presence of other antibiotics (not analysed in the present work) or with a direct input of genes via manure application.

3.5 Contamination of Guaporé soils versus contamination in other countries

The concentrations of antibiotics and resistance genes found in the Guaporé soils tend to be similar to those observed in other agricultural soils worldwide (see Bailey et al., 2015; Heuer et al., 2011; Hou et al., 2015; Li et al., 2013; Malik et al., 2008; Popowska et al., 2012; Thiele-Bruhn, 2003; Wei et al., 2016; Zhou et al., 2013). Indeed, animal production in feedlot systems (poultry and pigs) is based on similar technologies. Scientific advances in nutrition and disease control have been rapidly transformed into technologies adopted by almost all animal breeders in all countries (Shields & Orme-Evans, 2015). The system is based on confining large quantities of animals in specifically constructed buildings (Jong & Guémené, 2011; Rotta et al., 2009; Sather, Jones, Schaefer, Colyn, & Robertson, 1997), on a balanced diet (Benchaar, Pomar, & Chiquette, 2001) and with specific schedules to administer all supplements, including veterinary drugs, in order to obtain maximum feed conversion in the shortest time. The south of Brazil presents a large amount of concentrated production areas administrated by family farmers working in monoproduction systems (Tiecher, 2017). In Brazil, as in Canada or the United States, antibiotics are used as growth promotors, whereas in the European Union, the use of antibiotics for such purpose was banned in 2006 (Maron, Smith, & Nachman, 2013). As a consequence, manures with similar or different qualities are used to fertilise soils, depending on the specific laws and regulations.

The seasonal management and the type of the soil receiving the animal waste may vary between countries or regions within a given country. For example, in Brazil, the limits for manure application are related to the zinc and copper quantities, and the volume of the manure applied (m3/ha) is determined by the pH, the C/N ratio, and concentrations of total organic matter, total carbon, phosphorus, and potassium (IAP). In Germany, fertiliser application restrictions already exist to prevent the overland transport of fertiliser-based contaminants. For example, application should not take place in winter or directly before predicted heavy rainfall (Bailey et al., 2015).

However, the mechanisms of transformation/degradation, the adsorption/desorption processes, among others are identical (Thiele-Bruhn, 2003). The intensity of changes in veterinary drugs is certainly different, but the physicochemical or biochemical principles are comparable. Thus, it can be stated that practices and management strategies adopted in the Guaporé watershed are similar to those used in other countries. The values presented in this work are rather a result of soil management strategies than of the levels of pharmaceuticals in manure.

4 CONCLUSIONS

The application of animal manures is an important source of nutrients for agriculture. However, this intensive application of this practice in Brazil raises the question of possible soil alteration by the accumulation of pharmaceutical residues and the development of resistant microorganisms. Such land degradation could represent a progressive risk of persistence and of widespread antibiotic resistance.

In Brazil, agricultural soils are treated several times each year, resulting in the application of millions to billions of Mg of animal manure per year. This intensive application of manure represents also a large input of antibiotics and antibiotic-resistant bacteria not only into soils but also into the surrounding waters. The present work highlights the fact that regular application of manure is responsible for introducing antibiotic compounds into the agricultural soils of the Guaporé watershed, as demonstrated by the differences in resistance levels in manured and nonmanured soils (i.e., forest soils). Nevertheless, soil runoff probably facilitates the diffusion of veterinary pharmaceuticals from application sites to the surrounding soils.

The high levels of resistance genes present in soils receiving manures from antibiotic-fed animals strongly suggest that the application of manure amplifies the dissemination of resistances. This highlights the strong contribution of soil practices (i.e., manure-spreading type and frequency) and management (i.e., animal types and soil retention time) to the control of antibiotic resistance in the environment. We stress that resistance to antibiotics (macrolides, quinolones, and sulfonamides) in manure-treated or nontreated soils is consistent with the observed levels of pharmaceuticals and the land use history. However, despite the absence of a correlation between the concentrations of antibiotics and those of resistance genes in the studied soils, the results show that the type of manure can induce a ‘specific pollution fingerprint.’ In this sense, the application of pig manure seems to favour the accumulation of antibiotics in soils, whereas the application of dairy cow manure favours the accumulation of resistance genes to sulfonamide.

The amounts of antibiotics or resistance genes found in the Guaporé watershed soils suggest that physical land degradation by erosion—as observed in the south of Brazil—may be an aggravating factor for antibiotic distribution, especially the high concentrations of pharmaceuticals observed in soils receiving pig manure raise the question of the fate (e.g.) of these compounds in the soils and the water bodies.

The release of antibiotics in watersheds remains a major global issue in terms of the prevention of an expansion of resistant bacteria. This study revealed that the situation in Brazil is no more alarming than that in other agricultural countries in America, Asia, or Europe, because antibiotics and antibiotic-resistant bacteria levels in manure-treated soils are lower than those in similar soils of other parts of the world.

ACKNOWLEDGMENTS

This study was supported by the CAPES-COFECUB (Project 761/12), the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), the Fundação de Amparo à Pesquisa do Estado do Rio Grande do Sul (FAPERGS), Europen Communities (FEDER) and Région Nouvelle Aquitaine.

    APPENDIX A

    Land use and topography of the Guaporé watershed (yellow: crop, green: forest, red: city, salmon: pasture and crop, and blue: water)

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