One practice for handling farm dairy effluent (DE) comprises recycling them to the soil with the challenge of balancing the tradeoff associated with environmental pollution through nutrient and microorganism loading. This study investigated seasonal bacterial community composition, diversity, abundance, and pathogenic indicators in untreated (Raw) and lagoon-stabilized (Lagoon) DE. The correlation between bacterial profiles and DE physicochemical characteristics was also analyzed. Pathogen-indicator bacteria were studied by enumerating viable counts and the bacterial community structure by 16S rRNA gene sequence analysis. Lagoon storage effectively reduced total solids (64%), suspended solids (77%), organic carbon (40%), and total nitrogen (82%), along with total coliforms, Escherichia coli, and enterococci. However, this efficiency was compromised in winter. Lagoon and Raw sample bacterial communities presented different compositions, with several environmental variables correlating to microbial community differences. Lagoon-treated DE exhibited the most diverse bacterial community, dominated by Firmicutes (40%), Proteobacteria (30%), and Bacteroidota (7.6%), whereas raw DE was mainly composed of Firmicutes (76%). Regardless of the season, dominant genera included Trichococcus, Romboutsia, Corynebacterium, and Paeniclostridium. Overall, the study emphasizes the importance of lagoon treatment for DE stabilization, showcasing its role in altering bacterial community composition and mitigating environmental risks associated with pathogens and nutrients, particularly in summer.

The intensification of dairy production in Uruguay generates increasing volumes of organic waste that are difficult to handle and may entail health risks. Irrigation with farm dairy effluents (DE) is a recommended agricultural practice to improve soil fertility. The objective of this work was to evaluate the effect of the application of raw (RDE) and two-lagoon stabilized effluents (LDE), urea fertilization, or non-amendment to Festuca arundinacea on soil and plant nutrient content, as well as pathogenic bacterial indicators and persistence of antimicrobial resistance genes. In a greenhouse trial, four seasonal applications were made with a total dose equivalent to 200 kg N ha-1. Soil Na content increased after DE applications. There was no increase in the nutrient content of tall fescue caused by DE applications. The persistence of E. coli was low but still detected in soil receiving RDE. Beta-lactam genes blaTEM and blaOXA were detected in both DE, being highest in LDE. However, they were not detected in the soil. DE applications demonstrated effects comparable to those of control and urea fertilization on tall fescue biomass and nutrient content, and slightly altered the soil's chemical status. LDE reduced pathogenic bacteria load to the soil, underlining the safety of its application.

Dairy intensification produces a large amount of farm dairy effluents (FDE). The final disposal of FDE is generally to the soil as fertilizer. While this use of FDE as fertilizer has numerous benefits, such as reducing the application of synthetic fertilizers or improving soil quality, there are concerns about the environmental and health risks associated with microbial pathogens from animal waste, the spread of antibiotic resistance genes, nutrient losses and greenhouse gases (GHG) emissions. Furthermore, how this agricultural practice impacts the composition and functionality of soil microbial communities has not yet been elucidated. This thesis aimed to evaluate the impact of FDE applications on soil GHG emissions, the composition, activity and diversity of its microbial community, and health risks. The FDE were collected raw and from a two-stage stabilization lagoon. The N application rate normalized to 200 kg N ha−1 was divided into four seasonal applications compared to urea fertilization or a no-aggregate control. Soil samples were taken after each application for microbial and physicochemical characterization and GHG fluxes were measured up to twenty days after each application. The pasture was harvested according to typical grazing management. Repeated application of both types of FDE increased the soil nutrient status and enhanced microbial activity. Higher fescue pasture production and macronutrient content with FDE than the control positioned FDE application to soil as an alternative disposal. However, N2O emissions increased after applying both FDE’s, most notably with raw FDE. Soil microbial community composition was not significantly influenced by FDE applications, but functional diversity shifted with raw FDE. Lagoon storage effectively reduced organic C and total N along with pathogenic indicator bacteria and changed the bacterial community composition except in winter. Beta-lactam resistance genes were detected in both FDEs, but not in the soil after repeated applications.

Farm dairy effluents (FDE) from washing the milking parlor contain manure, urine, and chemicals and constitute a large amount of wastewater. Applying FDE as soil fertilizers to pastures can enhance forage yield and improve soil nutrient status. Since the dairy industry is increasingly attempting to maximize returns through better utilization of forage with lesser inputs, there is demand for a supply of FDE as fertilizers. Nevertheless, the impact of this practice on soil microbiota remains largely unexplored. It must be studied before large-scale soil disposal to avoid diminishing microbial diversity or enhancing pathogen abundance. This study evaluated the effects of applying lagoon-stored (Lagoon) and raw dairy effluents (Raw) at a rate of 50 kg N ha(-1) in four equal doses, in comparison to urea fertilization, on soil fertility and the activity, abundance, and community structure of soil microbiota. Raw was obtained after solid separation, and Lagoon corresponds to the Raw stationed in a two-lagoon system. Microbial activity was assessed as basal respiration, potentially mineralizable N, potential nitrification activity, and enzymatic activities. The catabolic activity of the microbial community was evaluated using Biolog Ecoplates T. Bacterial and fungal community composition and diversity were analyzed through amplicon sequencing of 16S rRNA and ITS2. The application of FDE benefited soil fertility and microbial activity. Lagoon had the most potent effects on soil available P and extractable K+, Na+, Mg2+ and Ca2+. Soil treated with Raw displayed higher microbial activities, such as dehydrogenase, basal respiration, urease, and potentially mineralizable N, than the other treatments. FDE did not significantly alter the microbial composition, abundance, or functional diversity. In conclusion, in this short-term trial, despite changes in soil chemical properties and microbial activity, the composition and diversity of the bacterial and fungal communities remained unaffected by FDE irrigation.

The use of farm dairy effluents (FDE) has become a promising alternative to increase pasture yield while reducing the environmental impact of waste accumulation into streams, but other environmental implications should be considered. The present study aimed to assess the effect of application of either raw FDE or lagoon-stored FDE compared to dissolved urea or a non-amended control on N2O emission, soil N dynamics, functional microbial activity, and the yield and N-use efficiency of a fescue pasture. The normalized N application rate of 200 kg N ha−1 was divided into four seasonal events in a greenhouse experiment. Similar fescue forage production with FDE or urea positioned FDE application to soil as an alternative disposal. The repeated application of raw effluent delivered more organic C to the soil which induced an increase in enzyme activities, a shift in the catabolic activity of the soil microbial community, and greater N mineralization potential. On the other hand, urea addition decreased the functional activity of the soil microbial community. However, N2O emissions were greater for the raw effluent, so lagoon-stored effluent is an alternative to manage FDE under these conditions, avoiding urea addition and enhancing soil metabolic activity.

Cyanobacteria play a relevant role in rice soils due to their contribution to soil fertility through nitrogen (N2) fixation and as a promising strategy to mitigate methane (CH4) emissions from these systems. However, information is still limited regarding the mechanisms of cyanobacterial modulation of CH4 cycling in rice soils. Here, we focused on the response of methane cycling microbial communities to inoculation with cyanobacteria in rice soils. We performed a microcosm study comprising rice soil inoculated with either of two cyanobacterial isolates (Calothrix sp. and Nostoc sp.) obtained from a rice paddy. Our results demonstrate that cyanobacterial inoculation reduced CH4 emissions by 20 times. Yet, the effect on CH4 cycling microbes differed for the cyanobacterial strains. Type Ia methanotrophs were stimulated by Calothrix sp. in the surface layer, while Nostoc sp. had the opposite effect. The overall pmoA transcripts of Type Ib methanotrophs were stimulated by Nostoc. Methanogens were not affected in the surface layer, while their abundance was reduced in the sub surface layer by the presence of Nostoc sp. Our results indicate that mitigation of methane emission from rice soils based on cyanobacterial inoculants depends on the proper pairing of cyanobacteria–methanotrophs and their respective traits.

Rotational rice systems, involving pastures, other crops and/or livestock, are common in temperate South America, exemplified by the rice-pasture-livestock system of Uruguay which combines very high rice yields with tight nitrogen (N) balances. The generally good nutrient use efficiency in these systems provides a template for nutrient management in other mixed farming systems, if the underlying processes can be sufficiently well quantified and understood. Here, we studied N balances in rice–non-rice rotations in a long-term experiment in Uruguay, with the aim of parameterizing and testing the DNDC model of N dynamics for such systems for use in future work. The experiment includes three rotations: continuous rice (RI-CONT), rice-soybean (RI-SOY) and rice-pasture (RI-PAST). We considered 9 years of data on N balances (NBAL), defined as all N inputs minus all N outputs; N surplus (NSURP), defined as all N inputs minus only N outputs in food products; and N use efficiency (NUE), defined as the fraction of N inputs removed in food products. We parameterized DNDC against measured yield and input and output data, with missing data on N losses inferred from the N balance and compared with literature values. The model performance was assessed using standard indices of mean error, agreement and efficiency. The model simulated crop yields and rice cumulative N uptake very well, and soil N reasonably well. The values of NBAL were +45 and−20 kg N ha−1 yr−1 in RI-CONT and RI-SOY, respectively, and close to zero in RI-PAST (−6 kg N ha−1 yr−1). Values of NSURP decreased in the order RI-CONT >> RI-SOY > RI-PAST (+115, +25 and +13 kg N ha−1 yr−1, respectively). Values of NUE (84, 54, and 48% for RI-SOY, RI-PAST, and RI-CONT, respectively) decreased as NBAL increased. The sensitivity of DNDC's predictions to the agronomic characteristics of the different crops, rotations and water regimes agreed with expectations. We conclude that the DNDC model as parameterized here is suitable for exploring how to optimize N management in these systems.

This review presents a summary of the work done in Uruguay on the diversity and agricultural use of rhizobia, a group of soil bacteria able to establish symbiotic associations almost exclusively with legumes and fix atmospheric nitrogen. Uruguay has a long tradition regarding the use of microbial inoculants for agriculture. It is worth mentioning that since 1960, Uruguay has formally regulated the use of microorganisms in agriculture, being considered one of the pioneer countries where state policies on microbial inoculants have been implemented. In general, the vast majority of the work carried out in Uruguay has focused on the selection and characterization of promising bacteria to be used as biofertilizers. Therefore, the most studied symbiotic associations were those established with legumes of agricultural interest for the country, such as alfalfa, clover, lotus and soybean. The studies carried out with autochthonous alpha- and beta- rhizobia associated with diverse legume species are also considered, taking into account their ecological importance and the interest in knowing and preserving native germplasm.

Irrigated rice fields are major sources of two important greenhouse gases (GHG), methane and nitrous oxide. As an initial step towards obtaining local information, emissions of CH4 and N2O from rice paddy soil were measured by the static chamber technique in greenhouse and field experiments conducted in eastern Uruguay. In the greenhouse experiment, the effect of two flooding moments (21 and 45 days after emergence) and nitrogen fertilization (0 and 50 kg N ha-1) on gas emissions was studied. Early flooding and nitrogen fertilization tended to increase N2O emissions. In the field experiment, effect of winter soil cover crop and nitrogen fertilization (0 and 82 kg N ha-1) were tested. Higher CH4 fluxes were observed mainly during the reproductive stage of the plant in the N-fertilized treatment with ryegrass winter crop. N2O flux peaked at flushing. Results indicate that the use of cover crops might increase GHG emissions during the rice cycle. Despite differences in agronomic management practices employed in Uruguay, CH4 and N2O fluxes are within magnitudes previously reported for rice fields worldwide.

Rice is an important source of methane (CH4) and other crops may be sources of nitrous oxide (N2O), both of which are powerful greenhouse gases. In Uruguay, irrigated rice rotates with perennial pastures and allows high productivity and low environmental impact. A long-term experiment with contrasting rice rotation intensification alternatives, including rice–soybean and continuous rice, was recently carried out in an Argialboll located in a temperate region of South America. To know if rotation systems influence soil microbial activity involved in CH4 and N2O emissions, the abundance and potential rate for gas production or consumption of microbial populations were measured during the rice crop season. CH4 was only emitted when rice was flooded and N2O emission was not detected. All rotational soils showed the highest rate for methanogenesis at tillering (30 days after rice emergence), while for methanotrophy, the maximum rate was reached at flowering. The abundance of related genes also followed a seasonal pattern with highest densities of mcrA genes being observed at rice flowering whereas pmoA genes were more abundant in dry soils after rice harvest, regardless of the rotation system. Differences were found mainly at tillering when soils with two consecutive summers under rice showed higher amounts of mcrA and pmoA gene copies. The potential denitrification rate was highest at the tillering stage, but the abundance of nirK and nirS genes was highest in winter. Regarding ammonium oxidation, bacterial amoA abundance was higher in winter while the archaeal amoA gene was similar throughout the year. A strong influence of the rice growth stage was registered for most of the parameters measured in rice paddy soils in this no-till rice intensification experiment. However, differences among rotations begin to be observed mainly at tillering when the abundance of populations of the methane and nitrous oxide cycles seemed to respond to the rice intensification.

EDITORIAL article Front. Agron., 23 November 2021 | https://doi.org/10.3389/fagro.2021.796717

Rice root exudates can control nitrification by releasing biological nitrification inhibitors (BNIs), reducing nitrogen losses in agricultural soils. However, the inhibitory effect on nitrification and the abundance of ammonia oxidisers in different soil types remain unclear. Two temperate paddy soils with different organic matter contents were collected to investigate the impact on nitrification rates of two rice cultivar root exudates, El Paso 144 (O. sativa ssp. indica) and Tacuari (O. sativa spp. japonica). Root exudates were extracted before the tillering growth stage, and their BNI potential was evaluated in a bioassay with luminescent Nitrosomonas europaea and in a 12-day soil microcosm incubation. While exudates from Tacuari showed stronger BNI activity in the bioassay, its nitrification inhibition in both soils was similar to that of DCD. El Paso did not show BNI activity in Salto whose organic matter content was higher. The abundance of ammonia oxidisers was not affected by root exudates or DCD, but only ammonia-oxidising bacteria had a significant positive relationship with soil nitrate. Our results demonstrated that although the bioassay showed high BNI activity, its expression in soils varied depending on the rice cultivar and the type of soil, particularly with its organic matter content.

Ten heterocyst cyanobacteria isolated from a temperate ricefield in Uruguay were characterized using a polyphasic approach. Based on major phenotypic features, the isolates were divided into two different morphotypes within the Order Nostocales, filamentous without true branching. The isolates were also phylogenetically evaluated by their 16S rRNA and hetR gene sequences. Although the morphological classification of cyanobacteria has not always been supported by the analysis of the 16S rRNA gene, in this case the morphological identification agreed with the 16S rRNA gene phylogenetic analysis and the ten isolates were ascribed at the genus level to Nostoc or Calothrix. Four isolates were identified at species level. As these cyanobacteria were intended to be used as biofertilizer for rice, several physiological parameters were studied. Growth rates, nitrogenase, nitrate reductase and glutamate synthase activities were evaluated. This information will be valuable to select strains to be used as inoculant for ricefields.

The practice of inoculating forage legumes with rhizobia strains is widespread. It is assumed that the inoculated strain determines the performance of the symbiosis and nitrogen fixation rates. However, native-naturalized strains can be competitive, and actual nodule occupancy is often scarcely investigated. In consequence, failures in establishment, and low productivity attributed to poor performance of the inoculant may merely reflect the absence of the inoculated strain in the nodules. This study lays out a strategy followed for selecting a Rhizobium leguminosarum sv. trifolii strain for white clover (Trifolium repens) with competitive nodule occupancy. First, the competitiveness of native-naturalized rhizobia strains selected for their efficiency to fix N2 in clover and tagged with gusA was evaluated in controlled conditions with different soils. Second, three of these experimental strains with superior nodule occupancy plus the currently recommended commercial inoculant, an introduced strain, were tested in the field in 2 years and at two sites. Plant establishment, herbage productivity, fixation of atmospheric N2 (15N natural abundance), and nodule occupancy (ERIC-PCR genomic fingerprinting) were measured. In both years and sites, nodule occupancy of the native-naturalized experimental strains was either higher or similar to that of the commercial inoculant in both primary and secondary roots. The difference was even greater in stolon roots nodules, where nodule occupancy of the native-naturalized experimental strains was at least five times greater. The amount of N fixed per unit plant mass was consistently higher with native-naturalized experimental strains, although the proportion of N derived from atmospheric fixation was similar for all strains. Plant establishment and herbage production, as well as clover contribution in oversown native grasslands, were either similar or higher in white clover inoculated with the native-naturalized experimental strains. These results support the use of our implemented strategy for developing a competitive inoculant from native-naturalized strains.

The burgeoning demand for rice in Latin America and Caribbean (LAC) exceeds supply, resulting in a rice deficit. To overcome this challenge, rice production should be increased, albeit sustainably. However, since rice production is associated with increases in the atmospheric concentration of two greenhouse gases (GHGs), namely methane (CH4) and nitrous oxide (N2O), the challenge is on ensuring that production increases are not associated with an increase in GHG emissions and thus do not cause an increase in GHG emission intensities. Based on current understanding of drivers of CH4 and N2O production, we provide here insights on the potential climate change mitigation benefits of management and technological options (i.e., seeding, tillage, irrigation, residue management) pursued in the LAC region. Studies conducted in the LAC region show intermittent irrigation or alternate wetting and drying of rice fields to reduce CH4 emissions by 25–70% without increasing N2O emissions. Results on yield changes associated with intermittent irrigation remain inconclusive. Compared to conventional tillage, no-tillage and anticipated tillage (i.e., fall tillage) cause a 21% and 25% reduction in CH4 emissions, respectively. From existing literature, it was unambiguous that the mitigation potential of most management strategies pursued in the LAC region need to be quantified while acknowledging country-specific conditions. While breeding high yielding and low emitting rice varieties may represent the most promising and possibly sustainable approach for achieving GHG emission reductions without demanding major changes in on-farm management practices, this is rather idealistic. We contend that a more realistic approach for realizing low GHG emitting rice production systems is to focus on increasing rice yields, for obvious food security reasons, which, while not reducing absolute emissions, should translate to a reduction in GHG emission intensities. Moreover, there is need to explore creative ways of incentivizing the adoption of promising combinations of management and technological options.

Denitrification is one of the main biological sources of N2O, a greenhouse gas. In paddies, water flooding provides anaerobic soil conditions that can boost denitrification. In this work, the influences of rice cultivar, water management and soil type on the abundance and community structure of denitrifying bacteria were evaluated; nirS and nirK-type denitrifiers were considered separately. Two microcosm experiments were performed, and the abundance and community structure for both nitrite reductase genes were assessed using qPCR and T-RFLP, respectively. In the first experiment, two rice cultivars and two water managements were evaluated; in the second experiment, two soils, which mainly differed in their organic matter content, and two flooding times were evaluated. The results show that sampling time was the main factor driving nirS and nirK abundances. The nirK:nirS ratio, recently proposed as an indicator of the soil N2O emission potential, was higher in samples taken at the flower primordium stage of rice in both experiments, suggesting that this stage could be a hot moment for N2O emissions. Soil type was the main factor influencing the nirS community structure, while it had no effect on nirK communities. Although the nirK community structure was not affected by cultivar or soil type, statistical analysis showed that some T-RFs were associated with each cultivar or soil type, indicating that these factors exerted effects on certain subsets of the denitrifying population rather than the whole community. The community structure of nirS-type denitrifiers was more sensitive to the analyzed factors than the nirK-type, and soil type was the main factor that influenced this community structure.

Microbial processes such as mineralization, nitrification and denitrification regulate nitrogen dynamics in the soil. The last two processes may produce nitrous oxide (N2O). In this work N2O fluxes were quantified at four moments of the rice cycle, sowing, tillering, panicle initiation and maturity, in two sites that differed mainly in their soil organic matter (OM) content, Salto (higher OM) and Treinta y Tres. Potential net N mineralization, ammonium oxidation and denitrification as well as the most probable numbers (MPN) of ammonia oxidizers and denitrifiers were determined. Potential N mineralization did not vary with the soil type and increased at rice maturity. Neither ammonia oxidation potential nor MPN were different among the soils. However, the soil with higher OM exhibited higher activity and MPN of denitrifiers, irrespective of the rice stage. In turn, at the latest phases of the crop, the MPN of denitrifiers increased coinciding with the highest mineralization potential and mineral N content of the soil. Significant differences in N2O flux were observed in Salto, where the highest emissions were detected at rice maturity, after the soil was drained (44.2 vs 20.8g N-N2O/ha d in Treinta y Tres). This work shows the importance of considering the soil type and end-of-season drainage of the rice field to elaborate GHGs (greenhouse gases) inventories.

Denitrifiers comprise a metabolically diverse group of microbes used as a resource for environmental engineering, due to their ability to perform anaerobic respiration. The main use of denitrification in environmental sustainability is the removal of nitrate and nitrite in water treatment plants.Heterotrophic denitrifiers are those that use organic molecules as C sources, including pollutants, a trait that makes them as a potential tool for many bioremediation processes. A notorious advantage of denitrifiers over other microorganisms is that they are able to degrade pollutants in anaerobic environments, which extend their potential usefulness.In this chapter, recent advances regarding the use of heterotrophic denitrifiers in environmental sustainability will be discussed. We end the chapter discussing the singularities of denitrifying strains of the genus Paracoccus and their potentiality in environmental sustainability.