Nitrogen source, transformation and fate within intensive dairy systems to inform sustainable intensification

Contamination and deterioration of natural water quality by nitrogen (N) from agricultural sources is a major threat to the environment. Globally, there is a societal expectation that sustainable food production should be achievable. The concept of sustainable intensification is based on to the equality between production and environmental targets. For this to become a reality, increased productivity must be accompanied by provision of clean water, air, habitats for biodiversity, recycling of nutrients and mitigation against climate change. Agriculture and food production rely heavily on external N inputs (e.g. fertilisers) and as agronomic systems generally have low use efficiency there is the risk of high N losses i.e. the leak of N excess to the environment. Agricultural landscapes contain many different soil/subsoil/bedrock typologies having heterogeneous N water attenuation capacities (intrinsic ability of soils to reduce contamination). Dairy farms represent complex environments, necessitating many techniques (isotopes, biogeochemical parameters, dissolved gases, bacterial gene abundances) used in combination, to provide a thorough characterisation of, examination of N source, transformation and fate along different subsurface pathways. These multiple techniques are currently seldom used in combination. In Ireland, 30% of milk production occurs in high rainfall conditions and heavy textured soil areas. For better grass growth, artificial drainage systems (shallow and groundwater systems) are installed. The role of land drainage in N transfer, transformation and fate is however relatively unexplored. These systems may reduce N transformation potential by, for example, creating unsuitable conditions for denitrification leading to greater nitrate (NO3--N) losses or by-passing zones of high soil N attenuation capacity further compromising sustainability targets. Indeed, the potential to use drainage systems as a monitoring tool, which covers large areas of contribution, has been neglected in terms of multiple techniques that could explore N transfer, transformation and fate. The concept of “sustainable intensification” includes all the aspects of agricultural productivity and environmental protection. The primary aim of this thesis was to examine this concept in terms of impacts and relationships of drainage systems installed at intensive sites on and with soil drainage classes, N transfer, transformation and fate and water quality to develop advises and a range of multiple techniques to improve and guide future management. Herein, this concept has been tested within a range of different contexts in terms of scale (farm, plot and laboratory), soil characteristics (from heterogeneous soils to heavy homogeneous types), drainage designs (from random to parallel and from single to multiple, from moles to piped systems) and techniques (gaseous emissions, biogeochemical parameters, isotopic signatures, gene abundances) in order to produce a more refined interpretation of artificial drainage systems and the role they play within the sustainable intensification framework. As agricultural landscapes contain many different soil types with heterogeneous nitrogen (N) attenuation capacity, a zone of contribution (ZOC) surrounding a borehole and an installed drainage system was used to interpret subsurface hydro-biogeochemical functional capacity within four hydrologically isolated plots. By using the drainage system as a monitoring tool in combination with multiple techniques, a disconnectivity and complexity of the system was highlighted in terms of contamination sources uncovered and separate water attenuation functionalities. This study showed that collating isotopic, dissolved gas and biophysical data from the drainage system and groundwater locations creates a clearer conceptual model of a site showing an interpretation of source and attenuation within these areas. Next, the study moved to five commercial farms where surface or groundwater gley soils were artificially drained (site specific designs) and monitored. This study aimed to investigate how drainage system design (e.g. shallow and groundwater) affected N transformation and how the multi-technique method could be broadened to rank commercial dairy farms in terms of their N attenuation capacity. These techniques showed the ability to divide sites into three distinct groups according to their respective water attenuation potential highlighting different sustainability for different drainage designs. A tool to compare or rank sites in terms of their N sustainability was created. From micro-plot and field this tool was then moved to farm scale on a heterogeneous soil landscape to infer further knowledge on attenuation within drained versus un-drained areas and future management to decrease N losses. The tool was able to divide the farm into several groups with different attenuation ability which was not disrupted by the imposed artificial drainage system. The identified groups and areas could be subjected to differential management to further move towards sustainability. The use of bacterial gene abundance was further tested as a tool to improve pour characterisation tool and lastly, an incubation experiment was conducted to examine more closely the effect of land drainage and saturation on an N problematic site and its gaseous phase component. Major findings of the present study include: • Techniques such as natural isotopic abundances, biogeochemical parameters, isotopomers, gaseous emissions, dissolved gasses, can be combined to elucidate sustainability of intensive dairy systems. • Drainage systems can be used, when analysed with the above techniques, to elucidate water quality but more interestingly can be used as a monitoring tool, in combination with groundwater monitoring networks, to interpret net N source, transformation and fate, over large areas, on agricultural landscapes. • Although surpluses of N were found to be uniform across intensive dairy sites on the present study, the soil water attenuation function and “net denitrification” varied considerably across sites. This means that there was considerable variation within dairy farms in terms of N sustainability, which will have consequences for sustainable intensification. • Drainage systems affect this water attenuation function differently depending on their design. This means that the presence of a drainage system on agricultural landscapes does not infer poor water quality, more importantly than absence/presence is the depth and type of drainage system present. • During this assessment the techniques used in combination with the present study worked well to characterise and rank sustainability

Medication use during pregnancy, gestational age and date of delivery: Agreement between maternal self-reports and health database information in a cohort

Supplemental tables. Table S1. Agreement between questionnaire and prescription redemption database for selected therapeutic classes by time of questionnaire completion. Table S2. Number of women with information on hypertension during pregnancy and agreement between questionnaire and birth certificate database. Table S3. Number of women with information on hypertension during pregnancy in questionnaire and in birth certificate database and use of antihypertensive medications according to questionnaire and prescription database. Positive Predictive Value and Negative Predictive Value of prescriptions for antihypertensive medications recorded in questionnaire and in birth certificate database. (DOCX 23 kb

Potential of the cyanobacteria Anabaena sp. and Dolichospermum sp. for being produced using wastewater or pig slurry: Validation using pilot-scale raceway reactors

Indoor trials using 0.3 L bubble columns were conducted to demonstrate the potential of two cyanobacterial strains, Anabaena sp. and Dolichospermum sp., for being produced using nutrients obtained from waste streams (wastewater or pig slurry). Filtered pig slurry diluted at a concentration of 5% (v/v) led to a biomass productivity comparable to that of the standard medium (0.72 ± 0.05 and 0.66 ± 0.09 g·L-1·day-1 for Anabaena sp. and Dolichospermum sp. respectively). When produced using wastewater, the productivity was around 0.40 g·L-1·day-1 for both strains. The process was up-scaled using a 1.04 m3 raceway reactor located outdoors and operated at a culture depth of 0.12 m. Dilution rates of 0.1-0.3 day-1 were evaluated, achieving maximum biomass productivities when operating at a dilution rate of 0.3 day-1: 20.9 and 28.0 g·m-2·day-1 for Anabaena sp. and Dolichospermum sp., respectively. The maximum total nitrogen (N-NH4+ plus N-NO3-) removal rates for Anabaena sp. and Dolichospermum sp. were 2,471 and 3,621 mg·m-2·day-1, achieved when operating at a dilution rate of 0.3 day-1. Nitrification and stripping contributed to the N-NH4+ removal. When operating at 0.3 day-1, maximum P-PO43- removal rates for cultures of Anabaena sp. and Dolichospermum sp. were 81.5 and 87.1 mg·m-2·day-1. Illumina sequencing results revealed that both strains dominated the prokaryotic community of both cultures with other notable eukaryotic and prokaryotic genus detected including human pathogens. However, annual studies are needed to assess the potential of producing biomass rich in these strains outdoors

Characterization of Two <i>Zymomonas mobilis</i> Wild Strains and Analysis of Populations Dynamics during Their Leavening of Bread-like Doughs

Two Zymomonas mobilis wild strains (UMB478 and 479) isolated from water kefir were characterized for their biomass production levels and leavening performance when used as the inoculum of a real bread-like dough formulation. The obtained baked product would be consumable by people with adverse responses to Saccharomyces cerevisiae. In liquid cultures, the two strains reached similar biomass concentration (0.7 g CDW/L). UMB479 showed an interesting resistance to NaCl (MBC 30 g/L), that may be useful in the bakery sector. When inoculated in doughs, UMB479 produced the maximum dough volume (650 mL) after 5 h, glucose was almost consumed and 1 g/100 g of ethanol produced, +200% respective to UMB478. Using S. cerevisiae for comparison purposes, the dough doubled its volume fast, in only 2 h, but reached a final level of 575 mL, lower than that achieved by Z. mobilis. The analysis of bacterial and fungal population dynamics during dough leavening was performed through the Automated Ribosomal Intergenic Spacer Analysis (ARISA); doughs leavened by UMB479 showed an interesting decrease in fungal richness after leavening. S. cerevisiae, instead, created a more complex fungal community, similar before and after leavening. Results will pave the way for the use of Z. mobilis UMB479 in commercial yeast-free leavened products

Biohazard identification: Profiling microalgal cultures growing on municipal wastewater and fertilizer medium in raceway photobioreactors

Microalgae provide a promising way to combine wastewater treatment and biomass production. They are often used as pre-treatment to reduce pathogenic loads: however, a full characterisation of the risks is still needed to develop safety guidelines. Two raceways were inoculated with Scenedesmus, one in a fertilizer medium and one in wastewater. Biohazards were then explored in three ways: NGS analysis, commercial qPCR array and plate counts. Media and sampling locations contributed to shape bacterial and eukaryotic structures and pathogenic loads. Communities were variable across time with a higher diversity between inlets than between biomass and outlets. A lower presence of pathogens was seen in fertilizer, while wastewater showed a distinct reduction from inlet to outlet. The main pathogenic genera detected were Arcobacter and Elizabethkingia with an important presence of Aeromonas. The three analyses together identified the necessity of preventive and protection measures and of post-harvest treatments

Autotrophic nitrogen removal for decentralized treatment of ammonia-rich industrial textile wastewater: process assessment, stabilization and modelling

Digital textile printing (DTP) is a game-changer technology that is rapidly expanding worldwide. On the other hand, process wastewater is rich in ammoniacal and organic nitrogen, resulting in relevant issues for discharge into sewer system and treatment in centralized plants. The present research is focused on the assessment of the partial nitritation/anammox process in a singlestage granular sequencing batch reactor for on-site decentralized treatment. The technical feasibility of the process was assessed by treating wastewater from five DTP industries in a laboratory-scale reactor, in one case investigating long-term process stabilization. While experimental results indicated nitrogen removal efficiencies up to about 70%, complying with regulations on discharge in sewer system, these data were used as input for process modelling, whose successful parameter calibration was carried out. The model was applied to the simulation of two scenarios: (i) the current situation of a DTP company, in which wastewater is discharged into the sewer system and treated in a centralized plant, (ii) the modified situation in which on-site decentralized treatment for DTP wastewater is implemented. The second scenario resulted in significant improvements, including reduced energy consumption (− 15%), reduced greenhouse gases emission, elimination of external carbon source for completing denitrification at centralized WWTP and reduced sludge production (− 25%)

Effects of the application of microbiologically activated bio-based fertilizers derived from manures on tomato plants and their rhizospheric communities

Abstract Bio-based fertilizers (BBFs) recovered from animal manure are promising products to optimise resources recovery and generate high agricultural yields. However, their fertilization value may be limited and it is necessary to enrich BBFs with microbial consortia to enhance their fertilization value. Three specific microbial consortia were developed according to the characteristics of three different BBFs produced from manure (bio-dried solid fraction, solid fraction of digestate and biochar) to enhance plant growth and product quality. A greenhouse pot experiment was carried out with tomato plants grown with microbiologically activated BBFs applied either as N-organic fertilizers or as an organic amendment. A next generation sequencing analysis was used to characterise the development of each rhizospheric community. All the activated BBFs gave enhanced tomato yields (fresh and dry weight) compared with the non-activated treatments and similar to, or higher than, chemical fertilization. Concerning the tomato fruits’ organoleptic quality, lycopene and carotenoids concentrations were improved by biological activation. Metagenomic analysis points at Trichoderma as the main driver of the positive effects, with the effects of added bacteria being negligible or limited at the early stages after fertilization. In the context of the circular economy, the activated BBFs could be used to replace synthetic fertilisers, reducing costs and environmental burdens and increasing production

An integrated assessment of nitrogen source, transformation and fate within an intensive dairy system to inform management change.

From an environmental perspective optimised dairy systems, which follow current regulations, still have low nitrogen (N) use efficiency, high N surplus (kg N ha-1) and enable ad-hoc delivery of direct and indirect reactive N losses to water and the atmosphere. The objective of the present study was to divide an intensive dairy farm into N attenuation capacity areas based on this ad-hoc delivery. Historical and current spatial and temporal multi-level data- sets (stable isotope and dissolved gas) were combined and interpreted. Results showed that the farm had four distinct attenuation areas: high N attenuation: characterised by ammonium-N (NH4+-N) below 0.23 mg NH4+-N l-1 and nitrate (NO3--N) below 5.65 mg NO3-- N l-1 in surface, drainage and groundwater, located on imperfectly to moderately-well drained soils with high denitrification potential and low nitrous oxide (N2O) emissions (av. 0.0032 mg N2O-N l-1); moderate N attenuation: characterised by low NO3--N concentration in drainage water but high N2O production (0.0317 mg N2O-N l-1) and denitrification potential lower than group 1 (av. &#948;15N-NO3-: 16.4 , av. &#948;18O-NO3-: 9.2 ), on well to moderately drained soils; low N attenuation area 1: characterised by high NO3--N (av. 6.90 mg NO3--N l-1) in drainage water from well to moderately-well drained soils, with low denitrification potential (av. &#948;15N-NO3-: 9.5 , av. &#948;18O-NO3-: 5.9 ) and high N2O emissions (0.0319 mg N2O l-1); and low N attenuation area 2: characterised by high NH4+-N (av. 3.93 mg NH4+-N l-1 and high N2O emissions (av. 0.0521 mg N2O l-1) from well to imperfectly drained soil. N loads on site should be moved away from low attenuation areas and emissions to air and water should be assessed.The authors thank S. Leach, C. Somers, D. Brennan, M.M.R. Jahangir and D. Peyton for assistance during the project. J. Patton provided data on the N balance and R. Fox and A. Lawless facilitated access to the research farm and helped with the management scenario section.peer-reviewe