Sustainable strategies: Nature-based solutions to tackle antibiotic resistance gene proliferation and improve agricultural productivity and soil quality

The issue of antibiotic resistance is now recognized by the World Health Organisation (WHO) as one of the major problems in human health. Although its effects are evident in the healthcare settings, the root cause should be traced back to the One Health link, extending from animals to the environment. In fact, the use of organic fertilizers in agroecosystems represents one, if not the primary, cause of the introduction of antibiotics and antibiotic-resistant bacteria into the soil. Since the concentrations of antibiotics introduced into the soil are residual, the agroecosystem has become a perfect environment for the selection and proliferation of antibiotic resistance genes (ARGs). The continuous influx of these emerging contaminants (i.e., antibiotics) into the agroecosystem results in the selection and accumulation of ARGs in soil bacteria, occasionally giving rise to multi-resistant bacteria. These bacteria may harbour ARGs related to various antibiotics on their plasmids. In this context, these bacteria can potentially enter the human sphere when individuals consume food from contaminated agroecosystems, leading to the acquisition of multi-resistant bacteria. Once introduced into the nosocomial environment, these bacteria pose a significant threat to human health. In this review, we analyse how the use of digestate as an organic fertilizer can mitigate the spread of ARGs in agroecosystems. Furthermore, we highlight how, according to European guidelines, digestate can be considered a Nature-Based Solution (NBS). This NBS not only has the ability to mitigate the spread of ARGs in agroecosystems but also offers the opportunity to further improve Microbial-Based Solutions (MBS), with the aim of enhancing soil quality and productivity.

Conventional activated sludge vs. photo-sequencing batch reactor for enhanced nitrogen removal in municipal wastewater: Microalgal-bacterial consortium and pathogenic load insights

Municipal wastewater treatment plants are mostly based on traditional activated sludge (AS) processes. These systems are characterised by major drawbacks: high energy consumption, large amount of excess sludge and high greenhouse gases emissions. Treatment through microalgal-bacterial consortia (MBC) is an alternative and promising solution thanks to lower energy consumption and emissions, biomass production and water sanitation. Here, microbial difference between a traditional anaerobic sludge (AS) and a consortium-based system (photo-sequencing batch reactor (PSBR)) with the same wastewater inlet were characterised through shotgun metagenomics. Stable nitrification was achieved in the PSBR ensuring ammonium removal > 95 % and significant total nitrogen removal thanks to larger flocs enhancing denitrification. The new system showed enhanced pathogen removal, a higher abundance of photosynthetic and denitrifying microorganisms with a reduced emissions potential identifying this novel PSBR as an effective alternative to AS.

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

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.

Microbial community acclimatization enhances bioplastics biodegradation and biogas production under thermophilic anaerobic digestion

This paper reports the results of a novel study of microbial acclimatization for bioplastics anaerobic degradation and conversion into biogas. Three sequential anaerobic digestion (AD) runs were carried out to favour microbial acclimatization to two different bioplastics, starch-based (SBS) and polyactic-acid (PLA). AD of SBS and PLA bioplastics was favoured by the acclimatization of the inoculum to the substrate after each run of AD. SBS conversion into biogas increased by 52 % (from 94 to 143 NL kgVS-1) and it was correlated with the enhanced growth of starch degrading bacteria such as Hydrogenispora, Halocella and Haloplasma. PLA anaerobic degradation increased by 97 % (from 395 to 779 NLbiogas kgVS-1) and it was related to the acclimatization of known PLA-degraders such as Tepidimicrobium, Methanothermobacter and Tepidanaerobacter. Microbial acclimatization appears a suitable and low-cost strategy to enhance bioplastics circularity by promoting their anaerobic biodegradation and conversion into biogas.

Structural and functional microbial diversity in deadwood respond to decomposition dynamics

We investigated the changes in microbial community diversities and functions in natural downed wood at different decay stages in a natural oak forest in the Italian Alps, through metagenomics analysis and in vitro analysis. Alfa diversity of bacterial communities was affected by the decay stage and log characteristics, while beta diversity was mainly driven by log diameter. Fungal and archaeal beta diversities were affected by the size of the sampled wood (log diameter), although, fungi were prominently driven by wood decay stage. The analysis of genes targeting cell wall degradation revealed higher abundances of cellulose and pectin-degrading enzymes in bacteria, while in fungi the enzymes targeting cellulose and hemicellulose were more abundant. The decay class affected the abundance of single enzymes, revealing a shift in complex hydrocarbons degradation pathways along the decay process. Moreover, we found that the genes related to Coenzyme M biosynthesis to be the most abundant especially at early stages of wood decomposition while the overall methanogenesis did not seem to be influenced by the decay stage. Intra- and inter-kingdom interactions between bacteria and fungi revealed complex pattern of community structure in response to decay stage possibly reflecting both direct and indirect interactions.

Influence of feedstock source on the development of polyhydroxyalkanoates-producing mixed microbial cultures in continuously stirred tank reactors

Polyhydroxyalkanoates (PHAs) are the new frontier of bioplastic production; however, research is needed to develop and characterise efficient mixed microbial communities (MMCs) for their application with a multi-feedstock approach. Here, the performance and composition of six MMCs developed from the same inoculum on different feedstocks were investigated through Illumina sequencing to understand community development and identify possible redundancies in terms of genera and PHA metabolism. High PHA production efficiencies (>80% mg COD_PHA mg^-1 COD_OA-consumed) were seen across all samples, but differences in the organic acids (OAs) composition led to different ratios of the monomers poly(3-hydroxybutyrate) (3HB) to poly(3-hydroxyvalerate) (3HV). Communities differed across all feedstocks, with enrichments in specific PHA-producing genera, but analysis of potential enzymatic activity identified a certain degree of functional redundancy, possibly leading to the general high efficiency seen in PHA production from all feedstocks. Leading PHAs producers across all feedstocks were identified in genera such as Thauera, Leadbetterella, Neomegalonema and Amaricoccus.

Pig Slurry Management Producing N Mineral Concentrates: A Full-Scale Case Study

Manure treatment to recover nutrients presents a great challenge to delocalize nutrients from overloaded areas to those needing such nutrients. To do this, approaches for the treatment of manure have been proposed, and currently, they are mostly under investigation before being upgraded to full scale. There are very few fully operating plants recovering nutrients and, therefore, very few data on which to base environmental and economic studies. In this work, a treatment plant carrying out full-scale membrane technology to treat manure to reduce its total volume and produce a nutrient-rich fraction, i.e., the concentrate, was studied. The concentrate fraction allowed the recovery of 46% of total N and 43% of total P. The high mineral N content, i.e., N-NH₄/total-N > 91%, allowed matching the REcovered Nitrogen from manURE (RENURE) criteria proposed by the European Commission to allow the potential substitution of synthetic chemical fertilizers in vulnerable areas characterized by nutrient overloading. Life cycle assessment (LCA) performed by using full-scale data indicated that nutrient recovery by the process studied, when compared with the production of synthetic mineral fertilizers, had a lower impact for the 12 categories studied. LCA also suggested precautions which might reduce environmental impacts even more, i.e., covering the slurry to reduce NH₃, N₂O, and CH₄ emissions and reducing energy consumption by promoting renewable production. The system studied presented a total cost of 4.3 € tons^-1 of slurry treated, which is relatively low compared to other similar technologies.

Wastewater from textile digital printing as a substrate for microalgal growth and valorization

This study aims at evaluating an innovative biotechnological process for the concomitant bioremediation and valorization of wastewater from textile digital printing technology based on a microalgae/bacteria consortium. Nutrient and colour removal were assessed in lab-scale batch and continuous experiments and the produced algae/bacteria biomass was characterized for pigment content and biomethane potential. Microbial community analysis provided insight of the complex community structure responsible for the bioremediation action. Specifically, a community dominated by Scenedesmus spp. and xenobiotic and dye degrading bacteria was naturally selected in continuous photobioreactors. Data confirm the ability of the microalgae/bacteria consortium to grow in textile wastewater while reducing the nutrient content and colour. Improvement strategies were eventually identified to foster biomass growth and process performances. The experimental findings pose the basis of the integration of a microalgal-based process into the textile sector in a circular economy perspective.

Impact of photobioreactor design on microalgae-bacteria communities grown on wastewater: Differences between thin-layer cascade and thin-layer raceway ponds

Thin-layer (TL) photobioreactors (PBRs) are characterised by high productivity. However, their use is limited to lab/pilot-scale, and a deeper level of characterisation is needed to reach industrial scale and test the resistance of multiple microalgae. Here, the performance and composition of eight microalgal communities cultivated in the two main TLs design (thin-layer cascade (TLC) and thin-layer raceway pond (RW)) were investigated through Illumina sequencing. Chlorella vulgaris showed robustness in both designs and often acted as an "invasive" species. Inoculum and reactor type brought variability. Eukaryotic microalgae inocula led to a more robust and stable community (higher similarity), however, RWs were characterised by a higher variability and did not favour the eukaryotic microalgae. The only cyanobacterial inoculum, Nostoc piscinale, was maintained, however the community was variable between designs. The reactor design had an effect on the N cycle with the TLC and RW configurations, enhancing nitrification and denitrification respectively.

Centrate as a sustainable growth medium: Impact on microalgal inocula and bacterial communities in tubular photobioreactor cultivation systems

Centrate is a low-cost alternative to synthetic fertilizers for microalgal cultivation, reducing environmental burdens and remediation costs. Adapted microalgae need to be selected and characterised to maximise biomass production and depuration efficiency. Here, the performance and composition of six microalgal communities cultivated both on synthetic media and centrate within semi-open tubular photobioreactors were investigated through Illumina sequencing. Biomass grown on centrate, exposed to a high concentration of ammonium, showed a higher quantity of nitrogen (5.6% dry weight) than the biomass grown on the synthetic media nitrate (3.9% dry weight). Eukaryotic inocula were replaced by other microalgae while cyanobacterial inocula were maintained. Communities were generally similar for the same inoculum between media, however, inoculation with cyanobacteria led to variability within the eukaryotic community. Where communities differed, centrate resulted in a higher richness and diversity. The higher nitrogen of centrate possibly led to higher abundance of genes coding for N metabolism enzymes.

Characterization of Two Zymomonas mobilis 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.

Profiling microalgal cultures growing on municipal wastewater and fertilizer media in raceway photobioreactors

Microalgae cultivation is proposed as an effective system for pathogens reduction and wastewater depuration, however, a full characterisation of the risks is still needed. Two raceways were inoculated with Scenedesmus, one using wastewater and the other using a fertilizer medium. Microbial community and pathogen presence were explored by next generation sequencing (NGS), commercial qPCR array and plate counts. These methods proved to be complementary for a full characterization of community structure and potential risks. Media and sampling locations contributed to shape communities and pathogenic loads. The main pathogenic genera detected were Arcobacter and Elizabethkingia (mainly in wastewater) with an important presence of Aeromonas (all samples). A lower presence of pathogens was detected in fertilizer samples, while wastewater showed a reduction from inlet to outlet. Raceways showed potential as an effective biotreatment, with most of the retained pathogens released in the outlet and only a minor part settled in the biomass.

Microbial community and performance of a partial nitritation/anammox sequencing batch reactor treating textile wastewater

Implementation of onsite bioremediation technologies is essential for textile industries due to rising concerns in terms of water resources and quality. Partial nitritation-anaerobic ammonium oxidation (PN/A) processes emerged as a valid, but unexplored, solution. In this study, the performance of a PN/A pilot-scale (9 m3) sequencing batch reactor treating digital textile printing wastewater (10-40 m3 d-1) was monitored by computing nitrogen (N) removal rate and efficiencies. Moreover, the structure of the bacterial community was assessed by next generation sequencing and quantitative polymerase chain reaction (qPCR) analyses of several genes, which are involved in the N cycle. Although anaerobic ammonium oxidation activity was inhibited and denitrification occurred, N removal rate increased from 16 to 61 mg N g VSS-1 d-1 reaching satisfactory removal efficiency (up to 70%). Ammonium (18-70 mg L-1) and nitrite (16-82 mg L-1) were detected in the effluent demonstrating an unbalance between the aerobic and anaerobic ammonia oxidation activity, while constant organic N was attributed to recalcitrant azo dyes. Ratio between nitrification and anammox genes remained stable reflecting a constant ammonia oxidation activity. A prevalence of ammonium oxidizing bacteria and denitrifiers suggested the presence of alternative pathways. PN/A resulted a promising cost-effective alternative for textile wastewater N treatment as shown by the technical-economic assessment. However, operational conditions and design need further tailoring to promote the activity of the anammox bacteria.

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 single-stage 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%).

Anaerobic biodegradation of phenol in wastewater treatment: achievements and limits

Anaerobic biodegradation of toxic compounds found in industrial wastewater is an attractive solution allowing the recovery of energy and resources but it is still challenging due to the low kinetics making the anaerobic process not competitive against the aerobic one. In this review, we summarise the present state of knowledge on the anaerobic biodegradation process for phenol, a typical target compound employed in toxicity studies on industrial wastewater treatment. The objective of this article is to provide an overview on the microbiological and technological aspects of anaerobic phenol degradation and on the research needs to fill the gaps still hindering the diffusion of the anaerobic process. The first part is focused on the microbiology and extensively presents and characterises phenol-degrading bacteria and biodegradation pathways. In the second part, dedicated to process feasibility, anaerobic and aerobic biodegradation kinetics are analysed and compared, and strategies to enhance process performance, i.e. advanced technologies, bioaugmentation, and biostimulation, are critically analysed and discussed. The final section provides a summary of the research needs. Literature data analysis shows the feasibility of anaerobic phenol biodegradation at laboratory and pilot scale, but there is still a consistent gap between achieved aerobic and anaerobic performance. This is why current research demand is mainly related to the development and optimisation of powerful technologies and effective operation strategies able to enhance the competitiveness of the anaerobic process. Research efforts are strongly justified because the anaerobic process is a step forward to a more sustainable approach in wastewater treatment.Key points• Review of phenol-degraders bacteria and biodegradation pathways.• Anaerobic phenol biodegradation kinetics for metabolic and co-metabolic processes.• Microbial and technological strategies to enhance process performance.

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 datasets (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. δ15N-NO3-: 16.4‰, av. δ18O-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. δ15N-NO3-: 9.5‰, av. δ18O-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.

Influence of artificial drainage system design on the nitrogen attenuation potential of gley soils: Evidence from hydrochemical and isotope studies under field-scale conditions

In North Atlantic Europe intensive dairy farms have a low nitrogen (N) use efficiency, with high N surpluses often negatively affecting water quality. Low feed input systems on heavy textured soils often need artificial drainage to utilise low cost grassland and remain profitable. Heavy textured soils have high but variable N attenuation potential, due to soil heterogeneity. Furthermore, drainage system design can influence the potential for N attenuation and subsequent N loadings in waters receiving drainage from such soils. The present study utilises end of pipe, open ditch and shallow groundwater sampling points across five sites in SW Ireland to compare and rank sites based on N surplus, water quality and "net denitrification", and to develop a conceptual framework for the improved management of heavy textured dairy sites to inform water quality N sustainability. This includes both drainage design and "net denitrification" criterion, as developed within this study.N surplus ranged from 211 to 292 kg N/ha (mean of 252 kg N/sourha) with a common source of organic N across all locations. The predicted soil organic matter (SOM) N release potential from top-subsoil layers was high, ranging from 115 to >146 kg N/ha. Stable isotopes analyses showed spatial variation in the extent of specific N-biotransformation processes, according to drainage location and design. Across all sites, nitrate (NO₃-N) was converted to ammonium (NH₄⁺-N), which migrated offsite through open ditch and shallow groundwater pathways. Using the ensemble data the potential for soil N attenuation could be discriminated by 3 distinct groups reflecting the relative dominance of in situ N-biotransformation processes deduced from water composition: Group 1 (2 farms, ranked with high sustainability, NH₄⁺ < 0.23 mg N/l, δ¹⁵N-NO₃^- > 5‰ and δ¹⁸O-NO₃^- > 10‰), low NH₄⁺-N concentration coupled with a high denitrification potential; Group 2 (1 farm with moderate sustainability, NH₄⁺ < 0.23 mg N/l, δ¹⁵N-NO₃^- < 8‰ and δ¹⁸O-NO₃^- < 8‰), low NH₄⁺-N concentration with a high nitrification potential and a small component of complete denitrification; Group 3 (2 farms, ranked with low sustainability, NH₄⁺ > 0.23 mg N/l, 14‰ > δ¹⁵N-NO₃^- > 5‰ and 25‰ > δ¹⁸O-NO₃^- > -2‰), high NH₄⁺-N concentration due to low denitrification. The installation of a shallow drainage system (e.g. mole or gravel moles at 0.4 m depth) reduced the "net denitrification" ranking of a site, leading to water quality issues. From this detailed work an N sustainability tool for any site, which presents the relationship between drainage class, drainage design (if present), completeness of denitrification, rate of denitrification and NH₄-N attenuation was developed. This tool allows a comparison or ranking of sites in terms of their N sustainability. The tool can also be used pre-land drainage and presents the consequences of future artificial land drainage on water quality and gaseous emissions at a given site.

Impact of pneumococcal conjugate vaccination: a retrospective study of hospitalization for pneumonia in North-East Italy

INTRODUCTION

Pneumonia remains a common reason for hospitalizing infants and the elderly worldwide, and streptococcal infection is often responsible. The aim of this study was to assess the burden of pneumonia in a large general population.

METHODS

All pneumonia-related hospitalizations from 2004 to 2013 in north-east Italy were identified from the hospital records with a first-listed diagnosis on discharge of bacterial pneumonia, or a first-listed diagnosis on discharge of meningitis, septicemia or empyema associated with a secondary diagnosis of bacterial pneumonia. We identified major comorbidities, calculated agespecific case-fatality rates (CFR), and estimated the related cost to the health care system.

RESULTS

Of the 125,722 hospitalizations identified, 96.9% were cases of pneumonia, 2.4% of septicemia, 0.4% of meningitis, and 0.3% of empyema; 75.3% of hospitalizations involved ≥ 65-yearolds. The overall CFR was 12.4%, and it increased with age, peaking in people over 80 (19.6%). The mean annual pneumonia-associated hospitalization rate was 204.6 per 100,000 population, and it peaked in 0- to 4-year-old children (325.6 per 100,000 in males, 288.9 per 100,000 in females), and adults over 65 (844.9 per 100,000 in males, 605.7 per 100,000 in females). Hospitalization rates dropped over the years for the 0-4 year-olds, and rose for people over 80. The estimated overall annual cost of these pneumonia-related hospitalizations was approximately € 41 million.

CONCLUSIONS

This study shows that the burden on resources for pneumonia-related hospitalization is an important public health issue. Prevention remains the most valuable tool for containing pneumonia, and vaccination strategies can help in the primary prevention of infection, possibly reducing the number of cases in all age groups.