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.

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.

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.

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 CODPHA mg-1 CODOA-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.

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.

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.

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 phenol biodegradation: kinetic study and microbial community shifts under high-concentration dynamic loading.

The anaerobic biodegradation of phenol has been realised in a sequencing batch reactor (SBR) under anaerobic conditions with phenol as sole carbon and energy source and with glucose as co-substrate. A step-change increase of phenol loading (from 100 up to 2000 mg/L of phenol concentration in the feed solution) has been applied during the acclimation phase in order to progressively induce the development of a specialised microbial consortium. This approach, combined with the dynamic sequence of operations characterising SBRs and with the high biomass retention time, led to satisfactory phenol and COD removal efficiencies with values > 70% for the highest phenol input (2000 mg/L) fed as the single carbon and energy source. Analysis of removal efficiencies and biodegradation rates suggested that the use of glucose as co-substrate did not induce a significant improvement in process performance. Kinetic tests have been performed at different initial phenol (400-1000 mg/L) and glucose (1880-0 mg/L) concentrations to kinetically characterise the developed biomass: estimated kinetic constants are suitable for application and no inhibitory effect due to high concentrations of phenol has been observed in all investigated conditions. The microbial community has been characterised at different operating conditions through molecular tools: results confirm the successful adaptation-operation approach of the microbial consortium showing a gradual increase in richness and diversity and the occurrence and selection of a high proportion of phenol-degrading genera at the end of the experimentation. Key Points • Anaerobic phenol removal in the range of 70-99% in a sequencing batch reactor. • Negligible effect of co-substrate on removal efficiencies and biodegradation rates. • No biomass inhibition due to phenol concentration in the range of 400-1000 mg/L. • Increasing phenol loads promoted the culture enrichment of phenol-degrading genera.

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.