Resilience of soil bacterial community to irrigation with water of different qualities under Mediterranean climate

Insights into the impact of 6PPD-Q and 6PPD on nitrogen metabolism and microbial community in the anammox system

N-(1,3-Dimethylbutyl)-N'-phenyl-p-phenylenediamine (6PPD) is an antioxidant commonly used in tire manufacturing, and its release into the environment has significantly increased due to rapid urbanization. When subjected to ozonation, 6PPD converts into the harmful pollutant 6PPD quinone (6PPDQ). These substances enter wastewater treatment plants (WWTPs) via stormwater runoff and pipelines, posing significant risks to the functional microorganisms. Anammox, a strictly controlled and sensitive microbial nitrogen removal process, is especially susceptible to the effects of the pollutants. This study investigates the comprehensive impact of 6PPD-Q and 6PPD on anammox communities based on characterization analysis and metagenomics. At environmental concentrations, 6PPD-Q at 200 ng/L-1000 ng/L led to the disintegration of anammox granules. Extended exposure to both 6PPD-Q and 6PPD significantly reduces the population of anammox bacteria (AnAOB). By utilizing organic matter from dead cells and incoming carbonate as a carbon source, the system evolved into a nitrogen metabolism network primarily focused on denitrification and dissimilatory nitrate reduction to ammonium (DNRA). This transformation was accompanied by a reshuffling of the microbial community and associated genes, resulting in an accumulation of NH4+-N. These findings underscore the toxicity of 6PPD-Q and 6PPD to anammox and stress the importance of incorporating 6PPD into regulatory and preventive strategies.

Soil Microbial Communities Changes Along Depth and Contrasting Facing Slopes at the Parque Nacional La Campana, Chile

The Parque Nacional La Campana (PNLC) was recently recognized for its high soil surface microbial richness. Here, we explored the microbial community structure in soil profiles from contrasting facing slopes where sclerophyllous forest (SF) and xerophytic shrubland (XS) develop. Soil physicochemical conditions (dry density, pH, and organic matter C and N isotopic soil signatures) were determined at three depths (5, 10, and 15 cm depths). Amplicon sequencing (16S rRNA and ITS1-5F) and specific quantification (qPCR bacteria, archaea and ammonia-oxidizing archaea, fungi) were used to profile the microbial community. Our results indicate that opposite slopes, with different vegetation types and soil conditions studied potentially explained the spatial variability of the microbial community composition, especially between sites than through soil depth. Discriminative taxa were observed to vary between sites, such as, C. nitrososphaera (ammonia-oxidizing archaea) and Sphingomonas, and bacteria associated with Actinobacteria and Bacteroidetes were predominant in SF and XS, respectively. Fungi affiliated with Humicola and Preussia were more abundant in SF, while Cladosporium and Alternaria were in XS. Higher ASV richness was observed in SF compared to XS, for both prokaryotes and fungi. Furthermore, SF showed a higher number of shared ASVs, while XS showed a decrease in unique ASVs in deeper soil layers. In XS, the genus DA101 (Verrucomicrobia) increases with soil depth, reaching higher levels in SF, while Kaistobacter shows the opposite trend. PNLC soils were a reservoir of redundant microbial functions related to biogeochemical cycles, including symbiotic and phytopathogenic fungi. In conclusion, as with the predominant vegetation, the structure and potential function of microbial life in soil profiles were associated with the contrasting the effect of facing slopes as toposequence effects.

Microbial Diversity of Soil in a Mediterranean Biodiversity Hotspot: Parque Nacional La Campana, Chile

Parque Nacional La Campana (PNLC) is recognized worldwide for its flora and fauna, rather than for its microbial richness. Our goal was to characterize the structure and composition of microbial communities (bacteria, archaea and fungi) and their relationship with the plant communities typical of PNLC, such as sclerophyllous forest, xerophytic shrubland, hygrophilous forest and dry sclerophyllous forest, distributed along topoclimatic variables, namely, exposure, elevation and slope. The plant ecosystems, the physical and chemical properties of organic matter and the soil microbial composition were characterized by massive sequencing (iTag-16S rRNA, V4 and ITS1-5F) from the DNA extracted from the soil surface (5 cm, n = 16). A contribution of environmental variables, particularly related to each location, is observed. Proteobacteria (35.43%), Actinobacteria (32.86%), Acidobacteria (10.07%), Ascomycota (76.11%) and Basidiomycota (15.62%) were the dominant phyla. The beta diversity (~80% in its axes) indicates that bacteria and archaea are linked to their plant categories, where the xerophytic shrub stands out with the most particular microbial community. More specifically, Crenarchaeote, Humicola and Mortierella were dominant in the sclerophyllous forest; Chloroflexi, Cyanobacteria and Alternaria in the xerophytic shrubland; Solicoccozyma in the dry sclerophyllous forest; and Cladophialophora in the hygrophilous forest. In conclusion, the structure and composition of the microbial consortia is characteristic of PNLC's vegetation, related to its topoclimatic variables, which suggests a strong association within the soil microbiome.

Water reuse of treated domestic wastewater in agriculture: Effects on tomato plants, soil nutrient availability and microbial community structure

The reuse of treated wastewater (TWW) in agriculture for crop irrigation is desirable. Crop responses to irrigation with TWW depend on the characteristics of TWW and on intrinsic and extrinsic soil properties. The aim of this study was to assess the response of tomato (Solanum lycopersicum L.) cultivated in five different soils to irrigation with TWW, compared to tap water (TAP) and an inorganic NPK solution (IFW). In addition, since soil microbiota play many important roles in plant growth, a metataxonomic analysis was performed to reveal the prokaryotic community structures of TAP, TWW and IFW treated soil, respectively. A 56-days pot experiment was carried out. Plant biometric parameters, and chemical, biochemical and microbiological properties of different soils were investigated. Shoot and root dry and fresh weights, as well as plant height, were the highest in plants irrigated with IFW followed by those irrigated with TWW, and finally with TAP water. Plant biometric parameters were positively affected by soil total organic carbon (TOC) and nitrogen (TN). Electrical conductivity was increased by TWW and IFW, being such an increase proportional to clay and TOC. Soil available P was not affected by TWW, whereas mineral N increased following their application. Total microbial biomass, as well as, main microbial groups were positively affected by TOC and TN, and increased according to the following order: IFW > TWW > TAP. However, the fungi-to-bacteria ratio was lowered in soil irrigated with TWW because of its adverse effect on fungi. The germicidal effect of sodium hypochlorite on soil microorganisms was affected by soil pH. Nutrients supplied by TWW are not sufficient to meet the whole nutrients requirement of tomato, thus integration by fertilization is required. Bacteria were more stimulated than fungi by TWW, thus leading to a lower fungi-to-bacteria ratio. Interestingly, IFW and TWW treatment led to an increased abundance of Proteobacteria and Acidobacteria phyla and Balneimonas, Rubrobacter, and Steroidobacter genera. This soil microbiota structure modulation paralleled a general decrement of fungi versus bacteria abundance ratio, the increment of electrical conductivity and nitrogen content of soil and an improvement of tomato growth. Finally, the potential adverse effect of TWW added with sodium chloride on soil microorganisms depends on soil pH.

Heterogeneous Antibiotic Resistance Gene Removal Impedes Evaluation of Constructed Wetlands for Effective Greywater Treatment

Microorganisms carrying antimicrobial resistance genes are often found in greywater. As the reuse of greywater becomes increasingly needed, it is imperative to determine how greywater treatment impacts antimicrobial resistance genes (ARGs). Using qPCR and SmartChip™ qPCR, we characterized ARG patterns in greywater microbial communities before, during, and after treatment by a recirculating vertical flow constructed wetland. In parallel, we examined the impact of greywater-treated irrigation on soil, including the occurrence of emerging micropollutants and the taxonomic and ARG compositions of microbial communities. Most ARGs in raw greywater are removed efficiently during the winter season, while some ARGs in the effluents increase in summer. SmartChip™ qPCR revealed the presence of ARGs, such as tetracycline and beta-lactam resistance genes, in both raw and treated greywater, but most abundantly in the filter bed. It also showed that aminoglycoside and vancomycin gene abundances significantly increased after treatment. In the irrigated soil, the type of water (potable or treated greywater) had no specific impact on the total bacterial abundance (16S rRNA gene). No overlapping ARGs were found between treated greywater and greywater-irrigated soil. This study indicates ARG abundance and richness increased after treatment, possibly due to the concentration effects of the filter beds.

Mitigating risks and maximizing sustainability of treated wastewater reuse for irrigation

Scarcity of freshwater for agriculture has led to increased utilization of treated wastewater (TWW), establishing it as a significant and reliable source of irrigation water. However, years of research indicate that if not managed adequately, TWW may deleteriously affect soil functioning and plant productivity, and pose a hazard to human and environmental health. This review leverages the experience of researchers, stakeholders, and policymakers from Israel, the United-States, and Europe to present a holistic, multidisciplinary perspective on maximizing the benefits from municipal TWW use for irrigation. We specifically draw on the extensive knowledge gained in Israel, a world leader in agricultural TWW implementation. The first two sections of the work set the foundation for understanding current challenges involved with the use of TWW, detailing known and emerging agronomic and environmental issues (such as salinity and phytotoxicity) and public health risks (such as contaminants of emerging concern and pathogens). The work then presents solutions to address these challenges, including technological and agronomic management-based solutions as well as source control policies. The concluding section presents suggestions for the path forward, emphasizing the importance of improving links between research and policy, and better outreach to the public and agricultural practitioners. We use this platform as a call for action, to form a global harmonized data system that will centralize scientific findings on agronomic, environmental and public health effects of TWW irrigation. Insights from such global collaboration will help to mitigate risks, and facilitate more sustainable use of TWW for food production in the future.

Dynamic Responses of Rhizosphere Microorganisms to Biogas Slurry Combined with Chemical Fertilizer Application during the Whole Life Cycle of Rice Growth

Biogas slurry combined with chemical fertilizer (BCF) is widely used as a fertilizer in paddy fields and rhizosphere microorganisms are key players in plant growth and reproduction. However, the dynamic responses of rhizosphere microorganisms of field-grown rice to BCF application still remain largely unknown. In this study, a field experiment was conducted in two proximate paddy fields in Chongming Island to study the impacts of BCF on the changes in rhizosphere microorganisms during the whole rice growth, including seedling, tillering, booting, and grain-filling stages, with solely chemical fertilizer (CF) treatment as control. The results showed BCF could increase the N-, P-, and C- levels in paddy water as well as the rhizosphere microbial abundance and diversity compared with control. In particular, the phosphate-solubilizing- and cellulose-decomposing-bacteria (e.g., Bacillus) and fungi (e.g., Mortierella) were more abundant in the rhizosphere of BCF than those of CF. Moreover, these microbes increased markedly at the booting and grain-filling stages in BCF, which could promote rice to obtain available nutrients (P and C). It was noted that denitrifying-like bacteria (e.g., Steroidobacteraceae) decreased and dissimilatory nitrate reduction to ammonia-related bacteria (e.g., Geobacter, Anaeromyxobacter, and Ignavibacterium) increased at the booting and filling stages, which could promote N-availability. TP in paddy water of BCF was most correlated to the bacteria, while COD was the most critical regulator for the fungi. Furthermore, correlation network analysis showed nutrient-cycling-related microorganisms were more closely interconnected in BCF than those in CF. These findings showed the application of biogas slurry plus chemical fertilizer could regulate rhizosphere microorganisms towards a beneficial fertilizer use for rice growth.

Effect of long-term influx of tertiary treated wastewater on native bacterial communities in a dry valley topsoil: 16S rRNA gene-based metagenomic analysis of composition and functional profile

Although dumping treated wastewater into soil might provide nutrients and organic matter, it can also expose the ecosystem to biological and chemical risks. A vital indication of soil health and quality is the soil microbial community. The current work used next-generation 16S rRNA gene amplicon sequencing to evaluate the effects of the long-term influx of tertiary treated wastewater (TWW) into Wadi Uranah, a dry valley in Makkah city, Saudi Arabia, on native topsoil bacterial community composition and predicted functions. The findings demonstrated that neither the compositions of microbial communities nor their predicted functions using PICRUSt2 differed significantly (p > 0.05) between polluted valley soil (PolVS) and unpolluted valley soil (UPVS). Alpha and beta diversity, however, showed that the PolVS samples had a considerably higher level of diversity and variability. Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidetes were the most prevalent phyla in both groups. Noticeable relative variations existed in some metabolic pathways such as cofactor, prosthetic group, electron carrier degradation, aldehyde degradation, and Entner-Doudoroff (ED) pathways. Overall, our findings suggest that because both groups have very similar core microbiomes and functions, the long-term disposal of tertiary TWW into Wadi Uranah may have little to no influence on the composition and function of soil bacterial communities. In addition, the long-term discharge of tertiary TWW after partially treated wastewater's initial disposal may have helped the native soil microbial community recover.

Valorisation of hydrothermal liquefaction wastewater in agriculture: effects on tobacco plants and rhizosphere microbiota

Industrial wastewater obtained from hydrothermal liquefaction (HTL-WW) of food wastes for biofuels production could represent a source of crop nutrients since it is characterized by a high amount of organic and inorganic compounds. In the present work, the potential use of HTL-WW as irrigation water for industrial crops was investigated. The composition of the HTL-WW was rich in nitrogen, phosphorus, and potassium with high level of organic carbon. A pot experiment with Nicotiana tabacum L. plants was conducted using diluted wastewater to reduce the concentration of some chemical elements below the official accepted threshold values. Plants were grown in the greenhouse under controlled conditions for 21 days and irrigated with diluted HTL-WW every 24 hours. Soils and plants were sampled every seven days to evaluate, over time, the effect of wastewater irrigation both on soil microbial populations, through high-throughput sequencing, and plant growth parameters, through the measurement of different biometric indices. Metagenomic results highlighted that, in the HTL-WW treated rhizosphere, the microbial populations shifted via their mechanisms of adaptation to the new environmental conditions, establishing a new balance among bacterial and fungal communities. Identification of microbial taxa occurring in the rhizosphere of tobacco plants during the experiment highlighted that the HTL-WW application improved the growth of Micrococcaceae, Nocardiaceae and Nectriaceae, which included key species for denitrification, organic compounds degradation and plant growth promotion. As a result, irrigation with HTL-WW improved the overall performance of tobacco plants which showed higher leaf greenness and increased number of flowers compared to irrigated control plants. Overall, these results demonstrate the potential feasibility of using of HTL-WW in irrigated agriculture.

River water influenced by shale gas wastewater discharge for paddy irrigation has limited effects on soil properties and microbial communities

The processes of hydraulic fracturing to extract shale gas generate a large amount of wastewater, and the potential impacts of wastewater discharge after treatment are concerning. In this field study, we investigated the effects of the irrigation of paddy fields for 2 consecutive years by river water that has been influenced by shale gas wastewater discharge on soil physicochemical properties, microbial community structure and function, and rice grain quality. The results showed that conductivity, chloride and sulfate ions in paddy soils downstream of the outfall showed an accumulative trend after two years of irrigation, but these changes occurred on a small scale (<500 m). Two-year irrigation did not cause the accumulation of trace metals (barium, cadmium, chromium, copper, lead, strontium, zinc, nickel, and uranium) in soil and rice grains. Among all soil parameters, the accumulation of chloride ions was the most pronounced, with concentrations in the paddy soil at the discharge site 13.3 times higher than at the upstream control site. The use of influenced river water for paddy irrigation positively increased the soil microbial diversity, but these changes occurred after two years of irrigation and did not occur after one year of irrigation. Overall, the use of river water affected by shale gas wastewater discharge for agricultural irrigation has limited effects on agroecosystems over a short period. Nevertheless, the possible negative effects of contaminant accumulation in soil and rice caused by longer-term irrigation should be seriously considered.

Integrated organic and inorganic fertilization and reduced irrigation altered prokaryotic microbial community and diversity in different compartments of wheat root zone contributing to improved nitrogen uptake and wheat yield

The effect of long-term water and integrated fertilization on prokaryotic microorganisms and their regulation for crop nutrient uptake remains unknown. Therefore, the impact of soil water and integrated fertilization after eight years on prokaryotic microbial communities in different compartments of root zone and their association with wheat nitrogen (N) absorption and yield were investigated. The results showed that compared with fertilization treatments (F), water regimes (W) more drastically modulated the prokaryotic microbial community structure and diversity in bulk soil, rhizosphere and endosphere. The increase of irrigation improved the prokaryotic diversity in the rhizosphere and endosphere while decreased the diversity in the bulk soil. Application of organic fertilizers significantly improved soil organic matter (SOM) and nutrient contents, increased rhizosphere and endophytic prokaryotic microbial diversity, and elevated the relative abundance of aerobic ammonia oxidation and nitrification-related functional microorganisms in rhizosphere and endosphere. Increasing irrigation elevated the relative abundance of functional microorganisms related to aerobic ammonia oxidation and nitrification in the rhizosphere and endosphere. Soil water content (SWC) and NH₄⁺-N as well as NO₃^--N were key predictors of prokaryotic microbial community composition under W and F treatments, respectively. Appropriate application of irrigation and organic fertilizers increased the relative abundance of some beneficial bacteria such as Flavobacterium. Water and fertilization treatments regulated the prokaryotic microbial communities of bulk soil, rhizosphere and endosphere by altering SWC and SOM, and provided evidence for the modulation of prokaryotic microorganisms to promote nitrogen uptake and wheat yield under long-term irrigation and fertilization. Conclusively, the addition of organic manure (50 %) with inorganic fertilizers (50 %) and reduced amount of irrigation (pre-sowing and jointing-period irrigation) decreased the application amount of chemical fertilizers and water, while increased SOM and nutrient content, improved prokaryotic diversity, and changed prokaryotic microbial community structure in the wheat root zone, resulting in enhanced nutrient uptake and wheat yield.

Changes of Microbial Diversity in Rhizosphere of Different Cadmium-Gradients Soil under Irrigation with Reclaimed Water

Water scarcity and the uneven distribution of water resources in China have resulted in water shortages for agricultural irrigation in arid and semi-arid areas. Reclaimed water used for agricultural irrigation has become an effective solution in the context of the global water shortage. In order to improve soil productivity and solve the shortage of water resources, we carried out reclaimed water irrigation experiments on polluted soil. Compared with full irrigation treatments, the EC value of reclaimed water under deficit irrigation treatments decreased by 2.89–42.90%, and the content of organic matter increased by 6.31–12.10%. The proportion of Acidobacteria community in soils with different cadmium concentration gradients irrigated with reclaimed water ranged from 13.6% to 30.5%, its relative abundance decreased with the increase of soil cadmium concentration. In particular, the relative abundance of Pseudomonas pathogens in deficit irrigation treatments was lower than that of the full irrigation treatments. RDA analysis showed that the environmental factors that played a leading role in the change of microbial community structure were organic matter and pH. Furthermore, the metabolic function potential of the rhizosphere soil bacterial community in deficit irrigation treatments was higher than that of full irrigation treatments with reclaimed water. This study proved that reclaimed water irrigation for cadmium contaminated soil did not aggravate the pollution level and promoted the soil ecological environment with better microbial community diversity.

Impact of repeated irrigation of lettuce cultures with municipal wastewater on soil bacterial community diversity and composition

The effect of wastewater irrigation on the diversity and composition of bacterial communities of soil mesocosms planted with lettuces was studied over an experiment made of five cultivation campaigns. A limited effect of irrigation with either raw or treated wastewater was observed in both α-diversity and β-diversity of soil bacterial communities. However, the irrigation with wastewater fortified with a complex mixture of fourteen relevant chemicals at 10 μg/L each, including pharmaceutical, biocide, and pesticide active substances, led to a drift in the composition of soil bacterial community. One hundred operational taxonomic units (OTUs) were identified as responsible for changes between treated and fortified wastewater irrigation treatments. Our findings indicate that under a realistic agronomical scenario, the irrigation of vegetables with domestic (treated or raw) wastewater has no effect on soil bacterial communities. Nevertheless, under the worst-case scenario tested here (i.e., wastewater fortified with a mixture of chemicals), non-resilient changes were observed suggesting that continuous/repeated irrigation with wastewater could lead to the accumulation of contaminants in soil and induce changes in bacterial communities with unknown functional consequences.

Response of Rhizosphere Microbial Community in High-PAH-Contaminated Soil Using Echinacea purpurea (L.) Moench

Under polycyclic aromatic hydrocarbon (PAH) pollution conditions (149.17–187.54 mg/kg), we had found the dominant flora of PAHs by observing the response of the soil microbial community after planting purple coneflower (Echinacea purpurea (L.) Moench). In this study, pot experiments were conducted in a growth chamber to explore the changes in the rhizosphere microbial community structure during remediation of heavily PAH-contaminated soil using purple coneflower (Echinacea purpurea (L.) Moench). The phospholipid fatty acid (PLFA) content in the soil was measured during four periods before and after planting, and the results showed that: (i) at 120 days, E. purpurea can regulate the microbial community structure but had no significant effect on soil microbial diversity, (ii) at 120 days, the number of PLFAs characterizing actinomycetes, bacteria, and fungi increased, and both Gram-negative bacteria and Arbuscular mycorrhizal fungi (AMF) were significant with the observed PLFA level (p < 0.05), and (iii) the results indicated that AMF and Gram-negative bacteria represent some of the main factors that can promote the degradation of PAHs. The results obtained in this work are important to future research on PAH-degradation-functional genes and degradation mechanisms of the selection of flora.

Irrigation and Nitrogen Fertilization Alter Soil Bacterial Communities, Soil Enzyme Activities, and Nutrient Availability in Maize Crop

Irrigation and nitrogen (N) fertilization rates are widely used to increase crop growth and yield and promote the sustainable production of the maize crop. However, our understanding of irrigation and N fertilization in the soil microenvironment is still evolving, and further research on soil bacterial communities under maize crop with irrigation and N management in subtropical regions of China is needed. Therefore, we evaluated the responses of two irrigation levels (low and high irrigation water with 60 and 80% field capacity, respectively) and five N fertilization rates [i.e., control (N0), N200 (200 kg N ha^-1), N250 (250 kg N ha^-1), N300 (300 kg N ha^-1), and N350 (350 kg N ha^-1)] on soil bacterial communities, richness, and diversity. We found that both irrigation and N fertilization significantly affected bacterial richness, diversity index, and number of sequences. Low irrigation with N300 treatment has significantly higher soil enzymes activities, soil nutrient content, and bacterial alpha and beta diversity than high irrigation. In addition, the Proteobacteria, Actinobacteriota, Chloroflexi, and Firmicutes were the dominant bacterial phyla under both irrigation regimes. The acidic phosphates, acidic invertase, β-glucosidase, catalase, cellulase, and urease were positively correlated with the Shannon index under both low and high irrigation. Therefore, low irrigation improves soil nutrient utilization by boosting soil enzyme activity, directly affecting soil bacterial communities. It was concluded that greater soil nutrients, enzyme activities with higher bacterial diversity are the main indicators of soil reactivity to low irrigation water and N300 for maintaining soil fertility and soil microbial community balance.

Variation of soil microbial carbon use efficiency (CUE) and its Influence mechanism in the context of global environmental change: a review

Soil microbial carbon utilization efficiency (CUE) is the efficiency with which microorganisms convert absorbed carbon (C) into their own biomass C, also referred to as microorganism growth efficiency. Soil microbial CUE is a critical physiological and ecological parameter in the ecosystem’s C cycle, influencing the processes of C retention, turnover, soil mineralization, and greenhouse gas emission. Understanding the variation of soil microbial CUE and its influence mechanism in the context of global environmental change is critical for a better understanding of the ecosystem’s C cycle process and its response to global changes. In this review, the definition of CUE and its measurement methods are reviewed, and the research progress of soil microbial CUE variation and influencing factors is primarily reviewed and analyzed. Soil microbial CUE is usually expressed as the ratio of microbial growth and absorption, which is divided into methods based on the microbial growth rate, microbial biomass, substrate absorption rate, and substrate concentration change, and varies from 0.2 to 0.8. Thermodynamics, ecological environmental factors, substrate nutrient quality and availability, stoichiometric balance, and microbial community composition all influence this variation. In the future, soil microbial CUE research should focus on quantitative analysis of trace metabolic components, analysis of the regulation mechanism of biological-environmental interactions, and optimization of the carbon cycle model of microorganisms’ dynamic physiological response process.

Ecotoxicological risk assessment of wastewater irrigation on soil microorganisms: Fate and impact of wastewater-borne micropollutants in lettuce-soil system

The implementation of the new Water Reuse regulation in the European Union brings to the forefront the need to evaluate the risks of using wastewater for crop irrigation. Here, a two-tier ecotoxicological risk assessment was performed to evaluate the fate of wastewater-borne micropollutants in soil and their ecotoxicological impact on plants and soil microorganisms. To this end, two successive cultivation campaigns of lettuces were irrigated with wastewater (at agronomical dose (not spiked) and spiked with a mixture of 14 pharmaceuticals at 10 and 100 µg/L each) in a controlled greenhouse experiment. Over the two cultivation campaigns, an accumulation of PPCPs was observed in soil microcosms irrigated with wastewater spiked with 100 μg/L of PPCPs with the highest concentrations detected for clarithromycin, hydrochlorothiazide, citalopram, climbazole and carbamazepine. The abundance of bacterial and fungal communities remained stable over the two cultivation campaigns and was not affected by any of the irrigation regimes applied. Similarly, no changes were observed in the abundance of ammonium oxidizing archaea (AOA) and bacteria (AOB), nor in clade A of commamox no matter the cultivation campaign or the irrigation regime considered. Only a slight increase was detected in clade B of commamox bacteria after the second cultivation campaign. Sulfamethoxazole-resistant and -degrading bacteria were not impacted either. The irrigation regimes had only a limited effect on the bacterial evenness. However, in response to wastewater irrigation the structure of soil bacterial community significantly changed the relative abundance of Acidobacteria, Chloroflexi, Verrucomicrobia, Beta-, Gamma- and Deltaprotebacteria. Twenty-eight operational taxonomic units (OTUs) were identified as responsible for the changes observed within the bacterial communities of soils irrigated with wastewater or with water. Interestingly, the relative abundance of these OTUs was similar in soils irrigated with either spiked or non-spiked irrigation solutions. This indicates that under both agronomical and worst-case scenario the mixture of fourteen PPCPs had no effect on soil bacterial community.

Irrigation has a higher impact on soil bacterial abundance, diversity and composition than nitrogen fertilization

The aim of this study was to assess the effects of irrigation frequency and nitrogen fertilization rate on the abundance, diversity, and composition of soil bacteria in winter wheat. Irrigation, but not nitrogen fertilization, significantly affected the bacterial alpha diversity index. Among the 50 phyla obtained in these treatments, Proteobacteria, Bacteroidetes, Actinobacteria, Acidobacteria, Gemmatimonadetes, and Firmicutes were the predominant phyla. The LEfSe analysis of different treatments indicated that irrigation had a stronger effect on soil bacteria community composition than nitrogen fertilization. Moreover, the soil pH, moisture, available phosphorus (AP), and available potassium (AK) significantly correlated with the relative abundance of dominant bacteria at the phylum, genus, and operational taxonomic unit (OTU) levels. Overall, after three years of irrigation and fertilization treatments, the effect of irrigation on soil bacteria abundance, diversity, and composition of winter wheat was stronger than that of nitrogen fertilization, highlighting the importance of water availability for bacteria communities in semi-arid ecosystems. Inorganic and organic fertilizers should be applied in rotation.

Plant and soil microbial community responses to different water management strategies in an almond crop

Climate change is one of the main challenges facing the agricultural sector as it strives to meet global food needs. In arid and semiarid areas, the scarcity of water imposes the use of alternative sources - such as reclaimed water (RW) or desalinated water (DW) - and of deficit irrigation strategies, such as regulated deficit irrigation (RDI), in order to maintain productivity. The impact of both alternative water sources and RDI strategies on soil microbial communities in conjunction with the crop response has been little studied, and far less in fruit trees. Here, we evaluated the effects of the irrigation water quantity (RDI or the optimal water amount) and quality (DW or saline RW) on: i) the biomass, composition, and activity of the soil microbial community, and ii) the plant agro-physiological response at the level of the water status, nutrients, vegetative growth, and yield of almond trees. The DW-RDI treatment had a lower vegetative growth than the rest, reducing the nutrient requirements and increasing the contents of organic carbon and nitrogen in soil. This coincided with a significant increase in the bacterial biomass and enzyme activities in soil, as well as with a decrease in plant nutrient use efficiencies and yield. Irrigation with RW increased the fungal biomass. When there were no water restrictions (RW-FI), none of the plant agro-physiological parameters were affected; when RDI was applied (RW-RDI), the highest soil sodicity was reached and vegetative growth and yield were negatively affected, although the plant nutrient use efficiencies did not decrease as much as with DW-RDI. In addition, the plant nutrient use efficiencies were negatively correlated with the soil enzyme activities. These results improve our knowledge of the functioning of plant-soil interactions in Mediterranean crops subjected to different irrigation strategies.

Hidden Resistome: Enrichment Reveals the Presence of Clinically Relevant Antibiotic Resistance Determinants in Treated Wastewater-Irrigated Soils

Treated-wastewater (TW) irrigation transfers antibiotic-resistant bacteria (ARB) to soil, but persistence of these bacteria is generally low due to resilience of the soil microbiome. Nonetheless, wastewater-derived bacteria and associated antibiotic resistance genes (ARGs) may persist below detection levels and potentially proliferate under copiotrophic conditions. To test this hypothesis, we exposed soils from microcosm, lysimeter, and field experiments to short-term enrichment in copiotroph-stimulating media. In microcosms, enrichment stimulated growth of multidrug-resistant Escherichia coli up to 2 weeks after falling below detection limits. Lysimeter and orchard soils irrigated in-tandem with either freshwater or TW were subjected to culture-based, qPCR and shotgun metagenomic analyses prior, and subsequent, to enrichment. Although native TW- and freshwater-irrigated soil microbiomes and resistomes were similar to each other, enrichment resulted in higher abundances of cephalosporin- and carbapenem-resistant Enterobacteriaceae and in substantial differences in the composition of microbial communities and ARGs. Enrichment stimulated ARG-harboring Bacillaceae in the freshwater-irrigated soils, whereas in TWW-irrigated soils, ARG-harboring γ-proteobacterial families Enterobacteriaceae and Moraxellaceae were more profuse. We demonstrate that TW-derived ARB and associated ARGs can persist at below detection levels in irrigated soils and believe that similar short-term enrichment strategies can be applied for environmental antimicrobial risk assessment in the future.

Plant Microbiota Beyond Farming Practices: A Review

Plants have always grown and evolved surrounded by numerous microorganisms that inhabit their environment, later termed microbiota. To enhance food production, humankind has relied on various farming practices such as irrigation, tilling, fertilization, and pest and disease management. Over the past few years, studies have highlighted the impacts of such practices, not only in terms of plant health or yields but also on the microbial communities associated with plants, which have been investigated through microbiome studies. Because some microorganisms exert beneficial traits that improve plant growth and health, understanding how to modulate microbial communities will help in developing smart farming and favor plant growth-promoting (PGP) microorganisms. With tremendous cost cuts in NGS technologies, metagenomic approaches are now affordable and have been widely used to investigate crop-associated microbiomes. Being able to engineer microbial communities in ways that benefit crop health and growth will help decrease the number of chemical inputs required. Against this background, this review explores the impacts of agricultural practices on soil- and plant-associated microbiomes, focusing on plant growth-promoting microorganisms from a metagenomic perspective.

Treated wastewater reuse for irrigation: Pros and cons

The appropriateness of using treated wastewater for crop or agricultural irrigation remains a bone of contention among experts and policymakers. Here, we outline and analyze not only the benefits but also the drawbacks of such a practice in order to suggest a way forward. To ensure that our review reflects the state-of-the-art in terms of technological advances and best practices, only literature published in the last decade is considered except for literature on the history of reuse. The review begins by highlighting growing water scarcity, the history of wastewater reuse in agriculture, and the limitations of existing studies. A short overview of the approach used in the write-up is outlined after the introduction. It then proceeds with an in-depth look at three broad areas: environmental impacts, public health impacts, and economic impacts. In terms of environmental impacts, effects on soil quality, water resources, plant growth, and soil microbial communities are analyzed. For each sub-area, the positive effects are described before the negative ones. The same approach is then applied to public health impacts, the focus of which is on human exposure to heavy metals and pathogens, and economic impacts, which are assessed with particular reference to investment cost, financial benefit to wastewater treatment plants (WWTPs), farm expenditure and income. Having weighed the advantages and disadvantages in each area, innovative measures are proposed for optimizing the benefits and mitigating the drawbacks of using treated wastewater for crop irrigation. Special consideration was given to contaminants of emerging concern and the known or perceived environmental and health risks associated with these contaminants.

Neutral electrolyzed oxidizing water is effective for pre-harvest decontamination of fresh produce

Pre-harvest sanitization of irrigation water has potential for reducing pathogen contamination of fresh produce. We compared the sanitizing effects of irrigation water containing neutral electrolyzed oxidizing water (EOW) or sodium hypochlorite (NaClO) on pre-harvest lettuce and baby spinach leaves artificially contaminated with a mixture of Escherichia coli, Salmonella Enteritidis and Listeria innocua (~1 × 108 colony-forming units/mL each resuspended in water containing 100 mg/L dissolved organic carbon, simulating a splash-back scenario from contaminated soil/manure). The microbial load and leaf quality were assessed over 7 days, and post-harvest shelf life evaluated for 10 days. Irrigation with water containing EOW or NaClO at 50 mg/L free chlorine significantly reduced the inoculated bacterial load by ≥ 1.5 log10, whereas tap water irrigation reduced the inoculated bacterial load by an average of 0.5 log10, when compared with untreated leaves. There were no visual effects of EOW or tap water irrigation on baby spinach or lettuce leaf surfaces pre- or post-harvest, whereas there were obvious negative effects of NaClO irrigation on leaf appearance for both plants, including severe necrotic zones and yellowing/browning of leaves. Therefore, EOW could serve as a viable alternative to chemical-based sanitizers for pre-harvest disinfection of minimally processed vegetables.

Domestic wastewater infiltration process in desert sandy soil and its irrigation prospect analysis

Although domestic wastewater and its reclaimed water are alternative water resources in arid region, investigation of their negative effect must be done to prevent environmental pollution. In this paper, a short-term column experiment was conducted to simulate the infiltration process of wastewater in desert soil. Alfalfa was planted and irrigated with fresh water for control (CK), tertiary treated domestic wastewater (TTW), secondary treated domestic wastewater (STW) and raw domestic wastewater untreated (RW). The effect of wastewater application on desert soil, drainage and plant properties was evaluated. Experimental results demonstrated that the tested desert soil has no soil structure, organic matter, nor microbial community while possess high infiltration rate. The use of wastewater significantly improved plant growth, and the biomass of TTW, RW, STW were 5.5, 4.3, 2.9 times of CK. The infiltration rate of water in bare soil was high (high to low: TTW, CK, RW, STW), while plant growth reduced infiltration rate (ca. 40% with TTW and RW). Wastewater irrigation and plant growth decreased soil zeta potential, while increased formation of aggregates and bacterial abundance and diversity in soil. Top soil (0-30 cm) accumulation of nitrogen (N), phosphorus (P), organic matter and E. coli was evidenced and all could go down to deep soil and drainage with constant wastewater use. It was concluded that domestic wastewater had big potential in desert soil vegetation recovering and function restoration. Nevertheless, the N, salt, P and organic matter and E. coli in wastewater could give rise to desert soil and groundwater contamination if improper treatment was used.

Comparative Study on Soil Microbial Diversity and Structure Under Wastewater and Groundwater Irrigation Conditions

Wastewater (WW) irrigation to agricultural soils is one of the most economical and effective water-saving strategies. The effects of WW irrigation on soil microbial communities have gained increasing focus as these effects are not well understood. In this study, the effects of WW and groundwater (GW) irrigation on microbial diversity and structure were compared using the high-throughput sequencing analysis of 16S rDNA amplicons. Soil samples irrigated by WW for several decades and maize soil (loamy) samples irrigated by GW were collected from Luancheng Town, Shijiazhuang City, China. Compared to the GW groups, WW groups exhibited non-significant soil bacterial community abundance at the 0-20 and 20-40 cm depths. WW irrigation significantly altered the bacterial community composition and structures compared to GW irrigation. The relative abundance of Proteobacteria and Firmicutes increased in WW irrigated soil, while Actinobacteria decreased. Moreover, 14 significantly abundant biomarkers from Proteobacteria and Firmicutes that corresponded with WW irrigation were identified. Additionally, WW irrigation enriched some KEGG pathways that corresponded with metabolism and human diseases. The physical and chemical properties of WW irrigated soil may shape the compositions and structures of soil bacterial communities. The findings of this study illuminated the effects of wastewater irrigation on microbial characteristics, which is important for estimating the effects of long-term wastewater irrigation on soil environmental health.

Linking the response of soil microbial community structure in soils to long-term wastewater irrigation and soil depth

Irrigation with treated wastewater (TWW) has become a prevailing agricultural practice due to the scarcity of fresh water resources, which may have a significant impact on the microbial communities that are critical to many biogeochemical processes in soils. However, it is unclear whether there are links between soil microbial responses to long-term irrigation with different sources of wastewater and soil depth. Here we assess the influence of treated domestic (DTWW), leather industry (LTWW) and pharmaceutical (PTWW) wastewater on microbial communities in vertical soil profiles using high-throughput sequencing based on 16S rRNA and internal transcribed spacer (ITS) gene profiling. We found that microbial α-diversity in the vertical profiles of soils was significantly influenced by TWW irrigation. Bacteria and fungi in different soil depths showed distinct responses to TWW; irrigation with TWW markedly increased abundance of bacterial OTUs and inhibited abundance of fungal OTUs. β-diversity analysis showed that the effect of TWW irrigation on microbial communities was greater than the effect of soil depth, and microbes in subsurface soil were more sensitive to different sources of irrigation water. We also found that, based on β-diversity analysis, irrigation with treated industrial wastewater, including LTWW and PTWW, had a greater impact on microbial community structures than DTWW. TWW irrigation significantly affected the composition of indigenous soil microbial communities at different depths and might introduce exogenous microbes into the soil environment. Our work explicitly demonstrates the vertical responses of bacterial and fungal communities in soils to irrigation with TWW from different sources, which can provides insights into the microbial-dominated geochemical processes from the perspective of the entire soil profile under the context of wastewater irrigation.

Effluents of wastewater treatment plants promote the rapid stabilization of the antibiotic resistome in receiving freshwater bodies

Treated wastewater discharged into the environment acts as a disturbance of the natural microbial communities in terms of taxonomic composition and of functional gene pool, including antibiotic resistance genes. We tested whether stochastic and heterogeneous site-specific trajectories or generalities, potentially driven by deterministic processes, control the fate of allochthonous bacteria from anthropogenic sources and the persistence of their functional traits in freshwater. Finding generalities would allow the identification of wastewater treatments that could be effective in abating determinants of antibiotic resistance. We analysed the short-term response of native bacterial communities in waters exposed to the disturbance of wastewater at different dilutions, using a metagenomic approach that revealed both microbial community composition and the scope and abundance of the resistome that can pose indirect risks to human health. We found that the taxonomic composition of the communities after the disturbance was driven by case-specific stochastic processes, whereas the resistome had a deterministic trajectory, rapidly stabilising its functional traits with higher proportions of wastewater effluents, regardless of differences in taxonomic composition, richness of antibiotic resistance genes and of bacterial taxa, phenotypic features of the bacterial communities, and type of wastewater treatment. The observed deterministic proliferation of resistomes in freshwater bodies receiving wastewater effluents, suggests that this process may contribute to the global propagation of antibiotic resistance, and thus calls for new legislations promoting alternative tertiary treatments for the wastewater reuse, and targeting bacterial functional traits and not only bacterial abundances.

Land Use and Seasonal Effects on the Soil Microbiome of a Brazilian Dry Forest

Drylands occupy approximately 41% of the Earth's terrestrial surface. Climate change and land use practices are expected to affect biogeochemical cycling by the soil microbiome in these ecosystems. Understanding how soil microbial community might respond to these drivers is extremely important to mitigate the processes of land degradation and desertification. The Caatinga, an exclusively Brazilian biome composed of an extensive seasonal tropical dry forest, is exposed to variable spatiotemporal rainfall patterns as well as strong human-driven pressures. Herein, an integrated analysis of shotgun metagenomics approach coupled to meteorological data was employed to unravel the impact of seasonality and land use change on soil microbiome from preserved and agriculture-affected experimental fields in Caatinga drylands. Multivariate analysis suggested that microbial communities of preserved soils under seasonal changes were shaped primarily by water deficit, with a strong increase of Actinobacteria and Proteobacteria members in the dry and rainy seasons, respectively. In contrast, nutrient availability notably played a critical role in driving the microbial community in agriculture-affected soils. The strong enrichment of bacterial genera belonging to the poorly-known phylum Acidobacteria ('Candidatus Solibacter' and 'Candidatus Koribacter') in soils from dry season affected by ferti-irrigation practices presupposes a contrasting copiotrophic lifestyle and ecological role in mitigating the impact of chemical fertilization. Functional analyses identify overrepresented genes related to osmotic stress response (synthesis of osmoprotectant compounds, accumulation of potassium ions) and preferential carbon and nitrogen utilization when comparing the microbiome of preserved soils under seasonal changes, reflecting differences in the genetic potential for nutrient cycling and C acquisition in the environment. However, the prevalence of nitrosative stress and denitrification functions in irrigation/fertilization-affected soils of the dry season clearly suggest that nutrient input and disruption of natural water regime may impact biogeochemical cycles linked to the microbial processes, with potential impacts on the ecosystem functionality. These findings help to better understand how natural seasonality and agricultural management differentially affect soil microbial ecology from dry forests, providing support for the development of more sustainable land management in dryland ecosystems.

Root microbiome response to treated wastewater irrigation

With increasing fresh water (FW) scarcity, the use of treated wastewater (TWW) for crop irrigation is expanding globally. Besides clear benefits, some undesired long-term effects of irrigation with this low quality water on plant performance have been reported. As the rhizosphere microbiome can mediate plant-soil interactions, an examination of the response of these organisms to TWW is necessary to understand the full effects of water quality. In the current study, the effects of irrigation water quality on the microbial community structure of soil and roots as well as edaphic properties and plant performance were evaluated. We compared soil and roots microbiomes of two different plant species (tomato and lettuce), each grown in two distinct soils, and irrigated with either FW or TWW. Irrigation with TWW significantly increase soil pH, EC, K, Na and DOC, and decrease plant fruit and shoot weight, relatively to samples irrigated with FW. We calculated the effect size of plant species, soil type, and irrigation water quality on microbial community structure in soil and root. In the roots, plant species and irrigation water were the dominant factors in shaping both total (DNA based) and active (RNA based) microbial communities, with both factors contributing similarly to the observed microbial population. Soil type and irrigation water were the dominant factors shaping the total microbial community in the soil and were of similar magnitude. Irrigation water quality is demonstrated to be a major force in shaping root-associated microbiome, leading to altered microbial community structure in the critical juncture between plant and soil.

The effect of moisture on soil microbial properties and nitrogen cyclers in Mediterranean sweet orange orchards under organic and inorganic fertilization

Water shortage and soil degradation are common environmental stressors encountered in the Mediterranean area. We evaluated how different soil moisture levels, dependent on distance from drip irrigation points, impact on the biological, chemical and physical properties of citrus soil under organic and inorganic fertilization. We measured soil physicochemical properties, basal soil respiration, soil microbial biomass carbon, soil microbial community structure (phospholipid fatty acid assay), bacterial load (16S rRNA gene abundance), enzymatic activities (urease, dehydrogenase, β-glucosidase and acid phosphatase) and abundance of microbial nitrogen cyclers (quantitative PCR). A field experiment was established in an orange orchard (Citrus sinensis) in southeast Spain and eighteen soil samples were taken from each plot to compare the impacts of soil moisture: near (wet, w) or away (dry, d) from drip-irrigation points, in plots with inorganic fertilizers under intensive ploughing (PI) or organic fertilization (OA). The results showed that changes in microbial properties and soil microbial indexes were strongly associated with soil moisture content under both organic and inorganic fertilization, and with organic carbon content. Soil moisture influenced soil aggregation, basal soil respiration, phosphatase activity, bacterial and fungal load (PLFAs) and the abundances of bacterial N cycling genes, including nifH (nitrogen fixation) nirS/K and nosZ genes (denitrification) and amoA-B (bacterial nitrification). The potential for N fixation and denitrification, two microbial processes that are crucial for determining the amount of N in the soil, were improved by increased soil moisture in the proximity of the drip irrigation. Soil OC and total N, which are higher under organic fertilization than under inorganic fertilization, were also shown to be highly correlated with the abundance of the N cycling genes. By controlling irrigation doses and applying organic amendments, it may be possible to increase the microbial abundance and function in soil and support greater fertility of soils.

Assessing Pathogen Presence in an Intensively Tile Drained, Agricultural Watershed

Increases in swine production and concomitant manure application provide beneficial nutrients for crops but also include the potential to spread pathogenic bacteria in the environment. While manure is known to contain a variety of pathogens, little is known regarding the long-term effect of manure application on fate and transport of this diverse set of pathogens into surrounding waterways. We report on the use of 16S-rRNA gene sequencing to detect pathogen-containing genera in the agriculturally dominated South Fork Iowa River watershed, home to approximately 840,000 swine in the 76,000-ha basin. DNA was extracted from monthly grab samples collected from three surface water sites and two main artificial drainage outlets. DNA sequences from water samples were matched with sequences from genera known to contain pathogens using targeted 16S rRNA amplicon sequencing. The specific genera known to contain pathogens were quantified by combining percentage of genera sequence matches with 16S rRNA gene quantitative polymerase chain reaction results. Specifically, abundances of , , and significantly increased in surface water after typical fall manure application. Additionally, the likely transport pathways for specific genera known to contain pathogens were identified. Surface water concentrations were influenced mainly by artificial drainage, whereas was primarily transported to surface waters by runoff events. The results of this study will help us to understand environmental pathways that may be useful for mitigation of the diverse set of pathogenic genera transported in agroecosystems and the capability of manure application to alter existing microbial community structures.

Impact of chlorine dioxide disinfection of irrigation water on the epiphytic bacterial community of baby spinach and underlying soil

The contamination of pathogenic bacteria through irrigation water is a recognized risk factor for fresh produce. Irrigation water disinfection is an intervention strategy that could be applied to reduce the probability of microbiological contamination of crops. Disinfection treatments should be applied ensuring minimum effective doses, which are efficient in inhibiting the microbial contamination while avoiding formation and accumulation of chemical residues. Among disinfection technologies available for growers, chlorine dioxide (ClO₂) represents, after sodium hypochlorite, an alternative disinfection treatment, which is commercially applied by growers in the USA and Spain. However, in most of the cases, the suitability of this treatment has been tested against pathogenic bacteria and low attention have been given to the impact of chemical residues on the bacterial community of the vegetable tissue. The aim of this study was to (i) to evaluate the continual application of chlorine dioxide (ClO₂) as a water disinfection treatment of irrigation water during baby spinach growth in commercial production open fields, and (ii) to determine the subsequent impact of these treatments on the bacterial communities in water, soil, and baby spinach. To gain insight into the changes in the bacterial community elicited by ClO₂, samples of treated and untreated irrigation water as well as the irrigated soil and baby spinach were analyzed using Miseq® Illumina sequencing platform. Next generation sequencing and multivariate statistical analysis revealed that ClO₂ treatment of irrigation water did not affect the diversity of the bacterial community of water, soil and crop, but significant differences were observed in the relative abundance of specific bacterial genera. This demonstrates the different susceptibility of the bacteria genera to the ClO₂ treatment. Based on the obtained results it can be concluded that the phyllosphere bacterial community of baby spinach was more influenced by the soil bacteria community rather than that of irrigation water. In the case of baby spinach, the use of low residual ClO₂ concentrations (approx. 0.25 mg/L) to treat irrigation water decreased the relative abundance of Pseudomonaceae (2.28-fold) and Enterobacteriaceae (2.5-fold) when comparing treated versus untreated baby spinach. Members of these two bacterial families are responsible for food spoilage and foodborne illnesses. Therefore, a reduction of these bacterial families might be beneficial for the crop and for food safety. In general it can be concluded that the constant application of ClO₂ as a disinfection treatment for irrigation water only caused changes in two bacterial families of the baby spinach and soil microbiota, without affecting the major phyla and classes. The significance of these changes in the bacterial community should be further evaluated.

A Review of Environmental Contamination and Health Risk Assessment of Wastewater Use for Crop Irrigation with a Focus on Low and High-Income Countries

Population densities and freshwater resources are not evenly distributed worldwide. This has forced farmers to use wastewater for the irrigation of food crops. This practice presents both positive and negative effects with respect to agricultural use, as well as in the context of environmental contamination and toxicology. Although wastewater is an important source of essential nutrients for plants, many environmental, sanitary, and health risks are also associated with the use of wastewater for crop irrigation due to the presence of toxic contaminants and microbes. This review highlights the harmful and beneficial impacts of wastewater irrigation on the physical, biological, and chemical properties of soil (pH, cations and anions, organic matter, microbial activity). We delineate the potentially toxic element (PTEs) build up in the soil and, as such, their transfer into plants and humans. The possible human health risks associated with the use of untreated wastewater for crop irrigation are also predicted and discussed. We compare the current condition of wastewater reuse in agriculture and the associated environmental and health issues between developing and developed countries. In addition, some integrated sustainable solutions and future perspectives are also proposed, keeping in view the regional and global context, as well as the grounded reality of wastewater use for crop production, sanitary and planning issues, remedial techniques, awareness among civil society, and the role of the government and the relevant stakeholders.

Impact of treated wastewater for irrigation on soil microbial communities

The use of treated wastewater (TWW) for irrigation has been suggested as an alternative to use of fresh water because of the increasing scarcity of fresh water in arid and semiarid regions of the world. However, significant barriers exist to widespread adoption due to some potential contaminants that may have adverse effects on soil quality and or public health. In this study, we investigated the abundance and diversity of bacterial communities and the presence of potential pathogenic bacterial sequences in TWW in comparison to synthetic fresh water (SFW) using pyrosequencing. The results were analyzed using UniFrac coupled with principal coordinate analysis (PCoA) to compare diversity and abundance of different bacterial groups in TWW irrigated soils to soils treated with SFW. Shannon diversity index values (H') suggest that microbial diversity was not significantly different (P<0.086) between soils with TWW and SFW. Pyrosequencing detected sequences of 17 bacterial phyla with Proteobacteria (32.1%) followed by Firmicutes (26.5%) and Actinobacteria (14.3%). Most of the sequences associated with nitrifying bacteria, nitrogen-fixing bacteria, carbon degraders, denitrifying bacteria, potential pathogens, and fecal indicator bacteria were more abundant in TWW than in SFW. Therefore, TWW effluent may contain bacterial that may be very active in many soil functions as well as some potential pathogens.

Quality of Irrigation Water Affects Soil Functionality and Bacterial Community Stability in Response to Heat Disturbance

Anthropogenic activities alter the structure and function of a bacterial community. Furthermore, bacterial communities structured by the conditions the anthropogenic activities present may consequently reduce their stability in response to an unpredicted acute disturbance. The present mesocosm-scale study exposed soil bacterial communities to different irrigation water types, including freshwater, fertilized freshwater, treated wastewater, and artificial wastewater, and evaluated their response to a disturbance caused by heat. These effectors may be considered deterministic and stochastic forces common in agricultural operations of arid and semiarid regions. Bacterial communities under conditions of high mineral and organic carbon availability (artificial wastewater) differed from the native bacterial community and showed a proteobacterial dominance. These bacterial communities had a lower resistance to the heat treatment disturbance than soils under conditions of low resource availability (high-quality treated wastewater or freshwater). The latter soil bacterial communities showed a higher abundance of operational taxonomic units (OTUs) classified as Bacilli These results were elucidated by soil under conditions of high resource availability, which lost higher degrees of functional potential and had a greater bacterial community composition change. However, the functional resilience, after the disturbance ended, was higher under a condition of high resource availability despite the bacterial community composition shift and the decrease in species richness. The functional resilience was directly connected to the high growth rates of certain Bacteroidetes and proteobacterial groups. A high stability was found in samples that supported the coexistence of both resistant OTUs and fast-growing OTUs.IMPORTANCE This report presents the results of a study employing a hypothesis-based experimental approach to reveal the forces involved in determining the stability of a soil bacterial community to disturbance. The resultant postdisturbance bacterial community composition dynamics and functionality were analyzed. The paper demonstrates the relatedness of community structure and stability under cultivation conditions prevalent in an arid area under irrigation with water of different qualities. The use of common agricultural practices to demonstrate these features has not been described before. The combination of a fundamental theoretical issue in ecology with common and concerning disturbances caused by agricultural practice makes this study unique. Furthermore, the results of the present study have applicable importance regarding soil conservation, as it enables a better characterization and monitoring of stressed soil bacterial communities and possible intervention to reduce the stress. It will also be of valued interest in coming years, as fresh water scarcity and the use of alternative water sources are expected to rise globally.

Drylands soil bacterial community is affected by land use change and different irrigation practices in the Mezquital Valley, Mexico

Dryland agriculture nourishes one third of global population, although crop irrigation is often mandatory. As freshwater sources are scarce, treated and untreated wastewater is increasingly used for irrigation. Here, we investigated how the transformation of semiarid shrubland into rainfed farming or irrigated agriculture with freshwater, dam-stored or untreated wastewater affects the total (DNA-based) and active (RNA-based) soil bacterial community composition, diversity, and functionality. To do this we collected soil samples during the dry and rainy seasons and isolated DNA and RNA. Soil moisture, sodium content and pH were the strongest drivers of the bacterial community composition. We found lineage-specific adaptations to drought and sodium content in specific land use systems. Predicted functionality profiles revealed gene abundances involved in nitrogen, carbon and phosphorous cycles differed among land use systems and season. Freshwater irrigated bacterial community is taxonomically and functionally susceptible to seasonal environmental changes, while wastewater irrigated ones are taxonomically susceptible but functionally resistant to them. Additionally, we identified potentially harmful human and phytopathogens. The analyses of 16 S rRNA genes, its transcripts and deduced functional profiles provided extensive understanding of the short-term and long-term responses of bacterial communities associated to land use, seasonality, and water quality used for irrigation in drylands.

Laboratory persistence in soil of thiacloprid, pendimethalin and fenarimol incubated with treated wastewater and dissolved organic matter solutions. Contribution of soil biota

Reutilization of treated wastewater (TWW) in agriculture has continued to grow, especially in areas prone to frequent drought periods. One of the major aspects derived from this practice is the addition of important amounts of organic carbon (OC) that could interfere with the fate of organic contaminants in soils. This study has evaluated the impact of irrigation with a secondary TWW and dissolved OC (DOC) solutions from sewage sludge in the dissipation of thiacloprid (THC), pendimethalin (PDM) and fenarimol (FEN) in an OC-poor agricultural soil under laboratory conditions. The effect on soil microbial activity was also assessed through the measurement of dehydrogenase activity. Biotic processes were the main responsible for the degradation of the three compounds. Results showed that while THC was rapidly degraded (DT₅₀ ≤ 5.5 d), PDM and FEN were moderately persistent in soil (DT₅₀ ≥ 93 d). Incubation with TWW did not modify the decay rate of the three pesticides, but initially inhibited soil biota. Solutions of DOC did not alter the dissipation of FEN, but contrasting effects were observed for THC and PDM. Low DOC concentrations (30 mg L^-1) accelerated THC disappearance, a fact explained by stimulation of endogenous biota rather than by the presence of exogenous microorganisms from the solution. On the other hand, high DOC concentrations (300 mg L^-1) had more influence on the activity of microorganisms at longer times, and showed a trend to enhance the disappearance of the moderately persistent PDM.

Impacts of Long-Term Irrigation of Domestic Treated Wastewater on Soil Biogeochemistry and Bacterial Community Structure

Freshwater scarcity and regulations on wastewater disposal have necessitated the reuse of treated wastewater (TWW) for soil irrigation, which has several environmental and economic benefits. However, TWW irrigation can cause nutrient loading to the receiving environments. We assessed bacterial community structure and associated biogeochemical changes in soil plots irrigated with nitrate-rich TWW (referred to as pivots) for periods ranging from 13 to 30 years. Soil cores (0 to 40 cm) were collected in summer and winter from five irrigated pivots and three adjacently located nonirrigated plots. Total bacterial and denitrifier gene abundances were estimated by quantitative PCR (qPCR), and community structure was assessed by 454 massively parallel tag sequencing (MPTS) of small-subunit (SSU) rRNA genes along with terminal restriction fragment length polymorphism (T-RFLP) analysis of nirK, nirS, and nosZ functional genes responsible for denitrification of the TWW-associated nitrate. Soil physicochemical analyses showed that, regardless of the seasons, pH and moisture contents (MC) were higher in the irrigated (IR) pivots than in the nonirrigated (NIR) plots; organic matter (OM) and microbial biomass carbon (MBC) were higher as a function of season but not of irrigation treatment. MPTS analysis showed that TWW loading resulted in the following: (i) an increase in the relative abundance of Proteobacteria, especially Betaproteobacteria and Gammaproteobacteria; (ii) a decrease in the relative abundance of Actinobacteria; (iii) shifts in the communities of acidobacterial groups, along with a shift in the nirK and nirS denitrifier guilds as shown by T-RFLP analysis. Additionally, bacterial biomass estimated by genus/group-specific real-time qPCR analyses revealed that higher numbers of total bacteria, Acidobacteria, Actinobacteria, Alphaproteobacteria, and the nirS denitrifier guilds were present in the IR pivots than in the NIR plots. Identification of the nirK-containing microbiota as a proxy for the denitrifier community indicated that bacteria belonged to alphaproteobacteria from the Rhizobiaceae family within the agroecosystem studied. Multivariate statistical analyses further confirmed some of the above soil physicochemical and bacterial community structure changes as a function of long-term TWW application within this agroecosystem.

Seasonal effect and anthropogenic impact on the composition of the active bacterial community in Mediterranean orchard soil

Several anthropogenic interventions, common in agriculture, may influence active bacterial communities in soil without affecting their total composition. Therefore, the composition of an active bacterial community in soil may reflect its relation to biogeochemical processes. This issue was addressed during two consecutive years in olive-orchard soil, irrigated with treated wastewater (TWW) in a Mediterranean climate, by following the active (rRNA) and total (rRNA gene) bacterial community in the soil. Although TWW irrigation did not affect the composition of the total soil bacterial community, it had an effect on the active fraction of the community. These results, based on 16S rRNA data, indicate that the organic matter and minerals in TWW were not directly utilized for the rapid proliferation of specific taxonomic groups. Activity levels, manifested by variance in the relative abundance of the active and total communities of selected operational taxonomic units, revealed annual and seasonal fluctuations and fluctuations dependent on the type of irrigation. The potential activity (nitrification rates) and community composition of ammonia-oxidizing bacteria were affected by TWW irrigation, and this group of bacteria was therefore further explored. It was concluded that irrigation with TWW had little effect on "who is there", i.e. which bacteria were present, but influenced "who is active", with a distinct effect on bacteria associated with the biochemical cycling of nitrogen.

Soil microbial community structure is unaltered by plant invasion, vegetation clipping, and nitrogen fertilization in experimental semi-arid grasslands

Global and regional environmental changes often co-occur, creating complex gradients of disturbance on the landscape. Soil microbial communities are an important component of ecosystem response to environmental change, yet little is known about how microbial structure and function respond to multiple disturbances, or whether multiple environmental changes lead to unanticipated interactive effects. Our study used experimental semi-arid grassland plots in a Mediterranean-climate to determine how soil microbial communities in a seasonally variable ecosystem respond to one, two, or three simultaneous environmental changes: exotic plant invasion, plant invasion + vegetation clipping (to simulate common management practices like mowing or livestock grazing), plant invasion + nitrogen (N) fertilization, and plant invasion + clipping + N fertilization. We examined microbial community structure 5-6 years after plot establishment via sequencing of >1 million 16S rRNA genes. Abiotic soil properties (soil moisture, temperature, pH, and inorganic N) and microbial functioning (nitrification and denitrification potentials) were also measured and showed treatment-induced shifts, including altered NO(-) 3 availability, temperature, and nitrification potential. Despite these changes, bacterial and archaeal communities showed little variation in composition and diversity across treatments. Even communities in plots exposed to three interacting environmental changes were similar to those in restored native grassland plots. Historical exposure to large seasonal and inter-annual variations in key soil properties, in addition to prior site cultivation, may select for a functionally plastic or largely dormant microbial community, resulting in a microbial community that is structurally robust to single and multiple environmental changes.

Effects of 100 years wastewater irrigation on resistance genes, class 1 integrons and IncP-1 plasmids in Mexican soil

Long-term irrigation with untreated wastewater can lead to an accumulation of antibiotic substances and antibiotic resistance genes in soil. However, little is known so far about effects of wastewater, applied for decades, on the abundance of IncP-1 plasmids and class 1 integrons which may contribute to the accumulation and spread of resistance genes in the environment, and their correlation with heavy metal concentrations. Therefore, a chronosequence of soils that were irrigated with wastewater from 0 to 100 years was sampled in the Mezquital Valley in Mexico in the dry season. The total community DNA was extracted and the absolute and relative abundance (relative to 16S rRNA genes) of antibiotic resistance genes (tet(W), tet(Q), aadA), class 1 integrons (intI1), quaternary ammonium compound resistance genes (qacE+qacEΔ1) and IncP-1 plasmids (korB) were quantified by real-time PCR. Except for intI1 and qacE+qacEΔ1 the abundances of selected genes were below the detection limit in non-irrigated soil. Confirming the results of a previous study, the absolute abundance of 16S rRNA genes in the samples increased significantly over time (linear regression model, p < 0.05) suggesting an increase in bacterial biomass due to repeated irrigation with wastewater. Correspondingly, all tested antibiotic resistance genes as well as intI1 and korB significantly increased in abundance over the period of 100 years of irrigation. In parallel, concentrations of the heavy metals Zn, Cu, Pb, Ni, and Cr significantly increased. However, no significant positive correlations were observed between the relative abundance of selected genes and years of irrigation, indicating no enrichment in the soil bacterial community due to repeated wastewater irrigation or due to a potential co-selection by increasing concentrations of heavy metals.

Wastewater reuse in irrigation: a microbiological perspective on implications in soil fertility and human and environmental health

The reuse of treated wastewater, in particular for irrigation, is an increasingly common practice, encouraged by governments and official entities worldwide. Irrigation with wastewater may have implications at two different levels: alter the physicochemical and microbiological properties of the soil and/or introduce and contribute to the accumulation of chemical and biological contaminants in soil. The first may affect soil productivity and fertility; the second may pose serious risks to the human and environmental health. The sustainable wastewater reuse in agriculture should prevent both types of effects, requiring a holistic and integrated risk assessment. In this article we critically review possible effects of irrigation with treated wastewater, with special emphasis on soil microbiota. The maintenance of a rich and diversified autochthonous soil microbiota and the use of treated wastewater with minimal levels of potential soil contaminants are proposed as sine qua non conditions to achieve a sustainable wastewater reuse for irrigation.

High throughput profiling of antibiotic resistance genes in urban park soils with reclaimed water irrigation

Reclaimed water irrigation (RWI) in urban environments is becoming popular, due to rapid urbanization and water shortage. The continuous release of residual antibiotics and antibiotic resistance genes (ARGs) from reclaimed water could result in the dissemination of ARGs in the downstream environment. This study provides a comprehensive profile of ARGs in park soils exposed to RWI through a high-throughput quantitative PCR approach. 147 ARGs encoding for resistance to a broad-spectrum of antibiotics were detected among all park soil samples. Aminoglycoside and beta-lactam were the two most dominant types of ARGs, and antibiotic deactivation and efflux pump were the two most dominant mechanisms in these RWI samples. The total enrichment of ARGs varied from 99.3-fold to 8655.3-fold compared to respective controls. Six to 60 ARGs were statistically enriched among these RWI samples. Four transposase genes were detected in RWI samples. TnpA-04 was the most enriched transposase gene with an enrichment was up to 2501.3-fold in Urumqi RWI samples compared with control soil samples. Furthermore, significantly positive correlation was found between ARGs and transposase abundances, indicating that transposase might be involved in the propagation of ARGs. This study demonstrated that RWI resulted in the enrichment of ARGs in urban park soils.

Wastewater irrigation increases the abundance of potentially harmful gammaproteobacteria in soils in Mezquital Valley, Mexico

Wastewater contains large amounts of pharmaceuticals, pathogens, and antimicrobial resistance determinants. Only a little is known about the dissemination of resistance determinants and changes in soil microbial communities affected by wastewater irrigation. Community DNAs from Mezquital Valley soils under irrigation with untreated wastewater for 0 to 100 years were analyzed by quantitative real-time PCR for the presence of sul genes, encoding resistance to sulfonamides. Amplicon sequencing of bacterial 16S rRNA genes from community DNAs from soils irrigated for 0, 8, 10, 85, and 100 years was performed and revealed a 14% increase of the relative abundance of Proteobacteria in rainy season soils and a 26.7% increase in dry season soils for soils irrigated for 100 years with wastewater. In particular, Gammaproteobacteria, including potential pathogens, such as Pseudomonas, Stenotrophomonas, and Acinetobacter spp., were found in wastewater-irrigated fields. 16S rRNA gene sequencing of 96 isolates from soils irrigated with wastewater for 100 years (48 from dry and 48 from rainy season soils) revealed that 46% were affiliated with the Gammaproteobacteria (mainly potentially pathogenic Stenotrophomonas strains) and 50% with the Bacilli, whereas all 96 isolates from rain-fed soils (48 from dry and 48 from rainy season soils) were affiliated with the Bacilli. Up to six types of antibiotic resistance were found in isolates from wastewater-irrigated soils; sulfamethoxazole resistance was the most abundant (33.3% of the isolates), followed by oxacillin resistance (21.9% of the isolates). In summary, we detected an increase of potentially harmful bacteria and a larger incidence of resistance determinants in wastewater-irrigated soils, which might result in health risks for farm workers and consumers of wastewater-irrigated crops.