bluuebunny/crossref_metadata_2025 huggingface dataset:
Isolation and Characterization of a Novel Siphoviridae Phage, vB_AbaS_TCUP2199, Infecting Multidrug-Resistant Acinetobacter baumannii
Authors: Mardiana Meity , Teh Soon-Hian , Lin Ling-Chun , Lin Nien-Tsung
Published: June 2022

Multidrug-resistant Acinetobacter baumannii (MDRAB) is a pathogen recognized as antimicrobial-resistant bacteria involved in healthcare-associated infections. Resistance to antibiotics has made alternative therapies necessary. Bacteriophage therapy is considered a potential solution to treat MDRAB. In this study, we isolated and characterized the phage vB_AbaS_TCUP2199 (TCUP2199), which can infect MDRAB. Morphological analysis revealed that TCUP2199 belongs to the Siphoviridae family. TCUP2199 has a wide host range, can adsorb rapidly (68.28% in 2 min), and has a burst size of 196 PFU/cell. At least 16 distinct structural proteins were visualized by SDS polyacrylamide gel electrophoresis. A stability test showed that TCUP2199 was stable at 37 °C and pH 7. Genome analysis of TCUP2199 showed that it consists of a double-stranded DNA genome of 79,572 bp with a G+C content of 40.39%, which contains 98 putative open reading frames, none of which is closely related to the bacteriophage genome sequence that was found in the public database. TCUP2199 shows similarity in genomic organization and putative packaging mechanism with Achromobacter phage JWF and Pseudoalteromonas phage KB12-38 based on protein BLAST and phylogenetic analysis. Because of those unique characteristics, we consider TCUP2199 to be a novel phage that is suitable for inclusion in a phage cocktail to treat A. baumannii infection.
Aptamer-Based High-Throughput Screening Model for Efficient Selection and Evaluation of Natural Ingredients against SGIV Infection
Authors: Wei Hongling , Guo Zhongbao , Long Yu , Liu Mingzhu , Xiao Jun , Huang Lin , Yu Qing , Li Pengfei
Published: June 2022

Singapore grouper iridovirus (SGIV) causes high economic losses in mariculture. Effective drugs for managing SGIV infection are urgently required. Medicinal plant resources are rich in China. Medicinal plants have a long history and significant curative effects in the treatment of many diseases. Reverse-transcription quantitative real-time PCR is the most commonly used method for detecting virus infection and assessing antiviral efficacy with high accuracy. However, their applications are limited due to high reagent costs and complex time-consuming operations. Aptamers have been applied in some biosensors to achieve the accurate detection of pathogens or diseases through signal amplification. This study aimed to establish an aptamer-based high-throughput screening (AHTS) model for the efficient selection and evaluation of medicinal plants components against SGIV infection. Q2-AHTS is an expeditious, rapid method for selecting medicinal plant drugs against SGIV, which was characterized as being dram, high-speed, sensitive, and accurate. AHTS strategy reduced work intensity and experimental costs and shortened the whole screening cycle for effective ingredients. AHTS should be suitable for the rapid selection of effective components against other viruses, thus further promoting the development of high-throughput screening technology.
Exploring New Routes for Genetic Resistances to Potyviruses: The Case of the Arabidopsis thaliana Phosphoglycerates Kinases (PGK) Metabolic Enzymes
Authors: Diop Mamoudou , Gallois Jean-Luc
Published: June 2022

The development of recessive resistance by loss of susceptibility is a consistent strategy to combat and limit damages caused by plant viruses. Susceptibility genes can be turned into resistances, a feat that can either be selected among the plant’s natural diversity or engineered by biotechnology. Here, we summarize the current knowledge on the phosphoglycerate kinases (PGK), which have emerged as a new class of susceptibility factors to single-stranded positive RNA viruses, including potyviruses. PGKs are metabolic enzymes involved in glycolysis and the carbon reduction cycle, encoded by small multigene families in plants. To fulfil their role in the chloroplast and in the cytosol, PGKs genes encode differentially addressed proteins. Here, we assess the diversity and homology of chloroplastic and cytosolic PGKs sequences in several crops and review the current knowledge on their redundancies during plant development, taking Arabidopsis as a model. We also show how PGKs have been shown to be involved in susceptibility—and resistance—to viruses. Based on this knowledge, and drawing from the experience with the well-characterized translation initiation factors eIF4E, we discuss how PGKs genes, in light of their subcellular localization, function in metabolism, and susceptibility to viruses, could be turned into efficient genetic resistances using genome editing techniques.
Characterization of SARS-CoV-2 Evasion: Interferon Pathway and Therapeutic Options
Authors: Znaidia Mariem , Demeret Caroline , van der Werf Sylvie , Komarova Anastassia V.
Published: June 2022

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is responsible for the current COVID-19 pandemic. SARS-CoV-2 is characterized by an important capacity to circumvent the innate immune response. The early interferon (IFN) response is necessary to establish a robust antiviral state. However, this response is weak and delayed in COVID-19 patients, along with massive pro-inflammatory cytokine production. This dysregulated innate immune response contributes to pathogenicity and in some individuals leads to a critical state. Characterizing the interplay between viral factors and host innate immunity is crucial to better understand how to manage the disease. Moreover, the constant emergence of new SARS-CoV-2 variants challenges the efficacy of existing vaccines. Thus, to control this virus and readjust the antiviral therapy currently used to treat COVID-19, studies should constantly be re-evaluated to further decipher the mechanisms leading to SARS-CoV-2 pathogenesis. Regarding the role of the IFN response in SARS-CoV-2 infection, in this review we summarize the mechanisms by which SARS-CoV-2 evades innate immune recognition. More specifically, we explain how this virus inhibits IFN signaling pathways (IFN-I/IFN-III) and controls interferon-stimulated gene (ISG) expression. We also discuss the development and use of IFNs and potential drugs controlling the innate immune response to SARS-CoV-2, helping to clear the infection.
Viruses of Economic Impact on Tomato Crops in Mexico: From Diagnosis to Management—A Review
Authors: García-Estrada Raymundo Saúl , Diaz-Lara Alfredo , Aguilar-Molina Vivian Hayde , Tovar-Pedraza Juan Manuel
Published: June 2022

Tomato is the most economically important vegetable crop worldwide and the second most important for Mexico. However, viral diseases are among the main limiting factors that affect the productivity of this crop, causing total losses in some cases. This review provides key information and findings on the symptoms, distribution, transmission, detection, and management of diseases caused by viruses of major importance in tomato crops in Mexico. Currently, about 25 viruses belonging to nine different families have been reported infecting tomato in Mexico, but not all of them cause economically significant diseases. Viruses of economic importance include tomato brown rugose fruit virus (ToBRFV), tomato spotted wilt virus (TSWV), tomato yellow leaf curl virus (TYLCV), pepino mosaic virus (PepMV), and tomato marchitez virus (ToMarV). The topics discussed here will provide updated information about the status of these plant viruses in Mexico as well as diverse management strategies that can be implemented according to the specific circumstances of each viral pathosystem. Additionally, a list of tomato-affecting viruses not present in Mexico that are continuous threats to the crop health is included.
Independent Evaluation of Cell Culture Systems for Hepatitis E Virus
Authors: Chew Nicholas , Situ Jianwen , Wu Shusheng , Yao Weiming , Sridhar Siddharth
Published: June 2022

Hepatitis E virus (HEV) infection in humans is primarily caused by genotypes within Paslahepevirus species balayani (HEV-A). Rocahepevirus species ratti (HEV-C1, otherwise known as rat HEV) can also infect humans. HEV grows poorly in cell culture. Recent studies have reported that hyper-confluent cell layers, amphotericin B, MgCl2, progesterone, and dimethyl sulfoxide (DMSO) increase HEV yield in vitro. Here, we describe an independent evaluation of the effectiveness of these modifications in improving the yield of HEV-A genotype 4 (HEV-A4) and HEV-C1 from clinical samples in PLC/PRF/5 cells. We found that amphotericin B, MgCl2, and DMSO increased HEV yield from high-viral-load patient stool samples, while progesterone was not effective. Yield of HEV-C1 was lower than HEV-A4 across all medium conditions, but was boosted by DMSO. HEV-A4 could be maintained for over 18 months in amphotericin B- and MgCl2-containing medium, with the demonstration of viral antigen in supernatants and infected cells. We also evaluated various protocols to remove pseudo-envelopes from cell culture-derived HEV. Treating cell culture supernatant with NP-40 was the most effective. Our findings identify key modifications that boost HEV growth in vitro and illustrate the importance of independent verification of such studies using diverse HEV variants and cell lines.
Filamentous Pseudomonas Phage Pf4 in the Context of Therapy-Inducibility, Infectivity, Lysogenic Conversion, and Potential Application
Authors: Gavric Damir , Knezevic Petar
Published: June 2022

More than 20% of all Pseudomonas aeruginosa are infected with Pf4-related filamentous phage and although their role in virulence of P. aeruginosa strain PAO1 is well documented, its properties related to therapy are not elucidated in detail. The aim of this study was to determine how phage and antibiotic therapy induce Pf4, whether the released virions can infect other strains and how the phage influences the phenotype of new hosts. The subinhibitory concentrations of ciprofloxacin and mitomycin C increased Pf4 production for more than 50% during the first and sixth hour of exposure, respectively, while mutants appearing after infection with obligatory lytic phage at low MOI produced Pf4 more than four times after 12–24 h of treatment. This indicates that production of Pf4 is enhanced during therapy with these agents. The released virions can infect new P. aeruginosa strains, as confirmed for models UCBPP-PA14 (PA14) and LESB58, existing both episomally and in a form of a prophage, as confirmed by PCR, RFLP, and sequencing. The differences in properties of Pf4-infected, and uninfected PA14 and LESB58 strains were obvious, as infection with Pf4 significantly decreased cell autoaggregation, pyoverdine, and pyocyanin production, while significantly increased swimming motility and biofilm production in both strains. In addition, in strain PA14, Pf4 increased cell surface hydrophobicity and small colony variants’ appearance, but also decreased twitching and swarming motility. This indicates that released Pf4 during therapy can infect new strains and cause lysogenic conversion. The infection with Pf4 increased LESB58 sensitivity to ciprofloxacin, gentamicin, ceftazidime, tetracycline, and streptomycin, and PA14 to ciprofloxacin and ceftazidime. Moreover, the Pf4-infected LESB58 was re-sensitized to ceftazidime and tetracycline, with changes from resistant to intermediate resistant and sensitive, respectively. The obtained results open a new field in phage therapy—treatment with selected filamentous phages in order to re-sensitize pathogenic bacteria to certain antibiotics. However, this approach should be considered with precautions, taking into account potential lysogenic conversion.
Systemic Neutralizing Antibodies and Local Immune Responses Are Critical for the Control of SARS-CoV-2
Authors: Chandrasekar Shaswath S. , Phanse Yashdeep , Riel Mariah , Hildebrand Rachel E. , Hanafy Mostafa , Osorio Jorge E. , Abdelgayed Sherein S. , Talaat Adel M.
Published: June 2022

Antibody measurements are primarily used to evaluate experimental and approved COVID-19 vaccines, which is unilateral considering our immune responses’ complex nature. Previously, we showed that nanoparticle plasmid DNA adjuvant system, QAC, and MVA based vaccines were immunogenic against SARS-CoV-2. Here, we report on the protective efficacy of systemic humoral and mucosal cell-mediated immune responses in transgenic mice models against SARS-CoV-2 following nanoparticle immunization. Parenteral, intramuscular administration of QAC-based plasmid DNA vaccine-encoding SARS-CoV-2 S and N led to the induction of significant serum neutralizing humoral responses, which reduced viral burden in the lungs and prevented viral dissemination to the brain. In contrast, the mucosal, intranasal administration of a heterologous vaccine elicited significant mucosal cell-mediated immune responses in the lungs that limited lung viral replication. The presented results demonstrate that serum neutralizing humoral and local lung T-cell immune responses are critical for the control of SARS-CoV-2 replication.
Redesign and Validation of a Real-Time RT-PCR to Improve Surveillance for Avian Influenza Viruses of the H9 Subtype
Authors: Panzarin Valentina , Marciano Sabrina , Fortin Andrea , Brian Irene , D’Amico Valeria , Gobbo Federica , Bonfante Francesco , Palumbo Elisa , Sakoda Yoshihiro , Le Kien Trung , Chu Duc-Huy , Shittu Ismaila , Meseko Clement , Haido Abdoul Malick , Odoom Theophilus , Diouf Mame Nahé , Djegui Fidélia , Steensels Mieke , Terregino Calogero , Monne Isabella
Published: June 2022

Avian influenza viruses of the H9 subtype cause significant losses to poultry production in endemic regions of Asia, Africa and the Middle East and pose a risk to human health. The availability of reliable and updated diagnostic tools for H9 surveillance is thus paramount to ensure the prompt identification of this subtype. The genetic variability of H9 represents a challenge for molecular-based diagnostic methods and was the cause for suboptimal detection and false negatives during routine diagnostic monitoring. Starting from a dataset of sequences related to viruses of different origins and clades (Y439, Y280, G1), a bioinformatics workflow was optimized to extract relevant sequence data preparatory for oligonucleotides design. Analytical and diagnostic performances were assessed according to the OIE standards. To facilitate assay deployment, amplification conditions were optimized with different nucleic extraction systems and amplification kits. Performance of the new real-time RT-PCR was also evaluated in comparison to existing H9-detection methods, highlighting a significant improvement of sensitivity and inclusivity, in particular for G1 viruses. Data obtained suggest that the new assay has the potential to be employed under different settings and geographic areas for a sensitive detection of H9 viruses.
Conformational Changes in Ff Phage Protein gVp upon Complexation with Its Viral Single-Stranded DNA Revealed Using Magic-Angle Spinning Solid-State NMR
Authors: Kedem Smadar , Hassid Roni Rene , Shamir Yoav , Goldbourt Amir
Published: June 2022

Gene V protein (gVp) of the bacteriophages of the Ff family is a non-specific single-stranded DNA (ssDNA) binding protein. gVp binds to viral DNA during phage replication inside host Escherichia coli cells, thereby blocking further replication and signaling the assembly of new phage particles. gVp is a dimer in solution and in crystal form. A structural model of the complex between gVp and ssDNA was obtained via docking the free gVp to structures of short ssDNA segments and via the detection of residues involved in DNA binding in solution. Using solid-state NMR, we characterized structural features of the gVp in complex with full-length viral ssDNA. We show that gVp binds ssDNA with an average distance of 5.5 Å between the amino acid residues of the protein and the phosphate backbone of the DNA. Torsion angle predictions and chemical shift perturbations indicate that there were considerable structural changes throughout the protein upon complexation with ssDNA, with the most significant variations occurring at the ssDNA binding loop and the C-terminus. Our data suggests that the structure of gVp in complex with ssDNA differs significantly from the structure of gVp in the free form, presumably to allow for cooperative binding of dimers to form the filamentous phage particle.
Complete Genome Sequencing of Tick-Borne Encephalitis Virus Directly from Clinical Samples: Comparison of Shotgun Metagenomic and Targeted Amplicon-Based Sequencing
Authors: Zakotnik Samo , Knap Nataša , Bogovič Petra , Zorec Tomaž Mark , Poljak Mario , Strle Franc , Avšič-Županc Tatjana , Korva Miša
Published: June 2022

The clinical presentation of tick-borne encephalitis virus (TBEV) infection varies from asymptomatic to severe meningoencephalitis or meningoencephalomyelitis. The TBEV subtype has been suggested as one of the most important risk factors for disease severity, but TBEV genetic characterization is difficult. Infection is usually diagnosed in the post-viremic phase, and so relevant clinical samples of TBEV are extremely rare and, when present, are associated with low viral loads. To date, only two complete TBEV genomes sequenced directly from patient clinical samples are publicly available. The aim of this study was to develop novel protocols for the direct sequencing of the TBEV genome, enabling studies of viral genetic determinants that influence disease severity. We developed a novel oligonucleotide primer scheme for amplification of the complete TBEV genome. The primer set was tested on 21 clinical samples with various viral loads and collected over a 15-year period using the two most common sequencing platforms. The amplicon-based strategy was compared to direct shotgun sequencing. Using the novel primer set, we successfully obtained nearly complete TBEV genomes (>90% of genome) from all clinical samples, including those with extremely low viral loads. Comparison of consensus sequences of the TBEV genome generated using the novel amplicon-based strategy and shotgun sequencing showed no difference. We conclude that the novel primer set is a powerful tool for future studies on genetic determinants of TBEV that influence disease severity and will lead to a better understanding of TBE pathogenesis.
Sudden Onset of IgA Vasculitis Affecting Vital Organs in Adult Patients following SARS-CoV-2 Vaccines
Authors: Choi Yunjung , Lee Chang Hun , Kim Kyoung Min , Yoo Wan-Hee
Published: June 2022

IgA vasculitis is an immune complex-mediated small-vessel vasculitis that mainly occurs in children and is characterized by palpable purpura, arthralgia, abdominal pain, and glomerulonephritis. We report three cases of new-onset IgA vasculitis involving major organs in adult patients after they received either the ChAdOx1 viral vector (Oxford/AstraZeneca) vaccine or the messenger RNA-1273 (Moderna) vaccine. These cases suggest that COVID-19 vaccines have the potential to trigger IgA vasculitis and indicate that physicians need to monitor for this possible complication.
Cost-Effectiveness of Extending the National Influenza Vaccination Program in South Korea: Does Vaccination of Older Adults Provide Health Benefits to the Entire Population?
Authors: Shin Gyeongseon , Kang Daewon , Cheong Hee Jin , Choi Sang-Eun
Published: June 2022

The South Korean government has successfully improved influenza vaccination coverage for individuals aged 65 years or older as part of its National Immunization Program (NIP). Those aged 50–64 years without funded vaccination care have significantly lower vaccination rates and face a substantial risk of influenza-related complications. We use a dynamic epidemiological and economic model to investigate the cost-effectiveness of expanding the universal vaccine fund to include those aged 50–64. The epidemiological model is estimated using the susceptibility-infection-recovery model and influenza and influenza-like illness incidence rates, which were calculated by the National Health Insurance Service–National Sample Cohort from the 2008/09 to 2012/13 influenza seasons but excluding the 2009/10 season for pandemic influenza A (H1N1). The decision tree economic model is assessed from societal and healthcare sector perspectives. The proposed policy would eliminate 340,000 annual influenza cases and prevent 119 unnecessary deaths. From a societal perspective, the proposed policy would reduce costs by USD 68 million. From a healthcare perspective, the cost is USD 4318 per quality-adjusted life years. Within the study range, sensitivity analyses found consistent cost-effectiveness results. The influenza vaccine for adults aged 50–64 appears to be cost-saving or cost-effective and, thus, should be considered for the NIP.
Reduction of Precautionary Behaviour following Vaccination against COVID-19: A Test on a British Cohort
Authors: Desrichard Olivier , Moussaoui Lisa , Ofosu Nana
Published: June 2022

Background: There is a risk that people vaccinated against COVID-19 will drop or reduce their precautionary behaviours (i.e., a phenomenon of risk homeostasis). Our aim is to assess the occurrence of this effect in a cohort of UK participants who were interviewed 141 days before and 161 days after the start of the vaccination programme. Methods: Of the 765 people who could be followed up before and after the start of the programme and whose vaccination status was known, 178 had not received any injection and 583 were more or less advanced in the process (one vs. two doses since less vs. more than 14 days). The frequency of 14 precautionary behaviours was assessed at both times of measurement, as well as potential covariates (gender, age, comorbidities and history of COVID-19). Results: Controlling for covariates, we didn’t find more decrease in precautionary behaviours among vaccinated individuals, regardless of how far along they were in the process. Conclusion: The results observed in this sample show little risk for a massive change in behaviours among early vaccinated individuals. The pressure to adopt precautionary behaviours remains strong and probably prevents the emergence of a risk homeostasis effect.
Spatial and Temporal Variations of the Water Quality of the Tiflet River, Province of Khemisset, Morocco
Authors: Elassassi Zahra , Ougrad Ihsane , Bedoui Imane , Kara Mohammed , El Bouch Mohmed , Assouguem Amine , Fadli Mohmed , Almeer Rafa , Mohamed Hanan R. H. , Peluso Ilaria , Chaouch Abdelaziz
Published: June 2022

Humanity’s water needs are constantly increasing, however, under the action of humanity themselves, the reserves of this substance are, constantly, deteriorating in quantity and quality. It is, therefore, necessary to preserve the water reserves. However, any development of a hydrosystem’s quality conservation strategy is based on determining the chemical characteristics of its waters. Therefore, the objective of this study is to investigate the spatial and temporal variations of water quality in the Tiflet River, a watercourse in the northwest of Morocco, to estimate its degree of pollution and to determine its main sources of pollution. Thus, eight stations, distributed along the watercourse and positioned taking into account the potential sources of pollution, were fixed, and eleven physicochemical parameters were, seasonally, evaluated. Multivariate statistical techniques were used to assess variations in water quality and identify the main factors responsible for pollution. The results showed that wastewater discharges into the river can increase the water salinity, phosphorus load and organic pollution load of the river. The total loads of nitrogen and nitrate pollution were higher compared to the standard norms in the stations exposed to agricultural pollution and to the leaching of the watersheds, which could aggravate the eutrophication state of the river and stimulate the growth of aquatic vegetation. The organic pollution load recorded in the wet season is low, compared to that recorded in the dry season. Whereas, the nutrient load recorded during the dry season is low, compared to that recorded in the wet season. An overall pollution index was used, classifying surface waters from sub-clean to moderately polluted.
Advances in Ecohydrology for Water Resources Optimization in Arid and Semi-Arid Areas
Authors: Castellini Mirko , Di Prima Simone , Stewart Ryan , Biddoccu Marcella , Rahmati Mehdi , Alagna Vincenzo
Published: June 2022

Conserving water resources is a current challenge that will become increasingly urgent in future due to climate change. The arid and semi-arid areas of the globe are expected to be particularly affected by changes in water availability. Consequently, advances in ecohydrology sciences, i.e., the interplay between ecological and hydrological processes, are necessary to enhance the understanding of the critical zone, optimize water resources’ usage in arid and semi-arid areas, and mitigate climate change. This Special Issue (SI) collected 10 original contributions on sustainable land management and the optimization of water resources in fragile environments that are at elevated risk due to climate change. In this context, the topics mainly concern transpiration, evapotranspiration, groundwater recharge, deep percolation, and related issues. The collection of manuscripts presented in this SI represents knowledge of ecohydrology. It is expected that ecohydrology will have increasing applications in the future. Therefore, it is realistic to assume that efforts to increase environmental sustainability and socio-economic development, with water as a central theme, will have a greater chance of success.
Impact of Participation in Groundwater Market on Farmland, Income, and Water Access: Evidence from Pakistan
Authors: Razzaq Amar , Xiao Meizhen , Zhou Yewang , Liu Hancheng , Abbas Azhar , Liang Wanqi , Naseer Muhammad Asad ur Rehman
Published: June 2022

Groundwater irrigation has a critical role in the sustainability of arable farming in many developing countries including Pakistan. Groundwater irrigation is generally practiced to supplement surface water supplies in Pakistan. Nevertheless, uninterrupted and extensive use of groundwater irrigation has raised several concerns about its sustainability and resultant environmental implications. Due to the scarcity of groundwater and heterogeneity in farmers’ resources, informal groundwater markets have emerged in Pakistan, where farmers trade water using a contractual system. Yet, the effects of these markets on agricultural productivity and equity remain largely unknown. This paper aims to analyze the impact of participation in the groundwater market on farmland utilization, cropping patterns, water access, and income. We analyze these impacts using primary data collected from 360 farmers in three different zones of the country’s largest province. The farmers were categorized as buyers, sellers, and self-users of water. Results indicate that participation in water markets increased agricultural land utilization, evinced by a higher cropping intensity among participants. A horizontal and vertical equity analysis of water markets shows that although large farmers have better access to groundwater irrigation, water market participation improves equity to water access. Based on income inequality measures such as the Gini coefficient and the Lorenz curve, water market participation also improves farmer incomes regardless of farm size. Propensity score matching revealed that wheat yield and income among water-market participants went up by approximately 150 kg and PKR 4503 per acre compared with non-participants. Groundwater market participants’ higher crop productivity and income level suggest that water markets need a thorough revisit in terms of policy focus and institutional support to ensure sustainable rural development.
Empirical Setting of the Water Stressed Baseline Increases the Uncertainty of the Crop Water Stress Index in a Humid Temperate Climate in Different Water Regimes
Authors: Godson-Amamoo Samuel , Kato Tasuku , Katsura Keisuke
Published: June 2022

Water productivity of rice is imperative for global water security. Currently, water saving management techniques have been proposed and applied to rice systems. The crop water stress index (CWSI) is a major index for evaluating crop water use. The utility of the CWSI in rice in a humid temperate climate has been given little attention. Previous studies have focused on upland crops and readily available constant reference baselines, primarily the water stressed baseline (WSB), which does not inherently reflect transpiration flux. This study examined the performance of the estimated non-water stressed baseline (NWSB) and WSB for rice in a humid climate and the CWSI sensitivity under variable reference baseline scenarios in a 2-year pot trial under phytotron and field environment conditions with two rice genotypes (IRAT109 and Takanari) in a flooded (FL) and aerobic (AR) water regime. We observed that the dynamics of CWSI is dependent not only on the water regimes but could be strongly influenced by genotype sensitivity to vapor pressure deficit (VPD). A higher slope (pooled data) in the field environment (−5.68 °C kPa−1) compared to the phytotron (−3.04 °C kPa−1) reflected transpiration water loss sensitivity to VPD thresholds. Further studies with diverse rice germplasms to explore generalizability to field conditions and reformulation of reference baselines considering the VPD threshold sensitivity could prove to be significant.
A Review and Analysis of Water Research, Development, and Management in Bangladesh
Authors: Rahman Ataur , Jahan Sayka , Yildirim Gokhan , Alim Mohammad A. , Haque Md Mahmudul , Rahman Muhammad Muhitur , Kausher A. H. M.
Published: June 2022

This paper presents a review of water research, development, and management in Bangladesh, with examples drawn from the past and present. A bibliometric analysis is adopted here to analyze the water-related publication data of Bangladesh. Water-quality-related research is the dominating research field in Bangladesh as compared to water-quantity (floods and droughts)-related ones. The most productive author was found to be Ahmed KM for water-related publication in Bangladesh. The arsenic contamination in Bangladesh has received the highest attention (13 out of the top 15 highly cited papers are related to arsenic contamination). Climate-change-related topics have been showing an increasing trend in research publications over the last 5 years. Bangladesh Delta Plan 2100, prepared recently, is a visionary master plan that is expected to shape water management in Bangladesh in the coming decades to adapt to climate change. A set of recommendations is made here to achieve sustainable water management in Bangladesh.
Coastal Scenic Quality Assessment of Moroccan Mediterranean Beaches: A Tool for Proper Management
Authors: Er-Ramy Noureddine , Nachite Driss , Anfuso Giorgio , Williams Allan T.
Published: June 2022

This paper focuses on the study of landscape quality of Moroccan Mediterranean coastal areas, with a view to distinguishing exceptional beaches with high scenic value. The main characteristics of 50 beaches along the studied coast were assessed using a coastal scenic evaluation system based on a set of 26 selected parameters, including physical (18) and human (8) parameters. Each parameter was examined via a five-point rating scale, ranging from presence/absence or poor quality (1) to excellent quality (5). A decision index (D) is afterward obtained and used to classify sites into five classes: Class I: D ≥ 0.85, which included 9 sites (18%); Class II: 0.85 > D ≥ 0.65, 10 sites (20%); Class III: 0.65 > D ≥ 0.40, 8 sites (16%); Class IV: 0.40 > D ≥ 0.00, 16 sites (32%); and Class V: D < 0.00, 7 sites (14%). The sites of Belyounech 2, Maresdar, El Hwad, and Dalya are the best examples of Class I and represent extremely attractive coastal landscapes. The sites of Ghandouri, Tangier Municipal, M’Diq, Martil, and Tangier Malabata are examples of degraded urban sites that are very unattractive due to high human pressures. Management efforts in Moroccan coastal landscapes can strengthen the control of human activities and improve the scenic value of the sites. Class II beaches, such as Mrisat, Souani, Taourirt, and Sfiha, could improve and upgrade to Class I through litter cleaning and a regular maintenance program. Using the same principle, Class III sites, such as Sidi Amer O Moussa and Sidi Driss, could improve and upgrade to Class II. Indeed, litter and sewage appear as the main factors of degradation of Moroccan coasts, and many excellent beaches are strongly affected by them. This should be a wakeup call to the Moroccan authorities to take urgent and appropriate management measures.
Quantifying the Trends and Drivers of Ice Thickness in Lakes and Rivers across North America
Authors: Imrit Mohammad Arshad , Yousaf Zahra , Sharma Sapna
Published: June 2022

Monitoring the timing of ice-on and ice-off has been instrumental in estimating the long-term effects of climate change on freshwater lakes and rivers. However, ice thickness has been studied less intensively, both spatially and temporally. Here, we quantified the trends and drivers of ice thickness from 27 lakes and rivers across North America. We found that ice thickness declined on average by 1.2 cm per decade, although ice thickness declined significantly in only four waterbodies. Local winter air temperature, cloud cover, and winter precipitation were the most important determinants of ice thickness, explaining over 81% of the variation in ice thickness. Ice thickness was lower in years and regions with higher air temperatures, high percentage of cloud cover, and high winter precipitation. Our results suggest that warming is contributing to thinning ice, particularly at high latitudes, with potential ramifications to the safety of humans and wildlife populations using freshwater ice for travel and recreation.
Characteristics and Causes of Changing Groundwater Quality in the Boundary Line of the Middle and Lower Yellow River (Right Bank)
Authors: Tong Xiaoxia , Tang Hui , Gan Rong , Li Zitao , He Xinlin , Gu Shuqian
Published: June 2022

The alluvial plain in the middle and lower reaches of the Yellow River is an important agricultural production base that affects groundwater quality. Groundwater quality in the region is related to the residential and production uses of water by local residents. Samples of shallow groundwater and river water were collected from the right bank of the middle and lower reaches of the Yellow River to determine the evolution and causes of hydrochemical characteristics, and the relationship between the hydrochemical evolution of river water and groundwater was explored. The results showed that the shallow groundwater in the area received lateral recharge from the Yellow River water. The closer to the Yellow River the groundwater was, the higher the SO42−, Cl−, and Na+ concentrations and the lower the HCO3− and Mg2+ concentrations were. Agriculture and aquaculture has influenced and complicated the hydrochemical types of shallow groundwater in recent decades. The groundwater in the area was jointly affected by water–rock interactions and evaporation concentrations; a strong cation exchange effect was detected. Arsenic exceeded the limit in some shallow groundwater, which was mainly distributed in the Yellow River alluvial plain and caused by the reductive sedimentary environment of the Yellow River alluvial plain. The “three nitrogen”, NH4+-N, NO2−-N, and NO3−-N, demonstrated sporadic local excesses in shallow groundwater, which were related to human activities, such as aquaculture.
Synergistic Effects and Ecological Responses of Combined In Situ Passivation and Macrophytes toward the Water Quality of a Macrophytes-Dominated Eutrophic Lake
Authors: Yu Wei , Yang Haiquan , Yang Yongqiong , Chen Jingan , Liao Peng , Wang Jingfu , Wu Jiaxi , He Yun , Xu Dan
Published: June 2022

Combined use of in situ passivation and macrophytes is a valuable technology that exerts remarkable effects on aquatic systems. However, the effectiveness and ecological functions of this combined technology for macrophytes-dominated eutrophic (MDE) lakes with organophosphorus-controlled internal phosphorus (P) loading were poorly understood. In this study, aquatic simulation experiments were performed to study the combination of La-modified materials (LMM; La-modified bentonite (LMB), and La/Al co-modified attapulgite (LAA)) with macrophytes (Myriophyllum verticillatum L. (MVL), Hydrilla verticillata (Linn. f.) royle (HVR), and Ceratophyllum demersum L. (CDL)) for the control of P mobility in the water column, and to investigate the passivator effects on the physiological characteristics of macrophytes. The mineralization of organophosphates (BD−Po, HCl−Po, and Res−Po) is an important factor for maintaining high internal P loadings and overlying water P concentrations in the experiments. Compared with individual treatment groups, the reduction of internal P release flux and porewater SRP concentrations was more obvious in the combined treatments. Moreover, the redox-sensitive P forms transformation is more pronounced in the surface sediments. In the LAA+M group, internal P release flux was reduced by 55% and 55% compared with individual passivators and macrophytes retreatment groups, respectively. In contrast, the LMB+M group decreased by 16% and 46%, respectively. Simultaneously, LMM had less effect on macrophytes traits compared with individual macrophytes group and enhanced the absorption of phosphate by macrophytes. The phosphate content of macrophytes in the LAA+M and LMB+M groups increased by 24% and 11%, respectively, in comparison with the individual macrophytes group. Results concluded that the combination of passivator and macrophytes enhanced the effect of ecological restoration and exerts a synergistic effect on internal P pollution with macrophytes.
Effects of Hybrid-Type Artificial Groundwater Recharge and Underground Barrier in a Small Basin
Authors: Choi Myoung-Rak , Kim Gyoo-Bum
Published: June 2022

Climate change is exacerbating water shortages in upstream basins in the Korean peninsula that lack agricultural water supply systems. The basin investigated in this study requires an extra 208 m3·d−1 of agricultural water during May (the busiest month for agriculture). The purpose of this study was to assess a hybrid-artificial recharge and circulation system, which was composed of a hybrid-recharge source and re-infiltration of pumped water in the field, and to estimate yield capacity by a field injection test and a numerical model. Injecting pretreated stream water for 42 d increased groundwater levels in the recharge basin. Water budget analysis in MODFLOW simulations revealed that injecting water increased groundwater levels as well as stream discharge due to the terrain’s gentle slope. To prevent downstream discharge and maintain groundwater levels after injection, we assumed the installation of an underground barrier at the basin outlet in the model, following which changes in groundwater levels and water balance were simulated. Water level was persistently maintained after a ~31-cm water level rise, and 590 m3·d−1 of water could be supplied from the collector well, which can ease water shortages. Therefore, it is necessary to develop structures to prevent recharged water escape when artificially recharging groundwater in small upstream basins. In upstream areas where reservoirs or water supply conduits are unfeasible, artificial recharge systems could solve water shortages.
Groundwater Vulnerability Assessment in the Metaponto Coastal Plain (Basilicata, Italy)
Authors: Canora Filomena , Muzzillo Rosalba , Sdao Francesco
Published: June 2022

This study aims at a groundwater vulnerability assessment of the Metaponto coastal plain, located in the Basilicata region (southern Italy). In the last century, intensive agriculture, zootechnical and industrial activities have significantly changed the plain. These changes led to negative impacts on the hydrogeological system intensifying the risk of the aquifer to pollution. The paper presents the assessment of the intrinsic vulnerability of the coastal aquifer carried out by the GIS-based application of the SINTACS method. It considers several aquifer parameters such as water table depth, effective infiltration, unsaturated conditions, soil media, aquifer media, hydraulic conductivity and topography. Furthermore, the anthropogenic influence in the study area was considered by applying the SINTACS-LU method, in which the parameter of land use (LU) was added. The SINTACS and SINTACS-LU vulnerability indexes were provided by summing the product of ratings and weights assigned to each parameter. The analysis of the intrinsic vulnerability map allowed for determining three classes ranging from low to high vulnerability. In both cases, the southeastern part of the coastal plain, closest to the sea, shows the highest vulnerability class, indicating that it is the most vulnerable to contamination due to the hydrogeological intrinsic factors. The wide central part of the study area shows a moderate class of vulnerability and the low class is scattered in small parts in the northern portion of the plain, which represents the areas less contaminable in space and time in the case of potential pollution. In the SINTACS-LU map, some areas classified as highly vulnerable in the SINTACS method show a minor vulnerability class. These areas are localized in natural and wooded sectors of the Metaponto plain, which are less populated, where human impact on the groundwater is minimal.
Nitrogen Removal of Water and Sediment in Grass Carp Aquaculture Ponds by Mixed Nitrifying and Denitrifying Bacteria and Its Effects on Bacterial Community
Authors: Han Dengfeng , Hu Zhenyi , Li Dapeng , Tang Rong
Published: June 2022

Nitrification and denitrification are important for nitrogen (N) cycling in fish ponds culture, but the effects of nitrifying and denitrifying bacteria concentrations on pond water and sediments remain largely unknown. Here, we used 0, 0.15, 0.30, 0.60 mg/L different concentrations of mixed nitrifying and denitrifying bacteria to repair the pond substrate through an enclosure experiment lasting 15 days. The results showed that the purification effect of nitrifying and denitrifying bacteria was most obvious on pond nitrogen from day 4 to day 7. The optimal relative concentration was 0.60 mg/L for nitrifying and denitrifying bacteria; NH4+-N (ammonia nitrogen) decreased by 75.83%, NO2−-N (nitrite) by 93.09%, NO3−-N (nitrate) by 38.02%, and TN (total nitrogen) by 45.16% in this concentration group on pond water. In one cycle, C/N (carbon/nitrogen) ratio of both water body and bottom sediment significantly increased, but C/N ratio of water body increased more significantly than that of sediment. Water C/N ratio increased by 76.00%, and sediment C/N ratio increased by 51.96% in the 0.60 mg/L concentration group. Amplicon sequencing of pond sediment showed that the change in nitrifying and denitrifying bacterium diversity was consistent with that in water quality index. Dominant nitrifying bacteria had a relatively high percentage, with significant differences in dominant bacterium percentage across different bacterial addition groups, while dominant denitrifying bacterium percentage was not high without significant differences among different groups. The dominant species of nitrifying bacteria were, respectively, Nitrosomonas, Nitrosovibrio, Nitrosospira, and Aeromonas, and the dominant species of denitrifying bacteria were Thauera, Azoarcus, Magnetospirillum, Azospira, and Idiomarina. The correlation analyses showed an aerobic nitrification and facultative anaerobic denitrification in pond sediments. Research shows that the addition of exogenous nitrifying and denitrifying bacteria can effectively reduce the nitrogen load of pond water and sediment. At the concentration of 0.6 mg/L, the nitrogen load of pond water and sediment decreased most obviously, which had the best effect on pond purification.
Conceptual Evaluation of Factors Controlling Groundwater Chemistry in Ad-Dawadmi, Saudi Arabia, Using Visualization and Multiple Lines of Evidence
Authors: Gomaa Hassan E. , Alotibi AbdAllah A. , Charni Mohamed , AlMarri Abdulhadi H. , Gomaa Fatma A.
Published: June 2022

Understanding the hydrogeochemical and physicochemical processes and factors controlling the chemical characteristics of groundwater (GW) is essential in water resources studies. In this work, the authors explored, applied, and evaluated the practicality of a series of analysis methods, exploring their ability to improve the representation of the generic GW chemical datasets. The demonstration resulted in a detailed explanation of findings and interpretations, which benefits newcomers who may not be experts in managing such data. Visualization-based, facile, readily readable, and interpretable graphs were tuned and applied to identify the interconnected controlling factors. The examined varieties were bubble diagrams, 3D surface plots, and scatter box plot matrices. Box plot matrices yielded intensive information about the significant interacting parameters in one graph. Employing bubble diagrams produced vast detail, allowing the identification of the significant processes and enabling the recognition of internally acting mechanisms that were otherwise hidden. The identified GW evolution processes include aerosol dissolution, evaporation, direct and reverse ion exchange, precipitation of calcium salts, flushing out of soil-bounded salts, and rock weathering. pH and HCO3− fluctuations coupled with evaporation were recognized as prominent factors giving rise to the vicious salinization cycle, which is thought to be the process causing the worst deterioration in the GW quality and the salinity within the study area.
Automated versus Manual Mapping of Gravel Pit Lakes from South-Eastern Romania for Detailed Morphometry and Vegetation
Authors: Bretcan Petre , Dunea Daniel , Vintescu Gabriel , Tanislav Danut , Zelenakova Martina , Predescu Laurențiu , Șerban Gheorghe , Borowiak Dariusz , Rus Ioan , Sabău Daniel , Mititelu-Ionuș Oana , Hueci Maria , Moreanu Alexandru , Samoila Eduardt , Nguyen Huu , Frasin Loredana , Mirea Ioana-Alexandra , Muntean Răzvan-Cristian
Published: June 2022

In recent years, the accelerated development of the remote sensing domain and the improvement of the resolution and frequency of satellite images allowed the increase in the accuracy of the evaluation of morphometric characteristics and the spatiotemporal distribution of pit lakes, including the small ones. Our study quantitatively analyzes small-scale pit lakes in the piedmont and subsidence plains from contact with the Getic and Curvature Subcarpathians from Romania using the normalized difference water index (NDWI) and data series, with different resolutions, from Landsat 8, Google Earth, and Sentinel 2A. The problems encountered in extracting the contours of the gravel pit lakes were determined by the different resolution of the images, the uneven quality of the images exported from Google Earth, and an additional challenge was given by the diversity of the analyzed land surfaces, the land use, and the optical properties of the lakes. A comparison of the obtained NDWI values using data series from Sentinel 2A and Landsat 8 highlighted the importance of resolution and also showed a larger spectral difference between the identified water bodies and the surrounding land in favor of Sentinel 2A. Regarding the vegetation-derived indices, superior leaf area index (1.8–3) was recorded in low-lying plains and mixed areas (tall shrubs, wetlands, etc.) because the river banks have increased moisture that supports taller species with denser foliage and the sparsely vegetated areas are located in agricultural crops and in/near villages. Changes in vegetation richness and abundance can be spatiotemporally monitored using indices derived from the spectral bands of satellite imagery.