68,492 results match your criteria soil bacteria


Impact of organic acids and sulfate on the biogeochemical properties of soil from urban subsurface environments.

J Environ Manage 2021 May 10;292:112756. Epub 2021 May 10.

Department of Earth and Environmental Sciences, Korea University, Seoul, South Korea. Electronic address:

Urban subsurface environments are often different from undisturbed subsurface environments due to the impacts of human activities. For example, deterioration of underground infrastructure can introduce elevated levels of Ca, Fe, and heavy metals into subsurface soils and groundwater. Likewise, leakage from sewer systems can lead to contamination by organic C, N, S, and P. Read More

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Heavy metal accumulation by roadside vegetation and implications for pollution control.

PLoS One 2021 13;16(5):e0249147. Epub 2021 May 13.

Department of Geology and Soil Science, Faculty of Forestry and Wood Technology, Mendel University in Brno, Brno, Czech Republic.

Vehicular emissions cause heavy metal pollution and exert negative impacts on environment and roadside vegetation. Wild plants growing along roadsides are capable of absorbing considerable amounts of heavy metals; thus, could be helpful in reducing heavy metal pollution. Therefore, current study inferred heavy metal absorbance capacity of some wild plant species growing along roadside. Read More

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Halotolerant Bacillus spizizenii FMH45 promoting growth, physiological, and antioxidant parameters of tomato plants exposed to salt stress.

Plant Cell Rep 2021 May 13. Epub 2021 May 13.

Laboratory of Environmental Sciences and Sustainable Development (LASED), Sfax Preparatory Engineering Institute, University of Sfax, BP 1172, 3018, Sfax, Tunisia.

Key Message: Bacillus spizizenii is for the first time described as a plant growth salt-tolerant bacterium able to alleviate salt stress in crop plants by improving physiological parameters and antioxidant defense mechanisms. Agricultural soil salinization is a serious issue worldwide affecting agricultural yield. Plant growth promoting bacteria can enhance salt tolerance and plant yield. Read More

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Prokaryotic reverse transcriptases: from retroelements to specialized defense systems.

FEMS Microbiol Rev 2021 May 13. Epub 2021 May 13.

Structure, Dynamics and Function of Rhizobacterial Genomes, Grupo de Ecología Genética de la Rizosfera, Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Profesor Albareda 1, 18008 Granada, Spain.

Reverse transcriptases (RTs) catalyze the polymerization of DNA from an RNA template. These enzymes were first discovered in RNA tumor viruses in 1970, but it was not until 1989 that they were found in prokaryotes as a key component of retrons. Apart from RTs encoded by the "selfish" mobile retroelements known as group II introns, prokaryotic RTs are extraordinarily diverse, but their function has remained elusive. Read More

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Assembly processes lead to divergent soil fungal communities within and among twelve forest ecosystems along a latitudinal gradient.

New Phytol 2021 May 13. Epub 2021 May 13.

Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia.

Latitudinal gradients provide opportunities to better understand soil fungal community assembly and its relationship with vegetation, climate, soil and ecosystem function. Understanding the mechanisms underlying community assembly is essential for predicting compositional responses to changing environments. We quantified the relative importance of stochastic and deterministic processes in structuring soil fungal communities using patterns of community dissimilarity observed within and between twelve natural forests and related these to environmental variation within and among sites. Read More

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[Effects and mechanisms of nitrogen fertilizers on soil and tritrophic interactions in Chinese medicinal plants ecosystem].

Zhongguo Zhong Yao Za Zhi 2021 Apr;46(8):1893-1900

State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences Beijing 100700, China.

Nitrogen is one of the most frequently used fertilizers in growth of Chinese medicinal plants(CMP). As in many other ecosystems, CMP ecosystem is also composed of plant-herbivore-natural enemy(tritrophic) interactions. Nitrogen fertilizer influences the growth and reproduction of CMP, and it is also able to heavily shape the ecosystem functions of CMP ecosystem through bottom-up forces. Read More

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Metagenome dataset of lateritic soil microbiota from Sadaipur, Birbhum, West Bengal, India.

Data Brief 2021 Jun 6;36:107041. Epub 2021 Apr 6.

Post Graduate Department of Biotechnology, St. Xavier's College (Autonomous), 30 Mother Teresa Sarani (Park Street), Kolkata, West Bengal 700016, India.

The data represents the bacterial community profile obtained through metagenomic sequencing of soil sample, collected from the 'Rarh' region of West Bengal, which is characterized by the lateritic badlands dating back to the late Pleistocene. Taxonomic binning and operational taxonomic unit (OTU) prediction of the Illumina sequencing data indicated the abundance Proteobacteria (61%) followed closely by Bacterioidetes (35%). The top two most abundant genera identified, were Sphingobacterium and Acinetobacter respectively. Read More

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Lsr2 and Its Novel Paralogue Mediate the Adjustment of Mycobacterium smegmatis to Unfavorable Environmental Conditions.

mSphere 2021 May 12;6(3). Epub 2021 May 12.

Department of Molecular Microbiology, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland

Lsr2 is a nucleoid-associated protein (NAP) that has been found strictly in actinobacteria, including mycobacteria. It is a functional homolog of histone-like nucleoid-structuring protein (H-NS); it acts as a DNA-bridging protein that plays a role in chromosomal organization and transcriptional regulation. To date, the studies on Lsr2 have focused mainly on In this study, we analyze the role of Lsr2 as a transcription factor in , a saprophytic bacterium whose natural habitat (soil and water) substantially differs from those of the obligatory mycobacterial pathogens. Read More

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Influence of plants and environmental variables on the diversity of soil microbial communities in the Yellow River Delta Wetland, China.

Chemosphere 2021 Jul 15;274:129967. Epub 2021 Feb 15.

Key Laboratory for Applied Technology of Sophisticated Analytical Instrument of Shandong Province, Shandong Analysis and Test Center, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250014, PR China.

Microorganisms play an important role in the biogeochemical cycle and ecological function regulation of wetlands, have a major impact on global climate change and are critical for maintaining the health of the global ecosystem. In order to investigate the relationships among plants, environmental variables, and microbial communities in coastal wetlands in the Yellow River Delta, we selected soils growing plants such as Suaeda salsa, Tamarix chinensis, Phragmites australis, and cotton etc. The results show that there were differences in microbial diversity among areas with different vegetation cover and the microbial abundance in Phragmites australis and Tamarix chinensis areas was higher than that in mudflat, Suaeda glauca and cotton field, plants increased the diversity of soil microorganisms. Read More

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Deciphering Potential Roles of Earthworms in Mitigation of Antibiotic Resistance in the Soils from Diverse Ecosystems.

Environ Sci Technol 2021 May 12. Epub 2021 May 12.

State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.

Earthworms are capable of redistributing bacteria and antibiotic resistance genes (ARGs) through soil profiles. However, our understanding of the earthworm gut microbiome and its interaction with the antibiotic resistome is still lacking. Here, we characterized the earthworm gut and soil microbiome and antibiotic resistome in natural and agricultural ecosystems at a national scale, and microcosm studies and field experiments were also employed to test the potential role of earthworms in dynamics of soil ARGs. Read More

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Effects of Dissolved Organic Matter on the Bioavailability of Heavy Metals During Microbial Dissimilatory Iron Reduction: A Review.

Rev Environ Contam Toxicol 2021 May 13. Epub 2021 May 13.

School of Resources, Environmental and Chemical Engineering, Nanchang University, Nanchang, China.

Dissolved organic matter (DOM), a type of mixture containing complex structures and interactions, has important effects on environmental processes such as the complexation and interface reactions of soil heavy metals. Furthermore, microbial dissimilatory iron reduction (DIR), a key process of soil biogeochemical cycle, is closely related to the migration and transformation of heavy metals and causes the release of DOM by carbon-ferrihydrite associations. This chapter considers the structural properties and characterization techniques of DOM and its interaction with microbial dissimilated iron. Read More

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Identification of c-di-GMP/FleQ-Regulated New Target Genes, Including , Encoding Adenylate Cyclase, in Pseudomonas putida.

mSystems 2021 May 11;6(3). Epub 2021 May 11.

State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China

The bacterial second messenger cyclic diguanylate (c-di-GMP) modulates plankton-to-biofilm lifestyle transition of species through its transcriptional regulatory effector FleQ. FleQ regulates transcription of biofilm- and flagellum-related genes in response to c-di-GMP. Through transcriptomic analysis and FleQ-DNA binding assay, this study identified five new target genes of c-di-GMP/FleQ in , including , , (), (), and Except encoding an outer membrane pore protein and encoding an adenylate cyclase, the functions of the other three genes encoding hypothetical proteins remain unknown. Read More

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Rapid Response of Nitrogen Cycling Gene Transcription to Labile Carbon Amendments in a Soil Microbial Community.

mSystems 2021 May 11;6(3). Epub 2021 May 11.

Center for Ecosystem Science and Society (ECOSS), Northern Arizona University, Flagstaff, Arizona, USA.

Episodic inputs of labile carbon (C) to soil can rapidly stimulate nitrogen (N) immobilization by soil microorganisms. However, the transcriptional patterns that underlie this process remain unclear. In order to better understand the regulation of N cycling in soil microbial communities, we conducted a 48-h laboratory incubation with agricultural soil where we stimulated the uptake of inorganic N by amending the soil with glucose. Read More

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Manure Microbial Communities and Resistance Profiles Reconfigure after Transition to Manure Pits and Differ from Those in Fertilized Field Soil.

mBio 2021 May 11;12(3). Epub 2021 May 11.

Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, Wisconsin, USA

In agricultural settings, microbes and antimicrobial resistance genes (ARGs) have the potential to be transferred across diverse environments and ecosystems. The consequences of these microbial transfers are unclear and understudied. On dairy farms, the storage of cow manure in manure pits and subsequent application to field soil as a fertilizer may facilitate the spread of the mammalian gut microbiome and its associated ARGs to the environment. Read More

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Bio-electrocatalytic remediation of hydrocarbons contaminated soil with integrated natural attenuation and chemical oxidant.

Chemosphere 2021 Apr 26;280:130649. Epub 2021 Apr 26.

Bioengineering and Environmental Sciences Lab (BEES), Department of Energy and Environmental Engineering (DEEE), CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India. Electronic address:

The present study aimed to assess the possibility of integrating natural attenuation (NA) and chemical oxidation (O) with the bio-electrocatalytic remediation (BET) process to remediate petroleum hydrocarbons contaminated soil. Six different reactors were operated, wherein in the first reactor was a NA system, and the second condition to the NA was supplemented with a chemical oxidant (NAO). These systems were compared with BET systems which were differentiated based on the position and distance between the electrodes. Read More

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Carboxylic acid reduction and sulfate-reducing bacteria stabilization combined remediation of Cr (VI)-contaminated soil.

Ecotoxicol Environ Saf 2021 May 8;218:112263. Epub 2021 May 8.

Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Science, Chengdu 610041, China; University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address:

For controlling heavy metal pollution, the utilization of carboxylic acids (CAs) combined with sulfate-reducing bacteria (SRB) for continuous and stable remediation of Cr (VI)-contaminated soil was comprehensively investigated. At pH 3, citrate and lactate had photocatalysis characteristics that enabled them to reduce high Cr (VI) concentrations. The reduction efficiencies of citrate and lactate were 99. Read More

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Evaluation of applying an alkaline green tea/ferrous iron system to lindane remediation impacts to soil and plant growth-promoting microbial community.

Sci Total Environ 2021 May 4;786:147511. Epub 2021 May 4.

Department of Environmental Engineering, National Chung Hsing University, 145 Xingda Road, Taichung 40227, Taiwan.

Application of in situ chemical oxidation or reduction (ISCO/ISCR) technologies for contaminated soil remediation and its subsequent impact on soil is gaining increased attention. Reductive reactivity, generated from green tea (GT) extract mixed with ferrous (Fe) ions under alkaline conditions (the alkaline GT/Fe system), has been considered as a promising ISCR process; however, its impact on soil has never been studied. In this study, the impact of applying the alkaline GT/Fe system on soil was evaluated by analyzing the variations of the soil microbial community, diversity, and richness using next-generation 16S rRNA amplicon sequencing while mimicking the lindane-contaminated soil remediation procedure. Read More

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Using farm management practices to predict Campylobacter prevalence in pastured poultry farms.

Poult Sci 2021 Mar 11;100(6):101122. Epub 2021 Mar 11.

Department of Food Science and Technology, University of Georgia, Athens, GA, USA. Electronic address:

Contamination of poultry products by Campylobacter is often associated with farm management practices and processing plant practices. A longitudinal study was conducted on 11 pastured poultry farms in southeastern United States from 2014 to 2017. In this study, farm practices and processing variables were used as predictors for a random forest (RF) model to predict Campylobacter prevalence in pastured poultry farms and processing environments. Read More

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Effective removal of heavy metals from industrial effluent wastewater by a multi metal and drug resistant Pseudomonas aeruginosa strain RA-14 using integrated sequencing batch reactor.

Environ Res 2021 May 8:111240. Epub 2021 May 8.

Grassland and Forage Division, National Institute of Animal Science, RDA, Seonghwan-Eup, Cheonan-Si, Chungnam, 330-801, Republic of Korea. Electronic address:

Sequencing batch reactor (SBR) is useful in removal of both non-biodegradable and biodegradable contaminants from wastewater. The main aim of the present investigation was to evaluate the potential of biocatalyst strain RA-14 on heavy metal removal under SBR. The selected strain was screened from the soil sediment contaminated with heavy metals. Read More

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Fulvic Acid-Mediated Interfacial Reactions on Exposed Hematite Facets during Dissimilatory Iron Reduction.

Langmuir 2021 May 11. Epub 2021 May 11.

National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, P. R. China.

Although the dual role of natural organic matter (NOM) as an electron shuttle and an electron donor for dissimilatory iron (Fe) reduction has been extensively investigated, the underlying interfacial interactions between various exposed facets and NOM are poorly understood. In this study, fulvic acid (FA), as typical NOM, was used and its effect on the dissimilatory reduction of hematite {001} and {100} by CN-32 was investigated. FA accelerates the bioreduction rates of hematite {001} and {100}, where the rate of hematite {100} is lower than that of hematite {001}. Read More

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The Interaction between Rice Genotype and Magnaporthe oryzae Regulates the Assembly of Rice Root-Associated Microbiota.

Rice (N Y) 2021 May 11;14(1):40. Epub 2021 May 11.

State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China.

Background: Utilizating the plant microbiome to enhance pathogen resistance in crop production is an emerging alternative to the use of chemical pesticides. However, the diversity and structure of the microbiota, and the assembly mechanisms of root-associated microbial communities of plants are still poorly understood.

Results: We invstigated the microbiota of the root endosphere and rhizosphere soils of the rice cultivar Nipponbare (NPB) and its Piz-t-transgenic line (NPB-Piz-t) when infected with the filamentous fungus Magnaporthe oryzae (M. Read More

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Taishania pollutisoli gen. nov., sp. nov., Isolated from Tetrabromobisphenol A-Contaminated Soil.

Curr Microbiol 2021 May 11. Epub 2021 May 11.

Key Lab of Microbiological Engineering of Agricultural Environment, Department of Microbiology, College of Life Sciences, Ministry of Agriculture, Nanjing Agricultural University, 210095, Nanjing, People's Republic of China.

Strain CZZ-1 was isolated from long-term TBBPA-contaminated soil Zaozhuang city, Shandong province, People's Republic of China. CZZ-1 was pink-pigmented, Gram-stain-negative, rod-shaped, non-motile and aerobic. The 16S rRNA gene analysis indicated that strain CZZ-1 shows high similarities to Fluviicola taffensis DSM 16823 (92. Read More

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Differentially expressed microRNAs that target functional genes in mature soybean nodules.

Plant Genome 2021 May 10:e20103. Epub 2021 May 10.

School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, Hong Kong.

MicroRNAs (miRNAs) are important regulators of biological functions in plants. To find out what roles miRNAs play in regulating symbiotic nitrogen fixation (SNF) in soybean [Glycine max (L.) Merr. Read More

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Stimulated saprotrophic fungi in arable soil extend their activities to the rhizosphere and root microbiomes of crop seedlings.

Environ Microbiol 2021 May 10. Epub 2021 May 10.

Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.

Saprotrophic fungi play an important role in ecosystem functioning and plant performance, but their abundance in intensively managed arable soils is low. Saprotrophic fungal biomass in arable soils can be enhanced with amendments of cellulose-rich materials. Here we examined if sawdust-stimulated saprotrophic fungi extend their activity to the rhizosphere of crop seedlings and influence the composition and activity of other rhizosphere and root inhabitants. Read More

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Planococcus soli sp. nov., isolated from antarctic soil.

Antonie Van Leeuwenhoek 2021 May 11. Epub 2021 May 11.

Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 100081, Beijing, People's Republic of China.

A novel bacterial strain, designated C23, was isolated from a soil sample obtained from King George Island, Antarctica. Phenotypic, phylogenetic, chemotaxonomic and molecular analyses were performed on the new isolate. Strain C23 formed orange colonies on agar plates and was Gram-stain-positive. Read More

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Distinctive in-planta acclimation responses to basal growth and acute heat stress were induced in Arabidopsis by cattle manure biochar.

Sci Rep 2021 May 10;11(1):9875. Epub 2021 May 10.

Department of Soil Chemistry, Plant Nutrition and Microbiology, Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, 7505101, Israel.

In-planta mechanisms of biochar (BC)-mediated improved growth were evaluated by examining oxidative stress, metabolic, and hormonal changes of Arabidopsis wild-type plants under basal or acute heat stress (-HS/ + HS) conditions with or without BC (+ BC/-BC). The oxidative stress was evaluated by using Arabidopsis expressing redox-sensitive green fluorescent protein in the plastids (pla-roGFP2). Fresh biomass and inflorescence height were greater in + BC(‒HS) plants than in the -BC(‒HS) plants, despite similar leaf nutrient levels, photosystem II (PSII) maximal efficiencies and similar oxidative poise. Read More

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Risk of groundwater contamination widely underestimated because of fast flow into aquifers.

Proc Natl Acad Sci U S A 2021 May;118(20)

Department of Civil Engineering, University of Bristol, BS8 1TR, Bristol, United Kingdom.

Groundwater pollution threatens human and ecosystem health in many regions around the globe. Fast flow to the groundwater through focused recharge is known to transmit short-lived pollutants into carbonate aquifers, endangering the quality of groundwaters where one quarter of the world's population lives. However, the large-scale impact of such focused recharge on groundwater quality remains poorly understood. Read More

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Bacterial composition, function and the enrichment of plant growth promoting rhizobacteria (PGPR) in differential rhizosphere compartments of Al-tolerant soybean in acidic soil.

Yi Chuan 2021 May;43(5):487-500

Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China.

Low pH with aluminum (Al) toxicity are the main limiting factors affecting crop production in acidic soil. Selection of legume crops with acid tolerance and nitrogen-fixation ability should be one of the effective measures to improve soil quality and promote agricultural production. The role of the rhizosphere microorganisms in this process has raised concerns among the research community. Read More

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A two-component monooxygenase for continuous denitration and dechlorination of chlorinated 4-nitrophenol in Ensifer sp. strain 22-1.

Environ Res 2021 May 7;198:111216. Epub 2021 May 7.

Department of Microbiology, Key Lab of Environmental Microbiology for Agriculture, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China; Jiangsu Key Lab for Solid Organic Waste Utilization, 210095, Nanjing, China. Electronic address:

The environmental fates of chlorinated 4-nitrophenols, 2,6-dichloro-4-nitrophenol (2,6-DCNP) and 2-chloro-4-nitrophenol (2C4NP), mediated via microbial catabolism have attracted great attention due to their high toxicity and persistence in the environment. In this study, a strain of Ensifer sp. 22-1 that was capable of degrading both 2,6-DCNP and 2C4NP was isolated from a halogenated aromatic-contaminated soil sample. Read More

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SARS-CoV-2 and other viruses in soil: An environmental outlook.

Environ Res 2021 May 7;198:111297. Epub 2021 May 7.

Department of Civil and Mechanical Engineering, University of Cassino and Southern Lazio, Via Di Biasio 43, 03043, Cassino, Italy. Electronic address:

In the present review, the authors shed light on the SARS-CoV-2 impact, persistence, and monitoring in the soil environment. With this purpose, several aspects have been deepened: i) viruses in soil ecosystems; ii) direct and indirect impact on the soil before and after the pandemic, and iii) methods for quantification of viruses and SARS-CoV-2 monitoring in soil. Viruses are present in soil (i. Read More

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