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Article ; Online: Legacy effects of rhizodeposits on soil microbiomes: A perspective

Nannipieri, Paolo / Hannula, S. Emilia / Pietramellara, Giacomo / Schloter, Michael / Sizmur, Tom / Pathan, Shamina Imran

Soil Biology and Biochemistry. 2023 Sept., v. 184 p.109107-

2023

Abstract: Plant legacy effects observed in plant-soil feedback experiments have largely been attributed to the root or litter material of the previous plant. The legacy effects of rhizodeposits are defined as changes in the soil microbiome that remain after a ... ...

Abstract	Plant legacy effects observed in plant-soil feedback experiments have largely been attributed to the root or litter material of the previous plant. The legacy effects of rhizodeposits are defined as changes in the soil microbiome that remain after a plant has died or been removed from the soil and caused by the release of substances of various compositions by living plants (rhizodeposits). Rhizodeposit-mediated legacy effects have been largely ignored mainly due to the high spatial and temporal variability of rhizodeposits and difficulties quantifying and tracking them in the rhizosphere. In this perspective article, we discuss what is known about the legacy effects of rhizodeposits and provide ideas for future experiments to improve understanding of this phenomenon. Only a few studies separate rhizodeposit-mediated plant legacy effects from legacy effects of root decomposition. Results from these experiments indicate that rhizodeposit-mediated legacy effects on soil microbial communities may persist for several months to several years, especially if the same crop is cultivated persistently for several years in a ‘conditioning’ phase. Rhizodeposit-mediated legacy effects on fungal communities usually last longer than those on bacterial communities due to fungal life-cycle strategies (spore formation) and slower reproduction rates, compared to bacterial communities. We highlight the need for further experimentation to investigate the influence that the length of a conditioning phase has on the persistence of the legacy effect, differentiate the effect of root exudates from the effects of sloughed root cells, separate the influence of simple sugars from that of high molecular-weight exudates and plant derived compounds with antimicrobial properties, and explore whether plant species diversity influences the nature of the legacy. To address these questions, we propose the use of contemporary tools such as stable isotope probing, plant genetics, and reverse microdialysis. We think that harnessing rhizodeposit-mediated plant legacy effects could be a promising approach to improve sustainable crop production by creating disease-suppressive soils and simulating plant growth-promoting micro-organisms within soil systems.
Keywords	biochemistry ; fungi ; microdialysis ; molecular weight ; plant genetics ; reproduction ; rhizosphere ; soil ; soil biology ; soil microorganisms ; soil-plant interactions ; species diversity ; spores ; stable isotopes ; sustainable agriculture ; temporal variation
Language	English
Dates of publication	2023-09
Publishing place	Elsevier Ltd
Document type	Article ; Online
ZDB-ID	280810-9
ISSN	0038-0717
ISSN	0038-0717
DOI	10.1016/j.soilbio.2023.109107
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Perspective on the status and behaviour of SARS-CoV-2 in soil

Giacomo Pietramellara / Shamina Imran Pathan / Rahul Datta / Valerie Vranová / MariaTeresa Ceccherini / Paolo Nannipieri

Saudi Journal of Biological Sciences, Vol 29, Iss 2, Pp 1014-

2022 Volume 1020

Abstract: Soil contamination by SARS-CoV-2 is highly probable because soil can collect several transporters of the virus, such as fallout aerosols, wastewaters, relatively purified sludges, and organic residues. However, the fate and status of SARS-CoV-2 in soil ... ...

Abstract	Soil contamination by SARS-CoV-2 is highly probable because soil can collect several transporters of the virus, such as fallout aerosols, wastewaters, relatively purified sludges, and organic residues. However, the fate and status of SARS-CoV-2 in soil and the possible risks for human health through contaminated food are unknown. Therefore, this perspective paper discusses the challenges of determining the SARS-CoV-2 in soil and the mechanisms concerning its adsorption, movement, and infectivity in soil, considering what has already been reported by perspective papers published up to May 2021. These issues are discussed, drawing attention to the soil virus bibliography and considering the chemical structure of the virus. The mechanistic understanding of the status and behavior of SARS-CoV-2 in soil requires setting up an accurate determination method. In addition, future researches should provide insights into i) plant uptake and movement inside the plant, ii) virus adsorption and desorption in soil with the relative infectivity, and iii) its effects on soil functions. Models should simulate spatial localization of virus in the soil matrix.
Keywords	SARS-CoV-2 ; Soil ; Virus adsorption ; Desorption ; Biology (General) ; QH301-705.5
Subject code	630
Language	English
Publishing date	2022-02-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
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Article: Perspective on the status and behaviour of SARS-CoV-2 in soil.

Pietramellara, Giacomo / Pathan, Shamina Imran / Datta, Rahul / Vranová, Valerie / Ceccherini, MariaTeresa / Nannipieri, Paolo

Saudi journal of biological sciences

2021 Volume 29, Issue 2, Page(s) 1014–1020

Abstract	Soil contamination by SARS-CoV-2 is highly probable because soil can collect several transporters of the virus, such as fallout aerosols, wastewaters, relatively purified sludges, and organic residues. However, the fate and status of SARS-CoV-2 in soil and the possible risks for human health through contaminated food are unknown. Therefore, this perspective paper discusses the challenges of determining the SARS-CoV-2 in soil and the mechanisms concerning its adsorption, movement, and infectivity in soil, considering what has already been reported by perspective papers published up to May 2021. These issues are discussed, drawing attention to the soil virus bibliography and considering the chemical structure of the virus. The mechanistic understanding of the status and behavior of SARS-CoV-2 in soil requires setting up an accurate determination method. In addition, future researches should provide insights into i) plant uptake and movement inside the plant, ii) virus adsorption and desorption in soil with the relative infectivity, and iii) its effects on soil functions. Models should simulate spatial localization of virus in the soil matrix.
Language	English
Publishing date	2021-09-30
Publishing country	Saudi Arabia
Document type	Journal Article ; Review
ZDB-ID	2515206-3
ISSN	2213-7106 ; 1319-562X
ISSN (online)	2213-7106
ISSN	1319-562X
DOI	10.1016/j.sjbs.2021.09.073
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Article ; Online: The extracellular DNA can baffle the assessment of soil bacterial community, but the effect varies with microscale spatial distribution.

Pathan, Shamina Imran / Arfaioli, Paola / Taskin, Eren / Ceccherini, Maria Teresa / Puglisi, Edoardo / Pietramellara, Giacomo

FEMS microbiology letters

2021 Volume 368, Issue 12

Abstract: Environmental DNA is made-up of intracellular (iDNA) and extracellular (eDNA) pools. In soils, eDNA can be present up to 40% and could distort the assessment of living microorganisms. Distribution of microbial community is inconsistent among different ... ...

Abstract	Environmental DNA is made-up of intracellular (iDNA) and extracellular (eDNA) pools. In soils, eDNA can be present up to 40% and could distort the assessment of living microorganisms. Distribution of microbial community is inconsistent among different size-aggregates, and the persistence and turnover of eDNA are thus uneven. Uneven persistence and distribution of eDNA could lead to heterogeneity in community analysis biases that arise due to eDNA sequences at micro-scale distribution. Here, we investigated the diversity and structure of eDNA and iDNA bacterial communities in bulk soil and different size-aggregates. Significant differences were observed between eDNA and iDNA bacterial diversity and composition. Changes in community composition are more important than the amount of eDNA to assess the biases caused by eDNA in community analysis. Furthermore, variations were also observed in aggregates-levels for eDNA and iDNA community which indicates that colonization pattern of iDNA community and protection of eDNA through absorbance on particle surface within soil-matrix is heterogeneous. Our work provides empirical evidence that eDNA presence could mask the detection of aggregates-level spatial dynamics in soil microbial community and have potential to qualitatively baffle observed live effects of given treatment by adequately muting the actual response dynamics of the soil microbiome.
MeSH term(s)	Bacteria/classification ; Bacteria/genetics ; Bacteria/isolation & purification ; Bias ; Cluster Analysis ; DNA, Bacterial/genetics ; Environmental DNA/genetics ; Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; Soil Microbiology
Chemical Substances	DNA, Bacterial ; Environmental DNA ; RNA, Ribosomal, 16S ; Soil
Language	English
Publishing date	2021-05-27
Publishing country	England
Document type	Journal Article
ZDB-ID	752343-9
ISSN	1574-6968 ; 0378-1097
ISSN (online)	1574-6968
ISSN	0378-1097
DOI	10.1093/femsle/fnab074
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Article ; Online: The pivotal role of cultivar affinity to arbuscular mycorrhizal fungi in determining mycorrhizal responsiveness to water deficit.

Ganugi, Paola / Pathan, Shamina Imran / Zhang, Leilei / Arfaioli, Paola / Benedettelli, Stefano / Masoni, Alberto / Pietramellara, Giacomo / Lucini, Luigi

Phytochemistry

2022 Volume 203, Page(s) 113381

Abstract: Arbuscular mycorrhizal fungi (AMF) have gained remarkable importance, having been proved to alleviate drought stress-induced damage in wheat due to their ability to ameliorate plant water use efficiency and antioxidant enzyme activity. However, despite ... ...

Abstract	Arbuscular mycorrhizal fungi (AMF) have gained remarkable importance, having been proved to alleviate drought stress-induced damage in wheat due to their ability to ameliorate plant water use efficiency and antioxidant enzyme activity. However, despite the current relevance of the topic, the molecular and physiological processes at the base of this symbiosis never consider the single cultivar affinity to mycorrhization as an influencing factor for the metabolic response in the AMF-colonized plant. In the present study, the mycorrhizal affinity of two durum wheat species (T. turgidum subsp. durum (Desf.)) varieties, Iride and Ramirez, were investigated. Successively, an untargeted metabolomics approach has been used to study the fungal contribution to mitigating water deficit in both varieties. Iride and Ramirez exhibited a high and low level of mycorrhizal symbiosis, respectively; resulting in a more remarkable alteration of metabolic pathways in the most colonised variety under water deficit conditions. However, the analysis highlighted the contribution of AMF to mitigating water deficiency in both varieties, resulting in the up- and down-regulation of many amino acids, alkaloids, phenylpropanoids, lipids, and hormones.
MeSH term(s)	Amino Acids/metabolism ; Antioxidants/metabolism ; Hormones/metabolism ; Lipids ; Mycorrhizae/physiology ; Plant Roots/metabolism ; Symbiosis/physiology ; Triticum/metabolism ; Water/metabolism
Chemical Substances	Amino Acids ; Antioxidants ; Hormones ; Lipids ; Water (059QF0KO0R)
Language	English
Publishing date	2022-08-27
Publishing country	England
Document type	Journal Article
ZDB-ID	208884-8
ISSN	1873-3700 ; 0031-9422
ISSN (online)	1873-3700
ISSN	0031-9422
DOI	10.1016/j.phytochem.2022.113381
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Article ; Online: Preliminary evidences of the presence of extracellular DNA single stranded forms in soil.

Pathan, Shamina Imran / Arfaioli, Paola / Ceccherini, Maria Teresa / Ascher-Jenull, Judith / Pietramellara, Giacomo

PloS one

2020 Volume 15, Issue 1, Page(s) e0227296

Abstract: The relevance of extracellular DNA (eDNA) in the soil ecosystem is becoming more and more evident to the scientific community by the progressive discovery of functions accompanying to natural gene transformation. However, despite the increased number of ... ...

Abstract	The relevance of extracellular DNA (eDNA) in the soil ecosystem is becoming more and more evident to the scientific community by the progressive discovery of functions accompanying to natural gene transformation. However, despite the increased number of published articles dedicated to eDNA in soil, so far only few are focused on its single stranded form (eDNAss). The present paper is the first to investigate the quantitative relevance of eDNAss in the total soil eDNA pool, discriminating between its linear (eDNAssl) and circular (eDNAssc) forms and the respective weakly (wa) and tightly (ta) adsorbed fractions. The results showed the prevalence of eDNAss and its linear form in both the total soil eDNA pool and its wa and ta fractions. Both of the eDNAss fractions (linear and circular) were characterized by small fragments.
MeSH term(s)	DNA, Circular/isolation & purification ; DNA, Single-Stranded/isolation & purification ; Environmental DNA/isolation & purification ; Italy ; Soil/chemistry
Chemical Substances	DNA, Circular ; DNA, Single-Stranded ; Environmental DNA ; Soil
Language	English
Publishing date	2020-01-07
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0227296
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Article ; Online: Extracellular DNA in natural environments: features, relevance and applications.

Nagler, Magdalena / Insam, Heribert / Pietramellara, Giacomo / Ascher-Jenull, Judith

Applied microbiology and biotechnology

2018 Volume 102, Issue 15, Page(s) 6343–6356

Abstract: Extracellular DNA (exDNA) is abundant in many habitats, including soil, sediments, oceans and freshwater as well as the intercellular milieu of metazoa. For a long time, its origin has been assumed to be mainly lysed cells. Nowadays, research is ... ...

Abstract	Extracellular DNA (exDNA) is abundant in many habitats, including soil, sediments, oceans and freshwater as well as the intercellular milieu of metazoa. For a long time, its origin has been assumed to be mainly lysed cells. Nowadays, research is collecting evidence that exDNA is often secreted actively and is used to perform a number of tasks, thereby offering an attractive target or tool for biotechnological, medical, environmental and general microbiological applications. The present review gives an overview on the main research areas dealing with exDNA, depicts its inherent origins and functions and deduces the potential of existing and emerging exDNA-based applications. Furthermore, it provides an overview on existing extraction methods and indicates common pitfalls that should be avoided whilst working with exDNA.
MeSH term(s)	DNA/analysis ; DNA/isolation & purification ; DNA/metabolism ; Environment ; Extracellular Space/chemistry ; Genetic Techniques/standards ; Genetic Techniques/trends ; Research/trends
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2018-06-01
Publishing country	Germany
Document type	Journal Article ; Review
ZDB-ID	392453-1
ISSN	1432-0614 ; 0171-1741 ; 0175-7598
ISSN (online)	1432-0614
ISSN	0171-1741 ; 0175-7598
DOI	10.1007/s00253-018-9120-4
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Article ; Online: The pivotal role of cultivar affinity to arbuscular mycorrhizal fungi in determining mycorrhizal responsiveness to water deficit

Ganugi, Paola / Pathan, Shamina Imran / Zhang, Leilei / Arfaioli, Paola / Benedettelli, Stefano / Masoni, Alberto / Pietramellara, Giacomo / Lucini, Luigi

Phytochemistry. 2022 Nov., v. 203 p.113381-

2022

Abstract	Arbuscular mycorrhizal fungi (AMF) have gained remarkable importance, having been proved to alleviate drought stress-induced damage in wheat due to their ability to ameliorate plant water use efficiency and antioxidant enzyme activity. However, despite the current relevance of the topic, the molecular and physiological processes at the base of this symbiosis never consider the single cultivar affinity to mycorrhization as an influencing factor for the metabolic response in the AMF-colonized plant. In the present study, the mycorrhizal affinity of two durum wheat species (T. turgidum subsp. durum (Desf.)) varieties, Iride and Ramirez, were investigated. Successively, an untargeted metabolomics approach has been used to study the fungal contribution to mitigating water deficit in both varieties. Iride and Ramirez exhibited a high and low level of mycorrhizal symbiosis, respectively; resulting in a more remarkable alteration of metabolic pathways in the most colonised variety under water deficit conditions. However, the analysis highlighted the contribution of AMF to mitigating water deficiency in both varieties, resulting in the up- and down-regulation of many amino acids, alkaloids, phenylpropanoids, lipids, and hormones.
Keywords	antioxidant enzymes ; biochemical pathways ; cultivars ; drought ; durum wheat ; enzyme activity ; fungi ; metabolomics ; phenylpropanoids ; plant biochemistry ; vesicular arbuscular mycorrhizae ; water use efficiency ; T. turgidum subsp. Durum (Desf.) Husn ; Poaceae ; UHPLC-ESI/QTOF-MS ; Multivariate analysis ; Differential metabolites ; Mycorrhizal affinity ; Water stress
Language	English
Dates of publication	2022-11
Publishing place	Elsevier Ltd
Document type	Article ; Online
ZDB-ID	208884-8
ISSN	1873-3700 ; 0031-9422
ISSN (online)	1873-3700
ISSN	0031-9422
DOI	10.1016/j.phytochem.2022.113381
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Genetic variability assessment of 127 Triticum turgidum L. accessions for mycorrhizal susceptibility-related traits detection.

Ganugi, Paola / Masoni, Alberto / Sbrana, Cristiana / Dell'Acqua, Matteo / Pietramellara, Giacomo / Benedettelli, Stefano / Avio, Luciano

Scientific reports

2021 Volume 11, Issue 1, Page(s) 13426

Abstract: Positive effects of arbuscular mycorrhizal fungi (AMF)-wheat plant symbiosis have been well discussed by research, while the actual role of the single wheat genotype in establishing this type of association is still poorly investigated. In this work, the ...

Abstract	Positive effects of arbuscular mycorrhizal fungi (AMF)-wheat plant symbiosis have been well discussed by research, while the actual role of the single wheat genotype in establishing this type of association is still poorly investigated. In this work, the genetic diversity of Triticum turgidum wheats was exploited to detect roots susceptibility to AMF and to identify genetic markers in linkage with chromosome regions involved in this symbiosis. A tetraploid wheat collection of 127 accessions was genotyped using 35K single-nucleotide polymorphism (SNP) array and inoculated with the AMF species Funneliformis mosseae (F. mosseae) and Rhizoglomus irregulare (R. irregulare), and a genome-wide association study (GWAS) was conducted. Six clusters of genetically related accessions were identified, showing a different mycorrhizal colonization among them. GWAS revealed four significant quantitative trait nucleotides (QTNs) involved in mycorrhizal symbiosis, located on chromosomes 1A, 2A, 2B and 6A. The results of this work enrich future breeding activities aimed at developing new grains on the basis of genetic diversity on low or high susceptibility to mycorrhization, and, possibly, maximizing the symbiotic effects.
MeSH term(s)	Fungi/physiology ; Genes, Plant ; Genetic Variation ; Genome-Wide Association Study ; Mycorrhizae/physiology ; Phylogeny ; Plant Breeding ; Plant Roots/microbiology ; Plant Shoots/growth & development ; Polymorphism, Single Nucleotide ; Quantitative Trait Loci ; Symbiosis/genetics ; Tetraploidy ; Triticum/genetics ; Triticum/microbiology
Language	English
Publishing date	2021-06-28
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-021-92837-1
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Preliminary evidences of the presence of extracellular DNA single stranded forms in soil.

Shamina Imran Pathan / Paola Arfaioli / Maria Teresa Ceccherini / Judith Ascher-Jenull / Giacomo Pietramellara

PLoS ONE, Vol 15, Iss 1, p e

2020 Volume 0227296

Abstract	The relevance of extracellular DNA (eDNA) in the soil ecosystem is becoming more and more evident to the scientific community by the progressive discovery of functions accompanying to natural gene transformation. However, despite the increased number of published articles dedicated to eDNA in soil, so far only few are focused on its single stranded form (eDNAss). The present paper is the first to investigate the quantitative relevance of eDNAss in the total soil eDNA pool, discriminating between its linear (eDNAssl) and circular (eDNAssc) forms and the respective weakly (wa) and tightly (ta) adsorbed fractions. The results showed the prevalence of eDNAss and its linear form in both the total soil eDNA pool and its wa and ta fractions. Both of the eDNAss fractions (linear and circular) were characterized by small fragments.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2020-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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