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Article ; Online: Short-Term Resilience of Soil Microbial Communities and Functions Following Severe Environmental Changes

Stefano Mocali / Antonio Gelsomino / Paolo Nannipieri / Roberta Pastorelli / Laura Giagnoni / Beatrix Petrovicova / Giancarlo Renella

Agriculture, Vol 12, Iss 268, p

2022 Volume 268

Abstract: Soil microorganisms are key drivers of soil biochemical processes, but the resilience of microbial communities and their metabolic activity after an extreme environmental change is still largely unknown. We studied structural (bacterial and fungal ... ...

Abstract	Soil microorganisms are key drivers of soil biochemical processes, but the resilience of microbial communities and their metabolic activity after an extreme environmental change is still largely unknown. We studied structural (bacterial and fungal communities) and functional responses (soil respiration, adenosine triphosphate (ATP) content, hydrolase activities involved in the mineralization of organic C, N, P and S, and microbial community-level physiological profiles (CLPPs)) during the microbial recolonization of three heat-sterilized forest soils followed by cross- or self-reinoculation and incubation for 1, 7 and 30 days. Soil ATP content, biochemical activities and CLPP were annihilated by autoclaving, whereas most of the hydrolase activities were reduced to varying extents depending on the soil and enzyme activity considered. During the incubation period, the combination of self- and cross-reinoculation of different sterilized soils produced rapid dynamic changes in enzymatic activity as well as in microbial structure and catabolic activity. Physicochemical properties of the original soils exerted a major influence in shaping soil functional diversity, while reinoculation of sterilized soils promoted faster and greater changes in bacterial community structure than in fungal communities, varying with incubation period and soil type. Our results also confirmed the importance of microbial richness in determining soil resilience under severe disturbances. In particular, the new microbial communities detected in the treated soils revealed the occurrence of taxa which were not detected in the original soils. This result confirmed that rare microbial taxa rather than the dominant ones may be the major drivers of soil functionality and resilience.
Keywords	microbial diversity ; enzymes ; catabolic activity ; soil recolonization ; sterilization ; resilience ; Agriculture (General) ; S1-972
Subject code	630
Language	English
Publishing date	2022-02-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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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
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Soil Pollution from Micro- and Nanoplastic Debris

Shamina Imran Pathan / Paola Arfaioli / Tommaso Bardelli / Maria Teresa Ceccherini / Paolo Nannipieri / Giacomo Pietramellara

Sustainability, Vol 12, Iss 7255, p

A Hidden and Unknown Biohazard

2020 Volume 7255

Abstract: The fate, properties and determination of microplastics (MPs) and nanoplastics (NPs) in soil are poorly known. In fact, most of the 300 million tons of plastics produced each year ends up in the environment and the soil acts as a log-term sink for these ... ...

Abstract	The fate, properties and determination of microplastics (MPs) and nanoplastics (NPs) in soil are poorly known. In fact, most of the 300 million tons of plastics produced each year ends up in the environment and the soil acts as a log-term sink for these plastic debris. Therefore, the aim of this review is to discuss MP and NP pollution in soil as well as highlighting the knowledge gaps that are mainly related to the complexity of the soil ecosystem. The fate of MPs and NPs in soil is strongly determined by physical properties of plastics, whereas negligible effect is exerted by their chemical structures. The degradative processes of plastic, termed ageing, besides generating micro-and nano-size debris, can induce marked changes in their chemical and physical properties with relevant effects on their reactivity. Further, these processes could cause the release of toxic oligomeric and monomeric constituents from plastics, as well as toxic additives, which may enter in the food chain, representing a possible hazard to human health and potentially affecting the fauna and flora in the environment. In relation to their persistence in soil, the list of soil-inhabiting, plastic-eating bacteria, fungi and insect is increasing daily. One of the main ecological functions attributable to MPs is related to their function as vectors for microorganisms through the soil. However, the main ecological effect of NPs (limited to the fraction size < than 50 nm) is their capacity to pass through the membrane of both prokaryotic and eukaryotic cells. Soil biota, particularly earthworms and collembola, can be both MPs and NPs carriers through soil profile. The use of molecular techniques, especially omics approaches, can gain insights into the effects of MPs and NPs on composition and activity of microbial communities inhabiting the soil and into those living on MPs surface and in the gut of the soil plastic-ingesting fauna.
Keywords	microplastics (MPs) ; nanoplastics (NPs) ; soil ; reactivity ; toxicity ; human health ; Environmental effects of industries and plants ; TD194-195 ; Renewable energy sources ; TJ807-830 ; Environmental sciences ; GE1-350
Subject code	630
Language	English
Publishing date	2020-09-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Community shift of microbial ammonia oxidizers in air-dried rice soils after 22 years of nitrogen fertilization

Jia, Zhongjun / Xiaojing Hu / Weiwei Xia / Dario Fornara / Paolo Nannipieri / James Tiedje

Biology and fertility of soils. 2019 May, v. 55, no. 4

2019

Abstract: In this study, we show that composition shifts of ammonia oxidizer communities imposed by a 22-year field fertilization regime could be well retained in both fresh and air-dried soils. The abundance and composition of ammonia-oxidizing bacteria (AOB) and ...

Abstract	In this study, we show that composition shifts of ammonia oxidizer communities imposed by a 22-year field fertilization regime could be well retained in both fresh and air-dried soils. The abundance and composition of ammonia-oxidizing bacteria (AOB) and archaea (AOA) were measured in fresh soils, which received no fertilization (CK), chemical fertilization (NPK), and chemical plus organic matter fertilization (NPK/OM) for 22 years. The air-drying treatment of fresh soil was also conducted for pairwise analysis. We found that in fresh soils DGGE fingerprints of AOB showed significant changes under both NPK and NPK/OM treatments when compared with control (CK) and that microbial shift was almost identical in air-dried soils. Long-term nutrient fertilization did not affect AOA communities in either air-dried or fresh soils. Compared to CK treatment, real-time PCR indicated that AOB amoA genes increased significantly in fresh soils of NPK (59-fold) and NPK/OM (48-fold) plots and in air-dried NPK and NPK/OM soils by 22-fold and 19-fold respectively. Our results demonstrate that community shifts of AOB in fresh soils under chronic N fertilization could be well preserved in air-dried soils, despite the apparent decline in absolute abundance of ammonia oxidizers. These results suggest that air-dried soil could be a useful resource for deciphering the adaptive strategy of ammonia oxidizers under N enrichment when the significant changes of community composition occurred in fresh soils.
Keywords	Archaea ; air drying ; ammonia ; community structure ; denaturing gradient gel electrophoresis ; fertilizer application ; genes ; nitrifying bacteria ; nitrogen ; nitrogen fertilizers ; organic matter ; quantitative polymerase chain reaction ; rice soils
Language	English
Dates of publication	2019-05
Size	p. 419-424.
Publishing place	Springer Berlin Heidelberg
Document type	Article
ZDB-ID	742137-0
ISSN	1432-0789 ; 0178-2762
ISSN (online)	1432-0789
ISSN	0178-2762
DOI	10.1007/s00374-019-01352-z
Database	NAL-Catalogue (AGRICOLA)

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Article: The Impact of the Diurnal Cycle on the Microbial Transcriptome in the Rhizosphere of Barley

Baraniya, Divyashri / Anne Schöler / Gisle Vestergaard / Michael Schloter / Paolo Nannipieri / Susanne Kublik

Microbial ecology. 2018 May, v. 75, no. 4

2018

Abstract: While root exudation follows diurnal rhythms, little is known about the consequences for the microbiome of the rhizosphere. In this study, we used a metatranscriptomic approach to analyze the active microbial communities, before and after sunrise, in the ...

Abstract	While root exudation follows diurnal rhythms, little is known about the consequences for the microbiome of the rhizosphere. In this study, we used a metatranscriptomic approach to analyze the active microbial communities, before and after sunrise, in the rhizosphere of barley. We detected increased activities of many prokaryotic microbial taxa and functions at the pre-dawn stage, compared to post-dawn. Actinomycetales, Planctomycetales, Rhizobiales, and Burkholderiales were the most abundant and therefore the most active orders in the barley rhizosphere. The latter two, as well as Xanthomonadales, Sphingomonadales, and Caulobacterales showed a significantly higher abundance in pre-dawn samples compared to post-dawn samples. These changes in taxonomy coincide with functional changes as genes involved in both carbohydrate and amino acid metabolism were more abundant in pre-dawn samples compared to post-dawn samples. This study significantly enhances our present knowledge on how rhizospheric microbiota perceives and responds to changes in the soil during dark and light periods.
Keywords	Actinomycetales ; amino acid metabolism ; barley ; Burkholderiales ; carbohydrates ; Caulobacterales ; exudation ; genes ; microbial communities ; microbiome ; microorganisms ; Planctomycetales ; Rhizobiales ; rhizosphere ; soil ; Sphingomonadales ; taxonomy ; transcriptome ; transcriptomics ; Xanthomonadales
Language	English
Dates of publication	2018-05
Size	p. 830-833.
Publishing place	Springer US
Document type	Article
ZDB-ID	1462065-0
ISSN	1432-184X ; 0095-3628
ISSN (online)	1432-184X
ISSN	0095-3628
DOI	10.1007/s00248-017-1101-0
Database	NAL-Catalogue (AGRICOLA)

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Article: Bacterial culturability and the viable but non-culturable (VBNC) state studied by a proteomic approach using an artificial soil

Giagnoni, Laura / Erica Galardi / Giancarlo Renella / Mariarita Arenella / Paolo Nannipieri

Soil biology & biochemistry. 2018 Mar., v. 118

2018

Abstract: Gram-negative bacteria in soil rapidly adapt to various stresses, including nutrient limitation and desiccation, by adopting the viable but non-culturable (VBNC) state as a survival strategy. Due to the physico-chemical and microbiological complexity of ... ...

Abstract	Gram-negative bacteria in soil rapidly adapt to various stresses, including nutrient limitation and desiccation, by adopting the viable but non-culturable (VBNC) state as a survival strategy. Due to the physico-chemical and microbiological complexity of soils, little is understood on the effects of nutrient availability and moisture level on the transition from the VBNC state to culturability in soil. We evaluated the effects of gluconate or water on the transition of the soil borne bacterium C. metallidurans strain CH34 from the VBNC state to culturability by experiments of inoculation into artificial soils and bacterial metaproteomic analysis. Incubation without water or nutrients reduced the bacterial culturability to zero in 12 d, and addition of both water or gluconate restored the bacterial culturability to high levels within 24 h. The proteomic analysis showed that under water and nutrient limitation, proteins related to the cell shape and protein synthesis were rapidly down-regulated and stress-related proteins were quickly up-regulated during the transition from culturability to VBNC state. Reversion from the VBNC state to a culturable state with water or gluconate led to highly different bacterial proteomic profiles of C. metallidurans. Gluconate availability restored main protein biosynthesis and energy metabolic pathways, whereas water addition led to up-regulation of only six proteins, one of which degrade sigma factors involved in expression of genes controlling bacterial resistance under nutrient limitation. Proteins regulated during the transition between culturable and VBNC states could also be involved in the phenotypic VBNC for other soil bacteria, and can highlight some of the microbial genetic mechanisms allowing the entering and exiting from the VBNC state. Implications of the VBNC in microbial diversity and soil functionality are discussed.
Keywords	biochemical pathways ; energy ; gene expression ; gluconates ; Gram-negative bacteria ; nutrients ; phenotype ; protein synthesis ; proteomics ; sigma factors ; soil ; soil bacteria ; water content
Language	English
Dates of publication	2018-03
Size	p. 51-58.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	280810-9
ISSN	0038-0717
ISSN	0038-0717
DOI	10.1016/j.soilbio.2017.12.004
Database	NAL-Catalogue (AGRICOLA)

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Article: Microbial indicators for soil quality

Schloter, Michael / Paolo Nannipieri / Søren J. Sørensen / Jan Dirk van Elsas

Biology and fertility of soils. 2018 Jan., v. 54, no. 1

2018

Abstract: The living soil is instrumental to key life support functions (LSF) that safeguard life on Earth. The soil microbiome has a main role as a driver of these LSF. Current global developments, like anthropogenic threats to soil (e.g., via intensive ... ...

Abstract	The living soil is instrumental to key life support functions (LSF) that safeguard life on Earth. The soil microbiome has a main role as a driver of these LSF. Current global developments, like anthropogenic threats to soil (e.g., via intensive agriculture) and climate change, pose a burden on soil functioning. Therefore, it is important to dispose of robust indicators that report on the nature of deleterious changes and thus soil quality. There has been a long debate on the best selection of biological indicators (bioindicators) that report on soil quality. Such indicators should ideally describe organisms with key functions in the system, or with key regulatory/connecting roles (so-called keystone species). However, in the light of the huge functional redundancy in most soil microbiomes, finding specific keystone markers is not a trivial task. The current rapid development of molecular (DNA-based) methods that facilitate deciphering microbiomes with respect to key functions will enable the development of improved criteria by which molecular information can be tuned to yield molecular markers of soil LSF. This review critically examines the current state-of-the-art in molecular marker development and recommends avenues to come to improved future marker systems.
Keywords	climate change ; genetic markers ; indicator species ; intensive farming ; keystone species ; microbiome ; soil ; soil quality
Language	English
Dates of publication	2018-01
Size	p. 1-10.
Publishing place	Springer Berlin Heidelberg
Document type	Article
ZDB-ID	742137-0
ISSN	1432-0789 ; 0178-2762
ISSN (online)	1432-0789
ISSN	0178-2762
DOI	10.1007/s00374-017-1248-3
Database	NAL-Catalogue (AGRICOLA)

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Article: Rare taxa of alkaline phosphomonoesterase-harboring microorganisms mediate soil phosphorus mineralization

Wei, Xiaomeng / Bahar S. Razavi / Jianlin Shen / Jinshui Wu / Juan Zhou / Paolo Nannipieri / Tida Ge / Yajun Hu

Soil biology & biochemistry. 2019 Apr., v. 131

2019

Abstract: As a homologous gene encoding microbial alkaline phosphomonoesterase, the expression of phoD is critically controlled by P availability and thus contributes to the mineralization of soil organic P under P-depleted condition. However, its role in the ... ...

Abstract	As a homologous gene encoding microbial alkaline phosphomonoesterase, the expression of phoD is critically controlled by P availability and thus contributes to the mineralization of soil organic P under P-depleted condition. However, its role in the regulation of soil P turnover is largely unknown due to the complex coupling of physiochemical and biological processes in the P cycle, especially in paddy field. We hypothesized that 1) P fertilization would decrease the abundance of phoD gene and change the composition of phoD-harboring microbial community and 2) the high abundance of phoD-harboring microorganisms in P-poor soil would stimulate the synthesis of alkaline phosphomonoesterase, thus mitigating P limitation via the mineralization of organic P. After 42 days of rice growth, the phoD abundance negatively correlated with soil P availability, and it was significantly higher in non-fertilized treatments than in P-fertilized treatments for both rhizosphere and bulk soils. A stronger competition among phoD-harboring microorganisms was detected in non-fertilized soil than in P-fertilized soil, with Bradyrhizobium, Methylobacterium, and Methylomonas being the dominant taxa in all samples. However, the high phoD gene abundance under P-poor condition was mainly due to the growth of rare operational taxonomic units (OTUs) affiliated to Actinobacteria and Cyanobacteria (relative abundance < 3%). Consistent with our hypothesis, the growth of phoD-harboring microorganisms stimulated the hydrolysis of organic P in non-fertilized soil. However, in the P-fertilized treatments, the increase in OTU abundance was accompanied by the depletion of exchangeable P and accumulation of microbial biomass P. Our findings suggest that phoD-harboring microorganisms have the potential to immobilize P in biomass when the supply is sufficient while mineralize organic P under P-poor condition, during which the rare taxa play an important role.
Keywords	Actinobacteria ; Bradyrhizobium ; Cyanobacteria ; enzymes ; fertilizer application ; genes ; hydrolysis ; Methylobacterium ; Methylomonas ; microbial biomass ; microbial communities ; microorganisms ; mineralization ; paddies ; phosphorus ; phosphorus fertilizers ; rhizosphere ; rice ; soil
Language	English
Dates of publication	2019-04
Size	p. 62-70.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	280810-9
ISSN	0038-0717
ISSN	0038-0717
DOI	10.1016/j.soilbio.2018.12.025
Database	NAL-Catalogue (AGRICOLA)

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Article: Microbial expression profiles in the rhizosphere of two maize lines differing in N use efficiency

Pathan, Shamina Imran / Tomáš Větrovský / Laura Giagnoni / Rahul Datta / Petr Baldrian / Paolo Nannipieri / Giancarlo Renella

Plant and soil. 2018 Dec., v. 433, no. 1-2

2018

Abstract: AIMS: Study of the microbial expression profile in the rhizosphere of two contrasting maize lines, differing in the Nitrogen Use efficiency (NUE). METHODS: The Lo5 and T250 inbred maize characterized by high and low NUE, respectively, were grown in ... ...

Abstract	AIMS: Study of the microbial expression profile in the rhizosphere of two contrasting maize lines, differing in the Nitrogen Use efficiency (NUE). METHODS: The Lo5 and T250 inbred maize characterized by high and low NUE, respectively, were grown in rhizoboxes allowing precise sampling of rhizosphere and bulk soils. We conducted metatranscriptomic of rhizosphere and bulk soil by m-RNA sequencing. RESULTS: High activity of bacteria was observed compared to archaea and fungi in both rhizosphere and bulk soils of both maize lines. Proteobacteria and Actinobacteria were involved in all processes, while significant shifts occurred in the expression of Bacteroidetes, Chloroflexi, Firmicutes, Acidobacteria, Cyanobacteria, archaea and fungi, indicating their possible role in specific processes occurring in rhizosphere of two maize lines. Maize plants with different NUE induced changes in microbial processes, especially in N cycling, with high NUE maize favouring ammonification and nitrification processes and low NUE maize inducing expression of genes encoding for denitrifying process, likely favoured by longer N residence time in the rhizosphere. CONCLUSIONS: Overall our results showed that maize lines with different NUE shaped not only microbial communities but also conditioned the microbial functions and the N cycle in their rhizosphere. While the plant NUE is genetically determined and an inherent plant physiological trait, it also stimulates changes in the microbial community composition and gene expression in the rhizosphere, favouring microbial processes that mineralize and oxidize N in the high NUE maize. These results can improve our understanding on plant-microbe interaction in the rhizosphere of crop plants with potential applications for improving the management practices of the agro-ecosystems.
Keywords	Acidobacteria ; Actinobacteria ; Archaea ; Bacteroidetes ; Chloroflexi ; Cyanobacteria ; Firmicutes ; Proteobacteria ; agroecosystems ; ammonification ; bacteria ; community structure ; corn ; crops ; denitrification ; fungi ; gene expression ; microbial communities ; nitrification ; nutrient use efficiency ; rhizosphere ; soil ; transcriptomics
Language	English
Dates of publication	2018-12
Size	p. 401-413.
Publishing place	Springer International Publishing
Document type	Article
ZDB-ID	208908-7
ISSN	1573-5036 ; 0032-079X
ISSN (online)	1573-5036
ISSN	0032-079X
DOI	10.1007/s11104-018-3852-x
Database	NAL-Catalogue (AGRICOLA)

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Article: Availability of different nitrogen forms changes the microbial communities and enzyme activities in the rhizosphere of maize lines with different nitrogen use efficiency

Giagnoni, Laura / Giancarlo Renella / Mariarita Arenella / Paolo Nannipieri / Roberta Pastorelli / Stefano Mocali

Applied soil ecology. 2016 Feb., v. 98

2016

Abstract: We studied how the Lo5 and T250 maize lines, characterized by high and low nitrogen use efficiency (NUE), respectively, modified the microbial biomass, enzymatic activities and microbial community structure in the rhizosphere after exposure to different ... ...

Abstract	We studied how the Lo5 and T250 maize lines, characterized by high and low nitrogen use efficiency (NUE), respectively, modified the microbial biomass, enzymatic activities and microbial community structure in the rhizosphere after exposure to different N forms. The two maize lines were grown for 4 weeks in rhizoboxes allowing precise sampling of rhizosphere and bulk soil with no nutrient additions, and then exposed to with nitric-, ammonium- and urea-N. After N exposure, the plants were inserted back into their original rhizoboxes to allow the root exudates diffusion into the rhizosphere. After 24h rhizosphere soil were sampled and analyzed. Microbial biomass and soil enzymatic activities were increased after the exposure to different N forms of both maize lines. The plant exposure to different N forms also induced changes in the rhizosphere bacterial and fungal communities composition. Plant responses to the availability of different N forms was a dominant factor regulating activity and composition of the rhizosphere microbial communities, likely due to changes in the rhizodepositions. Therefore different N forms used for fertilization of agriculturally relevant plants such as maize can result in different plant mediated effects on the microbial activity and community structure in the rhizosphere.
Keywords	community structure ; corn ; enzyme activity ; fungal communities ; microbial activity ; microbial biomass ; nitrogen ; nutrient use efficiency ; plant response ; rhizosphere ; root exudates ; soil ; soil nutrients ; urea nitrogen
Language	English
Dates of publication	2016-02
Size	p. 30-38.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	1196758-4
ISSN	0929-1393
ISSN	0929-1393
DOI	10.1016/j.apsoil.2015.09.004
Database	NAL-Catalogue (AGRICOLA)

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