Comparison of Two Molecular Methods to Assess Soil Microbial Diversity

Lenola, Martina Di; Grenni, Paola; Proença, Diogo Neves; Morais, Paula V.; Caracciolo, Anna Barra

doi:10.1007/978-3-319-63336-7_3

Cited by 8 publications

(11 citation statements)

References 58 publications

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“…Finally, as regards the species that can be involved in PCB transformation, among α-(e.g., Spingomonas), β-(e.g., Burkholderia, Alcaligenes, Achromobacter, Comamonas, Ralstonia), and γ-Proteobacteria (e.g., Pseudomonas, Acinetobacter), there are species reported to be able to degrade PCBs [74,75]. In some cases, the apparent discrepancy between the ELFA and FISH data for Gram-positive Bacteria was presumably because the FISH technique detects active bacteria with an adequate number of ribosomes [39,40], while the ELFA one produces a phenotypic fingerprinting of microbial communities, whatever their activity.…”

Section: Discussionmentioning

confidence: 99%

“…The fluorescence in situ hybridization (FISH) method was used for identifying under the epifluorescence microscope the structure of the active microbial community [32,39,40]. FISH was applied on fixed soil sub-samples (1 g), from each replicate microcosm, following the procedure described in detail in Barra Caracciolo et al [41].…”

Section: Microbial Community Structure Assessed By Fishmentioning

confidence: 99%

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Combined Effects of Compost and Medicago Sativa in Recovery a PCB Contaminated Soil

Lenola

Caracciolo

Ancona

et al. 2020

Water

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The effectiveness of adding compost and the plant Medicago sativa in improving the quality of a soil historically contaminated by polychlorinated biphenyls (PCBs) was tested in greenhouse microcosms. Plant pots, containing soil samples from an area contaminated by PCBs, were treated with the compost and the plant, separately or together. Moreover, un-treated and un-planted microcosms were used as controls. At fixed times (1, 133 and 224 days), PCBs were analysed and the structure (cell abundance, phylogenetic characterization) and functioning (cell viability, dehydrogenase activity) of the natural microbial community were also measured. The results showed the effectiveness of the compost and plant in increasing the microbial activity, cell viability, and bacteria/fungi ratio, and in decreasing the amount of higher-chlorinated PCBs. Moreover, a higher number of α-Proteobacteria, one of the main bacterial groups involved in the degradation of PCBs, was found in the compost and plant co-presence.

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Section: Discussionmentioning

confidence: 99%

Section: Microbial Community Structure Assessed By Fishmentioning

confidence: 99%

Combined Effects of Compost and Medicago Sativa in Recovery a PCB Contaminated Soil

Lenola

Caracciolo

Ancona

et al. 2020

Water

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“…To study the population structures and dynamics of microbial communities, genetic fingerprinting techniques such as Denaturing Gradient Gel Electrophoresis (DGGE) were developed (Muyzer et al, 1993 ). Nowadays, DGGE can be used as a first approach to visualize main differences in a given microbial community and subsequently high-throughput sequencing (HTS) can be applied to have a deeper understanding of the microbiota composition (Di Lenola et al, 2017 ; Proença et al, 2017a ). This methodology has been implemented in different fields and it is very common in soil microbiology studies (Bevivino et al, 2014 ; Ng et al, 2014 ), or to assess the aboveground microbial structure of trees (e.g., maritime pine, Pinus pinaster Ait.)…”

Section: Methodological Approaches To Unravel the Composition And Funmentioning

confidence: 99%

Belowground Microbiota and the Health of Tree Crops

et al. 2018

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Trees are crucial for sustaining life on our planet. Forests and land devoted to tree crops do not only supply essential edible products to humans and animals, but also additional goods such as paper or wood. They also prevent soil erosion, support microbial, animal, and plant biodiversity, play key roles in nutrient and water cycling processes, and mitigate the effects of climate change acting as carbon dioxide sinks. Hence, the health of forests and tree cropping systems is of particular significance. In particular, soil/rhizosphere/root-associated microbial communities (known as microbiota) are decisive to sustain the fitness, development, and productivity of trees. These benefits rely on processes aiming to enhance nutrient assimilation efficiency (plant growth promotion) and/or to protect against a number of (a)biotic constraints. Moreover, specific members of the microbial communities associated with perennial tree crops interact with soil invertebrate food webs, underpinning many density regulation mechanisms. This review discusses belowground microbiota interactions influencing the growth of tree crops. The study of tree-(micro)organism interactions taking place at the belowground level is crucial to understand how they contribute to processes like carbon sequestration, regulation of ecosystem functioning, and nutrient cycling. A comprehensive understanding of the relationship between roots and their associate microbiota can also facilitate the design of novel sustainable approaches for the benefit of these relevant agro-ecosystems. Here, we summarize the methodological approaches to unravel the composition and function of belowground microbiota, the factors influencing their interaction with tree crops, their benefits and harms, with a focus on representative examples of Biological Control Agents (BCA) used against relevant biotic constraints of tree crops. Finally, we add some concluding remarks and suggest future perspectives concerning the microbiota-assisted management strategies to sustain tree crops.

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“…The Fluorescence In Situ Hybridization (FISH) technique assesses the structure of the active microbial community in soil . FISH was applied to soil samples collected at day 900 after poplar planting, in order to identify firstly Archaea and Bacteria .…”

Section: Methodsmentioning

confidence: 99%

“…The Fluorescence In Situ Hybridization (FISH) technique assesses the structure of the active microbial community in soil. 60 FISH was applied to soil samples collected at day 900 after poplar planting, in order to identify firstly Archaea and Bacteria. Soil sub-samples (1 g) were collected from each contaminated plot (P2, P3 and P4) from the rhizosphere and bulk soil (D soil) and transferred to a test tube containing the fixing solution 56 in order to measure microbial abundance.…”

Section: Microbial Structure and Composition By Fishmentioning

confidence: 99%

Heavy metal phytoremediation of a poplar clone in a contaminated soil in southern Italy

Ancona

Caracciolo

Campanale

et al. 2019

J of Chemical Tech & Biotech

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BACKGROUND The Monviso clone previously tested successfully to remediate a lindane‐contaminated soil in central Italy was then applied in a historically heavy metal contaminated area in southern Italy. RESULTS The results obtained at 900 days from the poplar planting showed a strong decrease below Italian national legal limits (D.Lgs 152/06) for most heavy metals (HMs). The highest reduction of HM concentrations was observed in soil samples collected near the trunk (25 cm distant from poplar) and in the rhizosphere. The values of the HM bioaccumulation factor (BAF, considering roots and leaves) and of the translocation factor (TF) suggest that poplar trees were able to phytostabilize HMs. The soil organic carbon content increased compared to the previous sampling in all plots planted. The highest values were observed for the rhizosphere soils of each target tree, while the phosphorous available strongly decreased. Microbial results showed an overall increase in cell viability, dehydrogenase activity and microbial abundance of some bacterial groups. CONCLUSION Overall results showed that the poplar‐based phytoremediation strategy was able to promote the phytostabilization of the HMs and to improve the soil quality in terms of both organic carbon content and microbial community structure and activity. © 2019 Society of Chemical Industry

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Comparison of Two Molecular Methods to Assess Soil Microbial Diversity

Cited by 8 publications

References 58 publications

Combined Effects of Compost and Medicago Sativa in Recovery a PCB Contaminated Soil

Combined Effects of Compost and Medicago Sativa in Recovery a PCB Contaminated Soil

Belowground Microbiota and the Health of Tree Crops

Heavy metal phytoremediation of a poplar clone in a contaminated soil in southern Italy

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