Sub-Lethal Effects of Pesticides on the DNA of Soil Organisms as Early Ecotoxicological Biomarkers

Vischetti, Costantino; Casucci, Cristiano; Bernardi, Arianna De; Monaci, Elga; Tiano, Luca; Marcheggiani, Fabio; Ciani, Maurizio; Comitini, Francesca; Marini, Enrica; Taskin, Eren; Puglisi, Edoardo

doi:10.3389/fmicb.2020.01892

Cited by 32 publications

(20 citation statements)

References 122 publications

(186 reference statements)

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“…The activity of β-Glucosidase, phosphatase, and urease was found to be suitable for monitoring the alteration status of soils subject to different management [ 42 , 43 ]. Alteration Index 3 (AI3) [ 47 ] successfully integrated the activity of these enzymes to provide us with a comparative assessment tool for the evaluation of the impact of management practices on soil alteration status in our study.…”

Section: Discussionmentioning

confidence: 99%

“…This is especially relevant when considering that the majority of Kenyan farmers who cultivate AIVs, particularly those who are in remote rural areas, have only little to moderate adaptive capacity to climate change [ 39 ]. Soil microbial community structure and soil enzymes such as β-Glucosidase, phosphatase, and urease can act as early indicators of soil health and alteration because of their sensitivity to tillage, fertilization, cultivations, drought, pesticides, and pollution [ 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 ].…”

Section: Introductionmentioning

confidence: 99%

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Smallholder Farmers’ Practices and African Indigenous Vegetables Affect Soil Microbial Biodiversity and Enzyme Activities in Lake Naivasha Basin, Kenya

Taskin

Misci

Bandini

et al. 2021

Biology

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Loss of soil biodiversity and fertility in Sub-Saharan Africa (SSA) may put the food security of smallholder farmers in peril. Food systems in SSA are seeing the rise of African indigenous vegetables (AIVs) that are underexploited but locally consumed without being considered a primary source of food and income. Here we present a field study, a first of its kind, in which we investigated the effects of different cropping systems and inclusion of AIVs in the farming approach on bacterial and fungal biodiversity and community structures, enzymatic activity, and the alteration status of soils of the smallholder farmers in Kenya. When compared to mainstream farming approaches, the composition and biodiversity of bacteria and fungi under AIV cultivations was significantly different. Tillage had a significant impact only on the fungal communities. Fertilization and soil amendments caused shifts in microbial communities towards specialized degraders and revealed the introduction of specific microorganisms from amendments. Traditional homemade plant protection products did not cause any disturbance to either of soil bacteria or fungi. The soil alteration index based on enzyme activity successfully differentiated the alteration status for the first time in SSA. These findings could be useful for farmers to integrate AIVs with correct sustainable practices for a sustainable future.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Smallholder Farmers’ Practices and African Indigenous Vegetables Affect Soil Microbial Biodiversity and Enzyme Activities in Lake Naivasha Basin, Kenya

Taskin

Misci

Bandini

et al. 2021

Biology

Self Cite

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“…Currently, thorough assessment of genetic diversity of microbial communities is gained by high-throughput techniques such as NGS; however, PCR-DGGE (Muyzer et al, 1993) is a routine and commonly used technique in plant-soil ecosystem studies. Admitting that the technique has some limitations (Orlewska et al, 2018;Vischetti et al, 2020), recently a number of protocols are optimized for use with plant and soil DNA. They are confirmed to be reliable, do not require complex bioinformatics for the analyses of results, and present an overall picture on the main differences in microbial community composition when coupled with culture-dependent microbiological approaches (Sarhan et al, 2016;Vischetti et al, 2020).…”

Section: Discussionmentioning

confidence: 99%

“…Admitting that the technique has some limitations (Orlewska et al, 2018;Vischetti et al, 2020), recently a number of protocols are optimized for use with plant and soil DNA. They are confirmed to be reliable, do not require complex bioinformatics for the analyses of results, and present an overall picture on the main differences in microbial community composition when coupled with culture-dependent microbiological approaches (Sarhan et al, 2016;Vischetti et al, 2020). And, common to the NGS methods, different primer sets can be used in PCR-DGGE, to addressing microbial communities at the phylogenetic level (e.g., 16S primers for bacteria and archaea), or at the functional level, depending on functional selected genes (Valášková and Baldrian, 2009).…”

Section: Discussionmentioning

confidence: 99%

Culture Media Based on Leaf Strips/Root Segments Create Compatible Host/Organ Setup for in vitro Cultivation of Plant Microbiota

Nemr

Patz

Abdelwakeel

et al. 2021

Front. Sustain. Food Syst.

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Plant microbiota have co-evolved with their associated plants in the entire holobiont, and their assemblages support diversity and productivity on our planet. Of importance is in vitro cultivation and identification of their hub taxa for possible core microbiome modification. Recently, we introduced the in situ-similis culturing strategy, based on the use of plant leaves as a platform for in vitro growth of plant microbiota. Here, the strategy is further extended by exploring plant organ compatible cultivation of plant microbiota when grown on corresponding leaf/root-based culture media. Pooling the advantages of MPN enrichment methodology together with natural plant-only-based culture media, the introduced method efficiently constructed a nutritional milieu governed by vegan nutrients of plant origin, i.e., leaf strips/root segments, immersed in plain semi-solid water agar. MPN estimates exceeded log 7.0 and 4.0 g−1 of endo-rhizosphere and endo-phyllosphere, respectively, of maize and sunflower; being proportionate to those obtained for standard culture media. With sunflower, PCR-DGGE analyses indicated divergence in community composition of cultivable endophytes primarily attributed to culture media, signaling a certain degree of plant organ affinity/compatibility. Based on 16S rRNA gene sequencing of bacterial isolates, 20 genera comprising 32 potential species were enriched; belonged to Bacteroidetes, Firmicutes, and Alpha-/Gammaproteobacteria. The described cultivation strategy furnished diversified nutritive platform in terms of homologous/heterologous plant organ-based medium and ambient/limited oxygenic cultivation procedure. Duly, cultivability extended to > 8 genera: Bosea, Brevundimonas, Chitinophaga, Pseudoxanthomonas, Sphingobacterium Caulobacter, Scandinavium, and Starkeya; the latter three genera were not yet reported for Sunflower, and possible unknown species or even one new putative genus. Thus, both potential members of the major microbiome and rare isolates of satellite microbiomes can be isolated using the presented method. It is a feasible addition to traditional cultivation methods to explore new potential resources of PGPB for future biotechnological applications.

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“…DNA metabarcoding further allows assessing soil microbial biodiversity (also in terms of phylogenetic relatedness), and to compare soil communities subjected to experimental conditions or geographical distance. It is also a cost-effective method for biomonitoring as DNA metabarcoding is more frequently used for monitoring agricultural practices, restoration efforts or forensics [ 9 , 10 , 11 , 12 ]. Presently, it represents the most used molecular approach to characterize microbiota in environmental samples.…”

Section: Introductionmentioning

confidence: 99%

DNA Metabarcoding for the Characterization of Terrestrial Microbiota—Pitfalls and Solutions

et al. 2021

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Soil-borne microbes are major ecological players in terrestrial environments since they cycle organic matter, channel nutrients across trophic levels and influence plant growth and health. Therefore, the identification, taxonomic characterization and determination of the ecological role of members of soil microbial communities have become major topics of interest. The development and continuous improvement of high-throughput sequencing platforms have further stimulated the study of complex microbiota in soils and plants. The most frequently used approach to study microbiota composition, diversity and dynamics is polymerase chain reaction (PCR), amplifying specific taxonomically informative gene markers with the subsequent sequencing of the amplicons. This methodological approach is called DNA metabarcoding. Over the last decade, DNA metabarcoding has rapidly emerged as a powerful and cost-effective method for the description of microbiota in environmental samples. However, this approach involves several processing steps, each of which might introduce significant biases that can considerably compromise the reliability of the metabarcoding output. The aim of this review is to provide state-of-the-art background knowledge needed to make appropriate decisions at each step of a DNA metabarcoding workflow, highlighting crucial steps that, if considered, ensures an accurate and standardized characterization of microbiota in environmental studies.

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Sub-Lethal Effects of Pesticides on the DNA of Soil Organisms as Early Ecotoxicological Biomarkers

Cited by 32 publications

References 122 publications

Smallholder Farmers’ Practices and African Indigenous Vegetables Affect Soil Microbial Biodiversity and Enzyme Activities in Lake Naivasha Basin, Kenya

Smallholder Farmers’ Practices and African Indigenous Vegetables Affect Soil Microbial Biodiversity and Enzyme Activities in Lake Naivasha Basin, Kenya

Culture Media Based on Leaf Strips/Root Segments Create Compatible Host/Organ Setup for in vitro Cultivation of Plant Microbiota

DNA Metabarcoding for the Characterization of Terrestrial Microbiota—Pitfalls and Solutions

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