Temporal dynamics of total and active prokaryotic communities in two Mediterranean orchard soils treated with solid anaerobic digestate or managed under no-tillage

Pathan, Shamina Imran; Roccotelli, Angela; Petrovičovà, Beatrix; Romeo, Maurizio; Badagliacca, Giuseppe; Monti, Michele; Gelsomino, Antonio

doi:10.1007/s00374-021-01569-x

Cited by 15 publications

(9 citation statements)

References 91 publications

(117 reference statements)

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“…Likewise, in the cropland soil metagenomes, a higher proportion of Clostridia and Coriobacteriia was identified by DL-TODA compared to Centrifuge or Kraken2. The abundance of Clostridia and Coriobacteriia, as predicted by DL-TODA, aligns well with prior studies of diverse agricultural related soil types [ 34 , 35 , 36 ]. Due to the lack of ground truth data, it is difficult to fully assess the accuracy of different tools on the metagenomes.…”

Section: Discussionsupporting

confidence: 84%

DL-TODA: A Deep Learning Tool for Omics Data Analysis

et al. 2023

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Metagenomics is a technique for genome-wide profiling of microbiomes; this technique generates billions of DNA sequences called reads. Given the multiplication of metagenomic projects, computational tools are necessary to enable the efficient and accurate classification of metagenomic reads without needing to construct a reference database. The program DL-TODA presented here aims to classify metagenomic reads using a deep learning model trained on over 3000 bacterial species. A convolutional neural network architecture originally designed for computer vision was applied for the modeling of species-specific features. Using synthetic testing data simulated with 2454 genomes from 639 species, DL-TODA was shown to classify nearly 75% of the reads with high confidence. The classification accuracy of DL-TODA was over 0.98 at taxonomic ranks above the genus level, making it comparable with Kraken2 and Centrifuge, two state-of-the-art taxonomic classification tools. DL-TODA also achieved an accuracy of 0.97 at the species level, which is higher than 0.93 by Kraken2 and 0.85 by Centrifuge on the same test set. Application of DL-TODA to the human oral and cropland soil metagenomes further demonstrated its use in analyzing microbiomes from diverse environments. Compared to Centrifuge and Kraken2, DL-TODA predicted distinct relative abundance rankings and is less biased toward a single taxon.

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Section: Discussionsupporting

confidence: 84%

DL-TODA: A Deep Learning Tool for Omics Data Analysis

et al. 2023

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“…Whereas Chloroflexi , whose members exhibit an oligotrophic lifestyle, [ 93 , 94 ] were preferentially depleted in NPK-fertilized soil at panicle initiation. Thaumarchaeota , which also includes copiotrophic taxa [ 95 , 96 ], were preferentially enriched in N and NPK-fertilized soil at booting stage.…”

Section: Discussionmentioning

confidence: 99%

Rice developmental stages modulate rhizosphere bacteria and archaea co-occurrence and sensitivity to long-term inorganic fertilization in a West African Sahelian agro-ecosystem

Dondjou

Diédhiou

Mbodj

et al. 2023

Environmental Microbiome

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Background Rhizosphere microbial communities are important components of the soil-plant continuum in paddy field ecosystems. These rhizosphere communities contribute to nutrient cycling and rice productivity. The use of fertilizers is a common agricultural practice in rice paddy fields. However, the long-term impact of the fertilizers usage on the rhizosphere microbial communities at different rice developmental stages remains poorly investigated. Here, we examined the effects of long-term (27 years) N and NPK-fertilization on bacterial and archaeal community inhabiting the rice rhizosphere at three developmental stages (tillering, panicle initiation and booting) in the Senegal River Delta. Results We found that the effect of long-term inorganic fertilization on rhizosphere microbial communities varied with the rice developmental stage, and between microbial communities in their response to N and NPK-fertilization. The microbial communities inhabiting the rice rhizosphere at panicle initiation appear to be more sensitive to long-term inorganic fertilization than those at tillering and booting stages. However, the effect of developmental stage on microbial sensitivity to long-term inorganic fertilization was more pronounced for bacterial than archaeal community. Furthermore, our data reveal dynamics of bacteria and archaea co-occurrence patterns in the rice rhizosphere, with differentiated bacterial and archaeal pivotal roles in the microbial inter-kingdom networks across developmental stages. Conclusions Our study brings new insights on rhizosphere bacteria and archaea co-occurrence and the long-term inorganic fertilization impact on these communities across developmental stages in field-grown rice. It would help in developing strategies for the successful manipulation of microbial communities to improve rice yields.

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“…Main properties of the solid anaerobic digestate were as follows: dry matter 18.0%, ash 14.4%, pH 8.77, EC 2140 µS cm −1 , total C 39.0%, total N 1.6%, C/N 24.3, NH 4 + -N 5.59 g kg −1 , NO 3 − -N 0.034 g kg −1 , total P 1.24 g kg −1 , and total K 2.25 g kg −1 . An extended description of this organic by-product is reported by Pathan, et al [25].…”

Section: Solid Anaerobic Digestatementioning

confidence: 94%

Olive Tree Physiology and Productivity Responses under No-Tillage or Digestate Amendment in an Acid Clay Soil

Pittarello,

Dattola,

Gullo

et al. 2024

Soil Systems

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In Mediterranean countries characterized by increasingly extended hot and dry periods, olive trees are often conventionally practiced in low fertility and rainfed soils. This study investigated over a 15-month period how conventional tillage, combined with or without incorporated solid digestate, and no tillage affected selected soil properties, photosynthetic activity and productivity of mature olive trees growing in highly clayey acid soil with an unbalanced nutrient content and Mn excess. Neither in soil nor in drupes were Mn, Fe, Cu and Al contents affected by the managements. However, in soil, exchangeable Mn that was always larger than 200 mg kg−1 threshold and unbalanced Ca, Mg, and K contents were evidenced in all treatments. Non-tilled soil showed the highest (p < 0.05) stomatal conductance and photosynthetic rate, and the highest (p < 0.05) fruits and oil yields. Instead, conventional tillage negatively (p < 0.05) affected plant physiology and productivity, likely due to the tilled increase in aeration, enhancing soil water loss and organic C mineralization. Conversely, digestate addition increased TOC, TN and EC. Stomatal conductance, the photosynthetic rate and plant yield significantly recovered (albeit not to no-tillage values) in tillage combined with incorporated digestate, suggesting that digestate-derived organic matter created soil conditions less constraining to plant growth and productivity than the conventional tillage did. Dealing with soil properties and climatic conditions is the key for adopting the best management practice for preserving plant productivity and soil fertility.

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Temporal dynamics of total and active prokaryotic communities in two Mediterranean orchard soils treated with solid anaerobic digestate or managed under no-tillage

Cited by 15 publications

References 91 publications

DL-TODA: A Deep Learning Tool for Omics Data Analysis

DL-TODA: A Deep Learning Tool for Omics Data Analysis

Rice developmental stages modulate rhizosphere bacteria and archaea co-occurrence and sensitivity to long-term inorganic fertilization in a West African Sahelian agro-ecosystem

Olive Tree Physiology and Productivity Responses under No-Tillage or Digestate Amendment in an Acid Clay Soil

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