Search

Introduction: Agriculture is undergoing an agroecological transition characterized by adopting new practices to reduce chemical fertilizer inputs. In this context, digestates are emerging as sustainable substitutes for mineral fertilizers. However, large-scale application of digestates in agricultural fields requires rigorous studies to evaluate their long-term effects on soil microbial communities, which are crucial for ecosystem functioning and resilience., Material and Methods: This study presents provides a comparative analysis in long-term field conditions of fertilization strategies combining annual applications of raw digestate with biennial applications of different organic waste products (OWPs)-biowaste compost (BIO), farmyard manure (FYM), and urban sewage sludge (SLU)-and compares them to combinations of the same OWPs with mineral fertilizers. The cumulative effects of repeated OWP applications, paired with two nitrogen sources-organic (digestate) and chemical (mineral fertilizer)-were assessed through soil physicochemical and microbial analyses. We hypothesized that the combined effect varied according to the N-supply sources and that this effect also depended on the type of OWP applied. Soil microbial communities were characterized using high-throughput sequencing targeting 16S and 18S ribosomal RNA genes, following DNA extraction from soil samples collected in 2022, six years after the initial digestate application., Results: The results indicated that combining OWPs rich in stable and recalcitrant organic matter, such as BIO and FYM, with raw digestate, offers an improved fertilization practice. This approach maintains soil organic carbon (SOC) levels, increases soil phosphorus and potassium content, and stimulates microbial communities differently than nitrogen supplied via mineral fertilizers. While microbial biomass showed no significant variation across treatments, microbial diversity indices exhibited differences based on the type of OWP and nitrogen source. The fertilization strategies moderately influenced prokaryotic and fungal community structures, with distinct patterns depending on the OWP and nitrogen source. Notably, fungal communities responded more strongly to treatment variations than prokaryotic communities., Discussion: This study provides new insights into the cumulative effects of substituting mineral fertilizers with digestates on soil microbial communities and soil physicochemical parameters. The sustainable development of agroecosystems significantly depends on a better understanding of the complex responses of soil microbial communities to different fertilization regimes. Future research should continue to assess the long-term impact of digestate application on soil microbiota in real agronomic field conditions, considering associated agricultural practices., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2025 Mora-Salguero, Montenach, Gilles, Jean-Baptiste and Sadet-Bourgeteau.)

Anaerobic digestion represents an opportunity for converting organic waste (OW) into valuable products: renewable energy (biogas) and a fertilizer (digestate). However, the long-term effects of digestates on soil biota, especially microorganisms, need to be better documented to understand the impact of digestate on soil ecosystem functioning and resilience. This study assessed the cumulative effect of repeated pig slurry digestate applications on soil microbial communities over a decade, using an in-situ approach to compare digested feedstock with undigested feedstock and other fertilization treatments. Conducted from 2012 to 2022 at an experimental field site in France, the study involved plots with identical agricultural soil management practices, differing only in fertilization treatments: mineral fertilizer, three different OW (cattle manure, pig slurry, pig slurry digestate), and a control with no organic or mineral fertilizer input. Changes in soil microbial communities were analyzed through molecular microbial biomass and diversity assessments using high-throughput sequencing targeting 16S and 18S ribosomal RNA genes. DNA extraction and molecular analyses were performed on soil samples collected at the start of the trial in 2012 and subsequently in 2017 and 2022. The long-term effects of annual digestate application over a decade include a higher soil microbial diversity in digestate-treated plots than in pig slurry-treated plots, and changes in the soil's microbial community structure and taxonomic composition resembling those observed with mineral fertilizer. Differential abundance analysis at the phylum level revealed few significant differences between digestate- and mineral fertilizer-treated plots for both prokaryotic and fungal communities. Only plots amended with cattle manure exhibited higher soil organic carbon content. Agricultural practices, along with climatic and environmental fluctuations, can significantly influence the response of soil microbial communities, thereby buffering the effects of fertilization treatments. Further research is needed to better understand the effects on soil microbial communities, considering the interactions between repeated digestate applications, different pedological contexts, and agricultural practices., Competing Interests: The authors declare that they have no known competing financial interest or personal relationships that could have appeared to influence the work reported in this paper., (© 2024 The Authors.)

Changes in soil microbial communities may impact soil fertility and stability because microbial communities are key to soil functioning by supporting soil ecological quality and agricultural production. The effects of soil amendment with biochar on soil microbial communities are widely documented but studies highlighted a high degree of variability in their responses following biochar application. The multiple conditions under which they were conducted (experimental designs, application rates, soil types, biochar properties) make it difficult to identify general trends. This supports the need to better determine the conditions of biochar production and application that promote soil microbial communities. In this context, we performed the first ever meta-analysis of the biochar effects on soil microbial biomass and diversity (prokaryotes and fungi) based on high-throughput sequencing data. The majority of the 181 selected publications were conducted in China and evaluated the short-term impact (<3 months) of biochar. We demonstrated that a large panel of variables corresponding to biochar properties, soil characteristics, farming practices or experimental conditions, can affect the effects of biochar on soil microbial characteristics. Using a variance partitioning approach, we showed that responses of soil microbial biomass and prokaryotic diversity were highly dependent on biochar properties. They were influenced by pyrolysis temperature, biochar pH, application rate and feedstock type, as wood-derived biochars have particular physico-chemical properties (high C:N ratio, low nutrient content, large pores size) compared to non-wood-derived biochars. Fungal community data was more heterogenous and scarcer than prokaryote data (30 publications). Fungal diversity indices were rather dependent on soil properties: they were higher in medium-textured soils, with low pH but high soil organic carbon. Altogether, this meta-analysis illustrates the need for long-term field studies in European agricultural context for documenting responses of soil microbial communities to biochar application under diverse conditions combining biochar types, soil properties and conditions of use., Competing Interests: Declaration of competing interest This study was funded by the French National Research Agency (ANR, grant number 21-PRRD-0033-01) within the call for projects “France 2030 – Plan de relance – mesure de preservation de l'emploi R&D”, based on public fundings (83 %) and private fundings (Groupe Bordet, 17 %)., (Copyright © 2023. Published by Elsevier B.V.)

The soil microbial community plays important roles in nutrient cycling, plant pathogen suppression, decomposition of residues and degradation of pollutants; as such, it is often regarded as a good indicator of soil quality. Repeated applications of mixed organic and inorganic materials in agriculture improve the soil microbial quality and in turn crop productivity. The soil microbial quality following several years of repeated fertilizer inputs has received considerable attention, but the dynamic of this community over time has never been assessed. We used high-throughput sequencing targeting 16S ribosomal RNA genes to investigate the evolution of the bacterial and archaeal community throughout 6 years of repeated organic and inorganic fertilizer applications. Soils were sampled from a field experiment in La Mare (Reunion Island, France), where different mixed organic-inorganic fertilizer inputs characterized by more or less stable organic matter were applied regularly for 6 years. Soil samples were taken each year, more than 6 months after the latest fertilizer application. The soil molecular biomass significantly increased in some organically fertilized plots (by 35-45% on average), 3-5 years after the first fertilizers application. The significant variations in soil molecular microbial biomass were explained by the fertilization practices (cumulated organic carbon inputs) and sometimes by the soil parameters (sand and soil carbon contents). The structure of the bacterial and archaeal community was more influenced by time than by the fertilization type. However, repeated fertilizer applications over time tended to modify the abundance of the bacterial phyla Acidobacteria, Actinobacteria, Bacteroidetes, Firmicutes , and Proteobacteria. To conclude, the present study highlights that the soil bacterial and archaeal community is lastingly modified after 6 years of repeated fertilizer inputs. These changes depend on the nature of the organic input and on the fertilization practice (frequency and applied quantity)., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Sadet-Bourgeteau, Djemiel, Chemidlin Prévost-Bouré and Feder.)

Soils are fundamental resources for agricultural production and play an essential role in food security. They represent the keystone of the food value chain because they harbor a large fraction of biodiversity-the backbone of the regulation of ecosystem services and "soil health" maintenance. In the face of the numerous causes of soil degradation such as unsustainable soil management practices, pollution, waste disposal, or the increasing number of extreme weather events, it has become clear that (i) preserving the soil biodiversity is key to food security, and (ii) biodiversity-based solutions for environmental monitoring have to be developed. Within the soil biodiversity reservoir, microbial diversity including Archaea, Bacteria, Fungi and protists is essential for ecosystem functioning and resilience. Microbial communities are also sensitive to various environmental drivers and to management practices; as a result, they are ideal candidates for monitoring soil quality assessment. The emergence of meta-omics approaches based on recent advances in high-throughput sequencing and bioinformatics has remarkably improved our ability to characterize microbial diversity and its potential functions. This revolution has substantially filled the knowledge gap about soil microbial diversity regulation and ecology, but also provided new and robust indicators of agricultural soil quality. We reviewed how meta-omics approaches replaced traditional methods and allowed developing modern microbial indicators of the soil biological quality. Each meta-omics approach is described in its general principles, methodologies, specificities, strengths and drawbacks, and illustrated with concrete applications for soil monitoring. The development of metabarcoding approaches in the last 20 years has led to a collection of microbial indicators that are now operational and available for the farming sector. Our review shows that despite the recent huge advances, some meta-omics approaches (e.g., metatranscriptomics or meta-proteomics) still need developments to be operational for environmental bio-monitoring. As regards prospects, we outline the importance of building up repositories of soil quality indicators. These are essential for objective and robust diagnosis, to help actors and stakeholders improve soil management, with a view to or to contribute to combining the food and environmental quality of next-generation farming systems in the context of the agroecological transition., Competing Interests: BK was employed by the company Novasol Experts. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Djemiel, Dequiedt, Karimi, Cottin, Horrigue, Bailly, Boutaleb, Sadet-Bourgeteau, Maron, Chemidlin Prévost-Bouré, Ranjard and Terrat.)

Fibrous feeds are essential for horses. When developing feeding regimens promoting health and performance, we need to understand the digestion of plant cell walls and the functioning of the hindgut microbial ecosystem. Our objective was to investigate the effect of grass fibre maturity and legume forage on the hindgut microbiota and its activity. Six caecum and colon fistulated geldings were fed three diets differing in fibre composition: concentrate and late harvested grass haylage (35:65 energy ratio) (C); early and late harvested grass haylage (80:20) (G); lucerne and late harvested grass haylage (80:20) (L) for 28 days in a Latin-square design. No differences were measured in total bacteria concentrations, fungi and protozoa numbers nor in cellulolytic bacteria concentrations between the diets. Short-chain fatty acid concentrations did not differ between diets, but a lower (acetate + butyrate)/propionate ratio when the horses were fed Diet C, compared to G and L, was observed, suggesting lower fibrolytic and higher amylolytic activity. The pH increased when the horses were fed Diet L and decreased when fed C and G from caecum to faeces. The buffering capacity (BC) of hindgut digesta was five to fifteen-fold higher than that of the feeds, suggesting a decreased effect of feed BC as digesta travelled through the digestive tract. In conclusion, an early harvested forage opens up the possibility for forage-only diets, providing high energy without the negative effects of concentrate.

Microorganisms in soil are known to be a source and a sink of volatile organic compounds (VOCs). The role of the microbial VOCs on soil ecosystem regulation has been increasingly demonstrated in the recent years. Nevertheless, little is known about the influence of the microbial soil community structure and diversity on VOC emissions. This novel study analyzed the effect of reduced microbial diversity in soil on VOC emissions. We found that reduced levels of microbial diversity in soil increased VOC emissions from soils, while the number of different VOCs emitted decreased. Furthermore, we found that Proteobacteria, Bacteroidetes and fungi phyla were positively correlated to VOC emissions, and other prokaryotic phyla were either negatively correlated or very slightly positively correlated to VOCs emissions. Our interpretation is that Proteobacteria, Bacteroidetes and fungi were VOC producers while the other prokaryotic phyla were consumers. Finally, we discussed the possible role of VOCs as mediators of microbial interactions in soil.

This study assessed the time-scale variability of bacterial community structure in foal feces from birth to 365 days of age using Automated Ribosomal Intergenic Spacer Analysis (ARISA). Fecal samples were collected from five foals 2 h after birth (meconium) and in the morning at days 1, 2, 5, 10, 30, 60, 120, 179, 183, 194 and 365. The ARISA profiles were compared using an analysis of similarity (ANOSIM). Although both the age effect and the foal effect were highly significant (P < 0.010), the R-ANOSIM value for the foal effect was very low (R-ANOSIM = 0.089), while that of the age effect was much higher (R-ANOSIM = 0.309). Significant age-related changes were detected between days 0 and 2 (R-ANOSIM = 0.500), days 2 and 10 (R-ANOSIM = 0.475) and days 10 and 30 (R-ANOSIM = 0.519). No further shifts between consecutive times of sampling were detected in the bacterial community after day 30 and no changes were observed at weaning (day 180). These results show that the establishment of the intestinal bacterial community in foals is a sequential process, which reaches its climax state at around one month of age. Further studies using new generation sequencing based methods could be conducted to identify which bacterial genera are establishing in foals during the first month of life., (Copyright © 2013 Elsevier Ltd. All rights reserved.)