Beneficial and adverse effects of bio-inoculation on predicted functional microbial communities in salt-land restoration

Beneficial and adverse effects of bio-inoculation on predicted functional microbial communities in salt-land restoration | Authorea try { document.documentElement.classList.add('js'); } catch (e) { } var _gaq = _gaq || []; _gaq.push(['_setAccount', 'G-8VDV14Y67G']); _gaq.push(['_trackPageview']); (function() { var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true; ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js'; var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s); })(); Skip to main content Preprints Collections Wiley Open Research IET Open Research Ecological Society of Japan All Collections About About Authorea FAQs Contact Us Quick Search anywhere Search for preprint articles, keywords, etc. Search Search ADVANCED SEARCH SCROLL This is a preprint and has not been peer reviewed. Data may be preliminary. 2 September 2025 V1 Latest version Share on Beneficial and adverse effects of bio-inoculation on predicted functional microbial communities in salt-land restoration Authors : Pape Djighaly , Nathalie Diagne , Estelle Tournier , Mariama Ngom , Maimouna Cissoko , Pierre Tisseyre , Daouda Ngom , Valerie Hocher , Sergio SVISTOONOFF , and Hervé Sanguin 0000-0001-7160-2840 [email protected] Authors Info & Affiliations https://doi.org/10.22541/au.175681448.85560879/v1 Published Land Degradation & Development Version of record Peer review timeline 228 views 133 downloads Contents Abstract Information & Authors Metrics & Citations View Options References Figures Tables Media Share Abstract The potential impacts of bioinoculants on native soil microbiota—and consequently on soil functioning—represent a key issue for their large-scale adoption in land restoration. Yet, available data remain fragmented, especially for degraded ecosystems that are particularly vulnerable. In Senegal, a restoration program of salt-affected lands has been successfully implemented using Casuarinaceae species in association with salt-tolerant symbionts as bioinoculants. While previous studies demonstrated clear benefits for Casuarinaceae plantations and associated understory vegetation, their effects on soil functioning remain less understood. This study assessed changes in native soil microbiota under this restoration program. Results showed that bioinoculation reduced overall fungal diversity, though rare taxa were unaffected. In contrast, bacterial diversity was primarily shaped by salinity and Casuarinaceae species, with effects limited to dominant taxa. Functional predictions highlighted major shifts, including a bioinoculant-related reduction in bacterial pathogens, but an increase in fungal pathogens linked to salinity. Moreover, soil nitrogen cycling mediated by bacteria appeared sensitive to both salinity and Casuarinaceae species, while nitrogen-fixing bacterial taxa were specifically influenced by bioinoculation. The study demonstrates the environmental impacts of bioinoculation in salt-affected soils, highlighting the needs to routinely integrate the monitoring of soil microbiota in the requirements for the deployment of ecological restoration strategies. In addition, the results supported the importance of N-fixing symbionts as bioinoculant to positively improved N cycling and soil health in degraded landscapes. 1. Introduction The use of bioinoculants is expanding rapidly as there is an increasing need for sustainable alternatives to traditional inputs in human-managed ecosystems, such as agriculture, afforestation, and land restoration (Sessitsch et al., 2018). However, numerous environmental risks have been identified (Hart et al., 2017), including the potential alteration of native soil microbiota (Cornell et al., 2021; Mawarda et al., 2020). The interactions between bioinoculants and native soil microbiota can be either competitive or facilitative, potentially resulting in changes to ecosystem functioning (Cornell et al., 2021; Poppeliers et al., 2023). In degraded lands, native soil microbiota is hypothesized to exhibit greater sensitivity to bioinoculant introduction, potentially culminating in the complete displacement of native taxa (Hart et al., 2017; Wubs et al., 2016). In Senegal, approximately 1,700,000 hectares of land are degraded due to soil salinization (Diack et al., 2015), and restoration programs of salt-affected lands has been implemented based on the use of salt-tolerant plants, notably Casuarinaceae species (National Research Council, 1984; Barrett-Lennard, 2002; Dagar and Gupta, 2020). The capacity of Casuarinaceae species to colonize salt-affected lands was primarily attributed to symbiotic relationships with nitrogen-fixing bacteria of the genus Frankia , as well as mycorrhizal fungi, which enhance phosphate absorption and water uptake (Diagne et al., 2013). Consequently, bioinoculants composed of arbuscular mycorrhizal fungi (AMF) and nitrogen-fixing bacteria (NFB) were tested to promote stress resistance of Casuarinaceae species (Diagne et al., 2020; Djighaly et al., 2022). An experimental Casuarinaceae plantation set up in a saline ecosystem (Fatick, Senegal) demonstrated the benefits of a symbiotic consortium bioinoculant on the height and survival rate of two Casuarinaceae species (Djighaly et al., 2020). It has been observed than the use of consortia in bioinoculation strategies could have larger effects on native soil microbiota than single-strain bioinoculant (Hu et al., 2021). Consequently, adverse effects on salt-affected ecosystems due to inoculation of a consortia of salt-tolerant symbionts needs to be evaluate since these ecosystems are characterized by a diversity of bacteria and fungi adapted to extreme environmental conditions (Salwan et al., 2019; Yadav et al., 2020; Zhang et al., 2023). Microbial taxa belonging to the Firmicutes , Bacteroidetes and Gemmatimondetes are for example widely described for their prevalence in highly saline ecosystems (Guan et al., 2021; Zhang et al., 2023), whereas Gammaproteobacteria , Alphaproteobacteria , and Glomeromycota are known for their benefits in plant salinity tolerance (Evelin et al., 2019; Mishra et al., 2021). The goal of this study was the characterization of potential impacts of a bioinoculant based on a consortia of salt-tolerant symbionts (Djighaly et al., 2018; Ngom et al., 2016) on the native soil microbiota in the experimental trial described above, and to evaluate the contribution of salinity levels and Casuarinaceae species in mitigating the bioinoculant-mediated changes. Indeed, the level of salinity is known as strongly structuring soil microbial communities (Guan et al., 2021), and the salinity gradient of the experimental Casuarinaceae plantation may thus over the effect of bioinoculation. Similarly, plant species are major drivers of soil microbiome diversity and composition, notably through difference in the rate and composition of root exudates (Staszel-Szlachta et al., 2024), and consequently may mask the impact of bioinoculation. Potential multiple interactions between all three factors are however probable, highlighting the needs to fully encompass the diversity of biotic and abiotic interactions to trace the origins of soil microbiome changes. 2. Materials and Methods 2.1. Field study site and soil sampling The experimental plantation (2500 m 2 ) located in the Fatick region (Senegal; 14 °01’14 N, 16 °45’23 W) has been implemented in 2013 on a sandy loamy soil, characterized by salinity levels varying from 40 to 500 mM NaCl during the dry season, and subjected to periodic waterlogging during the rainy season (Djighaly et al., 2020). An ecological engineering strategy for soil restoration based on the plantation of two Casuarinaceae species, i.e. Casuarina glauca and Casuarina equisetifolia inoculated with a salt-tolerant bioinoculant composed of an arbuscular mycorrhizal strain ( Rhizophagus fasciculatus DAOM227130) and an actinorhizal strain ( Frankia CeD), was implemented as described in Djighaly et al. (2020). Soil samples surrounding Casuarinaceae trees were collected from the 3-year-old plantation, according to three different environmental factors, (i) the salinity (low salinity, 40 to 200 mM NaCl and high salinity, 200 to 500 mM NaCl), (ii) the use of symbiont inoculants (inoculated or not not), and (iii) the Casuarinaceae species. For each tree, a composite soil sample was constituted from three soil cores collected using a 7-cm-diameter soil corer to a depth of 30 cm, and sieved to 2 mm. 2.2. Metataxonomics and data processing Total DNA was extracted from 500 mg of soil using the FastDNA SPIN kit for soil (MP Biomedicals Europe, Illkirch, France) according to manufacturer’s instructions. Soil microbiota was assessed by MetaHealth expertise (Montpellier, France) using 16S rRNA gene and ITS2 amplification and Illumina Miseq PE250 sequencing, according a metataxonomic approach described in (Khassali et al., 2020). Illumina sequencing, base calling and demultiplexing were carried out using RTA v1.18.54.0, MCS 2.6.2.1 and bcl2fastq2.20. Paired reads were assembled with vsearch v2.26.1 (Rognes et al., 2016), and primer clipping was performed with cutadapt v4.6 (Martin, 2011). Clustering with SWARM v3.1.14 (Mahé et al., 2021), post-clustering curation with mumu 1.0.2 (https://github.com/frederic-mahe/mumu), chimera detection and taxonomic assignment as detailed in Khassali et al. (2020). The ribosomal database SILVA v138.1 (Quast et al., 2012) and a custom version of the ITS database UNITE v9.0 (Abarenkov et al., 2024) were used for the bacteria and fungi, respectively. Details of data processing steps are provided in Appendix. The raw data are available under the bioproject PRJEB72132 (https://www.ebi.ac.uk/ena/data/view/ PRJEB72132). 2.3. Statistics Data tables were transformed using the R tidyverse package version 1.3.2 (Wickham et al., 2019) and the plots were generated using the R ggplot2 package version 3.4.1 (Wickham, 2016). For soil bacterial and fungal communities analysis, global rarefaction (based on the samples with the smallest sizes) to 21897 and 13479 reads, respectively, were performed with the R vegan package version 2.6–4 (Oksanen et al., 2022) using the rrarefy() function for downstream statistical tests. Hill numbers ( q D ) were used to characterize soil microbial diversity with the R hilldiv package version 1.5.1 (Alberdi and Gilbert, 2019).\(D^{q}=\left(\sum_{i=1}^{R}p_{i}^{q}\right)^{\frac{1}{\left(1-q\right)}}\)), where q is the order of the Hill number, R is the total number of categories (i.e., unique numerical values in a numerical matrix), and p is the relative abundance of each category. Hill numbers express diversity as the effective number of species, ranging from richness ( q = 0) to abundance-weighted ( q = 1) and dominance-focused ( q = 2) measures. Soil microbiota structure analysis was performed by nonmetric multi-dimensional scaling (NMDS) with the R package vegan, and significance of differences according environmental variables was assessed by PERMANOVA using adonis2() function and HOMOVA using betadisper() and permutest() functions from the R package vegan. Predicted functional microbial groups were determined based on microbial taxonomy using FAPROTAX (Functional Annotation of Prokaryotic Taxa) (Louca et al., 2016) for bacterial taxa and FungalTraits (Põlme et al., 2020) for fungal taxa. The impact of environmental factors on soil microbial diversity or the abundance of functional microbial groups were estimated by three-way ANOVA as implemented in aov() function. 3. Results 3.1. Impact of ecological engineering strategies on native soil microbiota The influence of bioinoculation on native soil microbiota was assessed in comparison with salinity levels and the Casuarinaceae species established at the restoration site. Among these factors, salinity emerged as the stronger driver ( P < 0.05) of soil bacterial diversity, accounting for 9 to 16% of the varaiation (Figure 1A-C). Soil bacterial diversity was inversely correlated between salinity and pH (Figure 1D-F), with notably a significant increase of soil bacterial diversity in highest salinity levels (Table 1; Figure S1). The Casuarinaceae species also significantly contributed to changes of soil bacterial diversity but only for predominant taxa (Figure 1C; 12% of variability; P = 0.007). Higher diversity was measured for soil bacteria associated with C. glauca (Table 1; Figure S1). In contrast, changes in soil fungal diversity were mainly explained by bioinoculation (Figure 2B-C; 10 to 12% of variability), and no correlation was observed with salinity and pH (Figure 2D-F). Bioinoculation lead to a decrease of soil fungal diversity for common and dominant taxa (Figure Table 2, Table S2). Structure analysis of the soil microbiota revealed a broader impact of restoration program on both bacterial (Figure S2) and fungal (Figure S3) communities, with significant impacts of bioinoculation, salinity and plant species. In contrast to the impacts observed on alpha diversity, bioinoculation (R 2 = 0.1042; P = 1e−04) explained the main difference between bacterial communities whereas it was mainly salinity (R 2 = 0.0946; P = 1e−04), for fungal communities. For both communities, significant interactions were observed among the different environmental factors. 3.2. Impact of ecological engineering strategies on major predicted soil functional microbial groups Changes in the abundance of functional groups of soil microbiota were assessed using taxonomic-based functional or guild predictions. Predicted bacterial groups associated with pathotroph lifestyle were significantly ( P < 0.05) impacted (Figure 3), except by salinity for pathogens and parasites. Predicted bacterial groups classified according their source of energy were either impacted by Casuarina species for chemoheterotroph or bioinoculation for H-oxidizing bacteria (Figure S5). In terms of metabolism, bioinoculation significantly impacted the abundance of predicted bacterial groups involved in methane (CH 4 ) cycling or Casuarinaceae species in aromatic compound degradation (Figure S6). Nutrient cycling was mostly impacted by Casuarinaceae species (Figure S7), but also by salinity or bioinoculation for macronutrients ( i.e. N) and micronutrients (i.e. Fe, Mn) (Figure S7), respectively. A deeper investigation of impacts on N cycling revealed positive effect of bioinoculation on the abundance of bacterial taxa involved in N inputs, notably global N fixation (Figure 4), but with a negative effect on the abundance of actinorhizal N-fixers (Figure 4). Casuarinaceae species differentially impacted the abundance of legume and actinorhizal N-fixers. Nitrogen bioavailability content also promoted by bioinoculation through the increase of abundance of predicted bacterial groups involved in ureolysis (Figure 4). Differences in N loss was mainly related to Casuarinaceae species with an increase of predicted bacterial groups involved in nitrification for C. glauca (Figure S8), and salinity with an increase of predicted bacterial groups involved in denitrification (Figure S8). The abundance of predicted fungal groups involved in soil organic matter degradation was enhanced by bioinoculation (Figure S9), whereas predicted fungal groups known as plant saprotrophs were impacted by Casuarinaceae species, as well as uncharacterized saprotrophs (Figure S9). Contrary to bacteria, predicted fungal pathogens were mostly promoted by salinity but not Casuarinaceae species (Figure 5), and no impact was observed on predicted fungal parasites (Figure 5). Predicted animal and plant symbionts were differentially impacted by environmental factors, salinity and bioinoculation or Casuarinaceae species (Figure 6), respectively. On the other hand, the global predicted plant endophytes were strongly impacted by bioinoculation (Figure 6). 4. Discussion Salinity is expected to be one of the main factors affecting ecosystem functioning (He et al., 2025; Pereira et al., 2018; Shokri et al., 2024). Salinity tolerance in plants is widely depending on plant species and ecotypes (Beauchamp et al., 2009; Ribeiro-Barros et al., 2022), but also on plant-associated microorganisms (Tarolli et al., 2024), notably root-associated microbial symbionts (Dastogeer et al., 2020; Ngom et al., 2016). Consequently, ecological strategies based on the use of bioinoculants are developed to counteract negative effects of salt on plant growth and survival. Yet adverse impacts of bioinoculants on soil functioning were observed (Cornell et al., 2021; Gou et al., 2024), with in most cases no resilience of the native microbial community (Mawarda et al., 2020). In the current study, salinity was a major factor of bacterial diversity changes, but bioinoculation was the main factor for fungal diversity. Salinity was described as a key environmental factor driving bacterial community diversity in arid ecosystems (Zhang et al., 2019), but differential impacts are observed depending on salinity ranges (Zhang et al., 2019). Similarly, salinity and pH were shown as strongly correlated to bacterial community diversity, but inversely for pH compared to previous studies (Zhao et al., 2018). Differences in pH gradient might explain these opposite effects, since acid pH gradient (3 < pH gradient (7.9 < pH < 8.7) in Zhao et al. (2018). The difference in response between bacteria and fungi along a salinity gradient has been also described in other arid ecosystems (Lin et al., 2023), and contrasting toxicity effects of salt were between bacteria and fungi (Rath et al., 2016). The lack of effect of salinity gradient on the diversity of the fungal community might also be due to other environmental factors outweighing the effect of salinity (Zhao et al., 2019). The presence of vegetation cover, for example, could be one of those since the presence of cover plants can mitigate the effect of salinity on soil microbiota (Dasgupta et al., 2023). The plantation of Casuarinaceae on the current restoration site was indeed shown to enhance the development of herbaceous vegetation (Djighaly et al., 2020). In addition, soil fungal diversity tend to be more closely aligned with vegetation cover both for mutualists (Cassman et al., 2016; Zhang et al., 2021) and saprobes (Francioli et al., 2020), thus less changes are expected in their communities without concurrent changes to vegetation (van der Heijden et al., 1998; Beck et al., 2020). On the other hand, changes in diversity of the predominant bacterial taxa have been observed between Casuarinaceae species, which might be due to differences in root traits (exudates, genetic, tolerance to stress) between the two species. Bacterial community have been indeed shown as more strongly affected by differences in root traits than fungi (Alahmad et al., 2024; Merino-Martín et al., 2020). The changes in vegetation cover (richness diversity, composition) due to the different environmental factors (salinity, bioinoculation, Casuarinaceae species) remains unknown until now, but constitute undoubtedly an important explaining factors to explain variations in soil microbiota (Djighaly et al., 2020). However, the composition of each microbial compartment was globally influenced by the various environmental factors, suggesting that the use of bioinoculant, as well as the type of Casuarinaceae species determine the characteristics of community assembly in addition to salt stress. The consequences in terms of microbial functionalities and ecosystem services could be important (Catano et al., 2023), and have to be taken into account for restoration programs. Bacteria and fungi play indeed major roles in soil biogeochemical cycles, supporting soil fertility and plant health (Banerjee and van der Heijden, 2022; Saleem et al., 2019; Trivedi et al., 2020). Modifications of biotic and abiotic parameters can have a serious and lasting impact on soil functioning by altering general and specialized microbial functional groups (Griffiths and Philippot, 2013; Xun et al., 2021). For example, salinity, pH, soil moisture, or nutrients were shown to contribute to changes in fungal trophic guilds in saline soils (Zhao et al., 2019). Current results revealed significant impacts on several predicted microbial functional groups or guilds dependent on single or dual environmental factors. Saprotrophs, symbiotrophs and pathotrophs were mostly impacted by bioinoculation and / or Casuarinaceae species. Nevertheless, salinity affected the abundance of fungal plant pathogens, but not bacterial pathogens. Salt stress has also been shown to increase aggressiveness of certain fungal pathogens (Haddoudi et al., 2021). Opposite effects were observed on the abundance of actinorhizal N-fixers and free N-fixers in soils, highlighting complex plant-soil feedbacks, potentially due to priority effects between the competitive actinorhizal symbiont pre-inoculated on Casuarinaceae seedlings and native actinorhizal community on the restoration site, and plant-mediated promoting effect on other N-fixers. Nevertheless, N fixation in soils was reduced for high levels of salinity. The use of AM fungal inoculant combined with actinorhizal inoculant could also impact the soil microbial community through plant-soil feedbacks by enhancement of host plant growth and modification of the amount, timing, and form of carbon inputs into soil (De Gruyter et al., 2022). AM fungal inoculation was hypothesized to modify the native AM fungal community, as frequently observed (Islam et al., 2021; Thioye et al., 2021, 2019), but the extent of changes are related to properties of AM fungal inoculant and environmental factors (Hart et al., 2017; Islam et al., 2021; Martignoni et al., 2020). In the current study, Casuarinaceae species was the explicative factor of changes, with higher abundance of soil AM fungi associated with C. glauca compared to C. equisetifolia . Similar observation was obtained for native soil rhizobia. These results emphasize the necessity to set up trial with mixed plantation to evaluate the benefits of a range of Casuarinaceae species on soil functioning beyond the effects on tree growth. Changes in saprotroph abundance might be due to differences in vegetation cover promoted by Casuarinaceae plantation and consequently differences in organic matter composition or abundance. In addition, differential impacts of Casuarinaceae species were observed on bacterial and fungal saprotrophs. Bioinoculation impacted also differentially bacterial and fungal saprotrophs, favoring soil fungal saprotrophs and limiting plant bacterial saprotrophs. By digging deeper into the functions involved in biogeochemical cycles, significant impacts of environmental factors were observed on nutrient cycling and energy flows. Soil carbon content, notably CH 4 cycling and aromatic compound degradation, was affected by symbiont inoculant and Casuarinaceae species, respectively. Multiple microbial guilds are responsible of CH 4 fluxes in soils (Hartman et al., 2024), and the strong changes of soil bacterial community due to bioinoculation might have particularly impacted some of the guilds involved in CH 4 cycling. Differences in the abundance of bacteria involved in aromatic compound degradation is probably due to differences in root exudate composition and rates between the two Casuarinaceae species (Dennis et al., 2010; Staszel-Szlachta et al., 2024). On the other hand, salinity was the main factor negatively impacting soil bacterial community mediating N cycling confirming previous studies in highly salt-affected soils (Li et al., 2021). Nevertheless, impacts on N turnover is dependent on salinity levels, which can lead to inconsistency in conclusions (Tao et al., 2024). Moreover, changes in H-oxidizing bacteria abundance, which are generally associated with N fixation variations (Maimaiti et al., 2007), was not related to salinity levels, but to bioinoculation with opposite effects on N fixation. Bioavailability of soil N content for plant was also promoted by bioinoculation through ureolytic bacterial community, with probable major benefits on soil fertility (Hasan, 2000). Interestingly, the use of C. glauca promoted bacterial community involved in N cycling compared to C. equisetifolia , from N fixation to nitrification, whereas increasing salinity promoted mainly denitrification. 5. Conclusion The development of ecological engineering strategies based on the inoculation of symbionts has to be deployed with caution. Important impacts beyond salt stress were observed, with positive and negative effects on predicted functional groups of soil microbiota. These results highlight the importance of combining above- and below-ground monitoring of agronomic and environmental traits to evaluate the performance of restoration strategies in salt-affected soils. To go further, the set-up of preliminary monitoring of soil microbiota in sites to be rehabilitated could be a crucial pre-requisites in ecological engineering strategies since the initial status of native soil microbiota rather than the changes due to inoculants has been reported as a promising indicator to predict the benefits of inoculation strategies (Lutz et al., 2023). Acknowledgement We acknowledge the “Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés Aux Stress Environnementaux (LAPSE)” for providing supporting funds to this project. We thank the Palmarin town, its authorities and inhabitants for their welcome and for supporting and facilitating our trials. We also thank Camille Faye and Gilbert Ndong for their support in the field and for monitoring the trials. This work would not have been possible without them. Tables Table 1. Impact of environmental factors on soil bacterial diversity (Type III anova) Hill numbers Environmental factors F value Pr(>F) q = 0 Bioinoculant 3.069 0.0881 Salinity 8.357 0.0064** Casuarinaceae 3.201 0.0818 Bioinoculant × Salinity 0.219 0.6426 Bioinoculant × Casuarinaceae 0.914 0.3452 Casuarinaceae × Salinity 2.772 0.1044 q = 1 Bioinoculant 1.363 0.2504 Salinity 11.168 0.0019** Casuarinaceae 3.698 0.0622 Bioinoculant × Salinity 0.342 0.562 Bioinoculant × Casuarinaceae 2.834 0.1007 Casuarinaceae × Salinity 2.166 0.1495 q = 2 Bioinoculant 0.897 0.3498 Salinity 8.595 0.0058** Casuarinaceae 9.372 0.0041** Bioinoculant × Salinity 1.630 0.2097 Bioinoculant × Casuarinaceae 9.656 0.0036** Casuarinaceae × Salinity 0.599 0.4438 Table 2. Impact of environmental factors on soil fungal diversity (Type III anova) Hill numbers Environmental factors F value Pr(>F) q = 0 Bioinoculant 0.782 0.3828 Salinity 0.304 0.5852 Casuarinaceae 0.068 0.7965 Bioinoculant × Salinity 0.006 0.9395 Bioinoculant × Casuarinaceae 0.619 0.4367 Casuarinaceae × Salinity 2.289 0.0486* q = 1 Bioinoculant 6.897 0.0129* Salinity 0.149 0.7022 Casuarinaceae 2.029 0.1635 Bioinoculant × Salinity 0.890 0.3522 Bioinoculant × Casuarinaceae 1.805 0.1880 Casuarinaceae × Salinity 3.261 0.0798 q = 2 Bioinoculant 5.807 0.0215* Salinity 0.002 0.9644 Casuarinaceae 3.673 0.0637 Bioinoculant × Salinity 1.069 0.3084 Bioinoculant × Casuarinaceae 1.978 0.1687 Casuarinaceae × Salinity 1.716 0.1990 Figure 1. Relative contribution of environmental factors (salinity, bioinoculation, Casuarinaceae species) on Hill numbers ( q D ) from bacterial community estimated by variance partitioning analyses (A-C), and correlation analysis between Hill numbers and salinity (soil conductivity, µS/cm) or pH (D-F). (A-D) q = 0, (B-E), q = 1 and (C-F), q = 2. Residuals indicate the percentage of variance unexplained with the environmental factors. R (Spearman rank coefficient) and P values are estimated for comparison. Figure 2. Relative contribution of environmental factors (salinity, inoculation, Casuarinaceae species) on Hill numbers ( q D ) from fungal community estimated by variance partitioning analyses (A-C), and correlation analysis between Hill numbers and salinity or pH (D-F). (A-D) q = 0, (B-E), q = 1 and (C-F), q = 2. Residuals indicate the percentage of variance unexplained with the environmental factors. R (Spearman rank coefficient) and P values are estimated for comparison. Figure 3. Effect of environmental factors (salinity, bionoculation, Casuarinaceae species) on the relative abundance (read numbers) of bacterial groups involved in plant-insect material degradation and pathotroph trophic mode. Low salinity, 4500 to 18 000 µS/cm NaCl. Statistics are based on log (1+x) transformed abundance, subjected to three-way ANOVA, and variance distribution for each comparison is represented with the corresponding p-values (P). High salinity, 18,000 to 40,000 µS/cm NaCl. (-), no bioinoculation. (+) bioinoculation. Figure 4. Effect of environmental factors (salinity, boinoculation, Casuarinaceae species) on the relative abundance (read numbers) of bacterial groups involved in N inputs and N plant bioavailability. Statistics are based on log (1+x) transformed abundance, subjected to three-way ANOVA, and variance distribution for each comparison is represented with the corresponding p-values (P). Low salinity, 4500 to 18000 µS/cm NaCl. High salinity, 18000 to 40000 µS/cm NaCl. (-), no bioinoculation. (+) bioinoculation. Figure 5. Effect of environmental factors (salinity, bioinoculation, Casuarinaceae species) on the relative abundance (read numbers) of fungal guilds with pathotroph trophic mode. Statistics are based on log (1+x) transformed abundance, subjected to three-way ANOVA, and variance distribution for each comparison is represented with the corresponding p-values (P). Low salinity, 4500 to 18 000 µS/cm NaCl. High salinity, 18000 to 40000 µS/cm NaCl. (-), no bioinoculation. (+) bioinoculation. Figure 6. Effect of environmental factors (salinity, bioinoculation, Casuarinaceae species) on the relative abundance (read numbers) of fungal guilds with symbiotroph trophic mode. Low salinity, 4500 to 18 000 µS/cm NaCl. Statistics are based on log (1+x) transformed abundance, subjected to three-way ANOVA, and variance distribution for each comparison is represented with the corresponding p-values (P). Low salinity, 4500 to 18 000 µS/cm NaCl. High salinity, 18000 to 40000 µS/cm NaCl. (-), no bioinoculation. (+) bioinoculation. Supplementary Materials Figure S1. Effect of environmental factors (salinity, inoculation, Casuarinaceae species) on effective number of species, Hill numbers ( q D ), from bacterial community. Statistics are based on three-way ANOVA, and variance distribution for each comparison is represented with the corresponding p-values (P). Low salinity, 4500 to 18 000 µS/cm NaCl. High salinity, 18,000 to 40,000 µS/cm NaCl. (-), no bioinoculation. (+) bioinoculation. Figure S2. Effect of environmental factors (salinity, inoculation, Casuarinaceae species) on effective number of species, Hill numbers ( q D ), from fungal community. Statistics are based on three-way ANOVA, and variance distribution for each comparison is represented with the corresponding p-values (P). Low salinity, 4500 to 18 000 µS/cm NaCl. High salinity, 18,000 to 40,000 µS/cm NaCl. (-), no bioinoculation. (+) bioinoculation. Figure S3. Non-metric scale analysis (NMDS) of bacterial community structure (based on the Horn–Morisita dissimilarity index) associated two Casuarinaceae species inoculated or not with symbionts in saline soils (Low salinity, 4500 to 18 000 µS/cm NaCl; High salinity, 18,000 to 40,000 µS/cm NaCl). The top and right marginal density plots represent the density of samples according to low (pale blue) to high (dark blue) salinity levels. Figure S4. Non-metric scale analysis (NMDS) of fungal community structure (based on the Horn–Morisita dissimilarity index) associated two Casuarinaceae species inoculated or not with symbionts in saline soils (Low salinity, 4500 to 18 000 µS/cm NaCl; High salinity, 18,000 to 40,000 µS/cm NaCl). The top and right marginal density plots represent the density of samples according to low (pale blue) to high (dark blue) salinity levels. Figure S5. Effect of environmental factors (salinity, inoculation, Casuarinaceae species) on the relative abundance (read numbers) of bacterial groups according the energy source. Statistics are based on log (1+x) transformed abundance, subjected to three-way ANOVA, and variance distribution for each comparison is represented with the corresponding p-values (P). Low salinity, 4500 to 18 000 µS/cm NaCl. High salinity, 18,000 to 40,000 µS/cm NaCl. (-), no bioinoculation. (+) bioinoculation. Figure S6. Effect of environmental factors (salinity, inoculation, Casuarinaceae species) on the relative abundance (read numbers) of bacterial groups involved in C cycling. Statistics are based on log (1+x) transformed abundance, subjected to three-way ANOVA, and variance distribution for each comparison is represented with the corresponding p-values (P). Low salinity, 4500 to 18 000 µS/cm NaCl. High salinity, 18,000 to 40,000 µS/cm NaCl. (-), no bioinoculation. (+) bioinoculation. Figure S7. Effect of environmental factors (salinity, inoculation, Casuarinaceae species) on the relative abundance (read numbers) of bacterial groups involved in nutrient and micronutrient cycling. Statistics are based on log (1+x) transformed abundance, subjected to three-way ANOVA, and variance distribution for each comparison is represented with the corresponding p-values (P). Low salinity, 4500 to 18 000 µS/cm NaCl. High salinity, 18,000 to 40,000 µS/cm NaCl. (-), no bioinoculation. (+) bioinoculation. Figure S8. Effect of environmental factors (salinity, inoculation, Casuarinaceae species) on the relative abundance (read numbers) of bacterial groups involved in N loss. Statistics are based on log (1+x) transformed abundance, subjected to three-way ANOVA, and variance distribution for each comparison is represented with the corresponding p-values (P). Low salinity, 4500 to 18 000 µS/cm NaCl. High salinity, 18,000 to 40,000 µS/cm NaCl. (-), no bioinoculation. (+) bioinoculation. Figure S9. Effect of environmental factors (salinity, inoculation, Casuarinaceae species) on the relative abundance (read numbers) of fungal guilds with saprotroph trophic mode. Statistics are based on log (1+x) transformed abundance, subjected to three-way ANOVA, and variance distribution for each comparison is represented with the corresponding p-values (P). Low salinity, 4500 to 18 000 µS/cm NaCl. High salinity, 18,000 to 40,000 µS/cm NaCl. (-), no bioinoculation. (+) bioinoculation. References Abarenkov, K., Nilsson, R.H., Larsson, K.-H., Taylor, A.F.S., May, T.W., Frøslev, T.G., Pawlowska, J., Lindahl, B., Põldmaa, K., Truong, C., Vu, D., Hosoya, T., Niskanen, T., Piirmann, T., Ivanov, F., Zirk, A., Peterson, M., Cheeke, T.E., Ishigami, Y., Jansson, A.T., Jeppesen, T.S., Kristiansson, E., Mikryukov, V., Miller, J.T., Oono, R., Ossandon, F.J., Paupério, J., Saar, I., Schigel, D., Suija, A., Tedersoo, L., Kõljalg, U., 2024. The UNITE database for molecular identification and taxonomic communication of fungi and other eukaryotes: sequences, taxa and classifications reconsidered. Nucleic. Acids Res. 52, D791–D797. https://doi.org/10.1093/nar/gkad1039 Alahmad, A., Harir, M., Fochesato, S., Tulumello, J., Walker, A., Barakat, M., Ndour, P.M.S., Schmitt-Kopplin, P., Cournac, L., Laplaze, L., Heulin, T., Achouak, W., 2024. Unraveling the interplay between root exudates, microbiota, and rhizosheath formation in pearl millet. Microbiome 12, 1. https://doi.org/10.1186/s40168-023-01727-3 Alberdi, A., Gilbert, M.T.P., 2019. hilldiv: an R package for the integral analysis of diversity based on Hill numbers. bioRxiv 545665. https://doi.org/10.1101/545665 Banerjee, S., van der Heijden, M.G.A., 2022. Soil microbiomes and one health. Nat. Rev. Microbiol. https://doi.org/10.1038/s41579-022-00779-w Barrett-Lennard, E.G., 2002. Restoration of saline land through revegetation. Agric. Water Manag. 53, 213–226. https://doi.org/10.1016/S0378-3774(01)00166-4 Beauchamp, V.B., Walz, C., Shafroth, P.B., 2009. Salinity tolerance and mycorrhizal responsiveness of native xeroriparian plants in semi-arid western USA. Appl Soil Ecol 43, 175–184. https://doi.org/10.1016/j.apsoil.2009.07.004 Catano, C.P., Groves, A.M., Brudvig, L.A., 2023. Community assembly history alters relationships between biodiversity and ecosystem functions during restoration. Ecology 104. https://doi.org/10.1002/ecy.3910 Cornell, C., Kokkoris, V., Richards, A., Horst, C., Rosa, D., Bennett, J.A., Hart, M.M., 2021. Do bioinoculants affect resident microbial communities? A meta-analysis. Front. Agron. 3, 753474. https://doi.org/10.3389/fagro.2021.753474 Dagar, J.C., Gupta, S.R., 2020. Agroforestry interventions for rehabilitating salt-affected and waterlogged marginal landscapes, in: Dagar, J.C., Gupta, S.R., Teketay, D. (Eds.), Agroforestry for degraded landscapes. Springer Singapore, Singapore, pp. 111–162. https://doi.org/10.1007/978-981-15-6807-7_5 Dasgupta, D., Ries, M., Walter, K., Zitnick‐Anderson, K., Camuy‐Vélez, L.A., Gasch, C., Banerjee, S., 2023. Cover cropping reduces the negative effect of salinity on soil microbiomes. J. Sust. Agri. Env. 2, 140–152. https://doi.org/10.1002/sae2.12054 Dastogeer, K.M.G., Zahan, M.I., Tahjib-Ul-Arif, Md., Akter, M.A., Okazaki, S., 2020. Plant salinity tolerance conferred by arbuscular mycorrhizal fungi and associated mechanisms: A meta-analysis. Front. Plant Sci. 11, 588550. https://doi.org/10.3389/fpls.2020.588550 De Gruyter, J., Weedon, J.T., Elst, E.M., Geisen, S., van der Heijden, M.G.A., Verbruggen, E., 2022. Arbuscular mycorrhizal inoculation and plant response strongly shape bacterial and eukaryotic soil community trajectories. Soil Biol. Biochem. 165, 108524. https://doi.org/10.1016/j.soilbio.2021.108524 Dennis, P.G., Miller, A.J., Hirsch, P.R., 2010. Are root exudates more important than other sources of rhizodeposits in structuring rhizosphere bacterial communities? FEMS Microbiol. Ecol. 72, 313–27. Diack, M., Diop, T., Ndiaye, R., 2015. Restoration of degraded lands affected by salinization process under climate change conditions: impacts on food security in the Senegal River Valley, in: Lal, R., Singh, B.R., Mwaseba, D.L., Kraybill, D., Hansen, D.O., Eik, L.O. (Eds.), Sustainable intensification to advance food security and enhance climate Resilience in Africa. Springer International Publishing, Cham, pp. 275–288. https://doi.org/10.1007/978-3-319-09360-4_14 Diagne, N., Diouf, D., Svistoonoff, S., Kane, A., Noba, K., Franche, C., Bogusz, D., Duponnois, R., 2013. Casuarina in Africa: Distribution, role and importance of arbuscular mycorrhizal, ectomycorrhizal fungi and Frankia on plant development. J. Environ. Manage. 128, 204–209. https://doi.org/10.1016/j.jenvman.2013.05.009 Diagne, N., Ndour, M., Djighaly, P.I., Ngom, D., Ngom, M.C.N., Ndong, G., Svistoonoff, S., Cherif-Silini, H., 2020. Effect of plant growth promoting rhizobacteria (PGPR) and arbuscular mycorrhizal fungi (AMF) on salt stress tolerance of Casuarina obesa (Miq.). Front. Sustain. Food Syst. 4, 601004. https://doi.org/10.3389/fsufs.2020.601004 Djighaly, P.I., Diagne, N., Ngom, M., Ngom, D., Hocher, V., Fall, D., Diouf, D., Laplaze, L., Svistoonoff, S., Champion, A., 2018. Selection of arbuscular mycorrhizal fungal strains to improve Casuarina equisetifolia L. and Casuarina glauca Sieb. tolerance to salinity. Ann. For. Sci. 75, 72. https://doi.org/10.1007/s13595-018-0747-1 Djighaly, P.I., Diagne, N., Ngom, D., Cooper, K., Pignoly, S., Hocher, V., Farrant, J.M., Svistoonoff, S., 2022. Effect of symbiotic associations with Frankia and arbuscular mycorrhizal fungi on antioxidant activity and cell ultrastructure in C. equisetifolia and C. obesa under salt stress. J. For. Res. 27, 117–127. https://doi.org/10.1080/13416979.2022.2037837 Djighaly, P.I., Ngom, D., Diagne, N., Fall, D., Ngom, M., Diouf, D., Hocher, V., Laplaze, L., Champion, A., Farrant, J.M., Svistoonoff, S., 2020. Effect of Casuarina plantations inoculated with arbuscular mycorrhizal fungi and frankia on the diversity of herbaceous vegetation in saline environments in Senegal. Diversity 12, 293. https://doi.org/10.3390/d12080293 Evelin, H., Devi, T.S., Gupta, S., Kapoor, R., 2019. Mitigation of salinity stress in plants by arbuscular mycorrhizal symbiosis: Current understanding and new challenges. Front. Plant Sci. 10, 470. https://doi.org/10.3389/fpls.2019.00470 Gou, X., Kong, W., Sadowsky, M.J., Chang, X., Qiu, L., Liu, W., Shao, M., Wei, X., 2024. Global responses of soil bacteria and fungi to inoculation with arbuscular mycorrhizal fungi. CATENA 237, 107817. https://doi.org/10.1016/j.catena.2024.107817 Griffiths, B.S., Philippot, L., 2013. Insights into the resistance and resilience of the soil microbial community. FEMS Microbiol. Rev. 37, 112–129. https://doi.org/10.1111/j.1574-6976.2012.00343.x Guan, Y., Jiang, N., Wu, Y., Yang, Z., Bello, A., Yang, W., 2021. Disentangling the role of salinity-sodicity in shaping soil microbiome along a natural saline-sodic gradient. Sci. Total Environ. 765, 142738. https://doi.org/10.1016/j.scitotenv.2020.142738 Haddoudi, I., Mhadhbi, H., Gargouri, M., Barhoumi, F., Romdhane, S.B., Mrabet, M., 2021. Occurrence of fungal diseases in faba bean ( Vicia faba L.) under salt and drought stress. Eur. J. Plant Pathol. 159, 385–398. https://doi.org/10.1007/s10658-020-02169-5 Hart, M.M., Antunes, P.M., Chaudhary, V.B., Abbott, L.K., 2017. Fungal inoculants in the field: Is the reward greater than the risk? Funct. Ecol. https://doi.org/10.1111/1365-2435.12976 Hartman, W.H., Bueno De Mesquita, C.P., Theroux, S.M., Morgan-Lang, C., Baldocchi, D.D., Tringe, S.G., 2024. Multiple microbial guilds mediate soil methane cycling along a wetland salinity gradient. mSystems 9, e00936-23. https://doi.org/10.1128/msystems.00936-23 Hasan, H.A.H., 2000. Ureolytic microorganisms and soil fertility: A review. Commun. Soil Sci. Plan. 31, 2565–2589. https://doi.org/10.1080/00103620009370609 He, M., Li, D., Peng, S., Wang, Y., Ding, Q., Wang, Y., Zhang, J., 2025. Reduced soil ecosystem multifunctionality is associated with altered complexity of the bacterial-fungal interkingdom network under salinization pressure. Environ. Res. 269, 120863. doi: 10.1016/j.envres.2025.120863. 39848514. Islam, M.N., Germida, J.J., Walley, F.L., 2021. Survival of a commercial AM fungal inoculant and its impact on indigenous AM fungal communities in field soils. Appl. Soil Ecol. 166, 103979. https://doi.org/10.1016/j.apsoil.2021.103979 Khassali, H., Baumel, A., Mahé, F., Tournier, E., Tisseyre, P., Prin, Y., Ouahmane, L., Sanguin, H., 2020. The belowground bacterial and fungal communities differed in their significance as microbial indicator of Moroccan carob habitats. Ecol. Indic. 114, 106341. https://doi.org/10.1016/j.ecolind.2020.106341 Li, X., Wang, A., Wan, W., Luo, X., Zheng, L., He, G., Huang, D., Chen, W., Huang, Q., 2021. High salinity inhibits soil bacterial community mediating nitrogen cycling. Appl. Environ. Microbiol. 87, e01366-21. https://doi.org/10.1128/AEM.01366-21 Lin, L., Ruan, Z., Jing, X., Wang, Y., Feng, W., 2023. Soil salinization increases the stability of fungal not bacterial communities in the Taklamakan desert. Soil Ecol. Lett. 5, 230175. https://doi.org/10.1007/s42832-023-0175-5 Louca, S., Parfrey, L.W., Doebeli, M., 2016. Decoupling function and taxonomy in the global ocean microbiome. Science 353, 1272–1277. https://doi.org/10.1126/science.aaf4507 Lutz, S., Bodenhausen, N., Hess, J., Valzano-Held, A., Waelchli, J., Deslandes-Hérold, G., Schlaeppi, K., Van Der Heijden, M.G.A., 2023. Soil microbiome indicators can predict crop growth response to large-scale inoculation with arbuscular mycorrhizal fungi. Nat. Microbiol. 8, 2277–2289. https://doi.org/10.1038/s41564-023-01520-w Mahé, F., Czech, L., Stamatakis, A., Quince, C., de Vargas, C., Dunthorn, M., Rognes, T., 2021. Swarm v3: towards tera-scale amplicon clustering. Bioinformatics btab493. https://doi.org/10.1093/bioinformatics/btab493 Maimaiti, J., Zhang, Y., Yang, J., Cen, Y., Layzell, D.B., Peoples, M., Dong, Z., 2007. Isolation and characterization of hydrogen‐oxidizing bacteria induced following exposure of soil to hydrogen gas and their impact on plant growth. Environ. Microbiol. 9, 435–444. https://doi.org/10.1111/j.1462-2920.2006.01155.x Martignoni, M.M., Garnier, J., Hart, M.M., Tyson, R.C., 2020. Investigating the impact of the mycorrhizal inoculum on the resident fungal community and on plant growth. Ecol. Model. 109321. https://doi.org/10.1016/j.ecolmodel.2020.109321 Martin, M., 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17, 10–12. https://doi.org/10.14806/ej.17.1.200 Mawarda, P.C., Le Roux, X., Dirk Van Elsas, J., Salles, J.F., 2020. Deliberate introduction of invisible invaders: A critical appraisal of the impact of microbial inoculants on soil microbial communities. Soil Biol. Biochem. 148, 107874. https://doi.org/10.1016/j.soilbio.2020.107874 Merino-Martín, L., Griffiths, R.I., Gweon, H.S., Furget-Bretagnon, C., Oliver, A., Mao, Z., Le Bissonnais, Y., Stokes, A., 2020. Rhizosphere bacteria are more strongly related to plant root traits than fungi in temperate montane forests: insights from closed and open forest patches along an elevational gradient. Plant Soil 450, 183–200. https://doi.org/10.1007/s11104-020-04479-3 Mishra, P., Mishra, J., Arora, N.K., 2021. Plant growth promoting bacteria for combating salinity stress in plants – Recent developments and prospects: A review. Microbiol. Res. 252, 126861. https://doi.org/10.1016/j.micres.2021.126861 National Research Council, 1984. Casuarinas: Nitrogen-fixing trees for adverse sites. National Academies Press, Washington, D.C. https://doi.org/10.17226/19415 Ngom, M., Gray, K., Diagne, N., Oshone, R., Fardoux, J., Gherbi, H., Hocher, V., Svistoonoff, S., Laplaze, L., Tisa, L.S., Sy, M.O., Champion, A., 2016. Symbiotic performance of diverse Frankia strains on salt-stressed Casuarina glauca and Casuarina equisetifolia Plants. Front. Plant Sci. 7. https://doi.org/10.3389/fpls.2016.01331 Oksanen, J., Simpson, G.L., Blanchet, F.G., Kindt, R., Legendre, P., Friendly, M., Minchin, P.R., O’Hara, R.B., Solymos, P., Stevens, M.H.H., Szoecs, E., Barbour, M., Bedward, M., Bolker, B., Borcard, D., Carvalho, G., Chirico, M., De Caceres, M., Durand, S., Evangelista, H., Fitzjohn, R., Hill, M., Lahti, L., McGlinn, D., Ouellette, M., Ribeiro, C.E., Smith, T., Stier, A., Terbraak, C., Weedon, J., 2022. vegan: Community Ecology Package. R package version 2.6-4. Pereira, C.S., Lopes, I., Abrantes, I., Sousa, J.P., Chelinho, S., 2018. Salinization effects on coastal ecosystems: a terrestrial model ecosystem approach. Philos. Trans. R. Soc. Lond. B. Biol. Sci. 374(1764), 20180251. doi: 10.1098/rstb.2018.0251. Põlme, S., Abarenkov, K., Henrik Nilsson, R., Lindahl, B.D., Clemmensen, K.E., Kauserud, H., Nguyen, N., Kjøller, R., Bates, S.T., Baldrian, P., Frøslev, T.G., Adojaan, K., Vizzini, A., Suija, A., Pfister, D., Baral, H.-O., Järv, H., Madrid, H., Nordén, J., Liu, J.-K., Pawlowska, J., Põldmaa, K., Pärtel, K., Runnel, K., Hansen, K., Larsson, K.-H., Hyde, K.D., Sandoval-Denis, M., Smith, M.E., Toome-Heller, M., Wijayawardene, N.N., Menolli, N., Reynolds, N.K., Drenkhan, R., Maharachchikumbura, S.S.N., Gibertoni, T.B., Læssøe, T., Davis, W., Tokarev, Y., Corrales, A., Soares, A.M., Agan, A., Machado, A.R., Argüelles-Moyao, A., Detheridge, A., de Meiras-Ottoni, A., Verbeken, A., Dutta, A.K., Cui, B.-K., Pradeep, C.K., Marín, C., Stanton, D., Gohar, D., Wanasinghe, D.N., Otsing, E., Aslani, F., Griffith, G.W., Lumbsch, T.H., Grossart, H.-P., Masigol, H., Timling, I., Hiiesalu, I., Oja, J., Kupagme, J.Y., Geml, J., Alvarez-Manjarrez, J., Ilves, K., Loit, K., Adamson, K., Nara, K., Küngas, K., Rojas-Jimenez, K., Bitenieks, K., Irinyi, L., Nagy, L.G., Soonvald, L., Zhou, L.-W., Wagner, L., Aime, M.C., Öpik, M., Mujica, M.I., Metsoja, M., Ryberg, M., Vasar, M., Murata, M., Nelsen, M.P., Cleary, M., Samarakoon, M.C., Doilom, M., Bahram, M., Hagh-Doust, N., Dulya, O., Johnston, P., Kohout, P., Chen, Q., Tian, Q., Nandi, R., Amiri, R., Perera, R.H., dos Santos Chikowski, R., Mendes-Alvarenga, R.L., Garibay-Orijel, R., Gielen, R., Phookamsak, R., Jayawardena, R.S., Rahimlou, S., Karunarathna, S.C., Tibpromma, S., Brown, S.P., Sepp, S.-K., Mundra, S., Luo, Z.-H., Bose, T., Vahter, T., Netherway, T., Yang, T., May, T., Varga, T., Li, W., Coimbra, V.R.M., de Oliveira, V.R.T., de Lima, V.X., Mikryukov, V.S., Lu, Y., Matsuda, Y., Miyamoto, Y., Kõljalg, U., Tedersoo, L., 2020. FungalTraits: a user-friendly traits database of fungi and fungus-like stramenopiles. Fungal Divers. 105, 1–16. https://doi.org/10.1007/s13225-020-00466-2 Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., Peplies, J., Glöckner, F.O., 2012. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, D590–D596. https://doi.org/10.1093/nar/gks1219 Rath, K.M., Maheshwari, A., Bengtson, P., Rousk, J., 2016. Comparative Toxicities of Salts on Microbial Processes in Soil. Appl. Environ. Microbiol. 82, 2012–2020. https://doi.org/10.1128/AEM.04052-15 Ribeiro-Barros, A.I., Pawlowski, K., Ramalho, J.C., 2022. Mechanisms of salt stress tolerance in Casuarina : a review of recent research. J. For. Res. 27, 113–116. https://doi.org/10.1080/13416979.2022.2036416 Rognes, T., Flouri, T., Nichols, B., Quince, C., Mahé, F., 2016. VSEARCH: a versatile open source tool for metagenomics. PeerJ 4, e2584. https://doi.org/10.7717/peerj.2584 Sahab, S., Suhani, I., Srivastava, V., Chauhan, P.S., Singh, R.P., Prasad, V., 2021. Potential risk assessment of soil salinity to agroecosystem sustainability: Current status and management strategies. Sci. Total Environ. 764, 144164. https://doi.org/10.1016/j.scitotenv.2020.144164 Saleem, M., Hu, J., Jousset, A., 2019. More than the sum of its parts: Microbiome biodiversity as a driver of plant growth and soil health. Annu. Rev. Ecol. Evol. Syst. 50, 145–168. https://doi.org/10.1146/annurev-ecolsys-110617-062605 Salwan, R., Sharma, A., Sharma, V., 2019. Microbes mediated plant stress tolerance in saline agricultural ecosystem. Plant Soil 442, 1–22. https://doi.org/10.1007/s11104-019-04202-x Sessitsch, A., Brader, G., Pfaffenbichler, N., Gusenbauer, D., Mitter, B., 2018. The contribution of plant microbiota to economy growth. Microb. Biotechnol. 11, 801–805. https://doi.org/10.1111/1751-7915.13290 Shokri, N., Hassani, A., & Sahimi, M., 2024. Multi-scale soil salinization dynamics from global to pore scale: A review. Rev. Geophys. 62, e2023RG000804. https://doi.org/10.1029/2023RG000804 Singh, A., 2022. Soil salinity: A global threat to sustainable development. Soil Use Manag. 38, 39–67. https://doi.org/10.1111/sum.12772 Staszel-Szlachta, K., Lasota, J., Szlachta, A., Błońska, E., 2024. The impact of root systems and their exudates in different tree species on soil properties and microorganisms in a temperate forest ecosystem. BMC Plant Biol. 24, 45. https://doi.org/10.1186/s12870-024-04724-2 Tao, Y., Xie, W., Xu, L., Zhang, L., Wang, G., Wang, X., Shi, C., 2024. The characteristics of soil salinization effects on nitrogen mineralization and nitrification in upland fields. Front. Environ. Sci. 12, 1369554. https://doi.org/10.3389/fenvs.2024.1369554 Tarolli, P., Luo, J., Park, E., Barcaccia, G., Masin, R., 2024. Soil salinization in agriculture: Mitigation and adaptation strategies combining nature-based solutions and bioengineering. iScience. 27(2), 108830. https://doi:10.1016/j.isci.2024.108830. Thioye, B., Sanguin, H., Kane, A., de Faria, S.M., Fall, D., Prin, Y., Sanogo, D., Ndiaye, C., Duponnois, R., Sylla, S.N., Bâ, A.M., 2019. Impact of mycorrhiza-based inoculation strategies on Ziziphus mauritiana Lam. and its native mycorrhizal communities on the route of the Great Green Wall (Senegal). Ecol. Eng. 128, 66–76. https://doi.org/10.1016/j.ecoleng.2018.12.033 Thioye, B., Sanguin, H., Kane, A., Ndiaye, C., Fall, D., Sanogo, D., Duponnois, R., de Faria, S.M., Sylla, S.N., Bâ, A., 2021. Mycorrhizal inoculation increases fruit production without disturbance of native arbuscular mycorrhizal community in jujube tree orchards (Senegal). Symbiosis 83, 361–372. https://doi.org/10.1007/s13199-021-00757-5 Trivedi, P., Leach, J.E., Tringe, S.G., Sa, T., Singh, B.K., 2020. Plant–microbiome interactions: from community assembly to plant health. Nat. Rev. Microbiol. https://doi.org/10.1038/s41579-020-0412-1 Wickham, H., 2016. ggplot2: elegant graphics for data analysis, Second edition. ed, Use R! Springer, Cham. Wickham, H., Averick, M., Bryan, J., Chang, W., McGowan, L., François, R., Grolemund, G., Hayes, A., Henry, L., Hester, J., Kuhn, M., Pedersen, T., Miller, E., Bache, S., Müller, K., Ooms, J., Robinson, D., Seidel, D., Spinu, V., Takahashi, K., Vaughan, D., Wilke, C., Woo, K., Yutani, H., 2019. Welcome to the Tidyverse. JOSS 4, 1686. https://doi.org/10.21105/joss.01686 Xun, W., Liu, Y., Li, W., Ren, Y., Xiong, W., Xu, Z., Zhang, N., Miao, Y., Shen, Q., Zhang, R., 2021. Specialized metabolic functions of keystone taxa sustain soil microbiome stability. Microbiome 9, 35. https://doi.org/10.1186/s40168-020-00985-9 Yadav, A.N., Kaur, T., Kour, D., Rana, K.L., Yadav, N., Rastegari, A.A., Kumar, M., Paul, D., Sachan, S.G., Saxena, A.K., 2020. Saline microbiome: Biodiversity, ecological significance, and potential role in amelioration of salt stress, in: New and Future Developments in Microbial Biotechnology and Bioengineering. Elsevier, pp. 283–309. https://doi.org/10.1016/B978-0-12-820526-6.00018-X Zhang, G., Bai, J., Zhai, Y., Jia, J., Zhao, Q., Wang, W., Hu, X., 2023. Microbial diversity and functions in saline soils: A review from a biogeochemical perspective. J. Adv. Res. S2090123223001789. https://doi.org/10.1016/j.jare.2023.06.015 Zhang, K., Shi, Y., Cui, X., Yue, P., Li, K., Liu, X., Tripathi, B.M., Chu, H., 2019. Salinity is a key determinant for soil microbial communities in a desert ecosystem. mSystems 4, e00225-18. https://doi.org/10.1128/mSystems.00225-18 Zhao, S., Liu, J., Banerjee, S., White, J.F., Zhou, N., Zhao, Z., Zhang, K., Hu, M., Kingsley, K., Tian, C., 2019. Not by salinity alone: How environmental factors shape fungal communities in saline soils. Soil Sci. Soc. Amer. J 83, 1387–1398. https://doi.org/10.2136/sssaj2019.03.0082 Zhao, S., Liu, J.-J., Banerjee, S., Zhou, N., Zhao, Z.-Y., Zhang, K., Tian, C.-Y., 2018. Soil pH is equally important as salinity in shaping bacterial communities in saline soils under halophytic vegetation. Sci. Rep. 8, 4550. https://doi.org/10.1038/s41598-018-22788-7 Information & Authors Information Version history V1 Version 1 02 September 2025 Peer review timeline Published Land Degradation & Development Version of Record 24 Mar 2026 Published Copyright This work is licensed under a Non Exclusive No Reuse License. Keywords casuarinaceae functional guild microbiota n-cycling soil salinization Authors Affiliations Pape Djighaly Universite Assane SECK de Ziguinchor View all articles by this author Nathalie Diagne Universite Cheikh Anta Diop de Dakar View all articles by this author Estelle Tournier CIRAD Direction Regionale Montpellier-Occitanie View all articles by this author Mariama Ngom Universite Cheikh Anta Diop Faculte des Sciences et Techniques View all articles by this author Maimouna Cissoko Universite Cheikh Anta Diop de Dakar View all articles by this author Pierre Tisseyre Institut de recherche pour le developpement View all articles by this author Daouda Ngom Universite Cheikh Anta Diop Faculte des Sciences et Techniques View all articles by this author Valerie Hocher Universite Cheikh Anta Diop de Dakar View all articles by this author Sergio SVISTOONOFF Institut de recherche pour le developpement Senegal View all articles by this author Hervé Sanguin 0000-0001-7160-2840 [email protected] CIRAD Direction Regionale Montpellier-Occitanie View all articles by this author Metrics & Citations Metrics Article Usage 228 views 133 downloads .FvxKWukQNSOunydq8rnd { width: 100px; } Citations Download citation Pape Djighaly, Nathalie Diagne, Estelle Tournier, et al. Beneficial and adverse effects of bio-inoculation on predicted functional microbial communities in salt-land restoration. Authorea . 02 September 2025. DOI: https://doi.org/10.22541/au.175681448.85560879/v1 If you have the appropriate software installed, you can download article citation data to the citation manager of your choice. Simply select your manager software from the list below and click Download. For more information or tips please see 'Downloading to a citation manager' in the Help menu . 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