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Additional file 1. Result S1. Analysis of rhizosheath sand composition. Result S2. Analysis of cultivable bacteria. Table S1. Climatic conditions throughout the year in Ksar Ghilane, Sahara Desert (Tunisia); data elaborated from https://www.worldweatheronline.com ; data as reported as monthly average measurement from January 2019 to now. Table S2. List of FISH probes used and conditions applied; probe sequence (5’-3’), attached fluorochrome (fluor.), bacterial target group, percentage of formaldehyde (FA) used during treatment, and references are also reported. Table S3. Number of KTUs and sequences used for each sample. RH: rhizosphere, RS: rhizosheath, RT: root tissue, BS: bulk sand. Table S4. Humidity (RH%) and temperature (T°C) measured in summer (June, 2016) and winter (November, 2016) for bulk sand and belowground speargrasses (i.e., plant rhizosheath–root system, RS). Table S5. Physico-chemical analyses conducted on bulk sand (BS) and rhizosheath matrix (RS) collected in summer (S) and winter (W). Table S6. PERMANOVA pair-wise comparison test of physico-chemical conditions (Table S5) in rhizosheath (RS) and bulk sand (BS) collected during summer (S) and winter (W) seasons. Table S7. Multivariate test (pairwise comparison) of beta-diversity associated with root tissue, rhizosheath, rhizosphere, and bulk sand. Table S8. Mean and standard error of multivariate dispersions from centroid calculated for each compartment (within-betadiversity). Table S9. Relative importance of different ecological processes in the assembly of bacterial community associated with the rhizosheath-root system compartments and bulk sand in two contrasting seasons. Table S10. Generalized linear model univariate test indicates the KTUs contributing to the difference in bulk soil among summer and winter. Table S11. Tukey’s honest significance difference (TukeyHSD) pairwise comparison tests for the degree, betweenness and keystone species detected across the four co-occurrence networks, namely bulk sand winter, bulk sand winter summer, rhizosheath–root system winter and rhizosheath–root system summer. Table S12. List of bacterial isolates, PGP activity, and abiotic resistance tested in vitro. Figure S1. Stipagrostis pungens rhizosheath-root system. Figure S2. Rarefaction curves of bacterial reads obtained by pair-ends MiSeq Illumina sequencing in bulk sand, rhizosheath, rhizosphere, and root tissues. Figure S3. Visualization of Stipagrostis pungens rhizosheath with scanning electron microscopy (SEM). Figure S4. SEM images and electron micrographs of the sand grains and root tissue within the rhizosheath of Stipagrostis pungens using environmental scanning electron microscopy (ESEM) to reveal chemical composition. Figure S5. Localization of bacteria in rhizosheath-root system by confocal laser-scanning microscopy (CLSM) and fluorescence in situ hybridization (FISH). Figure S6. Bacterial KTUs distribution across samples. Figure S7. Venn diagram shows the distribution of bacterial KTUs across compartment categories. Figure S8. Alpha diversity expressed as richness (number of KTUs) and Shannon diversity across the compartment categories. Figure S9. Quantification of betadiversity components in bulk sand bacterial communities across seasons (summer and winter). Figure S10. Alpha diversity expressed as richness (number of KTUs) and Shannon diversity across the compartments in summer and winter. Figure S11. Venn diagrams showing the number of KTUs present in summer and/or in winter in each compartment category. Figure S12. Analysis of 2-fold change was performed to evaluate the KTUs that had a significantly (p < 0.01) different relative abundance (2-fold change) over summer and winter. Figure S13. Taxonomy of co-occurrence network degrees in bulk sand and rhizosheath matrix across seasons. Figure S14. Microcosms to evaluate sand wettability in vitro. Evaluation of sand weight at 48 h and along the entire incubation (0, 24 and 48 h).

Mangrove ecosystems are highly productive and provide important ecosystem services. However, in the Red Sea mangroves are under severe nutrient-limiting conditions, reflected in dwarf plants. The nutrient limitation is especially acute for iron, as verified experimentally, although the low carbon-to-nutrient stoichiometric ratios reported for Red Sea mangrove leaves are indicative of general nutrient depletion. Therefore, atmospheric nitrogen (N2) fixation in mangrove sediments might be particularly important considering the minimal nitrogen inputs from land. Here, we tested the effect of temperature and crab density on sediment N2 fixation rates in mature and juvenile mangrove (Avicennia marina) stands in the central Red Sea. The average N2 fixation rates (from 0.002 ± 0.002 to 0.46 ± 0.12 mg N m–2 d–1) fall in the low range of N2 fixation rates reported in mangroves elsewhere, which is in agreement with the small size of the mangrove plants. Mature mangrove sediments hold higher N2 fixation rates than the juvenile mangrove sediment, related to a higher sediment organic matter and carbon content. We found a detrimental effect of temperature and crab density on sediment N2 fixation rates. Maximum N2 fixation rates were detected at 28°C with a sharp decrease at 35°C. Similarly, high crab-density reduced N2 fixation, likely due to the sediment oxygenation or the grazing of cyanobacteria by crabs. This is supported by i) previously reported higher oxygen concentration and redox around burrows compared to undisturbed sediment and ii) lighter sediment carbon isotopic composition in high crab-density than in low crab-density sediments, indicating a higher contribution of microphytobenthos in the mature sediments supporting low crab-density. Our data document temperature and crab density as factors affecting N2 fixation in the Red Sea mangrove sediments.

The adaptation of sporeformers to extreme environmental conditions is frequently questioned due to their capacity to produce highly resistant endospores that are considered as resting contaminants, not representing populations adapted to the system. In this work, in order to gain a better understanding of bacterial adaptation to extreme habitats, we investigated the phenotypic and genomic characteristics of the halophile Virgibacillus sp. 21D isolated from the seawater-brine interface (SBI) of the MgCl2-saturated deep hypersaline anoxic basin Discovery located in the Eastern Mediterranean Sea. Vegetative cells of strain 21D showed the ability to grow in the presence of high concentrations of MgCl2, such as 14.28% corresponding to 1.5 M. Biolog phenotype MicroArray (PM) was adopted to investigate the strain phenotype, with reference to carbon energy utilization and osmotic tolerance. The strain was able to metabolize only 8.4% of 190 carbon sources provided in the PM1 and PM2 plates, mainly carbohydrates, in accordance with the low availability of nutrients in its habitat of origin. By using in silico DNA-DNA hybridization the analysis of strain 21D genome, assembled in one circular contig, revealed that the strain belongs to the species Virgibacillus dokdonensis. The genome presented compatible solute-based osmoadaptation traits, including genes encoding for osmotically activated glycine-betaine/carnitine/choline ABC transporters, as well as ectoine synthase enzymes. Osmoadaptation of the strain was then confirmed with phenotypic assays by using the osmolyte PM9 Biolog plate and growth experiments. Furthermore, the neutral isoelectric point of the reconstructed proteome suggested that the strain osmoadaptation was mainly mediated by compatible solutes. The presence of genes involved in iron acquisition and metabolism indicated that osmoadaptation was tailored to the iron-depleted saline waters of the Discovery SBI. Overall, both phenomics and genomics highlighted the potential capability of V. dokdonensis 21D vegetative cells to adapt to the environmental conditions in Discovery SBI.

Plants and animals have evolved unique morpho-physiological adaptions to cope with the harsh and steep environmental gradients that characterise the mangrove ecosystem. However, the capacity of these two main components of the system to thrive, and the extraordinary productivity of mangrove forests in extreme conditions, has been overlooked in terms of the role of the microbiome. By combining approaches that included molecular microbial ecology, biogeochemical analyses, microscopy, raman spectroscopy and microsensor measurements, this thesis aimed to investigate the potential role of bacterial symbiosis in the adaptation of mangrove crabs to their environment and subsequently how these different animals modify their environment. Finally, with a field-based approach monitoring microbial communities, sediment metabolism and plant performance, the thesis aimed to investigate the plant/animal/bacterial dynamics in relation to seasonal environmental changes to contribute to understand the mangrove plant productivity paradox of high productivity under conditions of limited nutrents. Crab species were associated with distinct gill-bacteria communities, that produced carotenoids, according with their level of terrestrial adaptation. These carotenoids may be involved in protecting the gills from oxidative stress during air exposure. The main groups of ecosystem engineering crabs in mangroves had significant but diverse effects on the sediment environment and microbiome predominantly related to their ecology (i.e. filter feeder vs herbivore). Burrows increase aerobic microbial activity in the immediate burrow wall with a cascade effect on sediment microbial communities and nutrient distribution observed consistently across mangroves in different locations and with diverse environmental conditions. Microorganisms play an important role in adapting crabs on their evolutionary path to land and could contribute to the success of their colonization. At high population densities, of more than 50 individuals per square meter in some mangroves, these crabs deeply impact the functioning of the mangrove ecosystem, affecting microbial networks and nutrient recycling in the sediment, which may ameliorate conditions for plant growth. The microbiome is an understudied component of mangroves that lies at the basis of the functioning of these systems, influencing the success of the animal inhabitants (ecosystem engineers) that deeply modify the sediment microbiome, therefore influencing ecosystem functioning and resilience and, potentially, the success of the plants themselves (ecosystem architects).

Background In hot deserts daily/seasonal fluctuations pose great challenges to the resident organisms. However, these extreme ecosystems host unique microenvironments, such as the rhizosheath–root system of desert speargrasses in which biological activities and interactions are facilitated by milder conditions and reduced fluctuations. Here, we examined the bacterial microbiota associated with this structure and its surrounding sand in the desert speargrass Stipagrostis pungens under the contrasting environmental conditions of summer and winter in the Sahara Desert. Results The belowground rhizosheath–root system has higher nutrient and humidity contents, and cooler temperatures than the surrounding sand. The plant responds to the harsh environmental conditions of the summer by increasing the abundance and diversity of extracellular polymeric substances (EPS) compared to the winter. On the contrary, the bacterial community associated with the rhizosheath–root system and its interactome remain stable and, unlike the bulk sand, are unaffected by the seasonal environmental variations. The rhizosheath–root system bacterial communities are consistently dominated by Actinobacteria and Alphaproteobacteria and form distinct bacteria communities from those of bulk sand in the two seasons. The microbiome-stabilization mediated by the plant host acts to consistently retain beneficial bacteria with multiple plant growth promoting functions, including those capable to produce EPS, which increase the sand water holding capacity ameliorating the rhizosheath micro-environment. Conclusions Our results reveal the capability of plants in desert ecosystems to stabilize their below ground microbial community under seasonal contrasting environmental conditions, minimizing the heterogeneity of the surrounding bulk sand and contributing to the overall holobiont resilience under poly-extreme conditions.