Aridity modulates belowground bacterial community dynamics in olive tree

Aridity negatively affects the diversity and abundance of edaphic microbial communities and their multiple ecosystem services, ultimately impacting vegetation productivity and biotic interactions. Investigation about how plant-associated microbial communities respond to increasing aridity is of particular importance, especially in light of the global climate change predictions. To assess the effect of aridity on plant associated bacterial communities, we investigated the diversity and co-occurrence of bacteria associated with the bulk soil and the root system of olive trees cultivated in orchards located in higher, middle and lower arid regions of Tunisia. The results indicated that the selective process mediated by the plant root system is amplified with the increment of aridity, defining distinct bacterial communities, dominated by aridity-winner and aridity-loser bacteria negatively and positively correlated with increasing annual rainfall, respectively. Aridity regulated also the co-occurrence interactions among bacteria by determining specific modules enriched with one of the two categories (aridity-winners or aridity-losers), which included bacteria with multiple PGP functions against aridity. Our findings provide new insights into the process of bacterial assembly and interactions with the host plant in response to aridity, contributing to understand how the increasing aridity predicted by climate changes may affect the resilience of the plant holobiont

Cultivation-Dependant Assessment, Diversity, and Ecology of Haloalkaliphilic Bacteria in Arid Saline Systems of Southern Tunisia

Haloalkaliphiles are polyextremophiles adapted to grow at high salt concentrations and alkaline pH values. In this work, we isolated 122 haloalkaliphilic bacteria upon enrichments of 23 samples from 5 distinct saline systems of southern Tunisia, growing optimally in media with 10% salt and at pH 10. The collection was classified into 44 groups based on the amplification of the 16S–23S rRNA internal transcribed spacers (ITS-PCR). Phylogenetic analysis and sequencing of the 16S rRNA genes allowed the identification of 13 genera and 20 distinct species. Three gram-positive isolates showing between 95 and 96% of 16S rRNA sequence homology with Bacillus saliphilus could represent new species or genus. Beside the difference in bacterial diversity between the studied sites, several species ecological niches correlations were demonstrated such as Oceanobacillus in salt crust, Nesterenkonia in sand, and Salinicoccus in the rhizosphere of the desert plant Salicornia. The collection was further evaluated for the production of extracellular enzymes. Activity tests showed that gram-positive bacteria were mostly active, particularly for protease, lipase, DNase, and amylase production. Our overall results demonstrate the huge phenotypic and phylogenetic diversity of haloalkaliphiles in saline systems of southern Tunisia which represent a valuable source of new lineages and metabolites

A Drought Resistance-Promoting Microbiome Is Selected by Root System under Desert Farming

<div><h3>Background</h3><p>Traditional agro-systems in arid areas are a bulwark for preserving soil stability and fertility, in the sight of “reverse desertification”. Nevertheless, the impact of desert farming practices on the diversity and abundance of the plant associated microbiome is poorly characterized, including its functional role in supporting plant development under drought stress.</p> <h3>Methodology/Principal Findings</h3><p>We assessed the structure of the microbiome associated to the drought-sensitive pepper plant (<em>Capsicum annuum</em> L.) cultivated in a traditional Egyptian farm, focusing on microbe contribution to a crucial ecosystem service, i.e. plant growth under water deficit. The root system was dissected by sampling root/soil with a different degree of association to the plant: the endosphere, the rhizosphere and the root surrounding soil that were compared to the uncultivated soil. Bacterial community structure and diversity, determined by using Denaturing Gradient Gel Electrophoresis, differed according to the microhabitat, indicating a selective pressure determined by the plant activity. Similarly, culturable bacteria genera showed different distribution in the three root system fractions. <em>Bacillus</em> spp. (68% of the isolates) were mainly recovered from the endosphere, while rhizosphere and the root surrounding soil fractions were dominated by <em>Klebsiella</em> spp. (61% and 44% respectively). Most of the isolates (95%) presented <em>in vitro</em> multiple plant growth promoting (PGP) activities and stress resistance capabilities, but their distribution was different among the root system fractions analyzed, with enhanced abilities for <em>Bacillus</em> and the rhizobacteria strains. We show that the <em>C. annuum</em> rhizosphere under desert farming enriched populations of PGP bacteria capable of enhancing plant photosynthetic activity and biomass synthesis (up to 40%) under drought stress.</p> <h3>Conclusions/Significance</h3><p>Crop cultivation provides critical ecosystem services in arid lands with the plant root system acting as a “resource island” able to attract and select microbial communities endowed with multiple PGP traits that sustain plant development under water limiting conditions.</p> </div

Diversity indexes of the microbial collection.

<p>The indexes were calculated for the sequences of bacterial strains isolated from the different fractions of the pepper root system and the non-cultivated arid soil. Sequences have been grouped in OTUs based on nucleotide similarity at 99%.</p

Rhizobacteria increased plant resistance to drought stress.

<p>Abbreviations for the figure: CP, (positive) abiotic control, irrigated at the water holding capacity of the soil along all the experiment; NC, (negative) abiotic control, subjected to drought by interrupting water supply for 12 days. (A) Representative images of plants exposed to rhizobacteria compared to untreated plants eight days after the induction of drought. (B) Leaf physiological parameters in treated and untreated plants eight days after the induction of drought.Abbreviations: Pn, net photosynthesis; E, evapo-transpiration; Gs, stomatal conductance; Ci, internal carbon dioxide (CO₂). Student t-test was adopted to statistically analyse the data. *:p≤0,05; **:p≤0,01; ***:p≤0,001. The data reported in the graphs are representative of one replicate experiment. (C) Percentage increase in root fresh weight (FW) and root length (L) of water stressed plants, compared to the abiotic stressed control, set as 0%.</p

Cluster analysis of total microbial communities according to 16S rRNA DGGE profiles.

<p>The cluster analysis of the plot line was obtained from 16S rRNA PCR-DGGE bacterial community profiles, according to Pearson correlation. The analyzed fractions were root tissues (E), rhizosphere (R), root-surrounding soil (S) and bulk soil (B) of three replicate plants of pepper.</p

PGP potential of the microbial collection.

<p>Percentage distribution of plant growth promoting activities and tolerance to abiotic stress among the isolates of the bacterial collection obtained from the different fractions of the pepper root system and the non-cultivated arid soil.</p><p>Auxin  =  auxin production; P Sol.  =  inorganic phosphate solubilization; EPS  =  exopolysaccharide release; Sid. = siderophores production; NH₃  =  ammonia production; Prot.  =  protease activity; PEG = poly-ethylen-glycol.</p

Abundance of culturable bacteria associated to the different fractions of the pepper root system.

<p>The isolation was performed on different cultivation media. In the table it is reported the amount of bacterial isolates composing the strain collection associated to pepper endosphere and root-associated soil fractions. E, Endosphere; R, rhizosphere; S, root-surrounding soil; B, non-cultivated arid soil.</p

Rhizocompetence of <i>gfp</i>-labelled bacteria on different plant models.

<p>Plant root colonization experiments performed with a <i>Klebsiella pneumoniae</i> strain isolated from the pepper rhizosphere genetically labeled with a <i>gfp</i>. (A) and (B) colonization of <i>Arabidospis thaliana</i> rhizoplane; (C) and (D) colonization of the pepper rhizoplane. Red spots represent root autofluorescence as acquired through the TRICT filter. The scale bars of the different images in the figure correspond to 100 µm.</p