Microbiome Dynamics Associated With the Atacama Flowering Desert

Abstract

In a desert, plants as holobionts quickly respond to resource pulses like precipitation. However, little is known on how environment and plants modulate the rhizosphereassociated microbiome. As a model species to represent the Atacama Desert bloom, Cistanthe longiscapa (Montiaceae family) was selected to study the influence of abiotic and biotic environment on the diversity and structure of the microbiota associated to its rhizosphere. We analyzed the rhizosphere and soil microbiome along a North-South precipitation gradient and between a dry and rainy year by using Illumina high−throughput sequencing of 16S rRNA gene fragments and ITS2 regions for prokaryotes and fungi, respectively. In the rhizosphere of C. longiscapa the microbiota clearly differs in composition and structure from the surrounding bulk soil. The fungal and bacterial communities respond differently to environmental conditions. The diversity and richness of fungal OTUs were negatively correlated with aridity, as predicted. The community structure was predominantly influenced by other soil characteristics (pH, organic matter content) but not by aridity. In contrast, diversity, composition, and structure of the bacterial community were not influenced by aridity or any other evaluated soil parameter. These findings coincide with the identification of mainly sitespecific microbial communities, not shared along the sites. These local communities contain a group of OTUs, which are exclusive to the rhizosphere of each site and presumably vertically inherited as seed endophytes. Their ecological functions and dispersal mechanisms remain unclear. The analysis of co-occurrence patterns highlights the strong effect of the desert habitat over the soil-and rhizosphere-microbiome. The site-independent enrichment of only a small bacterial cluster consistently associated with the rhizosphere of C. longiscapa further supports this conclusion. In a rainy year, the rhizosphere microbiota significantly differed from bulk and bare soil, whereas in a dry year, the community structure of the former rhizosphere approximates to the one found in the bulk. In the context of plant-microbe interactions in desert environments, our study contributes new insights into the importance of aridity in microbial community structure and composition, discovering the influence of other soil parameters in this complex dynamic network, which needs further to be investigated.

Composition, Predicted Functions and Co-occurrence Networks of Rhizobacterial Communities Impacting Flowering Desert Events in the Atacama Desert, Chile

“…However, Sporichthyaceae is one of the less studied bacterial group mostly owing to their slow growth rate and requirements (Normand, 2006). In relation to the diversity of rhizobacterial community among the FF and PF, no differences were observed in both phenological stages, except with Shannon index, which is consistent with the explanation given by Araya et al (2019) who indicate that a small group of bacteria is consistently associated with C. longiscapa rhizosphere. However, differences among phenological stages were evidenced when rhizobacterial communities were evaluated with some rhizosphere soils properties using NMDS analysis.…”

“…Shifts in functions of bacterial community might not be coincident with changes in taxonomic as observed by Jorquera et al (2014) and Marileo et al (2016) using phylogenetic (16S rRNA and rpoB) and functional (amoA, nif H, and APase) genes. The recruitment of specific microbial community by C. longiscapa seems to contribute a optimal plant development under unique Atacama Desert conditions (Araya et al, 2019). In this context, rhizobacterial community functions predicted by PICRUSt shows significant differences (P ≤ 0.05) in numbers of sequences involved in environmental and genetic information processing among 2014 and 2015 FD events.…”

“…Nonetheless, information concerning its physiology and association with microorganisms are extremely scarce. A recent study has reported that C. longiscapa microbiota significantly differed among rhizosphere soils and bulk soils in rainy year, but they are closer in dry year (Araya et al, 2019), suggesting differences in the ecological functions of microbial communities in each niche. Orlando et al (2010), proposed that the bacterial community during FD bloom was likely involved in nitrogen (N) cycling.…”

The Abundance and Diversity of Fungi in a Hypersaline Microbial Mat from Guerrero Negro, Baja California, México

“…The Shannon ( H ’) diversity index presented herein based on metagenomic read-based classifications averaged of 3.73. In other microbial ecosystems, based on varying measurements, values of Shannon ( H ’) ranged between 1.45 and 4.5 for conventional and non-conventional wastewater technology systems [ 33 , 35 ], 2 and 4 for a composting system [ 34 ], 2.52 and 5.38 for coastal wetland sediment [ 36 ], 3 and 5 for desert and mountains [ 37 , 38 ] and 6 and 7 for a soil ecosystem [ 39 ]. Though we note that diversity indices applied to sequencing data are heavily influenced at each stage from sample acquisition through to sequence processing, and metrics from different data types and studies are not necessarily comparable.…”

Natural Holobiome Engineering by Using Native Extreme Microbiome to Counteract the Climate Change Effects

“…Recently, some studies have investigated in the microbiome dynamics associated with the "Atacama Flowering Events, " which corresponds to an explosive bloom of dormant desert plants produced by the presence of water as precipitation (Vidiella et al, 1999). Studying this phenomenon, it was discovered that some bacterial groups and their activity can influence the growth and flowering of native plants (Araya et al, 2020;Astorga-Eló et al, 2020). Similarly, cold desert such as Antarctic have also been studied.…”