Microbiomes of Velloziaceae from phosphorus-impoverished soils of the campos rupestres, a biodiversity hotspot

Abstract

The rocky, seasonally-dry and nutrient-impoverished soils of the Brazilian campos rupestre s impose severe growth-limiting conditions on plants. Species of a dominant plant family, Velloziaceae, are highly specialized to low-nutrient conditions and seasonal water availability of this environment, where phosphorus (P) is the key limiting nutrient. Despite plant-microbe associations playing critical roles in stressful ecosystems, the contribution of these interactions in the campos rupestres remains poorly studied. Here we present the first microbiome data of Velloziaceae spp. thriving in contrasting substrates of campos rupestres . We assessed the microbiomes of Vellozia epidendroides , which occupies shallow patches of soil, and Barbacenia macrantha , growing on exposed rocks. The prokaryotic and fungal profiles were assessed by rRNA barcode sequencing of epiphytic and endophytic compartments of roots, stems, leaves and surrounding soil/rocks. We also generated root and substrate (rock/soil)-associated metagenomes of each plant species. We foresee that these data will contribute to decipher how the microbiome contributes to plant functioning in the campos rupestres , and to unravel new strategies for improved crop productivity in stressful environments.

From Microbiome to Traits: Designing Synthetic Microbial Communities for Improved Crop Resiliency

“…It is well accepted that the plant microbiome is shaped through a process of coevolution with its host under adverse environmental conditions ( Theis et al, 2016 ). Thus, further studies have suggested that plants in stressful ecosystems may harbor microorganisms capable of electing traits of tolerance to that unfavored condition ( Woodward et al, 2012 ; Camargo et al, 2019 ). A successful strategy of microbial selection aiming to further application in the field should consider microbiome origin as the first clue to microbial capabilities in an environmentally guided selection of traits.…”

Plant-associated microbiomes promote nutrient turnover in impoverished substrates of a biodiversity hotspot

“…The different microbiomes of the two plants, despite their geographic proximity [27], suggests that contrasting substrates and host biology shape plant-associated communities in the campos rupestres . Furthermore, the finding that particular taxa become specialized on their host indicates that host and environment-specific pressures select specific functions.…”

“…In addition, the siderophore repertoires of B. macrantha -associated communities were much larger, which could be interpreted as an indirect consequence of the higher abundance of the BGC-rich [56] Actinobacteriota in these microbiomes. We believe, however, that a complementary nutrient-driven explanation is also appropriate: as the iron content of the sampled rocks is around 8-fold lower than that of the soils [27] this nutrient is under increased demand in B. macrantha microbiomes, increasing the fitness of Actinobacteriota populations that are efficient at scavenging iron and, consequently, solubilizing phosphate.…”

“…We also found a large amount of nifH orthologs that were assigned to the Rhizobiales order, a lineage that comprised several known diazotrophs. Interestingly, only a few of these orthologs were retrieved from B. macrantha and rock metagenomes and, although several Bradyrhizobium MAGs were recovered from these environments, none had the metabolic potential to fix N. We believe that the lack of nif is an advantageous trait for rock-dwelling bacteria, as the N fixation reaction is very carbon-demanding [63] and could cripple their growth in a carbon-poor environment [27]. We found, however, indirect evidence for endophytic diazotrophs as read-level gene identification revealed an enrichment of Bradyrhizobium nifH abundance in the rhizosphere of both plants (Suppl.…”

“…Because the soil substrate contains higher organic matter content than the exposed rocks [27], we investigated the carbon cycling potential of the V. epidendroides and B. macrantha microbiomes with respect to carbohydrate degradation and carbon dioxide fixation (Suppl. Note 4, Suppl.…”