Soil Bacterial Communities From the Chilean Andean Highlands: Taxonomic Composition and Culturability

Abstract

The Atacama Desert is a highly complex, extreme ecosystem which harbors microorganisms remarkable for their biotechnological potential. Here, a soil bacterial prospection was carried out in the high Altiplano region of the Atacama Desert (>3,800 m above sea level; m a.s.l.), where direct anthropogenic interference is minimal. We studied: (1) soil bacterial community composition using high-throughput sequencing of the 16S rRNA gene and (2) bacterial culturability, by using a soil extract medium (SEM) under a factorial design of three factors: temperature (15 and 30°C), nutrient content (high and low nutrient disposal) and oxygen availability (presence and absence). A total of 4,775 OTUs were identified and a total of 101 isolates were selected for 16S rRNA sequencing, 82 of them corresponded to unique or non-redundant sequences. To expand our view of the Altiplano landscape and to obtain a better representation of its microbiome, we complemented our Operational Taxonomic Units (OTUs) and isolate collection with data from other previous data from our group and obtained a merged set of OTUs and isolates that we used to perform our study. Taxonomic comparisons between culturable microbiota and metabarcoding data showed an overrepresentation of the phylum Firmicutes (44% of isolates vs. 2% of OTUs) and an underrepresentation of Proteobacteria (8% of isolates vs. 36% of OTUs). Within the Next Generation Sequencing (NGS) results, 33% of the OTUs were unknown up to genus, revealing an important proportion of putative new species in this environment. Biochemical characterization and analysis extracted from the literature indicated that an important number of our isolates had biotechnological potential. Also, by comparing our results with similar studies on other deserts, the Altiplano highland was most similar to a cold arid desert. In summary, our study contributes to expand the knowledge of soil bacterial communities in the Atacama Desert and complements the pipeline to isolate selective bacteria that could represent new potential biotechnological resources.

Energetic Basis of Microbial Growth and Persistence in Desert Ecosystems

“…For instance, members of Actinobacteria and Firmicutes, Gram-positive bacterial phyla widely found in drylands (7,13,14,16), are well known for their ability to form highly stress-resistant spores (17,18). Consistently, these sporulating taxa are among the most common groups identified in desert soils (19)(20)(21)(22) based on both conventional cultivation studies and modern molecular phylogenetic analyses. Common Cyanobacteria isolated from desert biocrusts, such as Anabaena, Nostoc, and Cylindrospermum (23,24), can differentiate into specific spore-like structures termed akinetes, which tend to be much larger in size than their vegetative structures (25).…”

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

“…), available phosphorus (P Olsen ) or pH. Atacama Desert soils are characterized by their high salinity where commonly are isolated salt tolerance culturable bacteria (4-8% NaCl) (Okoro et al, 2009;Maza et al, 2019). Factors influencing the rapid variation and adaptation of rhizobacterial communities are identified as plant genotype, phenological stages of plants, composition of rhizodeposits, bacterial assemblages, microenvironment generated by a whole set of plants or bacterial interactions (Fernández-Gómez et al, 2019), especially considering that some bacterial taxa observed in this study are also influenced in their distribution and diversity in short periods of time by diurnal cycling (Staley et al, 2017).…”

Diversity and structure of soil microbiota of the Jinsha earthen relic

“…Acidobacteria may participate in the biodegradation process of cultural relics. Nitrifying bacteria and acidophilic bacteria were also found in the soil of the Jinsha earthen relic, and might contribute to surface degradation of soil through the conversion of ammonia in the extracellular matrix into nitrite and nitric acid [ 50 ], or the secretion of organic acids (under abnormal conditions, microorganisms may secrete citric acid and pyruvate) [ 51 , 52 ]. Additionally, Bacillus and Pseudomonas bacteria were also identified in the Jinsha earthen site samples.…”

“…conditions, microorganisms may secrete citric acid and pyruvate) [51,52]. Additionally, Bacillus and Pseudomonas bacteria were also identified in the Jinsha earthen site samples.…”