A Metagenomics Insight in the Cyanosphere of Edible Andean Macrocolonies (Llayta)

Research Article

Austin J Proteomics Bioinform & Genomics. 2023; 8(1): 1034.

A Metagenomics Insight in the Cyanosphere of Edible Andean Macrocolonies (Llayta)

Claudia Vilo C1,2; Galetovic A1; Dong Q3; Gómez-Silva B1*

¹Laboratory of Biochemistry, Biomedical Department, Health Sciences Faculty and Centre for Biotechnology and Bioengineering (CeBiB), Universidad de Antofagasta, Antofagasta, Chile

²Laboratory of Molecular and Cellular Biology of Cancer, Department of Biomedical Sciences, Faculty of Medicine, Universidad Católica del Norte, Coquimbo, Chile

³Center for Biomedical Informatics, Department of Medicine, Stritch School of Medicine, Loyola University of Chicago, Maywood, Illinois, USA

*Corresponding author: Gómez-Silva B Biomedical Department, Health Sciences Faculty and Centre for Biotechnology and Bioengineering (CeBiB), Universidad de Antofagasta, Antofagasta, Chile. Email: benito.gomez@uantof.clt

Received: July 26, 2023 Accepted: August 25, 2023 Published: September 01, 2023

Abstract

It is well stablished that some cyanobacterial biomasses have nutritious ingredients and have been consumed for centuries. In South America, macrocolonies of filamentous diazotrophic species, order Nostocales, known as Llayta, can be found at Andean wetlands and have been consumed since pre-Columbian times. Cyanocohniella sp. LLY has been identified as a major cyanobacterial member of the Llayta cyanosphere, however, the microflora colonizing these macrocolonies has been poorly explored. Genomic DNA from Gentamycin-treated cyanobacterial filaments purified from the rehydrated biomass of Llayta macrocolonies, were subjected to metagenomics studies to identify resilient members of the accompanying heterotrophic bacterial flora. Here, we report a metagenomics-based identification of five prominent bacterial members belonging to the genera Mesorhizobium, Microvirga, Paracoccus, Aquimonas, and Blastomonas, tightly adhered to Llayta trichomes. Their metagenome-assembled genomes and information on putative genes and genes clusters involved in primary and secondary metabolism is also provided. We expect this information on Llayta cyanosphere would help to further explore adaptive responses and role of cyanobacteria macrocolonies in ecosystem processes under the stressful environmental conditions prevailing at the Atacama Desert highlands.

Keywords: Andes wetlands; Cyanosphere; Edible cyanobacterial macrocolonies; Llayta; Metagenomics; Metal resistance genes; Microbiota; Nostocales

Introduction

Consumption of edible macrocolonies of filamentous cyanobacteria, locally known as Llayta, is a centenary Andean alimentary practice in South America [1-3]. Llayta macrocolonies can be found at Andean wetlands above 3,000 m of altitude, at sites not always readily accessible [4,5], but it is available nowadays as a dried natural product at food markets in northern Chile and southern Peru [6]. Also, Llayta is considered a safe natural food ingredient based on its biochemical content, absence of cyanotoxins, ethnographic testimonies, and absence of negative epidemiological evidence [4-7].

Filamentous diazotrophic cyanobacteria are ubiquitous to almost any ecosystem on Earth, including some under severe environmental conditions. Trichomes containing vegetative cells and N2-fixing heterocyst develop during the life cycle of diazotrophic Nostoc species and can form green to brown sheet-like or spherical macrocolony, depending up-on the species, dehydration state, and location [8,9]. In natural environments, colonial and filamentous cyanobacteria can be colonized by microorganisms emplaced around, within or outside the host colony, with varied composition [10-14], and involved in biogeochemical cycles, ecosystem services, and algicidal or stimulatory effects [10,14-16].

Recently, Vilo et al. [16] reported an improved metagenomics analysis identifying Cyanocohniella sp. LLY as the potential cyanobacterium responsible for forming Llayta macrocolonies at the Andes wetlands, providing the first Metagenome-Assembled Genome (MAG) for this genus. Nonetheless, Llayta cyanosphere is still a pending issue. The identi-fication and draft genome of a Bacillus bacterium from the microbiota associated to Llayta colonies [17] was the first approach to address physiological relationships within the Llayta microbiota and to gain insights into the survival and adaptive strategies to dryness, metals, metalloids, and UV radiation, among other prevalent extreme environmental con-ditions at the Andes wetlands.

Metagenomics is proper culture-independent tool that allows insights into the composition and genomic capabilities of the microbial community from natural settings [18-20], and prospection of natural products [18-21]. To improve our under standing on Llayta cyanosphere, we focused our metagenomics-based study on the resilient bacterial microflora associated with isolated, Gentamycin-treated Llayta filaments. Here we present the identification of microbial taxa tightly adhered to Llayta trichomes, the genome recon-struction of five prominent bacterial members, the identification and annotation of func-tional genes, and an insight into their metabolic capabilities.

Materials and Methods

Isolation of Llayta Filaments, Growth Conditions and Antibiotic Treatment

Dry biomass of Llayta macrocolonies were obtained during 2015 at the major farmer´s food market in Arica, Chile. Filament isolation procedures have been previously described [17]. Briefly, rehydrated Llayta samples were grown and enriched in liquid, ni-trogen-free Arnon mineral medium [4,5,22]. Aliquots were seeded in agar plates, isolated filaments were retrieved under a stereo microscope, grown in fresh medium as above, harvested after 3 weeks at the exponential growth phase, washed with fresh medium, and recovered as a pellet by centrifugation at 4,000 x g for 5 min, at room temperature. Our metagenomics studies were focused on genomic DNA recovered from bacteria closely associated to isolated Llayta trichomes. Then, metagenomics analyses were conducted on trichomes previously incubated with Gentamycin in the presence of carbon sources to stimulate growth of heterotrophic bacteria and in darkness to slow down cyanobacterial metabolic activity. Approximately, 10-15 mL of cultured Llayta filaments were collected at the exponential growth phase, washed with fresh medium, and suspended in 20 mL of fresh Arnon medium containing Gentamycin (1 mg/mL; Sigma Aldrich, Chile), Casamino acids (1.6 mg/mL; Sigma Aldrich, Chile), and D-glucose (0.8 mg/mL; Sigma Aldrich, Chile), and incubated for 48h in darkness at 30°C, and gently stirred (120 rpm). After this treatment, microbial contamination of Llayta filaments decreased by nearly four orders of magnitude (Gentamycin was the most efficient antibiotic tested). The biomass was recovered by centrifugation and used to extract total genomic DNA.

DNA Extraction and Sequencing

Total genomic DNA from the filament pellets was extracted with Ultra Clean Micro-bial DNA isolation kit (MoBio Labs. Inc., Carlsbad, CA, USA), following the manufactur-er´s instructions. DNA quality was evaluated by electrophoresis in 0.8 % agarose gel and quantified photometrically at 260 nm. The Llayta metagenome was sequenced via MiSeq sequencing technology using shotgun paired-end libraries, with an average insert size of 250 bp. Reads had an average length of 300 bp, with good quality scores, as evaluated by the FastQC program (version 0.10.0). The sequencing produced a total of 17,137,246 reads. Sequencing reads are available at the Sequence Read Archive (SRA) with accession num-ber SRR17916224. The Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession JAKOMP000000000, JAKOMQ000000000, JAKOMR000000000, JAKOMS000000000, JAKOMT000000000, and JAKOMU000000000.

Bioinformatic Analysis

The metagenomic sequences were submitted to the Rapid Annotation using Subsys-tems Technology for Metagenomes (MG-RAST) web server [23] for a taxonomic and func-tional assignment using default parameters. In addition, metagenomic assembly was done using MEGAHIT assembler v.1.2.9 [24], and binning was conducted using the PATRIC web server [25]. The complete genome was annotated using the Rapid Annotations using Subsystem Technology (RAST) server version 4.0. Secondary metabolites were searched with PRISM version 4.4.5 [26] and AntiSMASH version 6.1.1 software [27]. In addition, in-house BLAST analysis was done against customized metal resistance genes databases.

Results and Discussion

During our work, an abundant microflora with high bacterial titers was detected in attempts to isolate and purify axenic Llayta filaments; however, incubation of isolated Llayta filaments with Gentamycin decreased such titers by nearly four orders of magnitude. Then, we focused our metagenomics-based study on the resilient bacterial microflora associated with isolated and Gentamycin-treated Llayta filaments to improve our under-standing on Llayta cyanosphere.

Genomic DNA from Gentamycin-treated cyanobacterial filaments, purified from the rehydrated biomass of Llayta macrocolonies, were subjected to metagenomics studies to identify resilient members of the accompanying heterotrophic bacterial flora, construct the corresponding metagenomic-assembled genomes, and gain insights into their functional metabolic capabilities. We identified the antibiotic-resilient bacterial community associ-ated to Llayta filaments, reconstructed the genomes of five prominent bacteria, and de-tected putative biosynthetic genes related to primary and secondary metabolism and adaptive stress strategies.

Microbial Diversity in Llayta Trichomes

Taxonomic assignments obtained from metagenomics analyses of shotgun meta-genome showed that the microbiota associated with Llayta filaments was dominated by bacteria (99%), while representatives of the domains Archaea (0.2%) and Eukarya (0.1%) were present at a much lower extent. Predominant bacteria in Llayta trichomes belong to the phyla Proteobacteria (82%) and Cyanobacteria (16%) (Figure 1). Dominant genera were Xanthomonas (38%), Stenotrophomonas (15%), Methylobacterium (9.3%), Nostoc (40%), Anabaena (26%), and Nodularia (21%). Thus, Xanthomonas (38%) and Nostoc (40%) were the primary genera (Figure 1).