A review on viral metagenomics in extreme environments

Viruses are the most abundant biological entities in the biosphere, and have the ability to infect Bacteria, Archaea, and Eukaryotes. The virome is estimated to be at least ten times more abundant than the microbiome with 107 viruses per milliliter and 109 viral particles per gram in marine waters and sediments or soils, respectively. Viruses represent a largely unexplored genetic diversity, having an important role in the genomic plasticity of their hosts. Moreover, they also play a significant role in the dynamics of microbial populations. In recent years, metagenomic approaches have gained increasing popularity in the study of environmental viromes, offering the possibility of extending our knowledge related to both virus diversity and their functional characterization. Extreme environments represent an interesting source of both microbiota and their virome due to their particular physicochemical conditions, such as very high or very low temperatures and >1 atm hydrostatic pressures, among others. Despite the fact that some progress has been made in our understanding of the ecology of the microbiota in these habitats, few metagenomic studies have described the viromes present in extreme ecosystems. Thus, limited advances have been made in our understanding of the virus community structure in extremophilic ecosystems, as well as in their biotechnological potential. In this review, we critically analyze recent progress in metagenomic based approaches to explore the viromes in extreme environments and we discuss the potential for new discoveries, as well as methodological challenges and perspectives

Metagenomics of Atacama lithobiontic extremophile life unveils highlights on fungal communities, biogeochemical cycles and carbohydrate-active enzymes

Halites, which are typically found in various Atacama locations, are evaporitic rocks that are considered as micro-scaled salterns. Both structural and functional metagenomic analyses of halite nodules were performed. Structural analyses indicated that the halite microbiota is mainly composed of NaCl-adapted microorganisms. In addition, halites appear to harbor a limited diversity of fungal families together with a biodiverse collection of protozoa. Functional analysis indicated that the halite microbiome possesses the capacity to make an extensive contribution to carbon, nitrogen, and sulfur cycles, but possess a limited capacity to fix nitrogen. The halite metagenome also contains a vast repertory of carbohydrate active enzymes (CAZY) with glycosyl transferases being the most abundant class present, followed by glycosyl hydrolases (GH). Amylases were also present in high abundance, with GH also being identified. Thus, the halite microbiota is a potential useful source of novel enzymes that could have biotechnological applicability. This is the first metagenomic report of fungi and protozoa as endolithobionts of halite nodules, as well as the first attempt to describe the repertoire of CAZY in this community. In addition, we present a comprehensive functional metagenomic analysis of the metabolic capacities of the halite microbiota, providing evidence for the first time on the sulfur cycle in Atacama halites

Extremely chaotolerant and kosmotolerant Aspergillus atacamensis – a metabolically versatile fungus suitable for recalcitrant biosolid treatment

Obligate halophily is extremely rare in fungi. Nevertheless, Aspergillus atacamensis (strain EXF-6660), isolated from a salt water-exposed cave in the Coastal Range hills of the hyperarid Atacama Desert in Chile, is an obligate halophile, with a broad optimum range from 1.5 to 3.4 M of NaCl. When we tested its ability to grow at varied concentrations of both kosmotropic (NaCl, KCl, and sorbitol) and chaotropic (MgCl2, LiCl, CaCl2, and glycerol) solutes, stereoscopy and laser scanning microscopy revealed the formation of phialides and conidia. A. atacamensis EXF-6660 grew up to saturating levels of NaCl and at 2.0 M concentration of the chaotropic salt MgCl2. Our findings confirmed that A. atacamensis is an obligate halophile that can grow at substantially higher MgCl2 concentrations than 1.26 M, previously considered as the maximum limit supporting prokaryotic life. To assess the fungus’ metabolic versatility, we used the phenotype microarray technology Biolog FF MicroPlates. In the presence of 2.0 M NaCl concentration, strain EXF-6660 metabolism was highly versatile. A vast repertoire of organic molecules (~95% of the substrates present in Biolog FF MicroPlates) was metabolized when supplied as sole carbon sources, including numerous polycyclic aromatic hydrocarbons, benzene derivatives, dyes, and several carbohydrates. Finally, the biotechnological potential of A. atacamensis for xenobiotic degradation and biosolid treatment was investigated. Interestingly, it could remove biphenyls, diphenyl ethers, different pharmaceuticals, phenols, and polyaromatic hydrocarbons. Our combined findings show that A. atacamensis EXF-6660 is a highly chaotolerant, kosmotolerant, and xerotolerant fungus, potentially useful for xenobiotic and biosolid treatments

Kmers frequency match between <i>Exophiala chapopotensis</i> LBMH1013 and its closest phylogenetic neighbours.

Kmers frequency match between Exophiala chapopotensis LBMH1013 and its closest phylogenetic neighbours.</p

Maximum-likelihood tree from concatenated sequences (SSU, ITS, LSU and B-TUB).

Branch supports are represented in nodes (periwinkle circles) as SH-like approximate likelihood ratio test (SH-aLRT) (%). Bar (0.1) represents number of changes per site. The tree was edited in iTOL online Version 6.7.6. bPTP and GMYC speciation partition supports for E. chapopotensis are depicted in violet on the corresponding branch. The indigo background corresponds to Capronia representatives. Cyphellophora oxyspora was used as the outgroup.</p

Principal Components Analysis (PCA) performed on the representatives of the <i>Herpotrichiellaceae</i> family with genome metrics as factors.

Mash genomic distance, ANI, AAI, POCP. Analysis based on Correlations. Variances were computed as SS/N-1. Missing Data deletion: Casewise. No. of active Factors: 4; No. of active cases: 93. Eigenvalues: 2.84348 .830461 .314132. 011930. NSP: Non-Separable Data. (PDF)</p

Growth, carbon utilization and micromorphology of <i>E</i>. <i>chapopotensis</i> LBMH1013 under several conditions^b'*'.

Growth, carbon utilization and micromorphology of E. chapopotensis LBMH1013 under several conditionsb'*'.</p

Overall genome relatedness indices of the strain LBMH1013 against 92 representatives of the family <i>Herpotrichiellaceae</i>.

Overall genome relatedness indices of the strain LBMH1013 against 92 representatives of the family Herpotrichiellaceae.</p

UFCG tree from 59 concatenated fungal marker genes extracted from genomic sequences of the <i>Herpotrichiellaceae</i> assemblies.

The tree was rooted using the midpoint rooting method. Branches supports are represented by their Gene Support Index (GSI) values. The canonical monophyletic clades of the family identified by [16] are highlighted with coloured boxes. Bar (0.1) represents number of changes per site. The tree was edited in iTOL online version 6.7.6. bPTP speciation partition support for E. chapopotensis are depicted in violet on the corresponding branch. Contexts whose current nomenclature is incorrect are highlighted in yellow.</p