Metagenomic comparisons reveal a highly diverse and unique viral community in a seasonally fluctuating hypersaline microbial mat

Abstract

In spring 2016, a shallow hypersaline pond (50×25 m) was found in the Cuatro Cienegas Basin (CCB). This pond, known as Archaean Domes (AD) because of its elastic microbial mats that form dome-shaped structures due to the production of reducing gases reminiscent of the Archaean eon, such as methane and hydrogen sulfide, harbour a highly diverse microbial community, rich in halophilic and methanogenic archaea. AD is a seasonally fluctuating hypersaline site, with salinity ranging from low hypersaline (5.3%) during the wet season to high hypersaline (saturation) during the dry season. To characterize the viral community and to test whether it resembles those of other hypersaline sites (whose diversity is conditioned by salinity), or if it is similar to other CCB sites (with which it shares a common geological history), we generated 12 metagenomes from different seasons and depths over a 4 year period and compared them to 35 metagenomes from varied environments. Haloarchaeaviruses were detected, but were never dominant (average of 15.37 % of the total viral species), and the viral community structure and diversity were not affected by environmental fluctuations. In fact, unlike other viral communities at hypersaline sites, AD remained more diverse than other environments regardless of season. β-Diversity analyses show that AD is closely related to other CCB sites, although it has a unique viral community that forms a cluster of its own. The similarity of two surface samples to the 30 and 50 cm depth samples, as well as the observed increase in diversity at greater depths, supports the hypothesis that the diversity of CCB has evolved as a result of a long time environmental stability of a deep aquifer that functions as a ‘seed bank’ of great microbial diversity that is transported to the surface by sporadic groundwater upwelling events.

Comparative evaluation of bioinformatic tools for virus-host prediction and their application to a highly diverse community in the Cuatro Ciénegas Basin, Mexico

“…Such diversity is believed to have evolved as a result of the long-standing environmental stability of a deep aquifer that recreates an ancient ocean conditions, and which nourishes the aquatic systems of Cuatro Ciénegas Basin through the movement of groundwater produced by the magmatic pouch deep in the Sierra San Marcos y Pinos [59]. Specifically, the environment from which samples were extracted is a shallow pond characterized by high pH and salinity known as Archaen Domes [16, 17, 18]. It has been shown that Archaean Domes harbors a great diversity of bacteria on a short spatial scale [17] and is one of the most diverse archaeal communities in the world [16].…”

“…However, the lack of consistency of CrisprOpenDB and RaFAH with the other methods suggests that relying on a >11 million spacers database [5] or on a Random Forest classifier based on the protein content of viruses with known host [11], respectively, may be beneficial only when the hosts or the assembled viruses are already known, or are closely related to hosts or viruses represented in the corresponding databases. Therefore, for highly diverse datasets likely to have a high proportion of novel viruses as the one tested here [18], it may be more appropriate to use host-based tools, either alignment-based or alignment-free, such as CrisprCustomDB or PHP, with ad hoc databases built with archaea and bacteria MAGs from the same dataset whenever possible.…”

“…30 cm plastic tubes were used as sediment samplers to collect two additional microbial mat samples at 30 and 50 cm depth (D30 and D50). Three samples were collected at the shallow ellipsoid orange pools or orange circles (OC) [16, 17, 18]: one superficial water sample (C0) on a 50 mL conical tube and two more at depths of 30 and 50 cm (C30 and C50). All samples were stored in liquid nitrogen until processing.…”

“…Archaean Domes is a seasonally fluctuating pond characterized by high pH and salinity, where an extreme diversity of Bacteria and Archaea has been recently described [16,17]. In addition, its highly diverse viral community does not behave like those from other hypersaline or high pH sites in the face of environmental solid fluctuations [18], for which it is essential to characterize the virus-host relationships and interactions that may drive the microbial and viral diversity in such a unique site. The CRISPR spacers were obtained with the CRISPRDetect tool [19] to test their performance on the custom database (133 bacterial genomes) with the parameters recommended by Dion et al [5].…”

Comparative evaluation of bioinformatic tools for virus-host prediction and their application to a highly diverse community in the Cuatro Ciénegas Basin, Mexico

“…This diversity includes a high abundance of halotolerant bacteria, as well as halophilic and methanogenic archaea, which are rare in the rest of the CCB [ 8 , 9 ]. Finally, a highly diverse viral community has recently been described, in which haloarchaeaviruses appear to be an essential component, and which does not behave like those from other hypersaline or high pH sites in the face of environmental fluctuations [ 10 ]. However, viruses in AD have yet to be fully characterised, which is essential to dissect the virus-host relationships and interactions that may drive microbial and viral diversity in such a unique site.…”