Diversity of Archaea Domain in Cuatro Cienegas Basin: Archaean Domes

Abstract

23Herein we describe the Archaea diversity in a shallow pond in the Cuatro Ciénegas Basin (CCB), 24Northeast Mexico, with fluctuating hypersaline conditions containing elastic microbial mats that 25 can form small domes where their anoxic inside reminds us of the characteristics of the Archaean 26Eon, rich in methane and sulfur gases; thus, we named this site the Archaean Domes (AD). These 27 domes only form after heavy rains that are rare in the Chihuahuan desert. CCB is a unique oasis 28 with hundreds of ponds, containing endemic species of animals, plants and highly diverse and 29 unique microbial communities, despite its very biased stoichiometry, due mostly to extreme low 30 phosphorus content (soils, water columns and sediments). This extreme oligotrophy has favored 31 survival of ancestral microorganisms. Whole metagenome sequencing approach was performed for 32 this unusual site in three different seasons to assess the extent of the Archaea biodiversity, with a 33 focus on extremophiles, since members of the Archaea had been underrepresented in different study 34 sites within the oasis. We found a highly diverse Archaea community compassing ~5% of the 35 metagenomes. The archaeal portion in all three metagenomes maintained its abundance and most of 36 the strains showed to form a resilient core during three seasonal samplings (2016-2017), despite 37 environmental fluctuations. However, relative abundances of all 230 archaeal OTUs (defined using 38 a 97% cutoff) were low enough (<0.1%) to be considered part of the rare biosphere. AD finding and 39 their description within CCB confirms that this particular pond is the most diverse for Archaea that 40we are aware of and opens new paths for understanding the forces that once drove and keep shaping 41 microbial community assemblage. 42 43 44 45 . CC-BY-NC-ND 4.0 International license is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It . https://doi.org/10.1101/766709 doi: bioRxiv preprint Archaea domain remains largely unexplored [14] along with a diverse metabolism [15, 16], 64 unveiling new processes and key features involving microbes and community structure.65 Cuatro Cienegas Basin (CCB) is an endangered oasis within the northern zone of the 66 Chihuahuan Desert in Mexico, characterized by an extremely unbalanced nutrient stoichiometry of 67 the area (N:P = 159:1), similar to the conditions of the Precambrian sea [17-21]. Strikingly, despite 68 . CC-BY-NC-ND 4.0 International license is made available under aThe copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It . https://doi.org/10.1101/766709 doi: bioRxiv preprint this nutrient deficiency CCB is considered a biodiversity hotspot for macroorganisms [22] and one 69 of the most diverse sites for microorganisms in the world [23][24][25][26][27]; this microbial biodiversity is 70 mirrored by its extreme diversity in virus [28]. CCB biodiversity is believed to have evolved as a 71result of a long time en...

Diversity of an uncommon elastic hypersaline microbial mat along a small-scale transect

“…The internal microbial layer, insulated by an outer aerobic community, thrives under an anaerobic environment, rich in methane, hydrogen sulfide, and small volatile hydrocarbons that recreate the atmosphere of the Archaean Eon, hence we named these mats “Archaean Domes” ( Medina-Chávez et al, 2019 ). Similar types of elastic mats have previously been described in marine tidal zones ( Gerdes et al, 1993 ).…”

Conserved bacterial genomes from two geographically isolated peritidal stromatolite formations shed light on potential functional guilds

“…The biogenicity of stromatolites has been studied extensively in the hypersaline and marine formations of Shark Bay, Australia, and Exuma Cay, The Bahamas, respectively (Khodadad and Foster, 2012; Mobberley et al ., 2015; Centeno et al ., 2016; Gleeson et al ., 2016; Ruvindy et al ., 2016; Warden et al ., 2016; White et al ., 2016; Babilonia et al ., 2018; Wong et al ., 2018; Chen et al ., 2020). The presence of Archaea has been noted in several microbial mats and stromatolite systems (Casaburi et al ., 2016; Balci et al ., 2018; Medina‐Chávez et al ., 2019; Chen et al ., 2020), particularly in the stromatolites of Shark Bay, where they are hypothesized to potentially fulfil the role of nitrifiers and hydrogenotrophic methanogens (Wong et al ., 2017). Studies of freshwater microbialites in Mexico found that there were significantly more genes associated with phosphate uptake and metabolism than in other communities associated with fresh or marine waters (Breitbart et al ., 2009) and that nitrogen fixation by heterocystous cyanobacteria, sulfur‐reducing bacteria, and purple sulfur bacteria was important to the formation of these particular stromatolites (Falcón et al ., 2007).…”

Archaeal Communities: The Microbial Phylogenomic Frontier

“…After three seasons (wet-dry-wet), each one represented by one metagenomic analysis on a dome (AD1, AD2, and AD3), the results show a vast diversity of members of the Archaea domain. An average of 230 Archaeal species were found in the mat ( Medina-Chávez et al, 2020 ), covering five phyla, Euryarchaeaota, Crenarchaeota, and the unexpected Thaumarchaeota, Korarchaeota, and Nanoarchaeota phyla ( Medina-Chávez et al, 2019 ). Total Archaeal diversity was constant through seasons, appearing as a stable Archaeal core throughout time.…”

“…By defining the “ strictly rare ” biosphere as the taxa with relative abundances below 0.01%, we found 50 Archaeal OTUs with very interesting demographic behavior. Within this group, 11 OTUs seem to be conditionally rare ( Shade et al, 2014 ), maintaining their lower abundance in only one sampling time (the wet month) and reaching higher abundances in both dry samplings ( Figure 2A ) ( Medina-Chávez et al, 2019 ). The dynamics of this portion of the rare taxa lead us to speculate that those OTUs from the Archaeal dome formation and those that are more abundant may benefit from a saltier environment under drier conditions.…”

“…Additionally, 39 rare taxa were transiently rare since they were absent in one or two samples ( Figure 2B ) ( Medina-Chávez et al, 2019 ). We suggest that this type of rarity is driven by stochastic processes such as passive dispersal of lineages temporarily recruited from the microbial seed bank or due to immigration ( Lynch and Neufeld, 2015 ).…”