Abundance and Co-Distribution of Widespread Marine Archaeal Lineages in Surface Sediments of Freshwater Water Bodies across the Iberian Peninsula

Abstract

Archaea inhabiting marine and freshwater sediments have a relevant role in organic carbon mineralization, affecting carbon fluxes at a global scale. Despite current evidences suggesting that freshwater sediments largely contribute to this process, few large-scale surveys have been addressed to uncover archaeal diversity and abundance in freshwater sedimentary habitats. In this work, we quantified and high-throughput sequenced the archaeal 16S rRNA gene from surficial sediments collected in 21 inland waterbodies across the Iberian Peninsula differing in typology and trophic status. Whereas methanogenic groups were dominant in most of the studied systems, especially in organic-rich sediments, archaea affiliated to widespread marine lineages (the Bathyarchaeota and the Thermoplasmata) were also ubiquitous and particularly abundant in euxinic sediments. In these systems, Bathyarchaeota communities were dominated by subgroups Bathyarchaeota-6 (87.95 ± 12.71%) and Bathyarchaeota-15 (8.17 ± 9.2%) whereas communities of Thermoplasmata were mainly composed of members of the order Thermoplasmatales. Our results also indicate that Archaea accounted for a minor fraction of sedimentary prokaryotes despite remarkable exceptions in reservoirs and some stratified lakes. Copy numbers of archaeal and bathyarchaeotal 16S rRNA genes were significantly different when compared according to system type (i.e., lakes, ponds, and reservoirs), but no differences were obtained when compared according to their trophic status (from oligotrophy to eutrophy). Interestingly, we obtained significant correlations between the abundance of reads (Spearman r = 0.5, p = 0.021) and OTU richness (Spearman r = 0.677, p < 0.001) of Bathyarchaeota and Thermoplasmata across systems, reinforcing the hypothesis of a potential syntrophic interaction between members of both lineages.

Metabolic versatility of freshwater sedimentary archaea feeding on different organic carbon sources

“…The similar response of Bathyarchaeota and Thermoplasmata to all carbon sources points to similar substrate preferences and agrees with the co-occurrence of both groups in sediments worldwide [4,29]. The ability of Bathyarchaeota to feed on a wide range of organic substrates has already been observed in enrichment cultures [26].…”

“…Standards for archaeal 16S rRNA gene quantification were made using genomic DNA from Sulfolobus solfataricus DSM1616. Plasmids containing inserts of environmental 16S rRNA gene fragments previously isolated from clone libraries [29] were used as standards for the quantification of Bathyarchaeota and Thermoplasmata. Standard curves were obtained after serial dilutions of the corresponding DNA extracts containing known concentration of target gene ranging from 10 9 to 10 2 gene copies per μl.…”

“…In the present work, epiphytic biofilms on settled plant debris and sediment were collected from the bottom of a freshwater karstic lake where Bathyarchaeota and Thermoplasmata are prevalent [4,29]. Both type of samples were used to set up laboratory microcosms that were amended with different organic compounds (D-and L-arginine, tryptophan, protocatechuate, humic acids, and pectin) to assess the responsiveness of archaeal groups to these organic carbon sources.…”

Prokaryotic Diversity and Distribution in Different Habitats of an Alpine Rock Glacier-Pond System

“…Nevertheless, other phyla often poorly represented in the Zhang et al study, like Nitrospira, Gemmatimonadetes and Ignavibacteria had higher relative abundances in the Col d'Olen Rock Glacier pond.Freshwater ecosystems have been reported to harbour, on average, more rich and diverse archaeal communities if compared with soil[49], and this was also the case of Olen pond system, and differences in dominant archaeal taxonomic groups among alpine lacustrine ecosystems exist. For instance, sediment communities dominated by Bathyarchaeota and methanogenic Euryarchaeota (Methanomicrobia, Methanobacteria and Thermoplasmata classes) have been described in lakes of the Yunnan and Tibetan Plateau in China[48, 50, 51], or in a number of water systems in the Iberian Peninsula[52,53]. However, even if 16-38% of total archaea sequences affiliated to Euryarchaeota (mainly Methanomicrobia), Olen pond showed a quite different situation, with only small proportions of Bathyarchaeota (0.2-4%) and a prevalence of Woesarchaeota (49-63%).…”

Metal contaminations impact archaeal community composition, abundance and function in remote alpine lakes

“…In alpine lake sediments, these services are supported by diverse microbial communities insuring the recycling of carbon, nitrogen, phosphorus and sulfur back to the water column (Ingvorsen et al, 1981;Billen, 1982;Holmer and Storkholm, 2001). Among these microbes, sediments harbour a large diversity and abundance of uncultured Archaea (Auguet et al, 2010;Borrel et al, 2012;Fillol et al, 2015;Compte-Port et al, 2017). Some of these taxa, namely: Bathyarchaeota, Thermoplasmata (and their lineages Marine Benthic Group D and Methanomassilicoccales) have the genomic potentialities for the degradation of organic compounds and the production of methane, a greenhouse gas (GHG) with a global warming potential 28-fold higher that of carbon dioxide (Lloyd et al, 2013;Borrel et al, 2014;Meng et al, 2014;Evans et al, 2015;Lin et al, 2015;Lazar et al, 2016).…”