Abundant Taxa and Favorable Pathways in the Microbiome of Soda-Saline Lakes in Inner Mongolia

Abstract

Background: The chloride-carbonate-sulfate lakes (also called Soda-Saline lakes) are double-extreme ecological environments with high pH and high salinity values but can also exhibit high biodiversity and high productivity. The diversity of metabolic process that functioned well in such environments remains to be systematically investigated. Deep sequencing and species-level characterization of the microbiome in elemental cycling of carbon and sulfur will provide novel insights into the microbial adaptation in such saline-alkaline lakes. Results: In this study, we characterized environmental factors and performed deep metagenomic sequencing of the brine and sediment samples from nine ponds with different salinities of two chloride-carbonate-sulfate lakes in Inner Mongolia of China. The results showed that the concentration of chloride most significantly influenced the microbial community in both of the brine and sediment environments. Of 385 high-quality metagenome-assembled genomes (MAGs) belonging to archaea (56 Euryarchaeota, 12 Candidatus Nanohaloarchaeota, and 12 Candidatus Woesearchaeota) and bacteria (119 Proteobacteria and 186 other diverse bacterial phyla, including 18 from Candidate Phyla Radiation, CPR), 38 MAGs were observed to be abundant species at least in one of the eighteen niches. These abundant taxa represented most branches of a phylogenomic tree at phylum level. Interestingly, almost half of the abundant MAGs had the potential to drive dissimilatory sulfur cycling, including four autotrophic Ectothiorhodospiraceae MAGs, one Cyanobacteria MAG and nine heterotrophic MAGs with potential to oxidize sulfur, as well as four abundant MAGs containing genes for elemental sulfur respiration, which may increase the ability of environmental adaptation in such saline-alkaline environments. In addition, some subgroups in Ca. Nanohaloarchaeota and Ca. Woesearchaeota of the DPANN superphylum were also observed abundant. We found 1,4-alpha-glucans phosphorylation and complete glycolysis pathway in the abundant Nanohaloarchaeota MAG NHA-1, and this efficient energy regeneration pathway (compared with hydrolysis) may be a key factor for Ca. Nanohaloarchaeota in adaptation to hypersaline environments. Conclusions: The abundant taxa including carbon fixing microbes, versatile heterotrophs and the nanosized DPANN superphyla, and the superiority of energy production and thermodynamics of these abundant species were systematically investigated. This has provided novel insights into the microbial process in chloride-carbonate-sulfate lakes, and further understanding of the metabolic mechanism of adaptation to such extremely alkaline and saline conditions.

Abundant Taxa and Favorable Pathways in the Microbiome of Soda-Saline Lakes in Inner Mongolia

“…We thank Dr. Wenyu Shi for data submission to NCBI and gcMeta. This manuscript was released as a preprint at Research Square (Zhao et al, 2019).…”

Metagenomic Insights Into Ecological and Phylogenetic Significances of Candidatus Natranaeroarchaeales, a Novel Abundant Archaeal Order in Soda Lake Sediment

“…It was classi ed further into normal soda lake and soda-saline lake based on the concentration of sulfate or chloride [9]. It has been reported that class Halobacteria and Candidatus Nanohaloarchaeota were the abundant archaeal members in the hypersaline brine [10][11][12][13][14]. Both lineages were also predominant in the neutral saline lakes and saltern [14][15][16].…”

“…Very recently, culture-dependent and -independent researches revealed that Ca. Nanohaloarchaeota had the capability of poly-or oligo-saccharide degradation in hypersaline brines of saltern and soda lakes [12,21]. Besides, the methylotrophic methanogenesis was evidently a dominant process, and many haloalkaliphilic methylotrophic methanogens were isolated from soda lakes, including Methanolobus, Methanosalsum, Methanocalculus and Methanonatronarchaeum [22,23].…”

“…Nanohaloarchaeota were deduced from the draft genomes [10]. The sediments of soda lakes exhibited much more complex microbial community and higher biodiversity [12].…”

“…Recently, we have deciphered the abundant taxa and their favorable pathways in the brine and surface sediment of soda-saline lakes in Inner Mongolia of China [12]. In this article, we focus on the characteristic archaeal microbiome in the deep sediments of the same region.…”