Evolution and adaptation of SAR11 and Cyanobium in a saline Tibetan lake

Abstract

Lake Qinghai is a unique lacustrine ecosystem located on the Tibetan Plateau and exhibits oligotrophic, alkaline, and saline conditions. Previous studies have focused on the community phylogenetic diversity of bacterioplankton in the ecosystem. This study aimed to address the ecotype diversity of bacterioplankton populations in the unique microbial habitat, using metagenomic sequencing and analysis. Phylogenetic analysis revealed two major bacterial populations: SAR11 IIIa (14% of the total) and Cyanobium (14%). Although the two populations shared high 16S rRNA gene sequence identity (> 98% identity) with their closest marine counterparts, they displayed substantial genomic divergence (≤ 80% average amino acid sequence identity). Comparative genomic analysis identified conservation of carbon and energy storage metabolism (biosynthesis of polyphosphate and polyhydroxyalkanoate) gene operons in the SAR11 IIIa and a cyanate (potential nitrogen source in alkaline conditions) transporter gene operon in the Cyanobium. We further identified genetic signature of positive selection acting on an exodeoxyribonuclease gene of the SAR11 IIIa population, which is potentially associated with DNA repair responsive to strong UV radiation on the high altitude mountain. Taken together, our results revealed the ecosystem-specific gene content of the bacterioplankton populations and provided new insights into their adaptations unique to the Tibetan lake.

Re-evaluating the salty divide: phylogenetic specificity of transitions between marine and freshwater systems

“…The partial genome from Lake Baikal combined with our observations provide robust evidence of SAR11 lineages other than LD12 (SAR11 IIIb) inhabiting freshwater lakes. Prior to these findings, marine SAR11 had been observed in saline lakes (40, 42) and LD12 had been detected and determined to assimilate thymidine in the brackish Gulf of Gdańsk, which is located on the southern Baltic Sea coast and receives freshwater input from the Vistula River (43). The first cultured representative of LD12 was isolated from the coastal lagoon of Lake Borgne (44).…”

Metagenomics Uncovers a Core SAR11 Population in Brackish Surface Waters of the Baltic Sea

“…Genome bins were then obtained based on the metagenome sequence read coverage, occurrence of unique marker genes, and tetranucleotide frequency, using MaxBin as described previously [34]. In contrast to the successful recovery of draft genomes using a similar approach in previous studies [23,32] the genome bins obtained using the metagenomic datasets used in this study showed low genome completeness, unfortunately. Assembling metagenomic data into high-quality genomes can be a complex task, which can be attributable to the inherent biological complexity (e.g., intra-species level genomic diversity and mobile genetic elements) as well as the highly demanding requirement of computer memory [33].…”

“…To assess the relative abundance (expressed as coverage) of a SAR11 population, metagenomics reads were searched against the 12 genes (aligned regions) using BLASTn with a cutoff of >70% nucleotide identity and >95 match length. The length of all mapped metagenomic reads was summed and divided by the total length of the 12 genes, as described previously [22][23][24]. The value was subsequently normalized to one Gb of metagenomics sequence, which was expressed as coverage (×).…”

“…Recent works have shown the assembly of metagenomic sequences into genomes, which helps improve the current understanding of the ecology of microorganisms that are hardly cultivable in laboratory settings such as SAR11 bacteria. Our previous work constructed a metagenome-assembled genome (MAG) of a novel SAR11 population, QL1, dominating a mesohaline lacustrine ecosystem on Water 2020, 12, 501 7 of 11 the Tibetan plateau [23,32]. Both 16S rRNA genes and representative single copy genes demonstrated the close genomic relatedness of the core population occurring in the site (LMO) to QL1.…”

“…16S rRNA gene-based surveys reported that the QL1-like population is globally found in various marine and lacustrine environments [31]. In particular, a recent study revealed the dominance of the QL1-like population (>95% genomic relatedness) in the Caspian Sea [40], in addition to other brackish waters globally distributed (e.g., the Baltic Sea, Chesapeake Bay, Delaware Bay, Lake Nam Co, and Lake Qinghai) [23,31,41,42]. Metagenomics uncovered distinct features in phylogenetic diversity and gene content between freshwater and oceanic communities [43].…”