Microbiome of the deep Lake Baikal, a unique oxic bathypelagic habitat

Abstract

Lake Baikal is the deepest lake in the world. Its depth provides the only bathypelagic (> 1000 m deep) freshwater habitat on Earth and its oxic, ultra-oligotrophic features make it a freshwater counterpart of the deep ocean. Here we have analyzed metagenomes from 1250 and 1350 m deep samples and built 231 metagenome-assembled genomes (MAGs). We detected high fractions of Thaumarchaeota (ca. 20% of 16S rRNA reads) and members of the candidate phyla radiation (CPR) (3-4.5%). Among the MAGs, we obtained ammonia-oxidizing archaea (AOA, Nitrosopumilaceae) and bacteria (AOB, Nitrosomonadaceae), and nitrite-oxidizers (Nitrospirae) indicating very active nitrification. A new clade of freshwater SAR202 Chloroflexi and methanotrophs (Methyloglobulus) were also remarkably abundant, the latter reflecting a possible role of methane oxidation as well. Novel species of streamlined and cosmopolitan bacteria such as Ca. Fonsibacter or acI Actinobacteria were more abundant at the surface but also present in deep waters. Conversely, CPRs, Myxococcales, Chloroflexi, DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota and Nanohaloarchaeota) archaea, or Gammaproteobacteria were found only in bathypelagic samples. We noted various important taxonomic and metabolic differences between deep aphotic region of Lake Baikal and marine waters of similar depth: Betaproteobacteriales, CPR, and DPANN superphylum were only found in bathypelagic Baikal, while Deltaproteobacteria, Gammaproteobacteria, or Alphaproteobacteria prevailed in oceanic samples. The genes mediating ammonia and methane oxidation, aromatic compound degradation, or alkane/methanesulfonate monooxygenases were detected in higher numbers in deep Baikal compared to their oceanic counterparts or its own surface. Overall, depth seems to be less relevant than salinity in configuring the microbial community.

Microbiome of the Black Sea Water Column Analyzed by Genome Centric Metagenomics  

“…50% of the total reads mapped with the MAGs from the coastal epipelagic sample (BS301-5 m), 42% for the offshore epipelagic sample (BS307-5 m) and 34% for the DCM sample (BS307-30 m). These recovery values are in the range of what was previously obtained for other aquatic environments [14]. A Distance-based redundancy analysis (dbRDA) was conducted to statistically assess the main differences between different Black Sea strata (Fig.…”

A freshwater radiation of diplonemids

“…300 bp), we wondered if it was possible to identify longer assembled 18S rRNA sequences from freshwater diplonemids in assembled metagenomic contigs. Additionally, we also used previously available metagenomic samples from the Řimov reservoir (Kavagutti et al ., 2019) and other published metagenomic datasets from the deep Lake Baikal (Cabello‐Yeves et al ., 2018; Cabello‐Yeves et al ., 2019). Multiple long sequences were retrieved from all samples except for Lake Baikal and all of them were closely related to the amplicon‐derived sequences (see Fig.…”

“…Each metagenomic dataset (i.e., each sample) was assembled independently with MEGAHIT (v1.1.5) (Li et al ., 2016) using the k‐mer sizes: 49, 69, 89, 109, 129, 149, and default settings. Previously available metagenomes and assemblies from the Řimov reservoir (Kavagutti et al ., 2019) and Lake Baikal were included in the analysis (Cabello‐Yeves et al ., 2018; Cabello‐Yeves et al ., 2019).…”

New viral biogeochemical roles revealed through metagenomic analysis of Lake Baikal

“…We have analyzed a total of ten metagenomes sequenced from different habitats of Lake Baikal. The four datasets that represented winter microbiomes from sub-ice samples have previously been described in detail [5,6]. We expanded this set of samples by generating a new set of six metagenomes obtained from similar geographical coordinates but collected during summer.…”

“…In spring, the ice layer melts, and surface water temperature raises to nearly 12°C, only to decrease rapidly towards deeper waters (below 50 m) to the same 4°C that are kept all year around for the deep water mass. Recent metagenomic studies have analyzed the microbiome of sub-ice epipelagic and bathypelagic waters, revealing the key microbes that dwell at this ecosystem as well as the ecological processes in which they are involved [5,6]. These studies have shed light on the taxonomic composition of the Lake Baikal microbiome and the contributions of these microbes to biogeochemical cycles.…”