Microbial diversity and adaptive strategies in the Mars-like Qaidam Basin, North Tibetan Plateau, China

Hydrochemical and isotopic characteristics of water sources for biological activity across a massive evaporite basin on the Tibetan Plateau: Implications for aquatic environments on early Mars

Covered by vast eolian landforms, gravel deposits, and playas, the worldwide typical evaporite deposit land, Qaidam Basin, in northwestern China is analogous to early Mars when the aridification process had lasted for millions of years since the end of a wetter climate. This study aims to investigate the chemical and isotopic characteristics of waters in an evaporite-rich environment, as well as the habitable conditions therein, that have undergone a transformation similar to early Mars. In May 2023, a total of 26 water samples were collected across the representative central axis of a longitudinal aridity gradient in the Qaidam Basin, including categories of meteoric water, freshwater, standing water accumulated after precipitation, salty lacustrine water, and hypersaline brines to inspect compounds made up of carbon, nitrogen, phosphorus, sulfur, halogen, and metallic elements. As evaporation intensified, the salt types transformed from HCO3-Ca·Na to Cl·SO4-Na or ClMg. The dominance of carbonate will gradually be replaced by sulfate and chloride, leaving much more dilute and less detectable contents. The presence of trace ClO4-, ClO3-, ClO2-, and BrO3- was confirmed in a few of the sampled Qaidam waters, indicating the preservation of oxyhalides in waters within an arid region and possibly the presence of relevant microbial enzymes. The isotopes of water, carbonaceous, and nitrogenous compounds provide valuable references for either abiogenic or biogenic signatures. With undetectable amount, phosphorus was found to be the limiting nutrient in evaporative aquatic environments but not necessarily antibiosignatures. Overall, these results suggest that the paleo-lacustrine environments on Mars are more likely to preserve biosignatures if they feature the dominance of carbonate minerals, bioavailable nitrate, phosphorus, and organic carbon, the presence of thermodynamically unstable oxyhalides, and isotope ratios that point to the involvement of biological activity.

Bacterial community distribution and functional potentials provide key insights into their role in the ecosystem functioning of a retreating Eastern Himalayan glacier

Himalayan glaciers are receding at an exceptional rate, perturbing the local biome and ecosystem processes. Understanding the microbial ecology of an exclusively microbe-driven biome provides insights into their contributions to the ecosystem functioning through biogeochemical fluxes. Here, we investigated the bacterial communities and their functional potential in the retreating East Rathong Glacier (ERG) of Sikkim Himalaya. Amplicon-based taxonomic classification revealed the dominance of the phyla Proteobacteria, Bacteroidota, and candidate Patescibacteria in the glacial sites. Further, eight good-quality metagenome-assembled genomes (MAGs) of Proteobacteria, Patescibacteria, Acidobacteriota, and Choloflexota retrieved from the metagenomes elucidated the microbial contributions to nutrient cycling. The ERG MAGs showed aerobic respiration as a primary metabolic feature, accompanied by carbon fixation and complex carbon degradation potentials. Pathways for nitrogen metabolism, chiefly dissimilatory nitrate reduction and denitrification, and a complete sulphur oxidation enzyme complex for sulphur metabolism were identified in the MAGs. We observed that DNA repair and oxidative stress response genes complemented with osmotic and periplasmic stress and protein chaperones were vital for adaptation against the intense radiation and stress conditions of the extreme Himalayan niche. Current findings elucidate the microbiome and associated functional potentials of a vulnerable glacier, emphasizing their significant ecological roles in a changing glacial ecosystem.

Use of 16S rRNA gene sequences to identify cyanobacteria that can grow in far-red light

Although most cyanobacteria use visible light (VL; λ = 400-700 nm) for photosynthesis, some have evolved strategies to use far-red light (FRL; λ = 700-800 nm). These cyanobacteria are defined as far-red light-utilizing cyanobacteria (FRLCyano), including two groups: (1) chlorophyll d-producing Acaryochloris spp. and (2) polyphyletic cyanobacteria that produce chlorophylls d and f in response to FRL. Numerous ecological studies examine pigments, such as chlorophylls d and f, to investigate the presence of FRLCyano in the environment. This method is not ideal because it can only detect FRLCyano that have made chlorophylls d or f. Here we develop a new method, far-red cyanobacteria identification (FRCI), to identify FRLCyano based on 16S rRNA gene sequences. From public databases and published articles, 62 16S rRNA gene sequences of FRLCyano were extracted. Comparing with related lineages, we determined that 97% sequence identity is the optimal cut-off for distinguishing FRLCyano from other cyanobacteria. To test the method experimentally, we collected samples from 17 sites in Taipei, Taiwan, and conducted VL and FRL enrichments. Our results demonstrate that FRCI can detect FRLCyano during FRL enrichments more sensitively than pigment analysis. FRCI can also resolve the composition of FRLCyano at the genus level, which pigment analysis cannot do. In addition, we applied FRCI to published datasets and discovered putative FRLCyano in diverse environments, including soils, hot springs and deserts. Overall, our results indicate that FRCI is a sensitive and high-resolution method using 16S rRNA gene sequences to identify FRLCyano.

Metabolic versatility of soil microbial communities below the rocks of the hyperarid Dalangtan Playa

IMPORTANCE

The hyperarid Dalangtan Playa in the western Qaidam Basin, northwestern China, is a unique terrestrial analog of Mars. Despite the polyextreme environments of this area, habitats below translucent rocks capable of environmental buffering could serve as refuges for microbial life. In this study, the hybrid assembly of Illumina short reads and Nanopore long reads recovered high-quality and high-continuity genomes, allowing for high-accuracy analysis and a deeper understanding of extremophiles in the sheltered soils of the Dalangtan Playa. Our findings reveal self-supporting and metabolically versatile sheltered soil communities adapted to a hyperarid and hypersaline playa, which provides implications for the search for life signals on Mars.

Prokaryotic taxonomy and functional diversity assessment of different sequencing platform in a hyper-arid Gobi soil in Xinjiang Turpan Basin, China

Turpan Basin located in the eastern Xinjiang is a typical arid inland basin with extremely scarce water resources and a fragile ecosystem. Prokaryotic communities with unique genetic and physiological modifications can survive and function in such harsh environments, offering diverse microbial resources. However, numerous microbes can enter the viable but non-culturable state because of drought stress in the desert soil. In this work, next generation sequencing (NGS) technology based on DNA nanoball sequencing platform (DNBSEQ-G400) and sequencing-by-synthesis platform (NovaSeq 6000) were applied to analyze the prokaryotic diversity in three hyper-arid Gobi soils from Flaming Mountain, Toksun, and Kumtag. The comparison between two platforms indicated that DNBSEQ-G400 had better repeatability and could better reflect the prokaryotic community of this hyper-arid region. The diversity analysis based on DNBSEQ-G400 identified a total of 36 bacterial phyla, including Pseudomonadota, Bacteroidota, Bacillota, Actinomycetota, Methanobacteriota, Acidobacteriota, Nitrososphaerota, and Planctomycetota. The environmental factors, including soluble salt, available potassium, total nitrogen, and organic matter, were positively correlated with the abundance of most prokaryote. In addition, the prokaryotic community assembly in hyper-arid soil was well described by neutral-based models, indicating that the community assembly was mainly controlled by stochastic processes. Finally, the phylogenetic analysis of Actinomycetota proved that such extremophiles played an important role in the ecosystems they colonize. Overall, our result provides a reference for choosing the appropriate sequencing platform and a perspective for the utilization of soil microbial resources from hyper-arid regions.

Adaptive mechanisms of Bacillus to near space extreme environments

Earth's near space is an extreme atmosphere environment with high levels of radiation, low atmospheric pressure and dramatic temperature fluctuations. The region is above the flight altitude of aircraft but below the orbit of satellites, which has special and Mars-like conditions for investigating the survival and evolution of life. Technical limitations including flight devices, payloads and technologies/methodologies hinder microbiological research in near space. In this study, we investigated microbial survival and adaptive strategies in near space using a scientific balloon fight mission and multi-omics analyses. Methods for sample preparation, storage, protector and vessel were optimized to prepare the exposed microbial samples. After 3 h 17 min of exposure at a float altitude of ~32 km, only Bacillus strains were alive with survival efficiencies of 0-10^-6. Diverse mutants with significantly altered metabolites were generated, firstly proving that Earth's near space could be used as a new powerful microbial breeding platform. Multi-omics analyses of mutants revealed cascade changes at the genome, transcriptome and proteome levels. In response to environmental stresses, two mutants had similar proteome changes caused by different genomic mutations and mRNA expression levels. Metabolic network analysis combined with proteins' expression levels revealed that metabolic fluxes of EMP, PPP and purine synthesis-related pathways were significantly altered to increase/decrease inosine production. Further analysis showed that proteins related to translation, molecular chaperones, cell wall/membrane, sporulation, DNA replication/repair and anti-oxidation were significantly upregulated, enabling cells to efficiently repair DNA/protein damages and improve viability against environmental stress. Overall, these results revealed genetic and metabolic responses of Bacillus to the harsh conditions in near space, providing a research basis for bacterial adaptive mechanisms in extreme environments.

Trait biases in microbial reference genomes

Common culturing techniques and priorities bias our discovery towards specific traits that may not be representative of microbial diversity in nature. So far, these biases have not been systematically examined. To address this gap, here we use 116,884 publicly available metagenome-assembled genomes (MAGs, completeness ≥80%) from 203 surveys worldwide as a culture-independent sample of bacterial and archaeal diversity, and compare these MAGs to the popular RefSeq genome database, which heavily relies on cultures. We compare the distribution of 12,454 KEGG gene orthologs (used as trait proxies) in the MAGs and RefSeq genomes, while controlling for environment type (ocean, soil, lake, bioreactor, human, and other animals). Using statistical modeling, we then determine the conditional probabilities that a species is represented in RefSeq depending on its genetic repertoire. We find that the majority of examined genes are significantly biased for or against in RefSeq. Our systematic estimates of gene prevalences across bacteria and archaea in nature and gene-specific biases in reference genomes constitutes a resource for addressing these issues in the future.

Biosignatures Preserved in Carbonate Nodules from the Western Qaidam Basin, NW China: Implications for Life Detection on Mars

The search for organic matter on Mars is one of the major objectives of Mars exploration. However, limited detection of organic signals by Mars rovers to date demands further investigation on this topic. The Curiosity rover recently discovered numerous nodules in Gale Crater on Mars. These nodules have been considered to precipitate in the neutral-to-alkaline and saline diagenetic fluids and could be beneficial for organic preservation. Here, we examine this possibility by studying the carbonate nodules in the western Qaidam Basin, NW China, one of the terrestrial analog sites for Mars. Fourier transform infrared spectra of the carbonate nodules reveal that the aliphatic and aromatic molecules can be readily preserved inside nodules in Mars-like environments. The chain-branching index of the Qaidam nodules suggests that the diagenetic fluids where nodules precipitated were able to support diverse microbial communities that could vary with the water salinity. Findings of this study provide new perspectives on the astrobiological significance of nodules in Gale Crater and the further detection of organic matter on Mars.