Biology subjects

liu, r.

Publications and source records attributed to liu, r..

4 recordsLinked to original sources

bioRxiv2025

Isolation of the first cultured representative from a deep-branching phylum in serpentinite-hosted ecosystems

Serpentinization drives abiotic synthesis of organics (e.g., hydrocarbon) potentially conducive to the emergence of life, making serpentinite-hosted systems and associated microbial community key windows into nature of lifes origin. Although cultivation-independent studies uncovered the Candisdatus Bipolaricaulota widely distributed in serpentinizing environments, cultivation of this phylum has been unsuccessful. Here we cultured the first pure strain, J31, of Ca. Bipolaricaulota from the Lost City hydrothermal field, a well-characterized marine serpentinite system, using hydrocarbons as the primary nutrient source. As an early-branching bacterial lineage, strain J31 exhibits an unusual morphology composed of a central rod and elongated Toga-like extensions at both ends, and divides by binary fission. Strain J31 absorbs hexadecane through Toga ends via coordinated processes resembling inhalation and swallowing, after which hexadecane is efficiently transported to the central rod in the vesicle-like structures and subsequently converted into membrane lipids to support Toga synthesis and cellular growth. Hydrocarbon-degrading capability is widespread among the globally distributed members of Ca. Bipolaricaulota. Strain J31 colonizes serpentine minerals, facilitating the utilization of hydrocarbons derived from serpentines and promoting the release of soluble iron and silicon, thereby linking microbial activity to geochemical cycling. Thus, our study presents a novel strategy for cultivating deep-branching bacteria and offers insights into the metabolic foundations of early life on Earth--and potentially on other rocky planets undergoing serpentinization.

microbiology↗

bioRxiv2021

Cultivation and characterization of a novel clade of deep-sea Chloroflexi: providing a glimpse of the phylum Chloroflexi involved in sulfur cycling

Chloroflexi bacteria are abundant and globally distributed in various unexplored biospheres on Earth. However, only few Chloroflexi members have been cultivated, hampering further understanding of this important group. In the current study, we firstly clarify the high abundance of the phylum Chloroflexi in deep-sea sediments via the operational taxonomic units analysis. We further successfully isolate a novel Chloroflexi strain ZRK33 from cold seep sediments by using an enrichment medium constantly supplemented with rifampicin. Phylogenetic analyses based on 16S rRNA gene, genome, RpoB and EF-tu proteins indicate that strain ZRK33 represents a novel class, and the class is designated as Sulfochloroflexia because whole set of genes encoding key enzymes responsible for assimilatory sulfate reduction are identified in the genome of strain ZRK33. Indeed, assimilation of sulfate or thiosulfate by strain ZRK33 evidently benefits its growth and morphogenesis. Proteomic results suggest that metabolization of sulfate or thiosulfate significantly promotes the transport and degradation of various macromolecules and thereby stimulating the energy production. Notably, the putative genes associated with assimilatory and dissimilatory sulfate reduction ubiquitously distribute in the metagenome-assembled genomes of 27 Chloroflexi members derived from deep-sea sediments, strongly suggesting that Chloroflexi bacteria play undocumented key roles in deep-sea sulfur cycling.

microbiology↗

bioRxiv2020

Metagenomic insights into the metabolism and ecologic functions of the widespread DPANN archaea from deep-sea hydrothermal vents

Due to the particularity of metabolism and the importance of ecological roles, the archaea living in deep-sea hydrothermal system always attract great attention. Included, the DPANN superphylum archaea, which are massive radiation of organisms, distribute widely in hydrothermal environment, but their metabolism and ecology remain largely unknown. In this study, we assembled 20 DPANN genomes comprised in 43 reconstructed genomes from deep-sea hydrothermal sediments, presenting high abundance in the archaea kingdom. Phylogenetic analysis shows 6 phyla comprising Aenigmarchaeota, Diapherotrites, Nanoarchaeota, Pacearchaeota, Woesearchaeota and a new candidate phylum designated DPANN-HV-2 are included in the 20 DPANN archaeal members, indicating their wide diversity in this extreme environment. Metabolic analysis presents their metabolic deficiencies because of their reduced genome size, such as gluconeogenesis, de novo nucleotide and amino acid synthesis. However, they possess alternative and economical strategies to fill this gap. Furthermore, they were detected to have multiple capacities of assimilating carbon dioxide, nitrogen and sulfur compounds, suggesting their potentially important ecologic roles in the hydrothermal system. IMPORTANCEDPANN archaea show high distribution in the hydrothermal system. However, they possess small genome size and some incomplete biological process. Exploring their metabolism is helpful to know how such small lives adapt to this special environment and what ecological roles they play. It was ever rarely noticed and reported. Therefore, in this study, we provide some genomic information about that and find their various abilities and potential ecological roles. Understanding their lifestyles is helpful for further cultivating, exploring deep-sea dark matters and revealing microbial biogeochemical cycles in this extreme environment.

microbiology↗

bioRxiv2020

Genomic analyses reveal the origin of domestic ducks and identify different genetic underpinnings of wild ducks

Domestic ducks are considered to have been tamed from the mallard or a descendant of the mallard and the spot-billed duck. Domestic ducks show remarkable phenotypic variation in morphology, physiology and behaviour. However, the molecular genetics of the origin and phenotypic variation of ducks are still poorly studied. Here, we present mallard and spot-billed genomes and perform whole-genome sequencing on eight domestic duck breeds and eight wild duck species. Surprisingly, analyses of these data support a model in which domestic ducks diverged from their closest wild lineage (mallard ducks and spot-billed ducks) at the last glacial period (LGP, 100-300 kilo years ago (Kyr)). The wild lineage further speciated into mallard ducks and spot-billed ducks approximately 70 Kyr, whereas the domestic lineage population decreased through the LGP. A scan of wild duck genomes compared with domestic duck genomes identified numerous loci that may have been affected by positive selection in ancestral wild ducks after their divergence from domestic lineages. Function analyses suggested that genes usually affecting organ development and energy metabolism may involve long-distance flight ability. Further selective sweep analyses identified two genes associated with egg production and three genes related to feeding modulation under selection in domestic ducks. These analyses unravel a distinct evolutionary pattern of ducks and two wild duck de novo genomes, thus providing a novel resource for speciation studies.

genomics↗