Biology subjects

Luo, Z.-H.

Publications and source records attributed to Luo, Z.-H..

8 recordsLinked to original sources

bioRxiv2026

Biofilm Lifestyle Drives Ecophysiological Niche Expansion in an Archaeal Soil Nitrifier

As key drivers of nitrification, ammonia-oxidizing archaea (AOA) play a central role in the global nitrogen cycle and contribute significantly to the emissions of the potent greenhouse gas nitrous oxide (N2O). However, the ecological implications of AOA growth as biofilms, remain poorly understood. Since nitrite production can be used to follow cellular activities directly we were able to compare biofilms with planktonic cells of the terrestrial model AOA Nitrososphaera viennensis at ecologically and agriculturally relevant conditions. Biofilms were more resistant across nearly all tested conditions and remained active at lower temperatures, acidic pH, and high ammonium concentrations. Collectively, activities in biofilm help reconcile discrepancies between earlier laboratory and environmental observations of soil AOA. Additionally, biofilms showed a high general resilience and lowered sensitivities to nitrification inhibitors. Although in situ biofilms grown in microrespiratory chambers exhibited activity and ammonia affinity similar to planktonic cells, biofilm cultures produced only half as much N2O. The enhanced fitness of biofilms across all tested conditions vastly expands the potential ecophysiological niche of AOA and supports the hypothesis that biofilm growth represents the in situ phenotype of AOA in soil environments.

microbiology↗

bioRxiv2026

Active virus-host system in a Lokiarchaeon culture

Asgard archaea are considered the closest prokaryotic relatives of eukaryotes and having a crucial role in eukaryogenesis. Only few organisms have been cultivated from this group and their viruses were previously described only through metagenomic reconstructions. Here, we report the first successful cultivation of an Asgard archaeal virus infecting a novel strain of Ca. Lokiarchaeum ossiferum B36. The 16 kbp integrated provirus is capable to excise and replicate independently leading to the formation of virus particles. Network analysis of shared protein clusters with other archaeal viruses places it in a new family, Fylgjaviridae. The host encodes a distinctive repertoire of antiviral defense systems, including Septu, Wadjet, and type II CBASS system, all different from the defense systems of the related strain Ca. L. ossiferum B35. Our cultures provide the first opportunity to study interactions of a virus-host system in Asgards and hold significant potential for developing genetic tools.

microbiology↗

bioRxiv2025

Metabolic Response of a Chemolithoautotrophic Archaeon to Carbon Limitation

The ubiquitously distributed ammonia-oxidizing archaea generate energy from ammonia and build cell mass from inorganic carbon sources, thereby contributing to both the global nitrogen and carbon cycles. However, little is known about the regulation of their predicted core carbon metabolism. A thermodynamic model for Nitrososphaera viennensis was developed to estimate the consumption of inorganic carbon in relation to ammonia consumed for energy and was tested experimentally by growing cells in carbon-limited and excess conditions. A combined proteomic and metabolomic approach of the experimental conditions revealed distinct metabolic adaptation depending on the amount of carbon supplied, either in a catalase or pyruvate background as a reactive oxygen species scavenger. Integration of protein and metabolite dynamics revealed a cellular strategy under carbon limitation to maintain a pool of amino acids and an upregulation of proteins necessary for translation initiation to stay primed for protein synthesis. The combination of modelling and functional genomics fills gaps in the understanding of the central metabolism and its regulation in a chemolithoautotrophic, ammonia-oxidizing archaeon even in the absence of available genetic tools.

microbiology↗

bioRxiv2024

Biofilm lifestyle as a common trait of ammonia-oxidizing archaea

Although widespread in nature, growth in biofilms has been relatively little explored in the globally distributed ammonia oxidizing archaea (AOA). Here we investigated six representatives of three different terrestrial and marine clades of AOA in a longitudinal and quantitative study for their ability to form biofilm and studied gene expression patterns of three representatives. While all strains grew on a solid surface, soil strains exhibited the highest capacity for biofilm formation. Based on microscopic and gene expression data, two different colonization strategies could be distinguished. S-layer containing AOA (from both soil and marine habitats) initialized attachment as single cells and subsequently formed denser layers and three-dimensional structures, while the S-layer free species of the Nitrosocosmicus clade attached as suspended aggregates to the surface and henceforth showed fastest establishment of biofilm. Transcription profiles were significantly different between planktonic and biofilm growth in all strains and revealed individual reactions, often fulfilling shared functions. In particular the strong expression of different types of multicopper oxidases was observed in all strains indicating modifications of their cell coats. S-layer carrying AOA each additionally expressed a set of adhesion proteins supporting attachment. Detoxification of nitrous compounds, copper acquisition as well as the expression of transcription factor B were also shared reactions among biofilm producing strains. However, the majority of differentially expressed protein families was distinct among the three strains illustrating that individual solutions have evolved for the shared growth mode of biofilm formation in AOA, probably driven by the different ecological niches.

microbiology↗

bioRxiv2021

Structure of Vibrio phage XM1, a simple contractile DNA injection machine

Antibiotic resistance poses a growing risk to public health requiring new tools to combat pathogenic bacteria. Contractile injection systems, including bacteriophage tails, pyocins, and bacterial type VI secretion systems, can efficiently penetrate cell envelopes and become potential antibacterial agents. Bacteriophage XM1 is a dsDNA virus belonging to the Myoviridae family and infecting Vibrio bacteria. The XM1 virion, made of 18 different proteins, consists of an icosahedral head and a contractile tail, terminated with a baseplate. Here we report cryo-EM reconstructions of all components of the XM1 virion and describe atomic structures of 14 XM1 proteins. The XM1 baseplate is composed of a central hub surrounded by six wedge modules to which twelve spikes are attached. The XM1 tail contains a fewer number of smaller proteins compared with other reported phage baseplates, depicting the minimum requirements for building an effective cell-envelope-penetrating machine. We describe the tail sheath structure in the pre-infection post-infection states and its conformational changes during infection. In addition, we report, for the first time, the in situ structure of the phage neck region to near-atomic resolution. Based on these structures, we propose mechanisms of virus assembly and infection.

molecular biology↗

bioRxiv2020

GenOrigin: A Comprehensive Protein-coding Gene Origination Database on the Evolutionary Timescale of Life

The origination of new genes contributes to the biological diversity of life. New genes may quickly build their own network in the genomes, exert important functions, and generate novel phenotypes. Dating gene age and inferring the origination mechanisms of new genes, like primate-specific gene, is the basis for the functional study of the genes. However, no comprehensive resource of gene age estimates across species is available. Here, we systematically dated the age of 9,102,113 protein-coding genes from 565 species in the Ensembl and Ensembl Genomes databases, including 82 bacteria, 57 protists, 134 fungi, 58 plants, 56 metazoa, and 178 vertebrates, using protein-family-based pipeline with Wagner parsimony algorithm. We also collected gene age estimate data from other studies and uniformed the gene age estimates to time ranges in million years for comparison across studies. All the data were cataloged into GenOrigin (http://genorigin.chenzxlab.cn/), a userfriendly new database of gene age estimates, where users can browse gene age estimates by species, age and gene ontology. In GenOrigin, the information such as gene age estimates, annotation, gene ontology, ortholog and paralog, as well as detailed gene presence/absence views for gene age inference based on the species tree with evolutionary timescale, was provided to researchers for exploring gene functions.

evolutionary biology↗

bioRxiv2019

Genome and community-level interaction insights on wide carbon utilizing and element cycling function of Hydrothermarchaeota from hydrothermal sediment

Hydrothermal vents release reduced compounds and small organic carbons into surrounding seawaters, providing essential substrates for microbial-derived biosynthesis and bioenergy transformations. Despite the wide distribution of Marine Benthic Group-E archaea (referred to as Hydrothermarchaeota) in hydrothermal environments, little is known on their genome blueprints and ecofunctions. Here, we studied four relatively high-completeness (> 80%) metagenome-assembled genomes (MAGs) from a black smoker chimney and surrounding sulfide sediments in the Mid-Atlantic Ridge of the South Atlantic Ocean (BSmoChi-MAR) as well as publicly available datasets. Comparative genomics suggest that Hydrothermarchaeota members have versatile carbon metabolism, including assimilating proteins, lactate and acetate, degrading aromatics anaerobically, oxidizing C1 compounds (CO, formate, and formaldehyde), utilizing methyl-compounds, and incorporating CO2 by tetrahydromethanopterin-based Wood-Ljungdahl (WL) pathway and Calvin-Benson-Bassham (CBB) cycle with type III Ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO). They could oxidize sulfur, arsenic, and hydrogen, and respire anaerobically via sulfate reduction and denitrification based on genomic evidence. The redundancy of carbon utilizing and element cycling functions, and the interactive processes of syntrophic and sequential utilization of substrates from community-level metabolic prediction, enable wide accessibility of carbon and energy sources to microorganisms. Hydrothermarchaeota members derived important functional components from the community through lateral gene transfer, and became clade-distinctive on genome content, which might serve as a niche-adaptive strategy to metabolize potential heavy metals, C1 compounds, and reduced sulfur compounds.\n\nImportanceThis study provides comprehensive metabolic insights on Hydrothermarchaeota from comparative genomics, evolution and community-level aspects. Hydrothermarchaeota synergistically participates in a wide range of carbon utilizing and element cycling processes with other microbes in the community. We expand the current understanding of community interactions within hydrothermal sediment environments, suggesting that microbial interactions driven by functions are essential to nutrient and element cycling.

ecology↗

bioRxiv2018

pyMeSHSim: an integrative python package to realize biomedical named entity recognition, normalization and comparison

SummaryComputing semantic similarity between two texts, like disease descriptions, has become important for many biomedical text mining applications. Here, we present PyMeSHSim, which is an integrative, lightweight and data-rich MeSH toolkit that recognizes biomedical named entities (bio-NEs) from texts, maps the bio-NEs to the controlled vocabulary MeSH and measures the semantic similarity between the MeSH terms.\n\nAvailabilityPackages source code and test datasets are available under the GPLv3 license at https://github.com/luozhhub/pyMeSHSim\n\nContactzhen-xia.chen@mail.hzau.edu.cn or zhy630@mail.hzau.edu.cn

bioinformatics↗