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The expanding Asgard archaea invoke novel insights into Tree of Life and eukaryogenesis

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mLife 2022年第4期1卷 374-381页

作者： Zhichao Zhou Yang Liu Karthik Anantharaman Meng Li Department of Bacteriology University of Wisconsin–MadisonMadisonWisconsinUSA archaeal Biology Center Institute for Advanced StudyShenzhen UniversityShenzhenChina Shenzhen Key Laboratory of Marine Microbiome Engineering Institute for Advanced StudyShenzhen UniversityShenzhenChina.

The division of organisms on the Tree of Life into either a three-domain(3D)tree or a two-domain(2D)tree has been disputed for a long time.Ever since the discovery of archaea by Carl Woese in 1977 using 16S ribosomal RNA sequence as the evolutionary marker,there has been a great advance in our knowledge of not only the growing diversity of archaea but also the evolutionary relationships between different lineages of living organisms.Here,we present this perspective to summarize the progress of archaeal diversity and changing notion of the Tree of Life.Meanwhile,we provide the latest progress in genomics/physiology-based discovery of Asgard archaeal lineages as the closest relative of Eukaryotes.Furthermore,we propose three major directions for future research on exploring the“next one”closest Eukaryote relative,deciphering the function of archaeal eukaryotic signature proteins and eukaryogenesis from both genomic and physiological aspects,and understanding the roles of horizontal gene transfer,viruses,and mobile elements in eukaryogenesis.

关键词： archaea Carl Woese eukaryogenesis Tree of Life

Response of ammonia-oxidizing archaea to heavy metal contamination in freshwater sediment

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Journal of Environmental Sciences 2019年第3期31卷 392-399页

作者： Ningning Li Yao Chen Zhengke Zhang Sha Chang Dawei Huang Sili Chen Qingwei Guo Shuguang Xie Yongxin Bing State Key Joint Laboratory of Environmental Simulation and Pollution Control College of Environmental Sciences and Engineering Peking University South China Institute of Environmental Sciences (SCIES) Ministry of Environment Protection (MEP)

It has been well-documented that the distribution of ammonia-oxidizing bacteria(AOB) and archaea(AOA) in soils can be affected by heavy metal contamination, whereas information about the impact of heavy metal on these ammonia-oxidizing microorganisms in freshwater sediment is still lacking. The present study explored the change of sediment ammonia-oxidizing microorganisms in a freshwater reservoir after being accidentally contaminated by industrial discharge containing high levels of metals. Bacterial amoA gene was found to be below the quantitative PCR detection and was not successfully amplified by conventional PCR. The number of archaeal amoA gene in reservoir sediments were 9.62 × 10~2–1.35 × 10~7 copies per gram dry sediment. AOA abundance continuously decreased, and AOA richness, diversity and community structure also considerably varied with time. Therefore, heavy metal pollution could have a profound impact on freshwater sediment AOA community. This work could expand our knowledge of the effect of heavy metal contamination on nitrification in natural ecosystems.

关键词： Ammonia-oxidizing archaea Freshwater sediment Heavy metal Nitrosopumilus

Microbiologically influenced corrosion of 304 stainless steel by halophilic archaea Natronorubrum tibetense

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Journal of Materials Science & Technology 2020年第11期42卷 12-20页

作者： Hongchang Qian Lingwei Ma Dawei Zhang Ziyu Li Luyao Huang Yuntian Lou Cuiwei Du Beijing Advanced Innovation Center for Materials Genome Engineering Institute for Advanced Materials and TechnologyUniversity of Science and Technology BeijingBeijing100083China

The corrosion behavior of 304 stainless steel(SS)in the presence of aerobic halophilic archaea Natronorubrum tibetense was investigated.After 14 days of immersion,no obvious pitting pit was observed on the SS surface in the sterile medium.By contrast,the SS exhibited serious pitting corrosion with the largest pit depth of 5.0μm in the inoculated medium after 14 days.The results of electrochemical tests showed that the barrier property of the passive film decreased faster in the inoculated medium.The X-ray photoelectron spectroscopy results indicated that the detrimental Fe2+and Cr6+increased in the passive film under the influence of archaea N.tibetense,which resulted in the accelerated deterioration of passive film and promoted the pitting corrosion.Combined with the energy starvation tests,the microbiologically influenced corrosion mechanism of 304 SS caused by halophilic archaea N.tibetense was discussed finally.

关键词： Stainless Steel archaea Microbiological influenced corrosion

Weaning methods affect ruminal methanogenic archaea composition and diversity in Holstein calves

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Journal of Integrative Agriculture 2019年第5期18卷 1080-1092页

作者： DONG Li-feng MA Jun-nan TU Yan DIAO Qi-yu Feed Research Institute Chinese Academy of Agricultural Sciences/Beijing Key Laboratory for Dairy Cow Nutrition/Key Laboratory of Feed Biotechnology Ministry of Agriculture

The objective of the present study was to examine the effect of different weaning methods on the ruminal methanogenic archaea composition and diversity in Holstein calves.Thirty-six newborn Holstein bull calves were assigned to 1 of 3 treatments:(1)conventional weaning(d 56)and fed a high proportion of solid feed(CWS);(2)conventional weaning(d 56)and fed a high proportion of liquid feed(CWL);(3)early weaning(d 42)and fed with a high proportion of solid feed(EWS).High-throughput sequencing of the methyl coenzyme M reductase(mcr A)gene,which encodes theα-subunit of methyl coenzyme M reductase-the enzyme that catalyzes the final step in methanogenesis was used to determine the composition and diversity of rumen methanogens.No significant difference(P>0.05)was observed for operational taxonomic units(OTUs)or richness indices,but diversity indices increased(P<0.05)for calves fed high dietary solids.Predominant families across the three treatments were Methanobacteriaceae,Thermoplasmataceae and Methanomassiliicoccaceae.Calves in the EWS treatment had a higher(P<0.05)relative abundance of Methanobrevibacter sp.strain AbM4 and Methanosphaera stadtmanae,while calves in the CWL treatment had a higher(P<0.05)abundance of Methanosphaera sp.strain SM9.A positive(P<0.05)relationship was identified between butyrate and Methanobrevibacter sp.strain AbM4.In conclusion,the composition and diversity of methanogens in the rumen of Holstein calves varied under the different weaning methods.This study identified a positive relationship between butyrate and Methanobrevibacter sp.strain AbM4,potentially reflecting correlations between ruminal fermentation variables and methanogenesis function.These in-depth analyses provide further understanding of weaning methods for intensified production systems.

关键词： calf methyl coenzyme M reductase(mcrA)gene methanogenic archaea diversity rumen fermentation weaning methods

archaea, the tree of life, and cellular evolution in eukaryotes

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Science China Earth Sciences 2019年第3期62卷 489-506页

作者： Jing XIAO Lu FAN Dingfeng WU Yanbing XU Dengxun LAI William F.MARTIN Ruixin ZHU Chuanlun ZHANG Department of Bioinformatics Tongji University Shenzhen Key Laboratory of Marine archaea Geo-Omics Department of Ocean Science and Engineering Southern University of Science and Technology SUSTech Academy for Advanced Interdisciplinary Studies Southern University of Science and Technology Institute of Molecular Evolution Heinrich-Heine-University Universit?tsstr.1 Laboratory for Marine Geology Qingdao National Laboratory for Marine Science and Technology

The early history of life harbours many unresolved evolutionary questions, none more important than the genomic origin and cellular evolution of eukaryotes. An issue central to eukaryote origin concerns the position of eukaryotes in the tree of life and the relationship of the host lineage that acquired the mitochondrion some two billion years ago to lineages of modern-day archaea. Recent analyses indicate that the host lineage branches within the archaea, prompting the search for novel archaeal lineages that can improve our understanding of the cellular evolution of eukaryotes. Here we give a brief review of the studies on archaea, the tree of life and the cellular evolution of eukaryotes, which is followed by an overview of recent progress fueled by new genomic technologies and recent status of archaeal research in China. Future directions for the study of early evolution are considered.

关键词： archaea Tree of life Cellular evolution of eukaryotes Metagenomics Bioinformatics

Shifts in community structure and function of ammoniaoxidizing archaea in biological soil crusts along a revegetation chronosequence in the Tengger Desert

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Research in Cold and Arid Regions 2019年第2期11卷 139-149页

作者： LiNa Zhao XinRong Li ShiWei Yuan YuBing Liu Shapotou Desert Research and Experiment Station Northwest Institute of Eco-Environment and Resources Chinese Academy of Sciences Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions of Gansu Province Northwest Institute of Eco-Environment and Resources Chinese Academy of Sciences University of Chinese Academy of Sciences Key Laboratory of Remote Sensing of Gansu Province Northwest Institute of Eco-Environment and Resources Chinese Academy of Sciences

Metagenomic studies have demonstrated the existence of ammonia-oxidizing archaea(AOA) and revealed they are responsible for ammoxidation in some extreme environments. However, the changes in compositional structure and ammonia-oxidation capacity of AOA communities in biological soil crusts(BSCs) of desert ecosystems remain poorly understood.Here, we utilized Illumina MiSeq sequencing and microbial functional gene array(GeoChip 5.0) to assess the above changes along a 51-year revegetation chronosequence in the Tengger Desert, China. The results showed a significant difference in AOA-community richness between 5-year-old BSCs and older ones. The most dominant phylum during BSC development was Crenarchaeota, and the corresponding species were ammonia-oxidizing_Crenarchaeote and environmental_samples_Crenarchaeota. Network analysis revealed that the positive correlations among dominant taxa increased, and their cooperation was reinforced in AOA communities during BSC succession. Redundancy analysis showed that the dominant factor influencing the change in AOA-community structure was soil texture. GeoChip 5.0 indicated that the amoA gene abundances of AOA and ammonia-oxidizing bacteria(AOB) were basically the same, demonstrating that AOA and AOB played an equally important role during BSCs development. Our study of the long-term succession of BSC demonstrated a persistent response of AOA communities to revegetation development in desert ecosystems.

关键词： ammonia-oxidizing archaea biological soil crusts GeoChip 5.0 network analysis

Diversity,metabolism and cultivation of archaea in mangrove ecosystems

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Marine Life Science & Technology 2021年第2期3卷 252-262页

作者： Cui-Jing Zhang Yu-Lian Chen Yi-Hua Sun Jie Pan Ming-Wei Cai Meng Li Shenzhen Key Laboratory of Marine Microbiome Engineering Institute for Advanced StudyShenzhen UniversityShenzhen518060China

Mangroves comprise a globally significant intertidal ecosystem that contains a high diversity of microorganisms,including fungi,bacteria and archaea.archaea is a major domain of life that plays important roles in biogeochemical cycles in these ecosystems.In this review,the potential roles of archaea in mangroves are briefly highlighted.Then,the diversity and metabolism of archaeal community of mangrove ecosystems across the world are summarized and Bathyarchaeota,Euryarchaeota,Thaumarchaeota,Woesearchaeota,and Lokiarchaeota are confirmed as the most abundant and ubiquitous archaeal groups.The metabolic potential of these archaeal groups indicates their important ecological function in carbon,nitrogen and sulfur cycling.Finally,some cultivation strategies that could be applied to uncultivated archaeal lineages from mangrove wetlands are suggested,including refinements to traditional cultivation methods based on genomic and transcriptomic information,and numerous innovative cultivation techniques such as single-cell isolation and high-throughput culturing(HTC).These cultivation strategies provide more opportunities to obtain previously uncultured archaea.

关键词： archaea Mangroves Cultivation Diversity Metabolisms

Potential coexistence of both bacterial and eukaryotic small RNA biogenesis and functional related protein homologs in archaea

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Journal of Genetics and Genomics 2010年第8期37卷 493-503页

作者： Yan Li Xiuying Liu Li Huang Huishan Guo Xiu-Jie Wang State Key Laboratory of Plant Genomics and National Center for Plant Gene Research Institute of Microbiology Chinese Academy of Sciences Beijing 100101 China State Key Laboratory of Plant Genomics Institute of Genetics and Developmental Biology Chinese Academy of Sciences Beijing 100101 China State Key Laboratory of Microbial Resources Institute of Microbiology Chinese Academy of Sciences Beijing 100101 China Graduate University of Chinese Academy of Sciences Beijing 100049 China

RNA silencing plays crucial roles in both bacteria and eukaryotes, yet its machinery appears to differ in these two kingdoms. A couple of Argonaute protein homologs have been reported in some archaeal species in recent years. As Argonaute protein is the key component of eukaryotic RNA silencing pathways, such findings suggested the possibility of existence of eukaryotic RNA silencing like pathways in archaea, which present the life forms between prokaryotes and eukaryotes. To further explore such hypothesis, we systematically screened 71 fully sequenced archaeal genomes, and identified some proteins containing homologous regions to the functional domains of eukaryotic RNA silencing pathway key proteins. The phylogenetic relationships of these proteins were analyzed. The conserved functional amino acids between archaeal and eukaryotic Piwi domains suggested their fimctional similarity. Our results provide new clues to the evolution of RNA silencing pathways.

关键词： archaea small RNA RNA silencing Piwi RNase Ill

Community diversity and distribution of ammonia-oxidizing archaea in marsh wetlands in the black soil zone in North-east China

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Frontiers of Environmental Science & Engineering 2019年第4期13卷 123-138页

作者： Chunhong Chen Hong Liang Dawen Gao State Key Laboratory of Urban Water Resource and Environment Harbin Institute of TechnologyHarbin 150090China School of Environment Harbin Institute of TechnologyHarbin 150090China

Since its first detection, ammonia-oxidizing archaea (AOA) have been proven to be ubiquitous in aquatic and terrestrial ecosystems. In this study, two freshwater marsh wetlands- the Honghe wetland and Qixinghe wetland - in the black soil zone in North-east China were chosen to investigate the AOA community diversity and distribution in wetland soils with different vegetation and depth. In the Honghe wetland, two sampling locations were chosen as the dominant plant transited from Deyeuxia to Carex. In the Qixinghe wetland, one sample location that was dominated by Deyeuxia was chosen. Samples of each location were collected from three different depths, and Illumina MiSeq platform was used to generate the AOA amoA gene archive. The results showed that the AOA amoA genes in the soils of the two wetlands were affiliated with three lineages: Nitrososphaera, Nitrosotalea, and Nitrosopumilus clusters. The different dominant status of these AOA lineages indicated their differences in adapting to acidic habitat, oxygenic/hypoxic alternation, organic matter, and other environmental factors, suggesting high diversity among AOA in marsh soils. The main driver of the AOA community was pH, along with organic carbon and ammonium nitrogen, which also played an important role combined with many other environmental factors. Thus, soil physiochemical characteristics, rather than vegetation, were the main cause of AOA community diversity in the wetlands in the black soil zone in China.

关键词： Ammonia-oxidizing archaea amoA gene Freshwater marsh Diversity Distribution