Archaea are an understudied component of the human microbiome.In this study,the gut archaeome and bacteriome of 60 healthy adults from different region were analyzed by whole-genome shotgun sequencing.Archaea were ubi...Archaea are an understudied component of the human microbiome.In this study,the gut archaeome and bacteriome of 60 healthy adults from different region were analyzed by whole-genome shotgun sequencing.Archaea were ubiquitously found in a wide range of abundances,reaching up to 7.2%.The dominant archaeal phylum was Methanobacteriota,specifically the family Methanobacteriaceae,encompassing more than 50%of Archaea in 50 samples.The previously underestimated Thermoplasmatota,mostly composed of Methanomassiliicoccaceae,dominated in 10 subjects(>50%)and was present in all others except one.Halobacteriota,the sole other archaeal phylum,occurred in negligible concentration,except for two samples(4.6-4.8%).This finding confirmed that the human gut archaeome is primarily composed of methanogenic organisms and among the known methanogenic pathway:i)hydrogenotrophic reduction of CO_(2) is the predominant,being the genus Methanobrevibacter and the species Methanobrevibacter smithii the most abundant in the majority of the samples;ii)the second pathway,that involved Methanomassiliicoccales,was the hydrogenotrophic reduction of methyl-compounds;iii)dismutation of acetate or methyl-compounds seemed to be absent.Co-occurrence analysis allowed to unravel correlations between Archaea and Bacteria that shapes the overall structure of the microbial community,allowing to depict a clearer picture of the human gut archaeome.展开更多
With 85% of the global oyster reefs destroyed, there is an urgent need for large scale restoration to benefit from the ecosystem services provided by biogenic oyster reefs and their associated biodiversity, including ...With 85% of the global oyster reefs destroyed, there is an urgent need for large scale restoration to benefit from the ecosystem services provided by biogenic oyster reefs and their associated biodiversity, including microorganisms that drive marine biogeochemical cycles. This experiment established a baseline for the monitoring of the bacterial and archaeal community associated with wild oysters, using samples from their immediate environment of the Voordelta, with cohabiting Crassostrea gigas and Ostrea edulis, Duikplaats with only C. gigas attached to rocks, and the Dansk Skaldyrcentre, with no onsite oysters. The microbial profiling was carried out through DNA analysis of samples collected from the surfaces of oyster shells and their substrate, the sediment and seawater. Following 16S rRNA amplicon sequencing and bioinformatics, alpha indices implied high species abundance and diversity in sediment but low abundance in seawater. As expected, Proteobacteria, Bacteroidetes, Firmicutes and Thaumarchaeota dominated the top 20 OTUs. In the Voordelta, OTUs related to Colwellia, Shewanella and Psychrobium differentiated the oysters collected from a reef with those attached to rocks. Duikplaats were distinct for sulfur-oxidizers Sulfurimonas and sulfate-reducers from the Sva 0081 sediment group. Archaea were found mainly in sediments and the oyster associated microbiome, with greater abundance at the reef site, consisting mostly of Thaumarchaeota from the family Nitrosopumilaceae. The oyster free site displayed archaea in sediments only, and algal bloom indicator microorganisms from the Rhodobacteraceae, Flavobacteriaceae family and genus [Polaribacter] huanghezhanensis, in addition to the ascidian symbiotic partner, Synechococcus. This study suggests site specific microbiome shifts, influenced by the presence of oysters and the type of substrate.展开更多
Soil microbial communities are pivotal in permafrost biogeochemical cycles,yet the variations of abundant and rare microbial taxa and their impacts on greenhouse gas emissions in different seasons,remain elusive,espec...Soil microbial communities are pivotal in permafrost biogeochemical cycles,yet the variations of abundant and rare microbial taxa and their impacts on greenhouse gas emissions in different seasons,remain elusive,especially in the case of soil archaea.Here,we conducted a study on soil abundant and rare archaeal taxa during the growing and non-growing seasons in the active layer of alpine permafrost in the Qinghai-Tibetan Plateau.The results suggested that,for the archaeal communities in the sub-layer,abundant taxa exhibited higher diversity,while rare taxa maintained a more stable composition from the growing to non-growing season.Water soluble organic carbon and soil porosity were the most significant environmental variables affecting the compositions of abundant and rare taxa,respectively.Stochastic and deterministic processes dominated the assemblies of rare and abundant taxa,respectively.The archaeal ecological network influenced N_(2)O flux through different modules.Rare taxa performed an essential role in stabilizing the network and exerting important effects on N_(2)O flux.Our study provides a pioneering and comprehensive investigation aimed at unravelling the mechanisms by which archaea or other microorganisms influence greenhouse gas emissions in the alpine permafrost.展开更多
Subterranean estuaries(STEs)are characterized by the mixing of terrestrial fresh groundwater and seawater in coastal aquifers.Although microorganisms are important components of coastal groundwater ecosystems and play...Subterranean estuaries(STEs)are characterized by the mixing of terrestrial fresh groundwater and seawater in coastal aquifers.Although microorganisms are important components of coastal groundwater ecosystems and play critical roles in biogeochemical transformations in STEs,limited information is available about how their community dynamics interact with hydrological,geochemical and environmental characteristics in STEs.Here,we studied bacterial and archaeal diversities and distributions with 16S rRNA-based Illumina MiSeq sequencing technology between surface water and groundwater in a karstic STE.Principal-coordinate analysis found that the bacterial and archaeal communities in the areas where algal blooms occurred were significantly separated from those in other stations without algal bloom occurrence.Canonical correspondence analysis showed that nutrients and salinity can explain the patterns of bacterial and archaeal community dynamics.The results suggest that hydrological,geochemical and environmental characteristics between surface water and groundwater likely control the bacterial and archaeal diversities and distributions in STEs.Furthermore,we found that some key species can utilize terrestrial pollutants such as nitrate and ammonia in STEs,indicating that these species(e.g.,Nitrosopumilus maritimus,Limnohabitans parvus and Simplicispira limi)may be excellent candidates for in situ degradation/remediation of coastal groundwater contaminations concerned with the nitrate and ammonia.Overall,this study reveals the coupling relationship between the microbial communities and hydrochemical environments in STEs,and provides a perspective of in situ degradation/remediation for coastal groundwater quality management.展开更多
The apparent sulfur oxidation activities of four pure thermophilic archaea, Acidianus brierleyi （JCM 8954）, Metallosphaera sedula （YN 23）, Acidianus manzaensis （YN 25） and Sulfolobus metallicus （YN 24） and the...The apparent sulfur oxidation activities of four pure thermophilic archaea, Acidianus brierleyi （JCM 8954）, Metallosphaera sedula （YN 23）, Acidianus manzaensis （YN 25） and Sulfolobus metallicus （YN 24） and their mixture in bioleaching chalcopyrite were compared, which were characterized indirectly by the evolution of the cells concentration, pH value and sulfate ions concentration in solution. The results show that the mixed culture contributed significantly to the raising of leaching rate, which suggests that the mixed culture had a higher sulfur oxidation activity than the pure culture. Meanwhile, the results also indicate that the changes of parameters characterizing the sulfur oxidation activity of thermophilic archaea are often influenced by many factors, so it is hard to reflect accurately the specific sulfur oxidation activities among the different sulfur-oxidizing microbes when bioleaching chalcopyrite at different conditions. Accordingly, an efficient method to characterize microbial sulfur oxidation activity appears to be desirable.展开更多
基金partially funded by PIANO NAZIONALE DI RIPRESA E RESILIENZA(PNRR)-MISSIONE 4 COMPONENTE 2,“Dalla ricerca all’impresa”INVESTIMENTO 1.3,Creazione di“Partenariati estesi alle universita,ai centri di ricerca,alle aziende per il finanziamento di progetti di ricerca di base”,finanziato dall’Unione europea-NextGenerationEU”-Progetto identificato con codice PE00000019,Titolo“HEAL ITALIA”-Spoke 5-CUP E93C22001860006 Avviso MUR DD.341 del 15.03.2022.
文摘Archaea are an understudied component of the human microbiome.In this study,the gut archaeome and bacteriome of 60 healthy adults from different region were analyzed by whole-genome shotgun sequencing.Archaea were ubiquitously found in a wide range of abundances,reaching up to 7.2%.The dominant archaeal phylum was Methanobacteriota,specifically the family Methanobacteriaceae,encompassing more than 50%of Archaea in 50 samples.The previously underestimated Thermoplasmatota,mostly composed of Methanomassiliicoccaceae,dominated in 10 subjects(>50%)and was present in all others except one.Halobacteriota,the sole other archaeal phylum,occurred in negligible concentration,except for two samples(4.6-4.8%).This finding confirmed that the human gut archaeome is primarily composed of methanogenic organisms and among the known methanogenic pathway:i)hydrogenotrophic reduction of CO_(2) is the predominant,being the genus Methanobrevibacter and the species Methanobrevibacter smithii the most abundant in the majority of the samples;ii)the second pathway,that involved Methanomassiliicoccales,was the hydrogenotrophic reduction of methyl-compounds;iii)dismutation of acetate or methyl-compounds seemed to be absent.Co-occurrence analysis allowed to unravel correlations between Archaea and Bacteria that shapes the overall structure of the microbial community,allowing to depict a clearer picture of the human gut archaeome.
文摘With 85% of the global oyster reefs destroyed, there is an urgent need for large scale restoration to benefit from the ecosystem services provided by biogenic oyster reefs and their associated biodiversity, including microorganisms that drive marine biogeochemical cycles. This experiment established a baseline for the monitoring of the bacterial and archaeal community associated with wild oysters, using samples from their immediate environment of the Voordelta, with cohabiting Crassostrea gigas and Ostrea edulis, Duikplaats with only C. gigas attached to rocks, and the Dansk Skaldyrcentre, with no onsite oysters. The microbial profiling was carried out through DNA analysis of samples collected from the surfaces of oyster shells and their substrate, the sediment and seawater. Following 16S rRNA amplicon sequencing and bioinformatics, alpha indices implied high species abundance and diversity in sediment but low abundance in seawater. As expected, Proteobacteria, Bacteroidetes, Firmicutes and Thaumarchaeota dominated the top 20 OTUs. In the Voordelta, OTUs related to Colwellia, Shewanella and Psychrobium differentiated the oysters collected from a reef with those attached to rocks. Duikplaats were distinct for sulfur-oxidizers Sulfurimonas and sulfate-reducers from the Sva 0081 sediment group. Archaea were found mainly in sediments and the oyster associated microbiome, with greater abundance at the reef site, consisting mostly of Thaumarchaeota from the family Nitrosopumilaceae. The oyster free site displayed archaea in sediments only, and algal bloom indicator microorganisms from the Rhodobacteraceae, Flavobacteriaceae family and genus [Polaribacter] huanghezhanensis, in addition to the ascidian symbiotic partner, Synechococcus. This study suggests site specific microbiome shifts, influenced by the presence of oysters and the type of substrate.
基金This work was supported by Gansu Provincial Science and Technology Program(22ZD6FA005)"Light of the West"Cross-team Project of the Chinese Academy of Sciences(xbzgzdsys-202214)+1 种基金the National Natural Science Foundation of China(41871064)Qinghai Province High-level Innovative"Thousand Talents"Program.
文摘Soil microbial communities are pivotal in permafrost biogeochemical cycles,yet the variations of abundant and rare microbial taxa and their impacts on greenhouse gas emissions in different seasons,remain elusive,especially in the case of soil archaea.Here,we conducted a study on soil abundant and rare archaeal taxa during the growing and non-growing seasons in the active layer of alpine permafrost in the Qinghai-Tibetan Plateau.The results suggested that,for the archaeal communities in the sub-layer,abundant taxa exhibited higher diversity,while rare taxa maintained a more stable composition from the growing to non-growing season.Water soluble organic carbon and soil porosity were the most significant environmental variables affecting the compositions of abundant and rare taxa,respectively.Stochastic and deterministic processes dominated the assemblies of rare and abundant taxa,respectively.The archaeal ecological network influenced N_(2)O flux through different modules.Rare taxa performed an essential role in stabilizing the network and exerting important effects on N_(2)O flux.Our study provides a pioneering and comprehensive investigation aimed at unravelling the mechanisms by which archaea or other microorganisms influence greenhouse gas emissions in the alpine permafrost.
基金The National Key R&D Program of China under contract No.2022YFE0209300the National Natural Science Foundation of China under contract No.42006152+1 种基金the Zhejiang Provincial Natural Science Foundation of China under contract No.LQ21D060005the 111 Project under contract No.BP0820020.
文摘Subterranean estuaries(STEs)are characterized by the mixing of terrestrial fresh groundwater and seawater in coastal aquifers.Although microorganisms are important components of coastal groundwater ecosystems and play critical roles in biogeochemical transformations in STEs,limited information is available about how their community dynamics interact with hydrological,geochemical and environmental characteristics in STEs.Here,we studied bacterial and archaeal diversities and distributions with 16S rRNA-based Illumina MiSeq sequencing technology between surface water and groundwater in a karstic STE.Principal-coordinate analysis found that the bacterial and archaeal communities in the areas where algal blooms occurred were significantly separated from those in other stations without algal bloom occurrence.Canonical correspondence analysis showed that nutrients and salinity can explain the patterns of bacterial and archaeal community dynamics.The results suggest that hydrological,geochemical and environmental characteristics between surface water and groundwater likely control the bacterial and archaeal diversities and distributions in STEs.Furthermore,we found that some key species can utilize terrestrial pollutants such as nitrate and ammonia in STEs,indicating that these species(e.g.,Nitrosopumilus maritimus,Limnohabitans parvus and Simplicispira limi)may be excellent candidates for in situ degradation/remediation of coastal groundwater contaminations concerned with the nitrate and ammonia.Overall,this study reveals the coupling relationship between the microbial communities and hydrochemical environments in STEs,and provides a perspective of in situ degradation/remediation for coastal groundwater quality management.
基金Project(50974140) supported by the National Natural Science Foundation of ChinaProject(20090162110054) supported by Specialized Research Fund for the Doctoral Program of Higher Education of China
文摘The apparent sulfur oxidation activities of four pure thermophilic archaea, Acidianus brierleyi （JCM 8954）, Metallosphaera sedula （YN 23）, Acidianus manzaensis （YN 25） and Sulfolobus metallicus （YN 24） and their mixture in bioleaching chalcopyrite were compared, which were characterized indirectly by the evolution of the cells concentration, pH value and sulfate ions concentration in solution. The results show that the mixed culture contributed significantly to the raising of leaching rate, which suggests that the mixed culture had a higher sulfur oxidation activity than the pure culture. Meanwhile, the results also indicate that the changes of parameters characterizing the sulfur oxidation activity of thermophilic archaea are often influenced by many factors, so it is hard to reflect accurately the specific sulfur oxidation activities among the different sulfur-oxidizing microbes when bioleaching chalcopyrite at different conditions. Accordingly, an efficient method to characterize microbial sulfur oxidation activity appears to be desirable.
