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
This study was conducted to investigate the phylogenetic diversity of archaea in the rumen of adult and elderly yaks. Six domesticated female yaks, 3 adult yaks （（5.3±0.6） years old）, and 3 elderly yaks （（1...This study was conducted to investigate the phylogenetic diversity of archaea in the rumen of adult and elderly yaks. Six domesticated female yaks, 3 adult yaks （（5.3±0.6） years old）, and 3 elderly yaks （（10.7±0.6） years old）, were used for the rumen contents collection. Illumina MiSeq high-throughput sequencing technology was applied to examine the archaeal composition of rumen contents. A total of 92 901 high-quality archaeal sequences were analyzed, and these were assigned to 2 033 operational taxonomic units （OTUs）. Among these, 974 OTUs were unique to adult yaks while 846 OTUs were unique to elderly yaks; 213 OTUs were shared by both groups. At the phylum level, more than 99% of the obtained OTUs belonged to the Euryarchaeota phylum. At the genus level, the archaea could be divided into 7 archaeal genera. The 7 genera （i.e., Methanobrevibacter, Methanobacterium, Methanosphaera, Thermogymnomonas, Methanomicrobiu, Meth- animicrococcus and the unclassified genus） were shared by all yaks, and their total abundance accounted for 99% of the rumen archaea. The most abundant archaea in elderly and adult yaks were Methanobrevibacterand Thermogymnomonas, respectively. The abundance of Methanobacteria （class）, Methanobacteriales （order）, Methanobacteriaceae （family）, and Methanobrevibacter （genus） in elderly yaks was significantly higher than in adult yaks. In contrast, the abundance of Ther-mogymnomonas in elderly yaks was 34% lower than in adult yaks, though the difference was not statistically significant. The difference in abundance of other archaea was not significant between the two groups. These results suggested that the structure of archaea in the rumen of yaks changed with age. This is the first study to compare the phytogenetic differences of rumen archaeal structure and composition using the yak model.展开更多
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 a...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.展开更多
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.
基金the International Cooperation Project of the Ministry of Sciences and Technology of China(2014DFA32860)the National Natural Science Foundation of China(31402104)for their financial support
文摘This study was conducted to investigate the phylogenetic diversity of archaea in the rumen of adult and elderly yaks. Six domesticated female yaks, 3 adult yaks （（5.3±0.6） years old）, and 3 elderly yaks （（10.7±0.6） years old）, were used for the rumen contents collection. Illumina MiSeq high-throughput sequencing technology was applied to examine the archaeal composition of rumen contents. A total of 92 901 high-quality archaeal sequences were analyzed, and these were assigned to 2 033 operational taxonomic units （OTUs）. Among these, 974 OTUs were unique to adult yaks while 846 OTUs were unique to elderly yaks; 213 OTUs were shared by both groups. At the phylum level, more than 99% of the obtained OTUs belonged to the Euryarchaeota phylum. At the genus level, the archaea could be divided into 7 archaeal genera. The 7 genera （i.e., Methanobrevibacter, Methanobacterium, Methanosphaera, Thermogymnomonas, Methanomicrobiu, Meth- animicrococcus and the unclassified genus） were shared by all yaks, and their total abundance accounted for 99% of the rumen archaea. The most abundant archaea in elderly and adult yaks were Methanobrevibacterand Thermogymnomonas, respectively. The abundance of Methanobacteria （class）, Methanobacteriales （order）, Methanobacteriaceae （family）, and Methanobrevibacter （genus） in elderly yaks was significantly higher than in adult yaks. In contrast, the abundance of Ther-mogymnomonas in elderly yaks was 34% lower than in adult yaks, though the difference was not statistically significant. The difference in abundance of other archaea was not significant between the two groups. These results suggested that the structure of archaea in the rumen of yaks changed with age. This is the first study to compare the phytogenetic differences of rumen archaeal structure and composition using the yak model.
基金supported by the Key Program for International S&T Cooperation Projects of China(2016YFE0109000)the National Key R&D Program of China(2017YFF0211702)+1 种基金the National Natural Science Foundation of China(41475126 and 31802085)the Young Scientist Lifting Project,China(2017–2019)
文摘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.
