The response of archaeal communities to petroleum contamination in saline-alkali soil was characterized by analyses of three soil samples with different total petroleum hydrocarbon concentrations.Through the construct...The response of archaeal communities to petroleum contamination in saline-alkali soil was characterized by analyses of three soil samples with different total petroleum hydrocarbon concentrations.Through the construction and screening of 16S rRNA gene clone libraries based on DNA extracts from these soils,nine distinct phylogenetic groups were identified.Statistical analyses showed that the distribution of archaeal community structures differ significantly along the gradient of petroleum contamination in these three saline- alkali soils.Five phylogenetic groups were dominant in the control soil,two of which were also abundant in the lightly contaminated soil.Four phylogenetic groups were dominant in heavily contaminated soil,one of which was also abundant in the lightly contaminated soil.The halophilic genus of Haloferax and the haloalkaliphilic genus of Natronomonas were more abundant in heavily contaminated soil.These results suggested that the genera of Haloferax and Natronomonas may have a role in the natural attenuation of petroleum- contaminated saline-alkali soil.展开更多
The effects of different concentrations of oxytetracycline （OTC） on the dynamics of bacterial and archaeal communities during the mesophilic anaerobic digestion （37＆#176;C） of cow manure were investigated. Before...The effects of different concentrations of oxytetracycline （OTC） on the dynamics of bacterial and archaeal communities during the mesophilic anaerobic digestion （37＆#176;C） of cow manure were investigated. Before anaerobic digestion, OTC was added to digesters at concentrations of 20, 50, and 80 mg L-1, respectively. Compared with no-antibiotic control, all methane productions underwent different levels of inhibition at different concentrations of OTC. Changes in the bacterial and archaeal communities were discussed by using PCR-denaturing gradient gel electrophoresis （DGGE）. Results showed that OTC affected the richness and diversity of bacterial and archaeal communities. The bacterial genus Flavobacterium and an uncultured bacterium （JN256083.1） were detected throughout the entire process of anaerobic digestion and seemed to be the functional bacteria. Methanobrevibacter boviskoreani and an uncultured archaeon （FJ230982.1） dominated the archaeal communities during anaerobic digestion. These microorganisms may have high resistance to OTC and may play vital roles in methane production.展开更多
Saccharolobus islandicus REY15A represents one of the very few archaeal models with versatile genetic tools,which include efficient genome editing,gene silencing,and robust protein expression systems.However,plasmid v...Saccharolobus islandicus REY15A represents one of the very few archaeal models with versatile genetic tools,which include efficient genome editing,gene silencing,and robust protein expression systems.However,plasmid vectors constructed for this crenarchaeon thus far are based solely on the pRN2 cryptic plasmid.Although this plasmid coexists with pRN1 in its original host,early attempts to test pRN1-based vectors consistently failed to yield any stable host-vector system for Sa.islandicus.We hypothesized that this failure could be due to the occurrence of CRISPR immunity against pRN1 in this archaeon.We identified a putative target sequence in orf904 encoding a putative replicase on pRN1(target N1).Mutated targets(N1a,N1b,and N1c)were then designed and tested for their capability to escape the host CRISPR immunity by using a plasmid inter-ference assay.The results revealed that the original target triggered CRISPR immunity in this archaeon,whereas all three mutated targets did not,indicating that all the designed target mutations evaded host immunity.These mutated targets were then incorporated into orf904 individually,yielding corresponding mutated pRN1 backbones with which shuttle plasmids were constructed(pN1aSD,pN1bSD,and pN1cSD).Sa.islandicus transformation revealed that pN1aSD and pN1bSD were functional shuttle vectors,but pN1cSD lost the capability for replication.These results indicate that the missense mutations in the conserved helicase domain in pN1c inactivated the replicase.We further showed that pRN1-based and pRN2-based vectors were stably maintained in the archaeal cells either alone or in combination,and this yielded a dual plasmid system for genetic study with this important archaeal model.展开更多
It is important to understand the effects of temporal changes in microbial communities in the acidic soils of tea orchards with different fertilizers. A field experiment involving organic fertilizer （OF）, chemical f...It is important to understand the effects of temporal changes in microbial communities in the acidic soils of tea orchards with different fertilizers. A field experiment involving organic fertilizer （OF）, chemical fertilizer （CF）, and unfertilized control （CK） treatments was arranged to analyze the temporal changes in the bacterial and archaeal communities at bimonthly intervals based on the 16S ribosomal RNA （rRNA） gene using terminal restriction fragment length polymorphism （T-RFLP） profiling. The abundances of total bacteria, total archaea, and selected functional genes （bacterial and archaeal amoA, bacterial narG, nirK, nirS, and nosZ） were determined by quantitative poly- merase chain reaction （qPCR）. The results indicate that the structures of bacterial and archaeal communities varied significantly with time and fertilization based on changes in the relative abundance of dominant T-RFs. The abundancy of the detected genes changed with time. The total bacteria, total archaea, and archaeal amoA were less abundant in July. The bacterial amoA and denitrifying genes were less abundant in September, except the nirK gene. The OF treatment increased the abundance of the observed genes, while the CF treatment had little influence on them. The soil temperature significantly affected the bacterial and archaeal community structures. The soil moisture was signif- icantly correlated with the abundance of denitrifying genes. Of the soil chemical properties, soil organic carbon was the most important factor and was significantly correlated with the abundance of the detected genes, except the nirK gene. Overall, this study demonstrated the effects of both temporal alteration and organic fertilizer on the structures of mi- crobial communities and the abundance of genes involved in the nitrogen cycle.展开更多
Biofilm formation, one of the primary causes of biofouling, results in reduced membrane flux or increased transmembrane pressure and thus represents a major impediment to the wider implementation of membrane bioreact...Biofilm formation, one of the primary causes of biofouling, results in reduced membrane flux or increased transmembrane pressure and thus represents a major impediment to the wider implementation of membrane bioreactor （MBR） technologies for water purification. Most studies have focused on the role of bacteria in membrane fouling as they are the most dominant and best studied organisms present in the MBR. In contrast, there is limited information on the role of the archaeal community in biofilm formation in MBRs. This study investigated the composition of the archaeal community during the process of biofouling in an MBR. The archaeal community was observed to have lower richness and diversity in the biofilm than the sludge during the establishment ofbiofilms at low transmembrane pressure （TMP）. Clustering of the communities based on the Bray-Curtis similarity matrix indicated that a subset of the sludge archaeal community formed the initial biofilms. The archaeal community in the biofilm was mainly composed of Thermoprotei, Thermoplasmata, Thermococci, Methanopyri, Methanomicrobia and Halobacteria. Among them, the Thermoprotei and Thermoplasmata were present at higher relative proportions in the biofilms than they were in the sludge. Additionally, the Thermoprotei, Thermoplasmata and Thermococci were the dominant organisms detected in the initial biofilms at low TMP, while as the TMP increased, the Methanopyri, Methanomicrobia, Aciduliprofundum and Halobacteria were present at higher abundances in the biofilms at high TMP.展开更多
Anthropogenic activities usually contaminate water environments, and have led to the eutrophication of many estuaries and shifts in microbial communities. In this study, the temporal and spatial changes of the microbi...Anthropogenic activities usually contaminate water environments, and have led to the eutrophication of many estuaries and shifts in microbial communities. In this study, the temporal and spatial changes of the microbial community in an industrial effluent receiving area in Hangzhou Bay were investigated by 454 pyrosequencing. The bacterial community showed higher richness and biodiversity than the archaeal community in all sediments. Proteobacteria dominated in the bacterial communities of all the samples; MarineGroupⅠand Methanomicrobia were the two dominant archaeal classes in the effluent receiving area. PCoA and AMOVA revealed strong seasonal but minor spatial changes in both bacterial and archaeal communities in the sediments. The seasonal changes of the bacterial community were less significant than those of the archaeal community, which mainly consisted of fluctuations in abundance of a large proportion of longstanding species rather than the appearance and disappearance of major archaeal species. Temperature was found to positively correlate with the dominant bacteria, Betaproteobacteria, and negatively correlate with the dominant archaea,MarineGroupⅠ; and might be the primary driving force for the seasonal variation of the microbial community.展开更多
Seamounts are subsurface mountains in the ocean. Examination of the abundance and distribution of Archaea in seamount ecosystems may provide a better understanding of their ecological functions. Most studies of marine...Seamounts are subsurface mountains in the ocean. Examination of the abundance and distribution of Archaea in seamount ecosystems may provide a better understanding of their ecological functions. Most studies of marine archaeal assemblages in seamount area have focused on hydrothermal vents or ferromanganese crusts. We investigated the archaeal communities from a seamount of the Mariana Volcanic Arc, in the tropical western Pacific Ocean by using high-throughput sequencing. Thaumarchaeota was dominant in the sediments of all sample stations. Community diversity and species richness were greatest at stations near the top of the seamount, and lowest at the deepest station. One sample station on the steep southeast slope that faced the Yap-Mariana trench had a unique composition of Archaea. In summary, depth has an important influence on archaeal community structure, and the geographic properties and sediment characteristics may explain the unique distribution patterns of Archaea in this seamount. This study provides a foundation for future research on Archaea in seamounts.展开更多
Oxidative stress induced by factors such as ammonia nitrogen has become a major issue in shrimp farming.The effects of carotenoids on the growth and antioxidant capability of Litopenaeus vannamei juveniles were invest...Oxidative stress induced by factors such as ammonia nitrogen has become a major issue in shrimp farming.The effects of carotenoids on the growth and antioxidant capability of Litopenaeus vannamei juveniles were investigated in this study using dietary archaeal carotenoids supplementation.For four weeks,shrimp were given diets containing 0 mg/kg(Ctrl)and 55.98 mg/kg(Car)archaeal carotenoids.Dietary archaeal carotenoids significantly enhanced the astaxanthin content in shrimp muscles and carapaces,as well as the superoxide dismutase(SOD)and glutathione peroxidase(GSH-Px)activity(P<0.05).The malonaldehyde(MDA)content in Car group significantly decreased(P<0.05).The transcriptome analysis was conducted to determine the molecular processes in response to archaeal carotenoids supplementation.A total of 1536 differentially expressed genes(DEGs)were detected,including 538 upregulated DEGs and 998 downregulated DEGs.GO functional enrichment analysis between Ctrl and Car indicated that 26 GO terms including extracellular region,metabolic process,and proteolysis were enriched.The KEGG pathway enrichment analysis revealed that the amino sugar and nucleotide sugar metabolism,cysteine and methionine metabolism,glycine serine and threonine metabolism,and amino acid biosynthesis were enriched.Archaeal carotenoids influenced the expression of several important genes involved in reactive oxygen species(ROS)generation,Nrf2 signaling,and antioxidant enzymes.Seven DEGs were chosen to confirm the RNA-Seq data using qRT-PCR.The genes and pathways discovered in this work assist to elucidate the molecular processes through which archaeal carotenoid enhances L.vannamei antioxidative system.展开更多
This paper reports the recent findings related to the stability properties of tetraether lipid layers. Organizations moleculars of chemical structure modified of Langmuir-Blodgett layers of archael tetraether lipids f...This paper reports the recent findings related to the stability properties of tetraether lipid layers. Organizations moleculars of chemical structure modified of Langmuir-Blodgett layers of archael tetraether lipids from the archebacterium Sulfolobus acidocaldarius on the wafer silicon substrates are investigated stable and organized. The behavior of Langmuir-Blodgett layers of chemical structure modified of archaeal tetraether lipids on the wafer silicon substrates is characterization using Differential Scanning Calorimetry (DSC) and Atomic Force Microscopy (AFM). The thermodynamics behavior and stability of Langmuir-Blodgett layers of archael tetraether lipids on the wafer silicon substrates are shown. Stability of the lipid membranes is of great importance to a number of biomedical applications, including intravenous drug delivery, biomaterials, and biosensors.展开更多
Archaea regulate the biogeochemical processes of ocean systems.The Changjiang(Yangtze)River estuary(CRE) is a complex and dynamic area strongly affected by seawaters and ocean currents.In this study,the planktonic arc...Archaea regulate the biogeochemical processes of ocean systems.The Changjiang(Yangtze)River estuary(CRE) is a complex and dynamic area strongly affected by seawaters and ocean currents.In this study,the planktonic archaeal communities in the surface and bottom seawaters of the CRE were investigated.Significant differences in the archaeal community composition were found between the surface and bottom seawaters(P<0.001).Marine Group Ⅱ(MG-Ⅱ) was dominant in the surface layers,and Nitrosopumilales was enriched in the bottom layers.Marine Group Ⅲ(MG-Ⅲ) was more abundant in the bottom layers than in the surface ones(P<0.001).These results were completely different from previous findings in the CRE seawater.Instead of dissolved oxygen(DO),temperature and salinity were the most vital environmental variations in the distribution of the archacal communities.According to the predicted metabolic pathways,the following functional subcategories were enriched in the hypoxic condition:replication and repair,membrane transport,glycan biosynthesis and metabolism,amino acid metabolism,metabolism of cofactors and vitamins,and xenobiotics biodegradation and metabolism(P<0.001),which indicated the strong adaptability of archaea to the harsh environment in the bottom seawater.These findings expand the understanding on archaeal structure and functions in the surface and bottom seawaters,including the hypoxic zones in the CRE,and may contribute to further works of the archaeal community in the CRE.展开更多
Polycyclic aromatic hydrocarbons(PAHs)often occur in oil-contaminated soil,coke wastewater and domestic sludge;however,associated PAH degraders in these environments are not clear.Here we evaluated phenanthrene degrad...Polycyclic aromatic hydrocarbons(PAHs)often occur in oil-contaminated soil,coke wastewater and domestic sludge;however,associated PAH degraders in these environments are not clear.Here we evaluated phenanthrene degradation potential in the mixed samples of above environments,and obtained a methanogenic community with different microbial profile compared to those from sediments.Phenanthrene was efficiently degraded(1.26 mg/L/d)and nonstoichiometric amount of methane was produced simultaneously.16S rRNA gene sequencing demonstrated that bacterial populations were mainly associated with Comamonadaceae Nocardiaceae and Thermodesulfobiaceae,and that methanogenic archaea groups were dominated by Methanobacterium and Methanothermobacter.Substances such as hexane,hexadecane,benzene and glucose showed the most positive effects on phenanthrene degradation.Substrate utilization tests indicated that this culture could not utilize other PAHs.These analyses could offer us some suggestions on the putative phenanthrene-degrading microbes in such environments,and might help us develop strategies for the removal of PAHs from contaminated soil and sludge.展开更多
Hadal trenches are the least explored marine habitat on earth. Archaea has been shown to be the dominant group in trench sediments. However, the activity potentials and detailed diversity of these communities as well ...Hadal trenches are the least explored marine habitat on earth. Archaea has been shown to be the dominant group in trench sediments. However, the activity potentials and detailed diversity of these communities as well as their inter-trench variations are still not known. In this study, we combined datasets from two pairs of primers to investigate at high resolution the structure and activity potentials of the archaeal communities in vertically sectioned sediment cores taken from the deepest points of the Mariana (10,853 m) and Mussau (7011 m) trenches. The compositions of the potentially active communities revealed, via 16S ribosomal RNA gene (rDNA) and RNA (rRNA), significant differences between samples. Marine Group I (MGI), with nine identified subgroups, was the most dominant class in the active archaeal communities of the two trenches. Significantly different species composition and vertical variations were observed between the two trenches. Vertical transitions from aerobic MGI α to anaerobic MGI η and υ subgroups were observed in MST but not in MT sediments, which might be related to the faster microbial oxygen consumption in MST. These results provide a better understanding on archaeal activity and diversity in trench sediments.展开更多
Euryarchaeota and Crenarchaeota, the two main lineages of the domain Archaea, encode different chromatin proteins and differ in the use of replicative DNA polymerases. Crenarchaea possess a single family B DNA polymer...Euryarchaeota and Crenarchaeota, the two main lineages of the domain Archaea, encode different chromatin proteins and differ in the use of replicative DNA polymerases. Crenarchaea possess a single family B DNA polymerase(Pol B), which is capable of strand displacement modulated by the chromatin proteins Cren7 and Sul7 d. Euryarchaea have two distinct replicative DNA polymerases, PolB and PolD, a family D DNA polymerase. Here we characterized the strand displacement activities of Pol B and Pol D from the hyperthermophilic euryarchaeon Pyrococcus furiosus and investigated the influence of HPf A1, a homolog of eukaryotic histones from P. furiosus, on these activities. We showed that both Pol B and Pol D were efficient in strand displacement. HPf A1 inhibited DNA strand displacement by both DNA polymerases but exhibited little effect on the displacement of a RNA strand annealed to single-stranded template DNA. This is consistent with the finding that HPf A1 bound more tightly to double-stranded DNA than to a RNA:DNA hybrid. Our results suggest that, although crenarchaea and euryarchaea differ in chromosomal packaging, they share similar mechanisms in modulating strand displacement by DNA polymerases during lagging strand DNA synthesis.展开更多
基金supported by the Knowledge Innova-tion Program of the Chinese Academy of Sciences(No.KZCX1-YW-06-03)
文摘The response of archaeal communities to petroleum contamination in saline-alkali soil was characterized by analyses of three soil samples with different total petroleum hydrocarbon concentrations.Through the construction and screening of 16S rRNA gene clone libraries based on DNA extracts from these soils,nine distinct phylogenetic groups were identified.Statistical analyses showed that the distribution of archaeal community structures differ significantly along the gradient of petroleum contamination in these three saline- alkali soils.Five phylogenetic groups were dominant in the control soil,two of which were also abundant in the lightly contaminated soil.Four phylogenetic groups were dominant in heavily contaminated soil,one of which was also abundant in the lightly contaminated soil.The halophilic genus of Haloferax and the haloalkaliphilic genus of Natronomonas were more abundant in heavily contaminated soil.These results suggested that the genera of Haloferax and Natronomonas may have a role in the natural attenuation of petroleum- contaminated saline-alkali soil.
基金supported by the Major Science and Technology Program for Water Pollution Control and Treatment,China (2012ZX07202-004-02)
文摘The effects of different concentrations of oxytetracycline （OTC） on the dynamics of bacterial and archaeal communities during the mesophilic anaerobic digestion （37＆#176;C） of cow manure were investigated. Before anaerobic digestion, OTC was added to digesters at concentrations of 20, 50, and 80 mg L-1, respectively. Compared with no-antibiotic control, all methane productions underwent different levels of inhibition at different concentrations of OTC. Changes in the bacterial and archaeal communities were discussed by using PCR-denaturing gradient gel electrophoresis （DGGE）. Results showed that OTC affected the richness and diversity of bacterial and archaeal communities. The bacterial genus Flavobacterium and an uncultured bacterium （JN256083.1） were detected throughout the entire process of anaerobic digestion and seemed to be the functional bacteria. Methanobrevibacter boviskoreani and an uncultured archaeon （FJ230982.1） dominated the archaeal communities during anaerobic digestion. These microorganisms may have high resistance to OTC and may play vital roles in methane production.
基金funded by the National Key R&D Program of China(Grant No.2020YFA0906800 to Q.S.)the National Natural Science Foundation of China(Nos.32270040 to Q.S.,32001022 to X.F.,and 32370033 to Y.S.).
文摘Saccharolobus islandicus REY15A represents one of the very few archaeal models with versatile genetic tools,which include efficient genome editing,gene silencing,and robust protein expression systems.However,plasmid vectors constructed for this crenarchaeon thus far are based solely on the pRN2 cryptic plasmid.Although this plasmid coexists with pRN1 in its original host,early attempts to test pRN1-based vectors consistently failed to yield any stable host-vector system for Sa.islandicus.We hypothesized that this failure could be due to the occurrence of CRISPR immunity against pRN1 in this archaeon.We identified a putative target sequence in orf904 encoding a putative replicase on pRN1(target N1).Mutated targets(N1a,N1b,and N1c)were then designed and tested for their capability to escape the host CRISPR immunity by using a plasmid inter-ference assay.The results revealed that the original target triggered CRISPR immunity in this archaeon,whereas all three mutated targets did not,indicating that all the designed target mutations evaded host immunity.These mutated targets were then incorporated into orf904 individually,yielding corresponding mutated pRN1 backbones with which shuttle plasmids were constructed(pN1aSD,pN1bSD,and pN1cSD).Sa.islandicus transformation revealed that pN1aSD and pN1bSD were functional shuttle vectors,but pN1cSD lost the capability for replication.These results indicate that the missense mutations in the conserved helicase domain in pN1c inactivated the replicase.We further showed that pRN1-based and pRN2-based vectors were stably maintained in the archaeal cells either alone or in combination,and this yielded a dual plasmid system for genetic study with this important archaeal model.
基金supported by the Research Fund for the Doctoral Program of Higher Education of China(No.20130101110127)the Project of Zhejiang Key Scientific and Technological Innovation Team(No.2010R50039),China
文摘It is important to understand the effects of temporal changes in microbial communities in the acidic soils of tea orchards with different fertilizers. A field experiment involving organic fertilizer （OF）, chemical fertilizer （CF）, and unfertilized control （CK） treatments was arranged to analyze the temporal changes in the bacterial and archaeal communities at bimonthly intervals based on the 16S ribosomal RNA （rRNA） gene using terminal restriction fragment length polymorphism （T-RFLP） profiling. The abundances of total bacteria, total archaea, and selected functional genes （bacterial and archaeal amoA, bacterial narG, nirK, nirS, and nosZ） were determined by quantitative poly- merase chain reaction （qPCR）. The results indicate that the structures of bacterial and archaeal communities varied significantly with time and fertilization based on changes in the relative abundance of dominant T-RFs. The abundancy of the detected genes changed with time. The total bacteria, total archaea, and archaeal amoA were less abundant in July. The bacterial amoA and denitrifying genes were less abundant in September, except the nirK gene. The OF treatment increased the abundance of the observed genes, while the CF treatment had little influence on them. The soil temperature significantly affected the bacterial and archaeal community structures. The soil moisture was signif- icantly correlated with the abundance of denitrifying genes. Of the soil chemical properties, soil organic carbon was the most important factor and was significantly correlated with the abundance of the detected genes, except the nirK gene. Overall, this study demonstrated the effects of both temporal alteration and organic fertilizer on the structures of mi- crobial communities and the abundance of genes involved in the nitrogen cycle.
基金supported by a research grant (MEWRC651/ 06/177) from the Environment and Water Industry Programme Office of Singapore
文摘Biofilm formation, one of the primary causes of biofouling, results in reduced membrane flux or increased transmembrane pressure and thus represents a major impediment to the wider implementation of membrane bioreactor （MBR） technologies for water purification. Most studies have focused on the role of bacteria in membrane fouling as they are the most dominant and best studied organisms present in the MBR. In contrast, there is limited information on the role of the archaeal community in biofilm formation in MBRs. This study investigated the composition of the archaeal community during the process of biofouling in an MBR. The archaeal community was observed to have lower richness and diversity in the biofilm than the sludge during the establishment ofbiofilms at low transmembrane pressure （TMP）. Clustering of the communities based on the Bray-Curtis similarity matrix indicated that a subset of the sludge archaeal community formed the initial biofilms. The archaeal community in the biofilm was mainly composed of Thermoprotei, Thermoplasmata, Thermococci, Methanopyri, Methanomicrobia and Halobacteria. Among them, the Thermoprotei and Thermoplasmata were present at higher relative proportions in the biofilms than they were in the sludge. Additionally, the Thermoprotei, Thermoplasmata and Thermococci were the dominant organisms detected in the initial biofilms at low TMP, while as the TMP increased, the Methanopyri, Methanomicrobia, Aciduliprofundum and Halobacteria were present at higher abundances in the biofilms at high TMP.
基金supported by a General Project granted by the National Natural Science Foundation of China (No. 51178002)
文摘Anthropogenic activities usually contaminate water environments, and have led to the eutrophication of many estuaries and shifts in microbial communities. In this study, the temporal and spatial changes of the microbial community in an industrial effluent receiving area in Hangzhou Bay were investigated by 454 pyrosequencing. The bacterial community showed higher richness and biodiversity than the archaeal community in all sediments. Proteobacteria dominated in the bacterial communities of all the samples; MarineGroupⅠand Methanomicrobia were the two dominant archaeal classes in the effluent receiving area. PCoA and AMOVA revealed strong seasonal but minor spatial changes in both bacterial and archaeal communities in the sediments. The seasonal changes of the bacterial community were less significant than those of the archaeal community, which mainly consisted of fluctuations in abundance of a large proportion of longstanding species rather than the appearance and disappearance of major archaeal species. Temperature was found to positively correlate with the dominant bacteria, Betaproteobacteria, and negatively correlate with the dominant archaea,MarineGroupⅠ; and might be the primary driving force for the seasonal variation of the microbial community.
基金Supported by the National Natural Science Foundation of China(Nos.41806178,41776130,41776131)the Strategic Priority Research Programs(No.XDA11030202.2)+1 种基金the National Natural Science Foundation of China-Shandong Joint Fund(Nos.U1706208,U1606404)a grant for LIA-MagMC,from the Centre National de la Recherche Scientifique
文摘Seamounts are subsurface mountains in the ocean. Examination of the abundance and distribution of Archaea in seamount ecosystems may provide a better understanding of their ecological functions. Most studies of marine archaeal assemblages in seamount area have focused on hydrothermal vents or ferromanganese crusts. We investigated the archaeal communities from a seamount of the Mariana Volcanic Arc, in the tropical western Pacific Ocean by using high-throughput sequencing. Thaumarchaeota was dominant in the sediments of all sample stations. Community diversity and species richness were greatest at stations near the top of the seamount, and lowest at the deepest station. One sample station on the steep southeast slope that faced the Yap-Mariana trench had a unique composition of Archaea. In summary, depth has an important influence on archaeal community structure, and the geographic properties and sediment characteristics may explain the unique distribution patterns of Archaea in this seamount. This study provides a foundation for future research on Archaea in seamounts.
基金Supported by the Project of China One-Belt-One-Road Foreign Expert Research Collaboration,Ministry of Science and Technology,China (No.DL2021002001L)the Open Project Program of State Key Laboratory of Food Nutrition and Safety,Tianjin University of Science&Technology (No.SKLFNS-KF-202205)。
文摘Oxidative stress induced by factors such as ammonia nitrogen has become a major issue in shrimp farming.The effects of carotenoids on the growth and antioxidant capability of Litopenaeus vannamei juveniles were investigated in this study using dietary archaeal carotenoids supplementation.For four weeks,shrimp were given diets containing 0 mg/kg(Ctrl)and 55.98 mg/kg(Car)archaeal carotenoids.Dietary archaeal carotenoids significantly enhanced the astaxanthin content in shrimp muscles and carapaces,as well as the superoxide dismutase(SOD)and glutathione peroxidase(GSH-Px)activity(P<0.05).The malonaldehyde(MDA)content in Car group significantly decreased(P<0.05).The transcriptome analysis was conducted to determine the molecular processes in response to archaeal carotenoids supplementation.A total of 1536 differentially expressed genes(DEGs)were detected,including 538 upregulated DEGs and 998 downregulated DEGs.GO functional enrichment analysis between Ctrl and Car indicated that 26 GO terms including extracellular region,metabolic process,and proteolysis were enriched.The KEGG pathway enrichment analysis revealed that the amino sugar and nucleotide sugar metabolism,cysteine and methionine metabolism,glycine serine and threonine metabolism,and amino acid biosynthesis were enriched.Archaeal carotenoids influenced the expression of several important genes involved in reactive oxygen species(ROS)generation,Nrf2 signaling,and antioxidant enzymes.Seven DEGs were chosen to confirm the RNA-Seq data using qRT-PCR.The genes and pathways discovered in this work assist to elucidate the molecular processes through which archaeal carotenoid enhances L.vannamei antioxidative system.
文摘This paper reports the recent findings related to the stability properties of tetraether lipid layers. Organizations moleculars of chemical structure modified of Langmuir-Blodgett layers of archael tetraether lipids from the archebacterium Sulfolobus acidocaldarius on the wafer silicon substrates are investigated stable and organized. The behavior of Langmuir-Blodgett layers of chemical structure modified of archaeal tetraether lipids on the wafer silicon substrates is characterization using Differential Scanning Calorimetry (DSC) and Atomic Force Microscopy (AFM). The thermodynamics behavior and stability of Langmuir-Blodgett layers of archael tetraether lipids on the wafer silicon substrates are shown. Stability of the lipid membranes is of great importance to a number of biomedical applications, including intravenous drug delivery, biomaterials, and biosensors.
基金Supported by the National Key R&D Program of China(No.2019YFD0901305)the Science and Technology Program of Zhoushan(No.2019C21011)+4 种基金the Research Project of Ecological Environment Protection and Restoration of Yangtze River in Zhoushan(No.SZGXZS2020068)the National Natural Science Foundation of China(Nos.31270160,J1310037)the Natural Science Foundation of Zhejiang Province,China(No.LY12C03003)the Zhejiang Public Welfare Technology Application Research Project(No.2016C33084)the Province Key Research and Development Program of Zhejiang(No.2021C02047)。
文摘Archaea regulate the biogeochemical processes of ocean systems.The Changjiang(Yangtze)River estuary(CRE) is a complex and dynamic area strongly affected by seawaters and ocean currents.In this study,the planktonic archaeal communities in the surface and bottom seawaters of the CRE were investigated.Significant differences in the archaeal community composition were found between the surface and bottom seawaters(P<0.001).Marine Group Ⅱ(MG-Ⅱ) was dominant in the surface layers,and Nitrosopumilales was enriched in the bottom layers.Marine Group Ⅲ(MG-Ⅲ) was more abundant in the bottom layers than in the surface ones(P<0.001).These results were completely different from previous findings in the CRE seawater.Instead of dissolved oxygen(DO),temperature and salinity were the most vital environmental variations in the distribution of the archacal communities.According to the predicted metabolic pathways,the following functional subcategories were enriched in the hypoxic condition:replication and repair,membrane transport,glycan biosynthesis and metabolism,amino acid metabolism,metabolism of cofactors and vitamins,and xenobiotics biodegradation and metabolism(P<0.001),which indicated the strong adaptability of archaea to the harsh environment in the bottom seawater.These findings expand the understanding on archaeal structure and functions in the surface and bottom seawaters,including the hypoxic zones in the CRE,and may contribute to further works of the archaeal community in the CRE.
基金supported by the National Natural Science Foundation of China(Grant Nos.41573065 and 41773082)the Key Project of Natural Science Foundation of China(Grant No.21337001)the National Water Pollution Control and Treatment Science and Technology Major Project(Grant No.2017ZX07202002).
文摘Polycyclic aromatic hydrocarbons(PAHs)often occur in oil-contaminated soil,coke wastewater and domestic sludge;however,associated PAH degraders in these environments are not clear.Here we evaluated phenanthrene degradation potential in the mixed samples of above environments,and obtained a methanogenic community with different microbial profile compared to those from sediments.Phenanthrene was efficiently degraded(1.26 mg/L/d)and nonstoichiometric amount of methane was produced simultaneously.16S rRNA gene sequencing demonstrated that bacterial populations were mainly associated with Comamonadaceae Nocardiaceae and Thermodesulfobiaceae,and that methanogenic archaea groups were dominated by Methanobacterium and Methanothermobacter.Substances such as hexane,hexadecane,benzene and glucose showed the most positive effects on phenanthrene degradation.Substrate utilization tests indicated that this culture could not utilize other PAHs.These analyses could offer us some suggestions on the putative phenanthrene-degrading microbes in such environments,and might help us develop strategies for the removal of PAHs from contaminated soil and sludge.
基金supported by National Key R&D Program of China(Grant Number 2018YFC0310600)by the National Natural Science Foundation of China(Grant Numbers 91951210,41773069,41906134)by Shanghai Natural Science Foundation(Grant Number 20ZR1423700).
文摘Hadal trenches are the least explored marine habitat on earth. Archaea has been shown to be the dominant group in trench sediments. However, the activity potentials and detailed diversity of these communities as well as their inter-trench variations are still not known. In this study, we combined datasets from two pairs of primers to investigate at high resolution the structure and activity potentials of the archaeal communities in vertically sectioned sediment cores taken from the deepest points of the Mariana (10,853 m) and Mussau (7011 m) trenches. The compositions of the potentially active communities revealed, via 16S ribosomal RNA gene (rDNA) and RNA (rRNA), significant differences between samples. Marine Group I (MGI), with nine identified subgroups, was the most dominant class in the active archaeal communities of the two trenches. Significantly different species composition and vertical variations were observed between the two trenches. Vertical transitions from aerobic MGI α to anaerobic MGI η and υ subgroups were observed in MST but not in MT sediments, which might be related to the faster microbial oxygen consumption in MST. These results provide a better understanding on archaeal activity and diversity in trench sediments.
基金supported by the National Natural Science Foundation of China (31130003, 30921065)
文摘Euryarchaeota and Crenarchaeota, the two main lineages of the domain Archaea, encode different chromatin proteins and differ in the use of replicative DNA polymerases. Crenarchaea possess a single family B DNA polymerase(Pol B), which is capable of strand displacement modulated by the chromatin proteins Cren7 and Sul7 d. Euryarchaea have two distinct replicative DNA polymerases, PolB and PolD, a family D DNA polymerase. Here we characterized the strand displacement activities of Pol B and Pol D from the hyperthermophilic euryarchaeon Pyrococcus furiosus and investigated the influence of HPf A1, a homolog of eukaryotic histones from P. furiosus, on these activities. We showed that both Pol B and Pol D were efficient in strand displacement. HPf A1 inhibited DNA strand displacement by both DNA polymerases but exhibited little effect on the displacement of a RNA strand annealed to single-stranded template DNA. This is consistent with the finding that HPf A1 bound more tightly to double-stranded DNA than to a RNA:DNA hybrid. Our results suggest that, although crenarchaea and euryarchaea differ in chromosomal packaging, they share similar mechanisms in modulating strand displacement by DNA polymerases during lagging strand DNA synthesis.
