Archaea-An International Microbiological Journal最新文献

{"title":"Ribosomal Protein Cluster Organization in Asgard Archaea","authors":"Madhan R. Tirumalai, Raghavan V. Sivaraman, Layla A. Kutty, Eric L. Song, George E. Fox","doi":"10.1155/2023/5512414","DOIUrl":"https://doi.org/10.1155/2023/5512414","url":null,"abstract":"It has been proposed that the superphylum of Asgard Archaea may represent a historical link between the Archaea and Eukarya. Following the discovery of the Archaea, it was soon appreciated that archaeal ribosomes were more similar to those of Eukarya rather than Bacteria. Coupled with other eukaryotic-like features, it has been suggested that the Asgard Archaea may be directly linked to eukaryotes. However, the genomes of Bacteria and non-Asgard Archaea generally organize ribosome-related genes into clusters that likely function as operons. In contrast, eukaryotes typically do not employ an operon strategy. To gain further insight into conservation of the r-protein genes, the genome order of conserved ribosomal protein (r-protein) coding genes was identified in 17 Asgard genomes (thirteen complete genomes and four genomes with less than 20 contigs) and compared with those found previously in non-Asgard archaeal and bacterial genomes. A universal core of two clusters of 14 and 4 cooccurring r-proteins, respectively, was identified in both the Asgard and non-Asgard Archaea. The equivalent genes in the E. coli version of the cluster are found in the S10 and spc operons. The large cluster of 14 r-protein genes (uS19-uL22-uS3-uL29-uS17 from the S10 operon and uL14-uL24-uL5-uS14-uS8-uL6-uL18-uS5-uL30-uL15 from the spc operon) occurs as a complete set in the genomes of thirteen Asgard genomes (five Lokiarchaeotes, three Heimdallarchaeotes, one Odinarchaeote, and four Thorarchaeotes). Four less conserved clusters with partial bacterial equivalents were found in the Asgard. These were the L30e (str operon in Bacteria) cluster, the L18e (alpha operon in Bacteria) cluster, the S24e-S27ae-rpoE1 cluster, and the L31e, L12..L1 cluster. Finally, a new cluster referred to as L7ae was identified. In many cases, r-protein gene clusters/operons are less conserved in their organization in the Asgard group than in other Archaea. If this is generally true for nonribosomal gene clusters, the results may have implications for the history of genome organization. In particular, there may have been an early transition to or from the operon approach to genome organization. Other nonribosomal cellular features may support different relationships. For this reason, it may be important to consider ribosome features separately.","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135132419","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Archaea: Methods and Protocols","authors":"","doi":"10.1007/978-1-0716-2445-6","DOIUrl":"https://doi.org/10.1007/978-1-0716-2445-6","url":null,"abstract":"","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"51714282","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"VOLN27B: A New Head-Tailed Halovirus Isolated from an Underground Salt Crystal and Infecting <i>Halorubrum</i>.","authors":"Shaoxing Chen,&nbsp;Yongpei Dai,&nbsp;Jingwen Liu,&nbsp;Shimin Zhang,&nbsp;Feilong Chen,&nbsp;Fanjie Jin,&nbsp;Peiyao Ruan,&nbsp;Lu Li,&nbsp;Xiangdong Chen","doi":"10.1155/2021/8271899","DOIUrl":"https://doi.org/10.1155/2021/8271899","url":null,"abstract":"<p><p>A novel halovirus, VOLN27B, was isolated from a drill core sample taken at a depth of approximately 430 m, from a layer formed during the Cretaceous period (Anhui, China). VOLN27B infects the halophilic archaeon <i>Halorubrum</i> sp. LN27 and has a head-tailed morphotype with a contractile tail, typical of myoviruses. The average head diameter is 64 ± 2.0 nm, and uncontracted tails are 15 ± 1.0 × 65 ± 2.0 nm. The latent period is about 10 h. The maturing time of VOLN27B in cells of <i>Halorubrum</i> sp. LN27 was nearly 8 h. The adsorption time of VOLN27B on cells of <i>Halorubrum</i> sp. LN27 was less than 1 min. Virus particles are unstable at pH values less than 5 or when the NaCl concentration is below 12% (<i>w</i>/<i>v</i>). VOLN27B and <i>Halorubrum</i> sp. LN27 were recovered from the same hypersaline environment and provide a new virus-host system in haloarchaea.</p>","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2021-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8727067/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39792071","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Biological Processes for Pollution Control: Current Research and Emerging Technologies 2020.","authors":"Jin Li, Yu Tao, Guangbin Li, Cuijie Feng, Rong Chen, Ming Hua","doi":"10.1155/2021/9852531","DOIUrl":"10.1155/2021/9852531","url":null,"abstract":"","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2021-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8589500/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39622735","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Ability of Hop Extracts to Reduce the Methane Production of <i>Methanobrevibacter ruminantium</i>.","authors":"J A Blaxland,&nbsp;A J Watkins,&nbsp;L W J Baillie","doi":"10.1155/2021/5510063","DOIUrl":"https://doi.org/10.1155/2021/5510063","url":null,"abstract":"<p><strong>Background: </strong>Methane emissions from agriculture are responsible for over 40% of the world's greenhouse gas emissions. In the past, antibiotics were used to control methane production by animals, but concerns over the emergence and spread of antibiotic-resistant bacteria to humans have prompted a search for alternative approaches. Hops are the flowers of the hop plant <i>Humulus lupulus</i>. They have been used to feed cattle for many years and are known to contain antibacterial compounds, and their extracts have been shown to kill members of the <i>Mycobacterium</i> spp including <i>Mycobacterium bovis</i>, the causative agent of bovine tuberculosis as well as a number of human pathogens. In this study, hop extracts were studied for their ability to inhibit methane production from <i>Methanobrevibacter ruminantium</i>, a major methane-producing archaeon found in the rumen of cattle.</p><p><strong>Methods: </strong><i>Methanobrevibacter ruminantium</i> M1^T (DSM 1093) was grown at 37°C for 30 days, and the amount of methane produced at different time points during this period was measured using gas chromatography. The archaeon was exposed to commercial hop extracts (tetra-hydro-iso-alpha acid and beta acid) and to aqueous hop extracts of a range of hop variants, and their effect on methane production was determined.</p><p><strong>Results: </strong>All of the extracts reduced the level of methane production of <i>M. ruminantium</i> over the 30-day period compared to the negative control (sterile distilled water). The commercial hop extracts were the most effective at inhibiting methane production over the course of the experiment in contrast to the aqueous extracts, which showed a gradual reduction of inhibition with time.</p><p><strong>Conclusions: </strong>Hops contain compounds which inhibit methane production. Given that hops can be safely fed to cattle, this raises the possibility of rationally designing a feed strategy which could reduce greenhouse gas emissions and protect against bovine tuberculosis. This study recommends that further research be undertaken to further identifying bioactive components from hops and their efficacy against a range of archaea.</p>","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2021-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8589499/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39731113","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structural and Kinetic Characterization of Hyperthermophilic NADH-Dependent Persulfide Reductase from <i>Archaeoglobus fulgidus</i>.","authors":"Sherwin Shabdar, Bukuru Anaclet, Ana Garcia Castineiras, Neyissa Desir, Nicholas Choe, Edward J Crane, Matthew H Sazinsky","doi":"10.1155/2021/8817136","DOIUrl":"10.1155/2021/8817136","url":null,"abstract":"<p><p>NADH-dependent persulfide reductase (Npsr) has been proposed to facilitate dissimilatory sulfur respiration by reducing persulfide or sulfane sulfur-containing substrates to H₂S. The presence of this gene in the sulfate and thiosulfate-reducing <i>Archaeoglobus fulgidus</i> DSM 4304 and other hyperthermophilic <i>Archaeoglobales</i> appears anomalous, as <i>A. fulgidus</i> is unable to respire S⁰ and grow in the presence of elemental sulfur. To assess the role of Npsr in the sulfur metabolism of <i>A. fulgidus</i> DSM 4304, the Npsr from <i>A. fulgidus</i> was characterized. AfNpsr is specific for persulfide and polysulfide as substrates in the oxidative half-reaction, exhibiting <i>k</i> _cat/<i>K</i> _m on the order of 10⁴ M^-1 s^-1, which is similar to the kinetic parameters observed for hyperthermophilic CoA persulfide reductases. In contrast to the bacterial Npsr, AfNpsr exhibits low disulfide reductase activity with DTNB; however, similar to the bacterial enzymes, it does not show detectable activity with CoA-disulfide, oxidized glutathione, or cystine. The 3.1 Å X-ray structure of AfNpsr reveals access to the tightly bound catalytic CoA, and the active site Cys 42 is restricted by a flexible loop (residues 60-66) that is not seen in the bacterial homologs from <i>Shewanella loihica PV-4</i> and <i>Bacillus anthracis</i>. Unlike the bacterial enzymes, AfNpsr exhibits NADH oxidase activity and also shows no detectable activity with NADPH. Models suggest steric and electrostatic repulsions of the NADPH 2'-phosphate account for the strong preference for NADH. The presence of Npsr in the nonsulfur-reducing <i>A. fulgidus</i> suggests that the enzyme may offer some protection against S⁰ or serve in another metabolic role that has yet to be identified.</p>","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2021-03-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7969121/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25524497","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Analysis of a Methanogen and an Actinobacterium Dominating the Thermophilic Microbial Community of an Electromethanogenic Biocathode.","authors":"Hajime Kobayashi,&nbsp;Ryohei Toyoda,&nbsp;Hiroyuki Miyamoto,&nbsp;Yasuhito Nakasugi,&nbsp;Yuki Momoi,&nbsp;Kohei Nakamura,&nbsp;Qian Fu,&nbsp;Haruo Maeda,&nbsp;Takashi Goda,&nbsp;Kozo Sato","doi":"10.1155/2021/8865133","DOIUrl":"https://doi.org/10.1155/2021/8865133","url":null,"abstract":"<p><p>Electromethanogenesis refers to the bioelectrochemical synthesis of methane from CO₂ by biocathodes. In an electromethanogenic system using thermophilic microorganisms, metagenomic analysis along with quantitative real-time polymerase chain reaction and fluorescence <i>in situ</i> hybridization revealed that the biocathode microbiota was dominated by the methanogen <i>Methanothermobacter</i> sp. strain EMTCatA1 and the actinobacterium <i>Coriobacteriaceae</i> sp. strain EMTCatB1. RNA sequencing was used to compare the transcriptome profiles of each strain at the methane-producing biocathodes with those in an open circuit and with the methanogenesis inhibitor 2-bromoethanesulfonate (BrES). For the methanogen, genes related to hydrogenotrophic methanogenesis were highly expressed in a manner similar to those observed under H₂-limited conditions. For the actinobacterium, the expression profiles of genes encoding multiheme c-type cytochromes and membrane-bound oxidoreductases suggested that the actinobacterium directly takes up electrons from the electrode. In both strains, various stress-related genes were commonly induced in the open-circuit biocathodes and biocathodes with BrES. This study provides a molecular inventory of the dominant species of an electromethanogenic biocathode with functional insights and therefore represents the first multiomics characterization of an electromethanogenic biocathode.</p>","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2021-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7943316/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25500613","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Performance Analysis and Microbial Community Evolution of In Situ Biological Biogas Upgrading with Increasing H₂/CO₂ Ratio.","authors":"Viola Corbellini,&nbsp;Cuijie Feng,&nbsp;Micol Bellucci,&nbsp;Arianna Catenacci,&nbsp;Tatiana Stella,&nbsp;Anna Espinoza-Tofalos,&nbsp;Francesca Malpei","doi":"10.1155/2021/8894455","DOIUrl":"https://doi.org/10.1155/2021/8894455","url":null,"abstract":"<p><p>The effect of the amount of hydrogen supplied for the <i>in situ</i> biological biogas upgrading was investigated by monitoring the process and evolution of the microbial community. Two parallel reactors, operated at 37°C for 211 days, were continuously fed with sewage sludge at a constant organic loading rate of 1.5 gCOD∙(L∙d)^-1 and hydrogen (H₂). The molar ratio of H₂/CO₂ was progressively increased from 0.5 : 1 to 7 : 1 to convert carbon dioxide (CO₂) into biomethane via hydrogenotrophic methanogenesis. Changes in the biogas composition become statistically different above the stoichiometric H₂/CO₂ ratio (4 : 1). At a H₂/CO₂ ratio of 7 : 1, the methane content in the biogas reached 90%, without adversely affecting degradation of the organic matter. The possibility of selecting, adapting, and enriching the original biomass with target-oriented microorganisms able to biologically convert CO₂ into methane was verified: high throughput sequencing of 16S rRNA gene revealed that hydrogenotrophic methanogens, belonging to <i>Methanolinea</i> and <i>Methanobacterium</i> genera, were dominant. Based on the outcomes of this study, further optimization and engineering of this process is feasible and needed as a means to boost energy recovery from sludge treatment.</p>","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2021-02-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7889367/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25408409","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Production of Poly(3-Hydroxybutyrate) by <i>Haloarcula</i>, <i>Halorubrum</i>, and <i>Natrinema</i> Haloarchaeal Genera Using Starch as a Carbon Source.","authors":"Fatma Karray,&nbsp;Manel Ben Abdallah,&nbsp;Nidhal Baccar,&nbsp;Hatem Zaghden,&nbsp;Sami Sayadi","doi":"10.1155/2021/8888712","DOIUrl":"https://doi.org/10.1155/2021/8888712","url":null,"abstract":"<p><p>Microbial production of bioplastics, derived from poly(3-hydroxybutyrate) (PHB), have provided a promising alternative towards plastic pollution. Compared to other extremophiles, halophilic archaea are considered as cell factories for PHB production by using renewable, inexpensive carbon sources, thus decreasing the fermentation cost. This study is aimed at screening 33 halophilic archaea isolated from three enrichment cultures from Tunisian hypersaline lake, Chott El Jerid, using starch as the sole carbon source by Nile Red/Sudan Black staining and further confirmed by PCR amplification of <i>phaC</i> and <i>phaE</i> polymerase genes. 14 isolates have been recognized as positive candidates for PHA production and detected during both seasons. The identification of these strains through 16S rRNA gene analyses showed their affiliation to <i>Halorubrum</i>, <i>Natrinema</i>, and <i>Haloarcula</i> genera. Among them, three PHB-producing strains, CEJ34-14, CEJ5-14, and CEJ48-10, related to <i>Halorubrum chaoviator</i>, <i>Natrinema pallidum</i>, and <i>Haloarcula tradensis</i> were found to be the best ones reaching values of 9.25, 7.11, and 1.42% of cell dry weight (CDW), respectively. Our findings highlighted that <i>Halorubrum</i>, <i>Natrinema</i>, and <i>Haloarcula</i> genera were promising candidates for PHB production using soluble starch as a carbon source under high salinity (250 g L^-1 NaCl).</p>","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2021-01-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7860971/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25363100","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Flocculation Efficiency and Mechanism of Carbamazepine by Microbial Flocculant Extracted from <i>Klebsiella pneumoniae</i> J1.","authors":"Jie Xing,&nbsp;Nanzhe Song,&nbsp;Xiangwei Chen,&nbsp;Ang Li,&nbsp;Hongwei Ni","doi":"10.1155/2020/8811516","DOIUrl":"https://doi.org/10.1155/2020/8811516","url":null,"abstract":"<p><p>The microbial flocculant (MFX) extracted from <i>Klebsiella pneumoniae</i> J1 was used to remove carbamazepine in prepared wastewater and domestic sewage. The influence factors and flocculation mechanism were studied. The optimal carbamazepine removal conditions for MFX were pH of 7-8, 7 mL of flocculant, 0.1 mL of coagulant, and 35°C, and the removal rate reached 81.75%. MFX was efficient in the removal of carbamazepine in both domestic sewage (75.03%) and secondary sedimentation tank effluent (69.76%). The pseudo-first-order kinetic equation fitted the adsorption process better than the pseudo-second-order kinetic equation, which suggested that the adsorption was not pure chemical adsorption. The analysis of floc size suggested that the repulsive force between carbamazepine and MFX was weakened under alkalescent conditions, which can help the growth and coherence of flocs and increase the carbamazepine removal efficiency. Enough dosage of MFX can generate larger flocs, but excessive dosage of MFX will decrease the carbamazepine removal rate because of increase in electrostatic repulsion. The analysis of 3D-EEM and FTIR suggested that hydroxyl, amino, and carboxyl in MFX played an important role in the removal of carbamazepine. As an eco-friendly and highly efficient microbial flocculant, MFX has potential for practical applications in carbamazepine removal.</p>","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2020-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2020/8811516","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38692657","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}