Archaea-An International Microbiological Journal最新文献

{"title":"Functional Group Distribution of the Carrier Surface Influences Adhesion of <i>Methanothermobacter thermautotrophicus</i>.","authors":"Masaki Umetsu,&nbsp;Takaaki Sunouchi,&nbsp;Yasuhiro Fukuda,&nbsp;Hideyuki Takahashi,&nbsp;Chika Tada","doi":"10.1155/2020/9432803","DOIUrl":"https://doi.org/10.1155/2020/9432803","url":null,"abstract":"<p><p>Various support carriers are used for high-density retention of methanogenic archaea in anaerobic wastewater treatment systems. Although the physicochemical properties of carrier materials and microorganisms influence the adhesion of methanogenic archaea, details about the underlying mechanism remain poorly characterized. We applied seven types of chemical surface modifications to carbon felts to clarify the adhesion properties of <i>Methanothermobacter thermautotrophicus</i>, a representative thermophilic hydrogenotrophic methanogen. The relationship between carrier surface properties and methanogen adhesion was evaluated. <i>M. thermautotrophicus</i> adhesion was significantly increased up to 2.6 times in comparison with control on carbon felts treated with NaOH, HCl, H₂SO₄, or Na₂HPO₄. Treated carbon felts showed a lower water contact angle, but no correlation between the carrier surface contact angle and methanogen adhesion was observed. On the other hand, at the surface of the carrier that showed improved adhesion of methanogens, the ratio of -COOH : -OH was 1 : 0.65. Such a ratio was not observed with treated carriers for which methanogen adhesion was not improved. Therefore, in the adhesion of <i>M. thermautotrophicus</i>, the functional group abundance was important as well as physical surface properties such as the hydrophobicity. Hydrogenotrophic methanogens are involved in active methanation during the startup of anaerobic digestion. Additionally, these methanogenic archaea function as methanogenic cathode catalysts. Therefore, anaerobic digestion performance will greatly improve by controlling the adhesion of hydrogenotrophic methanogens such as <i>M. thermautotrophicus</i>.</p>","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2020-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2020/9432803","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37635091","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":"Community Structure and Abundance of Archaea in a <i>Zostera marina</i> Meadow: A Comparison between Seagrass-Colonized and Bare Sediment Sites.","authors":"Pengfei Zheng,&nbsp;Chuantao Wang,&nbsp;Xiaoli Zhang,&nbsp;Jun Gong","doi":"10.1155/2019/5108012","DOIUrl":"https://doi.org/10.1155/2019/5108012","url":null,"abstract":"<p><p>Seagrass colonization alters sediment physicochemical properties by depositing seagrass fibers and releasing organic carbon and oxygen from the roots. How this seagrass colonization-induced spatial heterogeneity affects archaeal community structure and abundance remains unclear. In this study, we investigated archaeal abundance, diversity, and composition in both vegetated and adjacent bare surface sediments of a <i>Zostera marina</i> meadow. High-throughput sequencing of 16S rDNA showed that <i>Woesearchaeota</i>, <i>Bathyarchaeota</i>, and <i>Thaumarchaeota</i> were the most abundant phyla across all samples, accounting for approximately 42%, 21%, and 17% of the total archaeal communities, respectively. In terms of relative abundance, <i>Woesearchaeota</i> and <i>Bathyarchaeota</i> were not significantly different between these two niches; however, specific subclades (Woese-3, Woese-21, Bathy-6, Bathy-18) were significantly enriched in vegetated sediments (<i>P</i> < 0.05), while <i>Thaumarchaeota</i> was favored in unvegetated sites (<i>P</i> = 0.02). The quantification of archaeal 16S rRNA genes showed that the absolute abundance of the whole archaeal community, <i>Bathyarchaeota</i>, and Woese-3, Woese-10, Woese-13, and Woese-21 was significantly more abundant in vegetated sediments than in bare sediments (<i>P</i> < 0.05). Our study expands the available knowledge of the distribution patterns and niche preferences of archaea in seagrass systems, especially for the different subclades of <i>Woesearchaeota</i> and <i>Bathyarchaeota</i>, in terms of both relative proportions and absolute quantities.</p>","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2019-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2019/5108012","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37448975","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":"Acetotrophic Activity Facilitates Methanogenesis from LCFA at Low Temperatures: Screening from Mesophilic Inocula.","authors":"Suniti Singh,&nbsp;Johanna M Rinta-Kanto,&nbsp;Riitta Kettunen,&nbsp;Piet Lens,&nbsp;Gavin Collins,&nbsp;Marika Kokko,&nbsp;Jukka Rintala","doi":"10.1155/2019/1751783","DOIUrl":"https://doi.org/10.1155/2019/1751783","url":null,"abstract":"<p><p>The inoculum source plays a crucial role in the anaerobic treatment of wastewaters. Lipids are present in various wastewaters and have a high methanogenic potential, but their hydrolysis results in the production of long chain fatty acids (LCFAs) that are inhibitory to anaerobic microorganisms. Screening of inoculum for the anaerobic treatment of LCFA-containing wastewaters has been performed at mesophilic and thermophilic conditions. However, an evaluation of inocula for producing methane from LCFA-containing wastewater has not yet been conducted at low temperatures and needs to be undertaken. In this study, three inocula (one granular sludge and two municipal digester sludges) were assessed for methane production from LCFA-containing synthetic dairy wastewater (SDW) at low temperatures (10 and 20°C). A methane yield (based on mL-CH₄/g-COD_added) of 86-65% with acetate and 45-20% with SDW was achieved within 10 days using unacclimated granular sludge, whereas the municipal digester sludges produced methane only at 20°C but not at 10°C even after 200 days of incubation. The acetotrophic activity in the inoculum was found to be crucial for methane production from LCFA at low temperatures, highlighting the role of <i>Methanosaeta</i> (acetoclastic archaea) at low temperatures. The presence of bacterial taxa from the family <i>Syntrophaceae</i> (<i>Syntrophus</i> and uncultured taxa) in the inoculum was found to be important for methane production from SDW at 10°C. This study suggests the evaluation of acetotrophic activity and the initial microbial community characteristics by high-throughput amplicon sequencing for selecting the inoculum for producing methane at low temperatures (up to 10°C) from lipid-containing wastewaters.</p>","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2019-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2019/1751783","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37324540","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 Impact of Pyroglutamate: <i>Sulfolobus acidocaldarius</i> Has a Growth Advantage over <i>Saccharolobus solfataricus</i> in Glutamate-Containing Media.","authors":"Anna M Vetter,&nbsp;Julia Helmecke,&nbsp;Dietmar Schomburg,&nbsp;Meina Neumann-Schaal","doi":"10.1155/2019/3208051","DOIUrl":"https://doi.org/10.1155/2019/3208051","url":null,"abstract":"<p><p>Microorganisms are well adapted to their habitat but are partially sensitive to toxic metabolites or abiotic compounds secreted by other organisms or chemically formed under the respective environmental conditions. Thermoacidophiles are challenged by pyroglutamate, a lactam that is spontaneously formed by cyclization of glutamate under aerobic thermoacidophilic conditions. It is known that growth of the thermoacidophilic crenarchaeon <i>Saccharolobus solfataricus</i> (formerly <i>Sulfolobus solfataricus</i>) is completely inhibited by pyroglutamate. In the present study, we investigated the effect of pyroglutamate on the growth of <i>S. solfataricus</i> and the closely related crenarchaeon <i>Sulfolobus acidocaldarius.</i> In contrast to <i>S. solfataricus</i>, <i>S. acidocaldarius</i> was successfully cultivated with pyroglutamate as a sole carbon source. Bioinformatical analyses showed that both members of the <i>Sulfolobaceae</i> have at least one candidate for a 5-oxoprolinase, which catalyses the ATP-dependent conversion of pyroglutamate to glutamate. In <i>S. solfataricus</i>, we observed the intracellular accumulation of pyroglutamate and crude cell extract assays showed a less effective degradation of pyroglutamate. Apparently, <i>S. acidocaldarius</i> seems to be less versatile regarding carbohydrates and prefers peptidolytic growth compared to <i>S. solfataricus</i>. Concludingly, <i>S. acidocaldarius</i> exhibits a more efficient utilization of pyroglutamate and is not inhibited by this compound, making it a better candidate for applications with glutamate-containing media at high temperatures.</p>","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2019-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2019/3208051","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37052444","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":"Primary Production in the Water Column as Major Structuring Element of the Biogeographical Distribution and Function of Archaea in Deep-Sea Sediments of the Central Pacific Ocean.","authors":"Franziska Wemheuer,&nbsp;Avril Jean Elisabeth von Hoyningen-Huene,&nbsp;Marion Pohlner,&nbsp;Julius Degenhardt,&nbsp;Bert Engelen,&nbsp;Rolf Daniel,&nbsp;Bernd Wemheuer","doi":"10.1155/2019/3717239","DOIUrl":"10.1155/2019/3717239","url":null,"abstract":"<p><p>Information on environmental conditions shaping archaeal communities thriving at the seafloor of the central Pacific Ocean is limited. The present study was conducted to investigate the diversity, composition, and function of both entire and potentially active archaeal communities within Pacific deep-sea sediments. For this purpose, sediment samples were taken along the 180° meridian of the central Pacific Ocean. Community composition and diversity were assessed by Illumina tag sequencing targeting archaeal 16S rRNA genes and transcripts. Archaeal communities were dominated by Candidatus <i>Nitrosopumilus</i> (<i>Thaumarchaeota</i>) and other members of the <i>Nitrosopumilaceae</i> (<i>Thaumarchaeota</i>), but higher relative abundances of the Marine Group II (<i>Euryarchaeota</i>) were observed in the active compared to the entire archaeal community. The composition of the entire and the active archaeal communities was strongly linked to primary production (chlorophyll content), explaining more than 40% of the variance. Furthermore, we found a strong correlation of the entire archaeal community composition to latitude and silicic acid content, while the active community was significantly correlated with primary production and ferric oxide content. We predicted functional profiles from 16S rRNA data to assess archaeal community functions. Latitude was significantly correlated with functional profiles of the entire community, whereas those of the active community were significantly correlated with nitrate and chlorophyll content. The results of the present study provide first insights into benthic archaeal communities in the Pacific Ocean and environmental conditions shaping their diversity, distribution, and function. Additionally, they might serve as a template for further studies investigating archaea colonizing deep-sea sediments.</p>","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2019-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2019/3717239","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37177532","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":"Optimization of an In Vitro Transcription/Translation System Based on <i>Sulfolobus solfataricus</i> Cell Lysate.","authors":"Giada Lo Gullo,&nbsp;Rosanna Mattossovich,&nbsp;Giuseppe Perugino,&nbsp;Anna La Teana,&nbsp;Paola Londei,&nbsp;Dario Benelli","doi":"10.1155/2019/9848253","DOIUrl":"https://doi.org/10.1155/2019/9848253","url":null,"abstract":"<p><p>A system is described which permits the efficient synthesis of proteins <i>in vitro</i> at high temperature. It is based on the use of an unfractionated cell lysate (S30) from <i>Sulfolobus solfataricus</i> previously well characterized in our laboratory for translation of pretranscribed mRNAs, and now adapted to perform coupled transcription and translation. The essential element in this expression system is a strong promoter derived from the <i>S. solfataricus</i> 16S/23S rRNA-encoding gene, from which specific mRNAs may be transcribed with high efficiency. The synthesis of two different proteins is reported, including the <i>S. solfataricus</i> DNA-alkylguanine-DNA-alkyl-transferase protein (<i>Ss</i>OGT), which is shown to be successfully labeled with appropriate fluorescent substrates and visualized in cell extracts. The simplicity of the experimental procedure and specific activity of the proteins offer a number of possibilities for the study of structure-function relationships of proteins.</p>","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2019-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2019/9848253","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37230601","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":"Long-Term Effects of Periodical Fires on Archaeal Communities from Brazilian Cerrado Soils.","authors":"Aline Belmok,&nbsp;Thiago Rodrigues-Oliveira,&nbsp;Fabyano A C Lopes,&nbsp;Heloisa S Miranda,&nbsp;Ricardo H Krüger,&nbsp;Cynthia M Kyaw","doi":"10.1155/2019/6957210","DOIUrl":"https://doi.org/10.1155/2019/6957210","url":null,"abstract":"<p><p>The Cerrado biome corresponds to an extensive area of Brazil and is considered a biodiversity hotspot. Frequent fires are a natural feature in this biome and have influences on vegetation structure and composition. However, continuous anthropogenic actions are promoting changes in fire frequency and seasonality. Despite the high biodiversity of the Cerrado, little is known about its microbiome, with few publications describing some aspects of the bacterial and fungal communities found on this biome and almost no references about archaea. In this study, we describe the archaeal diversity in Cerrado <i>sensu stricto</i> soils, comparing the archaeal communities from soils of an area long protected from fires to one exposed to biennial fires, using both 16S rRNA and <i>amoA</i> genes as molecular markers. Almost all 16S rRNA sequences from both studied areas were affiliated with I.1b and 1.1c <i>Thaumarchaeota</i>, groups commonly detected in terrestrial environments. A higher relative abundance of I.1b thaumarchaeal subgroup was detected in the frequently burned area even though no statistically significant differences were observed in archaeal 16S rRNA richness and diversity between the investigated areas. Many ammonia-oxidizing archaea (AOA) are affiliated with this group, which is consistent with the higher <i>amoA</i> diversity and OTU numbers detected in the area periodically burned. Taken together, our results suggest that, although total archaeal community richness and diversity do not seem to greatly differ between the investigated conditions, alterations in wood cover and vegetation structure caused by frequent fires likely cause long-term effects in AOA diversity in Cerrado soils.</p>","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2019-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2019/6957210","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37024563","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":"Crystal Structures of the Putative Isocitrate Dehydrogenase from <i>Sulfolobus tokodaii</i> Strain 7 in the Apo and NADP⁺-Bound Forms.","authors":"Hisanori Kondo,&nbsp;Midori Murakami","doi":"10.1155/2018/7571984","DOIUrl":"https://doi.org/10.1155/2018/7571984","url":null,"abstract":"<p><p>Isocitrate dehydrogenase is a catabolic enzyme that acts during the third step of the tricarboxylic acid cycle. The hypothetical protein ST2166 from the archaeon <i>Sulfolobus tokodaii</i> was isolated and crystallized. It shares high primary structure homology with prokaryotic NADP⁺-dependent IDHs, suggesting that these enzymes share a common enzymatic mechanism. The crystal structure of ST2166 was determined at 2.0 Å resolution in the apo form, and then the structure of the crystal soaked with NADP⁺ was also determined at 2.4 Å resolution, which contained NADP⁺ bound at the putative active site. Comparisons between the structures of apo and NADP⁺-bound forms and NADP-IDHs from other prokaryotes suggest that prokaryotic NADP-IDHs recognize their cofactors using conserved Lys335, Tyr336, and Arg386 in ST2166 at the opening cleft before the domain closure.</p>","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2018-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2018/7571984","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36923359","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":"Archaea in Wastewater Treatment: Current Research and Emerging Technology.","authors":"Jin Li,&nbsp;Rutao Liu,&nbsp;Yu Tao,&nbsp;Guangbin Li","doi":"10.1155/2018/6973294","DOIUrl":"https://doi.org/10.1155/2018/6973294","url":null,"abstract":"","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2018-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2018/6973294","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36809851","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 Occurrence of Putative Nitric Oxide Dismutase (Nod) in an Alpine Wetland with a New Dominant Subcluster and the Potential Ability for a Methane Sink.","authors":"Yanfen Zhang,&nbsp;Anzhou Ma,&nbsp;Wenzong Liu,&nbsp;Zhihui Bai,&nbsp;Xuliang Zhuang,&nbsp;Guoqiang Zhuang","doi":"10.1155/2018/6201541","DOIUrl":"https://doi.org/10.1155/2018/6201541","url":null,"abstract":"<p><p>Recently, a new oxygenic pathway has been proposed based on the disproportionation of NO with putative NO dismutase (Nod). In addition to a new process in nitrogen cycling, this process provides ecological advantages for the degradation of substrates in anaerobic conditions, which is of great significance for wastewater treatment. However, the Nod distribution in aquatic environments is rarely investigated. In this study, we obtained the <i>nod</i> genes with an abundance of 2.38 ± 0.96 × 10⁵ copies per gram of dry soil from the Zoige wetland and aligned the molecular characteristics in the corresponding Nod sequences. These Nod sequences were not only found existing in NC10 bacteria, but were also found forming some other clusters with Nod sequences from a WWTP reactor or contaminated aquifers. Moreover, a new subcluster in the aquifer-similar cluster was even dominant in the Zoige wetland and was named the Z-aquifer subcluster. Additionally, soils from the Zoige wetland showed a high potential rate (10.97 ± 1.42 nmol of CO₂ per gram of dry soil per day) for nitrite-dependent anaerobic methane oxidation (N-DAMO) with low abundance of NC10 bacteria, which may suggest a potential activity of Nod in other clusters when considering the dominance of the Z-aquifer subcluster Nod. In conclusion, we verified the occurrence of Nod in an alpine wetland for the first time and found a new subcluster to be dominant in the Zoige wetland. Moreover, this new subcluster of Nod may even be active in the N-DAMO process in this alpine wetland, which needs further study to confirm.</p>","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2018-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2018/6201541","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36811864","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}