Archaea is a peer-reviewed, Open Access journal that publishes original research articles as well as review articles dealing with all aspects of archaea, including environmental adaptation, enzymology, genetics and genomics, metabolism, molecular biology, molecular ecology, phylogeny, and ultrastructure. Bioinformatics studies and biotechnological implications of archaea will be considered. Published since 2002, Archaea provides a unique venue for exchanging information about these extraordinary prokaryotes.

Archaea is a peer-reviewed, Open Access journal that has been publishing since 2002. It focuses on all aspects of archaea, including environmental adaptation, enzymology, genetics and genomics, metabolism, molecular biology, molecular ecology, phylogeny, and ultrastructure. The journal also welcomes bioinformatics studies and the biotechnological implications of archaea. Archaea provides a unique platform for exchanging information about these extraordinary prokaryotes.

《Archaea》是一本经过同行评审的开放获取期刊，自2002年起出版，专注于古菌的各个方面，包括环境适应、酶学、遗传学与基因组学、代谢学、分子生物学、分子生态学、系统发育和超微结构。我们欢迎关于古菌的生物信息学研究和生物技术应用的文章。该期刊为研究这些非凡的原核生物提供了一个独特的信息交流平台。

Archaea

Lipid vectors are commonly used to facilitate the transfer of nucleic acids into mammalian cells. In this study, two fractions of tetraether lipids from the archaea Sulfolobus acidocaldarius were extracted and purified using different methods. The purified lipid fractions polar lipid fraction E (PLFE) and hydrolysed glycerol-dialkyl-nonitol tetraether (hGDNT) differ in their structures, charge, size, and miscibility from conventional lipids. Liposomes were prepared by mixing tetraether lipids with cholesterol (CH) and 1,2-dioleoyl-3-trimethylammonium-propane (DOTAP) resulting in stable vectors for gene delivery. Lipoplexes were prepared by complexation of liposomes with a luciferase expressing plasmid (pCMV-luc) at certain nitrogen-to-phosphorus (N/P) ratios and optimised for the transient transfection of ovarian adenocarcinoma cells (SK-OV-3). Complexation efficacy was investigated by gel-red fluorescence assay. Biophysical properties, like size, surface charge, and morphology, were investigated by differential light scattering (DLS), atomic force microscopy (AFM), and scanning electron microscopy (Cryo-SEM), respectively, revealing structural differences between liposomes and lipoplexes. A range of stable transfecting agents containing tetraether lipids were obtained by incorporating 5 mol% of tetraether lipids. Lipoplexes showed a decrease in free gel-red with increasing N/P ratios indicating efficient incorporation of plasmid DNA (pDNA) and remarkable stability. Transfection experiments of the lipoplexes revealed successful and superior transfection of SK-OV-3 cell line compared to the commercially available DOTAP and branched polyethyleneimine (25 kDa bPEI).

Konrad H. Engelhardt

Shashank Reddy Pinnapireddy

Elias Baghdan

Jarmila Jedelská

Udo Bakowsky

Transfection Studies with Colloidal Systems Containing Highly Purified Bipolar Tetraether Lipids fromSulfolobus acidocaldarius

利用含有高纯度双极四醚脂质的胶体系统进行转染研究：Sulfolobus acidocaldarius

Groundwater environments provide habitats for diverse microbial communities, and although Archaea usually represent a minor fraction of communities, they are involved in key biogeochemical cycles. We analysed the archaeal diversity within a mixed carbonate-rock/siliciclastic-rock aquifer system, vertically from surface soils to subsurface groundwater including aquifer and aquitard rocks. Archaeal diversity was also characterized along a monitoring well transect that spanned surface land uses from forest/woodland to grassland and cropland. Sequencing of 16S rRNA genes showed that only a few surface soil-inhabiting Archaea were present in the groundwater suggesting a restricted input from the surface. Dominant groups in the groundwater belonged to the marine group I (MG-I) Thaumarchaeota and the Woesearchaeota. Most of the groups detected in the aquitard and aquifer rock samples belonged to either cultured or predicted lithoautotrophs (e.g., Thaumarchaeota or Hadesarchaea). Furthermore, to target autotrophs, a series of 13CO2 stable isotope-probing experiments were conducted using filter pieces obtained after filtration of 10,000 L of groundwater to concentrate cells. These incubations identified the SAGMCG Thaumarchaeota and Bathyarchaeota as groundwater autotrophs. Overall, the results suggest that the majority of Archaea on rocks are fixing CO2, while archaeal autotrophy seems to be limited in the groundwater.

Cassandre Sara Lazar

Wenke Stoll

Robert Lehmann

Martina Herrmann

Valérie F. Schwab

Denise M. Akob

Ali Nawaz

Tesfaye Wubet

François Buscot

Kai-Uwe Totsche

Kirsten Küsel

Archaeal Diversity and CO2Fixers in Carbonate-/Siliciclastic-Rock Groundwater Ecosystems

碳酸盐/碎屑岩地下水生态系统中的古菌多样性与二氧化碳固定者

A 1.1 × 10 6 Da acidic exopolysaccharide (EPS) was purified from an extremely halophilic archaeon Haloarcula hispanica ATCC33960 with a production of 30 mg L −1 when grown in AS-168 medium, which mainly composed of mannose and galactose with a small amount of glucose in a molar ratio of 55.9 : 43.2 : 0.9. Two glycosyltransferase genes ( HAH_1662 and HAH_1667 ) were identified to be responsible for synthesis of the acidic EPS. Deletion of either HAH_1662 or HAH_1667 led to loss of the acidic EPS. The mutants displayed a different cell surface morphology, retarded growth in low salty environment, an increased adhesion, and swimming ability. Our results suggest that biosynthesis of the acidic EPS might act as an adaptable mechanism to protect the cells against harsh environments.

Yang Lü

Hua Lu

Shiwei Wang

Jing Han

Hua Xiang

Cheng Jin

An Acidic Exopolysaccharide fromHaloarcula hispanicaATCC33960 and Two Genes Responsible for Its Synthesis

来自Haloarcula hispanicaATCC33960的酸性胞外多糖及其合成相关的两个基因

Tetramethylammonium-degrading methanogenic consortia from a complete-mixing suspended sludge (CMSS) and an upflow anaerobic sludge blanket (UASB) reactors were studied using multiple PCR-based molecular techniques and shotgun proteomic approach. The prokaryotic 16S rRNA genes of the consortia were analyzed by quantitative PCR, high-throughput sequencing, and DGGE-cloning methods. The results showed that methanogenic archaea were highly predominant in both reactors but differed markedly according to community structure. Community and proteomic analysis revealed that Methanomethylovorans and Methanosarcina were the major players for the demethylation of methylated substrates and methane formation through the reduction pathway of methyl-S-CoM and possibly, acetyl-CoA synthase/decarbonylase-related pathways. Unlike high dominance of one Methanomethylovorans population in the CMSS reactor, diverse methylotrophic Methanosarcina species inhabited in syntrophy-like association with hydrogenotrophic Methanobacterium in the granular sludge of UASB reactor. The overall findings indicated the reactor-dependent community structures of quaternary amines degradation and provided microbial insight for the improved understanding of engineering application.

Wei-Yu Chen

Lucia Kraková

Jer-Horng Wu

Domenico Pangallo

Lenka Jeszeová

Bing Liu

Hidenari Yasui

Community and Proteomic Analysis of Anaerobic Consortia Converting Tetramethylammonium to Methane

厌氧共生体将四甲基铵转化为甲烷的社区与蛋白质组学分析

An integrated anaerobic fluidized-bed membrane bioreactor (IAFMBR) was investigated to treat synthetic high-strength benzothiazole wastewater (50 mg/L) at a hydraulic retention time (HRT) of 24, 18, and 12 h. The chemical oxygen demand (COD) removal efficiency (from 93.6% to 90.9%), the methane percentage (from 70.9% to 69.27%), and the methane yield (from 0.309 m 3 CH 4 /kg·COD removed to 0.316 m 3 CH 4 /kg·COD removed ) were not affected by decreasing HRTs. However, it had an adverse effect on membrane fouling (decreasing service period from 5.3 d to 3.2 d) and benzothiazole removal efficiency (reducing it from 97.5% to 82.3%). Three sludge samples that were collected on day 185, day 240, and day 297 were analyzed using an Illumina® MiSeq platform. It is striking that the dominant genus of archaea was always Methanosaeta despite of HRTs. The proportions of Methanosaeta were 80.6% (HRT 24), 91.9% (HRT 18), and 91.2% (HRT 12). The dominant bacterial genera were Clostridium in proportions of 23.9% (HRT 24), 16.4% (HRT 18), and 15.3% (HRT 12), respectively.

Yue Li

Qi Hu

Da-Wen Gao

Dynamics of Archaeal and Bacterial Communities in Response to Variations of Hydraulic Retention Time in an Integrated Anaerobic Fluidized-Bed Membrane Bioreactor Treating Benzothiazole Wastewater

厌氧流化床膜生物反应器处理苯并噻唑废水中水力停留时间变化对古菌和细菌群落动态的影响

Archaeal species encode a diversity of chromatin proteins that play distinct roles in genome compaction. Although our understanding of the individual proteins has been growing, their contributions to higher‐order folding in the archaeal chromosome remain to be explored. In this study, we investigated the chromatin structure of Thermoplasma volcanium, a euryarchaeon that encodes a heat‐unstable (HU) family protein (HUTvo) instead of histones. Atomic force microscopy revealed that the T. volcanium chromatin contains nucleoprotein structures of progressively increasing sizes, from 20 nm filaments to ~50 nm globules, indicative of higher‐order DNA folding. In vitro reconstitution showed that HUTvo wraps DNA similar to histones and forms highly compact yet disorganized nucleoprotein clusters on its own. Remarkably, HUTvo only dampens the formation of higher‐order structures by Alba. Our results provide an insight into how the interplay of chromatin proteins regulates genome compaction in histone‐free archaea.

Kirk Amerigo B. Aycardo

Eloise I. Prieto

Insights Into the Chromatin Structure of Thermoplasma volcanium: Archaeal HU Regulates Alba‐Mediated DNA Compaction

《Thermoplasma volcanium染色质结构的洞察：古菌HU调控Alba介导的DNA压缩》

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.

Madhan R. Tirumalai

Raghavan V. Sivaraman

Layla A. Kutty

Eric L. Song

George E. Fox

Ribosomal Protein Cluster Organization in Asgard Archaea

Asgard古菌中核糖体蛋白簇的组织结构

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 Halorubrum sp. LN27 and has a head-tailed morphotype with a contractile tail, typical of myoviruses. The average head diameter is <math xmlns="http://www.w3.org/1998/Math/MathML" id="M1"> <mn>64</mn> <mo>±</mo> <mn>2.0</mn> </math> nm, and uncontracted tails are <math xmlns="http://www.w3.org/1998/Math/MathML" id="M2"> <mn>15</mn> <mo>±</mo> <mn>1.0</mn> <mo>×</mo> <mn>65</mn> <mo>±</mo> <mn>2.0</mn> </math> nm. The latent period is about 10 h. The maturing time of VOLN27B in cells of Halorubrum sp. LN27 was nearly 8 h. The adsorption time of VOLN27B on cells of Halorubrum 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% ( <math xmlns="http://www.w3.org/1998/Math/MathML" id="M3"> <mi>w</mi> <mo>/</mo> <mi>v</mi> </math> ). VOLN27B and Halorubrum sp. LN27 were recovered from the same hypersaline environment and provide a new virus-host system in haloarchaea.

Shaoxing Chen

Yongpei Dai

Jingwen Liu

Shimin Zhang

Feilong Chen

Fanjie Jin

Peiyao Ruan

Lu Li

Xiangdong Chen

VOLN27B: A New Head-Tailed Halovirus Isolated from an Underground Salt Crystal and Infecting Halorubrum

VOLN27B：一种从地下盐晶体中分离的新型头尾噬菌体，感染盐生红球菌

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 Humulus lupulus. 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 Mycobacterium spp including Mycobacterium bovis, 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 Methanobrevibacter ruminantium, a major methane-producing archaeon found in the rumen of cattle.Methanobrevibacter ruminantium M1T (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.All of the extracts reduced the level of methane production of M. ruminantium 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.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.

J. A. Blaxland

A. J. Watkins

L. W. J. Baillie

The Ability of Hop Extracts to Reduce the Methane Production of Methanobrevibacter ruminantium

啤酒花提取物降低甲烷短杆菌甲烷产量的能力

Jin Li

Yu Tao

Guangbin Li

Cuijie Feng

Rong Chen

Ming Hua

Biological Processes for Pollution Control: Current Research and Emerging Technologies 2020

污染控制生物过程：当前研究与新兴技术 2020

Abbreviation
Journal Impact	2.26
Quartiles(Global)	MICROBIOLOGY(Q3)

ISSN	1472-3646, 1472-3654
h-index	48

Publication Information	Publisher: Hindawi Limited，Publishing cycle: ，Journal Type: journal，Open Access Journals: Yes
Basic data	Year of publication: 2023，Proportion of original research papers: 0.00%，Self Citation Rate:0.00%， Gold OA Rate: 100.00%
Journal Fees	$1550Details
Average review cycle	网友分享经验：>12周，或约稿
Average recruitment ratio	网友分享经验：较易

Archaea

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