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You searched for: Subject "Archaea" Remove constraint Subject: "Archaea"
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1. Coupling methanotrophic denitrification to anammox in a moving bed biofilm reactor for nitrogen removal under hypoxic conditions

Author:
Ting Xie; Xinyu Liu; Yiming Xu; Samuel Bryson; Lu Zhao; Kai Huang; Shiqi Huang; Xiaoming Li; Qi Yang; Huiyu Dong; Mari-Karoliina H. Winkler
Source:
Science of the total environment 2023 v.856 pp. 158795
ISSN:
0048-9697
Subject:
Archaea,   etc   ; Comamonadaceae; Ignavibacteriaceae; Methylobacter; Methylomonas; Methylophilaceae; Opitutaceae; Thauera; ammonium; anaerobic ammonium oxidation; biochemical pathways; biofilm; denitrification; denitrifying microorganisms; environment; fish; genes; methane; methanol; methanotrophs; nitrates; nitrites; nitrogen;     Show all 23 Subjects
Abstract:
... Simultaneous removal of ammonium and nitrate was achieved in a methane-fed moving bed biofilm reactor (MBBR). In the reactor, methanotrophic microorganisms oxidized methane under hypoxic conditions likely to methanol, hence providing an electron donor to denitrifiers to reduce nitrate to nitrite that then allowed anaerobic ammonium oxidizing bacteria (Anammox) to remove excess ammonium as N₂. The ...
DOI:
10.1016/j.scitotenv.2022.158795

2. Temporal profiling resolves the drivers of microbial nitrogen cycling variability in coastal sediments

Author:
Alexis J. Marshall; Lori Phillips; Andrew Longmore; Helen L. Hayden; Karla B. Heidelberg; Caixian Tang; Pauline Mele
Source:
Science of the total environment 2023 v.856 pp. 159057
ISSN:
0048-9697
Subject:
Archaea,   etc   ; DNA; RNA; ammonium; anaerobic ammonium oxidation; coastal zone management; detection limit; environment; genes; microbial activity; microbial nitrogen; nitrates; nitrites; nitrogen fixation; oxidation; phylogeny; seasonal variation; sediments; Australia;     Show all 19 Subjects
Abstract:
... Here we describe the potential for sediment microbial nitrogen-cycling gene (DNA) and activity (RNA) abundances to spatially resolve coastal areas impacted by seasonal variability in external nutrient inputs. Three sites were chosen within a nitrogen-limited embayment, Port Phillip Bay (PPB), Australia that reflect variability in both proximity to external nutrient inputs and the dominant form of ...
DOI:
10.1016/j.scitotenv.2022.159057

3. Exclusion of fast evolving genes or fast evolving sites produces different archaean phylogenies

Author:
A.A. Superson; F.U. Battistuzzi
Source:
Molecular phylogenetics and evolution 2022 v.170 pp. 107438
ISSN:
1055-7903
Subject:
Archaea,   etc   ; case studies; data collection; phylogeny;     Show all 4 Subjects
Abstract:
... The large size of modern datasets has inspired a variety of strategies to alter genes, sites and/or species compositions to improve the accuracy of phylogenetic reconstructions. Each of these data-filtering approaches leads to the exclusion of different types of data, which is known to affect phylogenetic outcome. However, the choice of a filtering strategy is often subjective and the robustness o ...
DOI:
10.1016/j.ympev.2022.107438

4. A Plea for Considering Processes That Take Place on the Micrometer Scale in Modelling the Groundwater Ecosystems’ Functions

Author:
Susanne I. Schmidt
Source:
Water 2022 v.14 no.12 pp. -
ISSN:
2073-4441
Subject:
Archaea,   etc   ; bioremediation; freshwater ecosystems; groundwater; models;     Show all 5 Subjects
Abstract:
... The largest freshwater ecosystem on earth is in the subsurface: the groundwater. It is populated by animals of almost all phyla and by bacteria, archaea, and fungi. Processes on the macro-, meso-, and micro-scale shape this ecosystem. Bioremediation, i.e., the degradation of contaminants, is steered on the scale of micrometers. However, processes that take place on the micrometer scale are still p ...
DOI:
10.3390/w14121850

5. Special Issue: The Role of Microorganisms in the Evolution of Animals and Plants

Author:
Eugene Rosenberg; Ilana Zilber-Rosenberg
Source:
Microorganisms 2022 v.10 no.2 pp. -
ISSN:
2076-2607
Subject:
Archaea,   etc   ; animals; bacteria; evolution; planting; viruses;     Show all 6 Subjects
Abstract:
... It is now well established that all animals and plants harbor abundant and diverse microorganisms, including bacteria, archaea, viruses, and eukaryotic microorganisms [...] ...
DOI:
10.3390/microorganisms10020250

6. How to Shut Down Transcription in Archaea during Virus Infection

Author:
Simona Pilotto; Finn Werner
Source:
Microorganisms 2022 v.10 no.9 pp. -
ISSN:
2076-2607
Subject:
Archaea,   etc   ; RNA; active sites; transcription termination; viruses;     Show all 5 Subjects
Abstract:
... Multisubunit RNA polymerases (RNAPs) carry out transcription in all domains of life; during virus infection, RNAPs are targeted by transcription factors encoded by either the cell or the virus, resulting in the global repression of transcription with distinct outcomes for different host–virus combinations. These repressors serve as versatile molecular probes to study RNAP mechanisms, as well as ai ...
DOI:
10.3390/microorganisms10091824

7. Diverse heliorhodopsins detected via functional metagenomics in freshwater Actinobacteria, Chloroflexi and Archaea

Author:
Ariel Chazan; Andrey Rozenberg; Kentaro Mannen; Takashi Nagata; Ran Tahan; Shir Yaish; Shirley Larom; Keiichi Inoue; Oded Béjà; Alina Pushkarev
Source:
Environmental microbiology 2022 v.24 no.1 pp. 110-121
ISSN:
1462-2912
Subject:
Archaea,   etc   ; Actinobacteria; Chloroflexi; freshwater; metagenomics; microbiology; rhodopsin;     Show all 7 Subjects
Abstract:
... The recently discovered rhodopsin family of heliorhodopsins (HeRs) is abundant in diverse microbial environments. So far, the functional and biological roles of HeRs remain unknown. To tackle this issue, we combined experimental and computational screens to gain some novel insights. Here, 10 readily expressed HeR genes were found using functional metagenomics on samples from two freshwater environ ...
DOI:
10.1111/1462-2920.15890

8. Feeding by heterotrophic flagellates on marine archaea

Author:
Moo Joon Lee; Yeong Du Yoo; Kyeong Ah Seong; Hee Yeon Yang; Yi Gu Kang; Sung-Keun Rhee; Jong-Geol Kim; Gyu Gil Lee; Sung Ki Lee; Woongghi Shin; Jong Seong Ryu
Source:
Regional studies in marine science 2022 v.56 pp. 102665
ISSN:
2352-4855
Subject:
Archaea,   etc   ; Oxyrrhis marina; ingestion; marine science; protists;     Show all 5 Subjects
Abstract:
... Archaea live in diverse habitats including extreme environments. Although they are sometimes the dominant heterotrophic organisms in microbial communities, relatively little is known about their ecological roles in microbial food webs. To explore predator–prey relationships between archaea and heterotrophic protists, we determined feeding occurrence by the heterotrophic nanoflagellates Bodo sp., G ...
DOI:
10.1016/j.rsma.2022.102665

9. Solar salterns as model systems to study the units of bacterial diversity that matter for ecosystem functioning

Author:
Konstantinos T Konstantinidis; Tomeu Viver; Roth E Conrad; Stephanus N Venter; Ramon Rossello-Mora
Source:
Current opinion in biotechnology 2022 v.73 pp. 151-157
ISSN:
0958-1669
Subject:
Archaea,   etc   ; biotechnology; ecosystems; genetic variation; metagenomics; time series analysis;     Show all 6 Subjects
Abstract:
... Microbial communities often harbor overwhelming species and gene diversity, making it challenging to determine the important units to study this diversity. We argue that the reduced, and thus tractable, microbial diversity of manmade salterns provides an ideal system to advance this cornerstone issue. We review recent time-series genomic and metagenomic studies of the saltern-dominating bacterial ...
DOI:
10.1016/j.copbio.2021.07.028

10. Structural characterisation of a MAPR‐related archaeal cytochrome b5M protein

Author:
Sarah Teakel; Michealla Marama; David Aragão; Sofiya Tsimbalyuk; Emily R. R. Mackie; Tatiana P. Soares da Costa; Jade K. Forwood; Michael A. Cahill
Source:
FEBS letters 2022 v.596 no.18 pp. 2409-2417
ISSN:
0014-5793
Subject:
Archaea,   etc   ; ancestry; crystal structure; genes; heme; mammals; progesterone receptors;     Show all 7 Subjects
Abstract:
... We recently reported that the membrane‐associated progesterone receptor (MAPR) protein family (mammalian members: PGRMC1, PGRMC2, NEUFC and NENF) originated from a new class of prokaryotic cytochrome b₅ (cytb₅) domain proteins, called cytb₅M (MAPR‐like). Relative to classical cytb₅ proteins, MAPR and ctyb₅M proteins shared unique sequence elements and a distinct heme‐binding orientation at an appr ...
DOI:
10.1002/1873-3468.14471

11. Archaea Carotenoids: Natural Pigments with Unexplored Innovative Potential

Author:
Antoine Grivard; Isabelle Goubet; Luiz Miranda de Souza Duarte Filho; Valérie Thiéry; Sylvie Chevalier; Raimundo Gonçalves de Oliveira-Junior; Noureddine El Aouad; Jackson Roberto Guedes da Silva Almeida; Przemysław Sitarek; Lucindo José Quintans-Junior; Raphaël Grougnet; Hélène Agogué; Laurent Picot
Source:
Marine drugs 2022 v.20 no.8 pp. -
ISSN:
1660-3397
Subject:
Archaea,   etc   ; biotechnology; carotenoids; ecological function; medicine; metabolism; metabolites; pharmacology;     Show all 8 Subjects
Abstract:
... For more than 40 years, marine microorganisms have raised great interest because of their major ecological function and their numerous applications for biotechnology and pharmacology. Particularly, Archaea represent a resource of great potential for the identification of new metabolites because of their adaptation to extreme environmental conditions and their original metabolic pathways, allowing ...
DOI:
10.3390/md20080524

12. Environmental similarity is more important than distance in community structuring processes of AOA in agricultural soils

Author:
Dorsaf KERFAHI; Yu SHI; Baozhan WANG; Hokyung SONG; Haiyan CHU; Jonathan M. ADAMS
Source:
Pedosphere 2022 pp. -
ISSN:
1002-0160
Subject:
Archaea,   etc   ; ammonia; community structure; genes; phylogeny; soil pH; China;     Show all 7 Subjects
Abstract:
... Archaeal ammonia oxidizers (AOA) are important in converting ammonia into nitrates in soils. While many aspects of their community structure have been studied, the relative importance of stochastic versus deterministic processes has been poorly understood. We compared AOA communities across the North China Plain, targeting the amoA gene. A phylogenetic null modelling approach was used to calculate ...
DOI:
10.1016/j.pedsph.2022.09.004

13. Microbial communities in crude oil phase and filter‐graded aqueous phase from a Daqing oilfield after polymer flooding

Author:
Yan‐Feng Wei; Lu Wang; Zi‐Yuan Xia; Min Gou; Zhao‐Yong Sun; Wei‐Feng Lv; Yue‐Qin Tang
Source:
Journal of applied microbiology 2022 v.133 no.2 pp. 842-856
ISSN:
1364-5072
Subject:
Archaea,   etc   ; bacterial communities; genes; oil fields; oils; petroleum; polymers;     Show all 7 Subjects
Abstract:
... AIMS: The aim was to characterize indigenous micro‐organisms in oil reservoirs after polymer flooding (RAPF). METHODS: The microbial communities in the crude oil phase (Oil) and in the filter‐graded aqueous phases Aqu0.22 (>0.22 μm) and Aqu0.1 (0.1–0.22 μm) were investigated by 16S rRNA gene high‐throughput sequencing. RESULTS: Indigenous micro‐organisms related to hydrocarbon degradation prevaile ...
DOI:
10.1111/jam.15603

14. Proton transfer reactions in donor site mutants of ESR, a retinal protein from Exiguobacterium sibiricum

Author:
Lada E. Petrovskaya; Evgeniy P. Lukashev; Sergey A. Siletsky; Eleonora S. Imasheva; Jennifer M. Wang; Mahir D. Mamedov; Elena A. Kryukova; Dmitriy A. Dolgikh; Andrei B. Rubin; Mikhail P. Kirpichnikov; Sergei P. Balashov; Janos K. Lanyi
Source:
Journal of photochemistry and photobiology 2022 v.234 pp. 112529
ISSN:
1011-1344
Subject:
Archaea,   etc   ; Exiguobacterium; glutamic acid; pH; photobiology; photochemistry; schiff bases;     Show all 7 Subjects
Abstract:
... Light-driven proton transport by microbial retinal proteins such as archaeal bacteriorhodopsin involves carboxylic residues as internal proton donors to the catalytic center which is a retinal Schiff base (SB). The proton donor, Asp96 in bacteriorhodopsin, supplies a proton to the transiently deprotonated Schiff base during the photochemical cycle. Subsequent proton uptake resets the protonated st ...
DOI:
10.1016/j.jphotobiol.2022.112529

15. Novel primers for 16S rRNA gene-based archaeal and bacterial community analysis in oceanic trench sediments

Author:
Na Yang; Chen Tian; Yongxin Lv; Jialin Hou; Zhifeng Yang; Xiang Xiao; Yu Zhang
Source:
Applied microbiology and biotechnology 2022 v.106 no.7 pp. 2795-2809
ISSN:
0175-7598
Subject:
Archaea,   etc   ; bacterial communities; biotechnology; computer simulation; genes; ribosomal RNA; topology;     Show all 7 Subjects
Abstract:
... High-throughput sequencing of the 16S ribosomal RNA (16S rRNA) gene has been successfully applied to explore the microbial structure and dynamics in various environments. The distinctive microbial communities in oceanic trench sediments are expected because of the extremely high pressure and V-shape topology that caused the isolation from the other marine sediments. However, they have only been pr ...
DOI:
10.1007/s00253-022-11893-3

16. From Surface to Subsurface: Diversity, Composition, and Abundance of Sessile and Endolithic Bacterial, Archaeal, and Eukaryotic Communities in Sand, Clay and Rock Substrates in the Laurentians (Quebec, Canada)

Author:
Julia Meyer; Sheri Zakhary; Marie Larocque; Cassandre S. Lazar
Source:
Microorganisms 2022 v.10 no.1 pp. -
ISSN:
2076-2607
Subject:
Archaea,   etc   ; DNA; aquifers; eukaryotic cells; groundwater; habitats; plankton; sand; Quebec;     Show all 9 Subjects
Abstract:
... Microbial communities play an important role in shallow terrestrial subsurface ecosystems. Most studies of this habitat have focused on planktonic communities that are found in the groundwater of aquifer systems and only target specific microbial groups. Therefore, a systematic understanding of the processes that govern the assembly of endolithic and sessile communities is still missing. This stud ...
DOI:
10.3390/microorganisms10010129

17. Diversity of Novel Uncultured Prokaryotes in Microbial Communities of the Yessentukskoye Underground Mineral Water Deposit

Author:
S. N. Gavrilov; E. G. Potapov; M. I. Prokof’eva; A. A. Klyukina; A. Yu. Merkel; A. A. Maslov; D. G. Zavarzina
Source:
Microbiology 2022 v.91 no.1 pp. 28-44
ISSN:
0026-2617
Subject:
Archaea,   etc   ; Actinobacteria; genes; genomics; hydrochemistry; metadata; mineral water; prokaryotic cells;     Show all 8 Subjects
Abstract:
... Caucasian Mineral Waters is a unique territory, where various types of mineral waters with overall daily flow over 16 000 m³ are concentrated in a relatively small area. The Yessentukskoye deposit is characterized by high diversity of water types, of which Yessentuki nos. 17 and 4 are produced in the greatest amounts. Biogeochemical activity of microorganisms inhabiting the subsurface hydrosphere ...
DOI:
10.1134/S0026261722010039

18. The Historical Development of Cultivation Techniques for Methanogens and Other Strict Anaerobes and Their Application in Modern Microbiology

Author:
Nikola Hanišáková; Monika Vítězová; Simon K. -M. R. Rittmann
Source:
Microorganisms 2022 v.10 no.2 pp. -
ISSN:
2076-2607
Subject:
Archaea,   etc   ; air; anaerobes; biotechnology; methanogens; microbial physiology; new species; oxygen;     Show all 8 Subjects
Abstract:
... The cultivation and investigation of strictly anaerobic microorganisms belong to the fields of anaerobic microbial physiology, microbiology, and biotechnology. Anaerobic cultivation methods differ from classic microbiological techniques in several aspects. The requirement for special instruments, which are designed to prevent the contact of the specimen with air/molecular oxygen by different means ...
DOI:
10.3390/microorganisms10020412

19. Metagenomic Assessment of DNA Viral Diversity in Freshwater Sponges, Baikalospongia bacillifera

Author:
Tatyana V. Butina; Ivan S. Petrushin; Igor V. Khanaev; Yurij S. Bukin
Source:
Microorganisms 2022 v.10 no.2 pp. -
ISSN:
2076-2607
Subject:
Archaea,   etc   ; DNA; Porifera; data collection; freshwater; host range; metagenomics; taxonomy;     Show all 8 Subjects
Abstract:
... Sponges (type Porifera) are multicellular organisms that give shelter to a variety of microorganisms: fungi, algae, archaea, bacteria, and viruses. The studies concerning the composition of viral communities in sponges have appeared rather recently, and the diversity and role of viruses in sponge holobionts remain largely undisclosed. In this study, we assessed the diversity of DNA viruses in the ...
DOI:
10.3390/microorganisms10020480

20. First evidence for anaerobic oxidation of methane process in landfill cover soils: Activity and responsible microorganisms

Author:
Sai Xu; Houhu Zhang
Source:
Science of the total environment 2022 v.841 pp. 156790
ISSN:
0048-9697
Subject:
Archaea,   etc   ; environment; landfills; methane; nitrates; nitrites; oxidation; quantitative polymerase chain reaction;     Show all 8 Subjects
Abstract:
... Landfill cover soils (LCS) play important roles in mitigating methane emissions from landfills. Anaerobic oxidation of methane (AOM) has been demonstrated as a potential methane removal process in aquatic ecosystems. However, whether AOM could occur in LCS is largely unknown. Here, microcosm incubations with ¹³CH₄ were applied to track the potential activities of AOM and quantitative PCR was used ...
DOI:
10.1016/j.scitotenv.2022.156790