NFDI4Microbiota – national research data infrastructure for microbiota research by Konrad U. Förstner, Anke Becker, Jochen Blom, Peer Bork, Thomas Clavel, Marius Dieckmann, Alexander Goesmann, Barbara Götz, Thomas Gübitz, Franziska Hufsky, Sebastian Jünemann, Marie-Louise Körner, Manja Marz, Ulisses Nunes Da Rocha, Jörg Overmann, Alfred Pühler, Dietrich Rebholz-Schuhmann, Alexander Sczyrba, Jens Stoye, Justine Vandendorpe, Thea Van Rossum, Alice McHardy

“…Microbes – bacteria, archaea, unicellular eukaryotes, and viruses – play an important role in human and environmental health. …”
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Metagenomic characterization of a novel non-ammonia-oxidizing Thaumarchaeota from hadal sediment by Ru-Yi Zhang, Yan-Ren Wang, Ru-Long Liu, Sung-Keun Rhee, Guo-Ping Zhao, Zhe-Xue Quan

“…While there have been several studies on Thaumarchaeota there, most of them have primarily focused on ammonia-oxidizing archaea (AOA). However, systematic metagenomic research specifically targeting heterotrophic non-AOA Thaumarchaeota is lacking. …”
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Effect of Post-Ruminal Urea Supply on Growth Performance of Grazing Nellore Young Bulls at Dry Season by Irene Alexandre Reis, Mailza Gonçalves de Souza, Yury Tatiana Granja-Salcedo, Isabela Pena Carvalho de Carvalho, Marco Aurélio De Felicio Porcionato, Laura Franco Prados, Gustavo Rezende Siqueira, Flávio Dutra De Resende

“…Animals supplemented with CONT showed a tendency to have more Bacteria and fewer Archaea (<i>p</i> = 0.086). In Exp. 2, there was a treatment effect for the disappearance rate of the supplement (<i>p</i> < 0.001). …”
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Linking Nitrous Oxide and Nitric Oxide Fluxes to Microbial Communities in Tropical Forest Soils and Oil Palm Plantations in Malaysia in Laboratory Incubations by Julia Drewer, Jun Zhao, Melissa M. Leduning, Peter E. Levy, Justin Sentian, Cécile Gubry-Rangin, Ute M. Skiba

“…Quantification of related gene transcripts implied that Proteobacterial nirS and AniA-nirK (betaproteobacterial clade of Neisseria) containing denitrifiers might continuously contribute to the N2O emissions, while the nitrifiers (ammonia oxidizing archaea in this study) are conditionally active to produce N2O. …”
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High-resolution vertical biogeochemical profiles in the hyporheic zone reveal insights into microbial methane cycling by T. Michaelis, A. Wunderlich, Ö. K. Coskun, W. Orsi, W. Orsi, T. Baumann, F. Einsiedl

“…Stable isotope measurements of CH<span class="inline-formula">₄</span> suggest that hydrogenotrophic methanogenesis represents a dominant pathway for CH<span class="inline-formula">₄</span> production in the HZ of the river Moosach, while a relatively high abundance of a novel group of methanogenic archaea, the <i>Candidatus</i> “Methanomethyliales” (phylum <i>Candidatus</i> “Verstraetearchaeota”), indicate that CH<span class="inline-formula">₄</span> production through H<span class="inline-formula">₂</span>-dependent methylotrophic methanogenesis might also be an important CH<span class="inline-formula">₄</span> source. …”
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Deletion of AA9 Lytic Polysaccharide Monooxygenases Impacts A. nidulans Secretome and Growth on Lignocellulose by César Rafael Fanchini Terrasan, Marcelo Ventura Rubio, Jaqueline Aline Gerhardt, João Paulo Franco Cairo, Fabiano Jares Contesini, Mariane Paludetti Zubieta, Fernanda Lopes de Figueiredo, Fernanda Lima Valadares, Thamy Lívia Ribeiro Corrêa, Mario Tyago Murakami, Telma Teixeira Franco, Gideon J. Davies, Paul H. Walton, Andre Damasio

“…ABSTRACT Lytic polysaccharide monooxygenases (LPMOs) are oxidative enzymes found in viruses, archaea, and bacteria as well as eukaryotes, such as fungi, algae and insects, actively contributing to the degradation of different polysaccharides. …”
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Effects of feed additives on rumen function and bacterial and archaeal communities during a starch and fructose challenge by H.M. Golder, S.E. Denman, C. McSweeney, P. Celi, I.J. Lean

“…A rumen sample was collected from each heifer via stomach tube weekly (d 0, 7, 14) and 5 times over a 3.6 h period at 5, 65, 115, 165, and 215 min after consumption of the challenge ration (d 21) and analyzed for pH, and ammonia, d- and l-lactate, volatile fatty acids (VFA), and histamine concentrations and total bacteria and archaea. The 16S rRNA gene spanning the V4 region was PCR amplified and sequenced. …”
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Genomics and prevalence of bacterial and archaeal isolates from biogas-producing microbiomes by Irena Maus, Andreas Bremges, Yvonne Stolze, Sarah Hahnke, Katharina G. Cibis, Daniela E. Koeck, Yong S. Kim, Jana Kreubel, Julia Hassa, Daniel Wibberg, Aaron Weimann, Sandra Off, Robbin Stantscheff, Vladimir V. Zverlov, Wolfgang H. Schwarz, Helmut König, Wolfgang Liebl, Paul Scherer, Alice C. McHardy, Alexander Sczyrba, Michael Klocke, Alfred Pühler, Andreas Schlüter

“…Results Novel cellulolytic, hydrolytic, and acidogenic/acetogenic Bacteria as well as methanogenic Archaea originating from different anaerobic digestion communities were analyzed on the genomic level to assess their role in biomass decomposition and biogas production. …”
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Student performance study: the outcomes of metabolic, molecular and physical-chemical characterization of intestinal tract microbiome on a four mammalian species model by Nataša CIBER, Tina ZUPANČIČ, Tamara ZORAN, Katarina ŠIMUNOVIĆ, Anja PUGELJ, Bojan PAPIĆ, Nika KLINEC, Andreja GAZVODA, Benjamin DRAKSLAR, Mateja DOLENC, Blaž STRES

“…Since the methodological approaches proved to be the largest source of systematic errors in comparisons of microbial communities among different organisms of the same species or between different species, we tested a number of methods on samples from different species of mammals in order to verify the feasibility of this approach for future routine analysis of microbiomes:(i) analyses of physical-chemical parameters;(ii)the metabolic properties of attached, planktonic fractions in comparison to the total;(iii)structure of microbial communities of bacteria and archaea; (iv)data analysis. We used a model of intestinal samples from four species of mammals, encompassing the differences between the various types of intestinal tracts: ruminants and rodents (such as pre- and post- peptic fermentors), omnivores and carnivores. …”
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Review: Diving into the cow hologenome to reduce methane emissions and increase sustainability by Oscar Gonzalez-Recio, Natalia Scrobota, Javier López-Paredes, Alejandro Saborío-Montero, Almudena Fernández, Evangelina López de Maturana, Beatriz Villanueva, Idoia Goiri, Raquel Atxaerandio, Aser García-Rodríguez

“…This study includes a genome-wide association analysis on the microbiota composition, considering the relative abundance of some microbial taxa previously associated to enteric methane in dairy cattle (Archaea, Dialister, Entodinium, Eukaryota, Lentisphaerae, Methanobrevibacter, Neocallimastix, Prevotella and Stentor). …”
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An in-depth investigation of the microbiota and its virulence factors associated with severe udder cleft dermatitis lesions by A.S. Vermeersch, M. Ali, Y. Gansemans, F. Van Nieuwerburgh, R. Ducatelle, P. Geldhof, D. Deforce, J. Callens, G. Opsomer

“…Through shotgun metagenomic sequencing, we found a high proportion of bacteria in addition to a low abundance of archaea. A distinct clustering of healthy udder skin versus UCD lesion samples was shown by applying principal component analysis and (sparse) partial least squares analysis on the metagenomic data. …”
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Investigating of the microbial communities in a red circle disease of sea cucumber based on metagenomic sequencing by Zhen Zhang, Yan Liu, Ziyan Wang, Zhonghua Wang, Jun Zhou, Jiaojiao Han, Chenyang Lu, Ye Li, Tinghong Ming, Xiurong Su

“…Metataxonomic analysis of ''red circle'' samples showed different domains, namely, bacteria (71.39%), virus (5.11%), archaea (0.15%), eukaryotes (0.06%), and some unclassified microbiota (23.29%). …”
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Comparative analysis of gut DNA viromes in wild and captive Himalayan vultures by Jundie Zhai, Jundie Zhai, You Wang, You Wang, Boyu Tang, Boyu Tang, Sisi Zheng, Shunfu He, Wenxin Zhao, Hanxi Chen, Hanxi Chen, Jun Lin, Jun Lin, Feng Li, Feng Li, Yuzi Bao, Yuzi Bao, Zhuoma Lancuo, Kirill Sharshov, Chuanfa Liu, Wen Wang

“…These families included viruses associated with bacteria, animals, plants, insects, and archaea. Phage communities, including Siphoviridae, Microviridae, Myoviridae, Inoviridae, and Herelleviridae, dominated the gut virome of Himalayan vultures. …”
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Rhizosphere soil nitrification ability controls nitrogen‐use efficiency in rice growth period by Haipeng Zhang, Fuxing Liao, Wanyi Li, Yunlong Li, Shuo Yang, Hongcheng Zhang, Yanju Yang, Yuhua Shan

“…The abundance of ammonia‐oxidizing bacteria (AOB), ammonia‐oxidizing archaea (AOA), and pH in YC rhizosphere soils were always higher than in JR rhizosphere soils. …”
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Genome-Wide Characterization of Nitrogenase Reductase (<i>nifH</i>) Genes in the Sweet Potato [<i>Ipomoea batatas</i> (L.) Lam] and Its Wild Ancestors by Zengzhi Si, Chong Wang, Mingming Zhao, Zhixin Ji, Yake Qiao, Lianjun Wang

“…Lam.) is an important and widely grown crop, and the nitrogenase reductase (<i>nifH</i>) gene is the most widely sequenced marker gene used to identify nitrogen-fixing bacteria and archaea. There have been many examples of the isolation of the diazotrophic endophytes in sweet potatoes, and there has been no report on whether sweet potatoes and their wild ancestors harbored <i>nifH</i> genes. …”
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An Endogenous Staphylococcus aureus CRISPR-Cas System Limits Phage Proliferation and Is Efficiently Excised from the Genome as Part of the SCCmec Cassette by Kasper Mikkelsen, Janine Zara Bowring, Yong Kai Ng, Frida Svanberg Frisinger, Julie Kjærsgaard Maglegaard, Qiuchun Li, Raphael N. Sieber, Andreas Petersen, Paal Skytt Andersen, Jakob T. Rostøl, Nina Molin Høyland-Kroghsbo, Hanne Ingmer

“…IMPORTANCE CRISPR-Cas is an adaptive immune system protecting bacteria and archaea against mobile genetic elements such as phages. …”
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Community composition and abundance of complete ammonia oxidation (comammox) bacteria in the Lancang River cascade reservoir by Hang Ding, Jiahui Zhang, Yuchun Wang, Mingming Hu, Jie Wen, Shanze Li, Yufei Bao, Jianwei Zhao

“…In these reservoirs, the average amoA gene abundance of clade A and clade B of comammox bacteria, ammonia-oxidizing archaea (AOA), and ammonia-oxidizing bacteria (AOB) was 4.16 ± 0.85 × 105, 1.15 ± 0.33 × 105, 7.39 ± 2.31 × 104, and 3.28 ± 0.99 × 105 copies g−1, respectively. …”
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Pathways of methane removal in the sediment and water column of a seasonally anoxic eutrophic marine basin by Olga M. Żygadłowska, Jessica Venetz, Robin Klomp, Robin Klomp, Wytze K. Lenstra, Niels A. G. M. van Helmond, Niels A. G. M. van Helmond, Thomas Röckmann, Anna J. Wallenius, Paula Dalcin Martins, Paula Dalcin Martins, Annelies J. Veraart, Mike S. M. Jetten, Caroline P. Slomp, Caroline P. Slomp

“…Analyses of 16S rRNA gene sequences retrieved from the water column reveal the presence of aerobic CH4 oxidizing bacteria (Methylomonadaceae) and anaerobic methanotrophic archaea (Methanoperedenaceae), with the latter potentially capable of NO3- and/or metal-oxide dependent CH4 oxidation, near the oxycline. …”
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A georeferenced rRNA amplicon database of aquatic microbiomes from South America by Sebastian Metz, Paula Huber, Erick Mateus-Barros, Pedro C. Junger, Michaela de Melo, Inessa Lacativa Bagatini, Irina Izaguirre, Mariana Câmara dos Reis, Maria E. Llames, Victoria Accattatis, María Victoria Quiroga, Melina Devercelli, María Romina Schiaffino, Juan Pablo Niño-García, Marcela Bastidas Navarro, Beatriz Modenutti, Helena Vieira, Martin Saraceno, Carmen Alejandra Sabio y García, Emiliano Pereira, Alvaro González-Revello, Claudia Piccini, Fernando Unrein, Cecilia Alonso, Hugo Sarmento

“…Measurement(s) taxonomic diversity assessment by targeted gene survey Technology Type(s) next generation DNA sequencing Sample Characteristic - Organism Bacteria • Archaea Sample Characteristic - Environment aquatic environment Sample Characteristic - Location South America…”
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Microbial Hotspots in Lithic Microhabitats Inferred from DNA Fractionation and Metagenomics in the Atacama Desert by Dirk Schulze-Makuch, Daniel Lipus, Felix L. Arens, Mickael Baqué, Till L. V. Bornemann, Jean-Pierre de Vera, Markus Flury, Jan Frösler, Jacob Heinz, Yunha Hwang, Samuel P. Kounaves, Kai Mangelsdorf, Rainer U. Meckenstock, Mark Pannekens, Alexander J. Probst, Johan S. Sáenz, Janosch Schirmack, Michael Schloter, Philippe Schmitt-Kopplin, Beate Schneider, Jenny Uhl, Gisle Vestergaard, Bernardita Valenzuela, Pedro Zamorano, Dirk Wagner

“…The gypsum crusts are dominated by methylotrophs and heterotrophic phototrophs, mostly Chloroflexi, and the salt rocks (halite nodules) by phototrophic and halotolerant endoliths, mostly Cyanobacteria and Archaea. The major environmental constraints in the organic-poor arid and hyperarid Atacama Desert are water availability and UV irradiation, allowing phototrophs and other extremophiles to play a key role in desert ecology.…”
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