{"entity": "journal", "iuid": "6b9f6f2bb240444cb6bfc51017bdda03", "timestamp": "2026-07-11T23:19:51.132Z", "links": {"self": {"href": "https://publications.scilifelab.se/journal/Syst.%20Appl.%20Microbiol..json"}, "display": {"href": "https://publications.scilifelab.se/journal/Syst.%20Appl.%20Microbiol."}}, "title": "Syst. Appl. Microbiol.", "issn": "1618-0984", "issn-l": "0723-2020", "publications_count": 2, "publications": [{"entity": "publication", "iuid": "405669a21c9d4811a34a94b06e265a98", "links": {"self": {"href": "https://publications.scilifelab.se/publication/405669a21c9d4811a34a94b06e265a98.json"}, "display": {"href": "https://publications.scilifelab.se/publication/405669a21c9d4811a34a94b06e265a98"}}, "title": "Depth-specific distribution of bacterial MAGs in permafrost active layer in Ny \u00c5lesund, Svalbard (79\u00b0N).", "authors": [{"family": "Sipes", "given": "Katie", "initials": "K"}, {"family": "Buongiorno", "given": "Joy", "initials": "J"}, {"family": "Steen", "given": "Andrew D", "initials": "AD"}, {"family": "Abramov", "given": "Andrey A", "initials": "AA"}, {"family": "Abuah", "given": "Chukwufumnanya", "initials": "C"}, {"family": "Peters", "given": "Samantha L", "initials": "SL"}, {"family": "Gianonne", "given": "Richard J", "initials": "RJ"}, {"family": "Hettich", "given": "Robert L", "initials": "RL"}, {"family": "Boike", "given": "Julia", "initials": "J"}, {"family": "Garcia", "given": "Sarahi L", "initials": "SL"}, {"family": "Vishnivetskaya", "given": "Tatiana A", "initials": "TA"}, {"family": "Lloyd", "given": "Karen G", "initials": "KG"}], "type": "journal article", "published": "2024-11-00", "journal": {"title": "Syst. Appl. Microbiol.", "issn": "1618-0984", "volume": "47", "issue": "6", "pages": "126544", "issn-l": "0723-2020"}, "abstract": "Arctic soil microbial communities may shift with increasing temperatures and water availability from climate change. We examined temperature and volumetric liquid water content (VWC) in the upper 80 cm of permafrost-affected soil over 2 years (2018-2019) at the Bayelva monitoring station, Ny \u00c5lesund, Svalbard. We show VWC increases with depth, whereas in situ temperature is more stable vertically, ranging from -5\u00b0C to 5 \u00b0C seasonally. Prokaryotic metagenome-assembled genomes (MAGs) were obtained at 2-4 cm vertical resolution collected while frozen in April 2018 and at 10 cm vertical resolution collected while thawed in September 2019. The most abundant MAGs were Acidobacteriota, Actinomycetota, and Chloroflexota. Actinomycetota and Chloroflexota increase with depth, while Acidobacteriota classes Thermoanaerobaculia Gp7-AA8, Blastocatellia UBA7656, and Vicinamibacteria Vicinamibacterales are found above 6 cm, below 6 cm, and below 20 cm, respectively. All MAGs have diverse carbon-degrading genes, and Actinomycetota and Chloroflexota have autotrophic genes. Genes encoding \u03b2 -glucosidase, N-acetyl-\u03b2-D-glucosaminidase, and xylosidase increase with depth, indicating a greater potential for organic matter degradation with higher VWC. Acidobacteriota dominate the top 6 cm with their classes segregating by depth, whereas Actinomycetota and Chloroflexota dominate below \u223c6 cm. This suggests that Acidobacteriota classes adapt to lower VWC at the surface, while Actinomycetota and Chloroflexota persist below 6 cm with higher VWC. This indicates that VWC may be as important as temperature in microbial climate change responses in Arctic mineral soils. Here we describe MAG-based Seqcode type species in the Acidobacteriota, Onstottus arcticum, Onstottus frigus, and Gilichinskyi gelida and in the Actinobacteriota, Mayfieldus profundus.", "doi": "10.1016/j.syapm.2024.126544", "pmid": "39303414", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0723-2020(24)00058-4"}], "notes": [], "created": "2024-10-18T07:13:55.740Z", "modified": "2025-02-28T14:13:09.272Z"}, {"entity": "publication", "iuid": "e416ac81a99a4283864d119c4bfdd9c0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e416ac81a99a4283864d119c4bfdd9c0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e416ac81a99a4283864d119c4bfdd9c0"}}, "title": "Tepidanaerobacter acetatoxydans sp. nov., an anaerobic, syntrophic acetate-oxidizing bacterium isolated from two ammonium-enriched mesophilic methanogenic processes.", "authors": [{"family": "Westerholm", "given": "Maria", "initials": "M"}, {"family": "Roos", "given": "Stefan", "initials": "S"}, {"family": "Schn\u00fcrer", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2011-06-00", "journal": {"volume": "34", "issn": "1618-0984", "issue": "4", "pages": "260-266", "title": "Syst. Appl. Microbiol.", "issn-l": "0723-2020"}, "abstract": "Four anaerobic syntrophic acetate-oxidizing bacteria, the thermotolerant strains Re1(T), Re2, T1 and T2, were isolated from two different mesophilic methanogenic systems. The strains originate from sludge of a continuously stirred laboratory-scale reactor containing high levels of ammonium and from a high ammonium enrichment culture. Comparative 16S rRNA gene sequence analysis confirmed that the strains belong to the Firmicutes-Clostridia class. The most closely related species to strains Re1(T), Re2, T1 and T2 was Tepidanaerobacter syntrophicus, with a 16S rRNA gene sequence identity of 96%. The DNA-DNA relatedness of strains Re2, T1 and T2 to strain Re1(T) was 92, 102, 81%, respectively. The gene encoding the acetogen key enzyme formyltetrahydrofolate synthetase (FTHFS) was detected and partly sequenced from the strains. In pure culture the bacteria used different organic compounds as carbon and energy source, such as organic acids, alcohols, sugars and amino acids. Furthermore, acetate-oxidizing ability was observed during co-cultivation with a hydrogen-consuming Methanoculleus sp. The bacteria were found to be spore-forming, rod-shaped and motile, and possessed Gram-positive cell walls. The four strains were thermotolerant and grew at temperatures between 25 and 55\u00b0C. Strain Re1(T) had a DNA G+C content of 38.4% and the major fatty acids were C(18:1) w7c, C(18:1) w9c, anteiso-C(17:0), C(16:1) w7c and C(18:0). The genetic and phenotypic properties of strains Re1(T), Re2, T1 and T2 suggest classification as representatives of a novel species of the genus Tepidanaerobacter; the name Tepidanaerobacter acetatoxydans sp. nov. is suggested. The type strain of T. acetatoxydans is Re1(T) (=DSM 21804(T)=JCM 16047(T)).", "doi": "10.1016/j.syapm.2010.11.018", "pmid": "21498020", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "S0723-2020(11)00014-2"}, {"db": "GENBANK", "key": "HQ290074"}, {"db": "GENBANK", "key": "HQ290075"}, {"db": "GENBANK", "key": "HQ290076"}, {"db": "GENBANK", "key": "HQ290077"}], "notes": [], "created": "2017-05-04T15:02:03.173Z", "modified": "2020-01-21T13:56:05.845Z"}], "created": "2017-05-09T09:12:07.713Z", "modified": "2020-11-27T13:14:06.180Z"}