Journal: The ISME Journal

Article Title: Quantification of archaea-driven freshwater nitrification from single cell to ecosystem levels

doi: 10.1038/s41396-022-01216-9

Figure Lengend Snippet: The phylogenomic maximum likelihood tree was re-constructed using the IQ-tree algorithm on the basis of a concatenated amino acid alignment of 122 translated single-copy genes that were established by the GTDB-based taxonomy for phylogenetic inference of archaea . Branch support was tested with the Shimodaira–Hasegawa approximate likelihood-ratio test (SH-aLRT; 1000 replicates) and ultrafast bootstrap (1000 replicates) using the IQ-tree software package . Branch support was set as significant at ≥80% for SH-aLRT and ≥95% for ultrafast bootstrap values (black semi-circles for significant and white for non-significant). Non-AOA “Thaumarchaeota” archaeon sp. BS3 (IMG Taxon ID 2721755844), unclassified “Thaumarchaeota” DRTY-7 bin 36 (2263082001), and “Thaumarchaeota” archaeon strain DS1 (2263082000) were used as outgroup. The scale bar indicates 10% estimated amino acid sequence divergence. Accession numbers or respective Taxon IDs can be found in Supplementary Table .

Article Snippet: Non-AOA “Thaumarchaeota” archaeon sp. BS3 (IMG Taxon ID 2721755844), unclassified “Thaumarchaeota” DRTY-7 bin 36 (2263082001), and “Thaumarchaeota” archaeon strain DS1 (2263082000) were used as outgroup.

Techniques: Construct, Software, Sequencing

Journal: Science Advances

Article Title: Genomic remnants of ancestral methanogenesis and hydrogenotrophy in Archaea drive anaerobic carbon cycling

doi: 10.1126/sciadv.abm9651

Figure Lengend Snippet: ( A ) Diagram of individual metabolic pathways comprising the different types of methanogenesis, AMO, and anaerobic alkane oxidation (AAO). Colored dots correspond to CO 2 -reducing hydrogenotrophic methanogenesis or AMO (red), acetoclastic methanogenesis (orange), methyl-dismutating methanogenesis (pink), methoxyl-dismutating methanogenesis (turquoise), methyl-dependent hydrogenotrophic methanogenesis (blue), and AAO (purple). We have adopted the following simplifications: (i) The dashed line connecting CO 2 with methyl-H 4 MPT corresponds to the WLP H 4 MPT methyl branch, disregarding small variations in the enzymes used, and the cases where formate is used as a substrate for methanogenesis; (ii) the dashed line from R-CH 2 -S-CoM to acetyl–coenzyme A (CoA) corresponds to β oxidation. The AAO pathways (long-chain alkanes, coupled to methanogenesis) are modeled after ; (iii) for the conversion from acetate to acetyl-CoA, we do not discriminate whether it is performed in one (acetyl-CoA synthetase) or two (acetate kinase and phosphate transacetylase) reactions and include it only for acetoclastic methanogens even if the genes are present elsewhere; (iv) we overlook the H 4 MPT branch and Mtr in Methanosphaera , as they are not used in its methyl-dependent hydrogenotrophic methanogenesis. ( B ) ML phylogeny of Archaea, based on a supermatrix of 36 Phylosift markers (6021 amino acid positions) rooted at the DPANN*. Euryarchaeota* contain Thermococci, Hadarchaeia, Methanomada*, Thermoplasmatota, and Halobacteriota. Black circles indicate strongly supported branches (ultrafast bootstrap ≥ 95, aLRT SH-like ≥ 80), and other colored circles correspond to the metabolisms in (A). Any non-GTDB nomenclature is marked with an asterisk. For GTDB names without standard taxonomic suffixes, we use the taxonomic rank double underscore designation of GTDB. GTDB names and taxonomy correspond to r202. In phylogeny labels or elsewhere where NCBI names are used in conjunction with assembly accessions, we omit asterisks. Additional remarks on the phylogeny are given in Supplementary Results and Discussion.

Article Snippet: The National Center for Biotechnology Information (NCBI) taxon “Euryarchaeota archaeon JdFR-21” possesses five remnant methanogenesis markers, more than any other nonmethane/alkane-metabolizing archaeon.

Techniques:

Journal: Scientific Reports

Article Title: Environmental selection of planktonic methanogens in permafrost thaw ponds

doi: 10.1038/srep31312

Figure Lengend Snippet: A Thaumarchaeota archaeon was used as the outgroup. The values at each node represent the percentage bootstrap confidence values using 1,000 replications; only values over 60% are shown. Branches containing methanogenic taxa are in red and for other Euryarchaeota are in blue.

Article Snippet: 10585 , 1255 , SAS (3%) , Methanoregula , 98 , JF304133 , uncultured archaeon , outfall sediment.

Techniques:

Journal: Scientific Reports

Article Title: Environmental selection of planktonic methanogens in permafrost thaw ponds

doi: 10.1038/srep31312

Figure Lengend Snippet: Identity of the 5 most abundant OTUs (based on 16S rRNA sequences) for each valley following the lowest taxonomic level of the SILVA modified database 52 .

Article Snippet: 10585 , 1255 , SAS (3%) , Methanoregula , 98 , JF304133 , uncultured archaeon , outfall sediment.

Techniques: Modification, Isolation