{"entity": "journal", "iuid": "f4ec4b00603848b094956f14e7524bac", "timestamp": "2026-08-15T12:37:18.244Z", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/journal/Environ%20Microbiol%20Rep.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/journal/Environ%20Microbiol%20Rep"}}, "title": "Environ Microbiol Rep", "issn": "1758-2229", "issn-l": "1758-2229", "publications_count": 4, "publications": [{"entity": "publication", "iuid": "056a4d2607254601b94545a99d3a0ad9", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/056a4d2607254601b94545a99d3a0ad9.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/056a4d2607254601b94545a99d3a0ad9"}}, "title": "The novel bacterial phylum Calditrichaeota is diverse, widespread and abundant in marine sediments and has the capacity to degrade detrital proteins.", "authors": [{"family": "Marshall", "given": "Ian P G", "initials": "IPG"}, {"family": "Starnawski", "given": "Piotr", "initials": "P"}, {"family": "Cupit", "given": "Carina", "initials": "C"}, {"family": "Fern\u00e1ndez C\u00e1ceres", "given": "Eva", "initials": "E"}, {"family": "Ettema", "given": "Thijs J G", "initials": "TJG"}, {"family": "Schramm", "given": "Andreas", "initials": "A"}, {"family": "Kjeldsen", "given": "Kasper U", "initials": "KU"}], "type": "journal article", "published": "2017-08-00", "journal": {"title": "Environ Microbiol Rep", "issn": "1758-2229", "volume": "9", "issue": "4", "pages": "397-403", "issn-l": "1758-2229"}, "abstract": "Calditrichaeota is a recently recognized bacterial phylum with three cultured representatives, isolated from hydrothermal vents. Here we expand the phylogeny and ecology of this novel phylum with metagenome-derived and single-cell genomes from six uncultivated bacteria previously not recognized as members of Calditrichaeota. Using 16S rRNA gene sequences from these genomes, we then identified 322 16S rRNA gene sequences from cultivation-independent studies that can now be classified as Calditrichaeota for the first time. This dataset was used to re-analyse a collection of 16S rRNA gene amplicon datasets from marine sediments showing that the Calditrichaeota are globally distributed in the seabed at high abundance, making up to 6.7% of the total bacterial community. This wide distribution and high abundance of Calditrichaeota in cold marine sediment has gone unrecognized until now. All Calditrichaeota genomes show indications of a chemoorganoheterotrophic metabolism with the potential to degrade detrital proteins through the use of extracellular peptidases. Most of the genomes contain genes encoding proteins that confer O", "doi": "10.1111/1758-2229.12544", "pmid": "28488795", "labels": {"Affiliated researcher": null}, "xrefs": [], "notes": [], "created": "2018-12-05T12:29:32.384Z", "modified": "2018-12-05T12:29:32.402Z"}, {"entity": "publication", "iuid": "1ed4406f20e54e6ebf7d30564860ae53", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1ed4406f20e54e6ebf7d30564860ae53.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1ed4406f20e54e6ebf7d30564860ae53"}}, "title": "Successful enrichment of the ubiquitous freshwater acI Actinobacteria.", "authors": [{"family": "Garcia", "given": "Sarahi L", "initials": "SL"}, {"family": "McMahon", "given": "Katherine D", "initials": "KD"}, {"family": "Grossart", "given": "Hans-Peter", "initials": "HP"}, {"family": "Warnecke", "given": "Falk", "initials": "F"}], "type": "journal article", "published": "2014-02-00", "journal": {"title": "Environ Microbiol Rep", "issn": "1758-2229", "volume": "6", "issue": "1", "pages": "21-27", "issn-l": "1758-2229"}, "abstract": "Actinobacteria of the acI lineage are often the numerically dominant bacterial phylum in surface freshwaters, where they can account for > 50% of total bacteria. Despite their abundance, there are no described isolates. In an effort to obtain enrichment of these ubiquitous freshwater Actinobacteria, diluted freshwater samples from Lake Grosse Fuchskuhle, Germany, were incubated in 96-well culture plates. With this method, a successful enrichment containing high abundances of a member of the lineage acI was established. Phylogenetic classification showed that the acI Actinobacteria of the enrichment belonged to the acI-B2 tribe, which seems to prefer acidic lakes. This enrichment grows to low cell densities and thus the oligotrophic nature of acI-B2 was confirmed.", "doi": "10.1111/1758-2229.12104", "pmid": "24596259", "labels": {"Sarahi Garcia": null, "SciLifeLab Fellow": null}, "xrefs": [], "notes": [], "created": "2020-11-05T17:27:28.307Z", "modified": "2022-11-07T11:37:23.498Z"}, {"entity": "publication", "iuid": "253339a994034a158b597aed566e09df", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/253339a994034a158b597aed566e09df.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/253339a994034a158b597aed566e09df"}}, "title": "Depth-discrete profiles of bacterial communities reveal pronounced spatio-temporal dynamics related to lake stratification.", "authors": [{"family": "Garcia", "given": "Sarahi L", "initials": "SL"}, {"family": "Salka", "given": "Ivette", "initials": "I"}, {"family": "Grossart", "given": "Hans-Peter", "initials": "HP"}, {"family": "Warnecke", "given": "Falk", "initials": "F"}], "type": "journal article", "published": "2013-08-00", "journal": {"title": "Environ Microbiol Rep", "issn": "1758-2229", "volume": "5", "issue": "4", "pages": "549-555", "issn-l": "1758-2229"}, "abstract": "With this work we intend to stress the importance of considering discrete depth sampling for bacterial community analysis of stratified aquatic systems. Depth is a very important parameter to consider when sampling bacterial communities, as their abundance and composition can change within the distinct water layers. Stratified lakes are good model systems to study these connections since changes in environmental parameters can occur on a cm-scale at the thermo- and/or chemocline. Lake Grosse Fuchskuhle was sampled at discrete fine-scale depths at three time points covering a stage in which the lake was stratified and the beginning of winter mixing. In this paper we present the most abundant bacterial groups at the different depths sampled and also the most abundant operational taxonomic units (OTUs). Overall, oxygen was found to be an important factor shaping the microbial community composition.", "doi": "10.1111/1758-2229.12044", "pmid": "23864569", "labels": {"Sarahi Garcia": null, "SciLifeLab Fellow": null}, "xrefs": [], "notes": [], "created": "2020-11-05T17:28:08.654Z", "modified": "2022-11-07T11:37:23.524Z"}, {"entity": "publication", "iuid": "63b34a99b6b24daf88b1141a6e3790fc", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/63b34a99b6b24daf88b1141a6e3790fc.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/63b34a99b6b24daf88b1141a6e3790fc"}}, "title": "Which sequencing depth is sufficient to describe patterns in bacterial \u03b1- and \u03b2-diversity?", "authors": [{"family": "Lundin", "given": "Daniel", "initials": "D"}, {"family": "Severin", "given": "Ina", "initials": "I"}, {"family": "Logue", "given": "J\u00fcrg Brendan", "initials": "JB"}, {"family": "Ostman", "given": "Orjan", "initials": "O"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}, {"family": "Lindstr\u00f6m", "given": "Eva S", "initials": "ES"}], "type": "journal article", "published": "2012-06-00", "journal": {"title": "Environ Microbiol Rep", "issn": "1758-2229", "volume": "4", "issue": "3", "pages": "367-372", "issn-l": "1758-2229"}, "abstract": "The vastness of microbial diversity implies that an almost infinite number of individuals needs to be identified to accurately describe such communities. Practical and economical constraints may therefore prevent appropriate study designs. However, for many questions in ecology it is not essential to know the actual diversity but rather the trends among samples thereof. It is, hence, important to know to what depth microbial communities need to be sampled to accurately measure trends in diversity. We used three data sets of freshwater and sediment bacteria, where diversity was explored using 454 pyrosequencing. Each data set contained 6-15 communities from which 15\u2003000-20\u2003000 16S rRNA gene sequences each were obtained. These data sets were subsampled repeatedly to 10 different depths down to 200 sequences per community. Diversity estimates varied with sequencing depth, yet, trends in diversity among samples were less sensitive. We found that 1000 denoised sequences per sample explained to 90% the trends in \u03b2-diversity (Bray-Curtis index) among samples observed for 15\u2003000-20\u2003000 sequences. Similarly, 5000 denoised sequences were sufficient to describe trends in \u03b1-diversity (Shannon index) with the same accuracy. Further, 5000 denoised sequences captured to more than 80% the trends in Chao1 richness and Pielou's evenness.", "doi": "10.1111/j.1758-2229.2012.00345.x", "pmid": "23760801", "labels": {"Affiliated researcher": null}, "xrefs": [], "notes": [], "created": "2018-12-05T08:47:26.820Z", "modified": "2018-12-05T08:47:26.853Z"}], "created": "2018-12-05T08:47:26.834Z", "modified": "2020-11-27T13:12:56.987Z"}