{"entity": "researcher", "timestamp": "2026-07-12T08:49:27.065Z", "family": "Peura", "given": "Sari", "initials": "S", "orcid": "0000-0003-3892-8157", "affiliations": ["Department of Forest Mycology and Plant Pathology, Science for Life Laboratory, Swedish University of Agricultural Sciences, Uppsala, Sweden. sari.peura@slu.se."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/c430ad5c3bd14387b768c588a9b12ce0.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/c430ad5c3bd14387b768c588a9b12ce0"}}, "publications": [{"entity": "publication", "iuid": "4884ce0dfe5f4ceaa6bbb3db4b417f92", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4884ce0dfe5f4ceaa6bbb3db4b417f92.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4884ce0dfe5f4ceaa6bbb3db4b417f92"}}, "title": "Aquatic fungal diversity assessment through metagenomics is still limited to current databases", "authors": [{"family": "Sanyal", "given": "Anushree", "initials": "A", "orcid": "0000-0002-8592-2164", "researcher": {"href": "https://publications.scilifelab.se/researcher/6dcb90d513c445008e914bb358678adf.json"}}, {"family": "Kluge", "given": "Mariana", "initials": "M"}, {"family": "Redondo", "given": "Miguel Angel", "initials": "MA"}, {"family": "Buck", "given": "Moritz", "initials": "M"}, {"family": "Mehrshad", "given": "Maliheh", "initials": "M"}, {"family": "Garcia", "given": "Sarahi L", "initials": "SL", "orcid": "0000-0002-8622-0308", "researcher": {"href": "https://publications.scilifelab.se/researcher/8aabc8c17d5b4ad7872c7380301d4562.json"}}, {"family": "Bertilsson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-4265-1835", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c17765c2a9f4383b5383138d11ae93f.json"}}, {"family": "Peura", "given": "Sari", "initials": "S", "orcid": "0000-0003-3892-8157", "researcher": {"href": "https://publications.scilifelab.se/researcher/c430ad5c3bd14387b768c588a9b12ce0.json"}}], "type": "journal-article", "published": "2025-11-00", "journal": {"title": "Limnol Oceanogr", "issn": "0024-3590", "volume": "70", "issue": "11", "pages": "3249-3260", "issn-l": null}, "abstract": null, "doi": "10.1002/lno.70205", "pmid": null, "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-28T10:40:31.710Z", "modified": "2025-11-28T10:40:31.816Z"}, {"entity": "publication", "iuid": "eac7874ed8294cfabb98f904d734dc74", "links": {"self": {"href": "https://publications.scilifelab.se/publication/eac7874ed8294cfabb98f904d734dc74.json"}, "display": {"href": "https://publications.scilifelab.se/publication/eac7874ed8294cfabb98f904d734dc74"}}, "title": "Comprehensive dataset of shotgun metagenomes from oxygen stratified freshwater lakes and ponds.", "authors": [{"family": "Buck", "given": "Moritz", "initials": "M"}, {"family": "Garcia", "given": "Sarahi L", "initials": "SL", "orcid": "0000-0002-8622-0308", "researcher": {"href": "https://publications.scilifelab.se/researcher/8aabc8c17d5b4ad7872c7380301d4562.json"}}, {"family": "Fernandez", "given": "Leyden", "initials": "L"}, {"family": "Martin", "given": "Ga\u00ebtan", "initials": "G", "orcid": "0000-0002-5289-6131", "researcher": {"href": "https://publications.scilifelab.se/researcher/3fa7c61072034af188ed3685ce83ca3c.json"}}, {"family": "Martinez-Rodriguez", "given": "Gustavo A", "initials": "GA"}, {"family": "Saarenheimo", "given": "Jatta", "initials": "J"}, {"family": "Zopfi", "given": "Jakob", "initials": "J", "orcid": "0000-0002-8437-7344", "researcher": {"href": "https://publications.scilifelab.se/researcher/fea1eab419af4e60b1455c0221a5b6e7.json"}}, {"family": "Bertilsson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-4265-1835", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c17765c2a9f4383b5383138d11ae93f.json"}}, {"family": "Peura", "given": "Sari", "initials": "S", "orcid": "0000-0003-3892-8157", "researcher": {"href": "https://publications.scilifelab.se/researcher/c430ad5c3bd14387b768c588a9b12ce0.json"}}], "type": "dataset", "published": "2021-05-14", "journal": {"title": "Sci Data", "issn": "2052-4463", "volume": "8", "issue": "1", "pages": "131", "issn-l": "2052-4463"}, "abstract": "Stratified lakes and ponds featuring steep oxygen gradients are significant net sources of greenhouse gases and hotspots in the carbon cycle. Despite their significant biogeochemical roles, the microbial communities, especially in the oxygen depleted compartments, are poorly known. Here, we present a comprehensive dataset including 267 shotgun metagenomes from 41 stratified lakes and ponds mainly located in the boreal and subarctic regions, but also including one tropical reservoir and one temperate lake. For most lakes and ponds, the data includes a vertical sample set spanning from the oxic surface to the anoxic bottom layer. The majority of the samples were collected during the open water period, but also a total of 29 samples were collected from under the ice. In addition to the metagenomic sequences, the dataset includes environmental variables for the samples, such as oxygen, nutrient and organic carbon concentrations. The dataset is ideal for further exploring the microbial taxonomic and functional diversity in freshwater environments and potential climate change impacts on the functioning of these ecosystems.", "doi": "10.1038/s41597-021-00910-1", "pmid": "33990618", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41597-021-00910-1"}, {"db": "pmc", "key": "PMC8121793"}], "notes": [], "created": "2021-06-01T20:55:20.891Z", "modified": "2024-01-16T13:48:39.756Z"}, {"entity": "publication", "iuid": "8cce79d935434ebf8878720309fe8b5b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8cce79d935434ebf8878720309fe8b5b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8cce79d935434ebf8878720309fe8b5b"}}, "title": "Freshwater Chlorobia Exhibit Metabolic Specialization among Cosmopolitan and Endemic Populations.", "authors": [{"family": "Garcia", "given": "Sarahi L", "initials": "SL", "orcid": "0000-0002-8622-0308", "researcher": {"href": "https://publications.scilifelab.se/researcher/8aabc8c17d5b4ad7872c7380301d4562.json"}}, {"family": "Mehrshad", "given": "Maliheh", "initials": "M"}, {"family": "Buck", "given": "Moritz", "initials": "M"}, {"family": "Tsuji", "given": "Jackson M", "initials": "JM"}, {"family": "Neufeld", "given": "Josh D", "initials": "JD", "orcid": "0000-0002-8722-8571", "researcher": {"href": "https://publications.scilifelab.se/researcher/fea734cbc1ad4f33bdc1da72d3a34c35.json"}}, {"family": "McMahon", "given": "Katherine D", "initials": "KD", "orcid": "0000-0002-7038-026X", "researcher": {"href": "https://publications.scilifelab.se/researcher/84f48c9a667f4b1d80d85ad7bc2694e2.json"}}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}, {"family": "Greening", "given": "Chris", "initials": "C", "orcid": "0000-0001-7616-0594", "researcher": {"href": "https://publications.scilifelab.se/researcher/48e65b0eddca4d029e24ac3b6bcbb965.json"}}, {"family": "Peura", "given": "Sari", "initials": "S", "orcid": "0000-0003-3892-8157", "researcher": {"href": "https://publications.scilifelab.se/researcher/c430ad5c3bd14387b768c588a9b12ce0.json"}}], "type": "journal article", "published": "2021-05-11", "journal": {"title": "mSystems", "issn": "2379-5077", "volume": "6", "issue": "3", "pages": null, "issn-l": "2379-5077"}, "abstract": "Photosynthetic bacteria from the class Chlorobia (formerly phylum Chlorobi) sustain carbon fixation in anoxic water columns. They harvest light at extremely low intensities and use various inorganic electron donors to fix carbon dioxide into biomass. Until now, most information on the functional ecology and local adaptations of Chlorobia members came from isolates and merely 26 sequenced genomes that may not adequately represent natural populations. To address these limitations, we analyzed global metagenomes to profile planktonic Chlorobia cells from the oxyclines of 42 freshwater bodies, spanning subarctic to tropical regions and encompassing all four seasons. We assembled and compiled over 500 genomes, including metagenome-assembled genomes (MAGs), single-amplified genomes (SAGs), and reference genomes from cultures, clustering them into 71 metagenomic operational taxonomic units (mOTUs or \"species\"). Of the 71 mOTUs, 57 were classified within the genus Chlorobium, and these mOTUs represented up to \u223c60% of the microbial communities in the sampled anoxic waters. Several Chlorobium-associated mOTUs were globally distributed, whereas others were endemic to individual lakes. Although most clades encoded the ability to oxidize hydrogen, many lacked genes for the oxidation of specific sulfur and iron substrates. Surprisingly, one globally distributed Scandinavian clade encoded the ability to oxidize hydrogen, sulfur, and iron, suggesting that metabolic versatility facilitated such widespread colonization. Overall, these findings provide new insight into the biogeography of the Chlorobia and the metabolic traits that facilitate niche specialization within lake ecosystems.IMPORTANCE The reconstruction of genomes from metagenomes has helped explore the ecology and evolution of environmental microbiota. We applied this approach to 274 metagenomes collected from diverse freshwater habitats that spanned oxic and anoxic zones, sampling seasons, and latitudes. We demonstrate widespread and abundant distributions of planktonic Chlorobia-associated bacteria in hypolimnetic waters of stratified freshwater ecosystems and show they vary in their capacities to use different electron donors. Having photoautotrophic potential, these Chlorobia members could serve as carbon sources that support metalimnetic and hypolimnetic food webs.", "doi": "10.1128/mSystems.01196-20", "pmid": "33975970", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "6/3/e01196-20"}, {"db": "pmc", "key": "PMC8125076"}], "notes": [], "created": "2021-06-01T20:56:01.234Z", "modified": "2024-01-16T13:48:39.770Z"}, {"entity": "publication", "iuid": "22914a13727a400bbc7bf78b4c9dfd22", "links": {"self": {"href": "https://publications.scilifelab.se/publication/22914a13727a400bbc7bf78b4c9dfd22.json"}, "display": {"href": "https://publications.scilifelab.se/publication/22914a13727a400bbc7bf78b4c9dfd22"}}, "title": "Archaea in boreal Swedish lakes are diverse, dominated by Woesearchaeota and follow deterministic community assembly.", "authors": [{"family": "Juottonen", "given": "Heli", "initials": "H", "orcid": "0000-0003-3769-239X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1af9df805f914a21be382248c50b9d03.json"}}, {"family": "Fontaine", "given": "Laurent", "initials": "L"}, {"family": "Wurzbacher", "given": "Christian", "initials": "C"}, {"family": "Drakare", "given": "Stina", "initials": "S"}, {"family": "Peura", "given": "Sari", "initials": "S", "orcid": "0000-0003-3892-8157", "researcher": {"href": "https://publications.scilifelab.se/researcher/c430ad5c3bd14387b768c588a9b12ce0.json"}}, {"family": "Eiler", "given": "Alexander", "initials": "A", "orcid": "0000-0001-9916-9567", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7286785c9334dcba90273b69f81c018.json"}}], "type": "journal article", "published": "2020-08-00", "journal": {"title": "Environ. Microbiol.", "issn": "1462-2920", "volume": "22", "issue": "8", "pages": "3158-3171", "issn-l": "1462-2912"}, "abstract": "Despite their key role in biogeochemical processes, particularly the methane cycle, archaea are widely underrepresented in molecular surveys because of their lower abundance compared with bacteria and eukaryotes. Here, we use parallel high-resolution small subunit rRNA gene sequencing to explore archaeal diversity in 109 Swedish lakes and correlate archaeal community assembly mechanisms to large-scale latitudinal, climatic (nemoral to arctic) and nutrient (oligotrophic to eutrophic) gradients. Sequencing with universal primers showed the contribution of archaea was on average 0.8% but increased up to 1.5% of the three domains in forest lakes. Archaea-specific sequencing revealed that freshwater archaeal diversity could be partly explained by lake variables associated with nutrient status. Combined with deterministic co-occurrence patterns this finding suggests that ecological drift is overridden by environmental sorting, as well as other deterministic processes such as biogeographic and evolutionary history, leading to lake-specific archaeal biodiversity. Acetoclastic, hydrogenotrophic and methylotrophic methanogens as well as ammonia-oxidizing archaea were frequently detected across the lakes. Archaea-specific sequencing also revealed representatives of Woesearchaeota and other phyla of the DPANN superphylum. This study adds to our understanding of the ecological range of key archaea in freshwaters and links these taxa to hypotheses about processes governing biogeochemical cycles in lakes.", "doi": "10.1111/1462-2920.15058", "pmid": "32372550", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2020-12-08T23:57:02.276Z", "modified": "2024-01-16T13:48:42.081Z"}, {"entity": "publication", "iuid": "3ceba61f89834bd284538a521f2c5781", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3ceba61f89834bd284538a521f2c5781.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3ceba61f89834bd284538a521f2c5781"}}, "title": "Decreased Snow Cover Stimulates Under-Ice Primary Producers but Impairs Methanotrophic Capacity.", "authors": [{"family": "Garcia", "given": "Sarahi L", "initials": "SL", "orcid": "0000-0002-8622-0308", "researcher": {"href": "https://publications.scilifelab.se/researcher/8aabc8c17d5b4ad7872c7380301d4562.json"}}, {"family": "Szekely", "given": "Anna J", "initials": "AJ"}, {"family": "Bergvall", "given": "Christoffer", "initials": "C"}, {"family": "Schattenhofer", "given": "Martha", "initials": "M"}, {"family": "Peura", "given": "Sari", "initials": "S", "orcid": "0000-0003-3892-8157", "researcher": {"href": "https://publications.scilifelab.se/researcher/c430ad5c3bd14387b768c588a9b12ce0.json"}}], "type": "journal article", "published": "2019-01-09", "journal": {"volume": "4", "issn": "2379-5042", "issue": "1", "pages": null, "title": "mSphere", "issn-l": "2379-5042"}, "abstract": "Climate change scenarios anticipate decreased spring snow cover in boreal and subarctic regions. Forest lakes are abundant in these regions and substantial contributors of methane emissions. To investigate the effect of reduced snow cover, we experimentally removed snow from an anoxic frozen lake. We observed that the removal of snow increased light penetration through the ice, increasing water temperature and modifying microbial composition in the different depths. Chlorophyll a and b concentrations increased in the upper water column, suggesting activation of algal primary producers. At the same time, Chlorobiaceae, one of the key photosynthetic bacterial families in anoxic lakes, shifted to lower depths. Moreover, a decrease in the relative abundance of methanotrophs within the bacterial family Methylococcaceae was detected, concurrent with an increase in methane concentration in the water column. These results indicate that decreased snow cover impacts both primary production and methane production and/or consumption, which may ultimately lead to increased methane emissions after spring ice off.IMPORTANCE Small lakes are an important source of greenhouse gases in the boreal zone. These lakes are severely impacted by the winter season, when ice and snow cover obstruct gas exchange between the lake and the atmosphere and diminish light availability in the water column. Currently, climate change is resulting in reduced spring snow cover. A short-term removal of the snow from the ice stimulated algal primary producers and subsequently heterotrophic bacteria. Concurrently, the relative abundance of methanotrophic bacteria decreased and methane concentrations increased. Our results increase the general knowledge of microbial life under ice and, specifically, the understanding of the potential impact of climate change on boreal lakes.", "doi": "10.1128/mSphere.00626-18", "pmid": "30626619", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "4/1/e00626-18"}, {"db": "pmc", "key": "PMC6327105"}], "notes": [], "created": "2019-04-23T10:01:18.250Z", "modified": "2024-01-16T13:48:44.837Z"}]}