{"entity": "journal", "iuid": "41abffa5b26d4fb9ae10454164ec6773", "timestamp": "2026-08-09T07:28:48.635Z", "links": {"self": {"href": "https://publications.scilifelab.se/journal/FEMS%20Microbiol.%20Lett..json"}, "display": {"href": "https://publications.scilifelab.se/journal/FEMS%20Microbiol.%20Lett."}}, "title": "FEMS Microbiol. Lett.", "issn": "1574-6968", "issn-l": "0378-1097", "publications_count": 8, "publications": [{"entity": "publication", "iuid": "50660d74b49b4131a8622208135d9542", "links": {"self": {"href": "https://publications.scilifelab.se/publication/50660d74b49b4131a8622208135d9542.json"}, "display": {"href": "https://publications.scilifelab.se/publication/50660d74b49b4131a8622208135d9542"}}, "title": "Effects of compost amendments and experimental drought on grassland soil microbial communities.", "authors": [{"family": "Guasconi", "given": "Daniela", "initials": "D", "orcid": "0000-0003-3739-0877", "researcher": {"href": "https://publications.scilifelab.se/researcher/1393c3be58a14d8b89434d38994fbef4.json"}}, {"family": "Hugelius", "given": "Gustaf", "initials": "G"}, {"family": "Clemmensen", "given": "Karina E", "initials": "KE"}, {"family": "Cousins", "given": "Sara A O", "initials": "SAO"}, {"family": "Juhanson", "given": "Jaanis", "initials": "J"}, {"family": "Manzoni", "given": "Stefano", "initials": "S"}, {"family": "Roth", "given": "Nina", "initials": "N"}, {"family": "Fransson", "given": "Petra", "initials": "P"}], "type": "journal article", "published": "2025-01-10", "journal": {"title": "FEMS Microbiol. Lett.", "issn": "1574-6968", "volume": "372", "issn-l": "0378-1097"}, "abstract": "Prolonged drought is a major stressor for grassland ecosystems. In addition to decreasing plant productivity, it can affect soil microbial activities and thus destabilize nutrient cycling and carbon (C) sequestration. Soil organic amendments (OAs), such as compost, can be used to enhance soil fertility and mitigate drought effects. In this study, we evaluated the responses of fungal and bacterial communities to a 3-year-long experimental drought and compost treatment across four soil depths in two Swedish grasslands and at an upper and a lower topographic position. Results showed that while drought reduced soil moisture and compost amendment increased C content in the topsoil, the effects on microbial abundance and community composition within this time frame were weak, and detectable only in the topsoil. Fungal abundance increased with compost addition, which also affected community composition, while fungal communities were resistant to drought. Bacterial communities were not significantly affected by any of the treatments. This suggests that microbial ecosystem functions were resistant to the experimentally reduced precipitation. Overall, variation between sampling sites was more important for microbial community composition than treatments, highlighting the need for a better understanding of small-spatial-scale environmental controls on soil microbial and plant communities and their ecosystem functions.", "doi": "10.1093/femsle/fnaf108", "pmid": "41051250", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "NGI Long read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12527337"}, {"db": "pii", "key": "8275753"}], "notes": [], "created": "2025-11-04T10:54:01.939Z", "modified": "2025-11-28T10:49:00.649Z"}, {"entity": "publication", "iuid": "c575b869292647788dd14aecde31fc5f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c575b869292647788dd14aecde31fc5f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c575b869292647788dd14aecde31fc5f"}}, "title": "Bacterial community responses to micropollutants in chemically stressed small rivers in Kenya using environmental DNA.", "authors": [{"family": "Verb\u00fccheln", "given": "Nicolai", "initials": "N", "orcid": "0009-0003-7017-9413", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd94f69e78414b1697902ed955a458d9.json"}}, {"family": "Schaufelberger", "given": "Sonja", "initials": "S"}, {"family": "Cardis", "given": "Tibaud", "initials": "T"}, {"family": "Tanui", "given": "Isaac C", "initials": "IC"}, {"family": "Kandie", "given": "Faith", "initials": "F"}, {"family": "Brack", "given": "Werner", "initials": "W"}, {"family": "Backhaus", "given": "Thomas", "initials": "T"}, {"family": "Inostroza", "given": "Pedro A", "initials": "PA", "orcid": "0000-0001-7399-8308", "researcher": {"href": "https://publications.scilifelab.se/researcher/9cea8a42ffc2454d86f5f829b5dd7eff.json"}}], "type": "journal article", "published": "2025-01-10", "journal": {"title": "FEMS Microbiol. Lett.", "issn": "1574-6968", "volume": "372", "issn-l": "0378-1097"}, "abstract": "The responses of bacterial communities to changing environmental conditions are manifold but can include structural as well as functional alterations depending on the environmental stressors and toxic chemicals they are exposed to (e.g. pharmaceuticals, personal care products, pesticides, and industrial chemicals). In this study, environmental DNA was extracted from surface water samples collected from four small rivers in the Lake Victoria South Basin (Western Kenya) to (i) evaluate whether alpha- and beta-diversity change in dependency of land-use types, (ii) identify the environmental variables that explain alterations in community structure, (iii) qualitatively and quantitatively assess the consequences of antimicrobial stress on bacterial communities, and (iv) evaluate bacterial functional changes related to the degradation of organic chemicals. Our findings suggest that bacterial community composition is a more sensitive indicator to reflect the impact of chemical pollution derived from different types of land use compared to alpha-diversity. Nutrients and stress from chemical pollution were the variables explaining the dissimilarities between bacterial communities in small, forested, urbanised, and agricultural rivers. Furthermore, an assessment of potential ecological functions associated with the biodegradation of toxic chemicals unveiled a season-specific decline in bacterial degradation potential in all four rivers.", "doi": "10.1093/femsle/fnaf113", "pmid": "41100179", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12598650"}, {"db": "pii", "key": "8287733"}], "notes": [], "created": "2025-11-28T10:49:05.709Z", "modified": "2025-11-28T10:49:05.762Z"}, {"entity": "publication", "iuid": "bb49b19b908c48f6b2159e5e8e208b77", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bb49b19b908c48f6b2159e5e8e208b77.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bb49b19b908c48f6b2159e5e8e208b77"}}, "title": "Novel and unusual genes for nitrogen and metal cycling in Planctomycetota- and KSB1-affiliated metagenome-assembled genomes reconstructed from a marine subsea tunnel.", "authors": [{"family": "Suarez", "given": "Carolina", "initials": "C", "orcid": "0000-0001-5988-4048", "researcher": {"href": "https://publications.scilifelab.se/researcher/86cadb16f7cf45eca8030af1a8ae860e.json"}}, {"family": "Hackl", "given": "Thomas", "initials": "T", "orcid": "0000-0002-0022-320X", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d7de95e834842c3b506c92f9ef648f5.json"}}, {"family": "Wilen", "given": "Britt-Marie", "initials": "BM", "orcid": "0000-0001-6155-7759", "researcher": {"href": "https://publications.scilifelab.se/researcher/17fcd853ec9d43bda259e8d440a92eb7.json"}}, {"family": "Persson", "given": "Frank", "initials": "F", "orcid": "0000-0002-0269-9375", "researcher": {"href": "https://publications.scilifelab.se/researcher/40290cae1a7e44c1939801323653b31c.json"}}, {"family": "Hagelia", "given": "Per", "initials": "P"}, {"family": "Jetten", "given": "Mike S M", "initials": "MSM", "orcid": "0000-0002-4691-7039", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b43ecab3b254c8eb61a10099e3fda63.json"}}, {"family": "Dalcin Martins", "given": "Paula", "initials": "P", "orcid": "0000-0003-1242-0267", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd51c24d64564b0ca5d066c5dcabbecd.json"}}], "type": "journal article", "published": "2023-01-17", "journal": {"title": "FEMS Microbiol. Lett.", "issn": "1574-6968", "volume": "370", "issn-l": "0378-1097"}, "abstract": "The Oslofjord subsea road tunnel is a unique environment in which the typically anoxic marine deep subsurface is exposed to oxygen. Concrete biodeterioration and steel corrosion in the tunnel have been linked to the growth of iron- and manganese-oxidizing biofilms in areas of saline water seepage. Surprisingly, previous 16S rRNA gene surveys of biofilm samples revealed microbial communities dominated by sequences affiliated with nitrogen-cycling microorganisms. This study aimed to identify microbial genomes with metabolic potential for novel nitrogen- and metal-cycling reactions, representing biofilm microorganisms that could link these cycles and play a role in concrete biodeterioration. We reconstructed 33 abundant, novel metagenome-assembled genomes (MAGs) affiliated with the phylum Planctomycetota and the candidate phylum KSB1. We identified novel and unusual genes and gene clusters in these MAGs related to anaerobic ammonium oxidation, nitrite oxidation, and other nitrogen-cycling reactions. Additionally, 26 of 33 MAGs also had the potential for iron, manganese, and arsenite cycling, suggesting that bacteria represented by these genomes might couple these reactions. Our results expand the diversity of microorganisms putatively involved in nitrogen and metal cycling, and contribute to our understanding of potential biofilm impacts on built infrastructure.", "doi": "10.1093/femsle/fnad049", "pmid": "37291701", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "7192431"}], "notes": [], "created": "2023-11-27T21:52:12.844Z", "modified": "2024-01-16T13:48:34.124Z"}, {"entity": "publication", "iuid": "8383855cef1648d89387cb75227edce1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8383855cef1648d89387cb75227edce1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8383855cef1648d89387cb75227edce1"}}, "title": "Transcriptomic markers of fungal growth, respiration and carbon-use efficiency.", "authors": [{"family": "Hasby", "given": "Fahri A", "initials": "FA", "orcid": "0000-0002-5722-9565", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e3638fa2bf144a88542258843b1711d.json"}}, {"family": "Barbi", "given": "Florian", "initials": "F"}, {"family": "Manzoni", "given": "Stefano", "initials": "S"}, {"family": "Lindahl", "given": "Bj\u00f6rn D", "initials": "BD", "orcid": "0000-0002-3384-4547", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7a40688d33545a19c3c666940bda255.json"}}], "type": "journal article", "published": "2021-08-19", "journal": {"title": "FEMS Microbiol. Lett.", "issn": "1574-6968", "volume": "368", "issue": "15", "issn-l": "0378-1097"}, "abstract": "Fungal metabolic carbon acquisition and its subsequent partitioning between biomass production and respiration, i.e. the carbon-use efficiency (CUE), are central parameters in biogeochemical modeling. However, current available techniques for estimating these parameters are all associated with practical and theoretical shortcomings, making assessments unreliable. Gene expression analyses hold the prospect of phenotype prediction by indirect means, providing new opportunities to obtain information about metabolic priorities. We cultured four different fungal isolates (Chalara longipes, Laccaria bicolor, Serpula lacrymans and Trichoderma harzianum) in liquid media with contrasting nitrogen availability and measured growth rates and respiration to calculate CUE. By relating gene expression markers to measured carbon fluxes, we identified genes coding for 1,3-\u03b2-glucan synthase and 2-oxoglutarate dehydrogenase as suitable markers for growth and respiration, respectively, capturing both intraspecific variation as well as within-strain variation dependent on growth medium. A transcript index based on these markers correlated significantly with differences in CUE between the fungal isolates. Our study paves the way for the use of these markers to assess differences in growth, respiration and CUE in natural fungal communities, using metatranscriptomic or the RT-qPCR approach.", "doi": "10.1093/femsle/fnab100", "pmid": "34338746", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "6335482"}, {"db": "pmc", "key": "PMC8374604"}], "notes": [], "created": "2022-11-09T15:40:46.347Z", "modified": "2024-01-16T13:48:38.690Z"}, {"entity": "publication", "iuid": "16b41862d1d943d0a122469df5db584f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/16b41862d1d943d0a122469df5db584f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/16b41862d1d943d0a122469df5db584f"}}, "title": "The genetic diversity and evolution of diatom-diazotroph associations highlights traits favoring symbiont integration.", "authors": [{"family": "Caputo", "given": "Andrea", "initials": "A"}, {"family": "Nylander", "given": "Johan A A", "initials": "JAA"}, {"family": "Foster", "given": "Rachel A", "initials": "RA"}], "type": "journal article", "published": "2019-01-09", "journal": {"volume": null, "issn": "1574-6968", "issue": null, "title": "FEMS Microbiol. Lett.", "issn-l": "0378-1097"}, "abstract": "Diatom diazotroph associations (DDAs) are a widespread marine planktonic symbiosis between several diatom genera and di-nitrogen-fixing bacteria. Combining single cell confocal microscopy observations and molecular genetic approaches on individual field collected cells, we determined the phylogenetic diversity, distribution, and evolution of the DDAs. Confocal analyses coupled with 3-D imaging re-evaluated the cellular location of DDA symbionts. DDA diversity was resolved by paired gene sequencing (18S rRNA and rbcL genes and 16S rRNA and nifH genes). A survey using the newly acquired sequences against public databases found sequences with high similarity (99-100%) to either host (18S rRNA) or symbiont (16S rRNA) in atypical regions for DDAs (high latitudes, anoxic basin, copepod gut). Concatenated phylogenies were congruent for the host and cyanobacteria sequences and implied co-evolution. Time-calibrated trees dated the appearance of N2 fixing planktonic symbiosis from 100-50Mya and were consistent with the symbiont cellular location: symbioses with internal partners are more ancient. An ancestral state reconstruction traced the evolution of traits in DDAs and highlight that the adaptive radiation to the marine environment was likely facilitated by the symbiosis. Our results present the evolutionary nature of DDAs and provide new genetic and phenotypic information for these biogeochemically relevant populations.", "doi": "10.1093/femsle/fny297", "pmid": "30629176", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "5281432"}], "notes": [], "created": "2019-01-15T07:57:27.997Z", "modified": "2020-01-21T13:53:22.358Z"}, {"entity": "publication", "iuid": "9b3c47e1ea0843e3a015238ec949a229", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9b3c47e1ea0843e3a015238ec949a229.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9b3c47e1ea0843e3a015238ec949a229"}}, "title": "Comparison of four DNA extraction methods for comprehensive assessment of 16S rRNA bacterial diversity in marine biofilms using high-throughput sequencing", "authors": [{"family": "Corcoll", "given": "Nat\u00e0lia", "initials": "N"}, {"family": "\u00d6sterlund", "given": "Tobias", "initials": "T"}, {"family": "Sinclair", "given": "Lucas", "initials": "L"}, {"family": "Eiler", "given": "Alexander", "initials": "A"}, {"family": "Kristiansson", "given": "Erik", "initials": "E"}, {"family": "Backhaus", "given": "Thomas", "initials": "T"}, {"family": "Eriksson", "given": "K Martin", "initials": "KM"}], "type": "journal-article", "published": "2017-08-01", "journal": {"volume": "364", "issn": "1574-6968", "issue": "14", "pages": null, "title": "FEMS Microbiol. Lett.", "issn-l": "0378-1097"}, "abstract": null, "doi": "10.1093/femsle/fnx139", "pmid": "28673033", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "BioProject", "description": null, "key": "PRJNA378915"}], "notes": [], "created": "2017-10-30T09:27:43.376Z", "modified": "2024-01-16T13:48:47.653Z"}, {"entity": "publication", "iuid": "9c7992409f3d425cb633929d763c1cc2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9c7992409f3d425cb633929d763c1cc2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9c7992409f3d425cb633929d763c1cc2"}}, "title": "RNA transcript sequencing reveals inorganic sulfur compound oxidation pathways in the acidophile Acidithiobacillus ferrivorans.", "authors": [{"family": "Christel", "given": "Stephan", "initials": "S"}, {"family": "Fridlund", "given": "Jimmy", "initials": "J"}, {"family": "Buetti-Dinh", "given": "Antoine", "initials": "A"}, {"family": "Buck", "given": "Moritz", "initials": "M"}, {"family": "Watkin", "given": "Elizabeth L", "initials": "EL"}, {"family": "Dopson", "given": "Mark", "initials": "M"}], "type": "journal article", "published": "2016-04-00", "journal": {"volume": "363", "issn": "1574-6968", "issue": "7", "title": "FEMS Microbiol. Lett.", "issn-l": "0378-1097"}, "abstract": "Acidithiobacillus ferrivorans is an acidophile implicated in low-temperature biomining for the recovery of metals from sulfide minerals. Acidithiobacillus ferrivorans obtains its energy from the oxidation of inorganic sulfur compounds, and genes encoding several alternative pathways have been identified. Next-generation sequencing of At. ferrivorans RNA transcripts identified the genes coding for metabolic and electron transport proteins for energy conservation from tetrathionate as electron donor. RNA transcripts suggested that tetrathionate was hydrolyzed by the tetH1 gene product to form thiosulfate, elemental sulfur and sulfate. Despite two of the genes being truncated, RNA transcripts for the SoxXYZAB complex had higher levels than for thiosulfate quinone oxidoreductase (doxDAgenes). However, a lack of heme-binding sites in soxX suggested that DoxDA was responsible for thiosulfate metabolism. Higher RNA transcript counts also suggested that elemental sulfur was metabolized by heterodisulfide reductase (hdrgenes) rather than sulfur oxygenase reductase (sor). The sulfite produced as a product of heterodisulfide reductase was suggested to be oxidized by a pathway involving the sat gene product or abiotically react with elemental sulfur to form thiosulfate. Finally, several electron transport complexes were involved in energy conservation. This study has elucidated the previously unknown At. ferrivorans tetrathionate metabolic pathway that is important in biomining.", "doi": "10.1093/femsle/fnw057", "pmid": "26956550", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "fnw057"}], "notes": [], "created": "2017-05-03T13:00:06.848Z", "modified": "2024-01-16T13:48:50.282Z"}, {"entity": "publication", "iuid": "4314e230f7e1454ea5921f5643f9ab2a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4314e230f7e1454ea5921f5643f9ab2a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4314e230f7e1454ea5921f5643f9ab2a"}}, "title": "Identification and expression of stressosomal proteins in Mycobacterium marinum under various growth and stress conditions.", "authors": [{"family": "Pettersson", "given": "B M Fredrik", "initials": "BMF"}, {"family": "Nitharwal", "given": "Ram G", "initials": "RG"}, {"family": "Das", "given": "Sarbashis", "initials": "S"}, {"family": "Behra", "given": "Krishna P R", "initials": "KPR"}, {"family": "Benedik", "given": "Evgen", "initials": "E"}, {"family": "Arasu", "given": "Uma T", "initials": "UT"}, {"family": "Islam", "given": "Nurul M", "initials": "NM"}, {"family": "Dasgupta", "given": "Santanu", "initials": "S"}, {"family": "Bhattacharya", "given": "Alok", "initials": "A"}, {"family": "Kirsebom", "given": "Leif A", "initials": "LA", "orcid": "0000-0002-5092-512X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e80849a89d0043b0b4daff9804c67332.json"}}], "type": "journal article", "published": "2013-05-00", "journal": {"volume": "342", "issn": "1574-6968", "issue": "2", "pages": "98-105", "title": "FEMS Microbiol. Lett.", "issn-l": "0378-1097"}, "abstract": "Like other bacteria, Mycobacterium spp. have developed different strategies in response to environmental changes such as nutrient limitations and other different stress situations. We have identified candidate genes (rsb genes) from Mycobacterium marinum involved in the regulation of the activity of the alternative sigma factor, \u03c3(F) . This is a homolog of the master regulator of general stress response, \u03c3(B) , and the sporulation-specific sigma factor, \u03c3(F) , in Bacillus subtilis. The organization of these genes in M.\u00a0marinum and B.\u00a0subtilis is similar. Transcriptome and qRT-PCR data show that these genes are indeed expressed in M.\u00a0marinum and that the levels of expression vary with growth phase and exposure to stress. In particular, cold stress caused a significant rise in the expression of all identified rsb and sigF genes. We discuss these data in relation to what is currently known for other Mycobacterium spp.", "doi": "10.1111/1574-6968.12118", "pmid": "23480639", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:57:54.149Z", "modified": "2021-06-16T14:51:44.583Z"}], "created": "2017-05-09T09:12:29.645Z", "modified": "2020-11-27T13:14:05.899Z"}