{"entity": "journal", "iuid": "8fa8b7529988403889218a63a63022b8", "timestamp": "2026-07-15T16:23:54.684Z", "links": {"self": {"href": "https://publications.scilifelab.se/journal/Environ%20Microbiol%20Rep.json"}, "display": {"href": "https://publications.scilifelab.se/journal/Environ%20Microbiol%20Rep"}}, "title": "Environ Microbiol Rep", "issn": "1758-2229", "issn-l": "1758-2229", "publications_count": 7, "publications": [{"entity": "publication", "iuid": "ae53f79971b5422e8d7b0c5ef5626fe0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ae53f79971b5422e8d7b0c5ef5626fe0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ae53f79971b5422e8d7b0c5ef5626fe0"}}, "title": "Primary and Secondary Symbionts of Cambodian Cicadellidae and the Role of Parasitisation.", "authors": [{"family": "Phauk", "given": "Sophany", "initials": "S", "orcid": "0000-0002-8019-3206", "researcher": {"href": "https://publications.scilifelab.se/researcher/80bf701bd9c14bd08c081d49b0d6ecad.json"}}, {"family": "Assentato", "given": "Lorenzo", "initials": "L", "orcid": "0000-0003-3699-0483", "researcher": {"href": "https://publications.scilifelab.se/researcher/69a8069f62434b128fb5837b139dbb56.json"}}, {"family": "Meas", "given": "Seanghun", "initials": "S", "orcid": "0009-0003-8813-8839", "researcher": {"href": "https://publications.scilifelab.se/researcher/829ed324071b46cc8720d6ffcf68b701.json"}}, {"family": "Terenius", "given": "Olle", "initials": "O", "orcid": "0000-0002-9909-1859", "researcher": {"href": "https://publications.scilifelab.se/researcher/3042a807e20d444cafee3f760c38d5d1.json"}}], "type": "journal article", "published": "2025-10-00", "journal": {"title": "Environ Microbiol Rep", "issn": "1758-2229", "volume": "17", "issue": "5", "pages": "e70196", "issn-l": "1758-2229"}, "abstract": "Leafhoppers (Hemiptera: Cicadellidae) are important vectors of plant pathogens in agricultural systems. Biological control via parasitisation is a key management strategy, but little is known about how microbial symbionts mediate host-parasitoid interactions. Here, we characterise the bacterial communities of six Cambodian leafhopper species (Cofana spectra, Exitianus sp., Goniagnathus punctifer, Maiestas dorsalis, Nephotettix virescens, and Stirellus sp.) and their parasitoids from the families Dryinidae (Hymenoptera) and Halictophagidae (Strepsiptera). We found that the bacterial symbiont Sulcia dominates cicadellid microbiotas, often coexisting with secondary symbionts. For example, Nasuia is present alongside Sulcia in Nephotettix, while Wolbachia is prevalent in Exitianus and Goniagnathus. Parasitoids exhibited distinct microbiotas with greater diversity; Rhodobacteraceae and Comamonadaceae were in dryinids, while Wolbachia was common in Halictophagidae. We analysed the microbiota of individual pairs of host-parasitoid and although parasitism did not significantly alter cicadellid overall microbiotas, some secondary symbionts (e.g., Arsenophonus, Wolbachia, Rickettsia, and Sodalis) were detected in both hosts and parasitoids, suggesting possible microbial transmission that warrants further investigation. These findings improve our understanding of host-parasitoid microbial interactions and highlight the relationship between primary and secondary symbiont communities.", "doi": "10.1111/1758-2229.70196", "pmid": "40957832", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12440678"}], "notes": [], "created": "2025-11-07T07:26:49.751Z", "modified": "2025-11-28T10:50:56.250Z"}, {"entity": "publication", "iuid": "20eb2f2bbb1c422eaa580402cd480382", "links": {"self": {"href": "https://publications.scilifelab.se/publication/20eb2f2bbb1c422eaa580402cd480382.json"}, "display": {"href": "https://publications.scilifelab.se/publication/20eb2f2bbb1c422eaa580402cd480382"}}, "title": "Fermentative Yeast Diversity at the Northern Range Limit of Their Oak Tree Hosts.", "authors": [{"family": "Pinto", "given": "Javier", "initials": "J"}, {"family": "Haberkorn", "given": "Chlo\u00e9", "initials": "C", "orcid": "0000-0002-7371-9177", "researcher": {"href": "https://publications.scilifelab.se/researcher/099838e4d3b94ee1af5cdfbf8ffea5d2.json"}}, {"family": "Franz\u00e9n", "given": "Markus", "initials": "M"}, {"family": "Tack", "given": "Ayco J M", "initials": "AJM"}, {"family": "Stelkens", "given": "Rike", "initials": "R", "orcid": "0000-0002-8530-0656", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8b3449c244a4c13b8610e401f4cbef4.json"}}], "type": "journal article", "published": "2025-06-00", "journal": {"title": "Environ Microbiol Rep", "issn": "1758-2229", "volume": "17", "issue": "3", "pages": "e70110", "issn-l": "1758-2229"}, "abstract": "Fermentative yeasts play important roles in both ecological and industrial processes, but their distribution and abundance in natural environments are not well understood. We investigated the diversity of yeasts at the northern range limit of their oak tree hosts (Quercus spp.) in Sweden, and identified climatic and ecological conditions governing their distribution. Yeasts were isolated from bark samples from 28 forests and identified to the species level using DNA metabarcoding. Most communities were dominated by species in the Saccharomycetaceae family, especially by species of Saccharomyces, Kluyveromyces and Pichia. Each genus showed a distinct latitudinal and longitudinal distribution, and both temperature and precipitation metrics predicted significant variation in their abundance. Consistent with this, laboratory assays revealed significant effects of temperature on the growth of strains collected from different longitudes and latitudes. We found that older trees harbour more diverse and more balanced fermentative yeast communities with more evenly distributed species abundances. Communities across trees were more similar when sharing a common dominant species. This work provides a baseline for future studies on the impact of climate change on the fermentative yeast biodiversity of temperate forests in northern latitudes and contributes to a growing collection of wild isolates for potential biotechnological applications.", "doi": "10.1111/1758-2229.70110", "pmid": "40410946", "labels": {"Bioinformatics Support for Computational Resources": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12102073"}], "notes": [], "created": "2025-11-28T10:50:51.200Z", "modified": "2025-12-05T11:26:12.741Z"}, {"entity": "publication", "iuid": "2a2ca50ec2b44ca99ee63649522c4aaf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2a2ca50ec2b44ca99ee63649522c4aaf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2a2ca50ec2b44ca99ee63649522c4aaf"}}, "title": "Diel Bacterioplankton Community Dynamics Under Contrasting Light Regimes.", "authors": [{"family": "Papadopoulou", "given": "Sofia", "initials": "S", "orcid": "0000-0001-7315-3671", "researcher": {"href": "https://publications.scilifelab.se/researcher/5f6cb7f8c28f4e0fbc030ee7311c6078.json"}}, {"family": "Linkhorst", "given": "Annika", "initials": "A", "orcid": "0000-0002-3609-5107", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ba8c037d8ba4defbfa03364e2e264e7.json"}}, {"family": "Balmonte", "given": "John Paul", "initials": "JP", "orcid": "0000-0001-5571-4893", "researcher": {"href": "https://publications.scilifelab.se/researcher/b3949f1396414e15a27c85460886d7ac.json"}}, {"family": "Csit\u00e1ri", "given": "Bianka", "initials": "B", "orcid": "0000-0002-5219-5829", "researcher": {"href": "https://publications.scilifelab.se/researcher/72ae1be693ac4900987f70a21a271494.json"}}, {"family": "Felf\u00f6ldi", "given": "Tam\u00e1s", "initials": "T", "orcid": "0000-0003-2009-2478", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a452e1d353649bc860f59485fc8bf03.json"}}, {"family": "M\u00e1rton", "given": "Zsuzsanna", "initials": "Z", "orcid": "0000-0002-7420-5039", "researcher": {"href": "https://publications.scilifelab.se/researcher/631b674f8b91403e95b1bbc8383fd8a8.json"}}, {"family": "Mershad", "given": "Maliheh", "initials": "M", "orcid": "0000-0002-1108-6888", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3eca2f7212a4c67bd7b251fa93848e1.json"}}, {"family": "Szab\u00f3", "given": "Attila", "initials": "A", "orcid": "0000-0002-7777-8166", "researcher": {"href": "https://publications.scilifelab.se/researcher/78425c54e73b4bc1bf8c8b900224d41d.json"}}, {"family": "Torstensson", "given": "Anders", "initials": "A", "orcid": "0000-0002-8283-656X", "researcher": {"href": "https://publications.scilifelab.se/researcher/352fd53b3b584caa95ee5ff4405498cf.json"}}, {"family": "Bertilsson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-4265-1835", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c17765c2a9f4383b5383138d11ae93f.json"}}, {"family": "Sz\u00e9kely", "given": "Anna J", "initials": "AJ", "orcid": "0000-0001-8063-7156", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9b2d69cfd6a4f41a978b38ddf66c8d5.json"}}], "type": "journal article", "published": "2025-06-00", "journal": {"title": "Environ Microbiol Rep", "issn": "1758-2229", "issn-l": "1758-2229", "volume": "17", "issue": "3", "pages": "e70099"}, "abstract": "In the Boreal region, extreme seasonal variations in day-night length expose communities to dynamic light and temperature fluctuations. Freshwater bacterioplankton, representing key ecosystem components, faces climate-driven shifts; yet the fixed day-length patterns determined by latitude underscore the importance of studying light's role in predicting ecosystem responses. We investigated bacterial community composition in a brown peat bog and a clear oligotrophic lake across seasons with contrasting light regimes: the summer solstice (> 20 h of daylight) and the autumn equinox (equal day-night length). Using amplicon sequencing of 16S rRNA transcripts, alongside measurements of physicochemical parameters, organic matter characterisation and dissolved carbon dioxide and methane gas measurements, we found no diel cycling in the lake during either period or in the peat bog near the summer solstice. However, the structure of bacterial peat bog communities exhibited cyclic changes over diel cycles at the autumn equinox. Twelve amplicon sequence variants, including both phototrophic and heterotrophic taxa, increased in abundance at all measured morning sampling times. These findings provide valuable insights into the diel patterns of boreal lentic habitats and their bacterioplankton communities, highlighting the absence of diel fluctuations in some systems and seasons, while revealing cyclic dynamics in others, driven by conditionally rare taxa.", "doi": "10.1111/1758-2229.70099", "pmid": "40344486", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12061850"}], "notes": [], "created": "2025-05-12T05:46:12.949Z", "modified": "2025-11-28T10:50:46.010Z"}, {"entity": "publication", "iuid": "c04a689a952745a7b20584f2293eece0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c04a689a952745a7b20584f2293eece0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c04a689a952745a7b20584f2293eece0"}}, "title": "Metagenome assembled-genomes reveal similar functional profiles of CPR/Patescibacteria phyla in soils.", "authors": [{"family": "Nascimento Lemos", "given": "Leandro", "initials": "L", "orcid": "0000-0002-0898-568X", "researcher": {"href": "https://publications.scilifelab.se/researcher/2d27ac7aa5124a0e891272bb955adde4.json"}}, {"family": "Manoharan", "given": "Lokeshwaran", "initials": "L", "orcid": "0000-0001-9751-5745", "researcher": {"href": "https://publications.scilifelab.se/researcher/000321fd81b9457db66140246bbd9066.json"}}, {"family": "William Mendes", "given": "Lucas", "initials": "L", "orcid": "0000-0003-0980-7006", "researcher": {"href": "https://publications.scilifelab.se/researcher/205efe9eca574e0fad7434a25b3bc028.json"}}, {"family": "Monteiro Venturini", "given": "Andressa", "initials": "A"}, {"family": "Satler Pylro", "given": "Victor", "initials": "V", "orcid": "0000-0003-2154-9150", "researcher": {"href": "https://publications.scilifelab.se/researcher/384c2ceb3ffb4e39a44a221f9830df60.json"}}, {"family": "Tsai", "given": "Siu Mui", "initials": "SM", "orcid": "0000-0002-3733-6312", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a40fb3d3e4d4b15b5a34c3d797ace3a.json"}}], "type": "journal article", "published": "2020-12-00", "journal": {"volume": "12", "issn": "1758-2229", "issue": "6", "title": "Environ Microbiol Rep", "pages": "651-655", "issn-l": "1758-2229"}, "abstract": "Soil microbiome is one of the most heterogeneous biological systems. State-of-the-art molecular approaches such as those based on single-amplified genomes (SAGs) and metagenome assembled-genomes (MAGs) are now improving our capacity for disentailing soil microbial-mediated processes. Here, we analysed publicly available datasets of soil microbial genomes and MAG's reconstructed from the Amazon's tropical soil (primary forest and pasture) and active layer of permafrost, aiming to evaluate their genome size. Our results suggest that the Candidate Phyla Radiation (CPR)/Patescibacteria phyla have genomes with an average size fourfold smaller than the mean identified in the RefSoil database, which lacks any representative of this phylum. Also, by analysing the potential metabolism of 888 soil microbial genomes, we show that CPR/Patescibacteria representatives share similar functional profiles, but different from other microbial phyla and are frequently neglected in the soil microbial surveys. Finally, we argue that the use of MAGs may be a better choice over SAGs to expand the soil microbial databases, like RefSoil.", "doi": "10.1111/1758-2229.12880", "pmid": "32815317", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2020-09-10T13:39:31.755Z", "modified": "2024-01-16T13:48:41.226Z"}, {"entity": "publication", "iuid": "8227f86545354fea8ca5dd31ad2322b1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8227f86545354fea8ca5dd31ad2322b1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8227f86545354fea8ca5dd31ad2322b1"}}, "title": "Remnants of marine bacterial communities can be retrieved from deep sediments in lakes of marine origin.", "authors": [{"family": "Langenheder", "given": "Silke", "initials": "S"}, {"family": "Comte", "given": "J\u00e9r\u00f4me", "initials": "J"}, {"family": "Zha", "given": "Yinghua", "initials": "Y"}, {"family": "Samad", "given": "Md Sainur", "initials": "MS"}, {"family": "Sinclair", "given": "Lucas", "initials": "L"}, {"family": "Eiler", "given": "Alexander", "initials": "A"}, {"family": "Lindstr\u00f6m", "given": "Eva S", "initials": "ES"}], "type": "journal article", "published": "2016-08-00", "journal": {"volume": "8", "issn": "1758-2229", "issue": "4", "pages": "479-485", "title": "Environ Microbiol Rep", "issn-l": "1758-2229"}, "abstract": "Some bacteria can be preserved over time in deep sediments where they persist either in dormant or slow-growing vegetative stages. Here, we hypothesized that such cells can be revived when exposed to environmental conditions similar to those before they were buried in the sediments. To test this hypothesis, we collected bacteria from sediment samples of different ages (140-8500 calibrated years before present, cal BP) from three lakes that differed in the timing of their physical isolation from the Baltic Sea following postglacial uplift. After these bacterial communities were grown in sterile water from the Baltic Sea, we determined the proportion of 16S rRNA sequence reads associated with marine habitats by extracting the environment descriptive terms of homologous sequences retrieved from public databases. We found that the proportion of reads associated with marine descriptive term was significantly higher in cultures inoculated with sediment layers formed under Baltic conditions and where salinities were expected to be similar to current levels. Moreover, a similar pattern was found in the original sediment layers. Our study, therefore, suggests that remnants of marine bacterial communities can be preserved in sediments over thousands of years and can be revived from deep sediments in lakes of marine origin.", "doi": "10.1111/1758-2229.12392", "pmid": "26929161", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-05-03T13:00:11.885Z", "modified": "2024-01-16T13:48:49.696Z"}, {"entity": "publication", "iuid": "3534aa7612d14facbf4c711dee15c226", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3534aa7612d14facbf4c711dee15c226.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3534aa7612d14facbf4c711dee15c226"}}, "title": "Transcriptional responses of the bacterial antagonist Serratia plymuthica to the fungal phytopathogen Rhizoctonia solani.", "authors": [{"family": "Neupane", "given": "Saraswoti", "initials": "S"}, {"family": "Finlay", "given": "Roger D", "initials": "RD"}, {"family": "Alstr\u00f6m", "given": "Sadhna", "initials": "S"}, {"family": "Elfstrand", "given": "Malin", "initials": "M"}, {"family": "H\u00f6gberg", "given": "Nils", "initials": "N"}], "type": "journal article", "published": "2015-02-00", "journal": {"volume": "7", "issn": "1758-2229", "issue": "1", "pages": "123-127", "title": "Environ Microbiol Rep", "issn-l": "1758-2229"}, "abstract": "Rhizobacteria with biocontrol ability exploit a range of mechanisms to compete successfully with other microorganisms and to ensure their growth and survival in the rhizosphere, ultimately promoting plant growth. The rhizobacterium Serratia plymuthica\u2005AS13 is able to promote oilseed rape growth and improve seedling survival in the presence of the fungal pathogen, Rhizoctonia solani\u2005AG 2-1; however, our understanding of the mechanisms underlying the antagonism of Serratia is limited. To elucidate possible mechanisms, genome-wide gene expression profiling of S.\u2009plymuthica\u2005AS13 was carried out in the presence or absence of R.\u2009solani. We used RNA sequencing methodology to obtain a comprehensive overview of Serratia gene expression in response to R.\u2009solani. The differential gene expression profiles of S.\u2009plymuthica\u2005AS13 revealed significantly increased expression of genes related to the biosynthesis of the antibiotic pyrrolnitrin (prnABCD), protease production and transporters. The results presented here provide evidence that antibiosis is a major functional mechanism underlying the antagonistic behaviour of S.\u2009plymuthica\u2005AS13.", "doi": "10.1111/1758-2229.12203", "pmid": "25139310", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [], "notes": [], "created": "2017-05-02T12:58:10.189Z", "modified": "2020-01-21T13:56:08.988Z"}, {"entity": "publication", "iuid": "ede8b83029ae429f9d2c02612ae27f3d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ede8b83029ae429f9d2c02612ae27f3d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ede8b83029ae429f9d2c02612ae27f3d"}}, "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": {"volume": "4", "issn": "1758-2229", "issue": "3", "pages": "367-372", "title": "Environ Microbiol Rep", "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": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:56:15.460Z", "modified": "2020-01-21T13:53:20.940Z"}], "created": "2017-05-09T09:12:45.437Z", "modified": "2020-11-27T13:14:06.987Z"}