{"entity": "journal", "iuid": "54c2ecf4778540a1a0641de4d00d5af8", "timestamp": "2026-06-15T17:11:46.329Z", "links": {"self": {"href": "https://publications.scilifelab.se/journal/Environ%20Microbiome.json"}, "display": {"href": "https://publications.scilifelab.se/journal/Environ%20Microbiome"}}, "title": "Environ Microbiome", "issn": "2524-6372", "issn-l": null, "publications_count": 6, "publications": [{"entity": "publication", "iuid": "c67e37951ff244288a56301faa275a0d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c67e37951ff244288a56301faa275a0d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c67e37951ff244288a56301faa275a0d"}}, "title": "Evidence for cable bacteria inhabiting deep in anoxic sediment reveals a novel ecological niche.", "authors": [{"family": "Fonseca", "given": "Alexis", "initials": "A"}, {"family": "Hermans", "given": "Martijn", "initials": "M"}, {"family": "Nascimento", "given": "Francisco J A", "initials": "FJA"}, {"family": "Stranne", "given": "Christian", "initials": "C"}, {"family": "Norkko", "given": "Alf", "initials": "A"}, {"family": "Gustafsson", "given": "Bo G", "initials": "BG"}, {"family": "Humborg", "given": "Christoph", "initials": "C"}], "type": "journal article", "published": "2026-04-15", "journal": {"title": "Environ Microbiome", "issn": "2524-6372", "volume": "21", "issue": "1", "issn-l": null}, "abstract": "Cable bacteria are filamentous sulphide-oxidisers capable of cm-scale electron transport. They are generally considered restricted to the upper few oxic-suboxic cm of marine sediments, where they couple sulphide oxidation to oxygen or nitrate reduction. Despite their influence on redox gradients, trace metal mobility, and nutrient cycling, their presence and activity in deeper anoxic sediment layers remain unknown. The presence and activity of marine cable bacteria (Candidatus Electrothrix) were investigated at four stations in Sweden and Finland, including deep vertical profiles of anoxic sediment layers, to assess their presence and activity under different environmental contexts.\n\nUsing metatranscriptomic data for rRNA-based community profiling and gene expression combined with porewater geochemistry, evidence of abundant and active cable bacteria was found, peaking below 20 cm depth in deep anoxic sediment layers of Kolj\u00f6 Fjord on the Swedish West Coast. This zone coincided with elevated gene expressions related to sulphide oxidation (including sqr) and nitrate reduction (napA), as well as an abundant presence of sulphide and a sharp nitrate peak. Phylogenetic analyses revealed a diverse assemblage of Ca. Electrothrix includes several potential novel taxa. The co-occurrence of cable bacteria activity, sulphide availability, and a nitrate peak at depth suggests that these organisms may be supported by local nitrate production under anoxic conditions.\n\nOur findings challenge the prevailing view that cable bacteria are restricted to shallow sediment horizons and demonstrate their activity and diversity in deep, anoxic layers. This expands the known ecological niche of cable bacteria and suggests that locally produced nitrate under anoxic conditions may facilitate their activity at depth. This discovery advances our understanding of ecology in anoxic marine environments, providing new insights into marine cable bacteria, sediment biogeochemistry, and analogues of early Earth microbial ecosystems.", "doi": "10.1186/s40793-026-00895-7", "pmid": "41987322", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13081432"}, {"db": "pii", "key": "10.1186/s40793-026-00895-7"}], "notes": [], "created": "2026-05-11T11:49:40.138Z", "modified": "2026-05-11T11:49:40.148Z"}, {"entity": "publication", "iuid": "16a8d45180854dfdb468144fa9775e34", "links": {"self": {"href": "https://publications.scilifelab.se/publication/16a8d45180854dfdb468144fa9775e34.json"}, "display": {"href": "https://publications.scilifelab.se/publication/16a8d45180854dfdb468144fa9775e34"}}, "title": "Generalist phyllosphere taxa dominate microbial communities on macrophytes across a natural salinity gradient", "authors": [{"family": "Herlemann", "given": "Daniel P R", "initials": "DPR"}, {"family": "Riedinger", "given": "David J", "initials": "DJ"}, {"family": "Fen\u00e1ndez-Ju\u00e1rez", "given": "Victor", "initials": "V"}, {"family": "Delgado", "given": "Luis F", "initials": "LF", "orcid": "0000-0001-7850-5285", "researcher": {"href": "https://publications.scilifelab.se/researcher/c90912060686401482b1079bd8251e60.json"}}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}, {"family": "Pansch", "given": "Christian", "initials": "C", "orcid": "0000-0001-8442-4502", "researcher": {"href": "https://publications.scilifelab.se/researcher/50129df0120e441081efa1a9649ffbd5.json"}}, {"family": "Riemann", "given": "Lasse", "initials": "L", "orcid": "0000-0001-9207-2543", "researcher": {"href": "https://publications.scilifelab.se/researcher/9fc561d1d5694c4c9fbc9a05dd741e17.json"}}, {"family": "Bengtsson", "given": "Mia M", "initials": "MM"}, {"family": "Gyraite", "given": "Greta", "initials": "G", "orcid": "0000-0002-7079-7997", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9fa8139fbc64e7e990587ca8e5f6d52.json"}}, {"family": "Reusch", "given": "Thorsten B H", "initials": "TBH", "orcid": "0000-0002-8961-4337", "researcher": {"href": "https://publications.scilifelab.se/researcher/39b27965acd74a7a95e97b77abee769d.json"}}, {"family": "Katarzyte", "given": "Marija", "initials": "M"}, {"family": "Kube", "given": "Sandra", "initials": "S"}, {"family": "Martin", "given": "Georg", "initials": "G", "orcid": "0000-0002-5289-6131", "researcher": {"href": "https://publications.scilifelab.se/researcher/3fa7c61072034af188ed3685ce83ca3c.json"}}, {"family": "Rakowski", "given": "Marcin", "initials": "M"}, {"family": "Labrenz", "given": "Matthias", "initials": "M", "orcid": "0000-0003-3452-8631", "researcher": {"href": "https://publications.scilifelab.se/researcher/38c42f1aada5411281b2bdc4d2f8e934.json"}}], "type": "journal-article", "published": "2026-04-04", "journal": {"title": "Environ Microbiome", "issn": "2524-6372", "volume": "21", "issue": "1", "issn-l": null}, "abstract": "Shallow coastal habitats are characterized by diverse macrophytes and often feature steep abiotic gradients, including salinity variations, which can shape the leaf- surface epi-microbiome (phyllosphere). To elucidate the effect of salinity and host identity on the phyllosphere of aquatic macrophytes in shallow water, we sampled the leaf surface microbiota across a salinity range of 6-15. Samples included the eelgrass Zostera marina, as well as the Eurasian water milfoil (Myriophyllum spicatum), muskgrass (Chara spp.), and sago pondweed (Stuckenia pectinata) in the brackish Baltic Sea during the summer of 2022. Microbial communities were characterized using 16S and 18S rRNA gene amplicon sequencing.\n\nAs hypothesized, the phyllosphere bacterial and protist community composition was distinct from the surrounding seawater microbiome. Typically associated taxa included the genera Loktanella, Pseudorhodobacter, the methylotrophic genus Methylotenera, unclassified Synechococcales, and Rhodobacteriaceae. Protist genera such as Picochlorum were consistently detected across all macrophyte hosts, while Cocconeis, Cyclotella, Mondous and unclassified Bacillariophyceae were present in all phyllospheres except Chara spp. Both, salinity and host species significantly influenced the composition and prevalence of the microbiota, primarily through shifts in the abundance of typical phyllosphere taxa. However, only 4-11% of phyllosphere taxa were uniquely associated with a specific salinity or macrophyte host.\n\nOur results demonstrate that aquatic macrophytes harbor a distinct and characteristic phyllosphere microbiome. The low proportion of host- or salinity specific taxa suggests that the most abundant members of this community are generalists, broadly adapted to the phyllosphere niche rather than being narrowly specialized. This implies that the presence of the macrophyte itself, providing a stable, nutrient-rich surface, exerts a stronger deterministic influence on the microbial community than the host identity or salinity fluctuations. Consequently, the phyllosphere appears relatively resilient to environmental variability, particularly salinity fluctuations. This highlights the robust nature of host-microbiome interactions and their importance for conservation of aquatic macrophyte ecosystems.", "doi": "10.1186/s40793-026-00881-z", "pmid": "41935342", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13067490"}, {"db": "pii", "key": "10.1186/s40793-026-00881-z"}], "notes": [], "created": "2026-04-10T12:05:26.160Z", "modified": "2026-04-16T09:42:39.411Z"}, {"entity": "publication", "iuid": "529c1d9b93b7499997f647488acac746", "links": {"self": {"href": "https://publications.scilifelab.se/publication/529c1d9b93b7499997f647488acac746.json"}, "display": {"href": "https://publications.scilifelab.se/publication/529c1d9b93b7499997f647488acac746"}}, "title": "Pronounced seasonal dynamics in transcription of vitamin B1 acquisition strategies diverge among Baltic Sea bacterioplankton.", "authors": [{"family": "P\u00e9rez-Mart\u00ednez", "given": "Clara", "initials": "C"}, {"family": "Pontiller", "given": "Benjamin", "initials": "B"}, {"family": "Mart\u00ednez-Garc\u00eda", "given": "Sandra", "initials": "S"}, {"family": "Hylander", "given": "Samuel", "initials": "S"}, {"family": "Paerl", "given": "Ryan W", "initials": "RW"}, {"family": "Lundin", "given": "Daniel", "initials": "D"}, {"family": "Pinhassi", "given": "Jarone", "initials": "J"}], "type": "journal article", "published": "2025-09-16", "journal": {"title": "Environ Microbiome", "issn": "2524-6372", "volume": "20", "issue": "1", "pages": "115", "issn-l": null}, "abstract": "Vitamin B1 (thiamin) is essential to life; yet little is known of the regulation of its availability in marine environments or how it varies seasonally. Since microbes are the key synthesizers of the vitamin in marine environments, we here used metatranscriptomics to examine the seasonal dynamics of B1 acquisition strategies (including both uptake and synthesis pathways) in Baltic Sea bacterioplankton.\n\nElevated B1-related gene expression was observed in summer, coinciding with increased temperatures and bacterial activity and decreased nutrient availability. Different bacterial taxa exhibited distinct B1 acquisition strategies. We identified filamentous Cyanobacteria of the order Nostocales as critical to sustaining B1 production during summer, potentially compensating for limited synthesis in heterotrophic bacteria, especially for 4-amino-5-hydroxymethylpyrimidine (HMP) synthesis. Also, Pelagibacterales accounted for major portions of the community transcription, primarily taking up and salvaging the B1 precursor HMP during summer. This study highlights the partitioning of B1 synthesis, salvage, and uptake among microbial taxa, underscoring that transcriptional activity was more dynamic over time than changes in the genomic potential.\n\nWe emphasize the influence of environmental conditions on microbial community dynamics and B1 cycling in general, and the potential implications of global change-induced increases in filamentous Cyanobacteria blooms on vitamin food web transfer in particular.", "doi": "10.1186/s40793-025-00780-9", "pmid": "40958120", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12442306"}, {"db": "pii", "key": "10.1186/s40793-025-00780-9"}], "notes": [], "created": "2025-11-21T13:08:52.937Z", "modified": "2025-11-21T13:08:52.943Z"}, {"entity": "publication", "iuid": "2d986718e5874eb7957b646b4e881227", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2d986718e5874eb7957b646b4e881227.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2d986718e5874eb7957b646b4e881227"}}, "title": "Low impact of Zostera marina meadows on sediment and water microbiota under brackish conditions.", "authors": [{"family": "Herlemann", "given": "Daniel P R", "initials": "DPR"}, {"family": "Delgado", "given": "Luis F", "initials": "LF"}, {"family": "Riedinger", "given": "David J", "initials": "DJ"}, {"family": "Fern\u00e1ndez-Ju\u00e1rez", "given": "V\u00edctor", "initials": "V"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}, {"family": "Pansch", "given": "Christian", "initials": "C"}, {"family": "Riemann", "given": "Lasse", "initials": "L"}, {"family": "Bengtsson", "given": "Mia M", "initials": "MM"}, {"family": "Gyrait\u0117", "given": "Greta", "initials": "G"}, {"family": "Katar\u017eyt\u0117", "given": "Marija", "initials": "M"}, {"family": "Kisand", "given": "Veljo", "initials": "V"}, {"family": "Kube", "given": "Sandra", "initials": "S"}, {"family": "Martin", "given": "Georg", "initials": "G"}, {"family": "Piwosz", "given": "Kasia", "initials": "K"}, {"family": "Rakowski", "given": "Marcin", "initials": "M"}, {"family": "Labrenz", "given": "Matthias", "initials": "M"}], "type": "journal article", "published": "2025-01-11", "journal": {"title": "Environ Microbiome", "issn": "2524-6372", "volume": "20", "issue": "1", "pages": "2", "issn-l": null}, "abstract": "Zostera marina is an important ecosystem engineer influencing shallow water environments and possibly shaping the microbiota in surrounding sediments and water. Z. marina is typically found in marine systems, but it can also proliferate under brackish conditions. Changes in salinity generally have a strong impact on the biota, especially at the salty divide between salinity 6 and 9. To better understand the impact of the salty divide on the interaction between Z. marina and the surrounding sediment and water microbiota, we investigated the effects of Z. marina meadows on the surrounding microbiota across a salinity range of 6-15 in the Baltic Sea during the summer using 16S and 18S rRNA gene amplicon sequencing.\n\nSalinity was the most important factor for structuring the microbiota within both water and sediment. The presence of Z. marina affected the composition of the bacterial and eukaryotic community and bacterial alpha diversity in the sediment. However, this effect was confined to alpha-mesohaline conditions (salinity 9-15). The impact of Z. marina below salinity 9 on water and sediment microbiota was insignificant.\n\nIncreasing salinity was associated with a longer leaf length of Z. marina, causing an increased canopy height, which affects the sediment microbiota through reduced water velocity. Hence, we propose that the canopy effect may be the major predictor explaining Z. marina's interactions with the surrounding microbiota at salinity 9-15. These findings emphasize the importance of the physical effects of Z. marina meadow ecosystem services and have important implications for Z. marina management under brackish conditions in a changing climate.", "doi": "10.1186/s40793-024-00662-6", "pmid": "39799374", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11724437"}, {"db": "pii", "key": "10.1186/s40793-024-00662-6"}], "notes": [], "created": "2025-11-21T13:50:12.826Z", "modified": "2025-11-21T13:50:12.830Z"}, {"entity": "publication", "iuid": "42b992446dbf48e7aa157bc279607840", "links": {"self": {"href": "https://publications.scilifelab.se/publication/42b992446dbf48e7aa157bc279607840.json"}, "display": {"href": "https://publications.scilifelab.se/publication/42b992446dbf48e7aa157bc279607840"}}, "title": "Microplastic exposure across trophic levels: effects on the host-microbiota of freshwater organisms.", "authors": [{"family": "Varg", "given": "Javier Edo", "initials": "JE", "orcid": "0000-0002-7895-4563", "researcher": {"href": "https://publications.scilifelab.se/researcher/72cb1019516e49f7b8f39b18924babc2.json"}}, {"family": "Outomuro", "given": "David", "initials": "D"}, {"family": "Kunce", "given": "Warren", "initials": "W"}, {"family": "Kuehrer", "given": "Lukas", "initials": "L"}, {"family": "Svanb\u00e4ck", "given": "Richard", "initials": "R"}, {"family": "Johansson", "given": "Frank", "initials": "F"}], "type": "journal article", "published": "2022-07-06", "journal": {"title": "Environ Microbiome", "issn": "2524-6372", "volume": "17", "issue": "1", "pages": "36", "issn-l": null}, "abstract": "Microplastics are a pervasive pollutant widespread in the sea and freshwater from anthropogenic sources, and together with the presence of pesticides, they can have physical and chemical effects on aquatic organisms and on their microbiota. Few studies have explored the combined effects of microplastics and pesticides on the host-microbiome, and more importantly, the effects across multiple trophic levels. In this work, we studied the effects of exposure to microplastics and the pesticide deltamethrin on the diversity and abundance of the host-microbiome across a three-level food chain: daphnids-damselfly-dragonflies. Daphnids were the only organism exposed to 1 \u00b5m microplastic beads, and they were fed to damselfly larvae. Those damselfly larvae were exposed to deltamethrin and then fed to the dragonfly larvae. The microbiotas of the daphnids, damselflies, and dragonflies were analyzed.\n\nExposure to microplastics and deltamethrin had a direct effect on the microbiome of the species exposed to these pollutants. An indirect effect was also found since exposure to the pollutants at lower trophic levels showed carry over effects on the diversity and abundance of the microbiome on higher trophic levels, even though the organisms at these levels where not directly exposed to the pollutants. Moreover, the exposure to deltamethrin on the damselflies negatively affected their survival rate in the presence of the dragonfly predator, but no such effects were found on damselflies fed with daphnids that had been exposed to microplastics.\n\nOur study highlights the importance of evaluating ecotoxicological effects at the community level. Importantly, the indirect exposure to microplastics and pesticides through diet can potentially have bottom-up effects on the trophic webs.", "doi": "10.1186/s40793-022-00429-x", "pmid": "35794681", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9258161"}, {"db": "pii", "key": "10.1186/s40793-022-00429-x"}], "notes": [], "created": "2022-11-29T09:37:16.537Z", "modified": "2022-11-29T09:37:16.572Z"}, {"entity": "publication", "iuid": "23d7ef3496e949c7b6f354ee8b433bbc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/23d7ef3496e949c7b6f354ee8b433bbc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/23d7ef3496e949c7b6f354ee8b433bbc"}}, "title": "Land-use intensification differentially affects bacterial, fungal and protist communities and decreases microbiome network complexity.", "authors": [{"family": "Romdhane", "given": "Sana", "initials": "S"}, {"family": "Spor", "given": "Aym\u00e9", "initials": "A"}, {"family": "Banerjee", "given": "Samiran", "initials": "S"}, {"family": "Breuil", "given": "Marie-Christine", "initials": "M"}, {"family": "Bru", "given": "David", "initials": "D"}, {"family": "Chabbi", "given": "Abad", "initials": "A"}, {"family": "Hallin", "given": "Sara", "initials": "S"}, {"family": "van der Heijden", "given": "Marcel G A", "initials": "MGA"}, {"family": "Saghai", "given": "Aur\u00e9lien", "initials": "A"}, {"family": "Philippot", "given": "Laurent", "initials": "L", "orcid": "0000-0003-3461-4492", "researcher": {"href": "https://publications.scilifelab.se/researcher/45ef457126a748aebd40ff834d20085c.json"}}], "type": "journal article", "published": "2022-01-06", "journal": {"title": "Environ Microbiome", "issn": "2524-6372", "issn-l": null, "volume": "17", "issue": "1", "pages": "1"}, "abstract": "Soil microbial communities are major drivers of cycling of soil nutrients that sustain plant growth and productivity. Yet, a holistic understanding of the impact of land-use intensification on the soil microbiome is still poorly understood. Here, we used a field experiment to investigate the long-term consequences of changes in land-use intensity based on cropping frequency (continuous cropping, alternating cropping with a temporary grassland, perennial grassland) on bacterial, protist and fungal communities as well as on their co-occurrence networks.\r\n\r\nWe showed that land use has a major impact on the structure and composition of bacterial, protist and fungal communities. Grassland and arable cropping differed markedly with many taxa differentiating between both land use types. The smallest differences in the microbiome were observed between temporary grassland and continuous cropping, which suggests lasting effects of the cropping system preceding the temporary grasslands. Land-use intensity also affected the bacterial co-occurrence networks with increased complexity in the perennial grassland comparing to the other land-use systems. Similarly, co-occurrence networks within microbial groups showed a higher connectivity in the perennial grasslands. Protists, particularly Rhizaria, dominated in soil microbial associations, as they showed a higher number of connections than bacteria and fungi in all land uses.\r\n\r\nOur findings provide evidence of legacy effects of prior land use on the composition of the soil microbiome. Whatever the land use, network analyses highlighted the importance of protists as a key element of the soil microbiome that should be considered in future work. Altogether, this work provides a holistic perspective of the differential responses of various microbial groups and of their associations to agricultural intensification.", "doi": "10.1186/s40793-021-00396-9", "pmid": "34991714", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s40793-021-00396-9"}, {"db": "pmc", "key": "PMC8740439"}], "notes": [], "created": "2022-03-29T13:48:27.073Z", "modified": "2022-08-19T08:54:32.507Z"}], "created": "2022-03-29T13:48:27.121Z", "modified": "2022-03-29T13:48:27.121Z"}