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Delgadillo-Nuno, E., Teira, E., Pontiller, B., Lundin, D., Joglar, V., Pedros-Alio, C., . . . Martinez-Garcia, S. (2024). Coastal upwelling systems as dynamic mosaics of bacterioplankton functional specialization. Frontiers in Marine Science, 10, Article ID 1259783.
Open this publication in new window or tab >>Coastal upwelling systems as dynamic mosaics of bacterioplankton functional specialization
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2024 (English)In: Frontiers in Marine Science, E-ISSN 2296-7745, Vol. 10, article id 1259783Article in journal (Refereed) Published
Abstract [en]

Coastal upwelling areas are extraordinarily productive environments where prokaryotic communities, the principal remineralizers of dissolved organic matter (DOM), rapidly respond to phytoplankton bloom and decay dynamics. Nevertheless, the extent of variability of key microbial functions in such dynamic waters remains largely unconstrained. Our metatranscriptomics analyses of 162 marker genes encoding ecologically relevant prokaryotic functions showed distinct spatial-temporal patterns in the NW Iberian Peninsula upwelling area. Short-term (daily) changes in specific bacterial functions associated with changes in biotic and abiotic factors were superimposed on seasonal variability. Taxonomic and functional specialization of prokaryotic communities, based mostly on different resource acquisition strategies, was observed. Our results uncovered the potential influence of prokaryotic functioning on phytoplankton bloom composition and development (e.g., Cellvibrionales and Flavobacteriales increased relative gene expression related to vitamin B12 and siderophore metabolisms during Chaetoceros and Dinophyceae summer blooms). Notably, bacterial adjustments to C- or N-limitation and DMSP availability during summer phytoplankton blooms and different spatial-temporal patterns of variability in the expression of genes with different phosphate affinity indicated a complex role of resource availability in structuring bacterial communities in this upwelling system. Also, a crucial role of Cellvibrionales in the degradation of DOM (carbohydrate metabolism, TCA cycle, proteorhodopsin, ammonium, and phosphate uptake genes) during the summer phytoplankton bloom was found. Overall, this dataset revealed an intertwined mosaic of microbial interactions and nutrient utilization patterns along a spatial-temporal gradient that needs to be considered if we aim to understand the biogeochemical processes in some of the most productive ecosystems in the world ' s oceans.

Place, publisher, year, edition, pages
Frontiers Media S.A., 2024
Keywords
bacterioplankton, upwelling systems, phytoplankton bloom, metatranscriptomics, metabarcoding
National Category
Microbiology Oceanography, Hydrology and Water Resources
Research subject
Ecology, Microbiology; Ecology, Aquatic Ecology
Identifiers
urn:nbn:se:lnu:diva-127387 (URN)10.3389/fmars.2023.1259783 (DOI)001143516000001 ()2-s2.0-85182436775 (Scopus ID)
Available from: 2024-02-01 Created: 2024-02-01 Last updated: 2024-03-13Bibliographically approved
Prager, M., Lundin, D., Ronquist, F. & Andersson, A. F. (2023). ASV portal: an interface to DNA-based biodiversity data in the Living Atlas. BMC Bioinformatics, 24(1), Article ID 6.
Open this publication in new window or tab >>ASV portal: an interface to DNA-based biodiversity data in the Living Atlas
2023 (English)In: BMC Bioinformatics, E-ISSN 1471-2105, Vol. 24, no 1, article id 6Article in journal (Refereed) Published
Abstract [en]

Background: The Living Atlas is an open source platform used to collect, visualise and analyse biodiversity data from multiple sources, and serves as the national biodiversity data hub in many countries. Although powerful, the Living Atlas has had limited func-tionality for species occurrence data derived from DNA sequences. As a step toward integrating this fast-growing data source into the platform, we developed the Ampli-con Sequence Variant (ASV) portal: a web interface to sequence-based biodiversity observations in the Living Atlas.Results: The ASV portal allows data providers to submit denoised metabarcoding output to the Living Atlas platform via an intermediary ASV database. It also enables users to search for existing ASVs and associated Living Atlas records using the Basic Local Alignment Search Tool, or via filters on taxonomy and sequencing details. The ASV portal is a Python-Flask/jQuery web interface, implemented as a multi-container docker service, and is an integral part of the Swedish Biodiversity Data Infrastructure. Conclusion: The ASV portal is a web interface that effectively integrates biodiversity data derived from DNA sequences into the Living Atlas platform.

Place, publisher, year, edition, pages
BioMed Central (BMC), 2023
Keywords
Biodiversity informatics, Species occurrence, Darwin core, Amplicon sequencing, Metabarcoding, eDNA, BLAST
National Category
Ecology
Research subject
Natural Science, Ecology
Identifiers
urn:nbn:se:lnu:diva-118840 (URN)10.1186/s12859-022-05120-z (DOI)000909501700001 ()36604610 (PubMedID)2-s2.0-85145645757 (Scopus ID)
Available from: 2023-01-30 Created: 2023-01-30 Last updated: 2024-01-17Bibliographically approved
Bensch, H., Tolf, C., Waldenström, J., Lundin, D. & Zöttl, M. (2023). Bacteroidetes to Firmicutes: captivity changes the gut microbiota composition and diversity in a social subterranean rodent. Animal Microbiome, 5(1), Article ID 9.
Open this publication in new window or tab >>Bacteroidetes to Firmicutes: captivity changes the gut microbiota composition and diversity in a social subterranean rodent
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2023 (English)In: Animal Microbiome, E-ISSN 2524-4671, Vol. 5, no 1, article id 9Article in journal (Refereed) Published
Abstract [en]

BackgroundIn mammals, the gut microbiota has important effects on the health of their hosts. Recent research highlights that animal populations that live in captivity often differ in microbiota diversity and composition from wild populations. However, the changes that may occur when animals move to captivity remain difficult to predict and factors generating such differences are poorly understood. Here we compare the bacterial gut microbiota of wild and captive Damaraland mole-rats (Fukomys damarensis) originating from a population in the southern Kalahari Desert to characterise the changes of the gut microbiota that occur from one generation to the next generation in a long-lived, social rodent species.ResultsWe found a clear divergence in the composition of the gut microbiota of captive and wild Damaraland mole-rats. Although the dominating higher-rank bacterial taxa were the same in the two groups, captive animals had an increased ratio of relative abundance of Firmicutes to Bacteroidetes compared to wild animals. The Amplicon Sequence Variants (ASVs) that were strongly associated with wild animals were commonly members of the same bacterial families as those strongly associated with captive animals. Captive animals had much higher ASV richness compared to wild-caught animals, explained by an increased richness within the Firmicutes.ConclusionWe found that the gut microbiota of captive hosts differs substantially from the gut microbiota composition of wild hosts. The largest differences between the two groups were found in shifts in relative abundances and diversity of Firmicutes and Bacteroidetes.

Place, publisher, year, edition, pages
BioMed Central (BMC), 2023
Keywords
Captivity, Wild, Gut microbiota, Damaraland mole-rat, 16S amplicon sequencing
National Category
Ecology Microbiology
Research subject
Ecology, Microbiology
Identifiers
urn:nbn:se:lnu:diva-119958 (URN)10.1186/s42523-023-00231-1 (DOI)000932695300001 ()36765400 (PubMedID)2-s2.0-85159590559 (Scopus ID)
Available from: 2023-03-27 Created: 2023-03-27 Last updated: 2023-08-24Bibliographically approved
Churakova, Y., Aguilera, A., Charalampous, E., Conley, D. J., Lundin, D., Pinhassi, J. & Farnelid, H. (2023). Biogenic silica accumulation in picoeukaryotes: Novel players in the marine silica cycle. Environmental Microbiology Reports, 15(4), 282-290
Open this publication in new window or tab >>Biogenic silica accumulation in picoeukaryotes: Novel players in the marine silica cycle
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2023 (English)In: Environmental Microbiology Reports, ISSN 1758-2229, E-ISSN 1758-2229, Vol. 15, no 4, p. 282-290Article in journal (Refereed) Published
Abstract [en]

It is well known that the biological control of oceanic silica cycling is dominated by diatoms, with sponges and radiolarians playing additional roles. Recent studies have revealed that some smaller marine organisms (e.g. the picocyanobacterium Synechococcus) also take up silicic acid (dissolved silica, dSi) and accumulate silica, despite not exhibiting silicon dependent cellular structures. Here, we show biogenic silica (bSi) accumulation in five strains of picoeukaryotes (<2-3 mu m), including three novel isolates from the Baltic Sea, and two marine species (Ostreococcus tauri and Micromonas commoda), in cultures grown with added dSi (100 mu M). Average bSi accumulation in these novel biosilicifiers was between 30 and 92 amol Si cell(-1). Growth rate and cell size of the picoeukaryotes were not affected by dSi addition. Still, the purpose of bSi accumulation in these smaller eukaryotic organisms lacking silicon dependent structures remains unclear. In line with the increasing recognition of picoeukaryotes in biogeochemical cycling, our findings suggest that they can also play a significant role in silica cycling.

Place, publisher, year, edition, pages
John Wiley & Sons, 2023
National Category
Microbiology
Research subject
Ecology, Microbiology
Identifiers
urn:nbn:se:lnu:diva-120915 (URN)10.1111/1758-2229.13144 (DOI)000966621000001 ()36992638 (PubMedID)2-s2.0-85152072762 (Scopus ID)
Available from: 2023-05-26 Created: 2023-05-26 Last updated: 2023-09-07Bibliographically approved
Aguilera, A., Alegria Zufia, J., Bas Conn, L., Gurlit, L., Śliwińska‐Wilczewska, S., Budzałek, G., . . . Farnelid, H. (2023). Ecophysiological analysis reveals distinct environmental preferences in closely related Baltic Sea picocyanobacteria. Environmental Microbiology, 25(9), 1674-1695
Open this publication in new window or tab >>Ecophysiological analysis reveals distinct environmental preferences in closely related Baltic Sea picocyanobacteria
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2023 (English)In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 25, no 9, p. 1674-1695Article in journal (Refereed) Published
Abstract [en]

Cluster 5 picocyanobacteria significantly contribute to primary productivity in aquatic ecosystems. Estuarine populations are highly diverse and consist of many co-occurring strains, but their physiology remains largely understudied. In this study, we characterized 17 novel estuarine picocyanobacterial strains. Phylogenetic analysis of the 16S rRNA and pigment genes (cpcBandcpeBA) uncovered multiple estuarine and freshwater-related clusters and pigment types. Assays with five representative strains (three phycocyanin rich and two phycoerythrin rich) under temperature (10–30°C), light(10–190 μmol  photons  m-2s-1), and salinity (2–14  PSU) gradients revealed distinct growth optima and tolerance, indicating that genetic variability was accompanied by physiological diversity. Adaptability to environmental conditions was associated with differential pigment content and photosynthetic performance. Amplicon sequence variants at a coastal and an offshore station linked population dynamics with phylogenetic clusters, supporting that strains isolated in this study represent key ecotypes within the Baltic Sea picocyanobacterial community. The functional diversity found within strains with the same pigment type suggests that understanding estuarine picocyanobacterial ecology requires analysis beyond the phycocyanin and phycoerythrin divide. This new knowledge of the environmental preferences in estuarine picocyanobacteria is important for understanding and evaluating productivity in current and future ecosystems.

Place, publisher, year, edition, pages
John Wiley & Sons, 2023
National Category
Environmental Sciences Ecology Microbiology
Research subject
Natural Science, Environmental Science; Ecology, Aquatic Ecology; Ecology, Microbiology
Identifiers
urn:nbn:se:lnu:diva-120317 (URN)10.1111/1462-2920.16384 (DOI)000973717000001 ()2-s2.0-85153326236 (Scopus ID)
Funder
Knut and Alice Wallenberg Foundation, 570630‐3095
Available from: 2023-04-19 Created: 2023-04-19 Last updated: 2023-09-07Bibliographically approved
Bensch, H., Lundin, D., Tolf, C., Waldenström, J. & Zöttl, M. (2023). Environmental effects rather than relatedness determine gut microbiome similarity in a social mammal. Journal of Evolutionary Biology, 36(12), 1753-1760
Open this publication in new window or tab >>Environmental effects rather than relatedness determine gut microbiome similarity in a social mammal
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2023 (English)In: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 36, no 12, p. 1753-1760Article in journal (Refereed) Published
Abstract [en]

In social species, group members commonly show substantial similarity in gut microbiome composition. Such similarities have been hypothesized to arise either by shared environmental effects or by host relatedness. However, disentangling these factors is difficult, because group members are often related, and social groups typically share similar environmental conditions. In this study, we conducted a cross-foster experiment under controlled laboratory conditions in group-living Damaraland mole-rats (Fukomys damarensis) and used 16S amplicon sequencing to disentangle the effects of the environment and relatedness on gut microbiome similarity and diversity. Our results show that a shared environment is the main factor explaining gut microbiome similarity, overshadowing any effect of host relatedness. Together with studies in wild animal populations, our results suggest that among conspecifics environmental factors are more powerful drivers of gut microbiome composition similarity than host genetics.

Place, publisher, year, edition, pages
John Wiley & Sons, 2023
Keywords
16S, environmental effects, group living, gut microbiome, relatedness
National Category
Ecology
Research subject
Natural Science, Ecology
Identifiers
urn:nbn:se:lnu:diva-124071 (URN)10.1111/jeb.14208 (DOI)001049289200001 ()37584218 (PubMedID)2-s2.0-85168146294 (Scopus ID)
Available from: 2023-09-05 Created: 2023-09-05 Last updated: 2024-01-18Bibliographically approved
Martinez-Varela, A., Casas, G., Berrojalbiz, N., Lundin, D., Pina, B., Dachs, J. & Vila-Costa, M. (2023). Metatranscriptomic responses and microbial degradation of background polycyclic aromatic hydrocarbons in the coastal Mediterranean and Antarctica. Environmental Science and Pollution Research, 30(57), 119988-119999
Open this publication in new window or tab >>Metatranscriptomic responses and microbial degradation of background polycyclic aromatic hydrocarbons in the coastal Mediterranean and Antarctica
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2023 (English)In: Environmental Science and Pollution Research, ISSN 0944-1344, E-ISSN 1614-7499, Vol. 30, no 57, p. 119988-119999Article in journal (Refereed) Published
Abstract [en]

Although microbial degradation is a key sink of polycyclic aromatic hydrocarbons (PAH) in surface seawaters, there is a dearth of field-based evidences of regional divergences in biodegradation and the effects of PAHs on site-specific microbial communities. We compared the magnitude of PAH degradation and its impacts in short-term incubations of coastal Mediterranean and the Maritime Antarctica microbiomes with environmentally relevant concentrations of PAHs. Mediterranean bacteria readily degraded the less hydrophobic PAHs, with rates averaging 4.72 +/- 0.5 ng L h-1. Metatranscriptomic responses showed significant enrichments of genes associated to horizontal gene transfer, stress response, and PAH degradation, mainly harbored by Alphaproteobacteria. Community composition changed and increased relative abundances of Bacteroidota and Flavobacteriales. In Antarctic waters, there was no degradation of PAH, and minimal metatranscriptome responses were observed. These results provide evidence for factors such as geographic region, community composition, and pre-exposure history to predict PAH biodegradation in seawater.

Place, publisher, year, edition, pages
Springer, 2023
Keywords
Polycyclic aromatic hydrocarbons (PAH), Metatranscriptomics, 16S amplicon sequencing, PAH biodegradation rates, Antarctica, Mediterranean
National Category
Microbiology Environmental Sciences
Research subject
Ecology, Microbiology; Natural Science, Environmental Science
Identifiers
urn:nbn:se:lnu:diva-125935 (URN)10.1007/s11356-023-30650-1 (DOI)001100586300004 ()37934408 (PubMedID)2-s2.0-85178995648 (Scopus ID)
Available from: 2023-12-08 Created: 2023-12-08 Last updated: 2024-01-18Bibliographically approved
Vila-Costa, M., Lundin, D., Fernandez-Pinos, M.-C., Iriarte, J., Irigoien, X., Pina, B. & Dachs, J. (2023). Responses to organic pollutants in the tropical Pacific and subtropical Atlantic Oceans by pelagic marine bacteria. Frontiers in Environmental Science, 11, Article ID 1110169.
Open this publication in new window or tab >>Responses to organic pollutants in the tropical Pacific and subtropical Atlantic Oceans by pelagic marine bacteria
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2023 (English)In: Frontiers in Environmental Science, E-ISSN 2296-665X, Vol. 11, article id 1110169Article in journal (Refereed) Published
Abstract [en]

Background and chronic pollution by organic pollutants (OPs) is a widespread threat in the oceans with still uncharacterized effects on marine ecosystems and the modulation of major biogeochemical cycles. The ecological impact and toxicity of this anthropogenic dissolved organic carbon (ADOC) is not related to the presence of a single compound but to the co-occurrence of a myriad of synthetic chemicals with largely unknown effects on heterotrophic microbial communities. We have analyzed the metabolic capacity of metagenome-assembled genomes (MAGs) of natural oceanic communities from the north Pacific (Costa Rica dome) and Atlantic oceans challenged with environmentally relevant levels of ADOC. In the Atlantic, ADOC-exposed MAGs responded transcriptionally more strongly compared to controls than in the Pacific, possibly mirroring the higher relevance of ADOC compounds as carbon source in oligotrophic environments. The largest proportions of transcripts originated from MAGs belonging in the families Rhodobacteraceae and Flavobacteriaceae, known to play a role on consumption of several OPs. In the Atlantic, archaeal Poseidoniales showed the highest transcription levels after 2 h of ADOC exposure, although no increase of relative abundances in the DNA pool was recorded after 24 h, whereas Methylophaga showed the opposite pattern. Both taxa are suggested to be actively involved in the consumption of biogenic alkanes produced by cyanobacteria. We observed similar gene expression profiles of alkane degradation and methylotrophy signature genes. These findings, plus the chemical degradation of alkanes measured in the experiments, provides experimental evidence of the consumption of anthropogenic hydrocarbons and synthetic chemicals at the low concentrations found in the ocean, and modulation of microbiomes by ADOC.

Place, publisher, year, edition, pages
Frontiers Media S.A., 2023
Keywords
organic pollutants, surface seawater, anthropogenic organic matter, alkane biodegradation, polycyclic aromatic hydrocarbon degradation, Poseidonales, Methylophaga
National Category
Microbiology
Research subject
Ecology, Microbiology; Ecology, Aquatic Ecology; Natural Science, Environmental Science
Identifiers
urn:nbn:se:lnu:diva-120968 (URN)10.3389/fenvs.2023.1110169 (DOI)000970927000001 ()2-s2.0-85153355471 (Scopus ID)
Available from: 2023-05-30 Created: 2023-05-30 Last updated: 2023-09-07Bibliographically approved
Osbeck, C. M. G., Lundin, D., Karlsson, C., Teikari, J. E., Moran, M. A. & Pinhassi, J. (2022). Divergent gene expression responses in two Baltic Sea heterotrophic model bacteria to dinoflagellate dissolved organic matter. PLOS ONE, 17(11), Article ID e0243406.
Open this publication in new window or tab >>Divergent gene expression responses in two Baltic Sea heterotrophic model bacteria to dinoflagellate dissolved organic matter
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2022 (English)In: PLOS ONE, E-ISSN 1932-6203, Vol. 17, no 11, article id e0243406Article in journal (Refereed) Published
Abstract [en]

Phytoplankton release massive amounts of dissolved organic matter (DOM) into the water column during recurring blooms in coastal waters and inland seas. The released DOM encompasses a complex mixture of both known and unknown compounds, and is a rich nutrient source for heterotrophic bacteria. The metabolic activity of bacteria during and after phytoplankton blooms can hence be expected to reflect the characteristics of the released DOM. We therefore investigated if bacterioplankton could be used as "living sensors" of phytoplankton DOM quantity and/or quality, by applying gene expression analyses to identify bacterial metabolisms induced by DOM. We used transcriptional analysis of two Baltic Sea bacterial isolates (Polaribacter sp. BAL334 [Flavobacteriia] and Brevundimonas sp. BAL450 [Alphaproteobacteria]) growing with DOM from axenic cultures of the dinoflagellate Prorocentrum minimum. We observed pronounced differences between the two bacteria both in growth and the expressed metabolic pathways in cultures exposed to dinoflagellate DOM compared with controls. Differences in metabolic responses between the two isolates were caused both by differences in gene repertoire between them (e.g. in the SEED categories for membrane transport, motility and photoheterotrophy) and the regulation of expression (e.g. fatty acid metabolism), emphasizing the importance of separating the responses of different taxa in analyses of community sequence data. Similarities between the bacteria included substantially increased expression of genes for Ton and Tol transport systems in both isolates, which are commonly associated with uptake of complex organic molecules. Polaribacter sp. BAL334 showed stronger metabolic responses to DOM harvested from exponential than stationary phase dinoflagellates (128 compared to 26 differentially expressed genes), whereas Brevundimonas sp. BAL450 responded more to the DOM from stationary than exponential phase dinoflagellates (33 compared to 6 differentially expressed genes). These findings suggest that shifts in bacterial metabolisms during different phases of phytoplankton blooms can be detected in individual bacterial species and can provide insights into their involvement in DOM transformations.

Place, publisher, year, edition, pages
Public Library of Science, 2022
National Category
Microbiology Ecology
Research subject
Ecology, Microbiology; Ecology, Aquatic Ecology
Identifiers
urn:nbn:se:lnu:diva-119804 (URN)10.1371/journal.pone.0243406 (DOI)000926013600001 ()36395342 (PubMedID)2-s2.0-85142148866 (Scopus ID)
Available from: 2023-03-16 Created: 2023-03-16 Last updated: 2023-05-05Bibliographically approved
Berggren, H., Tibblin, P., Yildirim, Y., Broman, E., Larsson, P., Lundin, D. & Forsman, A. (2022). Fish Skin Microbiomes Are Highly Variable Among Individuals and Populations but Not Within Individuals. Frontiers in Microbiology, 12, Article ID 767770.
Open this publication in new window or tab >>Fish Skin Microbiomes Are Highly Variable Among Individuals and Populations but Not Within Individuals
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2022 (English)In: Frontiers in Microbiology, E-ISSN 1664-302X, Vol. 12, article id 767770Article in journal (Refereed) Published
Abstract [en]

Fish skin-associated microbial communities are highly variable among populations and species and can impact host fitness. Still, the sources of variation in microbiome composition, and particularly how they vary among and within host individuals, have rarely been investigated. To tackle this issue, we explored patterns of variation in fish skin microbiomes across different spatial scales. We conducted replicate sampling of dorsal and ventral body sites of perch (Perca fluviatilis) from two populations and characterized the variation of fish skin-associated microbial communities with 16S rRNA gene metabarcoding. Results showed a high similarity of microbiome samples taken from the left and right side of the same fish individuals, suggesting that fish skin microbiomes can be reliably assessed and characterized even using a single sample from a specific body site. The microbiome composition of fish skin differed markedly from the bacterioplankton communities in the surrounding water and was highly variable among individuals. No ASV was present in all samples, and the most prevalent phyla, Actinobacteria, Bacteroidetes, and Proteobacteria, varied in relative abundance among fish hosts. Microbiome composition was both individual- and population specific, with most of the variation explained by individual host. At the individual level, we found no diversification in microbiome composition between dorsal and ventral body sites, but the degree of intra-individual heterogeneity varied among individuals. To identify how genetic and phenotypic characteristics of fish hosts impact the rate and nature of intra-individual temporal dynamics of the skin microbiome, and thereby contribute to the host-specific patterns documented here, remains an important task for future research.

Place, publisher, year, edition, pages
Frontiers Media S.A., 2022
Keywords
community ecology, diversity, fish, heterogeneity, repeatability, richness, skin microbiota, spatial variation
National Category
Microbiology Ecology
Research subject
Ecology, Microbiology
Identifiers
urn:nbn:se:lnu:diva-110468 (URN)10.3389/fmicb.2021.767770 (DOI)000751451900001 ()35126324 (PubMedID)2-s2.0-85124103536 (Scopus ID)2022 (Local ID)2022 (Archive number)2022 (OAI)
Available from: 2022-02-17 Created: 2022-02-17 Last updated: 2024-01-17Bibliographically approved
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ORCID iD: ORCID iD iconorcid.org/0000-0002-8779-6464

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