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Alneberg, J., Bennke, C., Beier, S., Bunse, C., Quince, C., Ininbergs, K., . . . Andersson, A. F. (2020). Ecosystem-wide metagenomic binning enables prediction of ecological niches from genomes. Communications Biology, 3(1), 1-10, Article ID 119.
Öppna denna publikation i ny flik eller fönster >>Ecosystem-wide metagenomic binning enables prediction of ecological niches from genomes
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2020 (Engelska)Ingår i: Communications Biology, E-ISSN 2399-3642, Vol. 3, nr 1, s. 1-10, artikel-id 119Artikel i tidskrift (Refereegranskat) Published
Abstract [en]

Alneberg et al. conduct metagenomics binning of water samples collected over major environmental gradients in the Baltic Sea. They use machine-learning to predict the placement of genome clusters along niche gradients based on the content of functional genes. The genome encodes the metabolic and functional capabilities of an organism and should be a major determinant of its ecological niche. Yet, it is unknown if the niche can be predicted directly from the genome. Here, we conduct metagenomic binning on 123 water samples spanning major environmental gradients of the Baltic Sea. The resulting 1961 metagenome-assembled genomes represent 352 species-level clusters that correspond to 1/3 of the metagenome sequences of the prokaryotic size-fraction. By using machine-learning, the placement of a genome cluster along various niche gradients (salinity level, depth, size-fraction) could be predicted based solely on its functional genes. The same approach predicted the genomes' placement in a virtual niche-space that captures the highest variation in distribution patterns. The predictions generally outperformed those inferred from phylogenetic information. Our study demonstrates a strong link between genome and ecological niche and provides a conceptual framework for predictive ecology based on genomic data.

Ort, förlag, år, upplaga, sidor
Nature Publishing Group, 2020
Nationell ämneskategori
Ekologi
Forskningsämne
Naturvetenskap, Ekologi
Identifikatorer
urn:nbn:se:lnu:diva-94014 (URN)10.1038/s42003-020-0856-x (DOI)000521060500003 ()32170201 (PubMedID)
Tillgänglig från: 2020-04-28 Skapad: 2020-04-28 Senast uppdaterad: 2020-04-28Bibliografiskt granskad
Martínez-García, S. & Pinhassi, J. (2019). Adaptations of microorganisms to low nutrient environments: managing life in the oligotrophic ocean (4ed.). In: Thomas M. Schmidt (Ed.), Encyclopedia of microbiology: (pp. 9-21). Elsevier
Öppna denna publikation i ny flik eller fönster >>Adaptations of microorganisms to low nutrient environments: managing life in the oligotrophic ocean
2019 (Engelska)Ingår i: Encyclopedia of microbiology / [ed] Thomas M. Schmidt, Elsevier, 2019, 4, s. 9-21Kapitel i bok, del av antologi (Övrigt vetenskapligt)
Abstract [en]

Low-nutrient environments are abundant and widespread across Earth, in terrestrial, freshwater, and marine environments, and from a microbial perspective may thus be regarded as the norm rather than an exception. Consequently, an extraordinary variety of adaptations have evolved among microorganisms to survive, and even reproduce, when nutrients are scarce. Here we first present an overview of the physicochemical and biological conditions that determine the transition from nutrient rich coastal environments to the low-nutrient (oligotrophic) situation that dominates the open ocean. We thereafter present genetic, physiological and metabolic adaptations important for marine bacteria to compete successfully in open ocean environments, noting that SAR11 group bacteria (Alphaproteobacteria) and cyanobacterial Prochlorococcus are among the most abundant organisms in the open ocean. Distinct adaptations are necessary for adjusting to limited availability of dissolved organic carbon, the macronutrients nitrogen and phosphorous, or micronutrients like iron (and other trace metals) or vitamins. Moreover, a multitude of distinct bacterial groups use photosystems based on rhodopsins or bacteriochlorophyll to harvest energy from sunlight. The spatial and temporal distribution of microorganisms, as influenced by nutrient availability, can be expected to have major importance in determining biogeochemical cycles of elements necessary for life and the flux of energy through ecosystems. © 2019 Elsevier Inc. All rights reserved.

Ort, förlag, år, upplaga, sidor
Elsevier, 2019 Upplaga: 4
Nyckelord
Adaptations, Carbon, Iron, Marine bacteria, Microplankton, Nitrogen, Nutrient availability, Oligotrophy, Phosphorus, Photoheterotrophy, Prochlorococcus, SAR11, Vitamins
Nationell ämneskategori
Ekologi
Forskningsämne
Ekologi, Akvatisk ekologi
Identifikatorer
urn:nbn:se:lnu:diva-94561 (URN)10.1016/B978-0-12-809633-8.90696-4 (DOI)9780128117378 (ISBN)
Anmärkning

Bidrag till encyklopedi

Tillgänglig från: 2020-05-11 Skapad: 2020-05-11 Senast uppdaterad: 2020-05-11Bibliografiskt granskad
Karlsson, C. M. G., Cerro-Galvez, E., Lundin, D., Karlsson, C., Vila-Costa, M. & Pinhassi, J. (2019). Direct effects of organic pollutants on the growth and gene expression of the Baltic Sea model bacterium Rheinheimera sp. BAL341. Microbial Biotechnology, 12(5), 892-906
Öppna denna publikation i ny flik eller fönster >>Direct effects of organic pollutants on the growth and gene expression of the Baltic Sea model bacterium Rheinheimera sp. BAL341
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2019 (Engelska)Ingår i: Microbial Biotechnology, ISSN 1751-7907, E-ISSN 1751-7915, Vol. 12, nr 5, s. 892-906Artikel i tidskrift (Refereegranskat) Published
Abstract [en]

Organic pollutants (OPs) are critically toxic, bioaccumulative and globally widespread. Moreover, several OPs negatively influence aquatic wildlife. Although bacteria are major drivers of the ocean carbon cycle and the turnover of vital elements, there is limited knowledge of OP effects on heterotrophic bacterioplankton. We therefore investigated growth and gene expression responses of the Baltic Sea model bacterium Rheinheimera sp. BAL341 to environmentally relevant concentrations of distinct classes of OPs in 2-h incubation experiments. During exponential growth, exposure to a mix of polycyclic aromatic hydrocarbons, alkanes and organophosphate esters (denoted MIX) resulted in a significant decrease (between 9% and 18%) in bacterial abundance and production compared with controls. In contrast, combined exposure to perfluorooctanesulfonic acids and perfluorooctanoic acids (denoted PFAS) had no significant effect on growth. Nevertheless, MIX and PFAS exposures both induced significant shifts in gene expression profiles compared with controls in exponential growth. This involved several functional metabolism categories (e.g. stress response and fatty acids metabolism), some of which were pollutant-specific (e.g. phosphate acquisition and alkane-1 monooxygenase genes). In stationary phase, only two genes in the MIX treatment were significantly differentially expressed. The substantial direct influence of OPs on metabolism during bacterial growth suggests that widespread OPs could severely alter biogeochemical processes governed by bacterioplankton.

Ort, förlag, år, upplaga, sidor
John Wiley & Sons, 2019
Nationell ämneskategori
Mikrobiologi
Forskningsämne
Ekologi, Mikrobiologi
Identifikatorer
urn:nbn:se:lnu:diva-86985 (URN)10.1111/1751-7915.13441 (DOI)000474143400001 ()31270938 (PubMedID)2-s2.0-85068617751 (Scopus ID)
Tillgänglig från: 2019-07-25 Skapad: 2019-07-25 Senast uppdaterad: 2019-11-25Bibliografiskt granskad
Broman, E., Asmala, E., Carstensen, J., Pinhassi, J. & Dopson, M. (2019). Distinct Coastal Microbiome Populations Associated With Autochthonous- and Allochthonous-Like Dissolved Organic Matter. Frontiers in Microbiology, 10, 1-15, Article ID 2579.
Öppna denna publikation i ny flik eller fönster >>Distinct Coastal Microbiome Populations Associated With Autochthonous- and Allochthonous-Like Dissolved Organic Matter
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2019 (Engelska)Ingår i: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 10, s. 1-15, artikel-id 2579Artikel i tidskrift (Refereegranskat) Published
Abstract [en]

Coastal zones are important transitional areas between the land and sea, where both terrestrial and phytoplankton supplied dissolved organic matter (DOM) are respired or transformed. As climate change is expected to increase river discharge and water temperatures, DOM from both allochthonous and autochthonous sources is projected to increase. As these transformations are largely regulated by bacteria, we analyzed microbial community structure data in relation to a 6-month long time-series dataset of DOM characteristics from Roskilde Fjord and adjacent streams, Denmark. The results showed that the microbial community composition in the outer estuary (closer to the sea) was largely associated with salinity and nutrients, while the inner estuary formed two clusters linked to either nutrients plus allochthonous DOM or autochthonous DOM characteristics. In contrast, the microbial community composition in the streams was found to be mainly associated with allochthonous DOM characteristics. A general pattern across the land-to-sea interface was that Betaproteobacteria were strongly associated with humic-like DOM [operational taxonomic units (OTUs) belonging to family Comamonadaceae], while distinct populations were instead associated with nutrients or abiotic variables such as temperature (Cyanobacteria genus Synechococcus) and salinity (Actinobacteria family Microbacteriaceae). Furthermore, there was a stark shift in the relative abundance of OTUs between stream and marine stations. This indicates that as DOM travels through the land-to-sea interface, different bacterial guilds continuously degrade it.

Ort, förlag, år, upplaga, sidor
Frontiers Media S.A., 2019
Nyckelord
16S rRNA gene, DOM, estuarial and coastal areas, DNA, water
Nationell ämneskategori
Mikrobiologi
Forskningsämne
Ekologi, Mikrobiologi
Identifikatorer
urn:nbn:se:lnu:diva-90507 (URN)10.3389/fmicb.2019.02579 (DOI)000498524600001 ()31787958 (PubMedID)
Tillgänglig från: 2019-12-12 Skapad: 2019-12-12 Senast uppdaterad: 2019-12-12Bibliografiskt granskad
Nilsson, E., Li, K., Fridlund, J., Sulcius, S., Bunse, C., Karlsson, C. M. G., . . . Holmfeldt, K. (2019). Genomic and Seasonal Variations among Aquatic Phages Infecting the Baltic Sea Gammaproteobacterium Rheinheimera sp. Strain BAL341. Applied and Environmental Microbiology, 85(18), 1-19, Article ID e01003-19.
Öppna denna publikation i ny flik eller fönster >>Genomic and Seasonal Variations among Aquatic Phages Infecting the Baltic Sea Gammaproteobacterium Rheinheimera sp. Strain BAL341
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2019 (Engelska)Ingår i: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 85, nr 18, s. 1-19, artikel-id e01003-19Artikel i tidskrift (Refereegranskat) Published
Abstract [en]

Knowledge in aquatic virology has been greatly improved by culture-independent methods, yet there is still a critical need for isolating novel phages to identify the large proportion of "unknowns" that dominate metagenomes and for detailed analyses of phage-host interactions. Here, 54 phages infecting Rheinheimem sp. strain BAL341 (Gammaproteobacteria) were isolated from Baltic Sea seawater and characterized through genome content analysis and comparative genomics. The phages showed a myovirus-like morphology and belonged to a novel genus, for which we propose the name Barbavirus. All phages had similar genome sizes and numbers of genes (80 to 84 kb; 134 to 145 genes), and based on average nucleotide identity and genome BLAST distance phylogeny, the phages were divided into five species. The phages possessed several genes involved in metabolic processes and host signaling, such as genes encoding ribonucleotide reductase and thymidylate synthase, phoH, and rnazG. One species had additional metabolic genes involved in pyridine nucleotide salvage, possibly providing a fitness advantage by further increasing the phages' replication efficiency. Recruitment of viral metagenomic reads (25 Baltic Sea viral metagenomes from 2012 to 2015) to the phage genomes showed pronounced seasonal variations, with increased relative abundances of barba phages in August and September synchronized with peaks in host abundances, as shown by 16S rRNA gene amplicon sequencing. Overall, this study provides detailed information regarding genetic diversity, phage-host interactions, and temporal dynamics of an ecologically important aquatic phage-host system. IMPORTANCE Phages are important in aquatic ecosystems as they influence their microbial hosts through lysis, gene transfer, transcriptional regulation, and expression of phage metabolic genes. Still, there is limited knowledge of how phages interact with their hosts, especially at fine scales. Here, a Rheinheimera phage-host system constituting highly similar phages infecting one host strain is presented. This relatively limited diversity has previously been seen only when smaller numbers of phages have been isolated and points toward ecological constraints affecting the Rheinheimera phage diversity. The variation of metabolic genes among the species points toward various fitness advantages, opening up possibilities for future hypothesis testing. Phage-host dynamics monitored over several years point toward recurring "kill-the-winner" oscillations and an ecological niche fulfilled by this system in the Baltic Sea. Identifying and quantifying ecological dynamics of such phage-host model systems in situ allow us to understand and study the influence of phages on aquatic ecosystems.

Ort, förlag, år, upplaga, sidor
American Society for Microbiology, 2019
Nyckelord
Baltic Sea, bacteriophage, genomics, temporal variation
Nationell ämneskategori
Ekologi Mikrobiologi
Forskningsämne
Ekologi, Mikrobiologi; Ekologi, Akvatisk ekologi
Identifikatorer
urn:nbn:se:lnu:diva-89282 (URN)10.1128/AEM.01003-19 (DOI)000483596700008 ()31324626 (PubMedID)
Tillgänglig från: 2019-09-25 Skapad: 2019-09-25 Senast uppdaterad: 2019-10-01Bibliografiskt granskad
Bunse, C., Israelsson, S., Baltar, F., Bertos-Fortis, M., Fridolfsson, E., Legrand, C., . . . Pinhassi, J. (2019). High Frequency Multi-Year Variability in Baltic Sea Microbial Plankton Stocks and Activities. Frontiers in Microbiology, 9, Article ID 3296.
Öppna denna publikation i ny flik eller fönster >>High Frequency Multi-Year Variability in Baltic Sea Microbial Plankton Stocks and Activities
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2019 (Engelska)Ingår i: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 9, artikel-id 3296Artikel i tidskrift (Refereegranskat) Published
Abstract [en]

Marine bacterioplankton are essential in global nutrient cycling and organic matter turnover. Time-series analyses, often at monthly sampling frequencies, have established the paramount role of abiotic and biotic variables in structuring bacterioplankton communities and productivities. However, fine-scale seasonal microbial activities, and underlying biological principles, are not fully understood. We report results from four consecutive years of high-frequency time-series sampling in the Baltic Proper. Pronounced temporal dynamics in most investigated microbial variables were observed, including bacterial heterotrophic production, plankton biomass, extracellular enzyme activities, substrate uptake rate constants of glucose, pyruvate, acetate, amino acids, and leucine, as well as nutrient limitation bioassays. Spring blooms consisting of diatoms and dinoflagellates were followed by elevated bacterial heterotrophic production and abundances. During summer, bacterial productivity estimates increased even further, coinciding with an initial cyanobacterial bloom in early July. However, bacterial abundances only increased following a second cyanobacterial bloom, peaking in August. Uptake rate constants for the different measured carbon compounds varied seasonally and inter-annually and were highly correlated to bacterial productivity estimates, temperature, and cyanobacterial abundances. Further, we detected nutrient limitation in response to environmental conditions in a multitude of microbial variables, such as elevated productivities in nutrient bioassays, changes in enzymatic activities, or substrate preferences. Variations among biotic variables often occurred on time scales of days to a few weeks, yet often spanning several sampling occasions. Such dynamics might not have been captured by sampling at monthly intervals, as compared to more predictable transitions in abiotic variables such as temperature or nutrient concentrations. Our study indicates that high resolution analyses of microbial biomass and productivity parameters can help out in the development of biogeochemical and food web models disentangling the microbial black box.

Ort, förlag, år, upplaga, sidor
Frontiers Media S.A., 2019
Nyckelord
marine bacteria, phytoplankton, cyanobacteria, production, substrate uptake, enzyme activity, biogeochemistry
Nationell ämneskategori
Mikrobiologi Ekologi
Forskningsämne
Ekologi, Mikrobiologi; Ekologi, Mikrobiologi
Identifikatorer
urn:nbn:se:lnu:diva-80150 (URN)10.3389/fmicb.2018.03296 (DOI)000455948100001 ()2-s2.0-85064405301 (Scopus ID)
Tillgänglig från: 2019-02-05 Skapad: 2019-02-05 Senast uppdaterad: 2019-08-29Bibliografiskt granskad
Cerro-Galvez, E., Casal, P., Lundin, D., Pina, B., Pinhassi, J., Dachs, J. & Vila-Costa, M. (2019). Microbial responses to anthropogenic dissolved organic carbon in the Arctic and Antarctic coastal seawaters. Environmental Microbiology, 21(4), 1466-1481
Öppna denna publikation i ny flik eller fönster >>Microbial responses to anthropogenic dissolved organic carbon in the Arctic and Antarctic coastal seawaters
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2019 (Engelska)Ingår i: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 21, nr 4, s. 1466-1481Artikel i tidskrift (Refereegranskat) Published
Abstract [en]

Thousands of semi-volatile hydrophobic organic pollutants (OPs) reach open oceans through atmospheric deposition, causing a chronic and ubiquitous pollution by anthropogenic dissolved organic carbon (ADOC). Hydrophobic ADOC accumulates in cellular lipids, inducing harmful effects on marine biota, and can be partially prone to microbial degradation. Unfortunately, their possible effects on microorganisms, key drivers of global biogeochemical cycles, remain unknown. We challenged coastal microbial communities from Ny-angstrom lesund (Arctic) and Livingston Island (Antarctica) with ADOC concentrations within the range of oceanic concentrations in 24 h. ADOC addition elicited clear transcriptional responses in multiple microbial heterotrophic metabolisms in ubiquitous groups such as Flavobacteriia, Gammaproteobacteria and SAR11. Importantly, a suite of cellular adaptations and detoxifying mechanisms, including remodelling of membrane lipids and transporters, was detected. ADOC exposure also changed the composition of microbial communities, through stimulation of rare biosphere taxa. Many of these taxa belong to recognized OPs degraders. This work shows that ADOC at environmentally relevant concentrations substantially influences marine microbial communities. Given that emissions of organic pollutants are growing during the Anthropocene, the results shown here suggest an increasing influence of ADOC on the structure of microbial communities and the biogeochemical cycles regulated by marine microbes.

Ort, förlag, år, upplaga, sidor
Wiley-Blackwell, 2019
Nationell ämneskategori
Mikrobiologi
Forskningsämne
Ekologi, Mikrobiologi
Identifikatorer
urn:nbn:se:lnu:diva-82417 (URN)10.1111/1462-2920.14580 (DOI)000464373000022 ()30838733 (PubMedID)2-s2.0-85063342177 (Scopus ID)
Tillgänglig från: 2019-05-03 Skapad: 2019-05-03 Senast uppdaterad: 2019-08-29Bibliografiskt granskad
Zhang, H., Yoshizawa, S., Sun, Y., Huang, Y., Chu, X., Gonzalez, J. M., . . . Luo, H. (2019). Repeated evolutionary transitions of flavobacteria from marine to non-marine habitats. Environmental Microbiology, 21(2), 648-666
Öppna denna publikation i ny flik eller fönster >>Repeated evolutionary transitions of flavobacteria from marine to non-marine habitats
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2019 (Engelska)Ingår i: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 21, nr 2, s. 648-666Artikel i tidskrift (Refereegranskat) Published
Abstract [en]

The taxonomy of marine and non-marine organisms rarely overlap, but the mechanisms underlying this distinction are often unknown. Here, we predicted three major ocean-to-land transitions in the evolutionary history of Flavobacteriaceae, a family known for polysaccharide and peptide degradation. These unidirectional transitions were associated with repeated losses of marine signature genes and repeated gains of non-marine adaptive genes. This included various Na+-dependent transporters, osmolyte transporters and glycoside hydrolases (GH) for sulfated polysaccharide utilization in marine descendants, and in non-marine descendants genes for utilizing the land plant material pectin and genes facilitating terrestrial host interactions. The K+ scavenging ATPase was repeatedly gained whereas the corresponding low-affinity transporter repeatedly lost upon transitions, reflecting K+ ions are less available to non-marine bacteria. Strikingly, the central metabolism Na+-translocating NADH: quinone dehydrogenase gene was repeatedly gained in marine descendants, whereas the H+-translocating counterpart was repeatedly gained in non-marine lineages. Furthermore, GH genes were depleted in isolates colonizing animal hosts but abundant in bacteria inhabiting other non-marine niches; thus relative abundances of GH versus peptidase genes among Flavobacteriaceae lineages were inconsistent with the marine versus non-marine dichotomy. We suggest that phylogenomic analyses can cast novel light on mechanisms explaining the distribution and ecology of key microbiome components.

Ort, förlag, år, upplaga, sidor
Wiley-Blackwell, 2019
Nationell ämneskategori
Mikrobiologi Ekologi
Forskningsämne
Ekologi, Mikrobiologi
Identifikatorer
urn:nbn:se:lnu:diva-81225 (URN)10.1111/1462-2920.14509 (DOI)000459172700011 ()30565818 (PubMedID)2-s2.0-85060014925 (Scopus ID)
Tillgänglig från: 2019-03-22 Skapad: 2019-03-22 Senast uppdaterad: 2019-08-29Bibliografiskt granskad
Alneberg, J., Sundh, J., Bennke, C., Beier, S., Lundin, D., Hugerth, L. W., . . . Andersson, A. F. (2018). BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic Sea. Scientific Data, 5, Article ID 180146.
Öppna denna publikation i ny flik eller fönster >>BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic Sea
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2018 (Engelska)Ingår i: Scientific Data, E-ISSN 2052-4463, Vol. 5, artikel-id 180146Artikel i tidskrift (Refereegranskat) Published
Abstract [en]

The Baltic Sea is one of the world's largest brackish water bodies and is characterised by pronounced physicochemical gradients where microbes are the main biogeochemical catalysts. Meta-omic methods provide rich information on the composition of, and activities within, microbial ecosystems, but are computationally heavy to perform. We here present the Baltic Sea Reference Metagenome (BARM), complete with annotated genes to facilitate further studies with much less computational effort. The assembly is constructed using 2.6 billion metagenomic reads from 81 water samples, spanning both spatial and temporal dimensions, and contains 6.8 million genes that have been annotated for function and taxonomy. The assembly is useful as a reference, facilitating taxonomic and functional annotation of additional samples by simply mapping their reads against the assembly. This capability is demonstrated by the successful mapping and annotation of 24 external samples. In addition, we present a public web interface, BalticMicrobeDB, for interactive exploratory analysis of the dataset. [GRAPHICS] .

Ort, förlag, år, upplaga, sidor
Nature Publishing Group, 2018
Nationell ämneskategori
Bioinformatik och systembiologi
Forskningsämne
Ekologi, Mikrobiologi
Identifikatorer
urn:nbn:se:lnu:diva-77392 (URN)10.1038/sdata.2018.146 (DOI)000440291200001 ()30063227 (PubMedID)2-s2.0-85051806706 (Scopus ID)
Tillgänglig från: 2018-08-29 Skapad: 2018-08-29 Senast uppdaterad: 2019-08-29Bibliografiskt granskad
Alneberg, J., Karlsson, C. M. G., Divne, A.-M., Bergin, C., Homa, F., Lindh, M. V., . . . Pinhassi, J. (2018). Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes. Microbiome, 6, Article ID 173.
Öppna denna publikation i ny flik eller fönster >>Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes
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2018 (Engelska)Ingår i: Microbiome, ISSN 0026-2633, E-ISSN 2049-2618, Vol. 6, artikel-id 173Artikel i tidskrift (Refereegranskat) Published
Abstract [en]

Background: Prokaryotes dominate the biosphere and regulate biogeochemical processes essential to all life. Yet, our knowledge about their biology is for the most part limited to the minority that has been successfully cultured. Molecular techniques now allow for obtaining genome sequences of uncultivated prokaryotic taxa, facilitating in-depth analyses that may ultimately improve our understanding of these key organisms. Results: We compared results from two culture-independent strategies for recovering bacterial genomes: single-amplified genomes and metagenome-assembled genomes. Single-amplified genomes were obtained from samples collected at an offshore station in the Baltic Sea Proper and compared to previously obtained metagenome-assembled genomes from a time series at the same station. Among 16 single-amplified genomes analyzed, seven were found to match metagenome-assembled genomes, affiliated with a diverse set of taxa. Notably, genome pairs between the two approaches were nearly identical (average 99.51% sequence identity; range 98.77-99.84%) across overlapping regions (30-80% of each genome). Within matching pairs, the single-amplified genomes were consistently smaller and less complete, whereas the genetic functional profiles were maintained. For the metagenome-assembled genomes, only on average 3.6% of the bases were estimated to be missing from the genomes due to wrongly binned contigs. Conclusions: The strong agreement between the single-amplified and metagenome-assembled genomes emphasizes that both methods generate accurate genome information from uncultivated bacteria. Importantly, this implies that the research questions and the available resources are allowed to determine the selection of genomics approach for microbiome studies.

Ort, förlag, år, upplaga, sidor
BioMed Central, 2018
Nyckelord
Single-amplified genomes, Metagenome-assembled genomes, Metagenomics, Binning, Single-cell genomics
Nationell ämneskategori
Mikrobiologi
Forskningsämne
Ekologi, Mikrobiologi
Identifikatorer
urn:nbn:se:lnu:diva-78465 (URN)10.1186/s40168-018-0550-0 (DOI)000446307400001 ()30266101 (PubMedID)2-s2.0-85054254141 (Scopus ID)
Tillgänglig från: 2018-10-24 Skapad: 2018-10-24 Senast uppdaterad: 2019-11-25Bibliografiskt granskad
Organisationer
Identifikatorer
ORCID-id: ORCID iD iconorcid.org/0000-0002-6405-1347

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