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Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes
KTH Royal Institute of Technology.
Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. (Ctr Ecol & Evolut Microbial Model Syst EEMiS)
Uppsala University.
Uppsala University.
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2018 (English)In: Microbiome, ISSN 0026-2633, E-ISSN 2049-2618, Vol. 6, article id 173Article in journal (Refereed) 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.

Place, publisher, year, edition, pages
BioMed Central, 2018. Vol. 6, article id 173
Keywords [en]
Single-amplified genomes, Metagenome-assembled genomes, Metagenomics, Binning, Single-cell genomics
National Category
Microbiology
Research subject
Ecology, Microbiology
Identifiers
URN: urn:nbn:se:lnu:diva-78465DOI: 10.1186/s40168-018-0550-0ISI: 000446307400001PubMedID: 30266101Scopus ID: 2-s2.0-85054254141OAI: oai:DiVA.org:lnu-78465DiVA, id: diva2:1258375
Available from: 2018-10-24 Created: 2018-10-24 Last updated: 2019-11-25Bibliographically approved
In thesis
1. Exploring gene expression responses of marine bacteria to environmental factors
Open this publication in new window or tab >>Exploring gene expression responses of marine bacteria to environmental factors
2019 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Bacterioplankton are abundant in marine ecosystems, where they as “masters of transformation” of dissolved organic matter (DOM) are important for energy fluxes and biogeochemical cycles. However, the performance of bacteria in a changing marine environment influenced by anthropogenic activities is poorly understood. In this thesis, I did experiments with model bacteria and natural assemblages of bacteria, using microbiology methods combined with modern molecular tools, to investigate responses of marine bacteria to changes in environmental conditions like ocean acidification, organic pollution and organic matter released by phytoplankton. Experiments with a model gammaproteobacterium demonstrated that bacteria in stationary phase showed little responses to organic pollutants, whereas pollutants caused decreased bacterial growth and had a broad physiological impact on actively growing bacteria (as deduced from gene expression analysis). In an experiment with two distantly related marine model bacteria, we identified several important bacterial mechanisms, such as uptake of macromolecules and phosphonates, by which bacteria respond when exposed to DOM produced by photosynthetic dinoflagellates. Using natural bacterial communities in a Baltic Sea mesocosm experiment with the addition of river water from a forested or an agriculture influenced catchment area, we showed important interactions between river water type and the development of phytoplankton blooms that caused different bacterial gene expression activities. In the fourth set of experiments, marine bacterial communities were subjected to elevated CO2, to mimic ocean acidification, under high and low nutrient conditions in a mesocosm study. We found increased bacterial gene expression activity focused on maintaining pH homeostasis, but only under low nutrient conditions, indicating that bacteria focus on cell maintenance instead of growth when challenged by lowered pH. Finally, in a computational analysis, we compared genomes from yet uncultivated prokaryotes by two different strategies: metagenome assembled and single amplified genomes. Importantly, the analysis showed that both methods selected abundant taxa and generated nearly identical sequences in overlapping regions. To conclude, this thesis presents discoveries that will help form a better understanding of marine bacterial responses to present and future anthropogenic disturbances of marine ecosystems.

Abstract [sv]

Marina bakterier är abundanta och återfinns i alla marina ekosystem, där de som nedbrytare av organiskt material spelar en avgörande roll i att reglera flödet av energi och näringsämnenas kretslopp. Dock saknar vi kunskap om hur bakterieplankton reagerar på miljöförändringar i haven. Därtill är de molekylära mekanismerna för omsättningen av löst organiskt material från olika källor ofullständigt kända. I denna avhandling har jag med hjälp av bakterieisolat och naturliga bakteriesamhällen undersökt hur marina bakterier svarar på miljöförändringar genom att kombinera metoder inom klassisk mikrobiologi och moderna molekylärbiologiska verktyg. Det övergripande syftet med denna avhandling var att få en bättre förståelse för hur bakterier svarar på havsförsurning, organiska föroreningar och löst organisk kol utsöndrat av växtplankton. Under ett experiment med ett bakterieisolat inom klassen Gammaproteobacteria, uppvisade bakterierna svagare respons för organiska föroreningar då de befann sig i stationär fas än i en aktiv tillväxtfas. Detta märktes både genom minskad tillväxt och fysiologiska ändringar uppmätta genom genuttryck i bakterien. Vidare experiment med två skilda modellbakterier kunde vi identifiera viktiga processer såsom upptag av makromolekyler och fosfonater, som svar på tillsats av löst organiskt material producerat av dinoflagellater. I ett annat experiment använde vi naturliga bakteriesamhällen i vatten från Östersjön i ett storskaligt experiment, där vatten från floder i avrinningsområden dominerade antingen av skog eller jordbruk tillsattes. I detta experiment kunde vi visa hur vattnets ursprung påverkade utvecklingen av algblomningarna som i sin tur orsakade olika aktivitet i bakteriernas genuttryck. Vidare så undersöktes hur marina bakteriesamhällen påverkas av förhöjda CO2-halter under låg och hög näringstillgång. Det visade sig att bakterierna ökade sin aktivitet för att bibehålla pH-homeostasen, men bara under låg koncentration av näringsämnen. Detta innebar att bakterierna behövde ställa om sin ämnesomsättning från tillväxt till att lägga energi på att hantera syran i oligotrofa miljöer. Slutligen genomfördes dataanalyser där två metoder för att studera arvsmassan i bakterier tagna direkt från haven jämfördes. Vår studie visade att de två metoderna i viss mån kompletterade varandra men framför allt kunde vi bekräfta att ingen av de två uppvisade några systematiska fel. Sammanfattningsvis presenterar denna avhandling upptäcker som ger oss en bättre förståelse för hur marina bakterier i marina ekosystem svarar på nutida och framtida miljöförändringar orsakade av människor.

Place, publisher, year, edition, pages
Växjö: Linnaeus University Press, 2019
Series
Linnaeus University Dissertations ; 371/2019
Keywords
Baltic Sea, dissolved organic matter, model bacteria, ocean acidification, organic pollutants, river loadings, transcriptomics
National Category
Ecology
Research subject
Ecology, Microbiology
Identifiers
urn:nbn:se:lnu:diva-90261 (URN)978-91-89081-19-2 (ISBN)978-91-89081-20-8 (ISBN)
Public defence
2019-12-18, Fregatten Ma117 campus Kalmar, Kalmar, 09:30 (English)
Opponent
Supervisors
Available from: 2019-11-25 Created: 2019-11-25 Last updated: 2019-12-03Bibliographically approved

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Karlsson, Christofer M. G.Lindh, Markus V.Pinhassi, Jarone

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