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Lindh, M. V., Sjöstedt, J., Ekstam, B., Casini, M., Lundin, D., Hugerth, L., . . . Pinhassi, J. (2017). Metapopulation theory identifies biogeographical patterns among core and satellite marine bacteria scaling from tens to thousands of kilometers. Environmental Microbiology, 19(3), 1222-1236
Open this publication in new window or tab >>Metapopulation theory identifies biogeographical patterns among core and satellite marine bacteria scaling from tens to thousands of kilometers
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2017 (English)In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 19, no 3, p. 1222-1236Article in journal (Refereed) Published
Abstract [en]

Metapopulation theory developed in terrestrial ecology provides applicable frameworks for interpreting the role of local and regional processes in shaping species distribution patterns. Yet, empirical testing of metapopulation models on microbial communities is essentially lacking. We determined regional bacterioplankton dynamics from monthly transect sampling in the Baltic Sea Proper using 16S rRNA gene sequencing. A strong positive trend was found between local relative abundance and occupancy of populations. Notably, the occupancy-frequency distributions were significantly bimodal with a satellite mode of rare endemic populations and a core mode of abundant cosmopolitan populations (e.g. Synechococcus, SAR11 and SAR86 clade members). Temporal changes in population distributions supported several theoretical frameworks. Still, bimodality was found among bacterioplankton communities across the entire Baltic Sea, and was also frequent in globally distributed datasets. Datasets spanning waters with widely different physicochemical characteristics or environmental gradients typically lacked significant bimodal patterns. When such datasets were divided into subsets with coherent environmental conditions, bimodal patterns emerged, highlighting the importance of positive feedbacks between local abundance and occupancy within specific biomes. Thus, metapopulation theory applied to microbial biogeography can provide novel insights into the mechanisms governing shifts in biodiversity resulting from natural or anthropogenically induced changes in the environment.

Place, publisher, year, edition, pages
Wiley-Blackwell, 2017
National Category
Ecology Microbiology
Research subject
Ecology, Microbiology; Natural Science, Ecology
Identifiers
urn:nbn:se:lnu:diva-61540 (URN)10.1111/1462-2920.13650 (DOI)000397525100031 ()28028880 (PubMedID)2-s2.0-85012069850 (Scopus ID)
Projects
EcoChange
Available from: 2017-03-21 Created: 2017-03-21 Last updated: 2019-08-29Bibliographically approved
Broman, E., Sjöstedt, J., Pinhassi, J. & Dopson, M. (2017). Shifts in coastal sediment oxygenation cause pronounced changes in microbial community composition and associated metabolism. Microbiome, 5, Article ID 96.
Open this publication in new window or tab >>Shifts in coastal sediment oxygenation cause pronounced changes in microbial community composition and associated metabolism
2017 (English)In: Microbiome, ISSN 0026-2633, E-ISSN 2049-2618, Vol. 5, article id 96Article in journal (Refereed) Published
Abstract [en]

Background

A key characteristic of eutrophication in coastal seas is the expansion of hypoxic bottom waters, often referred to as ‘dead zones’. One proposed remediation strategy for coastal dead zones in the Baltic Sea is to mix the water column using pump stations, circulating oxygenated water to the sea bottom. Although microbial metabolism in the sediment surface is recognized as key in regulating bulk chemical fluxes, it remains unknown how the microbial community and its metabolic processes are influenced by shifts in oxygen availability. Here, coastal Baltic Sea sediments sampled from oxic and anoxic sites, plus an intermediate area subjected to episodic oxygenation, were experimentally exposed to oxygen shifts. Chemical, 16S rRNA gene, metagenomic, and metatranscriptomic analyses were conducted to investigate changes in chemistry fluxes, microbial community structure, and metabolic functions in the sediment surface.

Results

Compared to anoxic controls, oxygenation of anoxic sediment resulted in a proliferation of bacterial populations in the facultative anaerobic genus Sulfurovum that are capable of oxidizing toxic sulfide. Furthermore, the oxygenated sediment had higher amounts of RNA transcripts annotated as sqr, fccB, and dsrA involved in sulfide oxidation. In addition, the importance of cryptic sulfur cycling was highlighted by the oxidative genes listed above as well as dsvA, ttrB, dmsA, and ddhAB that encode reductive processes being identified in anoxic and intermediate sediments turned oxic. In particular, the intermediate site sediments responded differently upon oxygenation compared to the anoxic and oxic site sediments. This included a microbial community composition with more habitat generalists, lower amounts of RNA transcripts attributed to methane oxidation, and a reduced rate of organic matter degradation.

Conclusions

These novel data emphasize that genetic expression analyses has the power to identify key molecular mechanisms that regulate microbial community responses upon oxygenation of dead zones. Moreover, these results highlight that microbial responses, and therefore ultimately remediation efforts, depend largely on the oxygenation history of sites. Furthermore, it was shown that re-oxygenation efforts to remediate dead zones could ultimately be facilitated by in situ microbial molecular mechanisms involved in removal of toxic H2S and the potent greenhouse gas methane.

Place, publisher, year, edition, pages
BioMed Central, 2017
National Category
Ecology
Research subject
Ecology, Aquatic Ecology; Ecology, Microbiology
Identifiers
urn:nbn:se:lnu:diva-67205 (URN)10.1186/s40168-017-0311-5 (DOI)000407724600002 ()28793929 (PubMedID)
Projects
EcoChange
Available from: 2017-08-09 Created: 2017-08-09 Last updated: 2019-02-27Bibliographically approved
Lindh, M. V., Sjöstedt, J., Casini, M., Andersson, A., Legrand, C. & Pinhassi, J. (2016). Local Environmental Conditions Shape Generalist But Not Specialist Components of Microbial Metacommunities in the Baltic Sea. Frontiers in Microbiology, 7, 1-10, Article ID 2078.
Open this publication in new window or tab >>Local Environmental Conditions Shape Generalist But Not Specialist Components of Microbial Metacommunities in the Baltic Sea
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2016 (English)In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 7, p. 1-10, article id 2078Article in journal (Refereed) Published
Abstract [en]

Marine microbes exhibit biogeographical patterns linked with fluxes of matter and energy. Yet, knowledge of the mechanisms shaping bacterioplankton community assembly across temporal scales remains poor. We examined bacterioplankton 16S rRNA gene fragments obtained from Baltic Sea transects to determine phylogenetic relatedness and assembly processes coupled with niche breadth. Communities were phylogenetically more related over time than expected by chance, albeit with considerable temporal variation. Hence, habitat filtering, i.e., local environmental conditions, rather than competition structured bacterioplankton communities in summer but not in spring or autumn. Species sorting (SS) was the dominant assembly process, but temporal and taxonomical variation in mechanisms was observed. For May communities, Cyanobacteria, Actinobacteria, Alpha- and Betaproteobacteria exhibited SS while Bacteroidetes and Verrucomicrobia were assembled by SS and mass effect. Concomitantly, Gammaproteobacteria were assembled by the neutral model and patch dynamics. Temporal variation in habitat filtering and dispersal highlights the impact of seasonally driven reorganization of microbial communities. Typically abundant Baltic Sea populations such as the NS3a marine group (Bacteroidetes) and the SAR86 and SAR11 clade had the highest niche breadth. The verrucomicrobial Spartobacteria population also exhibited high niche breadth. Surprisingly, variation in bacterioplankton community composition was regulated by environmental factors for generalist taxa but not specialists. Our results suggest that generalists such as NS3a, SAR86, and SAR11 are reorganized to a greater extent by changes in the environment compared to specialists and contribute more strongly to determining overall biogeographical patterns of marine bacterial communities.

Place, publisher, year, edition, pages
Frontiers Media, 2016
Keywords
metacommunity, assembly mechanism, net relatedness index, niche breadth, generalist, specialist, habitat filtering
National Category
Microbiology Ecology
Research subject
Ecology, Microbiology
Identifiers
urn:nbn:se:lnu:diva-60156 (URN)10.3389/fmicb.2016.02078 (DOI)000390658700001 ()2-s2.0-85009401593 (Scopus ID)
Projects
EcoChange
Available from: 2017-01-24 Created: 2017-01-24 Last updated: 2019-02-27Bibliographically approved
Lindh, M. V., Sjöstedt, J., Andersson, A. F., Baltar, F., Hugerth, L., Lundin, D., . . . Pinhassi, J. (2015). Disentangling seasonal bacterioplankton population dynamics by high-frequency sampling. Environmental Microbiology, 17(7), 2459-2476
Open this publication in new window or tab >>Disentangling seasonal bacterioplankton population dynamics by high-frequency sampling
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2015 (English)In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 17, no 7, p. 2459-2476Article in journal (Refereed) Published
Abstract [en]

Multiyear comparisons of bacterioplankton succession reveal that environmental conditions drive community shifts with repeatable patterns between years. However, corresponding insight into bacterioplankton dynamics at a temporal resolution relevant for detailed examination of variation and characteristics of specific populations within years is essentially lacking. During 1 year, we collected 46 samples in the Baltic Sea for assessing bacterial community composition by 16S rRNA gene pyrosequencing (nearly twice weekly during productive season). Beta-diversity analysis showed distinct clustering of samples, attributable to seemingly synchronous temporal transitions among populations (populations defined by 97% 16S rRNA gene sequence identity). A wide spectrum of bacterioplankton dynamics was evident, where divergent temporal patterns resulted both from pronounced differences in relative abundance and presence/absence of populations. Rates of change in relative abundance calculated for individual populations ranged from 0.23 to 1.79 day(-1). Populations that were persistently dominant, transiently abundant or generally rare were found in several major bacterial groups, implying evolution has favoured a similar variety of life strategies within these groups. These findings suggest that high temporal resolution sampling allows constraining the timescales and frequencies at which distinct populations transition between being abundant or rare, thus potentially providing clues about physical, chemical or biological forcing on bacterioplankton community structure.

Place, publisher, year, edition, pages
Society for Applied Microbiology and John Wiley & Sons Ltd, 2015
National Category
Ecology
Research subject
Ecology, Aquatic Ecology
Identifiers
urn:nbn:se:lnu:diva-45558 (URN)10.1111/1462-2920.12720 (DOI)000358114300023 ()2-s2.0-84937073236 (Scopus ID)
Projects
EcoChange
Funder
Swedish Research Council FormasSwedish Research CouncilEcosystem dynamics in the Baltic Sea in a changing climate perspective - ECOCHANGE
Available from: 2015-07-25 Created: 2015-07-25 Last updated: 2019-02-27Bibliographically approved
Sjöstedt, J., Martiny, J. B. H., Munk, P. & Riemann, L. (2014). Abundance of Broad Bacterial Taxa in the Sargasso Sea Explained by Environmental Conditions but Not Water Mass. Applied and Environmental Microbiology, 80(9), 2786-2795
Open this publication in new window or tab >>Abundance of Broad Bacterial Taxa in the Sargasso Sea Explained by Environmental Conditions but Not Water Mass
2014 (English)In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 80, no 9, p. 2786-2795Article in journal (Refereed) Published
Abstract [en]

To explore the potential linkage between distribution of marine bacterioplankton groups, environmental conditions, and water mass, we investigated the factors determining the abundance of bacterial taxa across the hydrographically complex Subtropical Convergence Zone in the Sargasso Sea. Based on information from 16S rRNA gene clone libraries from various locations and two depths, abundances of the predominant taxa (eubacteria, Archaea, Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes, and the Roseobacter, SAR11, and SAR86 clades) were quantified by real-time PCR. In addition, the abundances of Synechococcus, Prochlorococcus, and picoalgae were determined by flow cytometry. Linear multiple-regression models determining the relative effects of eight environmental variables and of water mass explained 35 to 86% of the variation in abundance of the quantified taxa, even though only one to three variables were significantly related to any particular taxon's abundance. Most of the variation in abundance was explained by depth and chlorophyll a. The predominant phototrophs, Prochlorococcus and picoalgae, were negatively correlated with phosphate, whereas eubacteria, heterotrophic bacteria, and SAR86 were negatively correlated with nitrite. Water mass showed limited importance for explaining the abundance of the taxonomical groups (significant only for Roseobacter, explaining 14% of the variation). The results suggest the potential for predicting the abundance of broad bacterioplankton groups throughout the Sargasso Sea using only a few environmental parameters.

National Category
Microbiology
Research subject
Ecology, Aquatic Ecology; Ecology, Microbiology
Identifiers
urn:nbn:se:lnu:diva-34474 (URN)10.1128/AEM.00099-14 (DOI)000334583300017 ()2-s2.0-84898605116 (Scopus ID)
Available from: 2014-05-28 Created: 2014-05-28 Last updated: 2019-02-27Bibliographically approved
Sjöstedt, J. (2013). Effect of environmental factors on bacterioplankton community composition, diversity and functionality. (Doctoral dissertation). Växjö, Kalmar: Linnaeus University Press
Open this publication in new window or tab >>Effect of environmental factors on bacterioplankton community composition, diversity and functionality
2013 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The ocean covers more than 70 % of the Earth surface and represents the largest ecosystem on Earth. Bacteria are an important part of the marine food web not only in remineralisation but also since they utilize dissolved organic matter (DOM) and make the energy available to higher trophic levels. Despite their small size, the total bacterial biomass exceeds the combined mass of zooplankton and fishes.

Bacterial communities are often sensitive to disturbance and the composition changes in response to variations in environmental factors. The diversity of microorganisms is high and the biodiversity is composed of a few abundant and a long tail of rare taxa. The rare taxa contribute most to the diversity, but form a seed bank that is not growing or growing extremely slow. Experimental manipulations showed that the change in community composition in response to disturbance was, at least to some respect, accomplished by rare species becoming abundant. Changes in community composition and diversity did not have an affect on broad scale functions, e.g. utilization of dissolved organic carbon (DOC), indicating that bacterial communities are functionally redundant.

Microorganisms are generally believed to be easily dispersed globally because of their small size, high abundance and short generation time. However, changes in community composition have been shown both on temporal and spatial scales but there is limited information about which factors are most important for distribution of bacterial taxa. A study of in situ samples from the Sargasso Sea showed that a large extent of the variation in the abundance of broad bacterial taxa could be explained by environmental factors, whereas abundances generally did not differ between water masses. In addition, an investigation of the phylogenetic structure of bacterial communities from the Baltic Sea and Skagerrak showed that bacterial communities in specific environments usually are more phylogenetic related to each other than expected by chance. Together these results indicate that the environment is an important factor forming the community and that phylogenetically related bacteria are functionally related, sharing similar traits.

Place, publisher, year, edition, pages
Växjö, Kalmar: Linnaeus University Press, 2013
Series
Linnaeus University Dissertations ; 113/2013
Keywords
marine microbiology, bacterioplankton, community composition, diversity, functionality, environmental factors, disturbance, distribution
National Category
Ecology Microbiology
Research subject
Ecology, Microbiology; Ecology, Aquatic Ecology
Identifiers
urn:nbn:se:lnu:diva-23020 (URN)978-91-87427-00-8 (ISBN)
Public defence
2013-02-01, Fullriggaren, Barlastgatan 11, Kalmar, 09:00 (English)
Opponent
Supervisors
Available from: 2013-01-10 Created: 2012-12-17 Last updated: 2019-02-27Bibliographically approved
Pontarp, M., Sjöstedt, J. & Lundberg, P. (2013). Experimentally induced habitat filtering in marine bacterial communities. Marine Ecology Progress Series, 477, 77-U406
Open this publication in new window or tab >>Experimentally induced habitat filtering in marine bacterial communities
2013 (English)In: Marine Ecology Progress Series, ISSN 0171-8630, E-ISSN 1616-1599, Vol. 477, p. 77-U406Article in journal (Refereed) Published
Abstract [en]

We tested the habitat filtering hypothesis by measuring the phylogenetic structure in marine bacterial communities before and after experimentally induced stress. The habitat filtering hypothesis predicts that phylogenetic clustering (mean relatedness) should increase as the environment becomes suitable for only a subset of the original community. We show that community composition and phylogenetic structure were considerably changed with changes in salinity and dissolved organic carbon. Community composition showed no consistent patterns, while the phylogenetic relatedness between species consistently increased with treatment. We have no information about species interactions in our system, but the phylogenetic signal is strong enough to suggest that habitat filtering is the dominant assembly process. Our results support the hypothesis that habitat characteristics and environmental stress can 'filter' a community so that only closely related species can persist. This non-random phylogenetic signal also implies a relationship between ecologically relevant characteristics and species relatedness.

Keywords
Habitat filtering, Phylogenetic structure, Niche conservatism, Microbial ecology
National Category
Microbiology
Research subject
Natural Science, Microbiology
Identifiers
urn:nbn:se:lnu:diva-25227 (URN)10.3354/meps10126 (DOI)000315953300007 ()2-s2.0-84875139410 (Scopus ID)
Available from: 2013-04-10 Created: 2013-04-05 Last updated: 2019-02-27Bibliographically approved
Sjöstedt, J., Pontarp, M., Tinta, T., Alfredsson, H., Turk, V., Lundberg, P., . . . Riemann, L. (2013). Reduced diversity and changed bacterioplankton community composition do not affect utilization of dissolved organic matter in the Adriatic Sea. Aquatic Microbial Ecology, 71(1), 15-U132
Open this publication in new window or tab >>Reduced diversity and changed bacterioplankton community composition do not affect utilization of dissolved organic matter in the Adriatic Sea
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2013 (English)In: Aquatic Microbial Ecology, ISSN 0948-3055, E-ISSN 1616-1564, Vol. 71, no 1, p. 15-U132Article in journal (Refereed) Published
Abstract [en]

To obtain insights into the coupling between community composition, diversity and community function, bacterioplankton assemblages from the Gulf of Trieste (Northern Adriatic Sea) were exposed to increasing environmental stress throughout 2 wk in continuous seawater cultures to construct communities differing in composition and diversity. The assemblages were exposed to (1) decreased temperature, (2) decreased temperature and phosphate addition or (3) decreased temperature, phosphate addition and lowered oxygen level. Bacterial and viral abundances as well as bacterial community composition stabilized during the second week of the experiment. Denaturing gradient gel electrophoresis and pyrosequencing of 16S rRNA genes showed dramatic reductions in bacterial diversity in all treatments and major compositional differences relative to the inoculum. Nevertheless, no differences in the ability to exploit dissolved organic carbon (DOC) were found for the acquired communities relative to the inoculum, indicating that the bacterial communities were functionally redundant. We speculate that oscillations in exploitation of the DOC pool in situ are mainly governed by factors limiting the overall bacterial growth, rather than perturbations affecting only subsets of the microbial biota.

Keywords
Diversity, Functional redundancy, Community structure, Continuous cultures, DOC
National Category
Ecology
Research subject
Natural Science, Aquatic Ecology
Identifiers
urn:nbn:se:lnu:diva-31322 (URN)10.3354/ame01660 (DOI)000327552900002 ()2-s2.0-84889049698 (Scopus ID)
Available from: 2013-12-19 Created: 2013-12-19 Last updated: 2019-02-27Bibliographically approved
Sjöstedt, J., Koch-Schmidt, P., Pontarp, M., Canbäck, B., Tunlid, A., Lundberg, P., . . . Riemann, L. (2012). Recruitment of members from the rare biosphere of marine bacterioplankton communities after an environmental disturbance.. Applied and Environmental Microbiology, 78(5), 1361-1369
Open this publication in new window or tab >>Recruitment of members from the rare biosphere of marine bacterioplankton communities after an environmental disturbance.
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2012 (English)In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 78, no 5, p. 1361-1369Article in journal (Refereed) Published
Abstract [en]

A bacterial community may be resistant to environmental disturbances if some of its species show metabolic flexibility and physiological tolerance to the changing conditions. Alternatively, disturbances can change the composition of the community and thereby potentially affect ecosystem processes. The impact of disturbance on the composition of bacterioplankton communities was examined in continuous seawater cultures. Bacterial assemblages from geographically closely connected areas, the Baltic Sea (salinity 7 and high dissolved organic carbon [DOC]) and Skagerrak (salinity 28 and low DOC), were exposed to gradual opposing changes in salinity and DOC over a 3-week period such that the Baltic community was exposed to Skagerrak salinity and DOC and vice versa. Denaturing gradient gel electrophoresis and clone libraries of PCR-amplified 16S rRNA genes showed that the composition of the transplanted communities differed significantly from those held at constant salinity. Despite this, the growth yields (number of cells ml(-1)) were similar, which suggests similar levels of substrate utilization. Deep 454 pyrosequencing of 16S rRNA genes showed that the composition of the disturbed communities had changed due to the recruitment of phylotypes present in the rare biosphere of the original community. The study shows that members of the rare biosphere can become abundant in a bacterioplankton community after disturbance and that those bacteria can have important roles in maintaining ecosystem processes.

National Category
Microbiology
Research subject
Natural Science, Microbiology
Identifiers
urn:nbn:se:lnu:diva-22845 (URN)10.1128/AEM.05542-11 (DOI)22194288 (PubMedID)2-s2.0-84857065812 (Scopus ID)
Available from: 2012-12-14 Created: 2012-12-12 Last updated: 2019-02-27Bibliographically approved
Sjöstedt, J., Hagström, Å. & Zweifel, U. L. (2012). Variation in cell volume and community composition of bacteria in response to temperature. Aquatic Microbial Ecology, 66(3), 237-246
Open this publication in new window or tab >>Variation in cell volume and community composition of bacteria in response to temperature
2012 (English)In: Aquatic Microbial Ecology, ISSN 0948-3055, E-ISSN 1616-1564, Vol. 66, no 3, p. 237-246Article in journal (Refereed) Published
Abstract [en]

Although temperature is a key parameter controlling the activity and growth of all microorganisms, information about how water temperature may structure the bacterioplankton community is not consistent. We examined the relationship between temperature and the community composition, cell volume, and morphology of marine bacterioplankton in 4 continuous cultures harbouring multispecies communities. All 4 cultures were maintained at a turnover time of 0.04 h(-1) but at different temperatures of 10, 15, 20, and 25 degrees C. Denaturing gradient gel electrophoresis analyses showed that the community composition shifted in response to temperature. Cell volumes were determined from digital photomicrographs using an image analysis program, which also allowed the identification of 3 morphological types of bacteria: cocci-, rod-, and vibrio-shaped bacteria. Mean bacterial cell volume decreased with increasing temperature, e.g., by 39% when the temperature was increased from 10 degrees C to 20 degrees C. When the temperature increased, the bacterial morphology also shifted from dominance by rod- and vibrio-shaped bacteria to dominance by coccoid bacteria. The results clearly indicate the potential role of temperature in driving the community succession of bacterioplankton and in selecting for smaller cells at higher temperatures.

National Category
Microbiology
Research subject
Natural Science, Microbiology
Identifiers
urn:nbn:se:lnu:diva-24313 (URN)10.3354/ame01579 (DOI)000306321900003 ()2-s2.0-84863901944 (Scopus ID)
Available from: 2013-02-13 Created: 2013-02-13 Last updated: 2019-02-27Bibliographically approved
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ORCID iD: ORCID iD iconorcid.org/0000-0003-0993-8305

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