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Comte, J., Berga, M., Severin, I., Logue, J. B. & Lindström, E. S. (2017). Contribution of different bacterial dispersal sources to lakes: Population and community effects in different seasons. Environmental Microbiology, 19(6), 2391-2404.
Open this publication in new window or tab >>Contribution of different bacterial dispersal sources to lakes: Population and community effects in different seasons
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2017 (English)In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 19, no 6, 2391-2404 p.Article in journal (Refereed) Published
Abstract [en]

The diversity and composition of lake bacterial communities are driven by the interplay between local contemporary environmental conditions and dispersal of cells from the surroundings, i.e. the metacommunity. Still, a conceptual understanding ofthe relative importance of the two types of factors is lacking. For instance, it is unknown which sources ofdispersal are most important and under which circumstances. Here, we investigated the seasonal variation in the importance of dispersal from different sources (mixing, precipitation, surface runoff and sediment resuspension) for lake bacterioplankton community and population dynamics. For that purpose, two small forest lakes and their dispersal sources were sampled over a period of 10 months.The influence of dispersal on communities and populations was determined by 454 sequencing of the 16S rRNA gene and Source Tracker analysis. On the community level direct effects of dispersal were questionable from all sources. Instead we found that the community of the preceding sampling occasion, representing growth of resident bacteria, was of great importance. On the population level, however, dispersal of individual taxa from the inlet could be occasionally important even under low water flow. The effect of sediment resuspension and precipitation appeared small.

National Category
Oceanography, Hydrology and Water Resources
Identifiers
urn:nbn:se:uu:diva-323624 (URN)10.1111/1462-2920.13749 (DOI)000404007700024 ()28401636 (PubMedID)
Funder
Swedish Research Council, 2009-5172Wenner-Gren FoundationsCarl Tryggers foundation Knut and Alice Wallenberg FoundationScience for Life Laboratory - a national resource center for high-throughput molecular bioscienceSwedish National Infrastructure for Computing (SNIC), b2010008
Available from: 2017-06-08 Created: 2017-06-08 Last updated: 2018-01-13Bibliographically approved
Comte, J., Langenheder, S., Berga, M. & Lindström, E. S. (2017). Contribution of different dispersal sources to the metabolic response of lake bacterioplankton following a salinity change. Environmental Microbiology, 19(1), 251-260.
Open this publication in new window or tab >>Contribution of different dispersal sources to the metabolic response of lake bacterioplankton following a salinity change
2017 (English)In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 19, no 1, 251-260 p.Article in journal (Refereed) Published
Abstract [en]

Dispersal can modify how bacterial community composition (BCC) changes in response to environmental perturbations, yet knowledge about the functional consequences of dispersal is limited. Here we hypothesize that changes in bacterial community production in response to a salinity disturbance depend on the possibility to recruit cells from different dispersal sources. To investigate this, we conducted an in situ mesocosm experiment where bacterial communities of an oligotrophic lake were exposed to different salinities (0, 18, 36 psu) for two weeks and subjected to dispersal of cells originating from sediments, air (mesocosms open to air deposition), both or none. BCC was determined using 454 pyrosequencing of the 16S rRNA gene and bacterial production was measured by 3H leucine uptake. Bacterial production differed significantly among salinity treatments and dispersal treatments, being highest at high salinity. These changes were associated with changes in BCC and it was found that the identity of the main functional contributors differed at different salinities. Our results further showed that after a salinity perturbation, the response of bacterial communities depended on the recruitment of taxa, including marine representatives (e.g. Alphaproteobacteria Loktanella, Erythrobacter and the Gammaproteobacterium Rheiheimera) from dispersal sources, in which atmospheric deposition appeared to play a major role.

National Category
Microbiology Oceanography, Hydrology and Water Resources
Identifiers
urn:nbn:se:uu:diva-309470 (URN)10.1111/1462-2920.13593 (DOI)000393587200028 ()27871136 (PubMedID)
Funder
Knut and Alice Wallenberg FoundationScience for Life Laboratory - a national resource center for high-throughput molecular bioscienceWenner-Gren FoundationsHelge Ax:son Johnsons stiftelse Swedish Research Council, 2009-5172Swedish Research Council Formas
Available from: 2016-12-05 Created: 2016-12-05 Last updated: 2018-01-13Bibliographically approved
Lindström, E. S. & Andersson, M. (2017). Effects of sterilization on composition and bacterial utilization of dissolved organic carbon. .
Open this publication in new window or tab >>Effects of sterilization on composition and bacterial utilization of dissolved organic carbon
2017 (English)Data set, Primary data
National Category
Ecology
Research subject
Biology with specialization in Limnology
Identifiers
urn:nbn:se:uu:diva-336146 (URN)
Available from: 2017-12-12 Created: 2017-12-12 Last updated: 2017-12-15Bibliographically approved
Lindström, E. S. & del Giorgio, P. A. (2017). Progress and perspectives in aquatic microbial ecology: highlights of the SAME 14, Uppsala, Sweden, 2015. Aquatic Microbial Ecology, 80, 101-103.
Open this publication in new window or tab >>Progress and perspectives in aquatic microbial ecology: highlights of the SAME 14, Uppsala, Sweden, 2015
2017 (English)In: Aquatic Microbial Ecology, ISSN 0948-3055, E-ISSN 1616-1564, Vol. 80, 101-103 p.Article in journal (Refereed) Published
Abstract [en]

The presentations and discussion during the Symposium of Aquatic Microbial Ecology (SAME) in Uppsala, Sweden, in August 2015 highlighted new directions and challenges in the study of aquatic microbial communities. In this virtual Special Issue, plenary speakers and meeting awardees explore these challenges. The contributions cover a wide range of topics from the use of molecular analyses of microbial communities to cultivation and stoichiometric analyses. The virtual Special also includes theoretical developments on the concept of rarity to community assembly. A common theme for the Special is, however, the importance of a combination of different approaches in order to deepen our understanding of the ecology of microbial communities

Keyword
SAME 14, Molecular tools, Cultivation, Stoichimetry, Assembly, Rarity, Community assembly, Ecological interactions
National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-334882 (URN)10.3354/ame01851 (DOI)000414556400009 ()
Available from: 2017-11-29 Created: 2017-11-29 Last updated: 2017-11-30Bibliographically approved
Lindström, E. S. (2017). Repeated disturbances affect functional but not compositional resistance and resilience in aquatic bacterioplankton communities - supporting data. .
Open this publication in new window or tab >>Repeated disturbances affect functional but not compositional resistance and resilience in aquatic bacterioplankton communities - supporting data
2017 (English)Data set
National Category
Ecology
Research subject
Biology with specialization in Limnology
Identifiers
urn:nbn:se:uu:diva-336981 (URN)
Available from: 2017-12-19 Created: 2017-12-19 Last updated: 2017-12-19Bibliographically approved
Lindström, E. S. (2017). Supporting data version 2. .
Open this publication in new window or tab >>Supporting data version 2
2017 (English)Data set, Aggregated data
National Category
Ecology
Identifiers
urn:nbn:se:uu:diva-336954 (URN)
Available from: 2017-12-19 Created: 2017-12-19 Last updated: 2017-12-19Bibliographically approved
Logue, J. B., Stedmon, C. A., Kellerman, A. M., Nielsen, N. J., Andersson, A. F., Laudon, H., . . . Kritzberg, E. S. (2016). Experimental insights into the importance of aquatic bacterial community composition to the degradation of dissolved organic matter. The ISME Journal, 10(3), 533-545.
Open this publication in new window or tab >>Experimental insights into the importance of aquatic bacterial community composition to the degradation of dissolved organic matter
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2016 (English)In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 10, no 3, 533-545 p.Article in journal (Refereed) Published
Abstract [en]

Bacteria play a central role in the cycling of carbon, yet our understanding of the relationship between the taxonomic composition and the degradation of dissolved organic matter (DOM) is still poor. In this experimental study, we were able to demonstrate a direct link between community composition and ecosystem functioning in that differently structured aquatic bacterial communities differed in their degradation of terrestrially derived DOM. Although the same amount of carbon was processed, both the temporal pattern of degradation and the compounds degraded differed among communities. We, moreover, uncovered that low-molecular-weight carbon was available to all communities for utilisation, whereas the ability to degrade carbon of greater molecular weight was a trait less widely distributed. Finally, whereas the degradation of either low-or high-molecular-weight carbon was not restricted to a single phylogenetic clade, our results illustrate that bacterial taxa of similar phylogenetic classification differed substantially in their association with the degradation of DOM compounds. Applying techniques that capture the diversity and complexity of both bacterial communities and DOM, our study provides new insight into how the structure of bacterial communities may affect processes of biogeochemical significance.

National Category
Ecology
Identifiers
urn:nbn:se:uu:diva-281481 (URN)10.1038/ismej.2015.131 (DOI)000370472500001 ()26296065 (PubMedID)
Funder
Swedish National Infrastructure for Computing (SNIC), b2010008Swedish Research Council, 2010-4081, 2011-5689Helge Ax:son Johnsons stiftelse Swedish Research Council for Environment, Agricultural Sciences and Spatial PlanningThe Kempe Foundations
Available from: 2016-03-30 Created: 2016-03-24 Last updated: 2017-11-30Bibliographically approved
Graham, E. B., Knelman, J. E., Schindlbacher, A., Siciliano, S., Breulmann, M., Yannarell, A., . . . Nemergut, D. R. (2016). Microbes as Engines of Ecosystem Function: When Does Community Structure Enhance Predictions of Ecosystem Processes?. Frontiers in Microbiology, 7, Article ID 214.
Open this publication in new window or tab >>Microbes as Engines of Ecosystem Function: When Does Community Structure Enhance Predictions of Ecosystem Processes?
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2016 (English)In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 7, 214Article in journal (Refereed) Published
Abstract [en]

Microorganisms are vital in mediating the earth's biogeochemical cycles; yet, despite our rapidly increasing ability to explore complex environmental microbial communities, the relationship between microbial community structure and ecosystem processes remains poorly understood. Here, we address a fundamental and unanswered question in microbial ecology: 'When do we need to understand microbial community structure to accurately predict function?' We present a statistical analysis investigating the value of environmental data and microbial community structure independently and in combination for explaining rates of carbon and nitrogen cycling processes within 82 global datasets. Environmental variables were the strongest predictors of process rates but left 44% of variation unexplained on average, suggesting the potential for microbial data to increase model accuracy. Although only 29% of our datasets were significantly improved by adding information on microbial community structure, we observed improvement in models of processes mediated by narrow phylogenetic guilds via functional gene data, and conversely, improvement in models of facultative microbial processes via community diversity metrics. Our results also suggest that microbial diversity can strengthen predictions of respiration rates beyond microbial biomass parameters, as 53% of models were improved by incorporating both sets of predictors compared to 35% by microbial biomass alone. Our analysis represents the first comprehensive analysis of research examining links between microbial community structure and ecosystem function. Taken together, our results indicate that a greater understanding of microbial communities informed by ecological principles may enhance our ability to predict ecosystem process rates relative to assessments based on environmental variables and microbial physiology.

Keyword
microbial diversity, functional gene, statistical modeling, microbial ecology, ecosystem processes, respiration, nitrification, denitrification
National Category
Microbiology
Identifiers
urn:nbn:se:uu:diva-282313 (URN)10.3389/fmich.2016.00214 (DOI)000370760300001 ()
Available from: 2016-04-05 Created: 2016-04-05 Last updated: 2017-11-30Bibliographically approved
Langenheder, S., Comte, J., Zha, Y., Samad, M. S., Sinclair, L., Eiler, A. & Lindström, E. S. (2016). Remnants of marine bacterial communities can be retrieved from deep sediments in lakes of marine origin. Environmental Microbiology Reports, 8(4), 479-485.
Open this publication in new window or tab >>Remnants of marine bacterial communities can be retrieved from deep sediments in lakes of marine origin
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2016 (English)In: Environmental Microbiology Reports, ISSN 1758-2229, E-ISSN 1758-2229, Vol. 8, no 4, 479-485 p.Article in journal (Refereed) Published
Abstract [en]

Some bacteria can be preserved over time in deep sediments where they persist either in dormant or slow-growing vegetative stages. Here, we hypothesized that such cells can be revived when exposed to environmental conditions similar to those before they were buried in the sediments. To test this hypothesis, we collected bacteria from sediment samples of different ages (140–8500 calibrated years before present, cal BP) from three lakes that differed in the timing of their physical isolation from the Baltic Sea following postglacial uplift. After these bacterial communities were grown in sterile water from the Baltic Sea, we determined the proportion of 16S rRNA sequence reads associated with marine habitats by extracting the environment descriptive terms of homologous sequences retrieved from public databases. We found that the proportion of reads associated with marine descriptive term was significantly higher in cultures inoculated with sediment layers formed under Baltic conditions and where salinities were expected to be similar to current levels. Moreover, a similar pattern was found in the original sediment layers. Our study, therefore, suggests that remnants of marine bacterial communities can be preserved in sediments over thousands of years and can be revived from deep sediments in lakes of marine origin.

National Category
Ecology Microbiology
Research subject
Biology with specialization in Limnology; Biology with specialization in Microbiology
Identifiers
urn:nbn:se:uu:diva-295751 (URN)10.1111/1758-2229.12392 (DOI)000379938900007 ()26929161 (PubMedID)
Funder
Swedish Research Council, 2009-5172Wenner-Gren FoundationsSwedish Institute of Computer Science, SICS, b2011032
Available from: 2016-06-09 Created: 2016-06-09 Last updated: 2017-11-30Bibliographically approved
Berga, M., Östman, Ö., Lindström, E. S. & Langenheder, S. (2015). Combined effects of zooplankton grazing and dispersal on the diversity and assembly mechanisms of bacterial metacommunities. Environmental Microbiology, 17(7), 2275-2287.
Open this publication in new window or tab >>Combined effects of zooplankton grazing and dispersal on the diversity and assembly mechanisms of bacterial metacommunities
2015 (English)In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 17, no 7, 2275-2287 p.Article in journal (Refereed) Published
Abstract [en]

Effects of dispersal and the presence of predators on diversity, assembly and functioning of bacterial communities are well studied in isolation. In reality, however, dispersal and trophic interactions act simultaneously and can therefore have combined effects, which are poorly investigated. We performed an experiment with aquatic metacommunities consisting of three environmentally different patches and manipulated dispersal rates among them as well as the presence or absence of the keystone species Daphnia magnaDaphnia magnareduced both local and regional diversity, whereas dispersal increased local diversity but decreased beta-diversity having no net effect on regional diversity. Dispersal modified the assembly mechanisms of bacterial communities by increasing the degree of determinism. Additionally, the combination of the D. magna and dispersal increased the importance of deterministic processes, presumably because predator-tolerant taxa were spread in the metacommunity via dispersal. Moreover, the presence of D. magna affected community composition, increased community respiration rates but did not affect bacterial production or abundance, whereas dispersal slightly increased bacterial production. In conclusion, our study suggests that predation by a keystone species such as D. magna and dispersal additively influence bacterial diversity, assembly processes and ecosystem functioning.

National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-252430 (URN)10.1111/1462-2920.12688 (DOI)000358114300010 ()25367396 (PubMedID)
Funder
Swedish Research Council FormasThe Royal Swedish Academy of Sciences
Note

Funding: Bioinformatics Infrastructure for Life Sciences (BILS), Marie Curie Reintegration Grant, Olsson Borgh foundation 

Available from: 2015-05-07 Created: 2015-05-07 Last updated: 2017-12-04Bibliographically approved
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ORCID iD: ORCID iD iconorcid.org/0000-0001-8920-3071

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