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  • 1.
    Beier, Sara
    et al.
    Leibniz Inst Baltic Sea Res Warnemunde IOW, Biol Oceanog, Rostock, Germany.;Sorbonne Univ, Observ Oceanol Banyuls, Lab Oceanog Microbienne LOMIC, CNRS, Banyuls Sur Mer, France..
    Andersson, Anders F.
    KTH Royal Inst Technol, Sch Engn Sci Chem Biotechnol & Hlth, Dept Gene Technol, Sci Life Lab, Stockholm, Sweden..
    Galand, Pierre E.
    Sorbonne Univ, Observ Oceanol Banyuls, Lab Ecogeochim Environm Benth LECOB, CNRS, Banyuls Sur Mer, France..
    Hochart, Corentin
    Sorbonne Univ, Observ Oceanol Banyuls, Lab Ecogeochim Environm Benth LECOB, CNRS, Banyuls Sur Mer, France..
    Logue, Jürg Brendan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    McMahon, Katherine
    Univ Wisconsin, Dept Civil & Environm Engn, Madison, WI 53706 USA.;Univ Wisconsin, Dept Bacteriol, Madison, WI 53706 USA..
    Bertilsson, Stefan
    Swedish Univ Agr Sci, Dept Aquat Sci & Assessment, Uppsala, Sweden..
    The environment drives microbial trait variability in aquatic habitats2020In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 29, no 23, p. 4605-4617Article in journal (Refereed)
    Abstract [en]

    A prerequisite to improve the predictability of microbial community dynamics is to understand the mechanisms of microbial assembly. To study factors that contribute to microbial community assembly, we examined the temporal dynamics of genes in five aquatic metagenome time-series, originating from marine offshore or coastal sites and one lake. With this trait-based approach we expected to find gene-specific patterns of temporal allele variability that depended on the seasonal metacommunity size of carrier-taxa and the variability of the milieu and the substrates to which the resulting proteins were exposed. In more detail, we hypothesized that a larger seasonal metacommunity size would result in increased temporal variability of functional units (i.e., gene alleles), as shown previously for taxonomic units. We further hypothesized that multicopy genes would feature higher temporal variability than single-copy genes, as gene multiplication can result from high variability in substrate quality and quantity. Finally, we hypothesized that direct exposure of proteins to the extracellular environment would result in increased temporal variability of the respective gene compared to intracellular proteins that are less exposed to environmental fluctuations. The first two hypotheses were confirmed in all data sets, while significant effects of the subcellular location of gene products was only seen in three of the five time-series. The gene with the highest allele variability throughout all data sets was an iron transporter, also representing a target for phage infection. Previous work has emphasized the role of phage-prokaryote interactions as a major driver of microbial diversity. Our finding therefore points to a potentially important role of iron transporter-mediated phage infections for the assembly and maintenance of diversity in aquatic prokaryotes.

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  • 2. Besemer, Katharina
    et al.
    Peter, Hannes
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Logue, Jürg B.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Langenheder, Silke
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Lindström, Eva S.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Tranvik, Lars J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Battin, Tom J.
    Unraveling assembly of stream biofilm communities2012In: The ISME Journal: multidisciplinary journal of microbial ecology, ISSN 1751-7362, Vol. 6, no 8, p. 1459-1468Article in journal (Refereed)
    Abstract [en]

    Microbial biofilms assemble from cells that attach to a surface, where they develop into matrix-enclosed communities. Mechanistic insights into community assembly are crucial to better understand the functioning of natural biofilms, which drive key ecosystem processes in numerous aquatic habitats. We studied the role of the suspended microbial community as the source of the biofilm community in three streams using terminal-restriction fragment length polymorphism and 454 pyrosequencing of the 16S ribosomal RNA (rRNA) and the 16S rRNA gene (as a measure for the active and the bulk community, respectively). Diversity was consistently lower in the biofilm communities than in the suspended stream water communities. We propose that the higher diversity in the suspended communities is supported by continuous inflow from various sources within the catchment. Community composition clearly differed between biofilms and suspended communities, whereas biofilm communities were similar in all three streams. This suggests that biofilm assembly did not simply reflect differences in the source communities, but that certain microbial groups from the source community proliferate in the biofilm. We compared the biofilm communities with random samples of the respective community suspended in the stream water. This analysis confirmed that stochastic dispersal from the source community was unlikely to shape the observed community composition of the biofilms, in support of species sorting as a major biofilm assembly mechanism. Bulk and active populations generated comparable patterns of community composition in the biofilms and the suspended communities, which suggests similar assembly controls on these populations.

  • 3.
    Comte, Jérôme
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Berga, Mercè
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Biological Oceanography, Leibniz-Institute for Baltic Sea Research, Germany.
    Severin, Ina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Logue, Jürg Brendan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Lindström, Eva S.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Contribution of different bacterial dispersal sources to lakes: Population and community effects in different seasons2017In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 19, no 6, p. 2391-2404Article in journal (Refereed)
    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.

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  • 4.
    Logares, Ramiro
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Lindström, Eva S.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Langenheder, Silke
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Logue, Jürg Brendan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Paterson, Harriet
    Laybourn-Parry, Johanna
    Rengefors, Karin
    Tranvik, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Biogeography of bacterial communities exposed to progressive long-term environmental change2013In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 7, no 5, p. 937-948Article in journal (Refereed)
    Abstract [en]

    The response of microbial communities to long-term environmental change is poorly understood. Here, we study bacterioplankton communities in a unique system of coastal Antarctic lakes that were exposed to progressive long-term environmental change, using 454 pyrosequencing of the 16S rDNA gene (V3-V4 regions). At the time of formation, most of the studied lakes harbored marine-coastal microbial communities, as they were connected to the sea. During the past 20 000 years, most lakes isolated from the sea, and subsequently they experienced a gradual, but strong, salinity change that eventually developed into a gradient ranging from freshwater (salinity 0) to hypersaline (salinity 100). Our results indicated that present bacterioplankton community composition was strongly correlated with salinity and weakly correlated with geographical distance between lakes. A few abundant taxa were shared between some lakes and coastal marine communities. Nevertheless, lakes contained a large number of taxa that were not detected in the adjacent sea. Abundant and rare taxa within saline communities presented similar biogeography, suggesting that these groups have comparable environmental sensitivity. Habitat specialists and generalists were detected among abundant and rare taxa, with specialists being relatively more abundant at the extremes of the salinity gradient. Altogether, progressive long-term salinity change appears to have promoted the diversification of bacterioplankton communities by modifying the composition of ancestral communities and by allowing the establishment of new taxa. The ISME Journal (2013) 7, 937-948; doi:10.1038/ismej.2012.168; published online 20 December 2012

  • 5.
    Logue, Jürg B.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Lindström, Eva S.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Species sorting affects bacterioplankton community composition as determined by 16S rDNA and 16S rRNA fingerprints2010In: The ISME Journal, ISSN 1751-7362, Vol. 4, no 6, p. 729-738Article in journal (Refereed)
    Abstract [en]

    To understand the mechanisms determining community composition, it is essential to distinctively unravel the importance of local from that of regional processes. In this effort, the mechanisms underlying bacterioplankton community assembly were analysed in eight lakes of short water residence time (WRT) during a four-season sampling campaign. Bacterioplankton community composition (BCC) was determined using terminal-restriction fragment length polymorphism (t-RFLP) on the 16S rRNA gene (16S rDNA) and 16S rRNA. The relationship between similarity in BCC between a lake and its major inlet on the one hand and cell import per cell production rate from the inlet to the lake epilimnion on the other was used as a measure of the importance of cell dispersal (mass effects) for community assembly. Low similarities in BCC between lakes and their inlets were observed even at short WRTs, and the degree of similarity correlated better with the environmental conditions in lakes and streams than with cell import per cell production rates. Thus, mass effects seemed less important for local lake BCC in comparison to environmental habitat characteristics (species sorting). Analyses of 16S rDNA and 16S rRNA community fingerprints yielded similar results, indicating that species-sorting dynamics exerted an equally important effect on both the abundant and active fraction within the studied bacterioplankton communities.

  • 6.
    Logue, Jürg Brendan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Empirical approaches to metacommunities: a review and comparison with theoryManuscript (preprint) (Other academic)
    Abstract [en]

    Metacommunity theory has advanced our understanding of how spatial dynamics and local interactions shape local community structure and biodiversity. The last decade has seen an increase in implementation of these ideas in empirical ecology to explain and understand the regulation of local community structure and dynamics. Here, we review the different empirical (experimental and observational) approaches to metacommunities to analyse their strengths and weaknesses in comparison to natural ecosystems and theoretical paradigms. Experimental approaches are extremely diverse, ranging from highly controlled laboratory microcosms to large-scale fragmentation studies in the field. The main body of experiments, however, favours downscaled, artificial designs, avoiding physical complexity. These approaches are often successful in mechanistically addressing local and regional species interactions but the preponderance of artificial dispersal treatments via transfer neglects the importance of species’ differences in dispersal ability for community structure. Observational approaches mainly focus on investigating smaller organisms in aquatic communities, which are predominantly assembled by local environmental processes. However, observational approaches often lack actual measurements of dispersal rates, which hamper the distinction of local and regional effects on community composition. More generally, empirical metacommunity data deviate from theory as – with the exception of the most artificial experimental systems – the data rarely reflect specific paradigms. Thus, the paradigms capture only parts of the observed spatial dynamics. Metacommunity theory has emerged as a highly successful framework to understand the assembly of local communities but we conclude that empirical and theoretical approaches need thorough harmonisation to utilise the potential of this framework in guiding our understanding of spatial dynamics in ecological communities.

  • 7.
    Logue, Jürg Brendan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Factors influencing the biogeography of bacteria in fresh waters - a metacommunity approach2010Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    One of ecology’s primary goals is to comprehend biodiversity and its patterns of distribution over space and time. Since microorganisms play a pivotal role in key ecological processes, the diversity of microbial communities may have important implications for the stability and functioning of Earth’s ecosystems. Thus, it is of utmost importance to develop a theoretical foundation but also a conceptual understanding for the mechanisms that generate and maintain microbial diversity.

    The aim of this thesis is to investigate to what extent local freshwater bacterioplankton diversity, i.e. richness and community composition, is structured by local environmental interactions and/or regional processes. The key objective is to identify ecological linkages between lake bacterioplankton and bacterial communities in connected streams and the surrounding terrestrial landscape, thereby applying a metacommunity approach. To do so, I studied several natural lake bacterioplankton assemblies within different regions of Sweden and assessed both local environmental properties and regional parameters (e.g. dispersal, landscape position). The genetic composition of freshwater bacterioplankton diversity was determined by means of terminal-restriction fragment length polymorphism or 454 pyrosequencing.

    From the review on the biogeography of bacterioplankton in inland waters it became clear that microbial diversity and its spatial distribution are governed by a complex interplay of both local and regional drivers. In one case, freshwater bacterioplankton communities were structured by local environmental conditions rather than by regional dispersal processes. These local environmental conditions seemed to be equally important in controlling both the total bacterioplankton community and its active fraction. In a study of bacterioplankton communities from five different regions, locally abundant aquatic bacteria were shown to be also regionally widespread, a pattern predicted by neutral theory. Yet, this degree of similarity decreased with increasing environmental heterogeneity. In another study, bacterioplankton richness was controlled mostly by nutrient content, indicating that productivity exerted influence on bacterioplankton richness. However, landscape position and productivity covaried, suggesting that the landscape dictates environmental properties, which then directly structure local bacterioplankton richness. Finally, a review synthesising results from empirical metacommunity approaches and comparing these to theory showed that yet a gap between empirics and theory exists. To conclude, local bacterioplankton diversity appeared to be mainly structured by local environmental properties. However, signatures of neutral processes driving local bacterioplankton community assembly were also recorded.

    List of papers
    1. Biogeography of bacterioplankton in inland waters.
    Open this publication in new window or tab >>Biogeography of bacterioplankton in inland waters.
    2008 (English)In: Freshwater Reviews, ISSN 1755-084X, Vol. 1, no 1, p. 99-114Article in journal (Refereed) Published
    Abstract [en]

    Bacteria are among the most abundant groups of organisms.  They mediate key ecological processes.  Recent molecular advances have provided greater insight into bacterial diversity as well as allowing a more thorough examination of patterns in the spatial and temporal distribution of bacteria.  Thus, the study of bacterial biodiversity and biogeographical distribution has stimulated considerable interest and dispute over the last decade. This review summarises the findings obtained from studies on the biogeography of bacterioplankton in inland waters.  We examine factors and processes that may determine and maintain bacterial diversity and biogeography, and relate these to the theoretical metacommunity framework. We conclude that the importance of local environmental factors (such as lake character) for local bacterioplankton community compositions (BCC) is much more intensively studied than the importance of regional factors, such as dispersal.  Further, few attempts have been made to evaluate simultaneously the relative importance of the two types of factors for BCC.  Finally, we summarise gaps in knowledge, delineate challenges and put forward possible future research directions.

    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-107690 (URN)10.1608/FRJ-1.1.9 (DOI)
    Available from: 2009-08-24 Created: 2009-08-24 Last updated: 2024-03-14
    2. Empirical approaches to metacommunities: a review and comparison with theory
    Open this publication in new window or tab >>Empirical approaches to metacommunities: a review and comparison with theory
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Metacommunity theory has advanced our understanding of how spatial dynamics and local interactions shape local community structure and biodiversity. The last decade has seen an increase in implementation of these ideas in empirical ecology to explain and understand the regulation of local community structure and dynamics. Here, we review the different empirical (experimental and observational) approaches to metacommunities to analyse their strengths and weaknesses in comparison to natural ecosystems and theoretical paradigms. Experimental approaches are extremely diverse, ranging from highly controlled laboratory microcosms to large-scale fragmentation studies in the field. The main body of experiments, however, favours downscaled, artificial designs, avoiding physical complexity. These approaches are often successful in mechanistically addressing local and regional species interactions but the preponderance of artificial dispersal treatments via transfer neglects the importance of species’ differences in dispersal ability for community structure. Observational approaches mainly focus on investigating smaller organisms in aquatic communities, which are predominantly assembled by local environmental processes. However, observational approaches often lack actual measurements of dispersal rates, which hamper the distinction of local and regional effects on community composition. More generally, empirical metacommunity data deviate from theory as – with the exception of the most artificial experimental systems – the data rarely reflect specific paradigms. Thus, the paradigms capture only parts of the observed spatial dynamics. Metacommunity theory has emerged as a highly successful framework to understand the assembly of local communities but we conclude that empirical and theoretical approaches need thorough harmonisation to utilise the potential of this framework in guiding our understanding of spatial dynamics in ecological communities.

    Keywords
    metacommunity, community ecology, experimental, observational, empirical, theory, review, literature survey
    National Category
    Biological Sciences
    Research subject
    Biology
    Identifiers
    urn:nbn:se:uu:diva-129366 (URN)
    Available from: 2010-08-12 Created: 2010-08-12 Last updated: 2011-11-15
    3. Species sorting affects bacterioplankton community composition as determined by 16S rDNA and 16S rRNA fingerprints
    Open this publication in new window or tab >>Species sorting affects bacterioplankton community composition as determined by 16S rDNA and 16S rRNA fingerprints
    2010 (English)In: The ISME Journal, ISSN 1751-7362, Vol. 4, no 6, p. 729-738Article in journal (Refereed) Published
    Abstract [en]

    To understand the mechanisms determining community composition, it is essential to distinctively unravel the importance of local from that of regional processes. In this effort, the mechanisms underlying bacterioplankton community assembly were analysed in eight lakes of short water residence time (WRT) during a four-season sampling campaign. Bacterioplankton community composition (BCC) was determined using terminal-restriction fragment length polymorphism (t-RFLP) on the 16S rRNA gene (16S rDNA) and 16S rRNA. The relationship between similarity in BCC between a lake and its major inlet on the one hand and cell import per cell production rate from the inlet to the lake epilimnion on the other was used as a measure of the importance of cell dispersal (mass effects) for community assembly. Low similarities in BCC between lakes and their inlets were observed even at short WRTs, and the degree of similarity correlated better with the environmental conditions in lakes and streams than with cell import per cell production rates. Thus, mass effects seemed less important for local lake BCC in comparison to environmental habitat characteristics (species sorting). Analyses of 16S rDNA and 16S rRNA community fingerprints yielded similar results, indicating that species-sorting dynamics exerted an equally important effect on both the abundant and active fraction within the studied bacterioplankton communities.

    Place, publisher, year, edition, pages
    Nature Publishing Group, 2010
    Keywords
    16S rDNA, 16S rRNA, biogeography, mass effects, metacommunity, species sorting
    National Category
    Biological Sciences
    Research subject
    Biology with specialization in Limnology
    Identifiers
    urn:nbn:se:uu:diva-129364 (URN)10.1038/ismej.2009.156 (DOI)000278104800002 ()20130658 (PubMedID)
    Available from: 2010-08-12 Created: 2010-08-12 Last updated: 2010-12-13Bibliographically approved
    4. Freshwater bacterioplankton richness in oligotrophic lakes depends on nutrient availability rather than on species-area relationships
    Open this publication in new window or tab >>Freshwater bacterioplankton richness in oligotrophic lakes depends on nutrient availability rather than on species-area relationships
    Show others...
    2012 (English)In: The ISME Journal, ISSN 1751-7362, Vol. 6, no 6, p. 1127-1136Article in journal (Refereed) Published
    Abstract [en]

    A central goal in ecology is to grasp the mechanisms that underlie and maintain biodiversity and patterns in its spatial distribution can provide clues about those mechanisms. Here, we investigated what might determine bacterioplankton richness (BR) in lakes by means of 454 pyrosequencing of the 16S rRNA gene. We further provide a BR estimate based upon a sampling depth and accuracy, which, to our knowledge, are unsurpassed for freshwater bacterioplankton communities. Our examination of 22 669 sequences per lake showed that freshwater BR in fourteen nutrient-poor lakes was positively influenced by nutrient availability. Our study is, thus, consistent with the finding that the supply of available nutrients is a major driver of species richness; a pattern that may well be universally valid to the world of both micro- and macro-organisms. We, furthermore, observed that BR increased with elevated landscape position, most likely as a consequence of differences in nutrient availability. Finally, BR decreased with increasing lake and catchment area that is negative species-area relationships (SARs) were recorded; a finding that re-opens the debate about whether positive SARs can indeed be found in the microbial world and whether positive SARs can in fact be pronounced as one of the few “laws” in ecology.

    Keywords
    bacterial richness, biogeography, freshwater, landscape position, productivity, species-area relationship
    National Category
    Microbiology Ecology
    Research subject
    Biology with specialization in Limnology
    Identifiers
    urn:nbn:se:uu:diva-130008 (URN)10.1038/ismej.2011.184 (DOI)000304047800005 ()
    Available from: 2010-08-26 Created: 2010-08-26 Last updated: 2013-01-14Bibliographically approved
    5. Regional invariance among microbial communities
    Open this publication in new window or tab >>Regional invariance among microbial communities
    Show others...
    2010 (English)In: Ecology Letters, ISSN 1461-023X, E-ISSN 1461-0248, Vol. 13, no 1, p. 118-127Article in journal (Refereed) Published
    Abstract [en]

    Microbial ecology has focused much on causes of between-site variation in community composition. By analysing five data-sets each of aquatic bacteria and phytoplankton, we demonstrated that microbial communities show a large degree of similarity in community composition and that abundant taxa were widespread, a typical pattern for many metazoan metacommunities. The regional abundance of taxa explained on average 85 and 41% of variation in detection frequency and 58 and 31% of variation in local abundances for bacteria and phytoplankton, respectively. However, regional abundance explained less variation in local abundances with increasing environmental variation between sites within data-sets. These findings indicate that the studies of microbial assemblages need to consider similarities between communities to better understand the processes underlying the assembly of microbial communities. Finally, we propose that the degree of regional invariance can be linked to the evolution of microbes and the variation in ecosystem functions performed by microbial communities.

    Keywords
    Abundance-occupancy, dispersal, freshwater, generalists, neutral models, species sorting, Sweden
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-121206 (URN)10.1111/j.1461-0248.2009.01413.x (DOI)000272996200013 ()19968693 (PubMedID)
    Available from: 2010-03-19 Created: 2010-03-19 Last updated: 2017-12-12Bibliographically approved
    Download full text (pdf)
    FULLTEXT01
  • 8.
    Logue, Jürg Brendan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Bürgmann, Helmut
    Robinson, Christopher T.
    Progress in the Ecological Genetics and Biodiversity of Freshwater Bacteria2008In: BioScience, ISSN 0006-3568, E-ISSN 1525-3244, Vol. 58, no 2, p. 103-113Article in journal (Refereed)
    Abstract [en]

    The field of microbial ecology has grown tremendously with the advent of novel molecular techniques, allowing the study of uncultured microbes in the environment, and producing a paradigm shift: now, rather than using bacteria cultures for evaluating cell-specific questions, researchers use RNA and DNA techniques to examine more broad-based ecological and evolutionary constructs such as biogeography and the long-debated biological species concept. Recent work has begun to relate bacteria functional genes to ecosystem processes and functioning, thereby enabling a better understanding of the interactive role of bacteria in different and often-changing environments. The field continues to mature and will most likely make substantial contributions in the future with additional efforts that include metagenomics and genomics. Here we review progress in the application of molecular techniques to study microbial communities in freshwater environments.

  • 9.
    Logue, Jürg Brendan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Langenheder, Silke
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Andersson, Anders F.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Drakare, Stina
    Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences (SLU).
    Lanzén, Anders
    Centre for Geobiology and Department of Biology, University of Bergen.
    Lindström, Eva S.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Freshwater bacterioplankton richness in oligotrophic lakes depends on nutrient availability rather than on species-area relationships2012In: The ISME Journal, ISSN 1751-7362, Vol. 6, no 6, p. 1127-1136Article in journal (Refereed)
    Abstract [en]

    A central goal in ecology is to grasp the mechanisms that underlie and maintain biodiversity and patterns in its spatial distribution can provide clues about those mechanisms. Here, we investigated what might determine bacterioplankton richness (BR) in lakes by means of 454 pyrosequencing of the 16S rRNA gene. We further provide a BR estimate based upon a sampling depth and accuracy, which, to our knowledge, are unsurpassed for freshwater bacterioplankton communities. Our examination of 22 669 sequences per lake showed that freshwater BR in fourteen nutrient-poor lakes was positively influenced by nutrient availability. Our study is, thus, consistent with the finding that the supply of available nutrients is a major driver of species richness; a pattern that may well be universally valid to the world of both micro- and macro-organisms. We, furthermore, observed that BR increased with elevated landscape position, most likely as a consequence of differences in nutrient availability. Finally, BR decreased with increasing lake and catchment area that is negative species-area relationships (SARs) were recorded; a finding that re-opens the debate about whether positive SARs can indeed be found in the microbial world and whether positive SARs can in fact be pronounced as one of the few “laws” in ecology.

  • 10.
    Logue, Jürg Brendan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Lindström, Eva S.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Biogeography of bacterioplankton in inland waters.2008In: Freshwater Reviews, ISSN 1755-084X, Vol. 1, no 1, p. 99-114Article in journal (Refereed)
    Abstract [en]

    Bacteria are among the most abundant groups of organisms.  They mediate key ecological processes.  Recent molecular advances have provided greater insight into bacterial diversity as well as allowing a more thorough examination of patterns in the spatial and temporal distribution of bacteria.  Thus, the study of bacterial biodiversity and biogeographical distribution has stimulated considerable interest and dispute over the last decade. This review summarises the findings obtained from studies on the biogeography of bacterioplankton in inland waters.  We examine factors and processes that may determine and maintain bacterial diversity and biogeography, and relate these to the theoretical metacommunity framework. We conclude that the importance of local environmental factors (such as lake character) for local bacterioplankton community compositions (BCC) is much more intensively studied than the importance of regional factors, such as dispersal.  Further, few attempts have been made to evaluate simultaneously the relative importance of the two types of factors for BCC.  Finally, we summarise gaps in knowledge, delineate challenges and put forward possible future research directions.

  • 11.
    Logue, Jürg Brendan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Mouquet, Nicolas
    Peter, Hannes
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Hillebrand, Helmut
    Empirical approaches to metacommunities: a review and comparison with theory2011In: Trends in Ecology & Evolution, ISSN 0169-5347, E-ISSN 1872-8383, Vol. 26, no 9, p. 482-491Article in journal (Refereed)
    Abstract [en]

    Metacommunity theory has advanced understanding of how spatial dynamics and local interactions shape community structure and biodiversity. Here, we review empirical approaches to metacommunities, both observational and experimental, pertaining to how well they relate to and test theoretical metacommunity paradigms and how well they capture the realities of natural ecosystems. First, we show that the species-sorting and mass-effects paradigms are the most commonly tested and supported paradigms. Second, the dynamics observed can often be ascribed to two or more of the four non-exclusive paradigms. Third, empirical approaches relate only weakly to the concise assumptions and predictions made by the paradigms. Consequently, we suggest major avenues of improvement for empirical metacommunity approaches, including the integration across theoretical approaches and the incorporation of evolutionary and meta-ecosystem dynamics. We hope for metacommunity ecology to thereby bridge existing gaps between empirical and theoretical work, thus becoming a more powerful framework to understand dynamics across ecosystems.

  • 12.
    Logue, Jürg Brendan
    et al.
    Swiss Federal Institute of Aquatic Science and Technology (EAWAG).
    Robinson, Christopher T.
    Swiss Federal Institute of Aquatic Science and Technology (EAWAG).
    Meier, Christoph
    Swiss Federal Institute of Aquatic Science and Technology (EAWAG).
    van der Meer, Jan Roelof
    Swiss Federal Institute of Aquatic Science and Technology (EAWAG).
    Relationship between sediment organic matter, bacteria composition, and the ecosystem metabolism of alpine streams2004In: Limnology and Oceanography, ISSN 0024-3590, E-ISSN 1939-5590, Vol. 49, no 6, p. 2001-2010Article in journal (Refereed)
    Abstract [en]

    We tested whether sediment bacteria abundance (4´,6-diamidino-2-phenylindole–stained cell counts) were related to sediment organic content (ash-free dry mass [AFDM]) in 11 nonforested streams of three different Alpine catchments during summer 2003. We used terminal restriction fragment–length polymorphism (T-RLFP, a moleculargenetic technique) to test for seasonal and spatial differences in bacterial composition in these same streams. We then related the above parameters, in conjunction with periphyton biomass and hyporheic respiration, to whole stream estimates of gross primary production (GPP) and ecosystem respiration (ER) in a glacial and nonglacial stream, representing environmental extremes, in one of the catchments. The percentage of organic matter of sediments was 4–14% (0.01–0.04 g AFDM ml sediment-1), and counts of bacteria cells per millimeter of sediment averaged 2x10^6–4x10^6. Bacteria counts correlated with sediment AFDM only for streams in the catchment with highest sediment AFDM levels. Bacteria composition (based on the presence and absence of terminal restriction fragments from T-RFLP analysis) changed seasonally in the different streams and differed between glacial- and groundwater-fed streams. In the one catchment, hyporheic respiration averaged 0.0004 and 0.0003 g O2 h-1 kg sediment-1 and was positively correlated with AFDM (r2=0.23). Ecosystem metabolism displayed a strong seasonality, with GPP averaging 4.5 and 8.4 and ER averaging 5.4 and 9.9 g O2 m-2 d-1 for the two sites, respectively, thus indicating a predominance of heterotrophy (P:R<1) in these high-elevation, open-canopied systems. Bacteria play a strong role in the trophic dynamics of alpine streams.

  • 13. Lundin, Daniel
    et al.
    Severin, Ina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Logue, Jürg Brendan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Östman, Örjan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Population and Conservation Biology.
    Andersson, Anders F
    Lindström, Eva S
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Which sequencing depth is sufficient to describe patterns in bacterial a- and b-diversity?2012In: Environmental Microbiology Reports, ISSN 1758-2229, E-ISSN 1758-2229, Vol. 4, no 3, p. 367-372Article in journal (Refereed)
    Abstract [en]

    The vastness of microbial diversity implies that an almost infinite number of individuals needs to be identified to accurately describe such communities. Practical and economical constraints may therefore prevent appropriate study designs. However, for many questions in ecology it is not essential to know the actual diversity but rather the trends among samples thereof. It is, hence, important to know to what depth microbial communities need to be sampled to accurately measure trends in diversity. We used three data sets of freshwater and sediment bacteria, where diversity was explored using 454 pyrosequencing. Each data set contained 6–15 communities from which 15 000–20 000 16S rRNA gene sequences each were obtained. These data sets were subsampled repeatedly to 10 different depths down to 200 sequences per community. Diversity estimates varied with sequencing depth, yet, trends in diversity among samples were less sensitive. We found that 1000 denoised sequences per sample explained to 90% the trends in β-diversity (Bray-Curtis index) among samples observed for 15 000–20 000 sequences. Similarly, 5000 denoised sequences were sufficient to describe trends in α-diversity (Shannon index) with the same accuracy. Further, 5000 denoised sequences captured to more than 80% the trends in Chao1 richness and Pielou's evenness.

  • 14.
    Lymer, David
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Logue, Jürg Brendan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Brussaard, Corina P. D.
    Baudoux, Anne-Claire
    Vrede, Katarina
    Lindström, Eva
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Temporal variation in freshwater viral and bacterial community composition2008In: Freshwater Biology, ISSN 0046-5070, E-ISSN 1365-2427, Vol. 53, no 6, p. 1163-1175Article in journal (Refereed)
    Abstract [en]

    1. The goal of this study conducted in three lakes differing in nutrient content and size was to assess the temporal variation in viral community composition and possible co-variation with compositional changes in bacterial communities.   

    2. The viral community composition differed among lakes and changed over the season. Changes could also be detected on short-time scales, i.e. over a few days. These changes were comparable in magnitude to the changes detected between months or seasons.   

    3. The most important environmental factors co-varying with viral community composition, as determined by multivariate analysis, differed over the year and among lakes. Temperature and concentrations of dissolved organic carbon (DOC), total phosphorus and soluble reactive phosphorus were the most important factors.

    4. Bacterial community composition also varied over the season and among lakes. The most important factors co-varying with bacterial community composition, as determined by multivariate analysis, were also temperature and DOC concentration.

    5. Correlation between viral and bacterial community composition was weak and appeared to be a result of an indirect connection rather than a direct relationship between bacteria and viruses.

  • 15.
    Östman, Örjan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Population and Conservation Biology.
    Drakare, Stina
    Kritzberg, Emma S.
    Langenheder, Silke
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Logue, Jürg B.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Lindström, Eva S.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Importance of space and the local environment for linking local and regional abundances of microbes2012In: Aquatic Microbial Ecology, ISSN 0948-3055, E-ISSN 1616-1564, Vol. 67, no 1, p. 35-45Article in journal (Refereed)
    Abstract [en]

    It is frequently observed that the local relative abundances of aquatic microbial taxa are correlated with their average relative abundance at the regional scale, which results in the composition of different communities being more similar than expected by chance or invariant. The degree to which communities within a region match the regional average community is variable and likely depends on several different mechanisms that control the process of microbial community assembly. Here, we show that environmental variables were associated with the community specific degree of regional invariance in 9 of 10 datasets of microbial communities in aquatic systems, being the main set of variables explaining differences in regional invariance in 5 of them. This indicates that variation in local environmental conditions across a region reduces the degree of regional invariance amongst communities. Spatial distances between communities were not related to the degrees of regional invariance, but in 7 of the datasets, regional invariance differed among different parts of the regions, particularly for phytoplankton communities. This suggests an influence of spatial or historical processes on the community specific degree of regional invariance. We conclude that both local environmental conditions and spatial/historical processes cause between-site differences in the degree of invariance between local and regional abundances in aquatic microbial metacommunities. We argue that studies of regional invariance can be an important complement to other statistical methods due to its propensity to detect variation in stochastic processes along gradients.

  • 16.
    Östman, Örjan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Population and Conservation Biology.
    Drakare, Stina
    Kritzberg, Emma S.
    Langenheder, Silke
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Logue, Jürg Brendan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Lindström, Eva S.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Regional invariance among microbial communities2010In: Ecology Letters, ISSN 1461-023X, E-ISSN 1461-0248, Vol. 13, no 1, p. 118-127Article in journal (Refereed)
    Abstract [en]

    Microbial ecology has focused much on causes of between-site variation in community composition. By analysing five data-sets each of aquatic bacteria and phytoplankton, we demonstrated that microbial communities show a large degree of similarity in community composition and that abundant taxa were widespread, a typical pattern for many metazoan metacommunities. The regional abundance of taxa explained on average 85 and 41% of variation in detection frequency and 58 and 31% of variation in local abundances for bacteria and phytoplankton, respectively. However, regional abundance explained less variation in local abundances with increasing environmental variation between sites within data-sets. These findings indicate that the studies of microbial assemblages need to consider similarities between communities to better understand the processes underlying the assembly of microbial communities. Finally, we propose that the degree of regional invariance can be linked to the evolution of microbes and the variation in ecosystem functions performed by microbial communities.

1 - 16 of 16
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