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The immigration history of communities can profoundly affect community composition. For instance, early‐arriving species can have a lasting effect on community structure by reducing the invasion success of late‐arriving ones through priority effects. This can be particularly important when early‐arriving communities coalesce with another community during dispersal (mixing) events. However, the outcome of such community coalescence is unknown as we lack knowledge on how different factors influence the persistence of early‐arriving communities and the invasion success of late‐arriving taxa. Therefore, we implemented a full‐factorial experiment with aquatic bacteria where temperature and dispersal rate of a better adapted community were manipulated to test their joint effects on the resistance of early‐arriving communities to invasion, both at community and population level. Our 16S rRNA gene sequencing‐based results showed that invasion success of better adapted late‐arriving bacteria equaled or even exceeded what we expected based on the dispersal ratios of the recipient and invading communities suggesting limited priority effects on the community level. Patterns detected at the population level, however, showed that resistance of aquatic bacteria to invasion might be strengthened by warming as higher temperatures (a) increased the sum of relative abundances of persistent bacteria in the recipient communities, and (b) restricted the total relative abundance of successfully established late‐arriving bacteria. Warming‐enhanced resistance, however, was not always found and its strengths differed between recipient communities and dispersal rates. Nevertheless, our findings highlight the potential role of warming in mitigating the effects of invasion at the population level. Title in thesis list of papers: Warming-enhanced priority effects at population and community levels in aquatic bacteria

During recent years, many studies have shown that different processes including drift, environmental selection and dispersal can be important for the assembly of bacterial communities in aquatic and terrestrial ecosystems. However, we lack a conceptual overview about the ecological context and factors that influence the relative importance of the different assembly mechanisms and determine their dynamics in time and space. Focusing on free-living, i.e., nonhost associated, bacterial communities, this minireview, therefore, summarizes and conceptualizes findings from empirical studies about how (i) environmental factors, such as environmental heterogeneity, disturbances, productivity and trophic interactions; (ii) connectivity and dispersal rates (iii) spatial scale, (iv) community properties and traits and (v) the use of taxonomic/phylogenetic or functional metrics influence the relative importance of different community assembly processes. We find that there is to-date little consistency among studies and suggest that future studies should now address how (i)-(v) differ between habitats and organisms and how this, in turn, influences the temporal and spatial-scale dependency of community assembly processes in microorganisms.

The sensitivity and spatial recovery of river sediment biofilms along 1 km after the input of two wastewater treatment plants (WWTPs) located in two river reaches with different degrees of anthropogenic influence were investigated. First, at the upper reach, we observed an inhibition of some microbial functions (microbial respiration and extracellular enzyme activities) and strong shifts in bacterial community composition (16S rRNA gene), whereas an increase in microbial biomass and activity and less pronounced effect on microbial diversity and community composition were seen at the lower reach. Second, at the lower reach we observed a quick spatial recovery (around 200 m downstream of the effluent) as most of the functions and community composition were similar to those from reference sites. On the other hand, bacterial community composition and water quality at the upper reach was still altered 1 km from the WWTP effluent. Our results indicate that biofilms in the upstream sites were more sensitive to the effect of WWTPs due to a lower degree of tolerance after a disturbance than communities located in more anthropogenically impacted sites.

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.

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 interact ...

There is now clear evidence that microorganisms present biogeographic patterns, yet the processes that create and maintain them are still not well understood. In particular, the contribution of dispersal and its exact impact on local community composition is still unclear. For example, dispersing cells may not thrive in recipient environments, but may still remain part of the local species pool. Here, we experimentally tested if marine bacteria can be retrieved from freshwater communities (pelagic and sediment) and the atmosphere by exposing bacteria from three lakes, that differ in their proximity to the Norwegian Sea, to marine conditions. We found that the percentage of freshwater taxa decreased with increasing salinities, whereas marine taxa increased along the same gradient. Our results further showed that this increase was stronger for lake and sediment compared with air communities. Further, significant increases in the average niche breadth of taxa were found for all sources, and in particular lake water and sediment communities, at higher salinities. Our results therefore suggests that marine taxa can readily grow from freshwater sources, but that the response was likely driven by the growth of habitat generalists that are typically found in marine systems. Finally, there was a greater proportion of marine taxa found in communities originating from the lake closest to the Norwegian Sea. In summary, this study shows that the interplay between bacterial dispersal limitation and dispersal from internal and external sources may have an important role for community recovery in response to environmental change.

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.

Many studies have shown that species sorting, that is, the selection by local environmental conditions is important for the composition and assembly of bacterial communities. On the other hand, there are other studies that could show that bacterial communities are neutrally assembled. In this study, we implemented a microcosm experiment with the aim to determine, at the same time, the importance of species sorting and neutral processes for bacterial community assembly during the colonisation of new, that is, sterile, habitats, by atmospheric bacteria. For this we used outdoor microcosms, which contained sterile medium from three different rock pools representing different environmental conditions, which were seeded by rainwater bacteria. We found some evidence for neutral assembly processes, as almost every 4th taxon growing in the microcosms was also detectable in the rainwater sample irrespective of the medium. Most of these taxa belonged to widespread families with opportunistic growth strategies, such as the Pseudomonadaceae and Comamonadaceae, indicating that neutrally assembled taxa may primarily be generalists. On the other hand, we also found evidence for species sorting, as one out of three media selected a differently composed bacterial community. Species sorting effects were relatively weak and established themselves via differences in relative abundance of generalists among the different media, as well as media-specific occurrences of a few specific taxa. In summary, our results suggest that neutral and species sorting processes interact during the assembly of bacterial communities and that their importance may differ depending on how many generalists and specialists are present in a community.

We present a survey on the distribution and habitat range of Polynucleobacter necessarius ssp. asymbioticus (PnecC), a numerically and functionally important taxon in the plankton of freshwater systems. We systematically sampled stagnant freshwater habitats in a heterogeneous 2000 km(2) area, together with ecologically different habitats outside this area. In total, 137 lakes, ponds and puddles were investigated, which represent an enormous diversity of habitats differing, e.g. in depth (< 10 cm-171 m) and pH (3.9-8.5). PnecC bacteria were detected by cultivation-independent methods in all investigated habitats, and their presence was confirmed by cultivation of strains from selected habitats representing the whole studied ecological range. The determined relative abundance of the subspecies ranged from values close to the detection limit of FISH (0.2%) to 67% (average 14.5%), and the highest observed absolute abundance was 5.3 x 10(6) cells ml(-1). Statistical analyses revealed that the abundance of PnecC bacteria was partially controlled by factors linked to concentrations of humic substances, which support the hypothesis that these bacteria utilize photodegradation products of humic substances. Based on the revealed statistical relationships, an average relative abundance of this subspecies of 20% in global freshwater habitats was extrapolated. Our study provides important implications for the current debate on ubiquity and biogeography in microorganisms.

Soil physicochemical properties and microbial communities are highly heterogeneous and vary widely over spatial scales, necessitating careful consideration of sampling strategies to provide representative and reproducible soil samples across field sites. To achieve this, the study aimed to establish appropriate sampling methodology and to determine links between the variability of parameters, utilising two sampling strategies. The first (design 1) involved extracting 25 cores from random locations throughout the field and pooling them into five sets of five cores. The second (design 2) involved a further 25 cores within five 1 m 2 sub-plots. Sub-samples from each sub-plot were pooled in order to determine between and within sub-plot variability. All samples were analysed independently and as pooled sub-samples. Results indicate that pooling spatially separated samples significantly reduced the variability in pH, compared to individual samples. Pooling samples from a small area resulted in lower within sub-plot variability than between sub-plots for pH and bacterial community composition assessed by terminalrestriction fragment length polymorphism analysis. Following multivariate statistical analysis, a large amount of variation in community composition was explained by soil pH, which is remarkable given the relatively small size of the sampling area and minor differences in pH. Moisture content was also important in determining bacterial communities in the random design (design 1). In the 1 m 2 sub-plot design (design 2), the spatial location of the plots explained a large degree of the variation in bacterial community composition between plots, which was due to spatial autocorrelation of pH and possible additional environmental parameters. This study emphasises the importance of sampling design for obtaining representative samples from soil.

Summary Resource availability is a key factor regulating biodiversity and ecosystem functioning, but the relationship between resource availability and diversity has only been rarely investigated in microbial communities. The aim of this study was to determine how diversity and community structure of a functional group of soil bacteria are influenced by resource concentration. To achieve this, we used soil microcosms to investigate degradation of benzoate, which served as a model compound, by soil bacterial communities. Microcosms were supplied with 13C-labelled benzoate at four concentrations and RNA-stable isotope probing followed by molecular fingerprinting analysis of 16S rRNA genes was employed to identify bacteria able to assimilate benzoate at different concentrations. The composition of the benzoate degrader community differed at different concentrations and there was a significant decrease in taxa evenness at the highest substrate concentration. Active organisms could be grouped into generalists, occurring at all substrate concentrations, specialists, active at one particular benzoate concentration only, and taxa that were active at either the two lowest or two highest concentrations. The study comprises the first explicit demonstration that resource availability has an effect on the diversity of a functional group of heterotrophic soil bacteria.

Bacteria are essential for many ecosystem services but our understanding of factors controlling their functioning is incomplete. While biodiversity has been identified as an important driver of ecosystem processes in macrobiotic communities, we know much less about bacterial communities. Due to the high diversity of bacterial communities, high functional redundancy is commonly proposed as explanation for a lack of clear effects of diversity. The generality of this claim has, however, been questioned. We present the results of an outdoor dilution-to-extinction experiment with four lake bacterial communities. The consequences of changes in bacterial diversity in terms of effective number of species, phylogenetic diversity, and functional diversity were studied for (1) bacterial abundance, (2) temporal stability of abundance, (3) nitrogen concentration, and (4) multifunctionality. We observed a richness gradient ranging from 15 to 280 operational taxonomic units (OTUs). Individual relationships between diversity and functioning ranged from negative to positive depending on lake, diversity dimension, and aspect of functioning. Only between phylogenetic diversity and abundance did we find a statistically consistent positive relationship across lakes. A literature review of 24 peer-reviewed studies that used dilution-to-extinction to manipulate bacterial diversity corroborated our findings: about 25% found positive relationships. Combined, these results suggest that bacteria-driven community functioning is relatively resistant to reductions in diversity.

It has been demonstrated that solar and particularly UV-radiation has strong effects on the production, activity and abundance of bacterioplankton, whereas effects on bacterial community composition (BCC) are unclear. We performed 3 independent experiments where humic water (either from a lake or a swamp) was incubated at different depths to create a gradient of intensity of exposure to natural solar radiation. Bacterial community composition, as assessed by terminal restriction fragment length polymorphism analysis (t-RFLP), changed gradually with increasing depth in parallel to decreasing sunlight exposure. Vertical changes in the production of dissolved inorganic carbon, oxygen consumption and bacterial production coincided with changes in BCC, suggesting a relationship between bacterial community composition and function.

The aim of this study was to compare two major hypotheses concerning the formation of bacterial community composition (BCC) at the local scale, i.e., whether BCC is determined by the prevailing local environmental conditions or by “metacommunity processes.” A batch culture experiment where bacteria from eight distinctly different aquatic habitats were regrown under identical conditions was performed to test to what extent similar communities develop under similar selective pressure. Differently composed communities emerged from different inoculum communities, as determined by terminal restriction fragment length polymorphism analysis of the 16S rRNA gene. There was no indication that similarity increased between communities upon growth under identical conditions compared to that for growth at the ambient sampling sites. This suggests that the history and distribution of taxa within the source communities were stronger regulating factors of BCC than the environmental conditions. Moreover, differently composed communities were different with regard to specific functions, such as enzyme activities, but maintained similar broad-scale functions, such as biomass production and respiration.

We performed food web manipulation experiments in three eutrophic Daphnia-dominated ponds, to compare the predation impact on planktonic bacteria exerted by metazoan and protozoan bacterial consumers. We analyzed the bacterial morphological composition by image analysis and the taxonomic composition by fluorescent in situ hybridization with group-specific oligonucleotide probes. The removal of Daphnia always resulted in a microbial succession in which first free-living bacteria and then heterotrophic nanoflagellates (HNFs) increased. Distinct stages of bacterial grazing either exclusively by Daphnia or by HNFs allowed a quantitative and qualitative comparison of their predation impact on the bacterial assemblage. Both bacterial consumers showed a strong size-selective impact that shifted the free-living bacterial community structure toward small cells. Suppression of bacterial biomass below the carrying capacity was similar with Daphnia or HNFs in one experiment and was significantly stronger with Daphnia as bacterial consumer in two experiments. This was due to the fact that bacteria that were resistant to protozoan predation partially compensated grazing mortality. Bacteria attached to aggregates and detrital particles were more important as grazing-resistant forms than bacterial filaments and constituted up to 50% of total bacterial biomass at the end of the experiments. Changes in predation pressure were also associated with shifts in bacterial community composition. Bacteria belonging to the beta subclass of the class Proteobacteria and to the Cytophaga/ Flavobacterium group dominated originally. The latter were most strongly reduced by HNF grazing, whereas other groups, in two experiments the alpha sublass (ALF) of Proteobacteria and in one experiment bacteria hybridizing with the probe for Archaea, even increased during HNF grazing. The composition also differed between bacteria associated with aggregates and freely suspended bacteria, the most obvious being the dominance of ALF growing on detrital aggregates. The experiments demonstrated that predation is a major structuring force for planktonic bacterial communities and that changes in predation regime probably have a much stronger impact on the structure of the bacterial community than on bacterial abundance and biomass.