Altitudinal patterns of diversity and functional traits of metabolically active microorganisms in stream biofilms

Wilhelm, Linda; Besemer, Katharina; Fragner, Lena; Peter, Hannes; Weckwerth, Wolfram; Battin, Tom J.

doi:10.1038/ismej.2015.56

Cited by 54 publications

(43 citation statements)

References 51 publications

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“…The study, which analysed 14 biofilms grown in laboratory-scale bioreactors mimicking the hyporheic zone, showed that the likelihood of sustaining such enzymatic multifunctionality decreases with decreasing microbial diversity, indicative of a low level of redundancy. Another study reconstructed artificial metagenomes to derive 140 orthologues related to carbohydrate and amino acid metabolism in benthic biofilms from alpine streams 81 . Analysing the association between inferred metabolic multifunctionality and bacterial diversity revealed a high degree of metabolic redundancy, which means that the biofilm microbiome is able to metabolize a wide range of DOM compounds in the streamwater, regardless of community composition.…”

Section: Diversity and Functionmentioning

confidence: 99%

The ecology and biogeochemistry of stream biofilms

et al. 2016

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The perception that most microorganisms live as complex communities that are attached to surfaces has profoundly changed microbiology over the past decades. Most, if not all, bacteria can form biofilms, which are communities of cells embedded in a porous extracellular matrix.Dental plaque, the microorganisms on catheters and implants that cause persistent infections and the fouling of ship hulls and pipework are all examples of biofilms with important implications for public health and industrial processes. Most contemporary biofilm research rests on the discovery made more than 35 years ago by Maurice Lock, Gill Geesey and Bill Costerton: bacteria attached to surfaces dominate microbial life in streams [1][2][3] . These microbiologists pioneered research into stream biofilms, also termed periphyton or epilithon, and described them as complex aggregates of bacteria, algae, protozoa, fungi and meiobenthos. The early study of stream biofilms also highlighted the relevance of interactions between microbial phototrophs and heterotrophs for energy fluxes and the role of the biofilm matrix as the site of extracellular enzyme activity and adsorption of dissolved organic matter (DOM) 3,4 .Since these early days, the study of the ecology and biogeochemistry of stream biofilms has slowly developed in the wake of thriving research on bacterial biofilms -often comprising 3 only a single strain, of interest to medical microbiology, rather than the polymicrobial communities found in stream biofilms -and on the microbial ecology of marine and lake planktonic communities 5 . Unlike bacterial biofilms grown in the laboratory, biofilms in streams are continuously exposed to a diverse inoculum that includes bacteria, archaea, algae, fungi, protozoa and even metazoa. These diverse biological 'building blocks', when combined with the dynamic flow of streamwater, generate biofilms with inherently complex and varying physical structures that have implications for microbial functioning and ecosystem processes 6 . In streams, biofilms are key sites of enzymatic activity 7 , including organic matter cycling, ecosystem respiration and primary production and, as such, form the basis of the food web.Why should we study the ecology and biogeochemistry of stream biofilms? Streams sculpt the continental surface, forming dense and conspicuous channel networks that can be thought of as ecological arteries that perfuse the landscape. Streams are connected to their catchments through various surface and subsurface flow paths and notably through the hyporheic zone in the streambed at the interface between groundwater and streamwater 8 . Microbial cells, solutes and particles enter streams through these flow paths and, en route to downstream ecosystems and ultimately to the oceans, they may interact with the biofilms that colonize the large surface area provided by the streambed as a 'microbial skin' (BOX 1). As a result, the streambed and its biofilm microbiome contribute to biogeochemical fluxes 8 . Indeed, stream biofilms are now recognized as su...

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Section: Diversity and Functionmentioning

confidence: 99%

The ecology and biogeochemistry of stream biofilms

et al. 2016

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“…The few recent studies considering such land-water linkages have shown not only that this connectivity with the terrestrial environment may influence aquatic microbial communities by providing nutrients and dissolved organic matter of different quality (Besemer et al, 2013;Berggren and del Giorgio, 2015;Ruiz-González et al, 2015a;Wilhelm et al, 2015), but also that the immigration of microbes from the surrounding catchment can largely explain the local composition of the receiving community. For example, terrestrial runoff causes the advection of high numbers of bacterial taxa to aquatic bodies, and consequently the systems most tightly connected to the landscape will be more strongly influenced by this transport of terrestrial bacteria.…”

Section: Introductionmentioning

confidence: 99%

Contrasting dynamics and environmental controls of dispersed bacteria along a hydrologic gradient

et al. 2017

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Freshwater bacterioplankton communities are influenced by the transport of bacteria from the surrounding terrestrial environments. It has been shown that, although most of these dispersed bacteria gradually disappear along the hydrologic continuum, some can thrive in aquatic systems and become dominant, leading to a gradual succession of communities. Here we aimed at exploring the environmental factors driving the structure of such contrasting bacterial populations as well as their functional properties. Using Illumina sequencing of the 16S rRNA gene, we characterized the taxonomic composition of bacterioplankton communities from 10 streams and rivers in Québec spanning the whole hydrologic continuum (river Strahler order 0 to 7), which were sampled in two occasions. With the aim to understand the fate and controls of the transported bacteria, among the taxa present at the origin of the hydrologic gradient (i.e., in the smallest headwater streams) we identified two types of dynamics: i) 'Tourist' taxa, which were those that decreased in abundance from the headwaters towards the largest rivers, and ii) 'Seed' taxa, those that increased their abundances along the hydrologic continuum. Communities changed gradually from the fast-flowing headwater streams dominated by 'Tourist' taxa (ca. 95% of the sequences) towards the largest rivers (Strahler order 4-7) where 'Seed' taxa comprised up to 80% of community sequences. Variation in taxonomic composition of the communities dominated by 'Tourist' taxa in streams seemed related to different degree of terrestrial inputs, whereas compositional changes in 'Seed' communities in the large rivers were linked to differences in autochthonous processes. Finally, the two types of communities differed significantly in their metabolic potential assessed through Biolog Ecoplates. All this suggests that hydrologic transport modulates the gradual replacement of two contrasting population types subjected to different environmental controls and with different metabolic potentials. Moreover, we show that the separate exploration of the two pools of taxa allows unveiling environmental drivers and processes operating on them that remain hidden if explored at the whole community level.

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“…Finger et al, 2012;Majone et al, 2016), determines the habitat suitability of numerous aquatic organisms (e.g. Short and Ward, 1980;Hari et al, 2006;Wilhelm et al, 2015;Padilla et al, 2015) and even plays a noticeable role in the global emission of carbon dioxide into the atmosphere (Butman and Raymond, 2011;Raymond et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

StreamFlow 1.0: an extension to the spatially distributed snow model Alpine3D for hydrological modelling and deterministic stream temperature prediction

Gallice

Bavay²,

Brauchli

et al. 2016

Geosci. Model Dev.

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Abstract. Climate change is expected to strongly impact the hydrological and thermal regimes of Alpine rivers within the coming decades. In this context, the development of hydrological models accounting for the specific dynamics of Alpine catchments appears as one of the promising approaches to reduce our uncertainty of future mountain hydrology. This paper describes the improvements brought to StreamFlow, an existing model for hydrological and stream temperature prediction built as an external extension to the physically based snow model Alpine3D. StreamFlow's source code has been entirely written anew, taking advantage of object-oriented programming to significantly improve its structure and ease the implementation of future developments. The source code is now publicly available online, along with a complete documentation. A special emphasis has been put on modularity during the re-implementation of StreamFlow, so that many model aspects can be represented using different alternatives. For example, several options are now available to model the advection of water within the stream. This allows for an easy and fast comparison between different approaches and helps in defining more reliable uncertainty estimates of the model forecasts. In particular, a case study in a Swiss Alpine catchment reveals that the stream temperature predictions are particularly sensitive to the approach used to model the temperature of subsurface flow, a fact which has been poorly reported in the literature to date. Based on the case study, StreamFlow is shown to reproduce hourly mean discharge with a Nash-Sutcliffe efficiency (NSE) of 0.82 and hourly mean temperature with a NSE of 0.78.

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Altitudinal patterns of diversity and functional traits of metabolically active microorganisms in stream biofilms

Cited by 54 publications

References 51 publications

The ecology and biogeochemistry of stream biofilms

The ecology and biogeochemistry of stream biofilms

Contrasting dynamics and environmental controls of dispersed bacteria along a hydrologic gradient

StreamFlow 1.0: an extension to the spatially distributed snow model Alpine3D for hydrological modelling and deterministic stream temperature prediction

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