Treeline displacement may affect lake dissolved organic matter processing at high latitudes and altitudes

Climate change induced shifts in treeline position, both towards higher altitudes and latitudes induce changes in soil organic matter. Eventually, soil organic matter is transported to alpine and subarctic lakes with yet unknown consequences for dissolved organic matter (DOM) diversity and processing. Here, we experimentally investigate the consequences of treeline shifts by amending subarctic and temperate alpine lake water with soil-derived DOM from above and below the treeline. We use ultra-high resolution mass spectrometry (FT-ICR MS) to track molecular DOM diversity (i.e., chemodiversity), estimate DOM decay and measure bacterial growth efficiency. In both lakes, soil-derived DOM from below the treeline increases lake DOM chemodiversity mainly through the enrichment with polyphenolic and highly unsaturated compounds. These compositional changes are associated with reductions in bulk and compound-level DOM reactivity and reduced bacterial growth efficiency. Our results suggest that treeline advancement has the potential to enrich a large number of lake ecosystems with less biodegradable DOM, affecting bacterial community function and potentially altering the biogeochemical cycling of carbon in lakes at high latitudes and altitudes.

The cost of adaptability: resource availability constrains functional stability under pulsed disturbances

Global change exposes ecosystems to changes in the frequency, magnitude, and concomitancy of disturbances, which impact the composition and functioning of these systems. Here, we experimentally evaluate the effects of salinity disturbances and eutrophication on bacterial communities from coastal ecosystems. The functional stability of these communities is critically important for maintaining water quality, productivity, and ecosystem services, such as fishery yields. Microbial functional stability can be maintained via resistance and resilience, which are reflected in genomic traits such as genome size and codon usage bias and may be linked to metabolic costs. However, little is known about the mechanisms that select these traits under varying nutrient regimes. To study the impact of pulsed disturbances on community assembly and functioning depending on metabolic costs, we performed a 41-day pulse disturbance experiment across two levels of resource availability. Our setup triggered stochastic community re-assembly processes in all treatments. In contrast, we observed consistent and resource availability-dependent patterns of superordinate community functioning and structural patterns, such as functional resistance in response to disturbances, genomic trait distributions, and species diversity. Predicted genomic traits reflected the selection for taxa possessing resistant- and resilience-related traits, particularly under high nutrient availability. Our findings are a step toward unraveling the compositional and genomic underpinnings of functional resistance in microbial communities after exposure to consecutive pulse disturbances. Our work demonstrates how resource availability alleviates metabolic constraints on resistance and resilience, and this has important consequences for predicting water quality and ecosystem productivity of environments exposed to global change.

IMPORTANCE

Understanding the communities' responses to disturbances is a prerequisite to predicting ecosystem dynamics and, thus, highly relevant considering global change. Microbial communities play key roles in numerous ecosystem functions and services, and the large diversity, rapid growth, and phenotypic plasticity of microorganisms are thought to allow high resistance and resilience. While potential metabolic costs associated with adaptations to fluctuating environments have been debated, little evidence supports trade-offs between resource availability, resistance, and resilience. Here, we experimentally assessed the compositional and functional responses of an aquatic microbial model community to disturbances and systematically manipulated resource availability. Our results demonstrate that the capacity to tolerate environmental fluctuations is constrained by resource availability and reflected in the selection of genomic traits.

Picoflare jets power the solar wind emerging from a coronal hole on the Sun

Coronal holes are areas on the Sun with open magnetic field lines. They are a source region of the solar wind, but how the wind emerges from coronal holes is not known. We observed a coronal hole using the Extreme Ultraviolet Imager on the Solar Orbiter spacecraft. We identified jets on scales of a few hundred kilometers, which last 20 to 100 seconds and reach speeds of ~100 kilometers per second. The jets are powered by magnetic reconnection and have kinetic energy in the picoflare range. They are intermittent but widespread within the observed coronal hole. We suggest that such picoflare jets could produce enough high-temperature plasma to sustain the solar wind and that the wind emerges from coronal holes as a highly intermittent outflow at small scales.

The dark side of the moon: first insights into the microbiome structure and function of one of the last glacier-fed streams in Africa

The glaciers on Africa's 'Mountains of the Moon' (Rwenzori National Park, Uganda) are predicted to disappear within the next decades owing to climate change. Consequently, the glacier-fed streams (GFSs) that drain them will vanish, along with their resident microbial communities. Despite the relevance of microbial communities for performing ecosystem processes in equatorial GFSs, their ecology remains understudied. Here, we show that the benthic microbiome from the Mt. Stanley GFS is distinct at several levels from other GFSs. Specifically, several novel taxa were present, and usually common groups such as Chrysophytes and Polaromonas exhibited lower relative abundances compared to higher-latitude GFSs, while cyanobacteria and diatoms were more abundant. The rich primary producer community in this GFS likely results from the greater environmental stability of the Afrotropics, and accordingly, heterotrophic processes dominated in the bacterial community. Metagenomics revealed that almost all prokaryotes in the Mt. Stanley GFS are capable of organic carbon oxidation, while greater than 80% have the potential for fermentation and acetate oxidation. Our findings suggest a close coupling between photoautotrophs and other microbes in this GFS, and provide a glimpse into the future for high-latitude GFSs globally where primary production is projected to increase with ongoing glacier shrinkage.

Ultra-high-resolution observations of persistent null-point reconnection in the solar corona

Magnetic reconnection is a key mechanism involved in solar eruptions and is also a prime possibility to heat the low corona to millions of degrees. Here, we present ultra-high-resolution extreme ultraviolet observations of persistent null-point reconnection in the corona at a scale of about 390 km over one hour observations of the Extreme-Ultraviolet Imager on board Solar Orbiter spacecraft. The observations show formation of a null-point configuration above a minor positive polarity embedded within a region of dominant negative polarity near a sunspot. The gentle phase of the persistent null-point reconnection is evidenced by sustained point-like high-temperature plasma (about 10 MK) near the null-point and constant outflow blobs not only along the outer spine but also along the fan surface. The blobs appear at a higher frequency than previously observed with an average velocity of about 80 km s^-1 and life-times of about 40 s. The null-point reconnection also occurs explosively but only for 4 minutes, its coupling with a mini-filament eruption generates a spiral jet. These results suggest that magnetic reconnection, at previously unresolved scales, proceeds continually in a gentle and/or explosive way to persistently transfer mass and energy to the overlying corona.

Glacier-Fed Stream Biofilms Harbor Diverse Resistomes and Biosynthetic Gene Clusters

Antimicrobial resistance (AMR) is a universal phenomenon the origins of which lay in natural ecological interactions such as competition within niches, within and between micro- to higher-order organisms. To study these phenomena, it is crucial to examine the origins of AMR in pristine environments, i.e., limited anthropogenic influences. In this context, epilithic biofilms residing in glacier-fed streams (GFSs) are an excellent model system to study diverse, intra- and inter-domain, ecological crosstalk. We assessed the resistomes of epilithic biofilms from GFSs across the Southern Alps (New Zealand) and the Caucasus (Russia) and observed that both bacteria and eukaryotes encoded twenty-nine distinct AMR categories. Of these, beta-lactam, aminoglycoside, and multidrug resistance were both abundant and taxonomically distributed in most of the bacterial and eukaryotic phyla. AMR-encoding phyla included Bacteroidota and Proteobacteria among the bacteria, alongside Ochrophyta (algae) among the eukaryotes. Additionally, biosynthetic gene clusters (BGCs) involved in the production of antibacterial compounds were identified across all phyla in the epilithic biofilms. Furthermore, we found that several bacterial genera (Flavobacterium, Polaromonas, Superphylum Patescibacteria) encode both atimicrobial resistance genes (ARGs) and BGCs within close proximity of each other, demonstrating their capacity to simultaneously influence and compete within the microbial community. Our findings help unravel how naturally occurring BGCs and AMR contribute to the epilithic biofilms mode of life in GFSs. Additionally, we report that eukaryotes may serve as AMR reservoirs owing to their potential for encoding ARGs. Importantly, these observations may be generalizable and potentially extended to other environments that may be more or less impacted by human activity. IMPORTANCE Antimicrobial resistance is an omnipresent phenomenon in the anthropogenically influenced ecosystems. However, its role in shaping microbial community dynamics in pristine environments is relatively unknown. Using metagenomics, we report the presence of antimicrobial resistance genes and their associated pathways in epilithic biofilms within glacier-fed streams. Importantly, we observe biosynthetic gene clusters associated with antimicrobial resistance in both pro- and eukaryotes in these biofilms. Understanding the role of resistance in the context of this pristine environment and complex biodiversity may shed light on previously uncharacterized mechanisms of cross-domain interactions.

Spatial patterns of benthic biofilm diversity among streams draining proglacial floodplains

Glacier shrinkage opens new proglacial terrain with pronounced environmental gradients along longitudinal and lateral chronosequences. Despite the environmental harshness of the streams that drain glacier forelands, their benthic biofilms can harbor astonishing biodiversity spanning all domains of life. Here, we studied the spatial dynamics of prokaryotic and eukaryotic photoautotroph diversity within braided glacier-fed streams and tributaries draining lateral terraces predominantly fed by groundwater and snowmelt across three proglacial floodplains in the Swiss Alps. Along the lateral chronosequence, we found that benthic biofilms in tributaries develop higher biomass than those in glacier-fed streams, and that their respective diversity and community composition differed markedly. We also found spatial turnover of bacterial communities in the glacier-fed streams along the longitudinal chronosequence. These patterns along the two chronosequences seem unexpected given the close spatial proximity and connectivity of the various streams, suggesting environmental filtering as an underlying mechanism. Furthermore, our results suggest that photoautotrophic communities shape bacterial communities across the various streams, which is understandable given that algae are the major source of organic matter in proglacial streams. Overall, our findings shed new light on benthic biofilms in proglacial streams now changing at rapid pace owing to climate-induced glacier shrinkage.

The microbiome of cryospheric ecosystems

The melting of the cryosphere is among the most conspicuous consequences of climate change, with impacts on microbial life and related biogeochemistry. However, we are missing a systematic understanding of microbiome structure and function across cryospheric ecosystems. Here, we present a global inventory of the microbiome from snow, ice, permafrost soils, and both coastal and freshwater ecosystems under glacier influence. Combining phylogenetic and taxonomic approaches, we find that these cryospheric ecosystems, despite their particularities, share a microbiome with representatives across the bacterial tree of life and apparent signatures of early and constrained radiation. In addition, we use metagenomic analyses to define the genetic repertoire of cryospheric bacteria. Our work provides a reference resource for future studies on climate change microbiology.

The cryosphere includes those parts of Earth where water or soil is frozen, such as snow, ice, glaciers and permafrost soils. Here, the authors present a global inventory of cryospheric microbial communities and their genetic repertoires.

Glacier shrinkage will accelerate downstream decomposition of organic matter and alters microbiome structure and function

The shrinking of glaciers is among the most iconic consequences of climate change. Despite this, the downstream consequences for ecosystem processes and related microbiome structure and function remain poorly understood. Here, using a space-for-time substitution approach across 101 glacier-fed streams (GFSs) from six major regions worldwide, we investigated how glacier shrinkage is likely to impact the organic matter (OM) decomposition rates of benthic biofilms. To do this, we measured the activities of five common extracellular enzymes and estimated decomposition rates by using enzyme allocation equations based on stoichiometry. We found decomposition rates to average 0.0129 (% d^-1 ), and that decreases in glacier influence (estimated by percent glacier catchment coverage, turbidity, and a glacier index) accelerates decomposition rates. To explore mechanisms behind these relationships, we further compared decomposition rates with biofilm and stream water characteristics. We found that chlorophyll-a, temperature, and stream water N:P together explained 61% of the variability in decomposition. Algal biomass, which is also increasing with glacier shrinkage, showed a particularly strong relationship with decomposition, likely indicating their importance in contributing labile organic compounds to these carbon-poor habitats. We also found high relative abundances of chytrid fungi in GFS sediments, which putatively parasitize these algae, promoting decomposition through a fungal shunt. Exploring the biofilm microbiome, we then sought to identify bacterial phylogenetic clades significantly associated with decomposition, and found numerous positively (e.g., Saprospiraceae) and negatively (e.g., Nitrospira) related clades. Lastly, using metagenomics, we found evidence of different bacterial classes possessing different proportions of EEA-encoding genes, potentially informing some of the microbial associations with decomposition rates. Our results, therefore, present new mechanistic insights into OM decomposition in GFSs by demonstrating that an algal-based "green food web" is likely to increase in importance in the future and will promote important biogeochemical shifts in these streams as glaciers vanish.

Genomic and metabolic adaptations of biofilms to ecological windows of opportunity in glacier-fed streams

In glacier-fed streams, ecological windows of opportunity allow complex microbial biofilms to develop and transiently form the basis of the food web, thereby controlling key ecosystem processes. Using metagenome-assembled genomes, we unravel strategies that allow biofilms to seize this opportunity in an ecosystem otherwise characterized by harsh environmental conditions. We observe a diverse microbiome spanning the entire tree of life including a rich virome. Various co-existing energy acquisition pathways point to diverse niches and the exploitation of available resources, likely fostering the establishment of complex biofilms during windows of opportunity. The wide occurrence of rhodopsins, besides chlorophyll, highlights the role of solar energy capture in these biofilms while internal carbon and nutrient cycling between photoautotrophs and heterotrophs may help overcome constraints imposed by oligotrophy in these habitats. Mechanisms potentially protecting bacteria against low temperatures and high UV-radiation are also revealed and the selective pressure of this environment is further highlighted by a phylogenomic analysis differentiating important components of the glacier-fed stream microbiome from other ecosystems. Our findings reveal key genomic underpinnings of adaptive traits contributing to the success of complex biofilms to exploit environmental opportunities in glacier-fed streams, which are now rapidly changing owing to global warming.

Viral diversity is linked to bacterial community composition in alpine stream biofilms

Biofilms play pivotal roles in fluvial ecosystems, yet virtually nothing is known about viruses in these communities. Leveraging an optimized sample-to-sequence pipeline, we studied the spatiotemporal turnover of dsDNA viruses associated with stream biofilms and found an astounding diversity to be structured by seasons and along the longitudinal gradient in the stream. While some vOTUs were region- or season-specific, we also identified a large group of permanent biofilm phages, taxonomically dominated by Myoviridae. Comparison of the observed viral distribution with predictions based on neutral community assembly indicated that chance and dispersal may be important for structuring stream biofilm viral communities. Deviation from neutral model predictions suggests that certain phages distribute efficiently across distant locations within the stream network. This dispersal capacity appears to be linked to EPS depolymerases that enable phages to efficiently overcome the biofilm barrier. Other phages, particularly vOTUs classified as Siphoviridae, appear locally overrepresented and to rely on a lysogenic life cycle, potentially to exploit the spatial distribution of bacterial populations in stream biofilms. Overall, biofilm viral and bacterial community turnover were significantly coupled. Yet, viral communities were linked to the presence of the most abundant bacterial community members. With this work, we provide a foundational ecological perspective on factors that structure viral diversity in stream biofilms and identify potentially important viral traits related to the biofilm mode of life.

Microdiversity characterizes prevalent phylogenetic clades in the glacier-fed stream microbiome

Glacier-fed streams (GFSs) are extreme and rapidly vanishing ecosystems, and yet they harbor diverse microbial communities. Although our understanding of the GFS microbiome has recently increased, we do not know which microbial clades are ecologically successful in these ecosystems, nor do we understand potentially underlying mechanisms. Ecologically successful clades should be more prevalent across GFSs compared to other clades, which should be reflected as clade-wise distinctly low phylogenetic turnover. However, methods to assess such patterns are currently missing. Here we developed and applied a novel analytical framework, “phyloscore analysis”, to identify clades with lower spatial phylogenetic turnover than other clades in the sediment microbiome across twenty GFSs in New Zealand. These clades constituted up to 44% and 64% of community α-diversity and abundance, respectively. Furthermore, both their α-diversity and abundance increased as sediment chlorophyll a decreased, corroborating their ecological success in GFS habitats largely devoid of primary production. These clades also contained elevated levels of putative microdiversity than others, which could potentially explain their high prevalence in GFSs. This hitherto unknown microdiversity may be threatened as glaciers shrink, urging towards further genomic and functional exploration of the GFS microbiome.

Morphogenesis and oxygen dynamics in phototrophic biofilms growing across a gradient of hydraulic conditions

Biofilms are surface-attached and matrix-enclosed microbial communities that dominate microbial life in numerous ecosystems. Using flumes and automated optical coherence tomography, we studied the morphogenesis of phototrophic biofilms along a gradient of hydraulic conditions. Compact and coalescent biofilms formed under elevated bed shear stress, whereas protruding clusters separated by troughs formed under reduced shear stress. This morphological differentiation did not linearly follow the hydraulic gradient, but a break point emerged around a shear stress of ~0.08 Pa. While community composition did not differ between high and low shear environments, our results suggest that the morphological differentiation was linked to biomass displacement and reciprocal interactions between the biofilm structure and hydraulics. Mapping oxygen concentrations within and around biofilm structures, we provide empirical evidence for biofilm-induced alterations of oxygen mass transfer. Our findings suggest that architectural plasticity, efficient mass transfer, and resistance to shear stress contribute to the success of phototrophic biofilms.

Patterns and Drivers of Extracellular Enzyme Activity in New Zealand Glacier-Fed Streams

Glacier-fed streams (GFSs) exhibit near-freezing temperatures, variable flows, and often high turbidities. Currently, the rapid shrinkage of mountain glaciers is altering the delivery of meltwater, solutes, and particulate matter to GFSs, with unknown consequences for their ecology. Benthic biofilms dominate microbial life in GFSs, and play a major role in their biogeochemical cycling. Mineralization is likely an important process for microbes to meet elemental budgets in these systems due to commonly oligotrophic conditions, and extracellular enzymes retained within the biofilm enable the degradation of organic matter and acquisition of carbon (C), nitrogen (N), and phosphorus (P). The measurement and comparison of these extracellular enzyme activities (EEA) can in turn provide insight into microbial elemental acquisition effort relative to environmental availability. To better understand how benthic biofilm communities meet resource demands, and how this might shift as glaciers vanish under climate change, we investigated biofilm EEA in 20 GFSs varying in glacier influence from New Zealand’s Southern Alps. Using turbidity and distance to the glacier snout normalized for glacier size as proxies for glacier influence, we found that bacterial abundance (BA), chlorophyll a (Chl a), extracellular polymeric substances (EPS), and total EEA per gram of sediment increased with decreasing glacier influence. Yet, when normalized by BA, EPS decreased with decreasing glacier influence, Chl a still increased, and there was no relationship with total EEA. Based on EEA ratios, we found that the majority of GFS microbial communities were N-limited, with a few streams of different underlying bedrock geology exhibiting P-limitation. Cell-specific C-acquiring EEA was positively related to the ratio of Chl a to BA, presumably reflecting the utilization of algal exudates. Meanwhile, cell-specific N-acquiring EEA were positively correlated with the concentration of dissolved inorganic nitrogen (DIN), and both N- and P-acquiring EEA increased with greater cell-specific EPS. Overall, our results reveal greater glacier influence to be negatively related to GFS biofilm biomass parameters, and generally associated with greater microbial N demand. These results help to illuminate the ecology of GFS biofilms, along with their biogeochemical response to a shifting habitat template with ongoing climate change.

Combining Fluidic Devices with Microscopy and Flow Cytometry to Study Microbial Transport in Porous Media Across Spatial Scales

Understanding the transport, dispersion and deposition of microorganisms in porous media is a complex scientific task comprising topics as diverse as hydrodynamics, ecology and environmental engineering. Modeling bacterial transport in porous environments at different spatial scales is critical to better predict the consequences of bacterial transport, yet current models often fail to up-scale from laboratory to field conditions. Here, we introduce experimental tools to study bacterial transport in porous media at two spatial scales. The aim of these tools is to obtain macroscopic observables (such as breakthrough curves or deposition profiles) of bacteria injected into transparent porous matrices. At the small scale (10-1000 µm), microfluidic devices are combined with optical video-microscopy and image processing to obtain breakthrough curves and, at the same time, to track individual bacterial cells at the pore scale. At larger scale, flow cytometry is combined with a self-made robotic dispenser to obtain breakthrough curves. We illustrate the utility of these tools to better understand how bacteria are transported in complex porous media such as the hyporheic zone of streams. As these tools provide simultaneous measurements across scales, they pave the way for mechanism-based models, critically important for upscaling. Application of these tools may not only contribute to the development of novel bioremediation applications but also shed new light on the ecological strategies of microorganisms colonizing porous substrates.

Optimised biomolecular extraction for metagenomic analysis of microbial biofilms from high-mountain streams

Glacier-fed streams (GFS) are harsh ecosystems dominated by microbial life organized in benthic biofilms, yet the biodiversity and ecosystem functions provided by these communities remain under-appreciated. To better understand the microbial processes and communities contributing to GFS ecosystems, it is necessary to leverage high throughput sequencing. Low biomass and high inorganic particle load in GFS sediment samples may affect nucleic acid extraction efficiency using extraction methods tailored to other extreme environments such as deep-sea sediments. Here, we benchmarked the utility and efficacy of four extraction protocols, including an up-scaled phenol-chloroform protocol. We found that established protocols for comparable sample types consistently failed to yield sufficient high-quality DNA, delineating the extreme character of GFS. The methods differed in the success of downstream applications such as library preparation and sequencing. An adapted phenol-chloroform-based extraction method resulted in higher yields and better recovered the expected taxonomic profile and abundance of reconstructed genomes when compared to commercially-available methods. Affordable and straight-forward, this method consistently recapitulated the abundance and genomes of a mock community, including eukaryotes. Moreover, by increasing the amount of input sediment, the protocol is readily adjustable to the microbial load of the processed samples without compromising protocol efficiency. Our study provides a first systematic and extensive analysis of the different options for extraction of nucleic acids from glacier-fed streams for high-throughput sequencing applications, which may be applied to other extreme environments.

Microbial Ecology of Methanotrophy in Streams Along a Gradient of CH4 Availability

Despite the recognition of streams and rivers as sources of methane (CH₄) to the atmosphere, the role of CH₄ oxidation (MOX) in these ecosystems remains poorly understood to date. Here, we measured the kinetics of MOX in stream sediments of 14 sites to resolve the ecophysiology of CH₄ oxidizing bacteria (MOB) communities. The streams cover a gradient of land cover and associated physicochemical parameter and differed in stream- and porewater CH₄ concentrations. Michealis–Menten kinetic parameter of MOX, maximum reaction velocity (V_max), and CH₄ concentration at half V_max (K_S) increased with CH₄ supply. K_S values in the micromolar range matched the CH₄ concentrations measured in shallow stream sediments and indicate that MOX is mostly driven by low-affinity MOB. 16S rRNA gene sequencing identified MOB classified as Methylococcaceae and particularly Crenothrix. Their relative abundance correlated with pmoA gene counts and MOX rates, underscoring their pivotal role as CH₄ oxidizers in stream sediments. Building on the concept of enterotypes, we identify two distinct groups of co-occurring MOB. While there was no taxonomic difference among the members of each cluster, one cluster contained abundant and common MOB, whereas the other cluster contained rare operational taxonomic units (OTUs) specific to a subset of streams. These integrated analyses of changes in MOB community structure, gene abundance, and the corresponding ecosystem process contribute to a better understanding of the distal controls on MOX in streams.

Trait-specific dispersal of bacteria in heterogeneous porous environments: from pore to porous medium scale

The dispersal of organisms controls the structure and dynamics of populations and communities, and can regulate ecosystem functioning. Predicting dispersal patterns across scales is important to understand microbial life in heterogeneous porous environments such as soils and sediments. We developed a multi-scale approach, combining experiments with microfluidic devices and time-lapse microscopy to track individual bacterial trajectories and measure the overall breakthrough curves and bacterial deposition profiles: we, then, linked the two scales with a novel stochastic model. We show that motile cells of Pseudomonas putida disperse more efficiently than non-motile mutants through a designed heterogeneous porous system. Motile cells can evade flow-imposed trajectories, enabling them to explore larger pore areas than non-motile cells. While transported cells exhibited a rotation in response to hydrodynamic shear, motile cells were less susceptible to the torque, maintaining their body oriented towards the flow direction and thus changing the population velocity distribution with a significant impact on the overall transport properties. We also found, in a separate set of experiments, that if the suspension flows through a porous system already colonized by a biofilm, P. putida cells are channelled into preferential flow paths and the cell attachment rate is increased. These two effects were more pronounced for non-motile than for motile cells. Our findings suggest that motility coupled with heterogeneous flows can be beneficial to motile bacteria in confined environments as it enables them to actively explore the space for resources or evade regions with unfavourable conditions. Our study also underlines the benefit of a multi-scale approach to the study of bacterial dispersal in porous systems.

Benchmarking protocols for the metagenomic analysis of stream biofilm viromes

Viruses drive microbial diversity, function and evolution and influence important biogeochemical cycles in aquatic ecosystems. Despite their relevance, we currently lack an understanding of their potential impacts on stream biofilm structure and function. This is surprising given the critical role of biofilms for stream ecosystem processes. Currently, the study of viruses in stream biofilms is hindered by the lack of an optimized protocol for their extraction, concentration and purification. Here, we evaluate a range of methods to separate viral particles from stream biofilms, and to concentrate and purify them prior to DNA extraction and metagenome sequencing. Based on epifluorescence microscopy counts of viral-like particles (VLP) and DNA yields, we optimize a protocol including treatment with tetrasodium pyrophosphate and ultra-sonication to disintegrate biofilms, tangential-flow filtration to extract and concentrate VLP, followed by ultracentrifugation in a sucrose density gradient to isolate VLP from the biofilm slurry. Viromes derived from biofilms sampled from three different streams were dominated by Siphoviridae, Myoviridae and Podoviridae and provide first insights into the viral diversity of stream biofilms. Our protocol optimization provides an important step towards a better understanding of the ecological role of viruses in stream biofilms.

Automated 3D Optical Coherence Tomography to Elucidate Biofilm Morphogenesis Over Large Spatial Scales

Biofilms are a most successful microbial lifestyle and prevail in a multitude of environmental and engineered settings. Understanding biofilm morphogenesis, that is the structural diversification of biofilms during community assembly, represents a remarkable challenge across spatial and temporal scales. Here, we present an automated biofilm imaging system based on optical coherence tomography (OCT). OCT is an emerging imaging technique in biofilm research. However, the amount of data that currently can be acquired and processed hampers the statistical inference of large scale patterns in biofilm morphology. The automated OCT imaging system allows covering large spatial and extended temporal scales of biofilm growth. It combines a commercially available OCT system with a robotic positioning platform and a suite of software solutions to control the positioning of the OCT scanning probe, as well as the acquisition and processing of 3D biofilm imaging datasets. This setup allows the in situ and non-invasive automated monitoring of biofilm development and may be further developed to couple OCT imaging with macrophotography and microsensor profiling.

Importance of mixotrophic flagellates during the ice-free season in lakes located along an elevational gradient

Mixotrophy seems to be widespread among phytoplankton, but whether this strategy is more relevant in oligotrophic lakes remains unclear. Here, we tested the hypothesis that the relative abundance of mixotrophic flagellates in lakes increases along an elevational gradient paralleling increasingly oligotrophic conditions. For this purpose, 12 lakes located between 575 and 2796 m above sea level were sampled in summer and fall to include two different seasonal windows in phytoplankton dynamics and environmental conditions. The degree of mixotrophy in phytoplankton was estimated in tracer experiments using fluorescently-labeled bacteria and done with composite samples collected in the euphotic zone and in samples obtained from the chlorophyll-a maximum. The results indicated the existence of a positive trend particularly in summer in the relative abundance of mixotrophic flagellates with elevation, however, this trend was not linear, and exceptions along the elevational gradient were found. Changes in the relative abundance of mixotrophic flagellates were related with significant changes in water transparency, DOC and phosphorus concentrations, as well as in bacterial and flagellate abundance. Overall, our results reveal that the harsh growth conditions found in oligotrophic high mountain lakes favor a mixotrophic trophic strategy among phytoplankton.

Unraveling the biophysical underpinnings to the success of multispecies biofilms in porous environments

Biofilms regulate critical processes in porous ecosystems. However, the biophysical underpinnings of the ecological success of these biofilms are poorly understood. Combining experiments with fluidic devices, sequencing and modeling, we reveal that architectural plasticity enhances space exploitation by multispecies biofilms in porous environments. Biofilms consistently differentiated into an annular base biofilm coating the grains and into streamers protruding from the grains into the pore space. Although different flow-related processes governed the differentiation of these architectures, both BB and streamers were composed of similar bacterial assemblages. This is evidence for architectural plasticity. Architectural plasticity allowed for complementary use of the space provided by the grain–pore complexes, which increased biofilm carrying capacity at the larger scale of the porous system. This increase comes potentially at the cost of a tradeoff. Contrasting time scales of oxygen replenishment and consumption, we show that streamers locally inhibit the growth of the BB downstream from the grains. Our study provides first insights into the biophysical underpinnings to the success of multispecies biofilms in porous environments.

Environmental heterogeneity promotes spatial resilience of phototrophic biofilms in streambeds

The loss of environmental heterogeneity threatens biodiversity and ecosystem functioning. It is therefore important to understand the relationship between environmental heterogeneity and spatial resilience as the capacity of ecological communities embedded in a landscape matrix to reorganize following disturbance. We experimented with phototrophic biofilms colonizing streambed landscapes differing in spatial heterogeneity and exposed to flow-induced disturbance. We show how streambed roughness and related features promote growth-related trait diversity and the recovery of biofilms towards carrying capacity (CC) and spatial resilience. At the scale of streambed landscapes, roughness and exposure to water flow promoted biofilm CC and growth trait diversity. Structural equation modelling identified roughness, post-disturbance biomass and a ‘neighbourhood effect’ to drive biofilm CC. Our findings suggest that the environment selecting for adaptive capacities prior to disturbance (that is, memory effects) and biofilm connectivity into spatial networks (that is, mobile links) contribute to the spatial resilience of biofilms in streambed landscapes. These findings are critical given the key functions biofilms fulfil in streams, now increasingly experiencing shifts in sedimentary and hydrological regimes.

Abstract P6-08-22: Frequency of equivocal Her2-test results after revision of the ASCO/CAP guidelines in a real-world setting. Results of a prospective cross-sectional study of primary breast cancers in Germany

Background

In 2013 the ASCO/CAP Guidelines for HER2 testing were updated and revised to improve the accuracy of Her2 testing and its utility as a predictive marker in breast cancer. In this prospective cross-sectional study, we assessed the proportion of Her2 positive and equivocal cases in a real-world setting in Germany. Patients' characteristics and tumor biological factors were evaluated. Furthermore, we analyzed the effect of the updated recommendations on the clinical management.

Methods

This IRB approved prospective analysis included patients with primary breast cancer. Patients with primary stage IV and recurrent breast cancer were excluded. Data was collected from 2012-2017 in six certified breast centers using a personal questionnaire and data from the patients' medical records.

Results

2705 primary breast cancer cases were analyzed. The groups consisted of 320(11.8%) TNBC, 1956 (72.31%) luminal breast cancer patients and 381 (14.08%)Her2 positive cancer patients. 18 (1%) patients were classified as equivocal. 30 patients did not meet the criteria of any of these groups. No significant difference was seen in positive lymph node status between all groups. Tumor size at diagnosis was larger for TNBC compared to the other groups. 81,9% of all TNBC, 65.1% of the Her2 type, 44.2% of the luminal type and 44.44% (8/18) of the equivocal cases were grade 3 tumors. 3 cases with unresolved Her2 status were diagnosed in 2013 and 6 cases in 2016. 17/18 equivocal cases were hormone receptor positive, 1/18 was hormone receptor negative. In 12/18 cases adjuvant or neoadjuvant chemotherapy was recommended. Trastuzumab was recommended in 9/18 of the cases. 2/18 patients were BRCA mutation carriers. 2/18 received an oncologic treatment for another cancer prior to their breast cancer diagnosis. 1/18 patient received primary endocrine therapy with an aromatase inhibitor. 6/18 patients had a positive family history for breast cancer.

Conclusions

Our study indicates that the 2013 ASCO/CAP update does not affect the overall Her2 positivity rate in breast cancer. Although the proportion of tests and retests increased, only few unresolved cases remained. Despite the fact that the benefit of anti-Her2 directed therapy in equivocal cases is unproven, oncologists were more likely to recommend Trastuzumab, if chemotherapy was indicated for high risk breast cancer. There are numerous factors that could explain equivocal findings. Interestingly, a significant number of our patients presented endogenous or exogenous risk factors for chromosomal aberrations that might be responsible for unresolved Her2 cases.

Citation Format: Kuehnle E, Wulf S, Kristina L, Iris S, Stefanie N, Alexander M, Jutta J, Thomas N, Momme A, Peter H, Thilo D-B, Tjoung-Won P-S. Frequency of equivocal Her2-test results after revision of the ASCO/CAP guidelines in a real-world setting. Results of a prospective cross-sectional study of primary breast cancers in Germany [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P6-08-22.

Changes in bacterioplankton community structure during early lake ontogeny resulting from the retreat of the Greenland Ice Sheet

Retreating glaciers and ice sheets are among the clearest signs of global climate change. One consequence of glacier retreat is the formation of new meltwater-lakes in previously ice-covered terrain. These lakes provide unique opportunities to understand patterns in community organization during early lake ontogeny. Here, we analyzed the bacterial community structure and diversity in six lakes recently formed by the retreat of the Greenland Ice Sheet (GrIS). The lakes represented a turbidity gradient depending on their past and present connectivity to the GrIS meltwaters. Bulk (16S rRNA genes) and putatively active (16S rRNA) fractions of the bacterioplankton communities were structured by changes in environmental conditions associated to the turbidity gradient. Differences in community structure among lakes were attributed to both, rare and abundant community members. Further, positive co-occurrence relationships among phylogenetically closely related community members dominate in these lakes. Our results show that environmental conditions along the turbidity gradient structure bacterial community composition, which shifts during lake ontogeny. Rare taxa contribute to these shifts, suggesting that the rare biosphere has an important ecological role during early lakes ontogeny. Members of the rare biosphere may be adapted to the transient niches in these nutrient poor lakes. The directionality and phylogenetic structure of co-occurrence relationships indicate that competitive interactions among closely related taxa may be important in the most turbid lakes.

Ecological strategies and metabolic trade-offs of complex environmental biofilms

Microorganisms aggregated into matrix-enclosed biofilms dominate microbial life in most natural, engineered, and medical systems. Despite this, the ecological adaptations and metabolic trade-offs of the formation of complex biofilms are currently poorly understood. Here, exploring the dynamics of bacterial ribosomal RNA operon (rrn) copy numbers, we unravel the genomic underpinning of the formation and success of stream biofilms that contain hundreds of bacterial taxa. Experimenting with stream biofilms, we found that nascent biofilms in eutrophic systems had reduced lag phases and higher growth rates, and more taxa with higher rrn copy number than biofilms from oligotrophic systems. Based on these growth-related traits, our findings suggest that biofilm succession was dominated by slow-but-efficient bacteria likely with leaky functions, such as the production of extracellular polymeric substances at the cost of rapid growth. Expanding our experimental findings to biofilms from 140 streams, we found that rrn copy number distribution reflects functional trait allocation and ecological strategies of biofilms to be able to thrive in fluctuating environments. These findings suggest that alternative trade-offs dominating over rate-yield trade-offs contribute to the evolutionary success of stream biofilms.

Analyzing natural biofilms containing many types of bacteria yields insights into microbial strategies for success in complex biofilms. The ecological adaptations and metabolic trade-offs involved in the formation of multi-bacterial biofilms in the environment are not well understood. Researchers in Switzerland and Austria, led by Tom Battin and Hannes Peter at the École Polytechnique Fédérale de Lausanne, performed genetic analysis of biofilms sampled from 140 streams. The biofilms contained hundreds of types of bacteria, unlike the mono-bacterial biofilms examined in many laboratory studies. Genetic analysis techniques revealed a diversity of metabolic strategies that allow bacteria to survive within the rich ecology of natural biofilms. Slow-growing but metabolically efficient bacteria that release more extracellular biofilm components thrive better than those adapted for quick growth alone. The findings significantly improve understanding of biofilm ecology in the natural environment.

Climate-related changes of soil characteristics affect bacterial community composition and function of high altitude and latitude lakes

Lakes at high altitude and latitude are typically unproductive ecosystems where external factors outweigh the relative importance of in-lake processes, making them ideal sentinels of climate change. Climate change is inducing upward vegetation shifts at high altitude and latitude regions that translate into changes in the pools of soil organic matter. Upon mobilization, this allochthonous organic matter may rapidly alter the composition and function of lake bacterial communities. Here, we experimentally simulate this potential climate-change effect by exposing bacterioplankton of two lakes located above the treeline, one in the Alps and one in the subarctic region, to soil organic matter from below and above the treeline. Changes in bacterial community composition, diversity and function were followed for 72 h. In the subarctic lake, soil organic matter from below the treeline reduced bulk and taxon-specific phosphorus uptake, indicating that bacterial phosphorus limitation was alleviated compared to organic matter from above the treeline. These effects were less pronounced in the alpine lake, suggesting that soil properties (phosphorus and dissolved organic carbon availability) and water temperature further shaped the magnitude of response. The rapid bacterial succession observed in both lakes indicates that certain taxa directly benefited from soil sources. Accordingly, the substrate uptake profiles of initially rare bacteria (copiotrophs) indicated that they are one of the main actors cycling soil-derived carbon and phosphorus. Our work suggests that climate-induced changes in soil characteristics affect bacterioplankton community structure and function, and in turn, the cycling of carbon and phosphorus in high altitude and latitude aquatic ecosystems.

Alpine glacier-fed turbid lakes are discontinuous cold polymictic rather than dimictic

Glacier retreat as a consequence of climate change influences freshwater ecosystems in manifold ways, yet the physical and chemical bases of these effects are poorly studied. Here, we characterize how water temperature differs between alpine lakes with and without direct glacier influence on seasonal and diurnal timescales. Using high temporal resolution monitoring of temperature in 4 lakes located in a catchment influenced by glacier retreat, we reported unexpectedly high surface temperatures, even in proglacial lakes located 2600 m a.s.l. Cold glacier meltwater and low nighttime air temperatures caused a distinct diurnal pattern of water temperature in the water column of glacier-influenced lakes. Precipitation onto glacier surfaces apparently leads to rapid cooling of the glacier-fed lakes and disrupts the thermal stratification with several mixing events during the summer. Taken together, these mechanisms contribute to the unique seasonal and diurnal dynamics of glacier-influenced lakes that contrast with the typical dimictic pattern of clear alpine lakes and represent an example of discontinuous cold polymictic lake type. This work contributes to the basic description of how climate and meteorology affect the physical properties of an increasingly common lake type.

Are viruses important in the plankton of highly turbid glacier-fed lakes?

Viruses are ubiquitous in aquatic ecosystems where they significantly contribute to microbial mortality. In glacier-fed turbid lakes, however, viruses not only encounter low host abundances, but also a high number of suspended mineral particles introduced by glacier meltwaters. We hypothesized that these particles potentially lead to unspecific adsorption and removal of free virus from the plankton, and thus significantly reduce their abundance in this type of lake. We followed the distribution of free virus-like particles (VLP) during the ice-free season across a turbidity gradient in four alpine lakes including one adjacent clear system where hydrological connectivity to the receding glacier is already lost. In the glacier-fed turbid lakes, VLP abundance increased with distance to the glacier, but the highest numbers were observed in the clear lake by the end of August, coinciding with the maximum in prokaryotic abundance. Our results suggest that viral loss by attachment to particles is less important than expected. Nevertheless, the relatively lower variability in VLP abundance and the lower virus-to-prokaryote ratio found in the turbid lakes than in the clear one point to a rather low temporal turnover and thus, to a reduced impact on microbial communities.

Shifts in diversity and function of lake bacterial communities upon glacier retreat

Global climate change is causing a wastage of glaciers and threatening biodiversity in glacier-fed ecosystems. The high turbidity typically found in those ecosystems, which is caused by inorganic particles and result of the erosive activity of glaciers is a key environmental factor influencing temperature and light availability, as well as other factors in the water column. Once these lakes loose hydrological connectivity to glaciers and turn clear, the accompanying environmental changes could represent a potential bottleneck for the established local diversity with yet unknown functional consequences. Here, we study three lakes situated along a turbidity gradient as well as one clear unconnected lake and evaluate seasonal changes in their bacterial community composition and diversity. Further, we assess potential consequences for community functioning. Glacier runoff represented a diverse source community for the lakes and several taxa were able to colonize downstream turbid habitats, although they were not found in the clear lake. Operational taxonomic unit-based alpha diversity and phylogenetic diversity decreased along the turbidity gradient, but metabolic functional diversity was negatively related to turbidity. No evidence for multifunctional redundancy, which may allow communities to maintain functioning upon alterations in diversity, was found. Our study gives a first view on how glacier-fed lake bacterial communities are affected by the melting of glaciers and indicates that diversity and community composition significantly change when hydrological connectivity to the glacier is lost and lakes turn clear.

Impact of TiO₂ nanoparticles on freshwater bacteria from three Swedish lakes

Due to the rapidly rising production and usage of nano-enabled products, aquatic environments are increasingly exposed to engineered nanoparticles (ENPs), causing concerns about their potential negative effects. In this study we assessed the effects of uncoated titanium dioxide nanoparticles (TiO2NPs) on the growth and activity of bacterial communities of three Swedish lakes featuring different chemical characteristics such as dissolved organic carbon (DOC) concentration, pH and elemental composition. TiO2NP exposure concentrations were 15, 100, and 1000 μg L(-1), and experiments were performed in situ under three light regimes: darkness, photosynthetically active radiation (PAR), and ambient sunlight including UV radiation (UVR). The nanoparticles were most stable in lake water with high DOC and low chemical element concentrations. At the highest exposure concentration (1000 μg L(-1) TiO2NP) the bacterial abundance was significantly reduced in all lake waters. In the medium and high DOC lake waters, exposure concentrations of 100 μg L(-1) TiO2NP caused significant reductions in bacterial abundance. The cell-specific bacterial activity was significantly enhanced at high TiO2NP exposure concentrations, indicating the loss of nanoparticle-sensitive bacteria and a subsequent increased activity by tolerant ones. No UV-induced phototoxic effect of TiO2NP was found in this study. We conclude that in freshwater lakes with high DOC and low chemical element concentrations, uncoated TiO2NPs show an enhanced stability and can significantly reduce bacterial abundance at relatively low exposure concentrations.

What can large-scale magnetohydrodynamic numerical experiments tell us about coronal heating?

The upper atmosphere of the Sun is governed by the complex structure of the magnetic field. This controls the heating of the coronal plasma to over a million kelvin. Numerical experiments in the form of three-dimensional magnetohydrodynamic simulations are used to investigate the intimate interaction between magnetic field and plasma. These models allow one to synthesize the coronal emission just as it would be observed by real solar instrumentation. Large-scale models encompassing a whole active region form evolving coronal loops with properties similar to those seen in extreme ultraviolet light from the Sun, and reproduce a number of average observed quantities. This suggests that the spatial and temporal distributions of the heating as well as the energy distribution of individual heat deposition events in the model are a good representation of the real Sun. This provides evidence that the braiding of fieldlines through magneto-convective motions in the photosphere is a good concept to heat the upper atmosphere of the Sun.

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

Resources structure ecological communities and potentially link biodiversity to energy flow. It is commonly believed that functional traits (generalists versus specialists) involved in the exploitation of resources depend on resource availability and environmental fluctuations. The longitudinal nature of stream ecosystems provides changing resources to stream biota with yet unknown effects on microbial functional traits and community structure. We investigated the impact of autochthonous (algal extract) and allochthonous (spruce extract) resources, as they change along alpine streams from above to below the treeline, on microbial diversity, community composition and functions of benthic biofilms. Combining bromodeoxyuridine labelling and 454 pyrosequencing, we showed that diversity was lower upstream than downstream of the treeline and that community composition changed along the altitudinal gradient. We also found that, especially for allochthonous resources, specialisation by biofilm bacteria increased along that same gradient. Our results suggest that in streams below the treeline biofilm diversity, specialisation and functioning are associated with increasing niche differentiation as potentially modulated by divers allochthonous and autochthonous constituents contributing to resources. These findings expand our current understanding on biofilm structure and function in alpine streams.

Bacterial diversity and composition during rain events with and without Saharan dust influence reaching a high mountain lake in the Alps

The diversity of airborne microorganisms that potentially reach aquatic ecosystems during rain events is poorly explored. Here, we used a culture-independent approach to characterize bacterial assemblages during rain events with and without Saharan dust influence arriving to a high mountain lake in the Austrian Alps. Bacterial assemblage composition differed significantly between samples with and without Saharan dust influence. Although alpha diversity indices were within the same range in both sample categories, rain events with Atlantic or continental origins were dominated by Betaproteobacteria, whereas those with Saharan dust intrusions were dominated by Gammaproteobacteria. The high diversity and evenness observed in all samples suggests that different sources of bacteria contributed to the airborne assemblage collected at the lake shore. During experiments with bacterial assemblages collected during rain events with Saharan dust influence, cell numbers rapidly increased in sterile lake water from initially ∼3 × 103 cell ml-1 to 3.6-11.1 x105 cells ml-1 within 4-5 days, and initially, rare taxa dominated at the end of the experiment. Our study documents the dispersal of viable bacteria associated to Saharan dust intrusions travelling northwards as far as 47° latitude.

Prevalence of small-scale jets from the networks of the solar transition region and chromosphere

As the interface between the Sun's photosphere and corona, the chromosphere and transition region play a key role in the formation and acceleration of the solar wind. Observations from the Interface Region Imaging Spectrograph reveal the prevalence of intermittent small-scale jets with speeds of 80 to 250 kilometers per second from the narrow bright network lanes of this interface region. These jets have lifetimes of 20 to 80 seconds and widths of ≤300 kilometers. They originate from small-scale bright regions, often preceded by footpoint brightenings and accompanied by transverse waves with amplitudes of ~20 kilometers per second. Many jets reach temperatures of at least ~10(5) kelvin and constitute an important element of the transition region structures. They are likely an intermittent but persistent source of mass and energy for the solar wind.

Hot explosions in the cool atmosphere of the Sun

The solar atmosphere was traditionally represented with a simple one-dimensional model. Over the past few decades, this paradigm shifted for the chromosphere and corona that constitute the outer atmosphere, which is now considered a dynamic structured envelope. Recent observations by the Interface Region Imaging Spectrograph (IRIS) reveal that it is difficult to determine what is up and down, even in the cool 6000-kelvin photosphere just above the solar surface: This region hosts pockets of hot plasma transiently heated to almost 100,000 kelvin. The energy to heat and accelerate the plasma requires a considerable fraction of the energy from flares, the largest solar disruptions. These IRIS observations not only confirm that the photosphere is more complex than conventionally thought, but also provide insight into the energy conversion in the process of magnetic reconnection.

Disturbance induced decoupling between host genetics and composition of the associated microbiome

BACKGROUND

Studies of oyster microbiomes have revealed that a limited number of microbes, including pathogens, can dominate microbial communities in host tissues such as gills and gut. Much of the bacterial diversity however remains underexplored and unexplained, although environmental conditions and host genetics have been implicated. We used 454 next generation 16S rRNA amplicon sequencing of individually tagged PCR reactions to explore the diversity of bacterial communities in gill tissue of the invasive Pacific oyster Crassostrea gigas stemming from genetically differentiated beds under ambient outdoor conditions and after a multifaceted disturbance treatment imposing stress on the host.

RESULTS

While the gill associated microbial communities in oysters were dominated by few abundant taxa (i.e. Sphingomonas, Mycoplasma) the distribution of rare bacterial groups correlated to relatedness between the hosts under ambient conditions. Exposing the host to disturbance broke apart this relationship by removing rare phylotypes thereby reducing overall microbial diversity. Shifts in the microbiome composition in response to stress did not result in a net increase in genera known to contain potentially pathogenic strains.

CONCLUSION

The decrease in microbial diversity and the disassociation between population genetic structure of the hosts and their associated microbiome suggest that disturbance (i.e. stress) may play a significant role for the assembly of the natural microbiome. Such community shifts may in turn also feed back on the course of disease and the occurrence of mass mortality events in oyster populations.

Fundamentals of microbial community resistance and resilience

Microbial communities are at the heart of all ecosystems, and yet microbial community behavior in disturbed environments remains difficult to measure and predict. Understanding the drivers of microbial community stability, including resistance (insensitivity to disturbance) and resilience (the rate of recovery after disturbance) is important for predicting community response to disturbance. Here, we provide an overview of the concepts of stability that are relevant for microbial communities. First, we highlight insights from ecology that are useful for defining and measuring stability. To determine whether general disturbance responses exist for microbial communities, we next examine representative studies from the literature that investigated community responses to press (long-term) and pulse (short-term) disturbances in a variety of habitats. Then we discuss the biological features of individual microorganisms, of microbial populations, and of microbial communities that may govern overall community stability. We conclude with thoughts about the unique insights that systems perspectives – informed by meta-omics data – may provide about microbial community stability.

Resistance and resilience of microbial communities--temporal and spatial insurance against perturbations

Bacteria play fundamental roles for many ecosystem processes; however, little empirical evidence is available on how environmental perturbations affect their composition and function. We investigated how spatial and temporal refuges affect the resistance and resilience of a freshwater bacterioplankton community upon a salinity pulse perturbation in continuous cultures. Attachment to a surface avoided the flushing out of cells and enabled re-colonization of the liquid phase after the perturbation, hence serving as a temporal refuge. A spatial refuge was established by introduction of bacteria from an undisturbed reservoir upstream of the continuous culture vessel, acting analogous to a regional species pool in a metacommunity. The salinity pulse affected bacterial community composition and the rates of respiration and the pattern of potential substrate utilization as well as the correlation between composition and function. Compared with the no-refuge treatment, the temporal refuge shortened return to pre-perturbation conditions, indicating enhanced community resilience. Composition and function were less disturbed in the treatment providing a spatial refuge, suggesting higher resistance. Our results highlight that spatial and temporal dynamics in general and refuges in particular need to be considered for conceptual progress in how microbial metacommunities are shaped by perturbations.

Unraveling assembly of stream biofilm communities

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.