Convergence of biofilm successional trajectories initiated during contrasting seasons.

Biofilm communities play a major role in explaining the temporal variation of biogeochemical conditions in freshwater ecosystems, and yet we know little about how these complex microbial communities change over time (aka succession), and from different initial conditions, in comparison to other stream communities. This has resulted in limited knowledge on how biofilm community structure and microbial colonization vary over relevant time scales to become mature biofilms capable of significant alteration of the freshwater environment in which they live. Here, we monitored successional trajectories of biofilm communities from summer and winter in a headwater stream and evaluated their structural state over time by DNA high-throughput sequencing. Significant differences in biofilm composition were observed when microbial colonization started in the summer vs. winter seasons, with higher percentage of algae (Bacillariophyta) and Bacteroidetes in winter-initiated samples but higher abundance of Proteobacteria (e.g., Rhizobiales, Rhodobacterales, Sphingomonadales, and Burkholderiales), Actinobacteria, and Chloroflexi in summer-initiated samples. Interestingly, results showed that despite seasonal effects on early biofilm succession, biofilm community structures converged after 70 days, suggesting the existence of a stable, mature community in the stream that is independent of the environmental conditions during biofilm colonization. Overall, our results show that algae are important in the early development of biofilm communities during winter, while heterotrophic bacteria play a more critical role during summer colonization and development of biofilms.

Wastewater microorganisms impact microbial diversity and important ecological functions of stream periphyton.

Effluents of wastewater treatment plants can impact microbial communities in the receiving streams. However, little is known about the role of microorganisms in wastewater as opposed to other wastewater constituents, such as nutrients and micropollutants. We aimed therefore at determining the impact of wastewater microorganisms on the microbial diversity and function of periphyton, key microbial communities in streams. We used a flow-through channel system to grow periphyton upon exposure to a mixture of stream water and unfiltered or ultra-filtered wastewater. Impacts were assessed on periphyton biomass, activities and tolerance to micropollutants, as well as on microbial diversity. Our results showed that wastewater microorganisms colonized periphyton and modified its community composition, resulting for instance in an increased abundance of Chloroflexi and a decreased abundance of diatoms and green algae. This led to shifts towards heterotrophy, as suggested by the changes in nutrient stoichiometry and the increased mineralization potential of carbon substrates. An increased tolerance towards micropollutants was only found for periphyton exposed to unfiltered wastewater but not to ultra-filtered wastewater, suggesting that wastewater microorganisms were responsible for this increased tolerance. Overall, our results highlight the need to consider the role of wastewater microorganisms when studying potential impacts of wastewater on the receiving water body.

Microbial biofilm community dynamics in five lowland streams.

Stream biofilms are complex aggregates of diverse organism groups that play a vital role in global carbon and nitrogen cycles. Most of the current studies on stream biofilm focus on a limited number of organism groups (e.g., bacteria and algae), and few have included both prokaryote and eukaryote communities simultaneously. In this study, we incubated artificial substrates in five Danish lowland streams exhibiting different hydrological and physico-chemical conditions and explored the dynamics of community composition and diversity of the benthic biofilm, including both prokaryotes and eukaryotes. We found that few phyla in the prokaryote (Gammaproteobacteria and Bacteroidetes) and eukaryote (Cercozoa) communities accounted for over two-thirds of the total abundance at most of the sites. Both prokaryotic and eukaryotic diversity displayed the same temporal patterns, i.e., diversity peaked in July and January. We also found that hydrological and physico-chemical variables significantly explained the variation in the community composition at phylum level for both prokaryotes and eukaryotes. However, a large proportion of variation remained unexplained, which can be ascribed to important but unmeasured variables like light intensity and biological factors such as trophic and non-trophic interactions as revealed by network analysis. Therefore, we suggest that use of a multitrophic level perspective is needed to study biofilm i.e., the "microbial jungles", where high occurrences of trophic and non-trophic interactions are expected.

Climate mediates continental scale patterns of stream microbial functional diversity.

BACKGROUND: Understanding the large-scale patterns of microbial functional diversity is essential for anticipating climate change impacts on ecosystems worldwide. However, studies of functional biogeography remain scarce for microorganisms, especially in freshwater ecosystems. Here we study 15,289 functional genes of stream biofilm microbes along three elevational gradients in Norway, Spain and China. RESULTS: We find that alpha diversity declines towards high elevations and assemblage composition shows increasing turnover with greater elevational distances. These elevational patterns are highly consistent across mountains, kingdoms and functional categories and exhibit the strongest trends in China due to its largest environmental gradients. Across mountains, functional gene assemblages differ in alpha diversity and composition between the mountains in Europe and Asia. Climate, such as mean temperature of the warmest quarter or mean precipitation of the coldest quarter, is the best predictor of alpha diversity and assemblage composition at both mountain and continental scales, with local non-climatic predictors gaining more importance at mountain scale. Under future climate, we project substantial variations in alpha diversity and assemblage composition across the Eurasian river network, primarily occurring in northern and central regions, respectively. CONCLUSIONS: We conclude that climate controls microbial functional gene diversity in streams at large spatial scales; therefore, the underlying ecosystem processes are highly sensitive to climate variations, especially at high latitudes. This biogeographical framework for microbial functional diversity serves as a baseline to anticipate ecosystem responses and biogeochemical feedback to ongoing climate change. Video Abstract.

Bacterial Communities in Stream Biofilms in a Degrading Grassland Watershed on the Qinghai-Tibet Plateau.

Grassland is among the largest terrestrial biomes and is experiencing serious degradation, especially on the Qinghai-Tibet Plateau (QTP). However, the influences of grassland degradation on microbial communities in stream biofilms are largely unknown. Using 16S rRNA gene sequencing, we investigated the bacterial communities in stream biofilms in sub-basins with different grassland status in the Qinghai Lake watershed. Grassland status in the sub-basins was quantified using the normalized difference vegetation index (NDVI). Proteobacteria, Bacteroidetes, Cyanobacteria, and Verrucomicrobia were the dominant bacterial phyla. OTUs, 7,050, were detected in total, within which 19 were abundant taxa, and 6,922 were rare taxa. Chao 1, the number of observed OTUs, and phylogenetic diversity had positive correlations with carbon (C), nitrogen (N), and/or phosphorus (P) in biofilms per se. The variation of bacterial communities in stream biofilms was closely associated with the rate of change in NDVI, pH, conductivity, as well as C, N, P, contents and C:N ratio of the biofilms. Abundant subcommunities were more influenced by environmental variables relative to the whole community and to rare subcommunities. These results suggest that the history of grassland degradation (indicated as the rate of change in NDVI) influences bacterial communities in stream biofilms. Moreover, the bacterial community network showed high modularity with five major modules (>50 nodes) that responded differently to environmental variables. According to the module structure, only one module connector and 12 module hubs were identified, suggesting high fragmentation of the network and considerable independence of the modules. Most of the keystone taxa were rare taxa, consistent with fragmentation of the network and with adverse consequences for bacterial community integrity and function in the biofilms. By documenting the properties of bacterial communities in stream biofilms in a degrading grassland watershed, our study adds to our knowledge of the potential influences of grassland degradation on aquatic ecosystems.

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.

Biogeochemistry and community ecology in a spring-fed urban river following a major earthquake.

In February 2011 a MW 6.3 earthquake in Christchurch, New Zealand inundated urban waterways with sediment from liquefaction and triggered sewage spills. The impacts of, and recovery from, this natural disaster on the stream biogeochemistry and biology were assessed over six months along a longitudinal impact gradient in an urban river. The impact of liquefaction was masked by earthquake triggered sewage spills (~20,000 m(3) day(-1) entering the river for one month). Within 10 days of the earthquake dissolved oxygen in the lowest reaches was <1 mg l(-1), in-stream denitrification accelerated (attenuating 40-80% of sewage nitrogen), microbial biofilm communities changed, and several benthic invertebrate taxa disappeared. Following sewage system repairs, the river recovered in a reverse cascade, and within six months there were no differences in water chemistry, nutrient cycling, or benthic communities between severely and minimally impacted reaches. This study highlights the importance of assessing environmental impact following urban natural disasters.