Publications by authors named "Ruben Sommaruga"

79 Publications

Widespread deoxygenation of temperate lakes.

Nature 2021 06 2;594(7861):66-70. Epub 2021 Jun 2.

Department of Biology, University of Hamburg, Hamburg, Germany.

The concentration of dissolved oxygen in aquatic systems helps to regulate biodiversity, nutrient biogeochemistry, greenhouse gas emissions, and the quality of drinking water. The long-term declines in dissolved oxygen concentrations in coastal and ocean waters have been linked to climate warming and human activity, but little is known about the changes in dissolved oxygen concentrations in lakes. Although the solubility of dissolved oxygen decreases with increasing water temperatures, long-term lake trajectories are difficult to predict. Oxygen losses in warming lakes may be amplified by enhanced decomposition and stronger thermal stratification or oxygen may increase as a result of enhanced primary production. Here we analyse a combined total of 45,148 dissolved oxygen and temperature profiles and calculate trends for 393 temperate lakes that span 1941 to 2017. We find that a decline in dissolved oxygen is widespread in surface and deep-water habitats. The decline in surface waters is primarily associated with reduced solubility under warmer water temperatures, although dissolved oxygen in surface waters increased in a subset of highly productive warming lakes, probably owing to increasing production of phytoplankton. By contrast, the decline in deep waters is associated with stronger thermal stratification and loss of water clarity, but not with changes in gas solubility. Our results suggest that climate change and declining water clarity have altered the physical and chemical environment of lakes. Declines in dissolved oxygen in freshwater are 2.75 to 9.3 times greater than observed in the world's oceans and could threaten essential lake ecosystem services.
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http://dx.doi.org/10.1038/s41586-021-03550-yDOI Listing
June 2021

Characterization of the Aerobic Anoxygenic Phototrophic Bacterium sp. AAP5.

Microorganisms 2021 Apr 6;9(4). Epub 2021 Apr 6.

Centre Algatech, Institute of Microbiology, Czech Academy of Sciences, 379 81 Třeboň, Czech Republic.

An aerobic, yellow-pigmented, bacteriochlorophyll -producing strain, designated AAP5 (=DSM 111157=CCUG 74776), was isolated from the alpine lake Gossenköllesee located in the Tyrolean Alps, Austria. Here, we report its description and polyphasic characterization. Phylogenetic analysis of the 16S rRNA gene showed that strain AAP5 belongs to the bacterial genus and has the highest pairwise 16S rRNA gene sequence similarity with (98.3%), (96.8%), and (96.5%). Its genomic DNA G + C content is 65.9%. Further, in silico DNA-DNA hybridization and calculation of the average nucleotide identity speaks for the close phylogenetic relationship of AAP5 and . The high percentage (76.2%) of shared orthologous gene clusters between strain AAP5 and NCTC 11030, the type species of the genus, supports the classification of the two strains into the same genus. Strain AAP5 was found to contain C7 (64.6%) as a predominant fatty acid (>10%) and the polar lipid profile contained phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid, six unidentified glycolipids, one unidentified phospholipid, and two unidentified lipids. The main respiratory quinone was ubiquinone-10. Strain AAP5 is a facultative photoheterotroph containing type-2 photosynthetic reaction centers and, in addition, contains a xathorhodopsin gene. No CO-fixation pathways were found.
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http://dx.doi.org/10.3390/microorganisms9040768DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8067484PMC
April 2021

Low temporal dynamics of mycosporine-like amino acids in benthic cyanobacteria from an alpine lake.

Freshw Biol 2021 Jan 15;66(1):169-176. Epub 2020 Oct 15.

Department of Ecology University of Innsbruck Innsbruck Austria.

Cyanobacteria are one of the oldest organisms on Earth and they originated at a time when damaging ultraviolet (UV) C radiation still reached the surface. Their long evolution led to several adaptations to avoid deleterious effects caused by exposure to solar UV radiation. Synthesis of sunscreen substances, such as mycosporine-like amino acids (MAAs), allows them to photosynthesise with reduced risk of cell damage. The interplay of solar UV radiation and MAAs is well documented for cyanobacteria in the plankton realm, but little is known for those in the benthic realm, particularly of clear alpine lakes.Here, we assessed the temporal dynamics of MAAs in the benthic algal community of one clear alpine lake dominated by cyanobacteria during the ice-free season and along a depth gradient using state-of-the-art analytical methods (high-performance liquid chromatography, nuclear magnetic resonance, liquid chromatography-mass spectrometry). We differentiated between the epilithic cyanobacterial community and the overlying loosely attached filamentous cyanobacteria, as we expected they will have an important shielding/shading effect on the former. We hypothesised that in contrast to the case of phytoplankton, benthic cyanobacteria will show less pronounced temporal changes in MAAs concentration in response to changes in solar UV exposure.Three UV-absorbing substances were present in both types of communities, whereby all were unknown. The chemical structure of the dominant unknown substance (maximum absorption at 334 nm) resulted in the identification of a novel MAA that we named aplysiapalythine-D for its similarity to the previously described aplysiapalythine-C.Chlorophyll--specific MAA concentrations for epilithic and filamentous cyanobacteria showed a significant decrease with depth, although only traces were found in the former community. The temporal dynamics in MAA concentrations of filamentous cyanobacteria showed no significant variations during the ice-free season.Our result on the low temporal MAA dynamics agrees with the reduced growth rates of benthic cyanobacteria reported for cold ecosystems. The permanent presence of this community, which is adapted to the high UV levels characteristic of clear alpine lakes, probably represents the most important primary producers of these ecosystems.
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http://dx.doi.org/10.1111/fwb.13627DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7821102PMC
January 2021

Correction to: Polinton-like viruses are abundant in aquatic ecosystems.

Microbiome 2021 Jan 27;9(1):30. Epub 2021 Jan 27.

Department of Ecology, University of Innsbruck, Technikerstrasse 25, A-6020, Innsbruck, Austria.

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http://dx.doi.org/10.1186/s40168-021-01004-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7841899PMC
January 2021

Polinton-like viruses are abundant in aquatic ecosystems.

Microbiome 2021 01 12;9(1):13. Epub 2021 Jan 12.

Department of Ecology, University of Innsbruck, Technikerstrasse 25, A-6020, Innsbruck, Austria.

Background: Polintons are large mobile genetic elements found in the genomes of eukaryotic organisms that are considered the ancient ancestors of most eukaryotic dsDNA viruses. Originally considered as transposons, they have been found to encode virus capsid genes, suggesting they may actually be integrated viruses; however, an extracellular form has yet to be detected. Recently, circa 25 Polinton-like viruses have been discovered in environmental metagenomes and algal genomes, which shared distantly related genes to both Polintons and virophages (Lavidaviridae). These entities could be the first members of a major class of ancient eukaryotic viruses; however, owing to the lack of available genomes for analysis, information on their global diversity, evolutionary relationships, eukaryotic hosts, and status as free virus particles is limited.

Results: Here, we analysed the metaviromes of an alpine lake to show that Polinton-like virus genome sequences are abundant in the water column. We identify major capsid protein genes belonging to 82 new Polinton-like viruses and use these to interrogate publicly available metagenomic datasets, identifying 543 genomes and a further 16 integrated into eukaryotic genomes. Using an analysis of shared gene content and major capsid protein phylogeny, we define large groups of Polinton-like viruses and link them to diverse eukaryotic hosts, including a new group of viruses, which possess all the core genes of virophages and infect oomycetes and Chrysophyceae.

Conclusions: Our study increased the number of known Polinton-like viruses by 25-fold, identifying five major new groups of eukaryotic viruses, which until now have been hidden in metagenomic datasets. The large enrichment (> 100-fold) of Polinton-like virus sequences in the virus-sized fraction of this alpine lake and the fact that their viral major capsid proteins are found in eukaryotic host transcriptomes support the hypothesis that Polintons in unicellular eukaryotes are viruses. In summary, our data reveals a diverse assemblage of globally distributed viruses, associated with a wide range of unicellular eukaryotic hosts. We anticipate that the methods we have developed for Polinton-like virus detection and the database of over 20,000 genes we present will allow for continued discovery and analysis of these new viral groups. Video abstract.
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http://dx.doi.org/10.1186/s40168-020-00956-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7805220PMC
January 2021

Simultaneous Presence of Bacteriochlorophyll and Xanthorhodopsin Genes in a Freshwater Bacterium.

mSystems 2020 Dec 22;5(6). Epub 2020 Dec 22.

Center Algatech, Institute of Microbiology of the Czech Academy of Science, Třeboň, Czechia

Photoheterotrophic bacteria represent an important part of aquatic microbial communities. There exist two fundamentally different light-harvesting systems: bacteriochlorophyll-containing reaction centers or rhodopsins. Here, we report a photoheterotrophic strain isolated from an oligotrophic lake, which contains complete sets of genes for both rhodopsin-based and bacteriochlorophyll-based phototrophy. Interestingly, the identified genes were not expressed when cultured in liquid organic media. Using reverse transcription quantitative PCR (RT-qPCR), RNA sequencing, and bacteriochlorophyll quantification, we document that bacteriochlorophyll synthesis was repressed by high concentrations of glucose or galactose in the medium. Coactivation of photosynthesis genes together with genes for TonB-dependent transporters suggests the utilization of light energy for nutrient import. The photosynthetic units were formed by ring-shaped light-harvesting complex 1 and reaction centers with bacteriochlorophyll and spirilloxanthin as the main light-harvesting pigments. The identified rhodopsin gene belonged to the xanthorhodopsin family, but it lacks salinixanthin antenna. In contrast to bacteriochlorophyll, the expression of xanthorhodopsin remained minimal under all experimental conditions tested. Since the gene was found in the same operon as a histidine kinase, we propose that it might serve as a light sensor. Our results document that photoheterotrophic bacteria use the energy of light under carbon-limited conditions, while under carbon-replete conditions, they cover all their metabolic needs through oxidative phosphorylation. Phototrophic organisms are key components of many natural environments. There exist two main phototrophic groups: species that collect light energy using various kinds of (bacterio)chlorophylls and species that utilize rhodopsins. Here, we present a freshwater bacterium sp. strain AAP5 which contains genes for both light-harvesting systems. We show that bacteriochlorophyll-based reaction centers are repressed by light and/or glucose. On the other hand, the rhodopsin gene was not expressed significantly under any of the experimental conditions. This may indicate that rhodopsin in may have other functions not linked to bioenergetics.
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http://dx.doi.org/10.1128/mSystems.01044-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7762795PMC
December 2020

Deeper waters are changing less consistently than surface waters in a global analysis of 102 lakes.

Sci Rep 2020 11 25;10(1):20514. Epub 2020 Nov 25.

Lake Ecosystems Group, UK Centre for Ecology & Hydrology, Lancaster, UK.

Globally, lake surface water temperatures have warmed rapidly relative to air temperatures, but changes in deepwater temperatures and vertical thermal structure are still largely unknown. We have compiled the most comprehensive data set to date of long-term (1970-2009) summertime vertical temperature profiles in lakes across the world to examine trends and drivers of whole-lake vertical thermal structure. We found significant increases in surface water temperatures across lakes at an average rate of + 0.37 °C decade, comparable to changes reported previously for other lakes, and similarly consistent trends of increasing water column stability (+ 0.08 kg m decade). In contrast, however, deepwater temperature trends showed little change on average (+ 0.06 °C decade), but had high variability across lakes, with trends in individual lakes ranging from - 0.68 °C decade to + 0.65 °C decade. The variability in deepwater temperature trends was not explained by trends in either surface water temperatures or thermal stability within lakes, and only 8.4% was explained by lake thermal region or local lake characteristics in a random forest analysis. These findings suggest that external drivers beyond our tested lake characteristics are important in explaining long-term trends in thermal structure, such as local to regional climate patterns or additional external anthropogenic influences.
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http://dx.doi.org/10.1038/s41598-020-76873-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7688658PMC
November 2020

Key rules of life and the fading cryosphere: Impacts in alpine lakes and streams.

Glob Chang Biol 2020 Dec 19;26(12):6644-6656. Epub 2020 Oct 19.

School of Biology and Ecology, Climate Change Institute, University of Maine, Orono, ME, USA.

Alpine regions are changing rapidly due to loss of snow and ice in response to ongoing climate change. While studies have documented ecological responses in alpine lakes and streams to these changes, our ability to predict such outcomes is limited. We propose that the application of fundamental rules of life can help develop necessary predictive frameworks. We focus on four key rules of life and their interactions: the temperature dependence of biotic processes from enzymes to evolution; the wavelength dependence of the effects of solar radiation on biological and ecological processes; the ramifications of the non-arbitrary elemental stoichiometry of life; and maximization of limiting resource use efficiency across scales. As the cryosphere melts and thaws, alpine lakes and streams will experience major changes in temperature regimes, absolute and relative inputs of solar radiation in ultraviolet and photosynthetically active radiation, and relative supplies of resources (e.g., carbon, nitrogen, and phosphorus), leading to nonlinear and interactive effects on particular biota, as well as on community and ecosystem properties. We propose that applying these key rules of life to cryosphere-influenced ecosystems will reduce uncertainties about the impacts of global change and help develop an integrated global view of rapidly changing alpine environments. However, doing so will require intensive interdisciplinary collaboration and international cooperation. More broadly, the alpine cryosphere is an example of a system where improving our understanding of mechanistic underpinnings of living systems might transform our ability to predict and mitigate the impacts of ongoing global change across the daunting scope of diversity in Earth's biota and environments.
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http://dx.doi.org/10.1111/gcb.15362DOI Listing
December 2020

The balance between deterministic and stochastic processes in structuring lake bacterioplankton community over time.

Mol Ecol 2020 08 24;29(16):3117-3130. Epub 2020 Jul 24.

Lake and Glacier Ecology Research Group, Department of Ecology, University of Innsbruck, Innsbruck, Austria.

One major goal in microbial ecology is to establish the importance of deterministic and stochastic processes for community assembly. This is relevant to explain and predict how diversity changes at different temporal scales. However, understanding of the relative quantitative contribution of these processes and particularly of how they may change over time is limited. Here, we assessed the importance of deterministic and stochastic processes based on the analysis of the bacterial microbiome in one alpine oligotrophic and in one subalpine mesotrophic lake, which were sampled over two consecutive years at different time scales. We found that in both lakes, homogeneous selection (i.e., a deterministic process) was the main assembly process at the annual scale and explained 66.7% of the bacterial community turnover, despite differences in diversity and temporal variability patterns between ecosystems. However, in the alpine lake, homogenizing dispersal (i.e., a stochastic process) was the most important assembly process at the short-term (daily and weekly) sampling scale and explained 55% of the community turnover. Alpha diversity differed between lakes, and seasonal stability of the bacterial community was more evident in the oligotrophic lake than in the mesotrophic one. Our results demonstrate how important forces that govern temporal changes in bacterial communities act at different time scales. Overall, our study validates on a quantitative basis, the importance and dominance of deterministic processes in structuring bacterial communities in freshwater environments over long time scales.
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http://dx.doi.org/10.1111/mec.15538DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7540538PMC
August 2020

Stable species boundaries despite ten million years of hybridization in tropical eels.

Nat Commun 2020 03 18;11(1):1433. Epub 2020 Mar 18.

Department of Biosciences, University of Salzburg, Hellbrunnerstrasse 34, 5020, Salzburg, Austria.

Genomic evidence is increasingly underpinning that hybridization between taxa is commonplace, challenging our views on the mechanisms that maintain their boundaries. Here, we focus on seven catadromous eel species (genus Anguilla) and use genome-wide sequence data from more than 450 individuals sampled across the tropical Indo-Pacific, morphological information, and three newly assembled draft genomes to compare contemporary patterns of hybridization with signatures of past introgression across a time-calibrated phylogeny. We show that the seven species have remained distinct for up to 10 million years and find that the current frequencies of hybridization across species pairs contrast with genomic signatures of past introgression. Based on near-complete asymmetry in the directionality of hybridization and decreasing frequencies of later-generation hybrids, we suggest cytonuclear incompatibilities, hybrid breakdown, and purifying selection as mechanisms that can support species cohesion even when hybridization has been pervasive throughout the evolutionary history of clades.
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http://dx.doi.org/10.1038/s41467-020-15099-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7080837PMC
March 2020

Contrasting diurnal patterns in antioxidant capacities, but not in expression of stress protein genes among copepod populations from clear versus glacially fed alpine and subalpine lakes.

J Plankton Res 2019 Nov 10;41(6):897-908. Epub 2019 Dec 10.

Molecular Genetics Group, Institute of Biology, Humboldt University of Berlin, 10115 Berlin, Germany.

Short-term changes in environmental conditions largely influence planktonic organisms, but their responses will depend on the habitat characteristics. Here we studied diurnal patterns in antioxidative metabolites (lipophilic and hydrophilic antioxidant capacities) and in the expression of stress protein genes (heat shock proteins, ) of copepods to identify short-term stress responses in clear and turbid alpine lakes, as well as in less transparent subalpine ones. showed diurnal variation in antioxidant capacities with maxima around noon in clear, but not in glacially fed, turbid lakes. Low fluctuations of these metabolites were also observed in another copepod, . Although levels of genes differed between populations living in clear or glacially fed lakes, there was no diurnal rhythmicity in gene expression. Our data show that when planktonic organisms may be at greatest risk of oxidative damage, such as during the daytime in high UV radiation environments, they activate antioxidant responses. Conversely, in less transparent lakes, the physiological response seems to be unnecessary. The difference in gene expression levels suggests an ecological, albeit not acute, role of these genes in copepods experiencing daily environmental fluctuations.
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http://dx.doi.org/10.1093/plankt/fbz061DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6946086PMC
November 2019

Microplastics modify the toxicity of glyphosate on Daphnia magna.

Sci Total Environ 2019 Dec 30;697:134194. Epub 2019 Aug 30.

Department of Ecology, University of Innsbruck, Technikerstr. 25, 6020 Innsbruck, Austria. Electronic address:

Plastic contamination is an environmental problem spreading to even the most remote aquatic and terrestrial habitats and in particular, microplastics represent an uncertain threat for organisms. Microplastics can have a direct negative effect, but they can also potentially modify the toxicity and bioavailability of pollutants. Here, we tested over 1 week the combined effect of three different glyphosate chemical formulations (glyphosate acid, glyphosate-monoisopropylamine salt, and Roundup Gran) and two types of microplastics (polyethylene (PE) microbeads and polyethylene terephthalate/polyamide (PET/PA) fibers), on Daphnia magna. Glyphosate-monoisopropylamine salt caused the highest mortality after 1 week exposure (23.3%), whereas glyphosate acid the lowest (12.5%), when tested in the absence of microplastics. These results were inverted, however, when the individuals were exposed in combination with the PE microbeads (glyphosate acid: 53.3% and glyphosate-monoisopropylamine salt: 18.3%) or the PET/PA fibers (glyphosate acid: 30.0% and glyphosate-monoisopropylamine salt: 8.3%). The mortality in the Roundup Gran formulation also increased when combined with the two microplastics, though the effect was less pronounced. In all experiments, the effect of the treatments and time was significant, though there was no significant interaction between them. In most treatments, negative effects were not observed after 48 h or later. The change in toxicity of the glyphosate formulations caused by microplastics can be linked to the different sorption properties of the glyphosate-based chemicals formulations. The outcome of this study highlights that beside the potential direct negative effects of microplastics, they can modify the toxicity of pollutants, such as herbicides.
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http://dx.doi.org/10.1016/j.scitotenv.2019.134194DOI Listing
December 2019

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

Aquat Sci 2019 16;81(3):45. Epub 2019 Apr 16.

1Department of Ecology, Lake and Glacier Research Group, University of Innsbruck, Technikerstr. 25, 6020 Innsbruck, Austria.

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- 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.
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http://dx.doi.org/10.1007/s00027-019-0643-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6469636PMC
April 2019

Bacterial Communities Associated With Spherical Macrocolonies.

Front Microbiol 2019 21;10:483. Epub 2019 Mar 21.

Lake and Glacier Ecology Research Group, Department of Ecology, University of Innsbruck, Innsbruck, Austria.

Species of the genus (Cyanobacteria) can form large colonies of up to several centimeters in diameter that may represent a unique habitat for bacteria in freshwaters. Bacteria inside the colony are probably segregated from the surrounding water and largely dependent on the metabolism of this primary producer. However, the existence of a specific bacterial community associated with free-living representatives of from lakes and streams is unknown. Here, we studied large spp. colonies (ca. 2-10 cm in diameter) from two adjacent, high altitude aquatic environments and assessed the diversity, and community composition of the bacterial community associated with the inner gelatinous matrix (GM). Further, we compared this community with that of the lake's littoral zone where the colonies live or with the outer layer (OL) of the colony in samples collected from a stream. Alpha bacterial diversity in the inner GM of the colonies from both sites was lower than in the littoral zone or than in the OL. Significant differences in community composition were found between the inner and the OL, as well as between the inner GM, and the littoral zone. Further, these differences were supported by the putative metabolic processes of the bacterial communities. Our results indicate the existence of a specific bacterial community inside macrocolonies of spp. and also imply that the inner environment exerts a strong selection. Finally, these large colonies represent not only a unique habitat, but probably also a hotspot of bacterial activity in an otherwise oligotrophic environment.
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http://dx.doi.org/10.3389/fmicb.2019.00483DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6437075PMC
March 2019

Legislation restricts research in Uruguay.

Science 2018 11;362(6418):1008

Sección Limnología, IECA, Facultad de Ciencias, Universidad de la República, Uruguay.

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http://dx.doi.org/10.1126/science.aav6122DOI Listing
November 2018

Bacterioplankton composition in tropical high-elevation lakes of the Andean plateau.

FEMS Microbiol Ecol 2018 03;94(3)

Lake and Glacier Ecology Research Group, Institute of Ecology, University of Innsbruck, Technikerstr 25, Innsbruck 6020, Austria.

High-elevation lakes in the tropics are subject to extreme environmental fluctuations and microbes may harbor a unique genomic repertoire, but their composition and diversity are largely unknown. Here, we compared the planktonic bacterial community composition (BCC) and diversity of three tropical lakes located in the high Andean plateau (≥4400 m above sea level) during the dry and wet season. Diversity in these lakes was higher in the cool and wet season than in the warm and dry one. Operational taxonomic units (OTUs) composition was significantly different among lakes and between seasons. Members of the class Opitutae, Spartobacteria, Burkholderiales and Actinobacteria were dominant, but only the hgcI clade (Actinobacteria) and the Comamonadaceae family (Burkholderiales) were shared between seasons among the three lakes. In general, a large percentage (up to 42%) of the rare OTUs was unclassified even at the family level. In one lake, a pycnocline and an anoxic water layer with high abundance of Thiocapsa sp. was found in the wet season indicating that the known polymictic thermal condition is not always given. Our study highlights the particular BCC of tropical high-elevation lakes and also how little is known about the variability in physico-chemical conditions of these ecosystems.
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http://dx.doi.org/10.1093/femsec/fiy004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6018938PMC
March 2018

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

ISME J 2017 Oct 31. Epub 2017 Oct 31.

Institute of Ecology, Lake and Glacier Ecology Research Group, University of Innsbruck, Innsbruck, Austria.

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.The ISME Journal advance online publication, 31 October 2017; doi:10.1038/ismej.2017.191.
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http://dx.doi.org/10.1038/ismej.2017.191DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5776470PMC
October 2017

Stoichiometry of natural bacterial assemblages from lakes located across an elevational gradient.

Sci Rep 2017 07 19;7(1):5875. Epub 2017 Jul 19.

University of Innsbruck, Institute of Ecology, Technikerstraße 25, 6020, Innsbruck, Austria.

Heterotrophic bacteria are thought to be phosphorus-rich organisms with relatively homeostatic stoichiometry, but the elemental composition of natural bacterial communities has rarely been assessed. Here we tested whether bacterial stoichiometry changes with the trophic status of lakes by assessing the elemental composition of the bacterial-dominated (hereafter microbial) fraction together with that of the dissolved and seston fractions in 11 lakes situated along an elevational gradient. The stoichiometry of these three size-fractions was analyzed during the thermal stratification and mixing periods in composite water samples and in the water layer of the deep chlorophyll-a maximum. In addition, we analyzed the relative abundance of the most common bacterial groups in the lakes. Our results show that the microbial fraction was always enriched in phosphorus compared to the dissolved fraction, irrespectively of the lake trophic status. Further, they indicate that the elemental composition of bacteria in mountain lakes is at least seasonally very dynamic, resulting not only from changes in the nutrient ratios of the resource itself, but probably from changes in the composition of the dominant bacterial taxa too, though at the taxonomic level analyzed, we did not find evidence for this.
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http://dx.doi.org/10.1038/s41598-017-06282-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5517659PMC
July 2017

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

Inland Waters 2017 Jan 2;7(1):45-54. Epub 2017 May 2.

Institute of Ecology, Lake and Glacier Ecology Research Group, University of Innsbruck, Innsbruck, Austria.

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.
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http://dx.doi.org/10.1080/20442041.2017.1294346DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5478930PMC
January 2017

Distribution and UV protection strategies of zooplankton in clear and glacier-fed alpine lakes.

Sci Rep 2017 07 3;7(1):4487. Epub 2017 Jul 3.

Lake and Glacier Research Group, Institute of Ecology, University of Innsbruck, 6020, Innsbruck, Austria.

Zooplankton, a group of aquatic animals important as trophic link in the food web, are exposed to high levels of UV radiation (UVR) in clear alpine lakes, while in turbid glacier-fed lakes they are more protected. To study the interplay between behavioral and physiological protection responses in zooplankton from those lakes, we sampled six lakes of different UVR transparency and glacial turbidity. Copepods were absent in the upper water layers of the clearest lake, while in glacier-fed lakes they were more evenly distributed in the water column. Across all lakes, the weighted copepod mean depth was strongly related to food resources (chlorophyll a and rotifers), whereas in the fishless lakes, glacial turbidity largely explained the vertical daytime distribution of these organisms. Up to ~11-times (mean 3.5) higher concentrations of photo-protective compounds (mycosporine-like amino acids, MAAs) were found in the copepods from the clear than from the glacier-fed lakes. In contrast to carotenoid concentrations and antioxidant capacities, MAA levels were strongly related to the lake transparency. Copepods from alpine lakes rely on a combination of behavioral and physiological strategies adapted to the change in environmental conditions taking place when lakes shift from glacially turbid to clear conditions, as glacier retreat proceeds.
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http://dx.doi.org/10.1038/s41598-017-04836-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5495746PMC
July 2017

Ciliate community structure and interactions within the planktonic food web in two alpine lakes of contrasting transparency.

Freshw Biol 2016 11 6;61(11):1950-1965. Epub 2016 Oct 6.

Ciliate Ecology and Taxonomy Group Research Institute for Limnology University of Innsbruck Mondsee Austria.

Climate warming is accelerating the retreat of glaciers and recently, many 'new' glacial turbid lakes have been created. In the course of time, the loss of the hydrological connectivity to a glacier causes, however, changes in their water turbidity and turns these ecosystems into clear ones.To understand potential differences in the food-web structure between glacier-fed turbid and clear alpine lakes, we sampled ciliates, phyto-, bacterio- and zooplankton in one clear and one glacial turbid alpine lake, and measured key physicochemical parameters. In particular, we focused on the ciliate community and the potential drivers for their abundance distribution.In both lakes, the zooplankton community was similar and dominated by the copepod and rotifers including , , and . The phytoplankton community structure differed and it was dominated by the planktonic diatom and the cryptophyte alga in the glacial turbid lake, while chrysophytes and dinoflagellates were predominant in the clear one.Ciliate abundance and richness were higher in the glacial turbid lake (∼4000-27 800 Ind L, up to 29 species) than in the clear lake (∼570-7150 Ind L, up to eight species). The dominant species were , cf. , cf. and cf. . The same species dominated in both lakes, except for cf. and some particle-associated ciliates, which occurred exclusively in the glacial turbid lake. The relative underwater solar irradiance (i.e. percentage of PAR and UVR at depth) significantly explained their abundance distribution pattern, especially in the clear water lake. In the glacial turbid lake, the abundance of the dominating ciliate taxa was mainly explained by the presence of predatory zooplankton.Our results revealed an unexpected high abundance and richness of protists (algae, ciliates) in the glacial turbid lake. This type of lake likely offers more suitable environmental conditions and resource niches for protists than the clear and highly UV transparent lake.
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http://dx.doi.org/10.1111/fwb.12828DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5082529PMC
November 2016

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

Glob Chang Biol 2017 06 25;23(6):2331-2344. Epub 2016 Nov 25.

Lake and Glacier Ecology Research Group, Institute of Ecology, University of Innsbruck, Technikerstraße 25, Innsbruck, Austria.

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.
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http://dx.doi.org/10.1111/gcb.13545DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5434934PMC
June 2017

Environment not dispersal limitation drives clonal composition of Arctic Daphnia in a recently deglaciated area.

Mol Ecol 2016 Dec 18;25(23):5830-5842. Epub 2016 Nov 18.

Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Ch. Deberiotstraat 32, B-3000, Leuven, Belgium.

One of the most prominent manifestations of the ongoing climate warming is the retreat of glaciers and ice sheets around the world. Retreating glaciers result in the formation of new ponds and lakes, which are available for colonization. The gradual appearance of these new habitat patches allows us to determine to what extent the composition of asexual Daphnia (water flea) populations is affected by environmental drivers vs. dispersal limitation. Here, we used a landscape genetics approach to assess the processes structuring the clonal composition of species in the D. pulex species complex that have colonized periglacial habitats created by ice-sheet retreat in western Greenland. We analysed 61 populations from a young (<50 years) and an old cluster (>150 years) of lakes and ponds. We identified 42 asexual clones that varied widely in spatial distribution. Beta-diversity was higher among older than among younger systems. Lineage sorting by the environment explained 14% of the variation in clonal composition whereas the pure effect of geographical distance was very small and statistically insignificant (Radj2 = 0.010, P = 0.085). Dispersal limitation did not seem important, even among young habitat patches. The observation of several tens of clones colonizing the area combined with environmentally driven clonal composition of populations illustrates that population assembly of asexual species in the Arctic is structured by environmental gradients reflecting differences in the ecology of clones.
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http://dx.doi.org/10.1111/mec.13843DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5737836PMC
December 2016

Large Differences in Bacterial Community Composition among Three Nearby Extreme Waterbodies of the High Andean Plateau.

Front Microbiol 2016 21;7:976. Epub 2016 Jun 21.

Lake and Glacier Ecology Research Group, Institute of Ecology, University of Innsbruck Innsbruck, Austria.

The high Andean plateau or Altiplano contains different waterbodies that are subjected to extreme fluctuations in abiotic conditions on a daily and an annual scale. The bacterial diversity and community composition of those shallow waterbodies is largely unexplored, particularly, of the ponds embedded within the peatland landscape (i.e., Bofedales). Here we compare the small-scale spatial variability (<1 m) in bacterial diversity and community composition between two of those ponds with contrasting apparent color, using 454 pyrosequencing of the 16S rRNA gene. Further, we compared the results with the nearest (80 m) main lagoon in the system to elucidate the importance of different environmental factors such as salinity and the importance of these ponds as a source of shared diversity. Bacterial diversity was higher in both ponds than in the lagoon and community composition was largely different among them and characterized by very low operational taxonomic unit sharing. Whereas the "green" pond with relatively low dissolved organic carbon (DOC) concentration (33.5 mg L(-1)) was dominated by Proteobacteria and Bacteroidetes, the one with extreme DOC concentration (424.1 mg L(-1)) and red hue was dominated by Cyanobacteria. By contrast, the lagoon was largely dominated by Proteobacteria, particularly by Gammaproteobacteria. A large percentage (47%) of all reads was unclassified suggesting the existence of large undiscovered bacterial diversity. Our results suggest that even at the very small-scale spatial range considered, local environmental factors are important in explaining differences in bacterial community composition in those systems. Further, our study highlights that Altiplano peatland ponds represent a hitherto unknown source of microbial diversity.
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http://dx.doi.org/10.3389/fmicb.2016.00976DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4914511PMC
July 2016

Differential utilization patterns of dissolved organic phosphorus compounds by heterotrophic bacteria in two mountain lakes.

FEMS Microbiol Ecol 2016 09 15;92(9). Epub 2016 Jun 15.

Institute of Ecology, Lake and Glacier Ecology Research Group, University of Innsbruck, Technikerstr. 25, 6020 Innsbruck, Austria.

Although phosphorus limitation is common in freshwaters and bacteria are known to use dissolved organic phosphorus (DOP), little is known about how efficiently DOP compounds are taken up by individual bacterial taxa. Here, we assessed bacterial uptake of three model DOP substrates in two mountain lakes and examined whether DOP uptake followed concentration-dependent patterns. We determined bulk uptake rates by the bacterioplankton and examined bacterial taxon-specific substrate uptake patterns using microautoradiography combined with catalyzed reporter deposition-fluorescence in situ hybridization. Our results show that in the oligotrophic alpine lake, bacteria took up ATP, glucose-6-phosphate and glycerol-3-phosphate to similar extents (mean 29.7 ± 4.3% Bacteria), whereas in the subalpine mesotrophic lake, ca. 40% of bacteria took up glucose-6-phosphate, but only ∼20% took up ATP or glycerol-3-phosphate. In both lakes, the R-BT cluster of Betaproteobacteria (lineage of genus Limnohabitans) was over-represented in glucose-6-phosphate and glycerol-3-phosphate uptake, whereas AcI Actinobacteria were under-represented in the uptake of those substrates. Alphaproteobacteria and Bacteroidetes contributed to DOP uptake proportionally to their in situ abundance. Our results demonstrate that R-BT Betaproteobacteria are the most active bacteria in DOP acquisition, whereas the abundant AcI Actinobacteria may either lack high affinity DOP uptake systems or have reduced phosphorus requirements.
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http://dx.doi.org/10.1093/femsec/fiw139DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4940451PMC
September 2016

Phosphate and ATP uptake by lake bacteria: does taxonomical identity matter?

Environ Microbiol 2016 12 8;18(12):4782-4793. Epub 2016 Jun 8.

Lake and Glacier Ecology Research Group, Institute of Ecology, University of Innsbruck, Technikerstraße 25, 6020, Innsbruck, Austria.

Phosphorus often limits bacterial production in freshwater ecosystems. However, little is known on whether different bacteria contribute to inorganic and organic phosphorus uptake proportionally to their relative abundance and production. Here, we followed the temporal dynamics of the main heterotrophic bacterial taxa taking up inorganic phosphate ( P-Pi) and organic phosphorus ( P-ATP) in two mountain lakes and compared them to their contribution to bacterial production ( H-leucine uptake). The short turnover times for Pi and ATP suggested that in both lakes, phosphorus was limiting most of the year. The bulk uptake rates and the fractions of cells labelled positive for Pi and ATP uptake followed a seasonal trend with minima in winter and maxima in summer. Generally, the bacterial taxa examined contributed to Pi and ATP uptake proportionally to their relative abundance, but not always to their contribution to bacterial production. For instance, AcI Actinobacteria were often underrepresented in phosphorus uptake compared with leucine incorporation suggesting they might have high intracellular C:P ratios. Our results emphasize that ATP utilization is widespread among freshwater bacteria and indicate that members within the dominant bacterial taxa (Actinobacteria and Betaproteobacteria) have variable phosphorus requirements, probably due to their different growth potential and variable degrees of homeostasis.
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http://dx.doi.org/10.1111/1462-2920.13368DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5213779PMC
December 2016

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

Sci Rep 2016 04 20;6:24608. Epub 2016 Apr 20.

University of Innsbruck, Institute of Ecology, Lake and Glacier Research Group, Technikerstr. 25, 6020 Innsbruck, Austria.

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.
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http://dx.doi.org/10.1038/srep24608DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4837353PMC
April 2016

Microbial eukaryote plankton communities of high-mountain lakes from three continents exhibit strong biogeographic patterns.

Mol Ecol 2016 05 14;25(10):2286-301. Epub 2016 May 14.

Department of Ecology, University of Kaiserslautern, Kaiserslautern, 67663, Germany.

Microbial eukaryotes hold a key role in aquatic ecosystem functioning. Yet, their diversity in freshwater lakes, particularly in high-mountain lakes, is relatively unknown compared with the marine environment. Low nutrient availability, low water temperature and high ultraviolet radiation make most high-mountain lakes extremely challenging habitats for life and require specific molecular and physiological adaptations. We therefore expected that these ecosystems support a plankton diversity that differs notably from other freshwater lakes. In addition, we hypothesized that the communities under study exhibit geographic structuring. Our rationale was that geographic dispersal of small-sized eukaryotes in high-mountain lakes over continental distances seems difficult. We analysed hypervariable V4 fragments of the SSU rRNA gene to compare the genetic microbial eukaryote diversity in high-mountain lakes located in the European Alps, the Chilean Altiplano and the Ethiopian Bale Mountains. Microbial eukaryotes were not globally distributed corroborating patterns found for bacteria, multicellular animals and plants. Instead, the plankton community composition emerged as a highly specific fingerprint of a geographic region even on higher taxonomic levels. The intraregional heterogeneity of the investigated lakes was mirrored in shifts in microbial eukaryote community structure, which, however, was much less pronounced compared with interregional beta-diversity. Statistical analyses revealed that on a regional scale, environmental factors are strong predictors for plankton community structures in high-mountain lakes. While on long-distance scales (>10 000 km), isolation by distance is the most plausible scenario, on intermediate scales (up to 6000 km), both contemporary environmental factors and historical contingencies interact to shift plankton community structures.
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http://dx.doi.org/10.1111/mec.13633DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4976798PMC
May 2016

When glaciers and ice sheets melt: consequences for planktonic organisms.

Authors:
Ruben Sommaruga

J Plankton Res 2015 May;37(3):509-518

LAKE AND GLACIER ECOLOGY RESEARCH GROUP, INSTITUTE OF ECOLOGY, UNIVERSITY OF INNSBRUCK, TECHNIKERSTR. 25, INNSBRUCK 6020, AUSTRIA.

The current melting of glaciers and ice sheets is a consequence of climatic change and their turbid meltwaters are filling and enlarging many new proglacial and ice-contact lakes around the world, as well as affecting coastal areas. Paradoxically, very little is known on the ecology of turbid glacier-fed aquatic ecosystems even though they are at the origin of the most common type of lakes on Earth. Here, I discuss the consequences of those meltwaters for planktonic organisms. A remarkable characteristic of aquatic ecosystems receiving the discharge of meltwaters is their high content of mineral suspensoids, so-called glacial flour that poses a real challenge for filter-feeding planktonic taxa such as and phagotrophic groups such as heterotrophic nanoflagellates. The planktonic food-web structure in highly turbid meltwater lakes seems to be truncated and microbially dominated. Low underwater light levels leads to unfavorable conditions for primary producers, but at the same time, cause less stress by UV radiation. Meltwaters are also a source of inorganic and organic nutrients that could stimulate secondary prokaryotic production and in some cases (e.g. in distal proglacial lakes) also phytoplankton primary production. How changes in turbidity and in other related environmental factors influence diversity, community composition and adaptation have only recently begun to be studied. Knowledge of the consequences of glacier retreat for glacier-fed lakes and coasts will be crucial to predict ecosystem trajectories regarding changes in biodiversity, biogeochemical cycles and function.
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http://dx.doi.org/10.1093/plankt/fbv027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4747089PMC
May 2015