Trade‐off between taxon diversity and functional diversity in European lake ecosystems

Großmann, Lars; Beißer, Daniela; Böck, Christina; Chatzinotas, Antonis; Jensen, Manfred; Preisfeld, Angelika; Psenner, Roland; Rahmann, Sven; Wodniok, Sabina; Boenigk, Jens

doi:10.1111/mec.13878

Cited by 26 publications

(27 citation statements)

References 57 publications

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“…These three sequences were used for the generation of a custom reference sequence database and are available at community composition of a natural ecosystem. With its broad application in many other environments (Grossmann et al 2016), it is striking how rarely such approaches have been used for psychrophilic algae. So far a few studies have targeted snow algal communities in the Arctic (Lutz et al 2015a;Lutz et al 2015b;Lutz et al 2016Lutz et al , 2017Segawa et al 2018), in the US (Brown et al 2016), in Japan (Terashima et al 2017 and in Antarctica (Segawa et al 2018).…”

Section: Methodsmentioning

confidence: 99%

Evaluating amplicon high-throughput sequencing data of microalgae living in melting snow: improvements and limitations

Lutz¹,

Procházková²,

Benning³

et al. 2019

Fottea

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Melting snowfields are dominated by closely related green algae. Although microscopy-based classification are evaluable distinction tools, they can be challenging and may not reveal the diversity. High-throughput sequencing (HTS) allows for a comprehensive community evaluation but has been rarely used in such ecosystems. We found that assigning taxonomy to DNA sequences strongly depends on the quality of the reference databases. Furthermore, for an accurate identification, a combination of manual inspection of automated assignments, and oligotyping of the abundant 18S OTUs and ITS2 secondary structure analyses were needed. The use of one marker can be misleading because of low variability (18S) or the scarcity of references (ITS2). Our evaluation reveals that HTS outputs need to be thoroughly checked when the organisms are poorly represented in databases. We recommend an optimized workflow including consistent sampling, a two-molecular marker approach, light microscopy-based guidance, generation of appropriate reference sequences and a final manual verification of taxonomic assignments as a best approach for accurate diversity analyses.

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Section: Methodsmentioning

confidence: 99%

Evaluating amplicon high-throughput sequencing data of microalgae living in melting snow: improvements and limitations

Lutz¹,

Procházková²,

Benning³

et al. 2019

Fottea

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“…Many natural processes are strongly influenced by characteristics of their surroundings, i.e., it is known that chemical composition, size of different habitats, and socio-economic features such as human population size, can influence the (microbial) biodiversity in ecosystems [2–5]. Therefore, having access to environmental characteristics and including them in analyses is crucial when trying to understand natural processes.…”

Section: Introductionmentioning

confidence: 99%

SEDE-GPS: socio-economic data enrichment based on GPS information

Sperlea¹,

Füser²,

Boenigk³

et al. 2018

BMC Bioinformatics

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BackgroundMicrobes are essentail components of all ecosystems because they drive many biochemical processes and act as primary producers. In freshwater ecosystems, the biodiversity in and the composition of microbial communities can be used as indicators for environmental quality. Recently, some environmental features have been identified that influence microbial ecosystems. However, the impact of human action on lake microbiomes is not well understood. This is, in part, due to the fact that environmental data is, albeit theoretically accessible, not easily available.ResultsIn this work, we present SEDE-GPS, a tool that gathers data that are relevant to the environment of an user-provided GPS coordinate. To this end, it accesses a list of public and corporate databases and aggregates the information in a single file, which can be used for further analysis. To showcase the use of SEDE-GPS, we enriched a lake microbial ecology sequencing dataset with around 18,000 socio-economic, climate, and geographic features. The sources of SEDE-GPS are public databases such as Eurostat, the Climate Data Center, and OpenStreetMap, as well as corporate sources such as Twitter. Using machine learning and feature selection methods, we were able to identify features in the data provided by SEDE-GPS that can be used to predict lake microbiome alpha diversity.ConclusionThe results presented in this study show that SEDE-GPS is a handy and easy-to-use tool for comprehensive data enrichment for studies of ecology and other processes that are affected by environmental features. Furthermore, we present lists of environmental, socio-economic, and climate features that are predictive for microbial biodiversity in lake ecosystems. These lists indicate that human action has a major impact on lake microbiomes. SEDE-GPS and its source code is available for download at http://SEDE-GPS.heiderlab.deElectronic supplementary materialThe online version of this article (10.1186/s12859-018-2419-4) contains supplementary material, which is available to authorized users.

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“…Freshwater lakes provide essential ecosystem services whose quality often depends on their microbial communities (Grossmann et al, ; Paix, Ezzedine, & Jacquet, ). Understanding the temporal scales of changes in prokaryote and protist communities can provide a deeper understanding of the processes operating in an ecosystem (Su et al, ).…”

Section: Discussionmentioning

confidence: 99%

“…Here, the timing of the response of prokaryotes and protists was not the same across habitats but was generally related to a gradient in precipitation. Despite changes in large‐scale temporal patterns, ecosystem functions might not be compromised because of functional redundancy of microbial communities (Allison & Martiny, ; Grossmann et al, ).…”

Section: Discussionmentioning

confidence: 99%

Multifaceted aspects of synchrony between freshwater prokaryotes and protists

2019

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Community composition of freshwater prokaryotes and protists varies through time. Few studies contemporarily investigate temporal variation of these freshwater communities for more than 1 year. We compared the temporal patterns of prokaryotes and protists in three distinct habitats for 4 years (2014–2017) in Lake Tovel, a cold‐water lake. This lake showed a marked temperature increase in 2017 linked to altered precipitation patterns. We investigated whether microbial communities reflected this change across habitats and whether changes occurred at the same time and to the same extent. Furthermore, we tested the concept of hydrological year emphasizing the ecological effect of water renewal on communities for its explanatory power of community changes. Microbe diversity was assessed by Illumina sequencing of the V3–V4 hypervariable region of the 16S rRNA gene and 18S rRNA gene, and we applied co‐inertia analysis and asymmetric eigenvector maps modelling to infer synchrony and temporal patterns of prokaryotes and protists. When considering community composition, microbes were invariable in synchrony across habitats and indicated a temporal gradient linked to decreasing precipitation; however, when looking at temporal patterns, the extent of synchrony was reduced. Small‐scale patterns were similar across habitats and microbes and linked to seasonally varying environmental variables, while large‐scale patterns were different and partially linked to an ecosystem change as indicated by increasing water transparency and temperature and decreasing dissolved oxygen. Our advanced statistical approach outlined the multifaceted aspect of synchrony when linked to community composition and temporal patterns.

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Trade‐off between taxon diversity and functional diversity in European lake ecosystems

Cited by 26 publications

References 57 publications

Evaluating amplicon high-throughput sequencing data of microalgae living in melting snow: improvements and limitations

Evaluating amplicon high-throughput sequencing data of microalgae living in melting snow: improvements and limitations

SEDE-GPS: socio-economic data enrichment based on GPS information

Multifaceted aspects of synchrony between freshwater prokaryotes and protists

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