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Book: Biodiversität zwischen Wasser und Land

Altermatt, Florian / Güsewell, Sabine / Holderegger, Rolf

Exkursionen zu Gewässern, Mooren und Auen der Schweiz

2024

Author's details	Florian Altermatt, Sabine Güsewell, Rolf Holderegger
Subject code	580
Language	German
Size	256 Seiten, ca. 250 Abbildungen, 22.5 cm x 15.5 cm
Edition	1. Auflage 2024
Publisher	Haupt Verlag
Publishing place	Bern
Publishing country	Switzerland
Document type	Book
HBZ-ID	HT030740750
ISBN	978-3-258-08368-1 ; 3-258-08368-1
Database	Catalogue ZB MED Nutrition, Environment, Agriculture

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Shelf mark	Loan status	Location
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Book: Hotspot Furka

Hiltbrunner, Erika / Körner, Christian / Altermatt, Florian

biologische Vielfalt im Gebirge

2018

Author's details	[Herausgeber] Erika Hiltbrunner und Christian Körner ; mit Beiträgen von Florian Altermatt [und vielen weiteren]
Language	German
Size	60 Seiten, Illustrationen, Diagramme, Karten
Publisher	Alpine Forschungs- und Ausbildungsstation Furka (ALPFOR)
Publishing place	Basel
Publishing country	Switzerland
Document type	Book
HBZ-ID	HT019774293
ISBN	978-3-033-06701-1 ; 3-033-06701-8
Database	Catalogue ZB MED Nutrition, Environment, Agriculture

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184/117	available for loan (reading room)	Freihandmagazin (U1)

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Article ; Online: Invasive species drive cross-ecosystem effects worldwide.

Peller, Tianna / Altermatt, Florian

Nature ecology & evolution

2024

Abstract: Invasive species are pervasive around the world and have profound impacts on the ecosystem they invade. Invasive species, however, can also have impacts beyond the ecosystem they invade by altering the flow of non-living materials (for example, nutrients ...

Abstract	Invasive species are pervasive around the world and have profound impacts on the ecosystem they invade. Invasive species, however, can also have impacts beyond the ecosystem they invade by altering the flow of non-living materials (for example, nutrients or chemicals) or movement of organisms across the boundaries of the invaded ecosystem. Cross-ecosystem interactions via spatial flows are ubiquitous in nature, for example, connecting forests and lakes, grasslands and rivers, and coral reefs and the deep ocean. Yet, we have a limited understanding of the cross-ecosystem impacts invasive species have relative to their local effects. By synthesizing emerging evidence, here we demonstrate the cross-ecosystem impacts of invasive species as a ubiquitous phenomenon that influences biodiversity and ecosystem functioning around the world. We identify three primary ways by which invasive species have cross-ecosystem effects: first, by altering the magnitude of spatial flows across ecosystem boundaries; second, by altering the quality of spatial flows; and third, by introducing novel spatial flows. Ultimately, the strong impacts invasive species can drive across ecosystem boundaries suggests the need for a paradigm shift in how we study and manage invasive species around the world, expanding from a local to a cross-ecosystem perspective.
Language	English
Publishing date	2024-03-19
Publishing country	England
Document type	Journal Article ; Review
ISSN	2397-334X
ISSN (online)	2397-334X
DOI	10.1038/s41559-024-02380-1
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Editorial. Environmental threats we can act upon. How to use the science-policy dialogue

Altermatt, Florian

Gaia

2021 Volume 30, Issue 3, Page(s) 137

Language	German ; English
Document type	Article
ZDB-ID	1114994-2
ISSN	0940-5550
Database	Current Contents Nutrition, Environment, Agriculture

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Article ; Online: Spatiotemporal dynamics in freshwater amphipod assemblages are associated with surrounding terrestrial land use type

Cereghetti, Eva / Altermatt, Florian

Ecosphere. 2023 Mar., v. 14, no. 3 p.e4469-

2023

Abstract: Biological assemblages are the result of dynamic processes that have explicit temporal and spatial dimensions. Although biodiversity patterns can be directly inferred from the structure of these assemblages, an assessment of changes through time and ... ...

Abstract	Biological assemblages are the result of dynamic processes that have explicit temporal and spatial dimensions. Although biodiversity patterns can be directly inferred from the structure of these assemblages, an assessment of changes through time and space is needed to understand how organisms initially assembled and how they are responding to local environmental and biotic factors. Small freshwater streams are particularly affected by contemporary anthropogenic activities and biological invasions, yet they are commonly less studied, as studies often focus on lakes and large streams. Here, we conducted a spatially explicit analysis of keystone shredder assemblages across eight years in 12 replicated small tributary streams. In each stream, we monitored multiple sites per kilometer of stream length. By assessing temporal beta diversity dynamics, defined by the gain or loss of species or abundance per species at individual sites, we show that changes in amphipod assemblages occur within the context of the surrounding terrestrial matrix and reflect recent amphipod colonization history. While amphipod composition was mostly constant in streams located in forested catchments, streams embedded in catchments with more extensive agricultural land use displayed more pronounced temporal changes, either driven by colonization of unoccupied upstream locations or by more pronounced but undirected fluctuations in gains and losses of species or abundance per species. Our study thus suggests that agricultural landscapes might destabilize aquatic amphipod assemblages, causing higher temporal changes in community structures and highlighting the vulnerability of aquatic ecosystems to terrestrial land use drivers.
Keywords	Amphipoda ; agricultural land ; freshwater ; land use ; species diversity ; streams
Language	English
Dates of publication	2023-03
Publishing place	John Wiley & Sons, Inc.
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	2572257-8
ISSN	2150-8925
ISSN	2150-8925
DOI	10.1002/ecs2.4469
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Management of DNA reference libraries for barcoding and metabarcoding studies with the R package refdb

Keck, François / Altermatt, Florian

Molecular Ecology Resources. 2023 Feb., v. 23, no. 2 p.511-518

2023

Abstract: DNA barcoding and metabarcoding are revolutionizing the study and survey of biodiversity. In order to assign taxonomic labels to the DNA sequence data retrieved, these methods are strongly dependent on comprehensive and accurate reference databases. ... ...

Abstract	DNA barcoding and metabarcoding are revolutionizing the study and survey of biodiversity. In order to assign taxonomic labels to the DNA sequence data retrieved, these methods are strongly dependent on comprehensive and accurate reference databases. Producing reliable databases linking biological sequences and taxonomic data can be—and often has been—done using mainstream tools such as spreadsheet software. However, spreadsheets quickly become insufficient when the amount of data increases to thousands of taxa and sequences to be matched, and validation operations become more complex and are error prone if done in a manual way. Thus, there is a clear need for providing scientists with user‐friendly, reliable and powerful tools to manipulate and manage DNA reference databases in tractable, sound and efficient ways. Here, we introduce the R package refdb as an environment for semi‐automatic and assisted construction of DNA reference libraries. The refdb package is a reference database manager offering a set of powerful functions to import, organize, clean, filter, audit and export the data. It is broadly applicable in metabarcoding data generally obtained in biodiversity and biomonitoring studies. We present the main features of the package and outline how refdb can speed up reference database generation, management and handling, and thus contribute to standardization and repeatability in barcoding and metabarcoding studies.
Keywords	DNA ; DNA barcoding ; biodiversity ; computer software ; databases ; environmental monitoring ; imports ; nucleotide sequences ; surveys
Language	English
Dates of publication	2023-02
Size	p. 511-518.
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	2406816-0
ISSN	1471-8286 ; 1755-098X
ISSN (online)	1471-8286
ISSN	1755-098X
DOI	10.1111/1755-0998.13723
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Management of DNA reference libraries for barcoding and metabarcoding studies with the R package refdb.

Keck, François / Altermatt, Florian

Molecular ecology resources

2022

Abstract	DNA barcoding and metabarcoding are revolutionizing the study and survey of biodiversity. In order to assign taxonomic labels to the DNA sequence data retrieved, these methods are strongly dependent on comprehensive and accurate reference databases. Producing reliable databases linking biological sequences and taxonomic data can be-and often has been-done using mainstream tools such as spreadsheet software. However, spreadsheets quickly become insufficient when the amount of data increases to thousands of taxa and sequences to be matched, and validation operations become more complex and are error prone if done in a manual way. Thus, there is a clear need for providing scientists with user-friendly, reliable and powerful tools to manipulate and manage DNA reference databases in tractable, sound and efficient ways. Here, we introduce the R package refdb as an environment for semi-automatic and assisted construction of DNA reference libraries. The refdb package is a reference database manager offering a set of powerful functions to import, organize, clean, filter, audit and export the data. It is broadly applicable in metabarcoding data generally obtained in biodiversity and biomonitoring studies. We present the main features of the package and outline how refdb can speed up reference database generation, management and handling, and thus contribute to standardization and repeatability in barcoding and metabarcoding studies.
Language	English
Publishing date	2022-10-14
Publishing country	England
Document type	Journal Article
ZDB-ID	2406833-0
ISSN	1755-0998 ; 1755-098X
ISSN (online)	1755-0998
ISSN	1755-098X
DOI	10.1111/1755-0998.13723
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Measuring the state of aquatic environments using eDNA-upscaling spatial resolution of biotic indices.

Blackman, Rosetta C / Carraro, Luca / Keck, François / Altermatt, Florian

Philosophical transactions of the Royal Society of London. Series B, Biological sciences

2024 Volume 379, Issue 1904, Page(s) 20230121

Abstract: Aquatic macroinvertebrates, including many aquatic insect orders, are a diverse and ecologically relevant organismal group yet they are strongly affected by anthropogenic activities. As many of these taxa are highly sensitive to environmental change, ... ...

Abstract	Aquatic macroinvertebrates, including many aquatic insect orders, are a diverse and ecologically relevant organismal group yet they are strongly affected by anthropogenic activities. As many of these taxa are highly sensitive to environmental change, they offer a particularly good early warning system for human-induced change, thus leading to their intense monitoring. In aquatic ecosystems there is a plethora of biotic monitoring or biomonitoring approaches, with more than 300 assessment methods reported for freshwater taxa alone. Ultimately, monitoring of aquatic macroinvertebrates is used to calculate ecological indices describing the state of aquatic systems. Many of the methods and indices used are not only hard to compare, but especially difficult to scale in time and space. Novel DNA-based approaches to measure the state and change of aquatic environments now offer unprecedented opportunities, also for possible integration towards commonly applicable indices. Here, we first give a perspective on DNA-based approaches in the monitoring of aquatic organisms, with a focus on aquatic insects, and how to move beyond traditional point-based biotic indices. Second, we demonstrate a proof-of-concept for spatially upscaling ecological indices based on environmental DNA, demonstrating how integration of these novel molecular approaches with hydrological models allows an accurate evaluation at the catchment scale. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.
MeSH term(s)	Animals ; Aquatic Organisms/genetics ; Biodiversity ; Biological Monitoring/methods ; DNA, Environmental/analysis ; Ecosystem ; Environmental Monitoring/methods ; Insecta/genetics
Chemical Substances	DNA, Environmental
Language	English
Publishing date	2024-05-06
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	208382-6
ISSN	1471-2970 ; 0080-4622 ; 0264-3839 ; 0962-8436
ISSN (online)	1471-2970
ISSN	0080-4622 ; 0264-3839 ; 0962-8436
DOI	10.1098/rstb.2023.0121
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Context‐dependent evolution of high trophic position drives functional disparity in subterranean crustaceans

Premate, Ester / Borko, Špela / Altermatt, Florian / Fišer, Cene

Functional Ecology. 2023 Sept., v. 37, no. 9 p.2523-2534

2023

Abstract: Species performance depends on the concerted interplay of their functional traits. Natural selection acts on the performance of the species and influences entire suits of interdependent functional traits, thereby driving the evolution of functional ... ...

Abstract	Species performance depends on the concerted interplay of their functional traits. Natural selection acts on the performance of the species and influences entire suits of interdependent functional traits, thereby driving the evolution of functional diversity (FD) within a clade. In a given habitat, interdependent functional traits are expected to integrate into only a few adaptive combinations. When a clade diversifies in different habitats, the FD within habitats (herein called α‐FD) diversifies in response to local selections, while between the habitats, alternative adaptive combinations of interdependent traits that are specific to the habitat emerge. This multivariate selection leads to two hypotheses. First, realized α‐FD within one habitat represents only a small fraction of the variation of functional traits, and second, realized FDs across habitats (hereafter called β‐FD) are equal to or greater than would be in the absence of the interdependence of functional traits. We tested these hypotheses using 185 species of the highly diverse subterranean amphipod genus Niphargus living in three habitats: river interstitial, cave lakes, and cave streams. We (i) explored integration of functional traits related to locomotion and feeding biology and tested (ii) if realized α‐FD within each habitat is lower than it would be without trait interdependence, and (iii) if realized β‐FD in pairwise comparisons of habitats is higher than it would be without trait interdependence. In all three habitats, the length of the appendages as a proxy of the locomotion speed was positively correlated with the trophic position of the species. On the contrary, the body shape correlations were habitat dependent: species in high trophic positions were slender, stout or invariant in shape in interstitial, cave streams and cave lakes, respectively. Using null models, we show that only a fraction of functional trait combinations was realized in each habitat, whereas β‐FD between habitats was equal to or greater than the null expectations. The results indicate preserved potential for diversification in species within and between habitats. This potential can be realized through hybridization and can drive diversification in adaptive radiations. Moreover, this perspective on the evolution of FD is compatible with several central ecological and evolutionary concepts, such as adaptive landscape or ecological niche theory. Read the free Plain Language Summary for this article on the Journal blog.
Keywords	Amphipoda ; functional diversity ; hybridization ; locomotion ; natural selection ; niches ; rivers
Language	English
Dates of publication	2023-09
Size	p. 2523-2534.
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	2020307-X
ISSN	1365-2435 ; 0269-8463
ISSN (online)	1365-2435
ISSN	0269-8463
DOI	10.1111/1365-2435.14407
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Optimizing laboratory cultures of Gammarus fossarum (Crustacea: Amphipoda) as a study organism in environmental sciences and ecotoxicology

Alther, Roman / Krähenbühl, Andrin / Bucher, Pascal / Altermatt, Florian

Science of the Total Environment. 2023 Jan., v. 855 p.158730-

2023

Abstract: Amphipods are among the most abundant macroinvertebrates in freshwater ecosystems of the Palaearctic and crucial for ecosystem functioning. Furthermore, their high sensitivity to environmental change and pollutants makes them widely used model organisms ... ...

Abstract	Amphipods are among the most abundant macroinvertebrates in freshwater ecosystems of the Palaearctic and crucial for ecosystem functioning. Furthermore, their high sensitivity to environmental change and pollutants makes them widely used model organisms in environmental sciences and ecotoxicology. In field studies and surveys across Eurasia, species of the genus Gammarus are commonly used, yet laboratory-based studies and ecotoxicological tests are often restricted to the in most parts of the world non-native Hyalella azteca, as Gammarus is much harder to breed and maintain under laboratory conditions. However, for direct comparisons and extrapolations of results of field- vs. laboratory-based studies, the use of the same species would be desirable. Here, we investigated different settings with respect to feeding, shelter and day length to successfully increase survival, juvenile production and their respective growth and survival, and ultimately multi-generation breeding of the amphipod Gammarus fossarum. Amphipod populations persisted and reproduced successfully under optimized husbandry conditions for 12 months and were partially maintained for another year in populations up to a few hundred individuals. Specifically, supplementing diet with protein-rich food sources as well as the provisioning of shelters improved survival rate of G. fossarum significantly. However, we found no significant effect of different day length treatments on the overall relative reproductive activity or on the total amphipod abundance maintained. We conclude that G. fossarum can be kept and reared under standardized conditions. Despite the longer generation times of G. fossarum and higher effort required for maintenance compared to H. azteca, direct ecological relevance and comparability of results to natural systems may justify its future use and development as a study organism for environmental sciences and ecotoxicology.
Keywords	Gammarus fossarum ; Hyalella azteca ; Palearctic region ; diet ; ecosystems ; ecotoxicology ; freshwater ; juveniles ; macroinvertebrates ; photoperiod ; survival rate ; Eurasia ; Breeding ; Gammaridae ; Feeding ; Method ; Rearing ; Reproduction
Language	English
Dates of publication	2023-01
Publishing place	Elsevier B.V.
Document type	Article ; Online
Note	Use and reproduction
ZDB-ID	121506-1
ISSN	1879-1026 ; 0048-9697
ISSN (online)	1879-1026
ISSN	0048-9697
DOI	10.1016/j.scitotenv.2022.158730
Database	NAL-Catalogue (AGRICOLA)

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