Fungal communities in Scandinavian lakes along a longitudinal gradient

Khomich, Maryia; Davey, Marie L.; Kauserud, Håvard; Rasconi, Séréna; Andersen, Tom

doi:10.1016/j.funeco.2017.01.008

Cited by 46 publications

(48 citation statements)

References 101 publications

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“…This indicates that the propagules and mycelial fragments in soil and plant materials (e.g., decomposing leaves) flow into the river via the surface current or with the direct addition of these substrates (Voronin 2014). Recent studies that investigated the environmental fungal DNA of lakes and rivers also detected a significant amount of DNA for terrestrial fungi, as well as for aquatic fungi (Deiner et al 2016, Khomich et al 2017LeBrun et al 2018). Our results are consistent with the results of these previous studies.…”

Section: Fungal Diversity In River Watersupporting

confidence: 91%

Spatial structure of fungal DNA assemblages revealed with eDNA metabarcoding in a forest river network in western Japan

Matsuoka¹,

Sugiyama²,

Sato³

et al. 2019

MBMG

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Growing evidence has revealed high diversity and spatial heterogeneity of fungal communities in local habitats of terrestrial ecosystems. Recently, the analysis of environmental DNA has been undertaken to study the biodiversity of organisms, such as animals and plants, in both aquatic and terrestrial habitats. In the present study, we investigated fungal DNA assemblages and their spatial structure using environmental DNA metabarcoding targeting the internal transcribed spacer 1 (ITS1) region of the rRNA gene cluster in habitats across different branches of rivers in forest landscapes. A total of 1,956 operational taxonomic units (OTUs) were detected. Of these, 770 were assigned as Ascomycota, 177 as Basidiomycota, and 38 as Chytridiomycota. The river water was found to contain functionally diverse OTUs of both aquatic and terrestrial fungi, such as plant decomposers and mycorrhizal fungi. These fungal DNA assemblages were more similar within, rather than between, river branches. In addition, the assemblages were more similar between spatially closer branches. This spatial structuring was significantly associated with geographic distances but not with vegetation of the catchment area and the elevation at the sampling points. Our results imply that information on the terrestrial and aquatic fungal compositions of watersheds, and therefore their spatial structure, can be obtained by investigating the fungal DNA assemblages in river water.

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Section: Fungal Diversity In River Watersupporting

confidence: 91%

Spatial structure of fungal DNA assemblages revealed with eDNA metabarcoding in a forest river network in western Japan

Matsuoka¹,

Sugiyama²,

Sato³

et al. 2019

MBMG

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show abstract

“…In TABLE S4 of REF 30 it is obvious that most fungi in a large number of lakes and ponds in northeast Germany are uncharacterized and hence unknown. A similar pattern has been also found by another study exploring biogeographical patterns and biases of fungal diversity 31 . Targeted isolation approaches have started to reveal that some of these novel lineages within the early diverging fungi represent parasitic fungi of phytoplankton 32,33 .…”

Section: Under-explored Diversity Of Aquatic Fungisupporting

confidence: 86%

“…In contrast to global fungal studies in soil ecosystems 35,36 , studies on aquatic fungi have mostly addressed distribution patterns at the regional scales (e.g. river basin 37 , Scandinavian lakes 31 , or ocean basin 38 ). Relatively recently, large-scale public datasets such as the International Census of Marine Microbes, the Tara Oceans Expeditions or the Earth Microbiome Project have become available, enabling a new era of analysing global drivers of, e.g., marine fungi 39,40 .…”

Section: Under-explored Diversity Of Aquatic Fungimentioning

confidence: 99%

Fungi in aquatic ecosystems

et al. 2019

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Fungi are phylogenetically and functionally diverse ubiquitous components of almost all ecosystems on Earth, including aquatic environments stretching from high montane lakes down to the deep ocean. Aquatic ecosystems, however, remain frequently overlooked as fungal habitats, although fungi potentially hold important roles for organic matter cycling and food web dynamics. Within a broad ecological framework, we conceptualize the spatio-temporal dimensions, diversity, functions and organismic interactions of fungi in structuring aquatic foodwebs. We focus on currently unexplored fungal diversity, highlighting poorly understood ecosystems, including emerging artificial aquatic habitats. Recent methodological improvements have facilitated a greater appreciation of the importance of fungi in many aquatic systems, yet a conceptual framework is still missing. To date, aquatic fungi and their interactions have largely remained "hidden" and require interdisciplinary efforts to be explored in an ecosystem context. There remain obvious methodological and knowledge gaps to explore potential functions of aquatic fungi, moving from the microscale to the global scale. This knowledge is urgently needed since we humans strongly interfere with structure and function of natural ecosystems by permanently reshaping most of the Earth's surface and creating vast areas of novel urban habitats. Introduction: Recent advances in DNA sequencing technology have revealed that fungi are abundant in many, if not all aquatic ecosystems, however their diversity, quantitative abundance, ecological function and, in particular, their interactions with other microorganisms, remain largely speculative, unexplored and missing from current general concepts in aquatic ecology and biogeochemistry 1-4. This is surprising since terrestrial-focused research has understood the outstanding ecological role of fungi for >100 years, and therefore fungi constitute a major component of general concepts in terrestrial science 5,6. In aquatic ecosystems, the systematic analysis of fungal diversity and their ecological roles has faced several setbacks due to methodological limitations and a too small scientific community, in particular in the marine environment 7-11. This review focusses on aquatic fungi, which form a morphologically, phylogenetically, and ecologically diverse group 7. We here broadly define "aquatic fungi" as fungi that rely for the whole or part of their life cycle on aquatic habitats (FIG. 1). Three groups (indwellers, periodic immigrants and versatile immigrants) based on their degree of adaptation and dependence on aquatic habitats have been previously defined 12. We highlight the numerous knowledge gaps in their diversity, interactions and functional roles, as well as methodological limitations. In this review we propose new research avenues to set aquatic fungi in a broad ecological framework. Here, we do not explore the many existing gaps in the fungal phylogenetic tree. In aquatic systems, fungi constitute a significant proportion of eukaryo...

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“…This means that fungal DNA assemblages are more similar between spatially closer branches than between distant ones. Such geographical structures have also been observed by Khomich et al (2017); fungal DNA assemblages along latitudes and longitudes were investigated in a lake in the Scandinavia Peninsula. In the lake, the surrounding rivers brought and accumulated the DNA of terrestrial fungi from the surrounding areas (Khomich et al, 2017).…”

Section: Discussionsupporting

confidence: 55%

“…Such geographical structures have also been observed by Khomich et al (2017); fungal DNA assemblages along latitudes and longitudes were investigated in a lake in the Scandinavia Peninsula. In the lake, the surrounding rivers brought and accumulated the DNA of terrestrial fungi from the surrounding areas (Khomich et al, 2017). Our study shows that such geographical structures can also be observed in streams, where water has a directional flow and is constantly replaced.…”

Section: Discussionsupporting

confidence: 55%

Spatial structures of fungal DNA assemblages revealed with eDNA metabarcoding in a forest river network in western Japan

Matsuoka

Sugiyama

Sato

et al. 2019

Preprint

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24Growing evidence has revealed high diversity and spatial heterogeneity of fungal 25 communities including in local habitats in terrestrial ecosystems. These findings highlight 26 the considerable sampling effort, analysis time, and costs required for the investigation 27 of fungal diversity over large spatial scales. Recently, the analysis of environmental DNA 28 in river water has been undertaken to study the biodiversity of organisms, such as animals 29 and plants, in both aquatic and terrestrial habitats. However, previous studies have not 30 investigated the spatial structure of fungal DNA assemblages in river water. In the present 31 study, we investigate fungal DNA assemblages and their spatial structure using 32 environmental DNA metabarcoding in water across different branches of river over forest 33 landscapes. The river water was found to contain both phylogenetically and functionally 34 diverse fungal DNA, including aquatic and terrestrial fungi, such as plant decomposers 35 and mycorrhizal fungi. These fungal DNA assemblages were more similar within, rather 36 than between, branches. In addition, the assemblages were more similar between spatially 37 closer branches. These results imply that information on the terrestrial and aquatic fungal 38 compositions of watersheds, and therefore their spatial structure can be obtained by 39 investigating the fungal DNA assemblages in river water. 40 41 Keywords 42 environmental DNA, fungi, forest river, metabarcoding, spatial structure 43 44 45 Information on biodiversity composition is essential to understand the ecological 46 processes and functions of ecosystems. Understanding patterns of biodiversity is 47 fundamental for the maintenance of ecological processes during this era of environmental 48 change (Margules and Pressey, 2000; Pecl et al., 2017). The Kingdom Fungi boasts high 49 species diversity and undertakes unique functions in both terrestrial and aquatic 50 ecosystems via the decomposition of organic substrates and symbiotic or parasitic 51 interactions with other organisms, such as animals and plants (Peay et al., 2016; 52 Hawksworth and Lücking, 2017; Grossart et al., 2019). Recently, with the growing use 53 of DNA metabarcoding techniques, an increasing number of studies are investigating 54 fungal diversity on a variety of substrates in terrestrial and aquatic habitats (Duarte et al., 55 2015; Peay et al., 2016; Nilsson et al., 2019). However, as fungi show high local diversity 56 and spatial heterogeneity (Bahram et al., 2015, 2016), the investigation of fungal diversity 57 over large spatial scales, such as landscape (tens of km) and regional scales (hundreds to 58 thousands of km) requires a significant amount of sampling effort, time for analysis, and 59 costs. 60 Recently, the availability of environmental DNA in river water for biodiversity 61 exploration has been discussed in several studies (Deiner et al., 2016; Nakagawa et al. 62 2018). Deiner et al. (2016) suggest that river water can integrate DNA from the catchment 63 ...

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Fungal communities in Scandinavian lakes along a longitudinal gradient

Cited by 46 publications

References 101 publications

Spatial structure of fungal DNA assemblages revealed with eDNA metabarcoding in a forest river network in western Japan

Spatial structure of fungal DNA assemblages revealed with eDNA metabarcoding in a forest river network in western Japan

Fungi in aquatic ecosystems

Spatial structures of fungal DNA assemblages revealed with eDNA metabarcoding in a forest river network in western Japan

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