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  • 1
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    Mycoplankton diversity in the Elbe River (2021)
    PANGAEA
    Details
    Publication Date: 2024-02-24
    Description: Rivers are important transport systems for nutrients and organic material and thus influence biogeochemical cycles and food web structures. Microorganismal biodiversity is an important parameter for the ecological balance of river ecosystems. Despite the knowledge that freshwater fungi perform important ecological functions, there is scarcely any fungal data available for river systems. In this study, we address the fundamental question of how mycoplankton communities are structured and assembled over a longer river section with strong environmental gradients and anthropogenic pressure and what variables control on it. The mycoplankton communities from the shallow freshwater to the coastal-oceanic transition zone were analyzed based on 18S rRNA gene tag-sequencing and the observed patterns were related to environmental and spatial factors by multivariate statistics. Finally, the underlying assembly processes were revealed by Quantitative Process Estimates (QPE) method. The partitioning of mycoplankton communities deviated from the previously described patterns of fluvial microbial communities, triggered by a strong influence of local environmental conditions, which were partly under spatial control. The deepening of the Elbe River for improved navigation purpose seemed to have a strong secondary effect. The salinity gradient was the most explaining variable and zoosporic fungi showed higher sensitivity to high salinity levels. Consequently, none of the zoosporic taxon groups occurred solely in the marine environment. Significant differences were found in the assemblage processes with a dominance of environmental selection in the upstream region compared to undominated processes in downstream and coastal transition regions. The results suggest that fungi play various ecological roles along the diverse river sections and that their biotic interactions become more complex in the estuary. These results provide an important framework to help predict the functional consequences of changes in mycoplankton community structure and to help conserve microbial biodiversity in river ecosystems.
    Keywords: Ammonium; brackish; Carbon, organic, dissolved; Chlorophyll a; Date/Time of event; Elbe; Elbe_mycoplankton_1; Elbe_mycoplankton_10; Elbe_mycoplankton_11; Elbe_mycoplankton_12; Elbe_mycoplankton_13; Elbe_mycoplankton_14; Elbe_mycoplankton_15; Elbe_mycoplankton_16; Elbe_mycoplankton_17; Elbe_mycoplankton_18; Elbe_mycoplankton_19; Elbe_mycoplankton_2; Elbe_mycoplankton_20; Elbe_mycoplankton_21; Elbe_mycoplankton_22; Elbe_mycoplankton_23; Elbe_mycoplankton_24; Elbe_mycoplankton_3; Elbe_mycoplankton_4; Elbe_mycoplankton_5; Elbe_mycoplankton_6; Elbe_mycoplankton_7; Elbe_mycoplankton_8; Elbe_mycoplankton_9; Elbe river; Estuary; Event label; freshwater; Fungi; Latitude of event; Longitude of event; marine; Nitrate; Nitrite; Optional event label; pH; Phosphate; Salinity; Sample1; Sample10; Sample11; Sample12; Sample13; Sample14; Sample15; Sample16; Sample17; Sample18; Sample19; Sample2; Sample20; Sample21; Sample22; Sample23; Sample24; Sample3; Sample4; Sample5; Sample6; Sample7; Sample8; Sample9; Silicate; Temperature, water
    Type: Dataset
    Format: text/tab-separated-values, 232 data points
    Location Call Number Limitation Availability
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    DATA PANGAEA
  • 2
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    Seawater carbonate chemistry and taxonomic assemblage of fungal communities from the southern North Sea (2017)
    PANGAEA
    In:  Supplement to: Reich, Marlis; Wichels, Antje; Panzer, Katrin; Krause, Evamaria; Giménez, Luis; Gerdts, Gunnar (2017): Impacts of a reduction in seawater pH mimicking ocean acidification on the structure and diversity of mycoplankton communities. Aquatic Microbial Ecology, 79(3), 221-233, https://doi.org/10.3354/ame01831
    Details
    Publication Date: 2024-03-15
    Description: Increases in atmospheric carbon dioxide (CO2) change ocean chemistry, as dissolved CO2 leads to a reduction in the seawater pH. Many marine taxa have been shown to be affected by ocean acidification; however, information on marine fungi is lacking. We analyzed the effect of pH on mycoplankton communities. The pH of microcosms was adjusted to a value mimicking the predicted ocean acidification in the near future. Fungal communities were analyzed using a double-marker gene approach, allowing a more detailed analysis of their response using 454 pyrosequencing. Mycoplankton communities in microcosms with in situ and adjusted water pH values differed significantly in terms of structure and diversity. The differences were mainly abundance shifts among the dominant taxa, rather than the exclusion of fungal groups. A sensitivity to lower pH values was reported for several groups across the fungal kingdom and was not phylogenetically conserved. Some of the fungal species that dominated the communities of microcosms with a lower pH were known pathogenic fungi. With the increasing awareness of the significant role fungi play in marine systems, including performing a diverse range of symbiotic activities, our results highlight the importance of including fungi in further research projects studying and modeling biotic responses to the predicted ocean acidification.
    Keywords: Abundance; Alkalinity, total; Alkalinity, total, standard deviation; Aragonite saturation state; Bicarbonate ion; Bottles or small containers/Aquaria (〈20 L); Calcite saturation state; Calculated using seacarb after Nisumaa et al. (2010); Carbon, inorganic, dissolved; Carbonate ion; Carbonate system computation flag; Carbon dioxide; Coast and continental shelf; Community composition and diversity; Entire community; Experiment duration; Fugacity of carbon dioxide (water) at sea surface temperature (wet air); Group; Incubation duration; Laboratory experiment; North Atlantic; OA-ICC; Ocean Acidification International Coordination Centre; Partial pressure of carbon dioxide, respiration, standard deviation; Partial pressure of carbon dioxide (water) at sea surface temperature (wet air); Pelagos; pH; pH, standard deviation; Salinity; Temperate; Temperature, water; Treatment; Type
    Type: Dataset
    Format: text/tab-separated-values, 7488 data points
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    DATA PANGAEA
  • 3
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    Identification of Habitat-Specific Biomes of Aquatic Fungal Communities Using a Comprehensive Nearly Full-Length 18S rRNA Dataset Enriched with Contextual Data (2015)
    Public Library of Science
    In:  PLoS ONE, 10 (7). e0134377.
    Details
    Publication Date: 2020-10-26
    Description: Molecular diversity surveys have demonstrated that aquatic fungi are highly diverse, and that they play fundamental ecological roles in aquatic systems. Unfortunately, comparative studies of aquatic fungal communities are few and far between, due to the scarcity of adequate datasets. We combined all publicly available fungal 18S ribosomal RNA (rRNA) gene sequences with new sequence data from a marine fungi culture collection. We further enriched this dataset by adding validated contextual data. Specifically, we included data on the habitat type of the samples assigning fungal taxa to ten different habitat categories. This dataset has been created with the intention to serve as a valuable reference dataset for aquatic fungi including a phylogenetic reference tree. The combined data enabled us to infer fungal community patterns in aquatic systems. Pairwise habitat comparisons showed significant phylogenetic differences, indicating that habitat strongly affects fungal community structure. Fungal taxonomic composition differed considerably even on phylum and class level. Freshwater fungal assemblage was most different from all other habitat types and was dominated by basal fungal lineages. For most communities, phylogenetic signals indicated clustering of sequences suggesting that environmental factors were the main drivers of fungal community structure, rather than species competition. Thus, the diversification process of aquatic fungi must be highly clade specific in some cases.The combined data enabled us to infer fungal community patterns in aquatic systems. Pairwise habitat comparisons showed significant phylogenetic differences, indicating that habitat strongly affects fungal community structure. Fungal taxonomic composition differed considerably even on phylum and class level. Freshwater fungal assemblage was most different from all other habitat types and was dominated by basal fungal lineages. For most communities, phylogenetic signals indicated clustering of sequences suggesting that environmental factors were the main drivers of fungal community structure, rather than species competition. Thus, the diversification process of aquatic fungi must be highly clade specific in some cases.
    Type: Article , PeerReviewed
    Format: text
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    DOI: 10.1371/journal.pone.0134377
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    OceanRep: Article in a Scientific Journal - peer-reviewed
  • 4
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    MYCOPLANKTON BIOME STRUCTURE AND ASSEMBLAGE PROCESSES ALONG A TRANSECT FROM THE SHALLOW FRESHWATER AREA OF THE ELBE RIVER DOWN TO THE ADJACENT MARINE WATERS (2021)
    In:  EPIC3ASLO, 2021-06
    Details
    Publication Date: 2021-03-24
    Description: Understanding the relative importance of dispersal and environmental selection in shaping aquatic mycoplankton communities can help to predict fungus-driven ecological processes such as mycoflux or mycoloop and to maintain biodiversity in river ecosystems. In the presented study, a transect of the Elbe River (7th stream order number) that extended from the shallow freshwater zone through the estuary up to the river plume, and to the adjacent ocean waters, was sampled. Mycoplankton community structure and underlying assemblage processes were investigated using tag sequencing and Quantitative Process Estimates (QPE) analysis. Mycoplankton communities formed three significantly different biomes, by which the most structuring factor of salinity was superimposed by secondary effects of the Elbe deepening works. The underlying processes differed drastically: migrations of taxa played only a minor role. Instead, the species present in upstream sections responded to the strong physico-chemical environmental changes and a change from an autotrophic to a heterotrophic system was observed. Downstream, neither selection nor dispersal dominated but microbial features such as the cell tolerance to salinity variability, host dependency, and life strategy could help to explain the observed patterns. The results showed that the assemblage processes can change over relatively short distances. It indicates that the processes are not static and that the relative importance of a process can vary under different conditions and between members of a community.++
    Repository Name: EPIC Alfred Wegener Institut
    Type: Conference , notRev
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    PAPER (OA)
  • 5
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    Seasonal Dynamics of Pelagic Mycoplanktonic Communities: Interplay of Taxon Abundance, Temporal Occurrence, and Biotic Interactions (2020)
    In:  EPIC3Frontiers in Microbiology, 11, pp. 1305
    Details
    Publication Date: 2021-02-24
    Description: Marine fungi are an important component of pelagic planktonic communities. However, it is not yet clear how individual fungal taxa are integrated in marine processes of the microbial loop and food webs. Most likely, biotic interactions play a major role in shaping the fungal community structure. Thus, the aim of our work was to identify possible biotic interactions of mycoplankton with phytoplankton and zooplankton groups and among fungi, and to investigate whether there is coherence between interactions and the dynamics, abundance and temporal occurrence of individual fungal OTUs. Marine surface water was sampled weekly over the course of 1 year, in the vicinity of the island of Helgoland in the German Bight (North Sea). The mycoplankton community was analyzed using 18S rRNA gene tag-sequencing and the identified dynamics were correlated to environmental data including phytoplankton, zooplankton, and abiotic factors. Finally, co-occurrence patterns of fungal taxa were detected with network analyses based on weighted topological overlaps (wTO). Of all abundant and persistent OTUs, 77% showed no biotic relations suggesting a saprotrophic lifestyle. Of all other fungal OTUs, nearly the half (44%) had at least one significant negative relationship, especially with zooplankton and other fungi, or to a lesser extent with phytoplankton. These findings suggest that mycoplankton OTUs are embedded into marine food web chains via highly complex and manifold relationships such as parasitism, predation, grazing, or allelopathy. Furthermore, about one third of all rare OTUs were part of a dense fungal co-occurrence network probably stabilizing the fungal community against environmental changes and acting as functional guilds or being involved in fungal cross-feeding. Placed in an ecological context, strong antagonistic relationships of the mycoplankton community with other components of the plankton suggest that: (i) there is a top-down control by fungi on zooplankton and phytoplankton; (ii) fungi serve as a food source for zooplankton and thereby transfer nutrients and organic material; (iii) the dynamics of fungi harmful to other plankton groups are controlled by antagonistic fungal taxa.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , peerRev
    Format: application/pdf
    Location Call Number Limitation Availability
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    PAPER (OA)
  • 6
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    Impacts of a reduction in seawater pH mimicking ocean acidification on the structure and diversity of mycoplankton communities (2017)
    Interscience
    In:  EPIC3Aquatic Microbial Ecology, Interscience, 79, pp. 221-233
    Details
    Publication Date: 2017-06-14
    Description: Increases in atmospheric carbon dioxide (CO2) change ocean chemistry, as dissolved CO2 leads to a reduction in the seawater pH. Many marine taxa have been shown to be affected by ocean acidification, while information on marine fungi is lacking. Here, we analyze the effect of pH on mycoplankton communities. The pH of microcosms was adjusted to a value mimicking the predicted ocean acidification in the near future. Fungal communities were analyzed using a double-marker gene approach, allowing a more detailed analysis of their response using 454 pyrosequencing. Mycoplankton communities in microcosms with in situ and adjusted water pH values differed significantly in terms of structure and diversity. The differences were mainly based on abundance shifts among the dominant taxa rather than the exclusion of fungal groups. A sensitivity to lower pH values was reported for several groups across the fungal kingdom and was not phylogenetically conserved. Some of the fungal species that dominated the communities of microcosms with a lower pH were known pathogenic fungi. With the increasing awareness of the significant role fungi play in marine systems, including performing a diverse range of symbiotic activities, our results highlight the importance of including fungi in further research projects studying and modeling biotic responses to the predicted ocean acidification.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
    Location Call Number Limitation Availability
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    PAPER (OA)
  • 7
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    Seasonal Dynamics of Pelagic Mycoplanktonic Communities: Interplay of Taxon Abundance, Temporal Occurrence, and Biotic Interactions (2020)
    In:  EPIC3Frontiers in MICROBIOLOGY, 11
    Details
    Publication Date: 2022-09-05
    Description: Marine fungi are an important component of pelagic planktonic communities. However, it is not yet clear how individual fungal taxa are integrated in marine processes of the microbial loop and food webs. Most likely, biotic interactions play a major role in shaping the fungal community structure. Thus, the aim of our work was to identify possible biotic interactions of mycoplankton with phytoplankton and zooplankton groups and among fungi, and to investigate whether there is coherence between interactions and the dynamics, abundance and temporal occurrence of individual fungal OTUs. Marine surface water was sampled weekly over the course of 1 year, in the vicinity of the island of Helgoland in the German Bight (North Sea). The mycoplankton community was analyzed using 18S rRNA gene tag-sequencing and the identified dynamics were correlated to environmental data including phytoplankton, zooplankton, and abiotic factors. Finally, co-occurrence patterns of fungal taxa were detected with network analyses based on weighted topological overlaps (wTO). Of all abundant and persistent OTUs, 77% showed no biotic relations suggesting a saprotrophic lifestyle. Of all other fungal OTUs, nearly the half (44%) had at least one significant negative relationship, especially with zooplankton and other fungi, or to a lesser extent with phytoplankton. These findings suggest that mycoplankton OTUs are embedded into marine food web chains via highly complex and manifold relationships such as parasitism, predation, grazing, or allelopathy. Furthermore, about one third of all rare OTUs were part of a dense fungal co-occurrence network probably stabilizing the fungal community against environmental changes and acting as functional guilds or being involved in fungal cross-feeding. Placed in an ecological context, strong antagonistic relationships of the mycoplankton community with other components of the plankton suggest that: (i) there is a top-down control by fungi on zooplankton and phytoplankton; (ii) fungi serve as a food source for zooplankton and thereby transfer nutrients and organic material; (iii) the dynamics of fungi harmful to other plankton groups are controlled by antagonistic fungal taxa.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , NonPeerReviewed
    Location Call Number Limitation Availability
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    PAPER (OA)
  • 8
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    Differential integration of members of marine mycoplankton communities into food webs and carbon cycling (2021)
    In:  EPIC3Aslo, online, 2021-06
    Details
    Publication Date: 2022-09-29
    Description: Marine fungi are prominent components of plankton communities, but to date little is known about how the different community members are integrated into trophic networks and whether fungal cell numbers/biomass reach a size that can be considered significant for the carbon cycling and food web chains. To shed light into this black box, we linked tag-sequencing based classification and CARD-FISH enumeration of mycoplankton communities sampled from a marine time series station in the North Sea in two successive studies and modeled fungal interactions with other plankton groups over complex weighted Topological Overlap (wTO) networks. The wTO analysis reported significant negative relationships for half of all fungal OTUs with phyto- and zooplankton groups, but also between fungi. Zoosporic fungi, including several newly identified clades, held a special position within the modeled food webs with highest numbers of connections. During the spring phytoplankton bloom, Rozellomycota zoospores reached values of 106 cells L-1 similar to what is reported for freshwater mycoloops. Furthermore, saprotrophic yeasts showed distant frequency patterns over the course of the year. At the end of the spring phytoplankton bloom, yeast cell number increased 11-fold within a week and reached biomass values with a maximum of 8.9 mg C m-3 comparable to values of filamentous fungi in the Chilean upwelling system. Our results suggest that marine mycoplankton is integrated into trophic networks over different planktonic interactions, causes trophic upgrading, and are part of the microbial loop.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Conference , notRev
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  • 9
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    Mycoplankton Biome Structure and Assemblage Processes Differ Along a Transect From the Elbe River Down to the River Plume and the Adjacent Marine Waters (2021)
    Frontiers
    In:  EPIC3Frontiers in Microbiology, Frontiers
    Details
    Publication Date: 2022-11-01
    Description: Rivers are transport systems and supply adjacent ecosystems with nutrients. They also serve human well-being, for example as a source of food. Microorganismic biodiversity is an important parameter for the ecological balance of river ecosystems. Despite the knowledge that fungi are key players in freshwater nutrient cycling and food webs, data on planktonic fungi of streams with higher stream order is scarce. This study aims to fill this knowledge gap by a fungi-specific 18S rRNA gene tag sequencing approach, investigating mycoplankton diversity in the Elbe River along a transect from shallow freshwater, to the estuary and river plume down to the adjacent marine waters (sections of 7th stream order number). Using multivariate analyses and the Quantitative Process Estimates (QPE) method, the questions of how mycoplankton communities as part of the river continuum change along the transect, what factors, spatial and environmental, play a role, and what assembly processes, such as selection or dispersion, operate along the transect were addressed. The partitioning of mycoplankton communities into three significant distant biomes was mainly driven by local environmental conditions that were partly under spatial control. The assembly processes underlying the biomes also differed significantly. Thus, variable selection dominated the upstream sections, while undominated processes like ecological drift dominated the sections close to the river mouth and beyond. Dispersal played a minor role. The results suggest that the ecological versatility of the mycoplankton communities changes along the transect as response for example to a drastic change from an autotrophic to a heterotrophic system caused by an abrupt increase in the river depth. Furthermore, a significant salinity-dependent occurrence of diverse basal fungal groups was observed, with no clade found exclusively in marine waters. These results provide an important framework to help understand patterns of riverine mycoplankton communities and serve as basis for a further in-depth work, so that fungi as an important ecological organism group can be integrated into models of e.g. usage-balance considerations of rivers
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
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  • 10
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    A comprehensive fungi-specific 18S rRNA gene sequence primer toolkit suited for diverse research issues and sequencing platforms (2018)
    Springer Science and Business Media LLC
    In:  EPIC3BMC Microbiology, Springer Science and Business Media LLC, 18(1), pp. 190-, ISSN: 1471-2180
    Details
    Publication Date: 2023-06-21
    Description: BACKGROUND: Several fungi-specific primers target the 18S rRNA gene sequence, one of the prominent markers for fungal classification. The design of most primers goes back to the last decades. Since then, the number of sequences in public databases increased leading to the discovery of new fungal groups and changes in fungal taxonomy. However, no reevaluation of primers was carried out and relevant information on most primers is missing. With this study, we aimed to develop an 18S rRNA gene sequence primer toolkit allowing an easy selection of the best primer pair appropriate for different sequencing platforms, research aims (biodiversity assessment versus isolate classification) and target groups. RESULTS: We performed an intensive literature research, reshuffled existing primers into new pairs, designed new Illumina-primers, and annealing blocking oligonucleotides. A final number of 439 primer pairs were subjected to in silico PCRs. Best primer pairs were selected and experimentally tested. The most promising primer pair with a small amplicon size, nu-SSU-1333-5'/nu-SSU-1647-3' (FF390/FR-1), was successful in describing fungal communities by Illumina sequencing. Results were confirmed by a simultaneous metagenomics and eukaryote-specific primer approach. Co-amplification occurred in all sample types but was effectively reduced by blocking oligonucleotides. CONCLUSIONS: The compiled data revealed the presence of an enormous diversity of fungal 18S rRNA gene primer pairs in terms of fungal coverage, phylum spectrum and co-amplification. Therefore, the primer pair has to be carefully selected to fulfill the requirements of the individual research projects. The presented primer toolkit offers comprehensive lists of 164 primers, 439 primer combinations, 4 blocking oligonucleotides, and top primer pairs holding all relevant information including primer's characteristics and performance to facilitate primer pair selection.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , NonPeerReviewed
    Format: application/pdf
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