Browsing by Subject "co-occurrence"

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  • Abrego, Nerea; Roslin, Tomas; Huotari, Tea; Tack, Ayco J. M.; Lindahl, Bjorn D.; Tikhonov, Gleb; Somervuo, Panu; Schmidt, Niels Martin; Ovaskainen, Otso (2020)
    Understanding the role of interspecific interactions in shaping ecological communities is one of the central goals in community ecology. In fungal communities, measuring interspecific interactions directly is challenging because these communities are composed of large numbers of species, many of which are unculturable. An indirect way of assessing the role of interspecific interactions in determining community structure is to identify the species co-occurrences that are not constrained by environmental conditions. In this study, we investigated co-occurrences among root-associated fungi, asking whether fungi co-occur more or less strongly than expected based on the environmental conditions and the host plant species examined. We generated molecular data on root-associated fungi of five plant species evenly sampled along an elevational gradient at a high arctic site. We analysed the data using a joint species distribution modelling approach that allowed us to identify those co-occurrences that could be explained by the environmental conditions and the host plant species, as well as those co-occurrences that remained unexplained and thus more probably reflect interactive associations. Our results indicate that not only negative but also positive interactions play an important role in shaping microbial communities in arctic plant roots. In particular, we found that mycorrhizal fungi are especially prone to positively co-occur with other fungal species. Our results bring new understanding to the structure of arctic interaction networks by suggesting that interactions among root-associated fungi are predominantly positive.
  • Pineda-Munoz, Silvia; Jukar, Advait M.; Toth, Aniko B.; Fraser, Danielle; Du, Andrew; Barr, W. Andrew; Amatangelo, Kathryn L.; Balk, Meghan A.; Behrensmeyer, Anna K.; Blois, Jessica; Davis, Matt; Eronen, Jussi T.; Gotelli, Nicholas J.; Looy, Cindy; Miller, Joshua H.; Shupinski, Alexandria B.; Soul, Laura C.; Villasenor, Amelia; Wing, Scott; Lyons, S. Kathleen (2021)
    The late Quaternary of North America was marked by prominent ecological changes, including the end-Pleistocene megafaunal extinction, the spread of human settlements and the rise of agriculture. Here we examine the mechanistic reasons for temporal changes in mammal species association and body size during this time period. Building upon the co-occurrence results from Lyons et al. (2016) - wherein each species pair was classified as spatially aggregated, segregated or random - we examined body mass differences (BMD) between each species pair for each association type and time period (Late Pleistocene: 40 000(14)C-11 700(14)C ybp, Holocene: 11 700(14)C-50 ybp and Modern: 50-0 yr). In the Late Pleistocene and Holocene, the BMD of both aggregated and segregated species pairs was significantly smaller than the BMD of random pairs. These results are consistent with environmental filtering and competition as important drivers of community structure in both time periods. Modern assemblages showed a breakdown between BMD and co-occurrence patterns: the average BMD of aggregated, segregated and random species pairs did not differ from each other. Collectively, these results indicate that the late Quaternary mammalian extinctions not only eliminated many large-bodied species but were followed by a re-organization of communities that altered patterns of species coexistence and associated differences in body size.
  • Saine, Sonja; Ovaskainen, Otso; Somervuo, Panu; Abrego, Nerea (2020)
    Inferring interspecific interactions indirectly from community data is of central interest in community ecology. Data on species communities can be surveyed using different methods, each of which may differ in the amount and type of species detected, and thus produce varying information on interaction networks. Since fruit bodies reflect only a fraction of the wood-inhabiting fungal diversity, there is an ongoing debate in fungal ecology on whether fruit body?based surveys are a valid method for studying fungal community dynamics compared to surveys based on DNA metabarcoding. In this paper, we focus on species-to-species associations and ask whether the associations inferred from data collected by fruit-body surveys reflect the ones found from data collected by DNA-based surveys. We estimate and compare the association networks resulting from different survey methods using a joint species distribution model. We recorded both raw and residual associations that respectively do not and do correct for the influence of the abiotic predictors when estimating the species-to-species associations. The analyses of the DNA data yielded a larger number of species-to-species associations than the analyses of the fruit body?based data as expected. Yet, we estimated unique associations also from the fruit-body data. Our results show that the directions of estimated residual associations were consistent between the data types, whereas the raw associations were much less consistent, highlighting the need to account for the influence of relevant environmental covariates when estimating association networks. We conclude that even though DNA-based survey methods are more informative about the total number of interacting species, fruit-body surveys are also an adequate method for inferring association networks in wood-inhabiting fungi. Since the DNA and fruit-body data carry on complementary information on fungal communities, the most comprehensive insights are obtained by combining the two survey methods. This article is protected by copyright. All rights reserved.
  • Marjakangas, Emma-Liina; Abrego, Nerea; Grøtan, Vidar; de Lima, Renato A. F.; Bello, Carolina; Bovendorp, Ricardo S.; Culot, Laurence; Hasui, Érica; Lima, Fernando; Muylaert, Renata Lara; Niebuhr, Bernardo Brandão; Oliveira, Alexandre A.; Pereira, Lucas Augusto; Prado, Paulo I.; Stevens, Richard D.; Vancine, Maurício Humberto; Ribeiro, Milton Cezar; Galetti, Mauro; Ovaskainen, Otso (2020)
    Abstract Aim Forest fragmentation is among the principal causes of global biodiversity loss, yet how it affects mutualistic interactions between plants and animals at large spatial scale is poorly understood. In particular, tropical forest regeneration depends on animal-mediated seed dispersal, but the seed-dispersing animals face rapid decline due to forest fragmentation and defaunation. Here, we assess how fragmentation influences the pairwise interactions between 407 seed disperser and 1,424 tree species in a highly fragmented biodiversity hotspot. Location Atlantic Forest, South America. Methods We predicted interaction networks in 912 sites covering the entire biome by combining verified interaction data with co-occurrence probabilities obtained from a spatially explicit joint species distribution model. We identified keystone seed dispersers by computing a species-specific keystone index and by selecting those species belonging to the top 5% quantile. Results We show that forest fragmentation affects seed dispersal interactions negatively, and the decreased area of functionally connected forest, rather than increased edge effects, is the main driver behind the loss of interactions. Both the seed disperser availability for the local tree communities and in particular the proportion of interactions provided by keystone seed dispersers decline with increasing degree of fragmentation. Importantly, just 21 keystone species provided >40% of all interactions. The numbers of interactions provided by keystone and non-keystone species, however, were equally negatively affected by fragmentation, suggesting that seed dispersal interactions may not be rewired under strong fragmentation effects. Conclusions We highlight the importance of understanding the fragmentation-induced compositional shifts in seed disperser communities as they may lead to lagged and multiplicative effects on tree communities. Our results illustrate the utility of model-based prediction of interaction networks as well as model-based identification of keystone species as a tool for prioritizing conservation efforts. Similar modelling approaches could be applied to other threatened ecosystems and interaction types globally.
  • Odriozola, Inaki; Abrego, Nerea; Tlaskal, Vojtech; Zrustova, Petra; Morais, Daniel; Vetrovsky, Tomas; Ovaskainen, Otso; Baldrian, Petr (2021)
    Fungal-bacterial interactions play a key role in the functioning of many ecosystems. Thus, understanding their interactive dynamics is of central importance for gaining predictive knowledge on ecosystem functioning. However, it is challenging to disentangle the mechanisms behind species associations from observed co occurrence patterns, and little is known about the directionality of such interactions. Here, we applied joint species distribution modeling to high-throughput sequencing data on co-occurring fungal and bacterial communities in deadwood to ask whether fungal and bacterial co-occurrences result from shared habitat use (i.e., deadwood's properties) or whether there are fungal-bacterial interactive associations after habitat characteristics are taken into account. Moreover, we tested the hypothesis that the interactions are mainly modulated through fungal communities influencing bacterial communities. For that, we quantified how much the predictive power of the joint species distribution models for bacterial and fungal community improved when accounting for the other community. Our results show that fungi and bacteria form tight association networks (i.e., some species pairs co-occur more frequently and other species pairs co-occur less frequently than expected by chance) in deadwood that include common (or opposite) responses to the environment as well as (potentially) biotic interactions. Additionally, we show that information about the fungal occurrences and abundances increased the power to predict the bacterial abundances substantially, whereas information about the bacterial occurrences and abundances increased the power to predict the fungal abundances much less. Our results suggest that fungal communities may mainly affect bacteria in deadwood. IMPORTANCE Understanding the interactive dynamics between fungal and bacterial communities is important to gain predictive knowledge on ecosystem functioning. However, little is known about the mechanisms behind fungal-bacterial associations and the directionality of species interactions. Applying joint species distribution modeling to high-throughput sequencing data on co-occurring fungal-bacterial communities in deadwood, we found evidence that nonrandom fungal-bacterial associations derive from shared habitat use as well as (potentially) biotic interactions. Importantly, the combination of cross-validations and conditional cross-validations helped us to answer the question about the directionality of the biotic interactions, providing evidence that suggests that fungal communities may mainly affect bacteria in deadwood. Our modeling approach may help gain insight into the directionality of interactions between different components of the microbiome in other environments.
  • Abrego, Nerea; Norberg, Anna; Ovaskainen, Otso (2017)
    1. The identification of traits that influence the responses of the species to environmental variation provides a mechanistic perspective on the assembly processes of ecological communities. While much research linking functional ecology with assembly processes has been conducted with animals and plants, the development of predictive or even conceptual frameworks for fungal functional community ecology remains poorly explored. Particularly, little is known about the contribution of traits to the occurrences of fungal species under different environmental conditions. 2. Wood-inhabiting fungi are known to strongly respond to habitat disturbance, and thus provide an interesting case study for investigating to what extent variation in occurrence patterns of fungi can be related to traits. We apply a trait-based joint species distribution model to a data set consisting of fruit-body occurrence data on 321 wood-inhabiting fungal species collected in 22 460 dead wood units from managed and natural forest sites. 3. Our results show that environmental filtering plays a big role on shaping wood-inhabiting fungal communities, as different environments held different communities in terms of species and trait compositions. Most importantly, forest management selected against species with large and long-lived fruit-bodies as well as late decayers, and promoted the occurrences of species with small fruit-bodies and early decayers. A strong phylogenetic signal in the data suggested the existence of also some other functionally important traits than the ones we considered. 4. We found that those species groups that were more prevalent in natural conditions had more associations to other species than species groups that were tolerant to or benefitted from forest management. Therefore, the changes that forest management causes on wood-inhabiting fungal communities influence ecosystem functioning through simplification of interactive associations among the fungal species. 5. Synthesis. Our results show that functional traits are linked to the responses of wood-inhabiting fungi to variation in their environment, and thus environmental changes alter ecosystem functions via promoting or reducing species with different fruit-body types. However, further research is needed to identify other functional traits and to provide conclusive evidence for the adaptive nature of the links from traits to occurrence patterns found here.
  • Mod, Heidi K.; Chevalier, Mathieu; Luoto, Miska; Guisan, Antoine (2020)
    A comprehensive understanding of the scale dependency of environmental filtering and biotic interactions influencing the local assembly of species is paramount to derive realistic forecasts of the future of biodiversity and efficiently manage ecological communities. A classical assumption is that environmental filters are more prevalent at coarser scales with diminishing effects towards the finest scales where biotic interactions become more decisive. Recently, a refinement was proposed stipulating that the scale dependency of biotic interactions should relate to the type of interaction. Specifically, the effect of negative interactions (e.g. competition) should diminish with coarsening scale, whereas positive interactions (i.e. facilitation) should be detected irrespective of the scale. We use multiple vascular plant species datasets sampled at nested spatial scales (plot size varying from 0.04 to 64 m(2)) and recently developed joint species distribution models to test the hypotheses. Our analyses indicate slightly stronger environmental filtering with increasing plot size. While the overall strength of biotic interactions did not vary consistently across scales, we found a tendency for negative interactions to fade away with increasing plot size slightly more than positive interactions. Synthesis. We provide partial, but not unambiguous, evidence of the scale dependency of ecological assembly rules. However, our correlative methodology only allows us to interpret the findings as indication of environmental filtering and biotic interactions.