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  • Herzon, Irina; Marja, Riho; Le Viol, Isabelle; Menshikova, Svetlana; Kondratyev, Aleksander (2018)
    Use of community trait-based metrics has been increasingly implemented for achieving an integrated view of biodiversity in conservation planning. We examined the extent, to which the use of community metrics based on species traits reflecting plausible sensitivity to change would contribute to our understanding of landscape characteristics of importance to the conservation of farmland birds in a poorly studied region of Northwest Russia. We collected species data on farmland from 230 transects covering a total 215 km for each year of 2008, 2010 and 2011 and analysed them using generalised linear mixed modelling. We derived community indices from species traits of habitat specialisation, trophic position, relative brain size and body mass. By relating these indices to the numbers of all species regarded farmland and Species of European Conservation Concern (SPEC), and by analysing them against the type of field and occurrence in typical non-cropped landscape elements, we showed consistent, albeit weak, congruence among the taxonomic and trait-based community descriptors. All community descriptors had their lowest estimates in arable fields. Community specialisation was the highest in open abandoned fields, which confirms the importance of such fields as refuges for regionally specialised species. Pastures were characterised by the highest community biomass, which indicates a particularly good resource base. Presence of ditches, of all non-cropped elements, had the strongest positive relationship with the community descriptors. The SPEC number strongly correlated with the overall species richness of farmland birds. A relatively weak congruence between taxonomic and trait-based community descriptors highlights their cornplementarity in understanding the underlying mechanisms of community changes. However, similarity in patterns among field types means that, under the current level of production in the region, accounting for the species richness of farmland birds seems to be sufficient to rapidly assess community sensitivity to agricultural change.
  • Jamoneau, Aurelien; Passy, Sophia I.; Soininen, Janne; Leboucher, Thibault; Tison-Rosebery, Juliette (2018)
    1. Understanding the mechanisms that drive beta diversity (i.e. beta-diversity), an important aspect of regional biodiversity, remains a priority for ecological research. beta-diversity and its components can provide insights into the processes generating regional biodiversity patterns. We tested whether environmental filtering or dispersal related processes predominated along the stream watercourse by analysing the responses of taxonomic and functional diatom beta-diversity to environmental and spatial factors. 2. We examined the variation in total beta-diversity and its components (turnover and nestedness) in benthic diatom species and ecological guilds (motile, planktonic, low-and high profile) with respect to watercourse position (up-, mid-and downstream) in 2,182 sites throughout France. We tested the effects of pure environmental and pure spatial factors on beta-diversity with partial Mantel tests. Environmental factors included eight physicochemical variables, while geographical distances between sites were used as spatial factors. We also correlated a and c-diversity, and the degree of nestedness (NODF metric) with environmental variables. 3. Total beta-diversity and its turnover component displayed higher values upstream than mid-and downstream. The nestedness component exhibited low values, even when NODF values increased from up-to downstream. Pure environmental factors were highly significant for explaining total beta-diversity and turnover regardless of watercourse position, but pure spatial factors were mostly significant mid-and downstream, with geographical distance being positively correlated with beta-diversity. Across sites, nutrient enrichment decreased turnover but increased the degree of nestedness. Motile and low profile diatoms comprised the most abundant guilds, but their beta-diversity patterns varied in an opposite way. The lowest guild beta-diversity was observed upstream for low profile species, and downstream for motile species. 4. In conclusion, environmental filtering seemed to play a major role in structuring metacommunities irrespective of site watercourse position. Filtering promoted strong turnover patterns, especially in disconnected upstream sites. The greater role of spatial factors mid-and downstream was consistent with mass effects rather than neutral processes because these sites had lower total beta-diversity than upstream sites. Motile species were most strongly affected by mass effects processes, whereas low profile species were primarily influenced by environmental conditions. Collectively, these findings suggest that partitioning of total beta-diversity into its components and the use of diatom ecological guilds provide a useful framework for assessing the mechanisms underlying metacommunity patterns along the stream watercourse.
  • Leboucher, Thibault; Budnick, William R.; Passy, Sophia; Boutry, Sebastien; Jannoneau, Aurelien; Soininen, Janne; Vyverman, Wim; Tison-Rosebery, Juliette (2019)
    Aim To quantify the relative contributions of local community assembly processes versus gamma-diversity to beta-diversity, and to assess how spatial scale and anthropogenic disturbance (i.e. nutrient enrichment) interact to dictate which driver dominates. Location France and the United States. Time period 1993-2011. Major taxa studied Freshwater stream diatoms. Methods beta-diversity along a nutrient enrichment gradient was examined across multiple spatial scales. beta-diversity was estimated using multi-site Sorensen dissimilarity. We assessed the relative importance of specialists versus generalists using Friedley coefficient, and the contribution of local community assembly versus gamma-diversity to beta-diversity across spatial scales, with a null model. Finally, we estimated the response of beta-diversity to environmental and spatial factors by testing the correlations between community, environmental and geographical distance matrices with partial Mantel tests. Results beta-diversity generally increased with spatial scale but the rate of increase depended on nutrient enrichment level. beta-diversity decreased significantly with increasing nutrient enrichment level due to the loss of specialist species. Local assembly was an important driver of beta-diversity especially under low nutrient enrichment. Significant partial Mantel correlations were observed between diatom beta-diversity and pure environmental distances under these conditions, highlighting the role of species sorting in local assembly processes. Conversely, in heavily enriched sites, only spatial distances were significantly correlated with beta-diversity, which indicated a substantial role of dispersal processes. Main conclusions Nutrient concentration mediated the expected increase in beta-diversity with spatial scales. Across spatial scales, beta-diversity was more influenced by local assembly processes rather than by gamma-diversity. Nutrient enrichment was associated with an overall decline in diatom beta-diversity and a shift in assembly processes from species sorting to dispersal, notably due to the elimination of some specialists and their subsequent replacement by generalists.
  • Tóth, Zsolt; Szlavecz, Katalin; Epp Schmidt, Dietrich J.; Hornung, Erzsébet; Setälä, Heikki; Yesilonis, Ian D.; Kotze, D. Johan; Dombos, Miklós; Pouyat, Richard; Mishra, Saket; Cilliers, Sarel; Yarwood, Stephanie; Csuzdi, Csaba (2020)
    In urban landscapes, humans are the most significant factor determining belowground diversity, including earthworms. Within the framework of the Global Urban Soil Ecology and Education Network (GLUSEEN), a multi-city comparison was carried out to assess the effects of soil disturbance on earthworms. In each of five cities (Baltimore, USA; Budapest, Hungary; Helsinki and Lahti, Finland; Potchefstroom, South Africa), covering four climatic and biogeographical regions, four habitat types (ruderal, turf/lawn, remnant and reference) were sampled. The survey resulted in 19 species belonging to 9 genera and 4 families. The highest total species richness was recorded in Baltimore (16), while Budapest and the Finnish cities had relatively low (5–6) species numbers. Remnant forests and lawns supported the highest earthworm biomass. Soil properties (i.e. pH and organic matter content) explained neither earthworm community composition nor abundance. Evaluating all cities together, earthworm communities were significantly structured by habitat type. Communities in the two adjacent cities, Helsinki and Lahti were very similar, but Budapest clearly separated from the Finnish cities. Earthworm community structure in Baltimore overlapped with that of the other cities. Despite differences in climate, soils and biogeography among the cities, earthworm communities were highly similar within the urban habitat types. This indicates that human-mediated dispersal is an important factor shaping the urban fauna, both at local and regional scales.
  • Milardi, Marco; Gavioli, Anna; Soininen, Janne; Castaldelli, Giuseppe (2019)
    Exotic species invasions often result in native biodiversity loss, i.e. a lower taxonomic diversity, but current knowledge on invasions effects underlined a potential increase of functional diversity. We thus explored the connections between functional diversity and exotic species invasions, while accounting for their environmental drivers, using a fine-resolution large dataset of Mediterranean stream fish communities. While functional diversity of native and exotic species responded similarly to most environmental constraints, we found significant differences in the effects of altitude and in the different ranking of constraints. These differences suggest that invasion dynamics could play a role in overriding some major environmental drivers. Our results also showed that a lower diversity of ecological traits in communities (about half of less disturbed communities) corresponded to a high invasion degree, and that the exotic component of communities had typically less diverse ecological traits than the native one, even when accounting for stream order and species richness. Overall, our results suggest that possible outcomes of severe exotic species invasions could include a reduced functional diversity of invaded communities, but analyzing data with finer ecological, temporal and spatial resolutions would be needed to pinpoint the causal relationship between invasions and functional diversity.
  • Abrego, Nerea; Crosier, Brittni; Somervuo, Panu; Ivanova, Natalia; Abrahamyan, Arusyak; Abdi, Amir; Hämäläinen, Karoliina; Junninen, Kaisa; Maunula, Minna; Purhonen, Jenna; Ovaskainen, Otso (2020)
    Increasing evidence suggests that degradation of biodiversity in human populated areas is a threat for the ecosystem processes that are relevant for human well-being. Fungi are a megadiverse kingdom that plays a key role in ecosystem processes and affects human well-being. How urbanization influences fungi has remained poorly understood, partially due to the methodological difficulties in comprehensively surveying fungi. Here we show that both aerial and soil fungal communities are greatly poorer in urban than in natural areas. Strikingly, a fivefold reduction in fungal DNA abundance took place in both air and soil samples already at 1 km scale when crossing the edge from natural to urban habitats. Furthermore, in the air, fungal diversity decreased with urbanization even more than in the soil. This result is counterintuitive as fungal spores are known to disperse over large distances. A large proportion of the fungi detectable in the air are specialized to natural habitats, whereas soil fungal communities comprise a large proportion of habitat generalists. The sensitivity of the aerial fungal community to anthropogenic disturbance makes this method a reliable and efficient bioindicator of ecosystem health in urban areas.
  • Hakkila, Matti; Abrego, Nerea; Ovaskainen, Otso; Monkkonen, Mikko (2018)
    Protected areas are meant to preserve native local communities within their boundaries, but they are not independent from their surroundings. Impoverished habitat quality in the matrix might influence the species composition within the protected areas through biotic homogenization. The aim of this study was to determine the impacts of matrix quality on species richness and trait composition of bird communities from the Finnish reserve area network and whether the communities are being subject of biotic homogenization due to the lowered quality of the landscape matrix. We used joint species distribution modeling to study how characteristics of the Finnish forest reserves and the quality of their surrounding matrix alter species and trait compositions of forest birds. The proportion of old forest within the reserves was the main factor in explaining the bird community composition, and the bird communities within the reserves did not strongly depend on the quality of the matrix. Yet, in line with the homogenization theory, the beta-diversity within reserves embedded in low-quality matrix was lower than that in high-quality matrix, and the average abundance of regionally abundant species was higher. Influence of habitat quality on bird community composition was largely explained by the species' functional traits. Most importantly, the community specialization index was low, and average body size was high in areas with low proportion of old forest. We conclude that for conserving local bird communities in northern Finnish protected forests, it is currently more important to improve or maintain habitat quality within the reserves than in the surrounding matrix. Nevertheless, we found signals of bird community homogenization, and thus, activities that decrease the quality of the matrix are a threat for bird communities.
  • Schmidt, Dietrich J. Epp; Kotze, David Johan; Hornung, Erzsebet; Setala, Heikki; Yesilonis, Ian; Szlavecz, Katalin; Dombos, Miklos; Pouyat, Richard; Cilliers, Sarel; Toth, Zsolt; Yarwood, Stephanie A. (2019)
    Urbanization results in the systemic conversion of land-use, driving habitat and biodiversity loss. The "urban convergence hypothesis" posits that urbanization represents a merging of habitat characteristics, in turn driving physiological and functional responses within the biotic community. To test this hypothesis, we sampled five cities (Baltimore, MD, United States; Helsinki and Lahti, Finland; Budapest, Hungary; Potchefstroom, South Africa) across four different biomes. Within each city, we sampled four land-use categories that represented a gradient of increasing disturbance and management (from least intervention to highest disturbance: reference, remnant, turf/lawn, and ruderal). Previously, we used amplicon sequencing that targeted bacteria/archaea (16S rRNA) and fungi (ITS) and reported convergence in the archaeal community. Here, we applied shotgun metagenomic sequencing and QPCR of functional genes to the same soil DNA extracts to test convergence in microbial function. Our results suggest that urban land-use drives changes in gene abundance related to both the soil N and C metabolism. Our updated analysis found taxonomic convergence in both the archaeal and bacterial community (16S amplicon data). Convergence of the archaea was driven by increased abundance of ammonia oxidizing archaea and genes for ammonia oxidation (QPCR and shotgun metagenomics). The proliferation of ammonia-oxidizers under turf and ruderal land-use likely also contributes to the previously documented convergence of soil mineral N pools. We also found a higher relative abundance of methanogens (amplicon sequencing), a higher relative abundance of gene sequences putatively identified as Ni-Fe hydrogenase and nickel uptake (shotgun metagenomics) under urban land-use; and a convergence of gene sequences putatively identified as contributing to the nickel transport function under urban turf sites. High levels of disturbance lead to a higher relative abundance of gene sequences putatively identified as multiple antibiotic resistance protein marA and multidrug efflux pump mexD, but did not lead to an overall convergence in antibiotic resistance gene sequences.
  • Florencio, Margarita; Lobo, Jorge M.; Cardoso, Pedro; Almeida-Neto, Mario; Borges, Paulo A. V. (2015)
    Human-caused disturbances can lead to the extinction of indigenous (endemic and native) species, while facilitating and increasing the colonisation of exotic species; this increase can, in turn, promote the similarity of species compositions between sites if human-disturbed sites are consistently invaded by a regionally species-poor pool of exotic species. In this study, we analysed the extent to which epigean arthropod assemblages of four islands of the Azorean archipelago are characterised by nestedness according to a habitat-altered gradient. The degree of nestedness represents the extent to which less ubiquitous species occur in subsets of sites occupied by the more widespread species, resulting in an ordered loss/gain of species across environmental or ecological gradients. A predictable loss of species across communities while maintaining others may lead to more similar communities (i.e. lower beta-diversity). In contrast, anti-nestedness occurs when different species tend to occupy distinct sites, thus characterising a replacement of species across such gradients. Our results showed that an increase in exotic species does not promote assemblage homogenisation at the habitat level. On the contrary, exotic species were revealed as habitat specialists that constitute new and well-differentiated assemblages, even increasing the species compositional heterogeneity within human-altered landscapes. Therefore, contrary to expectations, our results show that both indigenous and exotic species established idiosyncratic assemblages within habitats and islands. We suggest that both the historical extinction of indigenous species in disturbed habitats and the habitat-specialised character of some exotic invasions have contributed to the construction of current assemblages.