Increases in local richness (α-diversity) following invasion are offset by biotic homogenization in a biodiversity hotspot

Trophic rewilding as a restoration approach under emerging novel biosphere conditions

Rewilding is a restoration approach that aims to promote self-regulating complex ecosystems by restoring non-human ecological processes while reducing human control and pressures. Rewilding is forward-looking in that it aims to enhance functionality for biodiversity, accepting and indeed promoting the dynamic nature of ecosystems, rather than fixating on static composition or structure. Rewilding is thus especially relevant in our epoch of increasingly novel biosphere conditions, driven by strong human-induced global change. Here, we explore this hypothesis in the context of trophic rewilding - the restoration of trophic complexity mediated by wild, large-bodied animals, known as 'megafauna'. This focus reflects the strong ecological impacts of large-bodied animals, their widespread loss during the last 50,000 years and their high diversity and ubiquity in the preceding 50 million years. Restoring abundant, diverse, wild-living megafauna is expected to promote vegetation heterogeneity, seed dispersal, nutrient cycling and biotic microhabitats. These are fundamental drivers of biodiversity and ecosystem function and are likely to gain importance for maintaining a biodiverse biosphere under increasingly novel ecological conditions. Non-native megafauna species may contribute to these effects as ecological surrogates of extinct species or by promoting ecological functionality within novel assemblages. Trophic rewilding has strong upscaling potential via population growth and expansion of wild fauna. It is likely to facilitate biotic adaptation to changing climatic conditions and resilience to ecosystem collapse, and to curb some negative impacts of globalization, notably the dominance of invasive alien plants. Finally, we discuss the complexities of realizing the biodiversity benefits that trophic rewilding offers under novel biosphere conditions in a heavily populated world.

Planktonic eukaryotes in the Chesapeake Bay: contrasting responses of abundant and rare taxa to estuarine gradients

Phytoplankton are important drivers of aquatic ecosystem function and environmental health. Their community compositions and distributions are directly impacted by environmental processes and human activities, including in the largest estuary in North America, the Chesapeake Bay. It is crucial to uncover how planktonic eukaryotes play fundamental roles as primary producers and trophic links and sustain estuarine ecosystems. In this study, we investigated the detailed community structure and spatiotemporal variations of planktonic eukaryotes in the Chesapeake Bay across space and time for three consecutive years. A clear seasonal and spatial shift of total, abundant, and rare planktonic eukaryotes was evident, and the pattern recurred interannually. Multiple harmful algal species have been identified in the Bay with varied distribution patterns, such as Karlodinium, Heterosigma akashiwo, Protoperidinium sp., etc. Compared to abundant taxa, rare subcommunities were more sensitive to environmental disturbance in terms of richness, diversity, and distribution. The combined effects of temporal variation (13.3%), nutrient availability (10.0%), and spatial gradients (8.8%) structured the distribution of eukaryotic microbial communities in the Bay. Similar spatiotemporal patterns between planktonic prokaryotes and eukaryotes suggest common mechanisms of adjustment, replacement, and species interaction for planktonic microbiomes under strong estuarine gradients. To our best knowledge, this work represents the first systematic study on planktonic eukaryotes in the Bay. A comprehensive view of the distribution of planktonic microbiomes and their interactions with environmental processes is critical in understanding the underlying microbial mechanisms involved in maintaining the stability, function, and environmental health of estuarine ecosystems.

IMPORTANCE

Deep sequencing analysis of planktonic eukaryotes in the Chesapeake Bay reveals high community diversity with many newly recognized phytoplankton taxa. The Chesapeake Bay planktonic eukaryotes show distinct seasonal and spatial variability, with recurring annual patterns of total, abundant, and rare groups. Rare taxa mainly contribute to eukaryotic diversity compared to abundant groups, and they are more sensitive to spatiotemporal variations and environmental filtering. Temporal variations, nutrient availability, and spatial gradients significantly affect the distribution of eukaryotic microbial communities. Similar spatiotemporal patterns in prokaryotes and eukaryotes suggest common mechanisms of adjustment, substitution, and species interactions in planktonic microbiomes under strong estuarine gradients. Interannually recurring patterns demonstrate that diverse eukaryotic taxa have well adapted to the estuarine environment with a long residence time. Further investigations of how human activities impact estuarine planktonic eukaryotes are critical in understanding their essential ecosystem roles and in maintaining environmental safety and public health.

Identification of hybrids between the Japanese giant salamander (Andrias japonicus) and Chinese giant salamander (Andrias cf. davidianus) using deep learning and smartphone images

Human-mediated hybridization between native and non-native species is causing biodiversity loss worldwide. Hybridization has contributed to the extinction of many species through direct and indirect processes such as loss of reproductive opportunity and genetic introgression. Therefore, it is essential to manage hybrids to conserve biodiversity. However, specialized knowledge is required to identify the target species based on visual characteristics when two species have similar features. Although image recognition technology can be a powerful tool for identifying hybrids, studies have yet to utilize deep learning approaches. Hence, this study aimed to identify hybrids between the native Japanese giant salamander (Andrias japonicus) and the non-native Chinese giant salamander (Andrias cf. davidianus) using EfficientNetV2 and smartphone images. We used smartphone images of 11 individuals of native A. japonicus (five training and six test images) and 20 individuals of hybrids between A. japonicus and A. cf. davidianus (five training and 15 test images). In our experimental environment, an AI model constructed with EfficientNetV2 exhibited 100% accuracy in identifying hybrids. In addition, gradient-weighted class activation mapping revealed that the AI model was able to classify A. japonicus and hybrids between A. japonicus and A. cf. davidianus on the basis of the dorsal head spot patterning. Our approach thus enables the identification of hybrids against A. japonicus, which was previously considered difficult by non-experts. Furthermore, since this study achieved reliable identification using smartphone images, it is expected to be applied to a wide range of citizen science projects.

Limnological factors that affect waterbird assemblages in semi-arid reservoirs of Tigray National Regional State, northern Ethiopia

Published accounts of the conservation of biodiversity indicate that understanding patterns of species distribution and richness is crucial. However, what drives patterns of species composition in a landscape remains debatable. I examined the relationship between limnological characteristics of reservoirs, morpho-edaphic variables, biological variables, and patterns of bird species richness and distribution. Six limnological, three morpho-edaphic variables, and biological variables were recorded for 35 reservoirs and analyzed by multivariate statistical techniques. To investigate the most important explanatory factors influencing avian species richness and their distribution, redundancy analysis (RDA) was used. A total of 85 bird species from 54 genera, with a mean species richness 14.23 ± 6.72 (mean ± standard deviation) per reservoir, were recorded. The RDA analysis identified two significant RDA axes, and 34.4% of the variation in species richness is explained by environmental variation (R²_adj = 0.34375; P < 0.001). Bird species richness was positively correlated with the surface area of reservoirs. I showed here that reservoir size and environmental heterogeneity were the important features that affect bird species richness, thus providing an important insight into the ecological relationship between waterbird species richness and the limnological characteristics of reservoirs. The strong positive correlation between species richness and both size and environmental variables underscores the importance of these reservoir features in the management of wildlife conservation. Large, environmentally heterogeneous reservoirs can support more species than small, environmentally homogeneous reservoirs because large, environmentally heterogeneous limnetic ecosystems can provide different resources for nesting, foraging, and roosting habitats for a diversified bird species. The result here also plays a role towards strengthening our knowledge of aquatic bird ecology and the natural history of African-Eurasian Migratory waterbirds.

Elevated compositional change in plant assemblages linked to invasion

Alien species are widely linked to biodiversity change, but the extent to which they are associated with the reshaping of ecological communities is not well understood. One possible mechanism is that assemblages where alien species are found exhibit elevated temporal turnover. To test this, we identified assemblages of vascular plants in the BioTIME database for those assemblages in which alien species are either present or absent and used the Jaccard measure to compute compositional dissimilarity between consecutive censuses. We found that, although alien species are typically rare in invaded assemblages, their presence is associated with an increase in the average rate of compositional change. These differences in compositional change between invaded and uninvaded assemblages are not linked to differences in species richness but rather to species replacement (turnover). Rapid compositional restructuring of assemblages is a major contributor to biodiversity change, and as such, our results suggest a role for alien species in bringing this about.

Magnago LF, Heringer G, Viana Neri A, Buttschardt T, Dudeque Zenni R, Tavares de Menezes LF, Zamborlini Saiter F, Reynaud Schaefer CEG, Vieira Hissa Safar N, Pacheco Da Silva M, Simonelli M, Martins SV, Brancalion PHS, A. Meira-Neto JA. Invasive alien acacias rapidly stock carbon, but threaten biodiversity recovery in young second-growth forests

Under the UN-Decade of Ecosystem Restoration and Bonn Challenge, second-growth forest is promoted as a global solution to climate change, degradation and associated losses of biodiversity and ecosystem services. Second growth is often invaded by alien tree species and understanding how this impacts carbon stock and biodiversity recovery is key for restoration planning. We assessed carbon stock and tree diversity recovery in second growth invaded by two Acacia species and non-invaded second growth, with associated edge effects, in the Brazilian Atlantic Forest. Carbon stock recovery in non-invaded forests was threefold lower than in invaded forests. Increasingly isolated, fragmented and deforested areas had low carbon stocks when non-invaded, whereas the opposite was true when invaded. Non-invaded forests recovered threefold to sixfold higher taxonomic, phylogenetic and functional diversity than invaded forest. Higher species turnover and lower nestedness in non-invaded than invaded forests underpinned higher abundance of threatened and endemic species in non-invaded forest. Non-invaded forests presented positive relationships between carbon and biodiversity, whereas in the invaded forests we did not detect any relationship, indicating that more carbon does not equal more biodiversity in landscapes with high vulnerability to invasive acacias. To deliver on combined climate change and biodiversity goals, restoration planning and management must consider biological invasion risk. This article is part of the theme issue 'Understanding forest landscape restoration: reinforcing scientific foundations for the UN Decade on Ecosystem Restoration'.

Half-century trends in alpha and beta diversity of phytoplankton summer communities in the Helsinki Archipelago, the Baltic Sea

We analyzed phytoplankton biodiversity trends in a 52 year (1967-2018) monitoring time-series from the archipelago of Helsinki, Gulf of Finland, the Baltic Sea. The community ordination revealed strong ordering of samples along the time axis (generalized additive model-gam fit: R ² = 0.9). Species richness increased in time and was the most influential alpha diversity descriptor related to the community structure (gam fit: R ² = 0.56-0.70). Changes in species richness accounted for 35-36% of the mean between-sample beta diversity. The remaining 64-65% was due to species turnover-the dominant component of the biodiversity trend. The temporal beta diversity trend reflected the eutrophication history of the geographically confined region, with a turning point in mid-1990s demarking the adaptation and recovery phases of the phytoplankton community. Trends in spatial beta diversity revealed homogenization of the communities in the outer archipelago zone, but not in the inner bays. The temporal decay of community similarity revealed high turnover rate, with 23.6 years halving time in the outer archipelago and 11.3 years in the inner bays, revealing the differences in eutrophication strength. The observed phytoplankton trends manifest the regional eutrophication history, and dispersal of new species to the unsaturated brackish species pool.

Climate change effects on marginal savannas from central-north Brazil

This study estimated the potential effects of climate change on peripheral plant diversity by predicting the distribution of species from Cerrado of Northern Brazil. Ecological niche modeling was used to provide present and future projections of responses in terms of occurrence of ten woody species based on four algorithms and four future climate change scenarios for the year 2050. Potential refuge areas for conservation actions were identified, and evidence of the vulnerability of the flora was demonstrated based on the disparity between potential areas of climate stability amid current protected areas. The results suggested a lack of pattern between the scenarios and an idiosyncratic response of the species, indicating different impacts on plant communities and the existence of unequal stable alternative conditions, which could bring consequences to the ecological relationships and functionality of the floras. Even in the most pessimistic scenarios, most species presented an expansion of potential occurrence areas, suppressing or cohabiting with species of adjacent biomes. Typically marginal plants were the most sensitive. Overlapping adequate habitats are concentrated in the NBC. The analysis of habitats in relation to anthropized areas and PAs demonstrate low future effectiveness in the protection of these savannas.

Late quaternary biotic homogenization of North American mammalian faunas

Biotic homogenization—increasing similarity of species composition among ecological communities—has been linked to anthropogenic processes operating over the last century. Fossil evidence, however, suggests that humans have had impacts on ecosystems for millennia. We quantify biotic homogenization of North American mammalian assemblages during the late Pleistocene through Holocene (~30,000 ybp to recent), a timespan encompassing increased evidence of humans on the landscape (~20,000–14,000 ybp). From ~10,000 ybp to recent, assemblages became significantly more homogenous (>100% increase in Jaccard similarity), a pattern that cannot be explained by changes in fossil record sampling. Homogenization was most pronounced among mammals larger than 1 kg and occurred in two phases. The first followed the megafaunal extinction at ~10,000 ybp. The second, more rapid phase began during human population growth and early agricultural intensification (~2,000–1,000 ybp). We show that North American ecosystems were homogenizing for millennia, extending human impacts back ~10,000 years.

Biotic homogenization, which is increased similarity in the composition of species among communities, is rising due to human activities. Using North American mammal fossil records from the past 30,000 years, this study shows that this phenomenon is ancient, beginning between 12,000 and 10,000 years ago with the extinction of the mammal megafauna.

Moroccan Lagoon Microbiomes

Lagoons are fragile marine ecosystems that are considerably affected by anthropogenic pollutants. We performed a spatiotemporal characterization of the microbiome of two Moroccan lagoons, Marchica and Oualidia, both classified as Ramsar sites, the former on the Mediterranean coast and the latter on the Atlantic coast. We investigated their microbial diversity and abundance using 16S rRNA amplicon- and shotgun-based metagenomics approaches during the summers of 2014 and 2015. The bacterial microbiome was composed primarily of Proteobacteria (25–53%, 29–29%), Cyanobacteria (34–12%, 11–0.53%), Bacteroidetes (24–16%, 23–43%), Actinobacteria (7–11%, 13–7%), and Verrucomicrobia (4–1%, 15–14%) in Marchica and Oualidia in 2014 and 2015, respectively. Interestingly, 48 strains were newly reported in lagoon ecosystems, while eight unknown viruses were detected in Mediterranean Marchica only. Statistical analysis showed higher microbial diversity in the Atlantic lagoon than in the Mediterranean lagoon and a robust relationship between alpha diversity and geographic sampling locations. This first-ever metagenomics study on Moroccan aquatic ecosystems enriched the national catalog of marine microorganisms. They will be investigated as candidates for bioindication properties, biomonitoring potential, biotechnology valorization, biodiversity protection, and lagoon health assessment.

Long-term changes in temperate marine fish assemblages are driven by a small subset of species

The species composition of plant and animal assemblages across the globe has changed substantially over the past century. How do the dynamics of individual species cause this change? We classified species into seven unique categories of temporal dynamics based on the ordered sequence of presences and absences that each species contributes to an assemblage time series. We applied this framework to 14,434 species trajectories comprising 280 assemblages of temperate marine fishes surveyed annually for 20 or more years. Although 90% of the assemblages diverged in species composition from the baseline year, this compositional change was largely driven by only 8% of the species' trajectories. Quantifying the reorganization of assemblages based on species shared temporal dynamics should facilitate the task of monitoring and restoring biodiversity. We suggest ways in which our framework could provide informative measures of compositional change, as well as leverage future research on pattern and process in ecological systems.

Antigonon leptopus invasion is associated with plant community disassembly in a Caribbean island ecosystem

Invasions by non-native plant species are widely recognized as a major driver of biodiversity loss. Globally, (sub-)tropical islands form important components of biodiversity hotspots, while being particularly susceptible to invasions by plants in general and vines in particular. We studied the impact of the invasive vine A. leptopus on the diversity and structure of recipient plant communities on the northern Caribbean island St. Eustatius. We used a paired-plot design to study differences in species richness, evenness and community structure under A. leptopus-invaded and uninvaded conditions. Community structure was studied through species co-occurrence patterns. We found that in plots invaded by A. leptopus, species richness was 40–50% lower, and these plots also exhibited lower evenness. The magnitude of these negative impacts increased with increasing cover of A. leptopus. Invaded plots also showed higher degrees of homogeneity in species composition. Species co-occurrence patterns indicated that plant communities in uninvaded plots were characterized by segregation, whereas recipient plant communities in invaded plots exhibited random co-occurrence patterns. These observations suggest that invasion of A. leptopus is not only associated with reduced species richness and evenness of recipient communities in invaded sites, but also with a community disassembly process that may reduce diversity between sites. Given that A. leptopus is a successful invader of (sub-)tropical islands around the globe, these impacts on plant community structure highlight that this invasive species could be a particular conservation concern for these systems.

Global projections of the soil microbiome in the Anthropocene

AIM

Soil microbes are essential for maintenance of life-supporting ecosystem services, but projections of how these microbes will be affected by global change scenarios are lacking. Therefore, our aim was to provide projections of future soil microbial distribution using several scenarios of global change.

LOCATION

Global.

TIME PERIOD

1950-2090.

MAJOR TAXA STUDIED

Bacteria and fungi.

METHODS

We used a global database of soil microbial communities across six continents to estimate past and future trends of the soil microbiome. To do so, we used structural equation models to include the direct and indirect effects of changes in climate and land use in our predictions, using current climate (temperature and precipitation) and land-use projections between 1950 and 2090.

RESULTS

Local bacterial richness will increase in all scenarios of change in climate and land use considered, although this increase will be followed by a generalized community homogenization process affecting > 85% of terrestrial ecosystems. Changes in the relative abundance of functional genes associated with the increases in bacterial richness are also expected. Based on an ecological cluster analysis, our results suggest that phylotypes such as Geodermatophilus spp. (typical desert bacteria), Mycobacterium sp. (which are known to include important human pathogens), Streptomyces mirabilis (major producers of antibiotic resistance genes) or potential fungal soil-borne plant pathogens belonging to Ascomycota fungi (Venturia spp., Devriesia spp.) will become more abundant in their communities.

MAIN CONCLUSIONS

Our results provide evidence that climate change has a stronger influence on soil microbial communities than change in land use (often including deforestation and agricultural expansion), although most of the effects of climate are indirect, through other environmental variables (e.g., changes in soil pH). The same was found for microbial functions such as the prevalence of phosphate transport genes. We provide reliable predictions about the changes in the global distribution of microbial communities, showing an increase in alpha diversity and a homogenization of soil microbial communities in the Anthropocene.

Non-native Species Surrounding Protected Areas Influence the Community of Non-native Species Within Them

Protected areas (PAs) are a key element of global conservation strategies aiming to protect habitats and species from various threats such as non-natives species (NNS) with negative ecological impacts. Yet little is known about the mechanisms by which PAs are colonized by NNS, and more specifically the role of colonizing events from surrounding areas. Here, we compared terrestrial and freshwater non-native plants and animals recorded in Norwegian PAs and in 5-km belts around them, using the database of the Norwegian Biodiversity Information Centre Species Map Service. Our analysis included 1,602 NNS and 671 PAs. We found that NNS were recorded in only 23% of the PAs, despite the fact that 90% of the 5-km belts were colonized by at least one NNS. A Zero-inflated negative binomial regression model showed that the number of NNS in the 5-km belts was a strong explanatory variable of the NNS richness inside PAs. Other significant variables included the surface area of the PA, mean human population density in the PA, main type of habitat and accessibility of PAs. We also observed similarity in the species in and around the PAs, with, on average, two thirds of the NNS present in a specific PA also present in its 5-km belt. Furthermore, NNS were recorded in PAs on average 4.5 years after being recorded in the 0–5 km belts, suggesting a dynamic of rapid colonization from the belts to the PAs. Invasive NNS represented 12% of NNS in the belts but 40% in the PAs. This difference was related to the higher abundance of invasive NNS in the belts. Our results highlight the necessity of expanding the focus of NNS management in PAs beyond their boundaries, in particular to prevent incursions of NNS with high negative ecological impact.

Frenemy at the gate: Invasion by Pheidole megacephala facilitates a competitively subordinate plant ant in Kenya

Biological invasions can lead to the reassembly of communities and understanding and predicting the impacts of exotic species on community structure and functioning are a key challenge in ecology. We investigated the impact of a predatory species of invasive ant, Pheidole megacephala, on the structure and function of a foundational mutualism between Acacia drepanolobium and its associated acacia-ant community in an East African savanna. Invasion by P. megacephala was associated with the extirpation of three extrafloral nectar-dependent Crematogaster acacia ant species and strong increases in the abundance of a competitively subordinate and locally rare acacia ant species, Tetraponera penzigi, which does not depend on host plant nectar. Using a combination of long-term monitoring of invasion dynamics, observations and experiments, we demonstrate that P. megacephala directly and indirectly facilitates T. penzigi by reducing the abundance of T. penzigi's competitors (Crematogaster spp.), imposing recruitment limitation on these competitors, and generating a landscape of low-reward host plants that favor colonization and establishment by the strongly dispersing T. penzigi. Seasonal variation in use of host plants by P. megacephala may further increase the persistence of T. penzigi colonies in invaded habitat. The persistence of the T. penzigi-A. drepanolobium symbiosis in invaded areas afforded host plants some protection against herbivory by elephants (Loxodonta africana), a key browser that reduces tree cover. However, elephant damage on T. penzigi-occupied trees was higher in invaded than in uninvaded areas, likely owing to reduced T. penzigi colony size in invaded habitats. Our results reveal the mechanisms underlying the disruption of this mutualism and suggest that P. megacephala invasion may drive long-term declines in tree cover, despite the partial persistence of the ant-acacia symbiosis in invaded areas.

Plant biodiversity in the face of global change

Le Roux et al. suggest that documented increases in local plant richness in response to climate change should consider the nature of 'new' species. They find that species responsible for increases in richness in areas that have experienced significant disturbance and climate change are often invasive and/or weedy species.

Marked decline in forest-dependent small mammals following habitat loss and fragmentation in an Amazonian deforestation frontier

Agricultural frontier expansion into the Amazon over the last four decades has created million hectares of fragmented forests. While many species undergo local extinctions within remaining forest patches, this may be compensated by native species from neighbouring open-habitat areas potentially invading these patches, particularly as forest habitats become increasingly degraded. Here, we examine the effects of habitat loss, fragmentation and degradation on small mammal assemblages in a southern Amazonian deforestation frontier, while accounting for species-specific degree of forest-dependency. We surveyed small mammals at three continuous forest sites and 19 forest patches of different sizes and degrees of isolation. We further sampled matrix habitats adjacent to forest patches, which allowed us to classify each species according to forest-dependency and generate a community-averaged forest-dependency index for each site. Based on 21,568 trap-nights, we recorded 970 small mammals representing 20 species: 12 forest-dependents, 5 matrix-tolerants and 3 open-habitat specialists. Across the gradient of forest patch size, small mammal assemblages failed to show the typical species-area relationship, but this relationship held true when either species abundance or composition was considered. Species composition was further mediated by community-averaged forest-dependency, so that smaller forest patches were occupied by a lower proportion of forest-dependent rodents and marsupials. Both species richness and abundance increased in less isolated fragments surrounded by structurally simplified matrix habitats (e.g. active or abandoned cattle pastures). While shorter distances between forest patches may favour small mammal abundances, forest area and matrix complexity dictated which species could persist within forest fragments according to their degree of forest-dependency. Small mammal local extinctions in small forest patches within Amazonian deforestation frontiers are therefore likely offset by the incursion of open-habitat species. To preclude the dominance of those species, and consequent losses of native species and associated ecosystem functions, management actions should limit or reduce areas dedicated to pasture, additionally maintaining more structurally complex matrix habitats across fragmented landscapes.

Increases in local richness (α-diversity) following invasion are offset by biotic homogenization in a biodiversity hotspot

The world's ecosystems are experiencing unparalleled rates of biodiversity change, with invasive species implicated as one of the drivers that restructure local assemblages. Here we focus on the processes leading to biodiversity change in a biodiversity hotspot, the Brazilian Cerrado. The null expectation that invasion leads to increase in local species richness is supported by our investigation of the grass layer in two key habitats (campo sujo and campo úmido). Our analysis uncovered a linear relationship between total richness and invasive richness at the plot level. However, because the invasive species-even though few in number-are widespread, their contribution to local richness (α-diversity) is offset by their homogenizing influence on composition (β-diversity). We thus identify a mechanism that can help explain the paradox that species richness is not declining in many local assemblages, yet compositional change is exceeding the predictions of ecological theory. As such, our results emphasize the importance of quantifying both α-diversity and β-diversity in assessments of biodiversity change in the contemporary world.