Mapping the imprint of biotic interactions on β-diversity

Unravelling large-scale patterns and drivers of biodiversity in dry rivers

More than half of the world's rivers dry up periodically, but our understanding of the biological communities in dry riverbeds remains limited. Specifically, the roles of dispersal, environmental filtering and biotic interactions in driving biodiversity in dry rivers are poorly understood. Here, we conduct a large-scale coordinated survey of patterns and drivers of biodiversity in dry riverbeds. We focus on eight major taxa, including microorganisms, invertebrates and plants: Algae, Archaea, Bacteria, Fungi, Protozoa, Arthropods, Nematodes and Streptophyta. We use environmental DNA metabarcoding to assess biodiversity in dry sediments collected over a 1-year period from 84 non-perennial rivers across 19 countries on four continents. Both direct factors, such as nutrient and carbon availability, and indirect factors such as climate influence the local biodiversity of most taxa. Limited resource availability and prolonged dry phases favor oligotrophic microbial taxa. Co-variation among taxa, particularly Bacteria, Fungi, Algae and Protozoa, explain more spatial variation in community composition than dispersal or environmental gradients. This finding suggests that biotic interactions or unmeasured ecological and evolutionary factors may strongly influence communities during dry phases, altering biodiversity responses to global changes.

The development of terrestrial ecosystems emerging after glacier retreat

The global retreat of glaciers is dramatically altering mountain and high-latitude landscapes, with new ecosystems developing from apparently barren substrates1-4. The study of these emerging ecosystems is critical to understanding how climate change interacts with microhabitat and biotic communities and determines the future of ice-free terrains1,5. Here, using a comprehensive characterization of ecosystems (soil properties, microclimate, productivity and biodiversity by environmental DNA metabarcoding6) across 46 proglacial landscapes worldwide, we found that all the environmental properties change with time since glaciers retreated, and that temperature modulates the accumulation of soil nutrients. The richness of bacteria, fungi, plants and animals increases with time since deglaciation, but their temporal patterns differ. Microorganisms colonized most rapidly in the first decades after glacier retreat, whereas most macroorganisms took longer. Increased habitat suitability, growing complexity of biotic interactions and temporal colonization all contribute to the increase in biodiversity over time. These processes also modify community composition for all the groups of organisms. Plant communities show positive links with all other biodiversity components and have a key role in ecosystem development. These unifying patterns provide new insights into the early dynamics of deglaciated terrains and highlight the need for integrated surveillance of their multiple environmental properties5.

In silico assessment of 18S rDNA metabarcoding markers for the characterization of nematode communities

Nematodes are keystone actors of soil, freshwater and marine ecosystems, but the complexity of morphological identification has limited broad-scale monitoring of nematode biodiversity. DNA metabarcoding is increasingly used to assess nematode diversity but requires universal primers with high taxonomic coverage and high taxonomic resolution. Several primers have been proposed for the metabarcoding of nematode diversity, many of which target the 18S rRNA gene. In silico analyses have a great potential to assess key parameters of primers, including taxonomic coverage, resolution and specificity. Based on a recently-available reference database, we tested in silico the performance of fourteen commonly used and one newly optimized primer for nematode metabarcoding. Most primers showed very good coverage, amplifying most of the sequences in the reference database, while four markers showed limited coverage. All primers showed good taxonomic resolution. Resolution was particularly good if the aim was the identification of higher-level taxa, such as genera or families. Overall, species-level resolution was higher for primers amplifying long fragments. None of the primers was highly specific for nematodes as, despite some variation, they all amplified a large number of other eukaryotes. Differences in performance across primers highlight the complexity of the choice of markers appropriate for the metabarcoding of nematodes, which depends on a trade-off between taxonomic resolution and the length of amplified fragments. Our in silico analyses provide new insights for the identification of the most appropriate primers, depending on the study goals and the origin of DNA samples. This represents an essential step to design and optimize metabarcoding studies assessing nematode diversity.

Novel community data in ecology-properties and prospects

New technologies for monitoring biodiversity such as environmental (e)DNA, passive acoustic monitoring, and optical sensors promise to generate automated spatiotemporal community observations at unprecedented scales and resolutions. Here, we introduce 'novel community data' as an umbrella term for these data. We review the emerging field around novel community data, focusing on new ecological questions that could be addressed; the analytical tools available or needed to make best use of these data; and the potential implications of these developments for policy and conservation. We conclude that novel community data offer many opportunities to advance our understanding of fundamental ecological processes, including community assembly, biotic interactions, micro- and macroevolution, and overall ecosystem functioning.

Severe Prolonged Drought Favours Stress-Tolerant Microbes in Australian Drylands

Drylands comprise one-third of Earth's terrestrial surface area and support over two billion people. Most drylands are projected to experience altered rainfall regimes, including changes in total amounts and fewer but larger rainfall events interspersed by longer periods without rain. This transition will have ecosystem-wide impacts but the long-term effects on microbial communities remain poorly quantified. We assessed belowground effects of altered rainfall regimes (+ 65% and -65% relative to ambient) at six sites in arid and semi-arid Australia over a period of three years (2016-2019) coinciding with a significant natural drought event (2017-2019). Microbial communities differed significantly among semi-arid and arid sites and across years associated with variation in abiotic factors, such as pH and carbon content, along with rainfall. Rainfall treatments induced shifts in microbial community composition only at a subset of the sites (Milparinka and Quilpie). However, differential abundance analyses revealed that several taxa, including Acidobacteria, TM7, Gemmatimonadates and Chytridiomycota, were more abundant in the wettest year (2016) and that their relative abundance decreased in drier years. By contrast, the relative abundance of oligotrophic taxa such as Actinobacteria, Alpha-proteobacteria, Planctomycetes, and Ascomycota and Basidiomycota, increased during the prolonged drought. Interestingly, fungi were shown to be more sensitive to the prolonged drought and to rainfall treatment than bacteria with Basidiomycota mostly dominant in the reduced rainfall treatment. Moreover, correlation network analyses showed more positive associations among stress-tolerant dominant taxa following the drought (i.e., 2019 compared with 2016). Our result indicates that such stress-tolerant taxa play an important role in how whole communities respond to changes in aridity. Such knowledge provides a better understanding of microbial responses to predicted increases in rainfall variability and the impact on the functioning of semi-arid and arid ecosystems.

Tree communities and functional traits determine herbivore compositional turnover

There are many factors known to drive species turnover, although the mechanisms by which these operate are less clear. Based on comprehensive datasets from the largest tree diversity experiment worldwide (BEF-China), we used shared herbivore species (zeta diversity) and multi-site generalized dissimilarity modelling to investigate the patterns and determinants of species turnover of Lepidoptera herbivores among study plots across a gradient in tree species richness. We found that zeta diversity declined sharply with an increasing number of study plots, with complete changes in caterpillar species composition observed even at the fine spatial scale of our study. Plant community characteristics rather than abiotic factors were found to play key roles in driving caterpillar compositional turnover, although these effects varied with an increasing number of study plots considered, due to the varying contributions of rare and common species to compositional turnover. Our study reveals details of the impact of phylogeny- and trait-mediated processes of trees on herbivore compositional turnover, which has implications for forest management and conservation and shows potential avenues for maintenance of heterogeneity in herbivore communities.

Shifts in food webs and niche stability shaped survivorship and extinction at the end-Cretaceous

It has long been debated why groups such as non-avian dinosaurs became extinct whereas mammals and other lineages survived the Cretaceous/Paleogene mass extinction 66 million years ago. We used Markov networks, ecological niche partitioning, and Earth System models to reconstruct North American food webs and simulate ecospace occupancy before and after the extinction event. We find a shift in latest Cretaceous dinosaur faunas, as medium-sized species counterbalanced a loss of megaherbivores, but dinosaur niches were otherwise stable and static, potentially contributing to their demise. Smaller vertebrates, including mammals, followed a consistent trajectory of increasing trophic impact and relaxation of niche limits beginning in the latest Cretaceous and continuing after the mass extinction. Mammals did not simply proliferate after the extinction event; rather, their earlier ecological diversification might have helped them survive.

Succession comprises a sequence of threshold-induced community assembly processes towards multidiversity

Research on successions and community assembly both address the same processes such as dispersal, species sorting, and biotic interactions but lack unifying concepts. Recent theoretical advances integrated both research lines proposing a sequence of stochastic and deterministic processes along successional gradients. Shifts in ecosystem states along successional gradients are predicted to occur abruptly once abiotic and biotic factors dominate over dispersal as main driver. Considering the multidiversity composed of five organismal groups including plants, animals, and microbes, our results imply that stochastic, likely dispersal-dominated, processes are replaced by rather deterministic processes such as environmental filtering and biotic interactions after around 60 years of succession in a glacier forefield. The niche-based character of later successional processes is further supported by a decline in multi-beta-diversity. Our results may update concepts of community assembly by considering multiple taxa, help to bridge the gap between research on successions and community assembly, and provide insights into the emergence of multidiverse and complex ecosystems.

Linking soil fungi to bacterial community assembly in arid ecosystems

Revealing the roles of biotic factors in driving community assembly, which is crucial for the understanding of biodiversity and ecosystem functions, is a fundamental but infrequently investigated subject in microbial ecology. Here, combining a cross-biome observational study with an experimental microcosm study, we provided evidence to reveal the major roles of biotic factors (i.e., soil fungi and cross-kingdom species associations) in determining soil bacterial biogeography and community assembly in complex terrestrial ecosystems of the arid regions of northwest China. The results showed that the soil fungal richness mediates the balance of assembly processes of bacterial communities, and stochastic assembly processes decreased with increasing fungal richness. Our results further suggest that the predicted increase in aridity conditions due to climate change will reduce bacterial α-diversity, particularly in desert soils and subsurface layer, and induce more negative species associations. Together, our study represents a significant advance in linking soil fungi to the mechanisms underlying bacterial biogeographic patterns and community assembly in arid ecosystems under climate aridity and land-use change scenarios.

Refocusing multiple stressor research around the targets and scales of ecological impacts

Ecological communities face a variety of environmental and anthropogenic stressors acting simultaneously. Stressor impacts can combine additively or can interact, causing synergistic or antagonistic effects. Our knowledge of when and how interactions arise is limited, as most models and experiments only consider the effect of a small number of non-interacting stressors at one or few scales of ecological organization. This is concerning because it could lead to significant underestimations or overestimations of threats to biodiversity. Furthermore, stressors have been largely classified by their source rather than by the mechanisms and ecological scales at which they act (the target). Here, we argue, first, that a more nuanced classification of stressors by target and ecological scale can generate valuable new insights and hypotheses about stressor interactions. Second, that the predictability of multiple stressor effects, and consistent patterns in their impacts, can be evaluated by examining the distribution of stressor effects across targets and ecological scales. Third, that a variety of existing mechanistic and statistical modelling tools can play an important role in our framework and advance multiple stressor research.

DNA metabarcoding and morphological methods show complementary patterns in the metacommunity organization of lentic epiphytic diatoms

Diatoms are important organisms in freshwater ecosystems due to their position as primary producers and therefore, analyzing their assemblages provides relevant information on ecosystem functioning. Diatoms have historically been identified based on morphological traits, which is time-consuming and requires well-trained specialists. Nevertheless, DNA barcoding offers an alternative approach to overcome some limitations of the morphological method. Here, we assess if both approaches are comparable methods to study patterns and mechanisms (including environmental filtering and dispersal limitation) of epiphytic diatom metacommunities using a comprehensive dataset from 22 Mediterranean ponds at different taxonomic resolutions. We used a fragment of rbcL barcode gene combined with High-Throughput Sequencing to infer diatom community composition. The overall degree of correspondence between both approaches was assessed by Procrustean rotation analysis and Procrustean randomization tests, whereas the role of local environmental variables and geographical distances was studied using a comprehensive combination of BIOENV, Mantel tests and distance-based redundancy analysis. Our results showed a relatively poor correspondence in the compositional variation of diatom metacommunity between both approaches. We speculate that the incompleteness of the reference database and the bioinformatics processing are the biases most likely affecting the molecular approach, whereas the limited counting effort and the presence of cryptic species are presumably the major biases related with the morphological method. On the other hand, variation in diatom community composition detected with both approaches was strongly related to the environmental template, which may be related with the narrow community-environment relationships in diatoms. Nevertheless, we found no significant relationship between compositional variation and geographical distances. Overall, our work shows the complementary nature of both approaches and highlights the importance of DNA metabarcoding to address empirical research questions of community ecology in freshwaters, especially once the reference databases include most genotypes of occurring taxa and bioinformatics biases are overcome.

Soil protist function varies with elevation in the Swiss Alps

Protists are abundant and play key trophic functions in soil. Documenting how their trophic contributions vary across large environmental gradients is essential to understand and predict how biogeochemical cycles will be impacted by global changes. Here, using amplicon sequencing of environmental DNA in open habitat soil from 161 locations spanning 2600 m of elevation in the Swiss Alps (from 400 to 3000 m), we found that, over the whole study area, soils are dominated by consumers, followed by parasites and phototrophs. In contrast, the proportion of these groups in local communities shows large variations in relation to elevation. While there is, on average, three times more consumers than parasites at low elevation (400–1000 m), this ratio increases to 12 at high elevation (2000–3000 m). This suggests that the decrease in protist host biomass and diversity toward mountains tops impact protist functional composition. Furthermore, the taxonomic composition of protists that infect animals was related to elevation while that of protists that infect plants or of protist consumers was related to soil pH. This study provides a first step to document and understand how soil protist functions vary along the elevational gradient.

Spatial patterns and ecological drivers of soil nematode β-diversity in natural grasslands vary among vegetation types and trophic position

Understanding biogeographic patterns of community assemblages is a core objective in ecology, but for soil communities these patterns are poorly understood. To understand the spatial patterns and underlying mechanisms of β-diversity in soil communities, we investigated the β-diversity of soil nematode communities along a 3,200-km transect across semi-arid and arid grasslands. Spatial turnover and nested-resultant are the two fundamental components of β-diversity, which have been attributed to various processes of community assembly. We calculated the spatial turnover and nested-resultant components of soil nematode β-diversity based on the β-partitioning framework. Distance matrices for the dissimilarity of soil nematode communities were computed using the 'Sørensen' method. We fitted negative exponential models to compare the distance decay patterns in nematode community similarity with geographic distance and plant community distance in three vegetation types (desert, desert steppe and typical steppe) and along the whole transect. Variation partitioning was used to distinguish the contribution of geographic distance and environmental variables to β-diversity and the partitioned components. Geographic distance and environmental filtering jointly drove the β-diversity patterns of nematode community, but environmental filtering explained more of the variation in β-diversity in the desert and typical steppe, whereas geographic distance was important in the desert steppe. Nematode community assembly was explained more by the spatial turnover component than by the nested-resultant component. For nematode feeding groups, the β-diversity in different vegetation types increased with geographic distance and plant community distance, but the nested-resultant component of bacterial feeders in the desert ecosystem decreased with geographic distance and plant community distance. Our findings show that spatial variation in soil nematode communities is regulated by environmental processes at the vegetation type scale, while spatial processes mainly work on the regional scale, and emphasize that the spatial patterns and drivers of nematode β-diversity differ among trophic levels. Our study provides insight into the ecological processes that maintain soil biodiversity and biogeographic patterns of soil community assemblage at large spatial scales.

Coupled beta diversity patterns among coral reef benthic taxa

Unraveling the processes that drive diversity patterns remains a central challenge for ecology, and an increased understanding is especially urgent to address and mitigate escalating diversity loss. Studies have primarily focused on singular taxonomic groups, but recent research has begun evaluating spatial diversity patterns across multiple taxonomic groups and suggests taxa may have congruence in their diversity patterns. Here, we use surveys of the coral reef benthic groups: scleractinian corals, macroalgae, sponges and gorgonians conducted in the Bahamian Archipelago across 27 sites to determine if there is congruence between taxonomic groups in their site-level diversity patterns (i.e. alpha diversity: number of species, and beta diversity: differences in species composition) while accounting for environmental predictors (i.e. depth, wave exposure, market gravity (i.e. human population size and distance to market), primary productivity, and grazing). Overall, we found that the beta diversities of these benthic groups were significant predictors of each other. The most consistent relationships existed with algae and coral, as their beta diversity was a significant predictor of every other taxa's beta diversity, potentially due to their strong biotic interactions and dominance on the reef. Conversely, we found no congruence patterns in the alpha diversity of the taxa. Market gravity and exposure showed the most prevalent correlation with both alpha and beta diversity for the taxa. Overall, our results suggest that coral reef benthic taxa can have spatial congruence in species composition, but not number of species, and that future research on biodiversity trends should consider that taxa may have non-independent patterns.

The rise of a marine generalist predator and the fall of beta diversity

Determining the importance of physical and biological drivers in shaping biodiversity in diverse ecosystems remains a global challenge. Advancements have been made towards this end in large marine ecosystems with several studies suggesting environmental forcing as the primary driver. However, both empirical and theoretical studies point to additional drivers of changes in diversity involving trophic interactions and, in particular, predation. Moreover, a more integrated but less common approach to the assessment of biodiversity changes involves analyses of spatial β diversity, whereas most studies to date assess only changes in species richness (α diversity). Recent research has established that when cod, a dominant generalist predator, was overfished and collapsed in a northwest Atlantic food web, spatial β diversity increased; that is, the spatial structure of the fish assemblage became increasingly heterogeneous. If cod were to recover, would this situation be reversible, given the inherent complexity and non-linear dynamics that typify such systems? A dramatic increase of cod in an ecologically similar large marine ecosystem may provide an answer. Here we show that spatial β diversity of fish assemblages in the Barents Sea decreased with increasing cod abundance, while decadal scale changes in temperature did not play a significant role. These findings indicate a reversibility of the fish assemblage structure in response to changing levels of an apex predator and highlight the frequently overlooked importance of trophic interactions in determining large-scale biodiversity patterns. As increased cod abundance was largely driven by changes in fisheries management, our study also shows that management policies and practices, particularly those involving apex predators, can have a strong effect in shaping spatial diversity patterns, and one should not restrict the focus to effects of climate change alone.

Sedimentary DNA reveals over 150 years of ecosystem change by human activities in Lake Chao, China

Understanding the extent and directionality of the impact of human activities on ecosystems is directly related to their management and protection. However, the lack of historical data limits our understanding of ecosystem changes with long-term exposure to human activities. Recently, lake sedimentary DNA (sedDNA) has become a powerful tool for revealing changes in ecosystems at the century and millennium scales. Here, we used sedDNA to reveal the dynamic of the microbial community (including bacteria and micro-eukaryotes) in Lake Chao over the past 150 years, and further explored the effects of long-term nutrient and heavy metal loads on these communities. Our data show that nutrient and heavy metal loads in Lake Chao have increased by ca. 2 to 4-fold since the 1960s. In response, the community structure, diversity, and ecological network of bacteria and micro-eukaryotes changed significantly during the 1960s, the 1980s and the 2010s. Importantly, community structure was more sensitive to human activities than diversity. We also found that the relative abundance of some taxa associated with nitrification and algal blooms (e.g., taxa in Nitrospira sp., Peridinales) has increased ca. 100-fold since the 1960s. Nutrient could better explain the variation in the bacterial community (ca. twice as much as heavy metal), while heavy metal explained micro-eukaryotes better (ca. 3 or 5-fold as much as nutrient). In particular, based on parsimonious models from distance-based linear model (distLM), we further identified that Pb is the key factor affecting the bacterial and micro-eukaryotes community in Lake Chao in addition to nutrient. Our study reveals the impacts of long-term human activities on lake ecosystems from multiple perspectives of nutrient and heavy metal loads, community structure, diversity and ecological network, these findings will contribute to the management and conservation of lakes in the future.