Community assembly effects shape the biodiversity-ecosystem functioning relationships

Parent material influences soil properties to shape bacterial community assembly processes, diversity, and enzyme-related functions

Soil parent material is the second most influential factor in pedogenesis, influencing soil properties and microbial communities. Different assembly processes shape diverse functional microbial communities. The question remains unresolved regarding how these ecological assembly processes affect microbial communities and soil functionality within soils on different parent materials. We collected soil samples developed from typical parent materials, including basalt, granite, metamorphic rock, and marine sediments across soil profiles at depths of 0-20, 20-40, 40-80, and 80-100 cm, within rubber plantations on Hainan Island, China. We determined bacterial community characteristics, community assembly processes, and soil enzyme-related functions using 16S rRNA high-throughput sequencing and enzyme activity analyses. We found homogeneous selection, dispersal limitation, and drift processes were the dominant drivers of bacterial community assembly across soils on different parent materials. In soils on basalt, lower pH and higher moisture triggered a homogeneous selection-dominated assembly process, leading to a less diverse community but otherwise higher carbon and nitrogen cycling enzyme activities. As deterministic process decreased, bacterial community diversity increased with stochastic process. In soils on marine sediments, lower water, carbon, and nutrient content limited the dispersal of bacterial communities, resulting in higher community diversity and an increased capacity to utilize relative recalcitrant substrates by releasing more oxidases. The r-strategy Bacteroidetes and genera Sphingomonas, Bacillus, Vibrionimonas, Ochrobactrum positively correlated with enzyme-related function, whereas k-strategy Acidobacteria, Verrucomicrobia and genera Acidothermus, Burkholderia-Caballeronia-Paraburkholderia, HSB OF53-F07 showed negative correlations. Our study suggests that parent material could influence bacterial community assembly processes, diversity, and soil enzyme-related functions via soil properties.

Impacts of sequential salinity and heat stress are recovery time-specific in freshwater crustacean, Daphnia pulicaria

Stressors can interact to affect animal fitness, but we have limited knowledge about how temporal variation in stressors may impact their combined effect. This limits our ability to predict the outcomes of pollutants and future dynamic environmental changes. Elevated salinity in freshwater ecosystems has been observed worldwide. Meanwhile, heatwaves have become more frequent and intensified as an outcome of climate change. These two stressors can jointly affect organisms; however, their interaction has rarely been explored in the context of freshwater ecosystems. We conducted lab experiments using Daphnia pulicaria, a key species in lakes, to investigate how elevated salinity and heatwave conditions collectively affect freshwater organisms. We also monitored the impacts of various recovery times between the two stressors. Daphnia physiological conditions (metabolic rate, Na+-K+-ATPase (NKA) activity, and lipid peroxidation level) and life history traits (survival, fecundity, and growth) in response to salt stress as well as mortality in heat treatment were examined. We found that Daphnia responded to elevated salinity by upregulating NKA activity and increasing metabolic rate, causing a high lipid peroxidation level. Survival, fecundity, and growth were all negatively affected by this stressor. These impacts on physiological conditions and life history traits persisted for a few days after the end of the exposure. Heat treatments caused mortality in Daphnia, which increased with rising temperature. Results also showed that individuals that experienced salt exposure were more susceptible to subsequent heat stress, but this effect decreased with increasing recovery time between stressors. Findings from this work suggest that the legacy effects from a previous stressor can reduce individual resistance to a subsequent stressor, adding great difficulties to the prediction of outcomes of multiple stressors. Our work also demonstrates that cross-tolerance/susceptibility and the associated mechanisms remain unclear, necessitating further investigation.

Unsupervised biological integrity assessment by eDNA biomonitoring of multi-trophic aquatic taxa

The biological integrity of global freshwater ecosystems is threatened by ever-increasing environmental stressors due to increased human activities, such as land-use change, eutrophication, toxic pollutants, overfishing, and exploitation. Traditional ecological assessments of lake or riverine ecosystems often require human supervision of a pre-selected reference area, using the current state of the reference area as the expected state. However, selecting an appropriate reference area has become increasingly difficult with the expansion of human activities. Here, an unsupervised biological integrity assessment framework based on environmental DNA metabarcoding without a prior reference area is proposed. Taxon richness, species dominance, co-occurrence network density, and phylogenetic distance were used to assess the aquatic communities in the Taihu Lake basin. Multi-gene metabarcoding revealed comprehensive biodiversity at multiple trophic levels including algae, protists, zooplankton, and fish. Fish sequences were mainly derived from 12S, zooplankton mainly from mitochondrial cytochrome C oxidase subunit I, and algae and protists mainly from 18S. There were significant differences in community composition among lakes, rivers, and reservoirs but no significant differences in the four fundamental biological indicators. The algal and zooplankton integrities were positively correlated with protist and fish integrities, respectively. Additionally, the algal integrity of lakes was found to be significantly lower than that of rivers. The unsupervised assessment framework proposed in this study allows different ecosystems, including the same ecosystem in different seasons, to adopt the same indicators and assessment methods, which is more convenient for environmental management and decision-making.

The Complex Biodiversity-Ecosystem Function Relationships for the Qinghai-Tibetan Grassland Community

Despite the long history of the study of the biodiversity-ecosystem function relationship, uncertainty remains about the relationship of natural grassland ecosystems under stressful conditions. Recently, trait- and phylogenetic-based tests provide a powerful way to detect the relationship in different spaces but have seldom been applied to stressful zones on a large spatial scale. We selected Qinghai-Tibetan as the study area and collected a grassland community database involving 581 communities. We calculated biomass and species', functional, and phylogenetic diversity of each community and examined their relationships by using linear and non-linear regression models. Results showed an overall positive biodiversity-productivity relationship in species', functional and phylogenetic space. The relationship, however, was non-linear, in which biodiversity explained better the variation in community biomass when species diversity was more than a threshold, showing a weak effect of biodiversity on ecosystem function in low species diversity communities. We also found a filled triangle for the limit of the relationship between species and functional diversity, implying that functional diversity differs significantly among communities when their species diversity is low but finally converges to be a constant with increasing communities' species diversity. Our study suggests that multiple niche processes may structure the grassland communities, and their forces tend to balance in high-biodiversity communities.

Biodiversity has a positive but saturating effect on imperiled coral reefs

Species loss threatens ecosystems worldwide, but the ecological processes and thresholds that underpin positive biodiversity effects among critically important foundation species, such as corals on tropical reefs, remain inadequately understood. In field experiments, we manipulated coral species richness and intraspecific density to test whether, and how, biodiversity affects coral productivity and survival. Corals performed better in mixed species assemblages. Improved performance was unexplained by competition theory alone, suggesting that positive effects exceeded agonistic interactions during our experiments. Peak coral performance occurred at intermediate species richness and declined thereafter. Positive effects of coral diversity suggest that species’ losses on degraded reefs make recovery more difficult and further decline more likely. Harnessing these positive interactions may improve ecosystem conservation and restoration in a changing ocean.

Spatial distribution of planktonic ciliates in the western Pacific Ocean: along the transect from Shenzhen (China) to Pohnpei (Micronesia)

Planktonic ciliates have been recognized as major consumers of nano- and picoplankton in pelagic ecosystems, playing pivotal roles in the transfer of matter and energy in the microbial loop. However, due to the difficulties in identification, the species composition of ciliate assemblages, especially for the small, fragile, and naked species that usually dominate the ciliate communities in the oceanic waters, remains largely unknown. In the present study, 22 stations along the transect from Shenzhen (China) to Pohnpei (Micronesia) were sampled for the enumeration of picoplankton and nanoflagellates. In addition, pigment analysis of major phytoplankton groups along with the measurements of environmental variables including temperature, salinity, and nutrients were also carried out. Ciliates were identified at species level using quantitative protargol stain to reveal the species composition and their distribution patterns from off-shore to open ocean. Ciliate abundance was positively correlated with phosphate, silicate, and pico-sized pigmented eukaryotes (PPEs), whereas the biomass was closely related with PPEs, heterotrophic nanoflagellates, and chlorophytes. The combination of silicate and pigmented nanoflagellates was identified as the major factor driving the ciliate community composition. The close relationship between silicate and ciliate abundance and community structure needs further validation based on more data collected from oceanic waters. Our study showed the necessity of using techniques that can reveal the community composition at higher taxonomic resolutions in future studies on ciliates.

Grazing simplifies soil micro-food webs and decouples their relationships with ecosystem functions in grasslands

Livestock grazing often alters aboveground and belowground communities of grasslands and their mediated carbon (C) and nitrogen (N) cycling processes at the local scale. Yet, few have examined whether grazing-induced changes in soil food webs and their ecosystem functions can be extrapolated to a regional scale. We investigated how large herbivore grazing affects soil micro-food webs (microbes and nematodes) and ecosystem functions (soil C and N mineralization), using paired grazed and ungrazed plots at 10 locations across the Mongolian Plateau. Our results showed that grazing not only affected plant variables (e.g., biomass and C and N concentrations), but also altered soil substrates (e.g., C and N contents) and soil environment (e.g., soil pH and bulk density). Grazing had strong bottom-up effects on soil micro-food webs, leading to more pronounced decreases at higher trophic levels (nematodes) than at lower trophic levels (microbes). Structural equation modeling showed that changes in plant biomass and soil environment dominated grazing effects on microbes, while nematodes were mainly influenced by changes in plant biomass and soil C and N contents; the grazing effects, however, differed greatly among functional groups in the soil micro-food webs. Grazing reduced soil C and N mineralization rates via changes in plant biomass, soil C and N contents, and soil environment across grasslands on the Mongolian Plateau. Spearman's rank correlation analysis also showed that grazing reduced the correlations between functional groups in soil micro-food webs and then weakened the correlation between soil micro-food webs and soil C and N mineralization. These results suggest that changes in soil micro-food webs resulting from livestock grazing are poor predictors of soil C and N processes at regional scale, and that the relationships between soil food webs and ecosystem functions depend on spatial scales and land-use changes.

Plant functional assemblages as indicators of the resilience of grassland ecosystem service provision

Ecosystems provide a variety of ecosystem services (ES), which act as key linkages between social and ecological systems. ES respond spatially and temporally to abiotic and biotic variation, and to management. Thus, resistant and resilient ES provision is expected to remain within a stable range when facing disturbances. In this study, generic indicators to evaluate resistance, potential resilience and capacity for transformation of ES provision are developed and their relevance demonstrated for a mountain grassland system. Indicators are based on plant trait composition (i.e. functional composition) and abiotic parameters determining ES provision at community, meta-community and landscape scales. First the resistance of an ES is indicated by its normal operating range characterized by observed values under current conditions. Second its resilience is assessed by its potential operating range - under hypotheses of reassembly from the community's species pool. Third its transformation potential is assessed for reassembly at meta-community and landscape scales. Using a state-and-transition model, possible management-related transitions between mountain grassland states were identified, and indicators calculated for two provisioning and two regulating ES. Overall, resilience properties varied across individual ES, supporting a focus on resilience of specific ES. The resilience potential of the two provisioning services was greater than for the two regulating services, both being linked to functional complementarity within communities. We also found high transformation potential reflecting functional redundancy among communities within each meta-community, and across meta-communities in the landscape. Presented indicators are promising for the projection of future ES provision and the identification of management options under environmental change.

A combinatorial analysis using observational data identifies species that govern ecosystem functioning

Understanding the relationship between biodiversity and ecosystem functioning has so far resulted from two main approaches: the analysis of species' functional traits, and the analysis of species interaction networks. Here we propose a third approach, based on the association between combinations of species or of functional groups, which we term assembly motifs, and observed ecosystem functioning. Each assembly motif describes a biotic environment in which species interactions have particular effects on a given ecosystem function. Clustering species in functional groups generates a classification of ecosystems based on their assembly motif. We evaluate the quality of each species clustering, that is its ability to predict an ecosystem function, by the coefficient of determination of the ecosystem classification. An iterative process then enables identifying the species clustering in functional groups that best accounts for the functioning of the observed ecosystems. We test this approach using experimental and simulated datasets. We show that our combinatorial analysis makes it possible to identify the combinations of functional groups of species whose interactions govern ecosystem functioning without any a priori knowledge of the species themselves or their interactions. Our combinatorial approach reproduces the associative learning of empirical ecologists, and proves to be powerful and parsimonious.

Integrating community assembly and biodiversity to better understand ecosystem function: the Community Assembly and the Functioning of Ecosystems (CAFE) approach

The research of a generation of ecologists was catalysed by the recognition that the number and identity of species in communities influences the functioning of ecosystems. The relationship between biodiversity and ecosystem functioning (BEF) is most often examined by controlling species richness and randomising community composition. In natural systems, biodiversity changes are often part of a bigger community assembly dynamic. Therefore, focusing on community assembly and the functioning of ecosystems (CAFE), by integrating both species richness and composition through species gains, losses and changes in abundance, will better reveal how community changes affect ecosystem function. We synthesise the BEF and CAFE perspectives using an ecological application of the Price equation, which partitions the contributions of richness and composition to function. Using empirical examples, we show how the CAFE approach reveals important contributions of composition to function. These examples show how changes in species richness and composition driven by environmental perturbations can work in concert or antagonistically to influence ecosystem function. Considering how communities change in an integrative fashion, rather than focusing on one axis of community structure at a time, will improve our ability to anticipate and predict changes in ecosystem function.

Soil networks become more connected and take up more carbon as nature restoration progresses

Soil organisms have an important role in aboveground community dynamics and ecosystem functioning in terrestrial ecosystems. However, most studies have considered soil biota as a black box or focussed on specific groups, whereas little is known about entire soil networks. Here we show that during the course of nature restoration on abandoned arable land a compositional shift in soil biota, preceded by tightening of the belowground networks, corresponds with enhanced efficiency of carbon uptake. In mid- and long-term abandoned field soil, carbon uptake by fungi increases without an increase in fungal biomass or shift in bacterial-to-fungal ratio. The implication of our findings is that during nature restoration the efficiency of nutrient cycling and carbon uptake can increase by a shift in fungal composition and/or fungal activity. Therefore, we propose that relationships between soil food web structure and carbon cycling in soils need to be reconsidered.

Effects of habitat restoration on belowground organisms and ecosystem processes are poorly understood. Morriën and colleagues show that changes in the composition and network interactions of soil biota lead to improved carbon uptake efficiency when formerly cultivated land is restored.