Deciphering the biotic and abiotic drivers of coalescence asymmetry between soil and manure microbiomes

Manure application improves soil fertility, yet its implications on the success of invasion of manure-borne microorganisms in the soil are poorly understood. Here, we assessed the importance of abiotic and biotic factors in modulating the extent to which manure-borne fungal and bacterial communities can invade resident soil microbial communities. For this purpose, we applied varying frequencies of two different amounts of manure to nine soils differing in physico-chemical properties, as well as in land-use history, over 180 days and monitored changes in bacterial and fungal communities. Variance partitioning revealed differential contributions of abiotic and biotic factors to invasion success, which together accounted for up to 82 % of the variance explained. We showed that the effects of interactions between biotic and abiotic factors increased with coalescence frequency and manure amount for the bacterial and fungal communities, respectively. Both abiotic and biotic factors were important for modulating coalescence asymmetry for the bacterial community, whereas abiotic factors had a greater effect on the fungal community. These results provide new insights into the drivers of coalescence events between manure and resident soil microbial communities. Moreover, our findings highlight the roles of the mixing ratio and frequency of coalescence events in modulating the survival of manure-borne microorganisms.

Effect of Streptomyces JD211 application on soil physicochemical properties and N2O emission characteristics of rice rhizosphere

Biocontrol agent, as a pollution-free and sustainable plant disease control method, can inhibit the spread of soil-borne diseases and promote the growth of crops. However, there are few studies on the effect of biocontrol agent on N2O emission in rice soil. In this study, after the application of the biocontrol agent Streptomyces JD211, N2O emission from rice soil were measured, and the relationship between the agent and soil N2O emissions were studied in soil chemistry and molecular biology. The results showed that the application of Streptomyces JD211 can significantly reduce the rate of N2O emission from rice soil. The NH4+-N and NO3--N contents in rice soil decreased in a short period of time after the application of Streptomyces JD211, while the mineral N content in the soil remained stable with rice growth. 16S rRNA gene sequencing and metagenomic sequencing revealed Streptomyces JD211 application mainly increased the relative abundance of Burkholderia and Streptomyces in the soil microbial community, reduced the relative abundance of hao, norB, norC genes, and increased the relative abundance of nosZ and hcp genes. Streptomyces JD211 application promoted N2O transformation and weakened N2O production pathways, which ultimately reduced N2O emissions from rice soils. This study provided new insight of biocontrol agents to regulate soil N2O emissions, which is of great significance for the development and application of biocontrol bacteria and farmland environmental protection.

Darwin's naturalization conundrum reconciled by changes of species interactions

Although phylogenetic distance between native and exotic species has a close link with their interactions, it is still unclear how environmental stresses and species interactions influence the relationship between phylogenetic distance and biological invasions. Here we assessed the effect of invader-native phylogenetic distance on the growth of the invader (Symphyotrichum subulatum) under three levels of drought (no, moderate, or intense drought). Under no drought, interspecific competition between close relatives was the dominant process and native communities more closely related to the invader showed higher resistance to invasion, supporting Darwin's naturalization hypothesis. In contrast, under intense drought, facilitation between close relatives by mutualism with arbuscular mycorrhizal fungi (AMF) became more important, and the invader became more successful in their more closely related native communities, supporting the preadaptation hypothesis. The colonization rate of AMF of the invader was higher in more closely related native communities regardless of the drought treatment, but it was only positively related to invader biomass under intense drought. Therefore, the shift of species interactions from competition to facilitation may be ascribed to the promotion of AMF to invasion occurring under intense drought, which leads to the effect of closely related natives on the invader shifting from negative to positive. Our results provide a new angle to resolve Darwin's naturalization conundrum from the change of species interactions along a stress gradient, and provide important clues for invasion management when species interactions change in response to global climatic change.

Spatial scales of competition and a growth-motility trade-off interact to determine bacterial coexistence

The coexistence of competing species is a long-lasting puzzle in evolutionary ecology research. Despite abundant experimental evidence showing that the opportunity for coexistence decreases as niche overlap increases between species, bacterial species and strains competing for the same resources are commonly found across diverse spatially heterogeneous habitats. We thus hypothesized that the spatial scale of competition may play a key role in determining bacterial coexistence, and interact with other mechanisms that promote coexistence, including a growth-motility trade-off. To test this hypothesis, we let two Pseudomonas putida strains compete at local and regional scales by inoculating them either in a mixed droplet or in separate droplets in the same Petri dish, respectively. We also created conditions that allow the bacterial strains to disperse across abiotic or fungal hyphae networks. We found that competition at the local scale led to competitive exclusion while regional competition promoted coexistence. When competing in the presence of dispersal networks, the growth-motility trade-off promoted coexistence only when the strains were inoculated in separate droplets. Our results provide a mechanism by which existing laboratory data suggesting competitive exclusion at a local scale is reconciled with the widespread coexistence of competing bacterial strains in complex natural environments with dispersal.

Exotic fishes that are phylogenetically close but functionally distant to native fishes are more likely to establish

Since Darwin's time, degree of ecological similarity between exotic and native species has been assumed to affect the establishment success or failure of exotic species. However, a direct test of the effect of exotic-native similarity on establishment of exotics is scarce because of the difficulty in recognizing failures of species to establish in the field. Here, using a database on the establishment success and failure of exotic fish species introduced into 673 freshwater lakes, we evaluate the effect of similarity on the establishment of exotic fishes by combining phylogenetic and functional information. We illustrate that, relative to other biotic and abiotic factors, exotic-native phylogenetic and functional similarities were the most important correlates of exotic fish establishment. While phylogenetic similarity between exotic and resident fish species promoted successful establishment, functional similarity led to failure of exotics to become established. Those exotic species phylogenetically close to, but functionally distant from, native fishes were most likely to establish successfully. Our findings provide a perspective to reconcile Darwin's naturalization conundrum and suggest that, while phylogenetic relatedness allows exotic fish species to pre-adapt better to novel environments, they need to possess distinct functional traits to reduce competition with resident native fish species.

Advancing biological invasion hypothesis testing using functional diversity indices

Pioneering investigations on the effects of introduced populations on community structure, ecosystem functioning and services have focused on the effects of invaders on taxonomic diversity. However, taxonomic-based diversity metrics overlook the heterogeneity of species roles within and among communities. As the homogenizing effects of biological invasions on community and ecosystem processes can be subtle, they may require the use of functional diversity indices to be properly evidenced. Starting from the listing of major functional diversity indices, alongside the presentation of their strengths and limitations, we focus on studies pertaining to the effects of invasive species on native communities and recipient ecosystems using functional diversity indices. By doing so, we reveal that functional diversity of the recipient community may strongly vary at the onset of the invasion process, while it stabilizes at intermediate and high levels of invasion. As functional changes occurring during the lag phase of an invasion have been poorly investigated, we show that it is still unknown whether there are consistent changes in functional diversity metrics that could indicate the end of the lag phase. Thus, we recommend providing information on the invasion stage under consideration when computing functional diversity metrics. For the existing literature, it is also surprising that very few studies explored the functional difference between organisms from the recipient communities and invaders of the same trophic levels, or assessed the effects of non-native organism establishment into a non-analogue versus an analogue community. By providing valuable tools for obtaining in-depth diagnostics of community structure and functioning, functional diversity indices can be applied for timely implementation of restoration plans and improved conservation strategies. To conclude, our work provides a first synthetic guide for their use in hypothesis testing in invasion biology.

The role of phylogenetic relatedness on alien plant success depends on the stage of invasion

Darwin's naturalization hypothesis predicts successful alien invaders to be distantly related to native species, whereas his pre-adaptation hypothesis predicts the opposite. It has been suggested that depending on the invasion stage (that is, introduction, naturalization and invasiveness), both hypotheses, now known as Darwin's naturalization conundrum, could hold true. We tested this by analysing whether the likelihood of introduction for cultivation, as well as the subsequent stages of naturalization and spread (that is, becoming invasive) of species alien to Southern Africa are correlated with their phylogenetic distance to the native flora of this region. Although species are more likely to be introduced for cultivation if they are distantly related to the native flora, the probability of subsequent naturalization was higher for species closely related to the native flora. Furthermore, the probability of becoming invasive was higher for naturalized species distantly related to the native flora. These results were consistent across three different metrics of phylogenetic distance. Our study reveals that the relationship between phylogenetic distance to the native flora and the success of an alien species changes from one invasion stage to the other.

Ecological Interactions of Cyanobacteria and Heterotrophs Enhances the Robustness of Cyanobacterial Consortium for Carbon Sequestration

Lack of robustness is a major barrier to foster a sustainable cyanobacterial biotechnology. Use of cyanobacterial consortium increases biodiversity, which provides functional redundancy and prevents invading species from disrupting the production ecosystem. Here we characterized a cyanobacterial consortium enriched from microbial mats of alkaline soda lakes in BC, Canada, at high pH and alkalinity. This consortium has been grown in open laboratory culture for 4 years without crashes. Using shotgun metagenomic sequencing, 29 heterotrophic metagenome-assembled-genomes (MAGs) were retrieved and were assigned to Bacteroidota, Alphaproteobacteria, Gammaproteobacteria, Verrucomicrobiota, Patescibacteria, Planctomycetota, and Archaea. In combination with metaproteomics, the overall stability of the consortium was determined under different cultivation conditions. Genome information from each heterotrophic population was investigated for six ecological niches created by cyanobacterial metabolism and one niche for phototrophy. Genome-resolved metaproteomics with stable isotope probing using 13C-bicarbonate (protein/SIP) showed tight coupling of carbon transfer from cyanobacteria to the heterotrophic populations, specially Wenzhouxiangella. The community structure was compared to a previously described consortium of a closely related cyanobacteria, which indicated that the results may be generalized. Productivity losses associated with heterotrophic metabolism were relatively small compared to other losses during photosynthesis.

Post-epizootic microbiome associations across communities of neotropical amphibians

Microbiome-pathogen interactions are increasingly recognized as an important element of host immunity. While these host-level interactions will have consequences for community disease dynamics, the factors which influence host microbiomes at larger scales are poorly understood. We here describe landscape-scale pathogen-microbiome associations within the context of post-epizootic amphibian chytridiomycosis, a disease caused by the panzootic chytrid fungus Batrachochytrium dendrobatidis. We undertook a survey of Neotropical amphibians across altitudinal gradients in Ecuador ~30 years following the observed amphibian declines and collected skin swab-samples which were metabarcoded using both fungal (ITS-2) and bacterial (r16S) amplicons. The data revealed marked variation in patterns of both B. dendrobatidis infection and microbiome structure that are associated with host life history. Stream breeding amphibians were most likely to be infected with B. dendrobatidis. This increased probability of infection was further associated with increased abundance and diversity of non-Batrachochytrium chytrid fungi in the skin and environmental microbiome. We also show that increased alpha diversity and the relative abundance of fungi are lower in the skin microbiome of adult stream amphibians compared to adult pond-breeding amphibians, an association not seen for bacteria. Finally, stream tadpoles exhibit lower proportions of predicted protective microbial taxa than pond tadpoles, suggesting reduced biotic resistance. Our analyses show that host breeding ecology strongly shapes pathogen-microbiome associations at a landscape scale, a trait that may influence resilience in the face of emerging infectious diseases.

Biodiversity-ecosystem function relationships on bodies and in buildings

Biodiversity underpins the function of ecosystems. Here we discuss how biodiversity–ecosystem function theory could apply to our bodies and buildings, outline practical applications and call for further research.

Environmental harshness drives spatial heterogeneity in biotic resistance

Ecological communities often exhibit greater resistance to biological invasions when these communities consist of species that are not closely related. The effective size of this resistance, however, varies geographically. Here we investigate the drivers of this heterogeneity in the context of known contributions of native trees to the resistance of forests in the eastern United States of America to plant invasions. Using 42,626 spatially referenced forest community observations, we quantified spatial heterogeneity in relationships between evolutionary relatedness amongst native trees and both invasive plant species richness and cover. We then modelled the variability amongst the 91 ecological sections of our study area in the slopes of these relationships in response to three factors known to affect invasion and evolutionary relationships –environmental harshness (as estimated via tree height), relative tree density and environmental variability. Invasive species richness and cover declined in plots having less evolutionarily related native trees. The degree to which they did, however, varied considerably amongst ecological sections. This variability was explained by an ecological section’s mean maximum tree height and, to a lesser degree, SD in maximum tree height (R2GLMM = 0.47 to 0.63). In general, less evolutionarily related native tree communities better resisted overall plant invasions in less harsh forests and in forests where the degree of harshness was more homogenous. These findings can guide future investigations aimed at identifying the mechanisms by which evolutionary relatedness of native species affects exotic species invasions and the environmental conditions under which these effects are most pronounced.

Stochastic processes govern invasion success in microbial communities when the invader is phylogenetically close to resident bacteria

Despite recent efforts in identifying the determinants of invasion in microbial communities, experimental observations across different ecosystems are inconclusive. While relationships between resident community diversity and invasion success are often noted, community diversity says little about community assembly processes. Community assembly processes may provide a more inclusive framework to explain-and potentially prevent or facilitate-invasion. Here we let replicate nitrite-oxidizing bacterial guilds assemble under different conditions from a natural source community and study their compositional patterns to infer the relative importance of the assembly processes. Then, an invader strain from that same guild was introduced at one of three propagule pressures. We found no significant correlation between community diversity and invasion success. Instead, we observed that the effect of selection on invasion success was surpassed by the effect of drift, as inferred from the substantial influence of propagule pressure on invasion success. This dominance of drift can probably be generalized to other invasion cases with high phylogenetic similarity between invader and resident community members. In these situations, our results suggest that attempting to modulate the invasibility of a community by altering its diversity is futile because stochastic processes determine the invasion outcome. Increasing or reducing propagule pressure is then deemed the most efficient avenue to enhance or limit invasion success.

Preadaptation and Naturalization of Nonnative Species: Darwin's Two Fundamental Insights into Species Invasion

Predicting which nonnative species become invasive is critical for their successful management, and Charles Darwin provided predictions based on species' relatedness. However, Darwin provided two opposing predictions about the relatedness of introduced nonnatives to indigenous species. First, environmental fit is the dominant factor determining invader success; thus, we should expect that invasive species are closely related to local native residents. Alternatively, if competition is important, we should expect successful invaders are distantly related to the native residents. These opposing expectations are referred to as Darwin's naturalization conundrum. The results of studies that examine nonnative species relatedness to natives are largely inconsistent. This inconsistency arises from the fact that studies occur at different spatial and temporal scales, and at different stages of invasion, and so implicitly examine different mechanisms. Further, while species have evolved ecological differences, the mode and tempo of evolution can affect species' differences, complicating the predictions from simple hypotheses. We outline unanswered questions and provide guidelines for collecting the data required to test competing hypotheses.

Phylogenetic context determines the role of competition in adaptive radiation

Understanding ecological mechanisms regulating the evolution of biodiversity is of much interest to ecologists and evolutionary biologists. Adaptive radiation constitutes an important evolutionary process that generates biodiversity. Competition has long been thought to influence adaptive radiation, but the directionality of its effect and associated mechanisms remain ambiguous. Here, we report a rigorous experimental test of the role of competition on adaptive radiation using the rapidly evolving bacterium Pseudomonas fluorescens SBW25 interacting with multiple bacterial species that differed in their phylogenetic distance to the diversifying bacterium. We showed that the inhibitive effect of competitors on the adaptive radiation of P. fluorescens decreased as their phylogenetic distance increased. To explain this phylogenetic dependency of adaptive radiation, we linked the phylogenetic distance between P. fluorescens and its competitors to their niche and competitive fitness differences. Competitive fitness differences, which showed weak phylogenetic signal, reduced P. fluorescens abundance and thus diversification, whereas phylogenetically conserved niche differences promoted diversification. These results demonstrate the context dependency of competitive effects on adaptive radiation, and highlight the importance of past evolutionary history for ongoing evolutionary processes.