Functional diversity explores the maintenance mechanism and driving factors of the invasion equilibrium state of the icefish (Neosalanx taihuensis Chen) in Lake Fuxian, China

Biodiversity loss caused by biological invasions is an ecological problem on a global scale, and understanding the mechanism of biological invasion is the basis for managing non-native species. The biotic resistance hypothesis proposes that species-rich native communities are less susceptible to invasion because of the limited resources available to non-native species, therefore comparing the resource utilization patterns of different communities can reveal the invasion mechanisms of specific non-native species at the community level. We selected Lake Taihu, where icefish (Neosalanx taihuensis Chen) originated, and Lake Fuxian, where icefish invaded, as the research objects. We calculated the fish functional diversity indexes, including functional richness (FRic), functional evenness (FEve), and functional divergence (FDiv), to reflect differences in ecological niche and resource utilization based on four quarterly fish survey data from two lakes. The random forests model explored the relationship between functional diversity indexes and biotic and environmental variables. Our results showed that more diverse resource utilization (high FRic), more niche space (low FEve), and less competitive pressure (high FDiv) in Lake Fuxian were identified as the critical important factors for maintaining the current equilibrium state after successful invasion of icefish. The bottom-up effects mainly affected the functional diversity indexes in Lake Fuxian. They differed from those in Lake Taihu and were primarily influenced by top-down effects. Enhancing the top-down effects in Lake Fuxian and limiting the zooplankton available to icefish are critical to controlling the invasion of icefish. This study offers a new perspective for studying the non-native fish invasion mechanism, and provides scientific guidance for managing non-native fish in Lake Fuxian.

Naturally diverse plant communities do not resist invasion by the strong competitor, Microstegium vimineum

PREMISE

Theory predicts and empirical studies have shown that ecologically manipulated communities with high species diversity are resistant to invasion, but do these predictions and results hold true when applied to highly competitive invaders in natural communities? Few studies of diversity-mediated invasion resistance have measured both invasion resistance and invader impact in the same study.

METHODS

We used a two-year field experiment to test: (1) diversity-mediated competitive resistance to patch expansion by the grass, Microstegium vimineum; and (2) the competitive effect of M. vimineum on resident plant diversity. We examined responses of M. vimineum to two native plant density-reduction treatments that had opposite effects on species diversity: (1) reducing species richness via the removal of rare species; and (2) reducing dominance by reducing the density of the dominant resident species. We examined the effects of M. vimineum reduction by pre-emergent herbicide on resident diversity in the second year of the study.

RESULTS

Neither rare species removal nor dominant species reduction significantly increased M. vimineum density (relative growth rate). The pre-emergent herbicide dramatically reduced M. vimineum in year 2 of the study, but not most resident plants, which were perennials and indirectly benefited from the herbicide at a more productive site, presumably due to reduced competition from M. vimineum.

CONCLUSIONS

Diversity-mediated resistance did not effectively deter invasion by a highly competitive invader. In the case of M. vimineum and at more productive sites, it would appear that nearly complete removal of this invader is necessary to preserve plant species diversity.

Revisiting the invasion paradox: Resistance-richness relationship is driven by augmentation and displacement trends

Host-associated resident microbiota can protect their host from pathogens-a community-level trait called colonization resistance. The effect of the diversity of the resident community in previous studies has shown contradictory results, with higher diversity either strengthening or weakening colonization resistance. To control the confounding factors that may lead to such contradictions, we use mathematical simulations with a focus on species interactions and their impact on colonization resistance. We use a mediator-explicit model that accounts for metabolite-mediated interactions to perform in silico invasion experiments. We show that the relationship between colonization resistance and species richness of the resident community is not monotonic because it depends on two underlying trends as the richness of the resident community increases: a decrease in instances of augmentation (invader species added, without driving out resident species) and an increase in instances of displacement (invader species added, driving out some of the resident species). These trends hold consistently under different parameters, regardless of the number of compounds that mediate interactions between species or the proportion of the facilitative versus inhibitory interactions among species. Our results show a positive correlation between resistance and diversity in low-richness communities and a negative correlation in high-richness communities, offering an explanation for the seemingly contradictory trend in the resistance-diversity relationship in previous reports.

Comparing long-term patterns of spread of native and invasive plants in a successional forest

A fundamental question in invasive plant ecology is whether invasive and native plants have different ecological roles. Differences in functional traits have been explored, but we lack a comparison of the factors affecting the spread of co-occurring natives and invasives. Some have proposed that to succeed, invasives would colonize a wider variety of sites, would disperse farther, or would be better at colonizing sites with more available light and soil nutrients than natives. We examined patterns of spread over 70 years in a regenerating forest in Connecticut, USA, where both native and invasive species acted as colonizers. We compared seven invasive and 19 native species in the characteristics of colonized plots, variation in these characteristics, and the importance of site variables for colonization. We found little support for the hypotheses that invasive plants succeed by dispersing farther than native plants or by having a broader range of site tolerances. Colonization by invasives was also not more dependent on light than colonization by natives. Like native understory species, invasive plants spread into closed-canopy forest and species-rich communities despite earlier predictions that these communities would resist invasion. The biggest differences were that soil nitrate and the initial land cover being open field increased the odds of colonization for most invasives but only for some natives. In large part, though, the spread of native and invasive plants was affected by similar factors.

Native molluscs alleviate water quality impacts of invasive crayfish

Freshwaters are considered to be the most vulnerable ecosystems facing biological invasions, and the red swamp crayfish (Procambarus clarkii) is one of the most widespread aquatic invasive species in the world. P. clarkii has negative impacts on water quality in the lakes that it invades by, for instance, increasing their turbidity and nutrient concentrations and reducing macrophyte biomass. However, native taxa such as snails and mussels could potentially help to maintain a clear-water status in lakes by grazing on periphyton or by phytoplankton filtration. To examine the potential negative effects of P. clarkii on the clear-water state in lakes dominated by the macrophyte Vallisneria denseserrulata and the potential for native species to buffer these effects, we tested the crayfish impact in the absence and presence of the snail Bellamya aeruginosa and the mussel Sinanodonta woodiana at different biomasses. In the presence of crayfish, total suspended solids, total phosphorus, and chlorophyll a concentrations significantly increased compared to the control treatments without crayfish. However, when crayfish coexisted with snails or mussels, these three environmental variables all decreased in concentration compared to the crayfish-only treatment. Low (500 g/m2) and high (1500 g/m2) snail or mussel biomass had similar buffering effects. Macrophyte biomass in the crayfish and high mussel biomass treatment was 43 % higher than in the crayfish-only treatment. Native molluscs therefore alleviated the negative effects of crayfish on lake water quality and promoted native macrophyte growth. We conclude that a thriving native mollusc community may help in maintaining the clear-water state in lakes following crayfish invasion.

Shipping traffic, salinity and temperature shape non-native fish richness in estuaries worldwide

Non-native species threaten biodiversity conservation and ecosystem functioning. Management at early-invasion stages can prevent ecological and socioeconomic impacts, but rely on the identification of drivers of non-native species occurrence at distinct scales. Here, we identify environmental and anthropogenic correlates of non-native fish richness across estuaries worldwide. We performed model selection using proxies of colonization pressure, habitat availability and connectivity, anthropogenic disturbance and climate, to assess the primary mechanisms underlying non-native species occurrence. Latitudinal and guild-related trends in non-native occurrence were also investigated using species thermal and salinity affinities. Data retrieved from a literature review revealed 147 non-native fish species in 147 estuaries worldwide. Shipping traffic, salinity (minimum and range values) and temperature (minimum value) were the main predictors of non-native fish richness. Hotspots of non-native species were under heavy levels of shipping traffic, had higher salinity (both minimum and range values) and colder waters. We also found evidence of thermal limits to species' geographic area of introduction. Latitude of invaded estuaries was negatively correlated with species' minimum, mean and maximum thermal affinities, and positively correlated with thermal affinity ranges. Most non-native species recorded in estuaries were freshwater, but their minimum salinity affinities ranged from 2 to 35 pss. Moreover, species within marine guilds were mostly stenohaline and showed affinity for minimum salinities around 20-30 pss, which may be related to the positive relationship between non-native richness and estuary's increased salinity. Our results indicate that colonization pressure, disturbance (as result of multiple shipping impacts) and habitat filtering are the primary mechanisms underlying non-native fish richness in estuaries, contributing to the development of management strategies targeting early-invasion stages. Matching climate between native and non-native ranges was particularly important for predicting introductions at the global scale, whereas local fluctuations in salinity likely drove non-native richness in response to increased habitat availability.

Microbial transmission in the social microbiome and host health and disease

Although social interactions are known to drive pathogen transmission, the contributions of socially transmissible host-associated mutualists and commensals to host health and disease remain poorly explored. We use the concept of the social microbiome-the microbial metacommunity of a social network of hosts-to analyze the implications of social microbial transmission for host health and disease. We investigate the contributions of socially transmissible microbes to both eco-evolutionary microbiome community processes (colonization resistance, the evolution of virulence, and reactions to ecological disturbance) and microbial transmission-based processes (transmission of microbes with metabolic and immune effects, inter-specific transmission, transmission of antibiotic-resistant microbes, and transmission of viruses). We consider the implications of social microbial transmission for communicable and non-communicable diseases and evaluate the importance of a socially transmissible component underlying canonically non-communicable diseases. The social transmission of mutualists and commensals may play a significant, under-appreciated role in the social determinants of health and may act as a hidden force in social evolution.

Biotic resistance to fish invasions in southern China: Evidence from biomass, habitat, and fertility limitation

Understanding the mechanisms underlying the invasion success or failure of alien species can help to predict future invasions and cope with the invaders. The biotic resistance hypothesis posits that diverse communities are more resistant to invasion. While many studies have examined this hypothesis, the majority of them have focused on the relationship between alien and native species richness in plant communities, and results have often been inconsistent. In southern China, many rivers have been invaded by alien fish species, providing an opportunity to test the resistance of native fish communities to alien fish invasions. Using survey data for 60,155 freshwater fish collected from five main rivers of southern China for 3 years, we assessed the relationships between native fish richness and the richness and biomass of alien fishes at river and reach spatial scales, respectively. Based on two manipulative experiments, we further examined the impact of native fish richness on habitat selection and the reproductive ability of an exotic model species Coptodon zillii. We found no apparent relationship between alien and native fish richness, whereas the biomass of alien fish significantly decreased with increasing native fish richness. In experiments, C. zillii preferred to invade those habitats that had low native fish richness, given evenly distributed food resources; reproduction of C. zillii was strongly depressed by a native carnivorous fish Channa maculata. Together, our results indicate that native fish diversity can continue to provide biotic resistance to alien fish species in terms of limiting their growth, habitat selection, and reproduction when these aliens have successfully invaded southern China. We thus advocate for fish biodiversity conservation, especially for key species, to mitigate against the population development and ecological impact of alien fish species.

Towards a mathematical understanding of invasion resistance in multispecies communities

Multispecies community composition and dynamics are key to health and disease across biological systems, a prominent example being microbial ecosystems. Explaining the forces that govern diversity and resilience in the microbial consortia making up our body's defences remains a challenge. In this, theoretical models are crucial, to bridge the gap between species dynamics and underlying mechanisms and to develop analytic insight. Here we propose a replicator equation framework to model multispecies dynamics where an explicit notion of invasion resistance of a system emerges and can be studied explicitly. For illustration, we derive the conceptual link between such replicator equation and N microbial species' growth and interaction traits, stemming from micro-scale environmental modification. Within this replicator framework, mean invasion fitness arises, evolves dynamically, and may undergo critical predictable shifts with global environmental changes. This mathematical approach clarifies the key role of this resident system trait for invader success, and highlights interaction principles among N species that optimize their collective resistance to invasion. We propose this model based on the replicator equation as a powerful new avenue to study, test and validate mechanisms of invasion resistance and colonization in multispecies microbial ecosystems and beyond.

Meta-analysis identifies native priority as a mechanism that supports the restoration of invasion-resistant plant communities

The restoration of invasion-resistant plant communities is an important strategy to combat the negative impacts of alien invasions. Based on a systematic review and meta-analysis of seed-based ecological restoration experiments, here we demonstrate the potential of functional similarity, seeding density and priority effect in increasing invasion resistance. Our results indicate that native priority is the most promising mechanism to control invasion that can reduce the performance of invasive alien species by more than 50%. High-density seeding is effective in controlling invasive species, but threshold seeding rates may exist. Overall seeding functionally similar species do not have a significant effect. Generally, the impacts are more pronounced on perennial and grassy invaders and on the short-term. Our results suggest that biotic resistance can be best enhanced by the early introduction of native plant species during restoration. Seeding of a single species with high functional similarity to invasive alien species is unpromising, and instead, preference should be given to high-density multifunctional seed mixtures, possibly including native species favored by the priority effect. We highlight the need to integrate research across geographical regions, global invasive species and potential resistance mechanisms.

Generalist Predators Shape Biotic Resistance along a Tropical Island Chain

Islands offer exclusive prisms for an experimental investigation of biodiversity x ecosystem function interplay. Given that species in upper trophic layers, e.g., arthropod predators, experience a comparative disadvantage on small, isolated islands, such settings can help to clarify how predation features within biotic resistance equations. Here, we use observational and manipulative studies on a chain of nine Indonesian islands to quantify predator-mediated biotic resistance against the cassava mealybug Phenacoccus manihoti (Homoptera: Pseudococcidae) and the fall armyworm Spodoptera frugiperda (Lepidoptera: Noctuidae). Across island settings, a diverse set of generalist lacewing, spider and ladybeetle predators aggregates on P. manihoti infested plants, attaining max. (field-level) abundance levels of 1.0, 8.0 and 3.2 individuals per plant, respectively. Though biotic resistance-as imperfectly defined by a predator/prey ratio index-exhibits no inter-island differences, P. manihoti population regulation is primarily provided through an introduced monophagous parasitoid. Meanwhile, resident predators, such as soil-dwelling ants, inflict apparent mortality rates up to 100% for various S. frugiperda life stages, which translates into a 13- to 800-fold lower S. frugiperda survivorship on small versus large islands. While biotic resistance against S. frugiperda is ubiquitous along the island chain, its magnitude differs between island contexts, seasons and ecological realms, i.e., plant canopy vs. soil surface. Hence, under our experimental context, generalist predators determine biotic resistance and exert important levels of mortality even in biodiversity-poor settings. Given the rapid pace of biodiversity loss and alien species accumulation globally, their active conservation in farmland settings (e.g., through pesticide phasedown) is pivotal to ensuring the overall resilience of production ecosystems.

Native diversity buffers against severity of non-native tree invasions

Determining the drivers of non-native plant invasions is critical for managing native ecosystems and limiting the spread of invasive species1,2. Tree invasions in particular have been relatively overlooked, even though they have the potential to transform ecosystems and economies3,4. Here, leveraging global tree databases5-7, we explore how the phylogenetic and functional diversity of native tree communities, human pressure and the environment influence the establishment of non-native tree species and the subsequent invasion severity. We find that anthropogenic factors are key to predicting whether a location is invaded, but that invasion severity is underpinned by native diversity, with higher diversity predicting lower invasion severity. Temperature and precipitation emerge as strong predictors of invasion strategy, with non-native species invading successfully when they are similar to the native community in cold or dry extremes. Yet, despite the influence of these ecological forces in determining invasion strategy, we find evidence that these patterns can be obscured by human activity, with lower ecological signal in areas with higher proximity to shipping ports. Our global perspective of non-native tree invasion highlights that human drivers influence non-native tree presence, and that native phylogenetic and functional diversity have a critical role in the establishment and spread of subsequent invasions.

The Food Niche Overlap and Interspecific Relationship between the Sympatric Tibetan Macaque and Grey Snub-Nosed Monkey

Assessing the trophic niche and interspecific relationships between related species and determining how the species maintain differences in nutritional niches while coexisting in the same area are important topics in ecological research. Therefore, exploring the mechanism of food resource utilization, competition and coexistence among species distributed in the same region is important. In this study, we used fecal samples and metagenome sequencing technology to study the plant feeding habits and coexistence mechanisms of Tibetan macaques (Macaca thibetana) and grey snub-nosed monkeys (Rhinopithecus brelichi) within the same area. In the winter of 2020, we collected a total of 40 fecal samples from Tibetan macaques and grey snub-nosed monkeys; of those, 29 samples were considered valid and were analyzed using DNA metabarcoding. The results showed that in winter, Tibetan macaques consumed plants from 117 families and 184 genera, whereas grey snub-nosed monkeys consumed plants from 109 families and 165 genera. Diversity analysis revealed that there was a significant difference in the food composition of Tibetan macaques and grey snub-nosed monkeys. Tibetan macaques had a broader food niche width than grey snub-nosed monkeys at the family and genus levels. In winter, the food niches of Tibetan macaques and grey snub-nosed monkeys almost entirely overlapped (0.99). Our research provides detailed dietary data for Tibetan macaques and grey snub-nosed monkeys and valuable information that can aid in conservation efforts targeting these species.

Trait-based species richness: ecology and macroevolution

Understanding the origins of species richness patterns is a fundamental goal in ecology and evolutionary biology. Much research has focused on explaining two kinds of species richness patterns: (i) spatial species richness patterns (e.g. the latitudinal diversity gradient), and (ii) clade-based species richness patterns (e.g. the predominance of angiosperm species among plants). Here, I highlight a third kind of richness pattern: trait-based species richness (e.g. the number of species with each state of a character, such as diet or body size). Trait-based richness patterns are relevant to many topics in ecology and evolution, from ecosystem function to adaptive radiation to the paradox of sex. Although many studies have described particular trait-based richness patterns, the origins of these patterns remain far less understood, and trait-based richness has not been emphasised as a general category of richness patterns. Here, I describe a conceptual framework for how trait-based richness patterns arise compared to other richness patterns. A systematic review suggests that trait-based richness patterns are most often explained by when each state originates within a group (i.e. older states generally have higher richness), and not by differences in transition rates among states or faster diversification of species with certain states. This latter result contrasts with the widespread emphasis on diversification rates in species-richness research. I show that many recent studies of spatial richness patterns are actually studies of trait-based richness patterns, potentially confounding the causes of these patterns. Finally, I describe a plethora of unanswered questions related to trait-based richness patterns.

Microbiomes in the context of developing sustainable intensified aquaculture

With an ever-growing human population, the need for sustainable production of nutritional food sources has never been greater. Aquaculture is a key industry engaged in active development to increase production in line with this need while remaining sustainable in terms of environmental impact and promoting good welfare and health in farmed species. Microbiomes fundamentally underpin animal health, being a key part of their digestive, metabolic and defense systems, in the latter case protecting against opportunistic pathogens in the environment. The potential to manipulate the microbiome to the advantage of enhancing health, welfare and production is an intriguing prospect that has gained considerable traction in recent years. In this review we first set out what is known about the role of the microbiome in aquaculture production systems across the phylogenetic spectrum of cultured animals, from invertebrates to finfish. With a view to reducing environmental footprint and tightening biological and physical control, investment in "closed" aquaculture systems is on the rise, but little is known about how the microbial systems of these closed systems affect the health of cultured organisms. Through comparisons of the microbiomes and their dynamics across phylogenetically distinct animals and different aquaculture systems, we focus on microbial communities in terms of their functionality in order to identify what features within these microbiomes need to be harnessed for optimizing healthy intensified production in support of a sustainable future for aquaculture.

From waste to feed: Microbial fermented abalone waste improves the digestibility, gut health, and immunity in marron, Cherax cainii

New aquafeed ingredients produced by a circular economy approach are the opportunity for sustainable and resilient aquaculture. In the light of this approach, the mixture of abalone waste and Sargassum spp (9:1) fermented by Saccharomyces cereviceae and Lactobacillus casei (Yakult®) (FMAS) were used to replace 0% (FMAS0), 25% (FMAS-25), 50% (FMAS-50), 75% (FMAS-75), and 100% (FMAS-100) of fishmeal (FM) protein in marron, Cherax cainii diet. The marron was fed these diets in triplicate for 90 days. Growth, feed utilization and protein efficiency ratio were unchanged in marron-fed all test diets. Improvement in apparent protein digestibility was aligned with an increase in the size and number of B-cells in the hepatopancreas. Most of the immune responses, except for haemocyte clotting time, hyaline cells and neutral red retention time (NRR time) were unchanged by 42- and 90-days feeding trials compared to those of the control group. 90 days post-feeding marron with FMAS25 showed a lower haemocyte clotting time than the post 42 days feeding marron with the same diet. Hyaline cells increased in marron fed FMAS75 for 90 days compared to marron fed the same diet for 42 days. The challenge test involved injecting marron with Vibrio mimicus resulted in a 100% survival rate after 96 h of exposure. During the challenge test, phagocytosis activity in 24 and 48-h post-challenged marron fed FMAS75 decreased which recovered after 96 h post-challenge. Marron fed FMAS50 also recorded a significantly higher proportion of granular cells after 24 h and NRR time at 96 h compared with that of other treatments. Given the above indicators of bio-growth, feed efficiency and immune responses, total replacement of FM protein of marron practical feed with FMAS are considered feasible and optimum to maintain health status and resistance to disease.

Fungal succession in decomposing ash leaves colonized by the ash dieback pathogen Hymenoscyphus fraxineus or its harmless relative Hymenoscyphus albidus

Introduction

The ascomycete Hymenoscyphus fraxineus, originating from Asia, is currently threatening common ash (Fraxinus excelsior) in Europe, massive ascospore production from the saprotrophic phase being a key determinant of its invasiveness.

Methods

To consider whether fungal diversity and succession in decomposing leaf litter are affected by this invader, we used ITS-1 metabarcoding to profile changes in fungal community composition during overwintering. The subjected ash leaf petioles, collected from a diseased forest and a healthy ash stand hosting the harmless ash endophyte Hymenoscyphus albidus, were incubated in the forest floor of the diseased stand between October 2017 and June 2018 and harvested at 2-3-month intervals.

Results

Total fungal DNA level showed a 3-fold increase during overwintering as estimated by FungiQuant qPCR. Petioles from the healthy site showed pronounced changes during overwintering; ascomycetes of the class Dothideomycetes were predominant after leaf shed, but the basidiomycete genus Mycena (class Agaricomycetes) became predominant by April, whereas H. albidus showed low prevalence. Petioles from the diseased site showed little change during overwintering; H. fraxineus was predominant, while Mycena spp. showed increased read proportion by June.

Discussion

The low species richness and evenness in petioles from the diseased site in comparison to petioles from the healthy site were obviously related to tremendous infection pressure of H. fraxineus in diseased forests. Changes in leaf litter quality, owing to accumulation of host defense phenolics in the pathogen challenged leaves, and strong saprophytic competence of H. fraxineus are other factors that probably influence fungal succession. For additional comparison, we examined fungal community structure in petioles collected in the healthy stand in August 2013 and showing H. albidus ascomata. This species was similarly predominant in these petioles as H. fraxineus was in petioles from the diseased site, suggesting that both fungi have similar suppressive effects on fungal richness in petiole/rachis segments they have secured for completion of their life cycle. However, the ability of H. fraxineus to secure the entire leaf nerve system in diseased forests, in opposite to H. albidus, impacts the general diversity and successional trajectory of fungi in decomposing ash petioles.

Fish waste to sustainable additives: Fish protein hydrolysates alleviate intestinal dysbiosis and muscle atrophy induced by poultry by-product meal in Lates calcarifer juvenile

Valorising waste from the processing of fishery and aquaculture products into functional additives, and subsequent use in aquafeed as supplements could be a novel approach to promoting sustainability in the aquaculture industry. The present study supplemented 10% of various fish protein hydrolysates (FPHs), obtained from the hydrolysis of kingfish (KH), carp (CH) and tuna (TH) waste, with 90% of poultry by-product meal (PBM) protein to replace fishmeal (FM) completely from the barramundi diet. At the end of the trial, intestinal mucosal barriers damage, quantified by villus area (VA), lamina propria area (LPA), LPA ratio, villus length (VL), villus width (VW), and neutral mucin (NM) in barramundi fed a PBM-based diet was repaired when PBM was supplemented with various FPHs (p < 0.05, 0.01, and 0.001). PBM-TH diet further improved these barrier functions in the intestine of fish (p < 0.05 and 0.001). Similarly, FPHs supplementation suppressed PBM-induced intestinal inflammation by controlling the expression of inflammatory cytokines (tnf-α and il-10; p < 0.05 and 0.001) and a mucin-relevant production gene (i-mucin c; p < 0.001). The 16S rRNA data showed that a PBM-based diet resulted in dysbiosis of intestinal bacteria, supported by a lower abundance of microbial diversity (p < 0.001) aligned with a prevalence of Photobacterium. PBM-FPHs restored intestine homeostasis by enhancing microbial diversity compared to those fed a PBM diet (p < 0.001). PBM-TH improved the diversity (p < 0.001) further by elevating the Firmicutes phylum and the Ruminococcus, Faecalibacterium, and Bacteroides genera. Muscle atrophy, evaluated by fiber density, hyperplasia and hypertrophy and associated genes (igf-1, myf5, and myog), occurred in barramundi fed PBM diet but was repaired after supplementation of FPHs with the PBM (p < 0.05, 0.01, and 0.001). Similarly, creatine kinase, calcium, phosphorous, and haptoglobin were impacted by PBM-based diet (p < 0.05) but were restored in barramundi fed FPHs supplemented diets (p < 0.05 and 0.01). Hence, using circular economy principles, functional FPHs could be recovered from the fish waste applied in aquafeed formulations and could prevent PBM-induced intestinal dysbiosis and muscular atrophy.

GRAPHICAL ABSTRACT

Coexistence between similar invaders: The case of two cosmopolitan exotic insects

Biological invasions are usually examined in the context of their impacts on native species. However, few studies have examined the dynamics between invaders when multiple exotic species successfully coexist in a novel environment. Yet, long-term coexistence of now established exotic species has been observed in North American lady beetle communities. Exotic lady beetles Harmonia axyridis and Coccinella septempunctata were introduced for biological control in agricultural systems and have since become dominant species within these communities. In this study, we investigated coexistence via spatial and temporal niche partitioning among H. axyridis and C. septempunctata using a 31-year data set from southwestern Michigan, USA. We found evidence of long-term coexistence through a combination of small-scale environmental, habitat, and seasonal mechanisms. Across years, H. axyridis and C. septempunctata experienced patterns of cyclical dominance likely related to yearly variation in temperature and precipitation. Within years, populations of C. septempunctata peaked early in the growing season at 550 degree days, while H. axyridis populations grew in the season until 1250 degree days and continued to have high activity after this point. C. septempunctata was generally most abundant in herbaceous crops, whereas H. axyridis did not display strong habitat preferences. These findings suggest that within this region H. axyridis has broader habitat and abiotic environmental preferences, whereas C. septempunctata thrives under more specific ecological conditions. These ecological differences have contributed to the continued coexistence of these two invaders. Understanding the mechanisms that allow for the coexistence of dominant exotic species contributes to native biodiversity conservation management of invaded ecosystems.

Biotic resistance or invasional meltdown? Diversity reduces invasibility but not exotic dominance in southern California epibenthic communities

High community diversity may either prevent or promote the establishment of exotic species. The biotic resistance hypothesis holds that species-rich communities are more resistant to invasion than species-poor communities due to mechanisms including greater interspecific competition. Conversely, the invasional meltdown hypothesis proposes that greater exotic diversity increases invasibility via facilitative interactions between exotic species. To evaluate the degree to which biotic resistance or invasional meltdown influences marine community structure during the assembly period, we studied the development of marine epibenthic “fouling” communities at two southern California harbors. With a focus on sessile epibenthic species, we found that fewer exotic species established as total and exotic richness increased during community assembly and that this effect remained after accounting for space availability. We also found that changes in exotic abundance decreased over time. Throughout the assembly period, gains in exotic abundance were greatest when space was abundant and richness was low. Altogether, we found greater support for biotic resistance than invasional meltdown, suggesting that both native and exotic species contribute to biotic resistance during early development of these communities. However, our results indicate that biotic resistance may not always reduce the eventual dominance of exotic species.

[Introduction to the microbiome]

The human body is colonized by a multitude of different microbes that are collectively referred to as the human microbiome. Gut microbes account for the largest proportion of these. They constitute a barrier against foreign pathogens, carry out important metabolic functions and regulate the immune system, thereby making them essential for the maintenance of health. The most important determinants of the gut microbiome structure in the general population include exocrine pancreatic function, genetics, nutrition, age, sex, and obesity. Changes in the gut microbiome have also been linked to a variety of diseases not limited to gastrointestinal disorders. Typical microbiome changes in disease include a loss of diversity and beneficial bacteria or an increase in opportunistic pathogens. This may result in a proinflammatory and unstable microbiome. Knowledge about the microbiome is rapidly increasing and microbiome modulation therapies have already been implemented in clinical practice. Therefore, basic knowledge about the microbiome is essential for all medical professionals in order for them to advise and treat their patients properly.

Links between host genetics, metabolism, gut microbiome and amoebic gill disease (AGD) in Atlantic salmon

Background

Rapidly spreading parasitic infections like amoebic gill disease (AGD) are increasingly problematic for Atlantic salmon reared in aquaculture facilities and potentially pose a risk to wild fish species in surrounding waters. Currently, it is not known whether susceptibility to AGD differs between wild and farmed salmon. Wild Atlantic salmon populations are declining and this emerging disease could represent an additional threat to their long-term viability. A better understanding of how AGD affects fish health is therefore relevant for the accurate assessment of the associated risk, both to farming and to the well-being of wild populations. In this study, we assessed the impact of natural exposure to AGD on wild, hybrid and farmed post-smolt Atlantic salmon reared in a sea farm together under common garden conditions.

Results

Wild fish showed substantially higher mortality levels (64%) than farmed fish (25%), with intermediate levels for hybrid fish (39%) suggesting that AGD susceptibility has an additive genetic basis. Metabolic rate measures representing physiological performance were similar among the genetic groups but were significantly lower in AGD-symptomatic fish than healthy fish. Gut microbial diversity was significantly lower in infected fish. We observed major shifts in gut microbial community composition in response to AGD infections. In symptomatic fish the relative abundance of key taxa Aliivibrio, Marinomonas and Pseudoalteromonas declined, whereas the abundance of Polaribacter and Vibrio increased compared to healthy fish.

Conclusions

Our results highlight the stress AGD imposes on fish physiology and suggest that low metabolic-rate fish phenotypes may be associated with better infection outcomes. We consider the role increased AGD outbreak events and a warmer future may have in driving secondary bacterial infections and in reducing performance in farmed and wild fish.

Supplementary Information

The online version contains supplementary material available at 10.1186/s42523-022-00203-x.

Biotic resistance of native fouling communities to bioinvasions could not be demonstrated by transplant experiments in Northern Italy

Biotic resistance is considered an important driver in the establishment of non-indigenous species (NIS), but experiments in the marine environment have led to contradictory results. In this context, a transplant experiment of fouling communities was carried out over five months. Settlement panels were moved from low impact (species-rich native communities) to high impact sites by NIS in two Italian areas to test the biotic resistance hypothesis. Fouling communities displayed significant differences among treatments before and after the transplant, thus indicating the maintenance of a peculiar fouling community in transplanted panels. On the other hand, newly recruited species were similar between treatments and neither a facilitation nor a mitigation role from native fouling communities on NIS was observed. Our results highlight the importance to better investigate the factors affecting the high variability obtained in experiments testing this hypothesis, with the aim to identify potential solutions for NIS management in ports.

The Native Hymenoscyphus albidus and the Invasive Hymenoscyphus fraxineus Are Similar in Their Necrotrophic Growth Phase in Ash Leaves

The populations of European ash and its harmless fungal associate Hymenoscyphus albidus are in decline owing to ash dieback caused by the invasive Hymenoscyphus fraxineus, a fungus that in its native range in Asia is a harmless leaf endophyte of local ash species. To clarify the behavior of H. albidus and its spatial and temporal niche overlap with the invasive relative, we used light microscopy, fungal species-specific qPCR assays, and PacBio long-read amplicon sequencing of the ITS1-5.8S-ITS2 region to examine fungal growth and species composition in attached leaves of European ash. The plant material was collected from a healthy stand in central Norway, where ash saplings in late autumn showed leaflet vein necrosis like that commonly related to H. fraxineus. For reference, leaflet samples were analyzed from stands with epidemic level of ash dieback in southeastern Norway and Estonia. While H. albidus was predominant in the necrotic veins in the healthy stand, H. fraxineus was predominant in the diseased stands. Otherwise, endophytes with pathogenic potential in the genera Venturia (anamorph Fusicladium), Mycosphaerella (anamorph Ramularia), and Phoma, and basidiomycetous yeasts formed the core leaflet mycobiome both in the healthy and diseased stands. In necrotic leaf areas with high levels of either H. albidus or H. fraxineus DNA, one common feature was the high colonization of sclerenchyma and phloem, a region from which the ascomata of both species arise. Our data suggest that H. albidus can induce necrosis in ash leaves, but that owing to low infection pressure, this first takes place in tissues weakened by autumn senescence, 1-2 months later in the season than what is characteristic of H. fraxineus at an epidemic phase of ash dieback. The most striking difference between these fungi would appear to be the high fecundity of H. fraxineus. The adaptation to a host that is phylogenetically closely related to European ash, a tree species with high occurrence frequency in Europe, and the presence of environmental conditions favorable to H. fraxineus life cycle completion in most years may enable the build-up of high infection pressure and challenge of leaf defense prior to autumn senescence.

Reduced Invasiveness of Common Ragweed (Ambrosia artemisiifolia) Using Low-Dose Herbicide Treatments for High-Efficiency and Eco-Friendly Control

Common ragweed (Ambrosia artemisiifolia) is an invasive annual weed that invades heavily disturbed habitats and natural habitats less disturbed by human activities with native plant species in need of protection. Achieving effective control of A. artemisiifolia for the protection of native organisms and the local ecological environment is an ongoing challenge. Based on the growth and development characteristics of A. artemisiifolia, we examined the effectiveness of herbicides in controlling this species and the optimal time for application in the field with the aim of reducing herbicide dosage. Additionally, we analyzed whether the efficiency of low-dose applications for controlling this species might improve with increasing native plant species richness. Our findings indicate that aminopyralid (33 g ai ha^-1) was the most suitable herbicide for chemical control of A. artemisiifolia, with optimum application time being during vegetative growth (BBCH 32-35). Application of aminopyralid was found to kill approximately 52% of A. artemisiifolia plants, and more than 75% of the surviving plants did not bloom, thereby reducing seed yield of the population by more than 90%. Compared with the application of high-dose herbicide, the phytotoxicity of aminopyralid to native plants at the applied dose was substantially reduced. After 2 years of application, the relative coverage of A. artemisiifolia significantly decreased, with few plants remaining, whereas the relative coverage of native plants more than doubled, representing an eco-friendly control. Further, there was an increase in the A. artemisiifolia control rate in the plant community with higher native plant species richness at the same herbicide rates and a reduction in seed yield of A. artemisiifolia. Our findings help toward developing control measures to reduce the invasiveness of A. artemisiifolia with low-dose herbicides meanwhile protecting native plants, and then using the species richness of native plant communities to indirectly promote the effectiveness of low-dose herbicide application.

Competitive effects of plant invaders on and their responses to native species assemblages change over time

Alien plant invaders are often considered to be more competitive than natives, and species-rich plant communities are often considered to be more resistant to invaders than species-poor communities. However, the competitive interactions between invaders and assemblages of different species richness are unlikely to be static over time (e.g. during a growth season). To test this, we grew five alien and five native species as invaders in a total of 21 artificial assemblages of one, two or four native competitor species. To test for temporal changes in the reciprocal effects of invaders and the competitor assemblages on each other, and how these depend on the species richness of the assemblages, we harvested plants at three growth stages (weeks 4, 8 and 12). We found that the invaders and competitor assemblages had negative effects on each other. Aboveground biomass of invaders was reduced by the presence of a competitor assemblage, irrespective of its species richness, and this difference gradually increased over time. Alien invaders accumulated more aboveground biomass than the native invaders, but only after 12 weeks of growth. Meanwhile, the invaders also negatively affected the biomass of the competitor assemblages. For multi-species assemblages, the increase in the negative effect of the presence of the invader occurred mainly between weeks 4 and 8, whereas it happened mainly between weeks 8 and 12 for the one-species assemblages. Our results suggest that although alien invaders are more competitive than native invaders, the competitive effects of the invaders on and their responses to native competitor assemblages changed over time, irrespective of the origin of the invaders.

Climate change and niche unfilling tend to favor range expansion of Moina macrocopa Straus 1820, a potentially invasive cladoceran in temporary waters

Non-native species' introductions have increased in the last decades primarily due to anthropogenic causes such as climate change and globalization of trade. Moina macrocopa, a stress-tolerant cladoceran widely used in bioassays and aquaculture, is spreading in temporary and semi-temporary natural ponds outside its natural range. Here, we characterize the variations in the climatic niche of M. macrocopa during its invasions outside the native Palearctic range following introduction into the American continent. Specifically, we examined to what extent the climatic responses of this species have diverged from those characteristics for its native range. We also made predictions for its potential distribution under current and future scenarios. We found that the environmental space occupied by this species in its native and introduced distribution areas shares more characteristics than randomly expected. However, the introduced niche has a high degree of unfilling when displacing its original space towards the extension to drier and hotter conditions. Accordingly, M. macrocopa can invade new areas where it has not yet been recorded in response to warming temperatures and decreasing winter precipitation. In particular, temporary ponds are more vulnerable environments where climatic and environmental stresses may also lower biotic resistance.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s10750-022-04835-7.

Diversity and pathogenicity of Alternaria species associated with the invasive plant Ageratina adenophora and local plants

Pathogen accumulation after introduction is unavoidable for exotic plants over a long period of time. Therefore, it is important to understand whether plant invasion promotes novel pathogen emergence and increases the risk of pathogen movement among agricultural, horticultural, and wild native plants. In this study, we used multiple gene analysis to characterize the species composition of 104 isolates of Alternaria obtained from the invasive plant Ageratina adenophora and native plants from Yunnan, Hubei, Guizhou, Sichuan, and Guangxi in China. Phylogenetically, these strains were from A. alternata (88.5%), A. gossypina (10.6%) and A. steviae (0.9%). There was a high amount of sharing between strains associated with A. adenophora and with local plants. Pathogenicity tests indicated that most of these Alternaria strains are generalists; the isolates with a wider host range were more virulent to the plant. Woody plants were more resistant to these strains than herbaceous plants and vines. However, the invasive plant A. adenophora was highly sensitive to these strains. Our data are valuable for understanding how A. adenophora invasion impacts the Alternaria species composition of the native plant and whether A. adenophora invasion causes potential disease risks in invaded ecosystems.

Drivers of ecosystem vulnerability to Corbicula invasions in southeastern North America

Invasive species introduction is one of the major ongoing ecological global crises. Identifying factors responsible for the success of invasive species is key for the implementation of effective management actions. The invasive filter-feeding bivalve, Corbicula, is of particular interest because it has become ubiquitous in many river basins across North America and elsewhere. Here we sampled bivalve assemblages, environmental indicators, and land cover parameters in the Ouachita highlands in southeastern Oklahoma and southwestern Arkansas, and in the Gulf Coastal Plain of Alabama to test three working models (using structural equation modeling, SEM) based on a priori scientific knowledge regarding Corbicula invasions. Our models tested three competing hypotheses: (1) Native mussel declines are related to land use changes at the watershed level and subsequent Corbicula colonization is a result of an empty niche; (2) Corbicula abundance is one of the factors responsible for native mussel declines and has an interactive effect with land use change at the watershed level; (3) Native mussel declines and Corbicula success are both related to land use changes at the watershed level. We found no evidence for the first two hypotheses. However, we found that environmental indicators and land cover parameters at the watershed scale were robust predictors of Corbicula abundance. In particular, agricultural land cover was positively related with Corbicula density. These results suggest that further improvement of conventional agricultural practices including the optimization of fertilizer delivery systems may represent an opportunity to manage this species by limiting nutrient inputs to stream ecosystems. Preservation of extensive floodplain habitats may help buffer these inputs by providing key ecosystem services including sediment and nutrient retention.

Gut Dysbiosis and Clostridioides difficile Infection in Neonates and Adults

In this review, we focus on gut microbiota profiles in infants and adults colonized (CDC) or infected (CDI) with Clostridioides difficile. After a short update on CDI epidemiology and pathology, we present the gut dysbiosis profiles associated with CDI in adults and infants, as well as the role of dysbiosis in C. difficile spores germination and multiplication. Both molecular and culturomic studies agree on a significant decrease of gut microbiota diversity and resilience in CDI, depletion of Firmicutes, Bacteroidetes, and Actinobacteria phyla and a high abundance of Proteobacteria, associated with low butyrogenic and high lactic acid-bacteria levels. In symptomatic cases, microbiota deviations are associated with high levels of inflammatory markers, such as calprotectin. In infants, colonization with Bifidobacteria that trigger a local anti-inflammatory response and abundance of Ruminococcus, together with lack of receptors for clostridial toxins and immunological factors (e.g., C. difficile toxins neutralizing antibodies) might explain the lack of clinical symptoms. Gut dysbiosis amelioration through administration of “biotics” or non-toxigenic C. difficile preparations and fecal microbiota transplantation proved to be very useful for the management of CDI.

Anthropogenic and environmental determinants of alien plant species spatial distribution on an island scale

Mediterranean islands are considered especially vulnerable to biological invasions by alien plants. However, there is a lack of studies on island scale regarding the factors that determine alien plant's spatial distribution, and the way they affect invasion process. A roadside survey of alien plant species was conducted on Lesvos, the 8th largest island in Mediterranean basin. Data on species counts and explanatory variables were aggregated to a 1 sq. km vector grid and brought together into a single GIS layer. Alien species counts were modelled by using a Negative-binomial model while a Generalised Additive Model was used to examine possible non-linear relationships to the predictors by using splines. A subset of significant factors, related both to human activities and the environment, shaped the spatial distribution of aliens and influenced, in various ways, their future invasion outcome. Transformed areas with high levels of anthropogenic pressures and disturbances, including high population numbers, dense road network, ports, and intensive land use, as is the case for coastal zones, promoted the presence of alien species. Contrary, modified areas, such as grazed lands, seemed to restrict alien species occurrences, possibly due to the long grazing history these areas present, a regime in which aliens are not adapted. Alien plants presence was positively associated with high levels of NPP, diversity of geological substrates, and a west-facing aspect. Anthropogenic determinants of alien spatial patterns were primarily connected to increased propagule pressure, whereas environmental factors demonstrated the preference of alien plants for resource-rich environments.

Scale dependency in native-exotic richness relationships revisited

In their seminal paper, Shea and Chesson (Trends in Ecology & Evolution, 2002, 17, 170) developed a highly cited model (S&C model) showing scale dependency in the native-exotic richness relationships. Two decades later, extensive additional data have been accumulated, leading to new findings and insights. Accordingly, two updates were made here to the original S&C model: (1) changing the "negative" richness relationship between natives and exotics to "non-consistent" or "non-significant"; and (2) modifying the original diagram to correctly represent native and exotic species richness and their correlations across both small and large scales.

Diversity of resident plant communities could weaken their allelopathic resistance against alien and native invaders

Elton’s classic diversity-invasibility hypothesis posits that diversity of resident communities increases resistance against invaders. We tested whether the diversity-invasibility relationsip might be mediated by allelopathic effects of the resident species. In a large germination experiment, we exposed seeds of six alien and six native test species to leachates of one, three, six or twelve species. The leachates tended to slightly delay germination, and almost all single-species leachates reduced the proportion of germinated seeds. Nevertheless, the overall effect of the plant leachate mixtures on the proportion of germinated seeds was not significant. This was because a higher diversity of the leachates increased the proportion of germinated seeds, particularly for native test species. Among the six alien test species, it was only the most invasive one that benefited from increased diversity of the leachates, just like the natives did. Overall, our findings suggest that allelopathy of diverse communities does not provide resistance but could actually facilitate the germination of invaders.

Complex community responses underpin biodiversity change following invasion

How do invasive species change native biodiversity? One reason why this long-standing question remains challenging to answer could be because the main focus of the invasion literature has been on shifts in species richness (a measure of α-diversity). As the underlying components of community structure—intraspecific aggregation, interspecific density and the species abundance distribution (SAD)—are potentially impacted in different ways during invasion, trends in species richness provide only limited insight into the mechanisms leading to biodiversity change. In addition, these impacts can be manifested in distinct ways at different spatial scales. Here we take advantage of the new Measurement of Biodiversity (MoB) framework to reanalyse data collected in an invasion front in the Brazilian Cerrado biodiversity hotspot. We show that, by using the MoB multi-scale approach, we are able to link reductions in species richness in invaded sites to restructuring in the SAD. This restructuring takes the form of lower evenness in sites invaded by pines relative to sites without pines. Shifts in aggregation also occur. There is a clear signature of spatial scale in biodiversity change linked to the presence of an invasive species. These results demonstrate how the MoB approach can play an important role in helping invasion ecologists, field biologists and conservation managers move towards a more mechanistic approach to detecting and interpreting changes in ecological systems following invasion.