The Unified Neutral Theory of Biodiversity and Biogeography at Age Ten

Biogeography of larval trematodes in the freshwater snail, Semisulcospira libertina: a comparison of the morphological and molecular approaches

While biogeographic patterns of free-living organisms are well documented, the biogeography of parasitic fauna remains largely unclear. Due to morphological similarities, parasites are often difficult to identify without the aid of molecular genetics, further complicating the interpretation of their biogeographic patterns. We investigated trematode parasites infecting the East Asian freshwater snail Semisulcospira libertina to understand their biogeography and to evaluate how molecular approaches influence the interpretation of biogeographic patterns of the trematode fauna. We identified 46 genetically delimited species from 19 morphologically distinguishable trematodes infecting S. libertina and found that their species richness was negatively correlated to latitude. We also found that potential definitive host (fishes) richness and host body size were positively correlated with trematode species richness, suggesting that host attributes are essential factors shaping the biogeographic pattern in trematodes. These trends were observed irrespective of species identification methods, demonstrating that classical morphological identification can also effectively identify the latitudinal gradient pattern in trematodes. We further detected the distance decay of similarity in trematode communities, although this trend was only detectable in the biogeographic dataset based on molecular identification. Our study showed that morphological identification sufficiently reflects the latitudinal richness gradient while molecular identification is essential to estimate accurate local species richness and increase the resolution of the large-scale pattern of population similarities in the trematode communities.

Distribution patterns of soil bacteria, fungi, and protists emerge from distinct assembly processes across subcommunities

Environmental change exerts a profound effect on soil microbial domains-including bacteria, fungi, and protists-that each perform vital ecological processes. While these microbial domains are ubiquitous and extremely diverse, little is known about how they respond to environmental changes in urban soil ecosystems and what ecological processes shape them. Here we investigated the community assembly processes governing bacteria, fungi, and protists through the lens of four distinct subcommunities: abundant, conditionally rare, conditionally abundant, and rare taxa. We show that transient taxa, including the conditionally rare and conditionally rare or abundant taxa, were the predominant subcommunities. Deterministic processes (e.g., environmental filtering) had major roles in structuring all subcommunities of fungi, as well as conditionally rare and abundant protists. Stochastic processes had strong effects in structuring all subcommunities of bacteria (except rare taxa) and conditionally rare protists. Overall, our study underscores the importance of complementing the traditional taxonomy of microbial domains with the subcommunity approach when investigating microbial communities in urban soil ecosystems.

Regional uniqueness of tree species composition and response to forest loss and climate change

The conservation and restoration of forest ecosystems require detailed knowledge of the native plant compositions. Here, we map global forest tree composition and assess the impacts of historical forest cover loss and climate change on trees. The global occupancy of 10,590 tree species reveals complex taxonomic and phylogenetic gradients determining a local signature of tree lineage assembly. Species occupancy analyses indicate that historical forest loss has significantly restricted the potential suitable range of tree species in all forest biomes. Nevertheless, tropical moist and boreal forest biomes display the lowest level of range restriction and harbor extremely large ranged tree species, albeit with a stark contrast in richness and composition. Climate change simulations indicate that forest biomes are projected to differ in their response to climate change, with the highest predicted species loss in tropical dry and Mediterranean ecoregions. Our findings highlight the need for preserving the remaining large forest biomes while regenerating degraded forests in a way that provides resilience against climate change.

Coinfection frequency in water flea populations is a mere reflection of parasite diversity

In nature, parasite species often coinfect the same host. Yet, it is not clear what drives the natural dynamics of coinfection prevalence. The prevalence of coinfections might be affected by interactions among coinfecting species, or simply derive from parasite diversity. Identifying the relative impact of these parameters is crucial for understanding patterns of coinfections. We studied the occurrence and likelihood of coinfections in natural populations of water fleas (Daphnia magna). Coinfection prevalence was within the bounds expected by chance and parasite diversity had a strong positive effect on the likelihood of coinfections. Additionally, coinfection prevalence increased over the season and became as common as a single infection. Our results demonstrate how patterns of coinfection, and particularly their temporal variation, are affected by overlapping epidemics of different parasites. We suggest that monitoring parasite diversity can help predict where and when coinfection prevalence will be high, potentially leading to increased health risks to their hosts.

Patterns of Tadpole β Diversity in Temperate Montane Streams

Understanding the spatial variation and formation mechanism of biological diversity is a hot topic in ecological studies. Comparing with α diversity, β diversity is more accurate in reflecting community dynamics. During the past decades, β diversity studies usually focused on plants, mammals, and birds. Studies of amphibian β diversity in montane ecosystems, in particular, tadpoles, are still rare. In this study, Mount Emei, located in southwestern China, was selected as the study area. We explored the tadpole β diversity in 18 streams, based on a two-year survey (2018-2019). Our results indicated a high total β diversity in tadpole assemblages, which was determined by both turnover and nestedness processes, and the dominant component was turnover. Both the total β diversity and turnover component were significantly and positively correlated with geographical, elevational, and environmental distances, but no significant relationship was detected between these and the nestedness component. Moreover, the independent contributions of river width, current velocity, and chlorophyll α were larger than that of geographical and elevational distance. Overall, tadpole β diversity was determined by both spatial and environmental factors, while the contribution of environmental factors was larger. Future studies can focus on functional and phylogenetic structures, to better understand the tadpole assembly process.

Rare and common species contribute disproportionately to alpine meadow community construction and functional variation

It is widely accepted that rare species are the first species to become extinct after human-induced disturbances. However, the functional importance of rare species still needs to be better understood, especially in alpine meadow communities with harsher habitats, where the extinction rate of rare species may be higher. This study established a 1.85 × 105 m2 permanent research sample plot on the eastern Tibetan Plateau. We investigated data from 162 plots at 6 different sampling scales in alpine meadows to determine the contribution of rare and common species to alpine meadow communities' structural and functional variability. The results showed that (1) Asteraceae (Compositae) was the dominant family in the surveyed localities. The trends of species diversity indices were the same, and all of them increased with the increase of sampling scale, and the plant community showed apparent scale effects. (2) The community construction of rare species at small scales with high occupancy transitioned from neutral processes to ecological niche processes, while the community construction of common species at different sampling scales was all dominated by ecological niche processes. (3) The trait values of rare species at different sampling scales were different from those of common species, and their distribution in FEs (functional entities) was also different, indicating that they contributed differently to the ecological functions of the communities. Rare species with lower abundance in the surveyed communities had a higher proportion of FEs, indicating that rare species had a more significant proportion of contribution to FEs. The functional redundancy (FR) of rare species was lower than that of common species, and the functional vulnerability (FV) was higher than that of common species. Therefore, the loss of rare species is more likely to cause the loss of community ecological functions, affecting the function and resilience of alpine meadow ecosystems.

Succession of diversity, assembly mechanisms, and activities of the microeukaryotic community throughout Scrippsiella acuminata (Dinophyceae) bloom phases

Harmful algal bloom (HAB) is a rapidly expanding marine ecological hazard. Although numerous studies have been carried out about the ecological impact and the ecological mechanism of HAB outbreaks, few studies have comprehensively addressed the shifts of species composition, metabolic activity level, driving factors and community assembly mechanisms of microeukaryotic plankton in the course of the bloom event. To fill the gap of research, we conducted 18S ribosomal DNA and RNA sequencing during the initiation, development, sustenance and decline stages of a Scrippsiella acuminata (S. acuminata) bloom at the coastal sea of Fujian Province, China. We found that the bloom event caused a decrease in microeukaryotic plankton species diversity and increase in community homogeneity. Our results revealed that the RNA- and DNA-inferred communities were similar, but α-diversity was more dynamic in RNA- than in DNA-inferred communities. The main taxa with high projected metabolic activity (with RNA:DNA ratio as the proxy) during the bloom included dinoflagellates, Cercozoa, Chlorophyta, Protalveolata, and diatoms. The role of deterministic processes in microeukaryotic plankton community assembly increased during the bloom, but stochastic processes were always the dominant assembly mechanism throughout the bloom process. Our findings improve the understanding of temporal patterns, driving factors and assembly mechanisms underlying the microeukarytic plankton community in a dinoflagellate bloom.

Environmental DNA metabarcoding reveals the effect of environmental selection on phytoplankton community structure along a subtropical river

The Dongjiang River, a major tributary of the Pearl River system that supplies water to more than 40 million people in Guangdong Province and neighboring regions of China, harbors rich biodiversity, including many endemic and endangered species. However, human activities such as urbanization, agriculture, and industrialization have posed serious threats to its water quality and biodiversity. To assess the status and drivers of phytoplankton diversity, which is a key indicator of aquatic ecosystem health, this study used Environmental DNA (eDNA) metabarcoding combined with machine learning methods to explore spatial variations in the composition and structure of phytoplankton communities along the Dongjiang River, including its estuary. The results showed that phytoplankton diversity exhibited spatial distribution patterns, with higher community structure similarity and lower network complexity in the upstream than in the downstream regions. Environmental selection was the main mechanism shaping phytoplankton community composition, with natural factors driving the dominance of Pyrrophyta, Ochrophyta, and Cryptophyta in the upstream regions and estuaries. In contrast, the downstream regions was influenced by high concentrations of pollutants, resulting in increased abundance of Cryptophyta. The random forest model identified temperature, dissolved oxygen, chlorophyll a, NO2-, and NH4+ as the main factors influencing the primary phytoplankton communities and could be used to predict changes during wet periods. This study provides valuable insights into the factors influencing phytoplankton diversity and community composition in the Dongjiang River, and demonstrates the application value of eDNA metabarcoding technique in large-scale, long-distance river biodiversity monitoring.

Horizontal gene transfer is predicted to overcome the diversity limit of competing microbial species

Natural microbial ecosystems harbor substantial diversity of competing species. Explaining such diversity is challenging, because in classic theories it is extremely infeasible for a large community of competing species to stably coexist in homogeneous environments. One important aspect mostly overlooked in these theories, however, is that microbes commonly share genetic materials with their neighbors through horizontal gene transfer (HGT), which enables the dynamic change of species growth rates due to the fitness effects of the mobile genetic elements (MGEs). Here, we establish a framework of species competition by accounting for the dynamic gene flow among competing microbes. Combining theoretical derivation and numerical simulations, we show that in many conditions HGT can surprisingly overcome the biodiversity limit predicted by the classic model and allow the coexistence of many competitors, by enabling dynamic neutrality of competing species. In contrast with the static neutrality proposed by previous theories, the diversity maintained by HGT is highly stable against random perturbations of microbial fitness. Our work highlights the importance of considering gene flow when addressing fundamental ecological questions in the world of microbes and has broad implications for the design and engineering of complex microbial consortia.

The combination of multiple environmental stressors strongly alters microbial community assembly in aquatic ecosystems

Microorganisms play a critical role in maintaining the delicate balance of ecosystem services. However, the assembly processes that shape microbial communities are vulnerable to a range of environmental stressors, such as climate change, eutrophication, and the use of herbicides. Despite the importance of these stressors, little is known about their cumulative impacts on microbial community assembly in aquatic ecosystems. To address this knowledge gap, we established 48 mesocosm experiments that simulated shallow lake ecosystems and subjected them to warming (including continuous warming (W) and heat waves (H)), glyphosate-based herbicides (G), and nutrient loading (E). Our study revealed that in the control group, both deterministic and stochastic processes codominated the assembly of microbial communities in water, whereas in sediment, the processes were primarily stochastic. Interestingly, the effects of multiple stress factors on assembly in these two habitats were completely opposite. Specifically, stressors promoted the dominance of stochastic processes in water but increased the importance of deterministic processes in sediment. Furthermore, warming amplified the effects of herbicides but exerted an opposite and stronger influence on assembly compared to nutrients, emphasizing the complexity of these mechanisms and the significance of considering multiple stressors. The interaction of some factors significantly affected assembly (p < 0.05), with the effects of WEG being most pronounced in water. Both water and sediment exhibited homogeneous assembly of microbial communities (mean NTI >0), but the phylogenetic clustering of microbial communities in water was more closely related (NTI >2). Our research revealed the response model of microbial community assembly in aquatic ecosystems to multiple environmental stresses, such as agricultural pollution, climate change, and eutrophication, and indicated that microbial community changes in sediment may be an important predictor of lake ecosystem development. This provides scientific evidence that better environmental management can reduce impacts on aquatic ecosystems under the threat of future warming.

A computational framework for resolving the microbiome diversity conundrum

Recent empirical studies offer conflicting findings regarding the relation between host fitness and the composition of its microbiome, a conflict which we term 'the microbial β- diversity conundrum'. The microbiome is crucial for host wellbeing and survival. Surprisingly, different healthy individuals' microbiome compositions, even in the same population, often differ dramatically, contrary to the notion that a vital trait should be highly conserved. Moreover, gnotobiotic individuals exhibit highly deleterious phenotypes, supporting the view that the microbiome is paramount to host fitness. However, the introduction of almost arbitrarily selected microbiota into the system often achieves a significant rescue effect of the deleterious phenotypes. This is true even for microbiota from soil or phylogenetically distant host species, highlighting an apparent paradox. We suggest several solutions to the paradox using a computational framework, simulating the population dynamics of hosts and their microbiomes over multiple generations. The answers invoke factors such as host population size, the specific mode of microbial contribution to host fitness, and typical microbiome richness, offering solutions to the conundrum by highlighting scenarios where even when a host's fitness is determined in full by its microbiome composition, this composition has little effect on the natural selection dynamics of the population.

Inferring the ecological and evolutionary determinants of community genetic diversity

Understanding the relative contributions of ecological and evolutionary processes to the structuring of ecological communities is needed to improve our ability to predict how communities may respond to future changes in an increasingly human-modified world. Metabarcoding methods make it possible to gather population genetic data for all species within a community, unlocking a new axis of data to potentially unveil the origins and maintenance of biodiversity at local scales. Here, we present a new eco-evolutionary simulation model for investigating community assembly dynamics using metabarcoding data. The model makes joint predictions of species abundance, genetic variation, trait distributions and phylogenetic relationships under a wide range of parameter settings (e.g. high speciation/low dispersal or vice versa) and across a range of community states, from pristine and unmodified to heavily disturbed. We first demonstrate that parameters governing metacommunity and local community processes leave detectable signatures in simulated biodiversity data axes. Next, using a simulation-based machine learning approach we show that neutral and non-neutral models are distinguishable and that reasonable estimates of several model parameters within the local community can be obtained using only community-scale genetic data, while phylogenetic information is required to estimate those describing metacommunity dynamics. Finally, we apply the model to soil microarthropod metabarcoding data from the Troodos mountains of Cyprus, where we find that communities in widespread forest habitats are structured by neutral processes, while high-elevation and isolated habitats act as an abiotic filter generating non-neutral community structure. We implement our model within the ibiogen R package, a package dedicated to the investigation of island, and more generally community-scale, biodiversity using community-scale genetic data.

DNA metabarcoding reveals impact of local recruitment, dispersal, and hydroperiod on assembly of a zooplankton metacommunity

Understanding the environmental impact on the assembly of local communities in relation to their spatial and temporal connectivity is still a challenge in metacommunity ecology. This study aims to unravel underlying metacommunity processes and environmental factors that result in observed zooplankton communities. Unlike most metacommunity studies, we jointly examine active and dormant zooplankton communities using a DNA metabarcoding approach to overcome limitations of morphological species identification. We applied two-fragment (COI and 18S) metabarcoding to monitor communities of 24 kettle holes over a two-year period to unravel (i) spatial and temporal connectivity of the communities, (ii) environmental factors influencing local communities, and (iii) dominant underlying metacommunity processes in this system. We found a strong separation of zooplankton communities from kettle holes of different hydroperiods (degree of permanency) throughout the season, while the community composition within single kettle holes did not differ between years. Species richness was primarily dependent on pH and permanency, while species diversity (Shannon Index) was influenced by kettle hole location. Community composition was impacted by kettle hole size and surrounding field crops. Environmental processes dominated temporal and spatial processes. Sediment communities showed a different composition compared to water samples but did not differ between ephemeral and permanent kettle holes. Our results suggest that communities are mainly structured by environmental filtering based on pH, kettle hole size, surrounding field crops, and permanency. Environmental filtering based on specific conditions in individual kettle holes seems to be the dominant process in community assembly in the studied zooplankton metacommunity.

Ecological network structure in response to community assembly processes over evolutionary time

The dynamic structure of ecological communities results from interactions among taxa that change with shifts in species composition in space and time. However, our ability to study the interplay of ecological and evolutionary processes on community assembly remains relatively unexplored due to the difficulty of measuring community structure over long temporal scales. Here, we made use of a geological chronosequence across the Hawaiian Islands, representing 50 years to 4.15 million years of ecosystem development, to sample 11 communities of arthropods and their associated plant taxa using semiquantitative DNA metabarcoding. We then examined how ecological communities changed with community age by calculating quantitative network statistics for bipartite networks of arthropod-plant associations. The average number of interactions per species (linkage density), ratio of plant to arthropod species (vulnerability) and uniformity of energy flow (interaction evenness) increased significantly in concert with community age. The index of specializationH 2 ' has a curvilinear relationship with community age. Our analyses suggest that younger communities are characterized by fewer but stronger interactions, while biotic associations become more even and diverse as communities mature. These shifts in structure became especially prominent on East Maui (~0.5 million years old) and older volcanos, after enough time had elapsed for adaptation and specialization to act on populations in situ. Such natural progression of specialization during community assembly is probably impeded by the rapid infiltration of non-native species, with special risk to younger or more recently disturbed communities that are composed of fewer specialized relationships.

Deterministic processes dominate microbial community assembly in artificially bred Schizothorax wangchiachii juveniles after being released into wild

Fish artificial breeding and release is an important method to restore wild populations of endemic fish species around the world. Schizothorax wangchiachii (SW) is an endemic fish in the upper Yangtze River and is one of the most important species for the artificial breeding and release program implemented in the Yalong River drainage system in China. It is unclear how artificially bred SW adapts to the changeable wild environment post-release, after being in a controlled and very different artificial environment. Thus, the gut samples were collected and analyzed for food composition and microbial 16S rRNA in artificially bred SW juveniles at day 0 (before release), 5, 10, 15, 20, 25, and 30 after release to the lower reaches of the Yalong River. The results indicated that SW began to ingest periphytic algae from the natural habitat before day 5, and this feeding habit is gradually stabilized at day 15. Prior to release, Fusobacteria are the dominant bacteria in the gut microbiota of SW, while Proteobacteria and Cyanobacteria generally are the dominant bacteria after release. The results of microbial assembly mechanisms illustrated that deterministic processes played a more prominent role than stochastic processes in the gut microbial community of artificially bred SW juveniles after releasing into the wild. Overall, the present study integrates the macroscopic and microscopic methods to provide an insight into the food and gut microbial reorganization in the released SW. This study will be an important research direction to explore the ecological adaptability of artificially bred fish after releasing into the wild.

Composition and assembly mechanisms of prokaryotic communities in wetlands, and their relationships with different vegetation and reclamation methods

Coastal wetlands are undergoing substantial transformations globally as a result of increased human activities. However, compared to other ecosystems, diversity and functional characteristics of microbial communities in reclaimed coastal wetlands are not well studied compared to other ecosystems. This is important because it is known that microorganisms can play a crucial role in biogeochemical cycling within coastal wetland ecosystems. Hence, this study utilized the high-throughput sequencing technique to investigate the structure and assembly processes of microbial communities in reclaimed coastal wetlands. The results revealed a substantial change in soil properties following coastal wetland reclamation. Remarkably, the reclaimed soil exhibited significantly lower pH, soil organic carbon (SOC), and total salinity (TS) values (p < 0.05). The dominant phyla included Proteobacteria, Chloroflexi, Bacteroidetes, Acidobacteria, and Planctomycetes among study sites. However, the relative abundance of Proteobacteria increased from un-reclaimed coastal wetlands to reclaimed ones. The Proteobacteria, Chloroflexi, and Acidobacteria showed higher relative abundance in vegetated soil compared to bare soil, while Bacteroidetes and Planctomycetes exhibited the opposite trend. Notably, vegetation types exerted the strongest influence on microbial diversity, surpassing the effects of soil types and depth (F = 34.49, p < 0.001; F = 25.49, p < 0.001; F = 3.173, p < 0.078, respectively). Stochastic assembly processes dominated in un-reclaimed soil, whereas deterministic processes governed the assembly in artificial sea embankment wetlands (SEW). The presence of Spartina alterniflora in all soil types (except SEW soils) indicated stochastic assembly, while Phragmites australis in reclaimed soils pointed toward deterministic microbial assembly. Furthermore, environmental factors such as pH, soil water content (SWC), SOC, total carbon (TC), total nitrogen (TN), total phosphorus (TP), NH4+-N, vegetation types, soil depth, and geographic distance exhibited significant effects on microbial beta diversity indices. Co-occurrence network analysis revealed a stronger association between taxa in SEW compared to land reclaimed from wetlands (LRW) and natural coastal wetlands (NCW). The bottom soil layer exhibited more complex network interactions than the topsoil layer. Besides soil parameters, reclamation and varieties of vegetation were also substantial factors influencing the composition, diversity, and assembly processes of microbial communities in coastal wetlands.

Quantifying Stochastic Processes in Shaping Dissolved Organic Matter Pool with High-Resolution Mass Spectrometry

Natural dissolved organic matter (DOM) represents a ubiquitous molecular mixture, progressively characterized by spatiotemporal resolution. However, an inadequate comprehension of DOM molecular dynamics, especially the stochastic processes involved, hinders carbon cycling predictions. This study employs ecological principles to introduce a neutral theory to elucidate the fundamental processes involving molecular generation, degradation, and migration. A neutral model is thus formulated to assess the probability distribution of DOM molecules, whose frequencies and abundances follow a β-distribution relationship. The neutral model is subsequently validated with high-resolution mass spectrometry (HRMS) data from various waterbodies, including lakes, rivers, and seas. The model fitting highlights the prevalence of molecular neutral distribution and quantifies the stochasticity within DOM molecular dynamics. Furthermore, the model identifies deviations of HRMS observations from neutral expectations in photochemical and microbial experiments, revealing nonrandom molecular transformations. The ecological null model further validates the neutral modeling results, demonstrating that photodegradation reduces molecular stochastic dynamics at the surface of an acidic pit lake, while random distribution intensifies at the river surface compared with the porewater. Taken together, the DOM molecular neutral model emphasizes the significance of stochastic processes in shaping a natural DOM pool, offering a potential theoretical framework for DOM molecular dynamics in aquatic and other ecosystems.

Phylogenetic diversity and structure in moist and dry upland forests in the semi-arid region of Brazil

Understanding the factors influencing variation in the diversity and structure of rich biological communities (e.g., Neotropical upland forests) is essential in the context of climate change. In this study, we examine how environmental filters (temperature, precipitation, and elevation) and distinct habitats (moist upland forests - MUF and dry upland forests - DHF) influence the phylogenetic diversity and structure of 54 tree communities (28 MHF and 26 DHF). We used the standardized effect size (ses) of the metrics phylogenetic diversity (ses.PD), mean pairwise distance (ses.MPD), and mean nearest neighbor distance (ses.MNTD) to quantify changes in tree community diversity and structure. Then, we assessed the relationships of the phylogenetic metrics with the environmental filters as predictors using generalized linear models (GLMs). Our results indicate that increasing temperature negatively affects the phylogenetic indices analyzed, leading to less diverse and more clustered communities. In contrast, increasing precipitation and elevation showed a significant positive relationship with the analyzed indices, directing communities towards greater phylogenetic diversity and random or overdispersed structure. Our findings also reveal that phylogenetic diversity and structure vary with habitat type. For example, while MUFs exhibit higher phylogenetic diversity and random structure, DUFs display lower phylogenetic diversity and clustered structure. In conclusion, our results suggest that the phylogenetic patterns exhibited by upland communities in the semiarid region are strongly related to climatic conditions and the habitat in which they are found. Therefore, if the predicted temperature increases and precipitation decreases in climate change scenarios for the semi-arid region materialize, these communities may face significant biodiversity loss.

Mathematical bounds on Shannon entropy given the abundance of the ith most abundant taxon

The measurement of diversity is a central component of studies in ecology and evolution, with broad uses spanning multiple biological scales. Studies of diversity conducted in population genetics and ecology make use of analogous concepts and even employ equivalent mathematical formulas. For the Shannon entropy statistic, recent developments in the mathematics of diversity in population genetics have produced mathematical constraints on the statistic in relation to the frequency of the most frequent allele. These results have characterized the ways in which standard measures depend on the highest-frequency class in a discrete probability distribution. Here, we extend mathematical constraints on the Shannon entropy in relation to entries in specific positions in a vector of species abundances, listed in decreasing order. We illustrate the new mathematical results using abundance data from examples involving coral reefs and sponge microbiomes. The new results update the understanding of the relationship of a standard measure to the abundance vectors from which it is calculated, potentially contributing to improved interpretation of numerical measurements of biodiversity.

Climate factors and host chemical profiles jointly drives the bacterial community assembly in Mussaenda pubescens stems

Endophytic bacteria residing within host plants can significantly impact on the host's growth, health, and overall relationship with its surrounding environment. However, the process that shape the community assembly of stem bacterial endophytes (SBEs) remains poorly understood. This study explored the community structure, co-occurrence patterns, and ecological processes of the SBEs inhabiting the shrub host, Mussaenda pubescens, across seven locations in southeastern China. We found that the absolute abundances, alpha diversity, and community composition of SBE communities exhibited notable differences among various host populations. Stem chemical characteristics were the most important factors influencing SBE community distribution, followed by geographic distance and climatic factors. The beta diversity decomposition analyses indicated that SBE community dissimilarities between sites were nearly equally driven by similarity, replacement diversity, and richness difference. The co-occurrence network analysis revealed that the keystone taxa were mostly observed in rare species, which may be essential for preserving the ecosystem's functions. Conditionally abundant taxa (CAT) showcased the highest closeness centrality, while exhibiting the lowest degree centrality and betweenness centrality as opposed to rare taxa. In addition, stochastic processes also played an important role in structuring SBE communities, with ecological drift being the dominant factor for both abundant and rare taxa. This study would deepen our understanding of the ecological dynamics and microbial interactions within plant endophytic microbiomes.

Contrasting Mechanisms Determine the Microeukaryotic and Syndiniales Community Assembly in a Eutrophic bay

Syndiniales is a diverse parasitic group, increasingly gaining attention owing to its high taxonomic diversity in marine ecosystems and inhibitory effects on the dinoflagellate blooms. However, their seasonal dynamics, host interactions, and mechanisms of community assembly are largely unknown, particularly in eutrophic waters. Here, using 18S rRNA gene amplicon sequencing, we intended to elucidate the interactions between Syndiniales and microeukaryotes, as well as community assembly processes in a eutrophic bay. The results showed that Syndiniales group II was dominating throughout the year, with substantially higher abundance in the winter and spring, whereas Syndiniales group I was more abundant in the summer and autumn. Temperature and Dinoflagellata were the most important abiotic and biotic factors driving variations of the Syndiniales community, respectively. The assembly processes of microeukaryotes and Syndiniales were completely different, with the former being controlled by a balance between homogeneous selection and drift and the latter being solely governed by drift. Network analysis revealed that Syndiniales group II had the largest number of interactions with microeukaryotes, and they primarily associated with Dinoflagellata in the winter, while interactions with Chlorophyta and Bacillariophyta increased dramatically in summer and autumn. These findings provide significant insights in understanding the interactions and assembly processes of Syndiniales throughout the year, which is critical in revealing the roles of single-celled parasites in driving protist dynamics in eutrophic waters.

Negative frequency dependent selection unites ecology and evolution

From genes to communities, understanding how diversity is maintained remains a fundamental question in biology. One challenging to identify, yet potentially ubiquitous, mechanism for the maintenance of diversity is negative frequency dependent selection (NFDS), which occurs when entities (e.g., genotypes, life history strategies, species) experience a per capita reduction in fitness with increases in relative abundance. Because NFDS allows rare entities to increase in frequency while preventing abundant entities from excluding others, we posit that negative frequency dependent selection plays a central role in the maintenance of diversity. In this review, we relate NFDS to coexistence, identify mechanisms of NFDS (e.g., mutualism, predation, parasitism), review strategies for identifying NFDS, and distinguish NFDS from other mechanisms of coexistence (e.g., storage effects, fluctuating selection). We also emphasize that NFDS is a key place where ecology and evolution intersect. Specifically, there are many examples of frequency dependent processes in ecology, but fewer cases that link this process to selection. Similarly, there are many examples of selection in evolution, but fewer cases that link changes in trait values to negative frequency dependence. Bridging these two well-developed fields of ecology and evolution will allow for mechanistic insights into the maintenance of diversity at multiple levels.

Life history complementarity and the maintenance of biodiversity

Life history, the schedule of when and how fast organisms grow, die and reproduce, is a critical axis along which species differ from each other^1-4. In parallel, competition is a fundamental mechanism that determines the potential for species coexistence^5-8. Previous models of stochastic competition have demonstrated that large numbers of species can persist over long timescales, even when competing for a single common resource^9-12, but how life history differences between species increase or decrease the possibility of coexistence and, conversely, whether competition constrains what combinations of life history strategies complement each other remain open questions. Here we show that specific combinations of life history strategy optimize the persistence times of species competing for a single resource before one species overtakes its competitors. This suggests that co-occurring species would tend to have such complementary life history strategies, which we demonstrate using empirical data for perennial plants.

Coordination and divergence in community assembly processes across co-occurring microbial groups separated by cell size

Setting the pace of life and constraining the role of members in food webs, body size can affect the structure and dynamics of communities across multiple scales of biological organization (e.g., from the individual to the ecosystem). However, its effects on shaping microbial communities, as well as underlying assembly processes, remain poorly known. Here, we analyzed microbial diversity in the largest urban lake in China and disentangled the ecological processes governing microbial eukaryotes and prokaryotes using 16S and 18S amplicon sequencing. We found that pico/nano-eukaryotes (0.22-20 μm) and micro-eukaryotes (20-200 μm) showed significant differences in terms of both community composition and assembly processes even though they were characterized by similar phylotype diversity. We also found scale dependencies whereby micro-eukaryotes were strongly governed by environmental selection at the local scale and dispersal limitation at the regional scale. Interestingly, it was the micro-eukaryotes, rather than the pico/nano-eukaryotes, that shared similar distribution and community assembly patterns with the prokaryotes. This indicated that assembly processes of eukaryotes may be coupled or decoupled from prokaryotes' assembly processes based on eukaryote cell size. While the results support the important influence of cell size, there may be other factors leading to different levels of assembly process coupling across size classes. Additional studies are needed to quantitatively parse the influence of cell size versus other factors as drivers of coordinated and divergent community assembly processes across microbial groups. Regardless of the governing mechanisms, our results show that there are clear patterns in how assembly processes are coupled across sub-communities defined by cell size. These size-structured patterns could be used to help predict shifts in microbial food webs in response to future disturbance.

An integrative approach to understanding diversity patterns and assemblage rules in Neotropical bats

Understanding the mechanisms shaping species composition of assemblages is critical for incorporating ecological and evolutionary perspectives into biodiversity conservation. Thus, we quantified the relative support of community assembly mechanisms by assessing how species richness relates to the functional and phylogenetic biodiversity of Neotropical bat assemblages. We assessed the association of functional diversity for functional categories and phylogenetic diversity with species richness for 20 assemblages of Neotropical bats. In addition, we contrasted functional and phylogenetic diversity against null models to determine the mechanisms that structure the assemblages. We hypothesize functional/phylogenetic overdispersion for high species sites and a positive relationship between those dimensions of diversity and richness. Functional divergence increased with species richness, indicating that the variability in ecological attributes among abundant bats increases as the assemblages contain more species. Taxa were more distantly related as richness increases, but distances among closely related species remained constant. We found a consistent tendency of clustering of functional traits in site assemblages, particularly in abundant species. We proposed competition between clades as a possible mechanism modulating the community structure in Neotropical bat assemblages. Our results suggest that decreasing overlap in functional traits between abundant species could promote coexistence with rare species that can buffer ecosystem function due to species loss.

Abundance does not predict extinction risk in the fossil record of marine plankton

A major premise of ecological neutral theory is that population size is inversely related to extinction risk. This idea is central to modern biodiversity conservation efforts, which often rely on abundance metrics to partially determine species extinction risk. However, limited empirical studies have tested whether extinction is indeed more probable for species with low abundances. Here we use the fossil record of Neogene radiolaria to test the relationship between relative abundance and longevity (time from first to last occurrence). Our dataset includes abundance histories for 189 polycystine radiolarian species from the Southern Ocean, and 101 species from the tropical Pacific. Using linear regression analyses, we show that neither maximum nor average relative abundance are significant predictors of longevity in either oceanographic region. This suggests that neutral theory fails to explain the plankton ecological-evolutionary dynamics we observe. Extrinsic factors are likely more important than neutral dynamics in controlling radiolarian extinction.

What constitutes a community? A co-occurrence exploration of the Costa Rican avifauna

The concept of a "community" as a form of organization for natural biological systems is both widespread and widely accepted within the ecological and biological sciences. Communities have been defined as groups of organisms that interact in ways that denote interdependence between individuals and taxa (e.g. as defined by "food webs") but they have also been defined as groups of co-occurring organisms that are assumed to interact by virtue of their shared spatiotemporal existence. The latter definition has been debated and challenged in the literature, with mounting evidence for co-occurrence being more indicative of coincident ecological niches in space and time rather than being evidence of ecological interaction or dependency. Using a dataset of 460 Costa Rican bird species divided into breeding and non-breeding season datasets, we empirically demonstrate the ways in which co-occurrence can create illusory communities based on similar occupied ecological niches and similar patterns of co-occurrence at different times of year. We discuss the importance of discerning coincidental co-occurrence from true ecological interactions that would manifest a true community, and further address the importance of differentiating communities of co-occurrence from communities of demonstrable ecological interaction. While co-occurrence is a necessary aspect of interspecific interactions, we discuss and demonstrate here that such co-occurrence does not make a community, nor should explicit patterns of co-occurrence be seen as evidence for evolutionarily important ecological interactions.

Heterogeneity in the isolation of patches may be essential for the action of metacommunity mechanisms

The spatial isolation gradient of communities and the gradient in the species dispersal ability are recognized as determinants of biodiversity in metacommunities. In spite of this, mean field models, spatially explicit models, and experiments were mainly focused on idealized spatial arrangements of communities leaving aside the combining role of dispersal and isolation gradients in metacommunity processes. Consequently, we have an incipient understanding of the role of the real spatial arrangement of communities on biodiversity patterns. We focus on six metacommunities for which confident information about the spatial arrangement of water bodies is available. Using coalescent metacommunity models and null models that randomize the location of water bodies, we estimated the potential effect of the landscape on biodiversity and its dependence on species dispersal ability. At extremely low or high dispersal abilities, the location of ponds does not influence diversity because different communities are equally affected by the low or high incoming dispersal. At intermediate dispersal abilities, peripheral communities present a much lower richness and higher beta diversity than central communities. Moreover, metacommunities from real landscapes host more biodiversity than randomized landscapes, a result that is determined by the heterogeneity in the geographic isolation of communities. In a dispersal gradient, mass effects systematically increase the local richness and decrease beta diversity. However, the spatial arrangement of patches only has a large importance in metacommunity processes at intermediate dispersal abilities, which ensures access to central locations but limits dispersal in isolated communities. The ongoing reduction in spatial extent and simplification of the landscape may consequently undermine the metacommunity processes that support biodiversity, something that should be explicitly considered in preserving and restoring strategies.

Plant community phylogeny responses to protections and its main drivers in boreal forests, China: General pattern and implications

Patterns of the phylogenetic structure have been broadly applied to predict community assembly processes. However, the distribution pattern of evolutionary diversity and its drivers under nature conservation are still poorly understood in boreal forests. Here, we investigated 1738 sampling plots and subplots from distinct protection intensities (PIs) zones in five representative National Nature Reserves (NNRs). Multiple comparisons, redundancy analysis, and linear mixed model were performed to identify the changes in community phylogeny across different PIs and NNRs and the drivers for these variations. Our results showed considerable plant community phylogeny variations in different NNRs. As indicated by SesMPD (standardized mean pairwise distance) and SesMNTD (standardized the mean nearest taxon distance), trees, shrubs, and herbs presented overdispersed, clustered, and random distribution patterns, respectively, in different PIs. Protection resulted in the phylogenetic structure between the nearest species of trees showing a more overdispersed pattern (p < 0.05). Protection decreased the phylogenetically clustered degree between the nearest species of shrubs (p > 0.05), while the herbs still maintained a random pattern. Community traits explained the most to phylogeny variation of different communities (24 %-71 %, p < 0.01), followed by geoclimatic factors (2 %-24 %) and conservation processes (1 %-21 %). The higher mean annual precipitation and under branch height at the lower latitude area accompanied the higher SesMPD and SesMNTD. The higher PIs attended with higher tree SesMPD, and the longer protection time resulted in higher shrub PSR (phylogenetic species richness) and PSV (phylogenetic species variability). Including the location of NNRs, community traits, and years of protection, rather than only emphasizing PI itself, could optimize community phylogenetic structure and preserve the evolutionary potential of biodiversity.

Crop diversity promotes the recovery of fungal communities in saline-alkali areas of the Western Songnen Plain

Introduction

Phytoremediation is an effective strategy for saline land restoration. In the Western Songnen Plain, northeast China, soil fungal community recovery for saline phytoremediation has not been well documented among different cropping patterns. In this study, we tested how rotation, mixture, and monoculture cropping patterns impact fungal communities in saline-alkali soils to assess the variability between cropping patterns.

Methods

The fungal communities of the soils of the different cropping types were determined using Illumina Miseq sequencing.

Results

Mixture and rotation promoted an increase in operational taxonomic unit (OTU) richness, and OTU richness in the mixture system decreased with increasing soil depth. A principal coordinate analysis (PCoA) showed that cropping patterns and soil depths influenced the structure of fungal communities, which may be due to the impact of soil chemistry. This was reflected by soil total nitrogen (TN) and electrical conductivity (EC) being the key factors driving OTU richness, while soil available potassium (AK) and total phosphorus (TP) were significantly correlated with the relative abundance of fungal dominant genus. The relative abundance of Leptosphaerulina, Alternaria, Myrothecium, Gibberella, and Tetracladium varied significantly between cropping patterns, and Leptosphaerulina was significantly associated with soil chemistry. Soil depth caused significant differences in the relative abundance of Fusarium in rotation and mixture soils, with Fusarium more commonly active at 0-15 cm deep soil. Null-model analysis revealed that the fungal community assembly of the mixture soils in 0-15 cm deep soil was dominated by deterministic processes, unlike the other two cropping patterns. Furthermore, fungal symbiotic networks were more complex in rotation and mixture than in monoculture soils, reflected in more nodes, more module hubs, and connectors. The fungal networks in rotation and mixture soils were more stable than in monoculture soils, and mixture networks were obviously more connected than rotations. FUNGuild showed that the relative proportion of saprotroph in rotation and mixture was significantly higher than that in monocultures. The highest proportion of pathotroph and symbiotroph was exhibited in rotation and mixture soils, respectively.

Discussion

Overall, mixture is superior to crop rotation and monocultures in restoring fungal communities of the saline-alkali soils of the Western Songnen Plain, northeast China.

Improving the realism of neutral ecological models by incorporating transient dynamics with temporal changes in community size

Neutral models in ecology assume that all species are demographically equivalent, such that their abundances differ ultimately because of demographic stochasticity rather than selection. In spite of their simplicity, neutral models have been found to accurately reproduce static patterns of biodiversity for diverse communities. However, the same neutral models have been found to exhibit species abundance dynamics that are far too slow compared to reality, resulting in poor fits to temporally dynamic patterns of biodiversity. Here, we show that one of the root causes of these slow dynamics is the additional assumption that a community has reached an equilibrium with a fixed community size, with species that have a net growth rate close to zero. We removed this additional assumption by constructing and analyzing a neutral model with an expected community size that can change over time and is not necessarily at equilibrium, which thus allows the historical formation of a community to be represented explicitly. Our analysis demonstrated that for the general scenario where a small community rapidly grows in size to a carrying capacity, representing recovery from ecological disturbance or assembly of a new community, the model produced much larger changes in species abundances and much shorter species ages than a neutral model at an equilibrium with fixed community size. In addition, the species abundance distribution was biphasic with a subset of abundant species arising from a founder effect. We confirmed these new results in applications of the new model to the specific scenario of recovery of the Amazon tree community after the end-Cretaceous bolide impact, which involved periods of increasing and decreasing community size. We conclude that incorporating transient dynamics in neutral models improves realism by allowing explicit consideration of how a community is formed over realistic time-scales.

Stochastic and deterministic processes shape bioenergy crop microbiomes along a vertical soil niche

Sustainable biofuel cropping systems aim to address climate change while meeting energy needs. Understanding how soil and plant-associated microbes respond to these different cropping systems is key to promoting agriculture sustainability and evaluating changes in ecosystem functions. Here, we leverage a long-term biofuel cropping system field experiment to dissect soil and root microbiome changes across a soil-depth gradient in poplar, restored prairie and switchgrass to understand their effects on the microbial communities. High throughput amplicon sequencing of the fungal internal transcribed spacer (ITS) and prokaryotic 16S DNA regions showed a common trend of root and soil microbial community richness decreasing and evenness increasing with depth. Ecological niche (root vs. soil) had the strongest effect on community structure, followed by depth, then crop. Stochastic processes dominated the structuring of fungal communities in deeper soil layers while operational taxonomic units (OTUs) in surface soil layers were more likely to co-occur and to be enriched by plant hosts. Prokaryotic communities were dispersal limited at deeper depths. Microbial networks showed a higher density, connectedness, average degree and module size in deeper soils. We observed a decrease in fungal-fungal links and an increase of bacteria-bacteria links with increasing depth in all crops, particularly in the root microbiome.

Evaluating the hologenome concept by analyzing the root-endosphere microbiota of chimeric plants

The hologenome concept considers the entity formed by a host and its microbiota, the holobiont, as new level of hierarchical organization subject to neutral and selective forces. We used grafted plants to formally evaluate the hologenome concept. We analyzed the root-endosphere microbiota of two independent watermelon and grapevine plant systems, including ungrafted and reciprocal-grafting combinations. Grafted and ungrafted hosts harbor markedly different microbiota compositions. Furthermore, the results indicate a non-random assembly of bacterial communities inhabiting the root endosphere of chimeric plants with interactive effect of both the rootstock and scion on the recruitment of microorganisms. Because chimeric plants did not have a random microbiota, the null hypothesis that holobionts assemble randomly and hologenome concept is an intellectual construction only can be rejected. The study supports the relevance of hologenome as biological level of organization and opens new avenues for a better fundamental understanding of plants as holobionts.

Community assembly patterns and processes of microbiome responses to habitats and Mytilopsis sallei invasion in the tidal zones of the Pearl River Estuary

The sustainability of estuarine ecosystem functions depends on the stabilization of microbial ecological processes. However, due to the unique and variable habitat characteristics of estuarine areas, in-depth studies on ecological processes such as the spatial distribution and assembly patterns of microbial community structure are lacking. As methods to elucidate this structure, we used 16S rDNA, 18S rDNA and ITS sequencing technologies to study the composition, diversity, spatial pattern and aggregation mechanism of the bacterial, protist and fungal communities in the tidal zones of the Pearl River Estuary (PRETZ). The abundance of bacterial communities was much higher than that of protists and fungi, and the spatial pattern was obvious in PRETZ. The application of neutral and null models revealed the assembly process of three microbial communities dominated by stochastic processes. Among the stochastic processes, undominated processes (64.03 %, 62.45 %, and 59.29 %) were the most critical processes in the assembly of bacterial, fungal and protist communities. Meanwhile, environmental variables, geographic locations, and biological factors were associated with the composition and assembly of bacterial, protist, and fungal communities. Among the environmental variables, dissolved oxygen and salinity were the main predictors that jointly affected the differences in the community structure of the three microorganisms, and geographic location was the second predictor affecting the community structure of the three microorganisms and had a more pronounced effect on the diversity and network structure of the bacterial and fungal communities. However, biological factors exerted a weaker effect on the microbial community structure than spatial factors and only affected bacteria and protists; the invasive species Mytilopsis sallei only affected the process of protist community assembly. In addition, environmental variables affected the relative importance of stochastic processes. In summary, the formation of microbial communities in the PRETZ was affected by random processes, environmental variables, geographic location, and invasive species.

Stochastic processes dominate soil arbuscular mycorrhizal fungal community assembly along an elevation gradient in central Japan

Arbuscular mycorrhizal (AM) fungi play an important role in facilitating ecosystem function and stability. Yet, their community response patterns and ecological assembly processes along elevational gradients which cross a range of climates and soil conditions remain elusive. We used Illumina MiSeq sequencing to examine trends in soil AM fungal community along an elevational gradient from 100 m to 2300 m in central Japan. A total of 750 operational taxonomic units (OTUs) affiliated to 12 AM fungal genera were identified from soil samples, and the AM fungal community composition differed strongly with elevation, with variance explained more by climate, followed by soil and plant factors. The AM fungal α-diversity, network connectivity and complexity between AM fungal taxa and also with plant communities all exhibited a maximum at the mid-elevation of 800 m and then declined, principally influenced by soil pH and precipitation. Stochastic processes dominated AM fungal community assembly across the whole elevation gradient, with homogenizing dispersal being the main process. Only when AM fungal communities were contrasted across a relatively broad range of elevations, did variable selection (deterministic process) became significant, and even then in a mixed role with stochasticity. While OTUs of AM fungi are clearly adapted to particular environmental ranges, stochasticity due to rapid dispersal has a major role in determining their occurrence, suggesting that AM fungi may possess generalized and interchangeable niches, and can adjust their distribution rapidly - at least on the scale of a single mountain. This finding emphasizes that the roles of AM fungi in plant ecology may be non-specific and easily substituted, and furthermore that there is rapid local scale dispersal, which may allow plants to maintain effective AM associations under environmental change.

Eukaryotic plankton community assembly and influencing factors between continental shelf and slope sites in the northern South China Sea

Eukaryotic plankton are pivotal members of marine ecosystems playing crucial roles in marine food webs and biogeochemical cycles. However, understanding the patterns and drivers of their community assembly remains a grand challenge. A study was conducted in the northern South China Sea (SCS) to address this issue. Here, 49 samples were collected and size-fractionated from discrete depths at continental shelf and continental slope in the northern SCS over a diel cycle. From high throughput sequencing of the 18S rDNA gene V4 region, 2463 operational taxonomic units (OTUs) were retrieved. Alveolata and Opisthokonta overwhelmingly dominated the assemblages in the abundance (44.76%, 31.08%) and species richness (59%, 12%). Biodiversity was higher in the slope than the shelf and increased with depth. Temperature and salinity appeared to be the most important deterministic drivers of taxon composition. Community structure was influenced by multiple factors in the importance order of: environmental factors (temperature + salinity) > spatial factor > water depth > sampling time. Furthermore, the neutral model explained more variations in the smaller-sized (0.22-3 μm) community (24%) than larger-sized (3-200 μm) community (16%) but generally explained less variations than did deterministic processes. Additionally, our data indicated that the larger plankton might be more environmentally filtered and less plastic whereas the smaller plankton had stronger dispersal ability. This study sheds light on the differential contributions of the deterministic process and stochastic process and complexities of assembly mechanisms in shaping the community assembly of micro-nano and pico-eukaryotic biospheres in a subtropical ocean.

A basic community dynamics experiment: Disentangling deterministic and stochastic processes in structuring ecological communities

Community dynamics are governed by two opposed processes: species sorting, which produces deterministic dynamics leading to an equilibrium state, and ecological drift, which produces stochastic dynamics. Despite a great deal of theoretical and empirical work aiming to demonstrate the predominance of one or the other of these processes, the importance of drift in structuring communities and maintaining species diversity remains contested. Here, we present the results of a basic community dynamics experiment using floating aquatic plants, designed to measure the relative contributions of species sorting and ecological drift to community change over about a dozen generations. We found that species sorting became overwhelmingly dominant as the experiment progressed, and directed communities toward a stable equilibrium state maintained by negative frequency-dependent selection. The dynamics of any particular species depended on how far its initial frequency was from its equilibrium frequency, however, and consequently the balance of sorting and drift varied among species.

Seasonal variation significantly influenced the stochasticity of community assembly of amphibian symbiotic bacteria

Seasonal variation has been shown to influence symbiotic bacterial community composition and structure in amphibians. It is still unknown how the symbiotic bacterial community assembly changes during different seasons, especially for amphibians who are particularly sensitive to environmental change. We found significant differences in the composition and diversity (alpha and beta diversity) of amphibian skin and gut bacteria. Co-occurrences network analysis showed that seasonal variation reduced the microbial network complexity of amphibians from summer to autumn. The normalized stochastic ratio (NST) and phylogenetic bin-based null model analysis (iCAMP) models showed that the same result that stochastic processes was the major factor regulating the symbiotic bacterial community assembly mechanisms of amphibians. From summer to autumn, the symbiotic bacterial community assembly mechanisms declined in the contribution of stochastic processes, while increasing in the contribution of deterministic processes. Dispersal limitation was the dominant microbial assembly mechanism, followed by homogeneous selection, and then heterogeneous selection in the symbiotic bacterial community communities of amphibians between summer and autumn. Furthermore, higher niche width of the symbiotic bacterial community of amphibians was found in summer than autumn. Overall, these results demonstrated that seasonal variation influenced amphibian symbiotic bacterial community between summer and autumn.

The successional trajectory of bacterial and fungal communities in soil are fabricated by yaks’ excrement contamination in plateau, China

The soil microbiome is crucial in determining contemporary realistic conditions for future terrestrial ecological and evolutionary development. However, the precise mechanism between the fecal deposition in livestock grazing and changes in the soil microbiome remains unknown. This is the first in-depth study of bacterial and fungal taxonomic changes of excrement contaminated soils in the plateau (&gt;3,500 m). This suggests the functional shifts towards a harmful-dominated soil microbiome. According to our findings, excrement contamination significantly reduced the soil bacterial and fungal diversity and richness. Furthermore, a continuous decrease in the relative abundance of microorganisms was associated with nutrient cycling, soil pollution purification, and root-soil stability with the increasing degree of excrement contamination. In comparison, soil pathogens were found to have the opposite trend in the scenario, further deteriorating normal soil function and system resilience. Such colonization and succession of the microbiome might provide an important potential theoretical instruction for microbiome-based soil health protection measures in the plateau of China.

Disentangling the assembly mechanisms of bacterial communities in a transition zone between the alpine steppe and alpine meadow ecosystems on the Tibetan Plateau

Alpine meadows and alpine steppes are two major grassland types distributed on the Tibetan Plateau. Due in large part to the differences in hydrothermal and nutrient conditions following the thawing of lakeshore permafrost, alpine meadows and alpine steppes which are characterized by disparate above- and below-ground biomass, could emerge together in the grassland transition zone between meadows and steppes of the Tibetan Plateau. Bacterial communities are essential components of alpine grassland ecosystems and respond rapidly to environmental changes. Despite their ecological significance, it remains poorly elucidated whether and how the assembly patterns of bacterial communities differed between alpine meadows and alpine steppes. Here, to disentangle the assembly mechanisms of bacterial communities from alpine meadows and alpine steppes, we collected samples from three diverse habitats (i.e., sediments, rhizosphere soils and bulk soils) in both alpine meadow and steppe ecosystems on the Tibetan Plateau. Our results indicated that in both meadows and steppes, rhizosphere bacterial communities exhibited higher alpha-diversity but lower beta-diversity compared to the bacterial communities in sediments and bulk soils. However, the close relationships of bacterial communities between different habitats weakened from meadows to steppes. Null model analysis indicated that the importance of environmental selection shaping bacterial community assemblages in all habitats decreased from meadows to steppes, whereas the role of dispersal limitation showed an opposite pattern. Moreover, pH was the primary driver of phylogenetic turnover of bacterial communities in the steppes across all habitats, whereas the dominant drivers of phylogenetic turnover of bacterial communities in meadows varied with habitat types. Overall, our findings provide novel insights into understanding the differences in microbial communities between meadows and steppes in the grassland transition zone on the Tibetan Plateau.

Unraveling the ecological mechanisms of bacterial succession in epiphytic biofilms on Vallisneria natans and Hydrilla verticillata during bioremediation of phenanthrene and pyrene polluted wetland

In wetland ecosystem, the microbial succession in epiphytic biofilms of submerged macrophytes remains to be fully elucidated, especially submerged macrophytes used to remediate organic pollutants contaminated sediment. Herein, 16 S rRNA gene sequencing was used to investigate the bacterial dynamics and ecological processes in the biofilms of two typical submerged macrophytes (Vallisneria natans and Hydrilla verticillata) settled in sediment polluted by polycyclic aromatic hydrocarbons (PAHs) at two growth periods. The results presented that the variations of bacterial community in the biofilms were influenced by attached surfaces (explanation ratio: 17.30%), incubation time (32.30%) and environmental factors (39.10%). Bacterial community assembly was mainly driven by dispersal limitation which triggered more positive co-occurrence associations in microbial networks, maintaining ecological stability in the process of bioremediation of PAHs. Additionally, the functional redundancy strength of bacterial community was more affected by attached surface than incubation time. The structural equation model illustrated that community assembly drove β-diversity and explained a part of ecological functions. Environmental factors, community assembly, and β-diversity jointly affected microbial networks. Overall, our study offers new insights into the microbial ecology in biofilms attached on the submerged macrophytes settled in PAH-polluted sediment, providing important information for deeply understanding submerged macrophyte-biofilm complex and promoting sustainable phytoremediation in shallow lacustrine and marshy ecosystems.

Nitrogen and carbon stable isotope analysis sheds light on trophic competition between two syntopic land iguana species from Galápagos

Coexistence between closely related species can lead to intense competition for resources. Stable isotope analysis (SIA) is a reliable tool to estimate the extent of species competition. We employed SIA to evaluate niche partitioning among two syntopic species of Galápagos land iguanas: Conolophus subcristatus and C. marthae. Samples were collected on Wolf Volcano, Isabela Island, where C. marthae is endemic and syntopic with C. subcristatus. We determined δ¹³C and δ¹⁵N ratios and described the isotopic niche of each species using corrected standard ellipse area (SEA_c). We tested for differentiation between the isotopic niches, while controlling for sex, body size, spatial location of samples and mean annual primary productivity at capture points, using bivariate linear models. Despite the extensive overlap of the isotopic niches, we found species and sex to be a significant, interacting predictor of a sample’s location in the δ¹³C, δ¹⁵N space, indicating the existence of niche partitioning mechanisms acting between species and sexes. We also found that body size and productivity at the capture points, compounded with yet undetermined spatial effects, explain ca. 75% of the differences observed between species and sexes, providing evidence for differential microhabitat and food-items usage. Our study provides essential baselines for evaluating conservation actions for C. marthae, such as the potential translocation to a sanctuary area free of competition from C. subcristatus.

Deterministic processes shape bacterial community assembly in a karst river across dry and wet seasons

Karst rivers are particularly vulnerable to bacterial pollution because immigrations are easily diffused from the surrounding environments due to their strong hydraulic connectivity. However, the assembly mechanism in shaping riverine bacterial biogeography is still poorly understood, especially for an ecosystem in the karst area. Here, 16S rRNA genes were used to explore the spatiotemporal and biogeographical patterns of bacterial communities from the Chishui River in the dry and wet seasons, and explore the impact of external immigration on the assembly of water bacterial communities. Our results showed clear spatiotemporal patterns of bacterial communities with a more pronounced seasonal rather than spatial fluctuation, which appeared to be dependent on seasonal-related environmental factors (e.g., temperature and turbidity). The bacterial communities exhibited a significant (p < 0.05) distance–decay pattern in both seasons, and they had a stronger distance–decay relationship in the dry season than in the wet season. However, most of the biomarkers of different external immigrations did not show significant (p > 0.05) distance–decay patterns along the Chishui river, implying that the biomarkers could be used as indicators of external immigration (e.g., OTU_125 and OTU_536). Also, the tributaries were the main external immigration (20.44–83.68%) for the Chishui River, while other terrestrial immigration (e.g., livestock, the soil of the cropland, brewing wastewater treatment plant, and sewages) showed relatively little influence, which could be due to the hydrodynamic conditions (e.g., fragile rock–soil system and hydrological structure) of the karst river. Additionally, the assembly of water bacterial communities in the Chishui river was governed by more determinism (50.7–85.7%) than stochasticity (14.3–49.3%) in both the dry and wet seasons. We demonstrated that the bacterial community’s substantial variations are largely shaped by deterministic processes, thereby providing a better understanding of spatiotemporal patterns and mechanisms of the bacterial community in karst river waters.

Intraspecies characterization of bacteria via evolutionary modeling of protein domains

The ability to detect and characterize bacteria within a biological sample is crucial for the monitoring of infections and epidemics, as well as for the study of human health and its relationship with commensal microorganisms. To this aim, a commonly used technique is the 16S rRNA gene targeted sequencing. PCR-amplified 16S sequences derived from the sample of interest are usually clustered into the so-called Operational Taxonomic Units (OTUs) based on pairwise similarities. Then, representative OTU sequences are compared with reference (human-made) databases to derive their phylogeny and taxonomic classification. Here, we propose a new reference-free approach to define the phylogenetic distance between bacteria based on protein domains, which are the evolving units of proteins. We extract the protein domain profiles of 3368 bacterial genomes and we use an ecological approach to model their Relative Species Abundance distribution. Based on the model parameters, we then derive a new measurement of phylogenetic distance. Finally, we show that such model-based distance is capable of detecting differences between bacteria in cases in which the 16S rRNA-based method fails, providing a possibly complementary approach , which is particularly promising for the analysis of bacterial populations measured by shotgun sequencing.

Making the competitive exclusion principle operational at the biogeographical scale using fuzzy logic

In biogeography the competitive exclusion principle (CEP) has been confirmed in some cases but not in others. This has fueled an unresolved debate between those advocating niche theory or the neutral theory in biodiversity and biogeography. We suggest that this situation mainly arises from the use of crisp logic, where the CEP is defined as either completely true or false. We propose the application of the fuzzy concepts of favorability (the degree to which environmental conditions are propitious for the occurrence of individual species) and favorableness (the degree to which environmental conditions are simultaneously favorable for competing species) to operationalize a fuzzy version of the CEP. Favorability was obtained by performing species distribution models applying favorability functions, while favorableness was derived from the application of the fuzzy intersection between the favorability for competing species. Then we plotted individual favorability values along the gradient of favorableness. Two potentially competing species would coexist in high-favorableness locations, as the demands of both species would be well fulfilled. In locations of low favorableness, the result would be either autecological exclusion of both species or autecological segregation, as abiotic conditions are unfavorable for at least one of the species. Competitive exclusion would occur at the intermediate stretch of the favorableness gradient, as the conditions would be good enough for persistence of each species separately but not enough for permanent coexistence. According to this theoretical framework, the observed probability that a location belongs to the intermediate favorableness area given that the two species co-occur in this location should be lower than expected according to the environmental probability models for the two species. We tested this prediction on published data about the distribution of pairs of native and introduced deer species in Great Britain, using a Bayesian approach. In two thirds of comparisons between a native and an introduced deer species the predictions of the fuzzy CEP were corroborated, which suggests that these are the pairs of species and the specific geographical areas affected by competitive exclusion. This is important both theoretically and for biodiversity conservation planning.

Complex and unexpected outcomes of antibiotic therapy against a polymicrobial infection

Antibiotics are our primary approach to treating complex infections, yet we have a poor understanding of how these drugs affect microbial communities. To better understand antimicrobial effects on host-associated microbial communities we treated cultured sputum microbiomes from people with cystic fibrosis (pwCF, n = 24) with 11 different antibiotics, supported by theoretical and mathematical modeling-based predictions in a mucus-plugged bronchiole microcosm. Treatment outcomes we identified in vitro that were predicted in silico were: 1) community death, 2) community resistance, 3) pathogen killing, and 4) fermenter killing. However, two outcomes that were not predicted when antibiotics were applied were 5) community profile shifts with little change in total bacterial load (TBL), and 6) increases in TBL. The latter outcome was observed in 17.8% of samples with a TBL increase of greater than 20% and 6.8% of samples with an increase greater than 40%, demonstrating significant increases in community carrying capacity in the presence of an antibiotic. An iteration of the mathematical model showed that TBL increase was due to antibiotic-mediated release of pH-dependent inhibition of pathogens by anaerobe fermentation. These dynamics were verified in vitro when killing of fermenters resulted in a higher community carrying capacity compared to a no antibiotic control. Metagenomic sequencing of sputum samples during antibiotic therapy revealed similar dynamics in clinical samples. This study shows that the complex microbial ecology dictates the outcomes of antibiotic therapy against a polymicrobial infection.

Biogeography of terrestrial vertebrates and its conservation implications in a transitional region in western Mexico

Conservation biogeography, which applies principles, theories, and analyses of biodiversity distribution patterns to address conservation challenges, can provide valuable insight and guidance to policy making for protection of biodiversity at multiple scales. The temperate and tropical ecosystems of the Nearctic-Neotropical transition in the small western state of Colima, Mexico, support a mosaic of remarkably diverse fauna and flora and provide a rare opportunity to determine spatial distribution patterns of terrestrial vertebrate species, assess human-induced threats, and identify potential conservation strategies. We analyzed the spatial distribution patterns and correlated them with the current land cover and extent of the protected areas. Despite its limited geographic extension, 29% (866) of all vertebrates, and almost a quarter of both endemic and threatened species in Mexico, live in Colima. Our analysis identified clear high-richness concentration sites (i.e., “hotspots”) coincident for all groups and that elevation and both temperate and tropical ecosystems composition exert significant influence on richness patterns. Furthermore, current species´ distribution also showed significant correlation with natural and disturbed landcover. Significant hotspots for all species groups coincided poorly with the limited protected areas in the state (only 3.8%). The current state of natural land cover (less than 16%) in the state, coupled with its remarkable biological importance, highlights the need for further complementary conservation efforts including expansion and creation of new protected areas, significant restoration efforts and other conservation measures to maintain this uniquely biogeographic and biological diverse region of the country.