Community assembly and metaphylogeography of soil biodiversity: Insights from haplotype-level community DNA metabarcoding within an oceanic island.

The mechanisms of community assembly are a central focus in the field of microbial ecology. However, to what extent these mechanisms differ in importance by traits of groups is poorly understood. Here we quantified the importance of neutral and niche processes in community assembly for bacteria, habitat specialists and generalists in 21 plateau lakes of China. Results showed that both neutral and niche processes played a critical role in the assembly of entire bacterial communities, shaping a unique biogeographical pattern. A few habitat generalists and many specialists were identified. Interestingly, habitat specialists were only governed by niche process, with seven significant environmental variables-salinity, dissolved oxygen, water transparency, total phosphorus, ammonium-nitrogen, temperature and total nitrogen-independently explaining 40.3% of the biological variation. By contrast, habitat generalists were strongly driven by neutral process, with 50.9% of the variation of detection frequency explained in neutral community model. Only three environmental variables-salinity, total nitrogen and dissolved oxygen-significantly affected the distribution of habitat generalists, independently explaining 13.6% of the variation. Governed by different assembly mechanisms, habitat specialists and generalists presented disparate biogeographical patterns. Our result emphasizes the importance of investigating the bacterial community assembly at more refined levels than entire communities.

Inferring microbial community assembly in an urban river basin through geo-multi-omics and phylogenetic bin-based null-model analysis of surface water

Ecological specialization is an important mechanism enhancing species coexistence within a given community. Yet, unravelling the effect of multiple selective evolutionary and ecological factors leading the process of specialization remains a key challenge in ecology. Subterranean habitats provide highly replicated experimental arenas in which to disentangle the relative contribution of evolutionary history (convergent evolution vs. character displacement) and ecological setting (environmental filtering vs. competitive exclusion) in driving community assembly. We tested alternative hypotheses about the emergence of ecological specialization using the radiation of a lineage of sheet‐weaver cave‐dwelling spiders as model system. We observed that at the local scale, a differential specialization to cave microhabitats generally parallels moderate levels of morphological similarity and close phylogenetic relatedness among species. Conversely, geographic distance contributed little in explaining microhabitat occupation, possibly mirroring a limited role of competitive exclusion. Yet, compared to non‐coexisting species, co‐occurring species adapted to different microhabitats showed lower morphological niche overlap (i.e. higher dissimilarity) and deeper genetic distance. The framework here developed suggests that in the subterranean domain, habitat specialization is primarily driven by environmental filtering, secondarily by convergent evolution, and only marginally by character displacement or competitive exclusion. This pattern results in the establishment of replicated communities across geographical space, composed by ecologically equivalent species. Such process of community assembly well explains the numerous adaptive radiations observed in subterranean habitats, an eco‐evolutionary pattern well documented in oceanic islands or mountain summit communities. A free Plain Language Summary can be found within the Supporting Information of this article.

Using individual-based modeling to understand grassland diversity and resilience in the Anthropocene

BackgroundPrevious studies have found that coastal eutrophication increases the influence of homogeneous selection on bacterial community assembly. However, whether seasonal changes affect the dominance of homogenous selection in bacterial community assembly in eutrophic bays remains unclear. Sansha Bay is an enclosed bay with ongoing eutrophication, located in the southeast coast of China. We investigated the bacterial community composition at two depths of the enclosed bay across seasons and the seasonal variation in community assembly processes.ResultsDiversity analyses revealed that the bacterial community composition among seasons differed significantly. By contrast, there was little difference in the community composition between the two depths. The temperature was the key environmental factor influencing the community composition. The null model indicated that the relative importance of homogeneous selection decreased in the following order: spring > winter > autumn > summer. Homogeneous selection did not always dominate the community assembly among seasons in the eutrophic bay. The effects of pure spatial variables on the community assembly were prominent in autumn and winter.ConclusionsOur results showed the seasonal influence of eutrophication on bacterial community diversity. The seasonal variation in composition and structure of bacterial communities eclipsed the vertical variability. Eutrophication could enhance the importance of homogeneous selection in the assembly processes, but the seasonal environmental differences interfered with the steady-state maintained by ongoing eutrophication and changed the community assembly processes. Homogeneous selection was not always important in bacterial community in the eutrophic enclosed bay. The bacterial community was the most complex in summer, because the composition differed from other seasons, and the assembly process was the most intricate. These findings have contributed to understanding bacterial community composition and assembly processes in eutrophic coastal ecosystems.

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.

ABSTRACTRecent studies have highlighted the significant role of tree species' mycorrhizal traits on forest soil microbial communities and their associated ecosystem functions. However, our understanding of how tree species richness in mono‐mycorrhizal (arbuscular mycorrhiza [AM] or ectomycorrhiza [EcM]) or mixed‐mycorrhizal (AM and EcM = AE) stands affects the rooting zone microbial community assembly processes remains limited. We investigated this knowledge gap using the MyDiv tree diversity experiment, which comprises plantings of AM and EcM tree species and their mixture in one‐, two‐, and four‐species plots. Soil microbiomes in the target tree rooting zone were analyzed using meta‐barcoding of the fungal ITS2 and bacterial 16S V4 rRNA regions. We examined the effects of plot mycorrhizal type, tree species identity and richness on microbial diversity, community composition, and microbial community assembly processes. We found that AM plots exhibited higher fungal richness compared to EcM and mixed mycorrhizal type (AE) plots, whereas tree species identity and diversity showed no significant impact on fungal and bacterial alpha diversity within mono and mixed mycorrhizal type plots. The soil fungal community composition was shaped by tree species identity, tree diversity, and plot mycorrhizal type, while bacterial community composition was only affected by tree species identity. EcM tree species significantly impacted both soil fungal and bacterial community compositions. Plot mycorrhizal type and tree species richness displayed interactive effects on the fungal and bacterial community composition, with AM and EcM plots displaying contrasting patterns as tree diversity increased. Our results suggest that both stochastic and deterministic processes shape microbial community assemblage in mono and mixed mycorrhizal type tree communities. The importance of deterministic processes decreases from AM to EcM plots primarily due to homogeneous selection, while stochastic processes increase, mainly due to dispersal limitation. Stochastic processes affected fungal and bacterial community assembly differently, through dispersal limitation and homogenous dispersal, respectively. In fungi, the core, intermediate and rare abundance fungal taxa were mainly controlled by both stochastic and deterministic processes whereas bacterial communities were dominantly shaped by stochastic processes. These findings provide valuable insights into the role of tree species identity, diversity and mycorrhizal type mixture on the soil microbiome community composition and assembly processes, highlighting the differential impacts on core and rare microbial taxa. Understanding the balance between deterministic and stochastic processes can help forest ecosystem management by predicting microbial community responses to land‐use and environmental changes and influencing ecosystem functions critical for ecosystem health and productivity.

Dominant ecological processes and plant functional strategies change during the succession of a subtropical forest

Trait-based approaches present a promising avenue for improving our understanding of species coexistence and community assembly, while intraspecific trait variation (ITV) across different spatial scales is important in trait-based community assembly mechanisms, especially in extreme environments. In this study, we focused on the functional diversity and community assembly patterns of a desert community across different spatial scales and investigated whether ITV plays a significant role in community assembly processes in arid habitats. A 50 m × 50 m plot with different small quadrats was established in a typical desert community at the transition zone between the Tengger Desert and Loess Plateau in China. A total of 14 traits were selected to assess the trait-based functional diversity and assembly processes in the community. We found that functional diversity showed different patterns when considering ITV and related to different types of traits (chemical traits or morphological traits) and some soil factors (pH and nitrate nitrogen). Plant communities in this study showed stochastic distribution patterns and similar functional diversity patterns based on functional trait approaches, regardless of spatial scales. Also, the effect of ITV on community assembly did not show more effect with increasing scales. These results indicated that ITV diluted deterministic processes in community assembly across scales in arid habitats.

QuestionsSmall islands are outstanding model systems to study community assembly. Due to harsher environmental conditions on smaller islands compared to larger ones, environmental filtering may preclude some species, potentially resulting in island size‐dependent species pools. We tested whether the species pool size follows a similar species–area relationship as the observed richness. This can provide new insight into community assembly processes and the elusive small‐island effect (SIE), which states that species richness on smaller islands is less dependent on area than on larger islands.LocationRaja Ampat Archipelago, Indonesia.MethodsWe studied the woody vegetation on sixty small islands ranging from 3 m2 to 11,806 m2. For each recorded species, we estimated its area requirements and compared them against random colonization models. We developed a novel method to calculate probabilistic species pools for each island. We compared different species–area models for observed species richness and our index of species pool size to test whether the SIE results from differences in species pool size.ResultsWe found that most species were restricted to islands significantly larger than expected from random colonization. The occurrence probability of all species increased with island size, indicating a lack of species that are specialized to the conditions on small islands. We found a SIE in observed species richness, but not in species pool size.ConclusionWoody plants in the studied island system have specific requirements that are linked to island area and determine island‐specific species pools. Lower community completeness on smaller islands compared to larger ones indicated that the SIE is shaped by local limiting processes that have no impact on the species pool, but control how much of it is realized on an island. Together, these results clearly indicate non‐random plant community assembly on small islands.

Mulching drive changes in soil microbial community assembly processes and networks across aggregate fractions

QuestionsHow does the response to environmental filters change across the life cycle of pioneer plants through the early process of community assembly? Is there a threshold at any of the life‐history stages during roadcut primary colonization?LocationA very steep, sun‐exposed, low‐fertility and low water retention roadcut in a Mediterranean continental site in Madrid, central Spain.MethodsWe tracked density of individuals, plant cover, species richness and community composition throughout the sequential process of primary colonization of a newly‐exposed roadcut surface. We monitored from seed arrival to seedling emergence, seedling survival and plant growth across species over two growing seasons. We manipulated the intensity of environmental filters in 12 experimental plots (10 × 8 m) following a full‐factorial design of two treatments (topsoil spreading and shallow tillage).ResultsThe response to environmental filter manipulation varied throughout the individual life cycle. Under an equal seed rain, the higher carrying capacity caused by topsoil spreading gave rise to the emergence of a larger number of species, which either persisted or occasionally appeared in some of the stages of the early community assembly. Further, topsoil spreading enhanced seedling survival across species, as well as subsequent plant growth. We therefore detected two life‐history stages acting as thresholds in plant community assembly due to an ontogenetic niche shift across species. The first, at seedling emergence, in response to environmental cues with lasting consequences in community composition and species richness; and the second, at the transition to the adult stage in response to local resource availability, with consequences in subsequent plant growth and community cover.ConclusionsDuring primary colonization, ontogenetic development of pioneers was paralleled by the action of environmental filters throughout the community assembly process. On roadcuts, the confluence of both processes gives rise to a community ontogeny marked by two thresholds determining community richness and cover under Mediterranean conditions. Our findings shed light on the underlying mechanisms involved in technical solutions, such as topsoil spreading, and provide a more efficient approach to roadside restoration.

The effect of founders (the potential influence of initially colonizing species on the composition, functionality, and stability of communities) plays a crucial role in community assembly; many experimental studies on priority effects or artificially assembled species have suggested the existence of this effect, but direct experimental evidence at the community level remains limited. This study used sterilized and nonsterilized paocai soup (a traditional Chinese fermented vegetable soup) from the same source to simulate initial environments with and without founders. These were placed in beakers with varying opening sizes on an open rooftop for 15 days to explore the impact of founders on community assembly under different dispersal intensities. The 16S rRNA sequencing analysis revealed that communities with founders exhibited lower species richness (320) compared to communities without founders (645). Additionally, communities with founders showed reduced species turnover and richness variation (53.7%) compared to communities without founders (60.9%). Furthermore, the average variability degree (AVD) in communities with founders (0.446 ± 0.044) was significantly lower than in communities without founders (0.927 ± 0.466), indicating higher community stability. Finally, deterministic processes dominated communities with founders (with heterogeneous selection contributing 70%), whereas stochastic processes primarily governed communities without founders (homogeneous dispersal 10% and undominated processes 70%). These findings demonstrate that founderspresence reduces dispersal impacts, decreases community diversity, enhances stability, and deterministic processes. The effect of founders fundamentally shapes the direction of community assembly. This study helps further understanding of how founders influence biodiversity maintenance and community assembly processes.

Lentic systems are often small experiencing the wide range of consequences of climate change through shifts in chemistry and community assembly processes. Such vulnerable systems support a majority of regional freshwater biodiversity in the Finnish subarctic, highlighting their conservational value. Despite increasing research of subarctic freshwater diatoms focusing on the relationship between biodiversity and various factors, the effect of habitat size on benthic diatoms remains understudied. This study compared diatom diversity and water chemistry between and within subarctic lentic systems. Significant differences in species richness, water pH, conductivity, Ca, Cl, and Na were found between lakes and ponds but the variation within systems was insignificant. Our results suggest that there were size-dependent differences in community composition, assembly processes, and local contributions towards beta diversity. The results suggest that the different water chemistry between ponds and lakes helps shape the benthic diatom communities. Thus, surface area may be used as a proxy for water chemistry. Microhabitat abundance and environmental harshness are likely to cause such area-effects, but further investigation is required on isolation, dispersal limitations, and water depth. Studying the benthic communities of these vulnerable systems will provide insight into the effects of climate change. UNSTRUCTURED ABSTRACT Subarctic lentic systems are significantly different from each other in terms of water chemistry, which contributes to a distinct benthic diatom diversity.

QuestionsNumerous studies on community assembly processes have been conducted in natural ecosystems. However, we know little about community assembly processes in human‐dominated urban ecosystems. Here, we asked: (1) how are the composition and functional diversity of native and exotic plant species shaped by local environment and landscape factors across urban vacant lots; and (2) how is microbial (bacterial and fungal) community composition influenced by the local environment, landscape factors, and plant species composition across urban vacant lots?LocationWe investigated 69 urban vacant lots in Yokohama, Japan.MethodsBy using a variation partitioning approach, we examined the relative importance of local environmental and landscape factors (including land use and spatial structure) in explaining variation in plant species composition and functional diversity of native or exotic species. We also explored the relative importance of local environmental and landscape factors, and plant species composition in explaining variation in microbial community composition.ResultsThe spatial structure of vacant lots determined the species composition and functional diversity of plant communities, suggesting that plant community assembly is determined by dispersal limitation. However, the functional diversity of the exotic species varied randomly, which reduced the relative importance of the spatial structure of vacant lots. Plant species composition as well as the spatial structure of vacant lots were the important drivers of the composition of soil microbial communities, despite a higher proportion of unexplained variation in their composition. Finally, we found an essential contribution of earthmoving methods in explaining the variations in both plant and microbial community composition.ConclusionPlant and microbial community composition would be largely determined by dispersal limitation across urban vacant lots. Understanding urban community assembly is critical for predicting plant and microbial communities that play an essential role in regulating urban ecosystem functioning and services.