Marine Benthic Community Assembly Is Taxonomically Stochastic but Functionally Deterministic in a Dynamic Coastal Sea

BackgroundUnderstanding patterns of biodiversity is a longstanding challenge in ecology. Similar to other biotic groups, arthropod community structure can be shaped by deterministic and stochastic processes, with limited understanding of what moderates the relative influence of these processes. Disturbances have been noted to alter the relative influence of deterministic and stochastic processes on community assembly in various study systems, implicating ecological disturbances as a potential moderator of these forces.MethodsUsing a disturbance gradient along a 5-year chronosequence of insect-induced tree mortality in a subalpine forest of the southern Rocky Mountains, Colorado, USA, we examined changes in community structure and relative influences of deterministic and stochastic processes in the assembly of aboveground (surface and litter-active species) and belowground (species active in organic and mineral soil layers) arthropod communities. Arthropods were sampled for all years of the chronosequence via pitfall traps (aboveground community) and modified Winkler funnels (belowground community) and sorted to morphospecies. Community structure of both communities were assessed via comparisons of morphospecies abundance, diversity, and composition. Assembly processes were inferred from a mixture of linear models and matrix correlations testing for community associations with environmental properties, and from null-deviation models comparing observed vs. expected levels of species turnover (Beta diversity) among samples.ResultsTree mortality altered community structure in both aboveground and belowground arthropod communities, but null models suggested that aboveground communities experienced greater relative influences of deterministic processes, while the relative influence of stochastic processes increased for belowground communities. Additionally, Mantel tests and linear regression models revealed significant associations between the aboveground arthropod communities and vegetation and soil properties, but no significant association among belowground arthropod communities and environmental factors.DiscussionOur results suggest context-dependent influences of stochastic and deterministic community assembly processes across different fractions of a spatially co-occurring ground-dwelling arthropod community following disturbance. This variation in assembly may be linked to contrasting ecological strategies and dispersal rates within above- and below-ground communities. Our findings add to a growing body of evidence indicating concurrent influences of stochastic and deterministic processes in community assembly, and highlight the need to consider potential variation across different fractions of biotic communities when testing community ecology theory and considering conservation strategies.

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.

The role of deterministic and stochastic processes in community assembly is a key question in community ecology. We evaluated the effect of an abiotic filter (hydroperiod) on the partitioned diversity of three taxonomic groups (birds, vegetation, macroinvertebrates) from prairie pothole wetlands in Alberta, Canada, which naturally vary in water permanence. We observed that alpha and gamma diversity were higher in permanent than temporary wetlands (16–25% and 34–47% respectively, depending on the taxon). This suggests an influence of deterministic constraints on the number of species a wetland can support. Taxa which cannot persist in shallow, temporary wetlands are excluded by the deterministic constraints that a shortened hydroperiod imposes. In contrast, we observed that beta diversity was significantly higher (2–12%) in temporary wetlands than permanent ones, and temporary wetlands supported more unique combinations of community composition than permanent wetlands, despite having a smaller regional species pool. This observation contradicts prior mesocosm studies that found beta diversity mirrored the pattern in gamma diversity along an environmental filtering gradient. We conclude that deterministic processes are more influential in more stable permanent wetlands, whereas stochastic processes play a more important role in assembly in dynamic temporary wetlands that must disassemble and re‐establish annually. Considering three distinct taxonomic groups differing in their relative mobility, our large‐scale field study demonstrates that both stochastic and deterministic processes act together to influence the assembly of multiple communities and that the relative importance of the two processes varies consistently along a gradient of environmental filtering.

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

AimMountains are biodiversity hotspots and are among the most sensitive ecosystems to ongoing global change being thus of conservation concern. Under this scenario, assessing how biological communities vary over time along elevational gradients and the relative effects of niche‐based deterministic processes and stochastic events in structuring assemblages is essential. Here, we examined how the temporal trends of bird communities vary with elevation over a 20 year‐period (1999–2018). We also tested for differences in temporal dynamics among habitat types (among‐community variability) and functional groups (within‐community variability).Taxon97 species of common breeding birds.LocationSwiss Alps.MethodsWe used abundance data from the Swiss breeding bird survey to compute different temporal dynamic metrics (temporal turnover, synchrony, rate of community change and community‐level of covariance among species). We also examined the relative contribution of deterministic and stochastic processes in community assembly using the Raup‐Crick method and the normalized stochasticity ratio.ResultsWe found that, with greater elevation, temporal species turnover increased while the rate of overall community change over successive years decreased, suggesting that high‐elevation communities display more erratic dynamics with no clear trend. Despite this, we found a more deterministic assembly of alpine communities in comparison to those located at lower elevations. Deterministic processes had greater influence than stochastic processes on community assembly along the entire elevational gradient (80% of communities). Forest communities exhibited higher synchrony in comparison to the remaining habitats likely because they consisted of species with greater functional redundancy, whereas alpine communities were the least stable as a result of their low taxonomic richness (‘portfolio’ effect).Main conclusionsCommunity‐level synchrony was overall positive supporting the idea that compensatory mechanisms are rare in natural biological communities. Our results suggest that rather than competition, the existence of differences in the ecological strategies of species may have a stabilizing effect on bird communities by weakening the concordance of species responses to fluctuations in environmental conditions (i.e. enhanced interspecific temporal asynchrony). This study provides evidence that, although species turnover in metacommunities is frequent, a high temporal turnover does not necessarily imply the overriding importance of stochastic processes.

Background. Understanding patterns of biodiversity is a longstanding challenge in ecology. Similar to other biotic groups, arthropod community structure can be shaped by deterministic and stochastic processes, with limited understanding of what moderates the relative influence of these processes. Disturbances have been noted to alter the relative influence of deterministic and stochastic processes on community assembly in various study systems, implicating ecological disturbances as a potential moderator of these forces. Methods. Using a disturbance gradient along a 5-year chronosequence of insect-induced tree mortality in a subalpine forest of the southern Rocky Mountains, Colorado, USA, we examined changes in community structure and relative influences of deterministic and stochastic processes in the assembly of aboveground (surface and litter-active species) and belowground (species active in organic and mineral soil layers) arthropod communities. Arthropods were sampled for all years of the chronosequence via pitfall traps (aboveground community) and modified Winkler funnels (belowground community) and sorted to morphospecies. Community structure of both communities were assessed via comparisons of morphospecies diversity and assemblages. Assembly processes were inferred from a mixture of linear models and matrix correlations testing for community associations with environmental properties, and from null-deviation models calculated from observed vs. expected levels of species turnover (Beta diversity) among samples. Results. Tree mortality altered community structure in both aboveground and belowground arthropod communities, but null models suggested that aboveground communities experienced greater relative influences of deterministic processes, while the relative influence of stochastic processes increased for belowground communities. Additionally, Mantel tests and linear regression models revealed significant associations between the aboveground arthropod communities and vegetation and soil properties, but no significant association among belowground arthropod communities and environmental factors. Discussion. Our results suggest context-dependent influences of stochastic and deterministic community assembly processes across different fractions of a ground-dwelling arthropod community following a disturbance. This variation in assembly may be linked to contrasting ecological strategies and dispersal rates within above- and below-ground communities. Our findings add to a growing body of evidence indicating concurrent influences of different processes in community assembly, and highlight the need to consider potential variation across different fractions of biotic communities when testing community ecology theory.

Successional dynamics in plant community assembly may result from both deterministic and stochastic ecological processes. The relative importance of different ecological processes is expected to vary over the successional sequence, between different plant functional groups, and with the disturbance levels and land-use management regimes of the successional systems. We evaluate the relative importance of stochastic and deterministic processes in bryophyte and vascular plant community assembly after fire in grazed and ungrazed anthropogenic coastal heathlands in Northern Europe. A replicated series of post-fire successions (n=12) were initiated under grazed and ungrazed conditions, and vegetation data were recorded in permanent plots over 13years. We used redundancy analysis (RDA) to test for deterministic successional patterns in species composition repeated across the replicate successional series and analyses of co-occurrence to evaluate to what extent species respond synchronously along the successional gradient. Change in species co-occurrences over succession indicates stochastic successional dynamics at the species level (i.e., species equivalence), whereas constancy in co-occurrence indicates deterministic dynamics (successional niche differentiation). The RDA shows high and deterministic vascular plant community compositional change, especially early in succession. Co-occurrence analyses indicate stochastic species-level dynamics the first two years, which then give way to more deterministic replacements. Grazed and ungrazed successions are similar, but the early stage stochasticity is higher in ungrazed areas. Bryophyte communities in ungrazed successions resemble vascular plant communities. In contrast, bryophytes in grazed successions showed consistently high stochasticity and low determinism in both community composition and species co-occurrence. In conclusion, stochastic and individualistic species responses early in succession give way to more niche-driven dynamics in later successional stages. Grazing reduces predictability in both successional trends and species-level dynamics, especially in plant functional groups that are not well adapted to disturbance.

ABSTRACTComplete ammonia oxidizers (comammox) have been widely detected in riverine and estuarine ecosystems. However, knowledge about the process of comammox community assembly from freshwater to marine environments is still limited. Here, based on deep sequencing, we investigated the community composition of comammox along a salinity gradient in the Pearl River Estuary (PRE), South China. Our results showed that comammox microorganisms in the PRE sediments were extremely diverse and displayed distinct distributional patterns between upstream and downstream habitats. Quantitative PCR demonstrated that comammox was the dominant ammonia-oxidizing microorganism (AOM) in the PRE upstream sediments, and ammonia-oxidizing archaea (AOA) dominated the PRE downstream sediments, while ammonia-oxidizing bacteria (AOB) were not dominant in any section of the PRE. Neutral modeling revealed that stochastic processes explained a limited part of the variation in the comammox community. The majority of beta nearest-taxon index values were higher than 2, indicating that comammox community assembly in the PRE sediments was better explained through a deterministic process than through a stochastic process. Salinity and total nitrogen were the most important contributing factors that shaped the comammox community. This study expanded the current knowledge of the diversity and niche preference of comammox in the estuarine ecosystem, and further enhances our understanding of the assembly of comammox community from freshwater to marine environments.IMPORTANCE Microbial communities are shaped by stochastic (emigration, immigration, birth, death, and genetic drift of species) and deterministic (e.g., environmental factors) processes. However, it remains unknown as to which type of process is more important in influencing the comammox community assembly from freshwater to marine environments. In this study, we compared the relative importance of stochastic and deterministic processes in shaping the assembly of the comammox community, which demonstrated that the deterministic process was more important in determining the community assembly patterns in the PRE ecosystem.

ABSTRACTBackground: Tropical sand dunes are ideal systems for understanding drivers of community assembly as dunes are subject to both deterministic and stochastic processes. However, studies that evaluate the factors that mediate plant community assembly in these ecosystems are few.Aims: We evaluated phylogenetic community structure to elucidate the role of deterministic and stochastic processes in mediating the assembly of plant communities along the north of the Yucatan Peninsula, Mexico.Methods: We used plastid genetic markers to evaluate phylogenetic relationships in 16 sand-dune communities. To evaluate the role of climate in shaping plant community structure we carried out linear regressions between climatic variables and mean phylogenetic distance. We estimated the Net Relatedness Index and Nearest Taxon Index to identify ecological processes mediating community assembly.Results: Observed phylogenetic structure was not different from random, suggesting that stochastic processes are the major determinants of community assembly. Climate was slightly correlated with phylogenetic diversity suggesting that abiotic environment plays a minimal role in community assembly.Conclusions: Random assembly appears to be the primary factor structuring the studied sand dune plant communities. Environmental filters may represent a secondary factor contributing to the observed phylogenetic structure. Thus, both processes may act simultaneously to mediate the assembly of sand-dune plant communities.

Studies have revealed extensive taxonomic classifications and patterns of gut microbial diversity in snails, with limited focus on community assembly processes. To better understand the balance between stochastic and deterministic processes in the snail gut microbial assembly and their associations with snail fitness, we used the freshwater snail Biomphalaria straminea as a model and analyzed the gut bacterial communities from 118 samples via high-throughput sequencing of the 16S rRNA gene. This study reveals that Proteobacteria and Bacteroidota dominate the gut microbiota of B. straminea. Snails from different laboratory habitats exhibit similar gut bacterial diversity but significantly different community structures. The assembly of gut bacterial communities in both laboratory and wild samples is predominantly influenced by stochastic processes rather than deterministic processes, as evidenced by the neutral community model (NCM). Furthermore, during the snail invasion and adaptation to a new environment, stochastic processes are more crucial than deterministic ones in shaping the snail gut microbiota. This indicates that the interplay between stochastic and deterministic processes in the snail gut microbial assembly is associated with host fitness during snail adaptation to a new environment. Based on the null model analysis, we also found that stochastic processes (based on dispersal limitation, homogenizing dispersal, and undominated processes) play a larger role than deterministic (based on homogeneous selection and variable selection) in driving the snail gut bacterial community assembly. Furthermore, the significant difference in the proportions of dispersal limitation and undominated processes is linked to both adaptive and non-adaptive snails. This study demonstrates that stochastic processes govern the assembly of the gut microbiota in B. straminea. Furthermore, snail adaptation is associated with the interplay between stochastic and deterministic processes in gut microbial composition. This study provides a better understanding of the dynamic patterns of the gut microbial community in freshwater gastropods and may contribute to the development of strategies for controlling intermediate hosts and schistosomiasis.

Assessing the relative contributions of the interacting deterministic and stochastic ecological processes for phytoplankton community assembly is crucial in understanding and predicting community organization and succession at different temporal and spatial scales. In this study, we hypothesized that deterministic and stochastic ecological processes regulating phytoplankton, present seasonal and repeating patterns. This hypothesis was explored during a 5-year survey (287 samples) conducted at a small spatial scale (~15km) in a temperate coastal ecosystem (eastern English Channel). Microscopy and flow cytometry quantified phytoplankton abundance and biomass, while metabarcoding data allowed an extended evaluation of diversity and the exploration of the ecological processes regulating phytoplankton using null model analysis. Alpha diversity of phytoplankton was governed by the effect of environmental conditions (environmental filtering). Temporal community turnover (beta diversity) evidenced a consistent interannual pattern that determined the phytoplankton seasonal structure. In winter and early spring (from January to March), determinism (homogeneous selection) was the major process in the phytoplankton community assembly. The overall mean in the year was 38%. Stochastic processes (ecological drift) prevailed during the rest of the year from April to December, where the overall mean for the year was 55%. The maximum values were recorded in late spring and summer, which often presented recurrent and transient monospecific phytoplankton peaks. Overall, the prevalence of stochastic processes rendered less predictable seasonal dynamics of phytoplankton communities to future environmental change. IMPORTANCE While ecological deterministic processes are conducive to modeling, stochastic ones are far less predictable. Understanding the overall assembly processes of phytoplankton is critical in tracking and predicting future changes. The novelty of this study was that it addressed a long-posed question, on a pluriannual scale. Was seasonal phytoplankton succession influenced by deterministic processes (e.g., abiotic environment) or by stochastic ones (e.g., dispersal, or ecological drift)? Our results provided strong support for a seasonal and repeating pattern with stochastic processes (drift) prevailing during most of the year and periods with monospecific phytoplankton peaks.

Community assembly processes are complex and understanding them represents a challenge in microbial ecology. Here, we used Lascaux Cave as a stable, confined environment to quantify the importance of stochastic vs deterministic processes during microbial community dynamics across the three domains of life in relation to an anthropogenic disturbance that had resulted in the side-by-side occurrence of a resistant community (unstained limestone), an impacted community (present in black stains), and a resilient community (attenuated stains). Metabarcoding data showed that the microbial communities of attenuated stains, black stains, and unstained surfaces differed, with attenuated stains being in an intermediate position. We found four scenarios to explain community response to disturbance in stable conditions for the three domains of life. Specifically, we proposed the existence of a fourth, not-documented yet scenario that concerns the always-rare microbial taxa, where stochastic processes predominate even after disturbance but are replaced by deterministic processes during post-disturbance recovery. This suggests a major role of always-rare taxa in resilience, perhaps because they might provide key functions required for ecosystem recovery.IMPORTANCEThe importance of stochastic vs deterministic processes in cave microbial ecology has been a neglected topic so far, and this work provided an opportunity to do so in a context related to the dynamics of black-stain alterations in Lascaux, a UNESCO Paleolithic cave. Of particular significance was the discovery of a novel scenario for always-rare microbial taxa in relation to disturbance, in which stochastic processes are replaced later by deterministic processes during post-disturbance recovery, i.e., during attenuation of black stains.

Despite the importance of wood-inhabiting fungi on nutrient cycling and ecosystem functions, their ecology, especially related to their community assembly, is still highly unexplored. In this study, we analyzed the wood-inhabiting fungal richness, community composition, and phylogenetics using PacBio sequencing. Opposite to what has been expected that deterministic processes especially environmental filtering through wood-physicochemical properties controls the community assembly of wood-inhabiting fungal communities, here we showed that both deterministic and stochastic processes can highly contribute to the community assembly processes of wood-inhabiting fungi in this tropical forest. We demonstrated that the dynamics of stochastic and deterministic processes varied with wood decomposition stages. The initial stage was mainly governed by a deterministic process (homogenous selection), whereas the early and later decomposition stages were governed by the stochastic processes (ecological drift). Deterministic processes were highly contributed by wood physicochemical properties (especially macronutrients and hemicellulose) rather than soil physicochemical factors. We elucidated that fine-scale fungal-fungal interactions, especially the network topology, modularity, and keystone taxa of wood-inhabiting fungal communities, strongly differed in an initial and decomposing deadwood. This current study contributes to a better understanding of the ecological processes of wood-inhabiting fungi in tropical regions where the knowledge of wood-inhabiting fungi is highly limited.

Microbial community assembly is influenced by a continuum (actually the trade-off) between deterministic and stochastic processes. An understanding of this ecological continuum is of great significance for drawing inferences about the effects of community assembly processes on microbial community structure and function. Here, we investigated the driving forces of soil microbial community assembly in three different environmental contexts located on subalpine coniferous forests of the Loess Plateau in Shanxi, China. The variation in null deviations and phylogenetic analysis showed that a continuum existed between deterministic and stochastic processes in shaping the microbial community structure, but deterministic processes prevailed. By integrating the results of redundancy analysis (RDA), multiple regression tree (MRT) analysis and correlation analysis, we found that soil organic carbon (SOC) was the main driver of the community structure and diversity patterns. In addition, we also found that SOC had a great influence on the community assembly processes. In conclusion, our results show that deterministic processes always dominated assembly processes in shaping bacterial community structure along the three habitat contexts.

Both bottom-up (e.g., nutrients) and top-down (e.g., herbivory) forces structure plant communities, but it remains unclear how they affect the relative importance of stochastic and deterministic processes in plant community assembly. Moreover, different-sized herbivores have been shown to have contrasting effects on community structure and function, but their effects on the processes governing community assembly (i.e., how they generate the impacts on structure) remain largely unknown. We evaluated the influence of bottom-up and top-down forces on the relative importance of deterministic and stochastic processes during plant community assembly. We used the data of a 7-yr factorial experiment manipulating nutrient availability (ambient and increased) and the presence of vertebrate herbivores (>1kg) of different body size in a floodplain grassland in The Netherlands. We used a null model that describes a community composition expected by chance (i.e., stochastic assembly) and compared the plant community composition in the different treatments with this null model (the larger the difference, the more deterministically assembled). Our results showed that herbivore exclusion promoted a more stochastic plant community assembly, whereas increased nutrients played a relatively minor role in determining the relative importance of stochasticity in community assembly. Large herbivores facilitated intermediate-sized mammal herbivores, resulting in synergistic effects of enhanced grazing pressure and a more deterministic and convergent plant community assembly. We conclude that herbivores can act as strong deterministic forces during community assembly in natural systems. Our results also reveal that although large- and intermediate-sized mammal herbivores often have contrasting effects on many community and ecosystem properties, they can also synergistically homogenize plant communities.