Changes In Assembly Processes Research Articles

Changes in assembly processes and differential responses of soil microbial communities during mining disturbance in mining reclamation and surrounding grassland

Soil microbes play critical roles in regulating ecosystem-level functioning and responding to environmental changes after disturbance events. However, a systematic understanding of soil microbial community assembly processes and responses in the context of severe anthropogenic disturbance remains lacking. Here, microbial communities collected from the soil in the mining reclamation and surrounding grassland of the Baiyinhua #1 open-pit coal mine were profiled and compared by three-generation PacBio sequencing to identify the response characteristics of the soil microbial communities to mining-induced disturbance, microbial community assembly and their relevance to environmental variables. The results suggested that the five locations surveyed had heterogeneous microbial community structures, distribution patterns and network topological characteristics, especially exhibiting contrasting differences between the mining reclamation and the grassland surrounding the mine, and different survey sites supported the enrichment of different and adaptative bacterial and fungal taxa and biomarkers. In comparison to the bacterial community, the fungal community was more susceptible to the current mining disturbances, and the stability of the core fungal interaction network, fungal diversity and resistance index were relatively low. Redundancy analysis showed that the differences in microbial communities were driven by the joint impacts of soil alkaline phosphatase and total nitrogen, and differences in bacterial communities were also driven by pH. Stochastic processes dominated the microbial assemblies at the entire site across the mining reclamation and grasslands around the coal mine, and dispersal limitation and drift were the dominant processes of the bacterial and fungal assemblies, respectively, at most individual sites. The relative influences of deterministic and stochastic processes in terms of shaping microbial community assemblies shifted with soil enzyme activity and nutrients. These findings provide critical insights into the prediction of soil ecosystem recovery after disturbance and deepen our understanding of the responses and assembly rules associated with severe anthropogenic disturbance.

Microbiome assembly predictably shapes diversity across a range of disturbance frequencies in experimental microcosms

Diversity is often implied to have a positive effect on the functional stability of ecological communities. However, its relationship with stochastic and deterministic assembly mechanisms remains largely unknown, particularly under fluctuating disturbances. Here, we subjected complex bacterial communities in microcosms to different frequencies of alteration in substrate feeding scheme, tracking temporal dynamics in their assembly, structure and function. Activated sludge bioreactors were subjected to six different frequencies of double organic loading, either never (undisturbed), every 8, 6, 4, or 2 days (intermediately disturbed), or every day (press disturbed), and operated in daily cycles for 42 days. Null modeling revealed a stronger role of stochastic assembly at intermediate disturbance frequencies, with a peak in stochasticity that preceded the occurrence of a peak in α-diversity. Communities at extreme ends of the disturbance range had the lowest α-diversity and highest within-treatment similarity in terms of β-diversity, with stronger deterministic assembly. Increased carbon removal and microbial aggregate settleability (general functions) correlated with stronger deterministic processes. In contrast, higher stochasticity correlated with higher nitrogen removal (a specialized function) only during initial successional stages at intermediate disturbance frequencies. We show that changes in assembly processes predictably precede changes in diversity under a gradient of disturbance frequencies, advancing our understanding of the mechanisms behind disturbance–diversity–function relationships.

Changes in assembly processes of soil microbial communities in forest-to-cropland conversion in Changbai Mountains, northeastern China

In response to human-induced changes in the environment, it is crucial to assess the underlying factors of the impacts of forest conversion on ecosystem function. However, research is limited on bacteria and fungi diversity, functional properties, and community assembly mechanisms in response to forest-to-cropland conversion. We categorized soil bacterial and fungal communities from primary forest, secondary forest, and cropland in Changbai Mountains, China. We found that forest-to-cropland conversion altered the structure and composition of bacterial and fungal communities and might be associated with potential changes in function. The null models indicated that the conversion from forest to cropland enhanced the bacterial dispersal limitation process and weakened the fungal dispersal limitation processes. Furthermore, ecological drift dominates the ecological processes of cropland fungi. Both edaphic properties (the content of C: N ratio, available phosphorus, nitrate) significantly impacted on soil bacterial and fungal community structures. In addition, there were significant functional variations in the fungal community between forest-to-cropland. The ectomycorrhizal and saprotrophic fungi showed increased abundance in the forest microbial communities, whereas the endophytic and pathogenic fungal abundance was increased in cropland soil. Taken together, our data illustrate the differences in the response of bacteria and fungi to forest-to-cropland conversion in temperate forest areas and deepen our understanding of the effects of forest conversion on microbial functions and community assembly processes.

Multiple-Facet Diversity Patterns of Aquatic Vegetation in Lakes along a Trophic Gradient

The EU Water Framework Directive foresees the ecological assessment of surface waters against identified pressures. Nutrient loading is the main pressure impairing the ecological quality of lake ecosystems, and aquatic macrophytes are considered good indicators of ecological response. In this study, we statistically assessed different aspects of aquatic plant (macrophyte) diversity in response to different trophic levels in Mediterranean lakes. We used 5690 relevés of aquatic vegetation, distributed over 305 transects, sampled in 18 freshwater lake ecosystems during 2013–2016. Our results show a significant decrease in taxonomic alpha diversity in lakes with a total phosphorus content above 100 μg/L. Syntaxonomic diversity followed the species richness pattern as well. Functional richness decreased along the trophic gradient, while functional dispersion was higher in lakes with high trophic levels. Taxonomic and functional beta partitioning presented changes in assembly processes leading to greater community homogeneity in lakes with higher trophic levels. In summary, we found no redundancy between taxonomic and functional diversity indices. These results provide novel insights into aquatic plant assembly processes of impacted freshwater lakes needed to forward conservation and restoration practices.

Changes in assembly processes of soil microbial communities during secondary succession in two subtropical forests

Soil microbes re-establish plant diversity and ecosystem functions after disturbance events. Deterministic and stochastic processes are expected to contribute to microbial community assembly during long-term ecosystem recovery. We characterized soil prokaryotic and fungal communities, to determine their assembly patterns, along two chronosequences with early to later successional subtropical forests. Prokaryotic and fungal community composition was more variable in early successional forests but converged in the later successional forests. The community composition was governed by deterministic processes in the early stages, while the relative influence of stochasticity increased in the later stages. Environmental factors that predicted the shift in deterministic and stochastic balance varied within and across successional stages. In particular, the compositional dissimilarity of plant communities strongly predicted the relative influences of the two processes during succession. These findings suggest that the relative influences of deterministic and stochastic processes in shaping microbial community assembly shift during secondary succession. Consequently, plant communities are important predictors of assembly processes in soil microbial communities during long-term ecosystem recovery.

Using null models to compare bacterial and microeukaryotic metacommunity assembly under shifting environmental conditions

Temporal variations in microbial metacommunity structure and assembly processes in response to shifts in environmental conditions are poorly understood. Hence, we conducted a temporal field study by sampling rock pools in four-day intervals during a 5-week period that included strong changes in environmental conditions due to intensive rain. We characterized bacterial and microeukaryote communities by 16S and 18S rRNA gene sequencing, respectively. Using a suite of null model approaches (elements of metacommunity structure, Raup-Crick beta-diversity and quantitative process estimates) to assess dynamics in community assembly, we found that strong changes in environmental conditions induced small but significant temporal changes in assembly processes and triggered different responses in bacterial and microeukaryotic metacommunities, promoting distinct selection processes. Incidence-based approaches showed that the assemblies of both communities were mainly governed by stochastic processes. In contrast, abundance-based methods indicated the dominance of historical contingency and unmeasured factors in the case of bacteria and microeukaryotes, respectively. We distinguished these processes from dispersal-related processes using additional tests. Regardless of the applied null model, our study highlights that community assembly processes are not static, and the relative importance of different assembly processes can vary under different conditions and between different microbial groups.

Changes in assembly processes in soil bacterial communities following a wildfire disturbance

Although recent work has shown that both deterministic and stochastic processes are important in structuring microbial communities, the factors that affect the relative contributions of niche and neutral processes are poorly understood. The macrobiological literature indicates that ecological disturbances can influence assembly processes. Thus, we sampled bacterial communities at 4 and 16 weeks following a wildfire and used null deviation analysis to examine the role that time since disturbance has in community assembly. Fire dramatically altered bacterial community structure and diversity as well as soil chemistry for both time-points. Community structure shifted between 4 and 16 weeks for both burned and unburned communities. Community assembly in burned sites 4 weeks after fire was significantly more stochastic than in unburned sites. After 16 weeks, however, burned communities were significantly less stochastic than unburned communities. Thus, we propose a three-phase model featuring shifts in the relative importance of niche and neutral processes as a function of time since disturbance. Because neutral processes are characterized by a decoupling between environmental parameters and community structure, we hypothesize that a better understanding of community assembly may be important in determining where and when detailed studies of community composition are valuable for predicting ecosystem function.

A guide for using functional diversity indices to reveal changes in assembly processes along ecological gradients

AbstractQuestionWhich functional diversity indices have the power to reveal changes in community assembly processes along abiotic stress gradients? Is their power affected by stochastic processes and variations in species richness along stress gradients?MethodsWe used a simple community assembly model to explore the power of functional diversity indices across a wide range of ecological contexts. The model assumes that with declining stress the influence of niche complementarity on species fitness increases while that of environmental filtering decreases. We separately incorporated two trait‐independent stochastic processes – mass and priority effects – in simulating species occurrences and abundances along a hypothetical stress gradient. We ran simulations where species richness was constant along the gradient, or increased, decreased or varied randomly with declining stress. We compared observed values for two indices of functional richness – total functional dendrogram length (FD) and convex hull volume (FRic) – with a matrix‐swap null model (yielding indices SESFD and SESFRic) to remove any trivial effects of species richness. We also compared two indices that measure both functional richness and functional divergence – Rao quadratic entropy (Rao) and functional dispersion (FDis) – with a null model that randomizes abundances across species but within communities. This converts them to pure measures of functional divergence (SESRao and SESFDis).ResultsWhen mass effects operated, only SESRao and SESFDis gave reasonable power, irrespective of how species richness varied along the stress gradient. FD, FRic, Rao and FDis had low power when species richness was constant, and variation in species richness greatly influenced their power. SESFRic and SESFD were unaffected by variation in species richness. When priority effects operated, FRic, SESFRic, Rao and FDis had good power and were unaffected by variation in species richness. Variation in species richness greatly affected FD and SESFD. SESRao and SESFDis had low power in the priority effects model but were unaffected by variation in species richness.ConclusionsOur results demonstrate that a reliable test for changes in assembly processes along stress gradients requires functional diversity indices measuring either functional richness or functional divergence. We recommend using SESFRic as a measure of functional richness and either SESRao or SESFDis (which are very closely related mathematically) as a measure of functional divergence. Used together, these indices of functional richness and functional divergence provide good power to test for increasing niche complementarity with declining stress across a broad range of ecological contexts.

Sensor-Based Artificial Skills with Force and Vision Information

To add flexibility against changes in assembly processes to a manufacturing system, we introduce artificial skills with advanced sensor-based information. Tasks are divided into a phase in local (contact) and global (noncontact) states and we developed pseudo contact point monitoring and feature-oriented coordination to achieve artificial skills for tasks in each phase. Pseudo contact point monitoring is a new technique that detects contact states by monitoring a pseudo contact point calculated from a set of observed force and moment. Effectiveness of artificial skills is shown by experimental results of stamping, bearing roller positioning, and a peg-in-hole task. Feature-oriented coordination system is a new control method that does not require prior calibration between the vision system and manipulator. We detail system possibilities and limitations with simulation.