Explore the vast range of titles available.

Ecological theory aids in understanding how disturbances affect ecosystems. However, experimental data are often complex, with multiple post‐disturbance theories potentially applying simultaneously to the same ecosystem. This emphasizes the need for tools to experimentally test these theoretical predictions. We introduce MicroEcoTools, an R package designed to test ecological framework predictions using microbial community data. It assesses microbial diversity and evaluates the relative impacts of stochastic and deterministic assembly mechanisms through a taxa‐based null model approach for replicated designs. Furthermore, the package allows application of Grime's trait‐based life‐history categories—competitor, stress‐tolerant and ruderal (CSR)—to taxa, functional traits and ecosystem functions within microbial communities. MicroEcoTools also includes relevant statistical tests, numeric simulations and publicly available datasets for demonstration. To demonstrate MicroEcoTools' functionality, we applied the package to experimental data from microcosm‐scale perturbation experiments on an activated sludge microbial ecosystem (included in the R package). This enabled us to assess assembly mechanisms and assign CSR categories. Results generated by MicroEcoTools closely aligned with previous findings from manual analysis. In conclusion, MicroEcoTools facilitates the application of ecological frameworks, including community assembly mechanisms, diversity analysis, and life‐history strategies, to microbial ecosystems under disturbance. This R package, along with its source code, can be freely accessed on GitHub at https://www.github.com/Soheil‐A‐Neshat/MicroEcoTools.

Ecosystem management must be viewed in the context of increasing frequencies and magnitudes of various disturbances that occur at different scales. This work provides a glimpse of the changes in assembly mechanisms found in microbial communities exposed to sustained changes in their environment. These mechanisms, deterministic or stochastic, can cause communities to reach a similar or variable composition and function. For a comprehensive view, we use a joint evaluation of temporal dynamics in assembly mechanisms and community structure for both bacterial taxa and their functional genes at different abundance levels, in both disturbed and undisturbed states. We further reverted the disturbance state to contrast recovery of function with community structure. Our findings are relevant, as very few studies have employed such an approach, while there is a need to assess the relative importance of assembly mechanisms for microbial communities across different spatial and temporal scales, environmental gradients, and types of disturbance. Press disturbances are of interest in microbial ecology, as they can drive microbial communities to alternative stable states. However, the effect of press disturbances in community assembly mechanisms, particularly with regard to taxa and functional genes at different levels of abundance (i.e., common and rare), remains largely unknown. Here, we tested the effect of a continuous alteration in substrate feeding scheme on the structure, function, and assembly of bacterial communities. Two sets of replicate 5-liter sequencing batch reactors were operated at two different organic carbon loads for a period of 74 days, following 53 days of acclimation after inoculation with sludge from a full-scale treatment plant. Temporal dynamics of community taxonomic and functional gene structure were derived from metagenomics and 16S rRNA gene metabarcoding data. Disturbed reactors exhibited different community function, structure, and assembly compared to undisturbed reactors. Bacterial taxa and functional genes showed dissimilar α-diversity and community assembly patterns. Deterministic assembly mechanisms were generally stronger in disturbed reactors and in common fractions compared to rare ones. Function quickly recovered after the disturbance was removed, but community structure did not. Our results highlight that functional gene data from metagenomics can indicate patterns of community assembly that differ from those obtained from taxon data. This study reveals how a joint evaluation of assembly mechanisms and community structure of bacterial taxa and functional genes as well as ecosystem function can unravel the response of complex microbial systems to a press disturbance. IMPORTANCE Ecosystem management must be viewed in the context of increasing frequencies and magnitudes of various disturbances that occur at different scales. This work provides a glimpse of the changes in assembly mechanisms found in microbial communities exposed to sustained changes in their environment. These mechanisms, deterministic or stochastic, can cause communities to reach a similar or variable composition and function. For a comprehensive view, we use a joint evaluation of temporal dynamics in assembly mechanisms and community structure for both bacterial taxa and their functional genes at different abundance levels, in both disturbed and undisturbed states. We further reverted the disturbance state to contrast recovery of function with community structure. Our findings are relevant, as very few studies have employed such an approach, while there is a need to assess the relative importance of assembly mechanisms for microbial communities across different spatial and temporal scales, environmental gradients, and types of disturbance.

Revealing the assembly mechanisms of the soil microbial community, which is crucial to comprehend microbial biodiversity, is a central focus in ecology. The distribution patterns of microbial elevational diversity have been extensively studied, but their assembly processes and drivers remain unclear. Therefore, it is essential to unravel the relationship between the deterministic and stochastic processes of the microbial community assembly and elevational gradients. Here, our study built upon previous physicochemical analyses of soil samples collected along an elevational gradient (900–1500 m) in Daiyun mountain, a subtropical forest located in southeastern China. Using the phylogenetic-bin-based null model analysis (icamp) and multiple regression on matrices approach, we explored the major drivers that influence the assembly processes of soil bacterial and fungal community across elevations. The results showed that: (1) bacterial rare taxa exhibited a broad habitat niche breadth along the elevational gradient; (2) homogeneous selection and homogenizing dispersal proved to be the most important assembly processes for the bacterial and fungal community; (3) soil phosphorus availability mediated the relative importance of deterministic and stochastic processes in the soil microbial community. Notably, the relative abundance of dominant microbial taxa controlled by homogeneous selection and homogenizing dispersal increased with increasing soil phosphorus availability. Collectively, the assembly processes of microbial elevational communities of the subtropical mountains in China can be explained to some extent by variations in the soil phosphorus availability. This conclusion provides valuable insights into the prediction of soil microbial diversity and phosphorus nutrient cycling in subtropical montane forests.

Agricultural intensification in greenhouse systems leads to a substantial accumulation of pesticides, yet its role in reshaping soil microbial interactions and their network stability remains poorly understood. This study reveals a critical ecological paradox: contrary to classical theory, greenhouse soils under chronic pesticide contamination exhibit significantly enhanced network stability (quantified as the robustness of network global efficiency under targeted node removal simulations) despite a concurrent sharp decline in bacterial diversity. We investigated this counter-intuitive phenomenon by integrating 16S rRNA sequencing, motif-based network analysis, and resilience modeling. Our findings suggest that this enhanced stability is not explained by species richness but, rather, coincides with a fundamental restructuring of the network's local interaction architecture. Pesticide residues, acting as a strong deterministic selection pressure, shaped the microbial community into a \"low-aggregation, high-redundancy\" network topology. This was characterized by a decrease in highly clustered, \"brittle\" interaction motifs (e.g., M3-2) and an increase in sparse triangular anti-motifs (e.g., M3-1). This new architecture mitigates the risk of cascading failures, thereby elevating the network's collapse threshold. Triazole fungicides (e.g., Tricyclazole and Hexaconazole) were significantly associated with this structural shift. Our study establishes a novel mechanistic link from pesticide stress to motif-level restructuring and enhanced system stability, offering new insights for assessing the health of highly stressed agricultural ecosystems.

Successional phases describe changes in ecological communities that proceed in steps rather than continuously. Despite their importance for the understanding of ecosystem development, there still exists no reliable definition of phases and no quantitative measure of phase transitions. In order to obtain these data, we investigated primary succession in an artificial catchment (6 ha) in eastern Germany over a period of 6 years. The data set consists of records of plant species and their cover values, and initial substrate properties, both from plots in a regular grid (20 m × 20 m) suitable for spatial data analysis. Community assembly was studied by analyses of species co-occurrence and nestedness. Additionally, we correlated lognormal and log series distributions of species abundance to each community. We here introduce a new general method for detection of successional phases based on the degree of transient spatial homogeneity in the study system. Spatially coherent vegetation patterns revealed nonoverlapping partitions within this sequence of primary succession and were characterized as two distinct ecological phases. Patterns of species co-occurrence were increasingly less random, and hence the importance of demographic stochasticity and neutral community assembly decreased during the study period. Our findings highlight the spatial dimension of successional phases and quantify the degree of change between these steps. They are an element for advancing a more reliable terminology of ecological successions.

Since the microbiome has been shown to impact insect fitness, a mechanistic understanding of community assembly has potentially significant applications but remains largely unexplored. In this paper, we investigate bacterial and fungal community assembly in nine sympatric wild insect species that share a common diet. The main findings indicate that stochastic processes drive the divergence of microbiomes and mycobiomes in nine sympatric wild insect species. These findings offer novel insights into the assembly mechanisms of microbiomes and mycobiomes in wild insects.

Turkey is among the countries where sand flies (Diptera: Psychodidae) are responsible for the endemic presence of leishmaniasis. Understanding the feeding behaviour of haematophagous arthropods is crucial for revealing the transmission cycles of vector-borne diseases. However, research on the host preferences of sand fly species in Turkey has been limited. This study aims to determine the blood meal sources of sand fly species collected from a wide range of geographical areas and to identify their feeding patterns. For the blood meal analysis, Sanger sequencing targeting the vertebrate mitochondrial cytochrome b or mammalian 12 S rRNA genes was performed on 265 female specimens collected between 2006 and 2019. The feeding patterns of sand flies were determined using Null model analysis. Host assignments of 218 individuals revealed nine different vertebrate hosts for 14 sand fly taxa. Bos taurus was the predominant host (81.19%), followed by Gallus gallus (8.88%), Capra hircus (5.14%), Mus musculus (1.81%), Ovis aries (0.93%), Homo sapiens (0.47%), Canis lupus familiaris (0.47%), Felis catus (0.47%) and Sitta spp. (0.47%). We discovered an aggregated feeding pattern among sand fly taxa instead of random or segregated feeding. Most sand fly taxa predominantly fed on bovines as their hosts, highlighting the need for further research on the role of domestic animals in the transmission of sand fly-borne diseases. Paraphlebotomus specimens displayed a relatively broad host range, particularly favouring Avian hosts, which requires further investigation into their life history traits.

Nested structure, in which specialists interact with subsets of species with which generalists interact, has been repeatedly found in networks of mutualistic interactions and thus is considered a general feature of mutualistic communities. However, it is uncertain how exclusive nested structure is for mutualistic communities since few studies have evaluated nestedness in other types of networks. Here, we show that 31 published food webs consist of bipartite subwebs that are as highly nested as mutualistic networks, contradicting the hypothesis that antagonistic interactions disfavor nested structure. Our findings suggest that nested networks may be a common pattern of communities that include resource-consumer interactions. In contrast to the hypothesis that nested structure enhances biodiversity in mutualistic communities, we also suggest that nested food webs increase niche overlap among consumers and thus prevent their coexistence. We discuss potential mechanisms for the emergence of nested structure in food webs and other types of ecological networks.

Co-occurrence pattern of fish species plays an important role in understanding the spatio-temporal structure and the stability of fish community. Species coexistence may vary with time and space. The co-occurrence patterns of fish species were examined using the C -score under fixed-fixed null model for fish communities in spring and autumn over different years in the Haizhou Bay, China. The results showed that fish assemblages in the whole bay had non-random patterns in spring and autumn over different years. However, the fish co-occurrence patterns were different for the northern and southern fish assemblages in spring and autumn. The northern fish assemblage showed structured pattern, whereas the southern assemblage were randomly assembled in spring. The co-occurrence patterns of fish communities were relatively stable over different years, and the number of significant species pairs in northern assemblage was more than that in the southern assemblage. Environmental heterogeneity played an important role in determining the distributions of fish species that formed significant species pairs, which might affect the co-occurrence patterns of northern and southern assemblages further in the Haizhou Bay.

Plant community ecologists use the null model approach to infer assembly processes from observed patterns of species co‐occurrence. In about a third of published studies, the null hypothesis of random assembly cannot be rejected. When this occurs, plant ecologists interpret that the observed random pattern is not environmentally constrained – but probably generated by stochastic processes. The null model approach (using the C‐score and the discrepancy index) was used to test for random assembly under two simulation algorithms. Logistic regression, distance‐based redundancy analysis, and constrained ordination were used to test for environmental determinism (species segregation along environmental gradients or turnover and species aggregation). This article introduces an environmentally determined community of alpine hydrophytes that presents itself as randomly assembled. The pathway through which the random pattern arises in this community is suggested to be as follows: Two simultaneous environmental processes, one leading to species aggregation and the other leading to species segregation, concurrently generate the observed pattern, which results to be neither aggregated nor segregated – but random. A simulation study supports this suggestion. Although apparently simple, the null model approach seems to assume that a single ecological factor prevails or that if several factors decisively influence the community, then they all exert their influence in the same direction, generating either aggregation or segregation. As these assumptions are unlikely to hold in most cases and assembly processes cannot be inferred from random patterns, we would like to propose plant ecologists to investigate specifically the ecological processes responsible for observed random patterns, instead of trying to infer processes from patterns. An environmentally determined plant community can present itself as randomly assembled. This may occur if two simultaneous environmental processes, one leading to species aggregation and the other leading to species segregation, concurrently determine composition. The resultant pattern is hence neither aggregated nor segregated, but random (Explanatory sentence for the organism photograph: Sparganium angustifolium Michx, a common hydrophyte in Iberian alpine lakes. Author: GGB.).