The role of stochasticity in fungal community assembly – explaining apparent stochasticity by field experiments
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PROVIDER: PRJEB65750 | ENA |
REPOSITORIES: ENA
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Project description:Community assembly of crop-associated fungi is thought to be strongly influenced by deterministic selection exerted by the plant host, rather than stochastic processes. Here we use a simple, sorghum system with abundant sampling to show that stochastic forces (drift or stochastic dispersal) act on fungal community assembly in leaves and roots early in host development and when sorghum is drought stressed, conditions when mycobiomes are small. Unexpectedly, we find no signal for stochasticity when drought stress is relieved, likely due to renewed selection by the host. In our experimental system, the host compartment exerts the strongest effects on mycobiome assembly, followed by the timing of plant development and lastly by plant genotype. Using a dissimilarity-overlap approach, we find a universality in the forces of community assembly of the mycobiomes of the different sorghum compartments and in functional guilds of fungi.
| S-EPMC6946711 | biostudies-literature
Project description:Several factors act on community structure, so determining species composition and abundance patterns. Core processes operating at local scales, such as species-environment matching and species interactions, shape observed assemblages. Artificial habitats (simplified structure) are useful systems for assessing the main factors affecting community composition and disentangling their assembly rules. Drinking troughs (brickwork tanks for free-ranging cattle watering) are widespread in Italy and represent a suitable aquatic habitat for colonization by various aquatic organisms. Dragonflies larvae are usually found in drinking troughs and often exhibit strong species interactions and striking community assembly patterns. Our primary aim was to search for Odonata communities exhibiting non-random co-occurrence/segregation patterns in drinking troughs. We performed null-model analyses by measuring a co-occurrence index (C-score) on larval Odonata assemblages (13 species from 28 distinct troughs). Overall, we found a non-random structure for the studied dragonfly assemblages, which, given their fast generation time, must have been generated by short-term ecological processes (i.e. interspecific interactions). We thus analyzed potential competition/predation among and within ecological guilds. From the field data, we speculated that interactions within the sprawlers' guild is likely among the main drivers structuring the studied assemblages, especially the effect of intraguild predation between C. erythraea and Sympetrum spp larval stages. We then experimentally tested these interactions in laboratory and demonstrated that intraguild predation among larvae at different development stages may result in an effective exclusion/negative impact on density pattern, representing one of the processes to take into consideration when studying dragonfly assemblages.
| S-EPMC6588213 | biostudies-literature
Project description:Microbial community assembly is a complex process shaped by multiple factors, including habitat filtering, species assortment and stochasticity. Understanding the relative importance of these drivers would enable scientists to design strategies initiating a desired reassembly for e.g., remediating low diversity ecosystems. Here, we aimed to examine if a human fecal-derived defined microbial community cultured in bioreactors assembled deterministically or stochastically, by completing replicate experiments under two growth medium conditions characteristic of either high fiber or high protein diets. Then, we recreated this defined microbial community by matching different strains of the same species sourced from distinct human donors, in order to elucidate whether coadaptation of strains within a host influenced community dynamics. Each defined microbial ecosystem was evaluated for composition using marker gene sequencing, and for behavior using 1H-NMR-based metabonomics. We found that stochasticity had the largest influence on the species structure when substrate concentrations varied, whereas habitat filtering greatly impacted the metabonomic output. Evidence of coadaptation was elucidated from comparisons of the two communities; we found that the artificial community tended to exclude saccharolytic Firmicutes species and was enriched for metabolic intermediates, such as Stickland fermentation products, suggesting overall that polysaccharide utilization by Firmicutes is dependent on cooperation.
| S-EPMC6863822 | biostudies-literature
Project description:Precipitation change is often associated with climate warming, but its effects on soil microbial community assembly remain relatively underexplored. Traditionally, it is thought that increasing the magnitude of environmental changes will increase the importance of deterministic processes in community assembly. Here, while ±30% precipitation promoted deterministic processes in the assembly of soil prokaryotic community during a five-year semiarid grassland experiment, ±60% precipitation increased the importance of stochastic processes like random birth/death, countering to conventional thinking. Similarly, analysis of a multifactorial experiment showed that +54% precipitation stimulated a random bacterial birth process while other environmental change factors did not. In addition, the increased taxonomic stochasticity under ±60% precipitation translated into functional stochasticity at the gene, protein, and enzyme levels. Our results revealed the distinctive mechanism and critical role of precipitation in determining microbial assemblages, demonstrating the need to integrate microbial taxonomic information to better predict their functional responses to precipitation changes.
2020-12-13 | PXD023103 |
Project description:Here, we compare the fungal community composition and diversity in Amazonian Dark Earth (ADE) and the respective non-anthropogenic origin adjacent (ADJ) soils from four different sites in Brazilian Central Amazon using pyrosequencing of 18S ribosomal RNA (rRNA) gene. Fungal community composition in ADE soils were more similar to each other than their ADJ soils, except for only one site. Phosphorus and aluminum saturation were the main soil chemical factors contributing to ADE and ADJ fungal community dissimilarities. Differences in fungal richness were not observed between ADE and ADJ soil pairs regarding to the most sites. In general, the most dominant subphyla present in the soils were Pezizomycotina, Agaricomycotina, and Mortierellomycotina. The most abundant operational taxonomic units (OTUs) in ADE showed similarities with the entomopathogenic fungus Cordyceps confragosa and the saprobes Fomitopsis pinicola, Acremonium vitellinum, and Mortierellaceae sp., whereas OTUs similar to Aspergillus niger, Lithothelium septemseptatum, Heliocephala gracillis, and Pestalosphaeria sp. were more abundant in ADJ soils. Differences in fungal community composition were associated to soil chemical factors in ADE (P, Ca, Zn, Mg, organic matter, sum of bases, and base saturation) and ADJ (Al, potential acidity, Al saturation, B, and Fe) soils. These results contribute to a deeper view of the fungi communities in ADE and open new perspectives for entomopathogenic fungi studies.
| S-EPMC4823338 | biostudies-literature
Project description:CGGBP1-regulated cytosine methylation at CTCF-binding motifs resists stochasticity
| PRJNA606696 | ENA
Project description:Identifying the influence of stochastic processes and of deterministic processes, such as dispersal of individuals of different species and trait-based environmental filtering, has long been a challenge in studies of community assembly. Here, we present the Univariate Community Assembly Analysis (UniCAA) and test its ability to address three hypotheses: species occurrences within communities are (a) limited by spatially restricted dispersal; (b) environmentally filtered; or (c) the outcome of stochasticity-so that as community size decreases-species that are common outside a local community have a disproportionately higher probability of occurrence than rare species. The comparison with a null model allows assessing if the influence of each of the three processes differs from what one would expect under a purely stochastic distribution of species. We tested the framework by simulating "empirical" metacommunities under 15 scenarios that differed with respect to the strengths of spatially restricted dispersal (restricted vs. not restricted); habitat isolation (low, intermediate, and high immigration rates); and environmental filtering (strong, intermediate, and no filtering). Through these tests, we found that UniCAA rarely produced false positives for the influence of the three processes, yielding a type-I error rate ≤5%. The type-II error rate, that is, production of false negatives, was also acceptable and within the typical cutoff (20%). We demonstrate that the UniCAA provides a flexible framework for retrieving the processes behind community assembly and propose avenues for future developments of the framework.
| S-EPMC6374725 | biostudies-literature
Project description:Supplementary raw metabolomics files for "Ecological stochasticity and phage induction diversify bacterioplankton communities at the microscale," Rachel E. Szabo et al.
2021-09-24 | MSV000088151 | MassIVE
Project description:Understory vegetation accounts for the majority of plant species diversity and serves as a driver of overstory succession and nutrient cycling in boreal forest ecosystems. However, investigations of the underlying assembly processes of understory vegetation associated with stand development following a wildfire disturbance are rare, particularly in Eurasian boreal forests. In this study, we measured the phylogenetic and functional diversity and trait dispersions of understory communities and tested how these patterns changed with stand age in the Great Xing'an Mountains of Northeastern China. Contrary to our expectation, we found that understory functional traits were phylogenetically convergent. We found that random patterns of phylogenetic, functional, and trait dispersions were dominant for most of our surveyed plots, indicating that stochastic processes may play a crucial role in the determination of understory community assembly. Yet, there was an evidence that understory community assembly was also determined by competitive exclusion and environmental filtering to a certain degree, which was demonstrated by the observed clustered phylogenetic and functional patterns in some plots. Our results showed that phylogenetic diversity significantly decreased, while functional diversity increased with stand age. The observed shift trends in phylogenetic and functional patterns between random to clustering along with stand age, which suggested that understory community assembly shifted from stochasticity to competitive exclusion and environmental filtering. Our study presented a difference to community assembly and species coexistence theories insisted solely on deterministic processes. These findings indicated that Eurasian boreal understory communities may be primarily regulated by stochastic processes, providing complementary evidence that stochastic processes are crucial in the determination of community assembly both in tropical and boreal forests.
| S-EPMC6315132 | biostudies-literature
Project description:Global warming is resulting in increased frequency of weather extremes. Root-associated fungi play important roles in terrestrial biogeochemical cycling processes, but the way in which they are affected by extreme weather is unclear. Here, we performed long-term field monitoring of the root-associated fungus community of a short rotation coppice willow plantation, and compared community dynamics before and after a once in 100 yr rainfall event that occurred in the UK in 2012. Monitoring of the root-associated fungi was performed over a 3-yr period by metabarcoding the fungal internal transcribed spacer (ITS) region. Repeated soil testing and continuous climatic monitoring supplemented community data, and the relative effects of environmental and temporal variation were determined on the root-associated fungal community. Soil saturation and surface water were recorded throughout the early growing season of 2012, following extreme rainfall. This was associated with a crash in the richness and relative abundance of ectomycorrhizal fungi, with each declining by over 50%. Richness and relative abundance of saprophytes and pathogens increased. We conclude that extreme rainfall events may be important yet overlooked determinants of root-associated fungal community assembly. Given the integral role of ectomycorrhizal fungi in biogeochemical cycles, these events may have considerable impacts upon the functioning of terrestrial ecosystems.
| S-EPMC6282977 | biostudies-literature