Stochastic Assembly Processes Research Articles

Composition and assembly mechanisms of prokaryotic communities in wetlands, and their relationships with different vegetation and reclamation methods

Coastal wetlands are undergoing substantial transformations globally as a result of increased human activities. However, compared to other ecosystems, diversity and functional characteristics of microbial communities in reclaimed coastal wetlands are not well studied compared to other ecosystems. This is important because it is known that microorganisms can play a crucial role in biogeochemical cycling within coastal wetland ecosystems. Hence, this study utilized the high-throughput sequencing technique to investigate the structure and assembly processes of microbial communities in reclaimed coastal wetlands. The results revealed a substantial change in soil properties following coastal wetland reclamation. Remarkably, the reclaimed soil exhibited significantly lower pH, soil organic carbon (SOC), and total salinity (TS) values (p < 0.05). The dominant phyla included Proteobacteria, Chloroflexi, Bacteroidetes, Acidobacteria, and Planctomycetes among study sites. However, the relative abundance of Proteobacteria increased from un-reclaimed coastal wetlands to reclaimed ones. The Proteobacteria, Chloroflexi, and Acidobacteria showed higher relative abundance in vegetated soil compared to bare soil, while Bacteroidetes and Planctomycetes exhibited the opposite trend. Notably, vegetation types exerted the strongest influence on microbial diversity, surpassing the effects of soil types and depth (F = 34.49, p < 0.001; F = 25.49, p < 0.001; F = 3.173, p < 0.078, respectively). Stochastic assembly processes dominated in un-reclaimed soil, whereas deterministic processes governed the assembly in artificial sea embankment wetlands (SEW). The presence of Spartina alterniflora in all soil types (except SEW soils) indicated stochastic assembly, while Phragmites australis in reclaimed soils pointed toward deterministic microbial assembly. Furthermore, environmental factors such as pH, soil water content (SWC), SOC, total carbon (TC), total nitrogen (TN), total phosphorus (TP), NH4+-N, vegetation types, soil depth, and geographic distance exhibited significant effects on microbial beta diversity indices. Co-occurrence network analysis revealed a stronger association between taxa in SEW compared to land reclaimed from wetlands (LRW) and natural coastal wetlands (NCW). The bottom soil layer exhibited more complex network interactions than the topsoil layer. Besides soil parameters, reclamation and varieties of vegetation were also substantial factors influencing the composition, diversity, and assembly processes of microbial communities in coastal wetlands.

Importance of stochastic assembly processes influencing beetle communities increases after logging

Xerothermophilous beetles are one of the endangered ecological groups of animals, mainly because of the loss of suitable habitats for their development. Many species of these beetles are associated with specific light conditions. Those preferring higher insolation levels may find such conditions in coppices. Coppicing is a type of forest management with a long history, which allowed the survival of many species in the European landscape. After WWII coppicing management was widely abandoned and coppices were transformed into high forest, which caused a significant decline in forest biodiversity. In the Podyjí National Park at the border of Czechia and Austria, coppicing was re-established in two neglected coppices by cutting trees on areas of approximately one hectare in the winter of 2015/2016 to support heliophilous and endangered species of plants and animals. We carried out a study in these two areas by using flight interception traps during the year before the logging (2015), and two years after the logging (2016 and 2017). We analysed the effect of the logging and the following succession on beetle assemblages by comparing beetle taxocoenoses before and after logging. The creation of the clearings in closed-canopy forests had a positive effect on overall species richness and supported threatened species of beetles. We revealed that unlike α-diversity, which was highest during the first year after logging, spatial differentiation of the assemblage (β-diversity) was highest during the second year after logging. Co-occurrence analysis showed that beetle assemblages tended to co-occur more than expected by chance during all study years, indicating shared environmental preferences. On the other hand, after logging the species co-occurrence pattern was closer to random species distribution, showing that dispersal ability and random immigration also play important role in assembly processes.

Stochastic and Deterministic Assembly Processes in Seamount Microbial Communities.

Seamounts are ubiquitous in the ocean. However, little is known about how seamount habitat features influence the local microbial community. In this study, the microbial populations of sediment cores from sampling depths of 0.1 to 35 cm from 10 seamount summit sites with a water depth of 1,850 to 3,827 m across the South China Sea (SCS) Basin were analyzed. Compared with nonseamount ecosystems, isolated seamounts function as oases for microbiomes, with average moderate to high levels of microbial abundance, richness, and diversity, and they harbor distinct microbial communities. The distinct characteristics of different seamounts provide a high level of habitat heterogeneity, resulting in the wide range of microbial community diversity observed across all seamounts. Using dormant thermospores as tracers to study the effect of dispersal by ocean currents, the observed distance-decay biogeography across different seamounts shaped simultaneously by the seamounts' naturally occurring heterogeneous habitat and the limitation of ocean current dispersal was found. We also established a framework that links initial community assembly with successional dynamics in seamounts. Seamounts provide resource-rich and dynamic environments, which leads to a dominance of stochasticity during initial community establishment in surface sediments. However, a progressive increase in deterministic environmental selection, correlated with resource depletion in subsurface sediments, leads to the selective growth of rare species of surface sediment communities in shaping the subsurface community. Overall, the study indicates that seamounts are a previously ignored oasis in the deep sea. This study also provides a case study for understanding the microbial ecology in globally widespread seamounts. IMPORTANCE Although there are approximately 25 million seamounts in the ocean, surprisingly little is known about seamount microbial ecology. We provide evidence that seamounts are island-like habitats harboring microbial communities distinct from those of nonseamount habitats, and they exhibit a distance-decay pattern. Environmental selection and dispersal limitation simultaneously shape the observed biogeography. Coupling empirical data with a null mode revealed a shift in the type and strength, which controls microbial community assembly and succession from the seamount surface to the subsurface sediments as follows: (i) community assembly is initially primarily driven by stochastic processes such as dispersal limitation, and (ii) changes in the subsurface environment progressively increase the importance of environmental selection. This case study contributes to the mechanistic understanding essential for a predictive microbial ecology of seamounts.

Effect of the bacterial community assembly process on the microbial remediation of petroleum hydrocarbon-contaminated soil.

The accumulation of petroleum hydrocarbons (PHs) in the soil can reduce soil porosity, hinder plant growth, and have a serious negative impact on soil ecology. Previously, we developed PH-degrading bacteria and discovered that the interaction between microorganisms may be more important in the degradation of PHs than the ability of exogenous-degrading bacteria. Nevertheless, the role of microbial ecological processes in the remediation process is frequently overlooked. This study established six different surfactant-enhanced microbial remediation treatments on PH-contaminated soil using a pot experiment. After 30 days, the PHs removal rate was calculated; the bacterial community assembly process was also determined using the R language program, and the assembly process and the PHs removal rate were correlated. The rhamnolipid-enhanced Bacillus methylotrophicus remediation achieved the highest PHs removal rate, and the bacterial community assembly process was impacted by deterministic factors, whereas the bacterial community assembly process in other treatments with low removal rates was affected by stochastic factors. When compared to the stochastic assembly process and the PHs removal rate, the deterministic assembly process and the PHs removal rate were found to have a significant positive correlation, indicating that the deterministic assembly process of bacterial communities may mediate the efficient removal of PHs. Therefore, this study recommends that when using microorganisms to remediate contaminated soil, care should be taken to avoid strong soil disturbance because directional regulation of bacterial ecological functions can also contribute to efficient removal of pollutants.

Natural grassland conversion to cultivated pastures increases soil microbial niche specialization with consequences for ecological processes

The conversion of natural grasslands to cultivated pastures has a profound effect on the soil habitat conditions, influencing the proportion of soil specialist and generalist microbes, with consequences for the assembly of microbial communities. This often leads to the homogenization of the microbial community and thus favoring stochastic assembly processes. However, there is still a gap in understanding the effect of conversion from natural grasslands to cultivated pastures on soil microbial ecological processes. Therefore, we aimed to investigate the assembly patterns of microbial communities and evaluate the ecological models for generalists and specialist microbes along a grassland management intensification gradient. Through 16S rRNA amplicon sequencing, we found that the conversion of natural grasslands to cultivated pastures has increased the number of microbial specialists, resulting in stochastic assembly processes due to the decrease in plant diversity. Moreover, the ecological processes governing the assembly of microbial communities were affected by soil and vegetation management. The perennial pasture was more affected by homogenizing selection, owing to the lower plant diversity and uniform plant covering and root development. We have found that the generalists in the grasslands are shaped by niche-based models, while the specialists in natural grasslands are more stochastic in nature. For improved pastures, we have found that lognormal and preemption models are more predominant, suggesting that homogenizing dispersal is more predominant than variable selection. We highlight it is essential to comprehend these assembly models and ecological processes to ensure plant-microbe supporting and provisioning ecosystem services for cattle, and humans while establishing management strategies and conservation policy priorities.

Inter-basin water diversion homogenizes microbial communities mainly through stochastic assembly processes

Inter-basin water transfer is an effective manner to achieve the optimal allocation of water resources, while accompanied by some ecological effects. The responses of microorganisms to water diversion and the ecological processes in regulating the community assembly are still unclear. Taking the eastern route of South-to-North Water Diversion Project as the study area, we investigated the microbial community patterns and the underlying assemblage processes in habitats with different hydrological connectivity, including isolated lakes, connected lakes and man-made canal. The results showed that microbial communities in the canal had higher diversity, lower dissimilarity, weaker compositional variation, and stronger co-occurrence patterns compared with that in the connected and isolated lakes. These findings suggested that the increase of connectivity among natural aquatic habitats due to water diversion can homogenize microbial communities and reduce microbial heterogeneity. The neutral and null models demonstrated the importance of stochastic processes in shaping microbial community assembly. Dispersal limitation and variable selection were the predominant mechanisms structuring microbial communities in the isolated lakes. Due to the homogenized environmental condition and the enhanced hydrologic connectivity in the canal and the connected lakes, microbial communities had higher dispersal capability and ecological drift occurred more frequently in these lotic habitats. The variations in microbial community structure were mainly driven by biotic ecological succession than abiotic factors, with positive and negative cohesion explained 63% and 25% of variability, respectively. Six taxa were considered as the potential introduced microorganisms, which may favor the nutrient biogeochemical cycling and the organic matter degradation, but may also bring ecological risks. Overall, this study provides a deeper understanding of the ecological consequences of inter-basin water diversion, and helps the regulation and management of these projects.

Biofilm thickness controls the relative importance of stochastic and deterministic processes in microbial community assembly in moving bed biofilm reactors.

Deterministic and stochastic processes are believed to play a combined role in microbial community assembly, though little is known about the factors determining their relative importance. We investigated the effect of biofilm thickness on community assembly in nitrifying moving bed biofilm reactors using biofilm carriers where maximum biofilm thickness is controlled. We examined the contribution of stochastic and deterministic processes to biofilm assembly in a steady state system using neutral community modelling and community diversity analysis with a null-modelling approach. Our results indicate that the formation of biofilms results in habitat filtration, causing selection for phylogenetically closely related community members, resulting in a substantial enrichment of Nitrospira spp. in the biofilm communities. Stochastic assembly processes were more prevalent in biofilms of 200 µm and thicker, while stronger selection in thinner (50 µm) biofilms could be driven by hydrodynamic and shear forces at the biofilm surface. Thicker biofilms exhibited greater phylogenetic beta-diversity, which may be driven by a variable selection regime caused by variation in environmental conditions between replicate carrier communities, or by drift combined with low migration rates resulting in stochastic historical contingency during community establishment. Our results indicate that assembly processes vary with biofilm thickness, contributing to our understanding of biofilm ecology and potentially paving the way towards strategies for microbial community management in biofilm systems.

Strong Dispersal Limitation of Microbial Communities at Shackleton Glacier, Antarctica.

Microbial communities can be structured by both deterministic and stochastic processes, but the relative importance of these processes remains unknown. The ambiguity partly arises from an inability to disentangle soil microbial processes from confounding factors, such as aboveground plant communities or anthropogenic disturbance. In this study, we characterized the relative contributions of determinism and stochasticity to assembly processes of soil bacterial communities across a large environmental gradient of undisturbed Antarctic soils. We hypothesized that harsh soils would impose a strong environmental selection on microbial communities, whereas communities in benign soils would be structured largely by dispersal. Contrary to our expectations, dispersal was the dominant assembly mechanism across the entire soil environmental gradient, including benign environments. The microbial community composition reflects slowly changing soil conditions and dispersal limitation of isolated sites. Thus, stochastic processes, as opposed to deterministic, are primary drivers of soil ecosystem assembly across space at our study site. This is especially surprising given the strong environmental constraints on soil microorganisms in one of the harshest environments on the planet, suggesting that dispersal could be a driving force in microbial community assembly in soils worldwide. IMPORTANCE Because of their diversity and ubiquity, microbes provide an excellent means to tease apart how natural communities are structured. In general, ecologists believe that stochastic assembly processes, like random drift and dispersal, should dominate in benign environments while deterministic processes, like environmental filtering, should be prevalent in harsh environments. To help resolve this debate, we analyzed microbial community composition in pristine Antarctic soils devoid of human influence or plant communities for eons. Our results demonstrate that dispersal limitation is a surprisingly potent force of community limitation throughout all soil conditions. Thus, dispersal appears to be a driving force of microbial community assembly, even in the harshest of conditions.

Understanding stochastic and deterministic assembly processes in microbial communities along temporal, spatial and environmental scales.

Identifying the main drivers of community assembly remains an open fundamental question in ecology. Dispersal processes introduce randomness in community composition while selection for particular environments creates predictable assemblages. However, the interaction between selection and dispersal processes is still poorly understood. Here, we address this question in bacterial and microeukaryotic communities inhabiting a highly dynamic system of ephemeral (hyper)saline lakes. We show that the combination of beta-diversity decomposition methods and a temporal approach based on colonization and extinction dynamics yields new insights into the relative effect of selection and dispersal along environmental gradients. Selective pressure and dispersal-related processes simultaneously shape each local community with variable strength and effect. The dominance of selection vs. dispersal shifted from stochastic to deterministic assembly as salinity increased along the gradient. This transition also had an impact on the temporal dynamics of the lakes as community turnover decreased at high salinities because both colonization and extinction rates slowed down. Only microeukaryotic richness decreased along the gradient due to lower effective colonization at higher salinities, suggesting that the net effect of selection and dispersal is determined by both environmental conditions and the idiosyncrasy of the different microbial ecologies. Our results emphasize the use of temporal approaches in combination with standard statistical methods for a better understanding of the dynamic processes underlying community assembly.

Sedimentary, littoral and planktic diatoms show different diversity patterns and assembly mechanisms in mountain lakes of the northern European Alps

This study analysed diversity patterns of sedimentary, littoral and planktic diatoms in 43 mountain lakes in the northern European Alps and identified processes that contribute to these patterns. Linear regression models showed a significant increase of sedimentary α-diversity with lake area and conductivity and a negative trend with increasing elevation, whilst the littoral diatom α-diversity increased significantly with conductivity and lake water temperature. Planktic diatom α-diversity significantly decreased with lake area and depth. August water temperature, total phosphorus, conductivity and lake depth explained a significant part of the variation and were significantly correlated with pairwise β-diversities in the data sets, but spatial and shared effects of space and environment were more important for planktic and littoral diatoms. A null model approach based on assemblages’ dissimilarities revealed that the structure of littoral and planktic assemblages was predominantly stochastic. In contrast, sedimentary diatoms were formed by both deterministic and stochastic processes. Abundant and widespread species contributed a large part to the assemblage β-diversity. The results point to a stronger role of niche assembly in sedimentary than for littoral and planktic diatoms. Dispersal limitation, in turn, is likely to contribute to the spatial patterns and stochastic assembly processes observed for littoral and planktic diatoms.

The structure and assembly of rhizobacterial communities are influenced by poplar genotype.

The interaction between plants and microbes dominates plant growth and fitness in specific environments. The study of the relationship between plant genotypes and rhizobacterial community structure would provide a deep insight into the recruitment strategies of plants toward soil bacteria. In this study, three genotypes of 18-year-old mature poplar (H1, H2, and H3) derived from four different parents were selected from a germplasm nursery of Populus deltoides. Rhizosphere soil carbon, nitrogen, and phosphorus properties as well as the 16S rDNA sequences of rhizobacterial communities were analyzed to determine the relationship between poplar genotypes and rhizobacterial communities assembly. The results showed there were significant differences in the diversity (Chao1, ACE index, and Shannon index) of rhizobacterial communities between H1 and H2, as well as between H2 and H3, but no difference between H1 and H3. Principal component analysis also revealed a similar structure of rhizobacterial communities between H1 and H3, whereas the rhizobacterial communities of H2 demonstrated significant differences from H1 and H3. Linear discriminant effect size analysis indicated that there were 11 and 14 different biomarkers in the H1 and H3 genotype, respectively, but 42 in the H2 genotype. Co-occurrence network analysis indicated that the rhizobacterial communities of H2 had a distinct network structure compared to those of the other two genotypes, whereas H1 and H3 had a similar pattern of co-occurrence network. Threshold indicator taxa analysis revealed that 63 genera responded significantly to NO3 --N content and 58 genera to NH4 +-N/NO3 --N ratio. Moreover, the stochastic assembly process was found to be decreased with increasing NO3 --N content and fluctuated with increasing NH4 +-N/NO3 --N ratio. All results indicated that the structure of poplar rhizobacterial communities were influenced by host genotypes, and available nitrogen might play a dominant role in the assembly of rhizobacterial communities. This study would promote the future selection and utilization of rhizobacteria in poplar breeding.

Sediment sulfate content determines assembly processes and network stability of bacteria communities of coastal land-based shrimp aquaculture ponds

Sediment bacteria communities in shrimp pond are intricately linked to ecosystem function and the provision of services, such as nutrient cycling and excess nutrient metabolism in sediment. However, little is known about the main factor (assembly processes) governing abundant and rare bacterial diversity in land-based shrimp ponds. This study quantified the composition, spatial distribution, and assembly mechanisms of bacterial communities sampled from the sediment of 78 land-based shrimp ponds distributed along approximately 1700 km of the southeastern coastal zone of China. This was done using 16S rRNA gene amplicon sequencing. The bacterial community similarities decreased with spatial distance. Variation of bacterial community was mostly attributed to deterministic (environmental filtering) processes. Sediment sulfate concentrations regulated the balance between stochastic and deterministic bacterial community assembly processes, as indicated by the negative relationship between the stochasticity ratio, and network analysis highlighted increasingly sparse interconnections and less frequent co-occurrences among bacterial communities under greater sulfate concentrations. Our results demonstrate the negative impacts of sulfates associated with coastal aquaculture on sediment bacterial community dynamics, community assembly, and ecosystem function.

Microbial Community Succession Associated with Poplar Wood Discoloration.

Microbes are common inhabitants of wood, but little is known about the relationship between microbial community dynamics during wood discoloration. This study uses simulation experiments to examine the changes in the microbial communities in poplar wood at different succession stages. The composition and structure of the microbial communities changed significantly in different successional stages, with an overarching pattern of bacterial diversity decreasing and fungal diversity increasing from the early to the late successional stages. Nevertheless, succession did not affect the composition of the microbial communities at the phylum level: Proteobacteria and Acidobacteria dominated the bacterial communities, while Ascomycota and Basidiomycota dominated the fungal communities. However, at the genus level, bacterial populations of Sphingomonas and Methylobacterium, and fungal populations of Sphaeropsis were significantly more prevalent in later successional stages. Stochastic assembly processes were dominant in the early successional stages for bacteria and fungi. However, variable selection played a more critical role in the assembly processes as succession proceeded, with bacterial communities evolving towards more deterministic processes and fungal communities towards more stochastic processes. Altogether, our results suggest that bacteria and fungi exhibit different ecological strategies in poplar wood. Understanding those strategies, the resulting changes in community structures over time, and the relationship to the different stages of poplar discoloration, is vital to the biological control of that discoloration.

Patterns of denitrifier communities assembly and co-occurrence network regulate N2O emissions in soils with long-term contrasting tillage histories

Denitrification is reducing nitrate to nitrous oxide (N2O) and nitrogen (N2) under the action of denitrifying microorganisms, which are the main source of soil N2O emissions. However, the co-occurrence pattern and community assembly process of denitrifier communities have not been studied in agricultural soils with long-term contrasting tillage histories. Based on a continuous (> 11 yr) conservation experiment, we aimed to understand the community assembly process and co-occurrence network of nirK-, nirS-, nosZI- and nosZII-type denitrifier communities under conservation tillage (i.e., zero tillage (ZT) and chisel plough tillage (CPT)) and conventional tillage (i.e., plow tillage (PT)). Continuous in situ measurements showed that long-term conservation tillage significantly decreased the denitrification potential and N2O emission fluxes. CPT and ZT significantly increased the taxonomic and phylogenetic diversity of nirK, nosZI, and nosZII type communities, whereas consistently decreased the diversity of nirS-type communities, compared with PT. Although the assembly of nirK, nirS, nosZI, and nosZII type denitrifier communities were dominated by stochastic processes, the relative importance of stochastic assembly of denitrifying microbial communities was higher in conservation tillage soil. The co-occurrence network analyses further revealed clear tillage-induced ecological functions of N2O emissions, as evidenced by lower key nodes abundance and robustness of nirS and nirK communities network and higher key nodes abundance and robustness of nosZI and nosZII communities in conservation tillage soils. Variation partitioning analysis further indicated that the assembly processes significantly changed soil N2O emission intensity by regulating α-diversity and the key species abundances in the co-occurrence network of denitrifying communities. Overall, conservation tillage practices increased the diversity and the key nodes abundance of nosZI- and nosZII-type communities and decreased the diversity and the key nodes abundance of nirS- and nirK-type communities by regulating the relative importance of the stochastic assembly process of denitrifier communities, which is eventually likely to curb N2O emissions by strengthening the capacity of the N2O sink and weakening the capacity of the N2O source. These findings provide new insights into the formation of dryland microbial communities in agricultural soils with long-term contrasting tillage histories. Especially considering future climate change, this knowledge would prove useful in improving agroecosystem productivity and curbing greenhouse gas emissions.

Global landscape of gut microbiome diversity and antibiotic resistomes across vertebrates

Multiple factors influence gut microbiome diversity in vertebrate hosts. Most previous studies have only investigated specific factors and certain host species or taxa. However, a comprehensive assessment of the relative contributions of individual factors towards gut microbial diversity within a broader evolutionary context remains lacking. Here, 2202 16S rRNA gene sequencing samples of gut bacterial communities collected from 452 host species across seven classes were analyzed together to understand the factors broadly affecting vertebrate gut microbiomes across hosts with different diets, threatened status, captivity status, and habitat environmental factors. Among wild vertebrates, diet was most significantly associated with gut microbiome alpha diversity, while host phylogeny and diet were significantly associated with beta diversity, consistent with a previous study. Host threatened status and habitat environmental factors (e.g., geography and climate) were also associated with gut bacterial community beta diversity. Subsequent ecological modeling revealed a strong association between stochastic assembly processes and patterns of gut bacterial diversity among free-ranging vertebrates. In addition, metagenomic analysis of gut microbiomes from 62 captive vertebrates and sympatric humans revealed similar diversity and resistome profiles despite differences in host phylogeny, diet, and threatened status. These results thus suggest that captivity diminishes the effects of host phylogeny, diet, and threatened status on the diversity of vertebrate gut bacterial communities. The most overrepresented antibiotic resistant genes (ARGs) observed in these samples are involved in resistance to β-lactams, aminoglycosides, and tetracycline. These results also revealed potential horizontal transfers of ARGs between captive animals and humans, thereby jointly threatening public health and vertebrate conservation. Together, this study provides a comprehensive overview of the diversity and resistomes of vertebrate gut microbiomes. These combined analyses will help guide future vertebrate conservation via the rational manipulation of microbial diversity and reducing antibiotic usage.

Dancing with Douglas‐fir: Determinism dominates fungal community assembly processes

Abstract Fungal communities can influence the productivity, composition and survival of trees through cycling nutrients, providing resources and altering pathogens. Thus, shifts in fungal communities could impact forests by altering interactions between trees and their environments. Fungal community composition may be shaped by stochastic and deterministic processes such as dispersal limitation, environmental filtering and partner specificity between trees and fungi. For tree species with large geographical ranges, we expect fungal assembly processes to change with environmental variation across the range of the tree partner. Due to specificity between trees and symbiotic fungi, we expect deterministic to outweigh stochastic processes in root compared with soil fungi. As some tree species have exceptional longevity, we also expected tree age to influence fungal community assembly. We surveyed fungi in four stands of Pseudotsuga menziesii with tree ages up to 800 years along an 1,800 km transect. We sampled roots and soil around 12 P. menziesii in each stand, aged the trees, and sequenced fungal rDNA to determine composition and richness from which we calculated the relative role of deterministic and stochastic assembly processes. We used null models to evaluate the relative importance of deterministic variable and homogenizing selection, and stochastic dispersal limitation, drift and homogenizing dispersal in fungal community assembly. We detected 7,280 amplicon sequence variants with 5,270 associated with soil, 3,887 with roots and 1,877 found across both roots and soils. Deterministic processes dominated root and soil fungal communities at all sites except one where stochastic processes (i.e. dispersal limitation and drift) controlled root fungi. Despite the dominance of determinism in fungal community assembly, the proportion of processes differed by site. Assembly processes did not vary with tree age. Synthesis. Taken together, we suggest that the local environment, water limitation and partner‐preference between trees and their associated fungi, influence fungal community composition across the range of P. menziesii. We conclude that while fungal communities occurring near P. menziesii are dominated by homogenizing selection, the role of neutral processes still has a minor influence on community assembly and may be important in spatially isolated communities and those with strong gradients of fungal diversity.

Agricultural Management Drive Bacterial Community Assembly in Different Compartments of Soybean Soil-Plant Continuum.

Flowering stage of soybean is an important agronomic trait, which is important for soybean yield, quality and adaptability, and is the external expression of integrating external environmental factors and endogenous signals of the plant itself. Cropping system can change soil properties and fertility, which in turn determine plant growth and yield. The microbial community is the key regulator of plant health and production performance. Currently, there is limited understanding of the effects of cropping systems on microbial community composition, ecological processes controlling community assembly in different soil-plant continuum compartments of soybean. Here, we hope to clarify the structure and assembly process of different soybean compartments bacterial community at flowering stage through our work. The results showed that intercropping decreased the species diversity of rhizosphere and phyllosphere, and phylloaphere microbes mainly came from rhizosphere. FAPROTAX function prediction showed that indicator species sensitive to intercropping and crop rotation were involved in nitrogen/phosphorus cycle and degradation process, respectively. In addition, compared to the continuous cropping, intercropping increased the stochastic assembly processes of bacterial communities in plant-associated compartments, while crop rotation increased the complexity and stability of the rhizosphere network and the deterministic assembly process. Our study highlights the importance of intercropping and crop rotation, as well as rhizosphere and phyllosphere compartments for future crop management and sustainable agricultural regulation of crop microbial communities.

Brassica napus Bacterial Assembly Processes Vary with Plant Compartment and Growth Stage but Not between Lines.

ABSTRACTHolobiont bacterial community assembly processes are an essential element to understanding the plant microbiome. To elucidate these processes, leaf, root, and rhizosphere samples were collected from eight lines of Brassica napus in Saskatchewan over the course of 10 weeks. We then used ecological null modeling to disentangle the community assembly processes over the growing season in each plant part. The root was primarily dominated by stochastic community assembly processes, which is inconsistent with previous studies that suggest of a highly selective root environment. Leaf assembly processes were primarily stochastic as well. In contrast, the rhizosphere was a highly selective environment. The dominant rhizosphere selection process leads to more similar communities. Assembly processes in all plant compartments were dependent on plant growth stage with little line effect on community assembly. The foundations of assembly in the leaf were due to the harsh environment, leading to dominance of stochastic effects, whereas the stochastic effects in the root interior likely arise due to competitive exclusion or priority effects. Engineering canola microbiomes should occur during periods of strong selection assuming strong selection could promote beneficial bacteria. For example, engineering the microbiome to resist pathogens, which are typically aerially born, should focus on the flowering period, whereas microbiomes to enhance yield should likely be engineered postflowering as the rhizosphere is undergoing strong selection.IMPORTANCE In order to harness the microbiome for more sustainable crop production, we must first have a better understanding of microbial community assembly processes that occurring during plant development. This study examines the bacterial community assembly processes of the leaf, root, and rhizosphere of eight different lines of Brassica napus over the growing season. The influence of growth stage and B. napus line were examined in conjunction with the assembly processes. Understanding what influences the assembly processes of crops might allow for more targeted breeding efforts by working with the plant to manipulate the microbiome when it is undergoing the strongest selection pressure.

Spatial heterogeneity of the microbiome and metabolome profiles of high-temperature Daqu in the same workshop

High-temperature Daqu, usually used as a fermentation starter for sauce-flavor Baijiu production, plays an essential role in the yield and flavor quality of Baijiu. The environmental heterogeneity of different locations in the workshop during fermentation led to the final production of Daqu with three different types (i.e., white, yellow, and black Daqu). How to use these three types of Daqu in Baijiu production mainly depends on the workers’ experience so far. Here, we aimed to reveal the potential functions of different types of Daqu by comparing enzyme activity, volatile metabolites, and microbiota characteristics. White_Qu exhibited the highest liquefaction and saccharification enzyme activities, while the highest neutral proteinase and cellulase enzyme activities were detected in black_Qu. The total volatile content of yellow_Qu and black_Qu was roughly double that of white_Qu, and multivariate analysis revealed distinct volatile dissimilarities across different types of Daqu. Significant differences in bacterial and fungal community structures, assembly patterns, and potential functional profiles were discovered among different types of Daqu. At the genus level, Oceanobacillus and Thermomyces dominated the white_Qu microbiota, and the abundant microbes in yellow_Qu and black_Qu were scattered in Kroppenstedtia and Thermoascus. Bacterial and fungal communities were dominated by deterministic and stochastic assembly processes, respectively, suggesting that bacteria may be more affected by abiotic environmental factors and species interaction than fungi. Co-occurrence network analysis showed positive correlations characterized Daqu microbial networks, and network topological features indicated stronger interactions between bacterial taxa compared with fungal community. The Spearman correlation analysis revealed that four bacterial genera (Kroppenstedtia, Virgibacillus, Scopulibacillus, and Staphylococcus) and two fungal genera (Thermoascus and Aspergillus) exhibited positive correlations with almost all of the abundant volatiles. This work reveals that spatially varying environments lead to the microbiome and metabolome heterogeneity of high-temperature Daqu in the same workshop.

Differential microbial assembly processes and co-occurrence networks in the soil-root continuum along an environmental gradient.

Microorganisms of the soil-root continuum play key roles in ecosystem function. The Loess Plateau is well known for its severe soil erosion and thick loess worldwide, where mean annual precipitation (MAP) and soil nutrients decrease from the southeast to the northwest. However, the relative influence of environmental factors on the microbial community in four microhabitats (bulk soil, rhizosphere, rhizoplane, and endosphere) in the soil-root continuum along the environmental gradient in the Loess Plateau remains unclear. In this study, we investigated 82 field sites from warm-temperate to desert grasslands across the Loess Plateau, China, to assess the bacterial diversity, composition, community assembly, and co-occurrence networks in the soil-root continuum along an environmental gradient using bacterial 16S recombinant DNA amplicon sequencing. We discovered that the microhabitats explained the largest source of variations in the bacterial diversity and community composition in this region. Environmental factors (e.g., MAP, soil organic carbon, and pH) impacted the soil, rhizosphere, and rhizoplane bacterial communities, but their effects on the bacterial community decreased with increased proximity to roots from the soil to the rhizoplane, and the MAP enlarged the dissimilarity of microbial communities from the rhizosphere and rhizoplane to bulk soil. Additionally, stochastic assembly processes drove the endosphere communities, whereas the soil, rhizosphere, and rhizoplane communities were governed primarily by the variable selection of deterministic processes, which showed increased importance from warm-temperate to desert grasslands. Moreover, the properties of the microbial networks in the rhizoplane community indicate more stable networks in desert grasslands, likely conferring the resistance of microbial communities in higher stress environments. Collectively, our results showed that the bacterial communities in the soil-root continuum had different sensitivities and assembly mechanisms along an environmental gradient. These patterns are shaped simultaneously by the intertwined dimensions of proximity to roots and environmental stress change in the Loess Plateau.