Linking microbial community coalescence to ecological diversity, community assembly and species coexistence in a northern river catchment in China

Community coalescence denotes the amalgamation of biotic and abiotic factors across multiple intact ecological communities. Despite the growing attention given to the phenomenon of coalescence, there remains limited investigation into community coalescence in single and multiple source habitats and its impact on microbial community assemblages in sinks. This study focused on a major river catchment in northern China. We investigated microbial community coalescence across different habitats (i.e., water, sediment, biofilm, and riparian soil) and seasons (i.e., summer and winter). Using 16S rRNA gene amplicon sequence variants, we examined the relationship between community coalescence and microbial diversity, assembly processes, and species coexistence. The results showed that the intensity of microbial community coalescence was higher in the same habitat pairs compared to disparate habitat pairs in both summer and winter. During the occurrence of microbial community coalescence, the assembly processes regulated the intensity of coalescence. When the microbial community exhibited strong heterogeneous selection (heterogeneous environmental conditions leading to more dissimilar community structures), the intensity of community coalescence was low. With the assembly process shifted towards stochasticity, coalescence intensity increased gradually. However, when homogeneous selection (homogeneous environmental conditions leading to more similar community structures) predominantly shaped microbial communities, coalescence intensity exceeded the threshold of 0.25-0.30. Moreover, the enhanced intensity of community coalescence could increase the complexity of microbial networks, thereby enhancing species coexistence. Furthermore, the assembly processes mediated the relationship between community coalescence and species coexistence, underscoring the pivotal role of intermediate intensity of community coalescence in maintaining efficient species coexistence. In conclusion, this study highlights the crucial role of community coalescence originating from single and multiple source habitats in shaping microbial communities in sinks, thus emphasizing its central importance in watershed ecosystems.

Metagenomics-assembled analysis revealed the characteristics of antibiotic resistome and community coalescence in the soils irrigated with different irrigation materials

Antibiotic resistance has received widespread attention in recent years. Soil irrigation and fertilization are routine agricultural practices, but also lead to the spread of antibiotic resistance genes (ARGs) in soil-crop system such as via resistome coalescence. Despite community coalescence being ubiquitous and important in natural ecosystems, little research has been done to investigate resistome coalescence during soil irrigation activities. In this study, the characteristics of antibiotic resistome and community coalescence in the soils irrigated with different irrigation materials (wastewater, wastewater-river water, and wastewater-manure) have been revealed by utilizing microcosm experiments and high-throughput sequencing-based metagenomic assembly approaches. Results showed irrigation and coalescence changed soil quality and resistome. Totally, 789 unique ARGs were identified in the irrigation system, including some emerging ARGs. The abundance and diversity of ARGs increased in the coalesced soils, mainly due to the newly imported ARGs from irrigation materials. Relatively, the soils irrigated with wastewater and manure showed higher level of ARGs. Irrigation with the mixtures containing river water caused greater loss of indigenous taxa, while the community structure of mixing treatment with manure changed more dramatically. Interestingly, the succession of community in coalesced soils was influenced by transient competition for resources and ecological niche width, and the highest abundance and diversity of microorganisms and ARGs were found in the initial phase of coalescence, followed by a gradual succession towards the original community. With increasement of wastewater in the irrigation materials, the soil community showed a stepwise change rather than linear change. Notably, natural deposit of irrigation materials reduced their impacts on the ARGs in the coalesced soils. Findings provide new insights into the resistome coalescence during agricultural practices for reducing the spread risks of ARGs.

Experimental Evidence for Manure-Borne Bacteria Invasion in Soil During a Coalescent Event: Influence of the Antibiotic Sulfamethazine

The fertilization of agricultural soil by organic amendment that may contain antibiotics, like manure, can transfer bacterial pathogens and antibiotic-resistant bacteria to soil communities. However, the invasion by manure-borne bacteria in amended soil remains poorly understood. We hypothesized that this kind of process is both influenced by the soil properties (and those of its microbial communities) and by the presence of contaminants such as antibiotics used in veterinary care. To test that, we performed a microcosm experiment in which four different soils were amended or not with manure at an agronomical dose and exposed or not to the antibiotic sulfamethazine (SMZ). After 1 month of incubation, the diversity, structure, and composition of bacterial communities of the soils were assessed by 16S rDNA sequencing. The invasion of manure-borne bacteria was still perceptible 1 month after the soil amendment. The results obtained with the soil already amended in situ with manure 6 months prior to the experiment suggest that some of the bacterial invaders were established in the community over the long term. Even if differences were observed between soils, the invasion was mainly attributable to some of the most abundant OTUs of manure (mainly Firmicutes). SMZ exposure had a limited influence on soil microorganisms but our results suggest that this kind of contaminant can enhance the invasion ability of some manure-borne invaders.

Hydrodynamics-driven community coalescence determines ecological assembly processes and shifts bacterial network stability in river bends

Community coalescence, i.e., the mixing and merging of microbial communities and their surrounding environments, is prevalent in various ecosystems and potentially acts on ecological processes. River bends are distinguished by significant cross-stream velocities and spiral flow. The flow in river bends causes the mixing of microbial communities, thus making the resultant community (after mixing) different from its precursors (before mixing) through ecological processes. However, so far, no studies have explored the effect of community coalescence on ecological processes and network stability under the hydrodynamic processes of river bends. Here, we explored bacterial community assembly and community coalescence in river bends by coupling hydrodynamic profiling, aqueous biogeochemistry, DNA sequencing, and ecological theory. The results showed that the water flow dominated the community coalescence by regulating the movement of suspended sediments. The main ecological process determining the bacterial community compositions in water was the dispersal process, whereas in sediments it was the selection process. Furthermore, the negative cohesion results showed that community coalescence determined the stability of bacterial networks through competition and predation. This study depicted the bacterial community coalescence in river bends and highlighted their associations with network stability, which might provide new insights into bacterial community assembly and coalescence under complex hydrodynamics in the aquatic environment.

New insights into microbial community coalescence in the land-sea continuum

The land-sea continuum constitutes a mixing zone where soil microbial communities encounter, via runoff, those inhabiting marine coastal sediment resulting in community coalescence. Here, we propose an experimental approach, mimicking the land-sea continuum, to study the microbial community coalescence events in different situations, by 16S and 18S rRNA genes metabarcoding. The microbial community structure of sediment diverged with the soil inputs. For prokaryotes, phylogenetic enrichment and amplicon sequence variants (ASVs) replacements characterized the community changes in sediment receiving soil inputs. For fungi, despite phylogenetic enrichment was not observed, the fungal ASVs richness was maintained by soil inputs. Comparison of microbial communities revealed ASVs specific to sediment receiving soil inputs, and also ASVs shared with soil and/or runoff. Among these specific ASVs, four bacterial and one fungal ASVs were identified as indicators of coalescence. Our study provides evidences that coalescence involves the mixing of microorganisms and of the environment.

Per-, poly-fluoroalkyl substances (PFASs) and planktonic microbiomes: Identification of biotic and abiotic regulations in community coalescence and food webs

The importance of per-, poly-fluoroalkyl substances (PFASs) effects on riverine microbiomes is receiving increased recognition in the environmental sciences. However, few studies have explored how PFASs affect microbiomes across trophic levels, specifically through predator-prey interactions. This study examined the community profiles of planktonic archaea, bacteria, fungi, algae, protozoa, and metazoa in a semi-industrial and agricultural river alongside their interactions with 15 detected PFASs. As abiotic factors, PFASs affected community coalescence more than biogenic substances (p < 0.05). For biotic regulations, sub-communities in rare biospheres (including always rare taxa-ART and critically rare taxa-CRT) contributed to spatial community coalescence more than sub-communities in abundant biospheres (always abundant taxa-AAT and critically abundant taxa-CAT) (p < 0.05). Metazoa-bacteria (Modularity = 1.971) and protozoa-fungi (1.723) were determined to be the most stable predator-prey networks. Based on pathway models, short-chain PFBA (C4) was shown to weaken the trophic transfer efficiencies from heterotrophic bacteria (HB) to heterotrophic flagellates (HF) (p < 0.05). Long-chain PFTeDA (C14) promoted HB to amoeba (p < 0.05), which we postulate is the pathway for PFTeDA to enter the microbial food chain. Our preliminary results elucidated the influence of PFASs on planktonic microbial food webs and highlighted the need to consider protecting and remediating riverine ecosystems containing PFASs.

Perfluorinated compounds (PFCs) in regional industrial rivers: Interactions between pollution flux and eukaryotic community phylosymbiosis

Perfluorinated compounds (PFCs) pose serious threats to aquatic ecosystems, especially their microbial communities. However, little is known about the phylosymbiosis of aquatic fungal and viridiplantae communities in response to PFC accumulation. We quantified the distribution of 14 PFCs in rivers and found that PFBA was dominant in the transition from water to sediment. High through-put sequencing revealed that phyla Ascomycota, Basidiomycota, Anthophyta, and Chlorophyta were the predominant in eukaryotic community. The effects of PFCs on spatial community coalescence at taxonomic and phylogenetic levels (p < 0.05) were revealed. Fungal community coalescence triggered the spatial assembly of fungal and viridiplantae communities in riverine environments (p < 0.05). Null modeling indicated that PFBA, PFTrDA and PFOS, etc, mediated phylogenetic assembly (p < 0.05) and stochastic processes (86.67-100%) maintain phylogenetic turnover in the fungal community. Meanwhile, variable selection (27.78-54.44%) explained the viridiplantae community assemblage. Finally, we identified fungal genera Hannaella, Naganishia, Purpureocillium and Stachybotrys as indicators for PFC pollution (p < 0.001). These results help explain the effects of PFCs on riverine ecological remediation.

Microbial community coalescence: does it matter in the Three Gorges Reservoir?

The microbial community coalescence describes the mixing of microbial communities and the merging of their surrounding environments. Despite its prevalence in natural ecosystems and its potential influence on ecological processes, little research focused on the extent of coalescence between aquatic microbial communities. In this research, we analyzed the microbial communities in the Three Gorges Reservoir, a typical deep-water reservoir on the Yangtze River. The biogeography and the coalescence of microbial communities in water and sediment were illustrated and analyzed based on 16S rRNA gene amplicon sequence variants (ASVs). Differences in composition and diversity were identified between microbial communities in water and sediment, and microbial communities in sediment were more diverse than those in water. Between adjacent communities, by calculating the proportion of overlapped taxa, adopting the SourceTracker algorithm, and quantifying the connectivity of microbial cohesion, we found that the extent of intra-medium coalescence was strong (19.8%) and inter-media coalescence was faint (0.2%). 50 keystone species were selected using the cohesion metric. They displayed a stronger coalescence extent than average, and formed an accumulating pattern from upstream to downstream in the Three Gorges Reservoir, exhibiting their importance in the ecological network. Potential influencing factors of microbial community coalescence in aquatic environments were discussed, including environmental conditions, types of habitats, suspended particles in water, and microscale microbial activities. To summarize, this research depicted the coalescence of microbial communities in a deep-water reservoir and emphasized its ecological importance. We anticipate more attention and further research on the processes of microbial coalescence in the aquatic environment, which might provide new insights into turnover of microbial keystone species and changes in aquatic ecological conditions.

Potential for synergy in soil inoculation for nature restoration by mixing inocula from different successional stages

BACKGROUND AND AIMS

Soil inoculation is a powerful tool for the restoration of terrestrial ecosystems. However, the origin of the donor material may differentially influence early- and late-successional plant species. Donor soil from late-succession stages may benefit target plant species due to a higher abundance of soil-borne mutualists. Arable soils, on the other hand, may suppress ruderals as they support more root herbivores that preferentially attack ruderal plant species, while mid-succession soils may be intermediate in their effects on ruderals and target species performance. We hypothesized that a mixture of arable and late-succession inocula may outperform pure late-successional inocula for restoration, by promoting late-successional target plants, while simultaneously reducing ruderal species' performance.

METHODS

We conducted a glasshouse experiment and tested the growth of ruderal and target plant species on pure and mixed inocula. The inocula were derived from arable fields, mid-succession grasslands and late-succession heathlands and we created a replacement series testing different pairwise mixitures for each of these inocula types (ratios: 100:0, 75:25, 50:50, 25:75, 0:100 of inoculum A and B respectively).

RESULTS

In general, we found that a higher proportion of heathland material led to a higher aboveground biomass of target plant species, while responses of ruderal species were variable. We found synergistic effects when specific inocula were mixed. In particular, a 50:50 mixture of heathland and arable soil in the inoculum led to a significant reduction in ruderal species biomass relative to the two respective pure inocula. The overall response was driven by Myosotis arvensis, since the other two ruderal species were not significantly affected.

CONCLUSIONS

Mixing inocula from different successional stages can lead to synergistic effects on restoration, but this highly depends on the specific combination of inocula, the mixing ratio and plant species. This suggest that specific inocula may need to be developed in order to rapidly restore different plant communities.