Community Assembly Mechanisms Research Articles

Environmental heterogeneity caused by large-scale cultivation of Pyropia haitanensis shapes multi-group biodiversity distribution in coastal areas

The response of marine biodiversity to mariculture has long been a research focus in marine ecology. However, the effects of seaweed cultivation on biological community assembly are poorly understood, especially in diverse communities with distinct ecological characteristics. In this study, we used environmental DNA metabarcoding to investigate the spatial distribution patterns of bacterial, protistan, and metazoan diversity, aiming to reveal the mechanisms of community assembly in the Pyropia haitanensis cultivation zone along the Fujian coast, China. We found that, compared with the biological communities in control zones, those in P. haitanensis cultivation zones exhibited stronger geographic distance-decay patterns and displayed more complex and stable network structures. Deterministic processes (environmental selection) played a more important role in the assembly of bacterial, protistan, and metazoan communities in P. haitanensis cultivation zones, especially metazoan communities. Variance partitioning analysis showed that environmental variables made greater contributions to the diversity of the three types of communities within the P. haitanensis cultivation zones than in the control zones. Partial least squares path modeling analysis identified nitrate‑nitrogen (NO3-N), pH, particulate organic carbon (POC), and dissolved organic carbon (DOC) as the key environmental variables affecting biodiversity. Overall, the environmental heterogeneity caused by the large-scale cultivation of P. haitanensis could be the crucial factor influencing the composition and structure of various biological communities. Our results highlight the importance of the responses of multi-group organisms to the cultivation of seaweed, and provide insights into the coexistence patterns of biodiversity at the spatial scale.

Disease-induced changes in bacterial and fungal communities from plant below- and aboveground compartments

The plant microbes are an integral part of the host and play fundamental roles in plant growth and health. There is evidence indicating that plants have the ability to attract beneficial microorganisms through their roots in order to defend against pathogens. However, the mechanisms of plant microbial community assembly from below- to aboveground compartments under pathogen infection remain unclear. In this study, we investigated the bacterial and fungal communities in bulk soil, rhizosphere soil, root, stem, and leaf of both healthy and infected (Potato virus Y disease, PVY) plants. The results indicated that bacterial and fungal communities showed different recruitment strategies in plant organs. The number and abundance of shared bacterial ASVs between bulk and rhizosphere soils decreased with ascending migration from below- to aboveground compartments, while the number and abundance of fungal ASVs showed no obvious changes. Field type, plant compartments, and PVY infection all affected the diversity and structures of microbial community, with stronger effects observed in the bacterial community than the fungal community. Furthermore, PVY infection, rhizosphere soil pH, and water content (WC) contributed more to the assembly of the bacterial community than the fungal community. The analysis of microbial networks revealed that the bacterial communities were more sensitive to PVY infection than the fungal communities, as evidenced by the lower network stability of the bacterial community, which was characterized by a higher proportion of positive edges. PVY infection further increased the bacterial network stability and decreased the fungal network stability. These findings advance our understanding of how microbes respond to pathogen infections and provide a rationale and theoretical basis for biocontrol technology in promoting sustainable agriculture.Key points• Different recruitment strategies between plant bacterial and fungal communities.• Bacterial community was more sensitive to PVY infection than fungal community.• pH and WC drove the microbial community assembly under PVY infection.

Microplastics shaped performance, microbial ecology and community assembly in simultaneous nitrification, denitrification and phosphorus removal process

The widespread use of microplastics (MPs) has led to an increase in their discharge to wastewater treatment plants. However, the knowledge of impact of MPs on macro-performance and micro-ecology in simultaneous nitrification, denitrification, and phosphorus removal (SNDPR) systems is limited, hampering the understanding of potential risks posed by MPs. This study firstly comprehensively investigated the performance, species interactions, and community assembly under polystyrene (PS) and polyvinyl chloride (PVC) exposure in SNDPR systems. The results showed under PS (1, 10 mg/L) and PVC (1, 10 mg/L) exposure, total nitrogen removal was reduced by 3.38–10.15 %. PS and PVC restrained the specific rates of nitrite and nitrate reduction (SNIRR, SNRR), as well as the activities of nitrite and nitrate reductase enzymes (NIR, NR). The specific ammonia oxidation rate (SAOR) and activity of ammonia oxidase enzyme (AMO) were reduced only at 10 mg/L PVC. PS and PVC enhanced the size of co-occurrence networks, niche breadth, and number of key species while decreasing microbial cooperation by 5.85–13.48 %. Heterogeneous selection dominated microbial community assembly, and PS and PVC strengthened the contribution of stochastic processes. PICRUSt prediction further revealed some important pathways were blocked by PS and PVC. Together, the reduced TN removal under PS and PVC exposure can be attributed to the inhibition of SAOR, SNRR, and SNIRR, the restrained activities of NIR, NR, and AMO, the changes in species interactions and community assembly mechanisms, and the suppression of some essential metabolic pathways. This paper offers a new perspective on comprehending the effects of MPs on SNDPR systems.

Plant trait dissimilarity increases competitive interactions among co‐occurring plants

Abstract Plant–plant interactions, often studied in the context of plant traits, are considered crucial assembly mechanisms for plant communities and offer insights into how neighbours affect growth. Three key questions regarding these interactions have theoretical importance but limited empirical support: (1) does similarity in plant traits enhance competitive interactions among species, (2) is the “competitive environment” determined through plant traits of the resident species, and (3) do greater species diversity and niche use result in increased competition among co‐occurring species. Here we use a simple experimental design to directly test these foundational questions. In a mesocosm experiment using native grassland fragments, we investigated our questions simultaneously by manipulating trait relationships among resident and colonizing plants. To assess the net impact of neighbours on plant growth, we measured the degree of suppression experienced by focal plants compared to growth in the absence of neighbours. We further tested whether trait‐function relationships are context‐dependent by modifying available resources. Contrary to the limiting similarity hypothesis, we found that reduced overall dissimilarity mitigated neighbour‐induced growth suppression, with more negative effects occurring among dissimilar neighbours. The influence of trait dissimilarity depended on nutrient context and was stronger under increased resource availability. We found little support for the idea that specific plant traits are “functional” in creating competitive environments: no community traits (community weighted means) were associated with net neighbour effects. In contrast, resource supply significantly affected species interactions, with increased resources exacerbating negative neighbour effects on plant growth. We found that plant trait dissimilarity does function in competition but is contingent on resource context. However, trait values were not inherently competitive: traits may have physiological functions but did not function in focal plants' competitive response. We provide some of the limited data directly testing the core mechanisms of community assembly. We encourage such direct experimental tests as they are essential to building an understanding of ecological processes. Read the free Plain Language Summary for this article on the Journal blog.

New insights into substrates shaped nutrients removal, species interactions and community assembly mechanisms in tidal flow constructed wetlands treating low carbon-to-nitrogen rural wastewater

A limited understanding of microbial interactions and community assembly mechanisms in constructed wetlands (CWs), particularly with different substrates, has hampered the establishment of ecological connections between micro-level interactions and macro-level wetland performance. In this study, CWs with distinct substrates (zeolite, CW_A; manganese ore, CW_B) were constructed to investigate the nutrient removal efficiency, microbial interactions, metabolic mechanisms, and ecological assembly for treating rural sewage with a low carbon-to-nitrogen ratio. CW_B showed higher removal of ammonia nitrogen and total nitrogen by about 1.75–6.75 % and 3.42–5.18 %, respectively, compared to CW_A. Candidatus_Competibacter (denitrifying glycogen-accumulating bacteria) was the dominant microbial genus in CW_A, whereas unclassified_f_Blastocatellaceae (involved in carbon and nitrogen transformation) dominated in CW_B. The null model revealed that stochastic processes (drift) dominated community assembly in both CWs; however, deterministic selection accounted for a higher proportion in CW_B. Compared to those in CW_A, the interactions between microbes in CW_B were more complex, with more key microbes involved in carbon, nitrogen, and phosphorus conversion; the synergistic cooperation of functional bacteria facilitated simultaneous nitrification-denitrification. Manganese ores favour biofilm formation, increase the activity of the electron transport system, and enhance ammonia oxidation and nitrate reduction. These results elucidated the ecological patterns exhibited by microbes under different substrate conditions thereby contributing to our understanding of how substrates shape distinct microcosms in CW systems. This study provides valuable insights for guiding the future construction and management of CWs.

Local Community Assembly Mechanisms and the Size of Species Pool Jointly Explain the Beta Diversity of Soil Fungi

Fungi play vital regulatory roles in terrestrial ecosystems. Local community assembly mechanisms, including deterministic and stochastic processes, as well as the size of regional species pools (gamma diversity), typically influence overall soil microbial community beta diversity patterns. However, there is limited evidence supporting their direct and indirect effects on beta diversity of different soil fungal functional groups in forest ecosystems. To address this gap, we collected 1606 soil samples from a 25-ha subtropical forest plot in southern China. Our goal was to determine the direct effects and indirect effects of regional species pools on the beta diversity of soil fungi, specifically arbuscular mycorrhizal (AM), ectomycorrhizal (EcM), plant-pathogenic, and saprotrophic fungi. We quantified the effects of soil properties, mycorrhizal tree abundances, and topographical factors on soil fungal diversity. The beta diversity of plant-pathogenic fungi was predominantly influenced by the size of the species pool. In contrast, the beta diversity of EcM fungi was primarily driven indirectly through community assembly processes. Neither of them had significant effects on the beta diversity of AM and saprotrophic fungi. Our results highlight that the direct and indirect effects of species pools on the beta diversity of soil functional groups of fungi can significantly differ even within a relatively small area. They also demonstrate the independent and combined effects of various factors in regulating the diversities of soil functional groups of fungi. Consequently, it is crucial to study the fungal community not only as a whole but also by considering different functional groups within the community.

Fecal microbiota reveal adaptation of herbivores to the extreme environment of the Qinghai–Tibet Plateau

AbstractBackgroundGut microbiota is pivotal in regulating hosts' biological processes and maintaining homeostasis, but knowledge about its role in wild herbivores in extreme environments remains limited.MethodsGut bacteria and fungi were sequenced in ruminant (Chiru and Yak) and nonruminant (Kiang) herbivores on the Qinghai–Tibet Plateau, and their community structure, co‐occurrence networks, functions, and assembly mechanisms were investigated using multivariate ecological and statistical methods.ResultsKiang had lower gut microbial diversity than Chiru and Yak. Bacterial host‐specific exclusivity was greater than that of fungi. In addition to the evidence of glycan biosynthesis and carbohydrate metabolism, Chiru had a high Firmicutes/Bacteroidetes ratio and low animal pathogen abundance, suggesting better adaptation to the plateau's harsh environment. Additionally, members of gut microbiota tended to co‐occur rather than co‐exclude in all herbivores. Different network complexity and stability patterns were observed between bacterial and fungal communities. Furthermore, gut bacterial assembly was primarily controlled by stochastic dispersal limitation and drift, whereas fungal assembly was primarily controlled by deterministic homogeneous selection except in Chiru.ConclusionsOn the Qinghai–Tibet Plateau, Chiru and Yak exhibit more diverse gut microbiota and more diverse metabolic functions than Kiang, and gut bacteria are more divergent than gut fungi in these herbivores.

Role of generalists, specialists and opportunists in Nitrospira community assembly in soil aggregates from nearby cropland and grassland areas in a campus

Nitrospirota is an essential contributor to nitrification. However, the community assembly mechanism of such organisms in soil aggregates from nearby but different ecosystems is unclear. We quantitatively measured the relative contributions of generalists, opportunists and specialists to the Nitrospira community assembly. Nitrospira were more abundant in agricultural soils than in grasslands and were relatively enriched in microaggregates in both agricultural (AS) and grassland soils (GS). These findings could be explained by the neutral pH of AS and the relatively high organic carbon quantity of the aggregates. The community variation in Nitrospira was driven by both ecosystem and aggregate size fractions, with dispersal and drift dominating the assembly process, partly explained by macro- and microaggregates with higher organic quality that can reduce selection pressures to enrich Nitrospira species (indicated by a higher α diversity), supporting more stochastic processes (drift and dispersal limitations) in community assembly. Generalists belonging to Namibia soil cluster 2, followed by unknown Nitrospira and other lineage II members, contributed to the stochastic assembly, as indicated by a high normalized stochasticity ratio (NST) value of 0.618. A total of 89.7 % and 5.6 % of the ASVs were defined as opportunists and generalists, respectively. Opportunists expand their taxonomic affiliation from Nitrospira lineages I, II, V, and grassland metagenome lineages to unknown lineages, and almost all specialists cannot be assigned to a known lineage or a subcluster. We observed that the NSTs for Opportunists and specialists were approximately 0.472 and 0.247, respectively, suggesting that the assembly of opportunists was less dominated by stochastic processes than was that of generalists, while the assembly of specialists highly relied on deterministic processes. Indeed, limited variation in the abundances of opportunists and specialists was significantly explained by the soil properties, agreeing that variable selection slightly contributed to Nitrospira community assembly. We also highlighted that each specialist with an unknown affiliation could be a new species or variant from Nitrospira in “specific” micro-environments, as indicated by the fact that one species occurred in only a few soil aggregate size fractions. The present study presents a case in which the stochastic process of Nitrospira community assembly in soil aggregates from two nearby ecosystems with mild environmental conditions could be explained by a high proportion of opportunists plus generalists and a few microhabitat specialists.

Keystone taxa enhance the stability of soil bacterial communities and multifunctionality under steelworks disturbance

Continuous discharge of wastewater, emissions, and solid wastes from steelworks poses environmental risks to ecosystems. However, the role of keystone taxa in maintaining multifunctional stability during environmental disturbances remains poorly understood. To address this, we investigated the community diversity, assembly mechanisms, and soil multifunctionality of soils collected from within the steelworks (I), within 2.5 km radius from the steelworks (E), and from an undisturbed area (CK) in Jiangsu Province, China, via 16 S rRNA sequencing. Significant differences were found in the Chao1 and the richness indexes of the total taxa (p < 0.05), while the diversity of keystone taxa was not significant at each site (p > 0.05). The deterministic processes for total taxa were 42.9%, 61.9% and 47.7% in CK, E, and I, respectively. Steelworks stress increased the deterministicity of keystone taxa from 52.3% in CK to 61.9% in E and I soils. The average multifunctionality indices were 0.518, 0.506 and 0.513 for CK, E and I, respectively. Although the soil multifunctionality was positive correlated with α diversity of both the total and keystone taxa, the average degree of keystone taxa in functional network increased significantly (79.96 and 65.58, respectively), while the average degree of total taxa decreased (44.59 and 51.25, respectively) in the E and I. This suggests keystone taxa contribute to promoting the stability of ecosystems. With increasing disturbance, keystone taxa shift their function from basic metabolism (ribosome biogenesis) to detoxification (xenobiotics biodegradation, metabolism, and benzoate degradation). Here we show that keystone taxa are the most important factor in maintaining stable microbial communities and functions, providing new insights for mitigating pollution stress and soil health protection.

Historical and dispersal processes drive community assembly of multiple aquatic taxa in glacierized catchments in the Qinghai-Tibet plateau

Understanding the relative role of dispersal dynamics and niche constraints is not only a core task in community ecology, but also becomes an important prerequisite for bioassessment. Despite the recent progress in our knowledge of community assembly in space and time, patterns and processes underlying biotic communities in alpine glacierized catchments remain mostly ignored. To fill this knowledge gap, we combined the recently proposed dispersal-niche continuum index (DNCI) with traditional constrained ordinations and idealized patterns of species distributions to unravel community assembly mechanisms of different key groups of primary producers and consumers (i.e., phytoplankton, epiphytic algae, zooplankton, macroinvertebrates, and fishes) in rivers in the Qinghai-Tibet Plateau, the World's Third Pole. We tested whether organismal groups with contrasting body sizes differed in their assembly processes, and discussed their applicability in bioassessment in alpine zones. We found that community structure of alpine river biotas was always predominantly explained in terms of dispersal dynamics and historical biogeography. These patterns are most likely the result of differences in species-specific functional attributes, the stochastic colonization-extinction dynamics driven by multi-year glacier disturbances and the repeated hydrodynamic separation among alpine catchments after the rising of the Qilian mountains. Additionally, we found that the strength of dispersal dynamics and niche constraints was partially mediated by organismal body sizes, with dispersal processes being more influential for microscopic primary producers. Finding that zooplankton and macroinvertebrate communities followed clumped species replacement structures (i.e., Clementsian gradients) supports the notion that environmental filtering also contributes to the structure of high-altitude animal communities in glacierized catchments. In terms of the applied fields, we argue that freshwater bioassessment in glacierized catchments can benefit from incorporating the metacommunity perspective and applying novel approaches to (i) detect the optimal spatial scale for species sorting and (ii) identify and eliminate the species that are sensitive to dispersal-related processes.

Reproducible responses of geochemical and microbial successional patterns in the subsurface to carbon source amendment

Carbon amendments designed to remediate environmental contamination lead to substantial perturbations when injected into the subsurface. For the remediation of uranium contamination, carbon amendments promote reducing conditions to allow microorganisms to reduce uranium to an insoluble, less mobile state. However, the reproducibility of these amendments and underlying microbial community assembly mechanisms have rarely been investigated in the field. In this study, two injections of emulsified vegetable oil were performed in 2009 and 2017 to immobilize uranium in the groundwater at Oak Ridge, TN, USA. Our objectives were to determine whether and how the injections resulted in similar abiotic and biotic responses and their underlying community assembly mechanisms. Both injections caused similar geochemical and microbial succession. Uranium, nitrate, and sulfate concentrations in the groundwater dropped following the injection, and specific microbial taxa responded at roughly the same time points in both injections, including Geobacter, Desulfovibrio, and members of the phylum Comamonadaceae, all of which are well established in uranium, nitrate, and sulfate reduction. Both injections induced a transition from relatively stochastic to more deterministic assembly of microbial taxonomic and phylogenetic community structures based on 16S rRNA gene analysis. We conclude that geochemical and microbial successions after biostimulation are reproducible, likely owing to the selection of similar phylogenetic groups in response to EVO injection.

Variation and Correlation among Fine Root Traits of Desert Plants in Arid Areas of Northwest China

Variation and Correlation among Fine Root Traits of Desert Plants in Arid Areas of Northwest China

Phages in different habitats and their ability to carry antibiotic resistance genes

As the most abundant organisms on Earth, phages play a key role in the evolution of bacterial antibiotic resistance. Although previous studies have demonstrated the molecular mechanisms of horizontal gene transfer mediated by mobile genetic elements, our understanding of the intertwined relationships between antibiotic resistance genes (ARGs) and phages is limited. In this study, we analysed 2781 metagenomic samples to reveal the composition and species interactions of phage communities in different habitats as well as their capacity to carry ARGs with health risks. The composition of phage communities varies in different habitats and mainly depends on environmental conditions. Terrestrial habitats display more complex and robust interactions between phages than aquatic and human-associated habitats, resulting in the highest biodiversity of phages. Several types of phages in certain taxa (4.95–7.67%, mainly belonging to Caudoviricetes) have the capacity to carry specific ARGs and display a high potential risk to human health, especially in human-associated habitats. Overall, our results provide insights into the assembly mechanisms of phage communities and their effects on the dissemination of antibiotic resistance.

Microbial community structure in a constructed wetland based on a recirculating aquaculture system: Exploring spatio-temporal variations and assembly mechanisms

The diversity, composition and performance of microbial communities within constructed wetlands (CW) were markedly influenced by spatio-temporal variations. A pilot-scale integrated vertical-flow constructed wetland (IVCW) as the biological purification unit within a recirculating aquaculture system (RAS) was established and monitored in this study. The investigation aimed to elucidate the responses of community structure, co-occurrence networks, and assembly mechanisms of the microbial community to spatial and temporal changes. Spatially, all a-diversity indices and microbial networks complexity were significantly higher in the upstream pool of the IVCW than in the downstream pool. Temporally, the richness increased over time, while the evenness showed a decreasing trend. The number of nodes and edges of microbial networks increased over time. Notably, the stable pollutant removal efficiencies were observed during IVCW operations, despite a-diversity and bacterial community networks exhibited significant variations across time. Functional redundancy emerged as a likely mechanism contributing to the stability of microbial ecosystem functions. Null model and neutral model analyses revealed the dominance of deterministic processes shaping microbial communities over time, with deterministic influences being more pronounced at lower a-diversity levels. DO and inorganic nitrogen emerged as the principal environmental factor influencing microbial community dynamics. This study provides a theoretical foundation for the regulation of microbial communities and environmental factors within the context of IVCW.

Soil microbial subcommunity assembly mechanisms are highly variable and intimately linked to their ecological and functional traits.

Revealing the mechanisms underlying soil microbial community assembly is a fundamental objective in molecular ecology. However, despite increasing body of research on overall microbial community assembly mechanisms, our understanding of subcommunity assembly mechanisms for different prokaryotic and fungal taxa remains limited. Here, soils were collected from more than 100 sites across southwestern China. Based on amplicon high-throughput sequencing and iCAMP analysis, we determined the subcommunity assembly mechanisms for various microbial taxa. The results showed that dispersal limitation and homogenous selection were the primary drivers of soil microbial community assembly in this region. However, the subcommunity assembly mechanisms of different soil microbial taxa were highly variable. For instance, the contribution of homogenous selection to Crenarchaeota subcommunity assembly was 70%, but it was only around 10% for the subcommunity assembly of Actinomycetes, Gemmatimonadetes and Planctomycetes. The assembly of subcommunities including microbial taxa with higher occurrence frequencies, average relative abundance and network degrees, as well as wider niches tended to be more influenced by homogenizing dispersal and drift, but less affected by heterogeneous selection and dispersal limitation. The subcommunity assembly mechanisms also varied substantially among different functional guilds. Notably, the subcommunity assembly of diazotrophs, nitrifiers, saprotrophs and some pathogens were predominantly controlled by homogenous selection, while that of denitrifiers and fungal pathogens were mainly affected by stochastic processes such as drift. These findings provide novel insights into understanding soil microbial diversity maintenance mechanisms, and the analysis pipeline holds significant value for future research.

Higher stochasticity in comammox Nitrospira community assembly in upland soils than the adjacent paddy soils at a regional scale

Understanding the assembly mechanisms of microbial communities, particularly comammox Nitrospira, in agroecosystems is crucial for sustainable agriculture. However, the large-scale distribution and assembly processes of comammox Nitrospira in agricultural soils remain largely elusive. We investigated comammox Nitrospira abundance, community structure, and assembly processes in 16 paired upland peanuts and water-logged paddy soils in south China. Higher abundance, richness, and network complexity of comammox Nitrospira were observed in upland soils than in paddy soils, indicating a preference for upland soils over paddy soils among comammox Nitrospira taxa in agricultural environments. Clade A.2.1 and clade A.1 were the predominant comammox Nitrospira taxa in upland and paddy soils, respectively. Soil pH was the most crucial factor shaping comammox Nitrospira community structure. Stochastic processes were found to predominantly drive comammox Nitrospira community assembly in both upland and paddy soils, with deterministic processes playing a more important role in paddy soils than in upland soils. Overall, our findings demonstrate the higher stochasticity of comammox Nitrospira in upland soils than in the adjacent paddy soils, which may have implications for autotrophic nitrification in acidic agricultural soils.

Dispersal constrains the biotic connectivity of mountain assemblages

AbstractAimClimate warming is shifting the bioclimatic optima of species towards mountaintops, but the ability of organisms to track these changes also depends on their dispersal skills. Here, we assessed the role of dispersal over niche‐driven processes in connecting assemblages along mountain slopes and between mountain massifs.LocationCantabrian Mountains, Spain.TaxonBirds (Animalia; Aves) and Lichens (Fungi; Ascomycota, Basidiomycota).MethodsWe examined the change with elevation of community‐level traits that are dispersal proxies (wing shape in birds and type of dispersing propagule in lichens) and ecological niche proxies (micro‐habitat, substrate, and foraging features). We then permutate species composition within sites and massifs to create models of species distribution constrained by dispersal and niche processes. These models were compared with observed species distribution to disclose the relative contribution of dispersal and niche‐based processes in the biotic interchange along mountain slopes (vertical connectivity) and between isolated summits (horizontal connectivity).ResultsBoth bird and lichen communities were formed by species with traits that enhance dispersal at high elevations. These groups also showed similarities in the elevational patterns of niche diversity, which dropped at high elevations. Dispersal was by far the dominant assembly mechanism in both taxa. Pairwise community comparisons among elevation belts showed weak vertical connectivity, with predominant dispersal limitations but also niche barriers between the extremes of the gradient. Among massifs, horizontal connectivity was higher among high mountain assemblages than those from lower elevations.Main ConclusionDispersal was found to be the dominant assembly mechanism in mountain systems, even in taxa with high dispersal potential. Highland assemblages had low functional diversity but their species had high mobility. This permits biotic interchange between isolated summits and, potentially, colonization of other summits as climate warms. Our framework combining traits and occurrence‐permutation models improve the understanding of community assembly mechanisms along elevation gradients and points to dispersal limitations, especially at low‐middle elevations.

Anthropogenic vs. natural habitats: Higher microbial biodiversity pays the trade-off of lower connectivity

Climate change and anthropogenic disturbances are known to influence soil biodiversity. The objectives of this study were to compare the community composition, species coexistence patterns, and ecological assembly processes of soil microbial communities in a paired setting featuring a natural and an anthropogenic ecosystem facing each other at identical climatic, pedological, and vegetational conditions. A transect gradient from forest to seashore allowed for sampling across different habitats within both sites. The field survey was carried out at two adjacent strips of land within the Po River delta lagoon system (Veneto, Italy) one of which is protected within a natural preserve and the other has been converted for decades into a tourist resort. The anthropogenic pressure interestingly led to an increase in the α-diversity of soil microbes but was accompanied by a reduction in β-diversity. The community assembly mechanisms of microbial communities differentiate in natural and anthropic ecosystems: for bacteria, in natural ecosystems deterministic variables and homogeneous selection play a main role (51.92%), while stochastic dispersal limitation (52.15%) is critical in anthropized ecosystems; for fungi, stochastic dispersal limitation increases from 38.1% to 66.09% passing from natural to anthropized ecosystems. We are on calcareous sandy soils and in more natural ecosystems a variation of topsoil pH favors the deterministic selection of bacterial communities, while a divergence of K availability favors stochastic selection. In more anthropized ecosystems, the deterministic variable selection is influenced by the values of SOC. Microbial networks in the natural system exhibited higher numbers of nodes and network edges, as well as higher averages of path length, weighted degree, clustering coefficient, and density than its equivalent sites in the more anthropically impacted environment. The latter on the other hand presented a stronger modularity. Although the influence of stochastic processes increases in anthropized habitats, niche-based selection also proves to impose constraints on communities. Overall, the functionality of the relationships between groups of microorganisms co-existing in communities appeared more relevant to the concept of functional biodiversity in comparison to the plain number of their different taxa. Fewer but functionally more organized lineages displayed traits underscoring a better use of the resources than higher absolute numbers of taxa when those are not equally interconnected in their habitat exploitation. However, considering that network complexity can have important implications for microbial stability and ecosystem multifunctionality, the extinction of complex ecological interactions in anthropogenic habitats may impair important ecosystem services that soils provide us.

Successional changes in bacterial phyllosphere communities are plant-host species dependent.

Leaf surface microbiomes have the potential to influence agricultural and ecosystem productivity. We assessed their stability by determining composition, functional resistance, and resilience. Resistance is the degree to which communities remain unchanged as a result of disturbance, and resilience is the ability of a community to recover to pre-disturbance conditions. By understanding the mechanisms of community assembly and how they relate to the resistance and resilience of microbial communities under common environmental stresses such as drought, we can better understand how communities will adapt to a changing environment and how we can promote healthy agricultural microbiomes. In this study, phyllosphere compositional stability was highly related to plant host species phylogeny and, to a lesser extent, known stress tolerances. Phyllosphere community assembly and stability are a result of complex interactions of ecological processes that are differentially imposed by host species.

Microbial communities exhibit distinct diversities and assembly mechanisms in rainwater and tap-water storage systems

Roof-harvested rainwater stored for potable and nonpotable usages represent a clean and sustainable water supply resource. However, the microbial dynamics and mechanisms of community assembly in long-termed operated rainwater storage systems remain elusive. In this study, characteristics of microbial communities in different habitats were systematically compared within rainwater and tap-water simulated storage systems (SWSSs) constructed with different tank materials (PVC, stainless steel and cement). Distinct microbial communities were observed between rainwater and tap-water SWSSs for both water and biofilm samples (ANOSIM, p < 0.05), with lower diversity indexes noted in rainwater samples. Notably, a divergent potential pathogen profile was observed between rainwater and tap-water SWSSs, with higher relative abundances of potential pathogens noted in rainwater SWSSs. Moreover, tank materials had a notable impact on microbial communities in rainwater SWSSs (ANOSIM, p < 0.05), rather than tap-water SWSSs, illustrating the distinct interplay between water chemistry and engineering factors in shaping the SWSS microbiomes. Deterministic processes contributed predominantly to the microbial community assembly in cement rainwater SWSSs and all tap-water SWSSs, which might be ascribed to the high pH levels in cement rainwater SWSSs and low-nutrient levels in all tap-water SWSSs, respectively. However, microbial communities in the PVC and stainless-steel rainwater SWSSs were mainly driven by stochastic processes. Overall, the results provided insights to the distinct microbial assembly mechanisms and potential health risks in stored roof-harvested rainwater, highlighting the importance of developing tailored microbial management strategies for the storage and utilization of rainwater.