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• Plant microbiomes are essential to host health and productivity but the ecological processes that govern crop microbiome assembly are not fully known. • Here we examined bacterial communities across 684 samples from soils (rhizosphere and bulk soil) and multiple compartment niches (rhizoplane, root endosphere, phylloplane, and leaf endosphere) in maize (Zea mays)-wheat (Triticum aestivum)/barley (Hordeum vulgare) rotation system under different fertilization practices at two contrasting sites. • Our results demonstrate that microbiome assembly along the soil-plant continuum is shaped predominantly by compartment niche and host species rather than by site or fertilization practice. From soils to epiphytes to endophytes, host selection pressure sequentially increased and bacterial diversity and network complexity consequently reduced, with the strongest host effect in leaf endosphere. Source tracking indicates that crop microbiome is mainly derived from soils and gradually enriched and filtered at different plant compartment niches. Moreover, crop microbiomes were dominated by a few dominant taxa (c. 0.5% of bacterial phylotypes), with bacilli identified as the important biomarker taxa for wheat and barley and Methylobacteriaceae for maize. • Our work provides comprehensive empirical evidence on host selection, potential sources and enrichment processes for crop microbiome assembly, and has important implications for future crop management and manipulation of crop microbiome for sustainable agriculture.

Highly diverse exoenzymes mediate the energy flow from substrates to the multitrophic microbiota within the soil decomposer micro‐food web. Here, we used a “soil enzyme profile analysis” approach to establish a series of enzyme profile indices; those indices were hypothesized to reflect micro‐food web features. We systematically evaluated the shifts in enzyme profile indices in relation to the micro‐food web features in the restoration of an abandoned cropland to a natural area. We found that enzymatic C:N stoichiometry and decomposability index were significantly associated with substrate availability. Furthermore, the higher Shannon diversity index in the exoenzyme profile, especially for the C‐degrading hydrolase, corresponded to a greater microbiota community diversity. The increased complexity and stability of the exoenzyme network reflected similar changes with the micro‐food web networks. In addition, the gross activity of the enzyme profile as a parameter for soil multifunctionality, effectively predicted the substrate content, microbiota community size, diversity, and network complexity. Ultimately, the proposed enzymic channel index was closely associated with the traditional decomposition channel indices derived from microorganisms and nematodes. Our results showed that soil enzyme profile analysis reflected very well the decomposer food web features. Our study has important implications for projecting future climate change or anthropogenic disturbance impacts on soil decomposer micro‐food web features by using soil enzyme profile analysis. This study proposed the approach of a “soil enzyme profile analysis” whereby a series of enzyme profile indices were hypothesized to comprehensively reflect the micro‐food web features. Using a case study on the restored natural area of a post‐arable system, we systematically evaluated the shifts in enzyme profile indices in relation to the micro‐food web features. +, −, ↑, and ↓ represent positive correlation, negative correlation, increase, and decrease trends, respectively. Highlights Soil enzyme profile analysis for indicating decomposer micro‐food web features was first proposed. Diversity indication utilities for contrasting enzyme profiles were different. Protozoa channel index and enzymatic channel index were proposed.

Elevated CO2 (eCO2) stimulates productivity and nutrient demand of crops. Thus, comprehensively understanding the crop phosphorus (P) acquisition strategy is critical for sustaining agriculture to combat climate changes. Here, wheat (Triticum aestivum L) was planted in field in the eCO2 (550 µmol mol−1) and ambient CO2 (aCO2, 415 µmol mol−1) environments. We assessed the soil P fractions, root morphological and physiological traits and multitrophic microbiota [including arbuscular mycorrhizal fungi (AMF), alkaline phosphomonoesterase (ALP)‐producing bacteria, protozoa, and bacterivorous and fungivorous nematodes] in the rhizosphere and their trophic interactions at jointing stage of wheat. Compared with aCO2, significant 20.2% higher shoot biomass and 26.8% total P accumulation of wheat occurred under eCO2. The eCO2 promoted wheat root length and AMF hyphal biomass, and increased the concentration of organic acid anions and the ALP activity, which was accompanied by significant decreases in calcium‐bound inorganic P (Ca‐Pi) (by 16.7%) and moderately labile organic P (by 26.5%) and an increase in available P (by 14.4%) in the rhizosphere soil. The eCO2 also increased the growth of ALP‐producing bacteria, protozoa, and bacterivorous and fungivorous nematodes in the rhizosphere, governed their diversity and community composition. In addition, the eCO2 strengthened the trophic interactions of microbiota in rhizosphere; specifically, the eCO2 promoted the associations between protozoa and ALP‐producing bacteria, between protozoa and AMF, whereas decreased the associations between ALP‐producing bacteria and nematodes. Our findings highlighted the important role of root traits and multitrophic interactions among microbiota in modulating crop P‐acquisition strategies, which could advance our understanding about optimal P management in agriculture systems under global climate changes. The Elevated CO2 (eCO2) promoted wheat phosphorus (P) accumulation through increased root length and arbuscular mycorrhizal fungi (AMF) hyphal biomass, the concentration of organic acid anions and the alkaline phosphomonoesterase (ALP) activity. The eCO2 also increased the growth of ALP‐producing bacteria, protozoa and bacterivorous and fungivorous nematodes in the rhizosphere, and strengthened their trophic interactions. Highlights Elevated CO2 (eCO2) promoted wheat root length, organic acid anions, arbuscular mycorrhizal fungi (AMF) hyphal biomass, and wheat phosphorus (P) accumulation eCO2 decreased calcium‐bound inorganic P (Ca‐Pi) and moderately labile organic P but increased available P in the rhizosphere eCO2 increased the growth of alkaline phosphomonoesterase (ALP)‐producing bacteria, protozoa and bacterivorous and fungivorous nematodes and strengthened their trophic interactions

Since its initial release in 2022, ggClusterNet has become a vital tool for microbiome research, enabling microbial co‐occurrence network analysis and visualization in over 300 studies. To address emerging challenges, including multi‐factor experimental designs, multi‐treatment conditions, and multi‐omics data, we present a comprehensive upgrade with four key components: (1) A microbial co‐occurrence network pipeline integrating network computation (Pearson/Spearman/SparCC correlations), visualization, topological characterization of network and node properties, multi‐network comparison with statistical testing, network stability (robustness) analysis, and module identification and analysis; (2) Network mining functions for multi‐factor, multi‐treatment, and spatiotemporal‐scale analysis, including Facet.Network() and module.compare.m.ts(); (3) Transkingdom network construction using microbiota, multi‐omics, and other relevant data, with diverse visualization layouts such as MatCorPlot2() and cor_link3(); and (4) Transkingdom and multi‐omics network analysis, including corBionetwork.st() and visualization algorithms tailored for complex network exploration, including model_maptree2(), model_Gephi.3(), and cir.squ(). The updates in ggClusterNet 2 enable researchers to explore complex network interactions, offering a robust, efficient, user‐friendly, reproducible, and visually versatile tool for microbial co‐occurrence networks and indicator correlation patterns. The ggClusterNet 2R package is open‐source and available on GitHub (https://github.com/taowenmicro/ggClusterNet). ggClusterNet 2 drives the evolution of network analysis, offering researchers an accurate, efficient, convenient, reproducible, and visually compelling tool. Highlights The ggClusterNet 2 introduces a comprehensive microbial co‐occurrence network analysis pipeline. Enhanced network analysis workflow tailored for complex experimental designs and diverse data types. Enhanced visualization of microbiomes and their correlated environmental or host‐associated indicators. Introduced various visualization algorithms for transkingdom and multi‐omics interaction networks.

Background The contamination of the aquatic environment of urban rivers with industrial wastewater has affected the abiotic conditions and biological activities of the trophic levels of the ecosystem, particularly sediments. However, most current research about microorganism in urban aquatic environments has focused on indicator bacteria related to feces and organic pollution. Meanwhile, they ignored the interactions among microorganisms. To deeply understand the impact of industrial contamination on microbial community, we study the bacterial community structure and diversity in river sediments under the influence of different types of industrial pollution by Illumina MiSeq high-throughput sequencing technology and conduct a more detailed analysis of microbial community structure through co-occurrence networks. Results The overall community composition and abundance of individual bacterial groups differed between samples. In addition, redundancy analysis indicated that the structure of the bacterial community in river sediments was influenced by a variety of environmental factors. TN, TP, TOC and metals (Cu, Zn and Cd) were the most important driving factors that determined the bacterial community in urban river sediments ( P  < 0.01). According to PICRUSt analysis, the bacterial communities in different locations had similar overall functional profiles. It is worth noting that the 15 functional genes related to xenobiotics biodegradation and metabolism were the most abundant in the same location. The non-random assembly patterns of bacterial composition in different types of industrially polluted sediments were determined by a co-occurrence network. Environmental conditions resulting from different industrial pollutants may play an important role in determining their co-occurrence patterns of these bacterial taxa. Among them, the bacterial taxa involved in carbon and nitrogen cycles in module I were relatively abundant, and the bacterial taxa in module II were involved in the repair of metal pollution. Conclusions Our data indicate that long-term potential interactions between different types of industrial pollution and taxa collectively affect the structure of the bacterial community in urban river sediments.

Soil microbial communities are involved in and contribute to several processes in soil ecosystems. Nonetheless, how various forest management approaches and their timeframes influence soil microbial community composition and network complexity is poorly understood. Hence, in this study, a time‐series method examined how microbial populations in the soil of Carya cathayensis var. dabeishansis forests varied across different management practices (no management, extensive management, and intensive management) and over periods of 0, 3, 8, 15, and 20 years. High‐throughput sequencing determined the species composition of soil microbial communities, co‐occurrence network analysis assessed interrelationships between communities, and null model theory elucidated deterministic and stochastic processes governing community assembly. The results indicated that under both treatment methods, soil bacterial diversity indices increased compared to the control during short‐term management (3 years), but subsequently declined with further prolonged management duration. Moreover, soil acid phosphatase activity and total potassium levels primarily shaped the bacterial species in the soil, with Acidobacteriota (21.96%–31.45%), Proteobacteria (22.82%–31.12%), Actinobacteria (6.81%–13.05%), and Chloroflexi (6.68%–9.67%) representing the most prevalent bacterial taxa. Interactions between soil bacterial and fungal communities were predominantly cooperative across both management strategies (79.88%–100%). However, the degree of cooperation fluctuated throughout the duration. Stochastic processes, particularly diffusion limitation, played a key role in shaping the assembly of these microbial communities. The diffusion limitation of soil microorganisms was smaller in extensively managed forests than in intensively managed forests. These results highlight the need for balanced forest management strategies, where short‐term intensive practices could help preserve soil microbial diversity and sustain ecosystem functions. Therefore, we strongly recommend adopting an intermittent forest management approach, particularly in intensively managed forests, where it is necessary to allow the ecosystem adequate time for autonomous recovery. The interspecific relationships between soil bacterial and fungal communities were mainly collaborative in both extensive management and intensive management; Sustained forest management negatively affects soil microbial diversity, composition, and network complexity; Soil microbial community assembly processes diverge under different management methods.

Habitat and temporal variation can both influence microbial community dynamics, although their relative importance in reservoir buffer zones with complex hydrology regimes and dramatically altered environments remains controversial. To elucidate this, we investigated spatiotemporal variation in soil bacterial diversity and ecological processes from the flooding period to the dry period (April and June, respectively) using high‐throughput 16S amplicon sequencing in three habitats (abandoned cropland, grassland, and woodland) within the Chushandian Reservoir's buffer strip, China. The results showed that habitat was more important than temporal variation in shaping soil bacterial diversity and ecological processes in the reservoir buffer zone. Bacterial communities responded to temporal variation both in terms of species composition and function; temporal variation affected bacterial communities mostly by altering the abundance of shared species and by causing the resurgence or extinction of specific taxa within the same habitat. The main driver of these changes was the resilience capacity of habitats to the changing moisture environment. The magnitude and underlying mechanisms of the changes in bacterial community diversity and ecological processes differed markedly between the three habitats, owing mostly to the characteristics of their vegetation, thus the allocation ratios of different habitat vegetation types and landscape diversity should pay attention for the reservoir buffer zone management, improving the integrated ecological benefits of the reservoir ecosystem from a multiscale. Habitat is more important than temporal variation in shaping soil bacterial community diversity in reservoir buffer strips; the adaptive capacity of habitats to changes in the moisture environment is the main driver. Changes in the abundance of shared species and resurgence or extinction of some specific taxa in the same habitat.

Community composition is determined by four processes: drift, selection, dispersal, and speciation. The crucial issue in understanding community assembly is disentangling the relative importance of those processes. However, this issue has not been adequately addressed in benthic foraminiferal communities. A comprehensive study of benthic foraminiferal community composition, co‐occurrence network, and community assembly was conducted on the Xisha carbonate platform. The community composition was determined via the environmental DNA (eDNA) technique. Heavy metals (Co, Cr, Cu, Ni, Pb, V, and Zn), grain size, loss on ignition (LOI), organic carbon, and pH were chosen for environmental measurement. We evaluated the effects of environmental variables on the community composition and the co‐occurrence network, revealing that the former was affected only by organic carbon, whereas the latter was affected by both organic carbon and pH. Null and neutral models demonstrated that foraminiferal community assembly was driven by ecological drift instead of selection. The β‐NTI (a measure of the relative importance of deterministic and stochastic processes) had strong and positive correlations with community β‐diversity (compositional differences between pairs of communities) and network β‐diversity (structural differences between pairs of subnetworks). A conceptual model was offered to explain how heterogeneous selection and stochastic processes interact to affect the two β‐diversities. This study is the first to quantitatively assess the effects of variation in the relative importance of deterministic and stochastic processes on community β‐diversity and network β‐diversity in foraminifera; it provides new insight into the mechanisms underlying β diversity. We investigate benthic foraminiferal communities on the Xisha carbonate platform via the eDNA technique and conduct a comprehensive study, including community composition, co‐occurrence network, and community assembly. We assess the relative importance of deterministic and stochastic processes in foraminiferal community assembly and find that drift is the main driving force. We hypothesize that community β‐diversity and network β‐diversity increase with the strength of heterogeneous selection and provide a conceptual model to test our hypothesis.

The obstruction of lateral hydrologic connectivity poses a significant threat to floodplain ecosystems, with fishes being particularly susceptible to the impacts of such disturbances. Existing research about the effects of human activities on fish communities in the Yangtze River basin primarily focused on measures of diversity such as species diversity, functional diversity, and beta diversity. This study goes beyond by examining patterns of fish species and functional diversity variation, as well as revealing the pattern of species disappearance and its implications for maintaining fish community structure and function. Our findings highlight the importance of understanding the role of fish species in maintaining ecosystem function. We revealed a significant decrease in both fish species richness and functional richness across temporal (1960s, 1980s, and 2000s) and spatial (connected lakes, partially connected lakes, and disconnected lakes) scales. Among the disappearing fish species, those belonging to small‐sized and large‐sized genera exhibited a higher frequency of disappearance compared to those in moderate‐sized genera. Nevertheless, the complexity of fish communities' co‐occurrence networks does not exhibit a significant decrease with a decrease in species/functional richness, potentially due to the presence of niche overlap species (e.g., coexistence species within a single genus in our study). Our findings support the species redundancy hypothesis in elucidating the mechanisms that uphold fish community function. This study underscores the importance of considering fish species correlation within a community for the effective management of ecosystems, biodiversity conservation, and ecological restoration. We revealed a significant decrease in both fish species richness and functional richness across temporal (1950s, 1980s, and 2000s) and spatial (connected lakes, partially connected lakes, and disconnected lakes) scales. Nevertheless, the complexity of fish communities' co‐occurrence networks does not exhibit a significant decrease with a decrease in species/functional richness, potentially due to the presence of niche overlap species.

The collapse of large wild herbivores with replacement of livestock is causing global plant community and diversity shifts, resulting in altered food availability and diet composition of other sympatric small herbivores in grasslands. How diet shifts affect the gut microbiota of small mammals and whether these changes may translate into complex interactions among coexisting herbivores remain largely unknown. We conducted both a field experiment and a laboratory diet manipulation experiment to test whether sheep grazing induces a diet shift and thus alters the gut microbiota of a small rodent species living in grassland. We found that enclosures subjected to grazing were mostly dominated by Stipa krylovii (accounting for 53.6% of the total biomass) and that voles consumed significantly more S. krylovii and less Cleistogenes squarrosa in grazed enclosures. Voles in grazing enclosures exhibited significantly lower abundances of Firmicutes, higher abundances of Bacteroidetes and significantly lower measurements of alpha diversity. The microbiota from voles in the grazed enclosures had a smaller and more simplified co‐occurrence network with relatively higher percentage of positive interactions. Analysis based on dietary clusters indicated that grazing‐induced changes in diet composition contributed to the distinct gut microbial community of voles in enclosures. We verified our findings using laboratory experiments, in which voles were exclusively fed C. squarrosa (high carbohydrate, high fibre and high in secondary compounds), S. krylovii (low carbohydrate, low fibre and low in secondary compounds) or Leymus chinensis (nutritionally intermediate). We observed that the gut microbiota of voles changed with the three different diets, supporting the idea that the effects of sheep grazing on the gut microbiota of Brandt's voles may be related to grazing‐induced diet shifts. Our results highlighted the negative effects of livestock grazing on small mammals in grassland via changes in plant community and gut microbiota of small mammals and help to better understand the cascading consequences of realistic scenarios of world‐wide decline in large wild herbivores. The authors’ study provides an effective example of how the replacement of wildlife by livestock cascades to affect the coexisting small mammals. This work also explicitly highlights that gut microbes may modulate the population responses of small mammals to livestock.