Colonization ability and uniformity of resources and environmental factors determine biological homogenization of soil protists in human land-use systems.

Humans have substantially transformed the global land surface, resulting in the decline in variation in biotic communities across scales, a phenomenon known as "biological homogenization." However, different biota are affected by biological homogenization to varying degrees, but this variation and the underlying mechanisms remain little studied, particularly in soil systems. To address this topic, we used metabarcoding to investigate the biogeography of soil protists and their prey/hosts (prokaryotes, fungi, and meso- and macrofauna) in three human land-use ecosystem types (farmlands, residential areas, and parks) and natural forest ecosystems across subtropical and temperate regions in China. Our results showed that the degree of community homogenization largely differed between taxa and functional groups of soil protists, and was strongly and positively linked to their colonization ability of human land-use systems. Removal analysis showed that the introduction of widespread, generalist taxa (OTUs, operational taxonomic units) rather than the loss of narrow-ranged, specialist OTUs was the major cause of biological homogenization. This increase in generalist OTUs seemingly alleviated the negative impact of land use on specialist taxa, but carried the risk of losing functional diversity. Finally, homogenization of prey/host biota and environmental conditions were also important drivers of biological homogenization in human land-use systems, with their importance being more pronounced in phagotrophic than parasitic and phototrophic protists. Overall, our study showed that the variation in biological homogenization strongly depends on the colonization ability of taxa in human land-use systems, but is also affected by the homogenization of resources and environmental conditions. Importantly, biological homogenization is not the major cause of the decline in the diversity of soil protists, and conservation and study efforts should target at taxa highly sensitive to local extinction, such as parasites.

Distance-decay equations of antibiotic resistance genes across freshwater reservoirs.

Distance-decay (DD) equations can discern the biogeographical pattern of organisms and genes in a better way with advanced statistical methods. Here, we developed a data Compilation, Arrangement, and Statistics framework to advance quantile regression (QR) into the generation of DD equations for antibiotic resistance genes (ARGs) across various spatial scales using freshwater reservoirs as an illustration. We found that QR is superior at explaining dissemination potential of ARGs to the traditionally used least squares regression (LSR). This is because our model is based on the 'law of limiting factors', which reduces influence of unmeasured factors that reduce the efficacy of the LSR method. DD equations generated from the 99th QR model for ARGs were 'Sall = 90.03e-0.01Dall' in water and 'Sall = 92.31e-0.011Dall' in sediment. The 99th QR model was less impacted by uneven sample sizes, resulting in a better quantification of ARGs dissemination. Within an individual reservoir, the 99th QR model demonstrated that there is no dispersal limitation of ARGs at this smaller spatial scale. The QR method not only allows for construction of robust DD equations that better display dissemination of organisms and genes across ecosystems, but also provides new insights into the biogeography exhibited by key parameters, as well as the interactions between organisms and environment.

Assembly and succession of the phyllosphere microbiome and nutrient-cycling genes during plant community development in a glacier foreland.

The phyllosphere, particularly the leaf surface of plants, harbors a diverse range of microbiomes that play a vital role in the functioning of terrestrial ecosystems. However, our understanding of microbial successions and their impact on functional genes during plant community development is limited. In this study, considering core and satellite microbial taxa, we characterized the phyllosphere microbiome and functional genes in various microhabitats (i.e., leaf litter, moss and plant leaves) across the succession of a plant community in a low-altitude glacier foreland. Our findings indicate that phyllosphere microbiomes and associated ecosystem stability increase during the succession of the plant community. The abundance of core taxa increased with plant community succession and was primarily governed by deterministic processes. In contrast, satellite taxa abundance decreased during plant community succession and was mainly governed by stochastic processes. The abundance of microbial functional genes (such as C, N, and P hydrolysis and fixation) in plant leaves generally increased during the plant community succession. However, in leaf litter and moss leaves, only a subset of functional genes (e.g., C fixation and degradation, and P mineralization) showed a tendency to increase with plant community succession. Ultimately, the community of both core and satellite taxa collaboratively influenced the characteristics of phyllosphere nutrient-cycling genes, leading to the diverse profiles and fluctuating abundance of various functional genes during plant community succession. These findings offer valuable insights into the phyllosphere microbiome and plant-microbe interactions during plant community development, advancing our understanding of the succession and functional significance of the phyllosphere microbial community.

Lipid Metabolites as Potential Regulators of the Antibiotic Resistome in Tetramorium caespitum.

Antibiotic resistance genes (ARGs) are ancient but have become a modern critical threat to health. Gut microbiota, a dynamic reservoir for ARGs, transfer resistance between individuals. Surveillance of the antibiotic resistome in the gut during different host growth phases is critical to understanding the dynamics of the resistome in this ecosystem. Herein, we disentangled the ARG profiles and the dynamic mechanism of ARGs in the egg and adult phases of Tetramorium caespitum. Experimental results showed a remarkable difference in both gut microbiota and gut resistome with the development of T. caespitum. Meta-based metagenomic results of gut microbiota indicated the generalizability of gut antibiotic resistome dynamics during host development. By using Raman spectroscopy and metabolomics, the metabolic phenotype and metabolites indicated that the biotic phase significantly changed lipid metabolism as T. caespitum aged. Lipid metabolites were demonstrated as the main factor driving the enrichment of ARGs in T. caespitum. Cuminaldehyde, the antibacterial lipid metabolite that displayed a remarkable increase in the adult phase, was demonstrated to strongly induce ARG abundance. Our findings show that the gut resistome is host developmental stage-dependent and likely modulated by metabolites, offering novel insights into possible steps to reduce ARG dissemination in the soil food chain.

TRAPPC6B biallelic variants cause a neurodevelopmental disorder with TRAPP II and trafficking disruptions.

Highly conserved transport protein particle (TRAPP) complexes regulate subcellular trafficking pathways. Accurate protein trafficking has been increasingly recognized to be critically important for normal development, particularly in the nervous system. Variants in most TRAPP complex subunits have been found to lead to neurodevelopmental disorders with diverse but overlapping phenotypes. We expand on limited prior reports on TRAPPC6B with detailed clinical and neuroradiologic assessments, and studies on mechanisms of disease, and new types of variants. We describe 29 additional patients from 18 independent families with biallelic variants in TRAPPC6B. We identified seven homozygous nonsense (n = 12 patients) and eight canonical splice-site variants (n = 17 patients). In addition, we identified one patient with compound heterozygous splice-site/missense variants with a milder phenotype and one patient with homozygous missense variants. Patients displayed non-progressive microcephaly, global developmental delay/intellectual disability, epilepsy and absent expressive language. Movement disorders including stereotypies, spasticity and dystonia were also observed. Brain imaging revealed reductions in cortex, cerebellum and corpus callosum size with frequent white matter hyperintensity. Volumetric measurements indicated globally diminished volume rather than specific regional losses. We identified a reduced rate of trafficking into the Golgi apparatus and Golgi fragmentation in patient-derived fibroblasts that was rescued by wild-type TRAPPC6B. Molecular studies revealed a weakened interaction between mutant TRAPPC6B (c.454C>T, p.Q152*) and its TRAPP binding partner TRAPPC3. Patient-derived fibroblasts from the TRAPPC6B (c.454C>T, p.Q152*) variant displayed reduced levels of TRAPPC6B as well as other TRAPP II complex-specific members (TRAPPC9 and TRAPPC10). Interestingly, the levels of the TRAPPC6B homologue TRAPPC6A were found to be elevated. Moreover, co-immunoprecipitation experiments showed that TRAPPC6A co-precipitates equally with TRAPP II and TRAPP III, while TRAPPC6B co-precipitates significantly more with TRAPP II, suggesting enrichment of the protein in the TRAPP II complex. This implies that variants in TRAPPC6B may preferentially affect TRAPP II functions compared to TRAPP III functions. Finally, we assessed phenotypes in a Drosophila TRAPPC6B-deficiency model. Neuronal TRAPPC6B knockdown impaired locomotion and led to wing posture defects, supporting a role for TRAPPC6B in neuromotor function. Our findings confirm the association of damaging biallelic TRAPPC6B variants with microcephaly, intellectual disability, language impairments, and epilepsy. A subset of patients also exhibited dystonia and/or spasticity with impaired ambulation. These features overlap with disorders arising from pathogenic variants in other TRAPP subunits, particularly components of the TRAPP II complex. These findings suggest that TRAPPC6B is essential for brain development and function, and TRAPP II complex activity may be particularly relevant for mediating this function.

Adaptive shifts in plant traits associated with nitrogen removal driven by phytoremediation strategies in subtropical river restoration.

Phytoremediation, which is commonly carried out through hydroponics and substrate-based strategies, is essential for the effectiveness of nature-based engineered solutions aimed at addressing excess nitrogen in aquatic ecosystems. However, the performance and mechanisms of plants involving nitrogen removal between different strategies need to be deeply understood. Here, this study employed in-situ cultivation coupled with static nitrogen tracing experiments to elucidate the influence of both strategies on plant traits associated with nitrogen removal. The results indicated that removal efficiencies in plants with substrate-based strategies for ammonium nitrogen and nitrate nitrogen were 30.51-71.11 % and 16.82-99.95 %, respectively, which were significantly higher than those with hydroponics strategies (25.98-58.18 % and 7.29-79.19 %, respectively). Similarly, the plant nitrogen uptake rates in the substrate-based strategy also generally showed higher levels compared to hydroponics strategies (P < 0.05). Meanwhile, the microorganisms-mediated nitrous oxide emission rates in the substrate-based strategy during summer (unamended: 0.00-0.58 µg/g/d; potential: 3.35-7.65 µg/g/d) were obviously lower than those in the hydroponics strategy (unamended: 2.23-11.70 µg/g/d; potential: 9.72-43.09 µg/g/d) (P < 0.05). Notably, analysis of similarity tests indicated that the influences of strategy on the above parameters generally surpass the effects attributable to interspecies plant differences, particularly during summer (R > 0, P < 0.05). Based on statistical and metagenomic analyses, this study revealed that these differences were driven by the stabilizing influence of substrate-based strategy on plant roots and enhancing synergistic interplay among biochemical factors within plant-root systems. Even so, phytoremediation strategies did not significantly alter the characteristics of plants with regards to their tendency towards ammonium nitrogen uptake (up to 87.68 %) and dissimilatory nitrate reduction to ammonium as primary biological pathway for nitrogen transformation which accounted for 53.66-96.47 % nitrate removal. In summary, this study suggested that the substrate-based strategy should be a more effective strategy for enhancing the nitrogen removal ability of plants in subtropical river restoration practices.

Phagotrophic protists preserve antibiotic-resistant opportunistic human pathogens in the vegetable phyllosphere.

Food safety of leafy greens is an emerging public health issue as they can harbor opportunistic human pathogens (OHPs) and expose OHPs to consumers. Protists are an integral part of phyllosphere microbial ecosystems. However, our understanding of protist-pathogen associations in the phyllosphere and their consequences on public health remains poor. Here, we examined phyllosphere protists, human pathogen marker genes (HPMGs), and protist endosymbionts from four species of leafy greens from major supermarkets in Xiamen, China. Our results showed that Staphylococcus aureus and Klebsiella pneumoniae were the dominant human pathogens in the vegetable phyllosphere. The distribution of HPMGs and protistan communities differed between vegetable species, of which Chinese chive possessed the most diverse protists and highest abundance of HPMGs. HPMGs abundance positively correlated with the diversity and relative abundance of phagotrophic protists. Whole genome sequencing further uncovered that most isolated phyllosphere protists harbored multiple OHPs which carried antibiotic resistance genes, virulence factors, and metal resistance genes and had the potential to HGT. Colpoda were identified as key phagotrophic protists which positively linked to OHPs and carried diverse resistance and virulence potential endosymbiont OHPs including Pseudomonas nitroreducens, Achromobacter xylosoxidans, and Stenotrophomonas maltophilia. We highlight that phyllosphere protists contribute to the transmission of resistant OHPs through internalization and thus pose risks to the food safety of leafy greens and human health. Our study provides insights into the protist-OHP interactions in the phyllosphere, which will help in food safety surveillance and human health.

Urban greenspace types influence the microbial community assembly and antibiotic resistome more in the phyllosphere than in the soil.

Urban greenspace (UGS) is recognized to confer significant societal benefits, but few studies explored the microbial communities and antibiotic resistance genes (ARGs) from different urban greenspace types. Here, we collected leaf and soil samples from forest, greenbelt, and parkland to analyze microbial community assembly and ARG profile. For phyllosphere fungal community, the α-diversity was higher in forest, compared to those in greenbelt and parkland. Moreover, urban greenspace types altered the community assembly. Stochastic processes had a greater effect on phyllosphere fungal community in greenbelt and parkland, while in forest they were dominated by deterministic processes. In contrast, no significant differences in bacterial community diversity, community assembly were observed between the samples collected from different urban greenspace types. A total of 153 ARGs and mobile genetic elements (MGEs) were detected in phyllosphere and soil with resistance to the majority classes of antibiotics commonly applied to humans and animals. Structural equation model further revealed that a direct association between greenspace type and ARGs in the phyllosphere even after considering the effects of all other factors simultaneously. Our findings provide new insights into the microbial communities and antibiotic resistome of urban greenspaces and the potential risk linked with human health.

Rod-cone dystrophy in an adult with GNB1-related disorder: An expansion of the phenotype and natural history.

GNB1-related disorder is characterized by intellectual disability, abnormal tone, and other variable neurologic and systemic features. GNB1 encodes the ß1 subunit of the heterotrimeric G-protein, a complex with a key role in signal transduction. Consistent with its particularly high expression in rod photoreceptors, Gß1 forms a subunit of retinal transducin (Gαtß1γ1 ), which mediates phototransduction. In mice, GNB1 haploinsufficiency has been associated with retinal dystrophy. In humans, however, although vision and eye movement abnormalities are common in individuals with GNB1-related disorder, rod-cone dystrophy is not yet an established feature of this condition. We expand the phenotype of GNB1-related disorder with the first confirmed report of rod-cone dystrophy in an affected individual, and contribute to a further understanding of the natural history of this condition in a mildly affected 45-year-old adult.

Phyllosphere antibiotic resistome in a natural primary vegetation across a successional sequence after glacier retreat.

The spread of antibiotic-resistance genes (ARGs) has posed a significant threat to human health over the past decades. Despite the fact that the phyllosphere represents a crucial pool of microorganisms, little is known about the profile and drivers of ARGs in less human interference natural habitats. In order to minimize the influence of environmental factors, here we collected leaf samples from the early-, middle- and late-successional stages across a primary vegetation successional sequence within 2 km, to investigate how the phyllosphere ARGs develop in natural habitats. Phyllosphere ARGs were determined using high-throughput quantitative PCR. Bacterial community and leaf nutrient content were also measured to assess their contribution to the phyllosphere ARGs. A total of 151 unique ARGs were identified, covering almost all recognized major antibiotic classes. We further found that there was some stochastic and a core set of the phyllosphere ARGs during the plant community succession process, due to the fluctuant phyllosphere habitat and specific selection effect of plant individuals. The ARG abundance significantly decreased due to the reduction of the phyllosphere bacterial diversity, community complexity, and leaf nutrient content during the plant community succession process. While the closer links between soil and fallen leaf resulted in a higher ARG abundance in leaf litter than in fresh leaf. In summary, our study reveals that the phyllosphere harbors a broad spectrum of ARGs in the natural environment. These phyllosphere ARGs are driven by various environmental factors, including the plant community composition, host leaf properties, and the phyllosphere microbiome.

Characterization of microbial community, ecological functions and antibiotic resistance in estuarine plastisphere.

The plastisphere is a new ecological niche. Compared to the surrounding water, microbial community composition associated with the plastisphere is known to differ with functional consequences. Here, this study characterized the bacterial and fungal communities associated with four types of plastisphere (polyethylene, polystyrene, polypropylene and polyvinyl chloride) in an estuarine habitat; assessed ecological functions including carbon, nitrogen, phosphorus and sulfur cycling, and determined the presence of antibiotic resistance genes (ARGs) and human pathogens. Stochastic processes dominated the community assembly of microorganisms on the plastisphere. Several functional genera related to nutrient cycling were enriched in the plastisphere. Compared to surrounding water and other plastisphere, the abundances of carbon, nitrogen and phosphorus cycling genes (cdaR, nosZ and chpy etc.) and ARGs (aadA2-1, cfa and catB8 etc.) were significantly increased in polyvinyl chloride plastisphere. In contrast, the polystyrene plastisphere was the preferred substrate for several pathogens being enriched with for example, Giardia lamblia 18S rRNA, Klebsiella pneumoniae phoE and Legionella spp. 23S rRNA. Overall, this study showed that different plastisphere had different effects on ecological functions and health risk in estuaries and emphasizes the importance of controlling plastic pollution in estuaries. Data from this study support global policy drivers that seek to reduce plastic pollution and offer insights into ecological functions in a new ecological niche of the Anthropocene.

Plant identity shapes phyllosphere microbiome structure and abundance of genes involved in nutrient cycling.

The phyllosphere is a fluctuant micro-environment habitat that harbors diverse microbial communities that have the potential to influence plant growth through their effect on host fitness. However, we know little about the driving factors of phyllosphere microbial functional traits, e.g., genes related to nutrient cycling and microbial community structure under anthropic disturbance. Here, we characterized phyllosphere microbial communities and the abundance of genes related to nutrient cycling from diverse plant species between urban and natural habitats. We measured leaf functional traits to investigate the potential drivers of the phyllosphere microbial profile. Results indicated that phyllosphere microbial communities differed significantly between urban and natural habitats, and that this variation was dependent upon plant species. Host plant species had a greater influence on the abundance of genes involved in nutrient cycling in the phyllosphere than habitat. In addition, phyllosphere microbial diversity and functional gene abundance were significantly correlated. Furthermore, host leaf functional traits (e.g., specific leaf area and nutrient content) were potential driving factors of both phyllosphere microbial community structure and the abundance of genes involved in nutrient cycling. These findings contribute to a better understanding of the phyllosphere microbiome and its biotic and abiotic controlling factors, which improves our understanding of plant-microbe interactions and their ecosystem functions under anthropic disturbance.

Effect of phenol formaldehyde-associated microplastics on soil microbial community, assembly, and functioning.

Increasing investigations explore the effects of plastic pollutants on bacterial communities, diversity, and functioning in various ecosystems. However, the impact of microplastics (MPs) on the eukaryotic community, microbial assemblages, and interactions is still limited. Here, we investigated bacterial and micro-eukaryotic communities and functioning in soils with different concentrations of phenol formaldehyde-associated MPs (PF-MPs), and revealed the factors, such as soil properties, microbial community assembly, and interactions between microbes, influencing them. Our results showed that a high concentration (1%) of PF-MPs decreased the microbial interactions and the contribution of deterministic processes to the community assembly of microbes, and consequently changed the communities of bacteria, but not eukaryotes. A significant and negative relationship was determined between N2O emission rate and functional genes related to nitrification, indicating that the competitive interactions between functional microbes would affect the nitrogen cycling of soil ecosystem. We further found that vegetable biomass weakly decreased in treatments with a higher concentration of PF-MPs and positively related to the diversity of micro-eukaryotic communities and functional diversity of bacterial communities. These results suggest that a high concentration of the PF-MPs would influence crop growth by changing microbial communities, interactions, and eukaryotic and functional diversity. Our findings provide important evidence for agriculture management of phenol formaldehyde and suggest that we must consider their threats to microbial community compositions, diversity, and assemblage in soils due to the accumulation of PF-MPs widely used in the field.

Temporal dynamics of soil bacterial network regulate soil resistomes.

Soil bacteria are diverse and form complicated ecological networks through various microbial interactions, which play important roles in soil multi-functionality. However, the seasonal effects on the bacterial network, especially the relationship between bacterial network topological features and soil resistomes remains underexplored, which impedes our ability to unveil the mechanisms of the temporal-dynamics of antibiotic resistance genes (ARGs). Here, a field investigation was conducted across four seasons at the watershed scale. We observed significant seasonal variation in bacterial networks, with lower complexity and stability in autumn, and a wider bacterial community niche in summer. Similar to bacterial communities, the co-occurrence networks among ARGs also shift with seasonal change, particularly with respect to the topological features of the node degree, which on average was higher in summer than in the other seasons. Furthermore, the nodes with higher betweenness, stress, degree, and closeness centrality in the bacterial network showed strong relationships with the 10 major classes of ARGs. These findings highlighted the changes in the topological properties of bacterial networks that could further alter antibiotic resistance in soil. Together, our results reveal the temporal dynamics of bacterial ecological networks at the watershed scale, and provide new insights into antibiotic resistance management under environmental changes.

Distinct responses of airborne abundant and rare microbial communities to atmospheric changes associated with Chinese New Year.

Airborne microorganisms, including pathogens, would change with surrounding environments and become issues of global concern due to their threats to human health. Microbial communities typically contain a few abundant but many rare species. However, how the airborne abundant and rare microbial communities respond to environmental changes is still unclear, especially at hour scale. Here, we used a sequencing approach based on bacterial 16S rRNA genes and fungal ITS2 regions to investigate the high time-resolved dynamics of airborne bacteria and fungi and to explore the responses of abundant and rare microbes to the atmospheric changes. Our results showed that air pollutants and microbial communities were significantly affected by human activities related to the Chinese New Year (CNY). Before CNY, significant hour-scale changes in both abundant and rare subcommunities were observed, while only abundant bacterial subcommunity changed with hour time series during CNY. Air pollutants and meteorological parameters explained 61.5%-74.2% variations of abundant community but only 13.3%-21.6% variations of rare communities. These results suggested that abundant species were more sensitive to environmental changes than rare taxa. Stochastic processes predominated in the assembly of abundant communities, but deterministic processes determined the assembly of rare communities. Potential bacterial pathogens during CNY were the highest, suggesting an increased health risk of airborne microbes during CNY. Overall, our findings highlighted the "holiday effect" of CNY on airborne microbes and expanded the current understanding of the ecological mechanisms and health risks of microbes in a changing atmosphere.

Spatiotemporal variations of microbial assembly, interaction, and potential risk in urban dust.

Community and composition of dust-borne microbes would affect human health and are regulated by microbial community assembly. The dust in kindergarten is always collected to evaluate the microbial exposure of children, yet the microbial assembly, their interactions, and potential pathogens in kindergarten dust remain unclear. Here, we aim to investigate the microbial community assembly and structures, and potential bacterial pathogens in outdoor dust of kindergartens, and reveal the factors influencing the assembly and composition of microbial community. A total of 118 urban dust samples were collected on the outdoor impervious surfaces of 59 kindergartens from different districts of Xiamen in January and June 2020. We extracted microbial genomic DNA in these dusts and characterized the microbial (i.e., bacteria and fungi) community compositions and diversities using target gene-based (16S rRNA genes for bacterial community and ITS 2 regions for fungal community) high-throughput sequencing. Potential bacterial pathogens were identified and the interactions between microbes were determined through a co-occurrence network analysis. Our results showed the predominance of Actinobacteria and α-Proteobacteria in bacterial communities and Capnodiales in fungal communities. Season altered microbial assembly, composition, and interactions, with both bacterial and fungal communities exhibiting a higher heterogeneity in summer than those in winter. Although stochastic processes predominated in bacterial and fungal community assembly, the season-depended environmental factors (e.g., temperature) and interactions between microbes play important roles in dust microbial community assembly. Potential bacterial pathogens were detected in all urban dust, with significantly higher relative abundance in summer than that in winter. These results indicated that season exerted more profound effects on microbial community composition, assembly, and interactions, and suggested the seasonal changes of potential risk of microbes in urban dust. Our findings provide new insights into microbial community, community assembly, and interactions between microbes in the urban dust, and indicate that taxa containing opportunistic pathogens occur commonly in urban dust.

ROS as a key player in quinolone antibiotic stress on Arabidopsis thaliana: From the perspective of photosystem function, oxidative stress and phyllosphere microbiome.

With the increasing use of antibiotics, their ecological impacts have received widespread attention. However, research on the toxicity of quinolone antibiotics is still limited, especially regarding the oxidative stress and phyllosphere of plants. In this study, the toxic effects of enrofloxacin, norfloxacin, and levofloxacin on Arabidopsis thaliana and their underlying mechanisms were investigated. The toxicity of the three quinolone antibiotics decreased in the following order: enrofloxacin > norfloxacin > levofloxacin. Physiological cellular changes, such as plasmolysis and chloroplast swelling, were observed using electron microscopy. Photosynthetic efficiency was inhibited with a decline in the effective photochemical quantum yield of photosystem II (Y(II)) and non-photochemical quenching (NPQ), indicating that quinolone antibiotics might reduce light energy conversion efficiency and excess light energy dissipation. Oxidative stress occurred in A. thaliana after quinolone antibiotic treatment, with an increase in reactive oxygen species (ROS) levels and malondialdehyde (MDA) content. High ROS levels stimulated the over-expression of superoxide-responsive genes for self-protection. Structural equation modeling (SEM) analysis showed that photosynthesis inhibition and cellular damage caused by oxidative stress were critical factors for growth inhibition, suggesting that the antioxidant response activated by ROS might be a potential mechanism. Furthermore, the diversity of the phyllospheric microbial communities decreased after enrofloxacin exposure. Additionally, specific microbes were preferentially recruited to the phyllosphere because of the higher ROS levels.

Soil mesofauna alter the balance between stochastic and deterministic processes in the plastisphere during microbial succession.

Plastic debris, as a novel substrate, provides an avenue for enriching microbial growth. Although the structure of the aquatic plastisphere microbial community is well-characterised, linkages between microbial community assembly and species co-existence in the soil plastisphere vary and remain poorly understood, particularly when soil fauna is involved. This study investigated the soil plastisphere community, including bacteria, fungi, and protists, focusing on microbial succession and community assembly processes impacted by soil mesofauna. Certain soil plastisphere microbial taxa thrived at particular time points (e.g. Actinobacteria at 60 d), indicating the irreplaceable role of microplastic selection for time-sensitive taxa. Additionally, the biodiversity of keystone ecological clusters in the soil plastisphere was significantly associated with incubation time. Furthermore, the slopes of bacterial and fungal time-decay curves in soil plastisphere were steeper when treated with soil mesofauna than without soil mesofauna, whereas protist time-decay curves (total and abundant taxa) exhibited the opposite trend. Soil mesofauna increased the relative importance of determinacy in the soil plastisphere bacterial assembly process, while enhancing the stochasticity of fungal and protistan community assemblages. The study demonstrates the complex assembly patterns of soil plastisphere microbial communities, emphasising the importance of interactions between the plastisphere and local soil fauna from an ecological perspective.

Does Plant Identity Affect the Dispersal of Resistomes Above and Below Ground?

Resistomes are ubiquitous in natural environments. Previous studies have shown that both the plant phyllosphere and soil-borne nematodes were reservoirs of above- and below-ground resistomes, respectively. However, the influence of plant identity on soil, nematode, and phyllosphere resistomes remains unclear. Here, a microcosm experiment was used to explore the characteristics of bacterial communities and resistomes in soil, nematode, and phyllosphere associated with six different plant identities (Lactuca sativa, Cichorium endivia, Allium fistulosum, Coriandrum sativum, Raphanus sativus, and Mesembryanthemum crystallinum). A total of 222 antibiotic resistance genes (ARGs) and 7 mobile genetic elements (MGEs) were detected by high-throughput quantitative PCR from all samples. Plant identity not only significantly affected the diversity of resistomes in soil, nematode, and phyllosphere but also influenced the abundance of resistomes in nematodes. Shared bacteria and resistomes indicated a possible pathway of resistomes transfer through the soil-nematode-phyllosphere system. Structural equation models revealed that plant identity had no direct effect on phyllosphere ARGs, but altered indirectly through complex above- and below-ground interactions (soil-plant-nematode trophic transfer). Results also showed that bacteria and MGEs were key factors driving the above- and below-ground flow of resistomes. The study extends our knowledge about the top-down and bottom-up dispersal patterns of resistomes.

Microbial Multitrophic Communities Drive the Variation of Antibiotic Resistome in the Gut of Soil Woodlice (Crustacea: Isopoda).

Multitrophic communities inhabit in soil faunal gut, including bacteria, fungi, and protists, which have been considered a hidden reservoir for antibiotic resistance genes (ARGs). However, there is a dearth of research focusing on the relationships between ARGs and multitrophic communities in the gut of soil faunas. Here, we studied the contribution of multitrophic communities to variations of ARGs in the soil woodlouse gut. The results revealed diverse and abundant ARGs in the woodlouse gut. Network analysis further exhibited strong connections between key ecological module members and ARGs, suggesting that multitrophic communities in the keystone ecological cluster may play a pivotal role in the variation of ARGs in the woodlouse gut. Moreover, long-term application of sewage sludge significantly altered the woodlice gut resistome and interkingdom communities. The variation portioning analysis indicated that the fungal community has a greater contribution to variations of ARGs than bacterial and protistan communities in the woodlice gut after long-term application of sewage sludge. Together, our results showed that changes in gut microbiota associated with agricultural practices (e.g., sewage sludge application) can largely alter the gut interkingdom network in ecologically relevant soil animals, with implications for antibiotic resistance, which advances our understanding of the microecological drivers of ARGs in terrestrial ecosystem.