Insights into the roles of fungi and protist in the giant panda gut microbiome and antibiotic resistome

Pollution characteristics of heavy metals, antibiotic and antibiotic resistance genes in the crested ibis and their habitat across different lifestyle and geography

Antibacterial resistance in wild animals has been increasingly reported worldwide, even though they are usually not directly exposed to clinically relevant antibiotics. Crested ibis, one of the rarest birds in the world, usually forages in paddy fields and prefer to nest and breed near villages that is greatly influenced by anthropogenic activities. We sampled the feces of crested ibises, as well as their habitat environment samples, to explore the pollution characteristics of heavy metals, antibiotics and antibiotic resistance genes (ARGs). Results showed that the pollution characteristics of heavy metals, antibiotic, ARGs and gut microbiota of crested ibis were more related by host lifestyle and habitats. Captive ibises had higher relative abundances of the total ARGs and tetracycline concentrations compared with feralization and wild ibises, while the heavy metal contents had shown the opposite result. The Characteristics of pollutants in the corresponding environmental samples also exhibited high similarity with the results of fecal samples. The relative abundances of Proteobacteria and Actinobacteria were significantly different between captive and wild individuals, while the abundance of majority bacterial genera was generally higher in wild populations. The concentrations of heavy metals in soil (Cd, Cu and Zn) and water (Cd, Cu, Zn and Cr) were both exceeded the background soil levels or surface water quality standards, suggesting multi-element contamination in the habitat. Ecological risk assessments of soils by Igeo and Er showed that the habitats of wild ibises were heavily and moderately contaminated by Cd, which would possibly pose a threat to the health of ibises. PLS-PM analysis indicated that microbial compositions and residual antibiotics had the most substantial impact on the dynamic changes in ARGs of ibis. Overall, this work provides a comprehensive understanding of the characteristics, risks of those contaminations, and their effects on the ARGs in the habitat of crested ibis.

Seasonal variations affect the ecosystem functioning and microbial assembly processes in plantation forest soils

While afforestation mitigates climate concerns, the impact of afforestation on ecological assembly processes and multiple soil functions (multifunctionality) in afforested areas remains unclear. The Xiong'an New Area plantation forests (Pinus and Sophora forests) in North China were selected to examine the effects of plantation types across four distinct seasons on soil microbiomes. Three functional categories (nutrient stocks, organic matter decomposition, and microbial functional genes) of multifunctionality and the average (net) multifunctionality were quantified. All these categories are directly related to soil functions. The results showed that net soil multifunctionality as a broad function did not change seasonally, unlike other narrow functional categories. Bacterial communities were deterministically (variable selection and homogenous selection) structured, whereas the stochastic process of dispersal limitation was mainly responsible for the assembly and turnover of fungal and protist communities. In Pinus forests, winter initiates a sudden shift from deterministic to stochastic processes in bacterial community assembly, accompanied by decreased Shannon diversity and heightened nutrient cycling (nutrient stocks and organic matter decomposition). This indicates the potential vulnerability of deterministic assembly to seasonal fluctuations, particularly in environments rich in nutrients. The results predicted that protist community composition was uniquely structured with C-related functional activities relative to bacterial and fungal β-diversity variations, which were mostly explained by seasonal variations. Our study highlighted the importance of the protist phagocytosis process on soil microbial interactions through the predicted impact of protist α-diversity on microbial cooccurrence network parameters. This association might be driven by the high abundance of protist consumers as the main predators of bacterial and fungal lineages in our sampling plots. Our findings reveal that the complexity of microbial co-occurrence interactions was considerably higher in spring, perhaps attributing thermal variability and increased resource availability within spring that foster microbial diversity and network complexity. This study contributes to local ecosystem prospects to model the behavior of soil biota seasonally and their implied effects on soil functioning and microbial assembly processes, which will benefit global-scale afforestation programs by promoting novel, precise, and rational plantation forests for future environmental sustainability and self-sufficiency.

Urban greenspace types and climate factors jointly drive the microbial community structure and co-occurrence network

The benefits of urban green space are socially widely recognized as a direct link between plant-microbe interactions and the maintenance of biodiversity, community stability, and ecosystem functioning. Nevertheless, there is a lack of knowledge about the factors influencing microbial communities in urban green spaces, especially those related to phyllosphere epiphytes and stem epiphytes. In this study, we analyzed the microbial community assembly in leaf and stem bark samples collected from Square, Road, Campus, and Park. Illumina sequecing of 16S amplicons was performed to characterize microbial diversity and composition. The α-diversity was significantly higher in the bark epiphytic community, compared to the phyllosphere. Moreover, urban greenspaces'type altered the way communities gathered. The main soil and air properties factors of the urban greenhouse (e.g. soil temperature, atmospheric moisture, air temperature) were shaping the characteristics of bacterial communities on the leaf surface and bark epiphytic. In addition, in the co-occurrence network analysis, keystone taxa were not mostly observed in abundant species, which may be necessary to maintain ecosystem functions. Finally, our findings provide a deeper understanding of the ecological dynamics and microbial interactions within plant phyllosphere and stem epiphytes microbiomes.

Co-occurrence patterns of gut microbiome, antibiotic resistome and the perturbation of dietary uptake in captive giant pandas

The microbiome is a key source of antibiotic resistance genes (ARGs), significantly influenced by diet, which highlights the interconnectedness between diet, gut microbiome, and ARGs. Currently, our understanding is limited on the co-occurrence among gut microbiome, antibiotic resistome in the captive giant panda and the perturbation of dietary uptake, especially for the composition and forms in dietary nutrition. Here, a qPCR array with 384 primer sets and 16 S rRNA gene amplicon sequencing were used to characterize the antibiotic resistome and microbiomes in panda feces, dietary bamboo, and soil around the habitat. Diet nutrients containing organic and mineral substances in soluble and insoluble forms were also quantified. Organic and mineral components in water-unextractable fractions were 7.5 to 139 and 637 to 8695 times higher than those in water-extractable portions in bamboo and feces, respectively, while the latter contributed more to the variation (67.5 %) of gut microbiota. Streptococcus, Prevotellaceae, and Bacteroides were the dominant genera in giant pandas. The ARG patterns in panda guts showed higher diversity in old individuals but higher abundance in young ones, driven directly by the bacterial community change and mobile genetic element mediation and indirectly by dietary intervention. Our results suggest that dietary nutrition mainly accounts for the shift of gut microbiota, while bacterial community and mobile genetic elements influenced the variation of gut antibiotic resistome.

Effects of antibiotic resistance genes on health risks of rivers in habitat of wild animals under human disturbance - based on analysis of antibiotic resistance genes and virulence factors in microbes of river sediments

Studying the ecological risk of antibiotic resistance genes (ARGs) to wild animals from human disturbance (HD) is an important aspect of "One Health". The highest risk level of ARGs is reflected in pathogenic antibiotic-resistant bacteria (PARBs). Metagenomics was used to analyze the characteristics of PARBs in river sediments. Then, the total contribution of ARGs and virulence factors (VFs) were assessed to determine the health risk of PARBs to the rivers. Results showed that HD increased the diversity and total relative abundance of ARG groups, as well as increased the kinds of PARBs, their total relative abundance, and their gene numbers of ARGs and VFs. The total health risks of PARBs in wild habitat group (CK group), agriculture group (WA group), grazing group (WG group), and domestic sewage group (WS group) were 0.067 × 10-3, -1.55 × 10-3, 87.93 × 10-3, and 153.53 × 10-3, respectively. Grazing and domestic sewage increased the health risk of PARBs. However, agriculture did not increase the total health risk of the rivers, but agriculture also introduced new pathogenic mechanisms and increased the range of drug resistance. More serious was the increased transfer risk of ARGs in the PARBs from the rivers to wild animals under agriculture and grazing. If the ARGs in the PARBs are transferred from the rivers under HD to wild animals, then wild animals may face severe challenges of acquiring new pathogenic mechanisms and developing resistance to antibiotics. Further analysis showed that the total phosphorus (TP) and dissolved organic nitrogen (DON) were related to the risk of ARGs. Therefore, controlling human emissions of TP and DON could reduce the health risk of rivers.

The Potential of Co-Evolution and Interactions of Gut Bacteria-Phages in Bamboo-Eating Pandas: Insights from Dietary Preference-Based Metagenomic Analysis

Bacteria and phages are two of the most abundant biological entities in the gut microbiome, and diet and host phylogeny are two of the most critical factors influencing the gut microbiome. A stable gut bacterial community plays a pivotal role in the host's physiological development and immune health. A phage is a virus that directly infects bacteria, and phages' close associations and interactions with bacteria are essential for maintaining the stability of the gut bacterial community and the entire microbial ecosystem. Here, we utilized 99 published metagenomic datasets from 38 mammalian species to investigate the relationship (diversity and composition) and potential interactions between gut bacterial and phage communities and the impact of diet and phylogeny on these communities. Our results highlight the co-evolutionary potential of bacterial-phage interactions within the mammalian gut. We observed a higher alpha diversity in gut bacteria than in phages and identified positive correlations between bacterial and phage compositions. Furthermore, our study revealed the significant influence of diet and phylogeny on mammalian gut bacterial and phage communities. We discovered that the impact of dietary factors on these communities was more pronounced than that of phylogenetic factors at the order level. In contrast, phylogenetic characteristics had a more substantial influence at the family level. The similar omnivorous dietary preference and closer phylogenetic relationship (family Ursidae) may contribute to the similarity of gut bacterial and phage communities between captive giant panda populations (GPCD and GPYA) and omnivorous animals (OC; including Sun bear, brown bear, and Asian black bear). This study employed co-occurrence microbial network analysis to reveal the potential interaction patterns between bacteria and phages. Compared to other mammalian groups (carnivores, herbivores, and omnivores), the gut bacterial and phage communities of bamboo-eating species (giant pandas and red pandas) exhibited a higher level of interaction. Additionally, keystone species and modular analysis showed the potential role of phages in driving and maintaining the interaction patterns between bacteria and phages in captive giant pandas. In sum, gaining a comprehensive understanding of the interaction between the gut microbiota and phages in mammals is of great significance, which is of great value in promoting healthy and sustainable mammals and may provide valuable insights into the conservation of wildlife populations, especially endangered animal species.

Exploring ecological effects of arsenic and cadmium combined exposure on cropland soil: from multilevel organisms to soil functioning by multi-omics coupled with high-throughput quantitative PCR

Arsenic (As) and cadmium (Cd) pose potential ecological threats to cropland soils; however, few studies have investigated their combined effects on multilevel organisms and soil functioning. Here, we used collembolans and soil microbiota as test organisms to examine their responses to soil As and Cd co-contamination at the gene, individual, and community levels, respectively, and further uncovered ecological relationships between pollutants, multilevel organisms, and soil functioning. At the gene level, collembolan transcriptome revealed that elevated As concentrations stimulated As-detoxifying genes AS3MT and GST, whereas the concurrent Cd restrained GST gene expression. At the individual level, collembolan reproduction was sensitive to pollutants while collembolan survival wasn't. At the community level, significant but inconsistent correlations were observed between the biodiversity of different soil keystone microbial clusters and soil As levels. Moreover, soil functioning related to nutrient (e.g., carbon, nitrogen, phosphorus, and sulfur) cycles was inhibited under As and Cd co-exposure only through the mediation of plant pathogens. Overall, these findings suggested multilevel bioindicators (i.e., AS3MT gene expression in collembolans, collembolan reproduction, and biodiversity of soil keystone microbial clusters) in cropland soils co-contaminated with As and Cd, thus improving the understanding of the ecotoxicological impact of heavy metal co-contamination on soil ecosystems.

A comprehensive analysis of antibiotic resistance genes in the giant panda gut

In this study, we have successfully constructed a comprehensive database of metagenome-assembled genomes (MAGs) pertaining to the gut microbiota of the giant panda. Through our analysis, we have identified significant reservoirs of antibiotic resistance genes (ARGs), namely Escherichia coli, Citrobacter portucalensis, and Klebsiella pneumoniae. Furthermore, we have elucidated the primary contributors to ARGs, including Streptococcus alactolyticus and Clostridium SGBP116, in both captive and wild pandas. Additionally, our findings have demonstrated a higher prevalence of ARGs in the metagenome, with notable expression of the RPOB2 gene in S. alactolyticus. Crucially, 1217 ARGs shared homology with human gut ARGs, underscoring the interaction relationship between pandas and human microbiomes. These findings are instrumental in understanding the antibiotic resistance landscape in the giant panda's gut, providing a framework for developing strategies to combat antibiotic resistance and safeguard the health of this endangered species.

Parasitism-Induced Changes in Microbial Eukaryotes of Peruvian Alpaca Gastrointestinal Tract

Alpacas, important genetic resources in the Andean region of Peru, are vulnerable to diarrhea caused by pathogenic parasites such as Eimeria lamae and Giardia sp., which can be fatal, especially in neonates, due to their physiological immaturity and limited adaptability. The study investigated the diversity and abundance of intestinal fungi and protists in alpacas infected with Eimeria lamae and Giardia sp. compared to healthy alpacas. A total of 19 alpacas, aged between one and two months, were included. They were divided into two groups, one with pathological conditions (nine) and the other healthy (ten). Parasitological analyses for the detection of parasites and subsequent molecular analysis were performed on the collected fecal samples. The results revealed a greater diversity and abundance of protists in infected alpacas in comparison with healthy alpacas, while the fungal composition did not show significant changes. Therefore, parasitic infections affect the protist component of the alpaca gut microbiota. Also, it was observed that Blastocystis was identified in all healthy alpacas, serving as a possible marker of the health of the intestinal microbiota; in addition, Prussia and Pichia are beneficial fungi that help control diseases. This groundbreaking study in neonatal alpacas is the first to explore potential changes in the intestinal microbiota during an infectious state, underscoring the importance of further research to comprehend its effects on alpaca health and immune responses.

Core microbiota drive multi-functionality of the soil microbiome in the Cinnamomum camphora coppice planting

BACKGROUND

Cinnamomum camphora (L.) Presl (C. camphora) is an evergreen broad-leaved tree cultivated in subtropical China. The use of C. camphora as clonal cuttings for coppice management has become popular recently. However, little is known about the relationship between soil core microbiota and ecosystem multi-functionality under tree planting. Particularly, the effects of soil core microbiota on maintaining ecosystem multi-functionality under C. camphora coppice planting remained unclear.

MATERIALS AND METHODS

In this study, we collected soil samples from three points (i.e., the abandoned land, the root zone, and the transition zone) in the C. camphora coppice planting to investigate whether core microbiota influences ecosystem multi-functions.

RESULTS

The result showed a significant difference in soil core microbiota community between the abandoned land (AL), root zone (RZ), and transition zone (TZ), and soil ecosystem multi-functionality of core microbiota in RZ had increased significantly (by 230.8%) compared to the AL. Soil core microbiota played a more significant influence on ecosystem multi-functionality than the non-core microbiota. Moreover, the co-occurrence network demonstrated that the soil ecosystem network consisted of five major ecological clusters. Soil core microbiota within cluster 1 were significantly higher than in cluster 4, and there is also a higher Copiotrophs/Oligotrophs ratio in cluster 1. Our results corroborated that soil core microbiota is crucial for maintaining ecosystem multi-functionality. Especially, the core taxa within the clusters of networks under tree planting, with the same ecological preferences, had a significant contribution to ecosystem multi-functionality.

CONCLUSION

Overall, our results provide further insight into the linkage between core taxa and ecosystem multi-functionality. This enables us to predict how ecosystem functions respond to the environmental changes in areas under the C. camphora coppice planting. Thus, conserving the soil microbiota, especially the core taxa, is essential to maintaining the multiple ecosystem functions under the C. camphora coppice planting.

Effects of environmental disinfection on microbial population and resistance genes: A case study of the microecology within a panda enclosure

Widespread use of disinfectants raises concerns over their involvement in altering microbial communities and promoting antimicrobial resistance. This study explores the influence of disinfection protocols on microbial populations and resistance genes within an isolated enclosure environment and in the gut of giant pandas (GPs) held within. Samples of panda feces, air conditioning ducts, soil and bamboo were collected before and after disinfection. High-throughput sequencing characterized the microbial flora of GP gut and environmental microbes inside the artificial habitat. Microbial cultures showed that Escherichia coli (34.6%), Enterococcus (15.4%) and other pathogenic bacteria deposited in feces and the enclosure. Isolates exhibit a consistent resistance to disinfectant, with the greatest resistance shown to cyanuric acid, and the lowest to glutaraldehyde-dodecyl dimethyl ammonium bromide (GD-DDAB) and dodecyl dimethyl ammonium bromide (DDAB). The total number of the culturable bacteria in soil and bamboo were significantly diminished after disinfection but increased in the gut. After disinfection, the richness (Chao1 index) of environment samples increased significantly (P < 0.05), while the richness in gut decreased significantly (P < 0.05). Ten genera showed significant change in feces after disinfection. Metagenome sequencing showed that 126 types of virulence genes were present in feces before disinfection and 37 in soil. After disinfection, 110 virulence genes localized in feces and 53 in soil. Eleven virulence genes including ECP and T2SS increased in feces. A total of 182 antibiotic resistance genes (ARGs) subtypes, potentially conferring resistance to 20 classes of drugs, were detected in the soils and feces, with most belonging to efflux pump protein pathways. After disinfection, the number of resistance genes increased both in gut and soil, which suggests disinfection protocols increase the number of resistance pathways. Our study shows that the use of disinfectants helps to shape the microbial community of GPs and their habitat, and increases populations of resistant strain bacteria.

Human Disturbance Increases Health Risks to Golden Snub-Nosed Monkeys and the Transfer Risk of Pathogenic Antibiotic-Resistant Bacteria from Golden Snub-Nosed Monkeys to Humans

From the perspective of interactions in the human-animal-ecosystem, the study and control of pathogenic bacteria that can cause disease in animals and humans is the core content of "One Health". In order to test the effect of human disturbance (HD) on the health risk of pathogenic antibiotic-resistant bacteria (PARBs) to wild animals and transfer risk of the PARBs from wild animals to humans, golden snub-nosed monkeys (Rhinopithecus roxellana) were used as sentinel animals. Metagenomic analysis was used to analyze the characteristics of PARBs in the gut microbiota of golden snub-nosed monkeys. Then, the total contribution of antibiotic resistance genes (ARGs) and virulence factors (VFs) of the PARBs were used to assess the health risk of PARBs to golden snub-nosed monkeys, and the antimicrobial drug resistance and bacterial infectious disease of PARBs were determined to assess the transfer risk of PARBs from golden snub-nosed monkeys to humans. There were 18 and 5 kinds of PARBs in the gut microbiota of golden snub-nosed monkeys under HD (HD group) and wild habitat environments (W group), respectively. The total health risks of PARBs to the W group and the HD group were -28.5 × 10-3 and 125.8 × 10-3, respectively. There were 12 and 16 kinds of KEGG pathways of human diseases in the PARBs of the W group and the HD group, respectively, and the gene numbers of KEGG pathways in the HD group were higher than those in the W group. HD increased the pathogenicity of PARBs to golden snub-nosed monkeys, and the PARBs in golden snub-nosed monkeys exhibited resistance to lincosamide, aminoglycoside, and streptogramin antibiotics. If these PARBs transfer from golden snub-nosed monkeys to humans, then humans may acquire symptoms of pathogens including Tubercle bacillus, Staphylococcus, Streptococcus, Yersinia, Pertussis, and Vibrio cholera.

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.

The distribution variation of pathogens and virulence factors in different geographical populations of giant pandas

Intestinal diseases caused by opportunistic pathogens seriously threaten the health and survival of giant pandas. However, our understanding of gut pathogens in different populations of giant pandas, especially in the wild populations, is still limited. Here, we conducted a study based on 52 giant panda metagenomes to investigate the composition and distribution of gut pathogens and virulence factors (VFs) in five geographic populations (captive: GPCD and GPYA; wild: GPQIN, GPQIO, and GPXXL). The results of the beta-diversity analyzes revealed a close relationship and high similarity in pathogen and VF compositions within the two captive groups. Among all groups, Proteobacteria, Firmicutes, and Bacteroidetes emerged as the top three abundant phyla. By using the linear discriminant analysis effect size method, we identified pathogenic bacteria unique to different populations, such as Klebsiella in GPCD, Salmonella in GPYA, Hafnia in GPQIO, Pedobacter in GPXXL, and Lactococcus in GPQIN. In addition, we identified 12 VFs that play a role in the intestinal diseases of giant pandas, including flagella, CsrA, enterobactin, type IV pili, alginate, AcrAB, capsule, T6SS, urease, type 1 fimbriae, polar flagella, allantoin utilization, and ClpP. These VFs influence pathogen motility, adhesion, iron uptake, acid resistance, and protein regulation, thereby contributing to pathogen infection and pathogenicity. Notably, we also found a difference in virulence of Pseudomonas aeruginosa between GPQIN and non-GPQIN wild populations, in which the relative abundance of VFs (0.42%) of P. aeruginosa was the lowest in GPQIN and the highest in non-GPQIN wild populations (GPXXL: 23.55% and GPQIO: 10.47%). In addition to enhancing our understanding of gut pathogens and VFs in different geographic populations of giant pandas, the results of this study provide a specific theoretical basis and data support for the development of effective conservation measures for giant pandas.

Reductions in abundances of intracellular and extracellular antibiotic resistance genes by SiO2 nanoparticles during composting driven by mobile genetic elements

Applying exogenous additives during the aerobic composting of livestock manure is effective for slowing down the spread of antibiotic resistance genes (ARGs) in the environment. Nanomaterials have received much attention because only low amounts need to be added and they have a high capacity for adsorbing pollutants. Intracellular ARGs (i-ARGs) and extracellular ARGs (e-ARGs) comprise the resistome in livestock manure but the effects of nanomaterials on the fates of these different fractions during composting are still unclear. Thus, we investigated the effects of adding SiO₂ nanoparticles (SiO₂NPs) at four levels (0 (CK), 0.5 (L), 1 (M), and 2 g/kg (H)) on i-ARGs, e-ARGs, and the bacterial community during composting. The results showed that i-ARGs represented the main fraction of ARGs during aerobic composting of swine manure, and their abundance was lowest under M. Compared with CK, M increased the removal rates of i-ARGs and e-ARGs by 17.9% and 100%, respectively. SiO₂NPs enhanced the competition between ARGs hosts and non-hosts. M optimized the bacterial community by reducing the abundances of co-hosts (Clostridium_sensu_stricto_1, Terrisporobacter, and Turicibacter) of i-ARGs and e-ARGs (by 96.0% and 99.3%, respectively) and killing 49.9% of antibiotic-resistant bacteria. Horizontal gene transfer dominated by mobile genetic elements (MGEs) played a key role in the changes in the abundances of ARGs. i-intI1 and e-Tn916/1545 were key MGEs related closely to ARGs, and the maximum decreases of 52.8% and 100%, respectively, occurred under M, which mainly explained the decreased abundances of i-ARGs and e-ARGs. Our findings provide new insights into the distribution and main drivers of i-ARGs and e-ARGs, as well as demonstrating the possibility of adding 1 g/kg SiO₂NPs to reduce the propagation of ARGs.

Community assembly patterns and processes of microbiome responses to habitats and Mytilopsis sallei invasion in the tidal zones of the Pearl River Estuary

The sustainability of estuarine ecosystem functions depends on the stabilization of microbial ecological processes. However, due to the unique and variable habitat characteristics of estuarine areas, in-depth studies on ecological processes such as the spatial distribution and assembly patterns of microbial community structure are lacking. As methods to elucidate this structure, we used 16S rDNA, 18S rDNA and ITS sequencing technologies to study the composition, diversity, spatial pattern and aggregation mechanism of the bacterial, protist and fungal communities in the tidal zones of the Pearl River Estuary (PRETZ). The abundance of bacterial communities was much higher than that of protists and fungi, and the spatial pattern was obvious in PRETZ. The application of neutral and null models revealed the assembly process of three microbial communities dominated by stochastic processes. Among the stochastic processes, undominated processes (64.03 %, 62.45 %, and 59.29 %) were the most critical processes in the assembly of bacterial, fungal and protist communities. Meanwhile, environmental variables, geographic locations, and biological factors were associated with the composition and assembly of bacterial, protist, and fungal communities. Among the environmental variables, dissolved oxygen and salinity were the main predictors that jointly affected the differences in the community structure of the three microorganisms, and geographic location was the second predictor affecting the community structure of the three microorganisms and had a more pronounced effect on the diversity and network structure of the bacterial and fungal communities. However, biological factors exerted a weaker effect on the microbial community structure than spatial factors and only affected bacteria and protists; the invasive species Mytilopsis sallei only affected the process of protist community assembly. In addition, environmental variables affected the relative importance of stochastic processes. In summary, the formation of microbial communities in the PRETZ was affected by random processes, environmental variables, geographic location, and invasive species.

Ecological mechanisms of sedimental microbial biodiversity shift and the role of antimicrobial resistance genes in modulating microbial turnover

The mechanisms of phylogenetic turnover of microbial communities to environmental perturbations in sediments remain unclear. In this study, the molecular mechanisms of phylogenetic turnover, and impact of antibiotics and antibiotic resistance genes (ARGs) on the modification of microbial assemblages were unravelled. We investigated 306 ARGs, 8 transposases, and 4 integron integrases, bacteria, and eukaryotic diversity through high-throughput quantitative PCR and illumina sequencing, 21 antibiotics and 3 tetracycline byproducts. The freshwater and estuary ecosystems were mainly dominated by genus Sulfurovum and colonised by closely related species compared with the estuary (closeness centrality = 0.42 vs. 0.46), which was dominated by genus Mycobacterium. Eighty-six percent of the ecological process in the bacterial community was driven by stochastic processes, while the rest was driven by deterministic processes. Environmental-related concentrations of antibiotics (0.15-32.53 ng/g) stimulated the proliferation of ARGs which potentially modulated the microbial community assembly. ARG acquisition significantly (P < 0.001) increased eukaryotic diversity through protection mechanisms. ARGs showed complex interrelationships with the microbial communities, and phylum arthropods and Nematea demonstrated the strongest ARG acquisition potential. This study provides key insights for environmental policymakers into understanding the ecological impact of antibiotics and the role of ARGs in modulating the phylogenetic turnover of microbial communities and trophic transfer mechanisms.

The putative maintaining mechanism of gut bacterial ecosystem in giant pandas and its potential application in conservation

Animals living in captivity and the wild show differences in the internal structure of their gut microbiomes. Here, we performed a meta-analysis of the microbial data of about 494 fecal samples obtained from giant pandas (captive and wild giant pandas). Our results show that the modular structures and topological features of the captive giant panda gut microbiome differ from those of the wild populations. The co-occurrence network of wild giant pandas also contained more nodes and edges, indicating a higher complexity and stability compared to that of captive giant pandas. Keystone species analysis revealed the differences between geographically different wild populations, indicating the potential effect of geography on the internal modular structure. When combining all the giant panda samples for module analysis, we found that the abundant taxa (e.g., belonged to Flavobacterium, Herbaspirillum, and Escherichia-Shigella) usually acted as module hubs to stabilize the modular structure, while the rare taxa usually acted as connectors of different modules. We conclude that abundant and rare taxa play different roles in the gut bacterial ecosystem. The conservation of some key bacterial species is essential for promoting the development of the gut microbiome in pandas. The living environment of the giant pandas can influence the internal structure, topological features, and strength of interrelationships in the gut microbiome. This study provides new insights into the conservation and management of giant panda populations.

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.

Effects of Trophic Level and Land Use on the Variation of Animal Antibiotic Resistome in the Soil Food Web

In recent years, it has been increasingly recognized that soil animals are hidden reservoirs of antibiotic resistance genes (ARGs) and play a vital role in spreading ARGs in soil ecosystems. However, little is known about the variation of ARGs among different animals in the soil food web and effects of trophic levels and land uses on them. We characterized the antibiotic resistomes of 495 soil animal samples collected from six regions across China, including two different land uses. A total of 265 ARGs were detected in all animal samples, and relative abundances of ARGs in animals were significantly higher than in soils. In addition, significant differences in ARGs were observed among different animal groups. Twelve common ARGs were identified among all animal groups, accounting for 17.4% of total ARGs abundance. A positive and significant correlation was found between δ¹⁵N values (trophic level) and total ARGs abundance in animals. The relative abundance of ARGs in the soil food web from arable land was higher than forest land. Changes in soil antibiotics may indirectly affect animal resistome by altering soil ARGs. This study suggests that the risk of ARGs spreading through the food web is greater in arable than in forest ecosystems.

Tracking the influence of antibiotics, antibiotic resistomes, and salinity gradient in modulating microbial community assemblage of surface water and the ecological consequences

The ecological impacts of antibiotics and antibiotic resistance genes (ARGs) on water ecology remain elusive in natural environments. We investigated the influence of antibiotics, ARGs and salinity gradient on the surface water ecosystem. Cefquinome (104.2 ± 43.6 ng/L) and cefminox (16.2 ± 7.50 ng/L) cephalosporins were predominant in all sites. Antibiotic contamination was increased in the estuary ecosystems compared to the freshwater ecosystems by 6%. Bacterial diversity could resist changes in salinity, but the relative abundance of some bacterial genera; Pseudoalteromonas, Glaciecola, norank_f__Arcobacteraceae, and Pseudohongiella was increased in the estuary zone (salinity>0.2%). The eukaryotic composition was increased in the subsaline environments (<0.2%), but the higher salinity in the saline zone inhibited the eukaryotic diversity. The relative abundance of ARGs was significantly higher in the estuary than in freshwater ecosystems, and ARGs interactions and mobile elements (aac(6')-Ib(aka_aacA4)-01, tetR-02, aacC, intI1, intI-1(clinic), qacEdelta1-01, and strB) were the predominant factors responsible for the ARGs propagation. Antibiotics associated with corresponding and non-corresponding ARGs and potentially created an adverse environment that increased the predation and pathogenicity of the aquatic food web and inhibited the metabolic functions. Surface water are first-line-ecosystems receiving antibiotics and ARGs hence our findings provided vital insights into understanding their ecological consequences on surface water ecosystems.

Giant pandas' staple food bamboo phyllosphere fungal community and its influencing factors

Giant pandas have developed a series of foraging strategies to adapt to their special bamboo diets. Although bamboo is an important food resource for giant pandas in Liziping National Nature Reserve (Liziping NR), China, there are relatively few studies on their phyllosphere fungal community and its influencing factors. Herein, we used ITS1 amplification and metagenomic sequencing to analyze the phyllosphere fungi diversity and functions (KEGG, CAZyme, and antibiotic resistance gene) and explore the influencing factors for the three giant pandas foraging bamboo species (Arundinaria spanostachya, AS; Yushania lineolate, YL; and Fargesia ferax, FF) over different seasons (spring vs. autumn) in Liziping NR, China. We found that Ascomycota and Basidiomycota were the most dominant phyla in the bamboo phyllosphere. The alpha diversity (e.g., the Sobs index and Shannon index) was relatively higher in autumn samples than in spring samples, and the community structure differed significantly between the three bamboo species in spring and autumn. Some biotic and abiotic variables (e.g., the elevation and mean base diameter of bamboo) significantly influenced the abundance, diversity, and community structure of the bamboo phyllosphere fungal community. Moreover, the functional analysis showed the differences in the glycoside hydrolase community and antibiotic resistance gene (ARG) profile between spring and autumn samples. Co-occurrence network modeling suggested that AS phyllosphere fungal communities in autumn employed a much more complex network than that in spring, and the abundance of multidrug, tetracycline, and glycopeptide resistance genes was high and closely correlated with other ARGs. These results indicate that fungal community's abundance, diversity, and community structure are mainly affected by the season, host species, and elevation. The season and host species are major factors affecting the biological functions (KEGG and CAZyme), ARGs, and interactions between sympatric bacterial and fungal communities in bamboo phyllosphere. This integrated study can provide a reference basis for the seasonal management of bamboo resources foraged by wild giant pandas, and predict the risk of antibiotic resistance in bamboo phyllosphere fungal flora in Liziping NR (Xiaoxiangling mountains), China.

Global landscape of gut microbiome diversity and antibiotic resistomes across vertebrates

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

Effects of soil protists on the antibiotic resistome under long term fertilization

Soil protists are key in regulating soil microbial communities. However, our understanding on the role of soil protists in shaping antibiotic resistome is limited. Here, we considered the diversity and composition of bacteria, fungi and protists in arable soils collected from a long-term field experiment with multiple fertilization treatments. We explored the effects of soil protists on antibiotic resistome using high-throughput qPCR. Our results showed that long term fertilization had stronger effect on the composition of protists than those of bacteria and fungi. The detected number and relative abundance of antibiotic resistance genes (ARGs) were elevated in soils amended with organic fertilizer. Co-occurrence network analysis revealed that changes in protists may contribute to the changes in ARGs composition, and the application of different fertilizers altered the communities of protistan consumers, suggesting that effects of protistan communities on ARGs might be altered by the top-down impact on bacterial composition. This study demonstrates soil protists as promising agents in monitoring and regulating ecological risk of antibiotic resistome associated with organic fertilizers.

Adaptation of gut microbiome and host metabolic systems to lignocellulosic degradation in bamboo rats

Bamboo rats (Rhizomys pruinosus) are among the few mammals that lives on a bamboo-based diet which is mainly composed of lignocellulose. However, the mechanisms of adaptation of their gut microbiome and metabolic systems in the degradation of lignocellulose are largely unknown. Here, we conducted a multi-omics analysis on bamboo rats to investigate the interaction between their gut microbiomes and metabolic systems in the pre- and post-weaning periods, and observed significant relationships between dietary types, gut microbiome, serum metabolome and host gene expression. For comparison, published gut microbial data from the famous bamboo-eating giant panda (Ailuropoda melanoleuca) were also used for analysis. We found that the adaptation of the gut microbiome of the bamboo rat to a lignocellulose diet is related to a member switch in the order Bacteroidales from family Bacteroidaceae to family Muribaculaceae, while for the famous bamboo-eating giant panda, several aerobes and facultative anaerobes increase after weaning. The conversion of bacteria with an increased relative abundance in bamboo rats after weaning enriched diverse carbohydrate-active enzymes (CAZymes) associated with lignocellulose degradation and functionally enhanced the biosynthesis of amino acids and B vitamins. Meanwhile, the circulating concentration of short-chain fatty acids (SCFAs) derived metabolites and the metabolic capacity of linoleic acid in the host were significantly elevated. Our findings suggest that fatty acid metabolism, including linoleic acid and SCFAs, are the main energy sources for bamboo rats in response to the low-nutrient bamboo diet.

The ecological clusters of soil organisms drive the ecosystem multifunctionality under long-term fertilization

Long-term fertilization is known to impact the biodiversity and community structures of soil organisms, which are responsible for multiple soil ecosystem functions (multifunctionality). However the relationship between the alterations of soil organisms and ecosystem multifunctionality remains unclear, especially in the case of long-term fertilization. To explore the contribution of soil organismal biodiversity and community structures to ecosystem multifunctionality, we took soil samples from a nearly 25-year field fertilization experiment. Organic matter significantly improved the soil ecosystem multifunctionality. Ecosystem multifunctionality was found to be closely linked to the biodiversity and communities of soil organisms within the major ecological clustering of soil organisms (Module 1) according to the trophic co-occurrence network, rather than the entire community of soil organisms. This indicated that ecological clusters of soil organisms within the network were critical in maintaining soil ecosystem multifunctionality. The application of organic fertilization could enrich specialized soil organisms and increase interactions of soil organisms in the ecological cluster. As a result, our findings emphasize the role of ecological clusters in the soil organismal co-occurrence network in controlling soil multifunctionality after long-term fertilization, presenting a novel perspective on the link between soil biodiversity and ecosystem multifunctionality.

Disentangling the Effects of Physicochemical, Genetic, and Microbial Properties on Phase-Driven Resistome Dynamics during Multiple Manure Composting Processes

Composting alters manure-derived antibiotic resistance genes (ARGs) to a certain extent, which is largely dependent upon the composting phase, manure type, microbial phylogeny, and physicochemical properties. However, little is known about how these determinants influence the fate and dynamics of ARGs as well as the mechanisms underlying the ecological process of ARGs during composting. Here, we investigated the temporal patterns of ARGs and their correlations with a series of physicochemical, genetic, and microbial properties during pilot-scale composting of chicken, maggot, bovine, and swine manure. We detected 237 ARGs, 71 of which were co-occurring across all four composting processes and accounted for >80% of the sum of resistome abundance. In support of this ARG co-occurrence, variance partition analyses demonstrated that the manure type explained less resistome variations (5.6%) than the composting phase (21.6%). During the phase-driven resistome dynamics, ARGs showed divergent variations in abundance, and certain beta-lactams and multidrug ARGs were consistently enriched across multiple manure composting processes. Correlation analyses all led to the conclusion that the divergent ARG variations during composting were attributable to the unequal effects of physicochemical properties, mobile elements, and succession of indigenous microbiota, whereas antibiotic residues' effects were marginal. Ultimately, this study determines the relative importance of various key determinants in the phase-driven divergence of ARGs during multiple manure composting processes and demonstrates a clear need to evaluate risks posed by enriched ARGs toward their receiving environments.