Effects of cottonseed meal protein hydrolysate on intestinal microbiota of yellow-feather broilers.

We evaluated the effects of cottonseed meal protein hydrolysate (CPH) on the intestinal microbiota of yellow-feather broilers. We randomly divided 240 chicks into four groups with six replicates: basal diet with 0% (CON), 1% (LCPH), 3% (MCPH), or 5% (HCPH) CPH. The test lasted 63 days and included days 1-21, 22-42, and 43-63 phases. The ACE, Chao1, and Shannon indices in the MCPH and HCPH groups of 42-day-old broilers were higher than those in the CON group (p < 0.05), indicating that the cecum microbial diversity and richness were higher in these groups. Firmicutes and Bacteroidetes were the dominant phyla; however, the main genera varied during the different periods. The abundance of Lactobacillus in CPH treatment groups of 21-day-old broilers was high (p < 0.05); in the 42-day-old broilers, the abundances of Barnesiella, Clostridia_vadinBB60_group, and Parasutterella in the LCPH group, Desulfovibrio, Lactobacillus, Clostridia_vadinBB60_group, and Butyricicoccus in the MCPH group, and Megamonas and Streptococcus in the HCPH group increased; in the 63-day-old broilers, the abundance of Clostridia_UCG-014 and Synergistes in the LCPH and HCPH group, respectively, increased (p < 0.05), and that of Alistipes in the LCPH and MCPH groups decreased (p < 0.05). And changes in the abundance of probiotics were beneficial to improve the intestinal morphology and growth performance. In addition, the LCPH treatment increased the complexity of the microbial network, while the MCPH treatment had the same effect in 42-day-old broilers. Thus, CPH increased the relative abundance of beneficial intestinal microbiota and enhanced the richness and diversity of the bacterial microbiota in broilers aged <42 days; this effect was weakened after 42 days.

Impact of climate warming on soil microbial communities during the restoration of the inner Mongolian desert steppe.

Introduction: Grazer exclosure is widely regarded as an effective measure for restoring degraded grasslands, having positive effects on soil microbial diversity. The Intergovernmental Panel on Climate Change (IPCC) predicts that global surface temperatures will increase by 1.5-4.5°C by the end of the 21st century, which may affect restoration practices for degraded grasslands. This inevitability highlights the urgent need to study the effect of temperature on grassland soil microbial communities, given their critical ecological functions. Methods: Here, we assessed the effects of heavy grazing (control), grazer exclosure, and grazer exclosure plus warming by 1.5°C on soil microbial community diversity and network properties as well as their relationships to soil physicochemical properties. Results and discussion: Our results showed that grazer closure increased soil microbial richness relative to heavy grazing controls. Specifically, bacterial richness increased by 7.9%, fungal richness increased by 20.2%, and the number of fungal network nodes and edges increased without altering network complexity and stability. By contrast, grazer exclosure plus warming decreased bacterial richness by 9.2% and network complexity by 12.4% compared to heavy grazing controls, while increasing fungal network complexity by 25.8%. Grazer exclosure without warming increased soil ammonium nitrogen content, while warming increased soil nitrate nitrogen content. Soil pH and organic carbon were not affected by either exclosure strategy, but nitrate nitrogen was the dominant soil factor explaining changes in bacterial communities. Conclusion: Our findings show that grazer exclosure increases soil microbial diversity which are effective soil restoration measures for degraded desert steppe, but this effect is weakened under warming conditions. Thus, global climate change should be considered when formulating restoration measures for degraded grasslands.

Diversified crop rotations improve soil microbial communities and functions in a six-year field experiment.

Diversified crop rotations can help mitigate the negative impacts of increased agricultural intensity on the sustainability of agroecosystems. However, the impact of crop rotation diversity on the complexity of soil microbial association networks and ecological functions is still not well understood. In this study, a 6-year field experiment was conducted to evaluate how six different crop rotations change the composition and network complexity of soil microbial communities, as well as their related ecological functions. Microbial traits were measured in six crop rotations with different crop diversity index (CDI) during 2016-2022, including winter wheat-summer maize (CDI 1, WM) as the control, sweet potato→winter wheat-summer maize (CDI 1.5, SpWM), peanut→winter wheat-summer maize (CDI 1.5, PWM), soybean→winter wheat-summer maize (CDI 1.5, SWM), spring maize→winter wheat-summer maize (CDI 1.5, SmWM), and ryegrass-sweet sorghum→winter wheat-summer maize (CDI 2, RSWM). The study findings indicated that diversified crop rotations significantly increased ASV richness of both bacterial and fungal communities after 6-year treatments, and the ß-diversity profiles of bacterial and fungal communities significantly distinguished at the year of 2022 from 2016. The relative abundance of Acidobacteria and Chloroflexi was significantly enriched in SpWM rotation at 2022, while Basidiomycota significantly declined in five diversified rotations compared to WM. Diversified crop rotations at 2022 increased the complexity and density of bacterial and fungal networks than 2016. SpWM and PWM rotations had the highest functional groups involved in chemoheterotrophy and saprotroph, respectively. Structural equation modelling (SEM) also revealed that diversified crop rotations increased soil nutrients through improving the composition of bacterial communities and the augmented intricacy of the interconnections within both bacterial and fungal communities. This research underscores the importance of preserving the diversity and ecological functions of soil microorganisms in the nutrient-recycling processes for efficient agricultural practices.

Specialists regulate microbial network and community assembly in subtropical seagrass sediments under differing land use conditions.

Microorganisms in the sediment play a pivotal role in the functioning and stability of seagrass ecosystems and their dynamics are influenced by the nutrient acquisition strategies of host plants. While the distinct impacts of microbial generalists and specialists on community dynamics are recognized, their distribution patterns and ecological roles within seagrass ecosystems remain largely unexplored. To address this issue, we conducted an analysis of community assembly processes and co-occurrence relationships of both microbial generalists and specialists within sediment profiles (0-100 cm) from seagrass habitats subjected to differing land use conditions. The results revealed that seagrasses in Yifeng Estuary experienced the large proportion of cultivated land and exhibited higher organic carbon content in the 0-20 cm surface sediment layer. Nitrogen-cycling bacteria were predominantly associated with seagrasses from Yifeng Estuary, whereas Vibrio spp. was more prevalent in seagrasses from Liusha Bay. Notably, seagrass Halophia beccarii (YHB) in Yifeng Estuary harbored higher niche breadths for both microbial generalist and specialist compared to Halodule uninervis (LHU) and Halophia ovalis (LHO) from Liusha Bay. Stochastic processes were pivotal in shaping seagrass sediment microbial communities, with a higher immigration rate observed in YHB, suggesting greater microbial turnover in this area. Additionally, YHB sediment presented lower drift and higher dispersal limitation among generalists compared to LHU and LHO, whereas the pattern was reversed among specialists. Specialists were found to play a crucial role in shaping microbial interactions within YHB sediment, with genera Halioglobus identified as keystone species in the network. The specialists were further found to significantly influence microbial ß-diversity in seagrass sediment directly. Overall, our findings illustrated how microbial generalists and specialists were distributed in seagrass sediments in response to land use changes and provided new insights into the potential roles of microbial regulation in degraded seagrass ecosystems.

Sediment contamination alters the submersed macrophyte Vallisneria natans and root-associated microbiome profiles during phytoremediation.

The submerged plant Vallisneria natans plays an important role in the remediation of polycyclic aromatic hydrocarbon (PAH)-contaminated sediments. In this study, V. natans and sediments were collected from different V. natans natural vegetation zones, and sediment mesocosms were set up for phytoremediation tests. In addition, commercial-grade V. natans were obtained from the Fish-Bird-Flower market for comparison with phytoremediation. Phytoremediation using V. natans from natural growth significantly increased the degradation of PAHs in Dashui Harbor (0.0148±0.0015 d-1) and Taihu Lake bay sediments (0.0082±0.0010 d-1) but not in commercial-grade V. natans. Transplanted V. natans from natural growth had a significant (p=0.002) effect on PAH degradation, especially in highly PAH-contaminated sedimentary environments. The distinct bacterial communities were strongly affected by sediment type and V. natans type, which contributed to different phytoremediation patterns. Less complex but more stable microbial co-occurrence networks play key roles in improving PAH phytoremediation potential. In addition, V. natans from natural growth in highly PAH-contaminated sediment could adapt to PAH stress by exuding tryptophan metabolites to assemble health-promoting microbiomes. This study provides novel evidence that initial microbial and physicochemical characteristics of sediment and submerged plant types should be considered in the use of bioremediation management strategies for organic pollutant-contaminated sediments.

Seasonal succession of endophyte and the association with active ingredients in Rheum palmatum.

The endophyte is closely related to medicinal plant growth and development, stress resistance, and active ingredients' accumulation. However, a seasonal succession of endophytes and the association with active ingredients is still unclear. In this study, we used high-throughput sequencing methods to compare the endophyte diversity of Rheum palmatum under different seasons and analyze the association between endophytes and five active ingredients. The results show that the diversity of endophytic fungi increased and then decreased, while bacterial diversity increased with the change of season. Community composition showed that the dominant genera of endophytic fungi were different under the different seasons, while the dominant genera of endophytic bacteria were Delftia. Analysis of co-occurrence network maps showed that the connectivity and complexity of endophytic fungi and bacterial networks decreased with the change of season. Spearman analysis indicated that the active ingredients of R. palmatum were significantly positive correlation with genera of endophytic fungi (Chalara). FUNGuild and PICRUSt predictive analysis indicated that the function of endophytic fungi and bacteria, respectively, were symbiotroph and metabolism, and relative abundances were different under the different seasons. Our results help elucidate the mechanism of medicinal plant-endophyte interaction. IMPORTANCE: Through the investigation of the seasonal succession of endophytes and the association with active ingredients in Rheum palmatum, we found that the diversity and composition of endophytes in R. palmatum exhibited seasonal dynamics, and the active ingredients of R. palmatum showed a significantly positive correlation with the genus of endophytic fungi (Chalara). Our results may lay a foundation for understanding the interaction mechanism of endophyte and medicinal plant, and can also provide a theoretical basis for sustainable production of medicinal plants.

Microbial communities living inside plant leaves or on the leaf surface are differently shaped by environmental cues.

Leaf-associated microbial communities can promote plant health and resistance to biotic and abiotic stresses. However, the importance of environmental cues in the assembly of the leaf endo- and epi-microbiota remains elusive. Here, we aimed to investigate the impact of seasonal environmental variations, on the establishment of the leaf microbiome, focusing on long-term changes (five years) in bacterial, fungal, and nonfungal eukaryotic communities colonizing the surface and endosphere of six wild Arabidopsis thaliana populations. While leaf-microbial communities were found to be highly stochastic, the leaf niche had a predominant importance with endophytic microbial communities consistently exhibiting a lower diversity and variability. Among environmental factors, radiation- and humidity-related factors are the most important drivers of diversity patterns in the leaf, with stronger effects on epiphytic communities. Using linear models, we identified 30 important genera whose relative abundance in leaf compartments could be modeled from environmental variables, suggesting specific niche preferences for these taxa. With the hypothesis that environmental factors could impact interactions within microbial communities, we analyzed the seasonal patterns of microbial interaction networks across leaf compartments. We showed that epiphytic networks are more complex than endophytic and that the complexity and connectivity of these networks are partially correlated with the mentioned environmental cues. Our results indicate that humidity and solar radiation function as major environmental cues shaping the phyllosphere microbiome at both micro (leaf compartment) and macro (site) scales. These findings could have practical implications for predicting and developing field-adapted microbes in the face of global change.

Aridity shapes distinct biogeographic and assembly patterns of forest soil bacterial and fungal communities at the regional scale.

Climate change is exacerbating drought in arid and semi-arid forest ecosystems worldwide. Soil microorganisms play a key role in supporting forest ecosystem services, yet their response to changes in aridity remains poorly understood. We present results from a study of 84 forests at four south-to-north Loess Plateau sites to assess how increases in aridity level (1- precipitation/evapotranspiration) shapes soil bacterial and fungal diversity and community stability by influencing community assembly. We showed that soil bacterial diversity underwent a significant downward trend at aridity levels >0.39, while fungal diversity decreased significantly at aridity levels >0.62. In addition, the relative abundance of Actinobacteria and Ascomycota increased with higher aridity level, while the relative abundance of Acidobacteria and Basidiomycota showed the opposite trend. Bacterial communities also exhibited higher similarity-distance decay rates across geographic and environmental gradients than did fungal communities. Phylogenetic bin-based community assembly analysis revealed homogeneous selection and dispersal limitation as the two dominant processes in bacterial and fungal assembly. Dispersal limitation of bacterial communities monotonically increased with aridity levels, whereas homogeneous selection of fungal communities monotonically decreased. Importantly, aridity also increased the sensitivity of microbial communities to environmental disturbance and potentially decreased community stability, as evidenced by greater community similarity-environmental distance decay rates, narrower habitat niche breadth, and lower microbial network stability. Our study provides new insights into soil microbial drought response, with implications on the sustainability of ecosystems under environmental stress.

Organic management pattern improves microbial community diversity and alters microbial network structure in karst tea plantation.

Soil microbiomes play a crucial role in enhancing plant growth, health, and overall agricultural productivity. Nevertheless, the influence of distinct agricultural management practices on the microbial diversity and community structure within tea (Camellia sinensis) plantations has remained enigmatic. This study postulates that organic agricultural management models can enhance microbial diversity and optimise the microbial community structure within tea plantations, indirectly augmenting soil fertility and tea quality. We employed metagenome technology and conducted molecular ecological network analysis to explore the impact of organic management, pollution-free management, and conventional management on the microbial network structure of tea plantation soil in Weng'an County in the southwestern karst region. Soils subjected to organic management exhibited a higher relative abundance of soil microbial and carbohydrate-active enzyme functional genes than those subjected to other management regimes. Additionally, the relative abundance and diversity of dominant bacteria and keystone species were notably higher under organic management than under the other management regimes. Correlation analysis showed that soil microorganisms were closely related to soil fertility and tea quality, respectively. One-way analysis of variance and the structural equation modelling results showed significant variability in soil fertility under the three agricultural management modes and that soil fertility and soil microbial diversity had a direct impact on tea quality (P > 0.05). In conclusion, this study underscores the profound impact of management modes on microbial diversity and community structure within tea plantations. These management practices alter the soil microbial network structure and potential function, ultimately regulating the microecological dynamics of the soil community in tea plantations.

Plant diversity is more important than soil microbial diversity in explaining soil multifunctionality in Qinghai-Tibetan plateau wetlands.

The Qinghai-Tibetan Plateau harbors rich and diverse wetlands that provide multiple ecological functions simultaneously. Although the relationships between biodiversity and wetland functioning have been well studied in recent decades, the links between the multiple features of plant and microbial communities and soil multifunctionality (SMF) remain unknown in the high-altitude wetlands that are extremely sensitive to human disturbance. Here, using the single function, averaging, weighted, and multiple-threshold methods, we calculated the SMF of Qinghai-Tibetan wetlands based on 15 variables associated with soil nutrient status, nutrient cycle, and greenhouse gas emission. We then related SMF to multidimensional (species, phylogenetic, and functional) diversity of plants and soil microorganisms and microbial network modules. The results showed that plant diversity explained more variance in SMF than soil microbial diversity, and plant species richness and phylogenetic distance were positive predictors of SMF. Bacterial network modules were more positively related to SMF than fungal network modules, and the alpha diversity of bacterial network modules contributed more to SMF than the diversity of the whole bacterial community. Pediococcus, Hirsutella, and Rhodotorula were biomarkers for SMF and had significant relationships with nitrogen mineralization and greenhouse gas emissions. Together, these results highlight the importance of plant diversity and bacterial network modules in determining the SMF, which are crucial to predicting the response of ecosystem functioning to biodiversity loss under intensifying anthropogenic activities.

Soil fungal community has higher network stability than bacterial community in response to warming and nitrogen addition in a subtropical primary forest.

Global change factors are known to strongly affect soil microbial community function and composition. However, as of yet, the effects of warming and increased anthropogenic nitrogen deposition on soil microbial network complexity and stability are still unclear. Here, we examined the effects of experimental warming (3°C above ambient soil temperature) and nitrogen addition (5 g N m-2 year-1) on the complexity and stability of the soil microbial network in a subtropical primary forest. Compared to the control, warming increased |negative cohesion|:positive cohesion by 7% and decreased network vulnerability by 5%; nitrogen addition decreased |negative cohesion|:positive cohesion by 10% and increased network vulnerability by 11%. Warming and decreased soil moisture acted as strong filtering factors that led to higher bacterial network stability. Nitrogen addition reduced bacterial network stability by inhibiting soil respiration and increasing resource availability. Neither warming nor nitrogen addition changed fungal network complexity and stability. These findings suggest that the fungal community is more tolerant than the bacterial community to climate warming and nitrogen addition. The link between bacterial network stability and microbial community functional potential was significantly impacted by nitrogen addition and warming, while the response of soil microbial network stability to climate warming and nitrogen deposition may be independent of its complexity. Our findings demonstrate that changes in microbial network structure are crucial to ecosystem management and to predict the ecological consequences of global change in the future. IMPORTANCE: Soil microbes play a very important role in maintaining the function and health of forest ecosystems. Unfortunately, global change factors are profoundly affecting soil microbial structure and function. In this study, we found that climate warming promoted bacterial network stability and nitrogen deposition decreased bacterial network stability. Changes in bacterial network stability had strong effects on bacterial community functional potentials linked to metabolism, nitrogen cycling, and carbon cycling, which would change the biogeochemical cycle in primary forests.

Low Carbon Loss from Long-Term Manure-Applied Soil during Abrupt Warming Is Realized through Soil and Microbiome Interplay.

Manure application is a global approach for enhancing soil organic carbon (SOC) sequestration. However, the response of SOC decomposition in manure-applied soil to abrupt warming, often occurring during diurnal temperature fluctuations, remains poorly understood. We examined the effects of long-term (23 years) continuous application of manure on SOC chemical composition, soil respiration, and microbial communities under temperature shifts (15 vs 25 °C) in the presence of plant residues. Compared to soil without fertilizer, manure application reduced SOC recalcitrance indexes (i.e., aliphaticity and aromaticity) by 17.45 and 21.77%, and also reduced temperature sensitivity (Q10) of native SOC decomposition, plant residue decomposition, and priming effect by 12.98, 15.98, and 52.83%, respectively. The relative abundances of warm-stimulated chemoheterotrophic bacteria and fungi were lower in the manure-applied soil, whereas those of chemoautotrophic Thaumarchaeota were higher. In addition, the microbial network of the manure-applied soil was more interconnected, with more negative connections with the warm-stimulated taxa than soils without fertilizer or with chemical fertilizer applied. In conclusion, our study demonstrated that the reduced loss of SOC to abrupt warming by manure application arises from C chemistry modification, less warm-stimulated microorganisms, a more complex microbial community, and the higher CO2 intercepting capability by Thaumarchaeota.

Enhancement of nitrogen on core taxa recruitment by Penicillium oxalicum stimulated microbially-driven soil formation in bauxite residue.

Microbially-driven soil formation process is an emerging technology for the ecological rehabilitation of alkaline tailings. However, the dominant microorganisms and their specific roles in soil formation processes remain unknown. Herein, a 1-year field-scale experiment was applied to demonstrate the effect of nitrogen input on the structure and function of the microbiome in alkaline bauxite residue. Results showed that the contents of nutrient components were increased with Penicillium oxalicum (P. oxalicum) incorporation, as indicated by the increasing of carbon and nitrogen mineralization and enzyme metabolic efficiency. Specifically, the increasing enzyme metabolic efficiency was associated with nitrogen input, which shaped the microbial nutrient acquisition strategy. Subsequently, we evidenced that P. oxalicum played a significant role in shaping the assemblages of core bacterial taxa and influencing ecological functioning through intra- and cross-kingdom network analysis. Furthermore, a recruitment experiment indicated that nitrogen enhanced the enrichment of core microbiota (Nitrosomonas, Bacillus, Pseudomonas, and Saccharomyces) and may provide benefits to fungal community bio-diversity and microbial network stability. Collectively, these results demonstrated nitrogen-based coexistence patterns among P. oxalicum and microbiome and revealed P. oxalicum-mediated nutrient dynamics and ecophysiological adaptations in alkaline microhabitats. It will aid in promoting soil formation and ecological rehabilitation of bauxite residue. ENVIRONMENT IMPLICATION: Bauxite residue is a highly alkaline solid waste generated during the Bayer process for producing alumina. Attempting to transform bauxite residue into a stable soil-like substrate using low-cost microbial resources is a highly promising engineering. However, the dominant microorganisms and their specific roles in soil formation processes remain unknown. In this study, we evidenced the nitrogen-based coexistence patterns among Penicillium oxalicum and microbiome and revealed Penicillium oxalicum-mediated nutrient dynamics and ecophysiological adaptations in alkaline microhabitats. This study can improve the understanding of core microbes' assemblies that affect the microbiome physiological traits in soil formation processes.

Nanoplastics enhance the denitrification process and microbial interaction network in wetland soils.

With the widespread presence of plastic waste in ecosystems, it is imperative to understand the response of natural processes to micro- and nanoplastic pollution pressures. However, the effects of nanoplastics on biogeochemical cycles are still overlooked and controversial. This study investigated the effects of three particle sizes (100 µm, 7 µm, and 80 nm) of polystyrene (PS) micro/nanoplastics (0.08 % of mass concentration) on denitrification processes and nirS/nirK denitrifying bacterial communities in wetland soils. The results indicated that PS nanoplastics were found to significantly enhance denitrification rates from 21.30 to 54.73 µmol N2·h-1·kg-1, increasing by 1.57 times compared to the control. Exposure to nanoplastics caused shifts in the composition and structure of the nirS-type denitrifier community. LEfSe analysis, random forest, and Mantel tests revealed that nirS denitrifying bacteria, especially Sideroxydans, played a pivotal role in driving denitrification rates (Mantel's R = 0.24, p = 0.002), likely due to the faster release of organic substrates from nanoplastics. Microbial co-occurrence networks demonstrated that nanoplastic amendments fostered a denser denitrifier network and led to shifts in keystone species. Sideroxydans appeared more likely to cooperate with other bacteria, such as Burkholderiales, to complete denitrification processes. This study suggests that nanoplastics are a potentially stronger driver of denitrification than microplastics, providing insight into the impact of plastic pollutants on biogeochemical cycling in natural wetland ecosystems. Given the widespread distribution of wetlands, the potential increase in gaseous nitrogen emissions due to nanoplastics pollution warrants attention.

Biodegradable film mulching increases soil microbial network complexity and decreases nitrogen-cycling gene abundance.

Biodegradable plastic films have emerged as a substitute for conventional plastic films. Nevertheless, responses of plant-associated microbiomes to the application of biodegradable film mulching at field scale have received little attention. A field experiment was conducted to assess the influence of different film mulching treatments on various microbial attributes and nitrogen (N) cycling functional genes in bulk and rhizosphere soils. Biodegradable film mulching raised the bacterial Shannon index in bulk soils but not in rhizosphere soils. Biodegradable film mulching has led to an increase in the complexity and connectivity of microbial networks, as well as an enhancement in the positive association among microorganisms owing to raised soil nutrients and increased crop biomass. In biodegradable film-treated soils, both bacterial and fungal communities were primarily influenced by stochastic processes associated with dispersal limitation. Moreover, conventional plastic film mulching increased denitrification, anammox, N fixation, and dissimilatory nitrate-reduction (DNRA) gene abundance in bulk soils. In rhizosphere soils, biodegradable film mulching reduced nitrification, denitrification, anammox, N fixation, and DNRA gene abundance. Furthermore, keystone genera (e.g., Nitrosospira, Truepera, Adhaeribacter, Opitutus, and Fusarium) were affected by edaphic variables, contributing to decreased N-cycling gene abundance in biodegradable film-treated soils. Collectively, biodegradable film mulching transformed soil microbiome assembly and functional adaptation, and soil nutrient availability and plant biomass were the critical factors influencing the microbial community. These findings present a novel perspective on the diverse impacts of biodegradable and conventional film mulching on soil microbiome and N-cycling processes.

The effects of food provisioning on the gut microbiota community and antibiotic resistance genes of Yunnan snub-nosed monkey.

Yunnan snub-nosed monkeys (Rhinopithecus bieti) are the highest elevation lived non-human primate, and their survival has been threatened for decades. To promote their population growth, a reserve provides a typical monkey population with supplemental food. However, the influences of this food provisioning on their gut microbiota and antibiotic resistance genes (ARGs) were unknown. Therefore, we investigated the gut microbiota and ARGs of the food-provisioned monkey population compared with another wild foraging population. We found that food provisioning significantly increased the gut microbiota diversity and changed the community composition, particularly increased both the Firmicutes abundance and Firmicutes/Bacteroidetes ratio. Meanwhile, the food provisioning decreased the complex and stable gut microbiota network. KEGG functions were also influenced by food provisioning, with wild foraging monkeys showing higher functions of metabolism and genetic information processing, especially the carbohydrate metabolism, while food-provisioned monkeys exhibited increased environmental information processing, cellular processes, and organismal systems, including valine, leucine, and isoleucine degradation. In addition, food provisioning increased the abundance of ARGs in the gut microbiota, with most increasing the abundance of bacA gene and changing the correlations between specific ARGs and bacterial phyla in each population. Our study highlights that even food provisioning could promote wildlife nutrient intake, and it is necessary to pay attention to the increased ARGs and potential effects on gut microbiota stability and functions for this human conservation measure.

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

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

Revealing bioresponses of biofilm and flocs to salinity gradient in halophilic biofilm reactor.

Understanding the different biological responses to salinity gradient between coexisting biofilm and flocs is crucial for regulating the ecological function of biofilm system. This study investigated performance, dynamics, and community assembly of biofilm system under 3 %-7% salinity gradient. The removal efficiency of NH4+-N remained stable and exceeded 93 % at 3 %-6% salinity, but decreased to below 80 % at 7 % salinity. The elevated salinity promoted the synthesis of extracellular polymer substrates, inhibited microbial respiration, and significantly regulated the microbial community structure. Compared to flocs, biofilm exhibited greater species diversity and richer Nitrosomonas. It was found diffusion limitations dominated the microbial community assembly under the salinity gradient. And microbial network revealed positive interactions predominated the microbial relationships, designating norank Spirochaetaceae, unclassified Micrococcales, Corynebacterium, and Pusillimonas as keystone species. Moreover, distinct salinity preferences in nitrogen transformation-related genes were observed. This study can improve the understanding to the regulation of biofilm systems to salt stresses.

Rhizospheric microbiota of suppressive soil protect plants against Fusarium solani infection.

BACKGROUND: Fusarium infection has caused huge economic losses in many crops. The study aimed to compare the microbial community of suppressive and conducive soils and relate to the reduction of Fusarium wilt. RESULTS: High-throughput sequencing and microbial network analysis were used to investigate the differences in the rhizosphere microbiota of the suppressive and conducive soils and to identify the beneficial keystone taxa. Plant pathogens were enriched in the conducive soil. Potential plant-beneficial microorganisms and antagonistic microorganisms were enriched in the suppressive soil. More positive interactions and keystone taxa existed in the suppressive soil network. Thirty-nine and 16 keystone taxa were identified in the suppressive and conducive soil networks, respectively. Sixteen fungal strains and 168 bacterial strains were isolated from suppressive soil, some of which exhibited plant growth-promotion traits. Thirty-nine bacterial strains and 10 fungal strains showed antagonistic activity against F. solani. Keystone taxa Bacillus and Trichoderma exhibited high antifungal activity. Lipopeptides produced by Bacillus sp. RB150 and chitinase from Trichoderma spp. inhibited the growth of F. solani. Microbial consortium I (Bacillus sp. RB150, Pseudomonas sp. RB70 and Trichoderma asperellum RF10) and II (Bacillus sp. RB196, Bacillus sp. RB150 and T. asperellum RF10) effectively controlled root rot disease, the spore number of F. solani was reduced by 94.2% and 83.3%. CONCLUSION: Rhizospheric microbiota of suppressive soil protects plants against F. solani infection. Antagonistic microorganisms in suppressive soil inhibit pathogen growth and infection. Microbial consortia consisted of keystone taxa well control root rot disease. These findings help control Fusarium wilt. © 2024 Society of Chemical Industry.