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Simple Summary: The gut bacterial community of two captive ducks was investigated in this study across seasons. It was discovered that the composition of gut bacteria was significantly affected by seasonal variations, with greater diversity in winter. Different seasons yielded different biomarkers, with the majority found in winter when a more intricate bacterial network structure was seen. Ten important pathogenic bacterial species were discovered and appeared to be more abundant in the summer. The presence of significant pathogenic bacteria was demonstrated by this study, raising concerns for captive animals, and shedding light on how gut bacterial composition is affected by seasonal fluctuations. Vertebrates and their gut bacteria interact in complex and mutually beneficial ways. The intestinal microbial composition is influenced by several external influences. In addition to food, the abiotic elements of the environment, such as temperature, humidity, and seasonal fluctuation are also important determinants. Fecal samples were collected from two captive duck species, Baikal teal (Sibirionetta formosa) and common teal (Anas crecca) across four seasons (summer, autumn, winter, and spring). These ducks were consistently fed the same diet throughout the entire experiment. High throughput sequencing (Illumina Mi-seq) was employed to analyze the V4–V5 region of the 16sRNA gene. The dominant phyla in all seasons were Proteobacteria and Firmicutes. Interestingly, the alpha diversity was higher in winter for both species. The NMDS, PCoA, and ANOSIM analysis showed the distinct clustering of bacterial composition between different seasons, while no significant differences were discovered between duck species within the same season. In addition, LefSe analysis demonstrated specific biomarkers in different seasons, with the highest number revealed in winter. The co-occurrence network analysis also showed that during winter, the network illustrated a more intricate structure with the greatest number of nodes and edges. However, this study identified ten potentially pathogenic bacterial species, which showed significantly enhanced diversity and abundance throughout the summer. Overall, our results revealed that season mainly regulated the intestinal bacterial community composition and pathogenic bacteria of captive ducks under the instant diet. This study provides an important new understanding of the seasonal variations in captive wild ducks' intestinal bacterial community structure. The information available here may be essential data for preventing and controlling infections caused by pathogenic bacteria in captive waterbirds. [ABSTRACT FROM AUTHOR]

Simple Summary: The fungi community has received comparatively little attention compared to bacteria in previous studies on the avian gut microbiome. Even though fungi constitute a smaller proportion of the gastrointestinal (GIT) microbiota, changes in the diversity and composition of the gut microbial population have been associated with a number of diseases. This study, concentrating on captive migratory ducks, provides light on the gut fungal population, identifies potential animal pathogens and plant saprotrophs, and reveals that seasonal variations shape the dynamics of the gut fungal community more significantly than the host species. Understanding the dynamics of avian gut fungal communities and potentially pathogenic species across different seasons is crucial for assessing their health and ecological interactions. In this study, high-throughput sequencing was employed to examine the changes in gut fungal communities and the presence of potential pathogens between different seasons in captive Baikal teal and common teal. Between the summer and autumn seasons, both duck species showed significant differences in fungal diversity and community composition. A higher fungal diversity in both species was exhibited in the summer than in the autumn. Ascomycota and Basidiomycota were the two most common phyla, with a greater proportion of Ascomycota than Basidiomycota in both duck species in the summer. Interestingly, our study also identified animal pathogens and plant saprotrophs in the gut fungal communities. Seasonal variation had an effect on the diversity and abundance of both animal pathogens and saprotrophs. Specifically, during the summer season, the diversity and relative abundance were higher compared to the autumn season. In addition, there were differences between duck species in terms of animal pathogens, while no significant differences were observed in saprotrophs. Overall, the communities of the gut fungi, animal pathogens, and saprotrophs were found to be influenced by seasonal changes rather than host species. Therefore, seasonal variations might dominate over host genetics in shaping the gut microbiota of captive Baikal teal and common teal. This study underscores the importance of incorporating an understanding of seasonal dynamics and potential pathogens within the gut microbiota of captive ducks. Such considerations have the potential to drive progress in the development of sustainable and economically viable farming practices. [ABSTRACT FROM AUTHOR]

Driven by habitat loss from anthropogenic activities, wintering migratory birds forage together with poultry in paddy fields, and thus impose risks of cross transmitting pathogens. To date, there is little evidence for such risks of pathogen transmission between wild birds and poultry. Using the high‐throughput sequencing, we report on detected potential pathogens of both wild hooded cranes Grus monacha and sympatric domestic geese Anser anser domesticus during the wintering period, and infer the possibility of cross‐species pathogen transmission. The results revealed that the number of shared amplicon sequence variants (ASVs) of potential pathogens between the gut microbiota of the two species was low during the early wintering stage (17.2%; 5 ASVs shared) but increased to 56.3% (18 ASVs shared) during the late wintering stage. That is, potential pathogens in the gut microbial communities of the two species became more similar through co‐foraging in paddy fields, supporting cross transmission of pathogens between hooded cranes and domestic geese during the wintering period. Importantly, transmission appeared to be largely from wild hooded cranes to domestic geese, although some potential pathogens may have become specialized to the domestic goose in the late wintering stage. Humans are also face the risks of contracting these potential pathogens from migratory birds through their frequent contacts with domestic poultry. It is, therefore, necessary to closely monitor this pathway of pathogen transmission from wild birds to domestic animals and even to humans. [ABSTRACT FROM AUTHOR]

Background and aims: Wildfire is a primary driver of forest ecosystem functioning, and fire-induced changes in nutrient cycling and the balance of multiple nutrients may influence plant growth response to burning. However, the relationship between total and available soil stoichiometry and stoichiometric effects on the growth of fine roots following forest fires remain unclear. Methods: We measured the total and available soil C, N, and P concentrations, their ratios, and fine root biomass (FRB) at unburned control, 1-year-postfire, and 11-year-postfire sites in a Chinese boreal larch forest. We analyzed the relationship between soil stoichiometry and FRB. Results: Wildfire significantly reduced the total and available soil C:N:P ratios and FRB immediately postfire. Eleven years postfire, most indicators recovered to the prefire levels except for total soil C:P and N:P ratios, and available C:N ratio. Wildfire increased the associations between total and available soil C:N:P ratios, as well as between FRB and soil C:N:P ratios, but reduced the relationship between FRB and soil nutrient supply. However, these effects became weaker over time. Conclusions: The effects of wildfire on biogeochemical processes in boreal ecosystems extend to the relationship between total and available soil stoichiometry. Wildfires strengthen the linkage between fine roots and soil stoichiometry but weaken the effects of soil nutrient supply in the Great Xing'an Mountains. Therefore, the effects of wildfire on the coupling of soil C, N, and P cycling can produce a more complex soil-plant interaction in the early succession stage of boreal larch forest. [ABSTRACT FROM AUTHOR]

Grazing alters the plant communities, soil properties, and habitat conditions of the alpine grassland. Arbuscular mycorrhizal fungi (AMF) are involved in the nutrient cycling of grassland ecosystems and form a mutual symbiosis with their host plants. Thus, AMF are sensitive to the impact of livestock grazing. However, the effects of grazing intensity on the AMF community composition and the association between AMF and environmental factors, such as soil physicochemical properties, enzyme activity, and glomalin‐related soil proteins, remain unclear. Here, the response of the soil AMF community to grazing intensity gradients (i.e., light, moderate, and heavy grazing) was studied in an alpine grassland on the Qinghai‐Tibet Plateau. The dominant AMF families included Glomeraceae, Gigasporaceae, Claroideoglomeraceae, Diversisporaceae, and Ambisporaceae. Significant shifts in the AMF community composition in response to grazing intensity were found in both surface and subsurface soils. Soil C/N ratio, plant diversity, soil compactness, chitinase activity, aboveground biomass, total N, soil moisture, and NO3−–N significantly correlated with changes in the AMF community composition. Heavy grazing intensity was associated with the highest AMF alpha diversity, whereas moderate grazing intensity had the lowest AMF alpha diversity in both surface and subsurface soils. Grazing intensity, dominant plants, soil C and N concentrations, and soil compactness were significantly correlated with AMF diversity. These results demonstrated a significant response of the AMF community to grazing intensity, suggesting that plants increase their reliance on AMF symbioses with higher alpha diversity in the heavily degraded alpine grasslands of the Qinghai‐Tibet Plateau. Core Ideas: Grazing alters plant communities, soil properties, and AMF communities.Soil C/N and plant diversity are significantly correlated with AMF communities.Moderate grazing is associated with the lowest belowground AMF alpha diversity.Plants increase their reliance on AMF symbioses in heavily degraded alpine grassland. [ABSTRACT FROM AUTHOR]

Microbial degradation of fluorinated compounds raised significant attention because of their widespread distribution and potential environmental impacts. Here, we report a bacterial isolate, Rhodococcus sp. NJF-7 capable of defluorinating monofluorinated medium-chain length alkanes. This isolate consumed 2.29 ± 0.13 mmol L− 1 of 1-fluorodecane (FD) during a 52 h incubation period, resulting in a significant release of inorganic fluoride amounting to 2.16 ± 0.03 mmol L− 1. The defluorination process was strongly affected by the initial FD concentration and pH conditions, with lower pH increasing fluoride toxicity to bacterial cells and inhibiting enzymatic defluorination activity. Stoichiometric conversion of FD to fluoride was observed at neutral pH with resting cells, while defluorination was significantly lower at reduced pH (6.5). The discovery of the metabolites decanoic acid and methyl decanoate suggests that the initial attack by monooxygenases may be responsible for the biological defluorination of FD. The findings here provide new insights into microbial defluorination processes, specifically aiding in understanding the environmental fate of organic semi-fluorinated alkane chemicals. [ABSTRACT FROM AUTHOR]

Background: The intestinal microbiota play remarkable roles in maintaining the health of their hosts. Recent studies focused on gut bacterial diversity in birds and poultry, with little information about the ecological functions of their gut fungal community. Methods: The high-throughput sequencing was applied to compare intestinal fungal community structure between Hooded Crane (Grus monacha) and Domestic Goose (Anser anser domesticus), and infer the potential pathogens of each species at Shengjin Lake of China. Results: Intestinal fungal alpha diversity was higher in Hooded Crane than Greylag Goose (Anser anser). Gut fungal community composition showed dramatic shifts between the two species. Hooded Cranes mainly eat Vallisneria natans and Potamogeton malaianus, while artificial hurl food (i.e., paddy) was the main food resource for Domestic Geese, suggesting that the variations in fungal community might be induced by different diets between the two hosts. Two enriched genera (i.e., Acremonium and Rhodotorula) which could increase host's digestion were detected in guts of Hooded Cranes. In addition, there were 42 pathogenic amplicon sequence variants (ASVs), 17% of which shared in Hooded Crane and Greylag Goose. The Hooded Crane had higher gut fungal pathogenic diversity and abundance relative to Greylag Goose. Conclusions: The study demonstrated that divergence in intestinal fungal community structure might be induced by different diets between wintering Hooded Crane and Domestic Goose. Hooded Crane might rely more on their gut fungal taxa to acquire nutrients from indigestible food resources. Our study also implied that more research should focus on intestinal pathogens in wild birds and domestic poultry, as they might increase risk of disease in other animals, even human beings. The degree of cross infection in pathogens among wild birds and sympatric poultry should be clearly verified in future study. [ABSTRACT FROM AUTHOR]

Background: Gut microbiota play crucial roles in host health. Wild birds and domestic poultry often occupy sympatric habitats, which facilitate the mutual transmission of intestinal microbes. However, the distinct intestinal microbial communities between sympatric wild birds and poultry remain unknown. At present, the risk of interspecies transmission of pathogenic bacteria between wild and domestic host birds is also a research hotspot. Methods: This study compared the intestinal bacterial communities of the overwintering Hooded Crane (Grus monacha) and the Domestic Goose (Anser anser domesticus) at Shengjin Lake, China, using Illumina high-throughput sequencing technology (Mi-Seq platform). Results: Our results revealed that Firmicutes, Actinobacteria, Proteobacteria, Bacteroidetes and Chloroflexi were the dominant bacterial phyla in both hosts. The gut bacterial community composition differed significantly between sympatric Hooded Cranes and Domestic Geese. However, the hosts exhibited little variation in gut bacterial alpha-diversity. The relative abundance of Firmicutes was significantly higher in the guts of the Hooded Cranes, while the relative abundances of Actinobacteria, Proteobacteria, Bacteroidete and Chloroflexi were significantly higher in guts of Domestic Geese. Moreover, a total of 132 potential pathogenic operational taxonomic units (OTUs) were detected in guts of Hooded Cranes and Domestic Geese, and 13 pathogenic OTUs (9.8%) were found in both host guts. Pathogenic bacterial community composition and diversity differed significantly between hosts. Conclusions: The results showed that the gut bacterial community composition differs significantly between sympatric Hooded Cranes and Domestic Geese. In addition, potential pathogens were detected in the guts of both Hooded Cranes and Domestic Geese, with 13 pathogenic OTUs overlapping between the two hosts, suggesting that more attention should be paid to wild birds and poultry that might increase the risk of disease transmission in conspecifics and other mixed species. [ABSTRACT FROM AUTHOR]

Aims: The effects of shrub encroachment on plant and soil properties have been well studied. However, little is known about how shrub encroachment influences soil bacterial communities. We investigated the effects of shrub encroachment on grassland soil bacterial communities along a soil depth gradient in the Inner Mongolian region of China.Methods: The belowground bacterial communities were examined using high-throughput sequencing of the 16S rRNA gene (V4-V5 region, Illumina MiSeq).Results: Bacterial alpha-diversity was higher in shrub-encroached soils than in control grassland soils. Bacterial OTU richness was highest at 0-20 cm soil depths, while phylogenetic diversity was greatest at 10-20 cm soil depths. At each soil depth layer, shrub encroachment was associated with a significant shift in bacterial community composition. Change in soil pH was the factor most strongly related to change in bacterial community composition associated with shrub encroachment at all four depth horizons in the soils. Shrub encroachment appears to alter the distribution of bacterial life history strategies in the surface soil (i.e., showing an enrichment in copiotrophs and a depletion in oligotrophs) and shrubs are associated with an increase in nitrification potential in deeper soil horizons.Conclusions: Our results indicate that the influence of shrub encroachment on bacterial community composition extends deep into the soil. The intensity of shrub encroachment at this study site suggests that this ecosystem is undergoing dramatic succession towards shrub-dominance, which will likely trigger shifts in ecosystem function. [ABSTRACT FROM AUTHOR]

The alpine meadow on the Qinghai-Tibetan Plateau (QTP), which is sensitive to global climate change and human activities, is subjected to addition of nutrients such as nitrogen (N) and phosphorus (P) in the soil. The impacts of N or P on ecosystem structure and function depend at least partly on the response of soil fungal communities, although few studies have compared the effects of N and P addition, both separately and together. We examined the responses of composition of the soil fungal community to 3-year experimental nutrient additions (control, N, N plus P, and P) in a typical alpine meadow of the QTP. We found that P addition, regardless of N addition, significantly reduced fungal species richness and changed fungal community composition, while the effect of N was undetectable. Nitrogen plus phosphorus caused a more distinct community than either N or P addition alone. Multivariate regression tree, canonical correspondence analysis, and distance-based multivariate linear model analyses all suggested available P was a key parameter determining the diversity and composition of the fungal community. Other parameters such as dissolved organic N, aboveground net primary productivity of forbs, and dissolved organic C played important but secondary roles. The results indicated an important role of P in structuring soil fungal communities in the alpine meadow. Our results suggest that fungal diversity loss and long-term changes in ecosystem stability can result from fertilization management in the fragile alpine environment. [ABSTRACT FROM AUTHOR]

Aims: Wildfires are important disturbances that help to shape the structure and function of forest ecosystems, and arbuscular mycorrhizal fungi (AMF) are key players in the post-fire recovery of soils and understory vegetation. We aimed to investigate the response of AMF communities to wildfire over different timescales. Methods: Primer set AMV4.5NF/AMDGR was used to amplify soil 18S rRNA gene fragments for the 454 GS-FLX pyrosequencing platform to examine belowground AMF communities 1 and 11 years following low- and high-intensity wildfires in the Greater Khingan Mountains of China. Results: The majority of AMF sequences detected were annotated as Glomeraceae, Claroideoglomeraceae, Diversisporaceae and Acaulosporaceae. Both AMF community composition and alpha-diversity were correlated with herbaceous and shrubby biomass, available phosphorus (AP) and NH, which were in turn altered by wildfire. AMF community composition, alpha-diversity, and phylogenetic structure were significantly altered 1-year-post-fire. However, AMF communities were indistinguishable from unburned forest soils 11-year-post-fire. Conclusions: Our results indicated that AMF communities are resilient to wildfire on decadal timescales. This resilience appears to depend on the post-fire regrowth of understory vegetation and the subsequent recovery of soil chemical properties. [ABSTRACT FROM AUTHOR]

Lignin enhanced biodegradation of polycyclic aromatic hydrocarbons (PAHs) in soil, but collaboration among soil microorganisms during this process remains poorly understood. Here we explored the relations between microbial communities and PAH transformation in soil microcosms amended with lignin. Mineralization of the four-ring benzo(a)anthracene (BaA), which was selected as a model, was determined by using an isotope-labeled tracer. The eukaryotic inhibitor cycloheximide and redox mediator ABTS were used to validate the fungal role, while microbial communities were monitored by amplicon sequencing. The results demonstrated that lignin significantly promoted BaA mineralization to CO 2 , which was inhibited and enhanced by cycloheximide and ABTS, respectively. Together with the increased abundance of Basidiomycota, these observations suggested an essential contribution of fungi to BaA biodegradation, which possibly through a ligninolytic enzyme-mediated pathway. The enrichment of Methylophilaceae and Sphingomonadaceae supported bacterial utilization of methyl and aryl groups derived from lignin, implicating cometabolic BaA degradation. Co-occurrence network analysis revealed increased interactions between fungi and bacteria, suggesting they played synergistic roles in the transformation of lignin and BaA. Collectively, these findings demonstrate the importance of synergy between fungi and bacteria in PAH transformation, and further suggest that the modulation of microbial interplay may ameliorate soil bioremediation with natural materials such as lignin. [Display omitted] • Lignin enhances benzo(a)anthracene (BaA) mineralization in soil microcosms. • Fungal BaA transformation is related to ligninolytic enzyme-mediated reaction. • Bacteria utilizing methyl and aryl groups of lignin are stimulated. • Co-occurrence pattern suggests fungi-bacteria synergy in BaA cometabolism. [ABSTRACT FROM AUTHOR]

The long-term high intensity continuous cropping with heavy application of mineral fertilization resulted in soil degradation and accumulation of soil-borne plant pathogens. Fungi are key microbial components and closely related to soil health in agroecosystem. In this study, the responses of fungal communities to different agricultural practices were investigated in upland of Ultisol using quantitative polymerase chain reaction (qPCR) and high-throughput sequencing (Illumina MiSeq). The study involved four management treatments: no fertilization (Control), mineral NPK fertilizer (NPK), NPK fertilizer plus peanut straw (NPKS), and NPK fertilizer plus planting green manure (i.e., hairy vetch; NPKG). By comparison with the NPK, application of NPKG significantly increased soil fertility and peanut yield. The NPKS and NPKG significantly increased soil fungal abundance relative to the NPK. Different agricultural practices significantly altered soil fungal community composition in Ultisol. Soil pH and phosphorus content were the two most pivotal drivers shaping fungal community structure. Compared to the NPK, the NPKS and NPKG significantly increased the relative abundance of Basidiomycota. The NPKG increased the relative abundance of certain plant-beneficial fungal taxa and decreased the relative abundance and diversity of plant-pathogen relative to NPK and NPKS, thereby contributing to suppressing continuous cropping barriers and increasing peanut productivity. Overall, our results suggested that planting hairy vetch might outperform NPK or returning peanut straw for improving peanut yield by increasing soil fertility and altering fungal community structure in upland of Ultisol. • Different practices affected fungal abundance and community structure in Ultisol. • Shifts in soil P and pH led to divergence in fungal community among treatments. • Application of hairy vetch decreased the relative abundance of plant-pathogen. • Hairy vetch increased crop yield by improving soil fertility and fungal community. [ABSTRACT FROM AUTHOR]

• Hairy vetch and peanut straw altered soil bacterial community structure. • Hairy vetch rather than peanut straw altered soil bacterial potential function. • Hairy vetch increased the relative abundance of certain plant-beneficial bacteria. • Hairy vetch increased nutrient levels offsetting the baleful effect of soil acidification. Empirical studies have intensively clarified the effects of livestock manure on soil fertility, crop yield and microbial community, with little information about their response to application of peanut straw and green manure in dryland of Ultisols. In this study, quantitative polymerase chain reaction (qPCR) and next-generation sequencing were used to compare bacterial abundance, community structure and predicted metabolic function under four agricultural practices in Ultisol: without fertilization (control), mineral fertilization (NPK, conventional regime), mineral fertilization with returning composting peanut straw (NPKS) and with planting hairy vetch (NPKG). Compared to the control, the NPKS and NPKG significantly decreased soil pH. The NPKG was associated with the highest soil nutrient contents and peanut yield. Compared to control, the NPKS and NPKG increased bacterial abundance and decreased bacterial alpha-diversity. Fertility improvement and soil acidification were responsible for increasing bacterial abundance and decreasing alpha-diversity, respectively. Phylogenetic clustering was found in soil bacterial community, with the stronger clustering in NPKS and NPKG, suggesting that soil acidification might induce stronger niche-based filtering to decrease bacterial alpha-diversity. Compared to control, the NPKS and NPKG altered soil bacterial community composition, but only NPKG changed the predicted metabolic functions. The NPKG triggered larger changes in bacterial community composition than NPKS, implying that dramatic shifts in community composition might lead to modification of bacterial functions. Soil bacterial community composition and predicted function co-varied with soil pH and nutrient contents, but nutrient improvement had stronger (i.e., 23.3% vs. 11.5% in composition; 21.8% vs. 13.6% in function) and contrary effects (i.e., the opposite arrows) than soil acidification. In addition, the NPKG was associated with higher relative abundance of plant-beneficial bacterial taxa (Mycobacterium and Pseudomonas). Overall, mineral fertilization with planting hairy vetch might be an effective practice for improving soil fertility, optimizing bacterial community structure and increasing peanut yield in dryland of Ultisol. However, the further soil acidification should be taken into account following planting hairy vetch longer. [ABSTRACT FROM AUTHOR]

Simple Summary: The gut microbiota plays important roles for maintaining the health of the host. In this study, the results revealed significant differences in the gut bacterial communities among bean geese, hooded cranes, and domestic geese. In comparison to domestic geese, the gut bacterial community of bean geese and hooded cranes had a greater capacity for energy metabolism, suggesting that wild birds may rely more on their gut microbiota to survive in cold conditions. Furthermore, pathogens were discovered to overlap among the three hosts, reminding us to monitor the potential for pathogen transmission between poultry and wild birds. Hooded cranes showed the highest diversity and relative abundance of pathogens compared to the other two species. Due to its vulnerable status, more focus should be paid to the protection of the hooded crane species. These findings could help us gain a deeper understanding of the structure of gut bacterial and pathogenic communities in poultry and wild birds. The host's physiological well-being is intricately associated with the gut microbiota. However, previous studies regarding the intestinal microbiota have focused on domesticated or captive birds. This study used high-throughput sequencing technology to identify the gut bacterial communities of sympatric bean geese, hooded cranes, and domestic geese. The results indicated that the gut bacterial diversity in domestic geese and hooded cranes showed considerably higher diversity than bean geese. The gut bacterial community compositions varied significantly among the three hosts (p < 0.05). Compared to the hooded crane, the bean goose and domestic goose were more similar in their genotype and evolutionary history, with less difference in the bacterial community composition and assembly processes between the two species. Thus, the results might support the crucial role of host genotypes on their gut microbiota. The gut bacteria of wild hooded cranes and bean geese had a greater capacity for energy metabolism compared to domestic geese, suggesting that wild birds may rely more on their gut microbiota to survive in cold conditions. Moreover, the intestines of the three hosts were identified as harboring potential pathogens. The relative abundance of pathogens was higher in the hooded crane compared to the other two species. The hooded crane gut bacterial community assemblage revealed the least deterministic process with the lowest filtering/selection on the gut microbiota, which might have been a reason for the highest number of pathogens result. Compared to the hooded crane, the sympatric bean goose showed the least diversity and relative abundance of pathogens. The intestinal bacterial co-occurrence network showed the highest stability in the bean goose, potentially enhancing host resistance to adverse environments and reducing the susceptibility to pathogen invasion. In this study, the pathogens were also discovered to overlap among the three hosts, reminding us to monitor the potential for pathogen transmission between poultry and wild birds. Overall, the current findings have the potential to enhance the understanding of gut bacterial and pathogenic community structures in poultry and wild birds. [ABSTRACT FROM AUTHOR]

Stag beetles, recognized as common saproxylic insects, are valued for their vibrant coloration and distinctive morphology. These beetles play a crucial ecological role in decomposition and nutrient cycling, serving as a vital functional component in ecosystem functioning. Although previous studies have confirmed that stag beetles are predominantly fungivores, the fluctuations in their intestinal fungal communities at different developmental stages remain poorly understood. In the current study, high-throughput sequencing was employed to investigate the dynamic changes within intestinal fungal communities at various developmental stages in the stag beetle Dorcus hopei. Results showed that microbial diversity was higher during the larval stage than during the pupal and adult stages. Furthermore, significant differences were identified in the composition of the intestinal fungal communities across the larval, pupal, and adult stages, suggesting that developmental transitions may be crucial factors contributing to variations in fungal community composition and diversity. Dominant genera included Candida, Scheffersomyces, Phaeoacremonium, and Trichosporon. Functional predictions indicated a greater diversity and relative abundance of endosymbiotic fungi in the larval gut, suggesting a potential dependency of larvae on beneficial gut fungi for nutrient acquisition. Additionally, the application of abundance-based β-null deviation and niche width analyses revealed that the adult gut exerted a stronger selection pressure on its fungal community, favoring certain taxa. This selection process culminates in a more robust co-occurrence network of fungal communities within the adult gut, thereby enhancing their adaptability to environmental fluctuations. This study advances our understanding of the intestinal fungal community structure in stag beetles, providing a crucial theoretical foundation for the development of saproxylic beetle resources, biomass energy utilization, plastic degradation strategies, and beetle conservation efforts. [ABSTRACT FROM AUTHOR]

Simple Summary: Phalacrognathus muelleri is naturally distributed in Queensland (Australia) and New Guinea, and this species can be successfully bred under artificial conditions. In this study, we compared gut bacterial community structure among different life stages. There were dramatic shifts in gut bacterial community structure between larvae and adults, which was probably shaped by their diet. The significant differences between early instar and final instars larvae suggested that certain life stages are associated with a defined gut bacterial community. Our results contribute to a better understanding of the potential role of gut microbiota in a host's growth and development, and the data will benefit stag beetle conservation in artificial feeding conditions. Although stag beetles are popular saprophytic insects, there are few studies about their gut bacterial community. This study focused on the gut bacterial community structure of the rainbow stag beetle (i.e., Phalacrognathus muelleri) in its larvae (three instars) and adult stages, using high throughput sequencing (Illumina Miseq). Our aim was to compare the gut bacterial community structure among different life stages. The results revealed that bacterial alpha diversity increased from the 1st instar to the 3rd instar larvae. Adults showed the lowest gut bacterial alpha diversity. Bacterial community composition was significantly different between larvae and adults (p = 0.001), and 1st instar larvae (early instar) had significant differences with the 2nd (p= 0.007) and 3rd (p = 0.001) instar larvae (final instar). However, there was little difference in the bacterial community composition between the 2nd and 3rd instar larvae (p = 0.059). Our study demonstrated dramatic shifts in gut bacterial community structure between larvae and adults. Larvae fed on decaying wood and adults fed on beetle jelly, suggesting that diet is a crucial factor shaping the gut bacterial community structure. There were significant differences in bacterial community structure between early instar and final instars larvae, suggesting that certain life stages are associated with a defined gut bacterial community. [ABSTRACT FROM AUTHOR]

Simple Summary: Intestinal bacterial taxa play an important role in maintaining the normal physiological ecology of animals. Many factors affect the composition and diversity of the intestinal bacterial community, including diet, environment and season. However, the unique life cycle of birds makes it interesting to study their gut bacteria, especially migratory birds. Birds use many habitats and food resources, which may influence their intestinal bacterial community structure during seasonal migration. Hooded crane (Grus monacha) is one such migrant waterbird that traverses long distances and occupies varied habitats. In this study, we investigated the diversity and differences in intestinal bacterial communities of hooded cranes over the migratory season. The intestinal bacterial alpha-diversity of hooded cranes in winter was significantly higher than fall and spring. The gut bacterial community composition differed significantly across the three seasons (ANOSIM, P = 0.001). This study provides baseline information on the seasonal dynamics of intestinal bacteria in migratory hooded cranes. Intestinal bacterial communities form an integral component of the organism. Many factors influence gut bacterial community composition and diversity, including diet, environment and seasonality. During seasonal migration, birds use many habitats and food resources, which may influence their intestinal bacterial community structure. Hooded crane (Grus monacha) is a migrant waterbird that traverses long distances and occupies varied habitats. In this study, we investigated the diversity and differences in intestinal bacterial communities of hooded cranes over the migratory seasons. Fecal samples from hooded cranes were collected at a stopover site in two seasons (spring and fall) in Lindian, China, and at a wintering ground in Shengjin Lake, China. We analyzed bacterial communities from the fecal samples using high throughput sequencing (Illumina Mi-seq). Firmicutes, Proteobacteria, Tenericutes, Cyanobacteria, and Actinobacteria were the dominant phyla across all samples. The intestinal bacterial alpha-diversity of hooded cranes in winter was significantly higher than in fall and spring. The bacterial community composition significantly differed across the three seasons (ANOSIM, P = 0.001), suggesting that seasonal fluctuations may regulate the gut bacterial community composition of migratory birds. This study provides baseline information on the seasonal dynamics of intestinal bacterial community structure in migratory hooded cranes. [ABSTRACT FROM AUTHOR]

• Corn yield was closely coupled with soil fungal abundance and diversity. • Mineral and organic fertilization led to divergence in fungal communities. • Soil fungal community composition was primarily driven by SOC content. Fertilization maintains soil fertility and maximizes crop productivity, but changes soil microbial community structure and functions. However, little is known about the effects of long-term mineral and/or organic fertilization on fungal communities which regulate nutrient cycling and crop growth. The responses of fungal abundance and community structure to 29-year mineral and/or organic fertilization were investigated in Ultisol using quantitative polymerase chain reaction (qPCR) and high-throughput sequencing (Illumina Mi-Seq). Compared to the control, mineral N fertilization decreased fungal abundance by 44%, but showed little effect on crop yield and fungal diversity. The NPK fertilization increased crop yield by 4.5 times and fungal diversity by 1.4 times, but had little effect on fungal abundance relative to the control. Manure application increased crop yield by 8.4 times, fungal abundance by 1.8 times and fungal diversity by 1.5 times relative to the control. Application of manure plus NPK increased crop yield by 9.5 times, fungal abundance by 1.9 times and fungal diversity by 1.6 times relative to the control. Long-term fertilization led to dramatic shifts in fungal community composition. Compared to the control, mineral and organic fertilization decreased the relative abundance of Ascomycota and Basidiomycota, respectively. The fungal community composition diverged between soils with mineral and organic fertilization. Changes in soil organic carbon (SOC) and nutrient contents primarily shifted fungal abundance and community structure. Manure application resulted in higher SOC and nutrient contents, and thus affected fungal abundance and community structure more strongly than mineral fertilization. Manure application rather than mineral fertilization increased the relative abundance of certain favorable fungal taxa (e.g., Pseudaleuria and Hypocreales) which suppress crop pathogens. Overall, long-term manure application explained patterns in soil fertility, crop productivity, fungal abundance, diversity and community composition better than mineral fertilization. [ABSTRACT FROM AUTHOR]

Adequate exploitation of legume–rhizobia symbiosis for nitrogen fixation may help to alleviate the overuse of chemical nitrogen fertilizer and aid in sustainable agricultural development. However, controlling this beneficial interaction requires thorough characterization of the effects of soil rhizosphere microorganisms, especially core taxa, on the legume–rhizobia symbiosis. Here, we used Illumina sequencing to investigate the effects of cover crop (Raphanus sativus L. and Lolium perenne L.) residue on the rhizosphere soil microbial community and peanut nodulation ability. The results indicated that Raphanus sativus L. amendment (RS) significantly increased soil available phosphorus (AP) content and peanut nodulation ability, while the Lolium perenne L. amendment (LP) had no noticeable impact on peanut nodulation. LP and RS significantly elevated bacterial and rhizobial diversity, reduced fungal diversity, and shifted microbial community structure (bacteria, 14.7%, p = 0.001; rhizobia, 21.7%, p = 0.001; fungi, 25.5%, p = 0.001). Random forest analysis found that the core rhizosphere taxa, sharing similar ecological preferences, were the primary drivers of peanut nodulation. By least squares regression, soil AP content was found to be positively correlated with the relative abundance of key ecological clusters. Furthermore, RS was found to promote peanut nodulation by increasing the relative abundance of critical rhizosphere taxa. Overall, our findings emphasize that core microbial taxa might play an essential function in the modulation of legume nodulation and provide scientific evidence for the effective management of the plant microbiome. [ABSTRACT FROM AUTHOR]

Chemical fertilizers, especially nitrogen (N) and phosphorus (P), are used in grasslands to maximize plant biomass production for livestock. Despite a substantial body of work on how fertilization affects aboveground plant and belowground microbial communities, the short-term response of soil ammonia-oxidizing microbial communities, which play the central role in nitrification, to fertilization is not well understood. The responses of ammonia-oxidizing microbial communities to short-term (3 years) N and/or P additions were investigated in an alpine grassland of the Qinghai-Tibetan Plateau. Quantitative polymerase chain reaction (qPCR) analysis of the amoA genes showed that ammonia-oxidizing archaea (AOA) dominated over ammonia-oxidizing bacteria (AOB) in non-amended soil. Short-term urea addition significantly increased the abundance of AOB, whereas AOA abundance remained unchanged, resulting in a shift from AOA to AOB dominance, which suggests that AOB are likely to be more important in the first step of the nitrification following urea amendment. Pyrosequencing demonstrated a significant shift in AOB but not AOA community composition within short-term N fertilizer plots, indicating that AOB community composition was more sensitive than AOA in response to urea amendment. This study demonstrated that the abundance and composition of AOA and AOB communities responded differently to 3 years of urea addition, suggesting that N fertilizer may be an important controller of ammonia-oxidizing microbial communities in managed alpine grasslands, such as those of the Qinghai-Tibet Plateau. [ABSTRACT FROM AUTHOR]

The spatial distribution of bacteria in bulk soil has been well studied, but little is known about the bacterial biogeography in the rhizosphere of crops. Here, we investigated bacterial distribution in bulk soil, loosely- and tightly-bound soils, from wheat fields distributed across 800,000 km 2 of the North China Plain. Bacterial community composition differed dramatically among bulk and rhizospheric soils, and bacterial diversity decreased with the root proximity. Soil pH correlated with bacterial community composition and diversity in three compartments. Bacterial community in tightly bound soil formed a hub-based network topology with higher transitivity and greater number of central nodes compared with loosely bound and bulk soils, potentially as a result of more direct ecological interactions between the members of the tightly bound soil compartment. Bulk and rhizospheric soils maintained similar compositional distance decay patterns (with equal decay rates), but distinct phylogenetic distance decay patterns (with steeper slope of tightly bound soil). Geographical distance described a relatively greater proportion of bacterial spatial distribution in tightly bound soil, compared with loosely bound soil and bulk soil. Deterministic processes dominated the assemblage of bacterial communities in all soil compartments, while phylogenetic clustering was weaker in tightly bound soil. Taken together, our results suggest distinct bacterial network structure and distribution patterns among bulk soil, loosely bound soil and tightly bound rhizospheric soil, which could possibly result in potential functional differentiation. [ABSTRACT FROM AUTHOR]

Migratory birds travel long distance and link various pathogens. Due to habitat degradation, wintering waterfowls forage together with poultry, increasing the risk of pathogen transmission between hosts. We investigated the fungal communities between wintering Hooded Cranes and Domestic Geese by high-throughput sequencing, and inferred the potential gut pathogens for both hosts at different wintering stages. The fungal community compositions were significantly different between seasons and between the hosts. The negative correlation was found between fungal diversity and pathogenic diversity, with higher fungal diversity and less pathogenic diversity in early stage and less fungal diversity and higher pathogenic diversity in late stage for both hosts. The dissimilarity of pathogenic community compositions decreased from early to late stage, with the quantity of overlapping potential pathogenic OTUs increasing along wintering periods between the two hosts, demonstrating the existence of pathogen cross transmission between the two hosts. Furthermore, the transmission pathway of avian pathogens was mainly from Hooded Cranes to Domestic Geese while the transmission direction of human pathogens was primarily from Domestic Geese to wild cranes. Based on above results, we argued that pathogen cross transmission and underlying outbreak risk of disease should be closely monitored in migratory birds and domestic poultry. [ABSTRACT FROM AUTHOR]

Simple Summary: The gut microbiome is expected to adapt to the varying energetic and nutritional pressures in females of different reproductive states. Although the genus Macaca has the widest geographical range of nonhuman primates, few empirical studies are currently available that explore the relationship between female reproductive states and their gut microbiome in this genus. We have examined variation of gut bacterial microbiome in free-ranging female Tibetan macaques (Macaca thibetana) across different reproductive states (cycling, pregnancy and lactation). We found significant changes in gut bacterial taxonomic composition, structure and their potential functions in different reproductive states of our study species. In particular, the relative abundance of Proteobacteria increased significantly during pregnancy and lactation. In addition, the relative abundance of Succinivibrionaceae and Succinivibrio (Succinivibrionaceae) were overrepresented in pregnant females, whereas Bifidobacteriaceae and Bifidobacterium (Bifidobacteriaceae) were overrepresented in lactating females. Furthermore, predicted functional genes of several metabolic pathways related to host's energy and nutrition, such as metabolism of carbohydrates, cofactors and vitamins, glycans and other amino acids, were overrepresented in pregnancy and lactation. Thus, our results suggest that the gut microbiome may play an important role in the energetic and nutritional strategies of female reproductive ecology in the genus Macaca. Future studies of the "microbial reproductive ecology" of primates that incorporate food availability, reproductive seasonality, female reproductive physiology and gut inflammation are warranted. The gut microbiome is expected to adapt to the varying energetic and nutritional pressures in females of different reproductive states. Changes in the gut microbiome may lead to varying nutrient utilizing efficiency in pregnant and lactating female primates. In this study, we examined variation in the gut bacterial community composition of wild female Tibetan macaques (Macaca thibetana) across different reproductive states (cycling, pregnancy and lactation). Fecal samples (n = 25) were collected from ten adult females harvested across different reproductive states. Gut microbial community composition and potential functions were assessed using 16 S rRNA gene sequences. We found significant changes in gut bacterial taxonomic composition, structure and their potential functions in different reproductive states of our study species. In particular, the relative abundance of Proteobacteria increased significantly during pregnancy and lactation. In addition, the relative abundance of Succinivibrionaceae and Succinivibrio (Succinivibrionaceae) were overrepresented in pregnant females, whereas Bifidobacteriaceae and Bifidobacterium (Bifidobacteriaceae) were overrepresented in lactating females. Furthermore, the relative abundance of predicted functional genes of several metabolic pathways related to host's energy and nutrition, such as metabolism of carbohydrates, cofactors and vitamins, glycans and other amino acids, were enriched in pregnancy and lactation. Our findings suggest that changes in the gut microbiome may play an important role in meeting the energetic needs of pregnant and lactating Tibetan macaques. Future studies of the "microbial reproductive ecology" of primates that incorporate food availability, reproductive seasonality, female reproductive physiology and gut inflammation are warranted. [ABSTRACT FROM AUTHOR]

Simple Summary: Intestinal microbiota play crucial roles for their hosts. Odontolabis fallaciosa shows striking sexual dimorphism and male trimorphism, which represents an interesting system to study their gut microbiota. We have compared the intestinal bacterial community structure between the two sexes and among three male morphs of O. fallaciosa. The gut bacterial community structure was significantly different between males and females. The females were associated with higher bacterial alpha-diversity relative to males. Large males had a higher relative abundance of Firmicutes and Firmicutes/Bacteroides (F/B) ratio, which contributed to nutritional efficiency. The results increased our understanding of beetle–bacterial interactions of O. fallaciosa between the two sexes, and among three male morphs, which might reveal the relationship among the gut microbiota, nutrition level, and phenotypic evolution of the stag beetle. Odontolabis fallaciosa (Coleoptera: Lucanidae) is a giant and popular stag beetle with striking sexual dimorphism and male trimorphism. However, little is known about their intestinal microbiota, which might play an indispensable role in shaping the health of their hosts. The aim of this study was to investigate the intestinal bacterial community structure between the two sexes and among three male morphs of O. fallaciosa from China using high-throughput sequencing (Illumina MiSeq). The gut bacterial community structure was significantly different between males and females, suggesting that sex appeared to be the crucial factor shaping the intestinal bacterial community. Females had higher bacterial alpha-diversity than males. There was little difference in gut bacterial community structure among the three male morphs. However, compared to medium and small males, large individuals were associated with the higher relative abundance of Firmicutes and Firmicutes/Bacteroides (F/B) ratio, which might contribute to nutritional efficiency. Overall, these results might help to further our understanding of beetle–bacterial interactions of O. fallaciosa between the two sexes, and among the three male morphs. [ABSTRACT FROM AUTHOR]