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Non-parametric estimation of the classes in a population
... Alpha diversity was measured using the Simpson [84], Chao1 [85], and Shannon [86] indices. Two-way ANOVA was computed in R Studio (R version 2022.12.0) to determine alpha group significance across the cofactors, namely radiation dose (RD) and time since irradiation (TSI); the significance value cutoff was p < 0.05. ...
There is an escalating need to comprehend the long-term impacts of nuclear radiation exposure since the permeation of ionizing radiation has been frequent in our current societal framework. A system evaluation of the microbes that reside inside a host’s colon could meet this knowledge gap since the microbes play major roles in a host’s response to stress. Indeed, our past study suggested that these microbes might break their symbiotic association with moribund hosts to form a pro-survival condition exclusive to themselves. In this study, we undertook metagenomics and metabolomics assays regarding the descending colon content (DCC) of adult mice. DCCs were collected 1 month and 6 months after 7 Gy or 7.5 Gy total body irradiation (TBI). The assessment of the metagenomic diversity profile in DCC found a significant sex bias caused by TBI. Six months after 7.5 Gy TBI, decreased Bacteroidetes were replaced by increased Firmicutes in males, and these alterations were reflected in the functional analysis. For instance, a larger number of networks linked to small chain fatty acid (SCFA) synthesis and metabolism were inhibited in males than in females. Additionally, bioenergy networks showed regression dynamics in females at 6 months post-TBI. Increased accumulation of glucose and pyruvate, which are typical precursors of beneficial SCFAs coupled with the activated networks linked to the production of reactive oxygen species, suggest a cross-sex energy-deprived state. Overall, there was a major chronic adverse implication in male mice that supported the previous literature in suggesting females are more radioresistant than males. The sex-biased chronic effects of TBI should be taken into consideration in designing the pertinent therapeutics.
... Bacterial communities were classified using the SILVA database (version 132), and fungal communities were classified utilizing the UNITE database (version 8.0). Microbial community α-diversity and richness were calculated with Mothur 1.43.0 software, with the Shannon index used to quantify community diversity (Shannon, 1948) and the Chao index to estimate community richness (Chao, 1984). For OTU-based co-occurrence networks, OTUs with relative abundances above 0.1% in bacterial and fungal communities were included, while OTUs with zero abundance in two-thirds of the samples were excluded. ...
Introduction
The increasing rate of atmospheric nitrogen deposition has severely affected the structure and function of these ecosystems. Although nitrogen deposition is increasing globally, the responses of soil microbial communities in subtropical planted forests remain inadequately studied.
Methods
In this study, a four-year experimental simulation was conducted to assess the impacts of varying nitrogen deposition levels (CK: 0 g·N·m⁻²·a⁻¹; N10: 10 g·N·m⁻²·a⁻¹; N20: 20 g·N·m⁻²·a⁻¹; N25: 25 g·N·m⁻²·a⁻¹) on two subtropical tree species, Pinus yunnanensis Franch. and Pinus armandii Franch. High-throughput sequencing was performed using the Illumina MiSeq platform. Statistical analyses, including analysis of variance (ANOVA), linear mixed-effects models, principal coordinate analysis (PCoA), analysis of similarity (ANOSIM), redundancy analysis (RDA), random forest analysis, and structural equation modeling (SEM), were used to examine the short-term responses of soil nutrients, bacterial communities, and fungal community structures to nitrogen deposition.
Results and discussion
The results showed that species differences led to variations in soil properties between the two forests, particularly a significant increase in soil pH in P. yunnanensis Franch. forests and a significant decrease in soil pH in P. armandii Franch. forests. Nitrogen addition did not significantly affect microbial diversity in either P. yunnanensis Franch. or P. armandii Franch. soils; however, forest type differences had a significant impact on bacterial diversity. The nitrogen addition significantly affected the relative abundance of specific microbial communities in both forest types, particularly altering the fungal community structure in the P. yunnanensis Franch forests, while no significant changes were observed in the bacterial community structure in either forest type. Furthermore, nitrogen addition increased the network complexity of bacterial communities in P. yunnanensis Franch. forests while decreasing network complexity in P. armandii Franch. forests. Structural equation modeling indicated that nitrogen addition regulates soil bacterial and fungal diversity in both forest types by modifying nitrogen availability.
Purpose and significance
These findings provide insights into the potential long-term impacts of nitrogen deposition on subtropical planted forest ecosystems and offer a theoretical basis for sustainable forest management and regulatory practices.
This study explored how potted treatments (with and without Scleroderma bovista inoculation) shape rhizosphere microbial diversity in hazel across five soils using split-root cultivation. Three treatments (control, split-root, split-root with S. bovista) were analyzed for root growth and microbial dynamics. S. bovista inoculation consistently enhanced root parameters (number, tips) in all soils. Potted treatments (with and without S. bovista inoculation) altered microbial features (OTU/ASV), with only 0.9–3.3% of features remaining unchanged. At the class level, potting increased Agaricomycetes abundance while reducing Sordariomycetes, a trend amplified by S. bovista. Potting decreased species richness estimates (ACE and Chao1), while both treatments lowered diversity index (Shannon index). Potted treatments without S. bovista inoculation drove stronger shifts in species composition than inoculation. Findings reveal potting and S. bovista synergistically recruit symbiotic fungi via root exudates, establishing disease-suppressive communities that selectively inhibit pathotrophic fungi (particularly plant pathogen Coniothyrium and fungal parasite Cladobotryum) while roughly maintaining non-pathogenic saprotrophic microbes essential for organic matter decomposition. This work provides insights for optimizing hazel orchard management and ectomycorrhizal agent development.
Ecosystem function can be shaped by the relationship between plant and soil microbial communities. When invasive plants disrupt these plant–soil feedbacks, they can leave soil legacy effects that persist even after removal. However, such legacy effects vary among species, and links between aboveground and belowground recovery after invasive plant removal remain unclear. We examined the potential legacy effects of the invasive yellow bluestem ( Bothriochloa ischaemum var. songarica ) in a grassland in central Texas, USA. In a 9‐year removal experiment, we measured the diversity and composition of plant and soil microbial communities in invaded plots (dominated by the invasive grass), removal plots (where the invasive was continually removed), and native‐dominated plots. With only passive recovery (i.e. no active seeding or planting), plant richness, native grass cover, and native forb cover in removal plots became similar to native‐dominated plots in 1–3 years, although species composition was still different 8 years after removal. In contrast, soil microbial diversity and composition did not differ among the treatments, including no differences between invaded and native‐dominated plots. Plant species composition may be influenced by dispersal limitations because removal plots are still surrounded by the invasive grass. The observed decoupling between aboveground and belowground responses to invasion and removal efforts could be due to the soil microbial community's resistance to influence by the invasive grass. These results suggest that microbial soil legacy effects will likely not limit grassland restoration and that active seeding or planting may be required for a more complete restoration of native plant communities after yellow bluestem removal.
Mariculture is currently experiencing rapid growth in response to the rising global food demand, while simultaneously posing significant challenges to environmental issues, such as pollution stress and ecological degradation. To achieve a balance between ecosystem maintenance and seafood supply, marine ranching has flourished as a sustainable approach through the implementation of artificial reef construction, stock enhancement, and strategic releasing. However, few studies have evaluated the ecological impacts through a comparison of in situ survey data across geographical areas. Phytoplankton are vital organisms in marine ecosystems that function as essential indicators of seawater quality and biological diversity, reflecting environmental health and ecological sustainability. In this study, we investigated the species diversity, community structure, and co-occurrence network of phytoplankton based on 175 samples collected from 75 sites encompassing all 26 marine ranching seawater areas, along with their corresponding surrounding areas in Yantai’s coastal sea. A total of 112 species were identified across three phyla of diatoms, dinoflagellates, and chrysophytes; among them, diatoms dominated the community with a notably high proportion of 98.83%. Their diversity and structure exhibited significant variations across different seasons and geographic locations. Moreover, no preference was observed between the marine ranching seawater and the surrounding areas. Nevertheless, a co-occurrence network analysis demonstrated that lower values for average degree, clustering coefficient, and average path length were exhibited in marine ranching, indicating that aquaculture activities have reduced connectivity among potential interactions. Additionally, it showed reduced stability as indicated by the remaining nodes and the natural connectivity indices, regardless of the proportion of nodes removed. These findings illustrate that while marine ranching processes can mitigate species losses with maintaining phytoplankton community structure, they still alter association among species and reduce overall stability. This research recommends that scientifically informed expansion of marine ranching necessitates robust environmental monitoring datasets and systematic validation to ensure holistic sustainability.
Presently, very sparse information exists about the occurrences and diversity of microbes in the western Indian Ocean (WIO) relative to other areas of the ocean. In this study, high‐throughput sequencing of 16S rRNA genes and metagenomic approaches were utilised to examine microbial assemblages in Kenya and Tanzania. Results from 24 locations showed that Proteobacterial members made up the majority of the bacterial assemblages. Other dominant phyla were Bacteroidetes (9%–10%), Firmicutes (1.4%–8%), Actinobacteria (4%–6%) and Acidobacter (3.4%–3.6%). Combinations of diversity (alpha and beta) as well as Pearson correlation analyses showed that assemblages in Kenya clustered together and differed from those in Tanzania because of covariation with various environmental factors, such as temperature and salinity.
The value of small protected areas in urbanized environments for avian conservation is poorly documented, particularly in the Neotropics. We compared the composition of bird assemblages between two protected areas of limited size but specific local value, the Urban National Park of Martissant (UNPM) and the suburban Wynne Farm Ecological Reserve (WFER) in Haiti, one of the poorest countries in the world, plagued with severe deforestation and environmental degradation. Species were identified along transects without distance estimation. Overall, 718 birds belonging to 38 different species were censused (494 at UNPM and 224 at WFER, from 24 to 26 species, respectively). Bird species observation included two endemic and vulnerable species, Corvus leucognaphalus and Amazona ventralis, observed only at the urban site. Species richness, diversity, evenness, and species-abundance distributions did not differ significantly between sites. However, the composition of the two avian assemblages differed significantly, with only 31.6% species in common and a significant difference in their relative abundance. We found no evidence for a difference in the degree of forest dependency between the two assemblages. However, mainly and strict insectivorous species accounted for a larger proportion of observations at WFER (34.8%) compared to UNPM (19.6%). Factors influencing the contrast in avian assemblage composition between two sites include differences in elevation and associated vegetation, difference in water availability and variation in the
ability of species to adapt to the urban environment. Our results demonstrate the importance and complementarity of the two small protected areas for the conservation of avian diversity in Haiti.
Keywords Bird conservation · Caribbean · Hispaniola · Species-abundance distribution · Species richness · Urban ecology
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