Shannon Index Research Articles

Wild again: recovery of a beneficial Cannabis seed endophyte from low domestication genotypes.

Beyond carrying the plant embryo, seeds harbour intricate microbial communities whose transmission across successive plant generations can significantly influence the ecological and evolutionary dynamics of plant-microbe symbioses. The process of plant domestication has potential repercussions in genes involved in plant-microbiome interactions. However, the extent to which breeding can impact the seed microbiome is sparsely explored. Cannabis is a high-value crop but sparsely subjected to agricultural innovations established in other crop species during the last century. Here, we conduct a large-scale analysis of the bacterial seed microbiome of Cannabis across different domestication grades and investigate the potential of seed-associated endophytes as plant growth-promoting agents under both controlled and field conditions. Analysis of Cannabis seed endophyte composition and diversity across 46 plant genotypes revealed 813 different bacterial genera with a predominance of Gammaproteobacteria, Bacilli, Actinobacteria and Alphaproteobacteria but a genotype-specific microbiome. The assessment of domestication and breeding on microbial assembly revealed a higher bacterial diversity in low domestication genotypes (Shannon index, H': 1.21 vs. 1.05) and a higher homogeneity in bacterial composition caused by line development. Further, a seed bacterial isolate (Bacillus frigoritolerans C1141) associated with low domestication genotypes, and with genes associated with bio-fertilization, bioremediation and phytohormone production, increased plant growth by 42.3% at the time of harvest, under field conditions. This study addresses critical knowledge gaps related to the assembly of the Cannabis seed-endophytic microbiome. It reveals that Cannabis breeding is linked to alterations of seed microbial communities, which potentially led to the loss of bacteria with functional significance. These results highlight the importance of preserving seed microbiomes in plant breeding to support sustainable plant health and growth enhancement in Cannabis. Video Abstract.

Microbial and organic manure fertilization alters rhizosphere bacteria and carotenoids of Citrus reticulata Blanco 'Orah'.

Citrus reticulata Blanco 'Orah' is one of the most widely grown citrus varieties in southern China. It has been proven that microbial and organic manure fertilization improve the yields and appearances of 'Orah' fruits. However, details regarding the mechanisms underlying the effects of combined fertilization on the agronomic traits and rhizosphere bacterial community of plants still need to be elucidated. This study compared the rhizosphere bacterial community and carotenoids of 'Orah' with (WYT group) and without (WYCK group) combined fertilization in a local orchard in Wuming town from Nanning, Guangxi, China. The WYT group was sprayed with 50ml Strongreen and 250g of Yumeiren five times while WYCK group did not sprayed. Combined fertilization increased fruit weight and the Citrus color index (CCI) significantly (p < 0.05). By 16s rRNA sequencing, 7,126 operational taxonomic units (OTU) were obtained. A higher Shannon index was observed in the WYT group compared to that in the WYCK group. Comparison between the two groups showed that Pseudomonas was enriched in the WYT group with LDA (log10) score of 4.32, and Cyanobacteria was enriched in the WYCK group with LDA (log10) score of -4.11. At the family level, Phyllobacteriaceae (abundance mean: 0.0046 in WYCK vs. 0.0073 in WYT) was significantly abundant in the WYT group, whereas Thermosporothrix (abundance mean: 0.00053 in WYCK vs. 0.0019 in WYT) and Sphingobium (abundance mean: 0.00053 in WYCK vs. 0.0013 in WYT) were significantly abundant in the WYCK group. A total of 51 carotenoid components were tested by UPLC-MS/MS. In the pulp tissues, 37 carotenoid components were decreased in the WYT group compared to those in the WYCK group. In fruit skin, 24 significantly different components (7 downregulated and 17 upregulated) were identified in WYT compared to those in WYCK. Correlation analysis revealed that the network between OTUs and carotenoids contained seven carotenoid components and four OTUs. Four OTUs, strain TRA3-20 (a eubacterium), Roseiflexus, OPB35, and Fictibacillus correlated to carotenoid accumulation regulation in fruit skin. This study demonstrates the impact of the fertilization on soil microorganisms and carotenoid components. It constructs the regulatory network contained four OTUs for seven carotenoid components, providing evidence on precise fertilization in Orah.

Suppressed oncogenic molecules involved in the treatment of colorectal cancer by fecal microbiota transplantation

Dysbiosis of the intestinal microbiota is prevalent among patients with colorectal cancer (CRC). This study aims to explore the anticancer roles of the fecal microbiota in inhibiting the progression of colorectal cancer and possible mechanisms. The intestinal microbial dysbiosis in CRC mice was significantly ameliorated by fecal microbiota transplantation (FMT), as indicated by the restored ACE index and Shannon index. The diameter and number of cancerous foci were significantly decreased in CRC mice treated with FMT, along with the restoration of the intestinal mucosal structure and the lessening of the gland arrangement disorder. Key factors in oxidative stress (TXN1, TXNRD1, and HIF-1α); cell cycle regulators (IGF-1, BIRC5, CDK8, HDAC2, EGFR, and CTSL); and a critical transcription factor of the innate immune signal pathway (IRF5) were among the repressed oncogenic targets engaged in the FMT treatment of CRC. Correlation analysis revealed that their expressions were positively correlated with uncultured_bacterium_o_Mollicutes_RF39, Rikenellaceae_RC9_gut_group, and negatively correlated with Bacillus, Marvinbryantia, Roseburia, Angelakisella, Enterorhabdus, Bacteroides, Muribaculum, and genera of uncultured_bacterium_f_Eggerthellaceae, uncultured_bacterium_f_Xanthobacteraceae, Prevotellaceae_UCG-001, uncultured_bacterium_f_Erysipelotrichaceae, uncul-tured_bacterium_f_Lachnospiraceae, uncultured_bacterium_f_Ruminococcaceae, Eubacterium_coprostanoligenes_group, Ruminococcaceae_UCG-005, and uncultured_bacterium_f_Peptococcaceae. This study provides more evidence for the application of FMT in the clinical treatment of CRC.

Nonselective beta blockade enhances gut microbiome diversity in a rodent model of trauma, hemorrhage, and chronic stress

BACKGROUND Traumatic injury leads to gut dysbiosis with changes in microbiome diversity and conversion toward a “pathobiome” signature characterized by a selective overabundance of pathogenic bacteria. The use of non-selective beta antagonism in trauma patients has been established as a useful adjunct to reduce systemic inflammation. We sought to investigate whether beta-adrenergic blockade following trauma would prevent the conversion of microbiome to a “pathobiome” phenotype. METHODS Sprague-Dawley rats (n = 6–8/group) were subjected to routine daily handling (naïve), lung contusion with hemorrhagic shock (LCHS), or LCHS with daily chronic stress (LCHS/CS), each with or without administration of intraperitoneal propranolol (BB) (10 mg/kg/day). Fecal microbiome was measured on Days 0, 7, and 14 using high-throughput 16S rRNA sequencing and QIIME2 bioinformatics analyses. Alpha- and beta-diversity and microbiome composition were assessed with significance defined as *p &lt; 0.05. RESULTS Use of propranolol following LCHS or LCHS/CS demonstrated a significant increase in the number of bacterial species (Chao1 index), as well as overall richness and evenness (Shannon index) compared with their untreated counterparts at Day 7. By Day 14, these differences were no longer apparent between BB and untreated groups subjected to LCHS/CS. There was an abundance of commensal bacteria such as Oscillospiraceae and Clostridia in LCHS and LCHS/CS treated with BB after 7 days which persisted at 14 days. CONCLUSION These findings suggest a role for beta-antagonism in altering the diversity of the gut microbiome and the need for further studies to elucidate the cellular and molecular mechanisms underlying this intriguing connection of microbiome with trauma and beta-blockade.

Influence of combined application of tetracycline and streptomycin on microbial diversity and function in rice soil.

A microcosm experiment was performed to quantify the residues of antibiotics [tetracycline (TC), streptomycin (STR), and streptocycline (STC; a mixture of TC and STR)] in rice soil and to assess their impact on microbial community structure and function using Illumina-MiSeq metagenomic analysis. Antibiotics were applied at half the recommended dose (0.5RD), recommended dose (RD), and double the recommended dose (2RD). At RD, TC was degraded in soil within 9days of its application, whereas it took 21days for STR and STC to degrade below limit of quantification (LOQ) level. The residue data were fitted in decay models, and half-lives (DT50) were 46.5-53.3h and 177.6-198h for TC and STR, respectively. Soil enzyme activities (dehydrogenase, β-glucosidase, fluorescein diacetate hydrolase, acid phosphatase, alkaline phosphatase) were negatively affected in the antibiotic-treated soil. Targeted metagenomic analysis showed that the major bacterial phyla such as Chloroflexi, Actinobacteria, Planctomycetes, Crenarchaeota, and Gemmatimonadetes were suppressed by antibiotic treatments as compared to control. Shannon, Simpson, ACE, and Chao1 diversity indices showed that bacterial diversity decreased with the application of antibiotics, and decrease in bacterial diversity was more prominent in case of STC as compared to TC and STR. Overall, the combination of antibiotics negatively affected the soil microbial community structure and function in comparison to their individual application.

Sustainable use of agricultural residues to improve corn silage quality: Co-ensiling with oregano oil residues

The study aimed to evaluate the effect of oregano essential oil extraction residues (ORES) on the fermentation quality of corn silage. Non-fungal infected (NFI) and fungal infected (FI) corn were ensiled with 20% (wet weight) of ORES for 180 d. The inclusion of ORES delayed pH decline regardless of fungal infection. The inclusion of ORES did not adversely affect lactic acid (LA) production in NFI silages but retarded the initial LA fermentation of FI silages. Co-ensiling corn with ORES significantly decreased ethanol content. Co-ensiling FI corn with ORES significantly increased the fungal Chao1 and Shannon indices compared to FI-CON silages but did not affect the bacterial Chao1 and Shannon indices. The fungal infection aggravated the risk of Paenibacillus and Clostridium contamination, which was mitigated by co-ensiling with ORES. In conclusion, fungal infection suppressed ensiling fermentation, and heightened the risk of proliferation of undesirable bacteria, while ORES relieved these risks. Ensiling ORES with corn as forages is a potential and promising strategy for the efficient reusing of agro-industrial waste.

The scale effects of symbiotic relationships under complex driving factors: An empirical study in China

AbstractSymbiotic relationships between enterprises help mitigate resource and environmental impacts of industrial activities via exchanging waste or by‐products as material inputs among each other. However, the emergence of such symbiotic relationships under complex driving factors across different geographical scales remains hitherto not well understood. Here, we provide an analytic framework including a random forest model and Shannon index, to systematically describe and explain the scale effects of driving factors underlying the symbiotic relationships. Based on a questionnaire survey for 324 enterprises in Chun'an, a typical industrial city in eastern China, we applied this analytical framework. The results show that, first, the quantity of symbiotic relationships exhibits an inversely proportional function across various geographical scales. Second, there exist significant differences in the dominant factors at different scales. Finally, the diversity of importance of factors and the emergence of symbiotic relationships exhibit a consistent trend of fluctuation, providing evidence for the explanatory potential of our proposed analytical framework for the driving mechanisms of emergence. We find that when enterprises are simultaneously affected by multiple driving factors with potent forces (referred to as the diversity of importance), symbiotic behaviors are more likely to occur. Moreover, our results suggest that fostering symbiotic relationships necessitates considering the variations in driving factors across different scales comprehensively and formulating targeted promotional measures tailored to the specific driving factors of different enterprise types. Our proposed framework would help to maximize industrial symbiosis potentials in a specific region.

Diversity pattern and antibiotic activity of microbial communities inhabiting a karst cave from Costa Rica.

The studies of cave bacterial communities worldwide have revealed their potential to produce antibiotic molecules. In Costa Rica, ~400 caves have been identified; however, their microbial diversity and biotechnological potential remain unexplored. In this work, we studied the chemical composition and microbial diversity of a Costa Rican cave (known as the Amblipigida cave) located in Puntarenas, Costa Rica. Additionally, through culture-dependent methods, we evaluated the potential of its microbiota to produce antibiotic molecules. Mineralogical and elemental analyses revealed that the Amblipigida cave is primarily composed of calcite. However, small variations in chemical composition were observed as a result of specific conditions, such as light flashes or the input of organic matter. The 16S rRNA gene metabarcoding revealed an extraordinarily high microbial diversity (with an average Shannon index of ~6.5), primarily comprising bacteria from the phyla Pseudomonadota, Actinomycetota, Firmicutes and Acidobacteriota, with the family Pseudomonadaceae being the most abundant. A total of 93 bacteria were isolated, of which 15% exhibited antibiotic activity against at least one Gram-positive or yeast strain and were classified within the genera Lysobacter, Streptomyces, Pseudomonas, Brevundimonas and Bacillus. These findings underscore the highly diverse nature of cave microbiota and their significant biotechnological potential, particularly in the production of antibiotic compounds.

Responses of Legume‐Associated Rhizobacterial Communities to Plant Diversity and Soil Traits in Alpine Grassland

ABSTRACTLegume species are essential components of plant diversity and affect soil biodiversity across various ecosystems. Their effect on the diversity and traits of soil bacteria, particularly in degraded grasslands, remains unknown. This study analysed the relationships among plant diversity, soil traits and legume‐associated rhizobacterial communities in Xiahe (XH) and Maqu (MQ) in Gansu Province, Haibei (HB) in Qinghai Province and Hongyuan (HY) in Sichuan Province in the eastern Qinghai‐Tibetan Plateau (QTP). The diversity index values (coverage, richness, Shannon index and evenness) of legume species were positively correlated with plant diversity. Several soil nutrients (ammonia‐nitrogen, nitrate‐nitrogen, total nitrogen, available potassium, available phosphorus and soil organic matter) and enzymes (urease, sucrase, peroxidase and dehydrogenase) were lower in HB and HY than in XH and MQ. The Shannon index for rhizobacterial diversity was higher in HB and HY than in XH and MQ. In contrast, the diversity index values were higher for geographical locations than for sympatric plant species. Additionally, HB and HY showed 50% fewer positive and negative associations with rhizobacteria than XH and MQ. Functional Annotation of Prokaryotic Taxa analysis indicated a higher relative abundance of nitrate reduction occurred in HB and HY than in XH and MQ, whereas nitrogen fixation occurred at a lower level in HB and HY than in XH and MQ. The Simpson index value for bacterial diversity was positively correlated with plant diversity, legume species diversity and soil multifunctionality. However, the Shannon index value was negatively correlated with these parameters. Changes in the composition of legume‐associated rhizobacteria across different geographical locations are strongly influenced by plant diversity and soil nutrients, reflecting the distribution characteristics of legumes in alpine grasslands.

Eco-Habitat Assessment of One of the Most Expensive Edible Mushrooms (Tricholoma matsutake) in Genekha, Thimphu, Bhutan

Tricholoma matsutake (S. Ito &amp; Imai) Singer is most expensive edible mushroom, naturally grown dispersed in temperate oak pine forested areas in Bhutan. It is ectomycorrhizal fungi with high ecological and economic value requiring an important ecological niche and symbiotic tree associates. The present study is an attempt to give an account on floristic composition and vegetation structure of Tricholoma matsutake habitat in Genekha, Thimphu. A total of 10 plots were enumerated with plot size of 20m X 20m, 5m X 5m and 2m X 2m for trees, shrubs and herbs respectively. PAST (Paleontological Statistics) 4.10 software was used for diversity analysis. A total of 58 species under 44 genera belonging to 26 families were recorded in the natural habitat of matsutake. The study revealed that T. matsutake is associated with Quercus semecarpifolia Sm., Pinus wallichiana A.B. Jack., Rhododendron spp., and Pieris formosa (Wall.) D. Don. J-shaped distribution curve of DBH and height class with fair regeneration status is obtained for associated species in the habitat. The Menhinick’s species richness of (2.26, 2) for both North facing habitat (NFH) and South facing habitats (SFH) indicated high species richness. Moderate and low diversity is indicated with Simpsons index 0.94 (NFH) and 0.76 (SFH), Shannon index 3.06 (NFH) and 2.49 (SFH) with moderately even distribution 0.74(NFH) and 0.73 (SFH) of species in the habitats. Sorensens similarity index of 0.9 indicated highly similar species composition between two habitats. This research provides current floristic and vegetation structure of Tricholoma matsutake habitat, that will have high significance in habitat management and conservation.

Investigating Microbial Diversity in the Endosphere and Rhizoplane of Three Aromatic Rice Landraces: Implications for Biological Nitrogen Fixation.

Biological nitrogen fixation (BNF) occurring in the rhizosphere is a sustainable source of nitrogen for plants. BNF in cereal crops can be promoted by inoculation of a single or consortium of associative and endophytic diazotrophs. Creating a successful nitrogen-fixing biofertilizer necessitates the study of the core microbiome of the plant rhizosphere and the functional relationship of the members. This study compares the endosphere and rhizoplane microbial diversity of three aromatic landraces and one high-yielding variety of rice using culture-independent methods. The V3-V4 variable regions of 16S rRNA were used for amplicon sequencing of soil DNA. Patescibacteria, Planctomycetota, and Proteobacteria were the predominant phyla in all four genotypes. Richness (Chao-1 and ACE) and microbial diversity indices (Shannon and Simpson indices) showed that microbial diversity among the genotypes varies subtly at the phylum level. Beta diversity analysis with the phylum identified and comparisons of the microbiome at the genus level revealed a more prominent effect of plant genotype on microbial diversity. Canonical component analysis drew a correlation between microbial diversity in each genotype with the sugar and N content of these landraces. Paraburkholderia was identified as one of the major OTUs among the known nitrogen fixing followed by Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium group, Azospirillum, Hebarspirillum, and Azotobacter.

The relationship between body size and diet breadth in non‐web building spiders

Abstract The handling hypothesis assumes that large animals have broader diets than small animals because small animals are restricted to small prey while large animals can handle both small and large prey. On the other hand, the optimal foraging hypothesis assumes no relationship between predator body size and diet breadth because large predators should shift from small prey to large prey to maximize the net energy intake. Using the diets and body sizes of 89 non‐web building spider species obtained from public databases (World Spider Trait database, Spiders of Europe and World Spider Catalogue), we investigated the relationship between body size and diet breadth in this group of terrestrial arthropod predators. We found that the taxonomic niche diet breadth measured by Hill numbers (i.e., prey richness, Shannon index of diversity and Simpson index of equitability) had no significant relationship with spider body size. The minimum prey size did not show any relationship with spider body size. On the other hand, mean, maximum, range and variability in prey size increased with spider body size. The results provide support for both hypotheses. The pattern in prey taxonomic dimension supports the optimal foraging hypothesis, while the pattern in prey size dimension supports the handling hypothesis. Overall, the observed distinct patterns between the taxonomic and prey size niche axes can be caused by the fact that the non‐web building spiders utilize similar prey types that are however highly size‐structured.

Biological Nitrification Inhibition by Australian Tussock Grass and Its Impact on the Rhizosphere Ammonia-Oxidizing Microbiome

Certain plant species have developed the ability to express biological nitrification inhibition (BNI), suppressing the activity of nitrifying microbes and thereby reducing the conversion of ammonium to nitrate. This study assessed the BNI capacity and the rhizosphere ammonia-oxidizing microbiome of two grass species: the endemic Australian Barley Mitchell grass (Astrebla pectinata) and the introduced koronivia grass (Urochloa humidicola), using soils from both agricultural land and native vegetation. In agricultural soil, koronivia grass exhibited significantly higher BNI capacity compared with Barley Mitchell grass. However, in native soil, this trend was reversed, with Barley Mitchell grass demonstrating a significantly greater BNI capacity than koronivia grass (52% vs. 38%). Koronivia grass significantly altered the composition of the ammonia-oxidizing bacteria community in its rhizosphere, leading to a decrease in the Shannon index and bacteria number. Conversely, Barley Mitchell grass reduced the Shannon index (1.2 vs. 1.7) and population size (3.28 × 107 vs. 7.43 × 107 gene copy number g−1 dry soil) of the ammonia-oxidizing archaea community in its rhizosphere to a greater extent. These findings suggest that Australian Barley Mitchell grass may have evolved mechanisms to suppress soil archaeal nitrifiers, thereby enhancing its BNI capacity and adapting to Australia’s nutrient-poor soils.

Diversity and ethnobotanical study of homegarden plants in Goba district, Oromia region, Ethiopia

Homegardens are one of the most diverse agroforestry systems and make a vital contribution to meeting various household needs, especially for smallholder farmers in developing countries. The aim of this study was to record the diversity and use of homegarden plant species in the Goba District. The households were randomly selected from five kebeles, with the number selected proportionate to the size of each kebele using the probability proportional to size (PPS) calculation. Seventy-one homegarden owners were chosen for the detailed study and data collection. Of the fifteen kebeles in the Goba District, five kebeles were chosen at random. Observations, semi-structured interviews, preference rating, direct matrix rankings, and paired comparisons were the methods used to gather ethno-botanical data. Descriptive statistical approaches, including density, frequency, relative frequency, relative density, and the Shannon and Wiener indices for species diversity were used to analyze the data. A total of 67 plant species belonging to 31 families were identified. Of the 67 plant species, 36 (or 54%) were herbs, 15 (or 22%) were tree species, 22% shrubs, and 2% were climbers. Twenty-eight (20.8%) species collected from homegardens had food and forage value, 17 (25.3%) had fence value, 12 (18%) had shade value, and 23 (34.3%) had medicinal value; moreover, 90% of the homes had home gardens, indicating that farmers value gardening plants that helps improve household food security and revenue generation. The involvement of the local population and government institutions in providing awareness through instruction or training on the sustainable use and management of plant resources is vital to conserve homegarden plants.

Soil P-stimulating bacterial communities: response and effect assessment of long-term fertilizer and rhizobium inoculant application

BackgroundPhosphorus (P) plays a vital role in plant growth. The pqqC and phoD genes serve as molecular markers for inorganic and organic P breakdown, respectively. However, the understanding of how P-mobilizing bacteria in soil respond to long-term fertilization and rhizobium application is limited. Herein, soil that had been treated with fertilizer and rhizobium for 10 years was collected to investigate the characteristics of P-mobilizing bacterial communities. Five treatments were included: no fertilization (CK), phosphorus fertilizer (P), urea + potassium fertilizer (NK), NPK, and PK + Bradyrhizobium japonicum 5821 (PK + R).ResultsThe soybean nodule dry weight was highest in the P treatment (1.93 g), while the soybean yield peaked in the PK + R treatment (3025.33 kg ha− 1). The abundance of the pqqC gene increased in the rhizosphere soil at the flowering-podding stage and in the bulk soil at the maturity stage under the P treatment, while its abundance increased in the bulk soil at the flowering-podding stage and in the rhizosphere soil at the maturity stage under the PK + R treatment. The abundance of the phoD gene was enhanced in the bulk soil at the flowering-podding stage under the PK + R treatment. The Shannon and Ace indexes of pqqC- and phoD-harboring bacteria were higher in the rhizosphere soil at maturity under the PK + R treatment compared to other treatments. Furthermore, a comprehensive analysis of the neutral community model and co-occurrence pattern demonstrated that the application of P fertilizer alone led to an increase in the distribution and dynamic movement of pqqC-harboring bacteria, but resulted in a decrease in complexity of network structure. On the other hand, rhizobium inoculation enhanced the distribution and dynamic movement of phoD-harboring bacteria, as well as the stability and complexity of the network structure. Pseudomonas and Nitrobacter, as well as Steptomyces, Stella, and Nonomuraea, may be crucial genera regulating the composition and function of pqqC- and phoD-harboring communities, respectively.ConclusionsThese findings affirm the crucial role of fertilization and rhizobium inoculation in regulating pqqC- and phoD-harboring bacterial communities, and highlight the significance of long-term phosphate-only fertilization and rhizobium inoculation in enhancing dissolved inorganic phosphorus and mineralized organophosphorus, respectively.

Diversity Patterns and Drivers of Soil Bacterial and Fungal Communities in a Muddy Coastal Wetland of China

Elucidating the dynamics of soil microbial diversity in coastal wetlands is essential for understanding the changes in ecological functions within these ecosystems, particularly in the context of climate change and improper management practices. In this study, the diversity patterns and influencing factors of soil bacterial and fungal communities in a muddy coastal wetland in China were investigated using Illumina sequencing of 16S rRNA and ITS1, across wetlands dominated by different vegetations and varying proximity to the coastline. The wetlands include four plots dominated by Spartina alterniflora (SA1), four plots dominated by Suaeda glauca (SG2), additional four plots of Suaeda glauca (SG3), and four plots dominated by Phragmites australis (PA4), ranging from the nearest to the coast to those farther away. The results revealed significant differences in bacterial richness (Observed_species index) and fungal diversity (Shannon index) across different wetlands, with SG3 demonstrating the lowest bacterial Observed_species value (1430.05), while SA1 exhibited the highest fungal Shannon value (5.55) and PA4 showing the lowest fungal Shannon value (3.10). Soil bacterial and fungal community structures differed significantly across different wetlands. The contents of soil available phosphorus and total phosphorus were the main drivers for fungal Observed_species and Shannon index, respectively. Soil organic carbon, pH, and salinity were indicated as the best predictors of bacterial community structure, accounting for 28.1% of the total variation. The total nitrogen content and soil salinity contributed mostly to regulating fungal community structure across different wetlands, accounting for 19.4% of the total variation. The results of this study offer a thorough understanding of the response and variability in soil microbial diversity across the muddy coastal wetlands in China.

Effects of Dietary Fiber and Copper on the Performance and Gut Microbiota of Finishing Pigs

This study aimed to investigate the effects of dietary fiber (DF) levels and copper concentrations on the production performance and cecal microbial diversity of finishing pigs. A 2 × 2 factorial experimental design was used, with different levels of dietary fiber (low [23% DF]: L and high [30% DF]: H) and copper concentrations (normal [25 mg/kg]: N and supplemented [45 mg/kg]: S) resulting in four diets (LN, LS, HN, and HS). Forty-eight hybrid barrows (Duroc × Landrace × Yorkshire), with an initial body weight of 76 kg ± 1.5 kg, were randomly assigned to four groups: LN, LS, HN, and HS, with 12 replicates per group and one pig per replicate. There was a 7-day adaptation period followed by a 56-day feeding trial, after which all pigs were slaughtered for sampling. Results indicated that in finishing pigs, the low dietary fiber group exhibited a higher final weight, a higher average daily gain, and a lower feed-to-gain ratio compared to the high fiber group (p &lt; 0.05). The LS group showed higher digestibility of dry matter, crude protein, crude fiber, ash, neutral detergent fiber, and DF than the HN and HS groups (p &lt; 0.05). Blood total protein levels were higher in the high fiber group, whereas blood Cu levels were higher in the supplemented copper group (p &lt; 0.05). High dietary fiber increased the activities of colonic carboxymethylcellulase and β-glucanase (p &lt; 0.05). Concentrations of acetic acid, propionic acid, and total volatile fatty acids were elevated in the high fiber group (p &lt; 0.05). Microbial α-diversity indices (observed species, Chao 1, and Shannon indices) increased with fiber but decreased with copper supplementation (p &lt; 0.05). The Firmicutes/Bacteroidetes ratio increased with fiber levels, with a higher relative abundance of Lactobacillus in the LS group. In conclusion, appropriate copper supplementation in diets can mitigate the negative effects of high fiber levels on finishing pig production performance by enhancing nutrient digestibility, fiber-degrading enzyme activity, regulating the microbial community, and its metabolic products.

Rice husk biochar resuscitates the microecological functions of heavy–metal contaminated soil after washing by enriching functional bacteria

Biochar has great potential for simultaneously improving soil ecological functions and eliminating environmental pollutants. However, studies on this strategy in the restoration of ecological functions in chelator–washed soil are lacking, and the effect of biochar on the structure, functions, and microbial interactions of washed soil microbiomes are unclear. Hence, the effect of rice husk biochar (RHB, 2 %) on the physicochemical properties, heavy metal fractions, and microbial community structure of glutamate–N, N–diacetic acid (GLDA)– and ethylenediaminetetraacetic acid (EDTA)– washed remediated soil were investigated. Results showed that the RHB addition restored the washed soil physical structure (pores and agglomerates) and meanwhile, the soil colloidal sheet sweeps increased by 20.49 % and 102.07 % in the z–axis, respectively. Additionally, RHB significantly increased washed soil pH (P < 0.05) and alkaline phosphatase and urease activities, while decreased acid phosphatase and glucosidase activities. The Observed–species and Shannon index were significantly higher in soil treated by RHB combined with GLDA and EDTA than those treated with GLDA and EDTA alone (P < 0.05). GLDA washing coupled RHB treatment enriched key bacterial groups such as MND1, Chelativorans, and Ellin6067, while EDTA washing coupled RHB treatment enriched Sreroidobacter, Micromonospora, and Reyranella, that both related to C–, N–, and P– cycles. Importantly, RHB addition could enrich functional bacteria by increasing bacterial resistance, including glucose metabolic homeostasis and metal ion resistance. The observed enrichment of functional bacteria provided evidence for the enhancement of soil nutrient cycles, indicative of improved soil functions by combination of chelator washing and biochar amended.

Supplementation with inulin reverses cognitive flexibility alterations and modulates the gut microbiota in high-fat-fed mice

IntroductionAlterations in cognitive performance are associated with inadequate nutritional states and diet composition. Prebiotics, such as inulin, are substances that can modulate the gut microbiome and, consequently, brain function by producing metabolites such as short-chain fatty acids (SCFAs). This study aimed to evaluate the effect of supplementation with inulin on cognitive flexibility, body composition, and gut microbiota in a murine model exposed to a high-fat (HF) diet.MethodsCD1 mice were divided into five groups: control fed a standard diet (C), high-fat diet (HF), inulin (I), high-fat diet with inulin (HFI), and manipulation control (M). Dietary supplementation was administered for 6 weeks. Cognitive flexibility was assessed using the Attentional Set-Shifting Test (AST). In addition, body composition was measured via electrical bioimpedance and adipose tissue compartments of each mouse were removed and weighed. Finally, gut microbiota metataxonomic was analyzed through metataxonomic bacterial 16S rRNA sequencing.ResultsWe observed that HF group required more AST trials than the C, HFI, and I groups in the compound discrimination (CD) and extra-dimensional (ED) stages. Notably, the HFI group required fewer trials than the HF group in the ED stage (p = 0.0187). No significant differences in overall body composition were observed between the groups. However, the percentage of gonadal and peritoneal adipose tissue was significantly higher in the HF and I groups compared to the C group. Statistically significant differences in alpha diversity for gut microbiota were observed using the Shannon, Simpson, and Chao1 indices. The I group showed a decrease in bacterial diversity compared to the HF group. While no differences were observed between groups in the phyla Bacillota and Bacteroidotes, Clostridium bacteria represented a lower proportion of sequences in the I group compared to the C group. Additionally, Lactobacillus represented a lower proportion of sequences in the HF group compared to the C and I groups.DiscussionThese findings suggest that supplementation with inulin could be a useful approach to mitigate the negative effects of an HF diet on cognitive flexibility and modulate gut microbiota composition.

Deciphering the microbial communities in ticks of Inner Mongolia: ecological determinants and pathogen profiles

BackgroundTicks are vectors of numerous pathogens, with their bacterial composition, abundance, diversity, and interaction influencing both their growth and disease transmission efficiency. Despite the abundance of ticks in Inner Mongolia, China, comprehensive data on their microbial communities are lacking. This study aims to analyze the microbial communities within ticks from Inner Mongolia to inform innovative control strategies for interrupting pathogen transmission.MethodsTick samples were collected from animals and vegetation in multiple locations across Inner Mongolia and stored at − 80 °C. Ticks were identified using morphological keys and molecular biology methods. Full-length 16S rRNA gene sequencing was performed on collected samples. Bacterial community composition and diversity were mainly analyzed using bioinformatic tools such as QIIME, phyloseq, and DESeq2. Alpha diversity was assessed using Chao1, ACE, and Shannon indices, while beta diversity was evaluated using Bray-Curtis dissimilarity matrices. LEfSe analysis was applied to identify taxa associated with ecological and biological variables.ResultsA total of 5,048,137 high-quality read counts were obtained, forming an average of 789.3 OTUs per sample. Proteobacteria, Firmicutes, and Bacteroidetes were the most dominant phyla. Bacterial community composition varied significantly with geography, with Dermacentor nuttalli showing a higher abundance of Rickettsia in Xilingol League, while other regions had different dominant genera. The microbial community also differed based on the feeding status of ticks. Additionally, the microbiota of engorged ticks showed organ specificity. Pathogen detection efforts revealed the presence of nine pathogens across all three tick species. D. nuttalli was found to carry a significantly higher burden of pathogenic bacteria, making it the most potentially threatening tick species in Inner Mongolia.ConclusionsThe study highlights significant variations in tick microbiomes influenced by geographic location, feeding status, and tick species. It underscores the importance of enhancing tick and tick-borne disease surveillance in Inner Mongolia for early detection and control of emerging pathogens.Graphical