Relative Abundance Of Actinobacteria Research Articles

Kiwifruit resistance to gray mold is enhanced by yeast-induced modulation of the endophytic microbiome

The influence of endophytic microbial community on plant growth and disease resistance is of considerable importance. Prior research indicates that pre-treatment of kiwifruit with the biocontrol yeast Debaryomyces hansenii suppresses gray mold disease induced by Botrytis cinerea. However, the specific underlying mechanisms remain unclear. In this study, Metagenomic sequencing was utilized to analyze the composition of the endophytic microbiome of kiwifruit under three distinct conditions: the healthy state, kiwifruit inoculated with B. cinerea, and kiwifruit treated with D. hansenii prior to inoculation with B. cinerea. Results revealed a dominance of Proteobacteria in all treatment groups, accompanied by a notable increase in the relative abundance of Actinobacteria and Firmicutes. Ascomycota emerged as the major dominant group within the fungal community. Treatment with D. hansenii induced significant alterations in microbial community diversity, specifically enhancing the relative abundance of yeast and exerting an inhibitory effect on B. cinerea. The introduction of D. hansenii also enriched genes associated with energy metabolism and signal transduction, positively influencing the overall structure and function of the microbial community. Our findings highlight the potential of D. hansenii to modulate microbial dynamics, inhibit pathogenic organisms, and positively influence functional attributes of the microbial community.

The impact on Cd bioavailability and accumulation in rice (Oryza sativa L.) induced by dry direct-seeding cultivation method in field-scale experiments

Dry direct-seeded rice cultivation has gained popularity and expanded its cultivated area due to reduced labor requirements and water consumption. However, the impact of this cultivation method on cadmium (Cd) bioavailability in soil and the accumulation levels in grains remains uncertain. Field experiments were conducted in acidic soils at two locations in southern China to compare rice varieties and evaluate the dry direct-seeding method alongside the wet direct-seeding and traditional transplanting methods. Dry direct-seeded rice reached significantly higher Cd concentrations in its tissues starting from the heading stage than transplanted rice. Cd accumulation levels by the maturation stage in the brown rice of dry direct-seeded rice were 18.33 %–150.69 % higher than those of wet direct-seeded and transplanted rice, with a considerable ability to translocate Cd into brown rice. Furthermore, dry direct seeding decreased iron plaque formation, particularly in the amorphous Fe form; it resulted in high soil temperature and low moisture content during tillering, elevating Cd availability in the soil. Additionally, the proportion of ions and more labile forms of Cd in the soil solution was high. Moreover, the soil under dry direct seeding had high urease and acid phosphatase enzyme activities. However, low richness and diversity in the bacterial community were characterized by a significant increase in the relative abundance of Actinobacteria and Gammaproteobacteria at the class level, while exhibiting decreased relative abundances of Alphaproteobacteria, Bacilli, and KD4-96, along with fewer biomarkers. Nonetheless, these differences are gradually reduced during the maturation stage. Overall, although dry direct seeding offers several advantages, it is crucial to implement additional measures to mitigate the increased health risks linked to rice cultivation through this approach in Cd-contaminated areas.

Quinones-enhanced humification in food waste composting: A novel strategy for hazard mitigation and nitrogen retention

The harmless and high-value conversion of organic waste are the core problems to be solved by composting technology. This study introduced an innovative method of promoting targeted humification and nitrogen retention in composting by adding p-benzoquinone (PBQ), the composting without any additives was set as control group (CK). The results indicated that the addition of exogenous quinones led to a 30.1% increase in humic acid (HA) content during the heating and thermophilic phases of composting. Spectroscopic analyses confirmed that exogenous quinones form the core skeleton structure of amino-quinones in HA through composting biochemical reactions. This accelerated the transformation of quinones into recalcitrant HA in the early stages of composting, and reduced CO2 and NH3 by 8% and 78%, respectively. Redundancy analysis (RDA) revealed that the decrease in carbon and nitrogen losses primarily correlated with quinones enhancing HA formation and greater nitrogen incorporation into HA (P < 0.05). Furthermore, the compost treated with quinones demonstrated a decrease in phytotoxicity and earthworm mortality, alongside a significant increase in the relative abundance of actinobacteria, which are associated with the humification process. This research establishes and proposes that co-composting with quinones-containing waste is an effective approach for the sustainable recycling of hazardous solid waste.

Early life exposure of infants to benzylpenicillin and gentamicin is associated with a persistent amplification of the gut resistome

BackgroundInfant gut microbiota is highly malleable, but the long-term longitudinal impact of antibiotic exposure in early life, together with the mode of delivery on infant gut microbiota and resistome, is not extensively studied.MethodsTwo hundred and eight samples from 45 infants collected from birth until 2 years of age over five time points (week 1, 4, 8, 24, year 2) were analysed. Based on shotgun metagenomics, the gut microbial composition and resistome profile were compared in the early life of infants divided into three groups: vaginal delivery/no-antibiotic in the first 4 days of life, C-section/no-antibiotic in the first 4 days of life, and C-section/antibiotic exposed in first 4 days of life. Gentamycin and benzylpenicillin were the most commonly administered antibiotics during this cohort’s first week of life.ResultsNewborn gut microbial composition differed in all three groups, with higher diversity and stable composition seen at 2 years of age, compared to week 1. An increase in microbial diversity from week 1 to week 4 only in the C-section/antibiotic-exposed group reflects the effect of antibiotic use in the first 4 days of life, with a gradual increase thereafter. Overall, a relative abundance of Actinobacteria and Bacteroides was significantly higher in vaginal delivery/no-antibiotic while Proteobacteria was higher in C-section/antibiotic-exposed infants. Strains from species belonging to Bifidobacterium and Bacteroidetes were generally persistent colonisers, with Bifidobacterium breve and Bifidobacterium bifidum species being the major persistent colonisers in all three groups. Bacteroides persistence was dominant in the vaginal delivery/no-antibiotic group, with species Bacteroides ovatus and Phocaeicola vulgatus found to be persistent colonisers in the no-antibiotic groups. Most strains carrying antibiotic-resistance genes belonged to phyla Proteobacteria and Firmicutes, with the C-section/antibiotic-exposed group presenting a higher frequency of antibiotic-resistance genes (ARGs).ConclusionThese data show that antibiotic exposure has an immediate and persistent effect on the gut microbiome in early life. As such, the two antibiotics used in the study selected for strains (mainly Proteobacteria) which were multiple drug-resistant (MDR), presumably a reflection of their evolutionary lineage of historical exposures—leading to what can be an extensive and diverse resistome.31ajk8a-14RKZLdCXmKHuwVideo

Gut microbiota dysbiosis and protein energy wasting in patients on hemodialysis: an observational longitudinal study.

Protein energy wasting (PEW) is common in patients on hemodialysis, and its development may involve gut microbial dysbiosis. However, the exact relationship between the composition of different flora and the development of PEW remains unclear. This is an observational longitudinal study on 115 patients undergoing hemodialysis who were followed up for 1 year. All the patients were evaluated at baseline, and different microbiota compositions were determined. After a 1 year follow-up period, the correlations between clinical parameter variations and the relative abundance of different gut flora were assessed using Spearman correlation. Moreover, the associations of the abundance of different gut microbiota with decrease in lean tissue mass and the development of PEW were analyzed using ROC curve and logistical regression analyses. We found that the relative abundances of Actinobacteria and Bifidobacteriaceae were significantly lower in patients with PEW than in those who did not develop PEW (p < 0.05). The abundance of Actinobacteria and Bifidobacteriaceae correlated positively with variations in serum albumin levels (r = 0.213, p = 0.035 and r = 0.214, p = 0.034, respectively), lean tissue mass (r = 0.296, p = 0.007 and r = 0.238, p = 0.002, respectively), and lean tissue index (r = 0.377, p < 0.001 and r = 0.419, p < 0.001, respectively). The area under the ROC curve or AUC values of Actinobacteria and Bifidobacteriaceae for the prediction of lean tissue mass decrease ranged from 0.676 to 0.708 (p < 0.05). Thus, decrease in the abundance of Actinobacteria and Bifidobacteriaceae may be associated with decrease in lean tissue mass and the occurrence of PEW. The present findings imply Actinobacteria and Bifidobacteriaceae may be potential markers for predicting skeletal muscle mass decrease and PEW development in patients on hemodialysis.

Interactive dynamics between rhizosphere bacterial and viral communities facilitate soybean fitness to cadmium stress revealed by time-series metagenomics

The distinctive symbiotic relationship between rhizobacteria and soybean (Glycine max) can enhance soil fertility and assist soybean defense heavy metal stress, such as cadmium (Cd), in soils. Soil viruses are critical for modulating microbial activities and enhancing host adaptability to soil contamination by encoding auxiliary metabolic genes (AMGs). However, the community structure, functional diversity and ecological roles of soil viruses and their dynamic interactions with soil-dwelling microbes under Cd stress remain unclear. Here, we characterized the bulk and rhizosphere bacterial community in a Cd-contaminated soybean field at five growth stages and investigated the rhizosphere microbial functional traits and the viral community after flowering using metagenomics. We showed that the rhizosphere bacterial community exhibited a stronger soybean development-dependent diversity pattern relative to bulk soil and had a more critical role in predicting Cd accumulation. The relative abundance of Actinobacteria in the rhizosphere increased with soybean development, particularly in the families Nocardioidaceae and Intrasporangiaceae, which were further identified as the main contributors of amino acid transport E and secondary metabolites Q genes. Viral analysis suggested an interactive and complementary assembly between viral and bacterial communities. Importantly, viruses exhibited a broader host range during the flowering period, and infected specific functional taxa such as Bradyrhizobium and Nocardioides, highlighting their potential impact on the rhizobia-soybean symbiosis and soybean growth and fitness. Furthermore, AMGs related to element cycling and microbial metabolism were identified and functionally and phylogenetically characterized, suggesting the contribution of these virus-encoded genes to biogeochemical cycles and soybean fitness under Cd stress. Together, our results expand our understanding of the ecological functions of rhizosphere viruses in Cd pollution-stressed soils, and provide insights in developing new strategies for bioremediation of contaminated soils.

[Prediction of Soil Bacterial Community Structure and Function in Minqin Desert-oasis Ecotone Artificial Haloxylon ammodendron Forest].

Exploring the effects of artificial Haloxylon ammodendron forest planting on the structure and function of a desert soil bacterial community provides data reference for soil micro-ecological restoration and land quality improvement in desert oasis transition zones. Illumina high-throughput sequencing technology and PICRUSt2 functional prediction analysis were used to identify and analyze the structure and function of soil bacterial communities, and the Mantel correlation test and RDA analysis were used to explain the physicochemical factors affecting the structure and function of soil bacterial communities. The results showed that:① the soil bacterial OTU number, Chao1 index, and Shannon index were significantly higher in the H. ammodendron forest than in the mobile dune soil, and the PCoA analysis and Adonis test showed significant differences in the soil bacterial community structure between H. ammodendron and mobile dune soil (P=0.001). ② A total of 34 phyla, 89 classes, 174 orders, 262 families, and 432 genera of bacteria were detected in all samples, and the phyla Proteobacteria, Actinobacteria, Cyanobacteria, and Chloroflexi accounted for 76.05% of the relative abundance of soil bacteria, which belonged to the dominant soil bacteria, among which the relative abundance of Actinobacteria in H. ammodendron forest soil was extremely significantly higher than that in mobile dune soil (P &lt; 0.01). ③PICRUSt2 function prediction revealed that the soil bacterial community of H. ammodendron forest included six categories of primary functions and 28 categories of secondary functions, among which the metabolism of carbohydrates, metabolism of amino acids, and metabolism of cofactors and vitamins were all greater than 10% in relative abundance and were the main metabolic functions of H. ammodendron forest soil bacteria. ④ The planting of H. ammodendron forest significantly improved the nutrient content of soil organic matter and other nutrients. Soil pH, organic matter, total nitrogen, and fast-acting phosphorus were the main physicochemical factors affecting the bacterial community, with soil organic matter significantly affecting the soil bacterial community structure (P &lt; 0.05) and metabolic function (P &lt; 0.05). In conclusion, the artificial H. ammodendron forest helped to increase desert soil microbial diversity, increase the relative abundance of soil bacterial metabolic function genes, and improve the desert soil microenvironment.

Effects of blister blight disease on endophytic microbial diversity and community structure in tea (Camellia sinensis) leaves.

In this study, metagenomic sequencing technology was employed to analyze the ITS1 region sequence of the ITS rDNA gene of endophytic fungi and 16S sequence of endophytic bacteria in tea leaves with varying degrees of infection by tea blister blight disease as well as healthy tea leaves. Subsequently, a comparative analysis was conducted on the endophytic microbial diversity and the community structure in tea leaves. The findings of this investigation reveal a shift in the dominant endophytic fungal genera from Ascomycota to Basidiomycota as the disease progressed. Furthermore, a negative correlation was observed between Exobasidium and Talaromyce, with Talaromyce exhibiting potential as an antagonist against the disease. Meanwhile, our findings reveal that Proteobacteria, Firmicutes, and Actinobacteria were the three most abundant bacteria phyla in tea leaves. As the disease progressed, there was an increase in the relative abundance of Actinobacteria, while Variovorax, Sphingomonas, and Pseudomonas were found to have higher abundance in later stages. The diversity analysis results indicated that the endophytic microbial diversity and the community structure in tea leaves in the diseased group were lower than those in the healthy control group. In general, blister blight disease altered the community structure of endophytic microorganisms in tea leaves, resulting in a few species with high abundance. The study lays a foundation for investigating the pathogenic mechanism of tea blister disease and establishing a theoretical basis for controlling diseases in tea trees.

Effects of Vitamin A on Growth Performance, Antioxidants, Gut Inflammation, and Microbes in Weaned Piglets.

Piglet weaning is an important stage in production where changes in the environment and diet can cause problems such as intestinal inflammation and diarrhea. Vitamin A is an essential nutrient for human and animal growth and has immunomodulatory and inflammatory effects. A large body of literature has previously reported on the use of vitamin A in piglet production, so our experiment added different concentrations of vitamin A (0, 1100, 2200, 4400, 8800, and 17,600 IU/kg) to weaned piglet diets to study the effects of different doses on growth performance, intestinal barrier, inflammation, and flora in weaned piglets. We selected 4400 IU/kg as the optimum concentration of vitamin A in relation to average daily weight gain, feed intake, feed-to-weight ratio, and diarrhea rate, and subsequently tested the inflammatory factors, immunoglobulin content, antioxidant levels, and intestinal flora of weaned piglets. Results: We observed that the diarrhea rate of weaned piglets was significantly lower after the addition of 4400 IU/kg of vitamin A to the diet (p < 0.05). A control group and a 4400 IU/kg VA group were selected for subsequent experiments. We found that after the addition of vitamin A, the serum CAT level of weaned piglets increased significantly, the expression of Claudin-1 in the jejunum and ileum increased significantly, the expression of Occludin gene in the jejunum increased significantly, the expression of IL-5 and IL-10 in the ileum increased significantly (p < 0.05), and the expression of IL-4, IL-5, and IL-10 in the ileum increased significantly (p < 0.05). Meanwhile, in the colonic flora of vitamin A-added weaned piglets, the relative abundance of Actinobacteria and Erysipelotrichales decreased significantly, while the relative abundance of Bacteroidales increased significantly (p < 0.05). The results of this study indicated that vitamin A at 4400 IU/kg reduces diarrhea in weaned piglets by increasing antioxidant levels, increasing intestinal tight junction protein gene expression, and regulating colonic gut microbiota.

How do aeration mode and influent carbon/nitrogen ratio affect pollutant removal, gas emission, functional genes and bacterial community in subsurface wastewater infiltration systems?

Abstract This study investigated the influences of aeration mode and influent carbon/nitrogen ratio on matrix oxygen concentration, pollutant removal, greenhouse gas emission, functional gene abundances and bacterial community in subsurface wastewater infiltration systems (SWISs). Intermittent or continuous aeration enhanced oxygen supply at 0.6 m depth in the matrix, which improved organics removal, nitrogen removal, the abundances of bacterial 16S rRNA, amoA, nxrA, narG, napA, nirK, nirS, norB, nosZ genes, bacterial community Alpha diversity, the relative abundances of Actinobacteria at 0.6 m depth, the relative abundances of Chloroflexi, Gemmatimonadetes, Bacteroidetes and Firmicutes at 0.9 and 1.2 m depth and reduced CH4 and N2O conversion efficiencies, the abundance of mcrA gene with carbon/nitrogen ratio of 12 and 16 compared with non-aeration. Increased carbon/nitrogen ratio resulted in higher TN removal efficiencies and lower CH4 and N2O conversion efficiencies in aeration SWISs than those in non-aeration SWIS. Intermittent aeration SWIS obtained high removal efficiencies of 83.2, 85.4 and 90.8% for TN, NH4+ -N and COD and low conversion efficiency of 0.21 and 0.65% for N2O and CH4 with optimal carbon/nitrogen ratio of 12. However, high TN (82.6%), NH4+ -N (84.9%) and COD (92.2%) removal efficiencies and low CH4 (0.67%) and N2O (0.23%) conversion efficiencies were achieved in continuous aeration SWIS with carbon/nitrogen ratio of 16.

In vitro fermentation of kodo and kutki millets by human gut microbiota: Gut microbiota and metabolomic analysis

Millets are underutilised cereals packed with several bioactive components. The effect of Kodo millet (KOM) and Kutki millet (KUM) on the modulation of gut microbiota and metabolites produced during batch in vitro fermentation using human faecal samples was investigated. A two-fold increase in Firmicutes and an 18.95- and 9.74-fold increase in the relative abundance of Actinobacteria were observed in the KOM and KUM groups respectively. Furthermore, Bacteroidetes counts decreased by 17.4% in the KOM group and by 98.2% in the KUM group. Metabolomic analysis revealed different abundances of metabolites in different millet groups. The concentration of acetate, lactate and propionate increased significantly in the KOM group, while only a significant increase in lactate was recorded in the KOM group. Odd chain fatty acids (OCFAs) were abundant in both groups. The KUM group was enriched in tridecanoic acid, and pentadecanoic acid, while KOM had a higher concentration of dodecanoic acid and cis-10-heptadecenoic acid. Correlation analysis of gut microbiota and metabolome revealed the association of beneficial metabolites with Caproiciproducens, Lactobacillus, Veillonella, Blautia, Faecalibacterium and Prevotella. Furthermore, PICRust analysis confirmed the upregulation of various metabolic pathways including glycan biosynthesis and metabolism, lipid, carbohydrate and amino acids metabolism, etc in millet groups. Collectively, the study contributes to the understanding of the millets-human gut microbiota interaction and suggests that different millets can be used for the formulation of specialized food that targets specific gut microbiota.

145 Dose-Response and Functional Roles of Zinc Glycinate on Growth and Intestinal Health of Nursery Pigs Challenged with F18+Escherichia Coli

Abstract This study was to evaluate dose-response and supplemental effects of zinc glycinate (ZnGly) on growth and intestinal health of nursery pigs challenged with F18+Escherichia coli. Nursery pigs (n = 40; BW = 6.5 ± 0.5 kg) were allotted to 5 treatments in a randomized complete block design with BW and sex as blocks: 1) NC: no-challenge/no-supplement; (2) PC: F18+E. coli challenge/no-supplement; (3 to 5) F18+E. coli challenge/supplementations of ZnGly at 400, 800, and 1,200 mg/kg. On d 7, challenged groups were orally inoculated with F18+E. coli at 6 × 109 CFU/mL, whereas NC received saline solution. Pigs were fed for 28 d based on 2 phases (Phase 1: 14 d and phase 2: 14 d), and experimental diets were formulated to meet or exceed nutrient requirements suggested by NRC (2012). Pigs were euthanized on d 28 to collect tissues to evaluate TNF-α, IL-8, malondialdehyde, protein carbonyl, gene expression of Zn transporters, and mucosa-associated microbiota in the jejunum. Data were analyzed using contrasts in the MIXED procedure of SAS. The E. coli challenge tended to reduce (P = 0.065) ADG (308 to 244 g/d) and increase (P &amp;lt; 0.05) fecal score (3.2 to 4.1) of the pigs during the first week of post-challenge. Supplementation of ZnGly from 0 to 1,200 mg/kg linearly (P = 0.092) increased G:F (0.69 to 0.81) during phase 1 and decreased (P &amp;lt;0.05) fecal score (4.1 to 3.5) of the pigs during the first week of post-challenge. Supplementation of ZnGly from 0 to 1,200 mg/kg had quadratic effects on TNF-α (P = 0.065; minimum 1.51 pg/mg at 405 mg/kg of ZnGly), IL-8 (P = 0.093; minimum 0.53 ng/mg at 494 mg/kg), and protein carbonyl (P = 0.054; minimum 2.30 pg/mg at 675 mg/kg) and linearly increased mRNA expressions of (P = 0.057) ZIP4 (0.69 to 1.03) and (P = 0.075) ZnT5 (0.92 to 1.22) in the jejunum of the pigs. Supplementation of ZnGly from 0 to 1,200 mg/kg tended to linearly decrease (P = 0.065) Chao1 index (150.6 to 144.6) and linearly increased (P &amp;lt; 0.05) relative abundance of Actinobacteria (13.10 to 16.26%) and had quadratic effects (P &amp;lt; 0.05) on the relative abundance of Cyanobacteria (minimum 0.67 % at 625 mg/kg) and Proteobacteria (minimum 45.6% at 735 mg/kg) at the phylum level with Enterobacteriaceae (minimum 4.79% at 660 mg/kg) at family level in jejunal mucosa-associated microbiota of the pigs. In conclusion, supplementation of ZnGly at a range of 400 to 675 mg/kg could reduce the negative impacts of F18+E. coli on growth performance and diarrhea of nursery pigs. These positive changes are related to reducing jejunal inflammation and oxidative stress by enhancing jejunal Zn absorption with positive changes in jejunal mucosa-associated microbiota in the pigs.

Integrated Macrogenomics and Metabolomics Explore Alterations and Correlation between Gut Microbiota and Serum Metabolites in Adult Epileptic Patients: A Pilot Study.

Epilepsy (EP) is a complex brain disorder showing a lot of unknows reasons. Recent studies showed that gut microbiota can influence epilepsy via the brain-gut axis. Nevertheless, the mechanism by which gut microbiota affects adult epilepsy still remains unclear. In this study, fecal and serum samples were obtained from patients with epilepsy and normal controls. Using an integrated analysis, sequencing was performed by macrogenomics and high-throughput targeted metabolomics with various bioinformatics approaches. The macrogenomic sequencing revealed significant changes in microbial structure in patients suffering from epilepsy. For example, at the phylum level, the relative abundance of Actinobacteria, Bacteroidetes and Proteobacteria showed an increase in the patients with epilepsy, whereas that of Firmicutes decreased. In addition, the patients with epilepsy had significantly differential metabolite profiles compared to normal controls, and five clusters with 21 metabolites, mainly containing the upregulation of some fatty acids and downregulation of some amino acids. Tryptophan (AUC = 91.81, p < 0.0001), kynurenine (AUC = 79.09, p < 0.01) and 7Z,10Z,13Z,16Z-Docosatetraenoic acid (AUC = 80.95, p < 0.01) may be used as potential diagnostic markers for epilepsy. Differential serum metabolites have effects on tryptophan metabolism, iron death and other pathways. Furthermore, a multiomic joint analysis observed a statistically significant correlation between the differential flora and the differential serum metabolites. In our findings, a macrogenomic analysis revealed the presence of dysregulated intestinal flora species and function in adult epileptic patients. Deeper metabolomic analyses revealed differences in serum metabolites between patients with epilepsy and healthy populations. Meanwhile, the multiomic combination showed connection between the gut microbes and circulating metabolites in the EP patients, which may be potential therapeutic targets.

Effects of snow removal on seasonal dynamics of soil bacterial community and enzyme activity

High latitude regions are experiencing considerable winter climate change, and reduced snowpack will likely affect soil microbial communities and their function, ultimately altering microbial-mediated biogeochemical cycles. However, the current knowledge on the responses of soil microorganisms to snow cover changes in permafrost ecosystems remains limited. Here, we conducted a 2-year (six periods) snow manipulation experiment comprising ambient snow and snow removal treatments with three replications of each treatment to explore the immediate and legacy effects of snow removal on soil bacterial community and enzyme activity in secondary Betula platyphylla forests in the permafrost region of the Daxing'an Mountains. Generally, bacterial community diversity was not particularly sensitive to the snow removal. Seasonal fluctuations in the relative abundance of dominated bacterial taxa were observed, but snow removal merely exerted a significant impact on the bacterial community structure during the snow melting period and early vegetation growing season within two consecutive years, with a reduction in the relative abundance of Chloroflexi and an increase in the relative abundance of Actinobacteria, and no evidence of cross-season legacy effects was found. Moreover, snow removal significantly altered the soil enzyme activities in the snow stabilization period and snow melting period, with an increase in soil acid phosphatase (ACP) activity of snow melting period and a decrease in polyphenol oxidase (PPO) activity of snow stabilization period as well as β-glucosidase (BG) activity of snow stabilization period and snow melting period, but this effect did not persist into the vegetation growing periods. The seasonal variations in bacterial community and enzyme activity were mostly driven by changes in soil nutrient availability. Overall, our results suggest that soil bacterial communities have rather high resilience and rapid adaptability to snow cover changes in the forest ecosystems in the cold region of the Daxing'an Mountains.

Effects of dietary tryptophan supplementation on rectal temperature, humoral immunity, and cecal microflora composition of heat-stressed broilers.

This trial aimed to determine the effects of tryptophan (Trp) on the rectal temperature, hormone, humoral immunity, and cecal microflora composition in broiler chickens under heat stress (HS). One hundred and eighty 18 days-old female Arbor Acres broilers were randomly divided into three treatment groups, with six replicates of ten birds in each replicate. The broilers were either raised under thermoneutral conditions (TN, 23 ± 1°C) or subjected to heat stress (34 ± 1°C for 8 h daily). The TN group received a basal diet, and another two heat-stressed groups were fed the basal diet (HS) or the basal diet supplemented with 0.18% Trp (HS + 0.18% Trp) for 21 consecutive days. The basal diet contained 0.18% Trp. Results revealed that HS increased the rectal temperature, serum epinephrine (EPI), and corticotropin-releasing hormone (CRH) concentrations (p < 0.05), reduced the bursal index, the levels of serum immunoglobulin A (IgA), IgG, IgM, and serotonin (5-HT) as well as the relative abundance of Actinobacteria in cecum (p < 0.05) compared with the TN group. Dietary supplementation of Trp decreased the rectal temperature, serum dopamine (DA), EPI, and the levels of CRH and L-kynurenine (p < 0.05), increased the bursal index, the levels of serum IgA, IgM, and 5-HT as well as the relative abundance of Ruminococcus torques group in cecum of heat-stressed broilers (p < 0.05) compared to HS group. In conclusion, dietary Trp supplementation decreased rectal temperature, improved cecal microbiota community and Trp metabolism, and enhanced humoral immunity of heat-stressed broilers.

Viral but not bacterial community successional patterns reflect extreme turnover shortly after rewetting dry soils.

As central members of soil trophic networks, viruses have the potential to drive substantial microbial mortality and nutrient turnover. Pinpointing viral contributions to terrestrial ecosystem processes remains a challenge, as temporal dynamics are difficult to unravel in the spatially and physicochemically heterogeneous soil environment. In Mediterranean grasslands, the first rainfall after seasonal drought provides an ecosystem reset, triggering microbial activity during a tractable window for capturing short-term dynamics. Here, we simulated precipitation in microcosms from four distinct dry grassland soils and generated 144 viromes, 84 metagenomes and 84 16S ribosomal RNA gene amplicon datasets to characterize viral, prokaryotic and relic DNA dynamics over 10 days. Vastly different viral communities in each soil followed remarkably similar successional trajectories. Wet-up triggered a significant increase in viral richness, followed by extensive compositional turnover. Temporal succession in prokaryotic communities was much less pronounced, perhaps suggesting differences in the scales of activity captured by viromes (representing recently produced, ephemeral viral particles) and total DNA. Still, differences in the relative abundances of Actinobacteria (enriched in dry soils) and Proteobacteria (enriched in wetted soils) matched those of their predicted phages, indicating viral predation of dominant bacterial taxa. Rewetting also rapidly depleted relic DNA, which subsequently reaccumulated, indicating substantial new microbial mortality in the days after wet-up, particularly of the taxa putatively under phage predation. Production of abundant, diverse viral particles via microbial host cell lysis appears to be a conserved feature of the early response to soil rewetting, and results suggest the potential for 'Cull-the-Winner' dynamics, whereby viruses infect and cull but do not decimate dominant host populations.

Variations in the Intestinal Microbiota of the Chinese Soft-Shelled Turtle (Trionyx sinensis) between Greenhouse and Pond Aquaculture.

The microbial community structure in aquaculture water plays an important role in the intestinal microbial diversity of aquatic animals. The Chinese soft-shelled turtle (SST) (Trionyx sinensis) is an important aquaculture species of high economic value in the Asia-Pacific region. An intuitive understanding of the microbial diversity and abundances of SST aquaculture is crucial for comprehending these ecosystems. Herein, the evolutionary characteristics of the bacterial communities in the SST and its aquaculture water systems were investigated using Illumina MiSeq sequencing. This experiment sampled nine SSTs from a pond outside a greenhouse and was repeated three times. The sequencing results revealed significant differences in the microflora composition at the phylum and genus levels in both the intestine and aquaculture water of the SSTs in the greenhouse and pond aquaculture environments. A total of 1039 genera belonging to 65 phyla were identified. At the phylum level, the relative abundances of Chloroflexi (24%), Acidobacteria (5%), and Nitrospira (3%) were higher in the greenhouse water than in the pond water. The relative abundances of Bacteroidetes (35%), Actinobacteria (8%), and Cyanobacteria (4%) were higher in the pond water than in the greenhouse water. The intestinal microorganisms in the SSTs experienced significant changes after the SSTs were transferred from a greenhouse culture to a pond culture environment for 28 days. After the SSTs were cultured in the ponds, we observed decreases in the relative abundances of Actinobacteria (39% to 25%), Cyanobacteria (24% to 0.8%), Chlorobacteria (9% to 3%), and Firmicutes (5.5% to 0.8%. However, we observed increases in the relative abundances of Bacteroidetes (2% to 35%) and Acidobacteria (0.3% to 25%). These results showed that the bacterial diversity and richness compositions in the intestinal tract and aquaculture water were the same. However, the relative abundances of bacterial communities varied. The results of this study are of great significance in understanding how the environment affects SST cultures. These data may provide valuable instructions for Chinese soft-shelled turtle aquaculture management.

The diversity and function of microbial community in the sediment and terrestrial area of thermokarst lakes

Thermokarst lakes are widely distributed across the Qinghai-Tibet Plateau (QTP) and have been identified as an important source of greenhouse gases. However, previous studies on soil microbes have mainly focused on the aquatic area of thermokarst lakes, and the changes in microbial communities in the terrestrial area around thermokarst lakes are still unclear. We used high-throughput sequencing to analyse the soil microbial communities in the sediment and terrestrial area around three thermokarst lakes on the QTP. The results showed that the relative abundances of Bacteroidetes and Proteobacteria were high in the sediment areas, while the relative abundances of Actinobacteria and Acidobacteria were high in the terrestrial area around the thermokarst lakes. As the distance from the thermokarst lakes decreases, the α-diversity of the microbial communities increased in the mature thermokarst lake (MTL), whereas the α-diversity of the microbial communities decreased in the developing thermokarst lake (DTL). The β-diversity of the microbial communities also varied significantly as the distance from the thermokarst lakes decreases. As the distance from the thermokarst lakes decreases, the abundances of most genes responsible for C decomposition decreased in the MTL and were high in the middle lakeside areas and sediment of the DTL. Soil organic carbon (SOC), total nitrogen (TN), pH, soil water content (SWC) and the pore equivalent diameter were critical factors that affected the microbial community. The microbial richness increased in relatively arid areas (SWC < 60%) and decreased in relatively humid areas (SWC > 60%) as the distance from the thermokarst lakes decreases. These results suggest that the potential C decomposition was high in the far lakeside areas of the MTL and was high in the middle lakeside areas and sediment of the DTL.

[Spatial-temporal Changes and Driving Factors of Soil Microbial Communities in a Typical City of North China Plain].

The structure and function of microbial communities are affected by several environmental factors. To clarify the spatial-temporal changes and main influencing factors of soil microbial communities in a typical pharmaceutical city, it is urgent to study the spatial-temporal changes in microbial communities in soils for typical cities. Shijiazhuang City was selected as the study area, and 12 sampling sites were selected. The topsoil was collected in June (summer) and September (autumn) of 2021. The 16S rRNA high-throughput sequencing technology was used to study the structure and function of microbial communities in the soil and explore their spatial-temporal changes. Concurrently, Pearson correlation analysis was applied to establish the correlation between the microbial community and environmental factors, and identify the main driving factors of temporal and spatial changes in the microbial community. The results showed that:① Actinobaciota and Proteobateria were the main dominant bacteria in the surface soil of Shijiazhuang City; at the phylum level, the relative abundance of Actinobacteria and Proteobateria decreased from summer to autumn; at the genus level, the dominant genera were Arthrobacter and unknown genera in summer and Arthrobacter and Candidatus_Nitrocosmicus in autumn, which showed significant seasonal differences (P<0.05). ② For seasonal variation, the mean values of the Simpson, Ace, and Chao indices increased, whereas the mean values of OTU decreased; for spatial variation, the Shannon and Simpson indices showed significant spatial difference (P<0.01 and P<0.05). ③ There were no significant spatial-temporal differences in various functional genes; thereinto, the relative abundances of energy production and transformation functional genes were the highest (24.06%-24.84% in summer and 24.63%-25.98% in autumn, respectively). ④ The compositions of microbial community, diversity index, and functional genes were significantly correlated with quinolone antibiotics (QNs), total phosphorus (TP), and nitrate nitrogen (NO3--N), most significantly correlated with QNs (|r|>0.900), which indicated that antibiotics were the main driving factor of soil microbial communities. Therefore, to ensure the stability of microbial community structure and function in urban soil, the comprehensive management and control of antibiotic pollution in soil should be further strengthened.

The effects of lotus-fish co-culture on the gut microbiome of Hefang crucian carp (Carassis auratus)

Gut microbiome plays an important role in host's development and reproduction. Lotus-fish co-culture (LFC) is a popular integrated agriculture–aquaculture farming system in China. However, there is still a relative dearth of information on how changes of aquaculture modes will affect the fish gut microbiome. In the present study, metagenomic sequencing was used to compare gut bacteria of the hybrid fish Hefang crucian carp (Carassius cuuieri ♀ × C. auratus var. red ♂) cultured in LFC and intensive pond culture (IPC) systems. The results indicated that aquaculture modes exerted great influences on the fish gut bacterial community. A significantly higher gut bacterial diversity was found in LFC than that in IPC (P < 0.05). The relative abundances of Actinobacteria and Chloroflexi were apparently higher in LFC than those in IPC, whereas Planctomycetota, Firmicutes, and Verrucomicrobia showed opposite patterns. Besides, gut bacterial metabolic potentials involved in energy metabolism, carbohydrate metabolism, amino acid metabolism, environmental information processing, and cellular processes were significantly increased in LFC compared to those in IPC. On the contrary, the bacterial functional potentials related to nucleotide metabolism, DNA mismatch repair, as well as homologous recombination were significantly stimulated in the IPC system. Source‐tracking analysis suggested that fish gut bacterial community in IPC was originated mainly from water sources, whereas the gut bacterial community in LFC was originated from more unknown sources and soil sources. Our results provided new insight into the influence of aquaculture modes on the microbial community diversity and functionality in aquatic animals and highlighted the importance of environment microbiome in reshaping the gut microbes.