Effects of Dietary Supplementation with Prebiotics and Pediococcus Acidilactici on Gut Health, Transcriptome, Microbiome, and Metabolome in Atlantic Salmon (Salmo Salar L) after Seawater Transfer

BackgroundGiven the importance of gut microbiota for health, growth and performance of the host, the aquaculture industry has taken measures to develop functional fish feeds aiming at modulating gut microbiota and inducing the anticipated beneficial effects. However, present understanding of the impact of such functional feeds on the fish is limited. The study reported herein was conducted to gain knowledge on performance and gut health characteristics in post-smolt Atlantic salmon fed diets varying in content of functional ingredients. Three experimental diets, a diet containing fructo-oligosaccharides (FOS), a diet with a combination of FOS and Pediococcus acidilactici (BC) and a diet containing galacto-oligosaccharides (GOS) and BC, were used in a 10-weeks feeding trial. A commercial diet without functional ingredients was also included as a control/reference. Samples of blood plasma, mucosa and digesta were subjected to microbiome, transcriptome and metabolome profiling for evaluation of the diet effects. Results No significant growth differences were observed between fish fed the supplemented diets, but FOS-BC fed fish showed significantly higher growth than the control fed fish. The microbiome results showed that the BC was present in both the digesta and the mucosa samples of fish fed the FOS-BC and GOS-BC diets. Digesta-associated microbiota was altered, while mucosa-associated microbiota was relatively unaffected by diet. Replacing FOS with GOS increased the level of metabolites linked to phospholipid, fatty acid, carnitine and sphingolipid metabolism. Variation in metabolite levels between the treatments closely correlated with genera mainly belonging to Firmicutes and Actinobacteria phyla. The transcriptome analyses indicated diet effects of exchanging FOS with GOS on immune functions, oxidative defense and stress responses. No significant diet effect was observed on intestinal inflammation in the pyloric ceca or in the distal intestine, and no steatosis was observed in the pyloric ceaca. ConclusionsDietary supplementation with BC induced moderate effects on the microbiota of the digesta, while the effects of replacing FOS with GOS were more marked and was observed also for nutrient metabolism. Our data indicates therefore that the quality of a prebiotic may be of great importance for the effects of a probiotic on gut microbiota, function and health.

Isotopic and Chemical Assessment of the Dynamics of Methane Sources and Microbial Cycling during Early Development of an Oil Sands Pit Lake

Water-capped tailings technology (WCTT) is a key component of the reclamation strategies in the Athabasca oil sands region (AOSR) of northeastern Alberta, Canada. The release of microbial methane from tailings emplaced within oil sands pit lakes, and its subsequent microbial oxidation, could inhibit the development of persistent oxygen concentrations within the water column, which are critical to the success of this reclamation approach. Here, we describe the results of a four-year (2015–2018) chemical and isotopic (δ13C) investigation into the dynamics of microbial methane cycling within Base Mine Lake (BML), the first full-scale pit lake commissioned in the AOSR. Overall, the water-column methane concentrations decreased over the course of the study, though this was dynamic both seasonally and annually. Phospholipid fatty acid (PLFA) distributions and δ13C demonstrated that dissolved methane, primarily input via fluid fine tailings (FFT) porewater advection, was oxidized by the water column microbial community at all sampling times. Modeling and under-ice observations indicated that the dissolution of methane from bubbles during ebullition, or when trapped beneath ice, was also an important source of dissolved methane. The addition of alum to BML in the fall of 2016 impacted the microbial cycling in BML, leading to decreased methane oxidation rates, the short-term dominance of a phototrophic community, and longer-term shifts in the microbial community metabolism. Overall, our results highlight a need to understand the dynamic nature of these microbial communities and the impact of perturbations on the associated biogeochemical cycling within oil sands pit lakes.

Soil microbial respiration, biomass carbon and community composition data induced by substrate quality from an agricultural grassland

The data presented here are related to the research article entitled ‘Effects ofsubstrate quality on carbon partitioning and microbial community composition in soil from an agricultural grassland’ [1]. Data illustrate cumulative CO2 efflux, microbial biomass C (Cmic), priming effect expressed as priming index (PI) and total phospholipid fatty acid (PLFA) profiles. The data were measured during four soil laboratory incubations using a silty clay loam soil under permanent grassland from May until August 2015. The soil was treated with carbohydrates of different complexity (glucose, glucose-6-phosphate (G6P) or cellulose) alone or in conjunction with livestock slurry amended or non-amended with a biological additive. Our data may be of great significance for further studies on microbial respiration and biosynthesis, and microbial community structure following slurry application to soil, alongside the potential beneficial effects of the addition of slurry amended with biological additives.

Application of Livestock Slurry Significantly Influences Microbial Biosynthesis and Cumulative Respiration in Agricultural Grassland Soil

The long-term application of livestock slurry to intensive grassland soils may lead to positive effects, including an increase in soil organic matter and plant nutrient supply to soils. Further, there is increasing interest in the potential of biological slurry additives (mixtures of selected living or latent microorganisms added to slurry) to enhance soil fertility through mobilisation of key elements in slurry and soil. However, significant uncertainties remain surrounding the potential impacts of slurry amended with biological additives on carbon (C) partitioning within three pools: respired CO2, microbial biomass C (Cmic) and C retained in the soil, as well as composition of the microbial community in temperate grassland soils. We examined how slurry that has received a biological additive ultimately affects the partitioning of C within these pools and the composition of the soil microbial community, based on phospholipid fatty acid (PLFA) analysis. Four short-term incubations in which soil collected from a grassland field that has received livestock slurry treated with a commercial biological additive, alongside 14C-labelled carbohydrates of different complexity (14C-glucose, 14C-glucose 6-phosphate (G6P), and 14C-cellulose) were undertaken. Our results indicate that the addition of slurry to soil alongside carbohydrate compounds led to lower 14C biomass uptake and cumulative respiration of carbohydrate compounds, as well as greater residual 14C activities in soil, compared to the treatments in which slurry was not applied. A dominance of bacteria over fungi characterised soil microbial community composition in all treatments through time, with a prevalence of gram-negative over gram-positive bacteria. Our results also indicate that the addition of biological additives during slurry storage increased 14C biomass uptake following application of slurry to agricultural grasslands. Therefore, biological additives have the potential to create a favourable environment for maintaining and increasing soil fertility through modification of the microbial community associated with the slurry and influence of the soil microflora.

Fungi Dominated the Incorporation of 13C-CO2 into Microbial Biomass in Tomato Rhizosphere Soil under Different CO2 Concentrations

An elevated CO2 (eCO2) fumigation experiment was carried out to study the influence of various CO2 concentrations on microorganisms involved in the incorporation of root-derived C in greenhouse soil systems. In this study, 400 and 800 µmol·mol−1 CO2 fumigation treatments were conducted during tomato planting. Phospholipid fatty acid (PLFA) profiling based on the stable isotope probing (SIP) technique was applied to trace active microorganisms. The absolute total abundance of 13C-PLFAs was much higher under eCO2 treatment. Most of the 13C-CO2 was incorporated into the 13C-PLFAs 18:2ω6,9 (fungi), 16:0 (general PLFA), 18:1ω9c (Gram-negative bacteria, G−) and i17:0 (Gram-positive bacteria, G+) via rhizodeposition from tomato under ambient CO2 (aCO2) and eCO2 treatments, suggesting similar responses of active microorganisms to different CO2 treatments. However, the fungi (characterized by the 13C-PLFA 18:2ω6,9) played a much more dominant role in the incorporation of root-derived C under eCO2. Actinomycetes, marked by the 13C-PLFA 10-Me-18:0, occurred only on labeling day 15 under the eCO2 treatment, indicating that the actinomycetes fed on both soil organic carbon and fresh rhizodeposition. It was indicated that eCO2 significantly affected microbial biomass and microbial community structures involved in the incorporation of 13C-CO2 via tomato root secretions, as supported by Adonis analysis and the Mantel test.

Zinc Deficiency, Plasma Fatty Acid Profile and Desaturase Activities in Hemodialysis Patients: Is Supplementation Necessary?

Background: Desaturation and elongation are critical processes in endogenous metabolic fatty acid pathways. Zinc (Zn) is a cofactor for desaturases and elongases enzymes. There is limited evidence regarding the relationships between biomarkers of Zn status, nutritional intake, plasma phospholipid fatty acid profile and clinical outcomes among patients undergoing hemodialysis (HD).Objective: To examine the relationships between dietary and serum levels of Zn and Cu/Zn ratio and to explore associations of these micronutrients with PUFA profile and estimated desaturase and elongase enzyme activities in serum phospholipids among HD patients.Methods: This study included 40 adult patients undergoing hemodialysis treatment. Repeated 24-h recalls were applied for dietary intake assessment. Serum concentration of Zn and Cu were determined using inductively coupled plasma mass spectrometry and fatty acid composition by gas-liquid chromatography. Desaturase and elongase activities were calculated from product-precursor fatty acid ratios.Results: Inadequate dietary Zn intake was found in 55% of HD patients. They all had serum Zn concentration below the reference value of 60 μg/dL (mean 38.8 ± 7.72 μg/dL). Adequate zinc intake was accompanied with significantly higher intake of energy, total fats, SFA, MUFA and proteins. There was no correlation between Zn serum status and Zn intake estimates. Serum Cu/Zn ratio was high, (2.76 ± 0.68), directly and significantly associated with HD period, CRP, BMI, VFA, and inversely with Kt/V, albumin, iron, and iPTH. The n-6/n-3 ratio in plasma phospholipids was elevated (12.25 ± 3.45) and patients with inadequate Zn intake had lower n-3 PUFA intake and status compared to those with adequate intake. Serum Zn concentrations were inversely correlated with linoleic/dihomo-γ-linolenic acid ratio (LA/DGLA) (p = 0.037), related to D6-desaturase activity (p = 0.033) and directly with DGLA relative abundances (p = 0.024). Cu status was inversely associated with EPA level (p = 0.03) and estimates of elongase activity (p = 0.001). Furthermore, positive relationship was found between the Cu/Zn ratio and determined elongase value (p = 0.01).Conclusion: Findings of this study underpin the high prevalence of Zn deficiency and inadequate n-3 PUFA intake and status among subjects undergoing HD. The results obtained indicate that the assessment of Zn status should be a standard parameter of nutritional status screening in HD patients while emphasizing the importance of Cu/Zn determination. Although further research is warranted, Zn and-n-3 PUFA supplementation in HD patients might be beneficial for the prevention and attenuation of adverse health outcomes

Shifts in Soil Structure, Biological, and Functional Diversity Under Long-Term Carbon Deprivation

Soil organic matter is composed of a variety of carbon (C) forms. However, not all forms are equally accessible to soil microorganisms. Deprivation of C inputs will cause changes in the physical and microbial community structures of soils; yet the trajectories of such changes are not clear. We assessed microbial communities using phospholipid fatty acid profiling, metabarcoding, CO2 emissions, and functional gene microarrays in a decade-long C deprivation field experiment. We also assessed changes in a range of soil physicochemical properties, including using X-ray Computed Tomography imaging to assess differences in soil structure. Two sets of soils were deprived of C inputs by removing plant inputs for 10 years and 1 year, respectively. We found a reduction in diversity measures, after 10 years of C deprivation, which was unexpected based on previous research. Fungi appeared to be most impacted, likely due to competition for scarce resources after exhausting the available plant material. This suggestion was supported by evidence of bioindicator taxa in non-vegetated soils that may directly compete with or consume fungi. There was also a reduction in copies of most functional genes after 10 years of C deprivation, though gene copies increased for phytase and some genes involved in decomposing recalcitrant C and methanogenesis. Additionally, soils under C deprivation displayed expected reductions in pH, organic C, nitrogen, and biomass as well as reduced mean pore size, especially in larger pores. However, pore connectivity increased after 10 years of C deprivation contrary to expectations. Our results highlight concurrent collapse of soil structure and biodiversity following long-term C deprivation. Overall, this study shows the negative trajectory of continuous C deprivation and loss of organic matter on a wide range of soil quality indicators and microorganisms.

Impacts of Decaying Aromatic Plants on the Soil Microbial Community and on Tomato Seedling Growth and Metabolism: Suppression or Stimulation?

This study provides insight into changes in the features of tomato seedlings growing in soils enriched with spearmint, peppermint, or rosemary leaves and into changes in the microbial communities of these soils used as seedbeds; an organic amendment was also applied as a positive control. While the soil microbial community flourished in the presence of all three aromatic plants, tomato growth was inhibited or stimulated depending on the plant that was used. More specifically, phospholipid fatty acid (PLFA) analysis showed an increase in the total microbial biomass and in the biomass of all the groups examined, except for actinobacteria, and changes in the microbial community structure, with Gram-negative bacteria and fungi being favoured in the mint treatments, in which the microbial biomass was maximized. Seedlings from the rosemary treatment were entirely inhibited; they were at the open-cotyledon stage throughout the experiment. Seedlings from the mint treatments were the heaviest, longest, and had the highest chlorophyll content and photosynthetic yield. Metabolomic analysis showed metabolism enhancement associated with both growth and priming in seedlings from the mint treatments and disruption of metabolic pathways in those from the rosemary treatment. There is a great potential for applying these aromatic plants as soil amendments and as either biostimulants of plant growth or as herbicides.

Characteristics and influencing factors of soil microbial communities in different subtropical forest stands in Jinyun Mountain, Southwest China

BackgroundAn insight into the soil microbial functions and spatial distribution of soil resources is an important basis for evaluating and managing plant growth in subtropical forests. Soil samples were collected from five forest stands in Jinyun Mountain Natural Reserve (JMNR) in Chongqing located at the Three Gorges Reservoir area: Gordonia acuminata evergreen broad-leaved forest (GAEBF), Cunninghamia lanceolata forest (CLF), Phyllostachys pubescens forest (PPF), coniferous and broad-leaved mixed forest (CBLMF) dominated by Pinus massoniana and Gordonia acuminata (PM&GA), and the CBLMF dominated by Pinus massoniana and Symplocos setchuensis (PM&SS). Combined with phospholipid fatty acid (PLFA) analysis and Sherlock microbial identification system (MIS), the structure of soil microbial communities in different forest stands was investigated.ResultsThe results showed that the PLFAs of soil microorganisms under the forest in JMNR have a high diversity. The PLFA dominance values of the five stands were 16:0, 19:0 cyclo ω7c, 18:0, 15:0 iso and 16 :0 10-methyl. Furthermore, soil microorganisms are dominated by Gram-negative bacteria, and the PLFAs content of soil bacteria in different forest stands is higher than that of fungi PLFAs. Regarding the phospholipid fatty acid biomarkers, the two CBLMFs are the highest, followed by CLF and GAEBF and PPF is the least. Moreover, the proportion of microorganisms in the soil of different forest stands varies. Among them, MP&SS has the highest gram-negative bacteria, gram-positive bacteria, actinomycetes and fungi.ConclusionsRDA analysis shows that the main influencing factors of PLFAs in the soil of different forest stands are the content of iron oxide, aluminium oxide, organic matter and total nitrogen in the soil, which are considered to be able to reflect the soil nutrient status of JMNR effectively.

Exogenous Antioxidants Impact on UV-Induced Changes in Membrane Phospholipids and the Effectiveness of the Endocannabinoid System in Human Skin Cells

Natural antioxidants effectively counteract changes caused by UV radiation in human skin cells. However, their action is limited due to their lipo/hydrophilicity. Therefore, the aim of this study was to analyze the mutual protective action of hydrophilic ascorbic acid and partially lipophilic rutin against UVA/UVB-induced changes in membranes phospholipid and endocannabinoid system in keratinocytes and fibroblasts. Obtained results clearly showed that, despite the stronger antioxidant properties of ascorbic acid, the lipid membranes were more effectively protected against UV-induced oxidation by rutin, including changes in phospholipid fatty acid levels, prevention against reactive aldehydes formation and endocannabinoids degradation. Ascorbic acid more strongly prevented UV-induced endocannabinoid receptors expression in fibroblasts, especially CB1. However, the combined action of used antioxidants resulted in the greatest cytoprotective effect, which was evident in the inflammatory marker TNFα down-regulation and increased cell viability following cell irradiation. The applied mixture of antioxidants showed a stronger protective in relation to membrane phospholipids in keratinocytes and in the endocannabinoid system in fibroblasts. In conclusion, it can be suggested that combined antioxidant capacities of ascorbic acid and rutin protects against lipid peroxidation but also decreases the UV-induced inflammation by direct interaction with the endocannabinoid system, thus increasing skin cell viability.