Leaf carbon chemistry effectively manipulated soil microbial profiles and induced metabolic adjustments under different revegetation types in the loess Plateau, China.

Microorganisms are essential components of underground life systems and drive elemental cycling between plants and soil. Yet, in the ecologically fragile Loess Plateau, scant attention has been paid to the response of microbial communities to organic carbon (C) chemistry of both leaves and soils under different revegetation conditions, as well as subsequent alternation in their C metabolic functions. Here, Fourier transform infrared (FTIR) spectrum, amplicon sequencing of 16S rRNA and ITS, and temporal incubation with Biolog-Eco 96 plates were combined to explore the vegetative heterogeneity of microbial community properties and metabolic functions, as well as their regulatory mechanisms in three typical revegetation types including Robinia pseudoacacia L. (RF), Caragana korshinskii KOM. (SL), and abandoned grassland (AG). We observed higher bacterial-to-fungal ratios (B: F = 270.18) and richer copiotrophic bacteria (Proteobacteria = 33.08%) in RF soil than those in AG soil, suggesting that microbes were dominated by r-strategists in soil under RF treatment, which is mainly related to long-term priming of highly bioavailable leaf C (higher proportion of aromatic and hydrophilic functional groups and lower hydrophobicity). Conversely, microbial taxa in AG soil, which was characterized by higher leaf organic C hydrophobicity (1.39), were dominated by relatively more abundant fungi (lower B: F ratio = 149.49) and oligotrophic bacteria (Actinobacteria = 29.30%). The co-occurrence network analysis showed that microbial interactive associations in RF and AG soil were more complex and connective than in SL soil. Furthermore, Biolog-Eco plate experiments revealed that microorganisms tended to utilize labile C compounds (carbohydrates and amino acids) in RF soil and resistant C compounds (polymers) in AG soil, which were consistent with the substrate adaptation strategies of predominant microbial trophic groups in different revegetation environments. Meanwhile, we observed greater microbial metabolic activity and diversity advantages in RF vegetation. Collectively, we suggest that besides the nutrient variables in the leaf-soil system, the long-term regulation of the microbial community by the C chemistry of the leaf sequentially alters the microbial metabolic profiles in a domino-like manner. RF afforestation is more conducive to restoring soil microbial fertility (including microbial abundance, diversity, interactive association, and metabolic capacity). Our study potentially paves the way for achieving well-managed soil health and accurate prediction of C pool dynamics in areas undergoing ecological restoration of the Loess Plateau.

Seasonality regulates the effects of acid rain on microbial community in a subtropical agricultural soil of Southern China.

Acid rain alters soil carbon (C) cycling by influencing the soil microbial community structure and functions. However, the response of soil microbial communities to acid rain with time and underlying mechanisms are still poorly understood. Herein, we conducted a one-year intact soil core experiment to investigate the temporal changes of soil microbial community composition and C sources metabolism under acid rain (pH 5.0, pH 4.0, and pH 3.0) in an agricultural soil of southern China. We found that pH 3.0 acid rain increased the total, bacterial, gram-positive bacterial, and actinomycetal PLFAs at the early stage, but this effect diminished with time. Conversely, the gram-negative bacterial PLFAs contents were reduced under pH 3.0 acid rain at the later stage. Interestingly, pH 5.0 acid rain increased the total, bacterial, gram-positive bacterial, and actinomycetal PLFAs contents at the later stage. In addition, pH 3.0 and pH 5.0 acid rain treatments accordingly altered the soil microbial community structure at the early and later stage. However, acid rain did not change the microbial C sources utilization pattern. The principal response curve analysis revealed that the seasonal variation exerted a greater effect on the overall variance of soil microbial community structure than the acidity of acid rain. Our results demonstrate the asynchronous response of soil microbial community structure and function, which implies that the microbial functional redundancy may exist in the subtropical agricultural soil under acid rain.

Low-intensity alternating ventilation achieves effective humification during food waste composting by enhancing the intensity of microbial interaction and carbon metabolism.

Vertical static composting is an efficient and convenient technology for the treatment of food waste. Exploring the impact of oxygen concentration levels on microbial community structure and functional stability is crucial for optimizing ventilation technology. This study set three experimental groups with varying ventilation intensities based on self-made alternating ventilation composting reactor (AL2: 0.2 L kg-1 DM·min-1; AL4: 0.4 L kg-1 DM·min-1; AL6: 0.6 L kg-1 DM·min-1) to explore the optimal alternating ventilation rate. The results showed that the cumulative ammonia emission of AL2 group reduced by 25.13% and 12.59% compared to the AL4 and AL6 groups. The humification degree of the product was 1.18 times and 1.25 times higher than the other two groups. AL2 increased the relative abundance of the core species Saccharomonospora, thereby strengthening microbial interaction. Low-intensity alternating ventilation increased the carbon metabolism levels, especially aerobic_chemoheterotrophy, carbohydrate and lipid metabolism. However, it simultaneously reduced nitrogen metabolism. Structural equation model analysis demonstrated that alternating low-intensity ventilation effectively regulated both microbial diversity (0.81, p < 0.001) and metabolism (0.81, p < 0.001) by shaping the composting environment. This study optimized the intensity of alternating ventilation and revealed the regulatory mechanism of community structure and metabolism. This study provides guidance for achieving efficient and low-consumption composting.

The maturity, humus content, and microbial metabolic function of sheep manure compost on the Qinghai-Tibet Plateau can be significantly improved by reducing the moisture content.

The Qinghai-Tibet Plateau (QTP) is characterized by an extreme hypoxia, which may lead to lack of sufficient oxygen for compost production, and thus seriously affecting the compost quality. The moisture content (MC) has a direct effect on the oxygen content of composting pile. At present, the research on the optimum moisture content of compost production on the QTP is still lacking. This study aimed to investigate the influences of MC on fermentation quality of sheep manure composting on the QTP and to further analyze the changes of microbial metabolic function and enzyme activity under different MC. Composting experiment with low MC (45%) and conventional MC (60%) was conducted in both summer and autumn. The results showed that the composting efficiency of 45% MC was better than 60% in both seasons, which was mainly manifested as longer high-temperature period (summer:16 d vs 14 d, autumn: 7 d vs 2 d), higher germination index (summer:136.1% vs 128.6%, autumn:103.5% vs 81.2%), and more humus synthesis (summer:159.8 g/kg vs 151.2 g/kg, autumn:136.1 k/kg vs 115.5 k/kg). The 45% MC can improve microbial metabolism, including increasing the abundance of functional genes involved in carbohydrate metabolism, amino acid metabolism, and nucleotide metabolism and improving the activities of cellulase, ß-glucosidase, protease, polyphenol oxidase, and peroxidase. In conclusion, 45% MC can improve the fermentation efficiency and products quality of sheep manure compost on QTP.

Regulatory effects of different anionic surfactants on the transformation of heavy metal fractions and reduction of heavy metal resistance genes in chicken manure compost.

Surfactants are widely used as a passivating agent in heavy metal passivation process, but their effect on transformation of heavy metal fraction and reduction of heavy metal resistance genes (MRGs) in composting process is still unknown. The aim of this study was to compare the effects of two anionic surfactants (rhamnolipid and sodium dodecyl sulfate) on heavy metal passivation and resistance gene reduction in chicken manure composting. The results showed that the addition of surfactant can effectively enhance degradation of organic matter (OM). Both surfactants could effectively reduce the bioavailability of heavy metals (HMs) and the relative abundance of resistance genes, especially rhamnolipids. The potential functional bacteria affecting heavy metal passivation were identified by the changes of microbial community. Redundancy analysis (RDA) showed that protease (PRT) activity was the key factor affecting the fractions of the second group of HMs including ZnF1, CuF1, CuF2, PbF1 and PbF3. These findings indicate that addition of anionic surfactants can reduce the bioavailability of HMs and the abundance of resistance genes in compost products, which is of guiding significance for the reduction of health risks in the harmless utilization of livestock and poultry manure.

Metagenome-Assembled Genomes From Pyropia haitanensis Microbiome Provide Insights Into the Potential Metabolic Functions to the Seaweed.

Pyropia is an economically important edible red alga worldwide. The aquaculture industry and Pyropia production have grown considerably in recent decades. Microbial communities inhabit the algal surface and produce a variety of compounds that can influence host adaptation. Previous studies on the Pyropia microbiome were focused on the microbial components or the function of specific microbial lineages, which frequently exclude metabolic information and contained only a small fraction of the overall community. Here, we performed a genome-centric analysis to study the metabolic potential of the Pyropia haitanensis phycosphere bacteria. We reconstructed 202 unique metagenome-assembled genomes (MAGs) comprising all major taxa present within the P. haitanensis microbiome. The addition of MAGs to the genome tree containing all publicly available Pyropia-associated microorganisms increased the phylogenetic diversity by 50% within the bacteria. Metabolic reconstruction of the MAGs showed functional redundancy across taxa for pathways including nitrate reduction, taurine metabolism, organophosphorus, and 1-aminocyclopropane-1-carboxylate degradation, auxin, and vitamin B12 synthesis. Some microbial functions, such as auxin and vitamin B12 synthesis, that were previously assigned to a few Pyropia-associated microorganisms were distributed across the diverse epiphytic taxa. Other metabolic pathways, such as ammonia oxidation, denitrification, and sulfide oxidation, were confined to specific keystone taxa.

Soil salinity regulation of soil microbial carbon metabolic function in the Yellow River Delta, China.

The ecological consequences of soil salinization, one of the major causes of soil degradation worldwide, on soil carbon (C) emissions are well known, but less is known about the related microbial C metabolic function. We conducted laboratory incubation experiments on soil samples under a salt gradient at four levels (non-saline, low, medium, and high salinity soils) from coastal saline-alkaline soil of the Yellow River Delta, China, to assess the role of soil salinity in regulating C emissions and microbial abundance. We also evaluated the associations between salt content and the read number of microbial C metabolism genes by determining the soil metagenomes. We found that soil salinity was negatively related to soil C, nitrogen (N) content, C emissions, bacterial gene copy number, and the relative abundances of Actinobacteria, Thermoleophilia, and Betaproteobacteria, but positively related to the C/N ratio and the relative abundance of Gemaproteobacteria and Halobacteria. Increases in soil salinity correlated with decreases in carbohydrate metabolism and gene abundances of glycosyl transferases and glycoside hydrolases based on the metagenomic data. In contrast, the enzyme active genes of carbohydrate esterases and auxiliary activities were positively related to soil salinity. This study provides a clear understanding of the response of soil microbial communities and their C metabolic functions to soil salinity. We offer evidence that soil salinity has significant effects on microbial communities and soil C metabolic functions, resulting in an overall negative effect on soil C emissions.

Metaproteomics reveals persistent and phylum-redundant metabolic functional stability in adult human gut microbiomes of Crohn's remission patients despite temporal variations in microbial taxa, genomes, and proteomes.

BACKGROUND: The gut microbiome plays a fundamental role in the human host's overall health by contributing key biological functions such as expanded metabolism and pathogen defense/immune control. In a healthy individual, the gut microbiome co-exists within the human host in a symbiotic, non-inflammatory relationship that enables mutual benefits, such as microbial degradation of indigestible food products into small molecules that the host can utilize, and enhanced pathogen defense. In abnormal conditions, such as Crohn's disease, this favorable metabolic relationship breaks down and a variety of undesirable activities result, including chronic inflammation and other health-related issues. It has been difficult, however, to elucidate the overall functional characteristics of this relationship because the microbiota can vary substantially in composition for healthy humans and possibly even more in individuals with gut disease conditions such as Crohn's disease. Overall, this suggests that microbial membership composition may not be the best way to characterize a phenotype. Alternatively, it seems to be more informative to examine and characterize the functional composition of a gut microbiome. Towards that end, this study examines 25 metaproteomes measured in several Crohn's disease patients' post-resection surgery across the course of 1 year, in order to examine persistence of microbial taxa, genes, proteins, and metabolic functional distributions across time in individuals whose microbiome might be more variable due to the gut disease condition. RESULTS: The measured metaproteomes were highly personalized, with all the temporally-related metaproteomes clustering most closely by individual. In general, the metaproteomes were remarkably distinct between individuals and to a lesser extent within individuals. This prompted a need to characterize the metaproteome at a higher functional level, which was achieved by annotating identified protein groups with KEGG orthologous groups to infer metabolic modules. At this level, similar and redundant metabolic functions across multiple phyla were observed across time and between individuals. Tracking through these various metabolic modules revealed a clear path from carbohydrate, lipid, and amino acid degradation to central metabolism and finally the production of fermentation products. CONCLUSIONS: The human gut metaproteome can vary quite substantially across time and individuals. However, despite substantial intra-individual variation in the metaproteomes, there is a clear persistence of conserved metabolic functions across time and individuals. Additionally, the persistence of these core functions is redundant across multiple phyla but is not always observable in the same sample. Finally, the gut microbiome's metabolism is not driven by a set of discrete linear pathways but a web of interconnected reactions facilitated by a network of enzymes that connect multiple molecules across multiple pathways.