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Metabolic pathways for N and inositol P metabolism and other types of metabolism related to organic matter turnover. Metabolic map and relative abundances of each type of metabolism. Blue bars represent the total relative abundances in four treatments and the heatmap indicates the relative abundance in each treatment. In the metabolic map, green blocks indicate carbohydrate metabolism, yellow blocks indicate amino acid metabolism, red blocks indicate energy metabolism, and white blocks indicate other types of metabolism such as lipid metabolism, nucleotide metabolism, metabolism of cofactors and vitamins, and biosynthesis of other secondary metabolites
Source publication
We investigated the types of metabolism and genes involved with N and P reactions, and SOM turnover as well as their interaction was monitored in an apple orchard by metagenome sequencing. The field experiment included plots with and without a cover crop but with weed control, and two subplots with or without chemical fertilizer. The relative abund...
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Background:
Most organisms cannot be cultivated, as they live in unique ecological conditions that cannot be mimicked in the lab. Understanding the functionality of those organisms' genes and their interactions by performing large-scale measurements of transcription levels, protein-protein interactions or metabolism, is extremely difficult and, in...
Citations
... The main processes involved in the nitrogen cycle by microorganisms include nitrogen fixation, nitrate assimilation reduction, nitrate allotropic reduction, nitrification and denitrification processes, and biosynthesis and degradation of organic nitrogen 48,49 . The nitrogen cycling processes of returned straw of interest in this study mainly include the nitrogen fixation process, nitrification, assimilative nitrate reduction, allotropic nitrate reduction, and nitrate assimilation, and its functional genes also include regulatory-related functional genes associated with genes encoding related functional proteins. ...
Straw is an important source of organic fertilizer for soil enrichment, however, the effects of different nitrogen(N) application rates and depths on straw decomposition microorganisms and carbon and nitrogen cycling under full straw return conditions in cool regions of Northeast China are not clear at this stage. In this paper, we applied macro-genome sequencing technology to investigate the effects of different N application rates (110 kg hm⁻², 120 kg hm⁻², 130 kg hm⁻², 140 kg hm⁻², 150 kg hm⁻²) and depths (0–15 cm, 15–30 cm) on straw decomposing microorganisms and N cycling in paddy fields in the cool zone of Northeast China. The results showed that (1) about 150 functional genes are involved in the carbon cycle process of degradation during the degradation of returned straw, of which the largest number of functional genes are involved in the methane production pathway, about 42, the highest abundance of functional genes involved in the citric acid cycle pathway. There are 22 kinds of functional genes involved in the nitrogen cycle degradation process, among which there are more kinds involved in nitrogen fixation, with 4 kinds. (2) High nitrogen application (150 kg hm⁻²) inhibited the carbon and nitrogen conversion processes, and the abundance of straw-degrading microorganisms and nitrogen-cycling functional genes was relatively high at a nitrogen application rate of 130 kg hm⁻². (3) Depth-dependent heterogeneity of the microbial community was reduced throughout the vertical space. At 71 days of straw return, the nitrogen cycling function decreased and some carbon functional genes showed an increasing trend with the increase of straw return depth. The nitrogen cycle function decreased with the increase of straw returning depth. The microbial community structure was best and the abundance of functional genes involved in the nitrogen cycling process was higher under the conditions of 0–15 cm of returning depth and 130 kg hm⁻² of nitrogen application.
... Additionally, functional characteristics in bacterial and fungal communities were predicted using the PIC-RUSt2 tool. In accordance with the Kyoto Encyclopedia of Genes and Genomes (KEGG) (Zheng et al. 2019), the predicted functions were classified. Random forest analysis is appropriate for data from microbial communities with discrete and discontinuous distributions (Hooper et al. 2000;Ren et al. 2020). ...
Aims
Crop rotation, especially with legumes, is believed to boost soil organic carbon (SOC). However, studies in Northeast China indicated long-term maize-soybean rotation doesn’t improve SOC more than maize and soybean monocropped. Further study is needed to explore why rotation system don’t significantly increase SOC under conventional management.
Methods
Samples were collected from a 30-year field experiment to assess soil amino sugars for quantifying microbial necromass carbon (MNC), employ pyrolysis-gas chromatography mass spectrometry (Py-GC/MS) for detailed analysis of soil organic matter (SOM) chemical composition, and utilize high-throughput sequencing to depict soil microbial community structure and functions.
Results
Maize monocropped has the highest SOC, followed by maize-soybean rotation, and soybean monocropped is the lowest. The lower SOC content in the maize-soybean rotation system, compared to maize monocropped, could be attributed to specific factors: (i) increased Ascomycetes phylum abundance affecting SOC degradation; (ii) negative correlation between Mortierellomycota phylum and MNC; (iii) elevated N-acetyl-glucosaminidase activity, indicating increased SOC decomposition. Despite lower SOC, the maize-soybean rotation system showed enhanced SOM stability with: (i) a higher fungal-derived carbon (C) to SOC ratio, indicating effective fungal-derived C enrichment; and (ii) Py-GC/MS analysis revealing greater abundance of stable SOM compounds like nitrogen-containing compounds and aromatic hydrocarbons than maize and soybean monocropped.
Conclusion
This study demonstrated that the maize-soybean rotation system, by altering soil microbial communities, intensifies the decomposition of SOC, resulting in lower SOC content than continuous maize monocropped. However, the remaining SOM in this system exhibits greater stability, which is more conducive to long-term C sequestration.
... The soil nutrient framework could be beneficial to tree growth and fruit development. Many studies have demonstrated that intercropping in orchards promotes soil SOM content and SOM degradation-related enzymes and enhances N and P availability by increasing N-and P-related enzyme activities, resulting in an increase in fruit production (Cui et al., 2015;Gao et al., 2019;Liu et al., 2019;Zheng et al., 2019). These effects could not be decreased, although the mixed intercropping with aromatic plants could lead to a decrease in microbial biomass, core OTUs, abundance, network complexity and stability compared with monoplanting due to their litter chemical diversity through interspecific interactions of aromatic plants, which often contain various unique organic components, such as ocimene, linalool, patuletin, and menthol (Wahbi et al., 2016;Mao et al., 2017;Misra et al., 2019;Tang et al., 2021). ...
Intercropping systems improve the soil nutrient cycle through microbial community activity and then land productivity. However, their interactions mechanism underlying that the mixed aromatic plant species intercropping regulate the soil microbiome and nutrient cycling on the perennial woody orchard is still uncovered. We designed treatments with 0, 1, and 3 aromatic plant species intercropped in two scenarios of clean tillage (T model, T1, T2, and T4) and natural grass (G model, G1, G2, and G4) in apple orchards, and investigated intercrops effects at the branch growing stage (BGS) and fruit development stage (FDS), respectively. Compared with T model, G model in FDS increased alpha diversity of bacterial community and Shannon index fungal community, the relative abundance of dominant taxa, such as Acidobacteria and Actinobacteria, and also the numbers of up and down-regulated OTUs, the most of indices of co-occurrence network in both bacterial and fungal community, and then improved invertase activity and available nitrogen content. Relative to G1, G2 and G4 reduced diversity bacterial community in FDS, the relative abundance of dominant taxa, the most of indices of co-occurrence network, and then improved soil invertase activity and total phosphorus content in soil. Moreover, Shannon index of fungal community, the altered number of OTUs and the most indices of co-occurrence network were higher in G4 than those in G2 in FDS. These changes above in FDS were more markedly than those in BGS, suggesting that chemical diversity of litter from mixed species of aromatic plants in natural grass scenario led to diversity, complexity, and stability of soil microbial community and then nutrient cycling. It provided a novel highlight and method to modulate biocenosis and then improve the soil nutrient cycling.
... In addition, Pearson's correlation analysis was used to determine the relationship between alpha diversity and environmental factors and Mantel test was used to examine the relationship between beta diversity and environmental factors. Mantel tests, heatmaps, PCoA, redundancy analysis (RDA), and network analysis were performed using the "vegan" package in R v3.6.3 (Bargaz et al., 2017;Zheng et al., 2019). ...
Intercropping between sugarcane and soybean is widely used to increase crop yield and promote the sustainable development of the sugarcane industry. However, our understanding of the soil microenvironment in intercropping systems, especially the effect of crop varieties on rhizosphere soil bacterial communities, remains poor. We selected two excellent sugarcane cultivars, Zhongzhe1 (ZZ1) and Zhongzhe9 (ZZ9), from Guangxi and the local soybean variety GUIZAO2 from Guangxi for field interplanting experiments. These two cultivars of sugarcane have good drought resistance. Rhizosphere soil samples were collected from the two intercropping systems to measure physicochemical properties and soil enzyme activities and to extract total soil DNA for high-throughput sequencing. We found that the diversity of the rhizosphere bacterial community was significantly different between the two intercropping systems. Compared with ZZ1, the ZZ9 intercropping system enriched the nitrogen-fixing bacteria, increasing the available nitrogen content by 18% compared with that with ZZ1. In addition, ZZ9 intercropping with soybean formed a more compact rhizosphere environment than ZZ1, thus providing favorable conditions for sugarcane growth. These results provide guidance for the sugarcane industry, especially for the management of sugarcane and soybean intercropping in Guangxi, China.
... Therefore, improving potato crop productivity and quality can address the nutritional needs of a rising population (Dahal et al., 2018;Muleta and Aga, 2019). Various methods, such as the use of plant residues, chemical fertilizers, soil conditioners and beneficial microbial products, have been utilized to improve potato yield (Paul et al., 2016;Zheng et al., 2019). Using biocontrol agents is of great interest as this approach is eco-friendly and conforms with sustainable agricultural practices (Khan et al., 2019). ...
The effect of a microbial consortium‐based (MCB) biocontrol product, composed of Bacillus subtilis, Trichoderma harzianum strain and diatomaceous earth as a carrier, on potato yield, and potential modes of action for its effect were investigated. The MCB product (300 kg ha⁻¹) was added to furrows in which the potato seed tubers each year for 3 years (2016, 2017 and 2018), while potato planting without the MCB product treatment served as the control. A metagenomic analysis indicated that bacterial phylotypes dominated the microbial community, with a relatively small contribution of archaea and fungal taxa. The relative abundance of beneficial bacterial taxa increased significantly in response to the MCB product treatment. Notably, a higher relative abundance of bacterial taxa with carbon fixation, carbon‐degrading and nitrogen metabolism properties were observed in the MCB product‐treated potato rhizosphere. This was also reflected in the identification of a greater abundance of genes encoding enzymes involved in nitrogen metabolism, carbon fixation and carbon degradation pathways in the conducted metagenomic analysis. The greater relative abundance of these beneficial bacterial taxa in the rhizosphere of MCB product‐treated plots, as well as the higher abundance of genes associated with the indicated cellular processes, were associated with an increase in tuber yield. The observed changes in microbial community structure at an early stage of tuber development appears to have a beneficial impact on tuber yield.
... It is well established that there is great variability of microbial taxonomic and functional composition across contrasting ecological contexts [28,29], which highlights that the ecophysiological importance of specific microbial groups can vary across contrasting ecological environments [30]. Yet the importance of a given species in the degradation network is not a given. ...
Background
Microbial-driven decomposition of plant residues is integral to carbon sequestration in terrestrial ecosystems. Actinobacteria , one of the most widely distributed bacterial phyla in soils, are known for their ability to degrade plant residues in vitro. However, their in situ importance and specific activity across contrasting ecological environments are not known. Here, we conducted three field experiments with buried straw in combination with microcosm experiments with ¹³ C-straw in paddy soils under different soil fertility levels to reveal the ecophysiological roles of Actinobacteria in plant residue decomposition.
Results
While accounting for only 4.6% of the total bacterial abundance, the Actinobacteria encoded 16% of total abundance of carbohydrate-active enzymes (CAZymes). The taxonomic and functional compositions of the Actinobacteria were, surprisingly, relatively stable during straw decomposition. Slopes of linear regression models between straw chemical composition and Actinobacterial traits were flatter than those for other taxonomic groups at both local and regional scales due to holding genes encoding for full set of CAZymes, nitrogenases, and antibiotic synthetases. Ecological co-occurrence network and ¹³ C-based metagenomic analyses both indicated that their importance for straw degradation increased in less fertile soils, as both links between Actinobacteria and other community members and relative abundances of their functional genes increased with decreasing soil fertility.
Conclusions
This study provided DNA-based evidence that non-dominant Actinobacteria plays a key ecophysiological role in plant residue decomposition as their members possess high proportions of CAZymes and as a group maintain a relatively stable presence during plant residue decomposition both in terms of taxonomic composition and functional roles. Their importance for decomposition was more pronounced in less fertile soils where their possession functional genes and interspecies interactions stood out more. Our work provides new ecophysiological angles for the understanding of the importance of Actinobacteria in global carbon cycling.
... In the mangrove ecosystem, the abundance of the ODAS gene was extremely high; six and seven of the top 10 genes belong to this group in wet and dry seasons, respectively (Fig. 3). This finding is consistent with those of other ecosystem surveys (Tu et al., 2017;Zheng et al., 2019). Thus, organic nitrogen metabolism is active in the mangrove ecosystem and provides energy for other important life activities of microorganisms. ...
The amount of nitrogen compounds discharged into the natural environment has increased drastically due to frequent human activities and led to worsening pollution. The mangrove ecosystem can remove nitrogen pollution, in this regard, few studies had focused on the relationship among nitrogen cycling genes, environmental factors, and taxonomic composition. In this study, shotgun metagenomic sequencing and quantitative polymerase chain reaction were used to understand the nitrogen cycle in the subtropical mangrove ecosystem in the Beibu Gulf of China. Eight nitrogen cycling pathways were annotated. Nitrogen metabolism activities were significantly higher in the wet season than those in the dry season. The most abundant genes were those related to the synthesis and degradation of organic nitrogen, followed by the genes involved in nitrate reduction (denitrification, dissimilation/assimilation nitrate reduction). Furthermore, dissimilation nitrate reduction was the main nitrate reduction pathway. Desulfobacterales plays an important role in nitrogen cycling and contributes 12% of the genes of nitrogen pathways on average; as such, a strong coupling relationship exists among nitrogen cycling, sulfur cycling, and carbon cycling in the mangrove ecosystem. Nitrogen pollution in the mangrove wetland can be efficiently alleviated by nitrate reduction of Desulfobacterales. Nevertheless, only 50% of genes can be matched among the known species, suggesting that many unknown microorganisms in the mangrove ecosystem can perform nitrogen cycling. Total phosphorus, available iron, and total organic carbon are the key environmental factors that influence the distribution of nitrogen cycling genes, related pathways, and the taxonomic composition. Our study clearly illustrates how the mangrove ecosystem mitigates nitrogen pollution through Desulfobacterales. This finding could provide a research reference for the whole nitrogen cycling in the mangrove ecosystem.
... EC: 1.7.7.1, EC: 1.7.2.2), nitrate reductase (EC: 1.7.99.4), and nitric oxide reductase (EC: 1.7.2.5) were promoted (Fig. 10). It was in agreement with previous studies showing that N plus straw increased the abundance of nirB, nirD, and norB (Fracetto et al. 2017;Zheng et al. 2019), but Fracetto et al. (2017) found N plus straw also increased the abundance of nirK, nirS, and nosZ. In the present study, the relative abundance of key enzyme genes related to nitrification and denitrification in the N300+BC treatment was sim For most microorganisms, assimilation of ammonia is accomplished through the synthesis of glutamine and glutamate Fig. 8 An overall of N-transforming processes in soil, including the processes of nitrification (purple), denitrification (yellow), N fixation (red), nitrite reduction (green), glutamate synthesis (blue), and carbamoyl phosphate synthesis (pink) Fig. 7 Relative abundances of the top 21 orders as affected by different treatments. ...
Biochar has been widely accepted as a soil amendment to improve nitrogen (N) use efficiency, but the effect of biochar on N transformation metabolic pathways is unclear. A field experiment was conducted to evaluate the effect of biochar on N transformation in drip-irrigated cotton field. Four treatments were set as (1) no N fertilization (CK), (2) N fertilizer application at 300 kg ha−1 (N300), (3) N fertilizer application plus cotton straw (N300+ST), and (4) N fertilizer application plus cotton straw–derived biochar (N300+BC). Result showed that soil total N in N300+ST and N300+BC was 16.3% and 24.9% higher than that in N300, respectively. Compared with N300+ST, the nitrate N (NO3−-N) in N300+BC was significantly increased. Acidolyzable N and non-acidolyzable N in N300+ST and N300+BC were higher than those in CK and N300, while N300+BC performed better than N300+ST. Furthermore, the N fertilizer use efficiency of cotton in N300+ST and N300+BC was 15.1% and 23.2% higher than that in N300, respectively. Both N fertilizer incorporations with straw and biochar significantly altered the microbial community structures and N metabolic pathways. Genes related to denitrification and nitrate reduction in N300+ST were higher than those in N300, and N300+BC significantly increased nitrification and glutamate synthesis genes. Therefore, N fertilizer application plus cotton straw–derived biochar changed the microbial community composition, increased nitrification and glutamate synthesis enzyme genes which were beneficial to the accumulation of soil N content, and improved soil N retention capacity thus to increase N fertilizer use efficiency.
... A nearest-neighbor algorithm matched the relative abundance of our 16S rRNA gene sequences to the Kyoto Encyclopedia of Genes and Genomes (KEGG) microbial genetic database (updated October 2018) with a 97% identity cutoff to infer the metagenomic content of the bacteria(Iwai et al., 2016). Ninetyeight orthologs that are likely involved in the processing of lignin, cellulose, and hemicellulose(Kumar et al., 2018;Santos, Sarmento, de Miranda, Henrique-Silva, & Logares, 2019;Scully et al., 2013;Zheng et al., 2019) were selected for further analysis. MANOVAs were conducted on the relative abundance of the KEGG pathways, and representative orthologs present between catfish species, gut regions, and submerged wood, with an FDR correction of <0.05. ...
Neotropical wood‐eating catfishes (family Loricariidae) can occur in diverse assemblages with multiple genera and species feeding on the same woody detritus. As such, they present an intriguing system in which to examine the influence of host species identity on the vertebrate gut microbiome as well as to determine the potential role of gut bacteria in wood digestion. We characterized the gut microbiome of two co‐occurring catfish genera and four species: Panaqolus albomaculatus , Panaqolus gnomus , Panaqolus nocturnus, and Panaque bathyphilus , as well as that of submerged wood on which they feed. The gut bacterial community did not significantly vary across three gut regions (proximal, mid, distal) for any catfish species, although interspecific variation in the gut microbiome was significant, with magnitude of interspecific difference generally reflecting host phylogenetic proximity. Further, the gut microbiome of each species was significantly different to that present on the submerged wood. Inferring the genomic potential of the gut microbiome revealed that the majority of wood digesting pathways were at best equivalent to and more often depleted or nonexistent within the catfish gut compared to the submerged wood, suggesting a minimal role for the gut microbiome in wood digestion. Rather, these fishes are more likely reliant on fiber degradation performed by microbes in the environment, with their gut microbiome determined more by host identity and phylogenetic history.
Understanding the stoichiometry of extracellular enzymes in soil, particularly in relation to nutrient acquisition (e.g., carbon, nitrogen, phosphorus), provides valuable insights into microorganisms’ resource requirements. This study investigates the metabolic constraints of soil microorganisms in response to different growth stages of apple trees under various soil management practices. A 14-year long-term experiment with a split-plot design was conducted, where the main plots received different cover crop treatments (bare vs. cover crop), and subplots were subjected to four fertilizer treatments (CK, M, NPK, MNPK). The significant main and interactive effects of cover crops, fertilizer treatment, and growth period on soil nutrients were observed (p < 0.001). Both cover crop and fertilizer treatments significantly increased the soil organic matter content, with implications for orchard resilience to drought. However, the cover factor alone did not notably influence soil carbon–nitrogen ratios or microbial communities. Microbial carbon limitations were driven by soil water dynamics and microbial biomass, while microbial phosphorus limitations were closely linked to total nitrogen levels. The results underscore the combination of cover crops and MNPK fertilizer-enhanced soil nutrient levels and enzyme activities, mitigating microbial carbon and phosphorus limitations. These findings suggest practical strategies for optimizing fertilization practices to improve soil fertility and address nutrient constraints in orchard ecosystems.
