Robust, Precise, and Deep Proteome Profiling Using a Small Mass Range and Narrow Window Data-Independent-Acquisition Scheme.

In recent years, a plethora of different data-independent acquisition methods have been developed for proteomics to cover a wide range of requirements. Current deep proteome profiling methods rely on fractionations, elaborate chromatography, and mass spectrometry setups or display suboptimal quantitative precision. We set out to develop an easy-to-use one shot DIA method that achieves high quantitative precision and high proteome coverage. We achieve this by focusing on a small mass range of 430-670 m/z using small isolation windows without overlap. With this new method, we were able to quantify >9200 protein groups in HEK lysates with an average coefficient of variance of 3.2%. To demonstrate the power of our newly developed narrow mass range method, we applied it to investigate the effect of PGC-1α knockout on the skeletal muscle proteome in mice. Compared to a standard data-dependent acquisition method, we could double proteome coverage and, most importantly, achieve a significantly higher quantitative precision, as compared to a previously proposed DIA method. We believe that our method will be especially helpful in quantifying low abundant proteins in samples with a high dynamic range. All raw and result files are available at massive.ucsd.edu (MSV000092186).

Specific amino acid changes correlate with pathogenic flavobacteria.

Flavobacterium is a genus of microorganisms living in a variety of hosts and habitats across the globe. Some species are found in fish organs, and only a few, such as Flavobacterium psychrophilum and Flavobacterium columnare, cause severe disease and losses in fish farms. The evolution of flavobacteria that are pathogenic to fish is unknown, and the protein changes accountable for the selection of their colonization to fish have yet to be determined. A phylogenetic tree was constructed with the complete genomic sequences of 208 species of the Flavobacterium genus using 861 softcore genes. This phylogenetic analysis revealed clade CII comprising nine species, including five pathogenic species, and containing the most species that colonize fish. Thirteen specific amino acid changes were found to be conserved across 11 proteins within the CII clade compared with other clades, and these proteins were enriched in functions related to replication, recombination, and repair. Several of these proteins are known to be involved in pathogenicity and fitness adaptation in other bacteria. Some of the observed amino acid changes can be explained by preferential selection for certain codons and tRNA frequency. These results could help explain how species belonging to the CII clade adapt to fish environments.

Intracellular metabolomics and microRNAomics unveil new insight into the regulatory network for potential biocontrol mechanism of stress-tolerant Tricho-fusants interacting with phytopathogen Sclerotium rolfsii Sacc.

The present study employed microRNA (miRNA) sequencing and metabolome profiling of Trichoderma parental strains and fusants during normal growth and interaction with the phytopathogen Sclerotium rolfsii Sacc. In-vitro antagonism indicated that abiotic stress-tolerant Tricho-fusant FU21 was examined as a potent biocontroller with mycoparasitic action after 10 days. During interaction with the test pathogen, the most abundant uprising intracellular metabolite was recognized as l-proline, which corresponds to held-down l-alanine, associated with arginine and proline metabolism, biosynthesis of secondary metabolites, and nitrogen metabolism linked to predicted genes controlled by miRNAs viz., cel-miR-8210-3p, hsa-miR-3613-5p, and mml-miR-7174-3p. The miRNAs- mml-miR-320c and mmu-miR-6980-5p were found to be associated with phenylpropanoid biosynthesis, transcription factors, and signal transduction pathways, respectively, and were ascertained downregulated in potent FU21_IB compared with FU21_CB. The amino benzoate degradation and T cell receptor signaling pathways were regulated by miRNAs cel-miR-8210 and tca-miR-3824 as stress tolerance mechanisms of FU21. The intracellular metabolites l-proline, maleic acid, d-fructose, Myo-inositol, arabinitol, d-xylose, mannitol, and butane were significantly elevated as potential biocontrol and stress-tolerant constituents associated with miRNA regulatory pathways in potent FU21_IB. A network analysis between regulatory miRNA-predicted genes and intracellular metabolomics acknowledged possible biocontrol pathways/mechanisms in potent FU21_IB to restrain phytopathogen.

Valorization of Biomasses from Energy Crops for the Discovery of Novel Thermophilic Glycoside Hydrolases through Metagenomic Analysis.

The increasing interest for environmentally friendly technologies is driving the transition from fossil-based economy to bioeconomy. A key enabler for circular bioeconomy is to valorize renewable biomasses as feedstock to extract high value-added chemicals. Within this transition the discovery and the use of robust biocatalysts to replace toxic chemical catalysts play a significant role as technology drivers. To meet both the demands, we performed microbial enrichments on two energy crops, used as low-cost feed for extremophilic consortia. A culture-dependent approach coupled to metagenomic analysis led to the discovery of more than 300 glycoside hydrolases and to characterize a new α-glucosidase from an unknown hyperthermophilic archaeon. Aglu1 demonstrated to be the most active archaeal GH31 on 4Np-α-Glc and it showed unexpected specificity vs. kojibiose, revealing to be a promising candidate for biotechnological applications such as the liquefaction/saccharification of starch.

Bioinformatics analysis of differentially expressed genes and pathways in the development of cervical cancer.

BACKGROUND: This study aimed to explore and identify key genes and signaling pathways that contribute to the progression of cervical cancer to improve prognosis. METHODS: Three gene expression profiles (GSE63514, GSE64217 and GSE138080) were screened and downloaded from the Gene Expression Omnibus database (GEO). Differentially expressed genes (DEGs) were screened using the GEO2R and Venn diagram tools. Then, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed. Gene set enrichment analysis (GSEA) was performed to analyze the three gene expression profiles. Moreover, a protein-protein interaction (PPI) network of the DEGs was constructed, and functional enrichment analysis was performed. On this basis, hub genes from critical PPI subnetworks were explored with Cytoscape software. The expression of these genes in tumors was verified, and survival analysis of potential prognostic genes from critical subnetworks was conducted. Functional annotation, multiple gene comparison and dimensionality reduction in candidate genes indicated the clinical significance of potential targets. RESULTS: A total of 476 DEGs were screened: 253 upregulated genes and 223 downregulated genes. DEGs were enriched in 22 biological processes, 16 cellular components and 9 molecular functions in precancerous lesions and cervical cancer. DEGs were mainly enriched in 10 KEGG pathways. Through intersection analysis and data mining, 3 key KEGG pathways and related core genes were revealed by GSEA. Moreover, a PPI network of 476 DEGs was constructed, hub genes from 12 critical subnetworks were explored, and a total of 14 potential molecular targets were obtained. CONCLUSIONS: These findings promote the understanding of the molecular mechanism of and clinically related molecular targets for cervical cancer.

Soil acidification reduces the effects of short-term nutrient enrichment on plant and soil biota and their interactions in grasslands.

Soil nitrogen (N) and phosphorus (P) contents, and soil acidification have greatly increased in grassland ecosystems due to increased industrial and agricultural activities. As major environmental and economic concerns worldwide, nutrient enrichment and soil acidification can lead to substantial changes in the diversity and structure of plant and soil communities. Although the separate effects of N and P enrichment on soil food webs have been assessed across different ecosystems, the combined effects of N and P enrichment on multiple trophic levels in soil food webs have not been studied in semiarid grasslands experiencing soil acidification. Here we conducted a short-term N and P enrichment experiment in non-acidified and acidified soil in a semiarid grassland on the Mongolian Plateau. We found that net primary productivity was not affected by N or P enrichment alone in either non-acidified or acidified soil, but was increased by combined N and P enrichment in both non-acidified and acidified soil. Nutrient enrichment decreased the biomass of most microbial groups in non-acidified soil (the decrease tended to be greatest with combined N and P enrichment) but not in acidified soil, and did not affect most soil nematode variables in non-acidified or acidified soil. Nutrient enrichment also changed plant and microbial community structure in non-acidified but not in acidified soil, and had no effect on nematode community structure in non-acidified or acidified soil. These results indicate that the responses to short-term nutrient enrichment were weaker for higher trophic groups (nematodes) than for lower trophic groups (microorganisms) and primary producers (plants). The findings increase our understanding of the effects of nutrient enrichment on multiple trophic levels of soil food webs, and highlight that soil acidification, as an anthropogenic stressor, reduced the responses of plants and soil food webs to nutrient enrichment and weakened plant-soil interactions.

Application of culturomics to characterize diverse anaerobic bacteria from the gastrointestinal tract of broiler chickens in relation to environmental reservoirs.

Characterization of the microbiota of chickens is of current interest. The goals of the current study were to apply anaerobic isolation methods to comprehensively isolate and identify bacteria from the gastrointestinal tract of chickens and their environment. Bacterial communities within the drinking water were dominated by Escherichia, whereas communities in litter were more representative of the cecum. The crop and small intestine (jejunum and ileum) were dominated by Lactobacillus and Enterococcus spp., and the cecum was dominated by Proteus spp. The collection of bacteria isolated was dominated by Enterococcus spp., Escherichia/Shigella spp., Lactobacillus spp., and Proteus spp.; however, many rare taxa were observed. These included members of the Clostridiales and Clostridium spp., which were commonly isolated from the ileum and cecum. Bacteria isolated by enrichment and direct plating differed. The selective de Man-Rogosa-Sharpe agar was commonly associated with the isolation of Lactobacillus spp. and yielded the lowest diversity of all methods utilized. Increased diversity and frequency of Clostridium spp. was observed in enrichments of blood and mucus or by plating on Columbia agar supplemented with 10% blood and gentamicin. The bacteria isolated from this study provide source material for genomic and functional studies in chicken hosts.

Protein Extraction, Enrichment and MALDI MS and MS/MS Analysis from Bitter Orange Leaves (Citrus aurantium).

Citrus aurantium is a widespread tree in the Mediterranean area, and it is mainly used as rootstock for other citrus. In the present study, a vacuum infiltration centrifugation procedure, followed by solid phase extraction matrix-assisted laser desorption ionization tandem mass spectrometry (SPE MALDI MS/MS) analysis, was adopted to isolate proteins from leaves. The results of mass spectrometry (MS) profiling, combined with the top-down proteomics approach, allowed the identification of 78 proteins. The bioinformatic databases TargetP, SignalP, ChloroP, WallProtDB, and mGOASVM-Loc were used to predict the subcellular localization of the identified proteins. Among 78 identified proteins, 20 were targeted as secretory pathway proteins and 36 were predicted to be in cellular compartments including cytoplasm, nucleus, and cell membrane. The largest subcellular fraction was the secretory pathway, accounting for 25% of total proteins. Gene Ontology (GO) of Citrus sinensis was used to simplify the functional annotation of the proteins that were identified in the leaves. The Kyoto Encyclopedia of Genes and Genomes (KEGG) showed the enrichment of metabolic pathways including glutathione metabolism and biosynthesis of secondary metabolites, suggesting that the response to a range of environmental factors is the key processes in citrus leaves. Finally, the Lipase GDSL domain-containing protein GDSL esterase/lipase, which is involved in plant development and defense response, was for the first time identified and characterized in Citrus aurantium.

Enhanced Electrocatalytic Performance through Body Enrichment of Co-Based Bimetallic Nanoparticles In Situ Embedded Porous N-Doped Carbon Spheres.

Extending available body space loading active species and controllably tailoring the d-band center to Fermi level of catalysts are of paramount importance but extremely challenging for the enhancement of electrocatalytic performance. Herein, a melamine-bridged self-construction strategy is proposed to in situ embed Co-based bimetallic nanoparticles in the body of N-doped porous carbon spheres (CoM-e-PNC), and achieve the controllable tailoring of the d-band center position by alloying of Co and another transition metal M (M = Ni, Fe, Mn, and Cu). The enrichment and exposure of the active sites in the body interior of porous carbon spheres, and the best balance between the adsorption of OH species and the desorption of O2 induced by optimizing the d-band center position, collectively enhance the oxygen evolution reaction (OER) performance. Meanwhile, the relationship of d-band center position and OER activity is found to exhibit the volcano curve rule, where the CoNi-e-PNC catalyst shows optimal OER performance with an overpotential of 0.24 V at 10 mA cm-2 in alkaline media, outperforming those of the ever-reported CoNi-based catalysts. Besides, CoNi-e-PNC catalyst also demonstrates high OER stability with slight current decrease after 100 h.

Is phosphorus a limiting factor to regulate the growth of phytoplankton in Daya Bay, northern South China Sea: a mesocosm experiment.

Previous field investigations implied a potential phosphorus (P)-limitation on the growth of phytoplankton in Daya Bay, a mesotrophic bay in the northern South China Sea. Using a total of 15 mesocosms (3 × 3 × 1.5 m, with ~10.8 m3 natural seawater containing phytoplankton assemblages for each), we found P-enrichment caused no obvious effect on phytoplankton (Chl a) growth across 8-day's cultivation in neither winter nor summer, while nitrogen (N)-enrichment greatly increased Chl a in both seasons. N plus P-enrichment further increased Chl a content. The N- or N plus P-enrichments increased the allocation of nano-Chl a but decreased micro-Chl a in most cases, with no obvious effect by P-alone. Coincided with nutrients effect on Chl a content, N- or N plus P-enrichments significantly enhanced the maximum photochemical quantum yield of Photosystem II (FV/FM) and maximum relative electron transport rate (rETRmax), but declined the non-photochemical quenching (NPQ), as well as the threshold for light saturation of electron transport (EK); again, P-enrichment had no significant effect. Moreover, the absorption cross section for PSII photochemistry (σPSII) and electron transport efficiency (α) increased due to N- or N plus P-enrichments, indicating the increased nutrients enhance the light utilization efficiency through promoting PSII light harvesting ability, and thus to enhance phytoplankton growth. Our findings indicate that N- or N plus P-enrichments rigorously fuel phytoplankton blooms regardless of N:P ratios, making a note of caution on the expected P-deficiency or P-limitation on the basis of Redfield N:P ratios in Daya Bay.

Evaluating stream sediment chemistry within an agricultural catchment of Lebanon, Northeastern USA.

Recent arsenic pollution of drinking-water wells across Lebanon, northeastern USA has led to a growing concern about possible impact of agricultural activities on the hydrologic system. This study assessed the concentrations and distributions of arsenic and ten other elements (Al, Cd, Cr, Cu, Fe, K, Mn, P, Pb, and Zn) in stream sediments. The overall goal is to determine the extent of these elements within the fluvial systems, as well as overall sediment quality. A total of 65 stream sediments samples were collected, and analyzed for particle size distributions, organic matter contents, trace, and major elements concentrations. Results showed spatial variability in the concentrations of trace elements due to variation in sediments grain sizes, organic matter content, as well as land use activities within the study area. Calculation of sediment enrichment with respect to As, Cd, Cr, Cu, Mn, Pb, and Zn showed that about 48-52% of all the sampling locations are not enriched, nevertheless, approximately 2-11% of all the sampling locations are significantly enriched, an indication of anthropogenic input. However, results of ecological risk assessment showed no connection with sediment enrichment as most sampling locations have concentrations below the threshold probable effect concentration (PEC) value. Statistical analysis using principal component analysis (PCA) extracted three significant components explaining over 72% of total variance covering elements having origin in both natural and anthropogenic sources, thus suggesting that the concentrations and distribution of these elements within stream sediments are related to a combination of weathering processes on the bedrock geology, and anthropogenic activities.

GeneSCF: a real-time based functional enrichment tool with support for multiple organisms.

BACKGROUND: High-throughput technologies such as ChIP-sequencing, RNA-sequencing, DNA sequencing and quantitative metabolomics generate a huge volume of data. Researchers often rely on functional enrichment tools to interpret the biological significance of the affected genes from these high-throughput studies. However, currently available functional enrichment tools need to be updated frequently to adapt to new entries from the functional database repositories. Hence there is a need for a simplified tool that can perform functional enrichment analysis by using updated information directly from the source databases such as KEGG, Reactome or Gene Ontology etc. RESULTS: In this study, we focused on designing a command-line tool called GeneSCF (Gene Set Clustering based on Functional annotations), that can predict the functionally relevant biological information for a set of genes in a real-time updated manner. It is designed to handle information from more than 4000 organisms from freely available prominent functional databases like KEGG, Reactome and Gene Ontology. We successfully employed our tool on two of published datasets to predict the biologically relevant functional information. The core features of this tool were tested on Linux machines without the need for installation of more dependencies. CONCLUSIONS: GeneSCF is more reliable compared to other enrichment tools because of its ability to use reference functional databases in real-time to perform enrichment analysis. It is an easy-to-integrate tool with other pipelines available for downstream analysis of high-throughput data. More importantly, GeneSCF can run multiple gene lists simultaneously on different organisms thereby saving time for the users. Since the tool is designed to be ready-to-use, there is no need for any complex compilation and installation procedures.

Interspecific competition enhances microcystin production by Microcystis aeruginosa under the interactive influences of temperature and nutrients.

Global warming and eutrophication contribute to frequent occurrences of toxic algal blooms in freshwater systems globally, while there is a limited understanding of their combined impacts on toxin-producing algal species under interspecific competitions. This study investigated the influences of elevated temperatures, lights, nutrient enrichments and interspecific interactions on growth and microcystin (MC) productions of Microcystis aeruginosa in laboratory condition. Our results indicated that elevated temperatures and higher nutrient levels significantly boosted biomass and specific growth rates of Microcystis aeruginosa, which maintained a competitive edge over Chlorella sp. Specifically, with phosphorus levels between 0.10 and 0.70 mg P L-1, the growth rate of Microcystis aeruginosa in mixed cultures increased by 23 %-52 % compared to mono-cultures, while the growth rate of Chlorella sp. shifted from positive in mono-cultures to negative in mixed cultures. Redundancy and variance partition analyses suggested that Chlorella sp. stimulate MC production in Microcystis aeruginosa and nutrient levels outshine temperature for toxin productions during competition. Lotka‒Volterra model revealed a positive correlation between the intensities of competitions and MC concentration. Our findings indicate that future algal bloom mitigation strategies should consider combined influence of temperature, nutrients, and interspecific competition due to their synergistic effects on MC productions.

Soil microbial community response to corrinoids is shaped by a natural reservoir of vitamin B12.

Soil microbial communities perform critical ecosystem services through the collective metabolic activities of numerous individual organisms. Most microbes use corrinoids, a structurally diverse family of cofactors related to vitamin B12. Corrinoid structure influences the growth of individual microbes, yet how these growth responses scale to the community level remains unknown. Analysis of metagenome-assembled genomes suggests that corrinoids are supplied to the community by members of the archaeal and bacterial phyla Thermoproteota, Actinobacteria, and Proteobacteria. Corrinoids were found largely adhered to the soil matrix in a grassland soil, at levels exceeding those required by cultured bacteria. Enrichment cultures and soil microcosms seeded with different corrinoids showed distinct shifts in bacterial community composition, supporting the hypothesis that corrinoid structure can shape communities. Environmental context influenced both community- and taxon-specific responses to specific corrinoids. These results implicate corrinoids as key determinants of soil microbiome structure and suggest that environmental micronutrient reservoirs promote community stability.

Soil microbial community response to corrinoids is shaped by a natural reservoir of vitamin B12.

Soil microbial communities perform critical ecosystem services through the collective metabolic activities of numerous individual organisms. Most microbes use corrinoids, a structurally diverse family of cofactors related to vitamin B12. Corrinoid structure influences the growth of individual microbes, yet how these growth responses scale to the community level remains unknown. Analysis of metagenome-assembled genomes suggests corrinoids are supplied to the community by members of the archaeal and bacterial phyla Thermoproteota, Actinobacteria, and Proteobacteria. Corrinoids were found largely adhered to the soil matrix in a grassland soil, at levels exceeding those required by cultured bacteria. Enrichment cultures and soil microcosms seeded with different corrinoids showed distinct shifts in bacterial community composition, supporting the hypothesis that corrinoid structure can shape communities. Environmental context influenced both community and taxon-specific responses to specific corrinoids. These results implicate corrinoids as key determinants of soil microbiome structure and suggest that environmental micronutrient reservoirs promote community stability.

Resource availability governs polyhydroxyalkanoate (PHA) accumulation and diversity of methanotrophic enrichments from wetlands.

Aquatic environments account for half of global CH4 emissions, with freshwater wetlands being the most significant contributors. These CH4 fluxes can be partially offset by aerobic CH4 oxidation driven by methanotrophs. Additionally, some methanotrophs can convert CH4 into polyhydroxyalkanoate (PHA), an energy storage molecule as well as a promising bioplastic polymer. In this study, we investigate how PHA-accumulating methanotrophic communities enriched from wetlands were shaped by varying resource availability (i.e., C and N concentrations) at a fixed C/N ratio. Cell yields, PHA accumulation, and community composition were evaluated in high (20% CH4 and 10 mM NH4 +) and low resource (0.2% CH4 and 0.1 mM NH4 +) conditions simulating engineered and environmental settings, respectively. High resource availability decreased C-based cell yields, while N-based cell yields remained stable, suggesting nutrient exchange patterns differed between methanotrophic communities at different resource concentrations. PHA accumulation was only observed in high resource enrichments, producing approximately 12.6% ± 2.4% (m/m) PHA, while PHA in low resource enrichments remained below detection. High resource enrichments were dominated by Methylocystis methanotrophs, while low resource enrichments remained significantly more diverse and contained only a minor population of methanotrophs. This study demonstrates that resource concentration shapes PHA-accumulating methanotrophic communities. Together, this provides useful information to leverage such communities in engineering settings as well as to begin understanding their role in the environment.

Recent advances in mass spectrometry-based methods to investigate reversible cysteine oxidation.

The post-translational modification of cysteine to diverse oxidative states is understood as a critical cellular mechanism to combat oxidative stress. To study the role of cysteine oxidation, cysteine enrichments and subsequent analysis via mass spectrometry are necessary. As such, technologies and methods are rapidly developing for sensitive and efficient enrichments of cysteines to further explore its role in signaling pathways. In this review, we analyze recent developments in methods to miniaturize cysteine enrichments, analyze the underexplored disulfide bound redoxome, and quantify site-specific cysteine oxidation. We predict that further development of these methods will improve cysteine coverage across more diverse organisms than those previously studied and elicit novel roles cysteines play in stress response.

Perspectives on the semantics/pragmatics debate: insights from aphasia research.

In the philosophy of language, there are many ongoing controversies that stem from relying too heavily on an utterance-based framework. The traditional approach of rigidly partitioning the utterance's meaning into what is grammatically determined from what is not may not fully capture the complexity of human language in real-world communicative contexts. To address this issue, we suggest shifting focus toward a broader analysis level encompassing conversations and discourses. From this broader perspective, it is possible to obtain a more integrated view of how linguistic and extra-linguistic aspects dynamically interact and thus reconsider semantics/pragmatics dichotomy as complementary dimensions. Meaning is not confined to linguistic structures alone but emerges from the dynamic interplay of words, sociocultural knowledge, discursive situations, and psychological dispositions of speakers. Substantiating this perspective calls for embracing an interdisciplinary approach that synthesizes research from various domains, including linguistics, cognitive psychology, and philosophy of language. This paper focuses on a particularly compelling case study: aphasia. Speeches produced by individuals with aphasia represent complex scenarios where the balance between linguistic and extra-linguistic aspects is notably compromised, often to the former's detriment. Aphasics' productions represent a vivid example of how the interpretation of speeches can be far from involving fixed and static operations. Instead, it entails continuously reallocating cognitive resources toward the most readily available and accessible sources for the speakers. This case study ultimately demonstrates that the influence of semantic and pragmatic processes in shaping and conveying meanings displays remarkable adaptability, continuously adjusting to the ever changing demands placed upon speakers.

Evaluation of Physical Egg Quality Parameters of Commercial Brown Laying Hens Housed in Five Production Systems.

This study evaluates the effect of housing environment on the egg quality characteristics of brown egg layers as many different environments are currently used in the industry. Battery cages, barren colony cages, enriched colony cages, cage-free, and free-range environments were evaluated. Overall, all egg quality measurements were affected by housing environment (p < 0.01) except for vitelline membrane strength, elasticity, and egg solids. Eggshells and yolks were lightest in barren colony cages and darkest from free-range hens (p < 0.0001). Free-range eggs were heavier than eggs from all other environments (p < 0.0001). Cage-free eggs had lower albumen height and Haugh units than other environments (p < 0.0001). Lastly, cage-free and free-range eggs had stronger eggshells than the other environments (p < 0.0001), and free-range eggs had more elastic eggshells than eggs from conventional battery cages and barren colony cages (p < 0.01). Access to the range seemed to give free-range hens different nutritional advantages, which allowed for the darker yolks and shells. Furthermore, eggs from barren colony cages seemed to exhibit more negative characteristics. Simply adding enrichments to colony cages did not improve or detract from egg quality. From this research, it appears that, as the industry moves toward extensive environments, the egg quality of brown egg layers will improve.

Soil bacteria are more sensitive than fungi in response to nitrogen and phosphorus enrichment.

Anthropogenic activities have dramatically increased nitrogen (N) and phosphorous (P) enrichments in terrestrial ecosystems. However, it is still unclear on how bacterial and fungal communities would respond to the simultaneously increased N and P enrichment. In this study, we used a field experiment to simulate N and P input, and examined the effects of N and P additions on the abundance, alpha-diversity, and community composition of soil bacteria and fungi in a riparian forest. Six nutrient-addition treatments, including low N (30 kg N ha-1 year-1), high N (150 kg N ha -1 year-1), low P (30 kg P2O5 ha-1 year-1), high P (150 kg P2O5 ha -1 year-1), low N+P, high N+P, and a control (CK) treatment were set up. We found that the N and P additions significantly affected bacterial abundance, community composition, but not the alpha diversity. Specifically, 16S, nirK, and nirS gene copy numbers were significantly reduced after N and P additions, which were correlated with decreases in soil pH and NO- 3-N, respectively; Co-additions of N and P showed significantly antagonistic interactions on bacterial gene copies; Nutrient additions significantly increased the relative abundance of Proteobacteria while reduced the relative abundance of Chloroflexi. Mantel's test showed that the alteration in bacterial composition was associated with the changes in soil pH and NO- 3-N. The nutrient additions did not show significant effects on fungal gene copy numbers, alpha diversity, and community composition, which could be due to non-significant alterations in soil C/N and total P concentration. In conclusion, our results suggest that soil bacteria are more sensitive than fungi in response to N and P enrichment; the alterations in soil pH and NO- 3-N explain the effects of N and P enrichment on bacterial communities, respectively; and the co-addition of N and P reduces the negative effects of these two nutrients addition in alone. These findings improve our understanding of microbial response to N and P addition, especially in the context of simultaneous enrichment of anthropogenic nutrient inputs.