Microbial Patterns Research Articles

PM-profiler: a high-resolution and fast tool for taxonomy annotation of amplicon-based microbiome.

Amplicon sequencing stands as a cornerstone in microbiome profiling, yet concerns persist regarding its resolution and accuracy. The enhancement of reference databases and annotations marks a new era for 16S rRNA-based profiling. Capitalizing on this potential, we introduce PM-profiler, a novel tool for profiling amplicon short reads. PM-profiler is implemented by C++-based advanced algorithms, such as pre-allocated hash for reference construction, hybrid and dynamic short-read matching, big-data-guided dual-mode hierarchical taxonomy annotation strategy, and full-procedure parallel computing. This tool delivers species-level resolution and ultrafast speed for large-scale microbiomes, surpassing alignment-based approaches and the Naïve-Bayesian model. Furthermore, recognizing the global uneven distribution of microbes, we delineate optimal annotation strategies for each sampling habitat based on microbial patterns over 270,000 microbiomes. Integrated with the established workflow of Parallel-Meta Suite and the latest curated reference databases, this endeavor offers a swift and dependable solution for high-precision microbiome surveys.IMPORTANCEOur study introduces PM-profiler, a new tool that deciphers the complexity of microbial communities. With advanced algorithms, flexible annotation strategies, and well-organized big-data, PM-profiler provides a faster and more accurate way to study on microbiomes, paving the way for discoveries that could improve our understanding of microbiomes and their impact on the world.

EPITHELIAL REMODELING AND MICROBIAL DYSBIOSIS IN THE LOWER RESPIRATORY TRACT OF VITAMIN A-DEFICIENT MOUSE LUNGS.

The World Health Organization identified vitamin A deficiency (VAD) as a major public health issue in low-income communities and developing countries, while additional studies have shown dietary VAD leads to various lung pathologies. Once believed to be sterile, research now shows that transient microbial communities exist within healthy lungs and are often dysregulated in patients suffering from malnourishment, respiratory infections, and disease. The inability to parse vitamin A-mediated mechanisms from other metabolic mechanisms in humans with pathogenic endotypes, as well as the lack of data investigating how VAD affects the lung microbiome, remains a significant gap in the field. To address this unmet need, we compared molecular, metatranscriptomic, and morphometric data to identify how dietary VAD affects the lung as well as the lung microbiome. Our research shows structural and functional alterations in host-microbe-diet interactions in VAD lungs compared to vitamin A-sufficient (VAS) lungs; these changes are associated with epithelial remodeling, a breakdown in mucociliary clearance, microbial imbalance, and altered microbial colonization patterns after 8 weeks of vitamin A deficient diet. These findings confirm vitamin A is critical for lung homeostasis and provide mechanistic insights that could be valuable for the prevention of respiratory infections and disease.

Microbiological, Functional, and Chemico-Physical Characterization of Artisanal Kombucha: An Interesting Reservoir of Microbial Diversity.

Kombucha is a trending tea fermented via a complex microflora of yeasts and acetic acid bacteria. It can be a valid low-calorie substitute for soft drinks due to its sour, naturally carbonated, and sweet taste. Despite increased interest, the microflora and functional properties of kombucha have not yet been fully understood. The aim of this work was to characterize, from a microbiological, chemico-physical, and functional point of view, three types of artisanal kombucha obtained by fermenting green tea containing sugar by means of different starter cultures. Metagenomic analysis revealed a predominance of yeasts compared to bacteria, regardless of the sample. In particular, Brettanomyces spp. was found to be the dominant yeast. Moreover, the different types of kombucha had different microbial patterns in terms of acetic acid bacteria and yeasts. Ethanol and acetic acid were the dominant volatile molecules of the kombucha volatilome; the samples differed from each other in terms of their content of alcohols, esters, and acids. All the samples showed a high antioxidant potential linked to the high content of phenols. This study confirmed the positive chemico-physical and functional properties of kombucha and indicated that the microflora responsible for the fermentation process can significantly affect the characteristics of the final product.

The relationship between atmospheric particulate matter, leaf surface microstructure, and the phyllosphere microbial diversity of Ulmus L.

BackgroundPlants can retain atmospheric particulate matter (PM) through their unique foliar microstructures, which has a profound impact on the phyllosphere microbial communities. Yet, the underlying mechanisms linking atmospheric particulate matter (PM) retention by foliar microstructures to variations in the phyllosphere microbial communities remain a mystery. In this study, we conducted a field experiment with ten Ulmus lines. A series of analytical techniques, including scanning electron microscopy, atomic force microscopy, and high-throughput amplicon sequencing, were applied to examine the relationship between foliar surface microstructures, PM retention, and phyllosphere microbial diversity of Ulmus L.ResultsWe characterized the leaf microstructures across the ten Ulmus lines. Chun exhibited a highly undulated abaxial surface and dense stomatal distribution. Langya and Xingshan possessed dense abaxial trichomes, while Lieye, Zuiweng, and Daguo had sparsely distributed, short abaxial trichomes. Duomai, Qingyun, and Lang were characterized by sparse stomata and flat abaxial surfaces, whereas Jinye had sparsely distributed but extensive stomata. The mean leaf retention values for total suspended particulate (TSP), PM2.5, PM2.5-10, PM10-100, and PM> 100 were 135.76, 6.60, 20.10, 90.98, and 13.08 µg·cm− 2, respectively. Trichomes substantially contributed to PM2.5 retention, while larger undulations enhanced PM2.5-10 retention, as evidenced by positive correlations between PM2.5 and abaxial trichome density and between PM2.5-10 and the adaxial raw microroughness values. Phyllosphere microbial diversity patterns varied among lines, with bacteria dominated by Sediminibacterium and fungi by Mycosphaerella, Alternaria, and Cladosporium. Redundancy analysis confirmed that dense leaf trichomes facilitated the capture of PM2.5-associated fungi, while bacteria were less impacted by PM and struggled to adhere to leaf microstructures. Long and dense trichomes provided ideal microhabitats for retaining PM-borne microbes, as evidenced by positive feedback loops between PM2.5, trichome characteristics, and the relative abundances of microorganisms like Trichoderma and Aspergillus.ConclusionsBased on our findings, a three-factor network profile was constructed, which provides a foundation for further exploration into how different plants retain PM through foliar microstructures, thereby impacting phyllosphere microbial communities.

Targeted microbial collaboration to enhance key flavor metabolites by inoculating Clostridium tyrobutyricum and Saccharomyces cerevisiae in the strong-flavor Baijiu simulated fermentation system

Ethyl hexanoate and ethyl butyrate are indispensable flavor metabolites in strong-flavor Baijiu (SFB), but batch production instability in fermenting grains can reduce the quality of distilled Baijiu. Biofortification of the fermentation process by designing a targeted microbial collaboration pattern is an effective method to stabilize the quality of Baijiu. In this study, we explored the metabolism under co-culture liquid fermentation with Clostridium tyrobutyricum DB041 and Saccharomyces cerevisiae YS219 and investigated the effects of inoculation with two functional microorganisms on physicochemical factors, flavor metabolites, and microbial communities in solid-state simulated fermentation of SFB for the first time. The headspace solid-phase microextraction-gas chromatography-mass spectrometry results showed that ethyl butyrate and ethyl hexanoate significantly increased in fermented grain. High-throughput sequencing analysis showed that Pediococcus, Lactobacillus, Weissella, Clostridium_sensu_stricto_12, and Saccharomyces emerged as the dominant microorganisms at the end of fermentation. Co-occurrence analysis showed that ethyl hexanoate and ethyl butyrate were significantly correlated (|r| > 0.5, P < 0.05) with a cluster of interactions dominated by lactic acid bacteria (Pediococcus, Lactobacillus, Weissella, and Lactococcus), which was driven by the functional C. tyrobutyricum and S. cerevisiae. Mantel test showed that moisture and reducing sugars were the main physicochemical factor affecting microbial collaboration (|r| > 0.7, P < 0.05). Taken together, the collaborative microbial pattern of inoculation with C. tyrobutyricum and S. cerevisiae showed positive results in enhancing typical flavor metabolites and the synergistic effects of microorganisms in SFB.

NLRP3 promotes allergic responses to birch pollen extract in a model of intranasal sensitization.

Allergic sensitization is an essential step in the development of allergic airway inflammation to birch pollen (BP); however, this process remains to be fully elucidated. Recent scientific advances have highlighted the importance of the allergen context. In this regard, microbial patterns (PAMPs) present on BP have attracted increasing interest. As these PAMPs are recognized by specialized pattern recognition receptors (PRRs), this study aims at investigating the roles of intracellular PRRs and the inflammasome regulator NLRP3. We established a physiologically relevant intranasal and adjuvant-free sensitization procedure to study BP-induced systemic and local lung inflammation. Strikingly, BP-sensitized Nlrp3-deficient mice showed significantly lower IgE levels, Th2-associated cytokines, cell infiltration into the lung, mucin production and epithelial thickening than their wild-type counterparts, which appears to be independent of inflammasome formation. Intriguingly, bone-marrow chimera revealed that expression of NLRP3 in the hematopoietic system is required to trigger an allergic response. Overall, this study identifies NLRP3 as an important driver of BP-induced allergic immune responses.

Forest-to-Cropland Conversion Reshapes Microbial Hierarchical Interactions and Degrades Ecosystem Multifunctionality at a National Scale.

Conversion from natural lands to cropland, primarily driven by agricultural expansion, could significantly alter soil microbiome worldwide; however, influences of forest-to-cropland conversion on microbial hierarchical interactions and ecosystem multifunctionality have not been fully understood. Here, we examined the effects of forest-to-cropland conversion on intratrophic and cross-trophic microbial interactions and soil ecosystem multifunctionality and further disclosed their underlying drivers at a national scale, using Illumina sequencing combined with high-throughput quantitative PCR techniques. The forest-to-cropland conversion significantly changed the structure of soil microbiome (including prokaryotic, fungal, and protistan communities) while it did not affect its alpha diversity. Both intrakingdom and interkingdom microbial networks revealed that the intratrophic and cross-trophic microbial interaction patterns generally tended to be more modular to resist environmental disturbance introduced from forest-to-cropland conversion, but this was insufficient for the cross-trophic interactions to maintain stability; hence, the protistan predation behaviors were still disturbed under such conversion. Moreover, key soil microbial clusters were declined during the forest-to-cropland conversion mainly because of the increased soil total phosphorus level, and this drove a great degradation of the ecosystem multifunctionality (by 207%) in cropland soils. Overall, these findings comprehensively implied the negative effects of forest-to-cropland conversion on the agroecosystem, from microbial hierarchical interactions to ecosystem multifunctionality.

Absence of a pancreatic microbiome in intraductal papillary mucinous neoplasm

ObjectiveThis study aims to validate the existence of a microbiome within intraductal papillary mucinous neoplasm (IPMN) that can be differentiated from the taxonomically diverse DNA background of next-generation sequencing procedures.DesignWe...

A Comprehensive Pilot Study to Elucidate the Distinct Gut Microbial Composition and Its Functional Significance in Cardio-Metabolic Disease.

Cardio-metabolic disease is a significant global health challenge with increasing prevalence. Recent research underscores the disruption of gut microbial balance as a key factor in disease susceptibility. We aimed to characterize the gut microbiota composition and function in cardio-metabolic disease and healthy controls. For this purpose, we collected stool samples of 18 subjects (12 diseased, 6 healthy) and we performed metagenomics analysis and functional prediction using QIIME2 and PICRUSt. Furthermore, we carried out assessments of microbe-gene interactions, gene ontology, and microbe-disease associations. Our findings revealed distinct microbial patterns in the diseased group, particularly evident in lower taxonomic levels with significant variations in 14 microbial features. The diseased cohort exhibited an enrichment of Lachnospiraceae family, correlating with obesity, insulin resistance, and metabolic disturbances. Conversely, reduced levels of Clostridium, Gemmiger, and Ruminococcus genera indicated a potential inflammatory state, linked to compromised butyrate production and gut permeability. Functional analyses highlighted dysregulated pathways in amino acid metabolism and energy equilibrium, with perturbations correlating with elevated branch-chain amino acid levels-a known contributor to insulin resistance and type 2 diabetes. These findings were consistent across biomarker assessments, microbe-gene associations, and gene ontology analyses, emphasizing the intricate interplay between gut microbial dysbiosis and cardio-metabolic disease progression. In conclusion, our study unveils significant shifts in gut microbial composition and function in cardio-metabolic disease, emphasizing the broader implications of microbial dysregulation. Addressing gut microbial balance emerges as a crucial therapeutic target in managing cardio-metabolic disease burden.

Investigating gut microbiota-blood and urine metabolite correlations in early sepsis-induced acute kidney injury: insights from targeted KEGG analyses.

The interplay between gut microbiota and metabolites in the early stages of sepsis-induced acute kidney injury (SA-AKI) is not yet clearly understood. This study explores the characteristics and interactions of gut microbiota, and blood and urinary metabolites in patients with SA-AKI. Utilizing a prospective observational approach, we conducted comparative analyses of gut microbiota and metabolites via metabolomics and metagenomics in individuals diagnosed with SA-AKI compared to those without AKI (NCT06197828). Pearson correlations were used to identify associations between microbiota, metabolites, and clinical indicators. The Comprehensive Antibiotic Resistance Database was employed to detect antibiotic resistance genes (ARGs), while Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways informed on metabolic processes and microbial resistance patterns. Our study included analysis of four patients with SA-AKI and five without AKI. Significant disparities in bacterial composition were observed, illustrated by diversity indices (Shannon index: 2.0 ± 0.4 vs. 1.4 ± 0.6, P = 0.230; Simpson index: 0.8 ± 0.1 vs. 0.6 ± 0.2, P = 0.494) between the SA-AKI group and the non-AKI group. N6, N6, N6-Trimethyl-L-lysine was detected in both blood and urine metabolites, and also showed significant correlations with specific gut microbiota (Campylobacter hominis and Bacteroides caccae, R > 0, P < 0.05). Both blood and urine metabolites were enriched in the lysine degradation pathway. We also identified the citrate cycle (TCA cycle) as a KEGG pathway enriched in sets of differentially expressed ARGs in the gut microbiota, which exhibits an association with lysine degradation. Significant differences in gut microbiota and metabolites were observed between the SA-AKI and non-AKI groups, uncovering potential biomarkers and metabolic changes linked to SA-AKI. The lysine degradation pathway may serve as a crucial link connecting gut microbiota and metabolites.

Macrophages: Balancing Inflammation and Homeostasis in Health and Disease

: Inflammation is crucial for maintaining tissue homeostasis and responding to insults, yet dysregulated inflammation can lead to various diseases. Macrophages, central to the immune system, play key roles in initiating, regulating, and resolving inflammation. This review provides an overview of macrophage functions, including activation mechanisms, recruitment to inflamed tissues, interactions with other immune cells and mediators, and their roles in phagocytosis, clearance of apoptotic cells and debris, and secretion of anti-inflammatory cytokines. Additionally, it discusses macrophage-induced regulatory T-cell formation, the impact of pro-inflammatory and anti-inflammatory cytokines on macrophage behavior, and the influence of microbial products and pathogen-associated molecular patterns (PAMPs) on macrophage function. The review also identifies targeting macrophages as a promising strategy for managing inflammatory diseases while acknowledging challenges such as macrophage heterogeneity, limitations of in vitro models, and incomplete understanding of regulatory mechanisms. Finally, it suggests areas for further research, including identifying specific macrophage subsets, understanding macrophage plasticity, exploring resolution signaling pathways, and investigating the role of metabolism and microenvironmental cues in macrophage function, aiming to pave the way for more effective macrophage-targeted therapies in inflammatory diseases.

Microbial Detection and Antibiotic Susceptibility patterns of Clinical Isolates from Women With Urinary Tract Infection in AL-Nasiriyah City/Iraq

Microbial Detection and Antibiotic Susceptibility patterns of Clinical Isolates from Women With Urinary Tract Infection in AL-Nasiriyah City/Iraq

Temporal and spatial dynamics within the fungal microbiome of grape fermentation.

Over 6 years, we conducted an extensive survey of spontaneous grape fermentations, examining 3105 fungal microbiomes across 14 distinct grape-growing regions. Our investigation into the biodiversity of these fermentations revealed that a small number of highly abundant genera form the core of the initial grape juice microbiome. Consistent with previous studies, we found that the region of origin had the most significant impact on microbial diversity patterns. We also discovered that certain taxa were consistently associated with specific geographical locations and grape varieties, although these taxa represented only a minor portion of the overall diversity in our dataset. Through unsupervised clustering and dimensionality reduction analysis, we identified three unique community types, each exhibiting variations in the abundance of key genera. When we projected these genera onto global branches, it suggested that microbiomes transition between these three broad community types. We further investigated the microbial community composition throughout the fermentation process. Our observations indicated that the initial microbial community composition could predict the diversity during the early stages of fermentation. Notably, Hanseniaspora uvarum emerged as the primary non-Saccharomyces species within this large collection of samples.

Diversity of Hydrogen Sulfide Oxidizers in Biogas-Stream Fed Bioscrubber in Seafood Factory

Corrosive and harmful hydrogen sulfide (H2S) are major obstacles to biogas utilization. Bioscrubber system is the one of the most popular tecnologies for removing H2S from biogas. Sulfur oxidizing bacteria (SOB) play an important role in controlling the efficiency and stability of bioscrubber systems through sulfur oxidation (soxABXYZ) and flavocytochrome sulfide dehydrogenase (fccAB) enzyme catalyses. The main purpose of this research is to analyse microbial diversity and gene expression pattern of SOBs related to H2S oxidation. In this study, SOB population were collected from the full-scale bioscrubber system of the seafood factory (TKF). The richness and diversity of SOB strains were analyzed using next-generation sequencing analysis (NGS) based on 16S rRNA gene. DNA microarray was used to examine the expression of soxABXYZ and fccAB genes involved in the H2S oxidation. A number of readable sequences indicate SOB diversity and richness that cover the entire population of bacteria in the TKF factory. The phylum proteobacteria was found covered up to 60% of total bacteria. Interestingly, the highest abundance genus of SOB coexisting in biocrubber to oxidize H2S in biogas was Pseudomonas, MWH-UniP1_aquatic, Smithella, Thioalkalimicrobium, Hydrogenophaga and Acinetobacter. Paracoccus sediminis, Pseudomonas stutzeri and Paracoccus denitrificans were found having the soxAXYZ and soxB gene expression level up to 0.2754-fold, 0.0808-fold and 0.3819-fold respectively. On the other hand, the expression of fccAB genes of P. denitrificans was increased up to 0.3819-fold. Altogether, the predominance of these species-strains was associated with the excellent H2S removal efficiency of 99.3% in the TKF factory.

Pediatric Urinary Tract Infections at a Tertiary Care Center: Microbial Diversity and Antibiotic Resistance Patterns

Abstract Introduction: Urinary tract infection (UTI) remains a prevalent bacterial infection among the pediatric age group, ranking as the third-most common bacterial infection in children in developing countries, following gastrointestinal and respiratory tract infections. It continues to pose a significant health challenge. Materials and Methods: The urine samples underwent gross examination, wet mount, and Gram stain. Semiquantitative cultures were conducted on conventional media (MacConkey agar, blood agar, and CLED agar) and UTI chromogenic media. Uropathogen identification employed standard microbiological techniques. Antibiotic susceptibility was determined using the Kirby–Bauer disk diffusion method, with interpretation based on CLSI guidelines. Plates were incubated overnight, and clear zone diameters around antibiotic discs were measured for sensitivity or resistance determination. Results: The study comprised 64.75% male children and 35.25% female children. Analyzing the age distribution, the majority of participants fell within the age range of 1–5 years (35%), followed by those &lt;1 year (33.75%), and the age group of 5–12 years, accounting for 31.25% of the total 400 participants. The findings from our investigation revealed a UTI prevalence of 17.25%, with Escherichia coli and Klebsiella emerging as the predominant uropathogens. Notably, these pathogens exhibited a significant susceptibility to carbapenems, nitrofurantoin, and amikacin. Conclusion: Our study identified a male predominance and various age distributions among UTI patients. Antibiotic susceptibility patterns revealed E. coli and Klebsiella pneumoniae’s high sensitivity to key antibiotics, whereas Enterococcus spp. exhibited significant high-level aminoglycoside resistance. This study underscores the importance of tailored antibiotic strategies based on local resistance profiles to combat UTIs effectively.

Antibiotic Resistance Trends in Uropathogens during the COVID-19 Pandemic in Western Romania: A Cross-Sectional Study.

The emergence and spread of antimicrobial resistance have been significant global health challenges, exacerbated by the COVID-19 pandemic. As healthcare systems faced unprecedented pressures, the management of non-COVID conditions, including urinary tract infections (UTIs), also encountered obstacles due to changes in microbial flora and antibiotic usage patterns. This cross-sectional study aimed to characterize the antimicrobial resistance trends among bacterial uropathogens isolated from patients in the Western region of Romania, between January 2020 and December 2022. The objectives were to map the resistance patterns and observe the pandemic's influence on antimicrobial resistance, particularly among enterobacterial Gram-negative species, to guide treatment and infection control strategies. From a total of 2472 urine samples collected during the study period, 378 positive samples were analyzed. This study found that Escherichia coli was the most commonly isolated uropathogen, making up 46.3% of the cases (n = 175), with Klebsiella pneumoniae at 20.6% (n = 78). There was a high resistance of Klebsiella pneumoniae to several antibiotics, while carbapenemase production increased to 52.5% and extended-spectrum beta-lactamase (ESBL) present in 24.3% of the strains. Escherichia coli showed high resistance rates to amoxicillin-clavulanic acid (from 45.4% in 2020 to 53.8% in 2022) and trimethoprim/sulfamethoxazole (from 27.5% in 2020 to 47.2% in 2022). The increasing trend of antimicrobial resistance noted during the pandemic, especially in Gram-negative enterobacterial species, highlights the urgent need for robust infection control measures and rational antibiotic use. This study underscores the critical importance of continuous surveillance to adapt antibiotic therapies effectively and prevent the further spread of resistance, thereby ensuring effective management of UTIs in the evolving healthcare landscape influenced by the pandemic.

Microbial Pattern of Neonatal Sepsis in the Neonatal Intensive Care Unit of dr. Ramelan Navy Central Hospital.

The morbidity and mortality rates from neonatal sepsis remain high. However, there is limited information about the microbial pattern of neonatal sepsis in Indonesia. Microbial patterns can give an overview of the hygiene of an environment and act as a determinant for choosing definitive antibiotic treatment in neonatal sepsis patients. The organisms that cause neonatal sepsis differ from unit to unit and from time to time within the same unit. This study is aimed at discovering the microbial pattern of neonatal sepsis in the Neonatal Intensive Care Unit (NICU), dr. Ramelan Navy Central Hospital, in 2021-2022. This is a retrospective, cross-sectional study that takes secondary data from the NICU and clinical microbiology department of dr. Ramelan Navy Central Hospital. Data that met the inclusion and exclusion criteria available between January 1, 2021, and December 31, 2022, were collected. Patients whose blood cultures were positive for bacterial growth and diagnosed with sepsis were selected as the study sample. Out of 174 samples, 93 (53.4%) were found positive for bacterial infection and diagnosed as neonatal sepsis. Gram-negative isolates (96.8%) were predominant. Sixty-point-two percent of Klebsiella pneumoniae XDR, 19.4% of Klebsiella pneumoniae ESBL, and 8.6% of Burkholderia cepacia XDR were identified. The gram-positive isolates found in this study were only 3 samples (3.2%). Two-point-one percent of MRSA and 1.1% of Staphylococcus haemolyticus MDR were identified. The most common microorganisms causing neonatal sepsis in our NICU were gram-negative bacteria, particularly Klebsiella pneumoniae XDR. Following the recommended infection control procedures, practicing good hand hygiene, and having access to basic supplies and equipment are important to prevent and reduce the incidence of sepsis.

Effect of Plateau pika on Soil Microbial Assembly Process and Co-Occurrence Patterns in the Alpine Meadow Ecosystem.

Burrowing animals are a critical driver of terrestrial ecosystem functioning, but we know little about their effects on soil microbiomes. Here, we evaluated the effect of burrowing animals on microbial assembly processes and co-occurrence patterns using soil microbiota from a group of habitats disturbed by Plateau pikas (Ochtona curzoniae). Pika disturbance had different impacts on bacterial and fungal communities. Fungal diversity generally increased with patch area, whereas bacterial diversity decreased. These strikingly different species-area relationships were closely associated with their community assembly mechanisms. The loss of bacterial diversity on larger patches was largely driven by deterministic processes, mainly due to the decline of nutrient supply (e.g., organic C, inorganic N). In contrast, fungal distribution was driven primarily by stochastic processes that dispersal limitation contributed to their higher fungal diversity on lager patches. A bacterial co-occurrence network exhibited a positive relationship of nodes and linkage numbers with patch area, and the fungal network presented a positive modularity-area relationship, suggesting that bacteria tended to form a closer association community under pika disturbance, while fungi tended to construct a higher modularity network. Our results suggest that pikas affects the microbial assembly process and co-occurrence patterns in alpine environments, thereby enhancing the current understanding of microbial biogeography under natural disturbances.

Organic carbon negatively affects the diversity of soil nitrous oxide reducers in Chinese fir plantations at a regional scale

Large-scale planting of Chinese fir (Cunninghamia lanceolata) can bring considerable economic benefits but also seriously alters soil properties, disrupting soil microbial survival patterns and giving rise to distinct microbial communities. Nitrous oxide (N2O) reduction is the sole recognized biological sink for N2O, thereby playing a critical role in forest nitrogen cycling. However, the distribution of N2O reducers in Chinese fir plantation soils and the underlying factors at a regional scale remain unclear. Here, we assessed the abundance, diversity, and community structure of nosZ I-type N2O reducers in soil samples collected from nine state-owned forest farms in Fujian Province, China. The abundance of nosZ I-type reducers exhibited significant variation across sites, with altitude exerting the greatest influence, positively influencing their abundance. Soil organic carbon (SOC) and dissolved organic carbon (DOC) were the strongest predictors of alpha-diversity. Interestingly, SOC and DOC exhibited a negative association with nosZ I-type reducer alpha-diversity. Additionally, DOC played a significant role in influencing community structure. All nosZ I sequences were associated with Alphaprotebacteria and Betaproteobacteria, with Alphaproteobacteria dominating nosZ I-type reducer communities in all soils, accounting for over 90 % of the total sequences. Moreover, the modified stochasticity ratio values exceeded 0.5 at all sampling sites except for one, characterized by the lowest pH and relatively lower nutrient content, indicating the predominance of stochastic processes in community assembly. Taken together, our results provide novel evidence that the augmentation of organic carbon content could potentially reduce diversity and alter the structure of nosZ I-type reducer communities, with potential implications for N2O emissions in Chinese fir plantations.

Altered microbial diversity, interaction pattern, and nitrogen transformation processes response to different iron addition amounts in constructed wetlands

Microbial interactions affect the biogeochemical cycles, pollutant transformation, and stable operation of constructed wetlands (CWs), and these interaction networks are vulnerable to environmental stress. Iron (Fe)-based CWs have been demonstrated as an intensified nitrogen (N) removal system, however, whether and how the addition of Fe, an exogenous environmental stressor, and its amount affect the microbial interactions and functions are poorly understood, which inevitably determine the stability and sustainability of CW system. Herein, we demonstrated that higher Fe addition could effectively improve the stability and sustainability of the CW system by regulating the diversity and interactions of the microbial communities rather than the relative abundance of functional genes. Specifically, low Fe-addition reduced the complexity and robustness of microbial network and the number of keystone taxa, while the high Fe-addition CWs showed the opposite pattern. In CWs with low Fe-addition, N-Fe cycles were accomplished by increasing competition represented by a high proportion of negative links between the same function, whereas increased cooperation was observed in CWs with high Fe-addition. Moreover, Fe addition shaped divergent N transformation processes, with denitrification-dissimilatory nitrate reduction to ammonium (DNRA) dominating in control group, and nitrification-partial denitrification/anammox (PD/A) dominating in Fe-based CWs, and the intensity of nitrification-PD/A increased with the addition amount of Fe. Our study provided insights into the potential ways to improve the stability and sustainability of Fe-CWs for intensified pollutant elimination, which would be valuable to advance the design, sustainable operation, and application of Fe-CWs.