Changes In Microbial Community Structure Research Articles

Dynamic interplay between soil microbial communities, enzyme activities, and pear quality across planting years

Few studies have been reported on the effect of planting years on fruit quality and soil of pear trees. In this study, four planting years (T5, T20, T30, and T40) of Cuiguan pears were used to analyze fruit quality, rhizosphere soil enzymes, and microbial diversity of pear trees, and their correlations. The results showed that the content of sucrose, reducing sugar and ascorbic acid in Cuiguan Pear showed a tendency of increasing and then decreasing with the increase of planting years, in which the highest content was found in 20- and 30-year-old fruits, and the highest content of total acid was found in 5-year-old fruits. Rhizosphere soil enzyme activities varied with planting year, with the highest protease activity in 20-year-old soil, phosphatase and urease in 30-year-old soil, polyphenol oxidase in 5-year-old soil, and sucrase in 40-year-old soil. The microbial diversity index and the number of OTUs showed an increasing and decreasing trend with the increase of planting years. Among the top 11 bacteria in pear rhizosphere soil average relative abundance, with Bradyrhizobium decreasing in relative abundance at the peak pear fruiting stages (T20 and T30), while Acidothermus showed an increasing trend in relative abundance with increasing planting years. RDA analysis showed that there were differences in the microbial community structure of pear trees at different planting years, and that both sucrose and reducing sugar contents in pears were positively correlated with T20 and T30, ascorbic acid content was positively correlated with T40, whereas the total acid content was positively correlated with T5, and that T20 was positively correlated with soil protease and phosphate mono esterase activities, and that T30 was positively correlated with polyphenol oxidase and urease activities, whereas T40 was positively correlated with sucrase activity. In summary, with the increase of planting years, changes in soil microbial community structure and soil enzyme activity have a significant impact on pear quality formation, and the results of the study provide a theoretical basis for scientific management of pear orchards.

Effects of Water Level Fluctuations and Vegetation Restoration on Soil Prokaryotic Microbial Community Structure in the Riparian Zone of the Three Gorges Reservoir

Riparian zones are typical fragile and sensitive ecological areas. Fluctuations in water level are the main factor affecting the soil environment in these zones, and vegetation restoration is considered an important means of soil conservation there. However, the interactive effects of water level fluctuations and vegetation restoration on the soil microbial community structure in the reservoir riparian zone remain unclear. Therefore, we selected abandoned grassland and artificial forestland at different water level elevations as research objects in the riparian zone of the Three Gorges Reservoir. We used 16S rRNA high-throughput sequencing technology to explore the composition and diversity of soil prokaryotic microbial communities and investigated the main environmental factors driving the soil microbial community structure. The results showed that the α diversity of soil prokaryotes was the highest at the low water level of the riparian zone. The Pielou_e index, Shannon index, and Simpson index at the 163 m elevation were significantly higher than those at the 168 m elevation, and the Chao1 index and Shannon index were significantly higher than those at the 173 m elevation. However, no significant difference was found in the soil microbial community α diversity between abandoned grassland and artificial forestland. At the same time, water level fluctuations and vegetation restoration had significant effects on the community composition of soil prokaryotic microorganisms, and there were significant differences in biomarker categories in different study sites. Notably, the effects of vegetation restoration types on the soil prokaryotic microbial community structure were stronger than that of water level fluctuations. In addition, the results of hierarchical segmentation showed that soil pH was the main driving factor for the change in soil prokaryotic microbial community structure in the Three Gorges Reservoir. These results deepen our understanding of the variations in microbial community structure in the reservoir riparian zone and provide scientific reference for the restoration and reconstruction of the riparian zone ecosystem.

Nitrogen-fixing cyanobacteria enhance microbial carbon utilization by modulating the microbial community composition in paddy soils of the Mollisols region

Nitrogen-fixing cyanobacteria (NFC) are photosynthetic prokaryotic microorganisms capable of nitrogen fixation. They can be used as biofertilizers in paddy fields, thereby improving the rice tillering capacity and yield. To reveal the microbiological mechanisms by which nitrogen-fixing cyanobacteria alter soil carbon storage, we conducted a field experiment using NFC as a partial substitute for nitrogen fertilizer in paddy fields in the Sanjiang Plain of Northeast China's Mollisols region. Using metagenomic sequencing technology and Biolog Ecoplate™ carbon matrix metabolism measurements, we explored the changes in the soil microbial community structure and carbon utilization in paddy fields. The results indicated that the replacement of nitrogen fertilizer with NFC predisposed the soil microbial community to host a great number of copiotrophic bacterial taxa, and Proteobacteria and Actinobacteria were closely associated with the metabolism of soil carbon sources. Moreover, through co-occurrence network analysis, we found that copiotrophic bacteria clustered in modules that were positively correlated with the metabolic level of carbon sources. The addition of NFC promoted the growth of copiotrophic bacteria, which increased the carbon utilization level of soil microorganisms, improved the diversity of the microbial communities, and had a potential impact on the soil carbon stock. The findings of this study are helpful for assessing the impact of NFC on the ecological function of soil microbial communities in paddy fields in the black soil area of Northeast China, which is highly important for promoting sustainable agricultural development and providing scientific reference for promoting the use of algal-derived nitrogen fertilizers.

Soil bacterial community structure and co‐occurrence networks in response to the succession of secondary forests in subtropical regions

AbstractA large amount of secondary successional vegetation (subtropical evergreen broadleaved forests) has formed after the extensive deforestation and cultivation of coniferous forests in Wuyi Mountain, Southeast China. However, we lack a detailed understanding of the dynamic changes in microbial community structure and its co‐occurrence network during succession. The features that are responsible for alterations in the soil bacterial community remain poorly defined. Therefore, we compared the soil physicochemical properties, enzyme activities, and bacterial diversity among three different forests (a coniferous forest [CF], early stage of succession; a mixed conifer‐broadleaf forest [CBMF], middle stage of succession; an evergreen broadleaf forest [EBF]; late stage of succession). Results indicated that the contents of soil organic carbon and microbial biomass carbon (MBC) in CBMF were higher compared with those in CF. The alpha diversity indices were the highest in CBMF. Functional annotation of prokaryotic taxa predicted the relative abundances of chemoheterotrophy and aerobic chemoheterotrophy were lower in CF than in the other two forests. Bacterial network topology was affected by forest succession, with CBMF having more complex bacterial networks. Mantel's test indicated the soil nitrate nitrogen content (P = 0.03) was the most important property that shaped the bacterial community composition, bacterial diversity was influenced by soil pH (P = 0.026), and the contents of available phosphorus (P = 0.04) and MBC (P = 0.022) during the succession process. In conclusion, the succession of secondary forests promoted soil nutrient accumulation and improved bacterial diversity and network complexity.

Analysis of microbial community evolution, autolysis phenomena, and energy metabolism pathways in Pholiota nameko endophytes.

Pholiota nameko is a widely consumed edible fungus. This study focuses on two crucial developmental stages of Pholiota nameko, namely, mycelium and ascospores. The objectives of this research were to investigate changes in microbial diversity and community structure during the growth of Pholiota nameko and to analyze the adaptability of the dominant strains to their respective habitats through metabolic. Specifically, we conducted second-generation sequencing of the 16S rRNA gene (Illumina) on samples obtained from these stages. In addition, we isolated and characterized endophytes present in Pholiota nameko, focusing on examining the impact of dominant endophyte genera on autolysis. We also conducted a metabolic pathway analysis. The results unveiled 578,414 valid sequences of Pholiota nameko endophytic fungi. At the phylum level, the dominant taxa were Basidiomycota, Ascomycota, Zoopagomycota, and Mucoromycota. At the genus level, the dominant taxa observed were Pholiota, Inocybe, Fusarium, and Hortiboletus. For endophytic bacteria, we obtained 458,475 valid sequences. The dominant phyla were Proteobacteria, TM6, Firmicutes, and Bacteroidetes, while the dominant genera were Edaphobacter, Xanthomonas, Burkholderia, and Pseudomonas. Moreover, we identified the isolated strains in Pholiota nameko using 16S rDNA, and most of them were found to belong to the genus Pseudomonas, with Pseudomonas putida being the most prevalent strain. The findings revealed that the Pseudomonas putida strain has the ability to slow down the breakdown of soluble proteins and partially suppress the metabolic processes that generate superoxide anion radicals in Pholiota nameko, thereby reducing autolysis. Additionally, our results demonstrated that molybdenum enzyme-mediated anaerobic oxidative phosphorylation reactions were the primary energy metabolism pathway in the Pseudomonas putida strain. This suggests that the molybdenum cofactor synthesis pathway might be the main mechanism through which Pholiota nameko adapts to its complex and diverse habitats.

Research on the Microbial Community Structure and Evolutionary Changes During the Industrial Fermentation Process of Cigar Tobacco Leaves

Cigar tobacco leaves host a diverse bacterial community on their surfaces, playing a vital role in the fermentation process. This study aimed to investigate and analyze the bacterial community dynamics during the artificial fermentation of cigar tobacco leaves, recognizing the advantages of artificial over natural fermentation. The research focused on elucidating the structural composition of the bacterial community on the leaves, exploring their metabolic activities, understanding how they influence the characteristics of the leaves during artificial fermentation, and identifying potential metabolic pathways. Significant shifts in the microbial community were observed post-fermentation, with a marked increase in diversity. Notably, genera like Oceanobacillus, Terribacillus, and Corynebacterium exhibited substantial growth during the mid-phase of fermentation, suggesting their importance in the process. The insights derived from this study shed light on the artificial fermentation process of cigar tobacco leaves, offering opportunities for enhancing safety and quality.

Changes in the Soil Microbial Community Structure and Driving Factors during Post-Fire Recovery of the Larix gmelinii Rupr. Forest in Northern China

Fire is crucial for shaping northern forest ecosystems and can affect soil microbial community structure. However, there are few studies on the long-term effects of forest fire disturbance on soil microbial community diversity. In this study, we employed high-throughput sequencing of 16S rRNA and ITS1 to assess variations in the abundance of bacterial and fungal communities in dominant populations at 1, 6, and 11 years post-fire. Furthermore, a comprehensive analysis was conducted to examine the relationship between soil microenvironmental changes and soil microbial communities after fire disturbances, considering soil physicochemical properties, including bulk density, moisture content, pH, organic carbon, total nitrogen, ammonium nitrogen, nitrate nitrogen, available potassium, and available phosphorus. We found that fire significantly increased soil pH, NO3−-N, AP, and AK contents, in which the content of NO3−-N basically recovered to the pre-fire level at 11 years after fire. The soil SOC and TN contents decreased significantly 1 year after the fire. However, compared to the unfired site, the SOC content essentially recovered 11 years after the fire, while TN content was still significantly higher 11 years after fire. Furthermore, fire changed the diversity and richness of soil microbial communities to some extent. PCoA and NMDS analyses suggested that the bacterial community structures in soil samples from different burned areas with different recovery periods exhibited similarity. However, notable differences were observed in the fungal community structures between the 1-year and 6-year post-fire study sites when compared to the unburned control site. Bacterial communities predominantly comprised Proteobacteria, Actinobacteria, and Acidobacteria, while fungal communities were mainly dominated by Ascomycota and Basidiomycota. RDA confirmed the significant roles of SOC, TN, and NO3−-N in affecting the diversity of soil microbial communities. Therefore, our study not only enhances our understanding of the long-term effects of forest fire disturbances on soil properties and soil microbial community structure, but also provides insights for further utilizing and controlling carbon and nitrogen content to regulate soil microbial activity and accelerate the recovery process of burned areas.

Effects of the combined application of livestock manure and plant residues on soil organic carbon sequestration in the southern Loess Plateau of China

Increasing soil organic carbon (SOC) sequestration enhances the stability and productivity of agricultural ecosystems. Organic material application is a direct and effective way to maintain and improve SOC sequestration. However, currently, there is little knowledge on efficient practices for combined organic material application to improve SOC sequestration. In this study, we evaluated the effect of three organic materials alone or in combination on SOC sequestration in a 4-year field experiment. Eight treatments were included: control (CK, conventional chemical fertilizer), green manure (G), straw (S), decomposed sheep manure (M), green manure plus straw (GS), green manure plus sheep manure (GM), straw plus sheep manure (SM), green manure, and straw plus sheep manure (GSM). In 2020, decomposed sheep manure application (M, SM, GM and GSM) resulted in the greatest cumulative SOC sequestration (9.5–10.8 Mg C ha−1), followed by those in treatments S (6.1 Mg C ha−1) and GS (6.9 Mg C ha−1). The SOC sequestration efficiency in the M treatment (44.8 %) was greater than that in the others (15.2–34.8 %). A random forest model revealed that organic material quantity and quality, enzyme activity, and microbial community composition were the primary factors determining SOC sequestration. Sheep manure application increased SOC sequestration by increasing lignin quantity and proportion. Incorporating green manure and straw return enhanced SOC sequestration by promoting microbial growth and increasing soil C-acquiring enzyme activity. However, interactions between sheep manure and plant residues resulted in decreases in SOC sequestration efficiency compared with sheep manure application alone. This is because combined fertilization stimulated microbial growth and enzyme activity, causing changes in microbial community structure and accelerating organic material and SOC decomposition. Thus, we do not recommend combining livestock manure with straw or green manure to improve SOC sequestration and soil quality in the southern Loess Plateau.

Differential effects of warming on the complexity and stability of the microbial network in Phragmites australis and Spartina alterniflora wetlands in Yancheng, Jiangsu Province, China.

The impact of climate warming on soil microbial communities can significantly influence the global carbon cycle. Coastal wetlands, in particular, are susceptible to changes in soil microbial community structure due to climate warming and the presence of invasive plant species. However, there is limited knowledge about how native and invasive plant wetland soil microbes differ in their response to warming. In this study, we investigated the temporal dynamics of soil microbes (prokaryotes and fungi) under experimental warming in two coastal wetlands dominated by native Phragmites australis (P. australis) and invasive Spartina alterniflora (S. alterniflora). Our research indicated that short-term warming had minimal effects on microbial abundance, diversity, and composition. However, it did accelerate the succession of soil microbial communities, with potentially greater impacts on fungi than prokaryotes. Furthermore, in the S. alterniflora wetland, experimental warming notably increased the complexity and connectivity of the microbial networks. While in the P. australis wetland, it decreased these factors. Analysis of robustness showed that experimental warming stabilized the co-occurrence network of the microbial community in the P. australis wetland, but destabilized it in the S. alterniflora wetland. Additionally, the functional prediction analysis using the Faprotax and FunGuild databases revealed that the S. alterniflora wetland had a higher proportion of saprotrophic fungi and prokaryotic OTUs involved in carbon degradation (p < 0.05). With warming treatments, there was an increasing trend in the proportion of prokaryotic OTUs involved in carbon degradation, particularly in the S. alterniflora wetland. Therefore, it is crucial to protect native P. australis wetlands from S. alterniflora invasion to mitigate carbon emissions and preserve the health of coastal wetland ecosystems under future climate warming in China.

Intestinal microbial profiling and immune responses of hybrid snakehead (Channa maculata ♀ × Channa argus ♂) challenged with Nocardia seriolae strain

Nocardiosis in fish, caused by Nocardia seriolae (a kind of filamentous bacterium), is a severe disease in aquaculture, affecting over 40 species of marine and freshwater fish and causing great losses. To investigate the relationship between fish nocardiosis and the gut microbiota, we first artificially infected hybrid snakehead (female Channa maculata × male Channa argus) with N. seriolae (1.0 × 107 CFU/mL), then utilized techniques such as high-throughput sequencing of 16 S rRNA, histopathology, and quantitative reverse transcription-polymerase chain reaction (qRT-PCR) to analyze the changes in microbial community structure, intestinal histopathological characteristics, and related immune genes expression in hybrid snakehead. Changes in gut microbial community structure and diversity were observed starting from day 2, followed by fluctuations on day 4, and significant alterations on day 6. Four major phyla (Actinomycetes, Proteobacteria, Firmicutes, and Bacteroidetes), particularly Actinomycetes, reflected the temporal variations in the gut microbiota structure. The composition of the gut microbiota also underwent significant changes, with beneficial microorganisms such as Lactobacillus decreasing and harmful microorganisms such as Aeromonas and Nocardia increasing. The pathological sections showed that after N. seriolae injection, the fish intestinal villi became distorted and widely spaced, with increasing damage over time, leading to severe shrinkage and atrophy by the sixth day. Additionally, immune-related genes, such as TLR2 and IRF2, exhibited higher mRNA expression levels (P < 0.01) in the intestinal tissues of the infected fish. Overall, this study provides preliminary insights into the dynamic changes in gut microbial community, immune response, and intestinal pathogenic mechanisms during N. seriolae infection in hybrid snakehead, at both the levels of gut microbial composition and mRNA expression. These findings are important for better understanding and managing Nocardia infection in fish.

Ecological characteristics of sugar beet plant and rhizosphere soil in response to high boron stress: A study of the remediation potential

High boron (B) stress degrades the soil environment and reduces plant productivity. Sugar beet has a high B demand and potential for remediation of B-toxic soils. However, the mechanism regarding the response of sugar beet plants and rhizosphere soil microbiome to high B stress is not clear. In the potted soil experiment, we set different soil effective B environments (0.5, 5, 10, 30, 50, and 100 mg kg−1) to study the growth status of sugar beets under different B concentrations, as well as the characteristics of soil enzyme activity and microbial community changes. The results showed that sugar beet growth was optimal at 5 mg kg−1 of B. Exceeding this concentration the tolerance index decreased. The injury threshold EC20 was reached at an available B concentration of 35.8 mg kg−1. Under the treatment of 100 mg kg−1, the B accumulation of sugar beet reached 0.22 mg plant−1, and the tolerance index was still higher than 60%, which had not yet reached the lethal concentration of sugar beet. The abundance of Acidobacteriota, Chloroflexi and Patescibacteria increased, which was beneficial to the resistance of sugar beet to high B stress. In summary, under high B stress sugar beet had strong tolerance, enhanced capacity for B uptake and enrichment, and changes in soil microbial community structure. This study provides a theoretical basis for clarifying the mechanism of sugar beet resistance to high B stress and soil remediation.

The impact of microbial community structure changes on the migration and release of typical heavy metal (loid)s during the revegetation process of mercury-thallium mining waste slag

The effect of changes in microbial community structure on the migration and release of toxic heavy metal (loid)s is often ignored in ecological restoration. Here, we investigated a multi-metal (mercury and thallium, Tl) mine waste slag. With particular focus on its strong acidity, poor nutrition, and high toxicity pollution characteristics, we added fish manure and carbonate to the slag as environmental-friendly amendments. On this basis, ryegrass, which is suitable for the remediation of metal waste dumps, was then planted for ecological restoration. We finally explored the influence of changes in microbial community structure on the release of Tl and As in the waste slag during vegetation reconstruction. The results show that the combination of fish manure and carbonate temporarily halted the release of Tl, but subsequently promoted the release of Tl and arsenic (As), which was closely related to changes in the microbial community structure in the waste slag after fish manure and carbonate addition. The main reason for these patterns was that in the early stage of the experiment, Bacillaceae inhibited the release of Tl by secreting extracellular polymeric substances; with increasing time, Actinobacteriota became the dominant bacterium, which promoted the migration and release of Tl by mycelial disintegration of minerals. In addition, the exogenously added organic matter acted as an electron transport medium for reducing microorganisms and thus helped to reduce nitrate or As (Ⅴ) in the substrate, which reduced the redox potential of the waste slag and promoted As release. At the same time, the phylum Firmicutes, including specific dissimilatory As-reducing bacteria that are capable of converting As into a more soluble form, further promoted the release of As. Our findings provide a theoretical basis for guiding the ecological restoration of relevant heavy-metal (loid) mine waste dumps.

Seasonal changes of prokaryotic microbial community structure in Zhangjiayan Reservoir and its response to environmental factors

As a typical sub-deep reservoir in the upper reaches of the Yangtze River in the southwest region, Zhangjiayan Reservoir is also an important source of drinking water. Exploring the role of microorganisms in the material cycle of water bodies is of great significance for preventing the exacerbation of eutrophication in the reservoir. In this study, water samples from the overlying water of five points in the reservoir were collected four times in spring (April), summer (July), autumn (November), and winter (January) of 2022–2023 using a gas-tight water sampler. Physicochemical factors were measured, and the microbial community structure was analyzed by high-throughput MiSeq sequencing of the V3–V4 hypervariable region of 16S rRNA gene in order to explore the relationship between physicochemical factors and microbial community structure and the dominant microbial populations that affect eutrophication of the reservoir. The following results were obtained through analysis. Among the 20 overlying water samples from Zhangjiayan Reservoir, a total of 66 phyla, 202 classes, 499 orders, 835 families, 1716 genera, and 27,904 ASVs of the bacterial domain were detected. The phyla Proteobacteria and Actinobacteria were dominant in the microbial community of the overlying water in Zhangjiayan Reservoir. At the genus level, hgcI_clade and Actinobacteria had the highest abundance and was the dominant population. The microbial community in the water of Zhangjiayan Reservoir has a high level of diversity. The diversity index ranked by numerical order was winter > autumn > summer > spring. Significant differences were found in the composition and structure of the microbial community between the spring/summer and autumn/winter seasons (p < 0.05). Total phosphorus, dissolved total phosphorus, soluble reactive phosphorus, and dissolved oxygen have a significant impact on the composition and structure of the microbial community (p < 0.01). The bacterial community in the overlying water of Zhangjiayan Reservoir showed a mainly positive correlation. Sphingomonas, Brevundimonas, and Blastomonas were the central populations of the bacterial community in the overlying water of Zhangjiayan Reservoir. This study indicates that environmental factors, such as phosphorus and other nutrients, have a significant impact on the formation of the microbial community structure in different seasons. Sphingomonas, Brevundimonas, and Blastomonas are key populations that may have a significant impact on eutrophication in Zhangjiayan Reservoir.

Changes in soil microbial carbon fixation pathways along the oasification process in arid desert region: A confirmation based on metagenome analysis

Microbial carbon fixation has been proved to play a key role in soil carbon accumulation in arid desert oasis, but the fixation mechanism remains unclear. To solve it, we used metagenomic sequencing technology to measure the changes of soil microbial community structure, carbon fixation–related genes and carbon fixation pathway, as well as their relationships with soil properties between natural desert shrubbery (CK) and four oasis farmlands with different cultivation years (i.e., 3, 18 and 30 years) in the arid desert region of northwest China. The results showed that the contents of four soil carbon fraction (soil organic carbon/SOC, soil recalcitrant organic carbon/ROC, soil water solution carbon /WSC, and microbial biomass carbon/MBC) all significantly increased with the cultivation years (30 years ≥ 18 years > 6 years ≥ 3 years ≥ CK) (P < 0.05). Microbial composition was significant difference among CK, 3-, 6-, 18- and 30-years cultivated farmlands. Bacteria were the soil dominant taxa, and its relative abundance gradually decreased with the cultivation years. Proteobacteria, Actinobacteria, Bacteroidetes and Acidobacteria were the dominant phylum of soil microorganisms in desert shrubbery and oasis farmlands. Their relative abundance changed obviously with cultivation years. Six microbial carbon fixation pathways. i.e., the reductive tricarboxylic acid cycle (rTCA), dicarboxylate/4–hydroxybutyrate cycle (DC/4–HB cycle), 3–hydroxypropionate bicycle (3–HP bi–cycle), 3–hydroxypropionate/4–hydroxybutyrate cycle (3–HP/4–HB cycle), Calvin cycle and the Wood–Ljungdahl pathway (WL pathway), were found in all soils, but only the rTCA, DC/4–HB, 3–HP/4–HB cycles and WL pathway significantly changed with the cultivation years. The rTCA cycle was the most common fixation pathway, followed by DC/4–HB cycle and 3–HP/4–HB cycle, while WL pathway was least detected. Soil properties, especially pH, recalcitrant organic carbon, bulk density, total salinity and soil water contents, affected microbial community composition and carbon fixation–related genes in the oasification process. Our results suggested that oasification affected microbial carbon fixation by changing the soil environment due to human agricultural activities. Limited by energy supply in the nutrient–poor soils, rTCA and DC/4–HB cycles were mainly used by microorganisms to fix carbon in oasis farmlands.

Performance and interaction mechanism of integrating alkali pretreatment and immobilized electrodes on enhanced sludge digestion for methane production

Introduction of voltage or conductive materials have been proven to be effective strategies for enhancing the stability and efficiency of sludge digestion for methane recovery. This experiment simulated a two-phase anaerobic system, consisting of an acid-producing phase with alkali pretreatment and a methane-producing phase with immobilized electrodes and voltage enhancement. Various effective and comparative experiments were conducted to investigate the crucial roles of immobilized electrodes like carbon brush (CB) and nickel foam (NF), electroactive biofilm and voltage during the sludge methane-producing phase. The experimental results indicate that directly application of immobilized CB and NF electrode to promote sludge anaerobic digestion achieves better performance than additional voltage supply. The electrodes can increase methane production by 38% to 94%, whereas under additional voltage supply, methane production only increases by 22%–53% compared to the control. Through the analysis of key transformations in organic substrates and changes in microbial community structure, the inherent advantages of electrode materials in promoting the syntrophic methanogenesis processes are confirmed. Compared to suspended sludge, the types and relative abundance of typical syntrophic methane-producing microorganisms, Methanosarcina, and acetogenic bacteria, Syntrophomonas on the electrode surface significantly increase by 8.5% and 1.7%. This process is notably superior to the methane generation process dominated by hydrogenotrophic methanogensis after applying voltage. The results indicate that CB and NF are suitable conductive materials to promote anaerobic methane recovery, and their effectiveness surpasses that of applying voltage. These research outcomes provide new insights for the development of novel anaerobic digestion enhancement systems.

Aggregation/disaggregation of microalgal-bacterial flocs in high-rate oxidation ponds is a response to biotic/abiotic-induced changes in microbial community structure

AbstractDuring wastewater treatment by integrated algal pond systems (IAPS), microalgal-bacterial flocs (MaB-flocs) form naturally but periodically disaggregate, resulting in poor settling, low biomass recovery, and reduced effluent quality. This study investigates biotic/abiotic-induced changes in microbial community structure in high-rate algal oxidation ponds (HRAOP) of an IAPS on MaB-floc formation and stability during sewage treatment. Results show that dominance by Pseudopediastrum, Desmodesmus and Micractinium species in spring and summer and the chytrids, Paraphysoderma sp. in spring and Sanchytrium sp. in summer, occurred coincident with enhanced MaB-floc formation and biomass recovery (≥90%). In winter, poor floc formation and low biomass recovery were associated with dominance by Desmodesmus, Chlorella, and the Chlorella-like genus Micractinium. A principal components analysis (PCA) confirmed that combinations of colonial microalgae and associated parasitic chytrids underpin MaB-floc formation and stability in spring and summer and that unicells dominated in winter. Dominance by Thiothrix sp. coincided with floc disaggregation. Thus, changes in season, composition and abundance of colonial microalgae and associated parasitic fungi appeared to impact MaB-floc formation, whereas species composition of the bacterial population and emergence of Thiothrix coincided with floc instability and disaggregation.

Microbial metabolite trimethylamine-N-oxide induces intestinal carcinogenesis through inhibiting farnesoid X receptor signaling.

Microbial dysbiosis is considered as a hallmark of colorectal cancer (CRC). Trimethylamine-N-oxide (TMAO) as a gut microbiota-dependent metabolite has recently been implicated in CRC development. Nevertheless, evidence relating TMAO to intestinal carcinogenesis remains largely unexplored. Herein, we aimed to examine the crucial role of TMAO in CRC progression. Apcmin/+ mice were treated with TMAO or sterile PBS for 14 weeks. Intestinal tissues were isolated to evaluate the effects of TMAO on the malignant transformation of intestinal adenoma. The gut microbiota of mouse feces was detected by 16S rRNA sequencing analysis. HCT-116 cells were used to provide further evidence of TMAO on the progression of CRC. TMAO administration increased tumor cell and stem cell proliferation, and decreased apoptosis, accompanied by DNA damage and gut barrier impairment. Gut microbiota analysis revealed that TMAO induced changes in the intestinal microbial community structure, manifested as reduced microbiota diversity and beneficial bacteria. Mechanistically, TMAO bound to farnesoid X receptor (FXR), thereby inhibiting the FXR-fibroblast growth factor 15 (FGF15) axis and activating the Wnt/β-catenin signaling pathway, whereas the FXR agonist GW4064 could blunt TMAO-induced Wnt/β-catenin pathway activation. The microbial metabolite TMAO can enhance intestinal carcinogenesis by inhibiting the FXR-FGF15 pathway.

Disproportional oxidation rates of ammonia and nitrite deciphers the heterogeneity of fertilizer-induced N2O emissions in agricultural soils

Nitrous oxide (N2O) is a potent greenhouse gas and ozone-depleting chemical. Although nitrogen (N) fertilizer rate is the best single predictor of N2O emissions, the spatial heterogeneity of the emission factor is striking and poorly understood. Nitrite (NO2−) dynamics have been reported to be correlated with N2O production in many soils; however, NO2− is often overlooked owing to its rare accumulation, and the underlying mechanisms of NO2− accumulation and the relationship with spatiotemporal heterogeneity of N2O emissions in response to N addition remains unclear. Here, we collected upland agricultural soils that cover the main upland agricultural production regions of China and investigated the soil-specific effects on N2O emissions, changes in microbial abundances and community structures of nitrifiers, and co-occurrence networks for ammonium (NH4+)-based fertilizer addition. Our results showed that high NO2− accumulation and high N2O emissions were generally correlated with low nxrA/AOB gene ratios (R2 = 0.90 and 0.86, respectively, P < 0.01). Further network analyses revealed that NH4+ addition increased the network links of the nitrification functional communities by 23% and enhanced the interrelationship between AOB and nitrite oxidizers. By synthesizing our data with previous studies in the literature, we found that soil N2O emission rate and nxrA/AOB gene ratio exhibit a threshold behavior worldwide, suggesting that disproportionality of NH3 and NO2− oxidations rates are involved in the heterogeneity of fertilizer-induced N2O emissions in agricultural soils. These findings enhance our understanding of spatiotemporal heterogeneity in NO2− accumulation and N2O emissions within upland agricultural soils in view of nitrification functional communities.

Mechanical abrasion stimulation: Altered epidermal mucus composition and microbial community in grass carp (Ctenopharyngodon idella)

In modern high-density farming, seasonal change, fishing, transportation, and other conditions easily cause mechanical abrasion of fish skin. This leads to alterations in the material balance of the epidermal mucus composition of fish, preventing normal immune function. Subsequently, the risk of disease increases. In this study, grass carp (Ctenopharyngodon idella) was used as an object to investigate immune-related enzyme activities, structural characteristics, and physiological changes of its epidermal mucous cells caused by mechanical abrasion. Furthermore, we explored the changes in body surface mucus composition and microbial community diversity and structure. Our results showed that mechanical abrasion stimulation, significantly changed the activities of immune-related enzymes, such as lysozyme (LZM), alkaline phosphatase (AKP), and acid phosphatase (ACP) were within 24 h (P < 0.05). Their levels gradually recovered after 48 h. In contrast, no significant change was observed in superoxide dismutase (SOD) levels. The number of mucous cells increased, especially those of type I and type II mucous cells in the dorsal skin, which were significantly increased (P < 0.05). Meanwhile, the stimulation changed the metabolites composition of the fish epidermal mucus in the short term, upregulating 12-OPDA, indole, quinic acid and GSH, which are beneficial to antibacterial and anti-inflammatory, and downregulating L-saccharopine, L-2-aminoadipic acid, spermine, GSSG and ribose 5-phosphate, which disrupt protein synthesis, energy production and DNA synthesis. Additionally, these metabolite changes further affect the composition of microorganism communities, rising the abundance of certain disease-associated microorganisms, such as Acidovorax, Rhizobiaceae, Aurantimicrobium, and Leifsonia, which increases the risk of disease in fish. The findings of the present study provide a deeper understanding of the role of mucus as a component of the immune system in fish and provide a scientific basis for effective grass carp culture management and disease control.

Changes in microbial community structure and yield responses with the use of nano-fertilizers of nitrogen and zinc in wheat–maize system

The growing popularity of nano-fertilization around the world for enhancing yield and nutrient use efficiency has been realized, however its influence on soil microbial structure is not fully understood. The purpose of carrying out this study was to assess the combined effect of nano and conventional fertilizers on the soil biological indicators and crop yield in a wheat–maize system. The results indicate that the at par grain yield of wheat and maize was obtained with application of 75% of recommended nitrogen (N) with full dose of phosphorus (P) and potassium (K) through conventional fertilizers along with nano-N (nano-urea) or nano-N plus nano-Zn sprays and N100PK i.e. business as usual (recommended dose of fertilizer). Important soil microbial property like microbial biomass carbon was found statistically similar with nano fertilizer-based management (N75PK + nano-N, and N75PK + nano-N + nano-Zn) and conventional management (N100PK), during both wheat and maize seasons. The experimental data indicated that the application of foliar spray of nano-fertilizers along with 75% N as basal is a sustainable nutrient management approach with respect to growth, yield and rhizosphere biological activity. Furthermore, two foliar sprays of nano-N or nano-N + nano-Zn curtailed N requirement by 25%, furthermore enhanced soil microbial diversity and the microbial community structure. The specific microbial groups, including Actinobacteria, Bacteroidia, and Proteobacteria, were present in abundance and were positively correlated with wheat and maize yield and soil microbial biomass carbon. Thus, one of the best nutrient management approaches for sustaining productivity and maintaining sound microbial diversity in wheat–maize rotation is the combined use of nano-fertilizers and conventional fertilizers.