Synergistic mechanisms of denitrification in FeS2-based constructed wetlands: Effects of organic carbon availability under day-night alterations.

In constructed wetlands (CWs), carbon source availability profoundly affected microbial metabolic activities engaged in both iron cycle and nitrogen metabolism. However, research gaps existed in understanding the biotransformation of nitrogen and iron in response to fluctuations in organic carbon content under day-night alterations. Results demonstrated increased removal efficiency of NO3--N (95.7 %) and NH4+-N (75.70 %) under light conditions, attributed to increased total organic carbon (TOC). This enhancement promoted the relative abundance of bacteria involved in nitrogen and iron processes, establishing a more stable microbial network. Elevated TOC content also upregulated genes for iron metabolism and glycolysis, facilitating denitrification. Spearman correlation analysis supported the synergistic mechanisms between FeS2-based autotrophic denitrification and TOC-mediated heterotrophic denitrification under light conditions. The significant impact of carbon sources on microbial activities underscores the critical role of organic carbon availability in enhancing nitrogen removal efficiency, providing valuable insights for optimizing FeS2-based CWs design and operation strategies.

Ultrasonication as anaerobic digestion pretreatment to improve sewage sludge methane production: Performance and microbial characterization.

A large amount of sludge is inevitably produced during sewage treatment. Ultrasonication (US) as anaerobic digestion (AD) pretreatment was implemented on different sludges and its effects on batch and semi-continuous AD performance were investigated. US was effective in sludge SCOD increase, size decrease, and CH4 production in the subsequent AD, and these effects were enhanced with an elevated specific energy input. As indicated by semi-continuous AD experiments, the mean daily CH4 production of US-pretreated A2O-, A2O-MBR-, and AO-AO-sludge were 176.9, 119.8, and 141.7 NmL/g-VSadded, which were 35.1%, 32.1% and 78.2% higher than methane production of their respective raw sludge. The US of A2O-sludge achieved preferable US effects and CH4 production due to its high organic content and weak sludge structure stability. In response to US-pretreated sludge, a more diverse microbial community was observed in AD. The US-AD system showed negative net energy; however, it exhibited other positive effects, e.g., lower required sludge retention time and less residual total solids for disposal. US is a feasible option prior to AD to improve anaerobic bioconversion and CH4 yield although further studies are necessary to advance it in practice.

An in-situ biochar-enhanced anaerobic membrane bioreactor for swine wastewater treatment under various organic loading rates.

A biochar-assisted anaerobic membrane bioreactor (BC-AnMBR) was conducted to evaluate the performance in treating swine wastewater with different organic loading rates (OLR) ranging from 0.38 to 1.13 kg-COD/(m3.d). Results indicated that adding spent coffee grounds biochar (SCG-BC) improved the organic removal efficiency compared to the conventional AnMBR, with an overall COD removal rate of > 95.01%. Meanwhile, methane production of up to 0.22 LCH4/gCOD with an improvement of 45.45% was achieved under a high OLR of 1.13 kg-COD/(m3.d). Furthermore, the transmembrane pressure (TMP) in the BC-AnMBR system was stable at 4.5 kPa, and no irreversible membrane fouling occurred within 125 days. Microbial community analysis revealed that the addition of SCG-BC increased the relative abundance of autotrophic methanogenic archaea, particularly Methanosarcina (from 0.11% to 11.16%) and Methanothrix (from 16.34% to 24.05%). More importantly, Desulfobacterota and Firmicutes phylum with direct interspecific electron transfer (DIET) capabilities were also enriched with autotrophic methanogens. Analysis of the electron transfer pathway showed that the concentration of c-type cytochromes increased by 38.60% in the presence of SCG-BC, and thus facilitated the establishment of DIET and maintained high activity of the electron transfer system even at high OLR. In short, the BC-AnMBR system performs well under various OLR conditions and is stable in the recovery energy system for swine wastewater.

Metformin modifies plasma microbial-derived extracellular vesicles in polycystic ovary syndrome with insulin resistance.

INTRODUCTION: This study investigated changes in plasma microbial-derived extracellular vesicles (EVs) in patients with polycystic ovary syndrome and insulin resistance (PCOS-IR) before and after metformin treatment, and aimed to identify bacterial taxa within EVs that were biologically and statistically significant for diagnosis and treatment. METHODS: The case-control study was conducted at Xiamen Chang Gung Hospital, Hua Qiao University. Plasma samples were collected from five PCOS-IR patients of childbearing age before and after 3 months of metformin treatment, and the samples were sequenced. The diversity and taxonomic composition of different microbial communities were analyzed through full-length 16 S glycosomal RNA gene sequencing. RESULTS: After metformin treatment, fasting plasma glucose levels and IR degree of PCOS-IR patients were significantly improved. The 16 S analysis of plasma EVs from metformin-treated patients showed higher microbial diversity. There were significant differences in EVs derived from some environmental bacteria before and after metformin treatment. Notably, Streptococcus salivarius was more abundant in the metformin-treated group, suggesting it may be a potential probiotic. DISCUSSION: The study demonstrated changes in the microbial composition of plasma EVs before and after metformin treatment. The findings may offer new insights into the pathogenesis of PCOS-IR and provide new avenues for research.

An optimal combined slow-release nitrogen fertilizer and urea can enhance the decomposition rate of straw and the yield of maize by improving soil bacterial community and structure under full straw returning system.

Under a full straw returning system, the relationship between soil bacterial community diversity and straw decomposition, yield, and the combined application of slow-release nitrogen and urea remains unclear. To evaluate these effects and provide an effective strategy for sustainable agricultural production, a 2-year field positioning trial was conducted using maize as the research object. Six experimental treatments were set up: straw returning + no nitrogen fertilizer (S1N0), straw returning + slow-release nitrogen fertilizer:urea = 0:100% (S1N1), straw returning + slow-release nitrogen fertilizer:urea = 30%:70% (S1N2), straw returning + slow-release nitrogen fertilizer:urea = 60%:40% (S1N3), straw returning + slow-release nitrogen fertilizer:urea = 90%:10% (S1N4), and straw removal + slow-release nitrogen fertilizer:urea = 30%:70% (S0N2). Significant differences (p < 0.05) were observed between treatments for Proteobacteria, Acidobacteriota, Myxococcota, and Actinobacteriota at the jointing stage; Proteobacteria, Acidobacteriota, Myxococcota, Bacteroidota, and Gemmatimonadota at the tasseling stage; and Bacteroidota, Firmicutes, Myxococcota, Methylomirabilota, and Proteobacteria at the maturity stage. The alpha diversity analysis of the soil bacterial community showed that the number of operational taxonomic units (OTUs) and the Chao1 index were higher in S1N2, S1N3, and S1N4 compared with S0N2 at each growth stage. Additionally, the alpha diversity measures were higher in S1N3 and S1N4 compared with S1N2. The beta diversity analysis of the soil bacterial community showed that the bacterial communities in S1N3 and S1N4 were more similar or closely clustered together, while S0N2 was further from all treatments across the three growth stages. The cumulative straw decomposition rate was tested for each treatment, and data showed that S1N3 (90.58%) had the highest decomposition rate. At the phylum level, straw decomposition was positively correlated with Proteobacteria, Actinobacteriota, Myxococcota, and Bacteroidota but significantly negatively correlated with Acidobacteriota. PICRUSt2 function prediction results show that the relative abundance of bacteria in soil samples from each treatment differed significantly. The maize yield of S1N3 was 15597.85 ± 1477.17 kg/hm2, which was 12.80 and 4.18% higher than that of S1N1 and S0N2, respectively. In conclusion, a combination of slow-release nitrogen fertilizer and urea can enhance the straw decomposition rate and maize yield by improving the soil bacterial community and structure within a full straw returning system.

Composite additives regulate physicochemical and microbiological properties in green waste composting: A comparative study of single-period and multi-period addition modes.

Composting additives can significantly enhance green waste (GW) composting. However, their effectiveness is limited due to the short action duration of a single-period addition. Therefore, this study proposes that multi-period additive modes to prolong the action duration, expedite lignocellulose degradation, reduce composting time, and enhance product quality. This study conducted six treatments (T1-T6), introducing a compound additive (BLP) during the mesophilic (MP) and cooling periods (CP). Each treatment consistently maintained 25% total BLP addition of GW dry weight, with variations only in the BLP distribution in different periods. The composition of BLP consists of Wbiochar: Wlactic acid: Wpond sediment in a ratio of 10:1:40. Specifically, T1 added 25% BLP in CP, T2 added 5% in MP and 20% in CP, T3 added 10% in MP and 15% in CP, T4 added 15% in MP and 10% in CP, T5 added 20% in MP and 5% in CP, and T6 added 25% in MP. In this study, composting temperature, pH value, electrical conductivity, total porosity, the contents of lignin, cellulose, hemicellulose, and nutrient, scanning electron microscopy images, germination index, and the successions of different bacteria and fungi at the phylum and genus levels were detailed. Results showed T4 achieved two thermophilic periods and matured in just 25 days. T4 enhanced lignocellulose degradation rates (lignin: 16-53%, cellulose: 14-23%, hemicellulose: 9-48%) and improved nutrient content. The above results, combined with correlation analysis and structural equation model, indicated that T4 may promote the development of dominant bacteria (Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes) by regulating compost physicochemical properties and facilitate the growth of dominant fungi (Ascomycota and Basidiomycota) by modulating nutrient supply capacity. This ultimately leads to a microbial community structure more conducive to lignocellulose degradation and nutrient preservation. In summary, this study reveals the comprehensive effects of single-period and multi-period addition methods on GW composting, providing a valuable basis for optimizing the use of additives and enhancing the efficiency and quality of GW composting.

Microbial community succession and responses to internal environmental drivers throughout the operation of constructed wetlands.

Constructed wetlands (CWs) have been widely used to ensure effective domestic wastewater treatment. Microorganisms-derived CWs have received extensive attention as they play a crucial role. However, research on the succession patterns of microbial communities and the influencing mechanisms of internal environmental factors throughout entire CW operations remains limited. In this context, three parallel-operated CWs were established in this study to assess the microbial communities and their influencing environmental factors at different substrate depths throughout the operation process using 16S rRNA gene high-throughput sequencing and metagenomic sequencing. The results showed gradual reproduction and accumulation of the microbial communities throughout the CW operation. Although gradual increases in the richness and diversity of the microbial communities were found, there were decreases in the functional expression of the dominant microbial species. The excessive accumulation of microorganisms will decrease the oxidation-reduction potential (ORP) within CWs and attenuate their influence on effluent.. Dissolved oxygen (DO) was the major factor influencing the microbial community succession over the CW operation. The main identified functional bacterial genera responsible for the ammonium oxidation, nitrification, and denitrification processes in the CWs were Nitrosospira, Nitrobacter, Nitrospira, Rhodanobacter, and Nakamurella. The narG gene was identified as a key functional gene linking various components of nitrogen cycling, while pH, electrical conductivity (EC), and ORP were the major environmental factors affecting the metabolism characteristics of nitrogen functional microorganisms. This study provides a theoretical basis for the effective regulation of related microbial communities to achieve long-term, efficient, and stable CW operations.

Microbial fungicides can positively affect aubergine photosynthetic properties, soil enzyme activity and microbial community structure.

Background: This study examined the effects of microbial agents on the enzyme activity, microbial community construction and potential functions of inter-root soil of aubergine (Fragaria × ananassa Duch.). This study also sought to clarify the adaptability of inter-root microorganisms to environmental factors to provide a theoretical basis for the stability of the microbiology of inter-root soil of aubergine and for the ecological preservation of farmland soil. Methods: Eggplant inter-root soils treated with Bacillus subtilis (QZ_T1), Bacillus subtilis (QZ_T2), Bacillus amyloliquefaciens (QZ_T3), Verticillium thuringiensis (QZ_T4) and Verticillium purpureum (QZ_T5) were used to analyse the effects of different microbial agents on the inter-root soils of aubergine compared to the untreated control group (QZ_CK). The effects of different microbial agents on the characteristics and functions of inter-root soil microbial communities were analysed using 16S rRNA and ITS (internal transcribed spacer region) high-throughput sequencing techniques. Results: The bacterial diversity index and fungal diversity index of the aubergine inter-root soil increased significantly with the application of microbial fungicides; gas exchange parameters and soil enzyme activities also increased. The structural and functional composition of the bacterial and fungal communities in the aubergine inter-root soil changed after fungicide treatment compared to the control, with a decrease in the abundance of phytopathogenic fungi and an increase in the abundance of beneficial fungi in the soil. Enhancement of key community functions, reduction of pathogenic fungi, modulation of environmental factors and improved functional stability of microbial communities were important factors contributing to the microbial stability of fungicide-treated aubergine inter-root soils.

An in vitro model system for testing chemical effects on microbiome-immune interactions - examples with BPX and PFAS mixtures.

Introduction: More than 350,000 chemicals make up the chemical universe that surrounds us every day. The impact of this vast array of compounds on our health is still poorly understood. Manufacturers are required to carry out toxicological studies, for example on the reproductive or nervous systems, before putting a new substance on the market. However, toxicological safety does not exclude effects resulting from chronic exposure to low doses or effects on other potentially affected organ systems. This is the case for the microbiome-immune interaction, which is not yet included in any safety studies. Methods: A high-throughput in vitro model was used to elucidate the potential effects of environmental chemicals and chemical mixtures on microbiome-immune interactions. Therefore, a simplified human intestinal microbiota (SIHUMIx) consisting of eight bacterial species was cultured in vitro in a bioreactor that partially mimics intestinal conditions. The bacteria were continuously exposed to mixtures of representative and widely distributed environmental chemicals, i.e. bisphenols (BPX) and/or per- and polyfluoroalkyl substances (PFAS) at concentrations of 22 µM and 4 µM, respectively. Furthermore, changes in the immunostimulatory potential of exposed microbes were investigated using a co-culture system with human peripheral blood mononuclear cells (PBMCs). Results: The exposure to BPX, PFAS or their mixture did not influence the community structure and the riboflavin production of SIHUMIx in vitro. However, it altered the potential of the consortium to stimulate human immune cells: in particular, activation of CD8+ MAIT cells was affected by the exposure to BPX- and PFAS mixtures-treated bacteria. Discussion: The present study provides a model to investigate how environmental chemicals can indirectly affect immune cells via exposed microbes. It contributes to the much-needed knowledge on the effects of EDCs on an organ system that has been little explored in this context, especially from the perspective of cumulative exposure.

Effects of coagulation pre-treatment on chemical and microbial properties of water-soil-plant systems of constructed wetlands.

Chemical coagulation has gained recognition as an effective technique to enhance the removal efficiency of pollutants in wastewater prior to their entry into a constructed wetland (CW) system. However, its potential impact on the chemical and microbial properties of soil and plant systems within CWs requires further research. This study investigated the impact of using ferric chloride (FeCl3) as a pre-treatment stage for dairy wastewater (DWW) on the chemical and microbial properties of water-soil-plant systems of replicated pilot-scale CWs, comparing them to CWs treating untreated DWW. CWs treating amended DWW had better performance than CWs treating raw DWW for all water quality parameters (COD, TSS, TP, and TN), ensuring compliance with the EU wastewater discharge directives. Soil properties remained mostly unaffected except for pH, calcium and phosphorus (P), which were lower in CWs treating amended DWW. As a result of lower nitrogen (N) and P loads, the plants in CWs receiving FeCl3-amended DWW had lower N and P contents than the plants of raw DWW CWs. However, the lower loads of P into amended DWW CWs did not limit the growth of Phragmites australis, which were able to accumulate trace elements higher than CWs receiving raw DWW. Alpha and Beta-diversity analysis revealed minor differences in community richness and composition between both treatments, with only 3.7% (34 genera) showed significant disparities. Overall, the application of chemical coagulation produced superior effluent quality without affecting the properties of soil and plant of CWs or altering the functioning of the microbial community.

Disentangling the assembly patterns and drivers of microbial communities during thermal stratification and mixed periods in a deep-water reservoir.

Effect of periodic thermal stratification in deep-water reservoirs on aquatic ecosystems has been a research hotspot. Nevertheless, there is limited information on the response patterns of microbial communities to environmental changes under such specialized conditions. To fill this gap, samples were collected from a typical deep-water reservoir during the thermal stratification period (SP) and mixed period (MP). Three crucial questions were answered: 1) How microbial communities develop with stratified to mixed succession, 2) how the relative importance of stochastic and deterministic processes to microbial community assembly, shifted in two periods, and 3) how environmental variables drive microbial co-occurrence networks and functional group alteration. We used Illumina Miseq high-throughput sequencing to investigate the dynamics of the microbial community over two periods, constructed molecular ecological networks (MENs), and unraveled assembly processes based on null and neutral models. The results indicated that a total of 33.9 % and 27.7 % of bacterial taxa, and 23.1 % and 19.4 % of fungal taxa were enriched in the stratified and mixed periods, respectively. Nitrate, water temperature, and total phosphorus drove the variation of microbial community structure. During the thermal stratification period, stochastic processes (dispersal limitation) and deterministic processes (variable selection) dominated the assembly of bacterial and fungal communities, followed by a shift to stochastic processes dominated by dispersal limitation in two communities. The MENs results revealed that thermal stratification-induced environmental stresses increased the complexity of microbial networks but decreased its robustness, resulting in more vulnerable ecological networks. Therefore, this work provides critical ecological insights for the longevity and sustainability of water quality management in an artificially regulated engineered system.

Response of petroleum-contaminated soil to chemical oxidation combined with biostimulation.

In this study, a microcosm experiment was conducted to investigate the effects of Na2S2O8 preoxidation combined with biostimulation on petroleum-contaminated soil remediation. The response of microbial community during this process was explored using BIOLOG ECO microplate carbon utilization method and 16 s rDNA high-throughput sequencing. The results showed that use of 10 mg/g Na2S2O8 removed 19.8 % of the petroleum hydrocarbons, reduced soil biotoxicity and did not affect soil microbial activity compared to other concentrations. Therefore, sodium persulfate of ca. 10 mg/g was used to oxidize petroleum in soil before the biostimulation experiment with organic and inorganic fertilizers. Our finding showed that the content of total petroleum hydrocarbons (TPHs) in soil was reduced by 43.3 % in inorganic fertilizer treatment after 60 days. The results of BIOLOG ECO microplate carbon utilization analysis and 16 S rDNA high-throughput sequencing further confirmed that biostimulation quickly restored the microbial activities in oxidant treated soil. The main marker bacteria in chemical oxidation combined with biostimulation remediation were Arthrobacter and Paenarthrobacter, and their relative abundances were both significantly negatively correlated with the content of petroleum hydrocarbons in soil.

Response of soil microbial community structure and function to the sewage leakage：a case study of a 25-year-old cesspool.

Providing many millions of rural households with decentralized sanitation facilities remains challenging. In undeveloped areas, cesspools have still been widely used due to technologically simple and low-cost. However, the influence of cesspools on the surrounding soil remains unclear. In this study, we investigated the influence of a 25-year-old household cesspool on soil physicochemical factors, microbial community composition and function, pathogens and antibiotic resistance genes (ARGs). Soil at the depth around the sewage liquid level (D70) was mostly disturbed where TOC, NO3-N and TP was increased to 16.8 g/kg, 18.2 mg/kg and 1.02 mg/kg respectively. Correspondingly, the element cycling genes of carbon fixation, methanotrophy, nitrogen fixation, ammonia oxidation, and nitrate reduction etc., were increased at D70. Notably, human derived pathogens such as Enterobacter, Salmonella, Pseudomonas aeruginosa, Klebsiella pneumoniae, Prevotella, and Vibrio were highly enriched by 5-10 folders in D70, indicating the potential health risk to human. Mantel tests suggested that EC, TP, pH, NH3-N and particularly NO3-N are important factors that influence the microbial community and element cycling genes in cesspool-affected soil. Overall, this study revealed the impact of household cesspool leakage on the surrounding soil and provided information for the selection and construction of basic sanitation facilities in poor regions.

Impact of polystyrene nanoplastics on primary sludge fermentation under acidic and alkaline conditions: Significance of antibiotic resistance genes.

As a part of industrial or commercial discharge, the influx of nanoplastics (NPs) to the wastewater treatment plants is inevitable. Consequently, it has become a must to understand the effects of these NPs on different unit processes. This study aimed to investigate the impact of three different concentrations of polystyrene nano plastics (PsNPs) on the fermentation of primary sludge (PrS), implemented in batch anaerobic bioreactors, at pH 5 and 10, considering the pH-dependent nature of the fermentation process. The results showed that PsNPs stimulated hydrogen gas production at a lower dose (50 µg/L), while a significant gas suppression was denoted at higher concentrations (150 µg/L, 250 µg/L). In both acidic and alkaline conditions, propionic and acetic acid predominated, respectively, followed by n-butyric acid. Under both acidic and alkaline conditions, exposure to PsNPs boosted the propagation of various antibiotic resistance genes (ARGs), including tetracycline, macrolide, ß-lactam and sulfonamide resistance genes, and integrons. Notably, under alkaline condition, the abundance of sul2 gene in the 250 µg PsNPs/L batch exhibited a 2.4-fold decrease compared to the control batch. The response of the microbial community to PsNPs exposure exhibited variations at different pH values. Bacteroidetes prevailed at both pH conditions, with their relative abundance increasing after PsNPs exposure, indicating a positive impact of PsNPs on PrS solubilization. Adverse impacts, however, were detected in Firmicutes, Chloroflexi and Actinobacteria. The observed variations in the survival rates of various microbes stipulate that they do not have the same tolerance levels under different pH conditions.

Effects of forest age and season on soil microbial communities in Chinese fir plantations.

Understanding changes in the distribution patterns and diversity of soil microbial communities from the perspectives of age-related changes, seasonal variations, and the interaction between the two factors can facilitate the management of plantations. In Chinese fir plantations, we collected soils from different depths in over-mature forests, mature forests, near-mature forests, middle-aged forests, and young forests in summer, autumn, and winter in China's subtropical regions. As the forests developed, bacterial and fungal communities' diversity changed, reached a minimum value at near-mature forests, and then increased in mature forests or over-mature forests. Near-mature forests had the lowest topological properties. The Shannon index of microbial communities varied with seasonal changes (P < 0.05). Bacterial and fungal community composition at genus level was more closely related to temperature indicators (including daily average temperature, daily maximum temperature, and daily minimum temperature) (P < 0.01, 0.5554 < R2 <0.8185) than daily average precipitation (P > 0.05, 0.0321 < R2 <0.6773). Bacteria were clustered by season and fungi were clustered by forest age. We suggested that extending the tree cultivation time of plantations could promote microbial community recovery. In addition, we found some species worthy of attention, including Bacteroidetes in autumn in over-mature forests, and Firmicutes in summer in young forests.IMPORTANCEChinese fir [Cunninghamia lanceolata (Lamb.) Hook] is an important fast-growing species with the largest artificial forest area in China, with the outstanding problems of low quality in soil. Soil microorganisms play a crucial role in soil fertility by decomposing organic matter, optimizing soil structure, and releasing essential nutrients for plant growth. In order to maintain healthy soil quality and prevent nutrient depletion and land degradation, it is crucial to understand the changes of soil microbial composition and diversity. Our study determined to reveal the change of soil microbial community from stand age, season, and the interaction between the two aspects, which is helpful to understand how interannual changes in different years and seasonal changes in one year affect soil fertility restoration and sustainable forest plantation management. It is a meaningful exploration of soil microbial communities and provides new information for further research.

PUPpy: a primer design pipeline for substrain-level microbial detection and absolute quantification.

Characterizing microbial communities at high resolution and with absolute quantification is crucial to unravel the complexity and diversity of microbial ecosystems. This can be achieved with PCR assays, which enable highly selective detection and absolute quantification of microbial DNA. However, a major challenge that has hindered PCR applications in microbiome research is the design of highly specific primer sets that exclusively amplify intended targets. Here, we introduce Phylogenetically Unique Primers in python (PUPpy), a fully automated pipeline to design microbe- and group-specific primers within a given microbial community. PUPpy can be executed from a user-friendly graphical user interface, or two simple terminal commands, and it only requires coding sequence files of the community members as input. PUPpy-designed primers enable the detection of individual microbes and quantification of absolute microbial abundance in defined communities below the strain level. We experimentally evaluated the performance of PUPpy-designed primers using two bacterial communities as benchmarks. Each community comprises 10 members, exhibiting a range of genetic similarities that spanned from different phyla to substrains. PUPpy-designed primers also enable the detection of groups of bacteria in an undefined community, such as the detection of a gut bacterial family in a complex stool microbiota sample. Taxon-specific primers designed with PUPpy showed 100% specificity to their intended targets, without unintended amplification, in each community tested. Lastly, we show the absolute quantification of microbial abundance using PUPpy-designed primers in droplet digital PCR, benchmarked against 16S rRNA and shotgun sequencing. Our data shows that PUPpy-designed microbe-specific primers can be used to quantify substrain-level absolute counts, providing more resolved and accurate quantification in defined communities than short-read 16S rRNA and shotgun sequencing. IMPORTANCE: Profiling microbial communities at high resolution and with absolute quantification is essential to uncover hidden ecological interactions within microbial ecosystems. Nevertheless, achieving resolved and quantitative investigations has been elusive due to methodological limitations in distinguishing and quantifying highly related microbes. Here, we describe Phylogenetically Unique Primers in python (PUPpy), an automated computational pipeline to design taxon-specific primers within defined microbial communities. Taxon-specific primers can be used to selectively detect and quantify individual microbes and larger taxa within a microbial community. PUPpy achieves substrain-level specificity without the need for computationally intensive databases and prioritizes user-friendliness by enabling both terminal and graphical user interface applications. Altogether, PUPpy enables fast, inexpensive, and highly accurate perspectives into microbial ecosystems, supporting the characterization of bacterial communities in both in vitro and complex microbiota settings.

Performance and mechanistic study of biochar and magnesium-enhanced phytoremediation in cadmium-contaminated soil by alfalfa.

Recently, phytoremediation has been regarded as a green and environment friendly technique to treat metals contaminated soils. Thus, in this study, pot experiments were designed to investigate the combine effects of biochar and magnesium (MPs) to purify cadmium (Cd)-contaminated soils by Medicago sativa L. (alfalfa). The results showed that the combined use of biochar and Mg significantly increased the accumulation of Cd and promoted the transport of Cd from root to shoot in alfalfa, simultaneously. Importantly, the combined use of biochar and Mg could increase the accumulation of Cd in shoot and whole plant (shoot + root) of alfalfa up-to 59.1% and 23.1%, respectively. Moreover, the enhancement mechanism can be analyzed from several aspects. Firstly, the photosynthesis was enhanced, which was beneficial to plant growth. The product of photosynthesis provided energy for uptake and transport of Cd. Meanwhile, its transport in phloem could promote the transport of Cd. Secondly, the enhancement of antioxidant capacity of alfalfa effectively protected the membrane structure of alfalfa, which indicated that Cd could enter alfalfa from the channel on the cell membrane. Lastly, the chemical form of Cd and microbial community structure in soil were changed. Overall, these changes reduced the Cd toxicity in soil, enhanced the resistance capability of alfalfa, increased the Cd uptake by alfalfa and promoted the growth of alfalfa. Thus, the obtained results suggested that the combined use of biochar and Mg is an effective approach to enhance phytoremediation performance for purifying Cd-contaminated soils.

Effects of carrier surface hydrophilic modification on sludge granulation: From sludge characteristics, extracellular polymeric substances, and microbial community.

Aerobic granular sludge (AGS) is a powerful biotechnological tool capable of treating multiple pollutants simultaneously. However, the granulation process and pollutant removal efficiency still need to be further improved. In this study, Fe2O3- and MnO2-surface-modified straw foam-based AGS (Fe2O3@SF-AGS and MnO2@SF-AGS), with an average particle size of 3 mm, were developed and evaluated. The results showed that surface modification reduced the hydrophobic groups of carriers, facilitating the attachment and proliferation of microorganisms. Notably, MnO2@SF-AGS showed excellent granulation performance, reaching a stable state about one week earlier than the unmodified SF-AGS. The polymeric substance content of MnO2@SF-AGS was found to be 1.28 times higher than that of the control group. Furthermore, the removal rates for NH4+-N, TN, and TP were enhanced by 27.28%, 12.8%, and 32.14%, respectively. The bacterial communities exhibited significant variations in response to different surface modifications of AGS, with genera such as Saprospiraceae, Terrimonas, and Ferruginibacter playing a crucial role in the formation of AGS and the removal of pollutants specifically in MnO2@SF-AGS. The charge transfer of metal ions of MnO2@SF promotes the granulation process and pollutant removal. These results highlight that MnO2@SF-AGS is an effective strategy for improving nitrogen and phosphorus removal efficiency from wastewater.

The spatio-temporal accumulation of 6 PPD-Q in greenbelt soils and its effects on soil microbial communities.

6 PPD-Q (6 PPD-Quinone) is an ozone-induced byproduct derived from the degradation of N-(1,3-dimethylbutyl)-N'-phenyl-p-phenylenediamine (6 PPD), commonly found in road dust resulting from tire wear. However, the extent of 6 PPD-Q pollution in urban soil remains unclear. This study investigates the spatial and temporal accumulation patterns of 6 PPD-Q in greenbelt soils in Ningbo, and explores the correlation between 6 PPD-Q accumulation and soil microbial community composition and functions. Our findings indicate that 6 PPD-Q is present (ranging from 0.85 to 12.58 µg/kg) in soil samples collected from both sides of urban traffic arteries. Soil fungi exhibit higher sensitivity to 6 PPD-Q accumulation compared to bacteria, and associated fungi (Basidiomycota) may be potential biomarkers for environmental 6 PPD-Q contamination. Co-occurrence network analysis reveals that the bacterial microbial network in summer exhibits greater stability and resilience in response to 6 PPD-Q inputs than in winter. However, 6 PPD-Q accumulation disrupts the network structure of fungal communities to some extent, leading to reduced diversity in fungal microbial communities. Long-term accumulation of 6 PPD-Q weakens the nitrogen and phosphorus cycling potential within urban soil, while the enhancement of carbon cycling may further promote 6 PPD-Q degradation in urban soil. Taken together, this study provides new insights into the ecological risks of 6 PPD-Q in urban soils.

Exploring the Environmental Influences and Community Assembly Processes of Bacterioplankton in a Subtropical Coastal System: Insights from the Beibu Gulf in China.

Due to rapid urbanization, the Beibu Gulf, a semi-closed gulf in the northwestern South China Sea, faces escalating ecological and environmental threats. Understanding the assembly mechanisms and driving factors of bacterioplankton in the Beibu Gulf is crucial for preserving its ecological functions and services. In the present study, we investigated the spatiotemporal dynamics of bacterioplankton communities and their assembly mechanisms in the Beibu Gulf based on the high-throughput sequencing of the bacterial 16S rRNA gene. Results showed significantly higher bacterioplankton diversity during the wet season compared to the dry season. Additionally, distinct seasonal variations in bacterioplankton composition were observed, characterized by an increase in Cyanobacteria and Thermoplasmatota and a decrease in Proteobacteria and Bacteroidota during the wet season. Null model analysis revealed that stochastic processes governed bacterioplankton community assembly in the Beibu Gulf, with drift and homogenizing dispersal dominating during the dry and wet seasons, respectively. Enhanced deterministic assembly of bacterioplankton was also observed during the wet season. Redundancy and random forest model analyses identified the physical properties (e.g., salinity and temperature) and nutrient content (e.g., nitrate) of water as primary environmental drivers influencing bacterioplankton dynamics. Moreover, variation partitioning and distance-decay of similarity revealed that environmental filtering played a significant role in shaping bacterioplankton variations in this rapidly developed coastal ecosystem. These findings advance our understanding of bacterioplankton assembly in coastal ecosystems and establish a theoretical basis for effective ecological health management amidst ongoing global changes.