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The relationship between plants and soil microbial communities is complex and subtle, with microbes playing a crucial role in plant growth. Autochthonous bioaugmentation and nutrient biostimulation are promising bioremediation methods for herbicides in contaminated agricultural soils, but how microbes interact to promote biodegradation and plant growth on barren fields, especially in response to the treatment of the herbicide bromoxynil after wheat seedlings, remains poorly understood. In this study, we explored the microbial community reassembly process from the three-leaf stage to the tillering stage of wheat and put forward the idea of using the overlapping results of three methods (network Zi-Pi analysis, LEfSe analysis, and Random Forest analysis) as keystones for the simplification and optimization of key microbial species in the soil. Then we used genome-scale metabolic models (GSMMs) to design a targeted synthetic microbiome for promoting wheat seedling growing. The results showed that carbon source was more helpful in enriching soil microbial diversity and promoting the role of functional microbial communities, which facilitated the degradation of bromoxynil. Designed a multifunctional synthetic consortium consisting of seven non-degraders which unexpectedly assisted in the degradation of indigenous bacteria, which increased the degradation rate of bromoxynil by 2.05 times, and when adding nutritional supplementation, it increased the degradation rate by 3.65 times. In summary, this study provides important insights for rational fertilization and precise microbial consortium management to improve plant seedling growth in contaminated fields., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier B.V.)

Restoring submerged plants naturally has been a significant challenge in water ecology restoration programs. Some silicate-based mineral materials have shown promise in improving the substrate properties for plant growth. While it is well-established that silicate mineral materials enhance submerged plant growth by improving salt release and reducing salt stress, the influence of rhizosphere microorganisms on phytohormone synthesis and key enzyme activities has been underestimated. This study focused on two typical silicate mineral materials, bentonite and maifanite, to investigate their effects on Myriophyllum oguraense from both plant physiology and microbiome perspectives. The results demonstrated that both bentonite and maifanite regulated the synthesis of phytohormones such as gibberellin (GA) and methyl salicylate (MESA), leading to inhibition of cellular senescence and promotion of cell division. Moreover, these silicate mineral materials enhanced the activity of antioxidant enzymes, thereby reducing intracellular reactive oxygen species levels. They also optimized the structure of rhizosphere microbial communities, increasing the proportion of functional microorganisms like Nitrospirota and Sva0485, which indirectly influenced plant metabolism. Analysis of sediment physicochemical properties revealed increased rare earth elements, macronutrients, and oxygen content in pore water in the presence of silicate materials, creating favorable conditions for root growth. Overall, these findings shed light on the multifaceted mechanisms by which natural silicate mineral materials promote the growth of aquatic plants, offering a promising solution for restoring aquatic vegetation in eutrophic lake sediments., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Freeze-thaw cycle (FTC) is a naturally occurring phenomenon in high-latitude terrestrial ecosystems, which may exert influence on distribution and evolution of microbial community in the soil. The relationship between transmission of antibiotic resistance genes (ARGs) and microbial community was investigated upon the case study on the soil of cold-region dairy farm under seasonal FTC. The results demonstrated that 37 ARGs underwent decrease in the abundance of blaTEM from 80.4 % for frozen soil to 71.7 % for thawed soil, and that sul2 from 8.8 % for frozen soil to 6.5 % for thawed soil, respectively. Antibiotic deactivation was identified to be closely related to the highest relative abundance of blaTEM, and the spread of sulfonamide resistance genes (SRGs) occurred mainly via target modification. Firmicutes in frozen soil were responsible for dominating the abundance of ARGs by suppressing the native bacteria under starvation effect in cold regions, and then underwent horizontal gene transfer (HGT) among native bacteria through mobile genetic elements (MGEs). The TRB-C (32.6-49.1 %) and tnpA-06 (0.27-7.5 %) were significantly increased in frozen soil, while Int3 (0.67-10.6 %) and tnpA-04 (11.1-19.4 %) were up-regulated in thawed soil. Moreover, the ARGs in frozen soil primarily underwent HGT through MGEs, i.e. TRB-C and tnpA-06, with increased number of Firmicutes serving as carrier. The case study not only demonstrated relationship between transmission of ARGs and microbial community in the soil under practically relevant FTC condition, but also emphasized the importance for formulating better strategies for preventing FTC-induced ARGs in dairy farm in cold regions., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Sewages from duck farms are often recognized as a major source of antimicrobial resistance and pathogenic bacteria discharged to natural water bodies, but few studies depicted the dynamic changes in resistome and microbial communities in the rivers under immense exposure of sewage discharge. In this study, we investigated the ecological and environmental risks of duck sewages to the rivers that geographically near to the duck farms with short-distance (<1 km) using 16S rRNA amplicon and metagenomic sequencing. The results showed that a total of 20 ARG types were identified with abundances ranged from 0.61 to 1.33 cpc. Of note, the genes modulate resistances against aminoglycoside, bacitracin and beta-lactam were the most abundant ARGs. Limnohabitans, Fluviibacter and Cyanobium were the top 3 predominant genera in the microbial community. The alpha diversity of overall microbial community decrease while the abundance of pathogen increase during the input of sewage within 200 m. Sul1 and bacA were the dominant ARGs brought from duck farm sewage. The community variations of ARGs and microbiome were primarily driven by pH and temperature. Total phosphorus was significantly correlated to alpha diversity and top 30 ARGs subtype. Stochastic processes was the dominated microbial assembly pattern and did not be altered by sewage. We also highlighted the ecological risk caused by bla GES which possibly could be mitigated by Cyanobacteria, and the natural water body can purify partial ARGs as well as microbiome from duck farms sewage. These findings expanded our knowledge regarding the ecological risks by wastes from the livestock farm, and underscoring the necessity to monitor ARGs in farm-surrounding water bodies., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Microbial community diversity significantly varies with seasonality. However, little is known about seasonal variation of microbial community functions in lake sediments and their associated environmental influences. In this study, metagenomic sequencing of sediments collected from winter, summer, and autumn from Caohai Lake, Guizhou Plateau, were used to evaluate the composition and function of sediment microbial communities, the potential interactions of functional genes, key genes associated with seasons, and community assembly mechanisms. The average concentrations of nitrogen (TN) and phosphorus (TP) in lake sediments were higher, which were 6.136 and 0.501 g/kg, respectively. TN and organic matter (OM) were the primary factors associated with sediment community composition and functional profiles. The diversity and structure of the microbial communities varied with seasons, and Proteobacteria relative abundances were significantly lower in summer than in other seasons (58.43-44.12 %). Seasons were also associated with the relative abundances of functional genes, and in particular korA, metF, narC, nrfA, pstC/S, and soxB genes. Network complexity was highest in the summer and key genes in the network also varied across seasons. Neutral community model analysis revealed that the assembly mechanisms related to carbon (C), nitrogen (N), phosphorus (P), and sulfur (S) cycle-related genes were primarily associated with random processes. In summary, diverse functional genes were identified in lake sediments and exhibited evidence for synergistic interactions (Positive proportion: 74.91-99.82 %), while seasonal factors influenced their distribution. The results of this study provide new insights into seasonal impacts on microbial-driven biogeochemical cycling in shallow lakes., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Thermal remediation is an effective technology for organic contaminant remediation. However, the application of thermal remediation may have negative effects on soil properties and ecological functions, which requires further investigation. Based on a pilot test of electrical resistance heating remediation (ERH), soil samples were collected at different locations after heating for 116 days. Most soil physicochemical properties were less affected by the heating temperature difference. Application of high temperature increased microbial abundance but inhibited alpha diversity of the bacterial community. More significant changes in microbial communities were observed at temperatures above 60 °C. The genera mainly affected by heating temperature included Flavobacteria, Brockia, and S085, while the increase in temperature also inhibited the abundance of nitrochlorobenzene functional genes. At 140 days after the end of the pilot test, the bacterial community affected by thermal remediation could recover effectively, and the recovery of the bacterial community was not affected by temperature difference during the heating period. This study provides valuable field evidence of the long term impact of soil ERH treatment on soil properties and microbial communities, and provides further references for optimization of remediation performance with coupled technologies., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Silage is an excellent method of feed preservation; however, carbon dioxide, methane and nitrous oxide produced during fermentation are significant sources of agricultural greenhouse gases. Therefore, determining a specific production method is crucial for reducing global warming. The effects of four temperatures (10 °C, 20 °C, 30 °C, and 40 °C) on silage quality, greenhouse gas yield and microbial community composition of forage sorghum were investigated. At 20 °C and 30 °C, the silage has a lower pH value and a higher lactic acid content, resulting in higher silage quality and higher total gas production. In the first five days of ensiling, there was a significant increase in the production of carbon dioxide, methane, and nitrous oxide. After that, the output remained relatively stable, and their production at 20 °C and 30 °C was significantly higher than that at 10 °C and 40 °C. Firmicutes and Proteobacteria were the predominant silage microorganisms at the phylum level. Under the treatment of 20 °C, 30 °C, and 40 °C, Lactobacillus had already dominated on the second day of silage. However, low temperatures under 10 °C slowed down the microbial community succession, allowing, bad microorganisms such as Chryseobacterium, Pantoea and Pseudomonas dominate the fermentation, in the early stage of ensiling, which also resulted in the highest bacterial network complexity. According to random forest and structural equation model analysis, the production of carbon dioxide, methane and nitrous oxide is mainly affected by microorganisms such as Lactobacillus, Klebsiella and Enterobacter, and temperature influences the activity of these microorganisms to mediate gas production in silage. This study helps reveal the relationship between temperature, microbial community and greenhouse gas production during silage fermentation, providing a reference for clean silage fermentation., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Soil freeze-thaw cycles (FTCs) are common in temperate agricultural ecosystems during the non-growing season and are progressively influenced by climate change. The impact of these cycles on soil microbial communities, crucial for ecosystem functioning, varies under different agricultural management practices. Here, we investigated the dynamic changes in soil microbial communities in a Mollisol during seasonal FTCs and examined the effects of stover mulching and nitrogen fertilization. We revealed distinct responses between bacterial and fungal communities. The dominant bacterial phyla reacted differently to FTCs: for example, Proteobacteria responded opportunistically, Actinobacteria, Acidobacteria, Choroflexi and Gemmatimonadetes responded sensitively, and Saccharibacteria exhibited a tolerance response. In contrast, the fungal community composition remained relatively stable during FTCs, except for a decline in Glomeromycota. Certain bacterial OTUs acted as sensitive indicators of FTCs, forming keystone modules in the network that are closely linked to soil carbon, nitrogen content and potential functions. Additionally, neither stover mulching nor nitrogen fertilization significantly influenced microbial richness, diversity and potential functions. However, over time, more indicator species specific to these agricultural practices began to emerge within the networks and gradually occupied the central positions. Furthermore, our findings suggest that farming practices, by introducing keystone microbes and changing interspecies interactions (even without changing microbial richness and diversity), can enhance microbial community stability against FTC disturbances. Specifically, higher nitrogen input with stover removal promotes fungal stability during soil freezing, while lower nitrogen levels increase bacterial stability during soil thawing. Considering the fungal tolerance to FTCs, we recommend reducing nitrogen input for manipulating bacterial interactions, thereby enhancing overall microbial resilience to seasonal FTCs. In summary, our research reveals that microbial responses to seasonal FTCs are reshaped through land management to support ecosystem functions under environmental stress amid climate change., Competing Interests: Declaration of competing interest The authors declare that they have no competing interests., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Precise identification of species is fundamental in microbial genomics and is crucial for understanding the microbial communities. While the 16S rRNA gene, particularly its V3-V4 regions, has been extensively employed for microbial identification, however has limitations in achieving species-level resolution. Advancements in long-read sequencing technologies have highlighted the rRNA operon as a more accurate marker for microbial classification and analysis than the 16S rRNA gene. This study aims to compare the accuracy of species classification and microbial community analysis using the rRNA operon versus the 16S rRNA gene. We evaluated the species classification accuracy of the rRNA operon,16S rRNA gene, and 16S rRNA V3-V4 regions using a BLAST-based method and a k-mer matching-based method with public data available from NCBI. We further performed simulations to model microbial community analysis. We accessed the performance using each marker in community composition estimation and differential abundance analysis. Our findings demonstrate that the rRNA operon offers an advantage over the 16S rRNA gene and its V3-V4 regions for species-level classification within the genus. When applied to microbial community analysis, the rRNA operon enables a more accurate determination of composition. Using the rRNA operon yielded more reliable results in differential abundance analysis as well., Importance: We quantitatively demonstrated that the rRNA operon outperformed the 16S rRNA and its V3-V4 regions in accuracy for both individual species identification and species-level microbial community analysis. Our findings can provide guidelines for selecting appropriate markers in the field of microbial research., Competing Interests: The authors declare no conflict of interest.

Background: The interaction between soil characteristics and microbial communities is crucial for poplar growth under different planting densities. Yet, little is understood about their relationships and how they respond to primary environmental drivers across varying planting densities., Results: In this study, we investigated poplar growth metrics, soil characteristics, and community assembly of soil bacterial and fungal communities in four poplar genotypes (M1316, BT17, S86, and B331) planted at low, medium, and high densities. Our findings reveal that planting density significantly influenced poplar growth, soil nutrients, and microbial communities (P < 0.05). Lower and medium planting densities supported superior poplar growth, higher soil nutrient levels, increased microbial diversity, and more stable microbial co-occurrence networks. The assembly of bacterial communities in plantation soils was predominantly deterministic (βNTI < -2), while fungal communities showed more stochastic assembly patterns (-2 < βNTI < 2). Soil available phosphorus (AP) and potassium (AK) emerged as pivotal factors shaping microbial communities and influencing bacterial and fungal community assembly. Elevated AP levels promoted the recruitment of beneficial bacteria such as Bacillus and Streptomyces, known for their phosphate-solubilizing abilities. This facilitated positive feedback regulation of soil AP, forming beneficial loops in soils with lower and medium planting densities., Conclusions: Our study underscores the critical role of planting density in shaping soil microbial communities and their interaction with poplar growth. This research carries significant implications for enhancing forest management practices by integrating microbiological factors to bolster forest resilience and productivity., (© 2024. The Author(s).)

Activated sludge (AS) microbial communities are influenced by various environmental variables. However, a comprehensive analysis of how these variables jointly and nonlinearly shape the AS microbial community remains challenging. In this study, we employed advanced machine learning techniques to elucidate the collective effects of environmental variables on the structure and function of AS microbial communities. Applying Dirichlet multinomial mixtures analysis to 311 global AS samples, we identified four distinct microbial community types (AS-types), each characterized by unique microbial compositions and metabolic profiles. We used 14 classical linear and nonlinear machine learning methods to select a baseline model. The extremely randomized trees demonstrated optimal performance in learning the relationship between environmental factors and AS types (with an accuracy of 71.43%). Feature selection identified critical environmental factors and their importance rankings, including latitude (Lat), longitude (Long), precipitation during sampling (Precip), solids retention time (SRT), effluent total nitrogen (Effluent TN), average temperature during sampling month (Avg Temp), mixed liquor temperature (Mixed Temp), influent biochemical oxygen demand (Influent BOD), and annual precipitation (Annual Precip). Significantly, Lat, Long, Precip, Avg Temp, and Annual Precip, influenced metabolic variations among AS types. These findings emphasize the pivotal role of environmental variables in shaping microbial community structures and enhancing metabolic pathways within activated sludge. Our study encourages the application of machine learning techniques to design artificial activated sludge microbial communities for specific environmental purposes., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Pentachlorophenol (PCP) is a highly toxic and carcinogenic compound with significant environmental impact, necessitating effective treatment technologies. This study evaluates PCP removal mechanisms, including adsorption and biodegradation, during the startup of a horizontal-flow anaerobic immobilized biomass reactor (HAIB), and examines the impact of PCP concentration on microbial diversity using denaturing gradient gel electrophoresis (DGGE). The primary mechanism for PCP removal in the HAIB was adsorption, effectively described by the Freundlich isotherm model. Adsorption efficiency ranged from 86 to 104% for PCP concentrations between 0.2 and 5.0 mg/L, and 46% to 64% for concentrations between 0.098 and 0.05 mg/L. Additionally, PCP degradation intermediates such as 2,3-DCP and 2,6-DCP were detected, indicating that biodegradation also occurred in the HAIB. Organic matter degradation averaged 81 ± 9%, and methane content in the biogas averaged 46 ± 9%, confirming the anaerobic process. No inhibition of microbial activity was observed due to PCP toxicity, even at a PCP load of 5 mg PCP/g STV per day. While the archaeal community showed only slight changes, with similarity coefficients ranging from 88 to 95%, the bacterial community was significantly affected by PCP, with similarity coefficients ranging from 18 to 50%. Bacterial groups were responsible for the initial PCP degradation, while the archaeal community was involved in metabolizing the resulting byproducts. The use of indigenous inoculum from the Santos-São Vicente estuary demonstrated its potential for effective PCP removal. Polyurethane foam proved to be an effective support material, enhancing the adsorption process and reducing PCP toxicity to the microbial consortium. This study provides valuable insights into PCP adsorption and biodegradation mechanisms in HAIB, highlighting the effectiveness of indigenous inoculum and polyurethane foam for PCP removal., (© 2024. The Author(s), under exclusive licence to Springer Nature B.V.)

Heavy metal (HM) contaminants are the emerging driving force for reshaping the microflora of plants by eradicating the non-tolerance and non-resistant microbes via their lethal effects. Seeds served as a prime source of ancestral microbial diversity hereditary transfer from generation to generation. However, the problem arises when they got exposed to metal contamination, does metal pollutant disrupt the delicate balance of microbial communities within seeds and lead to shifts in their microflora across generations. In this study, the endophytic community within Zea mays seeds was compared across three distinct regions in Yunnan province, China: a HM-contaminated site Ayika (AK), less-contaminated site Sanduoduo (SD), and a non-contaminated Site Dali (DL). High-throughput sequencing techniques were employed to analyze the microbial communities. A total of 492,177 high-quality reads for bacterial communities and 1,001,229 optimized sequences for fungal communities were obtained. These sequences were assigned to 502 and 239 operational taxonomic units (OTUs) for bacteria and fungi, respectively. A higher diversity was recorded in AK samples than in SD and DL. Microbial community structure analysis showed higher diversity and significant fluctuation in specific taxa abundance in the metal-polluted samples exhibiting higher response of microbial flora to HM. In AK samples, bacterial genera such as Gordonia and Burkholderia-Caballeronia-Paraburkholderia were dominant, while in SD Pseudomonas and Streptomyces were dominant. Among the fungal taxa, Fusarium, Saccharomycopsis, and Lecanicillium were prevalent in HM-contaminated sites. Our finding revealed the influential effect of HM contaminants on reshaping the seed microbiome of the Zea mays, showing both the resilience of certain important microbial taxa as well the shifts in the diversity in the contaminated and pristine conditions. The knowledge will benefit to develop effective soil remediation, reclamation, and crop management techniques, and eventually assisting in the extenuation of metal pollution's adverse effects on plant health and agricultural productivity., (© 2024. The Author(s).)

Background: Crop rotation is an important agricultural practice that often affects the metabolic processes of soil microorganisms through the composition and combination of crops, thereby altering nutrient cycling and supply to the soil. Although the benefits of crop rotation have been extensively discussed, the effects and mechanisms of different crop combinations on the soil microbial community structure in specific environments still need to be analyzed in detail., Materials and Methods: In this study, six crop rotation systems were selected, for which the spring crops were mainly tobacco or gramineous crops: AT (asparagus lettuce and tobacco rotation), BT (broad bean and tobacco rotation), OT (oilseed rape and tobacco rotation), AM (asparagus lettuce and maize rotation), BM (broad bean and maize rotation), and OR (oilseed rape and rice rotation). All crops had been cultivated for > 10 years. Soil samples were collected when the rotation was completed in spring, after which the soil properties, composition, and functions of bacterial and fungal communities were analyzed., Results: The results indicate that spring cultivated crops play a more dominant role in the crop rotation systems than do autumn cultivated crops. Crop rotation systems with the same spring crops have similar soil properties and microbial community compositions. pH and AK are the most important factors driving microbial community changes, and bacteria are more sensitive to environmental responses than fungi. Rotation using tobacco systems led to soil acidification and a decrease in microbial diversity, while the number of biomarkers and taxonomic indicator species differed between rotation patterns. Symbiotic network analysis revealed that the network complexity of OT and BM was the highest, and that the network density of tobacco systems was lower than that of gramineous systems., Conclusions: Different crop rotation combinations influence both soil microbial communities and soil nutrient conditions. The spring crops in the crop rotation systems had stronger dominating effects, and the soil bacteria were more sensitive than the fungi were to environmental changes. The tobacco rotation system can cause soil acidification and thereby affect soil sustainability, while the complexity of soil microbial networks is lower than that of gramineous systems. These results provide a reference for future sustainable applications of rotation crop systems., (© 2024. The Author(s).)

High-throughput metagenomic sequence technology was employed to evaluate changes in microbial community composition and carbohydrate-active enzymes encoding gene enrichment status in Elymus nutans silages to altitudinal gradients in the world's highest alpine region of Qinghai-Tibetan Plateau (QTP). E. nutans were collected from three different altitudes in QTP: 2,600 m (low altitude), 3600 m (moderate altitude), and 4,600 m [high (H) altitude], and ensiled for 7, 14, 30, and 60 d. Results indicated an improvement in silage quality with the increasing altitude, although the acetic acid concentration and dry matter loss were greater in H altitude silages after 30 d of ensiling. Harmful bacteria or potential pathogens predominated in the microbial community on d 7 and 14 of fermentation, while genera belonging to lactic acid bacteria gradually became the main microorganisms with the increasing altitude on d 30 and 60 of ensiling. The abundance of carbohydrate-active enzymes genes responsible for macromolecular carbohydrate degradation in silage increased with increasing altitude, and those genes were mainly carried by Lactiplantibacillus and Pediococcus at 30 and 60 d of ensiling. The abundance of key enzymatic genes associated with glycolysis and organic acid production in carbohydrate metabolism pathway was higher in H altitude silages, and Lactiplantibacillus and Pediococcus were also the main hosts after 30 d of silage fermentation, except for the fact that acetic acid production was also related to genera Leuconostoc , Latilactobacillus , and Levilactobacillus ., Importance: The fermentation quality of Elymus nutans silage was getting better with the increase of altitude in the Qinghai-Tibetan Plateau. The abundance of hosts carrying carbohydrate-active enzymes genes and key enzyme genes related to organic acid production increased with increasing altitude during the later stages of fermentation. Lactiplantibacillus and Pediococcus were the core microorganisms responsible for both polysaccharide hydrolysis and silage fermentation in the late stage of ensiling. This study provided insights on the influence of different altitudes on the composition and function of silage microbiome in the Qinghai-Tibetan Plateau, and provided a reference approach for improving the quality and controllability of silage production in high altitude areas of the Qinghai-Tibetan Plateau., Competing Interests: The authors declare no conflict of interest.

The exchange of metabolites (i.e., metabolic interactions) between bacteria in the rhizosphere determines various plant-associated functions. Systematically understanding the metabolic interactions in the rhizosphere, as well as in other types of microbial communities, would open the door to the optimization of specific predefined functions of interest, and therefore to the harnessing of the functionality of various types of microbiomes. However, mechanistic knowledge regarding the gathering and interpretation of these interactions is limited. Here, we present a framework utilizing genomics and constraint-based modeling approaches, aiming to interpret the hierarchical trophic interactions in the soil environment. 243 genome scale metabolic models of bacteria associated with a specific disease-suppressive vs disease-conducive apple rhizospheres were drafted based on genome-resolved metagenomes, comprising an in silico native microbial community. Iteratively simulating microbial community members' growth in a metabolomics-based apple root-like environment produced novel data on potential trophic successions, used to form a network of communal trophic dependencies. Network-based analyses have characterized interactions associated with beneficial vs non-beneficial microbiome functioning, pinpointing specific compounds and microbial species as potential disease supporting and suppressing agents. This framework provides a means for capturing trophic interactions and formulating a range of testable hypotheses regarding the metabolic capabilities of microbial communities within their natural environment. Essentially, it can be applied to different environments and biological landscapes, elucidating the conditions for the targeted manipulation of various microbiomes, and the execution of countless predefined functions., Competing Interests: AG, MB, EC, SM, GC, AF, IS, OT, SD, TS, MM, HE, SF No competing interests declared

The effects of heavy metals on soil microbial communities have been extensively investigated, whereas the combined effects of heavy metals and nutrients on soil microbial communities and their interactions are rarely understood. In this study, we investigated the distribution patterns of heavy metals, nutrients and microbial communities in a typical contaminated farmland and explored their interaction mechanisms. The results showed that Cd and Pb were the main pollutants in this area, which mainly came from the smelter. Canonical correspondence analysis and variance decomposition analysis showed that the heavy metals played a more important role in restraining the microbial community structure of soils than other soil properties. Soil Cd, Pb, pH and available K content were the most important environmental factors affecting the microbial community structures in soil. Major Cd tolerant bacteria and fungi were detected including Actinobacteriota, Gemmatimonadota, Entorrhizomycota and Mortierellomycota. The analyses of molecular ecological networks showed that there were 84.1 % of negative correlations among microorganisms. Cd could regulate the abundance of key nodes in Cd-tolerant network modules, and these key nodes could improve the adaptability of the whole module to heavy metals through competition with other microorganisms. This study provides insights into the ecological effects of heavy metals and nutrients on soil microbial communities and will help to develop the bio-remediation technologies for contaminated soils., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier B.V.)

Soil microorganisms are critical to the occurrence of Cordyceps sinensis (Chinese Cordyceps ), a medicinal fungi used in Traditional Chinese Medicine. The over-collection of Chinese Cordyceps has caused vegetation degradation and impacted the sustainable occurrence of Cordyceps . The effects of Chinese Cordyceps collection on soil microorganisms have not been reported. Metagenomic analysis was performed on the soil of collecting and non-collecting areas of production and non-production areas, respectively. C . sinensis collection showed no alteration in alpha-diversity but significantly affected beta-diversity and the community composition of soil microorganisms. In Cordyceps production, Thaumarchaeota and Crenarchaeota were identified as the dominant archaeal phyla. DNA repair, flagellar assembly, propionate metabolism, and sulfur metabolism were affected in archaea, reducing the tolerance of archaea in extreme habitats. Proteobacteria, Actinobacteria, Acidobacteria, Verrucomicrobia, and Nitrospirae were identified as the dominant bacterial phyla. The collection of Chinese Cordyceps enhanced the bacterial biosynthesis of secondary metabolites and suppressed ribosome and carbon metabolism pathways in bacteria. A more complex microbial community relationship network in the Chinese Cordyceps production area was found. The changes in the microbial community structure were closely related to C, N, P and enzyme activities. This study clarified soil microbial community composition and function in the Cordyceps production area and established that collection clearly affects the microbial community function by altering microbial community structure. Therefore, it would be important to balance the relationship between cordyceps production and microbiology.

The rhizosphere microbiome plays a crucial role in the ability of plants to colonize and thrive in stressful conditions such as drought, which could be decisive for the success of exotic plant invasion in the context of global climate change. The aim of this investigation was to examine differences in the composition, structure, and functional traits of the microbial community of the invader Nicotiana glauca R.C. Graham and native species growing at seven different Mediterranean semiarid locations under two distinct levels of water availability, corresponding to the wet and dry seasons. The results show that the phylum Actinobacteriota was an indicator phylum of the dry season as well as for the community of N. glauca. The dominant indicator bacterial families of the dry season were 67-14 (unclassified family), Pseudonocardiaceae, and Sphingomonadaceae, being relatively more abundant in the invasive rhizosphere. The relative abundances of the indicator fungal families Aspergillaceae (particularly the indicator genus Aspergillus), Glomeraceae, and Claroideoglomeraceae were higher in the invasive rhizosphere. The relative abundance of mycorrhizal fungi was higher in the invasive rhizosphere in the dry season (by about 40 % in comparison to that of native plants), without significant differences between invasive and native plants in the wet season. Bacterial potential functional traits related to energy and precursor metabolites production and also biosynthesis of cell wall, cofactors, vitamins, and amino acids as well as catabolic enzymes involved in the P cycle prevailed in the invasive rhizosphere under drought conditions. This study shows that the pronounced and beneficial shifts in the microbiome assembly and functions in the rhizosphere of N. glauca under conditions of low soil water availability can represent a clear advantage for its establishment., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)

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., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

There is a lack of understanding about the bacterial, fungal and archaeal communities' composition of solid-phase denitrification (SPD) systems. We investigated four SPD systems with different carbon sources by analyzing microbial gene sequences based on operational taxonomic unit (OTU) and amplicon sequence variant (ASV). The results showed that the corncob-polyvinyl alcohol sodium alginate-polycaprolactone (CPSP, 0.86±0.04 mg NO 3 - -N/(g·day)) and corncob (0.85±0.06 mg NO 3 - -N/(g·day)) had better denitrification efficiency than polycaprolactone (PCL, 0.29±0.11 mg NO 3 - -N/(g·day)) and polyvinyl alcohol-sodium alginate (PVA-SA, 0.24±0.07 mg NO 3 - -N/(g·day)). The bacterial, fungal and archaeal microbial composition was significantly different among carbon source types such as Proteobacteria in PCL (OTU: 83.72%, ASV: 82.49%) and Rozellomycota in PVA-SA (OTU: 71.99%, ASV: 81.30%). ASV methods can read more microbial units than that of OTU and exhibit higher alpha diversity and classify some species that had not been identified by OTU such as Nanoarchaeota phylum, unclassified&#95; f&#95; Xanthobacteraceae genus, etc., indicating ASV may be more conducive to understand SPD microbial communities. The co-occurring network showed some correlation between the bacteria fungi and archaea species, indicating different species may collaborate in SPD systems. Similar KEGG function prediction results were obtained in two bioinformatic methods generally and some fungi and archaea functions should not be ignored in SPD systems. These results may be beneficial for understanding microbial communities in SPD systems., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023. Published by Elsevier B.V.)

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., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Mud volcanoes are dynamic geological features releasing methane (CH 4 ), carbon dioxide (CO 2 ), and hydrocarbons, harboring diverse methane and hydrocarbon-degrading microbes. However, the potential application of these microbial communities in chlorinated hydrocarbons bioremediation purposes such as trichloroethylene (TCE) has not yet been explored. Hence, this study investigated the mud volcano's microbial diversity functional potentiality in TCE degradation as well as their eco-physiological profiling using metabolic activity. Geochemical analysis of the mud volcano samples revealed variations in pH, temperature, and oxidation-reduction potential, indicating diverse environmental conditions. The Biolog Ecoplate™ carbon substrates utilization pattern showed that the Tween 80 was highly consumed by mud volcanic microbial community. Similarly, MicroResp® analysis results demonstrated that presence of additive C-substrates condition might enhanced the cellular respiration process within mud-volcanic microbial community. Full-length 16 S rRNA sequencing identified Proteobacteria as the dominant phylum, with genera like Pseudomonas and Hydrogenophaga associated with chloroalkane degradation, and methanotrophic bacteria such as Methylomicrobium and Methylophaga linked to methane oxidation. Functional analysis uncovered diverse metabolic functions, including sulfur and methane metabolism and hydrocarbon degradation, with specific genes involved in methane oxidation and sulfur metabolism. These findings provide insights into the microbial diversity and metabolic capabilities of mud volcano ecosystems, which could facilitate their effective application in the bioremediation of chlorinated compounds., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier Inc.)

The rot caused by pathogens during the storage of table grapes is an important factor that affects the development of the grape industry and food safety, and it cannot be ignored. The development of innovative methods for pathogen control should be based on a comprehensive understanding of the overall microbial community changes that occur during grape storage. The study aims to investigate the relationship between the native microbiota (including beneficial, pathogenic and spoilage microorganisms) on grape surfaces and the development of disease during grape storage. In this study, the bacteria and fungi present on grape surfaces were analyzed during storage under room temperature conditions using high-throughput sequencing. During the storage of grapes at room temperature, observable diseases and a noticeable decrease in quality were observed at 8 days. Microbial community analysis showed that 4996 bacterial amplicon sequence variants (ASVs) and 488 fungal ASVs were determined. The bacterial richness exhibited an initial increase followed by a subsequent decrease. However, the diversity exhibited a distinct pattern of gradual decrease. The fungal richness and community diversity both exhibit a gradual decrease during the storage of grapes. Fungal β-diversity analysis showed that despite the absence of rot and the healthy state of grapes on the first and fourth days, the fungal β-diversity exhibited a significant difference. The analysis of changes in genera abundances suggested that Candidatus Profftella and Aspergillus exhibited dominance in the rotting grape at 16 days, which are the main pathogens that caused disease in the present study. The co-occurrence networks among the microbial showed that the Candidatus proftella genera has a positive correlation with Aspergillus niger, indicating that they work together to cause disease and promote growth in grapes. Predicting the function of bacterial communities found that the microorganisms associated with lipid metabolism at 4 days play an important role in the process of postharvest decay of grapes., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Background: The Calakmul Biosphere Reserve (CBR) is known for its rich animal and plant biodiversity, yet its microbial communities remain largely unknown. The reserve does not possess permanent bodies of water; nevertheless, seasonal depressions associated with fractures create wetlands, known locally as aguadas. Given the recent construction of the Maya train that crosses the CRB, it is essential to assess the biodiversity of its microorganisms and recognize their potential as a valuable source of goods. This evaluation is pivotal in mitigating potential mismanagement of the forest ecosystem. To enhance comprehension of microbial communities, we characterized the microbiota in three different wetlands. Ag-UD1 and Ag-UD2 wetlands are located in a zone without human disturbances, while the third, Ag-SU3, is in a semi-urbanized zone. Sampling was carried out over three years (2017, 2018, and 2019), enabling the monitoring of spatiotemporal variations in bacterial community diversity. The characterization of microbiome composition was conducted using 16S rRNA metabarcoding. Concurrently, the genomic potential of select samples was examined through shotgun metagenomics., Results: Statistical analysis of alpha and beta diversity indices showed significant differences among the bacterial communities found in undisturbed sites Ag-UD1 and Ag-UD2 compared to Ag-SU3. However, no significant differences were observed among sites belonging to the undisturbed area. Furthermore, a comparative analysis at the zone level reveals substantial divergence among the communities, indicating that the geographic location of the samples significantly influences these patterns. The bacterial communities in the CBR wetlands predominantly consist of genera from phyla Actinobacteria, Acidobacteria, and Proteobacteria., Conclusion: This characterization has identified the composition of microbial communities and provided the initial overview of the metabolic capacities of the microbiomes inhabiting the aguadas across diverse conservation zones. The three sites exhibit distinct microbial compositions, suggesting that variables such as chemical composition, natural and anthropogenic disturbances, vegetation, and fauna may play a pivotal role in determining the microbial structure of the aguadas. This study establishes a foundational baseline for evaluating the impact of climatic factors and human interventions on critical environments such as wetlands., (© 2024. The Author(s).)

Plant environmental stress response has become a global research hotspot, yet there is a lack of clear understanding regarding the mechanisms that maintain microbial diversity and their ecosystem services under environmental stress. In our research, we examined the effects of moderate elevation on the rhizosphere soil characteristics, microbial community composition, and ecosystem multifunctionality (EMF) within agricultural systems. Our findings revealed a notable negative correlation between EMF and elevation, indicating a decline in multifunctionality at higher elevations. Additionally, our analysis across bacterial and protistan communities showed a general decrease in microbial richness with increasing elevation. Using random forest models, pH was identified as the key environmental stressor influencing microbial communities. Furthermore, we found that microbial community diversity is negatively correlated with stability by mediating complexity. Interestingly, while pH was found to affect the complexity within bacterial networks, it did not significantly impact the ecosystem stability along the elevation gradients. Using a Binary-State Speciation and Extinction (BiSSE) model to explore the evolutionary dynamics, we found that Generalists had higher speciation rates and lower extinction rates compared to specialists, resulting in a skewed distribution towards higher net diversification for generalists under increasing environmental stress. Moreover, structural equation modeling (SEM) analysis highlighted a negative correlation between environmental stress and community diversity, but showed a positive correlation between environmental stress and degree of cooperation & competition. These interactions under environmental stress indirectly increased community stability and decreased multifunctionality. Our comprehensive study offers valuable insights into the intricate relationship among environmental factors, microbial communities, and ecosystem functions, especially in the context of varying elevation gradients. These findings contribute significantly to our understanding of how environmental stressors affect microbial diversity and ecosystem services, providing a foundation for future ecological research and management strategies in similar contexts., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier Inc.)

Heavy metal pollution of the soil affects the environment and human health. Masson pine is a good candidate for phytoremediation of heavy metal in mining areas. Microorganisms in the rhizosphere can help with the accumulation of heavy metal in host plants. However, studies on its rhizosphere bacterial communities under heavy metal pollution are still limited. Therefore, in this study, the chemical and bacterial characteristics of Masson pine rhizosphere under four different levels of heavy metal pollution were investigated using 16 S rRNA gene sequencing, soil chemistry and analysis of plant enzyme activities. The results showed that soil heavy metal content, plant oxidative stress and microbial diversity damage were lower the farther they were from the mine dump. The co-occurrence network relationship of slightly polluted soils (C1 and C2) was more complicated than that of highly polluted soils (C3 and C4). Relative abundance analysis indicated Sphingomonas and Pseudolabrys were more abundant in slightly polluted soils (C1 and C2), while Gaiella and Haliangium were more abundant in highly polluted soils (C3 and C4). LEfSe analysis indicated Burkholderiaceae, Xanthobacteraceae, Gemmatimonadaceae, Gaiellaceae were significantly enriched in C1 to C4 site, respectively. Mantel analysis showed that available cadmium (Cd) contents of soil was the most important factor influencing the bacterial community assembly. Correlation analysis showed that eight bacterial genus were significantly positively associated with soil available Cd content. To the best of our knowledge, this is the first study to investigate the rhizospheric bacterial community of Masson pine trees under different degrees of heavy metal contamination, which lays the foundation for beneficial bacteria-based phytoremediation using Masson pines in the future., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

The Taihu Lake region has undergone intensive land-use conversions from natural wetlands (NW) to conventional rice-wheat rotation fields (RW) and further to greenhouse vegetable fields (GH). Nevertheless, the effects of these conversions on soil microbes, particularly in wetland ecosystem, are not well explicit. To explore the impact of land-use intensification on soil microbial communities, monthly soil samples were obtained from replicate plots representing three land-use types (NW, RW, and GH) in subtropical wetlands and then subjected to amplicon sequencing. Land-use intensification had direct effects on bacterial and fungal community composition, with a more pronounced impact on bacteria than on fungi. These changes in bacterial communities were closely correlated with variations in soil environmental variables, such as NO 3 - -N, pH, and electrical conductivity. Land-use intensification led to a decrease in bacterial deterministic processes, with an opposing trend observed in the fungal community. In addition, arable lands (RW and GH), which are affected by anthropogenic activities, exhibited more complex networks. Potential metabolic functional groups in GH had higher absolute abundance. Seasonal variations significantly influenced microbial diversity, composition, and potential metabolic functional groups within each land-use type, particularly in summer, although the magnitude of this impact was much smaller than the impact of land-use intensification. Our findings emphasize the importance of comprehending the ecological consequences of land-use intensification in wetlands for sustainable resource management and biodiversity conservation., Competing Interests: Declaration of competing interest The authors declare that they have no conflict of interest., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Microorganisms are crucial components of the aquatic ecosystem due to their immense diversity and abundance. They are vital in sustaining ecological services, especially in maintaining essential biogeochemical cycles. Recent years have seen a substantial increase in surplus nitrogenous pollutants in aquatic ecosystems due to the heightened occurrence of anthropogenic activities. Elevated levels of free ammonia (FA, NH 3 ), stemming from the discharge of excess nitrogenous pollutants, have caused notable fluctuations in aquatic ecosystems, leading to water eutrophication and various ecological challenges. The impact of these oscillations on microbial communities in aquatic ecosystems has not been extensively studied. This study employed 16S rRNA gene amplicon sequencing to systematically investigate the dynamics, co-occurrence networks, and assembly processes of microbial communities and their subcommunities (abundant, moderate, and rare) in the Luanhe River Diversion Project in China. Our findings indicate that NH 3 concentration significantly influences the dynamics of microbial communities, with a notable decrease in community Richness and Phylogenetic Distance alongside increased community dissimilarity under higher NH 3 conditions. The analysis revealed that certain microbial groups, particularly Actinobacteriaota, were notably more prevalent in environments with elevated NH 3 levels, suggesting their potential resilience or adaptive responses to NH 3 stress. Additionally, through co-occurrence network analysis, we observed dynamic changes in network topology and increased connectedness under NH 3 stress. Key nodes, identified as connectors and module hubs, played crucial roles in maintaining network structure, particularly Cyanobacteria and Actinobacteriaota. Furthermore, stochastic processes, particularly drift and dispersal limitation, predominantly shaped the microbial communities. Within the three subcommunities, the impact of drift became more pronounced as the effect of dispersal limitation diminished. Overall, elucidating the dynamics of microbial communities in aquatic ecosystems exposed to NH 3 can enhance our comprehension of the ecological mechanisms of microbial communities and provide new insights into the conservation of microbial community diversity and ecological functions., Importance: The research presented in this paper explores how varying concentrations of free ammonia impact microbial communities in aquatic ecosystems. By employing advanced gene sequencing techniques, the study reveals significant changes in microbial diversity and network structures in response to increased ammonia levels. Key findings indicate that high ammonia concentrations lead to a decrease in microbial richness and diversity while increasing community dissimilarity. Notably, certain microbial groups, like Actinobacteria, show resilience to ammonia stress. This research enhances our understanding of how pollution affects microbial ecosystems and underscores the importance of maintaining balanced ammonia levels to preserve microbial diversity and ecosystem health., Competing Interests: The authors declare no conflict of interest.

Model microbial communities are regularly used to test ecological and evolutionary theory as they are easy to manipulate and have fast generation times, allowing for large-scale, high-throughput experiments. A key assumption for most model microbial communities is that they stably coexist, but this is rarely tested experimentally. Here we report the (dis)assembly of a five-species microbial community from a metacommunity of soil microbes that can be used for future experiments. Using reciprocal invasion-from-rare experiments we show that all species can coexist and we demonstrate that the community is stable for a long time (~600 generations). Crucially for future work, we show that each species can be identified by their plate morphologies, even after >1 year in co-culture. We characterise pairwise species interactions and produce high-quality reference genomes for each species. This stable five-species community can be used to test key questions in microbial ecology and evolution.

This study elucidated the influence on a partial denitrification (PD) system under 0-1 mg/L sulfamethoxazole (SMX) stress in a sequencing batch reactor. The results showed that the nitrite accumulation rate (NAR) significantly (P ≤ 0.01) decreased from 68.68 ± 9.00% to 49.05 ± 11.68%, while the total nitrogen removal efficiency significantly (P ≤ 0.001) increased from 23.19 ± 4.42% to 31.36 ± 2.73% in presence of SMX. The results indicated that SMX exposure switched the PD process to complete denitrification through the deterioration of the nitrite accumulation and the promotion of further nitrite reduction. The SMX removal loading rate increased from 0.21 ± 0.04 to 5.03 ± 0.77 mg-SMX/(g-MLVSS·d) with the extended reactor operation under SMX stress. Low SMX concentration exposure increased extracellular polymeric substances (EPS) content from 107.69 ± 20.78 mg/g-MLVSS (0.05 mg-SMX/L) to 123.64 ± 9.66 mg/g-MLVSS (0.5 mg-SMX/L), while EPS secretion was inhibited under high SMX concentration exposure (i.e., 1 mg-SMX/L). Moreover, SMX exposure promoted the synthesis of aromatic protein-like compounds and changed the functional groups as revealed by EEM and FTIR analysis. Additionally, SMX exposure significantly shifted the microbial community structures at both phylum and genus levels. Particularly, the abundance of Thauera, i.e., functional bacteria related to PD, considerably decreased from 41.69% to 11.62% after SMX exposure, whereas the abundances of Denitratisoma and SM1A02 significantly rose under different SMX concentrations. These outcomes hinted that the addition of SMX resulted in the shifting of partial denitrification to complete denitrification., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier Ltd.)

Biological fluidized bed reactor (FBR) is a promising treatment option for removing selenium oxyanions from wastewater by converting them into elemental selenium. The process can achieve high rates and be efficiently operated at low hydraulic retention times (HRT). However, the effects of HRT on the changes in microbial community in the FBR process have not been previously explored. In this study, dynamic changes of microbial communities both on biofilm carrier and in suspension of a selenate-reducing FBR were explored at various HRTs (0.3-120 h). Based on partial 16S rRNA gene sequencing of the microbial communities, alpha diversity of microbial communities in suspension rather than in the biofilm were impacted by low HRTs (0.3 h-3 h). Members from genera Geobacter, Geoalkalibacter, and Geovibrio were the main selenate-reducing bacteria on carrier throughout the FBR process. Genus Geobacter was dominant in FBR carrier at HRT of 24 h-120 h, whereas Geoalkalibacter and Geovibrio dominated at low HRT of 0.3 h-6 h. Suspended microbial communities detected in the FBR effluent were more sensitive to HRT changes than that in biofilm. "Shock loading" at HRT of 0.3 h had a great impact on microbial community compositions both in the biofilm and effluent. Reactor operation in batch mode and long HRT of 24 h helped recover the community from "shock loading" and improved selenite reduction and ethanol oxidation. Redundancy analysis revealed that HRT, influent pH and selenate loading were key operational parameters impacting both the FBR performance and the composition of microbial communities associated with both the FBR carrier and effluent. Overall, the microbial communities in FBR biofilm flexibly responded to the changes of HRT and showed resilience to the temporary shock loading, enabling efficient selenate removal., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: The authors report financial support was provided by Ontario Research Fund and China Scholarship Council., (Copyright © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Moso bamboo is excellent candidate for cadmium (Cd)/lead (Pb) phytoremediation, while rhizosphere microbiome has significant impact on phytoremediation efficiency of host plant. However, little is known about the rhizosphere bacterial communities of moso bamboo in Cd/Pb contaminated soils. Therefore, this study investigated the assembly patterns and key taxa of rhizosphere bacterial communities of moso bamboo in Cd/Pb polluted and unpolluted soils, by field sampling, chemical analysis, and 16S rRNA gene sequencing. The results indicated α-diversity between Cd/Pb polluted and unpolluted soils showed a similar pattern ( p  > 0.05), while β-diversity was significantly different ( p  < 0.05). The relative abundance analysis indicated α-proteobacteria (37%) and actinobacteria (31%) were dominant in Cd/Pb polluted soils, while γ-proteobacteria (40%) and α-proteobacteria (22%) were dominant in unpolluted soils. Co-occurrence network analysis indicated microbial networks were less complex and more negative in polluted soils than in unpolluted soils. Mantel analysis indicated soil available phosphorus, organic matter, and available Pb were the most important environmental factors affecting microbial community structure. Correlation analysis showed 11 bacterial genera were significantly positively related to Cd/Pb. Overall, this study identified the bacterial community composition of bamboo rhizosphere in responding to Cd/Pb contamination and provides a theoretical basis for microbe-assistant phytoremediation in the future.

The active layer is the portion of soil overlaying the permafrost that freezes and thaws seasonally. It is a harsh habitat in which a varied and vigorous microbial population thrives. The high-altitude active layer soil in northern India is a unique and important cryo-ecosystem. However, its microbiology remains largely unexplored. It represents a unique reservoir for microbial communities with adaptability to harsh environmental conditions. In the Changthang region of Ladakh, the Tsokar area is a high-altitude permafrost-affected area situated in the southern part of Ladakh, at a height of 4530 m above sea level. Results of the comparison study with the QTP, Himalayan, Alaskan, Russian, Canadian and Polar active layers showed that the alpha diversity was significantly higher in the Ladakh and QTP active layers as the environmental condition of both the sites were similar. Moreover, the sampling site in the Ladakh region was in a thawing condition at the time of sampling which possibly provided nutrients and access to alternative nitrogen and carbon sources to the microorganisms thriving in it. Analysis of the samples suggested that the geochemical parameters and environmental conditions shape the microbial alpha diversity and community composition. Further analysis revealed that the cold-adapted methanogens were present in the Ladakh, Himalayan, Polar and Alaskan samples and absent in QTP, Russian and Canadian active layer samples. These methanogens could produce methane at slow rates in the active layer soils that could increase the atmospheric temperature owing to climate change., (© 2024. The Author(s) under exclusive licence to Sociedade Brasileira de Microbiologia.)

Saliva is a common biological examination material at crime scenes and has high application value in forensic case investigations. It can reflect the suspect's time of crime at the scene and provide evidence of the suspect's criminal facts. Even though many researchers have proposed their experimental protocols for estimating the time since deposition (TsD) of saliva, there is still a relative lack of research on the use of microorganisms to estimate TsD. In the current study, the succession change of microbial community in saliva with different TsD values was explored to discern the microbial markers related to TsD of saliva. We gathered saliva samples from six unrelated healthy Han individuals living in Guizhou, China and exposed these samples to indoor conditions at six time points (0, 1, 3, 7, 15, and 28 days). Temporal changes of microbial compositions in these samples were investigated by 16S rRNA sequencing (V3-V4 regions). By assessing temporal variation patterns of microbial abundance at the genus level, four bacteria (Brucella, Prevotella, Pseudomonas, and Fusobacterium) were observed to show good time dependence in these samples. In addition, the hierarchical clustering and principal co-ordinates analysis results revealed that these saliva samples could be classified into t-short (≤7 days) and t-long (>7 days) groups. In the end, the random forest model was developed to predict the TsD of these samples. For the model, the root mean square error, R 2 , and mean absolute error between predicted and actual TsD values were 1.5213, 0.9851, and 1.1969, respectively. To sum up, we identified TsD-related microbial markers in saliva samples, which could be viewed as valuable markers for inferring the TsD of saliva., (© 2024 Wiley‐VCH GmbH.)

Biofilms formed by spoilage and pathogenic bacteria increase microbial persistence, causing an adverse influence on the quality of seafood. The mono-species biofilms are widely reported, however, the contamination of multi-species biofilms and their matrix in food environments are still not fully understood. Here, we assessed the contamination of multi-species biofilms in three seafood processing environments with different hygiene levels by detecting bacterial number and three biofilm matrix components (carbohydrates, extracellular DNA (eDNA), and proteins). Samples comprising seven food matrix surfaces and eight food processing equipment surfaces were collected from two seafood processing plants (XY and XC) and one seafood market (CC). The results showed that the bacterial counts ranged from 1.89 to 4.91 CFU/cm 2 and 5.68 to 9.15 BCE/cm 2 in these surfaces by cultivation and real-time PCR, respectively. Six biofilm hotspots were identified, including four in CC and two in XY. Among the three processing environments, the amplicon sequence variants (ASVs) of Proteobacteria, Bacteroidetes, and Actinobacteria decreased with improved processing hygiene, while Firmicutes showed a decrease in the four most abundant phyla. The most prevalent bacteria belonged to genera Psychrobacter, Acinetobacter, and Pseudomonas, demonstrating the significant differences and alteration in bacterial community composition during different environments. From the biofilm hotspots, 15 isolates with strong biofilm forming ability were identified, including 7 Pseudomonas, 7 Acinetobacter, and 1 Psychrobacter. The Pseudomonas isolates exhibited the highest production of EPS components and three strong motilities, whose characteristics were positively correlated. Thus, this study verified the presence of multi-species biofilms in seafood processing environments, offering preliminary insights into the diversity of microbial communities during processing. It highlights potential contamination sources and emphasizes the importance of understanding biofilms composition to control biofilms formation in seafood processing environments., Competing Interests: Declaration of competing interest All authors listed in this paper declare no conflict of interest., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

In this study, the influence and relationship between the microbial structure composition at different spatial locations during soy sauce fermentation and the quality of soy sauce were investigated. Within 3-7 days of fermentation, the abundance of Chromohalobacter in the surface and upper layers of moromi was initially high but subsequently decreased. In contrast, Tetragenococcus exhibited low abundance on the surface of moromi at the beginning of fermentation but emerged as the absolute dominant bacteria by the end of the fermentation process. Throughout the fermentation period of 3-42 days, Staphylococcus and Bacillus were the predominant bacterial genera observed at the bottom of the moromi. In addition, Halanaerobium was the dominant bacterial genus in the crude soy sauce layer throughout the fermentation process. Tetragenococcus and Zygosaccharomyces were strongly positively correlated with total acid and ammonia nitrogen. Bacillus and Staphylococcus were significantly negatively correlated with the salt content., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Strong-flavor Baijiu (SFB) production has relied on pit mud (PM) as a starter culture. The maturation time of natural PM (NPM) is about 30 years, so artificial PM (APM) with a shorter maturation time has attracted widespread attention. This study reveals the microbial and functional dissimilarities of APM and NPM, and helps to elucidate the different metabolic roles of microbes during substrate degradation and flavor formation. Significant differences in the microbial community were observed between APM and NPM, manifesting as variations in the abundance of core microorganisms. Total of 187 high-quality metagenome-assembled genomes (MAGs) were obtained based on the metagenomic binning technology, mainly including Firmicutes (n = 106), Bacteroidota (n = 15) and Chloroflexota (n = 14). Furthermore, the relative concentration of flavor compounds in 4-year APM was similar to those in 30-year NPM, but different from those in 100-year NPMs. Methanosarcina, Methanobacterium, Methanoculleus, Anaerolineae bacterium and Aminobacterium were the key bacteria responsible for the flavor differences. From a functional perspective, amino acid and carbohydrate metabolism were key functions of PM microbial, and showed differences between APM and NPM. Finally, substrate degradation and flavor generation pathways were found to exist in multiple microorganisms. Combine the relative abundance of microorganisms with the absolute abundance of enzymes, Clostridium, Lactobacillus, Petrimonas, Methanoculleus, Prevotella, Methanobacterium, Methanosarcina, Methanothrix, Proteiniphilum, Bellilinea, Anaerolinea, Anaeromassilibacillus, Syntrophomonas and Brevefilum were identified as the key microorganisms in APM and NPM., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Background: The microbial community plays a crucial role in Chinese strong-flavor baijiu (SFB) fermentation. However, the seasonal dynamics of the microbial community in the SFB fermentation system and its contribution to the unique flavor of SFB have not been fully elucidated. In this study, we investigated the seasonal dynamics of the microbial community through 16S rRNA and ITS gene sequencing., Results: The results revealed significant temporal dynamics of microbial communities and environmental variables throughout the four seasons. The influence of seasons on fungal communities was found to be more significant than on bacterial communities. The diversity of bacteria was higher during the winter and summer, whereas fungal diversity was more prominent in summer and autumn. Stochastic processes maintained their dominance in microbial assembly throughout all four seasons but the significance of heterogeneous selection increased during summer for both bacteria and fungi, whereas homogeneous selection became more pronounced during winter for fungi. The pH and environmental temperature were important drivers of microbial community assembly across different seasons, primarily impacting the core genera responsible for the production of major volatile flavor compounds (VFCs), especially ethyl caproate., Conclusion: These findings provide new insights into the impact of seasons on microbial communities and hold promise for improving the quality-control measures for SFB brewed in different seasons. © 2024 Society of Chemical Industry., (© 2024 Society of Chemical Industry.)

Background: Penicillium oxalicum is an important fungal agent in the composting of cattle manure, but the changes that occur in the microbial community, physicochemical factors, and potential functions of microorganisms at different time points are still unclear. To this end, the dynamic changes occurring in the microbial community and physicochemical factors and their correlations during the composting of cattle manure with Penicillium oxalicum were analysed., Results: The results showed that the main phyla observed throughout the study period were Firmicutes, Actinobacteria, Proteobacteria, Bacteroidetes, Halanaerobiaeota, Apicomplexa and Ascomycota. Linear discriminant analysis effect size (LEfSe) illustrated that Chitinophagales and Eurotiomycetes were biomarker species of bacteria and eukaryote in samples from Days 40 and 35, respectively. Bacterial community composition was significantly correlated with temperature and pH, and eukaryotic microorganism community composition was significantly correlated with moisture content and NH 4 + -N according to redundancy analysis (RDA). The diversity of the microbial communities changed significantly, especially that of the main pathogenic microorganisms, which showed a decreasing trend or even disappeared after composting., Conclusions: In conclusion, a combination of high-throughput sequencing and physicochemical analysis was used to identify the drivers of microbial community succession and the composition of functional microbiota during cattle manure composting with Penicillium oxalicum. The results offer a theoretical framework for explaining microecological assembly during cattle manure composting with Penicillium oxalicum., (© 2024. The Author(s).)

Microplastics (MPs) are emerging contaminants in aquatic ecosystems that can profoundly affect carbon and nitrogen cycling. However, the impact mechanisms of MPs on sedimentary greenhouse gas (GHG) emissions at distinct altitudes remain poorly elucidated. Here, we investigated the effects of polyvinyl chloride (PVC) and polylactic acid (PLA) on sedimentary CO 2 , CH 4 , and N 2 O emissions at distinct altitudes of the Yellow River. PVC increased the relative abundance of denitrifiers (e.g., Xanthobacteriaceae, Rhodocyclaceae) to promote N 2 O emissions, whereas PLA reduced the abundance of AOA gene and denitrifiers (e.g., Pseudomonadaceae, Sphingomonadaceae), impeding N 2 O emissions. Both PVC and PLA stimulated the growth of microbes (Saprospiraceae, Aquabacterium, and Desulfuromonadia) associated with complex organics degradation, leading to increased CO 2 emissions. Notably, the concurrent inhibition of PLA on mcrA and pmoA genes led to its minimal impact on CH 4 emissions. High-altitude MQ sediments, characterized by abundant substrate and a higher abundance of functional genes (AOA, AOB, nirK, mcrA), demonstrated higher GHG emissions. Conversely, lower microbial diversity rendered the low-altitude LJ microbial community more susceptible to PVC, leading to a more significant promotion on GHG emissions. This study unequivocally confirms that MPs exacerbate GHG emissions via microbiome-mediated mechanisms, providing a robust theoretical foundation for microplastic control to mitigate global warming., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier B.V.)

Atmospheric nitrogen (N) deposition has been substantially reduced due to declines in the reactive N emission in major regions of the world. Nevertheless, the impact of reduced N deposition on soil microbial communities and the mechanisms by which they are regulated remain largely unknown. Here, we examined the effects of N addition and cessation of N addition on plant and soil microbial communities through a 17-year field experiment in a temperate grassland. We found that extreme N input did not irreversibly disrupt the ecosystem, but ceasing high levels of N addition led to greater resilience in bacterial and fungal communities. Fungi exhibited diminished resilience compared to bacteria due to their heightened reliance on changes in plant communities. Neither bacterial nor fungal diversity fully recovered to their original states. Their sensitivity and resilience were mainly steered by toxic metal ions and soil pH differentially regulating on functional taxa. Specifically, beneficial symbiotic microbes such as N-fixing bacteria and arbuscular mycorrhizal fungi experienced detrimental effects from toxic metal ions and lower pH, hindering their recovery. The bacterial functional groups involved in carbon decomposition, and ericoid mycorrhizal and saprotrophic fungi were positively influenced by soil metals, and demonstrated gradual recovery. These findings could advance our mechanistic understanding of microbial community dynamics under ongoing global changes, thereby informing management strategies to mitigate the adverse effects of N enrichment on soil function., (© 2024 John Wiley & Sons Ltd.)

Considering the adaptability and responsiveness of microorganisms to environmental changes, their indicator potential is still not acknowledged in European directives. This comprehensive study examined the changes of microbial communities in sediments and a range of geochemical parameters from pristine and anthropogenically impacted coastal areas in the eastern Adriatic Sea. Various analytical methods found evidence of sediment contamination (high toxicity level, enrichments of metals, tributyltin) in certain areas, leading to the categorization of sediments based on the level of anthropogenic disturbance. Prokaryotes were identified as the most promising group of microbes for further research, with specific bacterial families (Rhodobacteraceae, Ectothiorhodospiraceae, Cyclobacteriaceae) and genera (Boseongicola, B2M28, Subgroup 23, Sva0485, Thiogranum) proposed as potential indicators of environmental status. Finally, predictive models were developed to identify key indicator variables for assessing anthropogenic impact in sediments. This research represents an essential step toward incorporating microbial communities into assessments of benthic environmental health., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Triclocarban (TCC), an emerging contaminant in water environments, its effects on freshwater biofilms remain insufficiently understood. This study investigates the effects of TCC exposure (at concentrations of 10 μg L -1 and 10 mg L -1 ) on mature freshwater biofilms. TCC was found to inhibit biofilm activity as evidenced by changes in surface morphology and the ratio of live/dead cells. Moreover, both concentrations of TCC were observed to modify the structure of the biofilm community. Metabolomics analysis revealed an overlap in the toxicity mechanisms and detoxification strategies triggered by various concentrations of TCC in biofilms. However, the higher toxicity induced by 10 mg L -1 TCC resulted from the downregulation of proline betaine, disrupting the homeostasis of cellular osmotic pressure regulation in biofilms. Notably, lipid and lipid-like molecules showed high sensitivity to different concentrations of TCC, indicating their potential as biomarkers for TCC exposure. Annotation of the differential metabolites by KEGG revealed that alterations in amino acid and carbon metabolism constituted the primary response mechanisms of biofilms to TCC. Moreover, the biofilm demonstrated enhanced nucleic acid metabolism, which bolstered resistance against TCC stress and heightened tolerance. Furthermore, elevated TCC concentrations prompted more robust detoxification processes for self-defense. Overall, short-term exposure to TCC induced acute toxicity in biofilms, yet they managed to regulate their community structure and metabolic levels to uphold oxidative homeostasis and activity. This research contributes to a deeper comprehension of TCC risk assessment and policy control in aquatic environments., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Yam is an important medicinal and edible dual-purpose plant with high economic value. However, nematode damage severely affects its yield and quality. One of the major effects of nematode infestations is the secondary infection of pathogenic bacteria or fungi through entry wounds made by the nematodes. Understanding the response of the symbiotic microbial community of yam plants to nematodes is crucial for controlling such a disease. In this study, we investigated the rhizosphere and how endophytic microbiomes shift after nematode infection during the tuber expansion stage in the Dioscorea opposita Thunb. cultivar Tiegun. Our results revealed that soil depth affected the abundance of nematodes, and the relative number of Meloidogyne incognita was higher in the diseased soil at a depth of 16 to 40 cm than those at a depth of 0 to 15 and 41 to 70 cm. The abundance of and interactions among soil microbiota members were significantly correlated with root-knot nematode (RKN) parasitism at various soil depths. However, the comparison of the microbial α-diversity and composition between healthy and diseased rhizosphere soil showed no difference. Compared with healthy soils, the co-occurrence networks of M. incognita -infested soils included a higher ratio of positive correlations linked to plant health. In addition, we detected a higher abundance of certain taxonomic groups belonging to Chitinophagaceae and Xanthobacteraceae in the rhizosphere of RKN-infested plants. The nematodes, besides causing direct damage to plants, also possess the ability to act synergistically with other pathogens, especially Ramicandelaber and Fusarium , leading to the development of disease complexes. In contrast to soil samples, RKN parasitism specifically had a significant effect on the composition and assembly of the root endophytic microbiota. The RKN colonization impacted a wide variety of endophytic microbiomes, including Pseudomonas , Sphingomonas , Rhizobium , Neocosmospora , and Fusarium . This study revealed the relationship between RKN disease and changes in the rhizosphere and endophytic microbial community, which may provide novel insights that help improve biological management of yam RKNs., Competing Interests: The author(s) declare no conflict of interest.

Chromium pollution, particularly hexavalent chromium [Cr(VI)], may threaten the environment and human health. This study investigated the potential of Tagetes erecta L. (Aztec marigold) for phytoremediation of soil contaminated with Cr(VI), and focused on the effects of varying concentrations of Cr(VI) on both the physicochemical properties of soil and microbiome of Tagetes erecta L. We observed that Tagetes erecta L. showed tolerance to Cr(VI) stress and maintained normal growth under these conditions, as indicated by bioconcentration factors of 0.33-0.53 in shoots and 0.39-0.70 in roots. Meanwhile, the structure and diversity of bacterial communities were significantly affected by Cr(VI) pollution. Specifically, Cr(VI) had a more significant effect on the microbial community structure in the endophytic of Tagetes erecta L. than in the rhizosphere (p < 0.05). The genera Devosia and Methylobacillus were positively correlated with Cr(VI) concentrations. Biomarkers such as Bacilli and Pseudonocardia were identified under the different Cr(VI)-contaminated treatments using LEfSe. In addition, the interaction and stability of the endophytic microbiome were enhanced under Cr(VI) stress. This study explored the interactions between heavy metals, microorganisms, and plants, providing valuable insights for developing in situ bioremediation of Cr(VI)-contaminated soils., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

The high use of plastic wraps leads to significant environmental pollution. In this study, the surface structure and microbial community evolution of commercially available plastic wraps [polyethylene (PE), polyvinyl chloride (PVC), polyvinylidene chloride (PVDC), and polylactic acid (PLA)] in constructed wetlands (CWs) were investigated. The results indicated that all plastic wraps gradually decreased in molecular weight, crystallinity, melting, and crystallization temperatures, whereas a gradual increase was observed in the surface roughness, polymer dispersity index (PDI), carbonyl index (CI) and Shannon index of microorganisms colonizing the CWs. The aging rate of the plastic wrap was in the order: PLA > PVC > PE > PVDC, at the same site in the CWs, and it was in the order: soil surface > plant roots > subsoil, for the same plastic wrap. The diversity of microorganisms colonizing the same plastic wrap was in the order: plant roots > subsoil > soil surface. The Shannon indices of microorganisms on plastic wraps were lower than those in the soil, indicating that the diversity of microorganisms colonizing plastic wraps is limited. Additionally, the microbial community structure on the plastic surface was co-differentiated by the plastic type, placement position in the CWs, and aging time. Significantly different microbial community structures were found on the PVC and PVDC wrap surfaces, revealing that the chlorine in plastics limits microbial diversity. Unclassified members of Rhizobiaceae and Pseudomonadaceae were the dominant genera on the surface of the plastic wraps, suggesting that they may be the microorganisms involved in plastic degradation processes. The study provides valuable perspectives to facilitate a comprehensive understanding of the migration, fate, and environmental risks associated with microplastics (MPs) in wetlands., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Fertilizer input is one of the effective forest management practices, which improves soil nutrients and microbial community compositions and promotes forest productivity. However, few studies have explored the response of rhizosphere soil microbial communities to various fertilization regimes across seasonal dynamics. Here, we collected the rhizosphere soil samples from Phoebe bournei plantations to investigate the response of community assemblages and microbial interactions of the soil microbiome to the short-term application of four typical fertilizer practices (including chemical fertilizer (CF), organic fertilizer (OF), compound microbial fertilizer (CMF), and no fertilizer control (CK)). The amendments of organic fertilizer and compound microbial fertilizer altered the composition of rhizosphere soil bacterial and fungal communities, respectively. The fertilization regime significantly affected bacterial diversity rather than fungal diversity, and rhizosphere fungi responded more sensitively than bacteria to season. Fertilization-induced fungal networks were more complex than bacterial networks. Stochastic processes governed both rhizosphere soil bacterial and fungal communities, and drift and dispersal limitation dominated soil fungal and bacterial communities, respectively. Collectively, these findings demonstrate contrasting responses to community assemblages and interactions of rhizosphere bacteria and fungi to fertilizer practices. The application of organic fertilization strengthens microbial interactions and changes the succession of key taxa in the rhizosphere habitat. KEY POINTS: • Fertilization altered the key taxa and microbial interaction • Organic fertilizer facilitated the turnover of rhizosphere microbial communities • Stochasticity governed soil fungal and bacterial community assembly., (© 2024. The Author(s).)

Biodegradable plastic films have emerged as a substitute for conventional plastic films. Nevertheless, responses of plant-associated microbiomes to the application of biodegradable film mulching at field scale have received little attention. A field experiment was conducted to assess the influence of different film mulching treatments on various microbial attributes and nitrogen (N) cycling functional genes in bulk and rhizosphere soils. Biodegradable film mulching raised the bacterial Shannon index in bulk soils but not in rhizosphere soils. Biodegradable film mulching has led to an increase in the complexity and connectivity of microbial networks, as well as an enhancement in the positive association among microorganisms owing to raised soil nutrients and increased crop biomass. In biodegradable film-treated soils, both bacterial and fungal communities were primarily influenced by stochastic processes associated with dispersal limitation. Moreover, conventional plastic film mulching increased denitrification, anammox, N fixation, and dissimilatory nitrate-reduction (DNRA) gene abundance in bulk soils. In rhizosphere soils, biodegradable film mulching reduced nitrification, denitrification, anammox, N fixation, and DNRA gene abundance. Furthermore, keystone genera (e.g., Nitrosospira, Truepera, Adhaeribacter, Opitutus, and Fusarium) were affected by edaphic variables, contributing to decreased N-cycling gene abundance in biodegradable film-treated soils. Collectively, biodegradable film mulching transformed soil microbiome assembly and functional adaptation, and soil nutrient availability and plant biomass were the critical factors influencing the microbial community. These findings present a novel perspective on the diverse impacts of biodegradable and conventional film mulching on soil microbiome and N-cycling processes., Competing Interests: Declaration of competing interest This manuscript has not been published before nor submitted to another journal for the consideration of publication. The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Microplastics (MPs) are distributed widely in the ocean surface waters and sediments. Increasing MPs contamination in intertidal zone profoundly impacts microbial ecosystem services and biogeochemical process. Little is known about the response of tidal sediment microbiome to MPs. We conducted a 30-day laboratory microcosm study using five polymers (PE, PBS, PC, PLA and PET) at three concentrations (1 %, 2 % and 5 %, w/w). High throughput sequencing of 16 S rRNA, qPCR and enzyme activity test were applied to demonstrate the response of microbial community and nitrogen cycling functional genes to MPs. MPs reduced the microbial alpha diversity and the microbial dissimilarity while the effects of PLA-MPs were concentration dependent. LEfSe analysis indicated that the Proteobacteria predominated for all MP treatments. Mantel's test, RDA and correlation analysis implied that pH may be the key environmental factor for causing microbial alterations. MPs enhanced nitrogen fixation in tidal sediment. PLA levels of 1 % but not 5 % produced the most significant effects in nitrogen cycling functional microbiota and genes. PLS-PM revealed that impacts of MPs on tidal sediment microbial communities and nitrogen cycling were dominated by indirect effects. Our study deepened understanding and filled the knowledge gap of MP contaminants affecting tidal sediment microbial nitrogen cycling., Competing Interests: Declaration of Competing Interest No conflict of interest exists in the submission of this manuscript., (Copyright © 2024 Elsevier B.V. All rights reserved.)