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Straw return with nitrogen (N) fertilizer can generally regulate soil N cycling by affecting the microbial community, thereby influencing crop productivity. Bacteria and fungi play a key role in nitrification, while the effects of soil microbial interactions that include protists under the condition of straw return and N fertilizer remain uncertain. Here, we evaluated the importance of the soil microbiome, particularly protists and ammonia‐oxidizing bacteria (AOB), in regulating the soil N transformation potential and wheat yields under different fertilization practices. The results showed that the activity of β‐1,4‐N‐acetylglucosaminidase (NAG) and the potential nitrification rate (PNR) increased significantly by 156.4% ~ 312.3% and 183.1% ~ 402.6% with the addition of N fertilizer and straw, respectively. The effect on PNR was greater for straw than fertilizer addition. The fertilization practices changed the microbial community structure, and there were stronger responses from the protists and AOB. The soil microbiome formed three closely co‐occurring modules (Modules 0, 1 and 2). Among them, Module 0 showed strong positive correlations with the soil total N, NAG, PNR and crop yield and may be the key ecological cluster. Moreover, the predatory protists Cercozoa, Conosa and Ochrophyta in Module 0 were significantly positively associated with the activity of NAG and the PNR, yields and AOB. The predatory protists in Module 0 may change the soil potential nitrification rate and enhance the yield of wheat by preying on the competitors of AOB. The results suggest that the incorporation of straw promotes the N transformation potential and wheat yields linked to trophic interactions between predatory protists and AOB in fluvo‐aquic soil. [ABSTRACT FROM AUTHOR]

The non-ionic water-soluble X-ray contrast agent iomeprol (IOM) enters the water supply through sewage treatment plants, which can cause considerable environmental harm. In this study,Pseudomonassp. I-24 (I-24) was tested for its ability to remove IOM from water via co-metabolic pathways. The optimum removal rate of IOM by I-24 was 38.43% ± 3.70% when starch served as the source of external carbon, and its co-metabolism of IOM conformed to the first-order kinetics. The highest activity of intracellular enzyme (degrading enzyme) extracted from I-24 was 0.143 ± 0.005 mU in starch condition. The Michaelis constant of the degrading enzyme was found to be 91.08 μmol L−1. However, glucose and maltose showed the best promotive effects on the growth and electron transport activity of I-24, indicating that overgrowth may result in competitive inhibition and a reduced degradation rate of IOM. Adding I-24 and degrading enzymes to biological aerated filters increased IOM removal rates without affecting CODMnremoval. [ABSTRACT FROM PUBLISHER]

Aerobic composting is commonly used to dispose livestock manure and is an efficient way to reduce antibiotic resistance genes (ARGs). Here, the effects of different quality substrates on the fate of ARGs were assessed during manure composting. Results showed that the total relative abundances of ARGs and intI1 in additive treatments were lower than that in control, and high quality treatment with low C/N ratio and lignin significantly decreased the relative abundance of tetW , ermB , ermC , sul1 and sul2 at the end of composting. Additionally, higher quality treatment reduced the relative abundances of some pathogens such as Actinomadura and Pusillimonas , and some thermotolerant degrading-related bacteria comprising Pseudogracilibacillus and Sinibacillus on day 42, probably owing to the change of composting properties in piles. Structural equation models (SEMs) further verified that the physiochemical properties of composting were the dominant contributor to the variations in ARGs and they could also indirectly impact ARGs by influencing bacterial community and the abundance of intI1. Overall, these findings indicated that additives with high quality reduced the reservoir of antibiotic resistance genes of livestock manure compost. • High quality additive effectively reduced the relative abundance of total ARGs during composting. • Bacterial composition and intI1 exhibit positive relationships with ARGs. • Firmicutes were the main potential host bacteria for multiple ARGs. • Composting properties show the most significant contribution to the variation of ARGs. [ABSTRACT FROM AUTHOR]

The main contributors to antibiotic resistance genes (ARGs) profiles during the composting process under the addition of biochar (BC) and peat (PT) were not fully explored. This study investigated the influence of BC and PT amendment on ARGs fate, the bacterial community and heavy metals in sewage sludge compost. Compared to control, BC and PT declined the total abundances of ARGs by 17.6% and 43.0% after composting. Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria were the dominant phyla across the composting process, among which, members of Firmicutes (mainly Bacillaceae) were the potential hosts for multiple ARGs. BC and PT addition declined the abundance of bacterial pathogens such as Bacteroides and Pseudomonas. Besides, the concentrations of copper (Cu), zinc (Zn) and lead (Pb) were less in BC and PT treatments than control on day 40, and these metals displayed significant positive correlations to sul1 and intI1. Furthermore, variation partitioning analysis (VPA) revealed that the bacterial community exhibited the most contribution to the ARG patterns, as much as 34.0%, followed by heavy metals (10.8%) and intI1 gene (1.5%). These results suggested that biochar and peat can reduce the risks of ARGs in sewage sludge mainly by sharping the bacterial composition. • Biochar and peat reduced the abundance of ARGs during composting. • Biochar and peat promoted the removal of heavy metals. • The addition of biochar significantly declined the abundance of bacteria pathogens. • The bacterial community contributed the most to the ARGs profiles. [ABSTRACT FROM AUTHOR]

Cytochrome P450 genes are very important for plant-parasitic nematodes to reproduce and to metabolize xenobiotic compounds generated by their host plants. The pine wood nematode (PWN), Bursaphelenchus xylophilus, causes very high annual economic losses by killing large numbers of pine trees across Asia and into Europe. In this study, we used RNA interference (RNAi) to analyze the function of the cyp-33C9 gene of PWN. Our results showed that expression of the cyp-33C9 gene was suppressed successfully after soaking nematodes for 24 h in cyp-33C9 double-stranded RNA (dsRNA). The silencing of the cyp-33C9 gene significantly decreased the feeding, reproduction, oviposition and egg hatch of B. xylophilus. Meanwhile, the migration speed of B. xylophilus in Pinus thunbergii was reduced in the early stages when the cyp-33C9 gene was silenced in the nematodes. Moreover, knockdown of the cyp-33C9 gene in B. xylophilus caused a decrease in pathogenicity to pine trees. These results suggest that the cyp-33C9 gene plays an important role in the reproduction and pathogenicity of B. xylophilus. This discovery identified several functions of the cyp-33C9 gene in B. xylophilus and provided useful information for understanding the molecular mechanism behind pine wilt disease caused by PWN. [ABSTRACT FROM AUTHOR]

Highlights • Wheat and maize straw biochar addition improved the maturity and fertility of compost product. • Biochar addition influenced the structure and functions of microbial community during composting process. • Network analysis revealed the close associations between bacterial taxa and the properties of compost. Abstract The present study determined the dynamic changes of bacterial community structures and its metabolism functions in rice straw composting process with different types of biochar addition. Results showed that both wheat and maize straw biochar addition greatly increased the temperatures and germination index. Biochar addition influenced microbial community structure and metabolic characteristics of the compost. Firmicutes , Actinobacteria and Proteobacteria were the dominant phyla throughout the process, and both biochar addition significantly increased the relative abundance of Actinobacteria phylum, especially genus Saccharomonospora. The abundance of bacterial genes related to amino acid metabolism, carbohydrate metabolism and energy metabolism were also increased with biochar addition. Moreover, total nitrogen was strongly affected by biochar addition and had the greatest influence on the bacterial community structure. These results indicated that biochar addition improved the maturity and fertility of the compost product as well as significantly regulated the microbial community structure and functions during composting process. [ABSTRACT FROM AUTHOR]

As the causal agent of pine wilt disease (PWD), the pine wood nematode (PWN), Bursaphelenchus xylophilus, causes huge economic losses by devastating pine forests worldwide. However, the pathogenesis-related genes of B. xylophilus are not well characterized. Thus, DNA microarrays were used to investigate differential gene expression in PWN where Pinus thunbergii was inoculated with nematodes, compared with those cultured on Botrytis cinerea. The microarrays comprised 31121 probes, 1310 (4.2%) of which were differentially regulated (changes of >2-fold, P < 0.01) in the two growth conditions. Of these 1310 genes, 633 genes were upregulated, whereas 677 genes were downregulated. Gene Ontology (GO) categories were assigned to the classes Cellular Component, Molecular Function, and Biological Process. The comparative gene expression analysis showed that a large number of the pathogenesis-related genes of B. xylophilus, such as pectate lyase genes, cytochrome P450s, UGTs, and ABC transporter genes, were highly expressed when B. xylophilus infected P. thunbergii. Annotation analysis indicated that these genes contributed to cell wall degradation, detoxification, and the reproduction process. The microarray results were validated using quantitative RT-PCR (qRT-PCR). The microarray data confirmed the specific expression of B. xylophilus genes during infection of P. thunbergii, which provides basic information that facilitates a better understanding of the molecular mechanism of PWD. [ABSTRACT FROM AUTHOR]

Introduction: Soil microbes are central in governing soil multifunctionality and driving ecological processes. Despite biochar application has been reported to enhance soil biodiversity, its impacts on soil multifunctionality and the relationships between soil taxonomic biodiversity and ecosystem functioning remain controversial in paddy soil., Methods: Herein, we characterized the biodiversity information on soil communities, including bacteria, fungi, protists, and nematodes, and tested their effects on twelve ecosystem metrics (including functions related to enzyme activities, nutrient provisioning, and element cycling) in biochar-amended paddy soil., Results: The biochar amendment augmented soil multifunctionality by 20.1 and 35.7% in the early stage, while the effects were diminished in the late stage. Moreover, the soil microbial diversity and core modules were significantly correlated with soil multifunctionality., Discussion: Our analysis revealed that not just soil microbial diversity, but specifically the biodiversity within the identified microbial modules, had a more pronounced impact on ecosystem functions. These modules, comprising diverse microbial taxa, especially protists, played key roles in driving ecosystem functioning in biochar-amended paddy soils. This highlights the importance of understanding the structure and interactions within microbial communities to fully comprehend the impact of biochar on soil ecosystem functioning in the agricultural ecosystem., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Xiao, Zhou, Qiu, Liu, Chen and Zhang.)

Introduction: Ammonia oxidizing archaea (AOA) and ammonia oxidizing bacteria (AOB) have been proven to be key microorganisms driving the ammonia oxidation process. However, under different fertilization practices, there is a lack of research on the impact of interaction between predators and AOA or AOB on nitrogen cycling at the multi-trophic level., Methods: In this study, a network-oriented microscopic culture experiment was established based on four different long-term fertilization practices soils. We used the nitrification inhibitors 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxide-3-oxyl (PTIO) and 3, 4-Dimethylpyrazole phosphate (DMPP) inhibited AOA and AOB, respectively, to explore the impact of interaction between protists and AOA or AOB on nitrogen transformation., Results: The results showed that long-term nitrogen application promoted the potential nitrification rate (PNR) and nitrous oxide (N 2 O) emission, and significantly increased the gene abundance of AOB, but had no obvious effect on AOA gene abundance. DMPP significantly reduced N 2 O emission and PNR, while PTIO had no obvious effect on them. Accordingly, in the multi-trophic microbial network, Cercozoa and Proteobacteria were identified as keystone taxa of protists and AOB, respectively, and were significantly positively correlated with N 2 O, PNR and nitrate nitrogen. However, Nitrososphaerota archaeon as the keystone species of AOA, had an obvious negative linkage to these indicators. The structural equation model (SEM) showed that AOA and AOB may be competitors to each other. Protists may promote AOB diversity through direct trophic interaction with AOA., Conclusion: The interaction pattern between protists and ammonia-oxidizing microorganisms significantly affects potential nitrification rate and N 2 O emission, which has important implications for soil nitrogen cycle., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision., (Copyright © 2024 Jia, Zhou, Ma, Qiu, Zhang, Wang, Zhang, Chen, Ma, Zhao and Xue.)

As the causal agent of pine wilt disease (PWD), the pine wood nematode (PWN), Bursaphelenchus xylophilus, causes huge economic losses by devastating pine forests worldwide. However, the pathogenesis-related genes of B. xylophilus are not well characterized. Thus, DNA microarrays were used to investigate differential gene expression in PWN where Pinus thunbergii was inoculated with nematodes, compared with those cultured on Botrytis cinerea. The microarrays comprised 31121 probes, 1310 (4.2%) of which were differentially regulated (changes of >2-fold, P < 0.01) in the two growth conditions. Of these 1310 genes, 633 genes were upregulated, whereas 677 genes were downregulated. Gene Ontology (GO) categories were assigned to the classes Cellular Component, Molecular Function, and Biological Process. The comparative gene expression analysis showed that a large number of the pathogenesis-related genes of B. xylophilus, such as pectate lyase genes, cytochrome P450s, UGTs, and ABC transporter genes, were highly expressed when B. xylophilus infected P. thunbergii. Annotation analysis indicated that these genes contributed to cell wall degradation, detoxification, and the reproduction process. The microarray results were validated using quantitative RT-PCR (qRT-PCR). The microarray data confirmed the specific expression of B. xylophilus genes during infection of P. thunbergii, which provides basic information that facilitates a better understanding of the molecular mechanism of PWD.