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Abstract The soil environment plays an important role in urban ecosystems. To study the heavy metal contamination of soil in Beilun District, Ningbo, we collected soil samples from 60 points in urban and peri-urban areas of Beilun District and analyzed the spatiotemporal variation and sources of heavy metal pollution in various land-use types. The results shown that the heavy metal contents in 2015 and 2022 were higher than the background soil values of Ningbo city, and there was an accumulation of heavy metals over these 7 years. The contents of heavy metals in green belts and woodland in 2022 were higher than those in 2015, while there was no significant change in agricultural land. The heavy metal contents in both years were mainly in the order green belts > agricultural land > woodland. The spatiotemporal distribution of heavy metal content showed that heavy metal pollution in Beilun District was concentrated in five industrial areas, and there was a trend toward the disappearance of highly polluted points. But the single-factor pollution index, pollution load index (PLI), and geoaccumulation index (Igeo) indicated that there was no significant heavy metal pollution in Beilun District, and individual elements at specific points showed slight pollution. The source analysis results showed that the main source of Hg is chemical, As is mainly derived from agricultural, Cr, Ni and Cu are mainly derived from natural, the main sources of Zn and Cd are electroplating and machinery activities, and the main source of Pb is traffic. These results specify a reference for future investigation on urban soil heavy metals, and the source apportionment results provide a scientific foundation for subsequent soil heavy metal pollution treatment.

Simple anaerobic digestion is insufficient to completely remove residual parent antibiotics and antibiotic resistance genes (ARGs) from animal manure. ARG prevalence in swine biogas slurry-irrigated soils threatens human health. However, comprehensive analysis of antibiotic residues, high-resolution resistance gene profiles, and pathogenic microbiomes in biogas slurry-irrigated soils is very limited. Here, we comprehensively determined the antibiotics, resistome, and potential pathogens distribution in these soils, using high-performance liquid chromatography-tandem mass spectrometry, high-throughput quantitative PCR, and 16S rRNA gene sequencing. The results revealed a significant enrichment of tetracyclines and fluoroquinolones antibiotics and ARGs in soils with prolonged biogas slurry irrigation, with a total of 12 antibiotics, 175 unique ARGs, and 9 mobile genetic elements (MGEs) detected. Quantification of veterinary antibiotic residues (especially chlortetracycline) showed significant correlations with multiple ARGs. The abundance of ARGs and MGEs was highest in the biogas slurry-irrigated soils, denoting a tight link between the application of biogas slurry and the spread of antibiotic resistance. The presence of 50 potential pathogenic bacterial genera, including 13 with multidrug resistance, was identified. Variation partitioning, combined with hierarchical partitioning analysis, indicated that Firmicutes, MGEs, and tetracyclines were the key drivers shaping the ARG profiles in biogas slurry-irrigated soils. The findings offer insights into the mechanisms of antibiotic residue and ARGs spread from the agricultural practice of biogas slurry irrigation, underscoring the necessity of sustainable soil management to mitigate the spread of antibiotic resistance.

Straw return is regarded as a widely used field management strategy for improving soil health, but its comprehensive effect on crop grain yield and quality remains elusive. Herein, a meta-analysis containing 1822 pairs of observations from 78 studies was conducted to quantify the effect of straw return on grain yield and quality of three main crops (maize, rice, and wheat). On average, compared with no straw return, straw return significantly (p< 0.05) increased grain yield (+4.3%), protein content (+2.5%), total amino acids concentration (+1.2%), and grain phosphorus content (+3.6%), respectively. Meanwhile, straw return significantly (p< 0.05) decreased rice chalky grain rate (-14.4%), overall grain hardness (-1.9%), and water absorption of maize and wheat (-0.5%), respectively. Moreover, straw return effects on grain yield and quality traits were infected by cultivated crop types, straw return amounts, straw return methods, and straw return duration. Our findings illustrated that direct straw return increased three main crop grain yields and improved various quality traits among different agricultural production areas. Although improper straw return may increase plant disease risk and affect seed germination, our results suggest that full straw return with covered or plough mode is a more suitable way to enhance grain yield and quality. Our study also highlights that compared with direct straw return, straw burning or composting before application may also be beneficial to farmland productivity and sustainability, but comparative studies in this area are still lacking.

Summary: Microorganisms are critical to the stability of aquatic environments, and understanding the ecological mechanisms of microbial community is essential. However, the distinctions and linkages across biogeographic patterns, ecological processes, and formation mechanisms of microbes in rivers and lakes remain unknown. Accordingly, microbiome-centric analysis was conducted in rivers and lakes in the Yangtze River watershed. Results revealed significant differences in the structure and diversity of microbial communities between rivers and lakes, with rivers showing higher diversity. Lakes exhibited lower community stability, despite higher species interactions. Although deterministic processes dominated microbial community assembly both in rivers and lakes, higher stochastic processes of rare and abundant taxa exhibited in rivers. Spatial factors influenced river microbial community, while environmental factors drove differences in the lake bacterial community. This study deepened the understanding of microbial biogeography and formation mechanisms in large watershed rivers and lakes, highlighting distinct community aggregation patterns between river and lake microorganisms.

Rhizo-microbe recruited by hyperaccumulating plants are crucial for the extraction of metals from contaminated soils. It is important, but difficult, to identify the specific rhizosphere microbes of hyperaccumulators shaped by root exudation. Continuous 13CO2 labeling, microbial DNA-based stable isotope probing (DNA-SIP), and high throughput sequencing were applied to identify those rhizosphere microorganisms using exudates from the Cd hyperaccumulator Sedum alfredii. In contrast to its non-hyperaccumulating ecotype (NAE), the hyperaccumulating ecotype (HAE) of S. alfredii strongly changed the rhizosphere environment and extracted a 5-fold higher concentration of Cd from contaminated soil. Although both HAE and NAE harbored Streptomyces, Massilia, Bacillus, and WPS-2 Uncultured Bacteria with relative abundance of more than 1% in the rhizosphere associated with plant growth and immunity, the HAE rhizosphere specifically recruited Rhodanobacter (2.66%), Nocardioides (1.16%), and Burkholderia (1.01%) through exudates to benefit the extraction of Cd from soil. Different from the bacterial network with weak cooperation in the NAE rhizosphere, a closed-loop bacterial network shaped by exudates was established in the HAE rhizosphere to synergistically resist Cd. This research reveals a specific rhizosphere bacterial community induced by exudates assisted in the extraction of Cd by S. alfredii and provides a new perspective for plant regulation of the rhizo-microbe community beneficial for optimizing phytoremediation.

The presence of biodegradable microplastics (MPs) has the potential to affect soil pH, and possibly accelerate or inhibit the loss of soil inorganic carbon (SIC) in calcareous soils. However, most researchers have focused on the release of biotic carbon dioxide (CO2) from soils following MP amendments, and few studies have investigated SIC-derived CO2. In this experiment, three typical biodegradable MPs were applied to three calcareous soils amended with 1 % 13C-labeled (99 % atom) carbonate, and the release of CO2 originating from SIC was quantified. The total CO2 emissions, soil pH, and microbial functional genes involved in soil nitrification and denitrification were also detected. Throughout the experiment, the contribution of 13C-labeled carbonate to total CO2 emissions ranged from 0.42 % to 3.31 %. The impact of biodegradable MPs on SIC-derived CO2 varied with incubation period. At the early stage (≤20 days), the amendment of three biodegradable MPs increased the abiotic CO2 in some cases, and the CO2 emissions from 13C-labeled SIC were positively correlated with the total CO2 originating from the decomposition of SOC and MPs. At the late stage (20–70 days), the presence of biodegradable MPs inhibited the release of CO2 from 13C-labeled carbonate in most treatments. Moreover, there were negative relationships of SIC-derived CO2 with soil pH and the amoA gene of ammonia-oxidizing archaea (AOA), but positive correlations of SIC-derived CO2 with amoA of ammonia oxidizing bacteria (AOB) and nirK and nirS genes encoding nitrate reductase in denitrification. Our results indicate that long-term exposure to biodegradable MPs probably regulates the release of H+ in the nitrification process by controlling AOB, and then controlling the dynamics of SIC in calcareous soils.

Continuous cropping is the primary cultivation method in Chinese facility agriculture, and the challenge of it stands as a global issue in soil remediation. Growing tomatoes continuously on the same plot for an extended period can result in outbreaks of tomato bacterial wilt. It is caused by the soil-borne bacterium Ralstonia solanacearum, a widespread plant pathogen that inflicts considerable damage on economically significant crops worldwide. Simultaneously, this plant pathogen proves extremely resilient, as it can adhere to plant residues and persist through the winter, continuing to infect plants in subsequent years. Scientists have dedicated considerable efforts towards finding effective methods to manage this disease. This article delineates the characteristics of tomato bacterial wilt and the various types of pathogenic bacteria involved. It systematically reviews the progress in research aimed at controlling tomato bacterial wilt, encompassing both physical and biological aspects concerning soil and plants. Emphasis is placed on the principles and current applications of these control measures, alongside proposed improvements to address their limitations. It is anticipated that the future of tomato bacterial wilt control will revolve around the development of a novel environmental protection system and efficient control strategies, focusing on microecological management and enhancing tomato resistance against bacterial wilt through breeding.

Biochar applied to soil can reduce nitrous oxide (N2O) emissions produced by freeze–thaw processes. Nonetheless, how biochar modification affects N2O emissions during freeze–thaw cycles is not completely clear. In our research, during freeze–thaw cycles, microcosm experiments were conducted to investigate the effects of maize straw biochar (MB) or rice straw biochar (RB) addition on soil N2O emissions under different water conditions. The N2O emissions peaked at the initial stage of thawing in all the soils, and the total N2O emissions were considerably greater in the flooded soils than in the nonflooded soils. Compared with the soils without biochar addition, RB and MB amendments inhibited N2O emissions by 69 and 67%, respectively. Moreover, after biochar addition, the abundance of AOB amoA genes decreased by 9–13%. Biochar addition significantly decreased the content of microbial biomass nitrogen (MBN) in flooded soil during thawing, which was significantly correlated with N2O emissions and nitrification and denitrification communities. The PLS-PM further revealed that biochar can inhibit the production and emission of soil N2O by reducing soil MBN during soil thawing. In addition, soil moisture directly significantly affects N2O emissions and indirectly affects N2O emissions through its influence on soil physicochemical properties. Our results revealed the important function of biochar in decreasing the emission of N2O in flooded soil during freeze–thaw cycles.

Soil organic matter (SOM) plays an important role in the field of climate change and terrestrial ecosystems. SOM in large areas, especially in urban areas, is difficult to monitor and estimate by traditional methods. Urban land structure is complex, and soil is a mixture of organic and inorganic constituents with different physical and chemical properties. Previous studies showed that remote sensing techniques that provide diverse data in the visible-near-infrared (VNIR)-shortwave infrared (SWIR) spectral range, are promising in the prediction of SOM content on a large scale. Sentinel-2 covers the important spectral bands (VNIR-SWIR) for SOM prediction with a short revisit time. Thus, this article aimed to evaluate the capacity of Sentinel-2 for SOM prediction in an urban area (i.e., Shanghai). 103 bare soil samples filtrated from 398 soil samples at a depth of 20 cm were selected. Three methods, partial least square regression (PLSR), artificial neural network (ANN), and support vector machine (SVM), were applied. The root mean square error (RMSE) of modelling (mRMSE) and the coefficient of determination ( $R^{2}$ ) of modelling $(mR^{2})$ were used to reflect the accuracy of the model. The results show that PLSR has the poorest performance. ANN has the highest modelling accuracy (mRMSE = 7.387 g kg $^{-1}$ , $mR^{2}=0.446$ ). The ANN prediction accuracy of RMSE (pRMSE) is 4.713 g kg $^{-1}$ and the prediction accuracy of $R^{2}~(pR^{2})$ is 0.723. For SVR, the pRMSE is 4.638 g kg $^{-1}$ , and the $pR^{2}$ is 0.732. The prediction accuracy of SVR is slightly higher than that of ANN. The spatial distribution of SOM demonstrates that the value obtained by ANN is the closest to the range of the bare soil samples, and ANN performs better in vegetation-covered areas. Therefore, Sentinel-2 can be used to estimate SOM content in urban areas, and ANN is a promising method for SOM estimation.

Biofilms are microbial aggregation membranes that are formed when microorganisms attach to the surfaces of living or nonliving things. Importantly, biofilm properties provide microorganisms with protection against environmental pressures and enhance their resistance to antimicrobial agents, contributing to microbial persistence and toxicity. Thus, bacterial biofilm formation is part of the bacterial survival mechanism. However, if foodborne pathogens form biofilms, the risk of foodborne disease infections can be greatly exacerbated, which can cause major public health risks and lead to adverse economic consequences. Therefore, research on biofilms and their removal strategies are very important in the food industry. Food waste due to spoilage within the food industry remains a global challenge to environmental sustainability and the security of food supplies. This review describes bacterial biofilm formation, elaborates on the problem associated with biofilms in the food industry, enumerates several kinds of common foodborne pathogens in biofilms, summarizes the current strategies used to eliminate or control harmful bacterial biofilm formation, introduces the current and emerging control strategies, and emphasizes future development prospects with respect to bacterial biofilms.

Abstract Background N fixation is one of the most important microbially driven ecosystem processes on Earth, allowing N to enter the soil from the atmosphere, and regulating plant productivity. A question that remains to be answered is whether such a fundamental process would still be that important in an over-fertilized world, as the long-term effects of fertilization on N fixation and associated diazotrophic communities remain to be tested. Here, we used a 35-year fertilization experiment, and investigated the changes in N fixation rates and the diazotrophic community in response to long-term inorganic and organic fertilization. Results It was found that N fixation was drastically reduced (dropped by 50%) after almost four decades of fertilization. Our results further indicated that functionality losses were associated with reductions in the relative abundance of keystone and phylogenetically clustered N fixers such as Geobacter spp. Conclusions Our work suggests that long-term fertilization might have selected against N fixation and specific groups of N fixers. Our study provides solid evidence that N fixation and certain groups of diazotrophic taxa will be largely suppressed in a more and more fertilized world, with implications for soil biodiversity and ecosystem functions.

Intercropping systems can flexibly use resources such as sunlight, heat, water, and nutrients in time and space, improve crop yield and land utilization rates, effectively reduce continuous cropping obstacles and the occurrence of diseases and insect pests, and control the growth of weeds. Thus, intercropping is a safe and efficient ecological planting mode. The legume–cereal intercropping system is the most common planting combination. Legume crops fix nitrogen from the atmosphere through their symbiotic nitrogen fixation abilities, and the fixed nitrogen can be transferred to and utilized by cereal crops in various ways. The symbiotic nitrogen fixation efficiency of legume crops was improved by reducing the inhibition of soil nitrogen on nitrogenase activity through competitive absorption of soil nitrogen. However, the effects of nitrogen transformation and distribution in intercropping systems and microbial community structure characteristics on nitrogen transfer need to be further explored. In this review, (ⅰ) we present the transformation and distribution of nitrogen in the legume–cereal intercropping system; (ⅱ) we describe the soil microbial community characteristics in intercropping systems; and (ⅲ) we discuss the advantages of using modern biological molecular techniques to study soil microorganisms. We conclude that intercropping can increase the diversity of soil microorganisms, and the interaction between different plants has an important impact on the diversity and composition of the bacterial and fungal communities. The extensive application of modern biological molecular techniques in soil microbial research and the great contribution of intercropping systems to sustainable agriculture are particularly emphasized in this review.

Antibiotic bacterial residue is a unique hazardous waste, and its safe and effective disposal has always been a concern of pharmaceutical enterprises. This report presents the effective treatment of hazardous waste—antibiotic bacterial residue—by black soldier fly larvae (larvae), oxytetracycline bacterial residue (OBR), and soya meal with mass ratios of 0:1 (soya), 1:20 (OBRlow), and 1:2 (OBRhigh), which were used as substrates for larval bioconversion. Degradation of OBR and oxytetracycline, the bacterial community, the incidence of antibiotic resistance genes (ARGs) and the bacterial function in the gut were examined. When the larvae were harvested, 70.8, 59.3, and 54.5% of the substrates had been consumed for soya, OBRlow and OBRhigh; 65.9 and 63.3% of the oxytetracycline was degraded effectively in OBRlow and OBRhigh, respectively. The larval bacterial communities were affected by OBR, abundant and various ARGs were discovered in the gut, and metabolism was the major predicted function of the gut. These findings show that OBR can be digested and converted by larvae with gut bacteria, and the larvae can be used as a bioremediation tool for the treatment of hazardous waste. Finally, the abundant ARGs in the gut deserve further attention and consideration in environmental health risk assessments.

Metal oxide nanoparticles (NPs) have been widely used in industrial and agricultural production and introduced into soils. The impact of these nanoparticles on soil nitrous oxide (N2O) emission is unclear. We conducted a microcosm experiment to investigate the effects of titanium oxide nanoparticles (TiO2 NPs), copper oxide nanoparticles (CuO NPs), and aluminum oxide nanoparticles (Al2O3 NPs) on soil N2O emissions and the abundance of functional genes related to N2O production/reduction. Compared to the soil without NPs addition, TiO2 NPs applied to the soil produced no significant effect on N2O emissions. The denitrification process in the soil exposed to CuO NPs was inhibited by reducing the functional genes related to nitrite reductase (nirK) and increasing N2O reductase (nosZ), while CuO NPs added to the soil stimulated the cumulative N2O emissions by 92.7%. After the application of Al2O3 NPs to the soil, the nitrification process was inhibited by inhibiting the functional genes of ammonia-oxidizing bacteria (AOB amoA), and soil N2O emission was reduced by 48.6%. Large-scale application of CuO NPs in agricultural soils may stimulate the N2O emissions resulting in potential environmental risks.

Due to selective pressure from the widespread use of antibiotics, antibiotic resistance genes (ARGs) are found in human hosts, plants, and animals and virtually all natural environments. Their migration and transmission in different environmental media are often more harmful than antibiotics themselves. ARGs mainly move between different microorganisms through a variety of mobile genetic elements (MGEs), such as plasmids and phages. The soil environment is regarded as the most microbially active biosphere on the Earth’s surface and is closely related to human activities. With the increase in human activity, soils are becoming increasingly contaminated with antibiotics and ARGs. Soil plasmids play an important role in this process. This paper reviews the current scenario of plasmid-mediated migration and transmission of ARGs in natural environments and under different antibiotic selection pressures, summarizes the current methods of plasmid extraction and analysis, and briefly introduces the mechanism of plasmid splice transfer using the F factor as an example. However, as the global spread of drug-resistant bacteria has increased and the knowledge of MGEs improves, the contribution of soil plasmids to resistance gene transmission needs to be further investigated. The prevalence of multidrug-resistant bacteria has also made the effective prevention of the transmission of resistance genes through the plasmid-bacteria pathway a major research priority.

Soil organic carbon (SOC) is the largest carbon pool and a key property of ecosystems. Compared with traditional field surveys, remote sensing (RS) represents a more efficient approach to mapping SOC, especially in larger-scale areas. Hyperspectral imagery provides a great potential for SOC prediction, but predicting the SOC content at a regional scale for a given year remains a great challenge. Multispectral RS images (e.g., Landsat images) with middle spatial resolution can be used as an alternative to predict SOC amongst other images. However, multispectral images are commonly affected by cloud cover and lack information on the shallow soil surface and soil surface with vegetation. By contrast, synthetic aperture radar (SAR) images can capture shallow surface information, penetrate through vegetation and are not affected by cloud cover. In this study, a new approach was evaluated for the prediction of SOC content by integrating Landsat Thematic Mapper (TM) and Advanced Land Observing Satellite (ALOS) Phased Arrayed L-band Synthetic Aperture Radar (PALSAR) images. Mainland Spain (hereafter Spain) was used as the study site. Soil samples from the Land Use and Coverage Area frame Survey (LUCAS) European topsoil dataset in 2009 were utilized to fit a random forest (RF) model of the relationships between SOC content and several covariates in Spain. SOC prediction using only the Landsat TM image and only the ALOS PALSAR image was established as benchmarks to verify the efficiency of the proposed approach. The results for Spain showed that the integrated approach holds the highest prediction accuracy, with R2, RPD and RMSE of 0.59, 1.98 and 9.27 g kg−1, respectively. The correlations between the SOC content and various covariates were investigated and discussed, and the derived indices presented high relationships with SOC. The proposed method can accurately map the SOC content covering a large area by combining spectral information on land cover from the Landsat TM and topsoil information from the ALOS PALSAR. Land covers and elevation are closely related to SOC prediction, where lands with high vegetation canopy density have high SOC content, and the SOC content in areas with slopes within 15° is mainly concentrated between 3 and 26 g kg−1.

As a saprophytic insect, the black soldier fly can digest organic waste efficiently in an environmentally friendly way. However, the ability and efficiency of this insect, and the microbial mechanisms involved, in the degradation of antibiotics are largely uncharacterized. To obtain further details during the degradation of OTC (oxytetracycline) by black soldier fly larvae (larvae), the changes in intestinal bacterial communities were examined. Both ARGs (antibiotic resistance genes) and MGEs (mobile genetic elements) were found within the larval guts. At the end of the degradation period, 82.7%, 77.6% and 69.3% of OTC was degraded by larvae when the initial concentrations were 100, 1000 and 2000 mg kg−1 (dry weight), respectively, which was much higher than the degradation efficiencies (19.3–22.2%) without larvae. There was no obvious effect of OTC on the development of the larvae. Although the larval gut microorganisms were affected by OTC, they adapted to the altered environment. Enterococcus, Ignatzschineria, Providencia, Morganella, Paenalcaligenes and Actinomyces in the gut responded strongly to antibiotic exposure. Interestingly, numerous ARGs (specifically, 180 ARGs and 10 MGEs) were discovered, and significantly correlated with those of both integron-integrase gene and transposases in the larval gut. Of all the detected ARGs, tetracycline resistance genes expressed at relatively high levels and accounted for up to 67% of the total ARGs. In particular, Enterococcus, Ignatzschineria, Bordetella, Providencia and Proteus were all hosts of enzymatic modification genes of tetracycline in the guts that enabled effective degradation of OTC. These findings demonstrate that OTC can be degraded effectively and prove that the bioremediation of antibiotic contamination is enhanced by larvae. In addition, the abundance of ARGs and MGEs formed should receive attention and be considered in environmental health risk assessment systems.

E-waste generation has become a major environmental issue worldwide. Heavy metals (HMs) in e-waste can be released during inappropriate recycling processes. While their pollution characteristics have been studied, the migration and transformation of different multi-metal fractions in soil–plant system of e-waste dismantling sites is still unclear. In this study, pot experiments were conducted to investigate the migration and transformation of different multi-metal fractions (Cu, Pb, Zn and Al) in the soil–plant system using two Chinese cabbage cultivars (heavy metals low-accumulated variety of Z1 and non-low-accumulated Z2) treated with or without biochar. The result showed that the acid-soluble fraction of Cu, Pb, Zn and Al in soil decreased by 5.5%, 55.7%, 7.8% and 21.3%, but the residual fraction (ResF) of them increased by 48.5%, 1.8%, 30.9% and 43.1%, respectively, when treated with biochar and plants, compared to that of the blank soil (CK). In addition, Pb mainly existed as a reducible fraction, whereas Cu existed as an oxidisable fraction. Biochar combined with plants significantly increased the ResF of multi-metals, which reduced the migration ability of Pb among all other metals. The relative amount of labelled 13C in the soil of Z1 was higher than that of Z2 (25.4 fold); among them, the Gram-negative bacteria (18-1ω9c, 18-1ω7c) and fungi (18-2ω6c) were significantly labelled in the Z1-treated soil, and have high correlation with HM migration and transformation. In addition, Gemmatimonadete were significantly positive in the acid-soluble fraction of HMs, whereas Ascomycota mostly contributed to the immobilisation of HMs. Therefore, the distribution of fractions rather than the heavy metal type plays an important role in the HM migration in the soil–plant system of e-waste dismantling sites.

Soil fertility management is one of the most important factors affecting crop production. The use of organic manures, including green manure, is an important strategy to maintain and/or improve soil fertility for sustainable crop production. Green manure generally refers to crops that can provide fertilizer sources for agricultural cash crops and improve soil productivity. The application of green manure is a traditional and valuable practice for agroecosystem management, particularly in paddy systems where green manure is rotated with rice. This paper systematically reviews the effects of green manure on soil microenvironments and greenhouse gas emissions, and the role of green manure in the phytoremediation of paddy fields. The paper concludes that green manure can not only affect soil nutrients and the microbial community, but also reduce greenhouse gas emissions and enhance soil remediation to some extent. Moreover, this review provides theoretical guidance on the selection of green manure germplasm and tillage methods for paddy fields of different climates and textures. However, this review only provides a macro-overview of the effects of green manure on soil nutrients, greenhouse gas emissions, and soil remediation in rice paddies based on a large number of previous studies, and does not provide a comprehensive quantitative assessment due to differences in green manure varieties and soil texture. The prospects for quantitative analysis of the ecological and economic effects of the sustainable development of green manure cultivation are discussed.

An elevated CO2 (eCO2) fumigation experiment was carried out to study the influence of various CO2 concentrations on microorganisms involved in the incorporation of root-derived C in greenhouse soil systems. In this study, 400 and 800 µmol·mol−1 CO2 fumigation treatments were conducted during tomato planting. Phospholipid fatty acid (PLFA) profiling based on the stable isotope probing (SIP) technique was applied to trace active microorganisms. The absolute total abundance of 13C-PLFAs was much higher under eCO2 treatment. Most of the 13C-CO2 was incorporated into the 13C-PLFAs 18:2ω6,9 (fungi), 16:0 (general PLFA), 18:1ω9c (Gram-negative bacteria, G−) and i17:0 (Gram-positive bacteria, G+) via rhizodeposition from tomato under ambient CO2 (aCO2) and eCO2 treatments, suggesting similar responses of active microorganisms to different CO2 treatments. However, the fungi (characterized by the 13C-PLFA 18:2ω6,9) played a much more dominant role in the incorporation of root-derived C under eCO2. Actinomycetes, marked by the 13C-PLFA 10-Me-18:0, occurred only on labeling day 15 under the eCO2 treatment, indicating that the actinomycetes fed on both soil organic carbon and fresh rhizodeposition. It was indicated that eCO2 significantly affected microbial biomass and microbial community structures involved in the incorporation of 13C-CO2 via tomato root secretions, as supported by Adonis analysis and the Mantel test.

Intestinal bacteria are crucial for the healthy aquaculture of Litopenaeus vannamei, and the coastal areas of China are important areas for concentrated L. vannamei cultivation. In this study, we evaluated different compositions and structures, key roles, and functional potentials of the intestinal bacterial community of L. vannamei shrimp collected in 12 Chinese coastal cities and investigated the correlation between the intestinal bacteria and functional potentials. The dominant bacteria in the shrimp intestines included Proteobacteria, Bacteroidetes, Tenericutes, Firmicutes, and Actinobacteria, and the main potential functions were metabolism, genetic information processing, and environmental information processing. Although the composition and structure of the intestinal bacterial community, potential pathogenic bacteria, and spoilage organisms varied from region to region, the functional potentials were homeostatic and significantly (p < 0.05) correlated with intestinal bacteria (at the family level) to different degrees. The correlation between intestinal bacteria and functional potentials further suggested that L. vannamei had sufficient functional redundancy to maintain its own health. These findings help us understand differences among the intestinal bacterial communities of L. vannamei cultivated in different regions and provide a basis for the disease management and healthy aquaculture of L. vannamei.

Zinc oxide nanoparticles (ZnO NPs) are widely used and exposed to the soil environment, but their effect on soil nitrous oxide (N2O) emissions remains unclear. In this study, a microcosm experiment was conducted to explore the effects of different ZnO NPs concentrations (0, 100, 500, and 1000 mg kg−1) on N2O emissions and associated functional genes related to N2O amendment with carbon (C) or nitrogen (N) substrates. Partial least squares path modeling (PLS-PM) was used to explore possible pathways controlling N2O emissions induced by ZnO NPs. In the treatment without C or N substrates, 100 and 500 mg kg−1 ZnO NPs did not affect N2O production, but 1000 mg kg−1 ZnO NPs stimulated N2O production. Interestingly, compared with the soils without ZnO NPs, the total N2O emissions in the presence of different ZnO NPs concentrations increased by 2.36–4.85-, 1.51–1.62-, and 6.28–8.35-fold following C, N and both C & N substrate amendments, respectively. Moreover, ZnO NPs increased the functional genes of ammonia-oxidizing bacteria (AOB amoA) and nitrite reductase (nirS) and led to the exhaustion of nitrate but reduced the gene copies of ammonia-oxidizing archaea (AOA amoA). In addition, the redundancy analysis results showed that the AOB amoA and nirS genes were positively correlated with total N2O emissions, and the PLS-PM results showed that ZnO NPs indirectly affected N2O emissions by influencing soil nitrate content, nitrifiers and denitrifiers. Overall, our results showed that ZnO NPs increase N2O emissions by increasing nitrification (AOB amoA) and denitrification (nirS), and we highlight that the exposure of ZnO NPs in agricultural fields probably results in a high risk of N2O emissions when coupled with C and N substrate amendments, contributing to global climate warming.

Abstract Nitrification inhibitors and urease inhibitors, such as nitrapyrin and N-(n-butyl) thiophosphoric triamide (NBPT), can improve the efficiencies of nitrogen fertilizers in cropland. However, their effects on ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) across different soil pH levels are still unclear. In the present work, vegetable soils at four pH levels were tested to determine the impacts of nitrification and urease inhibitors on the nitrification activities, abundances and diversities of ammonia oxidizers at different pHs by real-time PCR, terminal restriction fragment length polymorphism (T-RFLP) and clone sequence analysis. The analyses of the abundance of ammonia oxidizers and net nitrification rate suggested that AOA was the dominate ammonia oxidizer and the key driver of nitrification in acidic soil. The relationships between pH and ammonia oxidizer abundance indicated that soil pH dominantly controlled the abundance of AOA but not that of AOB. The T-RFLP results suggested that soil pH could significantly affect the AOA and AOB community structure. Nitrapyrin decreased the net nitrification rate and inhibited the abundance of bacterial amoA genes in this vegetable soil, but exhibited no effect on that of the archaeal amoA genes. In contrast, NBPT just lagged the hydrolysis of urea and kept low NH4 +-N levels in the soil at the early stage. It exhibited no or slight effects on the abundance and community structure of ammonia oxidizers. These results indicated that soil pH, rather than the application of urea, nitrapyrin and NBPT, was a critical factor influencing the abundance and community structure of AOA and AOB.

Reductive soil disinfestation (RSD) has recently attracted much attention owing to its effectiveness for controlling pathogens. In this study, we aimed to evaluate the effects of different C/N substrates on RSD and to explore the changes in microbial community structure during RSD treatment. The experimental set up included 10 groups, as follows: CK, without substrates; RSD treatments with alfalfa (Medicago sativa L.)[AL], maize (Zea mays Linn. Sp.) straw [MS], and rice (Oryza sativa L.) straw [RS], with three levels of addition (0.5% [L], 2% [M], and 5% [H]), yielding ALL, ALM, ALH, MSL, MSM, MSH, RSL, RSM, and RSH groups. Compared with CK, RSD treatments significantly increased the content of NH4+-N, and effectively eliminated the accumulated NO3--N in the soil. The relative abundances of organic acid producers, including Clostridium, Coprococcus, and Oxobacter, in all RSD groups were significantly higher than those in the CK by day 21. Moreover, on day 21, Aspergillus and Fusarium in all RSD groups were significantly lower than those in the CK. In summary, RSD treatments clearly increased the relative abundances of organic acid generators and effectively inhibited pathogens; however, when the C/N was too low and the amount of addition too high, ammonia poisoning and rapid growth of some microorganisms (e.g., Pseudallescheria and Arthrographis) may occur.

Plant-derived carbon (C) is considered fundamental to understand the interaction between rhizosphere microbes and plants in terrestrial ecosystems. Biochar soil amendment may enhance plant performance via changing soil properties or microbial diversity in the rhizosphere. However, our knowledge of how plant-microbiome associations respond to biochar amendment remains rather limited. Herein, 13CO2 steady-state labeling combined with DNA stable-isotope probing was used to characterize soil bacterial communities in the rhizosphere contributing to the utilization of plant-derived C. The diversity of bacteria active in the utilization of root exudates was determined after biochar amendment in a legume-based intercropping system (Vicia faba L., with Zea mays L.). The results showed the biochar application not only changed the bacterial community structure and diversity in the rhizosphere, but also altered bacterial members actively assimilating plant-derived C. There were more labeled species in the biochar-amended soils than the control soils. Compared with the control, the biochar amendment increased the relative abundances of Firmicutes and Bacteroidetes members (i.e., Bacillus, Clostridium, Sporomusa, Desulfosporosinus, and Alicyclobacillus) while decreasing the abundances of Proteobacteria members (e.g., Methylobacterium and Sphingomonas) utilizing plant-derived C. In contrast, slow-growing species of the phyla Acidobacteria, Planctomycetes, and Gemmatimonadetes were barely labeled. The bacteria found stimulated by the biochar amendment are known for their ability to fix nitrogen, solubilize phosphorus, or reduce iron and sulfur, which may potentially contribute to the “biochar effect” in the rhizosphere. This study is the first to provide empirical evidence that biochar amendment can alter the soil bacterial community assimilating plant-derived C; this may have consequences for nutrient cycling and improving plant performance in intercropping systems.

Functional antimicrobial peptides (AMPs) are an important class of effector molecules of innate host immune defense against pathogen invasion. Inability of microorganisms to develop resistance against the majority of AMPs has made them alternatives to antibiotics, contributing to the development of a new generation of antimicrobials. Due to extensive biodiversity, insects are one of the most abundant sources of novel AMPs. Notably, black soldier fly insect (BSF; Hermetia illucens (Diptera: Stratiomyidae)) feeds on decaying substrates and displays a supernormal capacity to survive under adverse conditions in the presence of abundant microorganisms, therefore, BSF is one of the most promising sources for identification of AMPs. However, discovery, functional investigation, and drug development to replace antibiotics with AMPs from Hermetia illucens remain in a preliminary stage. In this review, we provide general information on currently verified AMPs of Hermetia illucens, describe their potential medical value, discuss the mechanism of their synthesis and interactions, and consider the development of bacterial resistance to AMPs in comparison with antibiotics, aiming to provide a candidate for substitution of antibiotics in livestock farming or, to some extent, for blocking the horizontal transfer of resistance genes in the environment, which is beneficial to human and animal welfare.

Soil salinization typically inhibits the ability of decomposer organisms to utilize soil organic matter, and an increase in soil clay content can mediate the negative effect of salinity on carbon (C) mineralization. However, the interactive effects of soil salt concentrations and properties on C mineralization remain uncertain. In this study, a laboratory experiment was performed to investigate the interactive effects of soil salt content (0.1%, 0.3%, 0.6% and 1.0%) and texture (sandy loam, sandy clay loam and silty clay soil with 6.0%, 23.9% and 40.6% clay content, respectively) on C mineralization and microbial community composition after cotton straw addition. With increasing soil salinity, carbon dioxide (CO2) emissions from the three soils decreased, but the effect of soil salinity on the decomposition of soil organic carbon varied with soil texture. Cumulative CO2 emissions in the coarse-textured (sandy loam and sandy clay loam) soils were more affected by salinity than those in the fine-textured (silty clay) soil. This difference was probably due to the differing responses of labile and resistant organic compounds to salinity across different soil texture. Increased salinity decreased the decomposition of the stable C pool in the coarse-textured soil, by reducing the proportion of fungi to bacteria, whereas it decreased the mineralization of the active C pool in the fine-textured soil through decreasing the Gram-positive bacterial population. Overall, our results suggest that soil texture controlled the negative effect of salinity on C mineralization through regulating the soil microbial community composition.

Although elevated CO2 (eCO2) in the atmosphere is one of the main factors influencing climate and ecosystem stability, less research on eCO2 in greenhouse soil systems has been conducted, despite their prevalence. In this article, phospholipid fatty acid (PLFA) profiling, 16S rRNA and Internally Transcribed Spacer (ITS) gene sequencing and high-throughput quantity polymerase chain reactions (HT-qPCRs) for 72 biogeochemical cycling-related genes were used to reveal the comprehensive responses of microbes to 23 days eCO2 fumigation in the soil of a tomato greenhouse. Our results indicated that eCO2 significantly increased microbial biomass (p < 0.05). The fungal community was more susceptible to eCO2 than the bacterial community; the fungal alpha diversity indices decreased significantly under eCO2 (p < 0.05) and the abundance of Ascomycota and its lower level taxa also increased significantly (p < 0.01). The absolute abundance of numerous C, N, P, S and methane cycling related genes increased significantly (p < 0.05) under eCO2. Furthermore, the microbial community structure and function were correlated with certain measured plant characteristics. Hence, the microbial ecosystem of the tomato greenhouse soil system was stimulated under eCO2. These results contribute to a greater understanding of how eCO2 in the atmosphere affects terrestrial ecosystem stability.

Both drought and flooding are unfavorable for soil microorganisms, but nevertheless, are highly relevant to the extreme weather events that have been predicted to increase in the future. The switch of soil water status from drought to flooding can happen rapidly and microbial activity might be either stimulated or further inhibited, but we have insufficient understanding of the underlying microbial processes. Here, we tracked the changes in soil bacterial and fungal abundance and their community structures, assaying the total (DNA-based) and potentially active (RNA-based) communities in response to abrupt flooding of dry soil. Also, rates of soil respiration and enzyme activity were measured after flooding. Results showed that the bacterial community was found to be more responsive than the fungal community to flooding. The bacterial community responses were clearly classified into three distinct patterns in which the intermediate pattern displayed highly phylogenetic clustering. A transient flourish of Bacilli which belongs to Firmicutes was detected at 8–48 h of flooding, suggesting its potential importance in the microbial assemblage and subsequent ecosystem functioning. Finally, the accumulative amount of CO2 released was more closely related than enzyme activity to the change in structure of the bacterial community after flooding. In conclusion, these findings extended our understanding of the underlying soil microbial processes following abrupt water condition changes.

Organic fertilizer is a major carrier that stores and transmits antibiotic resistance genes (ARGs). In the environment, due to the application of organic fertilizers in agriculture, the increasing diversity and abundance of ARGs poses a potential threat to human health and environmental safety. In this paper, the microbial community structure and ARGs in different types of organic fertilizer treated with composting were examined. We found that the abundance and diversity of ARGs in earthworm cast organic fertilizer were the lowest and the highest in chicken manure organic fertilizer. Interestingly, the abundance and diversity of ARGs, especially beta-lactam resistance genes, sulfonamide resistance genes, and macrolide-lincosamide-streptogramin B (MLSB) resistance genes, in organic fertilizers were reduced significantly, while composting caused no significant change in mobile genetic elements (MGEs), where antibiotic deactivation and the use of efflux pumps were the two most dominant mechanisms. It was clear that removal of ARGs became more efficient with increasing reduction in the bacterial abundances and diversity of potential ARG hosts, and integron-mediated horizontal gene transfers (HGTs) played an important role in the proliferation of most ARG types. Therefore, the reduction in ARGs was mainly driven by changes in bacterial community composition caused by composting. Furthermore, rather than HGTs, the diversity and abundance of bacterial communities affected by compost physical and chemical properties were the main drivers shaping and altering the abundance and diversity of ARGs, which was indicated by a correlation analysis of these properties, antibiotic residues, microbial community structure, and ARGs. In general, high-temperature composting effectively removed antibiotic residues and ARGs from these organic fertilizers; however, it cannot prevent the proliferation of MGEs. The insights gained from these results may be of assistance in the safe and rational use of organic fertilizers by indicating the changes in microbial community structure and ARGs in different types of organic fertilizer treated with composting.

The black soldier fly, Hermetia illucens (L.) (Diptera: Stratiomyidae), is a saprophytic insect that can digest organic wastes, such as animal manure, plant residues, and food and agricultural wastes. In the degradation process, organic wastes are converted into protein, grease, and polypeptides, which can be applied in medicine, the refining of chemicals, and the manufacturing of feedstuffs. After their conversion by the H. illucens, organic wastes not only become useful but also environmentally friendly. To date, the H. illucens has been widely used to treat food waste and to render manure harmless. The protein and grease obtained via this insect have been successfully used to produce livestock feed and biodiesel. In this article, the biological characteristics, resource utilization of protein and grease, and environmental functions of the H. illucens are summarized. This article provides a theoretical basis for investigating potential applications of the H. illucens.

Mapping land surface water bodies from satellite images is superior to conventional in situ measurements. With the mission of long-term and high-frequency water quality monitoring, the launch of the Ocean and Land Colour Instrument (OLCI) onboard Sentinel-3A and Sentinel-3B provides the best possible approach for near real-time land surface water body mapping. Sentinel-3 OLCI contains 21 bands ranging from visible to near-infrared, but the spatial resolution is limited to 300 m, which may include lots of mixed pixels around the boundaries. Sub-pixel mapping (SPM) provides a good solution for the mixed pixel problem in water body mapping. In this paper, an unsupervised sub-pixel water body mapping (USWBM) method was proposed particularly for the Sentinel-3 OLCI image, and it aims to produce a finer spatial resolution (e.g., 30 m) water body map from the multispectral image. Instead of using the fraction maps of water/non-water or multispectral images combined with endmembers of water/non-water classes as input, USWBM directly uses the spectral water index images of the Normalized Difference Water Index (NDWI) extracted from the Sentinel-3 OLCI image as input and produces a water body map at the target finer spatial resolution. Without the collection of endmembers, USWBM accomplished the unsupervised process by developing a multi-scale spatial dependence based on an unsupervised sub-pixel Fuzzy C-means (FCM) clustering algorithm. In both validations in the Tibet Plate lake and Poyang lake, USWBM produced more accurate water body maps than the other pixel and sub-pixel based water body mapping methods. The proposed USWBM, therefore, has great potential to support near real-time sub-pixel water body mapping with the Sentinel-3 OLCI image.