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Organic amendments can improve soil fertility and microbial diversity, making agroecosystems more resilient to stress. However, it is uncertain whether organic amendments will enhance the functional capacity of soil microbial communities, thereby mitigating fluctuations in microbial respiration caused by environmental changes. Here, we examined the impacts of long-term organic amendments on the dynamics of microbial catabolic capacity (characterized by enzyme activities and carbon source utilization) and microbial respiration, as well as their interrelationships during a period with fluctuating temperature and rainfall in the field. We then subjected the field soil samples to laboratory heating disturbances to further evaluate the importance of microbial catabolic capacity in explaining patterns of microbial respiration. In both field and laboratory experiments, organic amendments tended to increase the stability of microbial catabolic capacity, but significantly increased the vulnerability of microbial respiration to environmental changes. However, the direction and driving factors of microbial respiration affected by environmental changes differed between the field and laboratory experiments. Environmental changes in the field suppressed the promotional effects of organic amendments on microbial respiration mainly through reducing microbial catabolic capacity, while laboratory heating further enhanced microbial respiration mainly due to increased soil resource availability. Together, these findings suggest that increased microbial respiration variations under organic amendments may potentially increase the uncertainty in predicting soil carbon emissions in the scenario of ongoing climate/anthropogenic changes, and highlight the necessity of linking laboratory studies on environmental changes to field conditions., 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.)

Coexistence of antibiotics/heavy metals and the overexpression of resistance genes in the vermicompost has become an emerging environmental issue. Little is known about the interaction and correlation between chemical pollutants and biological macromolecular compounds. In this study, three typical vermicompost samples were selected from the Yangtze River Delta region in China to investigate the antibiotic, heavy metal and corresponding antibiotic resistance genes (ARGs) and heavy metal resistance genes (HRGs). The results indicated the prevalence of tetracycline (TC), copper (Cu), zinc (Zn), cadmium (Cd), corresponding TC-resistance genes (tetA, tetC, tetW, tetM, tetO, and tetS) and HRGs (copA, pcoA, cusA, czcA, czcB, and czcR) in the three vermicompost samples. In addition, the ARG level was positively associated with the water-soluble TC fraction in the vermicompost, and it was same between the HRG abundance and exchangeable heavy metal content (p < 0.05). Moreover, a positive correlation was found between ARG and HRG abundance in the vermicompost samples, suggesting a close regulation mechanism involving the expression of both genes. The result obtained here could provide new insight into the controlling risk of heavy metals, TC, and relevant resistance genes mixed contamination in the vermicompost., (Copyright © 2018 Elsevier Ltd. All rights reserved.)

Transgenic Bacillus thuringiensis (Bt) rice extends significant protection against insect pests and meets the increasing demands for food and energy. Many studies have been conducted investigating the impacts of Bt rice to the agricultural ecosystem, but much less attention has been given to efforts attempting to determine how the presence of Bt rice influences and shapes the microbial community, especially the active microbes. Stable isotope probing and high-throughput sequencing were employed to explore the active microbes involved in Bt-containing straw decomposition. Compared to its near isoline, the Bt straw contained higher contents of total N, total P, total K, lignin, cellulose, and Cry1Ab toxin protein. These chemical differences did not affect the decomposition rate but significantly changed the active microbial decomposer communities. During the decomposition of Bt-containing straw, fungi were more affected than bacteria. Agromyces, Terrabacter, Microbacterium, Glycomyces, and Kribbella were the most representative unique (existed only in the Bt treatments and appeared at the early stage) bacterial genera, and Trichoderma was the most representative unique fungal genus in the Bt straw decomposition. By using similarity index calculation and function prediction, the significant differences between Bt straw and non-Bt straw treatments were found to be transient for both microbial taxa and functional traits. These results suggested that Bt rice has a significant but transient impact on soil microbes in terms of microbial straw decomposition.

Nematode predation has important roles in determining bacterial community composition and dynamics, but the extent of the effects remains largely rudimentary, particularly in natural environment settings. Here, we investigated the complex microbial-microfaunal interactions in the rhizosphere of maize grown in red soils, which were derived from four long-term fertilization regimes. Root-free rhizosphere soil samples were separated into three aggregate fractions whereby the abundance and community composition were examined for nematode and total bacterial communities. A functional group of alkaline phosphomonoesterase (ALP) producing bacteria was included to test the hypothesis that nematode grazing may significantly affect specific bacteria-mediated ecological functions, that is, organic phosphate cycling in soil. Results of correlation analysis, structural equation modeling and interaction networks combined with laboratory microcosm experiments consistently indicated that bacterivorous nematodes enhanced bacterial diversity, and the abundance of bacterivores was positively correlated with bacterial biomass, including ALP-producing bacterial abundance. Significantly, such effects were more pronounced in large macroaggregates than in microaggregates. There was a positive correlation between the most dominant bacterivores Protorhabditis and the ALP-producing keystone 'species' Mesorhizobium. Taken together, these findings implicate important roles of nematodes in stimulating bacterial dynamics in a spatially dependent manner.

Mixed contamination of nitrate and antibiotics/antibiotic-resistant genes (ARGs) is an emerging environmental risk to farmland soil. This is the first study to explore the role of excessive anthropogenic nitrate input in the anoxic dissipation of soil antibiotic/ARGs. During the initial 10 days of incubation, the presence of soil antibiotics significantly inhibited NO 3 - dissipation, N 2 O production rate, and denitrifying genes (DNGs) abundance in soil (p < 0.05). Between days 10 and 30, by contrast, enhanced denitrification clearly prompted the decline in antibiotic contents and ARG abundance. Significantly negative correlations were detected between DNGs and ARGs, suggesting that the higher the DNG activity, the more dramatic is the denitrification and the greater are the antibiotic dissipation and ARG abundance. This study provides crucial knowledge for understanding the mutual interaction between soil DNGs and ARGs in the enhanced anoxic denitrification condition., (Copyright © 2016 Elsevier Ltd. All rights reserved.)

Background: Invasion-biology is largely based on non-experimental observation of larger organisms. Here, we apply an experimental approach to the subject. By using microbial-based microcosm-experiments, invasion-biology can be placed on firmer experimental, and hence, less anecdotal ground. A better understanding of the mechanisms that govern invasion-success of bacteria in soil communities will provide knowledge on the factors that hinder successful establishment of bacteria artificially inoculated into soil, e.g. for remediation purposes. Further, it will yield valuable information on general principles of invasion biology in other domains of life., Methodology/principal Findings: Here, we studied invasion and establishment success of GFP-tagged Pseudomonas fluorescens DSM 50090 in laboratory microcosms during a 42-day period. We used soil heating to create a disturbance gradient, and hypothesized that increased disturbance would facilitate invasion; our experiments confirmed this hypothesis. We suggest that the key factors associated with the heating disturbance that explain the enhanced invasion success are increased carbon substrate availability and reduced diversity, and thus, competition- and predation-release. In a second experiment we therefore separated the effects of increased carbon availability and decreased diversity. Here, we demonstrated that the effect of the indigenous soil community on bacterial invasion was stronger than that of resource availability. In particular, introduced bacteria established better in a long term perspective at lower diversity and predation pressure., Conclusion: We propose increased use of microbial systems, for experimental study of invasion scenarios. They offer a simple and cost-efficient way to study and understand biological invasion. Consequently such systems can help us to better predict the mechanisms controlling changes in stability of communities and ecosystems. This is becoming increasingly relevant since anthropogenic disturbance causes increasing global change, which promotes invasion. Moreover, a thorough understanding of factors controlling invasion and establishment of artificially amended micro-organisms will mean a major step forward for soil-remediation microbiology.

Long‐term chemical‐only fertilisation (NPK) decreases soil pH, but this soil acidification is rarely reported with manure fertilisation (M). Soil acidification always leads to a negative effect on sustainable development. As oxalate oxidation is accompanied by soil alkalisation, it is still unknown how and to what extent bacterial oxalate oxidation in soils with different fertilisation regimes contributes to buffering of soil acidification. To assess the potential role of oxalotrophy in buffering soil acidification, two soils that underwent contrasted fertilisation regimes for over 30 years were used. The oxalotrophic communities were characterised based on a biomarker of oxalotrophic taxa (the frc gene), and their responsiveness to calcium oxalate (CaOx) addition was assessed. In addition, stable isotope probing was employed to explore the active bacteria responding to CaOx addition. Despite similar abundances of oxalotrophic bacteria between NPK and M soils before microcosm incubation, the M soil harboured more oxalotrophic bacteria belonging to Deltaproteobacteria, and the NPK soil was colonised by more oxalotrophic bacteria affiliated with Actinobacteria, Alphaproteobacteria, and Betaproteobacteria. In the incubation experiments, the M soil took half of the time that the NPK soil needed to deplete the added CaOx. The faster CaOx consumption rate could be explained by the higher functional redundancy and higher proportion of fast‐response oxalotrophic taxa in M soil. The most dominant active oxalotrophic taxa were Oxalicibacterium and Burkholderia in the M and NPK soils, respectively. Furthermore, the better performance of oxalate oxidation was conjectured to contribute to a higher soil acidification buffering ability. This study obtained an important cue to the feasibility of active oxalotrophic taxa in buffering acidification in soils with different fertilisation regimes, which provides valuable evidence for exploring alternative ways for alleviating soil acidification. [ABSTRACT FROM AUTHOR]

Background and Aims: The importance of aboveground herbivores for modifying belowground ecosystems has prompted numerous studies; however, studies can be biased by context dependent conditions which lead to extremely inconsistent results. So far, the impacts of herbivory intensity by important rice pests on rice paddy soil ecosystems are lacking. The aim of this study was to test the hypothesis that intermediate herbivory intensity of the brown planthopper ( Nilaparvata lugens Stål) could promote soil labile resources and microbial biomass, while high intensity would show a reverse pattern, by mediating rice plant growth. This study will also help the development of integrative pest management. Methods: Four hopper infestation density treatments (0, 4, 8 and 12 nymphs per rice plant) and two infestation duration treatments (9 and 15 days after N. lugens infestation, DAI 9 and DAI 15) were established in a glasshouse experiment. Soil and plant were sampled destructively from four replicates and analysed for soil labile resources availability, soil microbial biomass and plant performance, respectively. Results: The infestation density significantly affected both shoot and root mass of rice ( P < 0.05), soil dissolved organic carbon (DOC) and nitrogen (DON), and microbial biomass carbon (MBC) and nitrogen (MBN), and the effects were further enhanced by prolonged infestation duration. Compared to the control (CK) without N. lugens, plant dry mass, DOC, DON, MBC and MBN increased under low (LD) and moderate hopper densities (MD) but decreased under high density (HD) on DAI 9. Moreover, the LD treatment exerted the most promotional effects on DAI 15. Rice root to shoot ratio generally increased in treatments subjected to herbivory. The labile resources and microbial biomass showed close relationships with both shoot and root mass across treatments, in particular with root mass on DAI 15. Such a trend indicated that the shift of photosynthate allocation to belowground contributed to changes of soil resource availability and microbial biomass. Conclusions: Intermediate herbivory intensity showed positive effects on rice seedling performance and, further, promoted soil labile resource availability and microbial biomass. The importance of extrapolating temporal and spatial scale, i.e. from the short-term greenhouse experiment to an entire rice growing season in the field, was highlighted. [ABSTRACT FROM AUTHOR]

Abstract: Plant-mediated effects of aboveground herbivory on the belowground ecosystem are well documented, but less attention has been paid to agro-ecosystems and in particular how crop cultivars with different traits (i.e. resistance to pests) shape such interactions. A fully factorial experiment was conducted using four rice cultivars with different insect-resistance, with and without the aboveground herbivore Nilaparvata lugens (brown planthopper), and to test two hypotheses (1) aboveground herbivory affects the soil microbial biomass and nematode community by altering plant performance and soil resource availability and (2) herbivory effects will depend on cultivar resistance traits. Our results suggested that cultivar resistance mediated both herbivory intensity and herbivore effects on plant performance. N. lugens decreased the availability of soil resources (soluble sugars, amino acids, organic acids, dissolved organic carbon and nitrogen), microbial biomass and percentages of bacterivores when feeding on a susceptible cultivar but increased them in a resistant cultivar. However, total nematode abundance and the percentage of plant-parasitic nematodes responded in the opposite way, increasing under a susceptible cultivar and decreasing under a resistant cultivar. The development of plant-parasites under resistant cultivars before aboveground herbivory might contribute to their resistance traits. Our findings provide evidence that N. lugens significantly reversed the pattern of soil resource availability, microbial biomass and nematode community structure (abundance and trophic composition) across cultivars with distinct resistance. In the presence of aboveground pests, the agronomic use of resistant rice cultivars could also control populations of plant-parasites and promote soil resource availability, further extended to higher trophic level of soil food web. [Copyright &y& Elsevier]

Graphical abstract Highlights • Biochar impeded the vertical migration of ARPB from top soil to lower soil. • Polyvalent phage targeted inactivation of ARPB along different soil layers. • Biochar amendment with phage therapy synergistically eliminated ARG risk. • Combined treatment maintained the diversity of the bacteria community. Abstract The vertical migration of antibiotic resistance pathogenic bacteria (ARPB) and antibiotic resistance genes (ARGs) in the surface soil-vadose soil system has become a new threat to ecological safety and public health; there is an imperative need to develop an efficient technique for targeted control and inactivation of ARPB in these systems. In this work, undisturbed soil columns (0 ∼ −5 m) were constructed to investigate the impact of biochar amendment or/and polyvalent bacteriophage (ΦYSZ-KK) therapy on the vertical control and inactivation of tetracycline-resistant Escherichia coli K-12 and chloramphenicol-resistant Klebsiella pneumonia K-6. The simultaneous application of polyvalent phage and biochar impeded the vertical migration of ARPB from the top soil to lower soil layers and stimulated the ARPB dissipation in the soil column. After 60-day incubation, levels of ARPB and ARGs decreased significantly in the soil column by magnitudes of 2-6. Additionally, high throughput sequencing indicated that the simultaneous application of biochar and phage clearly maintained the structure and diversity of the soil microbial communities (p < 0.05). This work therefore demonstrates that the application of a biochar/phage combination is an environmentally friendly, efficacious measure for the control and inactivation of ARPB/ARGs in vertical soil column systems. [ABSTRACT FROM AUTHOR]

Earthworms could affect soil C and N cycling process to balance their energy and nutrients requirements, and they could also regulate soil microbial community structure and microbial acquisition for C and N. However, the connection between faunal and microbial stoichiometry in the coupling soil C and N cycling remains poorly understood. In a controlled laboratory experiment, we amended soil with five litters differing in litter chemistry (clover, maize stover, wheat straw, Rumex and bagasse fiber) including a no litter control and treated them without or with earthworms ( Metaphire guillelmi ). After 90 d incubation, we examined changes in earthworm tissue and microbial stoichiometry and different soil C and N fractions. Earthworm tissue C content was rather stable compared with the fluctuation in tissue N, implying that C is under stronger control and associated with higher demand than N. The presence of earthworm significantly enhanced CO 2 emissions and decreased particulate organic carbon (POC) and soil organic carbon (SOC) contents in the low lignin litter species clover, maize stover and wheat straw. Meanwhile, earthworm presence increased N 2 O cumulative emissions but exerted negligible effects on particulate organic nitrogen (PON) and soil total nitrogen (TN) contents irrespective of litter species. Correspondingly, earthworm regulated microbial C and N acquisition as C to N-degrading enzyme activity ratio were nearly doubled in the low lignin litter species clover, maize stover and wheat straw, while it was decreased in the high lignin litter species Rumex and bagasse fiber. However, the structural equation modeling indicated C loss induced by earthworms was mainly attributed to their effects on soil fungi and bacteria abundance, while much less related to C-degrading enzyme activities. In conclusion, litter species controlled earthworm effects on soil C and N loss and associated microbial acquisition for C and N, highlighting the pivotal role of resource chemistry in the regulation of soil fauna impact on soil functioning and ecosystem services. [ABSTRACT FROM AUTHOR]

The emerging mixed contamination of antibiotics and microplastics in greenhouse soil has made the control of antibiotic resistant gene (ARG) transmission a novel challenge. In this work, surfactant sophorolipid was applied to enhance the dissipation of tetracycline (TC) and tet genes in the presence of microplastics in greenhouse soil. During 49 days of incubation, soil bacteria and phages were both found to be the crucial reservoirs of ARGs. Meanwhile, microplastic’s presence significantly inhibited the dissipation of TC and ARGs in the soil. However, sophorolipid application was proved to outweigh the negative impact caused by microplastic existence, and lead to the highest dissipation of soil TC and ARGs. Significant positive correlation was detected between the dissipation rate of water-soluble and exchangeable TC content and bacteria/phage co-mediated ARG levels. This also held true between the two fractions of soil TC and the ratio of ARG level in the bacteria to that in the phages (B ARGs /P ARGs ). The opposite impacts of microplastic presence and sophorolipid amendment on the TC/ARG dissipation found in this work provides new information for understanding ARG transmission between bacteria and phages in the mixed contaminated greenhouse soil. [ABSTRACT FROM AUTHOR]

Abstract: Microcosm experiments were carried out to study the effects of bacterial-feeding nematodes and prometryne on soil bacterial communities in contaminated soil. Prometryne (5 or 10mgkg−1 dry soil, that is, P5 or P10) and bacterial-feeding nematodes (5 or 10 individuals g−1 dry soil, that is, N5 or N10), singly and in combination (P5N5, P5N10, P10N5, P10N10), were added to a nematode-free soil. An uncontaminated nematode-free soil was studied for comparison (Control). Bacterial-feeding nematode grazing boosted soil enzyme activities in contaminated soils, thus speeding up prometryne degradation. In the initial stage of the experiment, prometryne enhanced the soil enzyme activities too, but served the opposite purpose later. Denaturing gradient gel electrophoresis (DGGE) analysis indicated that prometryne contamination and nematode grazing over the incubation period exerted an obvious impact on Species richness (S), Shannon–Wiener index (H′) and Evenness (E H ) of soil bacteria, which increased initially, then decreased and increased again later. The cluster analysis of DGGE profiles showed that the similarity of soil bacterial communities in all treatments with indigenous microbes, P5, P5N5, P5N10, P10, P10N5, and P10N10 and the Control was 75%, 44%, 78% and 49% at Day 0, Day 8, Day 18 and Day 30, respectively. Compared to the Control, DGGE profiles displayed a varying characteristic bands pattern in all treatments over the incubation period with certain bands present in the treatments while not in the Control and vice versa, suggesting that bacterial-feeding nematode grazing and prometryne contamination affected soil bacterial communities evidently. Consequently, when added to contaminated soil, bacterial-feeding nematodes can contribute to restoration of contaminated sites by degrading toxic compounds like prometryne through enhanced microbial activity. [Copyright &y& Elsevier]