•Bacterial-feeding nematodes exhibited a hierarchy of diet choice.•P. fluorescens was the most preferred food of bacterial-feeding nematodes.•Nematode diet choice related strongly to bacterial traits and quality.•Nematodes feeding on preferred bacteria resulted in higher reproduction.•Nematode diet choice may regulate rhizobacteria-plant interactions.The dietary choices of bacterial-feeding nematodes could control the structure and ecological functions of soil bacterial communities. However, the physiological basis for the selection of particular bacterial species as food, and the consequences of these dietary choices for the survival of bacterial-feeding nematodes, is poorly understood. The objectives of this study were (1) to determine how nematode feeding preference was related to bacterial traits (cell size, gram stain and growth rate) and quality (water content, carbohydrate content, protein content and metabolite concentration), and (2) to evaluate how dietary choices affected the reproduction and lifespan of two soil-dwelling bacterial-feeding nematodes of the species Mesorhabditis and Acrobeloides. Their food sources included one model bacterium, Escherichia coli OP50, and four soil-dwelling bacterial species: Bacillus amyloliquefaciens, Bacillus megaterium, Variovorax paradoxus and Pseudomonas fluorescens. Both nematode species exhibited a similar hierarchy of diet choice, with P. fluorescens and E. coli OP50 being the most preferred food, whereas B. megaterium was the least preferred bacteria. Nematode feeding preference was strongly related to the water content, growth rate and metabolite concentration of bacterial cells, which explained 63–75% of the variation in the feeding preference index (PI, which indicates the number of nematodes attracted to specific bacteria), and the rest of the variation was attributed to bacterial cell size, gram stain, carbohydrate content and protein content. We propose two physiological mechanisms to explain dietary choices of bacterial-feeding nematodes: 1) chemical attraction to higher carbon dioxide levels around rapidly-growing bacteria or repulsion to volatile organic molecules released from bacterial cells, and 2) selective ingestion of bacterial cells with preferred characteristics (e.g., high water content in cells). Nematodes feeding on preferred bacteria always had higher reproduction, but dietary choices were not a good predictor of their lifespan. For example, Acrobeloides feeding on their preferred food P. fluorescens had the largest brood size but a moderate survival time. However, when Acrobeloides consumed their least-preferred food B. megaterium, they produced the smallest brood size and had the shortest survival time. This may be due to the fact that dietary resources are allocated first towards reproduction, and second to prolong the lifespan of bacterial-feeding nematodes. Our findings suggest that dietary choices are important for the survival of bacterial-feeding nematodes, and their ability to find and selectively ingest preferred bacterial species may have implications for soil bacterial community structure and ecological functions.

Problems associated with Organochlorine pesticide (OCP)-contaminated soils have received wide attention. To understand the anaerobic biodegradation process constraints, innovative mathematical analysis methods are effective.Response surface methodology (RSM) and Tenax TA extraction method combined with the first-three-compartment model were employed to systematically investigate the role of nitrate concentration and bioaccessibility enhancer (methyl-β-cyclodextrin, MCD) in the anaerobic biodegradation of OCPs in contaminated soil.The sole addition of either KNO3 or MCD could facilitate the anaerobic biodegradation of OCPs. The highest biodegradation for total OCPs, hexachlorocyclohexanes, endosulfans, and chlordanes were 71.6, 82.1, 68.3, and 55.6 %, respectively, when 20 mM KNO3 and 3.0 % (w/w) MCD were applied simultaneously. As predicted by RSM, the theoretical maximum biodegradation for total OCPs ranged from 60 to 80 % when 20 to 25 mM KNO3 and >2.5 % (w/w) MCD were applied simultaneously. Tenax TA extraction method demonstrated the enhancement of OCP bioaccessibility caused by MCD addition. Changes in the soil microbial activities also suggested the positive effects of adding suitable amounts of KNO3 as a cosubstrate to facilitate the anaerobic biodegradation of OCPs.The amount of KNO3 and MCD are crucial in influencing OCP biodegradation. RSM was demonstrated to be a powerful tool to estimate and predicting the optimal OCP biodegradation under KNO3 and MCD application simultaneously.

•Soil iron and aluminum minerals showed great affinity for the laccase.•Adsorbed laccases retained 26–64% of the activity of the free enzyme, and showed increased Km values and decreased Vmax values versus the free laccase.•Mineral adsorption enhanced catalytic activity of laccase under extra acid conditions and decreased the thermal stability.•Mineral adsorption increased Ea and ΔHa values of laccase.•Mineral adsorption improved the resistance to proteolysis and extended the lifespan of laccase.Laccases play an important role in the degradation of soil phenol or phenol-like substance and can be potentially used in soil remediation through immobilization. Iron and aluminum minerals can adsorb extracellular enzymes in soil environment. In the present study, we investigated the adsorptive interaction of laccase, from the white-rot fungus Trametes versicolor, with soil iron and aluminum minerals and characterized the properties of the enzyme after adsorption to minerals. Results showed that both soil iron and aluminum minerals adsorbed great amount of laccase, independent of the mineral specific surface areas. Adsorbed laccases retained 26–64% of the activity of the free enzyme. Compared to the free laccase, all adsorbed laccases showed higher Km values and lower Vmax values, indicating a reduced enzyme-substrate affinity and a lower rate of substrate conversion in reactions catalyzed by the adsorbed laccase. Adsorbed laccases exhibited increased catalytic activities compared to the free laccase at low pH, implying the suitable application of iron and aluminum mineral-adsorbed T. versicolor laccase in soil bioremediation, especially in acid soils. In terms of the thermal profiles, adsorbed laccases showed decreased thermal stability and higher temperature sensitivity relative to the free laccase. Moreover, adsorption improved the resistance of laccase to proteolysis and extended the lifespan of laccase. Our results implied that adsorbed T. versicolor laccase on soil iron and aluminum minerals had promising potential in soil remediation.

Proper rice straw management in paddy fields is necessary in order to sustain soil productivity and reduce greenhouse gas emissions. A field experiment was carried out from 2008 to 2011 in subtropical China: (1) to monitor rice yield, soil available nutrients, CH4, and N2O emissions and (2) to evaluate the effects of timing of rice straw incorporation and joint N application rate in a double rice cropping system. The total amount of rice straw from one cropping season was incorporated in winter (WS) or in spring (SS) and mineral N was jointly applied with rice straw incorporation at rates of 0, 30, and 60 % of the basal fertilization rate (N0B, N30B, and N60B) for the first rice crop. Soil water was naturally drained during the period of winter fallow (PWF) and controlled under intermittent irrigation during the period of first rice growth (PFR). Compared with SS, WS significantly (P < 0.05) increased the first rice yield only in the flooding year (2010), and increased the soil available K concentration after PWF and PFR in 2008–2009 and the hydrolysable N concentration after PWF in 2010–2011. Meanwhile, WS significantly decreased the total CH4 emission by about 12 % in 2009–2010 and 2010–2011, but increased the total N2O emission by 15–43 % particularly during PWF in all 3 years, resulting in a lower GWP in WS in the flooding year and no differences in the nonflooding years. Compared with N0B, joint N application (N60B and N30B) increased the soil hydrolysable N after PWF in all 3 years. Meanwhile, it decreased the total CH4 emissions by 21 % and increased the N2O emissions during PWF by 75–150 % in the nonflooding years, but the net GWP was lower in N60B than in N0B. The results suggested that the rice straw incorporation with joint N application in winter is more sustainable compared with the local practices such as rice straw incorporation in spring or open-field burning.

Prometryne with moderate to low mobility in soil is a ubiquitous environmental pollutant in water and soil. Bioremediation is widely used to remove pollutants from contaminated soil. Bacterial-feeding nematodes have been tested on the decomposition of soil organic matter and the release of nutrients through their interaction with soil microorganisms, but little attention has been paid to their effects on the removal of herbicides in soil. In this study, we investigated the effects of bacterial-feeding nematodes (Cephalobus Bastian) on the dissipation of prometryne and microbial activity in prometryne contaminated soil.Cultured with prometryne for a period of 6 months, prometryne-degrading bacteria strains P-1 and P-2 were isolated from sediments obtained from Anhui Huaxing Chemical Industry Co., Ltd. (Anhui Province, China). Bacterial-feeding nematodes were reared on Nematode Growth Medium agar plates (NGM) supplemented with prometryne for 5 months. Gnotobiotic microcosm experiments were conducted by inoculating both nematodes and prometryne-degrading bacteria strains P-1 (Ochrobactrum sp.) and P-2 (Bacillus sp.) into the contaminated soil. Soil samples were analyzed for prometryne concentration, the number of bacteria and nematodes, basal soil respiration, and enzyme activities.The results show that (1) about 50–66% of the prometryne is dissipated in the treatments with nematodes and the dissipation rate is raised by 5–7% compared with the treatments without nematodes. The nematodes have positive effects on the dissipation of prometryne through their interaction with bacteria in soil; (2) the nematode grazing can increase the population size of bacteria; and (3) the introduction of nematodes can enhance basal soil respiration and soil enzyme activities, that is, soil microbial activity.The inoculation of nematodes enhanced microbial activity in contaminated soils and accelerated the dissipation of prometryne, and thus nematodes can be used in restoration of contaminated sites by accelerating pollutants dissipation in the future.

A CPE-HPLC (UV) method has been developed for the determination of Prometryne. In this method, non-ionic surfactant Triton X-114 was first used to extract and pre-concentrate Prometryne from water and soil samples. The separation and determination of Prometryne were then carried out in an HPLC–UV system with isocratic elution using a detector set at 254 nm wavelength. The parameters and variables that affected the extraction were also investigated and the optimal conditions were found to be 0.5% of Triton X-114 (w/v), 3% of NaCl (w/v) and heat-assisted at 50 °C for 30 min. Using these conditions, the recovery rates of Prometryne ranged from 92.84% to 99.23% in water and 85.48% to 93.67% in soil, respectively, with all the relative standard deviations less than 3.05%. Limit of detection (LOD) and limit of quantification (LOQ) were 3.5 μg L−1 and 11.0 μg L−1 in water and 4.0 μg kg−1 and 13.0 μg kg−1 in soil, respectively. Thus, we developed a method that has proven to be an efficient, green, rapid and inexpensive approach for extraction and determination of Prometryne from soil samples.

The effects of IAA-producing bacteria (Pseudomonas sp. and Burkholderia sp.) and bacterial-feeding nematodes (Cephalobus sp.) on Arabidopsis thaliana (Ecotype, Columbia) root growth were investigated in pots with natural soil under controlled conditions. The soil, nematodes and root morphology of Arabidopsis were analysed at regular intervals. In natural soil, the bacterial-feeding nematodes grazing on bacteria stimulated both the microbial growth and activity and increased the mineral nitrogen and IAA contents. The analysis of the root architecture (total length, the number of tips, average diameter and surface area) of the A. thaliana seedlings revealed a highly branched root system, with longer and thinner roots in the presence of the IAA-producing bacteria and bacterial-feeding nematodes. On the basis of the above findings, it was concluded that the IAA-producing bacteria and bacterial-feeding nematodes improved the root growth of the A. thaliana seedlings in natural soil. The validity of our conclusion may be extended to future applications in agriculture.Highlights► The addition of bacteria and nematodes stimulated microbial activity. ► The addition of bacteria and nematodes increased mineral nitrogen and IAA content. ► The addition of nematodes resulted in longer and thinner Arabidopsis roots. ► The promotion of Arabidopsis root growth was better for nematodes than bacteria. ► We suggest adding a combination of nematodes and bacteria to promote plant growth.

The influence of earthworms on nematodes and protozoan communities was determined during the wheat phase of a six year rice–wheat rotation agro-ecosystem. Experimental plots in the rotation had five treatments, i.e. incorporation or mulching of maize residues with or without added earthworms and a control. The addition of maize residues to soil strongly affected the abundance and community structure of nematodes and protozoa in the absence of earthworms. The presence of earthworms gave significantly lower total nematode numbers at all soil depths following maize residue incorporation than the same treatment without earthworms, and also gave lower (although not significantly) total nematode numbers in the upper soil layer following maize residue mulching than the same treatment without earthworms. This was mainly due to a significant decrease in bacterial-feeding nematode numbers. Earthworms also strongly affected the distribution of the number of total nematodes and two trophic groups (bacterial and plant feeders) with soil depth. In the presence of earthworms, total protozoan and flagellate numbers significantly increased at all soil depths following both incorporation and mulching of maize residues, while numbers of amoebae increased only when maize residues were mulched. Additionally, in earthworm casts total nematode numbers (mainly bacterial and fungal feeders) were significantly higher, whereas total protozoa numbers (mainly flagellates and amoebae) were significantly lower than that in soil from 0 to 5 cm layer.These results indicated that earthworm activity could affect the abundance and community structure of microfauna, and change their distribution between soil layers and cast material, depending on the mode of application of organic residues.

The effects of bacterial-feeding nematodes on nitrification and the ammonia-oxidizing bacteria (AOB) community composition were studied in soil microcosms. Sterilized soils were inoculated with mixed soil bacteria (obtained by filtering) or with bacteria and bacterial-feeding nematodes, after which the dynamic inorganic nitrogen concentration was measured weekly. After 28 days of incubation, denaturing gradient gel electrophoresis (DGGE) based on PCR amplification of the amoA gene was used to analyze the AOB community composition. In addition, a clone library from the amoA gene fragments was established using clones randomly selected and sequenced from the two treatments. The results showed that the presence of bacterial-feeding nematodes led to significantly greater NH4+ and NO3− contents over the entire incubation period, indicating that bacterial-feeding nematodes promoted both N mineralization and nitrification. The results of DGGE showed that the AOB community composition was significantly changed in the presence of bacterial-feeding nematodes. Furthermore, the sequencing results suggested that Nitrosospira sp. was the dominant species in the treatment without nematodes, while Nitrosomonas sp. and Nitrosospira sp. were the dominant species in the treatment with nematodes. Such changes in the AOB community may be one of explanation of the important role that nematodes play in promoting nitrification.

The effect of earthworms on soil hydrolases (protease, urease, invertase, and alkaline phosphatase) and dehydrogenase activities was investigated in maize residue amended rice–wheat rotation agro-ecosystem. Experimental plots in the rotation had five treatments, i.e. incorporation or mulching of maize residues with or without added earthworms and an untreated control. The application of maize residues to soil without earthworms significantly enhanced the five soil enzyme activities compared with the control treatment during rice and wheat cultivation. The presence of earthworms further significantly enhanced protease activity in the soils with both incorporated and mulched maize residues during two cultivation seasons, but only significantly increased alkaline phosphatase activity in the soil with incorporated maize residue during the rice cultivation season. Invertase activity was significantly enhanced by the presence of earthworms in the soil with maize residue incorporation during two cultivation seasons. There were no changes in dehydrogenase activity when earthworms were present. Additionally, the five enzyme activities in earthworm casts were significant higher than those in the surrounding soil, especially dehydrogenase and invertase activities. Whatever the treatment, the values obtained for the enzyme activities in both soil and casts, except for dehydrogenase activity in earthworm casts, were significantly higher under wheat than those in rice-cultivated soil. These results indicate that the presence of earthworms strongly affected soil enzyme activities, depending on the method of organic residue application, and the enhanced enzyme activities of earthworm casts probably contributed to the surrounding soil enzyme activities.

•Total nematode abundance increased by fertilization of rice and wheat.•Aerobic environment supports more bacterial- and fungal-feeding nematodes.•Anaerobic environment favors the growth of plant- and algae-feeding nematodes.•Straw addition benefits the growth of fungal-feeding nematodes.Nematodes exert top-down control on the microbially-mediated processes of decomposition and nutrient cycling due to their position in the soil food web. Fertilization of agricultural soils can increase substrates for nematode populations, but whether the nematode community response to fertilization is consistent under anaerobic and aerobic soil conditions is not known. Our study investigated how soil nematode abundance and community structure responded to fertilization of a double-cropping system with paddy rice, representing anaerobic soil conditions due to flooding, followed an upland wheat phase that was rainfed and predominantly aerobic. We examined nematode communities twice a year from 2011 to 2013 at the ripening stage of rice (October) or wheat (June). Five fertilizer treatments were compared, including control (CK), chemical fertilizer (CF), compound pig manure-chemical fertilizer (MCF), straw plus chemical fertilizer (SCF) and pig manure plus straw plus chemical fertilizer (MSCF). Total nematode abundance increased by fertilization consistently in the rice and wheat cropping phases, and straw addition (i.e. SCF and MSCF) showed higher increment than manure addition (i.e. MCF) and CF treatments. However, dominant nematode genera respond to fertilization differently, depending on the crop phase. This is because dominant genera in the anaerobic soils of the rice phase were the plant-feeding nematode Hirschmanniella and algae-feeding nematode Rhabdolaimus, whereas dominant genera in the aerobic soils of the wheat phase were the fungal-feeding nematode Filenchus and bacterial-feeding nematodes Cephalobus, Eucephalobus and Acrobeloides. The manure addition (i.e. MCF) significantly raised Hirschmanniella abundance (by 133–616%) but sharply reduced the Rhabdolaimus population by 115–774% in the rice phase. In addition, straw addition (i.e. SCF and MSCF) increased Filenchus numbers (18–118%) but decreased the Acrobeloides population (49–145%) in the wheat phase. Since the MCF, SCF and MSCF fertilizers supply organic substrates for microbes and nutrients for plants, both of which are consumed by nematodes, this implies that food resources are the key determinant of total nematode abundance, the population size of all trophic levels. Our findings show that the nematode community structure is distinctive for each crop grown under a particular soil moisture regime, and that food resources derived from fertilizer inputs act as a bottom-up modulator of nematode population size in paddy rice–upland wheat systems.

The effects of bacterial-feeding nematodes on bacterial number, activity, and community composition were studied through a microcosm experiment using sterilized soil inoculated with soil bacteria (soil suspension) and with bacteria and three species of bacterial-feeding nematodes (Cephalobus persegnis, Protorhabditis filiformis, and Caenorhabditis elegans). Catalyzed reporter deposition-fluorescence in situ hybridization, CO2 evolution, and denaturing gradient gel electrophoresis (DGGE) of PCR amplified 16S rRNA gene fragments were used to investigate bacterial numbers, activity, and community composition, respectively. Our results showed that bacterial numbers and activity significantly increased in the presence of bacterial-feeding nematodes, which indicated that bacterial-feeding nematodes had a significant positive effect on soil bacteria. The different nematode species had different effects on bacterial numbers and activity. C. persegnis and P. filiformis, isolated from native soil, increased the bacterial number and activity more than C. elegans. The DGGE analysis results showed that dominant bacterial species significantly differed among the treatments, which suggested that bacterial-feeding nematode species modified the bacterial community composition in soil. Further gene sequence analysis results showed that the dominant bacterial species in this study were gram-negative bacteria. Given the completely same conditions except nematode species, the varied selective feeding behavior of different nematode species was the most likely reason for the altered bacterial community composition. Overall, the alteration of bacterial numbers, activity and community composition resulting from the bacterial-feeding nematodes may ultimately affect soil ecological functioning and processes.

⿢We evaluated fertilizer effects on soil nematodes with a meta-analysis.⿢High inorganic N inputs simplified nematode community structure and functions.⿢C-rich crop residues supported a well-structured and diverse soil community.⿢N-rich animal manure was effective in controlling plant-feeding nematodes.Organic fertilizer applications that boost soil fertility and crop production are expected to enhance soil biodiversity, making ecosystems more resilient to stress. Numerous studies have compared biodiversity in soil receiving organic fertilizer to soil under other fertilizer regimes (inorganic fertilizers, unfertilized), yet the data were not analyzed systematically across studies. We evaluated fertilizer effects on soil nematode communities with a meta-analysis of more than 229 data points from 54 studies around the world that were published between 1996 and 2015. Data were from cropland and considered five fertilizer regimes. These regimes include unfertilized soils and those receiving inorganic fertilizers (2 regimes), as well as organic fertilizers (2 regimes). Species richness and total nematode abundance increased with increasing carbon (C) inputs from fertilizers, whereas greater nitrogen (N) application rates from fertilizers significantly reduced the species richness, Shannon⿿s diversity (H⿲), maturity index (MI) and omnivore-predator nematode abundance. This could indicate that high fertilizer N inputs simplifies the nematode community structure and functions. Species richness, omnivore-predator nematode abundance and structural index (SI) increased with the organically-fertilized regime and declined in inorganically-fertilized regimes, suggesting that organic fertilizers can buffer stresses and sustain soil food web functions. Furthermore, organic fertilizers differed in their impact on soil nematodes, as those with C-rich crop residues supported larger free-living nematode populations and greatly promoted H⿲, SI and enrichment index (EI), whereas N-rich animal manure was more effective in controlling plant-feeding nematodes. Our review suggests that the application of C-rich crop residues is the most effective practice to enhance soil biodiversity in intensively managed agroecosystems, highlighting the importance of regular applications of straw and other C-rich residues to preserve the ecological resilience of cropland.

•Different pollutants induce distinct patterns of protein expression in earthworms.•mRNA expression does not correlate well with protein expression.•Metallothionein gene expression was specifically induced by the Cd treatment.•Worms subjected to the BaP or Cd treatments exhibited opposite patterns of CAT expression.Different pollutants induce distinct toxic responses in earthworms (Eisenia fetida). Here, we used proteomics techniques to compare the responses of E. fetida to exposure to the 10% lethal concentration (14d-LC10) of benzo[a]pyrene (BaP) or cadmium (Cd) in natural red soil (China). BaP exposure markedly induced the expression of oxidation-reduction proteins, whereas Cd exposure mainly induced the expression of proteins involved in transcription- and translation-related processes. Furthermore, calmodulin-binding proteins were differentially expressed upon exposure to different pollutants. The calcium (Ca2 +)-binding cytoskeletal element myosin was down-regulated upon BaP treatment, whereas the Ca2 +-binding cytoskeletal element tropomyosin-1 was up-regulated upon Cd treatment. Some proteins exhibited opposite responses to the two pollutants. For instance, catalase (CAT) and heat shock protein 70 were up-regulated upon BaP treatment and down-regulated upon Cd treatment. A significant (p < 0.05, one-way ANOVA with least-significant difference (LSD) test) increase in the level of reactive oxygen species (ROS) and CAT activity further showed that BaP mainly induces oxidative stress. Real-time PCR analysis showed that mRNA expression often did not correlate well with protein expression in earthworms subjected to Cd or BaP treatment. In addition, the expression of the gene encoding the protein metallothionein, which was not detected in the protein analysis, was induced upon Cd treatment, but slightly reduced upon BaP treatment. Therefore, BaP and Cd have distinct effects on the protein profile of E. Fetida with BaP markedly inducing ROS activity, and Cd mainly triggering genotoxicity.Capsule summaryDistinct patterns of protein expression are induced in earthworms upon exposure to different pollutants; BaP markedly induces high levels of ROS, while Cd resultes in genotoxicity.Download high-res image (297KB)Download full-size image

•Different pollutants induce distinct patterns of protein expression in earthworms.•mRNA expression does not correlate well with protein expression.•Metallothionein gene expression was specifically induced by the Cd treatment.•Worms subjected to the BaP or Cd treatments exhibited opposite patterns of CAT expression.Different pollutants induce distinct toxic responses in earthworms (Eisenia fetida). Here, we used proteomics techniques to compare the responses of E. fetida to exposure to the 10% lethal concentration (14d-LC10) of benzo[a]pyrene (BaP) or cadmium (Cd) in natural red soil (China). BaP exposure markedly induced the expression of oxidation-reduction proteins, whereas Cd exposure mainly induced the expression of proteins involved in transcription- and translation-related processes. Furthermore, calmodulin-binding proteins were differentially expressed upon exposure to different pollutants. The calcium (Ca2 +)-binding cytoskeletal element myosin was down-regulated upon BaP treatment, whereas the Ca2 +-binding cytoskeletal element tropomyosin-1 was up-regulated upon Cd treatment. Some proteins exhibited opposite responses to the two pollutants. For instance, catalase (CAT) and heat shock protein 70 were up-regulated upon BaP treatment and down-regulated upon Cd treatment. A significant (p < 0.05, one-way ANOVA with least-significant difference (LSD) test) increase in the level of reactive oxygen species (ROS) and CAT activity further showed that BaP mainly induces oxidative stress. Real-time PCR analysis showed that mRNA expression often did not correlate well with protein expression in earthworms subjected to Cd or BaP treatment. In addition, the expression of the gene encoding the protein metallothionein, which was not detected in the protein analysis, was induced upon Cd treatment, but slightly reduced upon BaP treatment. Therefore, BaP and Cd have distinct effects on the protein profile of E. Fetida with BaP markedly inducing ROS activity, and Cd mainly triggering genotoxicity.Capsule summaryDistinct patterns of protein expression are induced in earthworms upon exposure to different pollutants; BaP markedly induces high levels of ROS, while Cd resultes in genotoxicity.Download high-res image (297KB)Download full-size image