•A dioxygenase PdoAB capable of oxidizing benzo[a]pyrene.•In silico molecular modeling analysis to characterization of PdoAB structure.•Binding energy may predict the substrate conversion toward HMW PAHs.Ring-hydroxylating dioxygenases (RHDs) play a critical role in the biodegradation of polycyclic aromatic hydrocarbons (PAHs). In this study, genes pdoAB encoding a dioxygenase capable of oxidizing various PAHs with up to five-ring benzo[a]pyrene were cloned from Mycobacterium sp. NJS-P. The α-subunit of the PdoAB showed 99% and 93% identity to that from Mycobacterium sp. S65 and Mycobacterium sp. py136, respectively. An Escherichia coli expression experiment revealed that the enzyme is able to oxidize anthracene, phenanthrene, pyrene and benzo[a]pyrene, but not to fluoranthene and benzo[a]anthracene. Furthermore, the results of in silico analysis showed that PdoAB has a large substrate-binding pocket satisfying for accommodation of HMW PAHs, and suggested that the binding energy of intermolecular interaction may predict the substrate conversion of RHDs towards HMW PAHs, especially those may have steric constraints on the substrate-binding pocket, such as benzo[a]pyrene and benzo[a]anthracene.

As a ubiquitous symbiotic fungus, the responses and the feedback of arbuscular mycorrhizal (AM) fungi to engineered nanoparticles (ENPs) remain unknown as well as the underlying mechanisms. The objective of this investigation was to figure out the influence of iron oxide magnetic nanoparticles (Fe3O4NPs) on AM fungal community, the underlying mechanisms, and the possible consequences of AM fungi-plant involved soil ecosystem.A greenhouse pot experiment was established to investigate the responses of maize (Zea may L.) growth and AM fungal community to differential application levels (0.1, 1.0, and 10.0 mg kg−1) of iron oxide magnetic nanoparticles (Fe3O4NPs) or microscale magnetic iron oxide (bulk Fe3O4). The AM fungal community composition and diversity were analyzed by high-throughput sequencing. The plant biomass, phosphorus (P) acquisitions, Fe concentration in plant shoots, catalase (CAT) activity, root mycorrhizal colonization rate, and glomalin-related soil protein (GRSP) contents were determined. In the meantime, the soil P supply efficiency, soil pH, and dissolved organic carbon contents (DOC) were analyzed as well as soil-soluble Fe content.Fe3O4NPs at 10.0 mg kg−1 (the high concentration) could be toxic to AM fungi by directly decreasing their diversity significantly (p < 0.05) and shifting their community structure, compared to the control and bulk Fe3O4. The similar toxicity was observed for host plant by the significant increases (p < 0.05) in Fe concentration in plant shoots and CAT activity. Consequently, the biomass of the host plant and the photosynthetic carbon left for AM fungi were obviously decreased (p < 0.05). The direct and indirect influences of Fe3O4NPs at high concentration result in the reduction of AM fungal ecological function, such as the significantly decreased (p < 0.05) root mycorrhizal colonization, soil GRSP content, and alkaline phosphatase activity. This process, in return, could deteriorate the nutrient provision of AM fungi for plant. As evidence, soil available P content and P nutrition in plants were significantly decreased (p < 0.05).The Fe3O4NPs at high concentration would destroy the mutual interaction of AM fungi-plant and negatively influence the soil carbon accumulation and P cycling, both of which go against crop yield and soil fertility.

Microcalorimetry and BIOLOG are common tools in the study of soil microbial metabolism. When used combined, they may reveal further details about soil microbial metabolic diversity than individually. Through this study, we demonstrated the advantages of such a combinatorial methodology by comparing soil samples from two locations in China, each with (OM samples) and without (control) organic fertilization. We used BIOLOG and microcalorimetry to study soil microbes’ ability to metabolize different C substrates. Microcalorimetric measurements helped us further reveal the differences in the microbial growth kinetics under different BIOLOG-identified C substrates. Results showed that soils differed in the preferred C substrates, as denoted by the thermodynamic parameters. Some C substrates stimulated the active microbial biomass, while some stimulated microbial growth rate. Most interestingly, certain C substrates (e.g., l-arginine for Shandong soil and glycogen for Henan soil) showed stimulating effects on both OM and control soils, which could be attributed to the pH value and P availability in soil. Hence, we believe microcalorimetry could be potentially used to explore the soil microbial metabolic diversity by combining BIOLOG measurement, especially in determining how microbes assimilate different nutrient sources.

Chronosequences of ancient rice terraces serve as an invaluable archive for reconstructions of historical human-environment interactions. Presently, however, these reconstructions are based on traditional soil physico-chemical properties. The microorganisms in palaeosols have been unexplored. We hypothesized that microbial information can be used as an additional proxy to complement and consolidate archaeological interpretations. To test this hypothesis, the palaeoenvironmental methanogenic archaeal DNA in Longji Terraces, one of the famous ancient terraces in China, dating back to the late Yuan Dynasty (CE 1361–1406), was chronosequenced by high-throughput sequencing. It was found that the methanogenic archaeal abundance, diversity and community composition were closely associated with the 630 years of rice cultivation and in line with changes in multi-proxy data. Particularly, the centennial- and decadal-scale influences of known historical events, including social turbulences (The Taiping Rebellion, CE 1850–1865), palaeoclimate changes (the Little Ice Age) and recorded natural disasters (earthquakes and inundation), on ancient agricultural society were clearly echoed in the microbial archives as variations in alpha and beta diversity. This striking correlation suggests that the microorganisms archived in palaeosols can be quantitatively and qualitatively analyzed to provide an additional proxy, and palaeo-microbial information could be routinely incorporated in the toolkit for archaeological interpretation.

•The influences of AgNPs on maize growth and the rhizosphere AM fungal community were evaluated.•Biomass of maize plant and the photosynthetic carbon for AM fungi were decreased.•AM fungal community was influenced by AgNPs through direct toxicity or affecting maize–AM fungi interaction.•The mutual interaction between maize and AM fungi were deteriorated.The effects of silver nanoparticles (AgNPs) on plants and soil microbial communities have been widely documented. However, the influence of AgNPs on plant growth and rhizospheric microbial communities, especially the important symbiotic microbes, such as arbuscular mycorrhizal (AM) fungi, remains under debate. In this study, a greenhouse pot experiment was established to investigate the responses of maize (Zea mays L.) growth and rhizospheric AM fungal assemblages to different application levels (0.025, 0.25 and 2.5 mg kg−1) of AgNPs or bulk Ag. The results indicated that 2.5 mg kg−1 of AgNPs significantly decreased (p < 0.05) plant biomass and dissolved organic carbon (DOC) content in rhizospheric soils compared to the control and bulk Ag conditions. Growth inhibition was associated with increased Ag accumulation in plant tissues and increased antioxidant enzyme activity. A similar toxicity for the AM fungal community was observed as a significant decrease (p < 0.05) in their diversity and remarkable variations in their structure, which were closely correlated with plant root biomass, soil soluble Ag and DOC content. Consequently, AgNPs caused a reduction in AM fungal growth and ecological function, characterized by a significantly decreased (p < 0.05) root mycorrhizal colonization rate, soil alkaline phosphatase activity, available phosphorus (P) content and P nutrition in plants. These results suggest that high concentrations of AgNPs can deteriorate the mutual interaction between plants and AM fungi and negatively influence the rhizospheric soil P cycling, both of which go against plant growth and soil fertility.

Manure application to agricultural soils can increase the abundance of antibiotic-resistance genes and resistant bacterial populations in soil. The aim of this study was to compare the contribution of nutrients and microorganisms of manure in the accumulation of tetracycline resistance in manure-treated soil. Soil microcosms were incubated for 77 days in a bench-scale mesocosm experiment and for 2 years in a greenhouse experiment and treated with manure or sterilized manure. In the manured soil, both aerobic tetracycline-resistant bacteria (TRB) and tetracycline-resistance genes (TRGs) (tetG, tetB(P), tetO, and tetL) were detected. Nutrients and TRGs not carried by live bacteria contribute little to the accumulation of TRB and TRGs, while microorganisms from manure contributed considerably. However, in soil with a long history of manure fertilization, the survival or dissemination of TRB and TRGs were prevented. The native soil microbial communities were probably more competitive than microbial species added with manure for nutrients of colonizing soil niches. Some bacterial species showed a significant negative correlation with the relative abundance of the four TRGs and TRB; probably, these bacterial species might have played a role in inhibiting the survival of TRB or dissemination of TRGs. These findings provide some clues for revealing the mechanisms of how manure application influences the abundance of TRGs and TRB in soil.

The extract of Stevia residue is an ideal substitute for cultivation of the purple nonsulfur bacterium, like Rhodopseudomonas palustris (R. palustris). But the influence of R. palustris grown under residue extract on its downstream application is still not well-characterized. The objective of this study was to assess the effect of foliar spray of R. palustris grown under Stevia residue extract on the plant growth and soil microbial properties.A pot experiment was carried out under the greenhouse condition, consisting of four treatments varying in the sprayed substances: sterilized water (control), R. palustris grown under the chemical medium supplemented with L-tryptophan (SyT), R. palustris grown under Stevia residue extract supplemented with L-tryptophan (ExT), and R. palustris grown under Stevia residue extract supplemented with NH4Cl (ExT). The net photosynthesis rate of the uppermost leaves was measured with a portable photosynthesis system. Soil microbial activity was analyzed by microcalorimetry. Soil bacterial community components were determined by real-time quantitative PCR (qPCR) and high-throughput sequencing techniques.Compared with SyT, the R. palustris grown under Stevia residue extract not only improved the plant biomass and the net photosynthetic rate to a large extent, but also increased soil microbial metabolic activity and altered community compositions as well. The treatments receiving R. palustris, especially ExT and ExN, increased the relative abundances of some functional guilds involved in C turnover and nutrient cycling in soil, including Acidobacteria, Actinobacteria, Proteobacteria, Gemmatimonadaetes, Nitrospirae, and Planctomycetes.R. palustris grown under the Stevia residue extract showed advantages over that under the chemical medium on both plant growth and soil microbial properties. One of the possible reasons could result from the increases in microbial activity and several bacterial keystone guilds involved into C and nutrient cycling, both of which potentially contribute to the improved plant growth. The results would be conducive to the downstream application of R. palustris in an economical way.

The application of organic manure can alleviate the deterioration of soil quality. However, it inevitably increases paddy CH4 emissions by introducing more CH4-producing precursors, which further restricts the amendment of organic manure in paddy fields. A 17-week greenhouse pot experiment was conducted to compare the effects of noncomposted manure (NCM), commonly composted manure (CCM), and rapidly composted manure (RCM) on rice yield and CH4 emission. To understand CH4 emissions of these three different manures, both the population size and the community structure of the methanogenic archaea in the soils were also investigated.The experiment was carried out in a greenhouse with three treatments: NCM, CCM, and RCM. The CH4 fluxes during rice cultivation were measured using the closed static chamber technique, and the CH4 concentration was determined by FID gas chromatography (Agilent 7890, USA). Soil DNA was extracted from 0.5 g of moist soil using a FastDNA® SPIN Kit for soil (MP Biomedicals, Santa Ana, CA) according to the manufacturer’s instructions. The population size of methanotrophs and methanogenic archaea was determined by real-time quantitative PCR (qPCR), and the community composition was analyzed using pyrosequencing technology.Rice yield and CH4 emission significantly differed between the groups (P < 0.05) as follows: CCM < NCM < RCM and CCM < RCM < NCM, respectively. These results are, in part, due to the adverse effects of RCM on the soil methanogenic archaeal community. RCM is abundant in nitrogen, which can promote crop growth. The number of methanotrophs with the RCM treatment was the lowest, with no significant difference relative to that with the CCM treatment but significantly lower than that with the NCM treatment. RCM amendment decreased the abundance of total soil methanogenic archaea, specifically decreasing the abundances of two acetoclastic methanogenic guilds (Methanosarcina and Methanosaeta), and differentially altered the paddy methanogenic archaeal community structure at the rice tillering stage. These negative responses by methanogens led to the lower CH4 emissions with RCM treatment compared to that with NCM treatment.RCM amendment can guarantee high grain yield and can significantly decrease CH4 emission compared to the effects of fresh manure amendment. This phenomenon could result from the unique characteristics of RCM and its adverse effects on paddy methanogenic archaeal communities. Overall, RCM can be a beneficial alternative organic fertilizer, which can resolve the problem of increased rice production that leads to increased CH4 emission caused by the application of organic manure in the paddy ecosystem.

Thaumarchaeota is an ecologically relevant archaeal phylum which may significantly contribute to global nitrogen cycling. Thaumarchaeotal abundance, composition, and activity can be changed by soil pH and pollutants such as toxic metals. This study aims to examine the responses of thaumarchaeotal community to soil pH variation and polycyclic aromatic hydrocarbon (PAH) pollution which may co-occur in agricultural soils.Field soil samples were collected from agricultural land impacted by both acidification and PAH contamination. Thaumarchaeotal abundance and composition were assessed using molecular approaches targeting 16S rRNA or amoA genes and were linked to environmental factors by correlation and canonical correspondence analysis (CCA). To evaluate the short-term responses of Thaumarchaeota to PAHs, additional soil microcosms amended with either three selected PAHs were established. Changes in thaumarchaeotal communities during the incubation were monitored.A significant correlation between thaumarchaeotal gene abundance and soil pH was observed within field samples, with the I.1a-associated group enriched when pH <5.0. CCA suggests that the community variation was primarily related to soil pH. In contrast, the effects of PAHs were minimal. In soil microcosms, high concentrations of PAHs persisted after the 4-week incubation. Independent of the PAHs added, thaumarchaeotal amoA abundance slightly increased and the compositions were stable at the end of the incubation. This might be associated with the pollutants bioavailability and potential microbe-PAH interactions in the soil.Soil pH variation strongly shapes the agricultural soil thaumarchaeotal community, whereas PAH effects appear to be marginal even in the presence of high concentrations of pollutants. The complicated interaction between soil matrix, pollutants, and Thaumarchaeota requires further study.

Fruiting vegetables are generally considered to be safer than other vegetables for planting on cadmium (Cd)-contaminated farms. However, the risk of transferring Cd that has accumulated in the stems and leaves of fruiting vegetables is a major issue encountered with the usage of such non-edible parts. The objective of this study was to resolve the contribution of arbuscular mycorrhizal (AM) fungi to the production of low-Cd fruiting vegetables (focusing on the non-edible parts) on Cd-contaminated fields.An 8-week pot experiment was conducted to investigate the acquisition and translocation of Cd by cucumber (Cucumis sativus L.) plants on an unsterilized Cd-contaminated (1.6 mg kg−1) soil in response to inoculation with the AM fungus, Funneliformis caledonium (Fc) or Glomus versiforme (Gv). Mycorrhizal colonization rates of cucumber roots were assessed. Dry biomass and Cd and phosphorus (P) concentrations in the cucumber shoots and roots were all measured. Soil pH, EC, total Cd, phytoavailable (DTPA-extractable) Cd, available P, and acid phosphatase activity were also tested.Both Fc and Gv significantly increased (P < 0.05) root mycorrhizal colonization rates and P acquisition efficiencies, and thus the total P acquisition and biomass of cucumber plants, whereas only Fc significantly increased (P < 0.05) soil acid phosphatase activity and the available P concentration. Both Fc and Gv significantly increased (P < 0.05) root to shoot P translocation factors, inducing significantly higher (P < 0.05) shoot P concentrations and shoot/root biomass ratios. In contrast, both Fc and Gv significantly decreased (P < 0.05) root and shoot Cd concentrations, resulting in significantly increased (P < 0.05) P/Cd concentration ratios, whereas only Gv significantly decreased (P < 0.05) the root Cd acquisition efficiency and increased (P < 0.05) the root to shoot Cd translocation factor. Additionally, AM fungi also tended to decrease soil total and phytoavailable Cd concentrations by elevating plant total Cd acquisition and soil pH, respectively.Inoculation with AM fungi increased the P acquisition and biomass of cucumber plants, but decreased plant Cd concentrations by reducing the root Cd acquisition efficiency, and resulted in a tendency toward decreases in soil phytoavailable and total Cd concentrations via increases in soil pH and total Cd acquisition by cucumber plants, respectively. These results demonstrate the potential application of AM fungi for the production of fruiting vegetables with non-edible parts that contain low Cd levels on Cd-contaminated soils.

Mechanisms of soil organic carbon (C) accumulation in response to no tillage (NT) are unclear. The extraradical hyphae of arbuscular mycorrhizal (AM) fungi are known to contribute to the formation and maintenance of soil aggregates through the exudation of glomalin. The objectives of this study were to evaluate the effects of different tillage management treatments on soil aggregates, AM fungal community, and glomalin contents and find out the main factors that influence aggregate C accumulation.A field experiment established in a sandy loam soil at Northern China has received 4-year continuous tillage treatments, including conventional tillage (CT), NT, and alternating tillage (AT, tillage in the wheat season and no tillage in the maize season). Undisturbed top soil samples (0–15 cm) from four individual plots per treatment were collected for the analysis of aggregates, which were separated according to the wet-sieving method. The organic C contents in different particle size aggregates were determined by the dichromate oxidization, and the glomalin-related soil protein (GRSP) was then extracted with citrate solution using bovine serum albumin (BSA) as a standard. The population size of AM fungi was determined by real-time PCR, and the community composition was analyzed using polymerase chain reaction plus denature gradient gel electrophoresis (PCR-DGGE), cloning, and sequencing techniques.Compared to CT, both NT and AT resulted in higher percentages of macroaggregates (>50 μm), and NT, rather than AT, significantly increased organic C contents in >250- and 50–2-μm aggregates, and also organic C contribution by macroaggregates. Both NT and AT significantly increased AM fungal population in 250–50-μm aggregates, but only NT increased it in >250-μm aggregates. NT, rather than AT, significantly increased easily extractable GRSP contents in 250–50- and <2-μm aggregates, and total GRSP content in 250–50-μm aggregates. In addition, the greatest changes of AM fungal community in response to NT or AT were observed in 250–50-μm aggregates, and the genus of Glomus registered the highest species number from the DGGE profiles.Four-year NT practice greatly enhanced soil aggregation and increased both AM fungal population and organic C contribution of soil macroaggregates. The contents of GRSP and organic C in aggregates were linearly related across particle sizes for all treatments, suggesting that NT played a vital role in maintaining AM fungal growth and GRSP production (notably in 250–50-μm aggregates), which might contribute to binding within microaggregates (<50 μm) and macroaggregates, and increasing soil organic C sequestration.

Monitoring the effects of no-tillage (NT) in comparison with conventional tillage (CT) on soil microbes could improve our understanding of soil biochemical processes and thus help us to develop sound management strategies. The objective of this study was to compare the species composition and ecological function of soil arbuscular mycorrhizal (AM) fungi during the growth and rotation of crops under NT and CT. From late June 2009 to early June 2010, 32 topsoil (0–15 cm) samples from four individual plots per treatment (CT and NT) were collected at both the jointing and maturation stages of maize (Zea mays L.) and wheat (Triticum aestivum L.) from a long-term experimental field that was established in an Aquic Inceptisol in North China in June 2006. The AM fungal spores were isolated and identified and then used to calculate species diversity indices, including the Shannon- Wiener index (H’), Evenness (E), and Simpson’s index (D). The root mycorrhizal colonization and soil alkaline phosphatase activity were also determined. A total of 34 species of AM fungi within nine genera were recorded. Compared with NT, CT negatively affected the soil AM fungal community at the maize sowing stage, leading to decreases in the average diversity indices (from 2.12, 0.79, and 0.82 to 1.79, 0.72, and 0.74 for H’, E, and D, respectively), root mycorrhizal colonization (from 28% to 20%), soil alkaline phosphatase activity (from 0.24 to 0.19 mg/g/24 h) and available phosphorus concentration (from 17.4 to 10.5 mg/kg) at the maize jointing stage. However, reductions in diversity indices of H’, E, and D were restored to 2.20, 0.81, and 0.84, respectively, at the maize maturation stage. CT should affect the community again at the wheat sowing stage; however, a similar restoration in the species diversity of AM fungi was completed before the wheat jointing stage, and the highest Jaccard index (0.800) for similarity in the species composition of soil AM fungi between CT and NT was recorded at the wheat maturation stage. Our results also demonstrated that NT resulted in the positive protection of the community structure of AM fungi and played an important role in maintaining their functionality especially for maize seedlings.

A knowledge gap still remains concerning the in situ influences of nanoparticles on plant systems, partly due to the absence of soil microorganisms. Arbuscular mycorrhizal fungi (AMF) can form a mutualistic symbiosis with the roots of over 90% of land plants. This investigation sought to reveal the responses of mycorrhizal clover (Trifolium repens) to silver nanoparticles (AgNPs) and iron oxide nanoparticles (FeONPs) along a concentration gradient of each. FeONPs at 3.2 mg/kg significantly reduced mycorrhizal clover biomass by 34% by significantly reducing the glomalin content and root nutrient acquisition of AMF. In contrast, no negative effects of AgNPs at concentrations over 0.1 mg/kg were observed; however, AgNPs at 0.01 mg/kg inhibited mycorrhizal clover growth. In response to the elevated AgNPs content, the ability of AMF to alleviate AgNPs stress (via increased growth and ecological behaviors) was enhanced, which decreased Ag content and the activities of antioxidant enzymes in plants. These results were further supported by X-ray microcomputed tomography. Our findings suggest that in soil ecosystem, the influence of nanometals on plant systems would be more complicated than expected, and more attention should be focused on plant responses in combination with those of soil microorganisms.

Arbuscular mycorrhizal (AM) fungi are crucial for ecosystem functioning and can contribute to the formation and maintenance of soil aggregates through the exudation of glomalin by extraradical hyphae. Monitoring fertilization effects on AM fungi may help us to develop sound management strategies. The objectives of this study were to investigate the impacts of long-term fertilization on AM fungal parameters and to find out the key factor that affects the diversity and function of AM fungi.A long-term fertilization experiment established in a sandy loam soil at northern China has received continuous fertilization treatments for 21 years, including control; mineral fertilizers of NK, PK, NP, and NPK; organic manure (OM); and half organic manure N plus half mineral fertilizer N (1/2 OMN). Top soil samples (0–15 cm) from three individual plots per treatment were collected for the analysis of chemical properties and fungal parameters. The population size of soil AM fungi was determined by real-time PCR, and the community composition was analyzed using PCR-denature gradient gel electrophoresis (DGGE), cloning, and sequencing techniques. The external mycelium of AM fungi was assessed using the grid-line intersect method, and the glomalin-related soil protein (GRSP) was extracted with citrate solution using bovine serum albumin as a standard.Long-term fertilization significantly increased (P < 0.05) soil organic C content, AM fungal population, species richness (R), Shannon–Wiener index (H), and GRSP content, except for the P-deficiency (NK) fertilization treatment. OM had a significantly greater (P < 0.05) impact on AM fungal population and GRSP content compared to mineral fertilizers but significantly decreased the length of external mycelium compared to the control (P < 0.05). Fertilization also changed the community composition of AM fungi, and the P-deficiency treatment again had the slightest influence. In addition, most species recovered from the DGGE profiles belonged to three genera, Glomus, Diversispora, and Archaeospora. Redundancy analysis showed that the population size and species richness of AM fungi and the GRSP content all significantly correlated to soil organic C content (P < 0.05).Long-term P-containing fertilization, especially the application of OM, greatly increased the population size, species richness, and species diversity of AM fungi, as well as the contents of GRSP and soil organic C, but tended to decrease the length of external mycelium, while the P-deficiency fertilization had no such effect, suggesting that P was the key factor to maintain soil fertility as well as soil AM fungal diversity in this sandy loam soil.

A post-harvest experiment was conducted further to our previous greenhouse pot study on upland kangkong (Ipomoea aquatica Forsk.) and Alfred stonecrop (Sedum alfredii Hance) intercropping system in Cd-contaminated soil inoculated with arbuscular mycorrhizal (AM) fungi. Previously, four treatments were established in the intercropping experiment, including monoculture of kangkong (control), intercropping with stonecrop (IS), and IS plus inoculation with Glomus caledonium (IS + Gc) or Glomus versiforme (IS + Gv). Both kangkong and stonecrop plants were harvested after growing for 8 weeks. Then, the tested soils were reclaimed for growing post-harvest kangkong for 6 weeks. In the post-harvest experiment, there were no significant differences between the IS and control treatments, except for a significantly decreased (p < 0.05) soil available P concentration with IS treatment. Compared with IS, both IS + Gc and IS + Gv significantly decreased (p < 0.05) soil DTPA-extractable (phytoavailable) Cd concentrations, but not total Cd, by elevating soil pH, causing significantly lower (p < 0.05) Cd concentrations in both the root and shoot of kangkong. In addition, both Gc and Gv significantly increased (p < 0.05) soil acid phosphatase activities and available P concentrations and hence resulted in significantly higher (p < 0.05) plant P acquisitions. However, only Gv significantly increased (p < 0.05) kangkong yield, while Gc only significantly elevated (p < 0.05) the shoot P concentration. It suggested that AM fungi have played key roles in Cd stabilization and P mobilization in the intercropping system, and such positive responses seemed to be sustainable and valuable in post-harvest soils.

Due to the ever-increasing worldwide plantation of sweet leaf Stevia rebaudiana (Bertoni), how to efficiently and effectively utilize the huge amounts of leaf residues that contain abundant nutrients after sweetener extraction becomes an eminent issue. One option is to return these residues into soil, as organic manure in the fresh or composted form, in order to both sustain soil fertility and avoid potential environmental pollution. In a field experiment, we studied if the Stevia leaf residue returning affected both plant and soil microbial growths as well as the possible change of soil microbial community composition. In doing so, four treatments were employed: (1) no chemical fertilization and no Stevia residue returning (no-fertilization control); (2) chemical N, P, and K fertilization (NPK); (3) fresh Stevia residue plus NPK (FS + NPK); and (4) composted Stevia residue plus NPK (CS + NPK). Responses of plant and soil microbial communities to Stevia residue input after 1-year fertilizations were investigated by multiple approaches, including soil enzyme assay, real-time quantitative polymerase chain reaction, and PCR–denaturing gradient gel electrophoresis. Our results showed that compared to the sole NPK and no-fertilization control, returning Stevia residues to soil stimulated the enzyme activities of dehydrogenase, invertase, and urease, except neutral phosphomonoesterase; thereby, both the Stevia leaf biomass and sweet glycoside of rebaudioside A were increased. The soil microbial community abundance was increased by the returning of Stevia residues, and their composition was shifted, evidenced by an increase of relative abundance of some genotypic groups, such as Bacillales. Further molecular analysis of Bacillus confirmed that this guild composition was positively influenced by Stevia residue returning, especially for Bacillaceae. Our results demonstrated an effective use of Stevia residues as organic manure for promoting Stevia yield and quality through stimulating soil microbial growth and enzyme activities.

A balanced fertilization can increase crop yields partly due to stimulated microbial activities and growths. In this study, we investigated arbuscular mycorrhizal fungi (AMF) in arable soils to determine the optimal practices for an effective fertilization. We used pyrosequencing-based approach to study AMF diversity, as well as their responses to different long-term (>20 years) fertilizations, including OM (organic manure) and mix chemical fertilizers of NP (nitrogen–phosphorus), NK (nitrogen–potassium), and NPK (nitrogen–phosphorus-potassium). Results revealed that 124 998 of 18S rRNA gene fragments were dominated by Glomeromycota with 59 611 sequences, generating 70 operational taxonomic units (OTUs), of which the three largest families were Glomeraceae, Gigasporaceae and Acaulosporaceae. In Control and NK plots, AMF diversity and richness significantly decreased under long-term P fertilizations, such as NP, NPK, and OM. Concomitantly, the AMF community structure shifted. Supported by canonical correspondence analysis, we hereby propose that long-term balanced fertilization, especially P fertilizer with additional N fertilizer, helps the build-up of soil nutrients. Consequently, some AMF community constituents are sacrificed, propelled by the self-regulation of plant-AMF-microbes system, resulting in an agro-ecosystem with a better sustainability. This knowledge would be valuable toward better understandings of AMF community in agro-ecosystem, and long-term ecosystem benefits of the balanced fertilization.

Modern agricultural science has greatly reduced the use of tillage. Monitoring conservation versus conventional tillage effects on soil microbes could improve our understanding of soil biochemical processes and thus help us to develop sound management strategies. The objective of this study was to investigate the effects of conservation tillage on the spore community structure and the diversity of soil arbuscular mycorrhizal (AM) fungi and to find out the main factors that influence these parameters.A long-term field experiment established in a sandy loam soil in Northern China has received continuous tillage management treatments for 3 years, including conventional tillage (CT), no tillage (NT), and alternating tillage (AT). Topsoil samples (0–15 cm) from four individual plots per treatment were collected for the analysis of chemical properties and fungal parameters. AM fungal spores were isolated using the wet-sieving method and identified to species level based on morphology by light microscopy. The community structure and the diversity of AM fungi were evaluated using the following parameters: spore density, relative abundance, species richness, Shannon–Wiener index (H′), evenness (E), and Simpson's index (D). Jaccard index (J) of similarity was calculated to compare AM fungal species composition under different treatments.Twenty-eight species of AM fungi within four genera, Glomus, Acaulospora, Scutellospora, and Entrophospora, were recovered from the 12 plots within the three tillage management treatments. Higher spore density, species richness, and species diversity (H′, E, and D) of AM fungi were observed in the two conservation tillage treatments, and the redundancy analysis showed that the species richness significantly correlated to soil organic carbon content (P < 0.05). The positive effects of NT and AT on the species richness were very close, while the AT had relatively greater beneficial impacts on the spore density and the evenness of AM fungi compared to the NT. The lowest Jaccard index (J) of similarity in species composition was also observed between the AT and CT treatments.Soil organic carbon, the spore density, and species richness and diversity of AM fungi increased in the two conservation tillage treatments. The species richness of AM fungi significantly correlated to soil organic carbon content (P < 0.05). Compared with the CT treatment, the AT rather than the NT significantly increased the spore density and the evenness of AM fungi (P < 0.05). Thus, alternating tillage practice may be more beneficial to agroecosystem in this region.

Salmonella causes the majority of infections in humans and homeothermic animals. This article describes a specific polymerase chain reaction (PCR) method developed for a rapid identification of Salmonella. A gyrB-targeted species-specific primer pair, S-P-for (5′-GGT GGT TTC CGT AAA AGT A-3′) and S-P-rev (5′-GAA TCG CCT GGT TCT TGC-3′), was successfully designed. PCR with all the Salmonella strains produced a 366- bp DNA fragment that was absent from all the non-Salmonella strains tested. The detection limit of the PCR was 0.01 ng with genomic DNA or 3.2 cells per assay. Good specificity was also demonstrated by fecal samples, from which only the gyrB gene of Salmonella was amplified. Using the culture-PCR method, 27 isolates on Salmonella-Shigella (SS) medium were rapidly identified as Salmonella, which was confirmed by the sequencing of the gyrB gene.

Organic and inorganic fertilizers are used primarily to increase nutrient availability to plants. Monitoring balanced versus unbalanced fertilization effects on soil microbes could improve our understanding of soil biochemical processes and thus help us to develop sound management strategies. The objective of this study was to investigate the effects of long-term fertilization regimes on soil microbial community functional diversity, metabolic activity, and metabolic quotient and to find out the main factors that influence these parameters.A long-term fertilization experiment established in a sandy loam soil at northern China has received continuous fertilization treatments for more than 20 years, including control, mineral fertilizers of NK, PK, NP, and NPK, organic amendment (OA), and half organic amendment plus half mineral fertilizer (1/2 OM). Top soil samples (0–15 cm) from four individual plots per treatment were collected for the analysis of chemical properties and microbial parameters. Microbial biomass C was analyzed using the fumigation–extraction method. Invertase activity and basal respiration were determined based on incubation method. Then, the microbial metabolic quotient was calculated as the ratio of basal respiration to microbial biomass C. To this end, microbial functional diversity was evaluated using the community level physiological profile method by Biolog Eco-microplate.Higher microbial biomass C, invertase activity, and basal respiration, but lower microbial metabolic quotient, were observed in P-fertilized soils, and OA had significantly greater (P < 0.05) impacts on the biomass, activity, and quotient compared with mineral fertilizers. Both the sole-carbon-source utilization activity and the functional diversity of soil microbial community were significantly increased (P < 0.05) by balanced fertilization (NPK, OA, or 1/2 OM), and species richness of community and relative abundance of the most common species in the K-deficient (NP) treatment were also significantly increased (P < 0.05). Principal component analysis and redundancy analysis showed that both organic and mineral fertilizers could affect microbial parameters by increasing soil organic C contents, and P was the key factor to increase soil microbial diversity and soil fertility.Long-term balanced fertilization greatly increased soil microbial biomass, functional diversity, and invertase activity and played an important role in decreasing soil microbial metabolic quotient, while P could be considered as the key factor to control soil microbial diversity as well as soil fertility. With regard to the different effects of OA and mineral fertilizer on soil organic C contents and root exudates, combined application of mineral and organic fertilizers is recommended in the region.

Light is a major driver of primary productivity in most ecosystems on Earth. Phototrophic microorganisms harvest light to synthesize organic biomass for sustaining the global energy and carbon flow. However, the bottom-up model of phototrophic microorganisms as primary production and food source for higher trophic levels remains unclear in the terrestrial environment.Rice soil microcosms treated with different carbon sources (13C-formate, 12C-formate, or a control without formate) were incubated for 21 days under illumination. For each microcosm, genomic DNA were extracted and fractionated by isopycnic ultracentrifugation. Subsequently, the analyses were conducted on these samples with real-time quantitative PCR, PCR-denaturant gradient gel electrophoresis fingerprinting, and sequencing analysis of bacterial 16S rRNA, eukaryotic 18S rRNA, and photosynthetic functional genes.Our analysis indicated that formate carbon was assimilated by a subset of bacteria and eukaryotes. Based on molecular fingerprinting and sequencing analysis, the primary producers were determined to be the microorganisms affiliated with purple phototrophic bacteria, cyanobacteria, and algae. The detection of protozoa and fungi-like 18S rRNA gene sequences in the 13C-enriched DNA fractions suggested that these organisms acted as consumers. They fed on nutrients derived from labeled phototrophic microorganisms.Molecular evidence suggests that in the light-driven microbial food web, the carbon flow from formate is initiated by phototrophic primary and secondary producers. Their biomasses subsequently sustain the growth of consumers in the rice soil.

Laccases produced by white rot fungi are capable of rapidly oxidizing benzo[a]pyrene. We hypothesize that the polycyclic aromatic hydrocarbon (PAH)-degrading bacteria producing laccase can enhance the degree of benzo[a]pyrene mineralization. However, fungal laccases are glycoproteins which cannot be glycosylated in bacteria, and there is no evidence to show that bacterial laccases can oxidize benzo[a]pyrene. In this study, the in vitro oxidation of PAHs by crude preparations of the bacterial laccase, CueO, from Escherichia coli was investigated. The results revealed that the crude CueO catalyzed the oxidation of anthracene and benzo[a]pyrene in the same way as the fungal laccase from Trametes versicolor, but showed specific characteristics such as thermostability and copper dependence. In the presence of 2,2′-azino-bis-(3-ethylbenzothiazoline-6-sulfonic acid), high amounts of anthracene and benzo[a]pyrene, 80% and 97%, respectively, were transformed under optimal conditions of 60°C, pH 5, and 5 mmol l−1 CuCl2 after a 24-h incubation period. Other PAHs including fluorene, acenaphthylene, phenanthrene, and benzo[a]anthracene were also oxidized by the crude CueO. These findings indicated the potential application of prokaryotic laccases in enhancing the mineralization of benzo[a]pyrene by PAH-degrading bacteria.

The influences of different fertilizer treatments on spore community structure and diversity of arbuscular mycorrhizal (AM) fungi (AMF) were investigated in a long-term fertilization experiment with seven treatments: organic manure (OM), half organic manure N plus half fertilizer N (1/2 OMN), fertilizer NPK, fertilizer NP, fertilizer NK, fertilizer PK, and the control (without fertilization). Fertilization generally increased the nutrient contained in the fertilizer and treatments with NPK and 1/2 OMN produced the highest crop yields. Thirty-five species of AMF within 6 genera, including 8 previously undescribed species, were recovered. Similarly in all seven treatments, the most abundant genus was Glomus, and followed by Acaulospora. All the fertilization treatments changed AM species composition, and NK treatment had the slightest influence. Fertilization with fertilizers NP, PK and NPK markedly increased AM fungal spore density, while 1/2 OMN, OM and NK treatments showed no significant influences. All the fertilizer treatments, especially OM, significantly decreased species richness and species diversity (Shannon-Weiner index). There were no significant correlations between AM fungal parameters (spore density, species richness and species diversity) and soil properties. The findings indicate that long-term fertilization all can change AM fungal community structure and decrease species diversity, while balanced fertilization with NPK or 1/2 OMN is the most suitable fertilization regime if taking both crop yields and AM species diversity into account.

The knowledge of the impact of elevated ground-level O3 below ground the agro-ecosystem is limited. A field experiment in China Ozone Free-Air Concentration Enrichment (FACE-O3) facility on a rice–wheat rotation system was carried out to investigate responses of anoxygenic phototrophic purple bacteria (AnPPB) to elevated ground-level O3. AnPPB community structures and sizes in paddy soil were monitored by molecular approaches including PCR–DGGE and real-time quantitative PCR based upon the pufM gene on three typical rice growth stages. Repetitive sequence-based PCR (rep-PCR) in combination with culture-reliant method was conducted to reveal changes in genotypic diversity. Elevated ground-level O3 statistically reduce AnPPB abundance and percentage in total bacterial community in flooded rice soil via decreasing their genotypic diversity and metabolic versatility. Concomitantly, their community composition changed after rice anthesis stage under elevated ground-level O3. Our results from AnPPB potential responses imply that continuously elevated ground-level O3 in the future would eventually harm the health of paddy ecosystem through negative effect on soil microorganisms.

Biodegradation of polycyclic aromatic hydrocarbons (PAHs) by pure laccase has been reported, but the high cost limited its application in environmental bioremediation. Here, we reported a study about PAHs degradation by crude extracts (CEs) containing laccase, which were obtained by extracting four spent mushroom (Agaricus bisporus, Pleurotus eryngii, Pleurotus ostreatus, and Coprinus comatus) substrates. The results showed that anthracene, benzo[a]pyrene, and benzo[a]anthracene were top three degradable PAHs by CEs while naphthalene was most recalcitrant. The PAHs oxidation was enhanced in the presence of 2,2-azino-bis-(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS). Laccase included in CE might play a major role in PAHs degradation. The maximum degradation rate of anthracene and benzo[a]pyrene was observed by using crude extracts from P. eryngii while the highest laccase activities were found in crude extracts from A. bisporus, moreover, crude extracts from P. eryngii, which contained less laccase activities, degraded more anthracene and benzo[a]pyrene than pure laccase with higher laccase activities. The lack of correlation between laccase activity and PAHs degradation rate indicated that other factors might also influence the PAHs degradation. Boiled CEs were added to determine the effect on PAHs degradation by laccase. The results showed that all four boiled CEs had improved the PAHs oxidation. The maximum improvement was observed by adding CEs from P. eryngii. It suggested that some mediators indeed existed in CEs and CEs from P. eryngii contained most. As a result, CEs from P. eryngii has the most application potential in PAHs bioremediation.

The P efficiency, crop yield, and response of wheat to arbuscular mycorrhizal fungus (AMF) Glomus caledonium were tested in an experimental field with long-term (19 years) fertilizer management. The experiment included five fertilizer treatments: organic amendment (OA), half organic amendment plus half mineral fertilizer (1/2 OM), mineral fertilizer NPK, mineral fertilizer NK, and the control (without fertilization). AMF inoculation responsiveness (MIR) of wheat plants at acquiring P were estimated by comparing plants grown in unsterilized soil inoculated with G. caledonium and in untreated soil containing indigenous AMF. Without AMF inoculation, higher crop yields but lower colonization rates were observed in the NPK and two OA-inputted treatments, and NPK had significantly (P < 0.05) lower impacts on organic C and available P in soils and thereby P acquisition of wheat plants compared with OA and 1/2 OM. G. caledonium inoculation significantly (P < 0.05) increased colonization rates with the NPK and two P-deficient treatments but significantly (P < 0.05) increased vegetative biomass, crop yield, and P acquisition of wheat as well as soil alkaline phosphatase (ALP) activity, only with the NPK treatment. This gave an MIR of ca. 45% on total P acquisition of wheat plants. There were no other remarkable MIRs. It suggested that the MIR is determined by soil available P status, and rational combination of AMF with chemical NPK fertilizer can compensate for organic amendments by improving P-acquisition efficiency in arable soils.

Purple phototrophic bacteria (PPB) are thought to be crucial in the nutrient cycling of rice field. However, it remains unclear how PPB would respond to the climate change associated with the projected atmospheric CO2 in the future. A factorial design of field experiments was set up with two levels of atmospheric CO2 concentration (350 and 550 μmol mol−1) and N application rate (150 and 250 kg N ha−1) to investigate the abundance and composition changes of PPB in rhizospheric and bulk soils in response to the rising atmospheric CO2 concentration. Based on denaturant gradient gel electrophoresis (DGGE) analysis of pufM gene encoding the M subunit of anoxygenic PPB light reaction center, elevated CO2 appeared to enhance the biodiversity of PPB in flooded paddy soils. This was further supported by canonical correspondence analysis (CCA) of DGGE fingerprinting pattern of pufM genes in paddy soils as well as Shannon diversity indices. Real-time quantitative PCR analysis of pufM gene further indicated that PPB abundance was stimulated by elevated CO2 in bulk soil, while the contrasting result was observed in rhizospheric soil. Our result for the first time demonstrated that elevated CO2 enhanced the biodiversity of PPB within α and β subdivisions of Proteobacteria.

Arbuscular mycorrhizal (AM) fungal spores were isolated and identified morphologically from soil samples collected from a wheat field at a suburb of Jiangdu, China. Only one speciesGlomus caledonium and a small proportion of its spores were occupied by other spores. The occupant spores all belonged toGlomus microaggregatum. The number ofG. microaggregatum spores inhabiting a singleG. caledonium spore was generally approximately from 5 to 50, depending on the size of the occupied spore and its inhabitants. To our knowledge, this is the first observation thatG. caledonium can be occupied byG. microaggregatum spores.

An environmentally friendly method using Rhodobacter capsulatus is proposed to deposit Aurum nanoparticles. Experiments of Au (III) bioreduction were conducted. There were three kinds of locations found of deposited Aurum nanoparticles, outside, inside and on the plasma membrane of the cell, which showed the diversified ability of R. capsulatus to reduce heavy metal. The mechanism for each of them had been discussed. The methods by which R. capsulatus reduced heavy metal could be more diverse than those of other microbes reported before. The capping agent was also found to stabilize the reduced Aurum in supernate. In conclusion PNSB has the powerful and diversified ability of high valent Aurum reduction.

A pot culture experiment was carried out to study the effects of land use history and inoculation with Fusarium oxysporum f. sp. cucumberinum Owen (Foc) on soil nematodes communities during the cucumber growing season in 2007. The results showed that land use history and inoculation had significant effects on the abundance and diversity of soil nematodes. Bacterivores were found to be the most dominant group in this study. Irrespective of inoculation, numbers of fungivores, plant-parasites and values of trophic diversity index (TD) and plant-parasites index (PPI) were greater in greenhouse soils (GH) than in open field vegetable soils (OF) during the growth period of cucumber. While, the number of omnivores-predators and values of richness (SR) and maturity index (MI) presented an opposite trend. Foc inoculation had noticeable effects on numbers of plant-parasites and some taxa, such as Helicotylenchus, Epidorlaimus at flowering stage and Aphelenchus, Tobrilus at fruiting stage. Besides, inoculation significantly affected values of PPI at flowering stage and TD at fruiting stage, respectively. The faunal analysis showed that soil food web in GH was highly disturbed and in OF was degraded.

Biosorption has been shown to be an eco-friendly approach to remove heavy metal ions. In this study, the photosynthetic bacteria Rhodobacter capsulatus was screened and found to have strong ability to adsorb Au(III). The maximum specific uptake of living cells was over 92.43 mg HAuCl4/g dry weight of cell in the logarithmic phase. Biosorpion ability would be enhanced by an acidic environment. As the main cations, during biosorption the quantity of Mg2+ exchanged was more than Na+. Biosorbed Au(III) could be reduced by carotenoid and enzymes embedded and/or excreted by R. capsulatus, which might be the mechanism of photosynthtic bacteria metal tolerance.

Microcalorimetric technique was used to investigate the effects of balanced versus nutrient-deficiency fertilization on soil microbial activity in a long-term (19-year) fertilizer experiment. The number of microorganisms in soils was measured by viable cell count, and the power-time curves were recorded for soil samples supplemented with glucose and ammonium sulphate, also with or without sodium dihydrogen phosphate for P-deficiency fertilization. Both the bacterial and the fungal populations were significantly higher (P < 0.05) under balanced fertilization than under nutrient-deficiency fertilization. The microbial activity presented by heat dissipation per cell unit indicated that microorganisms under balanced fertilizer treatments had more efficient metabolism, while decreased microbial activity under nutrient-deficiency treatments was firstly due to soil available P, followed by N and K (P < 0.05). In addition, microbial growth in soils under P-deficiency fertilization was stimulated by adding available P, while the lower growth rate, less peak heat, and longer peak time all indicated the low activity of soil microorganisms. We emphasize the importance of balanced fertilization, as well as the role of available P, in maintaining and promoting soil microbial activity.

Paddy fields are one of the largest anthropogenic sources of global CH4 emission. A decrease in paddy CH4 emission can contribute significantly towards the control of global warming. Recent studies have demonstrated that the application of biochar in paddy soils has such a capability, but its underlying mechanism has yet to be elucidated. In this investigation, we studied CH4 emission, methanogenic archaeal, as well as methanotrophic proteobacterial communities, from microcosms derived from two paddy soils, Inceptisol and Ultisol. Both soils were amended with biochar at different pyrolysis temperatures (300 °C, 400 °C and 500 °C) at field condition. The soil CH4 flux was monitored across whole rice season in 2010; the functional guilds communities were analyzed by PCR–DGGE and real-time quantitative PCR (qPCR). It is found that paddy CH4 emissions significantly decreased under biochar amendments, which, interestingly, didn't result from the inhibition of methanogenic archaeal growth. qPCR further revealed that biochar amendments (1) increased methanotrophic proteobacterial abundances significantly, and (2) decreased the ratios of methanogenic to methanotrophic abundances greatly. These results shed insight on the underlying mechanism of how biochar decreases paddy CH4 emission. This knowledge can be applied to develop a more effective greenhouse gas mitigation process for paddy fields.Highlights► Biochar amendment significantly decreased paddy CH4 emission. ► Biochar didn't inhibit, and, on the contrary, even stimulated paddy methanogens. ► The greater stimulated biochar effect on methanotrophic proteobacteria was observed. ► Biochar amendment can both sustain soil productivity and reduce global warming.

The transformation profiles of polycyclic aromatic hydrocarbons (PAHs) by pure laccases from Trametes versicolor and Pycnoporus sanguineus, and the optimal reaction conditions (acetonitrile concentration, pH, temperature and incubation time) were determined. Anthracene was the most transformable PAH by both laccases, followed by benzo[a]pyrene, and benzo[a]anthracene. Laccase-mediator system (LMS) could not only improve the PAH oxidation but also extend the substrate types compared to laccase alone. 5% or 10% (v/v) of acetonitrile concentration, pH 4, temperature of 40 °C, and incubation time of 24 h were most favorable for anthracene oxidation by laccase from T. versicolor or P. sanguineus. The gas chromatography-mass spectrometry analysis indicated that 9,10-anthraquinone was the main product of anthracene transformed by laccase from T. versicolor. Microtox test results showed that both anthracene and its laccase-transformation products were not acute toxic compounds, suggesting that laccase-treatment of anthracene would not increase the acute toxicity of contaminated site.

The characteristics of arbuscular mycorrhizal fungal (AMF) community structure in various soil depths and growing seasons of watermelon (Citrullus vulgaris) grown in commercial greenhouses in Daxing of Beijing and Weifang and Laiyang of Shandong, China were investigated using both morphological identification and denaturing gradient gel electrophoresis. The sampled soils had been used for continuous greenhouse production of watermelon for 0, 5, 10, 15, or 20 years. Glomus claroideum was the dominant species in the greenhouse soils planted for 5, 10, and 15 years in Laiyang, while Glomus mosseae and Glomus etunicatum were dominant in the nearby open farmland soil. Sorenson's similarity index of AMF community composition ranged from 0.67 to 0.84 in the soils planted for 5 years, and from 0.29 to 0.33 for 20 years among the three locations. Spore abundance, species richness, and the Shannon index were highest near the soil surface (0–10 cm) and decreased with soil depth, and higher in June and October than in August and December. Canonical correspondence analysis showed that available P and the number of years that soil had been used for greenhouse production were the main factors contributing to the variance of AMF community composition. It was concluded that the community structure of AMF was mainly influenced by soil available P and planting time of watermelon as well as by soil depth and seasonal variation in the commercial greenhouse.

Soil samples collected from a long-term (19-year) experimental field with seven treatments were analyzed for fatty acids methyl esters (FAMEs) to determine fertilization regime effects on microbial community structure in sandy loam soils. The amounts of FAMEs in bacteria, actinomycetes, and fungi were highest with the two organic manure (OM)-fertilized treatments (OM and 1/2 OMN – half OM plus half mineral fertilizer), lowest with the NK treatment, and fell in the middle levels with three mineral P-fertilized treatments (NPK, NP and PK) and the control with no fertilizer (CK), with the exception of fungi which showed no significant difference among the five treatments without OM fertilization. Principal component analysis of FAME patterns indicated that NPK was not significantly different from CK, but the two manure-containing treatments and the P-deficiency treatment (NK) were significantly different from CK and NPK. Redundancy analysis plot showed that FAME amounts significantly correlated to soil organic C and total N contents, while soil available P and total P contents, which were greatly decreased by the NK treatment, also had positive and substantial effects on soil microbial FAMEs. The results demonstrated the importance of P fertilization as well as organic manure in maintaining soil microbial biomass and impacting community structure.

The elevational patterns of diversity for plants and animals have been well established over the past century. However, it is unclear whether there is a general elevational distribution pattern for microbes. Changbai Mountain is one of few well conserved natural ecosystems, where the vertical distribution of vegetation is known to mirror the vegetation horizontal zonation from temperate to frigid zones on the Eurasian continent. Here, we present a comprehensive analysis of soil bacterial community composition and diversity along six elevations representing six typical vegetation types from forest to alpine tundra using a bar-coded pyrosequencing technique. The bacterial communities differed dramatically along elevations (vegetation types), and the community composition was significantly correlated with soil pH, carbon/nitrogen ratio (C/N), moisture or total organic carbon (TOC), respectively. Phylogenetic diversity was positively correlated with soil pH (P = 0.024), while phylotype richness was positively correlated with soil pH (P = 0.004), total nitrogen (TN) (P = 0.030), and negatively correlated with C/N ratio (P = 0.021). Our results emphasize that pH is a better predictor of soil bacterial elevational distribution and also suggest that vegetation types may indirectly affect soil bacterial elevational distribution through altering soil C and N status.Highlights► We examine soil bacterial distribution along elevation. ► Bacterial communities differed dramatically along elevation. ► Bacterial diversity and community composition were correlated with soil pH. ► Soil pH is a better predictor of bacterial elevational distribution.

The P efficiency, crop yield, and response of maize to arbuscular mycorrhizal fungus (AMF) Glomus caledonium were tested in an experimental field with long-term (18-year) fertilizer management. The experiment included five fertilizer treatments: organic amendment (OA), half organic amendment plus half mineral fertilizer (1/2 OM), mineral fertilizer NPK, mineral fertilizer NK, and the control (without fertilization). AMF inoculation responsiveness (MIRs) of plant growth and P-uptake of maize were estimated by comparing plants grown in unsterilized soil inoculated with G. caledonium and in untreated soil containing indigenous AMF. Soil total P, available P, microbial biomass P, alkaline phosphatase activity, plant biomass, crop yield and total P-uptake of maize were all significantly increased (P < 0.05) by the application of OA, 1/2 OM, and NPK, but not by the application of NK. Specifically, the individual crop yield of maize approached zero in the NK-fertilized soils, as well as in the control soils. All maize plants were colonized by indigenous AMF, and the root colonization at harvest time was not significantly influenced by fertilization. G. caledonium inoculation increased mycorrhizal colonization significantly (P < 0.05) only with the NK treatment, and produced low but demiurgic crop yield in the control and NK-fertilized soils. Compared to the inoculation in balanced-fertilized soils, G. caledonium inoculation in either the NK-fertilized soils or the control soils had significantly greater (P < 0.05) impacts on soil alkaline phosphatase activity, stem length, plant biomass, and total P-uptake of maize, indicating that AMF inoculation was likely more efficient in extremely P-limited soils. These results also showed that balanced mineral fertilizers and organic amendments did not differ significantly in their effects on MIRs in these soils.

The potential of mushroom cultivation substrate (MCS) in bioremediation was examined in polycyclic aromatic hydrocarbon (PAH)-contaminated soil. After a 60-day incubation, 32.9% dissipation of the 15 studied PAHs was observed in MCS-amended microcosms, with anthracene, benzo(a)pyrene and benzo(a)anthracene being the most degradable PAHs. MCS significantly increased the abundance and changed the community compositions of bacteria, fungi and aromatic hydrocarbon degraders. Two species belonging to the Sordariomycetes of the Ascomycota were enriched in all MCS-treated soil samples, and coupled with the unique changes in the PAH profile, this implies the involvement of laccase-like enzymes. Limited improvement was observed after adding Pleurotus ostreatus, possibly because of its poor colonization of the soil. In addition, alfalfa appeared to antagonize the bioremediation effects of MCS. The results of this study suggest that MCS can be a cost-effective and green biostimulation agent, thereby providing support for the development of MCS-based biostimulation of PAH-contaminated soil.Highlights► Biostimulation with mushroom cultivation substrate removes PAHs in soil effectively. ► MCS changes the abundance and community compositions of soil microflora. ► Alfalfa antagonizes the bioremediation effects of MCS. ► The changes in PAH profile suggest an involvement of fungal laccase.

The influences of arbuscular mycorrhizal fungi (AMF, Acaulospora spp. and Glomus spp.) and rice straw and earthworms (RE, Eisenia foetida) on nematode communities and arsenic (As) uptake by maize (Zea mays L.) in As-contaminated soils were examined in a field experiment conducted in Wujiang, Jiangsu Province, China. The experiment was designed as a 2 × 2 factorial with the factors of AMF (inoculated or uninoculated) and RE (added or not added). The results demonstrated that AMF inoculation led to significantly higher root colonization of AMF and root dry weight. Plants inoculated with both AMF and RE had the highest As concentrations in root. The number of total nematodes increased with AMF inoculation when RE was absent, and decreased with RE addition when AMF was inoculated. The improved abundance of nematodes with the AMF treatment implied that the tested AMF acted as food sources for fungivores. The abundances of omnivores-predators and plant parasites were reduced by earthworm activity. Twenty-seven genera of nematodes were identified, with Filenchus dominant in all treatments. Trophic diversity, Shannon-Weaver diversity, Simpson dominance index, and species richness indicated higher species diversity, more proportionate species composition, evenly distributed species, and more food sources in the AMF, RE, and their interaction treatments. Maturity index showed a moderately disturbed environment due to As pollution. Besides enhancing plant uptake of contaminants, AMF and RE amendments could also improve soil health by restoring the structure of soil communities, as reflected by more stable nematode community structure.

The influences of arbuscular mycorrhizal fungi (AMF, Acaulospora spp. and Glomus spp.) and rice straw and earthworms (RE, Eisenia foetida) on nematode communities and arsenic (As) uptake by maize (Zea mays L.) in As-contaminated soils were examined in a field experiment conducted in Wujiang, Jiangsu Province, China. The experiment was designed as a 2 × 2 factorial with the factors of AMF (inoculated or uninoculated) and RE (added or not added). The results demonstrated that AMF inoculation led to significantly higher root colonization of AMF and root dry weight. Plants inoculated with both AMF and RE had the highest As concentrations in root. The number of total nematodes increased with AMF inoculation when RE was absent, and decreased with RE addition when AMF was inoculated. The improved abundance of nematodes with the AMF treatment implied that the tested AMF acted as food sources for fungivores. The abundances of omnivores-predators and plant parasites were reduced by earthworm activity. Twenty-seven genera of nematodes were identified, with Filenchus dominant in all treatments. Trophic diversity, Shannon-Weaver diversity, Simpson dominance index, and species richness indicated higher species diversity, more proportionate species composition, evenly distributed species, and more food sources in the AMF, RE, and their interaction treatments. Maturity index showed a moderately disturbed environment due to As pollution. Besides enhancing plant uptake of contaminants, AMF and RE amendments could also improve soil health by restoring the structure of soil communities, as reflected by more stable nematode community structure.

The effects of organic manure, mineral fertilizer (NPK), and P-deficiency fertilization (NK) on the individual biomass of young wheat plants, arbuscular mycorrhizal (AM) colonization in wheat root systems, population sizes of soil organic phosphorus mineralizing bacteria (OPMB) and inorganic phosphate solubilizing bacteria (IPSB) as well as soil P-mineralization and -solubilization potential were investigated in a long-term (18-year) fertilizer experiment. The experiment included five treatments: organic manure, an equal mixture of organic manure and mineral fertilizer, fertilizer NPK, fertilizer NK, and the control (without fertilization). Plant biomass, population sizes of soil OPMB and IPSB were greatly increased (P<0.05) by the application of organic manure and slightly increased by the balanced application of mineral fertilizer, while undiminished AM colonization in wheat root system was only observed in the case of the NK treatment. Compared to balanced fertilization, P-deficiency fertilization resulted in a significant increase (P<0.05) of OPMB-specific mineralization potential (soil P-mineralization potential per OPMB cell) and highest IPSB-specific solubilization potential (soil P-solubilization potential per IPSB cell), suggesting that OPMB and IPSB are likely more metabolically active in P-deficiency fertilized soils after long-term fertilizer management, and mycorrhizal plants are more dependent on AM in P-poor soils than in P-fertilized soils. Our results also showed the different effects of mineral fertilizer versus organic manure on soil P-mineralization and -solubilization potentials, as well as specific potentials of OPMB and IPSB in arable soils.

A pot culture experiment was carried out to study the growth of and Cu uptake by maize (Zea mays) inoculated with or without arbuscular mycorrhizal (AM) fungus Acaulospora mellea in sterilized soil with different Cu amounts added (0, 100, 200, 400, 800 mg kg−1). Root colonization rates were significantly lower with the addition of 400 and 800 mg kg−1 Cu. AM inoculation increased shoot dry weights at 200 and 400 mg kg−1 Cu added but showed no effects at other levels, while increased root dry weights at all Cu addition levels except 800 mg kg−1. Compared with the nonmycorrhizal plants, shoot Cu concentrations in mycorrhizal plants were higher when no Cu was added but lower at other levels, while root Cu concentrations were lower at 400 and 800 mg kg−1 Cu added but not affected at other levels. Thus, shoot Cu uptake in mycorrhizal plants increased with no Cu added but decreased at other levels, while mycorrhizal effects on root Cu uptake varied. Compared with nonmycorrhizal controls, Cu uptake efficiency and phytoextraction efficiency in mycorrhizal plants were higher when no Cu was added but lower at other levels, and Cu translocation efficiency was lower at all Cu addition levels. AM inoculation improved shoot and root P nutrition at all Cu addition levels. Soil pH was higher in mycorrhizal treatment than in the control when 200 mg kg−1 or more Cu was added. These results indicate that A. mellea ZZ may be not suitable for Cu phytoextraction by maize, but shows a potential role in phytostabilization of soil moderately polluted by Cu.