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1.
J Microbiol Methods ; 173: 105938, 2020 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-32360380

RESUMO

DNA-SIP (DNA-based stable isotope probing) is increasingly being employed in soil microbial ecology to identify those microbes assimilating the 13C/15N labelled substrate. Isopycnic gradient centrifugation is the primary experimental process for conducting DNA-SIP. However, diverse centrifugal conditions have been used in various recent studies. In order to get the optimum conditions of centrifugation for DNA-SIP, centrifugation time (36, 42, 48, 60 h), speed (45,000, 55,000 rpm) and the initial buoyant density (1.69, 1.71, 1.725 g ml-1), as were used extensively in related studies, were tested in this experiment with the Vti 65.2 rotor. DNA with either 13C-labelling or unlabelled was extracted from a paddy soil pre-incubated with either 13C-labelled or natural abundance glucose. After ultracentrifugation, the gene abundance of bacterial 16S rRNA, fungal 18S rRNA, bacterial and archaeal amoA within the fractioned DNA was detected. The results showed that centrifugation for 48 h was enough for the DNA to reach stabilization in the CsCl solution. The initial density of the mixed solution was best adjusted to 1.71 g ml-1 to ensure that most of the genes were concentrated on the middle fractions of the density gradient. Increasing the centrifugation speed would increase the density gradient of fractions; therefore, 45,000 rpm (184,000 g) was recommended so as to obtain the more widespread pattern of DNA in the centrifugal tube. We hope these findings will assist future researchers to conduct optimum ultracentrifugation for DNA-SIP.

2.
Microb Ecol ; 79(2): 357-366, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31342100

RESUMO

Rice root-associated microbial community play an important role in plant nutrient acquisition, biomass production, and stress tolerance. Herein, root-associated community assembly was investigated under different phosphate input levels in phosphorus (P)-deficient paddy soil. Rice was grown in a long-term P-depleted paddy soil with 0 (P0), 50 (PL), or 200 (PH) mg P2O5 kg-1 application. DNA from root endophytes was isolated after 46 days, and PCR amplicons from archaea, bacteria, and fungi were sequenced by an Illumina Miseq PE300 platform, respectively. P application had no significant effect on rice root endophytic archaea, which were dominated by ammonia-oxidizing Candidatus Nitrososphaera. By contrast, rice root endophytic community structure of the bacteria and fungi was affected by soil P. Low P input increased endophytic bacterial diversity, whereas high P input increased rhizosphere fungi diversity. Bacillus and Pleosporales, associated with phosphate solubilization and P uptake, dominated in P0 and PH treatments, and Pseudomonas were more abundant in the PL treatment than in the P0 and PH treatments. Co-occurrence network analysis revealed a close interaction between endophytic bacteria and fungi. Soil P application affected both the rice root endosphere and soil rhizosphere microbial community and interaction between rice root endophytic bacteria, and fungi, especially species related to P cycling.

3.
Ying Yong Sheng Tai Xue Bao ; 30(12): 4323-4332, 2019 Dec.
Artigo em Chinês | MEDLINE | ID: mdl-31840479

RESUMO

Soil microbes play essential roles in maintaining terrestrial ecosystem services. Soil moisture is a primary determinant of soil microbial activities and ecosystem functions, which may fluctuate dramatically with the altered precipitation patterns and extreme drought caused by the ongoing global climate change. Due to the distinct soil microbial tolerance and life-strategy approaches to drought stress and different water status, fluctuation of soil moisture has a direct impact on microbial activities and community structure, thereby profoundly affecting microbial-mediated processes and ecosystem functions. Thus, it is of great significance to understand the dynamics and mechanisms that underlie the microbial responses to soil water status. In this review, we summarized recent progress in the study of responses of soil microbial activities (e.g. soil respiration and enzyme activities) and community structure to soil water status. We summarized underlying microbial physiological and ecological mechanisms, particularly 1) the cellular physiological accommodation such as osmolyte accumulation, exopolysaccharide production and transition into dormant states, and 2) the ecological strategies such as stress-resistant gene transfer and functional redundancy. Therefore, this investigation on the underlying relationship between soil microbial assembly and ecosystem functions under different water status could further demonstrate the microbially-mediated soil biogeochemical processes and provide a theoretical basis for future research and modelling of terrestrial ecosystem responses to climate change.


Assuntos
Ecossistema , Solo , Bactérias , Mudança Climática , Microbiologia do Solo , Água
4.
Microbiome ; 7(1): 143, 2019 10 31.
Artigo em Inglês | MEDLINE | ID: mdl-31672173

RESUMO

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

5.
Environ Sci Pollut Res Int ; 26(35): 35978-35987, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31709485

RESUMO

Biochar has been considered as a promising soil amendment for improving fertility and mitigating N2O emission from the arable land. However, biochar's effectiveness in acidic tea soil and underlying mechanisms are largely unknown. We conducted a short-term microcosm experiment using two biochars (1% w/w, LB, generated from legume and NLB, non-legume biomass, respectively) to investigate the effects of biochar amendments on soil chemical properties, N2O emission, and microbial community in an acidic soil. Soil and headspace gas samples were taken on 1, 10, and 30 day's incubation. Biochar amendment increased soil pH and DOC, however, significantly reduced soil inorganic N. Both biochars at ~ 1% addition had little effect on microbial CO2 respiration but suppressed soil N2O emission by ~ 40% during the incubation. The divergence in N2O efflux rates between soils with and without biochar addition aligned to some degree with changes in soil pH, inorganic N, and dissolved organic C (DOC). We also found that biochar addition significantly modified the fungal community structure, in particular the relative abundance of members of Ascomycota, but not the bacterial community. Furthermore, the copy number of nosZ, the gene encoding N2O reductase, was significantly greater in biochar-amended soils than the soil alone. Our findings contribute to better understanding of the impact of biochar on the soil chemical properties, soil N2O emission, and microbial community and the consequences of soil biochar amendment for improving the health of acidic tea soil.


Assuntos
Poluentes Atmosféricos/análise , Carvão Vegetal/química , Dióxido de Nitrogênio/análise , Microbiologia do Solo , Ácidos , Poluentes Atmosféricos/química , Bactérias , Biomassa , Microbiota , Dióxido de Nitrogênio/química , Solo/química , Chá
6.
Front Microbiol ; 10: 1361, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31316475

RESUMO

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

7.
Animals (Basel) ; 9(6)2019 Jun 13.
Artigo em Inglês | MEDLINE | ID: mdl-31200503

RESUMO

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

8.
Chemosphere ; 224: 805-815, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-30851532

RESUMO

Biochar is considered as a universal sorbent used for soil amendment but its impacts on organochlorine pesticides (OCPs) and microbial communities associated with soil and vegetables are unclear. The effects of different biochars (derived from sewage sludge biochar (SSBC), soybean straw biochar (SBBC), rice straw biochar (RSBC) and peanut shells biochar (PNBC)), on bioaccessible fractions of OCPs in a contaminated soil and their subsequent bioaccumulation into vegetables (Chinese cabbage and spring onion) were investigated in this research work. The influence of these amendments on vegetable yields and soil microbial community using Illumina next generation sequencing technology was also assessed. The application of selected biochars significantly (p < 0.01) reduced the bioaccessibility of ∑OCPs in contaminated soil: SSBC (52%), PNBC (51%), RSBC (60%), and SBBC (47%), as compared to the control. The results indicated that following biochar additions, the bio-uptake of ∑OCP bio-uptake was considerably (from 86 to 85%) reduced in grown vegetables. Risk assessment showed that biochar amendments markedly (p < 0.01) decreased the hazard quotient (HQ) indices and incremental lifetime cancer risk (ILTR) values for OCPs associated with the consumption of vegetables. In addition, the results of high-throughput sequencing showed significant differences in microbial community structure between the treatments, which was driven by differences in the relative abundances of soil microbes. The relative abundances of Acidobacteria, Chloroflexi, Nitrospirae and Verrucomicrobia decreased following biochar additions. However, biochar amendments increased the relative abundances of Actinobacteria, Proteobacteria, Planctomycetes, Bacteroidetes, Firmicutes, and Gemmatimonadetes, though the increase in relative abundances of these phyla was strongly dependent on the type of biochar used.


Assuntos
Bactérias/crescimento & desenvolvimento , Carvão Vegetal/metabolismo , Poluição Ambiental/análise , Hidrocarbonetos Clorados/análise , Praguicidas/análise , Poluentes do Solo/análise , Solo/química , Agricultura/métodos , Arachis/metabolismo , Bactérias/efeitos dos fármacos , Bactérias/metabolismo , Microbiota , Oryza/metabolismo , Esgotos/química , Microbiologia do Solo , Verduras
9.
Appl Microbiol Biotechnol ; 103(10): 4217-4227, 2019 May.
Artigo em Inglês | MEDLINE | ID: mdl-30911786

RESUMO

The planting of transgenic rice has aroused ongoing controversy, due to the public anxiety surrounding the potential risk of transgenic rice to health and the environment. The soil microbial community plays an important environmental role in the plant-soil-microbe system; however, few studies have focused on the effect of transgenic rice on the soil rhizospheric microbiome. We labeled transgenic gene rice (TT51, transformed with Cry1Ab/1Ac gene), able to produce the Bt (Bacillus thuringiensis) toxin, its parental variety (Minghui 63), and a non-parental variety (9931) with 13CO2. The DNA of the associated soil rhizospheric microbes was extracted, subjected to density gradient centrifugation, followed by high-throughput sequencing of bacterial 16S rRNA gene. Unweighted unifrac analysis of the sequencing showed that transgenic rice did not significantly change the soil bacterial community structure compared with its parental variety. The order Opitutales, affiliated to phylum Verrucomicrobia and order Sphingobacteriales, was the main group of labeled bacteria in soil planted with the transgenic and parental varieties, while the orders Pedosphaerales, Chthoniobacteraceae, also affiliated to Verrucomicrobia, and the genus Geobacter, affiliated to class Deltaproteobacteria, dominated in the soil of the non-parental rice variety. The non-significant difference in soil bacterial community structure of labeled microbes between the transgenic and parental varieties, but the comparatively large difference with the non-parental variety, suggests a limited effect of planting transgenic Bt rice on the soil microbiome.


Assuntos
Proteínas de Bactérias/metabolismo , Endotoxinas/metabolismo , Proteínas Hemolisinas/metabolismo , Microbiota , Oryza/crescimento & desenvolvimento , Plantas Geneticamente Modificadas/crescimento & desenvolvimento , Rizosfera , Microbiologia do Solo , Dióxido de Carbono/metabolismo , Isótopos de Carbono/metabolismo , Análise por Conglomerados , DNA Bacteriano/química , DNA Bacteriano/genética , DNA Ribossômico/química , DNA Ribossômico/genética , Sequenciamento de Nucleotídeos em Larga Escala , Marcação por Isótopo , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
10.
Artigo em Inglês | MEDLINE | ID: mdl-30813565

RESUMO

High-throughput quantitative PCR combined with Illumina sequencing and network analysis were used to characterize the antibiotic resistance gene (ARG) profiles in air-conditioning filters from different environments. In total, 177 ARGs comprising 10 ARG types were determined. The detectable numbers and the relative abundance of ARGs in hospitals and farms were significantly higher than those in city and village residences. Compared to hospitals, farms had a higher level of tetracycline, multidrug, integrase, and macrolide⁻lincosamide⁻streptogramin (MLS) B resistance genes but a lower level of beta-lactam resistance genes. The bl3_cpha gene was the most abundant resistance gene subtype in hospital samples with an abundance of 2.01 × 10-4 copies/16S rRNA, while a level of only 5.08 × 10-12 copies/16S rRNA was observed in farm samples. There was no significant difference in bacterial diversity among the hospitals, farms, and residences, and Proteobacteria was the most abundant phylum. Network analysis revealed that Proteobacteria and Actinobacteria were possible hosts of the beta-lactam, MLSB, aminoglycoside, multidrug, sulfonamide, and tetracycline resistance genes. The results demonstrate that ARGs exist in indoor environments and that farms and hospitals are important sources. This study provides a useful reference for understanding the distribution patterns and risk management of ARGs in indoor environments.


Assuntos
Ar Condicionado/estatística & dados numéricos , Bactérias/genética , Farmacorresistência Bacteriana/genética , Microbiologia Ambiental , Monitoramento Ambiental , Genes Bacterianos/genética , Filtros de Ar/microbiologia , Antibacterianos/farmacologia , Bactérias/classificação , Bactérias/efeitos dos fármacos , Fazendas/estatística & dados numéricos , Hospitais/estatística & dados numéricos , Habitação/estatística & dados numéricos , Prevalência
11.
Environ Sci Pollut Res Int ; 26(9): 8808-8820, 2019 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-30712208

RESUMO

A comprehensive study was conducted to appraise the concentrations of 30 endocrine disrupting pesticides (EDPs) in soil and vegetable samples collected from Khyber Pakhtunkhwa, Pakistan. The sum of 30 EDPs (Σ30EDPs) ranged from 192 to 2148 µg kg-1 in the collected soils. The selected EDP concentrations exceeded their respective limits in most of the tested soils and showed great variation from site to site. Similarly, high variations in Σ30EDP concentrations were also observed in vegetables with the highest mean concentration in lettuce (28.9 µg kg-1), followed by radish (26.6 µg kg-1), spinach (25.7 µg kg-1), onion (16.2 µg kg-1), turnip (15.6 µg kg-1), and garlic (14.7 µg kg-1). However, EDP levels in all studied vegetables were within FAO/WHO limits. The mean bioconcentration factor values were observed < 1 for all the studied vegetables. The health risk assessment revealed that the incremental lifetime cancer risk (ILCR) of Σ30EDPs associated with vegetable ingestion was below the acceptable risk level (1 × 10-6), showing no cancer risk to local inhabitants. However, exposure to endocrine disruptor and probable carcinogen heptachlor epoxide poses a potential non-cancer risk (hazard quotient (HQ > 1)) to children through vegetable consumption. The presence of banned EDPs in soils and vegetables of the study area indicates the stability of these legacy chemicals in the environment from over usage in the past or illegal current application for agricultural purposes. Graphical abstract.


Assuntos
Disruptores Endócrinos/toxicidade , Contaminação de Alimentos , Praguicidas/toxicidade , Poluentes do Solo/toxicidade , Solo/química , Verduras/química , Agricultura , Criança , Ingestão de Alimentos , Humanos , Paquistão , Medição de Risco , Poluentes do Solo/análise
12.
Sci Total Environ ; 647: 551-560, 2019 Jan 10.
Artigo em Inglês | MEDLINE | ID: mdl-30089277

RESUMO

Biochar can be used as a promising potential substance to reduce the availability of toxic elements and compounds in contaminated soils but its effects on the accessibility of pesticides and microbiological interactions still remain unclear. Here, 65 day incubation experiments were conducted to investigate the efficacy of biochars on the accessibility of 21 different organochlorine pesticides (OCPs), and also to evaluate their influence on soil microbial community. The tested soil was collected from an agricultural field, containing loamy sand texture, and historically contaminated with high concentrations of OCPs. The soil was amended with four different kinds of biochars: sewage sludge biochar (SSBC), peanut shells biochar (PNBC), rice straw biochar (RSBC), and soybean straw biochar (SBBC). The results indicated that biochar-amendments had strong effects upon OCP accessibility over time and can act as super sorbent. Despite greater persistence of OCPs in soil, the application of selected biochars significantly (p < 0.01) reduced the accessibility of ∑OCPs in the amended soil in the order of SSBC (8-69%), PNBC (11-75%), RSBC (6-67%), and SBBC (14-86%), as compared to the control soil during 0-65 d incubation period. Moreover, the findings from total phospholipid acid (PLFA) and Illumina next-generation sequencing revealed that the incorporation of biochar have altered the soil microbial community structure over time. Higher abundances of Proteobacteria, firmicutes, Gemmatimonadetes, and Actinobacteria were found in biochar amendments. However, the relative abundances of Acidobacteria and Chloroflexi decreased, following biochar addition. The findings of these experiments suggest that biochar addition to soil at the rate of 3% (w/w) could be advantageous for decreasing accessibility of OCPs, enhancing the soil microbial communities, and their subsequent risk to environment and food chain contamination.

13.
Environ Sci Pollut Res Int ; 25(3): 2932-2941, 2018 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-29147983

RESUMO

Paddy soil experiences repeated anaerobic and aerobic changes during rice growth, the dramatic dynamics of soil water status accompanied by changes in redox condition and O2 availability. However, the effect of rapid water status change on soil microbial biomass and community composition is not well explored. Here, we present a comprehensive study focusing on the short-term water status change in 13 Chinese paddy soils. In order to gain a reliable way to determine soil microbial biomass carbon (MBC) in flooded or water-saturated soils, we also evaluated two different procedures (nitrogen bubbled and 100 °C water bath) to remove chloroform in extracts during the fumigation process. Compared to non-flooded paddy soils, the flooded paddy soils tended to have a lower microbial biomass, and this was much clearer using adenosine 5'-triphosphate (ATP) and phospholipid fatty acid (PLFA) analysis compared to biomass measured by the fumigation method. Fungal biomass, which was indicated by both ergosterol and the PLFA 18:2ω6,9c, also decreased after short-term flooding. Changes in soil microbial community composition (determined by PLFA biomarkers) were observed after short-term flooding, but the extent varied between soils. This study indicates that the dynamics of short-term water status altered the soil microbial biomass (ATP, MBC, and total PLFA) and community composition. Finally, our results suggested that liquid fumigation combined with the nitrogen-bubbled method is the best choice for analyzing MBC concentrations in water-saturated soils.


Assuntos
Oryza/crescimento & desenvolvimento , Microbiologia do Solo , Solo/química , Água/análise , Bactérias/crescimento & desenvolvimento , Biomassa , China , Ergosterol/análise , Ácidos Graxos/análise , Fungos/crescimento & desenvolvimento , Consórcios Microbianos
14.
AMB Express ; 7(1): 129, 2017 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-28641404

RESUMO

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

15.
Sci Total Environ ; 559: 15-23, 2016 07 15.
Artigo em Inglês | MEDLINE | ID: mdl-27054490

RESUMO

The application of straw and biochar to soil has received great attention because of their potential benefits such as fertility improvement and carbon (C) sequestration. The abiotic effects of these materials on C and nitrogen (N) cycling in the soil ecosystem have been previously investigated, however, the effects of straw or its derived biochar on the soil microbial community structure and function are not well understood. For this purpose, a short-term incubation experiment was conducted using (13)C-labeled rice straw and its derived biochar ((13)C-labeled biochar) to deepen our understanding about soil microbial community dynamics and function in C sequestration and greenhouse gas emission in the acidic paddy soil amended with these materials. Regarding microbial function, biochar and straw applications increased CO2 emission in the initial stage of incubation and reached the highest level (0.52 and 3.96mgCkg(-1)soilh(-1)) at 1d and 3d after incubation, respectively. Straw amendment significantly (p<0.01) increased respiration rate, total phospholipid fatty acids (PLFAs) and (13)C-PLFA as compared to biochar amendment and the control. The amount and percent of Gram positive bacteria, fungi and actinomycetes were also significantly (p<0.05) higher in (13)C-labeled straw amended soil than the (13)C-labeled biochar amended soil. According to the (13)C data, 23 different PLFAs were derived from straw amended paddy soil, while only 17 PLFAs were derived from biochar amendments. The profile of (13)C-PLFAs derived from straw amendment was significantly (p<0.01) different from biochar amendment. The PLFAs18:1ω7c and cy17:0 (indicators of Gram negative bacteria) showed high relative abundances in the biochar amendment, while 10Me18:0, i17:0 and 18:2ω6,9c (indicators of actinomycetes, Gram positive bacteria and fungi, respectively) showed high relative abundance in the straw amendments. Our results suggest that the function, size and structure of the microbial community were strongly influenced by the substrate composition and availability.


Assuntos
Agricultura/métodos , Microbiologia do Solo , Carvão Vegetal/metabolismo , Ecossistema , Oryza , Solo/química
16.
Appl Microbiol Biotechnol ; 100(15): 6815-6826, 2016 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-27063014

RESUMO

Yellow clay paddy soil (Oxisols) is a typical soil with low productivity in southern China. Nitrification inhibitors and slow release fertilizers have been used to improve nitrogen fertilizer utilization and reduce environmental impaction of the paddy soil. However, their effects on ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in paddy soil have rarely been investigated. In the present work, we compared the influences of several slow release fertilizers and nitrification inhibitors on the community structure and activities of the ammonia oxidizers in yellow clay soil. The abundances and community compositions of AOA and AOB were determined with qPCR, terminal restriction fragment length polymorphism (T-RFLP), and clone library approaches. Our results indicated that the potential nitrification rate (PNR) of the soil was significantly related to the abundances of both AOA and AOB. Nitrogen fertilizer application stimulated the growth of AOA and AOB, and the combinations of nitrapyrin with urea (NPU) and urea-formaldehyde (UF) inhibited the growth of AOA and AOB, respectively. Compared with other treatments, the applications of NPU and UF also led to significant shifts in the community compositions of AOA and AOB, respectively. NPU showed an inhibitory effect on AOA T-RF 166 bp that belonged to Nitrosotalea. UF had a negative effect on AOB T-RF 62 bp that was assigned to Nitrosospira. These results suggested that NPU inhibited PNR and increased nitrogen use efficiency (NUE) by inhibiting the growth of AOA and altering AOA community. UF showed no effect on NUE but decreased AOB abundance and shifted AOB community.


Assuntos
Amônia/metabolismo , Archaea/metabolismo , Bactérias/metabolismo , Fertilizantes/microbiologia , Nitrificação/fisiologia , Archaea/genética , Archaea/crescimento & desenvolvimento , Bactérias/genética , Bactérias/crescimento & desenvolvimento , Oxirredução , Polimorfismo de Fragmento de Restrição/genética , Solo/química , Microbiologia do Solo
17.
Environ Sci Pollut Res Int ; 23(15): 15483-94, 2016 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-27117156

RESUMO

Landfills are always the most important part of solid waste management and bear diverse metabolic activities involved in element biogeochemical cycling. There is an increasing interest in understanding the microbial community and activities in landfill cover soils. To improve our knowledge of landfill ecosystems, we determined the microbial physiological profiles and communities in three landfill cover soils (Ninghai: NH, Xiangshan: XS, and Fenghua: FH) of different ages using the MicroResp(TM), phospholipid fatty acid (PLFA), and high-throughput sequencing techniques. Both total PLFAs and glucose-induced respiration suggested more active microorganisms occurred in intermediate cover soils. Microorganisms in all landfill cover soils favored L-malic acid, ketoglutarate, and citric acid. Gram-negative bacterial PLFAs predominated in all samples with the representation of 16:1ω7, 18:1ω7, and cy19:0 in XS and NH sites. Proteobacteria dominated soil microbial phyla across different sites, soil layers, and season samples. Canonical correspondence analysis showed soil pH, dissolved organic C (DOC), As, and total nitrogen (TN) contents significantly influenced the microbial community but TN affected the microbial physiological activities in both summer and winter landfill cover soils.


Assuntos
Metaboloma , Consórcios Microbianos , Microbiologia do Solo , Solo/química , Instalações de Eliminação de Resíduos , China , Ecossistema , Ácidos Graxos/análise , Nitrogênio/análise , Fosfolipídeos/análise , Proteobactérias/crescimento & desenvolvimento , Proteobactérias/metabolismo , Estações do Ano
18.
Appl Microbiol Biotechnol ; 100(13): 5989-98, 2016 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-26923143

RESUMO

Nitrogen fertilization and returning straw to paddy soil are important factors that regulate CH4 production. To evaluate the effect of rice straw and/or nitrate amendment on methanogens, a paddy soil was anaerobically incubated for 40 days. The results indicated that while straw addition increased CH4 production and the abundances of mcrA genes and their transcripts, nitrate amendment showed inhibitory effects on them. The terminal restriction fragment length polymorphism (T-RFLP) analysis based on mcrA gene revealed that straw addition obviously changed methanogenic community structure. Based on mcrA gene level, straw-alone addition stimulated Methanosarcinaceaes at the early stage of incubation (first 11 days), but nitrate showed inhibitory effect. The relative abundance of Methanobacteriaceae was also stimulated by straw addition during the first 11 days. Furthermore, Methanosaetaceae were enriched by nitrate-alone addition after 11 days, while Methanocellaceae were enriched by nitrate addition especially within the first 5 days. The transcriptional methanogenic community indicated more dynamic and complicated responses to straw and/or nitrate addition. Based on mcrA transcript level, nitrate addition alone resulted in the increase of Methanocellaceae and the shift from Methanosarcinaceae to Methanosaetaceae during the first 5 days of incubation. Straw treatments increased the relative abundance of Methanobacteriaceae after 11 days. These results demonstrate that nitrate addition influences methanogens which are transcriptionally and functionally active and can alleviate CH4 production associated with straw amendment in paddy soil incubations, presumably through competition for common substrates between nitrate-utilizing organisms and methanogens.


Assuntos
Archaea/metabolismo , Biodiversidade , Metano/metabolismo , Nitrogênio/metabolismo , Oryza/crescimento & desenvolvimento , Archaea/classificação , Archaea/genética , Archaea/isolamento & purificação , Fertilizantes/análise , Oryza/química , Filogenia , Caules de Planta/química , Solo/química , Microbiologia do Solo
19.
Environ Sci Pollut Res Int ; 23(6): 5941-8, 2016 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-26596827

RESUMO

Rice straw application and flooding are common practices in rice production, both of which can induce changes in the microbial community. This study used soil microcosms to investigate the impact of water status (saturated and nonsaturated) and straw application (10 g kg(-1) soil) on soil microbial composition (phospholipid fatty acid analysis) and activity (MicroResp(™) method). Straw application significantly increased total PLFA amount and individual PLFA components independent of soil moisture level. The amount of soil fungal PLFA was less than Gram-negative, Gram-positive, and actinomycete PLFA, except the drained treatment with rice straw application, which had higher fungal PLFA than actinomycete PLFA at the initial incubation stage. Straw amendment and waterlogging had different effects on microbial community structure and substrate-induced pattern. PLFA profiles were primarily influenced by straw application, whereas soil water status had the greater influence on microbial respiration. Of the variation in PLFA and respiration data, straw accounted for 30.1 and 16.7 %, while soil water status explained 7.5 and 29.1 %, respectively. Our results suggest that (1) the size of microbial communities in paddy soil is more limited by carbon substrate availability rather than by the anaerobic conditions due to waterlogging and (2) that soil water status is more important as a control of fungal growth and microbial community activity.


Assuntos
Oryza , Microbiologia do Solo , Água , Carbono/análise , Ácidos Graxos/análise , Fungos , Oryza/crescimento & desenvolvimento , Fosfolipídeos/análise , Solo/química , Água/análise
20.
Nat Commun ; 6: 8444, 2015 10 05.
Artigo em Inglês | MEDLINE | ID: mdl-26436640

RESUMO

The continuum hypothesis states that both deterministic and stochastic processes contribute to the assembly of ecological communities. However, the contextual dependency of these processes remains an open question that imposes strong limitations on predictions of community responses to environmental change. Here we measure community and habitat turnover across multiple vertical soil horizons at 183 sites across Scotland for bacteria and fungi, both dominant and functionally vital components of all soils but which differ substantially in their growth habit and dispersal capability. We find that habitat turnover is the primary driver of bacterial community turnover in general, although its importance decreases with increasing isolation and disturbance. Fungal communities, however, exhibit a highly stochastic assembly process, both neutral and non-neutral in nature, largely independent of disturbance. These findings suggest that increased focus on dispersal limitation and biotic interactions are necessary to manage and conserve the key ecosystem services provided by these assemblages.


Assuntos
Bactérias , Biota , Fungos , Microbiologia do Solo , Biodiversidade , Ecologia , Ecossistema , Processos Estocásticos
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