Actinobacterial community structure in soils receiving long-term organic and inorganic amendments.
Ontology highlight
ABSTRACT:
SUBMITTER: Piao Z
PROVIDER: S-EPMC2223251 | biostudies-literature | 2008 Jan
REPOSITORIES: biostudies-literature
Publications
Actinobacterial community structure in soils receiving long-term organic and inorganic amendments.
Piao Zhe Z Yang Linzhang L Zhao Liping L Yin Shixue S
Applied and environmental microbiology 20071012 2
The impact of long-term organic and inorganic amendments on the actinobacterial community in soils was studied. Denaturing gradient gel electrophoresis patterns based on the V3 region of 16S rRNA suggested that there was no significant difference between the communities occurring in the different amendments. However, analysis of the clone libraries of the actinobacterial communities by the use of multiple statistical approaches showed that these communities were significantly different from each ...[more]
Similar Datasets
Project description:BackgroundAddition of organic amendments has been commonly adopted as a means to restore degraded soils globally. More recently, the use of woody organic amendments has been recognized as a viable method of capturing and retaining water and restoring degraded and desertified soil, especially in semi-arid regions. However, the impacts of woody amendments on soil microbial community structure, versus other traditional organic supplements is less understood.MethodsThree locally available natural organic materials of different qualities, i.e., cow manure (CM), corn straw (CS), and chipped poplar branches (PB) were selected as treatments in Ningxia, Northern China and compared with control soils. Four microcosms served as replicates for each treatment. All treatments contained desertified soil; treatments with amendments were mixed with 3% (w/w) of one of the above organic materials. After 7 and 15 months from the start of the experiment, soil samples were analyzed for chemical and physical properties, along with biological properties, which included microbial α-diversity, community structure, and relative abundance of microbial phyla.ResultsBoth bacterial and fungal α-diversity indices were weakly affected by amendments throughout the experimental period. All amendments yielded different microbial community compositions than the Control soils. The microbial community composition in the CS and PB treatments also were different from the CM treatment. After 15 months of the experiment, CS and PB exhibited similar microbial community composition, which was consistent with their similar soil physical and chemical properties. Moreover, CS and PB also appeared to exert similar effects on the abundance of some microbial taxa, and both of these treatments yield different abundances of microbial taxa than the CM treatment.ConclusionNew local organic amendment with PB tended to affect the microbial community in a similar way to the traditional local organic amendment with CS, but different from the most traditional local organic amendment with CM in Ningxia, Northern China. Moreover, the high C/N-sensitive, and lignin and cellulose decompose-related microbial phyla increased in CS and PB have benefits in decomposing those incorporated organic materials and improving soil properties. Therefore, we recommend that PB should also be considered as a viable soil organic amendment for future not in Ningxia, but also in other places.
| S-EPMC6511227 | biostudies-literature
Project description:Soil management is fundamental to all agricultural systems and fertilization practices have contributed substantially to the impressive increases in food production. Despite the pivotal role of soil microorganisms in agro-ecosystems, we still have a limited understanding of the complex response of the soil microbiota to organic and mineral fertilization in the very long-term. Here, we report the effects of different fertilization regimes (mineral, organic and combined mineral and organic fertilization), carried out for more than a century, on the structure and activity of the soil microbiome. Organic matter content, nutrient concentrations, and microbial biomass carbon were significantly increased by mineral, and even more strongly by organic fertilization. Pyrosequencing revealed significant differences between the structures of bacterial and fungal soil communities associated to each fertilization regime. Organic fertilization increased bacterial diversity, and stimulated microbial groups (Firmicutes, Proteobacteria, and Zygomycota) that are known to prefer nutrient-rich environments, and that are involved in the degradation of complex organic compounds. In contrast, soils not receiving manure harbored distinct microbial communities enriched in oligotrophic organisms adapted to nutrient-limited environments, as Acidobacteria. The fertilization regime also affected the relative abundances of plant beneficial and detrimental microbial taxa, which may influence productivity and stability of the agroecosystem. As expected, the activity of microbial exoenzymes involved in carbon, nitrogen, and phosphorous mineralization were enhanced by both types of fertilization. However, in contrast to comparable studies, the highest chitinase and phosphatase activities were observed in the solely mineral fertilized soil. Interestingly, these two enzymes showed also a particular high biomass-specific activities and a strong negative relation with soil pH. As many soil parameters are known to change slowly, the particularity of unchanged fertilization treatments since 1902 allows a profound assessment of linkages between management and abiotic as well as biotic soil parameters. Our study revealed that pH and TOC were the majors, while nitrogen and phosphorous pools were minors, drivers for structure and activity of the soil microbial community. Due to the long-term treatments studied, our findings likely represent permanent and stable, rather than transient, responses of soil microbial communities to fertilization.
| S-EPMC5022044 | biostudies-literature
Project description:Agricultural soils with organic amendments (Raw sequence reads)
| PRJNA599559 | ENA
Project description:Fertilization has a large impact on the soil microbial communities, which play pivotal roles in soil biogeochemical cycling and ecological processes. While the effects of changes in nutrient availability due to fertilization on the soil microbial communities have received considerable attention, specific microbial taxa strongly influenced by long-term organic and inorganic fertilization, their potential effects and associations with soil nutrients remain unclear. Here, we use deep 16S amplicon sequencing to investigate bacterial community characteristics in a fluvo-aquic soil treated for 24 years with inorganic fertilizers and organics (manure and straw)-inorganic fertilizers, and uncover potential links between soil nutrient parameters and specific bacterial taxa. Our results showed that combined organic-inorganic fertilization increased soil organic carbon (SOC) and total nitrogen (TN) contents and altered bacterial community composition, while inorganic fertilization had little impact on soil nutrients and bacterial community composition. SOC and TN emerged as the major determinants of community composition. The abundances of specific taxa, especially Arenimonas, Gemmatimonas, and an unclassified member of Xanthomonadaceae, were substantially increased by organic-inorganic amendments rather than inorganic amendments only. A co-occurrence based network analysis demonstrated that SOC and TN had strong positive associations with some taxa (Gemmatimonas and the members of Acidobacteria subgroup 6, Myxococcales, Betaproteobacteria, and Bacteroidetes), and Gemmatimonas, Flavobacterium, and an unclassified member of Verrucomicrobia were identified as the keystone taxa. These specific taxa identified above are implicated in the decomposition of complex organic matters and soil carbon, nitrogen, and phosphorus transformations. The present work strengthens our current understanding of the soil microbial community structure and functions under long-term fertilization management and provides certain theoretical support for selection of rational fertilization strategies.
| S-EPMC5298992 | biostudies-literature
Project description:Organic fertilizers have been shown to stimulate CH4 uptake from agricultural soils. Managing fertilizer application to maximize this effect and to minimize emission of other greenhouse gasses offers possibilities to increase sustainability of agriculture. To tackle this challenge, we incubated an agricultural soil with different organic amendments (compost, sewage sludge, digestate, cover crop residues mixture), either as single application or in a mixture and subjected it to different soil moisture concentrations using different amounts of organic amendments. GHG fluxes and in vitro CH4 oxidation rates were measured repeatedly, while changes in organic matter and abundance of GHG relevant microbial groups (nitrifiers, denitrifiers, methanotrophs, methanogens) were measured at the end of the incubation. Overall the dynamics of the analyzed GHGs differed significantly. While CO2 and N2O differed considerably between the treatments, CH4 fluxes remained stable. In contrast, in vitro CH4 oxidation showed a clear increase for all amendments over time. CO2 fluxes were mostly dependent on the amount of organic residue that was used, while N2O fluxes were affected more by soil moisture. Several combinations of amendments led to reductions of CO2, CH4, and/or N2O emissions compared to un-amended soil. Most optimal GHG balance was obtained by compost amendments, which resulted in a similar overall GHG balance as compared to the un-amended soil. However, compost is not very nutrient rich potentially leading to lower crop yield when applied as single fertilizer. Hence, the combination of compost with one of the more nutrient rich organic amendments (sewage sludge, digestate) provides a trade-off between maintaining crop yield and minimizing GHG emissions. Additionally, we could observe a strong increase in microbial communities involved in GHG consumption in all amendments, with the strongest increase associated with cover crop residue mixtures. Future research should focus on the interrelation of plants, soil, and microbes and their impact on the global warming potential in relation to applied organic amendments.
| S-EPMC6292959 | biostudies-literature
Project description:Organic-inorganic perovskite materials have attracted extensive attention for wide range of applications such as solar cells, photo detectors, and memory devices. However, the lack of stability in ambient condition prevented the perovskite materials from applying to practical applications. Here, we demonstrate resistive switching memory devices based on organic-inorganic perovskite (CH3NH3PbI3) that have been passivated using thin metal-oxide-layers. CH3NH3PbI3-based memory devices with a solution-processed ZnO passivation layer retain low-voltage operation and, on/off current ratio for more than 30 days in air. Passivation with atomic-layer-deposited (ALD) AlOx is also demonstrated. The resistive switching memory devices with an ALD AlOx passivation layer maintained reliable resistive switching for 30 d in ambient condition, but devices without the passivation layer degraded rapidly and did not show memory properties after 3 d. These results suggest that encapsulation with thin metal-oxide layers is easy and commercially-viable methods to fabricate practical memory devices, and has potential to realize memory devices with long-term stability and reliable, reproducible programmable memory characteristics.
| S-EPMC5429663 | biostudies-literature
Project description:Actinobacteria are major producers of secondary metabolites; however, it is unclear how they are distributed in the environment. DNA was extracted from forest, pasture and cultivated soils, street sediments (dust and material in place), and sediments affected by animal activity (e.g. guano, vermicompost) and characterised with two actinobacterial and a bacterial-specific 16S rDNA primer set. Amplicons (140/156) generated with the two actinobacterial-specific and amplicons (471) generated with bacterial-specific primers were analysed. Amplicons from actinobacterial-specific primer were disproportionately actinomycetal from animal-affected (soil) samples and street sediments and either verrucomicrobial (i.e. non-actinobacterial) and from a novel non-actinomycetal actinobacterial group for soils. Actinobacterial amplified ribosomal DNA restriction analysis and terminal restriction fragment length polymorphism fingerprints clustered by land use, with cultivated soils clustering apart from uncultivated soils. Actinobacterial amplicons generated with eubacterial primers were overwhelmingly from (116/126) street sediments; acidobacterial amplicons from soils (74/75). In two street samples, >90% of clones were actinomycetal. Actinomycetes are selected in terrestrial soils and sediments by cultivation, urbanisation and animal activity.
| S-EPMC3232471 | biostudies-literature
Project description:Soil microorganisms play a pivotal role in carbon mineralization and their diversity is crucial to the function of soil ecosystems. However, the effects of long-term fertilization on microbial-mediated carbon mineralization are poorly understood. To identify the relative roles of microbes in carbon mineralization of yellow paddies, we investigated the long-term fertilization effects on soil properties and microbial communities and their relationships with carbon mineralization. The treatments included: no fertilization (CK), chemical fertilizer (NPK), organic fertilizer (M), and constant organic-inorganic fertilizer (MNPK). NPK treatment significantly increased soil water content (WC), while M and MNPK treatments significantly increased the content of soil organic carbon (SOC), total nitrogen (TN), soil microbial biomass carbon (SMBC), soil microbial biomass nitrogen (SMBN), and WC. Strong increases in CO2 emissions, potential mineralized carbon, and turnover rate constant were observed in both organic-fertilizer treatments (M and MNPK), relative to the CK treatment. These changes in soil properties can be attributed to the variation in microbial communities. NPK treatment had no significant effect. Different fertilization treatments changed soil microbial community; SOC and SMBN were the most important contributors to the variance in microbial community composition. The variations in community composition did not significant influence carbon mineralization; however, carbon mineralization was significantly influenced by the abundance of several non-dominant bacteria. The results suggest that SOC, SMBN, and non-dominant bacteria (Gemmatimonadetes and Latescibacteria), have a close relationship to carbon mineralization, and should be preferentially considered in predicting carbon mineralization under long-term fertilization.
| S-EPMC6347141 | biostudies-literature
Project description:The long-term emission impacts of the nickel processing industry in the Kola Peninsula, the largest source of sulfur dioxide and heavy metals emissions in Northern Europe, have created vast technogenic barrens near the mineral industry complexes. The pace of rehabilitation using the improved remediation technologies to enhance sustainable environmental management and regional economic development is of crucial social and economic importance. In a 120-day incubation experiment, we evaluated the prospects for the restoration of two soils at different degradation stages via carbon pool regulation comparing to mineral ameliorants - NPK fertilizer, and liming agent. Organic additives used included a humic preparation based on an alkaline brown coal extract, wood-derived biochar, and peat-derived gel, supplied by mycorrhizae fungi. The results demonstrate that the selected organic amendments are suitable for restoration of acidic metal contaminated soils. Specifically, the treatments provided a measurable increase in soil carbon content, a marked decrease in acidity, a decrease in extractable metal contents, together with an enhanced nutrient uptake and vegetative growth. A stabilization effect increased from biochar to peat-gel, liming agent and humic preparation, with an accompanying increase in soil pH. Although biochar showed a reduced ability to metal stabilization, the associated treatments were the most productive. The most effective amendments in multi-metallic contaminated soils need to be able to stabilize bioavailability of metals, adjust pH to the optimum for plant growth, and regulate nutrient consumption.
| S-EPMC7841320 | biostudies-literature
Project description:The application of organic amendments to mining soils has been shown to be a successful method of restoration, improving key physicochemical soil properties. However, there is a lack of a clear understanding of the soil bacterial community taxonomic and functional changes that are brought about by these treatments. We present further metagenomic sequencing (MGS) profiling of the effects of different restoration treatments applied to degraded, arid quarry soils in southern Spain which had previously been profiled only with 16S rRNA gene (16S) and physicochemical analyses. Both taxonomic and functional MGS profiles showed clear separation of organic treatment amendments from control samples, and although taxonomic differences were quite clear, functional redundancy was higher than expected and the majority of the latter signal came from the aggregation of minor (<0.1%) community differences. Significant taxonomic differences were seen with the presumably less-biased MGS-for example, the phylum Actinobacteria and the two genera Chloracidobacterium (Acidobacteria) and Paenibacillus (Firmicutes) were determined to be major players by the MGS and this was consistent with their potential functional roles. The former phylum was much less present, and the latter two genera were either minor components or not detected in the 16S data. Mapping of reads to MetaCyc/BioCyc categories showed overall slightly higher biosynthesis and degradation capabilities in all treatments versus control soils, with sewage amendments showing highest values and vegetable-based amendments being at intermediate levels, matching higher nutrient levels, respiration rates, enzyme activities, and bacterial biomass previously observed in the treated soils. IMPORTANCE The restoration of soils impacted by human activities poses specific challenges regarding the reestablishment of functional microbial communities which will further support the reintroduction of plant species. Organic fertilizers, originating from either treated sewage or vegetable wastes, have shown promise in restoration experiments; however, we still do not have a clear understanding of the functional and taxonomic changes that occur during these treatments. We used metagenomics to profile restoration treatments applied to degraded, arid quarry soils in southern Spain. We found that the assortments of individual functions and taxa within each soil could clearly identify treatments, while at the same time they demonstrated high functional redundancy. Functions grouped into higher pathways tended to match physicochemical measurements made on the same soils. In contrast, significant taxonomic differences were seen when the treatments were previously studied with a single marker gene, highlighting the advantage of metagenomic analysis for complex soil communities.
| S-EPMC8609970 | biostudies-literature