Different Responses of Soil Bacterial and Fungal Communities to 3 Years of Biochar Amendment in an Alkaline Soybean Soil.
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ABSTRACT:
SUBMITTER: Gao W
PROVIDER: S-EPMC8187762 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Improving soil structure, fertility, and production is of major concern for establishing sustainable agroecosystems. Further research is needed to evaluate whether different methods of straw returning determine the variations of soil aggregation and the microbial community in aggregates in the long term. In this study, we comparatively investigated the effects of long-term fertilization regimes performed over six years, namely, non-fertilization (CK), chemical fertilization (CF), continuous straw return (CS), and continuous straw-derived biochar amendment (CB), on soil aggregation and bacterial communities in rice-wheat rotation systems. The results showed that straw/biochar application increased soil nutrient content and soil aggregate size distribution and stability at both 0-20 cm and 20-40 cm soil depths, compared with those of CF and CK; CB performed better than CS. CB increased bacterial community diversity and richness in 0-20 cm soil, and evenness in 0-40 cm soil (p < 0.05); CS had no significant effect on these aspects. Variations in the relative abundance of Actinobacteria, Chloroflexi, Bacteroidetes, Nitrospirae, Gemmatimonadetes, and Latescibacteria in specific aggregates confirmed the different effects of straw/biochar on bacterial community structure. The partial least squares discrimination analysis and permutation multivariate analysis of variance revealed that fertilization, aggregate size fractions, and soil depth affected the bacterial community, although their effects differed. This study suggests that CB may reduce chemical fertilizer usage and improve the sustainability of rice-wheat cropping systems over the long term, with a better overall outcome than CS.
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Project description:Fertilizer application has contributed substantially to increasing crop yield. Despite the important role of soil fungi in agricultural production, we still have limited understanding of the complex responses of fungal taxonomic and functional groups to organic and mineral fertilization in long term. Here we report the responses of the fungal communities in an alkaline soil to 30-year application of mineral fertilizer (NP), organic manure (M) and combined fertilizer (NPM) by the Illumina HiSeq sequencing and quantitative real-time PCR to target fungal internal transcribed spacer (ITS) genes. The results show: (1) compared to the unfertilized soil, fertilizer application increased fungal diversity and ITS gene copy numbers, and shifted fungal community structure. Such changes were more pronounced in the M and NPM soils than in the NP soil (except for fungal diversity), which can be largely attributed to the manure induced greater increases in soil total organic C, total N and available P. (2) Compared to the unfertilized soil, the NP and NPM soils reduced the proportion of saprotrophs by 40%, the predominant taxa of which may potentially affect cellulose decomposition. (3) Indicator species analysis suggested that the indicator operational taxonomic units (OTUs) in the M soil occupied 25.6% of its total community, but that only accounted for 0.9% in the NP soil. Our findings suggest that fertilization-induced changes of total fungal community were more responsive to organic manure than mineral fertilizer. The reduced proportion of cellulose decomposition-related saprotrophs in mineral fertilizer treatments may potentially contribute to increasing their soil C stocks.
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Project description:Soybean continuous cropping (SC) leads to continuous cropping obstacles, and soil-borne fungal diseases occur frequently. Rotation can alleviate continuous cropping obstacles. However, the long-term effects of continuous cropping and rotation on the structure and function of the fungal community in soil are not clear. In this study, five cropping systems, SC, fallow (CK), fallow-soybean (FS), corn-soybean (CS), and wheat-soybean (WS), were implemented in the long-term continuous cropping area of soybean. After 13 years of planting, high-throughput sequencing was used to evaluate the structure and diversity of soil fungal communities and to study the relationship between fungal communities and soil environmental factors. The results showed that the abundance and diversity of fungal flora in SC soil were the highest. There were significant differences in the formation of soil fungal communities between soybean continuous cropping and the other treatments. There were 355 species of endemic fungi in SC soil. There were 231 and 120 endemic species in WS and CS, respectively. The relative abundance of the potential pathogens Lectera, Gibberella, and Fusarium in the SC treatment soil was significantly high, and the abundance of all potential pathogens in CK was significantly the lowest. The abundance of Lectera and Fusarium in CS was significantly the lowest. There was a positive correlation between potential pathogens in the soil. The relative abundance of potential pathogens in the soil was significantly positively correlated with the relative abundance of Ascomycetes and negatively correlated with the relative abundance of Basidiomycetes. Potential pathogenic genera had a significant negative correlation with soil OM, available Mn, K and soil pH and a significant positive correlation with the contents of soil available Cu, Fe, and Zn. In general, the fungal communities of SC, FS, WS, and CS were divided into one group, which was significantly different from CK. WS and CS were more similar in fungal community structure. The CK and CS treatments reduced the relative abundance of soil fungi and potential pathogens. Our study shows that SC and FS lead to selective stress on fungi and pathogenic fungi and lead to the development of fungal community abundance and diversity, while CK and CS can reduce this development, which is conducive to plant health.
| S-EPMC9260669 | biostudies-literature
Project description:Soil microorganisms play a crucial role in organic matter decomposition and nutrient cycling in cropping systems. Compared to bacteria, fungal community composition and the role of fungi in organic matter decomposition and nutrient cycling in agro-systems are, however, elusive. Silicon (Si) fertilization is essential to improve agronomic performance of rice. The effects of the Si fertilizer application on the soil fungal community composition and their contribution in soil organic matter (SOM) decomposition are not yet studied. We investigated the short-term (120 days) slag silicate fertilizer (SSF) amendment impacts on plant photosynthesis and soil biochemical changes, soil fungal communities (assessed by ITS amplicon illumina sequencing), hydrolytic and oxidase enzyme activities, CO2 emissions, and bacterial and fungal respiration in diverse eco-geographic races of rice (Oryza sativa L.), i.e., Japonica rice (O. sativa japonica) and Indica rice (O. sativa indica). The short-term SSF amendment significantly increased the relative abundance of saprotrophic fungi and accelerated organic matter decomposition. The increase in saprotrophic fungi was mostly attributed to greater labile C availability and Si availability. Higher organic matter decomposition was accompanied by an increase in both hydrolytic and oxidative enzyme activities in response to the SSF amendment. The stimulation of oxidative enzyme activities was explained by an increase in root oxidase activities and iron redox cycling, whereas stimulation of hydrolytic enzyme activities was explained by the greater labile C availability under SSF fertilization. We conclude that the short-term SSF amendment increases saprotrophic fungal communities and soil hydrolytic and oxidative enzyme activities, which in turn stimulates SOM mineralization and thus could have negative feedback impacts on soil C storage in submerged rice paddies.
| S-EPMC6932956 | biostudies-literature
Project description:The soil microbiome is a complex living network that plays essential roles in agricultural systems, regardless of the level of intensification. However, the effects of agricultural management on the soil microbiome and the association with plant productivity remain largely unclear. Here, we studied the responses of three soil systems displaying distinct levels of agriculture intensiveness (i.e., natural, organic, and conventional soil management regimes) to experimentally manipulated organic farming amendments (i.e., dung and earthworms). We aimed at (i) identifying the effect on plant productivity and (ii) elucidating the degree of shifts in bacterial communities in response to the applied organic amendments. We found plant productivity to be lower with increasing agricultural intensification. Bacterial communities shifted distinctively for each soil management regime to the organic amendments applied. In brief, greater changes were observed in the Conventional management comparatively to the Organic and Natural management, an effect largely driven by dung addition. Moreover, we found evidence that the level of agricultural intensiveness also affects the timespan for these shifts. For instance, while the Natural system reached a relatively stable community composition before the end of the experiment, treatments on the conventional soil management regime did not. Random forest analyses further revealed an increasing impact of introduced taxa from dung addition aligned with increasing agricultural intensification. These analyses suggested that earthworms regulate the introduction of species from dung into the soil bacterial community. Collectively, our results contribute to a better understanding of the outcomes of organic amendments on soils under distinct levels of agriculture intensiveness, with implications for further development in soil restorations practices.
| S-EPMC6220598 | biostudies-literature
Project description:Biochar amendment can influence the abundance, activity, and community structure of soil microbes. However, scare information is present about the effect of the combined application of biochar with synthetic nitrogen (N) fertilizer under paddy field condition. We aimed to resolve this research gap in rice field conditions through different biochar in combination with N fertilizers on soil nutrients, soil microbial communities, and rice grain yield. The present study involves eight treatments in the form of biochar (0, 10, 20, and 30 t ha-1) and N (135 and 180 kg ha-1) fertilizer amendments. The soil microbial communities were characterized using high-throughput sequencing of 16S and Internal transcribed spacer (ITS) ribosomal RNA gene amplicons. Experiential findings showed that the treatments had biochar amendments along with N fertilizer significantly advanced soil pH, soil organic carbon (SOC), total nitrogen (TN), soil microbial carbon (SMBC), soil microbial nitrogen (SMBN), and rice grain yield in comparison to sole N application. Furthermore, in comparison with control in the first year (2019), biochar amendment mixed with N fertilizer had more desirable relative abundance of microorganism, phyla Acidobacteria, Actinobacteria, Proteobacteria, and Verrucomicrobia with better relative abundance ranging from 8.49, 4.60, 46.30, and 1.51% in T7, respectively. Similarly, during 2020, bacteria phyla Acidobacteria, Actinobacteria, Bacteroidetes, Gemmatimonadetes, Planctomycetes, and Verrucomicrobia were resulted in higher and ranging from 8.69, 5.18, 3.5, 1.9, 4.0, and 1.6%, in biochar applied treatments, respectively, as compared to control (T1). Among the treatments, Sphingopyxis and Thiobacillus bacterial genus were in higher proportion in T7 and T3, respectively, as compared to other treatments and Bacillus was higher in T6. Interestingly, biochar addition significantly decreased the soil fungi phyla Ascomycota, Basidiomycota, Chytridiomycota, and Rozellomycota, in 2020 as compared to 2019. Whereas biochar addition to soil decreased Echria, Kohlmeyeriopsis, and Westerdykella fungal genus as compared to non-biochar treatments. The redundancy analysis showed that soil biochemical traits were positively correlated with soil bacteria. In addition, correlation analysis showed that soil bacteria including Acidobacteria, Actinobacteria, Bacteroidetes, Planctomycetes, and Proteobacteria strongly correlated with rice grain yield. This study demonstrated that soil nutrients and bacteria contribute to an increase in rice yield in combined biochar amendment with lower N treatments.
| S-EPMC8984124 | biostudies-literature
Project description:The functions and interactions of individual microbial populations and their genes in agricultural soils amended with biochar remain elusive but are crucial for a deeper understanding of nutrient cycling and carbon (C) sequestration. In this study, we coupled DNA stable isotope probing (SIP) with shotgun metagenomics in order to target the active community in microcosms which contained soil collected from biochar-amended and control plots under napiergrass cultivation. Our analyses revealed that the active community was composed of high-abundant and low-abundant populations, including Actinobacteria, Proteobacteria, Gemmatimonadetes, and Acidobacteria. Although biochar did not significantly shift the active taxonomic and functional communities, we found that the narG (nitrate reductase) gene was significantly more abundant in the control metagenomes. Interestingly, putative denitrifier genomes generally encoded one gene or a partial denitrification pathway, suggesting denitrification is typically carried out by an assembly of different populations within this Oxisol soil. Altogether, these findings indicate that the impact of biochar on the active soil microbial community are transient in nature. As such, the addition of biochar to soils appears to be a promising strategy for the long-term C sequestration in agricultural soils, does not impart lasting effects on the microbial functional community, and thus mitigates un-intended microbial community shifts that may lead to fertilizer loss through increased N cycling.
| S-EPMC7717982 | biostudies-literature
Project description:BackgroundCultivars of bahiagrass (Paspalum notatum Flüggé) are widely used for pasture in the Southeastern USA. Soil microbial communities are unexplored in bahiagrass and they may be cultivar-dependent, as previously proven for other grass species. Understanding the influence of cultivar selection on soil microbial communities is crucial as microbiome taxa have repeatedly been shown to be directly linked to plant performance.ObjectivesThis study aimed to determine whether different bahiagrass cultivars interactively influence soil bacterial and fungal communities.MethodsSix bahiagrass cultivars ('Argentine', 'Pensacola', 'Sand Mountain', 'Tifton 9', 'TifQuik', and 'UF-Riata') were grown in a randomized complete block design with four replicate plots of 4.6 × 1.8 m per cultivar in a Rhodic Kandiudults soil in Northwest Florida, USA. Three soil subsamples per replicate plot were randomly collected. Soil DNA was extracted and bacterial 16S ribosomal RNA and fungal ribosomal internal transcribed spacer 1 genes were amplified and sequenced with one Illumina Miseq Nano.ResultsThe soil bacterial and fungal community across bahiagrass cultivars showed similarities with communities recovered from other grassland ecosystems. Few differences in community composition and diversity of soil bacteria among cultivars were detected; none were detected for soil fungi. The relative abundance of sequences assigned to nitrite-oxidizing Nitrospira was greater under 'Sand Mountain' than 'UF-Riata'. Indicator species analysis revealed that several bacterial and fungal indicators associated with either a single cultivar or a combination of cultivars are likely to be plant pathogens or antagonists.ConclusionsOur results suggest a low impact of plant cultivar choice on the soil bacterial community composition, whereas the soil fungal community was unaffected. Shifts in the relative abundance of Nitrospira members in response to cultivar choice may have implications for soil N dynamics. The cultivars associated with presumptive plant pathogens or antagonists indicates that the ability of bahiagrass to control plant pathogens may be cultivar-dependent, however, physiological studies on plant-microbe interactions are required to confirm this presumption. We therefore suggest that future studies should explore the potential of different bahiagrass cultivars on plant pathogen control, particularly in sod-based crop rotation.
| S-EPMC6545100 | biostudies-literature
Project description:IntroductionContinuous nitrogen deposition increases the nitrogen content of terrestrial ecosystem and affects the geochemical cycle of soil nitrogen. Forest-grassland ecotone is the interface area of forest and grassland and is sensitive to global climate change. However, the structure composition and diversity of soil microbial communities and their relationship with soil environmental factors at increasing nitrogen deposition have not been sufficiently studied in forest-grassland ecotone.MethodsIn this study, experiments were carried out with four nitrogen addition treatments (0 kgN·hm-2·a-1, 10 kgN·hm-2·a-1, 20 kgN·hm-2·a-1 and 40 kgN·hm-2·a-1) to simulate nitrogen deposition in a forest-grassland ecotone in northwest Liaoning Province, China. High-throughput sequencing and qPCR technologies were used to analyze the composition, structure, and diversity characteristics of the soil microbial communities under different levels of nitrogen addition.Results and discussionThe results showed that soil pH decreased significantly at increasing nitrogen concentrations, and the total nitrogen and ammonium nitrogen contents first increased and then decreased, which were significantly higher in the N10 treatment than in other treatments (N:0.32 ~ 0.48 g/kg; NH4+-N: 11.54 ~ 13 mg/kg). With the increase in nitrogen concentration, the net nitrogen mineralization, nitrification, and ammoniation rates decreased. The addition of nitrogen had no significant effect on the diversity and structure of the fungal community, while the diversity of the bacterial community decreased significantly at increasing nitrogen concentrations. Ascomycetes and Actinomycetes were the dominant fungal and bacterial phyla, respectively. The relative abundance of Ascomycetes was negatively correlated with total nitrogen content, while that of Actinomycetes was positively correlated with soil pH. The fungal community diversity was significantly negatively correlated with nitrate nitrogen, while the diversity of the bacterial community was significantly positively correlated with soil pH. No significant differences in the abundance of functional genes related to soil nitrogen transformations under the different treatments were observed. Overall, the distribution pattern and driving factors were different in soil microbial communities in a forest-grassland ecotone in northwest Liaoning. Our study enriches research content related to factors that affect the forest-grassland ecotone.
| S-EPMC10510407 | biostudies-literature
Project description:This study determined the interactive effects of biochar and lead toxicity on the soil microbial community in a phytoextraction experiment. Arranged with a completely randomized design in a greenhouse, banana liners were planted singly in a sandy soil spiked with Pb(NO3)2 at 0, 400 and 1200 mg kg-1 and amended with bamboo biochar (pyrolyzing at 600 °C) at 0, 1, 3%. Soil samples were taken from triplicated pots five months after planting and measured for (i) content of lead and organic carbon; (ii) lead speciation; and (iii) microbial community composition through 16S rRNA gene sequencing. DNA sequencing results showed that lead and biochar treatments had significant individual and interactive effects on soil microbial dissimilarities from taxonomic levels of phyla to genera. While some specific taxa were lead resistant, biochar addition apparently alleviated lead toxicity and increased their richness (e.g., Alkanibacter, Muciaginibacter, Burkholderiaceae, and Beggiatoaceae). Soil analysis data indicated that biochar not only helped retain more lead in the soil matrix but created a soil environment inducive for transformation of lead into highly insoluble pyromorphite. This study highlights the effectiveness of biochar for lead remediation and the sensitivity of soil microorganisms in sensing changes in soil environment and lead bioavailability.
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