scholarly journals Biochar and compost effects on soil microbial communities and nitrogen induced respiration in turfgrass soils

PLoS ONE ◽  
2020 ◽  
Vol 15 (11) ◽  
pp. e0242209
Author(s):  
Muhammad Azeem ◽  
Lauren Hale ◽  
Jonathan Montgomery ◽  
David Crowley ◽  
Milton E. McGiffen
Keyword(s):  
Microbial Community ◽  
Soil Microbial Communities ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Community Structures ◽  
Soil Microbial Community Structure ◽  
Amended Soils ◽  
Soil Microbial ◽  
Compost Amendment ◽  
Microbial Community Structures

We examined the effect of a labile soil amendment, compost, and recalcitrant biochar on soil microbial community structure, diversity, and activity during turfgrass establishment. Two application rates of biochar (B1 at 12.5 t ha-1and B2 at 25 t ha-1), a 5 centimeter (cm) green waste compost treatment (CM) in top soil, a treatment with 12.5 t ha-1 biochar and 5 cm compost (B1+CM), and an unamended control (CK) treatment were prepared and seeded with tall fescue. Overall, results of phospholipid fatty acid analysis (PLFA) profiling and Illumina high-throughput sequencing of 16S rRNA genes amplified from soil DNA revealed significant shifts in microbial community structures in the compost amended soils whereas in biochar amended soils communities were more similar to the control, unamended soil. Similarly, increases in enzymatic rates (6–56%) and nitrogen-induced respiration (94%) were all largest in compost amended soils, with biochar amended soils exhibiting similar patterns to the control soils. Both biochar and compost amendments impacted microbial community structures and functions, but compost amendment, whether applied alone or co-applied with biochar, exhibited the strongest shifts in the microbial community metrics examined. Our results suggest application of compost to soils in need of microbiome change (reclamation projects) or biochar when the microbiome is functioning and long-term goals such as carbon sequestration are more desirable.

Microbial community analysis of soils under different soybean cropping regimes in the Argentinean south-eastern Humid Pampas

2021 ◽  
Author(s):  
Gabriela Fernandez-Gnecco ◽  
Kornelia Smalla ◽  
Lorrie Maccario ◽  
Søren J Sørensen ◽  
Pablo Barbieri ◽  
...  
Keyword(s):  
Microbial Community ◽  
Cover Crops ◽  
Microbial Community Composition ◽  
Soil Microbial Communities ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Temporal Shift ◽  
Soil Microbial ◽  
No Till

Abstract Soil microbial communities are key players of ecosystem processes and important for crop and soil health. The Humid Pampas region in Argentina concentrates 75% of the national soybean production, which is based on intensive use of agrochemicals, monocropping and no-till. A long-term field experiment under no-till management in the southeast of the Argentinean Pampas provides a unique opportunity to compare soybean under monocropping with cultivation including alternating cover crops or in a three-phase rotation. We hypothesized that cropping regimes and season affect soil microbial community composition and diversity. Amplicon sequencing of 16S rRNA genes and internal transcribed spacer fragments showed a stronger microbial seasonal dynamic in conservation regimes compared to monocropping. In addition, several bacterial (e.g. Catenulispora, Streptomyces and Bacillus) and fungal genera (e.g. Exophiala) with cropping regime-dependent differential relative abundances were identified. Despite a temporal shift in microbial and chemical parameters, this study shows that long-term cropping regimes shaped the soil microbiota. This might have important implications for soil quality and soybean performance and should therefore be considered in the development of sustainable agricultural managements.

Linking nitrification characteristic and microbial community structures in integrated fixed film activated sludge reactor by high-throughput sequencing

2016 ◽  
Vol 74 (6) ◽  
pp. 1354-1364 ◽  
Author(s):  
Bin Dong ◽  
Jie Tan ◽  
Yang Yang ◽  
Zishan Pang ◽  
Zhongtian Li ◽  
...  
Keyword(s):  
Microbial Community ◽  
Activated Sludge ◽  
Ammonia Removal ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Nitrifying Bacteria ◽  
Ammonia Oxidizing Bacteria ◽  
Community Structures ◽  
Microbial Community Structures ◽  
Fixed Film

The primary goal of this study is to investigate ammonia removal, abundance of nitrifying bacteria and microbial community structures in a laboratory-scale integrated fixed film activated sludge (IFAS) reactor. The results of Illumina MiSeq sequencing based on 16S rRNA genes showed Proteobacteria and Bacteroidetes were the dominant phyla in both biofilm and suspended sludge samples in the IFAS reactor. The dominant ammonia-oxidizing bacteria (AOB) species was Nitrosomonas and the dominant nitrite-oxidizing bacteria species was Nitrospira. The contribution of biofilm to ammonia removal increased from 4.0 ± 0.9% to 37.0 ± 2% when the temperature decreased from 25 °C to 10 °C. The real-time polymerase chain reaction (PCR) result showed the abundance of AOB in suspended sludge was higher than that in biofilm at the same time. However, nitrification is more dependent on attached growth than on suspended growth in the IFAS reactor at 15 °C and 10 °C and the abundance of AOB in biofilm was also higher than that in suspended sludge. The more robust ammonia removal rate at low temperatures by biofilm contributed to the relatively stable ammonia removal, and biofilm attached on carriers in the IFAS reactor is advantageous for nitrification in low-temperature environment.

scholarly journals Diversity and composition of the Panax ginseng rhizosphere microbiome in various cultivation modesand ages

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Ai-Zi Tong ◽  
Wei Liu ◽  
Qiang Liu ◽  
Guang-Qing Xia ◽  
Jun-Yi Zhu
Keyword(s):  
Microbial Community ◽  
Microbial Diversity ◽  
Panax Ginseng ◽  
Soil Microbial Communities ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Continuous Cropping ◽  
Soil Microbial Diversity ◽  
Soil Microbial ◽  
Soil Borne Pathogens

Abstract Background Continuous cropping of ginseng (Panax ginseng Meyer) cultivated in farmland for an extended period gives rise to soil-borne disease. The change in soil microbial composition is a major cause of soil-borne diseases and an obstacle to continuous cropping. The impact of cultivation modes and ages on the diversity and composition of the P. ginseng rhizosphere microbial community and technology suitable for cropping P. ginseng in farmland are still being explored. Methods Amplicon sequencing of bacterial 16S rRNA genes and fungal ITS regions were analyzed for microbial community composition and diversity. Results The obtained sequencing data were reasonable for estimating soil microbial diversity. We observed significant variations in richness, diversity, and relative abundances of microbial taxa between farmland, deforestation field, and different cultivation years. The bacterial communities of LCK (forest soil where P. ginseng was not grown) had a much higher richness and diversity than those in NCK (farmland soil where P. ginseng was not grown). The increase in cultivation years of P. ginseng in farmland and deforestation field significantly changed the diversity of soil microbial communities. In addition, the accumulation of P. ginseng soil-borne pathogens (Monographella cucumerina, Ilyonectria mors-panacis, I. robusta, Fusarium solani, and Nectria ramulariae) varied with the cropping age of P. ginseng. Conclusion Soil microbial diversity and function were significantly poorer in farmland than in the deforestation field and were affected by P. ginseng planting years. The abundance of common soil-borne pathogens of P. ginseng increased with the cultivation age and led to an imbalance in the microbial community.

scholarly journals STRUKTUR KOMUNITAS MIKROBA TANAH DAN IMPLIKASINYA DALAM MEWUJUDKAN SISTEM PERTANIAN BERKELANJUTAN

el–Hayah ◽  
2012 ◽  
Vol 1 (4) ◽  
Author(s):  
Prihastuti Prihastuti
Keyword(s):  
Microbial Community ◽  
Microbial Diversity ◽  
Microbial Communities ◽  
Soil Microbial Community ◽  
Soil Microbial Communities ◽  
Organic Soil ◽  
Plant Type ◽  
Soil Microbial Community Structure ◽  
Soil Microbial ◽  
Wide Range

<p>Soils are made up of organic and an organic material. The organic soil component contains all the living creatures in the soil and the dead ones in various stages of decomposition.  Biological activity in soil helps to recycle nutrients, decompose organic matter making nutrient available for plant uptake, stabilize humus, and form soil particles.<br />The extent of the diversity of microbial in soil is seen to be critical to the maintenance of soil health and quality, as a wide range of microbial is involved in important soil functions.  That ecologically managed soils have a greater quantity and diversity of soil microbial. The two main drivers of soil microbial community structure, i.e., plant type and soil type, are thought to exert their function in a complex manner. The fact that in some situations the soil and in others the plant type is the key factor determining soil microbial diversity is related to their complexity of the microbial interactions in soil, including interactions between microbial and soil and microbial and plants. <br />The basic premise of organic soil stewardship is that all plant nutrients are present in the soil by maintaining a biologically active soil environment. The diversity of microbial communities has on ecological function and resilience to disturbances in soil ecosystems. Relationships are often observed between the extent of microbial diversity in soil, soil and plant quality and ecosystem sustainability. Agricultural management can be directed toward maximizing the quality of the soil microbial community in terms of disease suppression, if it is possible to shift soil microbial communities.</p><p>Keywords: structure, microbial, implication, sustainable agriculture<br /><br /></p>

scholarly journals Changes in the Soil Microbiome in Eggplant Monoculture Revealed by High-Throughput Illumina MiSeq Sequencing as Influenced by Raw Garlic Stalk Amendment

2019 ◽  
Vol 20 (9) ◽  
pp. 2125 ◽  
Author(s):  
Muhammad Imran Ghani ◽  
Ahmad Ali ◽  
Muhammad Jawaad Atif ◽  
Muhammad Ali ◽  
Bakht Amin ◽  
...  
Keyword(s):  
Microbial Community ◽  
High Throughput ◽  
Soil Microbial Communities ◽  
Illumina Miseq ◽  
Soil Microbiome ◽  
Plant Residues ◽  
Illumina Miseq Sequencing ◽  
Miseq Sequencing ◽  
Community Structures ◽  
Microbial Community Structures

The incorporation of plant residues into soil can be considered a keystone sustainability factor in improving soil structure function. However, the effects of plant residue addition on the soil microbial communities involved in biochemical cycles and abiotic stress phenomena are poorly understood. In this study, experiments were conducted to evaluate the role of raw garlic stalk (RGS) amendment in avoiding monoculture-related production constraints by studying the changes in soil chemical properties and microbial community structures. RGS was applied in four different doses, namely the control (RGS0), 1% (RGS1), 3% (RGS2), and 5% (RGS3) per 100 g of soil. The RGS amendment significantly increased soil electrical conductivity (EC), N, P, K, and enzyme activity. The soil pH significantly decreased with RGS application. High-throughput Illumina MiSeq sequencing revealed significant alterations in bacterial community structures in response to RGS application. Among the 23 major taxa detected, Anaerolineaceae, Acidobacteria, and Cyanobacteria exhibited an increased abundance level. RGS2 increased some bacteria reported to be beneficial including Acidobacteria, Bacillus, and Planctomyces (by 42%, 64%, and 1% respectively). Furthermore, internal transcribed spacer (ITS) fungal regions revealed significant diversity among the different treatments, with taxa such as Chaetomium (56.2%), Acremonium (4.3%), Fusarium (4%), Aspergillus (3.4%), Sordariomycetes (3%), and Plectosphaerellaceae (2%) showing much abundance. Interestingly, Coprinellus (14%) was observed only in RGS-amended soil. RGS treatments effectively altered soil fungal community structures and reduced certain known pathogenic fungal genera, i.e., Fusarium and Acremonium. The results of the present study suggest that RGS amendment potentially affects the microbial community structures that probably affect the physiological and morphological attributes of eggplant under a plastic greenhouse vegetable cultivation system (PGVC) in monoculture.

scholarly journals Transformation of Soil Microbial Community Structure and Rhizoctonia-Suppressive Potential in Response to Apple Roots

1999 ◽  
Vol 89 (10) ◽  
pp. 920-927 ◽  
Author(s):  
Mark Mazzola
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Fungal Community ◽  
Soil Microbial Community ◽  
Burkholderia Cepacia ◽  
Soil Microbial Communities ◽  
Apple Trees ◽  
Soil Microbial Community Structure ◽  
Soil Microbial ◽  
Orchard Soil

Changes in the composition of soil microbial communities and relative disease-suppressive ability of resident microflora in response to apple cultivation were assessed in orchard soils from a site possessing trees established for 1 to 5 years. The fungal community from roots of apple seedlings grown in noncultivated orchard soil was dominated by isolates from genera commonly considered saprophytic. Plant-pathogenic fungi in the genera Phytophthora, Pythium, and Rhizoctonia constituted an increasing proportion of the fungal community isolated from seedling roots with increasing orchard block age. Bacillus megaterium and Burkholderia cepacia dominated the bacterial communities recovered from noncultivated soil and the rhizosphere of apple seedlings grown in orchard soil, respectively. Populations of the two bacteria in their respective habitats declined dramatically with increasing orchard block age. Lesion nematode populations did not differ among soil and root samples from orchard blocks of different ages. Similar changes in microbial communities were observed in response to planting noncultivated orchard soil to five successive cycles of ‘Gala’ apple seedlings. Pasteurization of soil had no effect on apple growth in noncultivated soil but significantly enhanced apple growth in third-year orchard block soil. Seedlings grown in pasteurized soil from the third-year orchard block were equal in size to those grown in noncultivated soil, demonstrating that suppression of plant growth resulted from changes in the composition of the soil microbial community. Rhizoctonia solani anastomosis group 5 (AG 5) had no effect on growth of apple trees in noncultivated soil but significantly reduced the growth of apple trees in soil from third-year orchard soil. Changes in the ability of the resident soil microflora to suppress R. solani AG 5 were associated with reductions in the relative populations of Burkholderia cepacia and Pseudomonas putida in the rhizosphere of apple.

scholarly journals Organic Mulching Can Suppress Litchi Downy Blight Through Modification of Soil Microbial Community Structure and Functional Potentials

2021 ◽  
Author(s):  
Dandan Xu ◽  
Jinfeng Ling ◽  
Pinggen Xi ◽  
Yani Zeng ◽  
Jianfan Zhang ◽  
...  
Keyword(s):  
Microbial Community ◽  
Soil Microbial Community ◽  
Management Practice ◽  
Disease Incidence ◽  
Soil Microbial Communities ◽  
Community Diversity ◽  
Soil Microbial Diversity ◽  
Soil Microbial Community Structure ◽  
Soil Microbial ◽  
Pests And Diseases

Abstract Organic mulching is an important management practice in agricultural production to improve soil quality, control crop pests and diseases and increase the biodiversity of soil microecosystem. However, the information about soil microbial diversity and composition in litchi plantation response to organic mulching and its attribution to litchi downy blight severity was limited. This study aimed to investigate the effect of organic mulching on litchi downy blight, and evaluate the biodiversity and antimicrobial potential of soil microbial community of litchi plantation soils under organic mulching. Our results showed that organic mulching could decrease the disease incidence in the litchi plantation. As a result of high-throughput 16S rRNA and ITS rDNA gene illumine sequencing, higher bacterial and fungal community diversity indexes were found in organic mulching soils, the relative abundance of norank f norank o Vicinamibacterales, norank f Vicinamibacteraceae, norank f Xanthobacteraceae, Unclassified c sordariomycetes, Aspergillus and Thermomyces were significant more than that in control soils. Isolation and analysis of antagonistic microorganism showed that 29 antagonistic bacteria strains and 37 antagonistic fungi strains were unique for mulching soils. Thus, we believe that organic mulching has a positive regulatory effect on the litchi downy blight and the soil microbial communities, and so, is more suitable for litchi plantation.

Long-term use of green manure legume and chemical fertiliser affect soil bacterial community structures but not the rate of soil nitrate decrease when excess carbon and nitrogen are applied

Soil Research ◽  
2017 ◽  
Vol 55 (6) ◽  
pp. 524 ◽  
Author(s):  
Misato Toda ◽  
Yoshitaka Uchida
Keyword(s):  
Microbial Community ◽  
Rice Straw ◽  
Soil Microbial Community ◽  
Green Manure ◽  
Community Structures ◽  
Hairy Vetch ◽  
Soil Microbial ◽  
Microbial Community Structures ◽  
Chemical Fertiliser

Legumes add not only nitrogen (N), but also carbon (C) to soils, so their effects on the soil microbial community may be different from those of chemical fertiliser. Soil microbes often compete with plants for N when excess C is applied due to their increased N immobilisation potentials and denitrification. In the present study we evaluated the effects of the 9-year use of a green manure legume (hairy vetch; Vicia villosa) in a greenhouse tomato system on soil microbial community structures as well as on the decrease of nitrate when rice straw was incorporated into the soil. Soil microbial community structures and their diversity were altered by the long-term use of legumes. The ratios of Acidobacteria, Gemmatimonadetes and Proteobacteria increased in the hairy vetch soils. The rates of decrease in nitrate were similar in soils with a history of chemical fertiliser and hairy vetch, following the addition of rice straw. In addition, during incubation with added rice straw, the difference between the two soil microbial community structures became less clear within 2 weeks. Thus, we conclude that even though growing a green manure legume changed soil bacterial community structures, this did not result in relatively faster loss of available N for plants when rice straw was added to the soils.

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