Alteration of crop rotation in continuous Pinellia ternate cropping soils profiled via fungal ITS amplicon sequencing

2019 ◽  
Vol 68 (6) ◽  
pp. 522-529 ◽  
Author(s):  
Z. He ◽  
H. Chen ◽  
L. Liang ◽  
J. Dong ◽  
Z. Liang ◽  
...  
Keyword(s):  
Crop Rotation ◽  
Amplicon Sequencing ◽  
Fungal Its

scholarly journals Limited added value of fungal ITS amplicon sequencing in the study of bovine abortion

Heliyon ◽  
2018 ◽  
Vol 4 (11) ◽  
pp. e00915 ◽  
Author(s):  
Sara Vidal ◽  
Bernd W. Brandt ◽  
Martina Dettwiler ◽  
Carlos Abril ◽  
Jenny Bressan ◽  
...  
Keyword(s):  
Amplicon Sequencing ◽  
Added Value ◽  
Bovine Abortion ◽  
Fungal Its

Preparation of Fungal ITS Amplicons from Soil Samples for Illumina Amplicon Sequencing v1 (protocols.io.nmgdc3w)

protocols.io ◽  
2018 ◽  
Author(s):  
Loreen Sommermann ◽  
Joerg Geistlinger ◽  
Jessica Zwanzig ◽  
Ingo Schellenberg
Keyword(s):  
Amplicon Sequencing ◽  
Soil Samples ◽  
Fungal Its ◽  
Illumina Amplicon Sequencing

scholarly journals Fungal community profiles in agricultural soils of a long-term field trial under different tillage, fertilization and crop rotation conditions analyzed by high-throughput ITS-amplicon sequencing

PLoS ONE ◽  
2018 ◽  
Vol 13 (4) ◽  
pp. e0195345 ◽  
Author(s):  
Loreen Sommermann ◽  
Joerg Geistlinger ◽  
Daniel Wibberg ◽  
Annette Deubel ◽  
Jessica Zwanzig ◽  
...  
Keyword(s):  
Crop Rotation ◽  
High Throughput ◽  
Fungal Community ◽  
Field Trial ◽  
Agricultural Soils ◽  
Amplicon Sequencing ◽  
Term Field

scholarly journals A Two-Step PCR Protocol Enabling Flexible Primer Choice and High Sequencing Yield for Illumina MiSeq Meta-Barcoding

Agronomy ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1274
Author(s):  
Ko-Hsuan Chen ◽  
Reid Longley ◽  
Gregory Bonito ◽  
Hui-Ling Liao
Keyword(s):  
Illumina Miseq ◽  
Amplicon Sequencing ◽  
Agricultural Systems ◽  
Specific Primers ◽  
Community Discovery ◽  
16S Ribosomal Dna ◽  
Genomic Regions ◽  
Internal Transcribed Spacer Rdna ◽  
Fungal Its ◽  
Illumina Amplicon Sequencing

High-throughput amplicon sequencing that primarily targets the 16S ribosomal DNA (rDNA) (for bacteria and archaea) and the Internal Transcribed Spacer rDNA (for fungi) have facilitated microbial community discovery across diverse environments. A three-step PCR that utilizes flexible primer choices to construct the library for Illumina amplicon sequencing has been applied to several studies in forest and agricultural systems. The three-step PCR protocol, while producing high-quality reads, often yields a large number (up to 46%) of reads that are unable to be assigned to a specific sample according to its barcode. Here, we improve this technique through an optimized two-step PCR protocol. We tested and compared the improved two-step PCR meta-barcoding protocol against the three-step PCR protocol using four different primer pairs (fungal ITS: ITS1F-ITS2 and ITS1F-ITS4, and bacterial 16S: 515F-806R and 341F-806R). We demonstrate that the sequence quantity and recovery rate were significantly improved with the two-step PCR approach (fourfold more read counts per sample; determined reads ≈90% per run) while retaining high read quality (Q30 > 80%). Given that synthetic barcodes are incorporated independently from any specific primers, this two-step PCR protocol can be broadly adapted to different genomic regions and organisms of scientific interest.

scholarly journals Non-biological synthetic spike-in controls and the AMPtk software pipeline improve mycobiome data

2017 ◽  
Author(s):  
Jonathan M Palmer ◽  
Michelle A Jusino ◽  
Mark T Banik ◽  
Daniel L Lindner
Keyword(s):  
Data Analysis ◽  
Amplicon Sequencing ◽  
Variable Length ◽  
Its Sequences ◽  
Synthetic Control ◽  
Mock Community ◽  
Software Pipeline ◽  
Sequencing Platforms ◽  
Fungal Its ◽  
Mock Communities

High throughput amplicon sequencing (HTAS) of conserved DNA regions is a powerful technique to characterize microbial communities. Recently, spike-in mock communities have been used to measure accuracy of sequencing platforms and data analysis pipelines. To assess the ability of sequencing platforms and data processing pipelines using fungal ITS amplicons, we created two ITS spike-in control mock communities composed of cloned DNA in plasmids: a biological mock community (BioMock), consisting of ITS sequences from fungal taxa, and a synthetic mock community (SynMock), consisting of non-biological ITS-like sequences. Using these spike-in controls we show that: 1) a non-biological synthetic control (e.g., SynMock) is the best solution for parameterizing bioinformatics pipelines, 2) pre-clustering steps for variable length amplicons are critically important, 3) a major source of bias is attributed to initial PCR reactions and thus HTAS read abundances are typically not representative of starting values. We developed AMPtk, a versatile software solution equipped to deal with variable length amplicons and quality filter HTAS data based on spike-in controls. While we describe herein a non-biological synthetic mock community for ITS sequences, the concept and AMPtk software can be widely applied to any HTAS dataset to improve data quality.

Crop rotations with clover and their productivity

2020 ◽  
Author(s):  
Ol'ga Gladysheva ◽  
Oksana Artyuhova ◽  
Vera Svirina
Keyword(s):  
Forest Soil ◽  
Crop Rotation ◽  
Gray Forest Soil ◽  
Arable Land ◽  
Perennial Grasses ◽  
Crop Rotations ◽  
Field Crop ◽  
Pure Steam ◽  
Positive Effect

The results of long-term research in experiments with crop rotations with different clover saturation are presented. It is shown that the cluster has a positive effect on the main indicators of vegetation of dark-gray forest soil. The introduction of two fields of perennial grasses into the six-field crop rotation significantly increases both the humus reserves and increases the productivity of arable land by 1.5–2 times compared to the crop rotation with a field of pure steam.

Modes of agricultural use, productivity and fertility of developed lowland peat soils

2020 ◽  
Author(s):  
Aleksandr Glubokovskih
Keyword(s):  
Crop Rotation ◽  
Peat Soil ◽  
Perennial Grasses ◽  
Peat Soils ◽  
Fodder Crop ◽  
Agrochemical Properties ◽  
Agricultural Use ◽  
Fodder Crop Rotation

The results of many years of research on the cultivation of crops in fodder crop rotation on dried peat soil are presented. A productive and agroecological assessment of crop rotation with various saturation with perennial grasses is given. The data on the reduction of peat reserves and changes in the agrochemical properties of the soil are presented.

Fertilization System as a Factor of Transforming the Humus State of the Soil

2015 ◽  
Vol 2 (2) ◽  
pp. 39-44
Author(s):  
V. Lopushniak
Keyword(s):  
Crop Rotation ◽  
Podzolic Soil ◽  
Humus Content ◽  
Organic Fertilizers ◽  
Mineral Fertilizers ◽  
Forest Steppe ◽  
Content Increase ◽  
Energy Reserves ◽  
Gross Energy ◽  
Stable Forms

Aim. To establish the effect of different fertilization systems in short fi eld crop rotation on the change in the state of humus in the dark gray podzolic soils in Western Forest-Steppe of Ukraine. Methods. Field studies were carried out in a stationary experiment of the Department of Soil Science and Agricultural Chemistry of the L’viv National Agrarian University; determination of humus content – according to DSTU 4289:2004, and that of its labile forms – in accordance with DSTU 4732:2007, fraction-group composition – by Ponomare- va-Plotnikova’s method, according to the measurement procedure 31-497058-008-2002. Results. The use of organo-mineral fertilizer system in short fi eld crop rotation with the saturation of organic fertilizers of 15 t/ha of crop rotation contributes to the humus content increase by 0.7 % after the third rotation in 0–40 cm layer of dark gray podzolic soil, the increase in the share of stable forms of humic compounds up to 57–59 % and the increase in the ratio of R HA :R FA to 1.3–1.4. The study demonstrated very high dependence of amount of gross energy reserves in the humus on the R HA :R FA ratio. Conclusions. The combined application of organic fertili- zers in the form of manure, non-market of the crop (straw) and siderate, along with mineral fertilizers is re- commended in short fi eld crop rotations of Western Forest-Steppe of Ukraine toensure expanded reproduction of fertility of dark gray podzolic soil, improvement of its humus status, increase in gross energy reserves and the share of the stable forms and humic acids in the humus.

Sequestration of carbon oxide in different fertilization systems in agrocenoses

2018 ◽  
Vol 5 (2) ◽  
pp. 37-51 ◽  
Author(s):  
O. Demydenko ◽  
Yu. Zapasna ◽  
V. Velychko
Keyword(s):  
Crop Rotation ◽  
Carbon Oxide ◽  
Organic Fertilizers ◽  
Forest Steppe ◽  
Organic Fertilization ◽  
Organic System ◽  
Capacity Level ◽  
Medium Level ◽  
Fertilization System ◽  
By Products

Aim. To substantiate the agroecological estimation of the performance of a short crop rotation in conditions of intense and organic system of fertilization on the basis of restoring normative parameters of emission and se- questration of С-СО 2 circulation while using by-products as organic fertilizers in conditions of modern climatic system of the Forest-Steppe of Ukraine. Methods. Field, statistical, laboratory. Results of Investigations. The performance of short crop rotations is determined by the capacity of С-СО 2 balance. Strong inverse correla- tion was found between the capacity of N and the ratio between C and N in the agrocenosis, which demon- strated that enhancing the humifi cation processes (ratio constriction) led to the increase in the capacity of С org balance and the decrease in the capacity level of С-СО 2 balance (enhancing mineralization), related to the reduction in the performance of crops in the agrocenosis of a crop rotation compared to the organic system of fertilization. The capacity of С-СО 2 and С org balance correlates at the medium level of inverse direction, and the yield of the main products, feed units and digestible protein correlates at the level of strong direct correlation. Conclusions. General mineralization of by-products and humus in the agrocenosis and humifi cation processes are antagonists, so extending the ratio between С and N at the intense fertilization system stimulates the in- crease in performance and reducing С to N similar to the organic fertilization system enhances the humifi cation process due to binding of С org into humus and limits mineralization which leads to the reduction in agrocenosis performance at the organic fertilization system.

NITROGEN CYCLES IN CROP ROTATIONS DIFFERING IN FERTILIZATION

2015 ◽  
Author(s):  
Saulius GUŽYS ◽  
Stefanija MISEVIČIENĖ
Keyword(s):  
Crop Rotation ◽  
Soil Nitrogen ◽  
Nitrogen Fertilizer ◽  
Nitrogen Balance ◽  
Mineral Soil ◽  
Crop Productivity ◽  
Drainage Water ◽  
Perennial Grasses ◽  
Crop Rotations ◽  
Cereal Crop

The use of nitrogen fertilizer is becoming a global problem; however continuous fertilization with nitrogen ensures large and constant harvests. An 8 year research (2006–2013) was conducted to evaluate the relationships between differently fertilized cultivated plant rotations. The research was conducted in Lipliunai (Lithuania) in the agroecosystem with nitrogen metabolism in fields with deeper carbonaceous soil, i.e. Endocalcari Endohypogleyic Cambisol (CMg-n-w-can). The research area covered three drained plots where crop rotation of differently fertilized cereals and perennial grasses was applied. Samples of soil, water and plants were investigated in the Chemical Analysis Laboratory of the Aleksandras Stulginskis University certified by the Environment Ministry of the Republic of Lithuania. The greatest productivity was found in a crop rotation with higher fertilization (N32-140). In crop rotation with lower fertilization (N24-90) productivity of cereals and perennial grasses (N0-80) was 11–35 % lower. The highest amount of mineral soil nitrogen was found in cereal crop rotation with higher fertilization. It was influenced by fertilization and crop productivity. The lowest Nmin and Ntotal concentrations in drainage water were found in grasses crop rotation. Crop rotations of differently fertilized cereals increased nitrogen concentration in drainage water. Nmin concentration in water depended on crop productivity, quantity of mineral soil nitrogen, fertilization, and nitrogen balance. The lowest nitrogen leaching was found in the crop rotation of grasses. Cereal crop rotation increased nitrogen leaching by 12–42 %. The usage of all crop rotations resulted in a negative nitrogen balance, which essentially depended on fertilization with nitrogen fertilizer.

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