scholarly journals Relative Abundances of Species or Sequence Variants Can Be Misleading: Soil Fungal Communities as an Example

2021 ◽  
Vol 9 (3) ◽  
pp. 589
Author(s):  
Lukas Beule ◽  
Markus Arndt ◽  
Petr Karlovsky
Keyword(s):  
Population Size ◽  
Soil Fungi ◽  
Alley Cropping ◽  
Amplicon Sequencing ◽  
Environmental Benefits ◽  
Plant Production ◽  
Sequence Variants ◽  
Sequencing Analysis ◽  
Temperate Agroforestry ◽  
Relative Abundances

Plant production systems that are more sustainable than conventional monoculture croplands are the vision of future agriculture. With numerous environmental benefits, agroforestry is among the most promising alternatives. Although soil fungi are key drivers of plant productivity and ecosystem processes, investigations of these microorganisms in temperate agroforestry systems are scarce, leaving our understanding of agricultural systems under agroforestry practice incomplete. Here, we assessed the composition and diversity of the soil fungal community as well as the frequency (relative abundance) of fungal groups in three paired temperate poplar-based alley cropping (agroforestry) and monoculture cropland systems by amplicon sequencing. Analysis of microbiomes using relative abundances of species or sequence variants obtained from amplicon sequencing ignores microbial population size, which results in several problems. For example, species stimulated by environmental parameters may appear unaffected or suppressed in amplicon counts. Therefore, we determined absolute abundances of selected fungal groups as well as total fungal population size by real-time polymerase chain reaction (PCR). Tree rows strongly affected the community composition and increased the population size and species richness of soil fungi. Furthermore, ectomycorrhiza were strongly promoted by the tree rows. We speculate that mycorrhiza improved the nutrient acquisition in unfertilized tree rows, thereby contributing to the total productivity of the system. Comparison of relative and absolute abundances revealed dramatic discrepancies, highlighting that amplicon sequencing alone cannot adequately assess population size and dynamics. The results of our study highlight the necessity of combining frequency data based on amplicon sequencing with absolute quantification.

scholarly journals Changes in the Bacterial Diversity of Human Milk during Late Lactation Period (Weeks 21 to 48)

Foods ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 1184
Author(s):  
Wendy Marin-Gómez ◽  
Mᵃ José Grande ◽  
Rubén Pérez-Pulido ◽  
Antonio Galvez ◽  
Rosario Lucas
Keyword(s):  
Bacterial Diversity ◽  
Single Mother ◽  
Variable Region ◽  
Sampling Period ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
Lactation Period ◽  
Relative Abundances ◽  
The 16S Rrna Gene

Breast milk from a single mother was collected during a 28-week lactation period. Bacterial diversity was studied by amplicon sequencing analysis of the V3-V4 variable region of the 16S rRNA gene. Firmicutes and Proteobacteria were the main phyla detected in the milk samples, followed by Actinobacteria and Bacteroidetes. The proportion of Firmicutes to Proteobacteria changed considerably depending on the sampling week. A total of 411 genera or higher taxons were detected in the set of samples. Genus Streptococcus was detected during the 28-week sampling period, at relative abundances between 2.0% and 68.8%, and it was the most abundant group in 14 of the samples. Carnobacterium and Lactobacillus had low relative abundances. At the genus level, bacterial diversity changed considerably at certain weeks within the studied period. The weeks or periods with lowest relative abundance of Streptococcus had more diverse bacterial compositions including genera belonging to Proteobacteria that were poorly represented in the rest of the samples.

Does temperate agroforestry reduce nutrient leaching losses compared to cropland monocultures?

2020 ◽  
Author(s):  
Marcus Schmidt ◽  
Marife D. Corre ◽  
Xiaohong Duan ◽  
Florian Heinlein ◽  
Edzo Veldkamp
Keyword(s):  
Large Scale ◽  
Resource Competition ◽  
Alley Cropping ◽  
Safety Net ◽  
Nutrient Leaching ◽  
Environmental Benefits ◽  
The European Union ◽  
Leaching Losses ◽  
Temperate Agroforestry ◽  
Wide Range

<p>Over the past decades, excessive use of fertilizers in cropland monocultures in combination with a decrease in fertilizer use efficiency, have led to an increase in nutrient leaching losses, especially for nitrate. Consequently, ground water pollution is widespread and starting to be recognized and potentially sanctioned by the European Union. Unfertilized tree rows alternating with crop rows (e.g. alley-cropping agroforestry) are hypothesized to act as a safety net by taking up excess nutrients below the crop-rooting zone. Here, we measured leaching losses of nitrogen (N), phosphorus (P) and potassium (K) during two growing seasons in agroforestry systems and adjacent monocultures at three sites in Germany, representing a wide range of soil characteristics. Leaching losses of N, P and K were generally lower under agroforestry tree rows at all sites compared to agroforestry crop rows or crop monocultures. Overall, agroforestry reduced nitrate leaching losses by up to 82% compared to monocultures, but showed comparable losses of P and K. Nutrient leaching losses were high in the agroforestry crop rows close to the tree rows where crop productivity is lowest due to resource competition with trees. An adjusted management, e.g. reduced fertilizer inputs close to the tree rows, may counteract these losses. Our results suggest that agroforestry has the potential to reduce nutrient leaching losses through the trees and the application of fertilizer should be reduced in the agroforestry crop row close to the trees. The reduction in nutrient leaching losses in agroforestry indicates an increase in the soil function of water filtration. In order to achieve large-scale implementation of temperate agroforestry, its environmental benefits need to be financially valued for farmers to adapt this widely applicable land use alternative. The presented project, SIGNAL (Sustainable intensification of agriculture through agroforestry) is part of the German research initiative BonaRes (Soil as a sustainable resource).</p>

scholarly journals Early response of soil fungal communities to the conversion of monoculture cropland to a temperate agroforestry system

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12236
Author(s):  
Lukas Beule ◽  
Petr Karlovsky
Keyword(s):  
Community Composition ◽  
Fungal Biomass ◽  
Soil Fungi ◽  
Alley Cropping ◽  
Arable Land ◽  
Agroforestry Systems ◽  
West Germany ◽  
Fungal Communities ◽  
Temperate Agroforestry ◽  
Fungal Populations

Background Alley-cropping systems in the temperate zone are a type of agroforestry in which rows of fast-growing trees are alternated with rows of annual crops. With numerous environmental benefits, temperate agroforestry is considered a promising alternative to conventional agriculture and soil fungi may play a key in maintaining productivity of these systems. Agroforestry systems that are established for more than 10 years have shown to increase the fungal biomass and impact the composition of soil fungal communities. Investigations of soil fungi in younger temperate agroforestry systems are scarce and the temporal dynamic of these changes is not understood. Methods Our study was conducted in a young poplar-based alley cropping and adjacent monoculture cropland system in an Arenosol soil in north-west Germany. We investigated the temporal dynamics of fungal populations after the establishment of agroforestry by collecting soil samples half, one, and one and a half years after conversion of cropland to agroforestry. Samples were collected within the agroforestry tree row, at 1, 7, and 24 m distance from the tree row within the crop row, and in an adjacent conventional monoculture cropland. The biomass of soil fungi, Asco-, and Basidiomycota was determined by real-time PCR. Soil fungal community composition and diversity were obtained from amplicon sequencing. Results Differences in the community composition of soil fungi in the tree row and arable land were detected as early as half a year following the conversion of monoculture cropland to agroforestry. In the tree row, soil fungal communities in the plots strongly diverged with the age of the system. The presence of young trees did not affect the biomass of soil fungi. Conclusions The composition of soil fungal communities responded rapidly to the integration of trees into arable land through agroforestry, whereas the fungal biomass was not affected during the first one and a half years after planting the trees. Fungal communities under the trees gradually diversified. Adaptation to spatially heterogeneous belowground biomass of the trees and understory vegetation or stochastic phenomena due to limited exchange among fungal populations may account for this effect; long-term monitoring might help unravelling the cause.

scholarly journals Workstation benchmark of Spark Capable Genome Analysis ToolKit 4 Variant Calling

2020 ◽  
Author(s):  
Marcus H. Hansen ◽  
Anita T. Simonsen ◽  
Hans B. Ommen ◽  
Charlotte G. Nyvold
Keyword(s):  
Dna Sequencing ◽  
Genome Analysis ◽  
High Speed ◽  
High Performance ◽  
Variant Calling ◽  
Amplicon Sequencing ◽  
Targeted Sequencing ◽  
Sequencing Analysis ◽  
Genome Analysis Toolkit ◽  
Order Of Magnitude

AbstractBackgroundRapid and practical DNA-sequencing processing has become essential for modern biomedical laboratories, especially in the field of cancer, pathology and genetics. While sequencing turn-over time has been, and still is, a bottleneck in research and diagnostics, the field of bioinformatics is moving at a rapid pace – both in terms of hardware and software development. Here, we benchmarked the local performance of three of the most important Spark-enabled Genome analysis toolkit 4 (GATK4) tools in a targeted sequencing workflow: Duplicate marking, base quality score recalibration (BQSR) and variant calling on targeted DNA sequencing using a modest hyperthreading 12-core single CPU and a high-speed PCI express solid-state drive.ResultsCompared to the previous GATK version the performance of Spark-enabled BQSR and HaplotypeCaller is shifted towards a more efficient usage of the available cores on CPU and outperforms the earlier GATK3.8 version with an order of magnitude reduction in processing time to analysis ready variants, whereas MarkDuplicateSpark was found to be thrice as fast. Furthermore, HaploTypeCallerSpark and BQSRPipelineSpark were significantly faster than the equivalent GATK4 standard tools with a combined ∼86% reduction in execution time, reaching a median rate of ten million processed bases per second, and duplicate marking was reduced ∼42%. The called variants were found to be in close agreement between the Spark and non-Spark versions, with an overall concordance of 98%. In this setup, the tools were also highly efficient when compared execution on a small 72 virtual CPU/18-node Google Cloud cluster.ConclusionIn conclusion, GATK4 offers practical parallelization possibilities for DNA sequence processing, and the Spark-enabled tools optimize performance and utilization of local CPUs. Spark utilizing GATK variant calling is several times faster than previous GATK3.8 multithreading with the same multi-core, single CPU, configuration. The improved opportunities for parallel computations not only hold implications for high-performance cluster, but also for modest laboratory or research workstations for targeted sequencing analysis, such as exome, panel or amplicon sequencing.

Agroforestry: The North American Perspective

2021 ◽  
Author(s):  
Sarah T. Lovell ◽  
Harold E. "Gene" Garrett
Keyword(s):  
Alley Cropping ◽  
Indigenous Communities ◽  
Environmental Benefits ◽  
Forest Understory ◽  
Herbaceous Plants ◽  
Ecological Knowledge ◽  
Specialty Crops ◽  
Wide Range ◽  
Trees And Shrubs ◽  
Edible Products

Agroforestry has a long, rich history that is rooted in activities practiced by indigenous communities around the world. Native peoples were known to gather fruits, nuts, and understory herbs from the forest, based on their deep ecological knowledge of the natural system, and they often cultivated preferred species. For modern applications, agroforestry can be defined as the intentional integration of trees and shrubs with crops or livestock to create a multifunctional system with a wide range of benefits. In temperate regions, agroforestry is characterized by six key practices: (1) alley cropping—planting rows of trees with a companion crop grown between the rows; (2) forest farming—growing high-value specialty crops in the shaded forest understory; (3) riparian buffers—protecting water resources such as streams with a zone of trees, shrubs, and herbaceous plants; (4) silvopasture—combining trees, forage, and livestock for multiple products; (5) windbreaks—planting rows of trees and shrubs to protect crops or livestock from wind and to reduce soil erosion; and (6) urban food forests—integrating trees, shrubs, and herbaceous plants that provide edible products for the good of the community. The environmental benefits of agroforestry have been widely studied and continue to be a source of great interest. Most recently, the potential for agroforestry to contribute to climate change adaption and mitigation is being explored. While the science of agroforestry has been influenced to a great extent by the field of ecology and related disciplines, social science dimensions are increasingly captured through the study of adoption behaviors, preferences, and cultural benefits. The investigation of the role of economic and policy drivers is critical to understanding strategies to motivate landowners to adopt these practices at a level that would expand agroforestry into the mainstream. Landscape-level planning and design could provide a vision and a pathway for a broader transformation to a system that encourages perennial habitats including specialty crops that supply edible products. Such a strategy could place agroforestry more directly into the growing call to support regional food systems and positive human health outcomes. This article focuses on the trends and directions in agroforestry research primarily in North America, with emphasis on developments in the early 21st century.

scholarly journals Temperate Agroforestry Development: The Case of Québec and of France

2020 ◽  
Vol 12 (17) ◽  
pp. 7227
Author(s):  
Noémie Hotelier-Rous ◽  
Geneviève Laroche ◽  
Ève Durocher ◽  
David Rivest ◽  
Alain Olivier ◽  
...  
Keyword(s):  
Environmental Benefits ◽  
Organizational Dynamics ◽  
Training Development ◽  
Temperate Agroforestry ◽  
Industrialized Nations ◽  
Development Paths ◽  
Further Development ◽  
And Training ◽  
Agroforestry Practices ◽  
The Eu

This study sought to shed light on the political and organizational dynamics favoring the deployment of agroforestry in temperate environments. Development paths of agroforestry practices in Québec (Canada) and France were analyzed regarding five different issues: political status and recognition, regulation and financing, knowledge acquisition, knowledge transfer and training, development actors and implementation in the field. Scientific studies and results continue to accumulate concerning temperate agroforestry and its environmental benefits. Political recognition of the field appears to be stronger in France (and the EU), which makes state financial aid conditional upon the adoption of the practices. In Québec, only the Ministry of Agriculture provides limited support. It financially assists research at a moderate level, as well as the installation and maintenance of trees by participating farmers to perform specific functions, i.e., erosion control, water quality, and biodiversity. A large number of actors are active in France, where efforts are being made to improve consultation and to reduce redundancy. Stakeholders in Québec are linked to the broader agri-environment field and act partially through agroforestry, according to varying degrees of competency, creating a disparity between regions. Recognition at the highest level, i.e., training for councillors and advisors, greater flexibility in obtaining assistance, inclusion of a greater diversity of systems, and a structure that ensures promotion and consultation, would favour the further development of agroforestry in the industrialized nations of the temperate zone.

Effects of restorative agroecosystems on soil characteristics and plant production on a degraded soil in the Georgia Piedmont, USA

2009 ◽  
Vol 24 (3) ◽  
pp. 186-196 ◽  
Author(s):  
K.L. Jacobsen ◽  
C.F. Jordan
Keyword(s):  
Management Practices ◽  
Alley Cropping ◽  
Conservation Tillage ◽  
Soil Characteristics ◽  
Plant Production ◽  
Hot Pepper ◽  
Organic Management ◽  
Soil C ◽  
Winter Cover ◽  
Georgia Piedmont

AbstractThis work presents the results of a three-year field study of agroecosystems designed to restore soil organic matter (SOM) to degraded soils of the Georgia Piedmont. The systems combine a suite of management practices previously demonstrated to increase SOM when studied individually, and examine the effects of these techniques when used in combination in a cropping systems context on soil characteristics, crop production and weed biomass. The systems' components include organic management, alley cropping with perennial legumes, conservation tillage, use of winter cover crops, straw mulch and two compost application rates. Vegetable crops grown were a rotation of okra, hot pepper and a corn and winter squash intercrop. The systems were not able to maintain soil C or N without the addition of compost. Systems incorporating alley cropping, organic management, conservation tillage and compost maintained soil C, and increased in soil C when mulch was not applied. In organic, conservation tillage without alley cropping, soil C did not change significantly, even with annual 44.8 Mg ha−1 of compost additions. Patterns for soil N followed those of soil C. The study demonstrated that alley cropping can maintain and sequester soil C and N beyond organic conservation tillage alone, and more than conventionally tilled, chemically fertilized treatments. Crop yields did not vary by treatment due to high variation within treatments. Winter cover crop residue provided an effective weed barrier for 4 to 6 weeks in the spring, but additional hand weeding was required throughout the summer. The results of this systems-level study demonstrated interactions between management practices when used in combination that would not have been observed when studied individually. It also demonstrates that agroforestry techniques, conservation tillage and compost applications can increase soil C in degraded, clayey soils while they are in cultivation.

scholarly journals RLIP76 Gene Variants are not Associated with Drug Response in Turkish Epilepsy Patients

2011 ◽  
Vol 14 (1) ◽  
pp. 25-30 ◽  
Author(s):  
E Manguoğlu ◽  
S Akdeniz ◽  
N Dündar ◽  
Ö Duman ◽  
B Aktekin ◽  
...  
Keyword(s):  
Drug Resistance ◽  
High Performance ◽  
Drug Response ◽  
Resistance Mechanism ◽  
Sequence Variants ◽  
Gene Variants ◽  
Sequencing Analysis ◽  
Transporter Protein ◽  
Epileptic Patients ◽  
Response Status

RLIP76Gene Variants are not Associated with Drug Response in Turkish Epilepsy PatientsApproximately 30% of epileptic patients remain untreated, in spite of trials with maximum tolerable doses of more than one drug. The RalA binding protein 1 (RALBP1/RLIP76), a multifunctional, anti-apoptotic, multidrug transporter protein, has been proposed as being responsible for the drug resistance mechanism in epilepsy. We have investigated polymorphic differences in the coding regions and exon-intron boundaries of theRLIP76gene, between 146 refractory and 155 non refractory epileptic patients in Turkey, using denaturing high performance liquid chromatography (HPLC) and sequencing analysis techniques. We have detected the following sequence variants: c.160-4G>A, c.187C>G, c.1562-38G>A, c.1670+107G>A, c.1670+93G>A, c.1670+96G>A, c.1670+100C>T, c.1670+130C>T, c.1670+131G>C, c.1670+140 G>C, and found no statistically significant correlation between allele frequencies and drug response status. We conclude that sequence variants of this gene are not involved in drug resistance in epilepsy.

scholarly journals Synthetic Sequencing Standards: A Guide to Database Choice for Rumen Microbiota Amplicon Sequencing Analysis

2020 ◽  
Vol 11 ◽  
Author(s):  
Paul E. Smith ◽  
Sinead M. Waters ◽  
Ruth Gómez Expósito ◽  
Hauke Smidt ◽  
Ciara A. Carberry ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Cost Effective ◽  
Amplicon Sequencing ◽  
Gas Production ◽  
Reference Database ◽  
Specific Reference ◽  
Sequencing Analysis ◽  
Sequencing Data ◽  
Rumen Microbiota ◽  
Reference Databases

Our understanding of complex microbial communities, such as those residing in the rumen, has drastically advanced through the use of high throughput sequencing (HTS) technologies. Indeed, with the use of barcoded amplicon sequencing, it is now cost effective and computationally feasible to identify individual rumen microbial genera associated with ruminant livestock nutrition, genetics, performance and greenhouse gas production. However, across all disciplines of microbial ecology, there is currently little reporting of the use of internal controls for validating HTS results. Furthermore, there is little consensus of the most appropriate reference database for analyzing rumen microbiota amplicon sequencing data. Therefore, in this study, a synthetic rumen-specific sequencing standard was used to assess the effects of database choice on results obtained from rumen microbial amplicon sequencing. Four DADA2 reference training sets (RDP, SILVA, GTDB, and RefSeq + RDP) were compared to assess their ability to correctly classify sequences included in the rumen-specific sequencing standard. In addition, two thresholds of phylogenetic bootstrapping, 50 and 80, were applied to investigate the effect of increasing stringency. Sequence classification differences were apparent amongst the databases. For example the classification of Clostridium differed between all databases, thus highlighting the need for a consistent approach to nomenclature amongst different reference databases. It is hoped the effect of database on taxonomic classification observed in this study, will encourage research groups across various microbial disciplines to develop and routinely use their own microbiome-specific reference standard to validate analysis pipelines and database choice.

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