scholarly journals Taxonomic and Functional Diversity of Rhizosphere Microbiome Recruited From Compost Synergistically Determined by Plant Species and Compost

2022 ◽  
Vol 12 ◽  
Author(s):  
Ning Wang ◽  
Huixiu Li ◽  
Bo Wang ◽  
Jia Ding ◽  
Yingjie Liu ◽  
...  
Keyword(s):  
Amino Acids ◽  
Plant Species ◽  
Gene Clusters ◽  
Amplicon Sequencing ◽  
Sequencing Analysis ◽  
Shotgun Metagenomics ◽  
Antimicrobial Substances ◽  
Rhizosphere Microbiome ◽  
Study Recruitment ◽  
Rhizosphere Bacterial Community

Compost is frequently served as the first reservoir for plants to recruit rhizosphere microbiome when used as growing substrate in the seedling nursery. In the present study, recruitment of rhizosphere microbiome from two composts by tomato, pepper, or maize was addressed by shotgun metagenomics and 16S rRNA amplicon sequencing. The 16S rRNA amplicon sequencing analysis showed that 41% of variation in the rhizosphere bacterial community was explained by compost, in contrast to 23% by plant species. Proteobacterial genera were commonly recruited by all three plant species with specific selections for Ralstonia by tomato and Enterobacteria by maize. These findings were confirmed by analysis of 16S rRNA retrieved from the shotgun metagenomics library. Approximately 70% of functional gene clusters differed more than sevenfold in abundance between rhizosphere and compost. Functional groups associated with the sensing and up-taking of C3 and C4 carboxylic acids, amino acids, monosaccharide, production of antimicrobial substances, and antibiotic resistance were over-represented in the rhizosphere. In summary, compost and plant species synergistically shaped the composition of the rhizosphere microbiome and selected for functional traits associated with the competition on root exudates.

scholarly journals Microbial Communities of Cladonia Lichens and Their Biosynthetic Gene Clusters Potentially Encoding Natural Products

2021 ◽  
Vol 9 (7) ◽  
pp. 1347
Author(s):  
Tânia Keiko Shishido ◽  
Matti Wahlsten ◽  
Pia Laine ◽  
Jouko Rikkinen ◽  
Taina Lundell ◽  
...  
Keyword(s):  
Natural Products ◽  
Microbial Communities ◽  
High Throughput Sequencing ◽  
Indigenous Communities ◽  
Gene Clusters ◽  
Amplicon Sequencing ◽  
Metagenomic Data ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Shotgun Metagenomics

Lichens have been widely used in traditional medicine, especially by indigenous communities worldwide. However, their slow growth and difficulties in the isolation of lichen symbionts and associated microbes have hindered the pharmaceutical utilisation of lichen-produced compounds. Advances in high-throughput sequencing techniques now permit detailed investigations of the complex microbial communities formed by fungi, green algae, cyanobacteria, and other bacteria within the lichen thalli. Here, we used amplicon sequencing, shotgun metagenomics, and in silico metabolomics together with compound extractions to study reindeer lichens collected from Southern Finland. Our aim was to evaluate the potential of Cladonia species as sources of novel natural products. We compared the predicted biosynthetic pathways of lichen compounds from isolated genome-sequenced lichen fungi and our environmental samples. Potential biosynthetic genes could then be further used to produce secondary metabolites in more tractable hosts. Furthermore, we detected multiple compounds by metabolite analyses, which revealed connections between the identified biosynthetic gene clusters and their products. Taken together, our results contribute to metagenomic data studies from complex lichen-symbiotic communities and provide valuable new information for use in further biochemical and pharmacological studies.

scholarly journals Development of a time-series shotgun metagenomics database for monitoring microbial communities at the Pacific coast of Japan

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kazutoshi Yoshitake ◽  
Gaku Kimura ◽  
Tomoko Sakami ◽  
Tsuyoshi Watanabe ◽  
Yukiko Taniuchi ◽  
...  
Keyword(s):  
Time Series ◽  
Microbial Communities ◽  
Pacific Coast ◽  
Three Dimensional ◽  
Amplicon Sequencing ◽  
Metagenomic Data ◽  
Shotgun Metagenomics ◽  
Functional Features ◽  
Pacific Coast Of Japan ◽  
Marine Microbial Communities

AbstractAlthough numerous metagenome, amplicon sequencing-based studies have been conducted to date to characterize marine microbial communities, relatively few have employed full metagenome shotgun sequencing to obtain a broader picture of the functional features of these marine microbial communities. Moreover, most of these studies only performed sporadic sampling, which is insufficient to understand an ecosystem comprehensively. In this study, we regularly conducted seawater sampling along the northeastern Pacific coast of Japan between March 2012 and May 2016. We collected 213 seawater samples and prepared size-based fractions to generate 454 subsets of samples for shotgun metagenome sequencing and analysis. We also determined the sequences of 16S rRNA (n = 111) and 18S rRNA (n = 47) gene amplicons from smaller sample subsets. We thereafter developed the Ocean Monitoring Database for time-series metagenomic data (http://marine-meta.healthscience.sci.waseda.ac.jp/omd/), which provides a three-dimensional bird’s-eye view of the data. This database includes results of digital DNA chip analysis, a novel method for estimating ocean characteristics such as water temperature from metagenomic data. Furthermore, we developed a novel classification method that includes more information about viruses than that acquired using BLAST. We further report the discovery of a large number of previously overlooked (TAG)n repeat sequences in the genomes of marine microbes. We predict that the availability of this time-series database will lead to major discoveries in marine microbiome research.

scholarly journals Reduced metagenome sequencing for strain-resolution taxonomic profiles

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Lars Snipen ◽  
Inga-Leena Angell ◽  
Torbjørn Rognes ◽  
Knut Rudi
Keyword(s):  
Microbial Community ◽  
Microbial Community Composition ◽  
Amplicon Sequencing ◽  
Good Alternative ◽  
Shotgun Sequencing ◽  
Least Square ◽  
Full Potential ◽  
Shotgun Metagenomics ◽  
Metagenome Sequencing ◽  
Reference Genomes

Abstract Background Studies of shifts in microbial community composition has many applications. For studies at species or subspecies levels, the 16S amplicon sequencing lacks resolution and is often replaced by full shotgun sequencing. Due to higher costs, this restricts the number of samples sequenced. As an alternative to a full shotgun sequencing we have investigated the use of Reduced Metagenome Sequencing (RMS) to estimate the composition of a microbial community. This involves the use of double-digested restriction-associated DNA sequencing, which means only a smaller fraction of the genomes are sequenced. The read sets obtained by this approach have properties different from both amplicon and shotgun data, and analysis pipelines for both can either not be used at all or not explore the full potential of RMS data. Results We suggest a procedure for analyzing such data, based on fragment clustering and the use of a constrained ordinary least square de-convolution for estimating the relative abundance of all community members. Mock community datasets show the potential to clearly separate strains even when the 16S is 100% identical, and genome-wide differences is < 0.02, indicating RMS has a very high resolution. From a simulation study, we compare RMS to shotgun sequencing and show that we get improved abundance estimates when the community has many very closely related genomes. From a real dataset of infant guts, we show that RMS is capable of detecting a strain diversity gradient for Escherichia coli across time. Conclusion We find that RMS is a good alternative to either metabarcoding or shotgun sequencing when it comes to resolving microbial communities at the strain level. Like shotgun metagenomics, it requires a good database of reference genomes and is well suited for studies of the human gut or other communities where many reference genomes exist. A data analysis pipeline is offered, as an R package at https://github.com/larssnip/microRMS.

scholarly journals A plant endophyte Staphylococcus hominis strain MBL_AB63 produces a novel lantibiotic, homicorcin and a position one variant

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
M. Aftab Uddin ◽  
Shammi Akter ◽  
Mahbuba Ferdous ◽  
Badrul Haidar ◽  
Al Amin ◽  
...  
Keyword(s):  
Gene Clusters ◽  
Antimicrobial Activities ◽  
Whole Genome Sequence ◽  
Antimicrobial Substances ◽  
The Core ◽  
Rp Hplc ◽  
Ring Structures ◽  
Core Peptide ◽  
Staphylococcus Hominis ◽  
Epilancin 15X

AbstractHere we report a jute endophyte Staphylococcus hominis strain MBL_AB63 isolated from jute seeds which showed promising antimicrobial activity against Staphylococcus aureus SG511 when screening for antimicrobial substances. The whole genome sequence of this strain, annotated using BAGEL4 and antiSMASH 5.0 to predict the gene clusters for antimicrobial substances identified a novel antimicrobial peptide cluster that belongs to the class I lantibiotic group. The predicted lantibiotic (homicorcin) was found to be 82% similar to a reported peptide epicidin 280 having a difference of seven amino acids at several positions of the core peptide. Two distinct peaks obtained at close retention times from a RP-HPLC purified fraction have comparable antimicrobial activities and LC–MS revealed the molecular mass of these peaks to be 3046.5 and 3043.2 Da. The presence of an oxidoreductase (homO) similar to that of epicidin 280- associated eciO or epilancin 15X- associated elxO in the homicorcin gene cluster is predicted to be responsible for the reduction of the first dehydrated residue dehydroalanine (Dha) to 2-hydroxypropionate that causes an increase of 3 Da mass of homicorcin 1. Trypsin digestion of the core peptide and its variant followed by ESI–MS analysis suggests the presence of three ring structures, one in the N-terminal and other two interlocking rings at the C-terminal region that remain undigested. Homicorcin exerts bactericidal activity against susceptible cells by disrupting the integrity of the cytoplasmic membrane through pore formation as observed under FE-SEM.

scholarly journals Analysis of field-grown Panax ginseng rhizosphere microbiome provides clues for preventing red skin root syndrome

2021 ◽  
Author(s):  
Xingbo Bian ◽  
Ling Dong ◽  
Yan Zhao ◽  
He Yang ◽  
Yonghua Xu ◽  
...  
Keyword(s):  
Biological Control ◽  
Ecological Niche ◽  
Interaction Network ◽  
Pathogenic Fungi ◽  
Niche Overlap ◽  
Amplicon Sequencing ◽  
Soil Improvement ◽  
Niche Separation ◽  
Key Factors ◽  
Rhizosphere Microbiome

Abstract Background Ginseng red skin root syndrome (GRS) is one of the most common ginseng diseases. It leads to a severe decline in ginseng quality and seriously affects the ginseng industry in China. However, as a root disease, the characteristics of GRS rhizosphere microbiome are still unclear. Methods The amplicon sequencing technology, combined with bioinformatics analysis, was used to explore the relationship between soil ecological environment and GRS. Results There were significant differences in the diversity and richness of soil microorganisms between the rhizosphere with different degrees of disease, especially between healthy ginseng (HG) and heavily diseased groups. We also found that bacterial communities underwent multiple changes between complex stability and simple instability in different ginseng rhizospheres through the established interaction networks. The GRS group also had more competition with each other and ecological niche separation than the HG group. The fungal community's stability decreased significantly in the early stages of the disease, followed by the formation of a stable and complex fungal community. The GRS groups significantly increased interspecies cooperation and ecological niche overlap in the fungal network than the HG group. Microbes closely related to potential pathogenic fungi were also identified according to the interaction network, which provided clues for looking for biological control agents. Finally, the Distance-based redundancy analysis (dbRDA) results indicated that total P (TP), available K (AK), available P (AP), catalase (CAT), invertase (INV) are the key factors that influence the microbial communities. Conclusions This study collectively analyzed the changing characteristics in ginseng rhizosphere and provided the basis for soil improvement and biological control of field-grown ginseng.

scholarly journals Relative and quantitative rhizosphere microbiome profiling result in distinct abundance patterns

2021 ◽  
Author(s):  
Hamed Azarbad ◽  
Julien Tremblay ◽  
Luke D. Bainard ◽  
Etienne Yergeau
Keyword(s):  
Water Stress ◽  
Relative Abundance ◽  
Its Region ◽  
Cost Effective ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Real Time Quantitative Pcr ◽  
Rhizosphere Microbiome ◽  
History Of ◽  
Almost All

AbstractNext-generation sequencing is recognized as one of the most popular and cost-effective way of characterizing microbiome in multiple samples. However, most of the currently available amplicon sequencing approaches are inherently limited, as they are often presented based on the relative abundance of microbial taxa, which may not fully represent actual microbiome profiles. Here, we combined amplicon sequencing (16S rRNA gene for bacteria and ITS region for fungi) with real-time quantitative PCR (qPCR) to characterize the rhizosphere microbiome of wheat. We show that the increase in relative abundance of major microbial phyla does not necessarily result in an increase in abundance. One striking observation when comparing relative and quantitative abundances was a substantial increase in the abundance of almost all phyla associated with the rhizosphere of plants grown in soil with no history of water stress as compared with the rhizosphere of plants growing in soil with a history of water stress, which was in contradiction with the trends observed in the relative abundance data. Our results suggest that the estimated absolute abundance approach gives a different perspective than the relative abundance approach, providing complementary information that helps to better understand the rhizosphere microbiome.

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.

scholarly journals Constructing a Reference Genome in a Single Lab: The Possibility to Use Oxford Nanopore Technology

Plants ◽  
2019 ◽  
Vol 8 (8) ◽  
pp. 270 ◽  
Author(s):  
Yun Gyeong Lee ◽  
Sang Chul Choi ◽  
Yuna Kang ◽  
Kyeong Min Kim ◽  
Chon-Sik Kang ◽  
...  
Keyword(s):  
Plant Species ◽  
Genome Sequencing ◽  
Reference Genome ◽  
Genome Structure ◽  
Plant Genome ◽  
Sequence Information ◽  
Sequencing Analysis ◽  
Oxford Nanopore ◽  
A Genome ◽  
Long Read

The whole genome sequencing (WGS) has become a crucial tool in understanding genome structure and genetic variation. The MinION sequencing of Oxford Nanopore Technologies (ONT) is an excellent approach for performing WGS and it has advantages in comparison with other Next-Generation Sequencing (NGS): It is relatively inexpensive, portable, has simple library preparation, can be monitored in real-time, and has no theoretical limits on reading length. Sorghum bicolor (L.) Moench is diploid (2n = 2x = 20) with a genome size of about 730 Mb, and its genome sequence information is released in the Phytozome database. Therefore, sorghum can be used as a good reference. However, plant species have complex and large genomes when compared to animals or microorganisms. As a result, complete genome sequencing is difficult for plant species. MinION sequencing that produces long-reads can be an excellent tool for overcoming the weak assembly of short-reads generated from NGS by minimizing the generation of gaps or covering the repetitive sequence that appears on the plant genome. Here, we conducted the genome sequencing for S. bicolor cv. BTx623 while using the MinION platform and obtained 895,678 reads and 17.9 gigabytes (Gb) (ca. 25× coverage of reference) from long-read sequence data. A total of 6124 contigs (covering 45.9%) were generated from Canu, and a total of 2661 contigs (covering 50%) were generated from Minimap and Miniasm with a Racon through a de novo assembly using two different tools and mapped assembled contigs against the sorghum reference genome. Our results provide an optimal series of long-read sequencing analysis for plant species while using the MinION platform and a clue to determine the total sequencing scale for optimal coverage that is based on various genome sizes.

Formation and occurrence of N-malonylphenylalanine and related compounds in plants

1968 ◽  
Vol 46 (8) ◽  
pp. 797-806 ◽  
Author(s):  
N. Rosa ◽  
A. C. Neish
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Glutamic Acid ◽  
Plant Species ◽  
Isolation Procedure ◽  
Plant Kingdom ◽  
Feeding Experiments ◽  
Leucine Isomers ◽  
Related Compounds

Shoots of barley seedlings when fed D-phenylalanine convert the amino acid to N-malonylphenylalanine. Some N-acetylphenylalanine is obtained at the same time but this may be an artifact of the isolation procedure since it is readily formed by decarboxylation of the malonylphenylalanine. Feeding experiments with the D- and L-isomers of phenylalanine, valine, leucine, isoleucine, tyrosine, tryptophan, alanine, and glutamic acid showed that barley shoots form the malonyl derivative from all the D-isomers whereas little, if any, is formed from the L-isomers. Similar experiments with phenylalanine and leucine isomers, using seven different plant species, showed that the ability to conjugate the D-isomers (but not the L-isomers) was found in all of the plants tested. It was also observed that the ether-soluble acidic conjugates of a variety of amino acids, possibly malonyl derivatives, occur widely throughout the plant kingdom.

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