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Journal articles on the topic "Tag-pyrosequencing 454"
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Gonzalez-Martinez, Alejandro, Alejandro Rodriguez-Sanchez, M. C. M. van Loosdrecht, Jesus Gonzalez-Lopez, and Riku Vahala. "Detection of comammox bacteria in full-scale wastewater treatment bioreactors using tag-454-pyrosequencing." Environmental Science and Pollution Research 23, no. 24 (October 26, 2016): 25501–11. http://dx.doi.org/10.1007/s11356-016-7914-4.
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Kim, Ji Eun, Frederick C. Leung, Jingwei Jiang, Amy H. Y. Kwok, Darin C. Bennett, and Kimberly M. Cheng. "Expressed sequence tag analysis of the emu (Dromaius novaehollandiae) pituitary by 454 GS Junior pyrosequencing." Poultry Science 92, no. 1 (January 2013): 90–96. http://dx.doi.org/10.3382/ps.2012-02594.
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Hail, D., W. B. Hunter, S. E. Dowd, and B. R. Bextine. "Expressed Sequence Tag (EST) Survey of Life Stages of the Potato Psyllid,Bactericera cockerelli, using 454 Pyrosequencing." Southwestern Entomologist 35, no. 3 (October 2010): 463–66. http://dx.doi.org/10.3958/059.035.0333.
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Vohník, Martin, Ondřej Borovec, Zuzana Kolaříková, Radka Sudová, and Martina Réblová. "Extensive sampling and high-throughput sequencing reveal Posidoniomyces atricolor gen. et sp. nov. (Aigialaceae, Pleosporales) as the dominant root mycobiont of the dominant Mediterranean seagrass Posidonia oceanica." MycoKeys 55 (June 26, 2019): 59–86. http://dx.doi.org/10.3897/mycokeys.55.35682.
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Seagrasses provide invaluable ecosystem services yet very little is known about their root mycobiont diversity and distribution. Here we focused on the dominant Mediterranean seagrass Posidoniaoceanica and assessed its root mycobiome at 32 localities covering most of the ecoregions in the NW Mediterranean Sea using light and scanning electron microscopy and tag-encoded 454-pyrosequencing. Microscopy revealed that the recently discovered dark septate endophytic association specific for P.oceanica is present at all localities and pyrosequencing confirmed that the P.oceanica root mycobiome is dominated by a single undescribed pleosporalean fungus, hitherto unknown from other hosts and ecosystems. Its numerous slow-growing isolates were obtained from surface-sterilised root segments at one locality and after prolonged cultivation, several of them produced viable sterile mycelium. To infer their phylogenetic relationships we sequenced and analysed the large (LSU) and small (SSU) subunit nrDNA, the ITS nrDNA and the DNA-directed RNA polymerase II (RPB2). The fungus represents an independent marine biotrophic lineage in the Aigialaceae (Pleosporales) and is introduced here as Posidoniomycesatricolorgen. et sp. nov. Its closest relatives are typically plant-associated saprobes from marine, terrestrial and freshwater habitats in Southeast Asia and Central America. This study expands our knowledge and diversity of the Aigialaceae, adds a new symbiotic lifestyle to this family and provides a formal name for the dominant root mycobiont of the dominant Mediterranean seagrass.
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Noh, Eun Soo, Young-Sam Kim, Dong-Hyun Kim, and Kyoung-Ho Kim. "Bacterial Diversity in the Guts of Sea Cucumbers (Apostichopus japonicus) and Shrimps (Litopenaeus vannamei) Investigated with Tag-Encoded 454 Pyrosequencing of 16S rRNA Genes." Korean Journal of Microbiology 49, no. 3 (September 30, 2013): 237–44. http://dx.doi.org/10.7845/kjm.2013.3044.
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La Duc, Myron T., Parag Vaishampayan, Henrik R. Nilsson, Tamas Torok, and Kasthuri Venkateswaran. "Pyrosequencing-Derived Bacterial, Archaeal, and Fungal Diversity of Spacecraft Hardware Destined for Mars." Applied and Environmental Microbiology 78, no. 16 (June 22, 2012): 5912–22. http://dx.doi.org/10.1128/aem.01435-12.
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ABSTRACTSpacecraft hardware and assembly cleanroom surfaces (233 m2in total) were sampled, total genomic DNA was extracted, hypervariable regions of the 16S rRNA gene (bacteria and archaea) and ribosomal internal transcribed spacer (ITS) region (fungi) were subjected to 454 tag-encoded pyrosequencing PCR amplification, and 203,852 resulting high-quality sequences were analyzed. Bioinformatic analyses revealed correlations between operational taxonomic unit (OTU) abundance and certain sample characteristics, such as source (cleanroom floor, ground support equipment [GSE], or spacecraft hardware), cleaning regimen applied, and location about the facility or spacecraft. National Aeronautics and Space Administration (NASA) cleanroom floor and GSE surfaces gave rise to a larger number of diverse bacterial communities (619 OTU; 20 m2) than colocated spacecraft hardware (187 OTU; 162 m2). In contrast to the results of bacterial pyrosequencing, where at least some sequences were generated from each of the 31 sample sets examined, only 13 and 18 of these sample sets gave rise to archaeal and fungal sequences, respectively. As was the case for bacteria, the abundance of fungal OTU in the GSE surface samples dramatically diminished (9× less) once cleaning protocols had been applied. The presence of OTU representative of actinobacteria, deinococci, acidobacteria, firmicutes, and proteobacteria on spacecraft surfaces suggests that certain bacterial lineages persist even following rigorous quality control and cleaning practices. The majority of bacterial OTU observed as being recurrent belonged to actinobacteria and alphaproteobacteria, supporting the hypothesis that the measures of cleanliness exerted in spacecraft assembly cleanrooms (SAC) inadvertently select for the organisms which are the most fit to survive long journeys in space.
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NEBEL, MARKUS E., SEBASTIAN WILD, MICHAEL HOLZHAUSER, LARS HÜTTENBERGER, RAPHAEL REITZIG, MATTHIAS SPERBER, and THORSTEN STOECK. "JAGUC — A SOFTWARE PACKAGE FOR ENVIRONMENTAL DIVERSITY ANALYSES." Journal of Bioinformatics and Computational Biology 09, no. 06 (December 2011): 749–73. http://dx.doi.org/10.1142/s0219720011005781.
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Background: The study of microbial diversity and community structures heavily relies on the analyses of sequence data, predominantly taxonomic marker genes like the small subunit of the ribosomal RNA (SSU rRNA) amplified from environmental samples. Until recently, the "gold standard" for this strategy was the cloning and Sanger sequencing of amplified target genes, usually restricted to a few hundred sequences per sample due to relatively high costs and labor intensity. The recent introduction of massive parallel tag sequencing strategies like pyrosequencing (454 sequencing) has opened a new window into microbial biodiversity research. Due to its swift nature and relatively low expense, this strategy produces millions of environmental SSU rDNA sequences granting the opportunity to gain deep insights into the true diversity and complexity of microbial communities. The bottleneck, however, is the computational processing of these massive sequence data, without which, biologists are hardly able to exploit the full information included in these sequence data. Results: The freely available standalone software package JAGUC implements a broad regime of different functions, allowing for efficient and convenient processing of a huge number of sequence tags, including importing custom-made reference data bases for basic local alignment searches, user-defined quality and search filters for analyses of specific sets of sequences, pairwise alignment-based sequence similarity calculations and clustering as well as sampling saturation and rank abundance analyses. In initial applications, JAGUC successfully analyzed hundreds of thousands of sequence data (eukaryote SSU rRNA genes) from aquatic samples and also was applied for quality assessments of different pyrosequencing platforms. Conclusions: The new program package JAGUC is a tool that bridges the gap between computational and biological sciences. It enables biologists to process large sequence data sets in order to infer biological meaning from hundreds of thousands of raw sequence data. JAGUC offers advantages over available tools which are further discussed in this manuscript.
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Koopman, Margaret M., Danielle M. Fuselier, Sarah Hird, and Bryan C. Carstens. "The Carnivorous Pale Pitcher Plant Harbors Diverse, Distinct, and Time-Dependent Bacterial Communities." Applied and Environmental Microbiology 76, no. 6 (January 22, 2010): 1851–60. http://dx.doi.org/10.1128/aem.02440-09.
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ABSTRACT The ability of American carnivorous pitcher plants (Sarracenia) to digest insect prey is facilitated by microbial associations. Knowledge of the details surrounding this interaction has been limited by our capability to characterize bacterial diversity in this system. To describe microbial diversity within and between pitchers of one species, Sarracenia alata, and to explore how these communities change over time as pitchers accumulate and digest insect prey, we collected and analyzed environmental sequence tag (454 pyrosequencing) and genomic fingerprint (automated ribosomal intergenic spacer analysis and terminal restriction fragment length polymorphism) data. Microbial richness associated with pitcher plant fluid is high; more than 1,000 unique phylogroups were identified across at least seven phyla and 50 families. We documented an increase in bacterial diversity and abundance with time and observed repeated changes in bacterial community composition. Pitchers from different plants harbored significantly more similar bacterial communities at a given time point than communities coming from the same genetic host over time. The microbial communities in pitcher plant fluid also differ significantly from those present in the surrounding soil. These findings indicate that the bacteria associated with pitcher plant leaves are far from random assemblages and represent an important step toward understanding this unique plant-microbe interaction.
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Pellissier, Loïc, Anne Oppliger, Alexandre H. Hirzel, Dessislava Savova-Bianchi, Guilain Mbayo, Fabio Mascher, Stefan Kellenberger, and Hélène Niculita-Hirzel. "Airborne and Grain Dust Fungal Community Compositions Are Shaped Regionally by Plant Genotypes and Farming Practices." Applied and Environmental Microbiology 82, no. 7 (January 29, 2016): 2121–31. http://dx.doi.org/10.1128/aem.03336-15.
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ABSTRACTChronic exposure to airborne fungi has been associated with different respiratory symptoms and pathologies in occupational populations, such as grain workers. However, the homogeneity in the fungal species composition of these bioaerosols on a large geographical scale and the different drivers that shape these fungal communities remain unclear. In this study, the diversity of fungi in grain dust and in the aerosols released during harvesting was determined across 96 sites at a geographical scale of 560 km2along an elevation gradient of 500 m by tag-encoded 454 pyrosequencing of the internal transcribed spacer (ITS) sequences. Associations between the structure of fungal communities in the grain dust and different abiotic (farming system, soil characteristics, and geographic and climatic parameters) and biotic (wheat cultivar and previous crop culture) factors were explored. These analyses revealed a strong relationship between the airborne and grain dust fungal communities and showed the presence of allergenic and mycotoxigenic species in most samples, which highlights the potential contribution of these fungal species to work-related respiratory symptoms of grain workers. The farming system was the major driver of the alpha and beta phylogenetic diversity values of fungal communities. In addition, elevation and soil CaCO3concentrations shaped the alpha diversity, whereas wheat cultivar, cropping history, and the number of freezing days per year shaped the taxonomic beta diversity of these communities.
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Thiele, Stefan, Bernhard M. Fuchs, Nagappa Ramaiah, and Rudolf Amann. "Microbial Community Response during the Iron Fertilization Experiment LOHAFEX." Applied and Environmental Microbiology 78, no. 24 (October 12, 2012): 8803–12. http://dx.doi.org/10.1128/aem.01814-12.
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ABSTRACTIron fertilization experiments in high-nutrient, low-chlorophyll areas are known to induce phytoplankton blooms. However, little is known about the response of the microbial community upon iron fertilization. As part of the LOHAFEX experiment in the southern Atlantic Ocean,BacteriaandArchaeawere monitored within and outside an induced bloom, dominated byPhaeocystis-like nanoplankton, during the 38 days of the experiment. The microbial production increased 1.6-fold (thymidine uptake) and 2.1-fold (leucine uptake), while total cell numbers increased only slightly over the course of the experiment. 454 tag pyrosequencing of partial 16S rRNA genes and catalyzed reporter deposition fluorescencein situhybridization (CARD FISH) showed that the composition and abundance of the bacterial and archaeal community in the iron-fertilized water body were remarkably constant without development of typical bloom-related succession patterns. Members of groups usually found in phytoplankton blooms, such asRoseobacterandGammaproteobacteria, showed no response or only a minor response to the bloom. However, sequence numbers and total cell numbers of the SAR11 and SAR86 clades increased slightly but significantly toward the end of the experiment. It seems that although microbial productivity was enhanced within the fertilized area, a succession-like response of the microbial community upon the algal bloom was averted by highly effective grazing. Only small-celled members like the SAR11 and SAR86 clades could possibly escape the grazing pressure, explaining a net increase of those clades in numbers.
Dissertations / Theses on the topic "Tag-pyrosequencing 454"
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Byers, Robert L. "Marker Discovery in Allotetraploid Cotton Using 454 Pyrosequencing." BYU ScholarsArchive, 2011. https://scholarsarchive.byu.edu/etd/2663.
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A narrow germplasm base and a complex allotetraploid genome have historically made the discovery of single nucleotide polymorphism (SNP) markers difficult in cotton (Gossypium hirsutum). We conducted a genome reduction experiment to identify SNPs from two accessions of G. hirsutum and two accessions of G. barbadense. Approximately 2 million sequence reads were assembled into contigs with an N50 of 508 bp and analyzed for SNPs. A total of 11,834 and 1,679 SNPs between the accessions G. hirsutum and G. barbadense, respectively, were identified with highly conservative parameters (a minimum read depth of 8x at each SNP and a 100% identity of all reads within an accession at the SNP). Additionally, 4,327 SNPs were identified between accessions of G. hirsutum in and assembly of Expressed Sequence Tags (ESTs). 320 and 252 KASPAR assays were designed for SNP mapping in non-genic and genic regions respectively. 187 markers in total (136 non-genic, 51 genic) were mapped using KBioscience KASPar genotyping assays in a segregating F2 population using the Fluidigm EP1 system. EST The target genome of EST markers was successfully predicted bioinformaticly diploid reference sequences. Examination of nucleotide substitutions and SNP frequencies further confirms validity of new markers. A genetic map was constructed using a large G. hirsutum segregating F2 population. Genetic maps generated by these newly identified markers will be used to locate quantitative, economically important regions within the cotton genome.
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Georges, Clément. "Les communautés de protistes au sein d'un bloom phytoplanctonique dans la région naturellement fertilisée en fer des îles de Kerguelen (Océan Australe)." Thesis, Littoral, 2015. http://www.theses.fr/2015DUNK0415.
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Depuis les années 90, les études portant sur les différentes zones HNLC ont permis d'étudier les effets biologiques et biogéochimiques qu'entrainaient les enrichissements artificiels ou naturels en fer. Il est maintenant bien documenté que l'enrichissement en fer induit des blooms phytoplanctoniques et notamment des blooms de diatomées. En dehors des diatomées, très peu d'informations sont disponibles concernant les autres groupes de protistes et en particulier les protistes hétérotrophes consommateur du phytoplancton. Ce travail a été effectué dans un contexte de fertilisation naturelle en fer, dans la région des îles de Kerguélen (Océan Australe) pendant la campagne KEOPS 2 (Kerguelen Ocean and Plateau compared Study 2) lors de l'initiation du bloom phytoplanctonique et s'est focalisé en particulier sur les protistes hétérotrophes. Des approches moléculaires (tag-pyroséquençages 454) et morphologiques (microscopie) ont été utilisées afin de caractériser la structure des communautés de protistes dans la zone de référence HNLC et dans les différents blooms phytoplanctoniques. l'approche moléculaire a permis (i) de caractériser les communautés de protistes présentes (ii) de mettre en évidence des différences notables entre les structures de protistes dans la région HNLC et la région naturellement enrichie en fer, mais également entre les différents blooms. Les observations microscopiques ont révélé des tendances similaires entre les différentes régions mais aussi des liens significatifs entre les communautés microzooplanctoniques et leurs proies phytoplanctoniques. Les observations microscopiques ont également fournis des valeurs de biomasses des différents compatiments qui ont permis d'estimer le potentiel du microzooplancton en tant que consommateur du phytoplancton ou en tant que source nutritive pour le mésozooplancton. Ce travail représente la première étude caractérisant la communauté des protistes planctoniques dans son ensemble dans un contexte de fertilisation naturelle en ferSince the 90s, studies on different HNLC areas allowed to investigated the biological and biogeochemical effects due to artificial or natural iron-enrichment. It is now well documented that iron enrichment induced phytoplankton blooms and more specifically diatom blooms. With the exception of diatoms, very few information is available concerning other protists groups e. g. heterotrophic protists which are consumers of phytoplankton.This work was performed is a natural iron-fertilization context in the Kerguelen Island area (Southern Ocean) during the KEOPS 2 (Kerguelen Ocean and Plateau compared Study 2) cruise at the beginning of the phytoplankton bloom and focused specifically on heterotrophic protists. Molecular (tag-pyrosequencing 454) and morphological (microscopy) approaches were used to characterize the structure of protist communities in the HNLC reference area and in the phytoplankton blooms. The molecular approach allowed (i) to provide a complete picture of the protist communities (ii) to evidence significant differences in protists structures between HNLC and the naturally iron-fertilized area, but also between the different blooms. Microscopic observation revealed similar trends between regions but also significant links between microzooplanctonic communities and their phytoplankton preys. Microscopic observations also provided biomass values from different compartments allowing an estimation of the potential of microzooplankton as phytoplankton consumer or as a nutrient source for mesozooplankton. Above all, this work represents the first study characterizing the global planktonic protists community in the context of natural iron fertilization
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Zajac, Pawel. "Parallel target selection by trinucleotide threading." Doctoral thesis, KTH, Genteknologi, 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-11284.
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DNA is the code for all life. Via intermediary RNA the information encoded by the genome is relayed to proteins executing the various functions in a cell. Together, this repertoire of inherently linked biological macromolecules determines all characteristics and features of a cell. Technological advancements during the last decades have enabled the pursuit of novel types of studies and the investigation of the cell and its constituents at a progressively higher level of detail. This has shed light on numerous cellular processes and on the underpinnings of several diseases. For the majority of studies focusing on nucleic acids, an amplification step has to be implemented before an analysis, scoring or interrogation method translates the amplified material into relevant biological information. This information can, for instance, be the genotype of particular SNPs or STRs, or the abundance level of a set of interesting transcripts. As such, amplification plays a significant role in nucleic acid assays. Over the years, a number of techniques – most notably PCR – has been devised to meet this amplification need, specifically or randomly multiplying desired regions. However, many of the approaches do not scale up easily rendering comprehensive studies cumbersome, time-consuming and necessitating large quantities of material.Trinucleotide threading (TnT) – forming the red thread throughout this thesis – is a multiplex amplification method, enabling simultaneous targeted amplification of several nucleic acid regions in a specific manner. TnT begins with a controlled linear DNA thread formation, each type of thread corresponding to a segment of interest, by a gap-fill reaction using a restricted trinucleotide set. The whole collection of created threads is subsequently subjected to an exponential PCR amplification employing a single primer pair. The generated material can thereafter be analyzed with a multitude of readout and detection platforms depending on the issue or characteristic under consideration.TnT offers a high level of specificity by harnessing the inherent specificities of a polymerase and a ligase acting on a nucleotide set encompassing three out of the four nucleotide types. Accordingly, several erroneous events have to occur in order to produce artifacts. This necessitates override of a number of control points.The studies constituting this thesis demonstrate integration of the TnT amplification strategy in assays for analysis of various aspects of DNA and RNA. TnT was adapted for expression profiling of intermediately-sized gene sets using both conventional DNA microarrays and massively parallel second generation 454 sequencing for readout. TnT, in conjunction with 454 sequencing, was also employed for allelotyping, defined as determination of allele frequencies in a cohort. In this study, 147 SNPs were simultaneously assayed in a pool comprising genomic DNA of 462 individuals. Finally, TnT was recruited for parallel amplification of STR loci with detection relying on capillary gel electrophoresis. In all investigations, the material generated with TnT was of sufficient quality and quantity to produce reliable and accurate biological information.Taken together, TnT represents a viable multiplex amplification technique permitting parallel amplification of genomic segments, for instance harboring polymorphisms, or of expressed genes. In addition to these, this versatile amplification module can be implemented in assays targeting a range of other features of genomes and transcriptomes.QC 20100819
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Pettersson, Erik. "Interrogation of Nucleic Acids by Parallel Threading." Doctoral thesis, Stockholm : Bioteknologi, Alba Nova, Kungliga Tekniska högskolan, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-4546.
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Hu, Ping. "Effects of Oilseed Meals and Isothiocyanates (ITCS) on Phymatotrichopsis omnivora (Cotton Root Rot) and Soil Microbial Communities." Thesis, 2012. http://hdl.handle.net/1969.1/ETD-TAMU-2012-05-10932.
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The meals from many oilseed crops contain biocidal chemicals that are known to inhibit the growth and activity of several soil pathogens, though little is known concerning impacts on whole soil microbial communities. We investigated the effect of oilseed meals (SMs) from both brassicaceous plants, including mustard and camelina, as well as non-brassicaceous plants, including jatropha and flax, on P. omnivora (the casual agent of cotton root rot) in Branyon clay soil (at 1 and 5% application rates). We also investigated the effect of SMs from camelina, jatropha, flax, and wheat straw on microbial communities in Weswood loam soil. We also used four types of isothiocyanates (ITCs) including allyl, butyl, phenyl, and benzyl ITC to test their effects on P. omnivora growth on potato dextrose agar (PDA), as well as on soil microbial communities in a microcosm study. Community qPCR assays were used to evaluate relative abundances of soil microbial populations. Soil microbial community composition was determined through tag-pyrosequencing using 454 GS FLX titanium technology, targeting ITS and 16S rRNA gene regions for fungal and bacterial communities, respectively.
The results showed that all tested brassicaceous and jatropha SMs were able to inhibit P. omnivora sclerotial germination and hyphal growth, with mustard SM being the most effective. Flax didn't show any inhibitory effects on sclerotial germination. All tested ITCs inhibited P. omnivora OKAlf8 hyphal growth, and the level of inhibition varied with concentration and ITC type. Total soil fungal populations were reduced by ITC addition, and microbial community compositions were changed following SM and ITC application. These changes varied according to the type of SM or ITC added. Our results indicated that SMs of several brassicaceous species as well as jatropha may have potential for reducing cotton root rot as well as some other pathogens. Different SMs releasing varied ITCs may result in differential impacts on soil microorganisms including some pathogens.