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Captured metagenomics of fungi in agricultural soils

Arnellos, Dimitrios (2017) BINP30 20162
Degree Projects in Bioinformatics
Abstract
Soil microbial communities play an important role in the functioning of soils by degrading soil organic matter and making nutrients ac-cessible to plants. An in-depth knowledge of their structure and pro-cesses are of particular interest to agriculture. Fungi as soil organic matter decomposers draw attention to focus on this particular group of microorganisms. Here we studied the differences of genes in-volved in carbon metabolism and taxa that occur between wheat cultural soils and grassland soils. Fungal sequences were being isolated from sequences previously obtained by the “captured meta-genomics” method from the soil samples and were taxonomically and functionally annotated. We performed exploratory analyses that grouped functions... (More)
Soil microbial communities play an important role in the functioning of soils by degrading soil organic matter and making nutrients ac-cessible to plants. An in-depth knowledge of their structure and pro-cesses are of particular interest to agriculture. Fungi as soil organic matter decomposers draw attention to focus on this particular group of microorganisms. Here we studied the differences of genes in-volved in carbon metabolism and taxa that occur between wheat cultural soils and grassland soils. Fungal sequences were being isolated from sequences previously obtained by the “captured meta-genomics” method from the soil samples and were taxonomically and functionally annotated. We performed exploratory analyses that grouped functions between the wheat cultural soil samples and grassland soil samples from the functional perspective, however, subsequent statistical power was too weak to further validate the results. A clear distinction was achieved on the taxonomical level where patterns previously observed are being confirmed. (Less)
Popular Abstract
Differences in fungal communities between two soil types

In Lund University a method was developed where instead of sequencing the whole genomes of microorganisms in soil samples, we would target only specific regions of interest on all of the genomes. This is achieved by developing probes that target these specific regions, which subsequently can be isolated and sequenced on their own. The method targets genes from carbon catabolising pathways and proteases and it is developed specifically for soil samples. A first study was done, in which the targeted DNA was sequenced and which was dominated by bacteria (98%).

In this study, we wanted to focus on fungi. Fungi occupy a special niche as soil organic matter decomposers and their... (More)
Differences in fungal communities between two soil types

In Lund University a method was developed where instead of sequencing the whole genomes of microorganisms in soil samples, we would target only specific regions of interest on all of the genomes. This is achieved by developing probes that target these specific regions, which subsequently can be isolated and sequenced on their own. The method targets genes from carbon catabolising pathways and proteases and it is developed specifically for soil samples. A first study was done, in which the targeted DNA was sequenced and which was dominated by bacteria (98%).

In this study, we wanted to focus on fungi. Fungi occupy a special niche as soil organic matter decomposers and their functions improve plant growth. Thus, since the DNA from the previous study was already sequenced, the goal now was to identify only the fungal sequences and compare the differences between the samples. The comparison was made by measuring the differences in the functional and taxonomical aspects between the samples. There were two types of samples: wheat agricultural soil samples and grassland soil samples. By comparing the differences between these two soil samples, we would see how intensive agricultural practices affect the fungal communities.

The sequences that were determined to be fungal, were searched against online databases to be mapped to pathways and protein domains. In this way, we could assess the functionalities that the fungal communities possessed.

The results were that, from the taxonomical perspective, we had more fungi in wheat cultural soils than grassland soils. In terms of functionality, exploratory analyses suggested that grassland soils do indeed differentiate from wheat cultural soils. However, when a more definitive approach was attempted, the data were too few to yield statistically significant results.

The method that creates probes for targeting genes gives an enrichment for the genes with the functions that we are looking for. However, when we want to target a taxonomical group that is only a fraction of the sequences, then the sample is not big enough for a thorough analysis. It is necessary in this occasion that the sampling stage is repeated by having created probes only for fungi for this analysis to be successful.

Master’s Degree Project in Bioinformatics 30 credits 2017
Department of Biology, Lund University

Advisor: Dag Ahrén
Department of Biology, Lund University (Less)
Please use this url to cite or link to this publication:
author
Arnellos, Dimitrios
supervisor
organization
course
BINP30 20162
year
type
H2 - Master's Degree (Two Years)
subject
language
English
id
8928780
date added to LUP
2017-11-23 15:02:08
date last changed
2017-11-23 15:02:08
@misc{8928780,
  abstract     = {Soil microbial communities play an important role in the functioning of soils by degrading soil organic matter and making nutrients ac-cessible to plants. An in-depth knowledge of their structure and pro-cesses are of particular interest to agriculture. Fungi as soil organic matter decomposers draw attention to focus on this particular group of microorganisms. Here we studied the differences of genes in-volved in carbon metabolism and taxa that occur between wheat cultural soils and grassland soils. Fungal sequences were being isolated from sequences previously obtained by the “captured meta-genomics” method from the soil samples and were taxonomically and functionally annotated. We performed exploratory analyses that grouped functions between the wheat cultural soil samples and grassland soil samples from the functional perspective, however, subsequent statistical power was too weak to further validate the results. A clear distinction was achieved on the taxonomical level where patterns previously observed are being confirmed.},
  author       = {Arnellos, Dimitrios},
  language     = {eng},
  note         = {Student Paper},
  title        = {Captured metagenomics of fungi in agricultural soils},
  year         = {2017},
}