Diversity of soil microbial communities: In the perspective of targeting functional genes

Abstract

Abstract



Intensive land use in agriculture can lead to higher loss of biodiversity in soils and subsequently carbon due to tillage and application of pesticides and fertilizers. The microbial communities are pivotal to ecosystem processes in soil such as nutrient cycling, soil formation and plant productivity and thus are affected by land use. The main aim of this thesis is to understand the effects of land-use management on the diversity of both functions and taxonomy of soil microbial communities.

Diversity of microbial enzymes involved is key to understand processes such as carbon cycling in soil. Due to current inefficient methods in obtaining the vast diversity in functional enzymes from environmental samples, we developed a molecular method based on sequence capture to address this issue. As this method is based on oligonucleotide probes, a bioinformatics pipeline to generate probes for targeting mainly diverse functional genes in environmental communities was designed. A web-based implementation of this pipeline was established to make it possible for other researchers to design custom oligos for their own study of interest in understanding ecosystems. The laboratory method ‘captured metagenomics’ was developed and optimized using two soils samples from probes designed to target genes coding for enzymes involved in organic matter degradation. Captured metagenomics was validated and it was superior to current genetic methods such as whole metagenome sequencing.

The land-use management of soils affected the functional composition of microbes in degrading organic matter observed using captured metagenomics. The amount of nitrogen played an important role in defining the functional composition of SOM degrading enzymes while the amount of carbon played a role in defining the taxonomic composition of microbes in the soils. There was no correlation between the functional and taxonomic diversity of microbial communities in the soils that were part of this study. Land-use management also affected the taxonomic composition of AMF and agricultural practices decrease their diversity tremendously. Among the different farming systems, organic farming maintained a higher phylogenetic diversity of AMF with similar cereal production as other strategies. However, the land-use management of soils in this study did not affect bacterial taxonomic composition. These approaches have to be extended to understand microbial responses using enzyme expression to infer their behaviour and adaptation to environmental changes. Similar approaches on functional composition and diversity of microbes in more diverse soils would help us to understand different ecosystems and their functions more clearly.

Abstract (Swedish)

Popular Abstract in English

Soil as an ecosystem is a reservoir for several living organisms including microorganisms, earthworms, collembolans, nematodes and protozoans. They are involved in cycling the nutrients through degrading the organic compounds (source of carbon essential for all living organisms) like plant residues and respire part of it as carbon dioxide. Organic compounds get stored in the biomass of the organisms and contribute to the soil organic pool. Agricultural practices like tillage destroy the biological structure of soils and disrupt connections of fungal hyphae. Mainly microorganisms such as bacteria and fungi degrade the organic material and make nutrients including nitrogen and phosphorus available for plants. Agricultural intensification due to the growing need for food together with global population, these practices including application of pesticides, have caused several environmental issues like soil erosion, increased atmospheric carbon dioxide and loss of biodiversity in soils. It is important to understand these processes and how they affect the organisms in order to find a way towards sustainable agriculture.

As part of this thesis, the effects of different agricultural practices on a particular group of microorganism known as arbuscular mycorrhizal fungi were analysed. These fungi are known to colonize the roots of plants such as barley and wheat and they are specialized in helping them get nutrients from places the plant roots wont be able to reach by forming a tissue structure called hyphae that acts like a pipeline. These fungal communities were mainly affected by the conventional agricultural practices with inorganic fertilizers and pesticides and the fungal diversity was highest in grassland soils. It was also found from a greenhouse experiment that the organic farming produced same amount of barley grains as the conventional farming while maintaining a higher fungal diversity.

In order to understand the microbial processes in environments such as nutrient cycling in soil, it is important to understand the genetic potentials of these microbes through which they would be able to carryout these processes. Most research that was being done on environmental communities was based on the different kinds of organisms that survive in those environments. This is mainly because it is technically easier to measure the different kinds of organisms than to measure their possible potential. It is much harder to look into the genetic potential of various kinds of organisms that live in those conditions that would also have various genetic potentials.



This issue was addressed in this thesis by developing a method based on a genetic method that is well established in medical research to select and look particularly in certain region of a human genome for disease related modifications in the genome. Here in this thesis, we took that method and developed a similar method for researchers that are interested in understanding biological processes carried out by multiple organisms together, as we call it communities. Here they could select and look particularly into the genetic potential of these communities to carry out the biological processes of interest. This is of course based on the genetic information that is available about the different organisms to carry out the specific tasks in those processes. We have also developed a webpage that will assist the researchers in using this method for the processes that they are interested in studying mainly related to environmental and ecological studies.

In this thesis, this method was also applied on soils from grasslands and conventional agriculture to understand and find the differences in microbial potential in degrading organic compounds from these soils. It was found that the different management of these soils affected the ability of the organisms in degrading the organic compounds and not the kinds of organisms in the soils. The amount of nitrogen in the organic compounds present in these soils changes the genetic potential of the microbial community and amount of carbon changes the kinds of organisms populated in those soils. The potential and the diversity of the organisms in these soils were not related. This shows that it is important to look at the potential rather than kinds of the organism in these kinds of environments. With this knowledge of their potential, the microbial responses to environmental changes, such as application of fertilizers where only the active microbes will respond, is currently being measured using the same approach. It will also improve our understanding of these organisms, once we use similar approaches in different soils like rainforest and peatland that are currently under the threat and prevent from loosing organic materials in these soils due to global changes.

• author: Manoharan, Lokeshwaran
• supervisor: Katarina Hedlund
• opponent: Professor Hallin, Sara, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala
• organization: Biodiversity; Soil Ecology (research group)
• publishing date: 2016
• type: Thesis
• publication status: published
• subject: Ecology
• keywords: Soil, metagenomics, sequence capture, microbial communities, functional diversity, taxonomic diversity
• pages: 123 pages
• defense location: Blue Hall, Ecology Building, Sölvegatan 37, Lund 22362
• defense date: 2016-04-29 13:00:00
• ISBN: 978-91-7623-759-5
• ISBN: 978-91-7623-760-1
• language: English
• LU publication?: yes
• id: 1e11f828-321d-4c2e-9eed-0ffd79fbc1b1 (old id 8865963)
• date added to LUP: 2016-05-24 10:03:39
• date last changed: 2020-09-23 15:03:37