Metagenomics for Study of Fungal Ecology

Lindahl, Björn D.; Kuske, Cheryl R.

doi:10.1002/9781118735893.ch13

Cited by 14 publications

(10 citation statements)

References 103 publications

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“…Given how widespread sterol synthesis is in eukaryotes, we had expected to detect more eukaryotic Osc sequences than bacterial sequences in metagenomic databases. However, it has been documented that metagenomic sequencing tends to recover few eukaryotic sequences in general (Lindahl and Kuske, 2013 ). Therefore, the low number of eukaryotic metagenomic sequences more likely reflects a limited number of eukaryotic sequences in metagenome databases rather than the true prevalence of eukaryotic sterol producers in the environment.…”

Section: Resultsmentioning

confidence: 99%

Sterol Synthesis in Diverse Bacteria

2016

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Sterols are essential components of eukaryotic cells whose biosynthesis and function has been studied extensively. Sterols are also recognized as the diagenetic precursors of steranes preserved in sedimentary rocks where they can function as geological proxies for eukaryotic organisms and/or aerobic metabolisms and environments. However, production of these lipids is not restricted to the eukaryotic domain as a few bacterial species also synthesize sterols. Phylogenomic studies have identified genes encoding homologs of sterol biosynthesis proteins in the genomes of several additional species, indicating that sterol production may be more widespread in the bacterial domain than previously thought. Although the occurrence of sterol synthesis genes in a genome indicates the potential for sterol production, it provides neither conclusive evidence of sterol synthesis nor information about the composition and abundance of basic and modified sterols that are actually being produced. Here, we coupled bioinformatics with lipid analyses to investigate the scope of bacterial sterol production. We identified oxidosqualene cyclase (Osc), which catalyzes the initial cyclization of oxidosqualene to the basic sterol structure, in 34 bacterial genomes from five phyla (Bacteroidetes, Cyanobacteria, Planctomycetes, Proteobacteria, and Verrucomicrobia) and in 176 metagenomes. Our data indicate that bacterial sterol synthesis likely occurs in diverse organisms and environments and also provides evidence that there are as yet uncultured groups of bacterial sterol producers. Phylogenetic analysis of bacterial and eukaryotic Osc sequences confirmed a complex evolutionary history of sterol synthesis in this domain. Finally, we characterized the lipids produced by Osc-containing bacteria and found that we could generally predict the ability to synthesize sterols. However, predicting the final modified sterol based on our current knowledge of sterol synthesis was difficult. Some bacteria produced demethylated and saturated sterol products even though they lacked homologs of the eukaryotic proteins required for these modifications emphasizing that several aspects of bacterial sterol synthesis are still completely unknown.

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Section: Resultsmentioning

confidence: 99%

Sterol Synthesis in Diverse Bacteria

2016

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“…By targeting transcription ratios of specific ‘keystone’ genes at the ecosystem scale (i.e. meta‐transcriptomics), information about the interplay between the fungal communities and their environment may be derived that could be used to decipher the role of fungi as mediators of ecosystem responses to environmental change (Lindahl and Kuske, ; Treseder and Lennon, ).…”

Section: Discussionmentioning

confidence: 99%

Fungal ecological strategies reflected in gene transcription ‐ a case study of two litter decomposers

Barbi

Kohler

Barry

et al. 2019

Environmental Microbiology

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Summary Microbial communities interplay with their environment through their functional traits that can be a response or an effect on the environment. Here, we explore how a functional trait—the decomposition of organic matter, can be addressed based on genetic markers and how the expression of these markers reflect ecological strategies of two fungal litter decomposer Gymnopus androsaceus and Chalara longipes. We sequenced the genomes of these two fungi, as well as their transcriptomes at different steps of Pinus sylvestris needles decomposition in microcosms. Our results highlighted that if the gene content of the two species could indicate similar potential decomposition abilities, the expression levels of specific gene families belonging to the glycoside hydrolase category reflected contrasting ecological strategies. Actually, C. longipes, the weaker decomposer in this experiment, turned out to have a high content of genes involved in cell wall polysaccharides decomposition but low expression levels, reflecting a versatile ecology compare to the more competitive G. androsaceus with high expression levels of keystone functional genes. Thus, we established that sequential expression of genes coding for different components of the decomposer machinery indicated adaptation to chemical changes in the substrate as decomposition progressed.

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“…To do this while minimizing the known effects of vegetation biome types on microbial community structure and function (9, 57), we chose to focus on forests dominated by a single plant family, the Pinaceae (Table S1). The Pinaceae are ideal for exploring environmentcommunity-function relationships across the fungal kingdom because they have a broad distribution across North America and show low levels of host specificity for mycorrhizal fungi within the family (47,58). For example, North American pines readily associate with European ectomycorrhizal fungi (44), and co-occurring Pinaceae and angiosperms often share most common ectomycorrhizal fungi (59).…”

Section: Methodsmentioning

confidence: 99%

Endemism and functional convergence across the North American soil mycobiome

Talbot

Bruns

Taylor

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

468

437

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Identifying the ecological processes that structure communities and the consequences for ecosystem function is a central goal of ecology. The recognition that fungi, bacteria, and viruses control key ecosystem functions has made microbial communities a major focus of this field. Because many ecological processes are apparent only at particular spatial or temporal scales, a complete understanding of the linkages between microbial community, environment, and function requires analysis across a wide range of scales. Here, we map the biological and functional geography of soil fungi from local to continental scales and show that the principal ecological processes controlling community structure and function operate at different scales. Similar to plants or animals, most soil fungi are endemic to particular bioregions, suggesting that factors operating at large spatial scales, like dispersal limitation or climate, are the first-order determinants of fungal community structure in nature. By contrast, soil extracellular enzyme activity is highly convergent across bioregions and widely differing fungal communities. Instead, soil enzyme activity is correlated with local soil environment and distribution of fungal traits within the community. The lack of structure-function relationships for soil fungal communities at continental scales indicates a high degree of functional redundancy among fungal communities in global biogeochemical cycles.T he structure and function of ecological communities are intimately linked, such that the number and identity of species within a community often affect the key ecosystem properties of primary productivity (1), resistance and resilience to disturbance (2), and rates of nutrient cycling (3). However, understanding the extent to which structure-function relationships hold across communities and over large spatial scales continues to be a major goal of ecological research. Identifying these relationships for microbial organisms is particularly critical, because these organisms control rates of key ecosystem processes (the cycling of nitrogen, phosphorus, and carbon) (4) and directly affect the community structure of plants and animals through pathogenic or mutualistic interactions (5). As such, microbial activity is also intrinsic to Earth system models that inform citizens and policy makers of ecosystem dynamics and energy exchange between the biosphere and the atmosphere (6). As in plant communities of tropical rainforests (7), the incredible number of microbial taxa on Earth has been a challenge for understanding the link between diversity and function. Advances in DNA sequencing technology have recently allowed for a robust characterization of bacterial biogeographic patterns (8); however, to date, studies have examined structure-function relationships at a fixed scale (9-12). As a result, it is not yet clear how microbial function is linked to largescale biogeographic patterns, whether or not this link is a more reliable determinant of microbial function in global biogeochemical cycl...

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Metagenomics for Study of Fungal Ecology

Cited by 14 publications

References 103 publications

Sterol Synthesis in Diverse Bacteria

Sterol Synthesis in Diverse Bacteria

Fungal ecological strategies reflected in gene transcription ‐ a case study of two litter decomposers

Endemism and functional convergence across the North American soil mycobiome

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