High diversity of lysis‐resistant cells upon the application of targeted physical and chemical lysis to environmental samples originating from three different water bodies

Junier, Thomas; Paul, Christophe; Ramírez, Andrea Corona; Filippidou, Sevasti; Fatton, Mathilda; Lehmann, Anaël; Chain, Patrick; Ariztegui, Daniel; Vennemann, Torsten; Viollier, Patrick H.; Junier, Pilar

doi:10.1002/edn3.309

Cited by 4 publications

(4 citation statements)

References 125 publications

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“…Figure 6E and F showed that most ASVs in both environments (lake sediments and microbial mats) were either enriched in the total community or in the lysis-resistant fraction, with only a small proportion of them showing similar abundance in both fractions (index values 0.2-0.8). However, in contrast to Bacteria where OTUs would tend to be consistently found in either fraction [28], for Fungi, this is not the case and ASVs were found equally in both fractions in different environmental samples (Additional Fig. 3).…”

Section: Beyond Known Taxamentioning

confidence: 89%

“…This was the basis to develop a method that uses physical and chemical treatments to lyse non-resistant cells and to enrich lysis-resistant structures [27]. When applied to bacterial communities, the procedure results in the enrichment of endospores from Firmicutes, but also lysis-resistant spores from other bacteria such as Actinobacteria or Cyanobacteria [28]. Even though in the case of the various structures promoting survival in fungi, their enhanced resistance to lysis has not been assessed systematically, previous studies have shown that lysis of survival structures such as spores requires harsher conditions [29], and that modifications in the spore wall composition and structure promote resistance [30].…”

Section: Introductionmentioning

confidence: 99%

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Assessment of fungal spores and spore-like diversity in environmental samples by targeted lysis

et al. 2023

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At particular stages during their life cycles, fungi use multiple strategies to form specialized structures to survive unfavorable environmental conditions. These strategies encompass sporulation, as well as cell-wall melanization, multicellular tissue formation or even dimorphism. The resulting structures are not only used to disperse to other environments, but also to survive long periods of time awaiting favorable growth conditions. As a result, these specialized fungal structures are part of the microbial seed bank, which is known to influence the microbial community composition and contribute to the maintenance of diversity. Despite the importance of the microbial seed bank in the environment, methods to study the diversity of fungal structures with improved resistance only target spores dispersing in the air, omitting the high diversity of these structures in terms of morphology and environmental distribution. In this study, we applied a separation method based on cell lysis to enrich lysis-resistant fungal structures (for instance, spores, sclerotia, melanized yeast) to obtain a proxy of the composition of the fungal seed bank. This approach was first evaluated in-vitro in selected species. The results obtained showed that DNA from fungal spores and from yeast was only obtained after the application of the enrichment method, while mycelium was always lysed. After validation, we compared the diversity of the total and lysis-resistant fractions in the polyextreme environment of the Salar de Huasco, a high-altitude athalassohaline wetland in the Chilean Altiplano. Environmental samples were collected from the salt flat and from microbial mats in small surrounding ponds. Both the lake sediments and microbial mats were dominated by Ascomycota and Basidiomycota, however, the diversity and composition of each environment differed at lower taxonomic ranks. Members of the phylum Chytridiomycota were enriched in the lysis-resistant fraction, while members of the phylum Rozellomycota were never detected in this fraction. Moreover, we show that the community composition of the lysis-resistant fraction reflects the diversity of life cycles and survival strategies developed by fungi in the environment. To the best of our knowledge this is the first time that the fungal diversity is explored in the Salar de Huasco. In addition, the method presented here provides a simple and culture independent approach to assess the diversity of fungal lysis-resistant cells in the environment.

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Section: Beyond Known Taxamentioning

confidence: 89%

Section: Introductionmentioning

confidence: 99%

Assessment of fungal spores and spore-like diversity in environmental samples by targeted lysis

et al. 2023

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“…Firmicutes are spore formers; and further, spore formation is a survival trait to survive challenging environments such as the cold. Firmicutes have been reported to be lysis resistant during the DNA extraction process (Junier et al 2022). Therefore, it is possible during the DNA extraction procedure that we were unsuccessful in lysing Firmicutes, leading to their absence in the microbial-community data.…”

Section: Microorganisms Isolated From Snow Containing Particulate Mattermentioning

confidence: 99%

Microbial activity in dust-contaminated Antarctic snow

Thurston,

Foley,

Rosten

et al. 2023

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During weather events, particles can accumulate on the snow near the Pegasus ice and Phoenix compacted-snow Runways at the US McMurdo Station in Antarctica. The deposited particles melt into the surface, initially forming steep-sided holes, which can widen into patches of weak and rotten snow and ice. These changes negatively impact the ice and snow runways and snow roads trafficked by vehicles. To understand the importance of microbes on this process, we examined deposited dust particles and their microbial communities in snow samples collected near the runways. Snow samples were analyzed at the Cold Regions Research and Engineering Laboratory where we performed a respiration study to measure the microbial activity during a simulated melt, isolated microorganisms, examined particle-size distribution, and performed 16S rRNA gene sequencing. We measured higher levels of carbon dioxide production from a sample containing more dust than from a sample containing less dust, a finding consistent with viable dust-associated microbial communities. Additionally, eleven microorganisms were isolated and cultured from snow samples containing dust particles. While wind patterns and satellite images suggest that the deposited particles originate from nearby Black Island, comparisons of the particle size and chemical composition were inconclusive.

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“…This method uses physical and chemical treatments to lyse non-resistant cells and to enrich lysis-resistant structures. The procedure results in the enrichment of endospores from Firmicutes, but also lysis-resistant cell forms from other bacteria (25). Moreover, the use of the lysis-enrichment method has been recently extended to study lysis-resistant communities in archaea.…”

Section: Introductionmentioning

confidence: 99%

Assessment of Fungal spores and spore-like diversity in Environmental Samples by Targeted Lysis

Ramírez

Bregnard

Junier

et al. 2022

Preprint

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Resistant cells, such as spores are a vital part of the life cycle of fungi with essential roles in ecology and reproduction. These structures help fungi not only to disperse to other environments but also to survive long periods of time awaiting favorable growth conditions. As a result, fungal spores and resistant cells are part of the microbial seed bank, which is known to influence the microbial community composition, and contribute to the maintenance of diversity. Despite the importance of resistant cells in the life-cycles of fungi, and more largely, of microbial seed banks in the environment, the methods to study the diversity of fungal resistant cells only target spores dispersing in the air, omitting the diversity of these cells elsewhere. In this study, we applied a separation method based on lysis-resistance to enrich fungal spores and resistant cells to obtain a proxy of the composition of the fungal seed bank. This approach was first evaluated in selected species. The results obtained showed that DNA from fungal spores and from yeast is only obtained after the application of the lysis-resistant enrichment method, while mycelium is always lysed. After validation, we compared the total and fungal seed bank diversity in the polyextreme environment of the Salar de Huasco, a high-altitude athalassohaline wetland in the Chilean Altiplano. Environmental samples were collected from a salt flat and from microbial mats in small surrounding ponds. Both the lake sediments and microbial mats were dominated by Ascomycota and Basidiomycota, however, the diversity and composition of each environment differed. Members of the phylum Chytridiomycota were enriched in the lysis-resistant fraction, while members of the phylum Rozellomycota were never detected in this fraction. Moreover, we show that the community composition of the lysis-resistant fraction reflects the diversity of life cycles and survival strategies developed by fungi in the environment. To the best of our knowledge this is the first time that the fungal diversity is explored in the Salar de Huasco. In addition, the method presented here provides a simple and culture independent approach to assess the diversity of fungal lysis-resistant cells in the environment.

show abstract

High diversity of lysis‐resistant cells upon the application of targeted physical and chemical lysis to environmental samples originating from three different water bodies

Cited by 4 publications

References 125 publications

Assessment of fungal spores and spore-like diversity in environmental samples by targeted lysis

Assessment of fungal spores and spore-like diversity in environmental samples by targeted lysis

Microbial activity in dust-contaminated Antarctic snow

Assessment of Fungal spores and spore-like diversity in Environmental Samples by Targeted Lysis

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