Large-Scale Integration of Amplicon Data Reveals Massive Diversity within Saprospirales, Mostly Originating from Saline Environments

Abstract

The order Saprospirales, a group of bacteria involved in complex degradation pathways, comprises three officially described families: Saprospiraceae, Lewinellaceae, and Haliscomenobacteraceae. These collectively contain 17 genera and 31 species. The current knowledge on Saprospirales diversity is the product of traditional isolation methods, with the inherited limitations of culture-based approaches. This study utilized the extensive information available in public sequence repositories combined with recent analytical tools to evaluate the global evidence-based diversity of the Saprospirales order. Our analysis resulted in 1183 novel molecular families, 15,033 novel molecular genera, and 188 K novel molecular species. Of those, 7 novel families, 464 novel genera, and 1565 species appeared in abundances at ≥0.1%. Saprospirales were detected in various environments, such as saline water, freshwater, soil, various hosts, wastewater treatment plants, and other bioreactors. Overall, saline water was the environment showing the highest prevalence of Saprospirales, with bioreactors and wastewater treatment plants being the environments where they occurred with the highest abundance. Lewinellaceae was the family containing the majority of the most prevalent species detected, while Saprospiraceae was the family with the majority of the most abundant species found. This analysis should prime researchers to further explore, in a more targeted way, the Saprospirales proportion of microbial dark matter.

Global diversity and biogeography of Lyophyllum inferred from amplicon datasets

“…Ongoing research involves the extensive survey of ITS sequences in public databases, leading to the design of new ITS primers. These primers, compared to existing ones, exhibit improved coverage across different fungal taxa, enabling selective investigation of fungal communities in mycorrhizal, soil, and other environmental samples (Mourgela et al, 2023). This contributes to laying the groundwork for ecological studies on fungal diversity and community structure in the era of large-scale DNA sequencing.…”

“…Furthermore, the massive number of amplicon sequencing samples means a vast number of geographic locations sampled. Our method is not limited to the study of Lyophyllum, and other fungal potential diversity; in general, research on the diversity of bacteria, fungi, and plant pathogens can also benefit from this approach (Koch and Herr, 2021;Li P. et al, 2023;Mourgela et al, 2023). Given the increasing amount of data generated by amplicon sequencing, although resources can be saved based on existing sequence databases, it should be noted that amplicon sequencing itself is costly and has clear disadvantages compared to field research, such as difficulty in accurately identifying species, and the greater difficulty of distinguishing closely related species (Lam et al, 2020).…”

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“…Ongoing research involves the extensive survey of ITS sequences in public databases, leading to the design of new ITS primers. These primers, compared to existing ones, exhibit improved coverage across different fungal taxa, enabling selective investigation of fungal communities in mycorrhizal, soil, and other environmental samples (Mourgela et al, 2023). This contributes to laying the groundwork for ecological studies on fungal diversity and community structure in the era of large-scale DNA sequencing.…”

“…Furthermore, the massive number of amplicon sequencing samples means a vast number of geographic locations sampled. Our method is not limited to the study of Lyophyllum, and other fungal potential diversity; in general, research on the diversity of bacteria, fungi, and plant pathogens can also benefit from this approach (Koch and Herr, 2021;Li P. et al, 2023;Mourgela et al, 2023). Given the increasing amount of data generated by amplicon sequencing, although resources can be saved based on existing sequence databases, it should be noted that amplicon sequencing itself is costly and has clear disadvantages compared to field research, such as difficulty in accurately identifying species, and the greater difficulty of distinguishing closely related species (Lam et al, 2020).…”

DataSheet_1.zip

“…Ongoing research involves the extensive survey of ITS sequences in public databases, leading to the design of new ITS primers. These primers, compared to existing ones, exhibit improved coverage across different fungal taxa, enabling selective investigation of fungal communities in mycorrhizal, soil, and other environmental samples (Mourgela et al, 2023). This contributes to laying the groundwork for ecological studies on fungal diversity and community structure in the era of large-scale DNA sequencing.…”