Fungal Diversity in Sediments From Deep-Sea Extreme Ecosystems: Insights Into Low- and High-Temperature Hydrothermal Vents, and an Oxygen Minimum Zone in the Southern Gulf of California, Mexico

Abstract

Deep-sea sediments are vast microbial habitats that cover almost two-thirds of the planet’s surface. Particularly, sediments in hydrothermal vents and oxygen minimum zones (OMZ) represent emblematic, and poorly understood extreme niches that pose strong selective pressures to life, representing untapped reservoirs of a unique microbial diversity. Nonetheless, the mycobiota in these systems remains relatively unknown. Here, we explored fungal diversity and community structure in deep-sea sediments collected from low- and high-temperature vent systems (Pescadero Basin, Pescadero Transform Fault, and Alarcón Rise) and an OMZ (Alfonso Basin) in the southern Gulf of California, by using high-throughput Illumina sequencing of the ITS1 region. We identified 102 fungal amplicon sequence variants (ASVs), principally affiliated to the Ascomycota and Basidiomycota. Our results also evidenced a high proportion of widely distributed, uncultured phylotypes (e.g., unknown clades closely related to the Basidiomycota such as Fungi sp. 18 and 19 formerly reported from deep-sea), evidencing the copious occurrence of novel fungal lineages with limited distribution to deep-sea sediments. Overall, the largest number of ASVs was recovered from high-temperature vent systems, corroborating these as diversity hotspots. In addition, clustering patterns across samples and the FUNGuild analysis revealed characteristic assemblages in each ecosystem, which could be linked to site-specific processes. This study provides baseline data paving the way for a better understanding of deep-sea fungal diversity, evidencing its potential importance in ecosystem functioning.

OMICS and Other Advanced Technologies in Mycological Applications

“…Several fungal microorganisms, including anaerobic fungi, lichen-forming fungi, true marine/marine-derived fungi, black fungi, halotolerant yeast, and Aspergillus , possess unique physiological and morphological adaptations that enable them to thrive in extreme conditions [ 131 , 132 , 133 , 134 ]. They are also known to produce a wide range of bioactive compounds such as enzymes, pigments, antibiotics, and other secondary metabolites that have potential applications in the pharmaceutical, cosmeceutical, and chemical industries [ 94 , 135 , 136 ].…”

“…Furthermore, the application of omics technologies, including glycomics (the study of carbohydrates and their biological functions), has played a pivotal role in enhancing our comprehension of fungi, their diversity, and their behavior in underexplored marine environments, specifically the deep sea (greater than 1000 m below sea level), which is considered as one of the most extreme environments of the ocean [ 20 ]. These technologies have proven to be a valuable source of bioactive molecules from marine fungi [ 132 , 133 , 134 ]. These techniques can be used to identify potential anti-infective drugs derived from extreme and unique environments [ 146 ].…”

Fungal Abundance and Diversity in the Mariana Trench, the Deepest Ecosystem on Earth

“…Fungi are a ubiquitous component of deep-sea ecosystems, and they span from hypersaline anoxic basins [28,29] to cold seeps [30] and hydrothermal vents [31,32] either in surface and subsurface sediments [33][34][35][36], playing an important role in deep-sea biogeochemical processes and nutrient cycling [37][38][39][40][41]. In particular, fungi are known to contribute to the degradation of complex organic polymers [42,43] and denitrification processes [44], and their diversity is influenced by a variety of environmental factors (e.g., temperature, salinity, nutrient availability [45,46]).…”

Mycobiota in the Bottom Grounds of the Goryachinsky Thermal Spring

“…При использовании современных приемов секвенирования тотальной ДНК в образцах воды и донных грунтов горячих источников обнаружены, кроме аскомицетов, базидиомицетов и мукоромицетов, операционнотаксономические единицы (ОТЕ), принадлежащие и к другим отделам грибов [Kambura et al, 2016;Velez et al, 2022]. Так, в донных отложениях и воде горячих источников содового озера Магади (Кения) из 151 ОТЕ, идентифицированных до вида, большинство (80%) отнесены к отделу Ascomycota, 11.5% к Basidiomycota, остальные относились к отделам Glomeromycota, Chytridiomycota и ранним эволюционным линиям грибов [Kambura et al, 2016].…”

“…Работы по характеристике состава грибов в горячих источниках, в которых одновременно применяли методы посева на питательные среды и технологии NGS при анализе выделенных из природы образцов, единичны. В них изучали микобиоту гидротермальных источников на больших глубинах в океанах Velez et al, 2022].…”