Comparison of Deep-Sea Picoeukaryotic Composition Estimated from the V4 and V9 Regions of 18S rRNA Gene with a Focus on the Hadal Zone of the Mariana Trench

Han, Yuye; Guo, Cui; Guan, Xuran; McMinn, Andrew; Liu, Lu; Zheng, Guiliang; Jiang, Yong; Liang, Yantao; Tian, Jie

doi:10.1007/s00248-021-01747-2

Cited by 7 publications

(3 citation statements)

References 91 publications

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“…In addition, phosphorus and pH strongly influenced the dynamics of microeukaryotes and archaea, respectively. This pattern is consistent with previous studies ( 15 , 32 , 33 ), demonstrating vertical gradients as the most important environmental factor shaping the distribution of microbial communities in the Mariana Trench. Hadal environments, distinguished by their elevated hydrostatic pressure and isolated from the hydro-topography, are comparable to abyssal oceans in terms of physical and chemical conditions such as temperature, salinity, dissolved oxygen, and nutrients ( 34 ).…”

Section: Discussionsupporting

confidence: 93%

Depth shapes microbiome assembly and network stability in the Mariana Trench

Li,

Kan,

Liu

et al. 2024

Microbiol Spectr

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The Mariana Trench, a stable marine ecosystem minimally impacted by human activities, has the greatest vertical depth in the ocean. Depth gradients profoundly influence the physical, chemical, and biotic conditions in the deep oceans. Therefore, elucidating the depth-related effects on microbiome assembly and interaction is integral to understanding marine hadal ecosystems. In this study, eight samples were collected along vertical gradients to compare the assembly and associations of bacteria, archaea, and microeukaryotes, in the Marina Trench using high-throughput sequencing. There is no significant difference in the niche breadth occupied by bacteria, archaea, and microeukaryotes, indicating that microorganisms from the surface to the hadal water of the trench are well adapted to this environment. Stochastic processes significantly influenced the distribution of bacteria and microeukaryotes as well as archaea when the phylogenetic distance was considered. Although diversities of all three microbial domains were consistent across depth, distinct bacterial and archaeal community structures occurred between hadal waters (3,699–8,727 m) and upper bathypelagic waters (≤1,000 m). Bacteria and archaea in upper bathypelagic zones were more affected by a random process and exhibited higher phylogenetic distance than those in hadal waters. In contrast, stochasticity in assembly and phylogenetic distance of microeukaryotes remained unchanged. Bacteria made vital contributions to the stability of trench microbiomes, while consistent community stability was observed between the upper bathypelagic and hadal zones. Our results reveal the complexity of community assembly and associations of multi-domain microbiomes in hadal ecosystems and also highlight the differential adaptations and contributions of prokaryotes vs. microeukaryotes to microbiome community stability and robustness. IMPORTANCE Exploring microbial interactions and their stability/resilience from the surface to the hadal ocean is critical for further understanding of the microbiome structure and ecosystem function in the Mariana Trench. Vertical gradients did not destabilize microbial communities after long-term evolution and adaption. The uniform niche breadth, diversity, community complexity, and stability of microbiomes in both upper bathypelagic and hadal waters suggest the consistent roles of microbiomes in elemental cycling and adaptive strategies to overcome extreme environmental conditions. Compared with microeukaryotes, bacteria and archaea play a pivotal role in shaping the stability of the hadal microbiome. The consistent co-occurrence stability of microbiomes across vertical gradients was observed in the Mariana Trench. These results illuminate a key principle of microbiomes inhabiting the deepest trench: although distinct microbial communities occupy specific habitats, the interactions within microbial communities remain consistently stable from the upper bathypelagic to the hadal waters.

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Section: Discussionsupporting

confidence: 93%

Depth shapes microbiome assembly and network stability in the Mariana Trench

Li,

Kan,

Liu

et al. 2024

Microbiol Spectr

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“…The composition and diversity of protists and fungal communities in the soil were determined by amplifying the V4 regions of 18S riboso-mal RNA (rRNA) genes. The primers 528 F (5 -GCGGTAATTCCAGCTCCAA-3 ) and 706 R (5 -AATCCRAGAATTTCACCTCT-3 ) and the DNA extracted from the samples as templates were used for amplification [21].…”

Section: Dna Extraction and Pcr Amplificationsmentioning

confidence: 99%

Exploring Microeukaryote Community Characteristics and Niche Differentiation in Arid Farmland Soil at the Northeastern Edge of the Tibetan Plateau

Chen,

Han,

Wang

et al. 2023

Microorganisms

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The northeastern edge of the Tibetan Plateau exhibits diverse climate and landform variations, and has experienced substantial recent environmental changes, which may significantly impact local agricultural practices. Understanding the microeukaryote community structure within agricultural soils is crucial for finding out the biological responses to such changes and may guide future agricultural practices. In this study, we employed high-throughput amplicon sequencing to examine 29 agricultural soil samples from seven research areas around the northeastern edge of the Tibetan Plateau. The findings revealed that the predominant biological communities in these soils were characterized by a high abundance of Alveolata, Amoebozoa, and Rhizaria. Ascomycota displayed the highest relative abundance among fungal communities. Moreover, notable distinctions in microeukaryote community composition were observed among the study sites. Co-occurrence network analysis highlighted interactions between the biological communities. Furthermore, our results elucidated that deterministic and stochastic processes exerted diverse influences on the distribution of protozoan and fungal communities. This study provides valuable insight into the microeukaryote structure in the agricultural soils of the northeastern edge of the Tibetan Plateau, shedding light on the intricate relationships between environmental factors, microeukaryote communities, and agricultural productivity.

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“…High hydrostatic pressure (HHP) acts as one of the key parameters in the deep sea but also becomes an obstruction for most macrobiotic species to reach greater depths. However, recent studies have highlighted the abundance of fungal diversity even in the deep sea using both culture-dependent and culture-independent approaches ( 2 – 5 ). In addition, evidence indicates that deep-sea fungi not only exhibit robust biological activity ( 6 ) but also play an essential role in ecological functions ( 7 , 8 ).…”

Section: Introductionmentioning

confidence: 99%

Insight into the adaptation mechanisms of high hydrostatic pressure in physiology and metabolism of hadal fungi from the deepest ocean sediment

Zhong,

Li,

Deng

et al. 2024

mSystems

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High hydrostatic pressure (HHP) influences the life processes of organisms living at depth in the oceans. While filamentous fungi are one of the essential members of deep-sea microorganisms, few works have explored their piezotolerance to HHP. Here, we obtained three homogeneous Aspergillus sydowii from terrestrial, shallow, and hadal areas, respectively, to compare their pressure resistance. A set of all-around evaluation methods including determination of growth rate, metabolic activity, and microscopic staining observation was established and indicated that A. sydowii DM1 from the hadal area displayed significant piezotolerance. Global analysis of transcriptome data under elevated HHP revealed that A. sydowii DM1 proactively modulated cell membrane permeability, hyphae morphology, and septal quantities for seeking a better livelihood under mild pressure. Besides, differentially expressed genes were mainly enriched in the biosynthesis of amino acids, carbohydrate metabolism, cell process, etc., implying how the filamentous fungi respond to elevated pressure at the molecular level. We speculated that A. sydowii DM1 could acclimatize itself to HHP by adopting several strategies, including environmental response pathway HOG-MAPK, stress proteins, and cellular metabolisms. IMPORTANCE Fungi play an ecological and biological function in marine environments, while the physiology of filamentous fungi under high hydrostatic pressure (HHP) is an unknown territory due to current technologies. As filamentous fungi are found in various niches, Aspergillus sp. from deep-sea inspire us to the physiological trait of eukaryotes under HHP, which can be considered as a prospective research model. Here, the evaluation methods we constructed would be universal for most filamentous fungi to assess their pressure resistance, and we found that Aspergillus sydowii DM1 from the hadal area owned better piezotolerance and the active metabolisms under HHP indicated the existence of undiscovered metabolic strategies for hadal fungi. Since pressure-related research of marine fungi has been unexpectedly neglected, our study provided an enlightening strategy for them under HHP; we believed that understanding their adaptation and ecological function in original niches will be accelerated in the perceivable future.

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Comparison of Deep-Sea Picoeukaryotic Composition Estimated from the V4 and V9 Regions of 18S rRNA Gene with a Focus on the Hadal Zone of the Mariana Trench

Cited by 7 publications

References 91 publications

Depth shapes microbiome assembly and network stability in the Mariana Trench

Depth shapes microbiome assembly and network stability in the Mariana Trench

Exploring Microeukaryote Community Characteristics and Niche Differentiation in Arid Farmland Soil at the Northeastern Edge of the Tibetan Plateau

Insight into the adaptation mechanisms of high hydrostatic pressure in physiology and metabolism of hadal fungi from the deepest ocean sediment

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