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Shoemaker A, Maritan A, Cosar S, Nupp S, Menchaca A, Jackson T, Dang A, Baxter BK, Colman DR, Dunham EC, Boyd ES. Wood-Ljungdahl pathway encoding anaerobes facilitate low-cost primary production in hypersaline sediments at Great Salt Lake, Utah. FEMS Microbiol Ecol 2024; 100:fiae105. [PMID: 39054286 PMCID: PMC11287216 DOI: 10.1093/femsec/fiae105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 07/03/2024] [Accepted: 07/24/2024] [Indexed: 07/27/2024] Open
Abstract
Little is known of primary production in dark hypersaline ecosystems despite the prevalence of such environments on Earth today and throughout its geologic history. Here, we generated and analyzed metagenome-assembled genomes (MAGs) organized as operational taxonomic units (OTUs) from three depth intervals along a 30-cm sediment core from the north arm of Great Salt Lake, Utah. The sediments and associated porewaters were saturated with NaCl, exhibited redox gradients with depth, and harbored nitrogen-depleted organic carbon. Metabolic predictions of MAGs representing 36 total OTUs recovered from the core indicated that communities transitioned from aerobic and heterotrophic at the surface to anaerobic and autotrophic at depth. Dark CO2 fixation was detected in sediments and the primary mode of autotrophy was predicted to be via the Wood-Ljungdahl pathway. This included novel hydrogenotrophic acetogens affiliated with the bacterial class Candidatus Bipolaricaulia. Minor populations were dependent on the Calvin cycle and the reverse tricarboxylic acid cycle, including in a novel Thermoplasmatota MAG. These results are interpreted to reflect the favorability of and selectability for populations that operate the lowest energy requiring CO2-fixation pathway known, the Wood-Ljungdahl pathway, in anoxic and hypersaline conditions that together impart a higher energy demand on cells.
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Affiliation(s)
- Anna Shoemaker
- Department of Earth Sciences, Montana State University, P.O. Box 173480, Bozeman, MT 59717, United States
| | - Andrew Maritan
- Department of Microbiology and Cell Biology, Montana State University, P.O. Box 173520, Bozeman, MT 59717, United States
| | - Su Cosar
- Department of Microbiology and Cell Biology, Montana State University, P.O. Box 173520, Bozeman, MT 59717, United States
| | - Sylvia Nupp
- Department of Chemistry and Biochemistry, Montana State University, P.O. Box 173400, Bozeman, MT 59717, United States
| | - Ana Menchaca
- Department of Microbiology and Cell Biology, Montana State University, P.O. Box 173520, Bozeman, MT 59717, United States
| | - Thomas Jackson
- Department of Microbiology and Cell Biology, Montana State University, P.O. Box 173520, Bozeman, MT 59717, United States
| | - Aria Dang
- Department of Chemistry and Biochemistry, Montana State University, P.O. Box 173400, Bozeman, MT 59717, United States
| | - Bonnie K Baxter
- Great Salt Lake Institute, Westminster University, 1840 South 1300 East, Salt Lake City, UT 84105, United States
| | - Daniel R Colman
- Department of Microbiology and Cell Biology, Montana State University, P.O. Box 173520, Bozeman, MT 59717, United States
| | - Eric C Dunham
- Department of Microbiology and Cell Biology, Montana State University, P.O. Box 173520, Bozeman, MT 59717, United States
| | - Eric S Boyd
- Department of Microbiology and Cell Biology, Montana State University, P.O. Box 173520, Bozeman, MT 59717, United States
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Jung J, Loschko T, Reich S, Rassoul-Agha M, Werner MS. Newly identified nematodes from the Great Salt Lake are associated with microbialites and specially adapted to hypersaline conditions. Proc Biol Sci 2024; 291:20232653. [PMID: 38471558 PMCID: PMC10932707 DOI: 10.1098/rspb.2023.2653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 02/09/2024] [Indexed: 03/14/2024] Open
Abstract
Extreme environments enable the study of simplified food-webs and serve as models for evolutionary bottlenecks and early Earth ecology. We investigated the biodiversity of invertebrate meiofauna in the benthic zone of the Great Salt Lake (GSL), Utah, USA, one of the most hypersaline lake systems in the world. The hypersaline bays within the GSL are currently thought to support only two multicellular animals: brine fly larvae and brine shrimp. Here, we report the presence, habitat, and microbial interactions of novel free-living nematodes. Nematode diversity drops dramatically along a salinity gradient from a freshwater river into the south arm of the lake. In Gilbert Bay, nematodes primarily inhabit reef-like organosedimentary structures built by bacteria called microbialites. These structures likely provide a protective barrier to UV and aridity, and bacterial associations within them may support life in hypersaline environments. Notably, sampling from Owens Lake, another terminal lake in the Great Basin that lacks microbialites, did not recover nematodes from similar salinities. Phylogenetic divergence suggests that GSL nematodes represent previously undescribed members of the family Monhysteridae-one of the dominant fauna of the abyssal zone and deep-sea hydrothermal vents. These findings update our understanding of halophile ecosystems and the habitable limit of animals.
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Affiliation(s)
- Julie Jung
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Tobias Loschko
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
- Max Planck Institute for Biology, Tübingen, Germany
| | - Shelley Reich
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Maxim Rassoul-Agha
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Michael S. Werner
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
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Zeng F, Zhu Y, Zhang D, Zhao Z, Li Q, Ma P, Zhang G, Wang Y, Wu S, Guo S, Sun G. Metagenomic analysis of the soil microbial composition and salt tolerance mechanism in Yuncheng Salt Lake, Shanxi Province. Front Microbiol 2022; 13:1004556. [PMID: 36225369 PMCID: PMC9549588 DOI: 10.3389/fmicb.2022.1004556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 09/08/2020] [Indexed: 11/13/2022] Open
Abstract
The soil in Yuncheng Salt Lake has serious salinization and the biogeographic environment affects the composition and distribution of special halophilic and salt-tolerant microbial communities in this area. Therefore, this study collected soils at distances of 15, 30, and 45 m from the Salt Lake and used non-saline soil (60 m) as a control to explore the microbial composition and salt tolerance mechanisms using metagenomics technology. The results showed that the dominant species and abundance of salt-tolerant microorganisms changed gradually with distance from Salt Lake. The salt-tolerant microorganisms can increase the expression of the Na+/H+ antiporter by upregulating the Na+/H+ antiporter subunit mnhA-G to respond to salt stress, simultaneously upregulating the genes in the betaine/proline transport system to promote the conversion of choline into betaine, while also upregulating the trehalose/maltose transport system encode genes to promote the synthesis of trehalose to resist a high salt environment.
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Affiliation(s)
- Feifeng Zeng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yonghong Zhu
- Cotton Research Institute, Shanxi Agricultural University, Shanxi, China
| | - Dongling Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zengqiang Zhao
- Xinjiang Academy of Agricultural and Reclamation, Xinjiang, China
| | - Quansheng Li
- Xinjiang Academy of Agricultural and Reclamation, Xinjiang, China
| | - Panpan Ma
- Xinjiang Academy of Agricultural and Reclamation, Xinjiang, China
| | - Guoli Zhang
- Xinjiang Academy of Agricultural and Reclamation, Xinjiang, China
| | - Yuan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shenjie Wu
- Cotton Research Institute, Shanxi Agricultural University, Shanxi, China
| | - Sandui Guo
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guoqing Sun
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Guoqing Sun,
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Saccò M, White NE, Harrod C, Salazar G, Aguilar P, Cubillos CF, Meredith K, Baxter BK, Oren A, Anufriieva E, Shadrin N, Marambio-Alfaro Y, Bravo-Naranjo V, Allentoft ME. Salt to conserve: a review on the ecology and preservation of hypersaline ecosystems. Biol Rev Camb Philos Soc 2021; 96:2828-2850. [PMID: 34747117 DOI: 10.1111/brv.12780] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 07/06/2021] [Accepted: 07/07/2021] [Indexed: 02/01/2023]
Abstract
When it comes to the investigation of key ecosystems in the world, we often omit salt from the ecological recipe. In fact, despite occupying almost half of the volume of inland waters and providing crucial services to humanity and nature, inland saline ecosystems are often overlooked in discussions regarding the preservation of global aquatic resources of our planet. As a result, our knowledge of the biological and geochemical dynamics shaping these environments remains incomplete and we are hesitant in framing effective protective strategies against the increasing natural and anthropogenic threats faced by such habitats. Hypersaline lakes, water bodies where the concentration of salt exceeds 35 g/l, occur mainly in arid and semiarid areas resulting from hydrological imbalances triggering the accumulation of salts over time. Often considered the 'exotic siblings' within the family of inland waters, these ecosystems host some of the most extremophile communities worldwide and provide essential habitats for waterbirds and many other organisms in already water-stressed regions. These systems are often highlighted as natural laboratories, ideal for addressing central ecological questions due to their relatively low complexity and simple food web structures. However, recent studies on the biogeochemical mechanisms framing hypersaline communities have challenged this archetype, arguing that newly discovered highly diverse communities are characterised by specific trophic interactions shaped by high levels of specialisation. The main goal of this review is to explore our current understanding of the ecological dynamics of hypersaline ecosystems by addressing four main research questions: (i) why are hypersaline lakes unique from a biological and geochemical perspective; (ii) which biota inhabit these ecosystems and how have they adapted to the high salt conditions; (iii) how do we protect biodiversity from increasing natural and anthropogenic threats; and (iv) which scientific tools will help us preserve hypersaline ecosystems in the future? First, we focus on the ecological characterisation of hypersaline ecosystems, illustrate hydrogeochemical dynamics regulating such environments, and outline key ecoregions supporting hypersaline systems across the globe. Second, we depict the diversity and functional aspects of key taxa found in hypersaline lakes, from microorganisms to plants, invertebrates, waterbirds and upper trophic levels. Next, we describe ecosystem services and discuss possible conservation guidelines. Finally, we outline how cutting-edge technologies can provide new insights into the study of hypersaline ecology. Overall, this review sheds further light onto these understudied ecosystems, largely unrecognised as important sources of unique biological and functional diversity. We provide perspectives for key future research avenues, and advocate that the conservation of hypersaline lakes should not be taken with 'a grain of salt'.
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Affiliation(s)
- Mattia Saccò
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA, 6102, Australia
| | - Nicole E White
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA, 6102, Australia
| | - Chris Harrod
- Instituto de Ciencias Naturales Alexander von Humboldt, Universidad de Antofagasta, Avenida Angamos 601, Antofagasta, Chile.,Núcleo Milenio INVASAL, Concepción, 3349001, Chile
| | - Gonzalo Salazar
- Instituto de Ciencias Naturales Alexander von Humboldt, Universidad de Antofagasta, Avenida Angamos 601, Antofagasta, Chile.,Núcleo Milenio INVASAL, Concepción, 3349001, Chile
| | - Pablo Aguilar
- Núcleo Milenio INVASAL, Concepción, 3349001, Chile.,Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, Avenida Angamos 601, Antofagasta, Chile
| | - Carolina F Cubillos
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, Avenida Angamos 601, Antofagasta, Chile
| | - Karina Meredith
- Australian Nuclear Science and Technology Organisation (ANSTO), Locked Bag 2001, Kirrawee DC, NSW, 2232, Australia
| | - Bonnie K Baxter
- Great Salt Lake Institute, Westminster College, Salt Lake City, UT, 84105, U.S.A
| | - Aharon Oren
- Department of Plant and Environmental Sciences, The Institute of Life Sciences, the Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Elena Anufriieva
- A.O. Kovalevsky Institute of Biology of the Southern Seas, Russian Academy of Sciences, 2 Nakhimov Avenue 2, Sevastopol, 299011, Russia
| | - Nickolai Shadrin
- A.O. Kovalevsky Institute of Biology of the Southern Seas, Russian Academy of Sciences, 2 Nakhimov Avenue 2, Sevastopol, 299011, Russia
| | - Yeri Marambio-Alfaro
- Instituto de Ciencias Naturales Alexander von Humboldt, Universidad de Antofagasta, Avenida Angamos 601, Antofagasta, Chile
| | - Víctor Bravo-Naranjo
- Facultad de Ciencias, Universidad de La Serena, Benavente 980, La Serena, Coquimbo, Chile
| | - Morten E Allentoft
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA, 6102, Australia.,Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
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