1
|
Lennartz Née Rybarski AE, Nitsche F, Schoenle A, Voigt C, Staubwasser M, Arndt H. High diversity and isolated distribution of aquatic heterotrophic protists in salars of the Atacama Desert at different salinities. Eur J Protistol 2023; 89:125987. [PMID: 37245304 DOI: 10.1016/j.ejop.2023.125987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/24/2023] [Accepted: 04/11/2023] [Indexed: 05/30/2023]
Abstract
The species richness of eukaryotes in the hypersaline environment is generally thought to be low. However, recent studies showed a high degree of phylogenetic novelty at these extreme conditions with variable chemical parameters. These findings call for a more thorough look into the species richness of hypersaline environments. In this study, various hypersaline lakes (salars, 1-348 PSU) as well as further aquatic ecosystems of northern Chile were investigated regarding diversity of heterotrophic protists by metabarcoding studies of surface water samples. Investigations of genotypes of 18S rRNA genes showed a unique community composition in nearly each salar and even among different microhabitats within one salar. The genotype distribution showed no clear connection to the composition of main ions at the sampling sites, but protist communities from similar salinity ranges (either hypersaline, hyposaline or mesosaline) clustered together regarding their OTU composition. Salars appeared to be fairly isolated systems with only little exchange of protist communities where evolutionary lineages could separately evolve.
Collapse
Affiliation(s)
- Alexandra E Lennartz Née Rybarski
- Department of General Ecology, Institute of Zoology, Biocenter Cologne, University of Cologne, Zuelpicher Straße 47b, D-50674 Cologne, Germany
| | - Frank Nitsche
- Department of General Ecology, Institute of Zoology, Biocenter Cologne, University of Cologne, Zuelpicher Straße 47b, D-50674 Cologne, Germany
| | - Alexandra Schoenle
- Department of General Ecology, Institute of Zoology, Biocenter Cologne, University of Cologne, Zuelpicher Straße 47b, D-50674 Cologne, Germany
| | - Claudia Voigt
- Department of Geosciences, Institute of Geology and Mineralogy, University of Cologne, Zuelpicher Straße 49b, D-50674 Cologne, Germany; Department of Biology and Geology, Universidad de Almería, Carretera de Sacramento s.n, La Cañada de San Urbano, Almería 04120, Spain
| | - Michael Staubwasser
- Department of Geosciences, Institute of Geology and Mineralogy, University of Cologne, Zuelpicher Straße 49b, D-50674 Cologne, Germany
| | - Hartmut Arndt
- Department of General Ecology, Institute of Zoology, Biocenter Cologne, University of Cologne, Zuelpicher Straße 47b, D-50674 Cologne, Germany.
| |
Collapse
|
2
|
Li X, Liu Q, Yu X, Zhang C, Liu M, Zhou X, Gu C, Wang M, Shao H, Li J, Jiang Y. Spatial pattern and co-occurrence network of microbial community in response to extreme environment of salt lakes on the Qinghai-Tibet Plateau. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:20615-20630. [PMID: 36255574 DOI: 10.1007/s11356-022-23572-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
Abstract
Microbial communities are important components of alpine lakes, especially in extreme environments such as salt lakes. However, few studies have examined the co-occurrence network of microbial communities and various environmental factors in the water of salt lakes on the Qinghai-Tibet Plateau. From May to June 2019, nine samples from seven salt lakes with water salinity ranges from 13 to 267‰ on the Qinghai-Tibet Plateau were collected. There were great differences between low-salinity samples and high-salinity samples in the inorganic salt ion concentration, pH, and biodiversity. In addition, the microbial community sturcture in low-salinity samples and high-salinity samples differed, suggesting that each sample has its own specific species. The co-occurrence network suggests that salinity was the most important forcing factor. We believe that salinity and inorganic salt ions can result in differences in microbial community in different salt lakes. This sequencing survey of multiple salt lakes with various salinities on the Qinghai-Tibet Plateau enhances our understanding of the response of microbial communities to environmental heterogeneity.
Collapse
Affiliation(s)
- Xianrong Li
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Qian Liu
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, 266100, China
| | - Xiaowen Yu
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Chenru Zhang
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Mingjian Liu
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Xinhao Zhou
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Chengxiang Gu
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Min Wang
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 2661000, China
| | - Hongbing Shao
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Jiansen Li
- Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining, 810008, China
| | - Yong Jiang
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
| |
Collapse
|
3
|
Lee HB, Jeong DH, Cho BC, Park JS. The Diversity Patterns of Rare to Abundant Microbial Eukaryotes Across a Broad Range of Salinities in a Solar Saltern. MICROBIAL ECOLOGY 2022; 84:1103-1121. [PMID: 34779881 PMCID: PMC9747883 DOI: 10.1007/s00248-021-01918-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 11/04/2021] [Indexed: 06/13/2023]
Abstract
Solar salterns are excellent artificial systems for examining species diversity and succession along salinity gradients. Here, the eukaryotic community in surface water of a Korean solar saltern (30 to 380 practical salinity units) was investigated from April 2019 to October 2020 using Illumina sequencing targeting the V4 and V9 regions of 18S rDNA. A total of 926 operational taxonomic units (OTUs) and 1,999 OTUs were obtained with the V4 and V9 regions, respectively. Notably, most of the OTUs were microbial eukaryotes, and the high-abundance groups (> 5% relative abundance (RA), Alveolata, Stramenopila, Archaeplastida, and Opisthokonta) usually accounted for > 90% of the total cumulative read counts and > 80% of all OTUs. Moreover, the high-abundance Alveolata (larger forms) and Stramenopila (smaller forms) groups displayed a significant inverse relationship, probably due to predator-prey interactions. Most of the low-abundance (0.1-5% RA) and rare (< 0.1% RA) groups remained small portion during the field surveys. Taxonomic novelty (at < 90% sequence identity) was high in the Amoebozoa, Cryptista, Haptista, Rhizaria, and Stramenopila groups (69.8% of all novel OTUs), suggesting the presence of a large number of hidden species in hypersaline environments. Remarkably, the high-abundance groups had little overlap with the other groups, implying the weakness of rare-to-prevalent community dynamics. The low-abundance Discoba group alone temporarily became the high-abundance group, suggesting that it is an opportunistic group. Overall, the composition and diversity of the eukaryotic community in hypersaline environments may be persistently stabilized, despite diverse disturbance events.
Collapse
Affiliation(s)
- Hyeon Been Lee
- Department of Oceanography, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Dong Hyuk Jeong
- Department of Oceanography, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Byung Cheol Cho
- School of Earth and Environmental Sciences, Seoul National University, Seoul, 08826, Republic of Korea
- Saemangeum Environmental Research Center, Kunsan National University, Kunsan, 54150, Republic of Korea
| | - Jong Soo Park
- Department of Oceanography, Kyungpook National University, Daegu, 41566, Republic of Korea.
| |
Collapse
|
4
|
Schoenle A, Hohlfeld M, Rybarski A, Sachs M, Freches E, Wiechmann K, Nitsche F, Arndt H. Cafeteria in extreme environments: investigations on C. burkhardae and three new species from the atacama desert and the deep ocean. Eur J Protistol 2022; 85:125905. [DOI: 10.1016/j.ejop.2022.125905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 06/10/2022] [Accepted: 06/15/2022] [Indexed: 11/03/2022]
|
5
|
Triangulopteris lacunata gen. et sp. nov. (Centroplasthelida), a New Centrohelid Heliozoan from Soil. DIVERSITY 2021. [DOI: 10.3390/d13120658] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A new genus and species of centrohelid heliozoans, Triangulopteris lacunata gen. et sp. nov. (Pterocystidae Cavalier-Smith and Heyden, 2007), from four geographically remote locations (the Crimean Peninsula, the Dnieper Lowland (the East European Plain), Franz Josef Land, and the Kolyma Lowland (North–Eastern Siberia) was examined using light and electron microscopy. The novel centrohelid is characterized by round shape, 4.3–16.3 μm in diameter, covered with two types of scales: 1.06–4.54 μm long triangular spine scales and 1.22–2.05 μm oval plate scales. Studied centrohelid heliozoan possesses a unique spine scale morphology. The base of scales is represented by a horse hoof-shaped basal plate. The inner surface and lateral wings of spine scales have numerous radial ribs with two ‘pockets’ that are located on both sides of the spine shaft. These pockets are formed by the lateral wings and ends of the basal plate. The cyst formation and transition to a spicules-bearing stage were noted. Additionally, phylogenetic tree was constructed based on SSU rRNA sequences including the strain HF-25 from the permafrost of Kolyma Lowland. The resulting phylogeny recovered it within the clade Pterista, while forming a separate sister lineage to H2 clade, which only had included freshwater environmental sequences.
Collapse
|
6
|
Menéndez-Serra M, Triadó-Margarit X, Casamayor EO. Ecological and Metabolic Thresholds in the Bacterial, Protist, and Fungal Microbiome of Ephemeral Saline Lakes (Monegros Desert, Spain). MICROBIAL ECOLOGY 2021; 82:885-896. [PMID: 33725151 DOI: 10.1007/s00248-021-01732-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 03/08/2021] [Indexed: 05/20/2023]
Abstract
We studied the 16S and 18S rRNA genes of the bacterial, protist, and fungal microbiomes of 131 samples collected in 14 ephemeral small inland lakes located in the endorheic area of the Monegros Desert (NE Spain). The sampling covered different temporal flooding/desiccation cycles that created natural salinity gradients between 0.1% (w/v) and salt saturation. We aimed to test the hypothesis of a lack of competitive advantage for microorganisms using the "salt-in" strategy in highly fluctuating hypersaline environments where temperature and salinity transitions widely vary within short time periods, as in ephemeral inland lakes. Overall, 5653 bacterial zOTUs and 2658 eukaryal zOTUs were detected heterogeneously distributed with significant variations on taxonomy and general energy-yielding metabolisms and trophic strategies along the gradient. We observed a more diverse bacterial assembly than initially expected at extreme salinities and a lack of dominance of a few "salt-in" organisms. Microbial thresholds were unveiled for these highly fluctuating hypersaline environments with high selective pressures. We conclude that the extremely high dynamism observed in the ephemeral lakes of Monegros may have given a competitive advantage for more versatile ("salt-out") organisms compared to those better adapted to stable high salinities usually more common in solar salterns. Ephemeral inland saline lakes offered a well-suited natural framework for highly detailed evolutionary and ecological studies.
Collapse
Affiliation(s)
- Mateu Menéndez-Serra
- Integrative Freshwater Ecology Group, Centro de Estudios Avanzados de Blanes (CEAB-CSIC), Acces Cala Sant Francesc 14, 17300, Blanes, Spain
| | - Xavier Triadó-Margarit
- Integrative Freshwater Ecology Group, Centro de Estudios Avanzados de Blanes (CEAB-CSIC), Acces Cala Sant Francesc 14, 17300, Blanes, Spain
| | - Emilio O Casamayor
- Integrative Freshwater Ecology Group, Centro de Estudios Avanzados de Blanes (CEAB-CSIC), Acces Cala Sant Francesc 14, 17300, Blanes, Spain.
| |
Collapse
|
7
|
Rybarski AE, Nitsche F, Soo Park J, Filz P, Schmidt P, Kondo R, Gb Simpson A, Arndt H. Revision of the phylogeny of Placididea (Stramenopiles): Molecular and morphological diversity of novel placidid protists from extreme aquatic environments. Eur J Protistol 2021; 81:125809. [PMID: 34673437 DOI: 10.1016/j.ejop.2021.125809] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 04/30/2021] [Accepted: 05/11/2021] [Indexed: 11/17/2022]
Abstract
Recent studies suggested that the diversity of microbial eukaryotes in hypersaline environments is widely underestimated. Placidids are a group of heterotrophic stramenopile flagellates that are frequently found in these environments, but up to now only very few species were isolated and fully described, mostly from marine or brackish water sites. In this study, we extend the known diversity of Placididea by three new genera (Allegra, Haloplacidia, and Placilonga) compromising nine new species, isolated from athalassic, mostly hypersaline environments (Allegra dunaii, Allegra atacamiensis, Allegra hypersalina, Haloplacidia cosmopolita, Suigetsumonas keniensis) and marine waters (Placilonga atlantica, Placidia azorensis, Placidia abyssalis, Wobblia pacifica) including a description of their morphology and molecular phylogeny. In total, 36 strains were comparatively analysed. Studies from athalassic waters revealed an especially high number of different genotypes. A multigene analysis based on a ten genes dataset revealed a clear separation into marine, athalassic and brackish water clades. Several representatives were found to cope with hypersaline conditions from 20 to 250 PSU, even up to 284 PSU, suggesting that they may form a halotolerant group.
Collapse
Affiliation(s)
- Alexandra E Rybarski
- Department of General Ecology, Institute of Zoology, Biocenter Cologne, University of Cologne, Zuelpicher Straße 47b, D-50674 Cologne, Germany
| | - Frank Nitsche
- Department of General Ecology, Institute of Zoology, Biocenter Cologne, University of Cologne, Zuelpicher Straße 47b, D-50674 Cologne, Germany
| | - Jong Soo Park
- Department of Oceanography, School of Earth System Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Paulina Filz
- Department of General Ecology, Institute of Zoology, Biocenter Cologne, University of Cologne, Zuelpicher Straße 47b, D-50674 Cologne, Germany
| | - Patricia Schmidt
- Department of General Ecology, Institute of Zoology, Biocenter Cologne, University of Cologne, Zuelpicher Straße 47b, D-50674 Cologne, Germany
| | - Ryuji Kondo
- Department of Marine Science and Technology, Fukui Prefectural University, Obama, Fukui 917-0003, Japan
| | | | - Hartmut Arndt
- Department of General Ecology, Institute of Zoology, Biocenter Cologne, University of Cologne, Zuelpicher Straße 47b, D-50674 Cologne, Germany.
| |
Collapse
|
8
|
Schiwitza S, Gutsche L, Freches E, Arndt H, Nitsche F. Extended divergence estimates and species descriptions of new craspedid choanoflagellates from the Atacama Desert, Northern Chile. Eur J Protistol 2021; 79:125798. [PMID: 33984646 DOI: 10.1016/j.ejop.2021.125798] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 04/01/2021] [Accepted: 04/12/2021] [Indexed: 11/15/2022]
Abstract
In contrast to previous perspectives, hypersaline environments have been proven to harbour a variety of potentially highly adapted microorganisms, in particular unicellular eukaryotes. The isolated, hypersaline waterbodies in the Atacama Desert, Northern Chile are exposed to high UV radiation and deposition of toxic heavy metals, making them of great interest regarding studies on speciation and evolutionary processes. In the past two years, among a variety of other protist species, five new species of heterotrophic choanoflagellates were described and analysed from this area, showing an adaptation to a broad range of salinities. Morphological data alone does not allow for species delineation within craspedid species, additional molecular data is essential for modern taxonomy. In addition, molecular clock analyses pointed towards a strong selection force of the extreme environmental conditions. Within this study, we describe three additional craspedid choanoflagellate species, isolated from different aquatic environments. Phylogenetic analyses show two distinct clades of choanoflagellates from the Atacama, suggesting two independent invasions of at least two ancestral marine species, and, as indicated by our new data, a possible dispersal by Andean aquifers. The extended molecular clock analysis based on transcriptomic data of choanoflagellate strains from the Salar de Llamará, a hypersaline basin within the Central Depression of the Atacama Desert, reflects colonisation and divergence events which correspond to geological data of the paleohydrology.
Collapse
Affiliation(s)
- Sabine Schiwitza
- University of Cologne, Cologne Biocenter, Institute of Zoology, General Ecology, Zuelpicher Str. 47b, D-50674 Cologne, Germany
| | - Lennart Gutsche
- University of Cologne, Cologne Biocenter, Institute of Zoology, General Ecology, Zuelpicher Str. 47b, D-50674 Cologne, Germany
| | - Eric Freches
- University of Cologne, Cologne Biocenter, Institute of Zoology, General Ecology, Zuelpicher Str. 47b, D-50674 Cologne, Germany
| | - Hartmut Arndt
- University of Cologne, Cologne Biocenter, Institute of Zoology, General Ecology, Zuelpicher Str. 47b, D-50674 Cologne, Germany
| | - Frank Nitsche
- University of Cologne, Cologne Biocenter, Institute of Zoology, General Ecology, Zuelpicher Str. 47b, D-50674 Cologne, Germany.
| |
Collapse
|
9
|
Menéndez-Serra M, Ontiveros VJ, Triadó-Margarit X, Alonso D, Casamayor EO. Dynamics and ecological distributions of the Archaea microbiome from inland saline lakes (Monegros Desert, Spain). FEMS Microbiol Ecol 2020; 96:5719565. [PMID: 32006018 DOI: 10.1093/femsec/fiaa019] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 01/30/2020] [Indexed: 11/15/2022] Open
Abstract
We characterized the rich Archaea microbiome of shallow inland lakes (Monegros Desert, NE Spain) by 16S rRNA gene tag sequencing covering a wide salinity range (0.1%-40% w/v) along 3 years. Up to 990 operational taxonomic units (OTUs; >97% identity) were detected allocated in 14 major archaeal phyla and heterogeneously distributed along the salt gradient. Dynamics and idiosyncratic ecological distributions were uncovered for the different phyla. A high genetic richness was observed for Woesearchaeota and Pacearchaeota (>370 OTUs each), followed by Halobacteria (105), Nanohaloarchaeota (62) and Thermoplasmata (19). Overall, the distribution of genetic richness was strongly correlated with environmental niche amplitude, but not with occurrence. We unveiled high occurrence for a very rich Woesearchaeota assemblage, and an unexpected positive correlation of Pacearchaeota abundance with salinity at >15% dissolved salt content. The estimated dynamic behaviour (temporal 'turnover' rates of presence/absence data) unveiled Thaumarchaeota and Halobacteria as the most dynamic groups, and Aenigmarchaeota and Thermoplasmata as the most stable. The DPANN Pacearchaeota, Woesearchaeota, and Nanohaloarchaeota showed intermediate rates, suggesting higher resilience to environmental perturbations. A rich and dynamic Archaea microbiome was unveiled, including unseen ecological traits for relevant members of the still largely unknown DPANN group, supporting a strong ecological differentiation between Pacearchaeota and Woesearchaeota.
Collapse
Affiliation(s)
- Mateu Menéndez-Serra
- Integrative Freshwater Ecology Group, Centre of Advanced Studies of Blanes (CEAB), Spanish Research Council (CSIC), 17300 Blanes, Catalonia, Spain
| | - Vicente J Ontiveros
- Theoretical and Computational Ecology Group, Centre of Advanced Studies of Blanes (CEAB), Spanish Research Council (CSIC), 17300 Blanes, Catalonia, Spain
| | - Xavier Triadó-Margarit
- Integrative Freshwater Ecology Group, Centre of Advanced Studies of Blanes (CEAB), Spanish Research Council (CSIC), 17300 Blanes, Catalonia, Spain
| | - David Alonso
- Theoretical and Computational Ecology Group, Centre of Advanced Studies of Blanes (CEAB), Spanish Research Council (CSIC), 17300 Blanes, Catalonia, Spain
| | - Emilio O Casamayor
- Integrative Freshwater Ecology Group, Centre of Advanced Studies of Blanes (CEAB), Spanish Research Council (CSIC), 17300 Blanes, Catalonia, Spain
| |
Collapse
|
10
|
Gooday AJ, Schoenle A, Dolan JR, Arndt H. Protist diversity and function in the dark ocean - Challenging the paradigms of deep-sea ecology with special emphasis on foraminiferans and naked protists. Eur J Protistol 2020; 75:125721. [PMID: 32575029 DOI: 10.1016/j.ejop.2020.125721] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/13/2020] [Accepted: 05/21/2020] [Indexed: 11/27/2022]
Abstract
The dark ocean and the underlying deep seafloor together represent the largest environment on this planet, comprising about 80% of the oceanic volume and covering more than two-thirds of the Earth's surface, as well as hosting a major part of the total biosphere. Emerging evidence suggests that these vast pelagic and benthic habitats play a major role in ocean biogeochemistry and represent an "untapped reservoir" of high genetic and metabolic microbial diversity. Due to its huge volume, the water column of the dark ocean is the largest reservoir of organic carbon in the biosphere and likely plays a major role in the global carbon budget. The dark ocean and the seafloor beneath it are also home to a largely enigmatic food web comprising little-known and sometimes spectacular organisms, mainly prokaryotes and protists. This review considers the globally important role of pelagic and benthic protists across all protistan size classes in the deep-sea realm, with a focus on their taxonomy, diversity, and physiological properties, including their role in deep microbial food webs. We argue that, given the important contribution that protists must make to deep-sea biodiversity and ecosystem processes, they should not be overlooked in biological studies of the deep ocean.
Collapse
Affiliation(s)
- Andrew J Gooday
- National Oceanography Centre, University of Southampton Waterfront Campus, Southampton, UK; Life Sciences Department, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Alexandra Schoenle
- University of Cologne, Institute of Zoology, General Ecology, 50674 Cologne, Germany
| | - John R Dolan
- Sorbonne Université, CNRS UMR 7093, Laboratoroire d'Océanographie de Villefranche-sur-Mer, Villefranche-sur-Mer, France
| | - Hartmut Arndt
- University of Cologne, Institute of Zoology, General Ecology, 50674 Cologne, Germany.
| |
Collapse
|
11
|
Zhang Y, Li Q, Chen Y, Dai Q, Hu J. Mudflat reclamation causes change in the composition of fungal communities under long-term rice cultivation. Can J Microbiol 2019; 65:530-537. [DOI: 10.1139/cjm-2019-0005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Fungi play a critical role in farmland ecosystems, especially in improving soil fertility; however, little is known about the changes in fungal communities caused by mudflat reclamation under rice cultivation. In this study, mudflats located in Yancheng, China, which were divided into nine plots with 0, 11, and 20 years of successive rice cultivation histories, were sampled to determine the fungal community composition by using Illumina MiSeq sequencing. Results show that the Shannon diversity of the fungal communities did not change significantly but the species richness increased under mudflat reclamation with long-term rice cultivation. Ascomycota was the dominant phylum throughout the reclaimed mudflats samples, while Sordariomycetes was the dominant class. Fungal functional prediction found that the relative abundance of saprotrophs gradually increased with mudflat reclamation and mainly belonged to Ascomycota after 20 years of successive reclamation. Redundancy analysis showed that electrical conductivity, organic matter, and total nitrogen were the main factors affecting the composition and ecological function of the fungal community during mudflat reclamation. In short, a fungal community dominated by Ascomycota was established during mudflat reclamation under rice cultivation, which is more conducive to promoting soil fertility because of the higher proportion of saprotrophic fungi in Ascomycota.
Collapse
Affiliation(s)
- Yang Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops/Research Institute of Rice Industry Engineering Technology, Yangzhou University, Yangzhou 225009, P.R. China
| | - Qing Li
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops/Research Institute of Rice Industry Engineering Technology, Yangzhou University, Yangzhou 225009, P.R. China
| | - Yinglong Chen
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops/Research Institute of Rice Industry Engineering Technology, Yangzhou University, Yangzhou 225009, P.R. China
| | - Qigen Dai
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops/Research Institute of Rice Industry Engineering Technology, Yangzhou University, Yangzhou 225009, P.R. China
| | - Jian Hu
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou 225127, P.R. China
| |
Collapse
|
12
|
First description of an euryoecious acanthoecid choanoflagellate species, Enibas tolerabilis gen. et sp. nov. from a salar in the Chilean Andes based on morphological and transcriptomic data. Eur J Protistol 2019; 67:106-113. [DOI: 10.1016/j.ejop.2018.11.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 11/16/2018] [Accepted: 11/26/2018] [Indexed: 01/13/2023]
|
13
|
Schiwitza S, Arndt H, Nitsche F. Four new choanoflagellate species from extreme saline environments: Indication for isolation-driven speciation exemplified by highly adapted Craspedida from salt flats in the Atacama Desert (Northern Chile). Eur J Protistol 2018; 66:86-96. [DOI: 10.1016/j.ejop.2018.08.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 08/06/2018] [Accepted: 08/08/2018] [Indexed: 10/28/2022]
|
14
|
Zhao F, Filker S. Characterization of protistan plankton diversity in ancient salt evaporation ponds located in a volcanic crater on the island Sal, Cape Verde. Extremophiles 2018; 22:943-954. [DOI: 10.1007/s00792-018-1050-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/08/2018] [Indexed: 01/21/2023]
|
15
|
Ortiz-Álvarez R, Triadó-Margarit X, Camarero L, Casamayor EO, Catalan J. High planktonic diversity in mountain lakes contains similar contributions of autotrophic, heterotrophic and parasitic eukaryotic life forms. Sci Rep 2018. [PMID: 29535368 PMCID: PMC5849755 DOI: 10.1038/s41598-018-22835-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
A rich eukaryotic planktonic community exists in high-mountain lakes despite the diluted, oligotrophic and cold, harsh prevailing conditions. Attempts of an overarching appraisal have been traditionally hampered by observational limitations of small, colorless, and soft eukaryotes. We aimed to uncover the regional eukaryotic biodiversity of a mountain lakes district to obtain general conclusions on diversity patterns, dominance, geographic diversification, and food-web players common to oligotrophic worldwide distributed freshwater systems. An unprecedented survey of 227 high-altitude lakes comprising large environmental gradients was carried out using Illumina massive tag sequencing of the 18S rRNA gene. We observed a large Chrysophyceae dominance in richness, abundance and novelty, and unveiled an unexpected richness in heterotrophic phagotrophs and parasites. In particular, Cercozoa and Chytridiomycota showed diversity features similar to the dominant autotrophic groups. The prominent beta-dispersion shown by parasites suggests highly specific interactions and a relevant role in food webs. Interestingly, the freshwater Pyrenean metacommunity contained more diverse specific populations than its closest marine oligotrophic equivalent, with consistently higher beta-diversity. The relevance of unseen groups opens new perspectives for the better understanding of planktonic food webs. Mountain lakes, with remarkable environmental idiosyncrasies, may be suitable environments for the genetic diversification of microscopic eukaryotic life forms.
Collapse
Affiliation(s)
- Rüdiger Ortiz-Álvarez
- Integrative Freshwater Ecology Group, Center for Advanced Studies of Blanes-CSIC. Acc. Cala St Francesc 14, E-17300, Blanes, Catalonia, Spain
| | - Xavier Triadó-Margarit
- Integrative Freshwater Ecology Group, Center for Advanced Studies of Blanes-CSIC. Acc. Cala St Francesc 14, E-17300, Blanes, Catalonia, Spain
| | - Lluís Camarero
- Integrative Freshwater Ecology Group, Center for Advanced Studies of Blanes-CSIC. Acc. Cala St Francesc 14, E-17300, Blanes, Catalonia, Spain
| | - Emilio O Casamayor
- Integrative Freshwater Ecology Group, Center for Advanced Studies of Blanes-CSIC. Acc. Cala St Francesc 14, E-17300, Blanes, Catalonia, Spain.
| | - Jordi Catalan
- CREAF - CSIC, Campus UAB, Edifici C, 08193, Cerdanyola del Vallès, Catalonia, Spain
| |
Collapse
|
16
|
Harding T, Simpson AGB. Recent Advances in Halophilic Protozoa Research. J Eukaryot Microbiol 2018; 65:556-570. [PMID: 29266533 DOI: 10.1111/jeu.12495] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 11/14/2017] [Accepted: 12/08/2017] [Indexed: 11/30/2022]
Abstract
Most research on microorganisms adapted to hypersaline habitats has focused on Archaea and Bacteria, with microbial eukaryotes receiving much less attention. Over the past 15 yr, our knowledge of phagotrophic microbial eukaryotes, i.e. protozoa, from hypersaline habitats has greatly improved through combinations of microscopy, molecular phylogenetics, environmental sequencing, transcriptomics and growth experiments. High salinity waters from salterns, other landlocked water masses and deep hypersaline anoxic basins contain unique and diverse halophilic protozoan assemblages. These have the potential to exert substantial grazing pressure on prokaryotes and other eukaryotes. They represent many separate evolutionary lineages; species of Heterolobosea, Bicosoecida, and Ciliophora have been most intensively characterized, with several proven to be extreme (or borderline extreme) halophiles. Transcriptomic examinations of the bicosoecid Halocafeteria (and the heteroloboseid Pharyngomonas) indicate that high-salt adaptation is associated with a subtle shift in protein amino acid composition, and involves the differential expression of genes participating in ion homeostasis, signal transduction, stress management, and lipid remodeling. Instances of gene duplication and lateral transfer possibly conferring adaptation have been documented. Indirect evidence suggests that these protozoa use "salt-out" osmoadaptive strategies.
Collapse
Affiliation(s)
- Tommy Harding
- Department of Biochemistry and Molecular Biology, Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Alastair G B Simpson
- Department of Biology, and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| |
Collapse
|
17
|
Filker S, Forster D, Weinisch L, Mora-Ruiz M, González B, Farías ME, Rosselló-Móra R, Stoeck T. Transition boundaries for protistan species turnover in hypersaline waters of different biogeographic regions. Environ Microbiol 2017; 19:3186-3200. [PMID: 28574222 DOI: 10.1111/1462-2920.13805] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 05/26/2017] [Indexed: 11/28/2022]
Abstract
The identification of environmental barriers which govern species distribution is a fundamental concern in ecology. Even though salt was previously identified as a major transition boundary for micro- and macroorganisms alike, the salinities causing species turnover in protistan communities are unknown. We investigated 4.5 million high-quality protistan metabarcodes (V4 region of the SSU rDNA) obtained from 24 shallow salt ponds (salinities 4%-44%) from South America and Europe. Statistical analyses of protistan community profiles identified four salinity classes, which strongly selected for different protistan communities: 4-9%, 14-24%, 27-36% and 38-44%. The proportion of organisms unknown to science is highest in the 14-24% salinity class, showing that environments within this salinity range are an unappreciated reservoir of as yet undiscovered organisms. Distinct higher-rank taxon groups dominated in the four salinity classes in terms of diversity. As increasing salinities require different cellular responses to cope with salt, our results suggest that different evolutionary lineages of protists have evolved distinct haloadaptation strategies. Salinity appears to be a stronger selection factor for the structuring of protistan communities than geography. Yet, we find a higher degree of endemism in shallow salt ponds compared with less isolated ecosystems such as the open ocean. Thus, rules for biogeographic structuring of protistan communities are not universal, but depend on the ecosystem under consideration.
Collapse
Affiliation(s)
- Sabine Filker
- Department of Molecular Ecology, University of Kaiserslautern, 67663, Kaiserslautern, Germany
| | - Dominik Forster
- Department of Ecology, University of Kaiserslautern, 67663, Kaiserslautern, Germany
| | - Lea Weinisch
- Department of Ecology, University of Kaiserslautern, 67663, Kaiserslautern, Germany
| | - Merit Mora-Ruiz
- Marine Microbiology Group, Department of Ecology and Marine Resources, Institut Mediterrani d'Estudis Avançats, IMEDEA (CSIC-UIB), 07190 Esporles, Illes Balears, Spain
| | - Bernardo González
- Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez - Center of Applied Ecology and Sustainability, Santiago de Chile, Chile
| | - María Eugenia Farías
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CCT, CONICET, San Miguel de Tucumán, Tucumán, Argentina
| | - Ramon Rosselló-Móra
- Marine Microbiology Group, Department of Ecology and Marine Resources, Institut Mediterrani d'Estudis Avançats, IMEDEA (CSIC-UIB), 07190 Esporles, Illes Balears, Spain
| | - Thorsten Stoeck
- Department of Ecology, University of Kaiserslautern, 67663, Kaiserslautern, Germany
| |
Collapse
|
18
|
Llorens-Marès T, Triadó-Margarit X, Borrego CM, Dupont CL, Casamayor EO. High Bacterial Diversity and Phylogenetic Novelty in Dark Euxinic Freshwaters Analyzed by 16S Tag Community Profiling. MICROBIAL ECOLOGY 2016; 71:566-574. [PMID: 26552395 DOI: 10.1007/s00248-015-0696-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 10/26/2015] [Indexed: 06/05/2023]
Abstract
Microbial communities growing under extreme low redox conditions are present in anoxic and sulfide-rich (euxinic) environments such as karstic lakes and experience limitation of electron acceptors. The fine natural chemical gradients and the large diversity of organic and inorganic compounds accumulated in bottom waters are impossible to mimic under laboratory conditions, and only a few groups have been cultured. We investigated the bacterial composition in the oxic-anoxic interface and in the deep waters of three sulfurous lakes from the Lake Banyoles karstic area (NE Spain) through 16S rRNA gene tag sequencing and identified the closest GenBank counterpart. High diversity indices were found in most of the samples with >15 phyla/classes and >45 bacterial orders. A higher proportion of operational taxonomic units (OTUs) of the "highest novelty" was found in the hypolimnia (38 % of total sequences) than in the metalimnia (17 %), whereas the percentage of OTUs closer to cultured counterparts (i.e., 97 % identity in the 16S rRNA gene) was 6 to 21 %, respectively. Elusimicrobia, Chloroflexi, Fibrobacteres, and Spirochaetes were the taxa with the highest proportion of novel sequences. Interestingly, tag sequencing results comparison with metagenomics data available from the same dataset, showed a systematic underestimation of sulfur-oxidizing Epsilonproteobacteria with the currently available 907R "universal" primer. Overall, despite the limitation of electron acceptors, a highly diverse and novel assemblage was present in dark and euxinic hypolimnetic freshwaters, unveiling a hotspot of microbial diversity with a remarkable gap with cultured counterparts.
Collapse
Affiliation(s)
- Tomàs Llorens-Marès
- Integrative Freshwater Ecology Group, Centro de Estudios Avanzados de Blanes, CEAB-CSIC, Accés Cala Sant Francesc, 14, 17300, Blanes, Girona, Spain
| | - Xavier Triadó-Margarit
- Integrative Freshwater Ecology Group, Centro de Estudios Avanzados de Blanes, CEAB-CSIC, Accés Cala Sant Francesc, 14, 17300, Blanes, Girona, Spain
| | - Carles M Borrego
- Water Quality and Microbial Diversity, Catalan Institute for Water Research (ICRA), Girona, Spain
- Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Girona, Spain
| | - Chris L Dupont
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, San Diego, CA, USA
| | - Emilio O Casamayor
- Integrative Freshwater Ecology Group, Centro de Estudios Avanzados de Blanes, CEAB-CSIC, Accés Cala Sant Francesc, 14, 17300, Blanes, Girona, Spain.
| |
Collapse
|
19
|
Zhong ZP, Liu Y, Miao LL, Wang F, Chu LM, Wang JL, Liu ZP. Prokaryotic Community Structure Driven by Salinity and Ionic Concentrations in Plateau Lakes of the Tibetan Plateau. Appl Environ Microbiol 2016; 82:1846-1858. [PMID: 26746713 PMCID: PMC4784034 DOI: 10.1128/aem.03332-15] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Accepted: 12/31/2015] [Indexed: 02/06/2023] Open
Abstract
The prokaryotic community composition and diversity and the distribution patterns at various taxonomic levels across gradients of salinity and physiochemical properties in the surface waters of seven plateau lakes in the Qaidam Basin, Tibetan Plateau, were evaluated using Illumina MiSeq sequencing. These lakes included Lakes Keluke (salinity, <1 g/liter), Qing (salinity, 5.5 to 6.6 g/liter), Tuosu (salinity, 24 to 35 g/liter), Dasugan (salinity, 30 to 33 g/liter), Gahai (salinity, 92 to 96 g/liter), Xiaochaidan (salinity, 94 to 99 g/liter), and Gasikule (salinity, 317 to 344 g/liter). The communities were dominated by Bacteria in lakes with salinities of <100 g/liter and by Archaea in Lake Gasikule. The clades At12OctB3 and Salinibacter, previously reported only in hypersaline environments, were found in a hyposaline lake (salinity, 5.5 to 6.6 g/liter) at an abundance of ∼1.0%, indicating their ecological plasticity. Salinity and the concentrations of the chemical ions whose concentrations covary with salinity (Mg(2+), K(+), Cl(-), Na(+), SO4 (2-), and Ca(2+)) were found to be the primary environmental factors that directly or indirectly determined the composition and diversity at the level of individual clades as well as entire prokaryotic communities. The distribution patterns of two phyla, five classes, five orders, five families, and three genera were well predicted by salinity. The variation of the prokaryotic community structure also significantly correlated with the dissolved oxygen concentration, pH, the total nitrogen concentration, and the PO4 (3-) concentration. Such correlations varied depending on the taxonomic level, demonstrating the importance of comprehensive correlation analyses at various taxonomic levels in evaluating the effects of environmental variable factors on prokaryotic community structures. Our findings clarify the distribution patterns of the prokaryotic community composition in plateau lakes at the levels of individual clades as well as whole communities along gradients of salinity and ionic concentrations.
Collapse
Affiliation(s)
- Zhi-Ping Zhong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Ying Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Li-Li Miao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Fang Wang
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing, People's Republic of China
| | - Li-Min Chu
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing, People's Republic of China
| | - Jia-Li Wang
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing, People's Republic of China
- Institute of Shandong River Wetlands, Laiwu, People's Republic of China
| | - Zhi-Pei Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People's Republic of China
| |
Collapse
|
20
|
Oren A. Life in Hypersaline Environments. THEIR WORLD: A DIVERSITY OF MICROBIAL ENVIRONMENTS 2016. [DOI: 10.1007/978-3-319-28071-4_8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
21
|
|
22
|
Gimmler A, Stoeck T. Mining environmental high-throughput sequence data sets to identify divergent amplicon clusters for phylogenetic reconstruction and morphotype visualization. ENVIRONMENTAL MICROBIOLOGY REPORTS 2015; 7:679-686. [PMID: 26061246 DOI: 10.1111/1758-2229.12307] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Accepted: 06/03/2015] [Indexed: 06/04/2023]
Abstract
Environmental high-throughput sequencing (envHTS) is a very powerful tool, which in protistan ecology is predominantly used for the exploration of diversity and its geographic and local patterns. We here used a pyrosequenced V4-SSU rDNA data set from a solar saltern pond as test case to exploit such massive protistan amplicon data sets beyond this descriptive purpose. Therefore, we combined a Swarm-based blastn network including 11 579 ciliate V4 amplicons to identify divergent amplicon clusters with targeted polymerase chain reaction (PCR) primer design for full-length small subunit of the ribosomal DNA retrieval and probe design for fluorescence in situ hybridization (FISH). This powerful strategy allows to benefit from envHTS data sets to (i) reveal the phylogenetic position of the taxon behind divergent amplicons; (ii) improve phylogenetic resolution and evolutionary history of specific taxon groups; (iii) solidly assess an amplicons (species') degree of similarity to its closest described relative; (iv) visualize the morphotype behind a divergent amplicons cluster; (v) rapidly FISH screen many environmental samples for geographic/habitat distribution and abundances of the respective organism and (vi) to monitor the success of enrichment strategies in live samples for cultivation and isolation of the respective organisms.
Collapse
Affiliation(s)
- Anna Gimmler
- Department of Ecology, University of Kaiserslautern, Erwin-Schrödinger-Straße 14, Kaiserslautern, D-67633, Germany
| | - Thorsten Stoeck
- Department of Ecology, University of Kaiserslautern, Erwin-Schrödinger-Straße 14, Kaiserslautern, D-67633, Germany
| |
Collapse
|
23
|
Filker S, Gimmler A, Dunthorn M, Mahé F, Stoeck T. Deep sequencing uncovers protistan plankton diversity in the Portuguese Ria Formosa solar saltern ponds. Extremophiles 2014; 19:283-95. [DOI: 10.1007/s00792-014-0713-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 11/16/2014] [Indexed: 11/24/2022]
|
24
|
Wang J, Wang F, Chu L, Wang H, Zhong Z, Liu Z, Gao J, Duan H. High genetic diversity and novelty in eukaryotic plankton assemblages inhabiting saline lakes in the Qaidam basin. PLoS One 2014; 9:e112812. [PMID: 25401703 PMCID: PMC4234628 DOI: 10.1371/journal.pone.0112812] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2014] [Accepted: 10/19/2014] [Indexed: 12/21/2022] Open
Abstract
Saline lakes are intriguing ecosystems harboring extremely productive microbial communities in spite of their extreme environmental conditions. We performed a comprehensive analysis of the genetic diversity (18S rRNA gene) of the planktonic microbial eukaryotes (nano- and picoeukaryotes) in six different inland saline lakes located in the Qaidam Basin. The novelty level are high, with about 11.23% of the whole dataset showing <90% identity to any previously reported sequence in GenBank. At least 4 operational taxonomic units (OTUs) in mesosaline lakes, while up to eighteen OTUs in hypersaline lakes show very low CCM and CEM scores, indicating that these sequences are highly distantly related to any existing sequence. Most of the 18S rRNA gene sequence reads obtained in investigated mesosaline lakes is closely related to Holozoa group (48.13%), whereas Stramenopiles (26.65%) and Alveolates (10.84%) are the next most common groups. Hypersaline lakes in the Qaidam Basin are also dominated by Holozoa group, accounting for 26.65% of the total number of sequence reads. Notably, Chlorophyta group are only found in high abundance in Lake Gasikule (28.00%), whereas less represented in other hypersaline lakes such as Gahai (0.50%) and Xiaochaidan (1.15%). Further analysis show that the compositions of planktonic eukaryotic assemblages are also most variable between different sampling sites in the same lake. Out of the parameters, four show significant correlation to this CCA: altitude, calcium, sodium and potassium concentrations. Overall, this study shows important gaps in the current knowledge about planktonic microbial eukaryotes inhabiting Qaidam Basin (hyper) saline water bodies. The identified diversity and novelty patterns among eukaryotic plankton assemblages in saline lake are of great importance for understanding and interpreting their ecology and evolution.
Collapse
Affiliation(s)
- Jiali Wang
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing, China
- Institute of Shandong River Wetlands, Laiwu, China
| | - Fang Wang
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing, China
- * E-mail:
| | - Limin Chu
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing, China
- College of Hydrology and Water Resource, Hohai University, Nanjing, China
| | - Hao Wang
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing, China
| | - Zhiping Zhong
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zhipei Liu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | | | | |
Collapse
|
25
|
Comparison of Artemia–bacteria associations in brines, laboratory cultures and the gut environment: a study based on Chilean hypersaline environments. Extremophiles 2014; 19:135-47. [DOI: 10.1007/s00792-014-0694-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 08/28/2014] [Indexed: 10/24/2022]
|
26
|
Oren A, Hallsworth JE. Microbial weeds in hypersaline habitats: the enigma of the weed-likeHaloferax mediterranei. FEMS Microbiol Lett 2014; 359:134-42. [DOI: 10.1111/1574-6968.12571] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 07/30/2014] [Accepted: 08/01/2014] [Indexed: 11/29/2022] Open
Affiliation(s)
- Aharon Oren
- Department of Plant & Environmental Sciences; The Alexander Silberman Institute of Life Sciences; The Hebrew University of Jerusalem; Jerusalem Israel
| | - John E. Hallsworth
- Institute for Global Food Security; School of Biological Sciences; MBC; Queen's University Belfast; Belfast UK
| |
Collapse
|
27
|
Comparison of bacterial diversity from solar salterns and a simulated laboratory study. ANN MICROBIOL 2014. [DOI: 10.1007/s13213-014-0944-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
|
28
|
Genitsaris S, Kormas KA, Christaki U, Monchy S, Moustaka-Gouni M. Molecular diversity reveals previously undetected air-dispersed protist colonists in a Mediterranean area. THE SCIENCE OF THE TOTAL ENVIRONMENT 2014; 478:70-79. [PMID: 24530586 DOI: 10.1016/j.scitotenv.2014.01.071] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 12/24/2013] [Accepted: 01/20/2014] [Indexed: 06/03/2023]
Abstract
The molecular diversity of air-dispersed protists was examined through the 18S rRNA gene clone library construction in air samples and samples from experimental water containers passively collecting air-dispersed microorganisms, from July 2007 till October 2008 in three different sites of Northern Greece. The majority of the samplings took place in an urban industrialized coastal city (Thessaloniki). In all the samples, a total of 29 unique phylotypes were detected belonging to 10 known major taxonomic groups. The most abundant phylotypes were affiliated to known taxa of Ciliophora and Chlorophyceae, commonly found in various habitats. Additionally, various previously unnoticed and under-studied taxa, such as Bicosoecida, Oomycetes and Labyrinthulomycetes, were detected. These taxa are potentially important in ecological processes, through dispersal and colonization of various habitats. Multivariate statistical analysis associated the most abundant phylotypes with rainfall, suggesting that rain is a favorable means for reposition of air-dispersed protists. This is the first study investigating the molecular diversity of air-dispersed protists, including algae and heterotrophic protists.
Collapse
Affiliation(s)
- Savvas Genitsaris
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece; Université du Littoral Côte d'Opale, ULCO, Laboratoire d' Océanologie et Géoscience, LOG, UMR CNRS 8187, 32 av. Foch, F-62930 Wimereux, France
| | - Konstantinos Ar Kormas
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 384 46 Volos, Greece
| | - Urania Christaki
- Université du Littoral Côte d'Opale, ULCO, Laboratoire d' Océanologie et Géoscience, LOG, UMR CNRS 8187, 32 av. Foch, F-62930 Wimereux, France
| | - Sebastien Monchy
- Université du Littoral Côte d'Opale, ULCO, Laboratoire d' Océanologie et Géoscience, LOG, UMR CNRS 8187, 32 av. Foch, F-62930 Wimereux, France
| | - Maria Moustaka-Gouni
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece.
| |
Collapse
|
29
|
Liu K, Ding X, Wang HF, Zhang X, Hozzein WN, Wadaan MAM, Lan A, Zhang B, Li W. Eukaryotic microbial communities in hypersaline soils and sediments from the alkaline hypersaline Huama Lake as revealed by 454 pyrosequencing. Antonie van Leeuwenhoek 2014; 105:871-80. [PMID: 24563154 DOI: 10.1007/s10482-014-0141-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Accepted: 02/13/2014] [Indexed: 12/23/2022]
Abstract
In hypersaline ecosystems, microbial assemblages are structurally distinctive and play important roles in many microbiological and ecological processes. Here, eukaryotic microorganisms in hypersaline samples were investigated by 454 pyrosequencing of internal transcribed spacer (ITS) gene libraries. In total, 4,645, 1,677, and 5,912 reads were obtained from ITS libraries of waterlogged samples, salt crusts, and saline loess from the alkaline Huama Lake in Shaanxi, China. Analyses of pyrosequencing data revealed that the dominant genera were Dunaliella, Alternaria and Chlamydomonas, which dominated the microbial assemblages in the waterlogged sediments, the salt crusts and the saline loess from the lake banks, respectively. The various infrequent species were not commonly shared by the three types of samples, demonstrating that the eukaryotic microbial compositions of the different environments were distinct. However, the micro-eukaryotic assemblages associated with similar environmental conditions shared some components and were phylogenetically related. The eukaryotic microbial community composition was correlated with the pH value of the site (p = 0.001; r(2) = 0.99), but not with the concentration of total nitrogen or the inorganic ions investigated in this study. The results of this study demonstrated that the hypersaline ecosystems hosted surprisingly diverse eukaryotic microbial community.
Collapse
Affiliation(s)
- Kaihui Liu
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, China
| | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Casamayor EO, Triadó-Margarit X, Castañeda C. Microbial biodiversity in saline shallow lakes of the Monegros Desert, Spain. FEMS Microbiol Ecol 2013; 85:503-18. [DOI: 10.1111/1574-6941.12139] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 04/18/2013] [Accepted: 04/19/2013] [Indexed: 11/29/2022] Open
Affiliation(s)
- Emilio O. Casamayor
- Biodiversity and Biogeodynamics Group; Centre d'Estudis Avançats de Blanes; CSIC; Blanes Spain
| | - Xavier Triadó-Margarit
- Biodiversity and Biogeodynamics Group; Centre d'Estudis Avançats de Blanes; CSIC; Blanes Spain
| | | |
Collapse
|