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Zhang H, Wei T, Li Q, Fu L, Li M, He L, Wang Y. Metagenomic 18S rDNA reads revealed zonation of eukaryotic communities in the Yongle blue hole. Front Microbiol 2024; 15:1420899. [PMID: 39135873 PMCID: PMC11317397 DOI: 10.3389/fmicb.2024.1420899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Accepted: 07/15/2024] [Indexed: 08/15/2024] Open
Abstract
The Yongle blue hole (YBH), situated in the South China Sea, represents a compelling subject of study in marine microbiology due to its unique redox-layered microbial ecosystems. However, the diversity and ecology of microbial eukaryotes within the YBH remains underexplored. This study endeavors to bridge this gap through the application of the in situ microbial filtration and fixation (ISMIFF) device to collect 0.22-30 μm microbial samples from 21 water layers of YBH. Subsequent extraction of 18S rRNA metagenomic reads of 21 metagenomes and 10 metatranscriptomes facilitated a comprehensive analysis of community structures. Findings revealed a pronounced superiority in the diversity and richness of eukaryotic microorganisms in the oxic zone compared to its suboxic and anoxic counterparts. Notably, Dinophyceae and Maxillopoda emerged as the predominant taxa based on the analysis of the 18S rRNA reads for the V4 and V9 regions, which showed stratification In their relative abundance and suggested their potential role in the thermo-halocline boundaries and oxic-anoxic interface. Specifically, In these eukaryotic microbial communities, Dinophyceae exhibited significant abundance at 20 m (20.01%) and 105 m (26.13%) water depths, while Maxillopoda was prevalent at 40 m (22.84%), 80 m (23.19%), and 100 m (15.42%) depths. A part of these organisms, identified as larvae and protists, were likely attracted by swarming chemosynthetic bacterial prey prevailing at the thermo-halocline boundaries and oxic-anoxic interface. Furthermore, the phylogenetic relationships of the major 18S operational taxonomic units (OTUs) showed a close adjacency to known species, except for three Dinophyceae OTUs. In conclusion, this study provides critical insights into the vertical distribution and transcriptional activity of <30-μm eukaryotic microbes, shedding light on the taxonomic novelty of eukaryotic microorganisms within the semi-enclosed blue holes.
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Affiliation(s)
- Hongxi Zhang
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Taoshu Wei
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Qingmei Li
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Liang Fu
- Sansha Track Ocean Coral Reef Conservation Research Institute Co., Ltd., Sansha, China
| | - Manjie Li
- Institute for Ocean Engineering, Shenzhen International Graduate School, Shenzhen, China
- Shenzhen Key Laboratory of Advanced Technology for Marine Ecology, Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Lisheng He
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Yong Wang
- Institute for Ocean Engineering, Shenzhen International Graduate School, Shenzhen, China
- Shenzhen Key Laboratory of Advanced Technology for Marine Ecology, Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
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Li J, Xie N, Liu X, Bai M, Hunt DE, Wang G. Oxygen levels differentially attenuate the structure and diversity of microbial communities in the oceanic oxygen minimal zones. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 948:174934. [PMID: 39047843 DOI: 10.1016/j.scitotenv.2024.174934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 07/18/2024] [Accepted: 07/19/2024] [Indexed: 07/27/2024]
Abstract
Global change mediated shifts in ocean temperature and circulation patterns, compounded by human activities, are leading to the expansion of marine oxygen minimum zones (OMZs) with concomitant alterations in nutrient and climate-active trace gas cycling. While many studies have reported distinct bacterial communities within OMZs, much of this research compares across depths rather with oxygen status and does not include eukayrotic microbes. Here, we investigated the Bay of Bengal (BoB) OMZ, where low oxygen conditions are persistent, but trace levels of oxygen remain (< 20 μM from 200 to 500 m). As other environmental variables are similar between OMZ and non-OMZ (NOZ) stations, we compared the abundance, diversity, and community composition of several microbial groups (bacterioplankton, Labyrinthulomycetes, and fungi) across oxygen levels. While prokaryote abundance decreased with depth, no significant differences existed across oxygen groups. In contrast, Labyrinthulomycetes abundance was significantly higher in non-OMZ stations but did not change significantly with depth, while fungal abundance was patchy without clear depth or oxygen-related trends. Bacterial and fungal diversity was lower in OMZ stations at 500 m, while Labyrinthulomycetes diversity only showed a depth-related profile, decreasing below the euphotic zone. Surprisingly, previously reported OMZ-associated bacterial taxa were not significantly more abundant at OMZ stations. Furthermore, compared to the bacterioplankton, fewer Labyrinthulomycetes and fungi taxa showed responses to oxygen status. Thus, this research identifies stronger oxygen-level linkages within the bacterioplankton than in the examined microeukaryotes.
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Affiliation(s)
- Jiaqian Li
- School of Environmental Science & Engineering, Center for Marine Environmental Ecology, Tianjin University, China; Duke University Marine Lab, Beaufort, NC, USA
| | - Ningdong Xie
- School of Environmental Science & Engineering, Center for Marine Environmental Ecology, Tianjin University, China
| | - Xiuping Liu
- School of Environmental Science & Engineering, Center for Marine Environmental Ecology, Tianjin University, China
| | - Mohan Bai
- School of Environmental Science & Engineering, Center for Marine Environmental Ecology, Tianjin University, China
| | - Dana E Hunt
- Duke University Marine Lab, Beaufort, NC, USA.
| | - Guangyi Wang
- School of Environmental Science & Engineering, Center for Marine Environmental Ecology, Tianjin University, China.
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3
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Nakanishi H, Seto K, Takeuchi N, Kagami M. Novel parasitic chytrids infecting snow algae in an alpine snow ecosystem in Japan. Front Microbiol 2023; 14:1201230. [PMID: 37408638 PMCID: PMC10318532 DOI: 10.3389/fmicb.2023.1201230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 05/30/2023] [Indexed: 07/07/2023] Open
Abstract
Introduction Microbial communities are important components of glacier and snowpack ecosystems that influence biogeochemical cycles and snow/ice melt. Recent environmental DNA surveys have revealed that chytrids dominate the fungal communities in polar and alpine snowpacks. These could be parasitic chytrids that infect snow algae as observed microscopically. However, the diversity and phylogenetic position of parasitic chytrids has not been identified due to difficulties in establishing their culture and subsequent DNA sequencing. In this study, we aimed to identify the phylogenetic positions of chytrids infecting the snow algae, Chloromonas spp., bloomed on snowpacks in Japan. Methods By linking a microscopically picked single fungal sporangium on a snow algal cell to a subsequent sequence of ribosomal marker genes, we identified three novel lineages with distinct morphologies. Results All the three lineages belonged to Mesochytriales, located within "Snow Clade 1", a novel clade consisting of uncultured chytrids from snow-covered environments worldwide. Additionally, putative resting spores of chytrids attached to snow algal cells were observed. Discussion This suggests that chytrids may survive as resting stage in soil after snowmelt. Our study highlights the potential importance of parasitic chytrids that infect snow algal communities.
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Affiliation(s)
- Hiroaki Nakanishi
- Graduate School of Environment and Information Sciences, Yokohama National University, Yokohama, Kanagawa, Japan
| | - Kensuke Seto
- Faculty of Environment and Information Sciences, Yokohama National University, Yokohama, Kanagawa, Japan
| | - Nozomu Takeuchi
- Department of Earth Sciences, Graduate School of Science, Chiba University, Chiba, Japan
| | - Maiko Kagami
- Faculty of Environment and Information Sciences, Yokohama National University, Yokohama, Kanagawa, Japan
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4
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DNA metabarcoding data reveals harmful algal-bloom species undescribed previously at the northern Antarctic Peninsula region. Polar Biol 2022. [DOI: 10.1007/s00300-022-03084-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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5
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Lin YC, Chin CP, Yang JW, Chiang KP, Hsieh CH, Gong GC, Shih CY, Chen SY. How Communities of Marine Stramenopiles Varied with Environmental and Biological Variables in the Subtropical Northwestern Pacific Ocean. MICROBIAL ECOLOGY 2022; 83:916-928. [PMID: 34269858 PMCID: PMC9015972 DOI: 10.1007/s00248-021-01788-7] [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: 12/02/2020] [Accepted: 06/01/2021] [Indexed: 06/13/2023]
Abstract
MArine STramenopiles (MASTs) have been recognized as parts of heterotrophic protists and contribute substantially to protist abundances in the ocean. However, little is known about their spatiotemporal variations with respect to environmental and biological factors. The objectives of this study are to use canonical correspondence analysis to investigate how MASTs communities are shaped by environmental variables, and co-occurrence networks to examine their potential interactions with prokaryotic communities. Our dataset came from the southern East China Sea (sECS) in the subtropical northwestern Pacific, and involved 14 cruises along a coastal-oceanic transect, each of which sampled surface water from 4 to 7 stations. MASTs communities were revealed by metabarcoding of 18S rDNA V4 region. Most notably, MAST-9 had a high representation in warm waters in terms of read number and diversity. Subclades of MAST-9C and -9D showed slightly different niches, with MAST-9D dominating in more coastal waters where concentrations of nitrite and Synechococcus were higher. MAST-1C was a common component of colder water during spring. Overall, canonical correspondence analysis showed that MASTs communities were significantly influenced by temperature, nitrite and Synechococcus concentrations. The co-occurrence networks showed that certain other minor prokaryotic taxa can influence MAST communities. This study provides insight into how MASTs communities varied with environmental and biological variables.
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Affiliation(s)
- Yun-Chi Lin
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung, Taiwan
| | | | - Jinny Wu Yang
- Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, USA
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan
| | - Kuo-Ping Chiang
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung, Taiwan.
| | - Chih-Hao Hsieh
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan
| | - Gwo-Ching Gong
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung, Taiwan
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan
| | - Chi-Yu Shih
- Institute of Marine Biology, National Taiwan Ocean University, Keelung, Taiwan
| | - Szu-Ying Chen
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan
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6
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Schiwitza S, Thomsen HA. Morphological and molecular reinvestigation of acanthoecid species I. – Enibas urnula ( ) comb. nov. (= Stephanoeca urnula ). Eur J Protistol 2022; 83:125865. [DOI: 10.1016/j.ejop.2022.125865] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/07/2022] [Accepted: 01/08/2022] [Indexed: 11/15/2022]
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7
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Long AM, Jurgensen SK, Petchel AR, Savoie ER, Brum JR. Microbial Ecology of Oxygen Minimum Zones Amidst Ocean Deoxygenation. Front Microbiol 2021; 12:748961. [PMID: 34777296 PMCID: PMC8578717 DOI: 10.3389/fmicb.2021.748961] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 10/06/2021] [Indexed: 01/05/2023] Open
Abstract
Oxygen minimum zones (OMZs) have substantial effects on the global ecology and biogeochemical processes of marine microbes. However, the diversity and activity of OMZ microbes and their trophic interactions are only starting to be documented, especially in regard to the potential roles of viruses and protists. OMZs have expanded over the past 60 years and are predicted to expand due to anthropogenic climate change, furthering the need to understand these regions. This review summarizes the current knowledge of OMZ formation, the biotic and abiotic factors involved in OMZ expansion, and the microbial ecology of OMZs, emphasizing the importance of bacteria, archaea, viruses, and protists. We describe the recognized roles of OMZ microbes in carbon, nitrogen, and sulfur cycling, the potential of viruses in altering host metabolisms involved in these cycles, and the control of microbial populations by grazers and viruses. Further, we highlight the microbial community composition and roles of these organisms in oxic and anoxic depths within the water column and how these differences potentially inform how microbial communities will respond to deoxygenation. Additionally, the current literature on the alteration of microbial communities by other key climate change parameters such as temperature and pH are considered regarding how OMZ microbes might respond to these pressures. Finally, we discuss what knowledge gaps are present in understanding OMZ microbial communities and propose directions that will begin to close these gaps.
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Affiliation(s)
- Andrew M. Long
- Department of Oceanography and Coastal Sciences, Louisiana State University, Baton Rouge, LA, United States
| | | | | | | | - Jennifer R. Brum
- Department of Oceanography and Coastal Sciences, Louisiana State University, Baton Rouge, LA, United States
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8
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Block KR, O'Brien JM, Edwards WJ, Marnocha CL. Vertical structure of the bacterial diversity in meromictic Fayetteville Green Lake. Microbiologyopen 2021; 10:e1228. [PMID: 34459548 PMCID: PMC8330806 DOI: 10.1002/mbo3.1228] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 07/16/2021] [Accepted: 07/19/2021] [Indexed: 11/08/2022] Open
Abstract
The permanently stratified water columns in euxinic meromictic lakes produce niche environments for phototrophic sulfur oxidizers and diverse sulfur metabolisms. While Green Lake (Fayetteville, New York, NY) is known to host a diverse community of ecologically important sulfur bacteria, analyses of its microbial communities, to date, have been largely based on pigment analysis and smaller datasets from Sanger sequencing techniques. Here, we present the results of next-generation sequencing of the eubacterial community in the context of the water column geochemistry. We observed abundant purple and green sulfur bacteria, as well as anoxygenic photosynthesis-capable cyanobacteria within the upper monimolimnion. Amidst the phototrophs, we found other sulfur-cycling bacteria including sulfur disproportionators and chemotrophic sulfur oxidizers, further detailing our understanding of the sulfur cycle and microbial ecology of euxinic, meromictic lakes.
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Affiliation(s)
| | - Joy M. O'Brien
- Department of BiologyNiagara UniversityLewistonNew YorkUSA
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9
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Schiwitza S, Nitsche F. A Needle in the Haystack – Mapping Sequences to Morphology Exemplified by the Loricate Choanoflagellate Enibas thessalia sp. nov. (Acanthoecida, Acanthoecidae). Protist 2021; 172:125782. [DOI: 10.1016/j.protis.2020.125782] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 11/16/2020] [Accepted: 11/22/2020] [Indexed: 01/28/2023]
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10
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Reboul G, Moreira D, Bertolino P, Hillebrand-Voiculescu AM, López-García P. Microbial eukaryotes in the suboxic chemosynthetic ecosystem of Movile Cave, Romania. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:464-473. [PMID: 30969022 PMCID: PMC6697535 DOI: 10.1111/1758-2229.12756] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 03/26/2019] [Accepted: 04/08/2019] [Indexed: 06/09/2023]
Abstract
Movile Cave is a small system of partially inundated galleries in limestone settings close to the Black Sea in Southeast Romania. Isolated from the surface for 6 million years, its sulfidic, methane and ammonia-rich waters harbour unique chemosynthetic prokaryotic communities that include sulphur and ammonium-metabolizing chemolithotrophs, methanogens, methanotrophs and methylotrophs. The cave also harbours cave-dwelling invertebrates and fungi, but the diversity of other microbial eukaryotes remained completely unknown. Here, we apply an 18S rRNA gene-based metabarcoding approach to study the composition of protist communities in floating microbial mats and plankton from a well-preserved oxygen-depleted cave chamber. Our results reveal a wide protist diversity with, as dominant groups, ciliates (Alveolata), Stramenopiles, especially bicosoecids, and jakobids (Excavata). Ciliate sequences dominated both, microbial mats and plankton, followed by either Stramenopiles or excavates. Stramenopiles were more prominent in microbial mats, whereas jakobids dominated the plankton fraction of the oxygen-depleted water column. Mats cultured in the laboratory were enriched in Cercozoa. Consistent with local low oxygen levels, Movile Cave protists are most likely anaerobic or microaerophilic. Several newly detected OTU clades were very divergent from cultured species or environmental sequences in databases and represent phylogenetic novelty, notably within jakobids. Movile Cave protists likely cover a variety of ecological roles in this ecosystem including predation, parasitism, saprotrophy and possibly diverse prokaryote-protist syntrophies.
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Affiliation(s)
- Guillaume Reboul
- Unité d’Ecologie, Systématique et Evolution, CNRS, Université Paris-Sud, Université Paris-Saclay, AgroParisTech, bâtiment 360, 91400 Orsay, France
| | - David Moreira
- Unité d’Ecologie, Systématique et Evolution, CNRS, Université Paris-Sud, Université Paris-Saclay, AgroParisTech, bâtiment 360, 91400 Orsay, France
| | - Paola Bertolino
- Unité d’Ecologie, Systématique et Evolution, CNRS, Université Paris-Sud, Université Paris-Saclay, AgroParisTech, bâtiment 360, 91400 Orsay, France
| | - Alexandra Maria Hillebrand-Voiculescu
- Department of Biospeleology and Karst Edaphobiology, Emil Racovita Institute of Speleology, Bucharest, Romania
- Group for Underwater and Speleological Exploration, Bucharest, Romania
| | - Purificación López-García
- Unité d’Ecologie, Systématique et Evolution, CNRS, Université Paris-Sud, Université Paris-Saclay, AgroParisTech, bâtiment 360, 91400 Orsay, France
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11
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Singh D, Slik JWF, Jeon YS, Tomlinson KW, Yang X, Wang J, Kerfahi D, Porazinska DL, Adams JM. Tropical forest conversion to rubber plantation affects soil micro- & mesofaunal community & diversity. Sci Rep 2019; 9:5893. [PMID: 30971738 PMCID: PMC6458137 DOI: 10.1038/s41598-019-42333-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 03/25/2019] [Indexed: 11/10/2022] Open
Abstract
Tropical rainforests play important roles in carbon sequestration and are hot spots for biodiversity. Tropical forests are being replaced by rubber (Hevea brasiliensis) plantations, causing widespread concern of a crash in biodiversity. Such changes in aboveground vegetation might have stronger impacts on belowground biodiversity. We studied tropical rainforest fragments and derived rubber plantations at a network of sites in Xishuangbanna, China, hypothesizing a major decrease in diversity with conversion to plantations. We used metabarcoding of the 18S rRNA gene and recovered 2313 OTUs, with a total of 449 OTUs shared between the two land-use types. The most abundant phyla detected were Annelida (66.4% reads) followed by arthropods (15.5% reads) and nematodes (8.9% reads). Of these, only annelids were significantly more abundant in rubber plantation. Taken together, α- and β-diversity were significantly higher in forest than rubber plantation. Soil pH and spatial distance explained a significant portion of the variability in phylogenetic community structure for both land-use types. Community assembly was primarily influenced by stochastic processes. Overall it appears that forest replacement by rubber plantation results in an overall loss and extensive replacement of soil micro- and mesofaunal biodiversity, which should be regarded as an additional aspect of the impact of forest conversion.
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Affiliation(s)
- Dharmesh Singh
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, 666303, China
- Environmental Biotechnology & Genomics Division, CSIR-NEERI, Nehru Marg, Nagpur, MH, 440020, India
| | - J W Ferry Slik
- Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku, BE1410, Brunei Darussalam
| | - Yoon-Seong Jeon
- ChunLab Inc., Bldg. 105-1, Suite #307, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 151-742, Republic of Korea
| | - Kyle W Tomlinson
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, 666303, China
| | - Xiaodong Yang
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, 666303, China
| | - Jin Wang
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, 666303, China
| | - Dorsaf Kerfahi
- Department of Biological Sciences, College of Natural Sciences, Seoul National University, Gwanak-Gu, Seoul, 151-742, Republic of Korea
| | - Dorota L Porazinska
- Department of Entomology and Nematology, University of Florida, IFAS, 1881 Natural Area Drive, Gainesville, 32611, Florida, USA
| | - Jonathan M Adams
- School of Geography and Ocean Sciences, Nanjing University, Nanjing, 210023, Jiangsu Province, China.
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12
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Glukhova LB, Frank YA, Danilova EV, Avakyan MR, Banks D, Tuovinen OH, Karnachuk OV. Isolation, Characterization, and Metal Response of Novel, Acid-Tolerant Penicillium spp. from Extremely Metal-Rich Waters at a Mining Site in Transbaikal (Siberia, Russia). MICROBIAL ECOLOGY 2018; 76:911-924. [PMID: 29663040 DOI: 10.1007/s00248-018-1186-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 04/06/2018] [Indexed: 06/08/2023]
Abstract
The role of fungi in metal cycling in acidic environments has been little explored to date. In this study, two acid-tolerant and metal-resistant Penicillium isolates, strains ShG4B and ShG4C, were isolated from a mine site in the Transbaikal area of Siberia (Russia). Waters at the mine site were characterized by extremely high metal concentrations: up to 18 g l-1 Fe and > 2 g l-1 each of Cu, Zn, Al, and As. Both isolates were identified as Penicillium spp. by phylogenetic analyses and they grew well in Czapek medium acidified to pH 2.5. Resistance to Cu, Cd, Ni, Co, and arsenate was in the range of 1-10 g l-1. Further experiments with Penicillium strain ShG4C demonstrated that growth in Cu-containing media was accompanied by the precipitation of Cu-oxalate (moolooite) and the formation of extracellular vesicles enriched in Cu on the mycelia. Vesicles were greatly reduced in size in Cd-containing media and were not formed in the presence of Ni or Co. Cd-oxalate was detected as a crystalline solid phase in Cd-exposed mycelia. Hydrated Ni-sulfate (retgersite) and Co-sulfate (bieberite) were detected in mycelia grown in the presence of Ni and Co, respectively. The results demonstrated that acid-tolerant and metal-resistant Penicillium constitute a component in extremophilic microbiomes, contributing to organic matter breakdown and formation of secondary solid phases at pH ranges found in acid rock drainage.
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Affiliation(s)
- Lubov B Glukhova
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Lenin Ave. 36, Tomsk, Russia, 634050
| | - Yulia A Frank
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Lenin Ave. 36, Tomsk, Russia, 634050
| | - Ehrzena V Danilova
- Institute of General and Experimental Biology, Russian Academy of Sciences, Sakhyanovoy St. 6, Ulan-Ude, Russia, 670047
| | - Marat R Avakyan
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Lenin Ave. 36, Tomsk, Russia, 634050
| | - David Banks
- School of Engineering, Systems Power & Energy, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK
- Holymoor Consultancy Ltd., 360 Ashgate Road, Chesterfield, Derbyshire, S40 4BW, UK
| | - Olli H Tuovinen
- Department of Microbiology, Ohio State University, Columbus, OH, 43210, USA
| | - Olga V Karnachuk
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Lenin Ave. 36, Tomsk, Russia, 634050.
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13
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Cai J, Bai C, Tang X, Dai J, Gong Y, Hu Y, Shao K, Zhou L, Gao G. Characterization of bacterial and microbial eukaryotic communities associated with an ephemeral hypoxia event in Taihu Lake, a shallow eutrophic Chinese lake. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:31543-31557. [PMID: 30206827 DOI: 10.1007/s11356-018-2987-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 08/15/2018] [Indexed: 06/08/2023]
Abstract
While the important roles of microbial communities in oceanic hypoxic zones were beginning to be understood, little is known about microbial community associated with this phenomenon in shallow lakes. To address this deficit, both the bacterial and microbial eukaryotic communities of an ephemeral hypoxic area of Taihu Lake were characterized. The hypoxia provided nutritional niches for various bacteria, which results in high abundance and diversity. Specific bacterial groups, such as vadinBC27 subgroup of Bacteroidetes, Burkholderiales, Rhodocyclales, Pseudomonas, and Parcubacteria, were dominated in hypoxic sites and relevant to the fermentation, denitrification, nitrification, and sulfur metabolism. Conversely, most of microbial eukaryotes disappeared along with the decline of DO. An unexpected dominance of fungi was observed during hypoxia, which partly explained by the accumulation of toxic algae. Mucor was the single dominant genus in the hypoxic zone. We proposed that this group might cooperate with bacterial communities in the anaerobic degradation of algal biomass and woody materials. Generally, the hypoxic microbiome in shallow lakes is mainly involved in fermentative metabolism depending on phytodetritus and is potentially influenced by terrestrial sources. This study provided new insights into the unique microbiome in short-term hypoxia in shallow lakes and lays the foundation for studies that will enhance our understanding of the microbial players associated with hypoxia and their adaption strategy on the global scale.
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Affiliation(s)
- Jian Cai
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, People's Republic of China
| | - Chengrong Bai
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, People's Republic of China
| | - Xiangming Tang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, People's Republic of China
| | - Jiangyu Dai
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing, 210029, People's Republic of China
| | - Yi Gong
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, People's Republic of China
| | - Yang Hu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, People's Republic of China
| | - Keqiang Shao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, People's Republic of China
| | - Lei Zhou
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, People's Republic of China
| | - Guang Gao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, People's Republic of China.
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14
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Heger TJ, Giesbrecht IJW, Gustavsen J, Del Campo J, Kellogg CTE, Hoffman KM, Lertzman K, Mohn WW, Keeling PJ. High-throughput environmental sequencing reveals high diversity of litter and moss associated protist communities along a gradient of drainage and tree productivity. Environ Microbiol 2018; 20:1185-1203. [PMID: 29417706 DOI: 10.1111/1462-2920.14061] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Revised: 01/25/2018] [Accepted: 01/29/2018] [Indexed: 11/29/2022]
Abstract
Although previous studies, mostly based on microscopy analyses of a few groups of protists, have suggested that protists are abundant and diverse in litter and moss habitats, the overall diversity of moss and litter associated protists remains elusive. Here, high-throughput environmental sequencing was used to characterize the diversity and community structure of litter- and moss-associated protists along a gradient of soil drainage and forest primary productivity in a temperate rainforest in British Columbia. We identified 3262 distinct protist OTUs from 36 sites. Protists were strongly structured along the landscape gradient, with a significant increase in alpha diversity from the blanket bog ecosystem to the zonal forest ecosystem. Among all investigated environmental variables, calcium content was the most strongly associated with the community composition of protists, but substrate composition, plant cover and other edaphic factors were also significantly correlated with these communities. Furthermore, a detailed phylogenetic analysis of unicellular opisthokonts identified OTUs covering most lineages, including novel OTUs branching with Discicristoidea, the sister group of Fungi, and with Filasterea, one of the closest unicellular relatives to animals. Altogether, this study provides unprecedented insight into the community composition of moss- and litter-associated protists.
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Affiliation(s)
- Thierry J Heger
- Soil Science Group, CHANGINS, University of Applied Sciences and Arts Western Switzerland, Delémont, Switzerland.,Botany Department, University of British Columbia, Vancouver, BC, Canada.,Hakai Institute, Heriot Bay, BC, Canada
| | - Ian J W Giesbrecht
- Hakai Institute, Heriot Bay, BC, Canada.,School of Resource and Environmental Management, Simon Fraser University, Burnaby, BC, Canada
| | - Julia Gustavsen
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Javier Del Campo
- Botany Department, University of British Columbia, Vancouver, BC, Canada.,Hakai Institute, Heriot Bay, BC, Canada
| | - Colleen T E Kellogg
- Hakai Institute, Heriot Bay, BC, Canada.,Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Kira M Hoffman
- Hakai Institute, Heriot Bay, BC, Canada.,School of Environmental Studies, University of Victoria, Victoria, BC, Canada
| | - Ken Lertzman
- Hakai Institute, Heriot Bay, BC, Canada.,School of Resource and Environmental Management, Simon Fraser University, Burnaby, BC, Canada
| | - William W Mohn
- Hakai Institute, Heriot Bay, BC, Canada.,Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Patrick J Keeling
- Botany Department, University of British Columbia, Vancouver, BC, Canada.,Hakai Institute, Heriot Bay, BC, Canada
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15
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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.
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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
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16
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Shiratori T, Thakur R, Ishida KI. Pseudophyllomitus vesiculosus (Larsen and Patterson 1990) Lee, 2002, a Poorly Studied Phagotrophic Biflagellate is the First Characterized Member of Stramenopile Environmental Clade MAST-6. Protist 2017; 168:439-451. [PMID: 28822908 DOI: 10.1016/j.protis.2017.06.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 06/20/2017] [Accepted: 06/21/2017] [Indexed: 01/17/2023]
Abstract
There are many eukaryotic lineages that are exclusively composed of environmental sequences and lack information about which species are included. Regarding stramenopiles, at least 18 environmental lineages, known as marine stramenopiles (MAST), have been recognized. Since each MAST lineage forms deep branches in the stramenopiles, the characterization of MAST members is key to understanding the diversity and evolution of stramenopiles. In this study, we established a culture of Pseudophyllomitus vesiculosus, which is a poorly studied phagotrophic flagellate of uncertain taxonomic position. Our molecular phylogenetic analyses based on small subunit ribosomal RNA gene sequences robustly supported the inclusion of P. vesiculosus in the MAST-6 clade. Our microscopic observations indicated that P. vesiculosus shared characteristics with stramenopiles, including an anterior flagellum that exhibits sinusoidal waves and bears tubular mastigonemes. The flagellar apparatus of P. vesiculosus was also similar to that of other stramenopiles in having a transitional helix and five microtubular roots (R1-R4 and S tubules) including R2 that split into two bands. On the other hand, P. vesiculosus was distinguished from other deep-branching stramenopiles by the combination of flagellar apparatus characteristics. Based on the phylogenetic analyses and microscopic observations, we established Pseudophyllomitidae fam. nov in stramenopiles.
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Affiliation(s)
- Takashi Shiratori
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan.
| | - Rabindra Thakur
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Ken-Ichiro Ishida
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
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17
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Being right on Q: shaping eukaryotic evolution. Biochem J 2017; 473:4103-4127. [PMID: 27834740 PMCID: PMC5103874 DOI: 10.1042/bcj20160647] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Revised: 08/18/2016] [Accepted: 08/31/2016] [Indexed: 12/11/2022]
Abstract
Reactive oxygen species (ROS) formation by mitochondria is an incompletely understood eukaryotic process. I proposed a kinetic model [BioEssays (2011) 33, 88–94] in which the ratio between electrons entering the respiratory chain via FADH2 or NADH (the F/N ratio) is a crucial determinant of ROS formation. During glucose breakdown, the ratio is low, while during fatty acid breakdown, the ratio is high (the longer the fatty acid, the higher is the ratio), leading to higher ROS levels. Thus, breakdown of (very-long-chain) fatty acids should occur without generating extra FADH2 in mitochondria. This explains peroxisome evolution. A potential ROS increase could also explain the absence of fatty acid oxidation in long-lived cells (neurons) as well as other eukaryotic adaptations, such as dynamic supercomplex formation. Effective combinations of metabolic pathways from the host and the endosymbiont (mitochondrion) allowed larger varieties of substrates (with different F/N ratios) to be oxidized, but high F/N ratios increase ROS formation. This might have led to carnitine shuttles, uncoupling proteins, and multiple antioxidant mechanisms, especially linked to fatty acid oxidation [BioEssays (2014) 36, 634–643]. Recent data regarding peroxisome evolution and their relationships with mitochondria, ROS formation by Complex I during ischaemia/reperfusion injury, and supercomplex formation adjustment to F/N ratios strongly support the model. I will further discuss the model in the light of experimental findings regarding mitochondrial ROS formation.
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18
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Zhao D, Cao X, Huang R, Zeng J, Shen F, Xu H, Wang S, He X, Yu Z. The heterogeneity of composition and assembly processes of the microbial community between different nutrient loading lake zones in Taihu Lake. Appl Microbiol Biotechnol 2017; 101:5913-5923. [PMID: 28523397 DOI: 10.1007/s00253-017-8327-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 05/02/2017] [Accepted: 05/05/2017] [Indexed: 11/29/2022]
Abstract
To investigate the differences in the microbial community composition and assembly process in two lake zones (Meiliang Bay (MLB) and Xukou Bay (XKB) in Taihu Lake, China) with different nutrient loadings, water samples were collected. Both the 16S ribosomal RNA (rRNA) gene for the bacterial community and the 18S rRNA gene for the microeukaryote community were investigated using the Illumina second-generation sequencing platform (2 × 250 paired-end). The results indicated that both the bacterioplankton and microeukaryote community composition derived from the two lake zones were significantly different. Significantly higher operational taxonomic unit (OTU) richness (P < 0.01) and phylogenetic diversity (P < 0.05) were found for the bacterioplankton community of MLB. However, a comparable alpha diversity was found between the microeukaryote communities of MLB and XKB (P > 0.05). Environmental factors significantly affected the community compositions in XKB for both the bacterioplankton and microeukaryotes. However, they did not significantly influence the microbial community composition in MLB, except for a weak correlation between dissolved organic carbon (DOC) and the microeukaryote community. The microbial communities tended to be more phylogenetically clustered than expected by chance in the two lake zones. Moreover, the results of the phylogenetic structure suggest that deterministic processes played overwhelming roles in driving the assembly of both the bacterioplankton and microeukaryote community in XKB.
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Affiliation(s)
- Dayong Zhao
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China. .,College of Hydrology and Water Resources, Hohai University, Nanjing, 210098, China. .,Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.
| | - Xinyi Cao
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China.,College of Hydrology and Water Resources, Hohai University, Nanjing, 210098, China.,State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Rui Huang
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China.,College of Hydrology and Water Resources, Hohai University, Nanjing, 210098, China.,State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Jin Zeng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Feng Shen
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China.,College of Hydrology and Water Resources, Hohai University, Nanjing, 210098, China.,State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Huimin Xu
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China.,College of Hydrology and Water Resources, Hohai University, Nanjing, 210098, China.,State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Sichen Wang
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China.,College of Hydrology and Water Resources, Hohai University, Nanjing, 210098, China.,State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Xiaowei He
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China.,College of Hydrology and Water Resources, Hohai University, Nanjing, 210098, China.,State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Zhongbo Yu
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China. .,College of Hydrology and Water Resources, Hohai University, Nanjing, 210098, China.
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19
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Deterministic processes dominate nematode community structure in the Fynbos Mediterranean heathland of South Africa. Evol Ecol 2016. [DOI: 10.1007/s10682-016-9837-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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20
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Lepère C, Domaizon I, Hugoni M, Vellet A, Debroas D. Diversity and Dynamics of Active Small Microbial Eukaryotes in the Anoxic Zone of a Freshwater Meromictic Lake (Pavin, France). Front Microbiol 2016; 7:130. [PMID: 26904006 PMCID: PMC4748746 DOI: 10.3389/fmicb.2016.00130] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Accepted: 01/25/2016] [Indexed: 11/13/2022] Open
Abstract
Microbial eukaryotes play a crucial role in ecosystem functioning and oxygen is considered to be one of the strongest barriers against their local dispersal. However, diversity of microbial eukaryotes in freshwater habitats with oxygen gradients has previously received very little attention. We applied high-throughput sequencing (V4 region of the 18S rRNA gene) in conjunction with quantitative PCR (DNA and RNA) and fluorescent in situ hybridization (FISH) analyses, to provide an unique spatio-temporal analysis of microbial eukaryotes diversity and potential activity in a meromictic freshwater lake (lake Pavin). This study revealed a high genetic diversity of unicellular eukaryotes in the permanent anoxic zone of lake Pavin and allowed the discrimination of active vs. inactive components. Forty-two percent of the OTUs (Operational Taxonomic Units) are exclusively present in the monimolimnion, where Alveolata (Ciliophora and Dinophyceae) and Fungi (Dikarya and Chytrids) are the most active phyla and are probably represented by species capable of anaerobic metabolism. Pigmented eukaryotes (Haptophyceae and Chlorophyceae) are also present and active in this zone, which opens up questions regarding their metabolism.
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Affiliation(s)
- Cécile Lepère
- Laboratoire "Microorganismes: Génome et Environnement", Clermont Université, Université Blaise PascalClermont-Ferrand, France; Centre National de la Recherche Scientifique, UMR 6023, LMGEAubière, France
| | - Isabelle Domaizon
- Institut National de la Recherche Agronomique, UMR 42 CARRTELThonon-les-Bains, France; Université Savoie MontBlancChambéry, France
| | - Mylène Hugoni
- Laboratoire "Microorganismes: Génome et Environnement", Clermont Université, Université Blaise PascalClermont-Ferrand, France; Centre National de la Recherche Scientifique, UMR 6023, LMGEAubière, France
| | - Agnès Vellet
- Laboratoire "Microorganismes: Génome et Environnement", Clermont Université, Université Blaise PascalClermont-Ferrand, France; Centre National de la Recherche Scientifique, UMR 6023, LMGEAubière, France
| | - Didier Debroas
- Laboratoire "Microorganismes: Génome et Environnement", Clermont Université, Université Blaise PascalClermont-Ferrand, France; Centre National de la Recherche Scientifique, UMR 6023, LMGEAubière, France
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21
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Pasulka AL, Levin LA, Steele JA, Case DH, Landry MR, Orphan VJ. Microbial eukaryotic distributions and diversity patterns in a deep-sea methane seep ecosystem. Environ Microbiol 2016; 18:3022-43. [PMID: 26663587 DOI: 10.1111/1462-2920.13185] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 12/03/2015] [Accepted: 12/08/2015] [Indexed: 11/30/2022]
Abstract
Although chemosynthetic ecosystems are known to support diverse assemblages of microorganisms, the ecological and environmental factors that structure microbial eukaryotes (heterotrophic protists and fungi) are poorly characterized. In this study, we examined the geographic, geochemical and ecological factors that influence microbial eukaryotic composition and distribution patterns within Hydrate Ridge, a methane seep ecosystem off the coast of Oregon using a combination of high-throughput 18S rRNA tag sequencing, terminal restriction fragment length polymorphism fingerprinting, and cloning and sequencing of full-length 18S rRNA genes. Microbial eukaryotic composition and diversity varied as a function of substrate (carbonate versus sediment), activity (low activity versus active seep sites), sulfide concentration, and region (North versus South Hydrate Ridge). Sulfide concentration was correlated with changes in microbial eukaryotic composition and richness. This work also revealed the influence of oxygen content in the overlying water column and water depth on microbial eukaryotic composition and diversity, and identified distinct patterns from those previously observed for bacteria, archaea and macrofauna in methane seep ecosystems. Characterizing the structure of microbial eukaryotic communities in response to environmental variability is a key step towards understanding if and how microbial eukaryotes influence seep ecosystem structure and function.
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Affiliation(s)
- Alexis L Pasulka
- Integrative Oceanography Division and Center for Marine Biodiversity and Conservation, Scripps Institution of Oceanography, University of California, San Diego, CA, USA. .,Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA.
| | - Lisa A Levin
- Integrative Oceanography Division and Center for Marine Biodiversity and Conservation, Scripps Institution of Oceanography, University of California, San Diego, CA, USA
| | - Josh A Steele
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA.,Southern California Coastal Water Research Project, Costa Mesa, CA, USA
| | - David H Case
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - Michael R Landry
- Integrative Oceanography Division and Center for Marine Biodiversity and Conservation, Scripps Institution of Oceanography, University of California, San Diego, CA, USA
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
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22
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Pánek T, Táborský P, Pachiadaki MG, Hroudová M, Vlček Č, Edgcomb VP, Čepička I. Combined Culture-Based and Culture-Independent Approaches Provide Insights into Diversity of Jakobids, an Extremely Plesiomorphic Eukaryotic Lineage. Front Microbiol 2015; 6:1288. [PMID: 26635756 PMCID: PMC4649034 DOI: 10.3389/fmicb.2015.01288] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 11/03/2015] [Indexed: 11/13/2022] Open
Abstract
We used culture-based and culture-independent approaches to discover diversity and ecology of anaerobic jakobids (Excavata: Jakobida), an overlooked, deep-branching lineage of free-living nanoflagellates related to Euglenozoa. Jakobids are among a few lineages of nanoflagellates frequently detected in anoxic habitats by PCR-based studies, however only two strains of a single jakobid species have been isolated from those habitats. We recovered 712 environmental sequences and cultured 21 new isolates of anaerobic jakobids that collectively represent at least ten different species in total, from which four are uncultured. Two cultured species have never been detected by environmental, PCR-based methods. Surprisingly, culture-based and culture-independent approaches were able to reveal a relatively high proportion of overall species diversity of anaerobic jakobids—60 or 80%, respectively. Our phylogenetic analyses based on SSU rDNA and six protein-coding genes showed that anaerobic jakobids constitute a clade of morphologically similar, but genetically and ecologically diverse protists—Stygiellidae fam. nov. Our investigation combines culture-based and environmental molecular-based approaches to capture a wider extent of species diversity and shows Stygiellidae as a group that ordinarily inhabits anoxic, sulfide- and ammonium-rich marine habitats worldwide.
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Affiliation(s)
- Tomáš Pánek
- Department of Zoology, Faculty of Science, Charles University in Prague Prague, Czech Republic
| | - Petr Táborský
- Department of Zoology, Faculty of Science, Charles University in Prague Prague, Czech Republic
| | - Maria G Pachiadaki
- Geology and Geophysics Department, Woods Hole Oceanographic Institution Woods Hole, MA, USA
| | - Miluše Hroudová
- Department of Genomics and Bioinformatics, Institute of Molecular Genetics, Czech Academy of Sciences Prague, Czech Republic
| | - Čestmír Vlček
- Department of Genomics and Bioinformatics, Institute of Molecular Genetics, Czech Academy of Sciences Prague, Czech Republic
| | - Virginia P Edgcomb
- Geology and Geophysics Department, Woods Hole Oceanographic Institution Woods Hole, MA, USA
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University in Prague Prague, Czech Republic
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23
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Yu L, Zhang W, Liu L, Yang J. Determining Microeukaryotic Plankton Community around Xiamen Island, Southeast China, Using Illumina MiSeq and PCR-DGGE Techniques. PLoS One 2015; 10:e0127721. [PMID: 26020532 PMCID: PMC4447373 DOI: 10.1371/journal.pone.0127721] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 04/20/2015] [Indexed: 12/02/2022] Open
Abstract
Microeukaryotic plankton are important components of aquatic environments and play key roles in marine microbial food webs; however, little is known about their genetic diversity in subtropical offshore areas. Here we examined the community composition and genetic diversity of the microeukaryotic plankton in Xiamen offshore water by PCR-DGGE (polymerase chain reaction-denaturing gradient gel electrophoresis), clone-based sequencing and Illumina based sequencing. The Illumina MiSeq sequencing revealed a much (approximately two orders of magnitude) higher species richness of the microeukaryotic community than DGGE, but there were no significant difference in species richness and diversity among the northern, eastern, southern or western stations based on both methods. In this study, Copepoda, Ciliophora, Chlorophyta, Dinophyceae, Cryptophyta and Bacillariophyta (diatoms) were the dominant groups even though diatoms were not detected by DGGE. Our Illumina based results indicated that two northern communities (sites N2 and N3) were significantly different from others in having more protozoa and fewer diatoms. Redundancy analysis (RDA) showed that both temperature and salinity were the significant environmental factors influencing dominant species communities, whereas the full microeukaryotic community appeared to be affected by a complex of environmental factors. Our results suggested that extensive sampling combined with more deep sequencing are needed to obtain the complete diversity of the microeukaryotic community, and different diversity patterns for both abundant and rare taxa may be important in evaluating the marine ecosystem health.
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Affiliation(s)
- Lingyu Yu
- Laboratory of Marine Biodiversity and Global Change (MBiGC), College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Wenjing Zhang
- Laboratory of Marine Biodiversity and Global Change (MBiGC), College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- * E-mail:
| | - Lemian Liu
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Jun Yang
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
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24
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Duret MT, Pachiadaki MG, Stewart FJ, Sarode N, Christaki U, Monchy S, Srivastava A, Edgcomb VP. Size-fractionated diversity of eukaryotic microbial communities in the Eastern Tropical North Pacific oxygen minimum zone. FEMS Microbiol Ecol 2015; 91:fiv037. [DOI: 10.1093/femsec/fiv037] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/29/2015] [Indexed: 11/14/2022] Open
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25
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Oikonomou A, Filker S, Breiner HW, Stoeck T. Protistan diversity in a permanently stratified meromictic lake (Lake Alatsee, SW Germany). Environ Microbiol 2014; 17:2144-57. [PMID: 25330396 DOI: 10.1111/1462-2920.12666] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 09/26/2014] [Accepted: 10/08/2014] [Indexed: 11/28/2022]
Abstract
Protists play a crucial role for ecosystem function(ing) and oxygen is one of the strongest barriers against their local dispersal. However, protistan diversity in freshwater habitats with oxygen gradients received very little attention. We applied high-throughput sequencing of the V9 region (18S rRNA gene) to provide a hitherto unique spatiotemporal analysis of protistan diversity along the oxygen gradient of a freshwater meromictic lake (Lake Alatsee, SW Germany). In the mixolimnion, the communities experienced most seasonal structural changes, with Stramenopiles dominating in autumn and Dinoflagellata in summer. The suboxic interface supported the highest diversity, but only 23 OTUs95% (mainly Euglenozoa, after quality check and removal of operational taxonomic units (OTUs) with less than three sequences) were exclusively associated with this habitat. Eukaryotic communities in the anoxic monimolimnion showed the most stable seasonal pattern, with Chrysophyta and Bicosoecida being the dominant taxa. Our data pinpoint to the ecological role of the interface as a short-term 'meeting point' for protists, contributing to the coupling of the mixolimnion and the monimolimnion. Our analyses of divergent genetic diversity suggest a high degree of previously undescribed OTUs. Future research will have to reveal if this result actually points to a high number of undescribed species in such freshwater habitats.
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Affiliation(s)
- Andreas Oikonomou
- Department of Ecology, University of Kaiserslautern, Erwin Schroedinger Str. 14, D-67663, Kaiserslautern, Germany
| | - Sabine Filker
- Department of Ecology, University of Kaiserslautern, Erwin Schroedinger Str. 14, D-67663, Kaiserslautern, Germany
| | - Hans-Werner Breiner
- Department of Ecology, University of Kaiserslautern, Erwin Schroedinger Str. 14, D-67663, Kaiserslautern, Germany
| | - Thorsten Stoeck
- Department of Ecology, University of Kaiserslautern, Erwin Schroedinger Str. 14, D-67663, Kaiserslautern, Germany
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Youssef NH, Couger MB, McCully AL, Criado AEG, Elshahed MS. Assessing the global phylum level diversity within the bacterial domain: A review. J Adv Res 2014; 6:269-82. [PMID: 26257925 PMCID: PMC4522544 DOI: 10.1016/j.jare.2014.10.005] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 10/06/2014] [Accepted: 10/23/2014] [Indexed: 12/11/2022] Open
Abstract
Microbial ecology is the study of microbes in the natural environment and their interactions with each other. Investigating the nature of microorganisms residing within a specific habitat is an extremely important component of microbial ecology. Such microbial diversity surveys aim to determine the identity, physiological preferences, metabolic capabilities, and genomic features of microbial taxa within a specific ecosystem. A comprehensive review of various aspects of microbial diversity (phylogenetic, functional, and genomic diversities) in the microbial (bacterial, archaeal, and microeukaryotic) world is clearly a daunting task that could not be aptly summarized in a single review. Here, we focus on one aspect of diversity (phylogenetic diversity) in one microbial domain (the Bacteria). We restrict our analysis to the highest taxonomic rank (phylum) and attempt to investigate the extent of global phylum level diversity within the Bacteria. We present a brief historical perspective on the subject and highlight how the adaptation of molecular biological and phylogenetic approaches has greatly expanded our view of global bacterial diversity. We also summarize recent progress toward the discovery of novel bacterial phyla, present evidences that the scope of phylum level diversity in nature has hardly been exhausted, and propose novel approaches that could greatly facilitate the discovery process of novel bacterial phyla within various ecosystems.
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Affiliation(s)
- Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - M B Couger
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Alexandra L McCully
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | | | - Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
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Pachiadaki MG, Yakimov MM, LaCono V, Leadbetter E, Edgcomb V. Unveiling microbial activities along the halocline of Thetis, a deep-sea hypersaline anoxic basin. ISME JOURNAL 2014; 8:2478-89. [PMID: 24950109 DOI: 10.1038/ismej.2014.100] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 04/30/2014] [Accepted: 05/11/2014] [Indexed: 11/09/2022]
Abstract
Deep-sea hypersaline anoxic basins (DHABs) in the Eastern Mediterranean Sea are considered some of the most hostile environments on Earth. Little is known about the biochemical adaptations of microorganisms living in these habitats. This first metatranscriptome analysis of DHAB samples provides significant insights into shifts in metabolic activities of microorganisms as physicochemical conditions change from deep Mediterranean sea water to brine. The analysis of Thetis DHAB interface indicates that sulfate reduction occurs in both the upper (7.0-16.3% salinity) and lower (21.4-27.6%) halocline, but that expression of dissimilatory sulfate reductase is reduced in the more hypersaline lower halocline. High dark-carbon assimilation rates in the upper interface coincided with high abundance of transcripts for ribulose 1,5-bisphosphate carboxylase affiliated to sulfur-oxidizing bacteria. In the lower interface, increased expression of genes associated with methane metabolism and osmoregulation is noted. In addition, in this layer, nitrogenase transcripts affiliated to uncultivated putative methanotrophic archaea were detected, implying nitrogen fixation in this anoxic habitat, and providing evidence of linked carbon, nitrogen and sulfur cycles.
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Affiliation(s)
| | | | - Violetta LaCono
- CNR-Institute for Coastal Marine Environment, Messina, Italy
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28
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Edgcomb VP, Pachiadaki M. Ciliates along Oxyclines of Permanently Stratified Marine Water Columns. J Eukaryot Microbiol 2014; 61:434-45. [DOI: 10.1111/jeu.12122] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Revised: 02/28/2014] [Accepted: 02/28/2014] [Indexed: 11/30/2022]
Affiliation(s)
- Virginia P. Edgcomb
- Department of Geology and Geophysics; Woods Hole Oceanographic Institution; Woods Hole Massachusetts 02543
| | - Maria Pachiadaki
- Department of Geology and Geophysics; Woods Hole Oceanographic Institution; Woods Hole Massachusetts 02543
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29
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Dunthorn M, Stoeck T, Clamp J, Warren A, Mahé F. Ciliates and the Rare Biosphere: A Review. J Eukaryot Microbiol 2014; 61:404-9. [DOI: 10.1111/jeu.12121] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 03/14/2014] [Accepted: 03/14/2014] [Indexed: 11/27/2022]
Affiliation(s)
- Micah Dunthorn
- Department of Ecology; University of Kaiserslautern; D-67663 Kaiserslautern Germany
| | - Thorsten Stoeck
- Department of Ecology; University of Kaiserslautern; D-67663 Kaiserslautern Germany
| | - John Clamp
- Department of Biology; North Carolina Central University; Durham North Carolina 27707 USA
| | - Alan Warren
- Department of Life Sciences Department; Natural History Museum; London SW7 5BD United Kingdom
| | - Frédéric Mahé
- Department of Ecology; University of Kaiserslautern; D-67663 Kaiserslautern Germany
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Living at the Limits: Evidence for Microbial Eukaryotes Thriving under Pressure in Deep Anoxic, Hypersaline Habitats. ACTA ACUST UNITED AC 2014. [DOI: 10.1155/2014/532687] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The advent of molecular tools in microbial ecology paved the way to exploit the diversity of microbes in extreme environments. Here, we review these tools as applied in one of the most polyextreme habitats known on our planet, namely, deep hypersaline anoxic basins (DHABs), located at ca. 3000–3500 m depth in the Eastern Mediterranean Sea. Molecular gene signatures amplified from environmental DHAB samples identified a high degree of genetic novelty, as well as distinct communities in the DHABs. Canonical correspondence analyses provided strong evidence that salinity, ion composition, and anoxia were the strongest selection factors shaping protistan community structures, largely preventing cross-colonization among the individual basins. Thus, each investigated basin represents a unique habitat (“isolated islands of evolution”), making DHABs ideal model sites to test evolutionary hypotheses. Fluorescence in situ hybridization assays using specifically designed probes revealed that the obtained genetic signatures indeed originated from indigenous polyextremophiles. Electron microscopy imaging revealed unknown ciliates densely covered with prokaryote ectosymbionts, which may enable adaptations of eukaryotes to DHAB conditions. The research reviewed here significantly advanced our knowledge on polyextremophile eukaryotes, which are excellent models for a number of biological research areas, including ecology, diversity, biotechnology, evolutionary research, physiology, and astrobiology.
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Wang Y, Tian RM, Gao ZM, Bougouffa S, Qian PY. Optimal eukaryotic 18S and universal 16S/18S ribosomal RNA primers and their application in a study of symbiosis. PLoS One 2014; 9:e90053. [PMID: 24594623 PMCID: PMC3940700 DOI: 10.1371/journal.pone.0090053] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Accepted: 01/28/2014] [Indexed: 11/19/2022] Open
Abstract
Eukaryotic 18S ribosomal RNA (rRNA) gene primers that feature a wide coverage are critical in detecting the composition of eukaryotic microscopic organisms in ecosystems. Here, we predicted 18S rRNA primers based on consecutive conserved sites and evaluated their coverage efficiency and scope of application to different eukaryotic groups. After evaluation, eight of them were considered as qualified 18S primers based on coverage rate. Next, we examined common conserved regions in prokaryotic 16S and eukaryotic 18S rRNA sequences to design 16S/18S universal primers. Three 16S/18S candidate primers, U515, U1390 and U1492, were then considered to be suitable for simultaneous amplification of the rRNA sequences in three domains. Eukaryotic 18S and prokaryotic 16S rRNA genes in a sponge were amplified simultaneously using universal primers U515 and U1390, and the subsequent sorting of pyrosequenced reads revealed some distinctive communities in different parts of the sample. The real difference in biodiversity between prokaryotic and eukaryotic symbionts could be discerned as the dissimilarity between OTUs was increased from 0.005 to 0.1. A network of the communities in external and internal parts of the sponge illustrated the co-variation of some unique microbes in certain parts of the sponge, suggesting that the universal primers are useful in simultaneous detection of prokaryotic and eukaryotic microbial communities.
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Affiliation(s)
- Yong Wang
- Division of Life Sciences, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
- Sanya Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, San Ya, Hai Nan, China
| | - Ren Mao Tian
- Division of Life Sciences, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Zhao Ming Gao
- Division of Life Sciences, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Salim Bougouffa
- Division of Life Sciences, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Pei-Yuan Qian
- Division of Life Sciences, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
- * E-mail:
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Wang Y, Zhang WP, Cao HL, Shek CS, Tian RM, Wong YH, Batang Z, Al-Suwailem A, Qian PY. Diversity and distribution of eukaryotic microbes in and around a brine pool adjacent to the Thuwal cold seeps in the Red Sea. Front Microbiol 2014; 5:37. [PMID: 24575081 PMCID: PMC3922051 DOI: 10.3389/fmicb.2014.00037] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 01/20/2014] [Indexed: 11/25/2022] Open
Abstract
A hypoxic/suboxic brine pool at a depth of about 850 m was discovered near the Thuwal cold seeps in the Red Sea. Filled with high concentrations of hydrogen sulfide and ammonia, such a brine pool might limit the spread of eukaryotic organisms. Here, we compared the communities of the eukaryotic microbes in a microbial mat, sediments and water samples distributed in 7 sites within and adjacent to the brine pool. Taxonomic classification of the pyrosequenced 18S rRNA amplicon reads showed that fungi highly similar to the species identified along the Arabic coast were almost ubiquitous in the water and sediment samples, supporting their wide distribution in various environments. The microbial mat displayed the highest species diversity and contained grazers and a considerable percentage of unclassified species. Phylogeny-based methods revealed novel lineages representing a majority of the reads from the interface between the sea water and brine pool. Phylogenetic relationships with more reference sequences suggest that the lineages were affiliated with novel Alveolata and Euglenozoa inhabiting the interface where chemosynthetic prokaryotes are highly proliferative due to the strong chemocline and halocline. The brine sediments harbored abundant species highly similar to invertebrate gregarine parasites identified in different oxygen-depleted sediments. Therefore, the present findings support the uniqueness of some microbial eukaryotic groups in this cold seep brine system.
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Affiliation(s)
- Yong Wang
- Division of Life Science, Hong Kong University of Science and Technology Hong Kong, China ; Sanya Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences San Ya, China
| | - Wei Peng Zhang
- Division of Life Science, Hong Kong University of Science and Technology Hong Kong, China
| | - Hui Luo Cao
- Division of Life Science, Hong Kong University of Science and Technology Hong Kong, China
| | - Chun Shum Shek
- Division of Life Science, Hong Kong University of Science and Technology Hong Kong, China
| | - Ren Mao Tian
- Division of Life Science, Hong Kong University of Science and Technology Hong Kong, China
| | - Yue Him Wong
- Division of Life Science, Hong Kong University of Science and Technology Hong Kong, China
| | - Zenon Batang
- Coastal and Marine Resources Core Laboratory, King Abdullah University of Science and Technology Jeddah, Saudi Arabia
| | - Abdulaziz Al-Suwailem
- Coastal and Marine Resources Core Laboratory, King Abdullah University of Science and Technology Jeddah, Saudi Arabia
| | - Pei-Yuan Qian
- Division of Life Science, Hong Kong University of Science and Technology Hong Kong, China
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Yu Z, Yang J, Zhou J, Yu X, Liu L, Lv H. Water stratification affects the microeukaryotic community in a subtropical deep reservoir. J Eukaryot Microbiol 2013; 61:126-33. [PMID: 24373024 DOI: 10.1111/jeu.12090] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 09/21/2013] [Accepted: 09/30/2013] [Indexed: 11/28/2022]
Abstract
Producers, consumers, and decomposers are the three key functional groups that form the basis of all ecosystems. But, little is known about how these functional groups coexist with each other in aquatic environments, particularly in subtropical reservoirs. In this study, we describe the nature of microeukaryotic communities in a subtropical deep reservoir during the strongly stratified period. Denaturing gradient gel electrophoresis gel band sequencing, pyrosequencing, and light microscopy were used together to facilitate an in-depth investigation of the community structure of phytoplankton, zooplankton, and fungi. Our results showed that thermal and oxygen stratification shaped the composition of the phytoplankton, zooplankton, and fungi populations in the reservoir. Stratification was evident among ecological functional groups in autumn: producers and consumers were overwhelmingly dominant in the epilimnion characterized by high temperatures and oxygen levels, whereas decomposers were inclined to inhabit the hypolimnion. These results contribute to our understanding of the relationship of ecosystem functional groups in the man-made aquatic systems and have important practical implications for reservoir management. Results suggest that the strategies for the control of eutrophication and harmful algal bloom prevention should focus on a fuller understanding of the consequences of both thermal stratification and vertical distribution of microplankton.
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Affiliation(s)
- Zheng Yu
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China; University of Chinese Academy of Sciences, Beijing, 100049, China
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Oikonomou A, Pachiadaki M, Stoeck T. Protistan grazing in a meromictic freshwater lake with anoxic bottom water. FEMS Microbiol Ecol 2013; 87:691-703. [DOI: 10.1111/1574-6941.12257] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 10/29/2013] [Accepted: 11/13/2013] [Indexed: 01/26/2023] Open
Affiliation(s)
- Andreas Oikonomou
- Department of Ecology; University of Kaiserslautern; Kaiserslautern Germany
| | - Maria Pachiadaki
- Department of Ecology; University of Kaiserslautern; Kaiserslautern Germany
| | - Thorsten Stoeck
- Department of Ecology; University of Kaiserslautern; Kaiserslautern Germany
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35
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Stock A, Edgcomb V, Orsi W, Filker S, Breiner HW, Yakimov MM, Stoeck T. Evidence for isolated evolution of deep-sea ciliate communities through geological separation and environmental selection. BMC Microbiol 2013. [PMID: 23834625 DOI: 10.1186/1471‐2180‐13‐150] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Deep hypersaline anoxic basins (DHABs) are isolated habitats at the bottom of the eastern Mediterranean Sea, which originate from the ancient dissolution of Messinian evaporites. The different basins have recruited their original biota from the same source, but their geological evolution eventually constituted sharp environmental barriers, restricting genetic exchange between the individual basins. Therefore, DHABs are unique model systems to assess the effect of geological events and environmental conditions on the evolution and diversification of protistan plankton. Here, we examine evidence for isolated evolution of unicellular eukaryote protistan plankton communities driven by geological separation and environmental selection. We specifically focused on ciliated protists as a major component of protistan DHAB plankton by pyrosequencing the hypervariable V4 fragment of the small subunit ribosomal RNA. Geospatial distributions and responses of marine ciliates to differential hydrochemistries suggest strong physical and chemical barriers to dispersal that influence the evolution of this plankton group. RESULTS Ciliate communities in the brines of four investigated DHABs are distinctively different from ciliate communities in the interfaces (haloclines) immediately above the brines. While the interface ciliate communities from different sites are relatively similar to each other, the brine ciliate communities are significantly different between sites. We found no distance-decay relationship, and canonical correspondence analyses identified oxygen and sodium as most important hydrochemical parameters explaining the partitioning of diversity between interface and brine ciliate communities. However, none of the analyzed hydrochemical parameters explained the significant differences between brine ciliate communities in different basins. CONCLUSIONS Our data indicate a frequent genetic exchange in the deep-sea water above the brines. The "isolated island character" of the different brines, that resulted from geological events and contemporary environmental conditions, create selective pressures driving evolutionary processes, and with time, lead to speciation and shape protistan community composition. We conclude that community assembly in DHABs is a mixture of isolated evolution (as evidenced by small changes in V4 primary structure in some taxa) and species sorting (as indicated by the regional absence/presence of individual taxon groups on high levels in taxonomic hierarchy).
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Affiliation(s)
- Alexandra Stock
- University of Kaiserslautern, School of Biology, Erwin-Schroedinger-Str, 14, D-67663 Kaiserslautern, Germany
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Stock A, Edgcomb V, Orsi W, Filker S, Breiner HW, Yakimov MM, Stoeck T. Evidence for isolated evolution of deep-sea ciliate communities through geological separation and environmental selection. BMC Microbiol 2013; 13:150. [PMID: 23834625 PMCID: PMC3707832 DOI: 10.1186/1471-2180-13-150] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Accepted: 05/15/2013] [Indexed: 12/01/2022] Open
Abstract
Background Deep hypersaline anoxic basins (DHABs) are isolated habitats at the bottom of the eastern Mediterranean Sea, which originate from the ancient dissolution of Messinian evaporites. The different basins have recruited their original biota from the same source, but their geological evolution eventually constituted sharp environmental barriers, restricting genetic exchange between the individual basins. Therefore, DHABs are unique model systems to assess the effect of geological events and environmental conditions on the evolution and diversification of protistan plankton. Here, we examine evidence for isolated evolution of unicellular eukaryote protistan plankton communities driven by geological separation and environmental selection. We specifically focused on ciliated protists as a major component of protistan DHAB plankton by pyrosequencing the hypervariable V4 fragment of the small subunit ribosomal RNA. Geospatial distributions and responses of marine ciliates to differential hydrochemistries suggest strong physical and chemical barriers to dispersal that influence the evolution of this plankton group. Results Ciliate communities in the brines of four investigated DHABs are distinctively different from ciliate communities in the interfaces (haloclines) immediately above the brines. While the interface ciliate communities from different sites are relatively similar to each other, the brine ciliate communities are significantly different between sites. We found no distance-decay relationship, and canonical correspondence analyses identified oxygen and sodium as most important hydrochemical parameters explaining the partitioning of diversity between interface and brine ciliate communities. However, none of the analyzed hydrochemical parameters explained the significant differences between brine ciliate communities in different basins. Conclusions Our data indicate a frequent genetic exchange in the deep-sea water above the brines. The “isolated island character” of the different brines, that resulted from geological events and contemporary environmental conditions, create selective pressures driving evolutionary processes, and with time, lead to speciation and shape protistan community composition. We conclude that community assembly in DHABs is a mixture of isolated evolution (as evidenced by small changes in V4 primary structure in some taxa) and species sorting (as indicated by the regional absence/presence of individual taxon groups on high levels in taxonomic hierarchy).
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Affiliation(s)
- Alexandra Stock
- University of Kaiserslautern, School of Biology, Erwin-Schroedinger-Str, 14, D-67663 Kaiserslautern, Germany
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Coyne KJ, Countway PD, Pilditch CA, Lee CK, Caron DA, Cary SC. Diversity and Distributional Patterns of Ciliates in Guaymas Basin Hydrothermal Vent Sediments. J Eukaryot Microbiol 2013; 60:433-47. [DOI: 10.1111/jeu.12051] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Revised: 03/18/2013] [Accepted: 03/18/2013] [Indexed: 11/29/2022]
Affiliation(s)
- Kathryn J. Coyne
- College of Earth, Ocean, and Environment; University of Delaware; 700 Pilottown Road Lewes Delaware 19958 USA
| | - Peter D. Countway
- Department of Biological Sciences; University of Southern California; Los Angeles California 90089-0371 USA
| | - Conrad A. Pilditch
- Department of Biological Sciences; University of Waikato; Private Bag 3105 Hamilton 3240 New Zealand
| | - Charles K. Lee
- Department of Biological Sciences; University of Waikato; Private Bag 3105 Hamilton 3240 New Zealand
| | - David A. Caron
- Department of Biological Sciences; University of Southern California; Los Angeles California 90089-0371 USA
| | - Stephen C. Cary
- College of Earth, Ocean, and Environment; University of Delaware; 700 Pilottown Road Lewes Delaware 19958 USA
- Department of Biological Sciences; University of Waikato; Private Bag 3105 Hamilton 3240 New Zealand
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Terrado R, Scarcella K, Thaler M, Vincent WF, Lovejoy C. Small phytoplankton in Arctic seas: vulnerability to climate change. ACTA ACUST UNITED AC 2013. [DOI: 10.1080/14888386.2012.704839] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Modeo L, Fokin SI, Boscaro V, Andreoli I, Ferrantini F, Rosati G, Verni F, Petroni G. Morphology, ultrastructure, and molecular phylogeny of the ciliate Sonderia vorax with insights into the systematics of order Plagiopylida. BMC Microbiol 2013; 13:40. [PMID: 23418998 PMCID: PMC3626617 DOI: 10.1186/1471-2180-13-40] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 02/08/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Ciliates of the family Sonderiidae are common members of the eukaryotic communities in various anoxic environments. They host both ecto- and endosymbiotic prokaryotes (the latter associated with hydrogenosomes) and possess peculiar morpho-ultrastructural features, whose functions and homologies are not known. Their phylogenetic relationships with other ciliates are not completely resolved and the available literature, especially concerning electron microscopy and molecular studies, is quite scarce. RESULTS Sonderia vorax Kahl, 1928 is redescribed from an oxygen-deficient, brackish-water pond along the Ligurian Sea coastlines of Italy. Data on morphology, morphometry, and ultrastructure are reported. S. vorax is ovoid-ellipsoid in shape, dorsoventrally flattened, 130 x 69 μm (mean in vivo); it shows an almost spherical macronucleus, and one relatively large micronucleus. The ventral kinetom has a "secant system" including fronto-ventral and fronto-lateral kineties. A distinctive layer of bacteria laying between kineties covers the ciliate surface. Two types of extrusomes and hydrogenosomes-endosymbiotic bacteria assemblages are present in the cytoplasm. The phylogeny based on 18S rRNA gene sequences places S. vorax among Plagiopylida; Sonderiidae clusters with Plagiopylidae, although lower-level relationships remain uncertain. The studied population is fixed as neotype and the ciliate is established as type species of the genus, currently lacking. CONCLUSIONS This is the first description of a representative of Sonderiidae performed with both morphological and molecular data. To sum up, many previous hypotheses on this interesting, poorly known taxon are confirmed but confusion and contradictory data are as well highlighted.
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Affiliation(s)
- Letizia Modeo
- Unit of Protistology-Zoology, Department of Biology, University of Pisa, via A. Volta 4/6, Pisa 56126, Italy
| | - Sergei I Fokin
- Unit of Protistology-Zoology, Department of Biology, University of Pisa, via A. Volta 4/6, Pisa 56126, Italy
- Department of Invertebrate Zoology, St. Petersburg State University, Universitetskaya emb. 7/9, St. Petersburg, 199034, Russia
| | - Vittorio Boscaro
- Unit of Protistology-Zoology, Department of Biology, University of Pisa, via A. Volta 4/6, Pisa 56126, Italy
| | - Ilaria Andreoli
- Unit of Protistology-Zoology, Department of Biology, University of Pisa, via A. Volta 4/6, Pisa 56126, Italy
| | - Filippo Ferrantini
- Unit of Protistology-Zoology, Department of Biology, University of Pisa, via A. Volta 4/6, Pisa 56126, Italy
| | - Giovanna Rosati
- Unit of Protistology-Zoology, Department of Biology, University of Pisa, via A. Volta 4/6, Pisa 56126, Italy
| | - Franco Verni
- Unit of Protistology-Zoology, Department of Biology, University of Pisa, via A. Volta 4/6, Pisa 56126, Italy
| | - Giulio Petroni
- Unit of Protistology-Zoology, Department of Biology, University of Pisa, via A. Volta 4/6, Pisa 56126, Italy
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Manohar CS, Raghukumar C. Fungal diversity from various marine habitats deduced through culture-independent studies. FEMS Microbiol Lett 2013; 341:69-78. [PMID: 23363246 DOI: 10.1111/1574-6968.12087] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 01/09/2013] [Accepted: 01/10/2013] [Indexed: 11/28/2022] Open
Abstract
Studies on the molecular diversity of the micro-eukaryotic community have shown that fungi occupy a central position in a large number of marine habitats. Environmental surveys using molecular tools have shown the presence of fungi from a large number of marine habitats such as deep-sea habitats, pelagic waters, coastal regions, hydrothermal vent ecosystem, anoxic habitats, and ice-cold regions. This is of interest to a variety of research disciplines like ecology, evolution, biogeochemistry, and biotechnology. In this review, we have summarized how molecular tools have helped to broaden our understanding of the fungal diversity in various marine habitats. Majority of the environmental phylotypes could be grouped as novel clades within Ascomycota, Basidiomycota, and Chytridiomycota or as basal fungal lineages. Deep-branching novel environmental clusters could be grouped within Ascomycota as the Pezizomycotina clone group, deep-sea fungal group-I, and soil clone group-I, within Basidiomycota as the hydrothermal and/or anaerobic fungal group, and within Chytridiomycota as Cryptomycota or the Rozella clade. However, a basal true marine environmental cluster is still to be identified as most of the clusters include representatives from terrestrial regions. The challenge for future research is to explore the true marine fungi using molecular techniques.
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Affiliation(s)
- Cathrine Sumathi Manohar
- Biological Oceanography Division, National Institute of Oceanography - Council of Scientific and Industrial Research, Dona Paula, Goa, India.
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Anderson R, Wylezich C, Glaubitz S, Labrenz M, Jürgens K. Impact of protist grazing on a key bacterial group for biogeochemical cycling in Baltic Sea pelagic oxic/anoxic interfaces. Environ Microbiol 2013; 15:1580-94. [PMID: 23368413 DOI: 10.1111/1462-2920.12078] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Revised: 12/17/2012] [Accepted: 12/20/2012] [Indexed: 11/27/2022]
Abstract
Barrier zones between oxic and anoxic water masses (redoxclines) host highly active prokaryotic communities with important roles in biogeochemical cycling. In Baltic Sea pelagic redoxclines, Epsilonproteobacteria of the genus Sulfurimonas (subgroup GD17) have been shown to dominate chemoautotrophic denitrification. However, little is known on the loss processes affecting this prokaryotic group. In the present study, the protist grazing impact on the Sulfurimonas subgroup GD17 was determined for suboxic and oxygen/hydrogen sulphide interface depths of Baltic Sea redoxclines, using predator exclusion assays and bacterial amendment with the cultured representative 'Sulfurimonas gotlandica' strain GD1. Additionally, the principal bacterivores were identified by RNA-Stable Isotope Probing (RNA-SIP). The natural Sulfurimonas subgroup GD17 population grew strongly under oxygen/hydrogen sulphide interface conditions (doubling time: 1-1.5 days), but protist grazing could consume the complete new cell production per day. In suboxic samples, little or no growth of Sulfurimonas subgroup GD17 was observed. RNA-SIP identified five active grazers, belonging to typical redoxcline ciliates (Oligohymenophorea, Prostomatea) and globally widespread marine flagellate groups (MAST-4, Chrysophyta, Cercozoa). Overall, we demonstrate for the first time that protist grazing can control the growth, and potentially the vertical distribution, of a chemolithoautotrophic key-player of oxic/anoxic interfaces.
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Affiliation(s)
- Ruth Anderson
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research, Seestrasse 15, 18119, Rostock-Warnemünde, Germany.
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Rocke E, Jing H, Liu H. Phylogenetic composition and distribution of picoeukaryotes in the hypoxic northwestern coast of the Gulf of Mexico. Microbiologyopen 2012; 2:130-43. [PMID: 23281331 PMCID: PMC3584219 DOI: 10.1002/mbo3.57] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Revised: 10/28/2012] [Accepted: 11/12/2012] [Indexed: 11/05/2022] Open
Abstract
Coastal marine hypoxic, or low-oxygen, episodes are an increasing worldwide phenomenon, but its effect on the microbial community is virtually unknown by far. In this study, the community structure and phylogeny of picoeukaryotes in the Gulf of Mexico, which are exposed to severe hypoxia in these areas was explored through a clone library approach. Both oxic surface waters and suboxic bottom waters were collected in August 2010 from three representative stations on the inner Louisiana shelf near the Atchafalaya and Mississippi River plumes. The bottom waters of the two more western stations were much more hypoxic in comparison to those of the station closest to the Mississippi River plume, which were only moderately hypoxic. A phylogenetic analysis of a total 175 sequences, generated from six 18S rDNA clone libraries, demonstrated a clear dominance of parasitic dinoflagellates from Marine alveolate clades I and II in all hypoxic waters as well as in the surface layer at the more western station closest to the Atchafalaya River plume. Species diversity was significantly higher at the most hypoxic sites, and many novel species were present among the dinoflagellate and stramenopile clades. We concluded that hypoxia in the Gulf of Mexico causes a significant shift in picoeukaryote communities, and that hypoxia may cause a shift in microbial food webs from grazing to parasitism.
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Affiliation(s)
- Emma Rocke
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
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Charvet S, Vincent WF, Comeau A, Lovejoy C. Pyrosequencing analysis of the protist communities in a High Arctic meromictic lake: DNA preservation and change. Front Microbiol 2012; 3:422. [PMID: 23267353 PMCID: PMC3526917 DOI: 10.3389/fmicb.2012.00422] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Accepted: 11/24/2012] [Indexed: 11/30/2022] Open
Abstract
High Arctic meromictic lakes are extreme environments characterized by cold temperatures, low nutrient inputs from their polar desert catchments and prolonged periods of low irradiance and darkness. These lakes are permanently stratified with an oxygenated freshwater layer (mixolimnion) overlying a saline, anoxic water column (monimolimnion). The physical and chemical properties of the deepest known lake of this type in the circumpolar Arctic, Lake A, on the far northern coast of Ellesmere Island, Canada, have been studied over the last 15 years, but little is known about the lake’s biological communities. We applied high-throughput sequencing of the V4 region of the 18S ribosomal RNA gene to investigate the protist communities down the water column at three sampling times: under the ice at the end of winter in 2008, during an unusual period of warming and ice-out the same year, and again under the ice in mid-summer 2009. Sequences of many protist taxa occurred throughout the water column at all sampling times, including in the deep anoxic layer where growth is highly unlikely. Furthermore, there were sequences for taxonomic groups including diatoms and marine taxa, which have never been observed in Lake A by microscopic analysis. However, the sequences of other taxa such as ciliates, chrysophytes, Cercozoa, and Telonema varied with depth, between years and during the transition to ice-free conditions. These seasonally active taxa in the surface waters of the lake are thus sensitive to depth and change with time. DNA from these taxa is superimposed upon background DNA from multiple internal and external sources that is preserved in the deep, cold, largely anoxic water column.
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Affiliation(s)
- Sophie Charvet
- Département de Biologie, Université Laval, Québec QC, Canada ; Québec-Océan, Québec QC, Canada
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Filker S, Stock A, Breiner HW, Edgcomb V, Orsi W, Yakimov MM, Stoeck T. Environmental selection of protistan plankton communities in hypersaline anoxic deep-sea basins, Eastern Mediterranean Sea. Microbiologyopen 2012; 2:54-63. [PMID: 23239531 PMCID: PMC3584213 DOI: 10.1002/mbo3.56] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Revised: 10/31/2012] [Accepted: 11/12/2012] [Indexed: 11/25/2022] Open
Abstract
High salt concentrations, absence of light, anoxia, and high hydrostatic pressure make deep hypersaline anoxic basins (DHABs) in the Eastern Mediterranean Sea one of the most polyextreme habitats on Earth. Taking advantage of the unique chemical characteristics of these basins, we tested the effect of environmental selection and geographic distance on the structure of protistan communities. Terminal restriction fragment length polymorphism (T-RFLP) analyses were performed on water samples from the brines and seawater/brine interfaces of five basins: Discovery, Urania, Thetis, Tyro, and Medee. Using statistical analyses, we calculated the partitioning of diversity among the ten individual terminal restriction fragment (T-RF) profiles, based on peak abundance and peak incidence. While a significant distance effect on spatial protistan patterns was not detected, hydrochemical gradients emerged as strong dispersal barriers that likely lead to environmental selection in the DHAB protistan plankton communities. We identified sodium, magnesium, sulfate, and oxygen playing in concerto as dominant environmental drivers for the structuring of protistan plankton communities in the Eastern Mediterranean DHABs.
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Affiliation(s)
- Sabine Filker
- School of Biology, University of Kaiserslautern, Erwin-Schroedinger-Str. 14, D-67663, Kaiserslautern, Germany
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Wylezich C, Karpov SA, Mylnikov AP, Anderson R, Jürgens K. Ecologically relevant choanoflagellates collected from hypoxic water masses of the Baltic Sea have untypical mitochondrial cristae. BMC Microbiol 2012; 12:271. [PMID: 23171165 PMCID: PMC3579758 DOI: 10.1186/1471-2180-12-271] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Accepted: 11/08/2012] [Indexed: 11/17/2022] Open
Abstract
Background Protist communities inhabiting oxygen depleted waters have so far been characterized through both microscopical observations and sequence based techniques. However, the lack of cultures for abundant taxa severely hampers our knowledge on the morphology, ecology and energy metabolism of hypoxic protists. Cultivation of such protists has been unsuccessful in most cases, and has never yet succeeded for choanoflagellates, even though these small bacterivorous flagellates are known to be ecologically relevant components of aquatic protist communities. Results Quantitative data for choanoflagellates and the vertical distribution of Codosiga spp. at Gotland and Landsort Deep (Baltic Sea) indicate its preference for oxygen-depleted zones. Strains isolated and cultivated from these habitats revealed ultrastructural peculiarities such as mitochondria showing tubular cristae never seen before for choanoflagellates, and the first observation of intracellular prokaryotes in choanoflagellates. Analysis of their partial 28S rRNA gene sequence complements the description of two new species, Codosiga minima n. sp. and C. balthica n. sp. These are closely related with but well separated from C. gracilis (C. balthica and C. minima p-distance to C. gracilis 4.8% and 11.6%, respectively). In phylogenetic analyses the 18S rRNA gene sequences branch off together with environmental sequences from hypoxic habitats resulting in a wide cluster of hypoxic Codosiga relatives so far only known from environmental sequencing approaches. Conclusions Here, we establish the morphological and ultrastructural identity of an environmental choanoflagellate lineage. Data from microscopical observations, supplemented by findings from previous culture-independent methods, indicate that C. balthica is likely an ecologically relevant player of Baltic Sea hypoxic waters. The possession of derived mitochondria could be an adaptation to life in hypoxic environments periodically influenced by small-scale mixing events and changing oxygen content allowing the reduction of oxygen consuming components. In view of the intricacy of isolating and cultivating choanoflagellates, the two new cultured species represent an important advance to the understanding of the ecology of this group, and mechanisms of adaptations to hypoxia in protists in general.
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Affiliation(s)
- Claudia Wylezich
- IOW-Leibniz Institute for Baltic Sea Research Warnemünde, Rostock, Germany.
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Forster D, Behnke A, Stoeck T. Meta-analyses of environmental sequence data identify anoxia and salinity as parameters shaping ciliate communities. SYST BIODIVERS 2012. [DOI: 10.1080/14772000.2012.706239] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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Jensen S, Bourne DG, Hovland M, Colin Murrell J. High diversity of microplankton surrounds deep-water coral reef in the Norwegian Sea. FEMS Microbiol Ecol 2012; 82:75-89. [DOI: 10.1111/j.1574-6941.2012.01408.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Revised: 04/24/2012] [Accepted: 05/06/2012] [Indexed: 11/30/2022] Open
Affiliation(s)
- Sigmund Jensen
- Department of Biology; University of Bergen; Bergen; Norway
| | - David G. Bourne
- Australian Institute of Marine Science; Townsville; Qld; Australia
| | | | - J. Colin Murrell
- School of Environmental Sciences; University of East Anglia; Norwich; UK
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Orsi W, Song YC, Hallam S, Edgcomb V. Effect of oxygen minimum zone formation on communities of marine protists. ISME JOURNAL 2012; 6:1586-601. [PMID: 22402396 DOI: 10.1038/ismej.2012.7] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Changes in ocean temperature and circulation patterns compounded by human activities are leading to oxygen minimum zone (OMZ) expansion with concomitant alteration in nutrient and climate active trace gas cycling. Here, we report the response of microbial eukaryote populations to seasonal changes in water column oxygen-deficiency using Saanich Inlet, a seasonally anoxic fjord on the coast of Vancouver Island British Columbia, as a model ecosystem. We combine small subunit ribosomal RNA gene sequencing approaches with multivariate statistical methods to reveal shifts in operational taxonomic units during successive stages of seasonal stratification and renewal. A meta-analysis is used to identify common and unique patterns of community composition between Saanich Inlet and the anoxic/sulfidic Cariaco Basin (Venezuela) and Framvaren Fjord (Norway) to show shared and unique responses of microbial eukaryotes to oxygen and sulfide in these three environments. Our analyses also reveal temporal fluctuations in rare populations of microbial eukaryotes, particularly anaerobic ciliates, that may be of significant importance to the biogeochemical cycling of methane in OMZs. Eukaryotic 18S rRNA gene sequences recovered from the Saanich Inlet water column on were deposited in Genbank under accession numbers HQ864863–HQ871151.
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Affiliation(s)
- William Orsi
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
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Sequencing our way towards understanding global eukaryotic biodiversity. Trends Ecol Evol 2012; 27:233-43. [PMID: 22244672 DOI: 10.1016/j.tree.2011.11.010] [Citation(s) in RCA: 236] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2011] [Revised: 11/23/2011] [Accepted: 11/24/2011] [Indexed: 02/01/2023]
Abstract
Microscopic eukaryotes are abundant, diverse and fill critical ecological roles across every ecosystem on Earth, yet there is a well-recognized gap in understanding of their global biodiversity. Fundamental advances in DNA sequencing and bioinformatics now allow accurate en masse biodiversity assessments of microscopic eukaryotes from environmental samples. Despite a promising outlook, the field of eukaryotic marker gene surveys faces significant challenges: how to generate data that are most useful to the community, especially in the face of evolving sequencing technologies and bioinformatics pipelines, and how to incorporate an expanding number of target genes.
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Jebaraj CS, Forster D, Kauff F, Stoeck T. Molecular Diversity of Fungi from Marine Oxygen-Deficient Environments (ODEs). PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2012; 53:189-208. [PMID: 22222833 DOI: 10.1007/978-3-642-23342-5_10] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Molecular diversity surveys of marine fungi have demonstrated that the species richness known to date is just the tip of the iceberg and that there is a large extent of unknown fungal diversity in marine habitats. Reports of novel fungal lineages at higher taxonomic levels are documented from a large number of marine habitats, including the various marine oxygen-deficient environments (ODEs). In the past few years, a strong focus of eukaryote diversity research has been on a variety of ODEs, as these environments are considered to harbor a large number of organisms, which are highly divergent to known diversity and could provide insights into the early eukaryotic evolution. ODEs that have been targeted so far include shallow water sediments, hydrothermal vent systems, deep-sea basins, intertidal habitats, and fjords. Most, if not all, molecular diversity studies in marine ODEs have shown, that contrary to previous assumptions, fungi contribute significantly to the micro-eukaryotic community in such habitats. In this chapter, we have reanalyzed the environmental fungal sequences obtained from the molecular diversity survey in 14 different sites to obtain a comprehensive picture of fungal diversity in these marine habitats. The phylogenetic analysis of the fungal environmental sequences from various ODEs have grouped these sequences into seven distinct clades (Clade 1-7) clustering with well-known fungal taxa. Apart from this, four environmental clades (EnvClade A, B, C, and D) with exclusive environmental sequences were also identified. This has provided information on the positioning of the environmental sequences at different taxonomic levels within the major fungal phylums. The taxonomic distribution of these environmental fungal sequences into clusters and clades has also shown that they are not restricted by geographical boundaries. The distribution pattern together with the reports on the respiratory abilities of fungi under reduced oxygen conditions shows that they are highly adaptive and may have a huge ecological role in these oxygen deficient habitats.
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Affiliation(s)
- Cathrine Sumathi Jebaraj
- National Institute of Oceanography, Council of Scientific and Industrial Research, Dona Paula, 403 004, Goa, India,
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