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Karlicki M, Bednarska A, Hałakuc P, Maciszewski K, Karnkowska A. Spatio-temporal changes of small protist and free-living bacterial communities in a temperate dimictic lake: insights from metabarcoding and machine learning. FEMS Microbiol Ecol 2024; 100:fiae104. [PMID: 39039016 DOI: 10.1093/femsec/fiae104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 06/21/2024] [Accepted: 07/19/2024] [Indexed: 07/24/2024] Open
Abstract
Microbial communities, which include prokaryotes and protists, play an important role in aquatic ecosystems and influence ecological processes. To understand these communities, metabarcoding provides a powerful tool to assess their taxonomic composition and track spatio-temporal dynamics in both marine and freshwater environments. While marine ecosystems have been extensively studied, there is a notable research gap in understanding eukaryotic microbial communities in temperate lakes. Our study addresses this gap by investigating the free-living bacteria and small protist communities in Lake Roś (Poland), a dimictic temperate lake. Metabarcoding analysis revealed that both the bacterial and protist communities exhibit distinct seasonal patterns that are not necessarily shaped by dominant taxa. Furthermore, machine learning and statistical methods identified crucial amplicon sequence variants (ASVs) specific to each season. In addition, we identified a distinct community in the anoxic hypolimnion. We have also shown that the key factors shaping the composition of analysed community are temperature, oxygen, and silicon concentration. Understanding these community structures and the underlying factors is important in the context of climate change potentially impacting mixing patterns and leading to prolonged stratification.
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Affiliation(s)
- Michał Karlicki
- Institute of Evolutionary Biology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Anna Bednarska
- Institute of Evolutionary Biology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warsaw, Poland
- Department of Hydrobiology, Institute of Functional Biology and Ecology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Paweł Hałakuc
- Institute of Evolutionary Biology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Kacper Maciszewski
- Institute of Evolutionary Biology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warsaw, Poland
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská 1160/31, 370 05 České Budějovice, Czech Republic
| | - Anna Karnkowska
- Institute of Evolutionary Biology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warsaw, Poland
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Wang SH, Yuan SW, Che FF, Wan X, Wang YF, Yang DH, Yang HJ, Zhu D, Chen P. Strong bacterial stochasticity and fast fungal turnover in Taihu Lake sediments, China. ENVIRONMENTAL RESEARCH 2023; 237:116954. [PMID: 37619629 DOI: 10.1016/j.envres.2023.116954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 08/07/2023] [Accepted: 08/21/2023] [Indexed: 08/26/2023]
Abstract
Understanding the assembly and turnover of microbial communities is crucial for gaining insights into the diversity and functioning of lake ecosystems, a fundamental and central issue in microbial ecology. The ecosystem of Taihu Lake has been significantly jeopardized due to urbanization and industrialization. In this study, we examined the diversity, assembly, and turnover of bacterial and fungal communities in Taihu Lake sediment. The results revealed strong bacterial stochasticity and fast fungal turnover in the sediment. Significant heterogeneity was observed among all sediment samples in terms of environmental factors, especially ORP, TOC, and TN, as well as microbial community composition and alpha diversity. For instance, the fungal richness index exhibited an approximate 3-fold variation. Among the environmental factors, TOC, TN, and pH had a more pronounced influence on the bacterial community composition compared to the fungal community composition. Interestingly, species replacement played a dominant role in microbial beta diversity, with fungi exhibiting a stronger pattern. In contrast, stochastic processes governed the community assembly of both bacteria and fungi, but were more pronounced for bacteria (R2 = 0.7 vs. 0.5). These findings deepen the understanding of microbial assembly and turnover in sediments under environmental stress and provide essential insights for maintaining the multifunctionality of lake ecosystems.
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Affiliation(s)
- Shu-Hang Wang
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Sheng-Wu Yuan
- National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Fei-Fei Che
- National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Xin Wan
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Yi-Fei Wang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China
| | - Dian-Hai Yang
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China.
| | - Hai-Jiang Yang
- Key Laboratory of Western China's Environmental Systems (MOE), College of Earth and Environmental Sciences, Lanzhou University, China
| | - Dong Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China
| | - Peng Chen
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.
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3
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Widespread Occurrence of Two Planktonic Ciliate Species (Urotricha, Prostomatida) Originating from High Mountain Lakes. DIVERSITY 2022. [DOI: 10.3390/d14050362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Ciliates of the genus Urotricha are widely distributed and occur in almost any freshwater body. Thus far, almost all species have been described from morphology only. Here, we applied an integrative approach on the morphology, molecular phylogeny and biogeography of two species isolated from high mountain lakes in the Central Alps, Austria. As these remote lakes are known to have water temperatures <15 °C, our hypothesis was that these urotrichs might prefer ‘cold’ environments. We studied the morphological details from living and silver-stained individuals, and their molecular sequences (ribosomal operon, ITS), and screened available datasets for their biogeography. The two Urotricha species resembled morphological features of several congeners. An accurate species assignment was difficult due to several overlapping characteristics. However, we tentatively attributed the investigated species to Urotricha nais and Urotricha globosa. The biogeographic analyses revealed their occurrence in Europe, Africa and Asia, and no correlations to (cold) temperatures were found. Our findings suggest that these two urotrichs, originating from two cold and remote habitats, are probably cryptic species well adapted to their harsh environment.
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Sachs C, Kanaparthi D, Kublik S, Szalay AR, Schloter M, Damgaard LR, Schramm A, Lueders T. Tracing long-distance electron transfer and cable bacteria in freshwater sediments by agar pillar gradient columns. FEMS Microbiol Ecol 2022; 98:6567839. [PMID: 35416241 DOI: 10.1093/femsec/fiac042] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/20/2022] [Accepted: 04/11/2022] [Indexed: 11/14/2022] Open
Abstract
Cable bacteria (CB) perform electrogenic sulphur oxidation (e-SOX) by spatially separating redox-half-reactions over cm-distances. For freshwater systems, the ecology of CB is not yet well understood, partly because they proved difficult to cultivate. This study introduces a new "agar pillar" approach to selectively enrich and investigate CB-populations. Within sediment columns, a central agar pillar is embedded, providing a sediment-free gradient-system in equilibrium with the surrounding sediment. We incubated freshwater sediments from a streambed, a sulfidic lake, and a hydrocarbon polluted aquifer in such agar pillar columns. Microprofiling revealed typical patterns of e-SOx, such as the development of a suboxic zone and the establishment of electric potentials. The bacterial communities in the sediments and agar pillars were analysed over depth by PacBio near-full-length 16S rRNA gene amplicon sequencing, allowing for a precise phylogenetic placement of taxa detected. The selective niche of the agar pillar was preferentially colonized by CB related to Candidatus Electronema for surface-water sediments, including several potentially novel species, but not for putative groundwater CB affiliated with Desulfurivibrio spp. The presence of CB was seemingly linked to co-enriched fermenters, hinting at a possible role of e-SOx-populations as an electron sink for heterotrophic microbes. These findings add to our current understanding of the diversity and ecology of CB in freshwater systems, and to a discrimination of CB from surface and groundwater sediments. The agar pillar approach provides a new strategy that may facilitate the cultivation of redox gradient-dependent microorganisms, including previously unrecognized CB populations.
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Affiliation(s)
- Corinna Sachs
- Chair of Ecological Microbiology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Germany.,Institute of Groundwater Ecology, Helmholtz Zentrum München - German Research Center for Environmental Health, Germany
| | - Dheeraj Kanaparthi
- Chair of Ecological Microbiology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Germany.,Institute of Groundwater Ecology, Helmholtz Zentrum München - German Research Center for Environmental Health, Germany
| | - Susanne Kublik
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München - German Research Center for Environmental Health, Germany
| | - Anna Roza Szalay
- Institute of Groundwater Ecology, Helmholtz Zentrum München - German Research Center for Environmental Health, Germany
| | - Michael Schloter
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München - German Research Center for Environmental Health, Germany
| | - Lars Riis Damgaard
- Center for Electromicrobiology, Section for Microbiology, Department of Biology, Aarhus University, Denmark
| | - Andreas Schramm
- Center for Electromicrobiology, Section for Microbiology, Department of Biology, Aarhus University, Denmark
| | - Tillmann Lueders
- Chair of Ecological Microbiology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Germany
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Han Y, Guo C, Guan X, McMinn A, Liu L, Zheng G, Jiang Y, Liang Y, Shao H, Tian J, Wang M. Comparison of Deep-Sea Picoeukaryotic Composition Estimated from the V4 and V9 Regions of 18S rRNA Gene with a Focus on the Hadal Zone of the Mariana Trench. MICROBIAL ECOLOGY 2022; 83:34-47. [PMID: 33811505 DOI: 10.1007/s00248-021-01747-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 03/25/2021] [Indexed: 06/12/2023]
Abstract
Diversity of microbial eukaryotes is estimated largely based on sequencing analysis of the hypervariable regions of 18S rRNA genes. But the use of different regions of 18S rRNA genes as molecular markers may generate bias in diversity estimation. Here, we compared the differences between the two most widely used markers, V4 and V9 regions of the 18S rRNA gene, in describing the diversity of epipelagic, bathypelagic, and hadal picoeukaryotes in the Challenger Deep of the Mariana Trench, which is a unique and little explored environment. Generally, the V9 region identified more OTUs in deeper waters than V4, while the V4 region provided greater Shannon diversity than V9. In the epipelagic zone, where Alveolata was the dominant group, picoeukaryotic community compositions identified by V4 and V9 markers are similar at different taxonomic levels. However, in the deep waters, the results of the two datasets show clear differences. These differences were mainly contributed by Retaria, Fungi, and Bicosoecida. The primer targeting the V9 region has an advantage in amplifying Bicosoecids in the bathypelagic and hadal zone of the Mariana Trench, and its high abundance in V9 dataset pointed out the possibility of Bicosoecids as a dominant group in this environment. Chrysophyceae, Fungi, MALV-I, and Retaria were identified as the dominant picoeukaryotes in the bathypelagic and hadal zone and potentially play important roles in deep-sea microbial food webs and biogeochemical cycling by their phagotrophic, saprotrophic, and parasitic life styles. Overall, the use of different markers of 18S rRNA gene allows a better assessment and understanding of the picoeukaryotic diversity in deep-sea environments.
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Affiliation(s)
- Yuye Han
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Cui Guo
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China.
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China.
| | - Xuran Guan
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Andrew McMinn
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
| | - Lu Liu
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Guiliang Zheng
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Yong Jiang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Yantao Liang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Hongbing Shao
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Jiwei Tian
- Key Laboratory of Physical Oceanography, Ministry of Education, Ocean University of China, Qingdao, China
- Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Min Wang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China.
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China.
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6
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Zhang Q, Wu Z, Zhao J, Wang G, Hao J, Wang S, Lin Y, Guan H, Zhang J, Jian S, Li A. Composition and Functional Characteristics and Influencing Factors of Bacterioplankton Community in the Huangshui River, China. Microorganisms 2021; 9:microorganisms9112260. [PMID: 34835386 PMCID: PMC8623840 DOI: 10.3390/microorganisms9112260] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 10/22/2021] [Accepted: 10/26/2021] [Indexed: 11/16/2022] Open
Abstract
Bacterial community plays a key role in environmental and ecological processes of river ecosystems. Given the special climatic and geographical conditions, studying the compositional characteristics of microorganisms in highland rivers and the relationship between such microorganisms and water physicochemical factors is important for an in-depth understanding of microbial ecological mechanisms. In the present study, high-throughput sequencing was used to investigate and study the bacterioplankton community of the Huangshui River in the ecotone zone of the Qinghai Plateau and Loess Plateau. The results showed that the Huangshui River had significantly lower alpha diversity than the plain rivers. Despite the similarity in their environmental conditions, the main taxonomic compositions of the bacterial communities were distinct between the Huangshui River and polar regions (the Arctic and Antarctica). Proteobacteria accounted for the largest proportion (30.79–99.98%) of all the sequences, followed by Firmicutes (0–49.38%). Acidiphilium was the most numerous genera, which accounted for 0.03–86.16% of the assigned 16S reads, followed by Acidocella (0–95.9%), both belonging to Alphaproteobacteria. The diverse taxa of potential pathogens, such as Acinetobacter, Pseudomonas, and Aeromonas, were also identified. A principal coordinates analysis, coupled with a canonical correspondence analysis, showed spatial variations in the bacterial community composition. The water physical properties (e.g., Cr6+, total phosphorus, and CODMn); altitude; and land use (e.g., urban land cover and aquaculture) determined the distribution of the bacterioplankton composition. PICRUSt2 revealed that the overall functional profiles of the bacterial communities in different samples were similar, and our results suggested the potential health risks of water sources in this area. This work provided valuable insight into the composition of the plankton bacterial community and its relationship with the environmental factors in the Huangshui River in the ecotone zone of the Qinghai Plateau and Loess Plateau and a theoretical foundation for ecological health management.
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Affiliation(s)
- Qianqian Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (Q.Z.); (Z.W.); (J.H.); (S.W.); (Y.L.)
| | - Zhenbing Wu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (Q.Z.); (Z.W.); (J.H.); (S.W.); (Y.L.)
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Juan Zhao
- Qinghai Provincial Fishery Environmental Monitoring Center, Xining 810012, China; (J.Z.); (G.W.); (H.G.)
- Key Laboratory of Plateau Aquatic and Ecological Environmental in Qinghai Province, Xining 810012, China
| | - Guojie Wang
- Qinghai Provincial Fishery Environmental Monitoring Center, Xining 810012, China; (J.Z.); (G.W.); (H.G.)
- Key Laboratory of Plateau Aquatic and Ecological Environmental in Qinghai Province, Xining 810012, China
| | - Jingwen Hao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (Q.Z.); (Z.W.); (J.H.); (S.W.); (Y.L.)
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuyi Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (Q.Z.); (Z.W.); (J.H.); (S.W.); (Y.L.)
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yaoyao Lin
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (Q.Z.); (Z.W.); (J.H.); (S.W.); (Y.L.)
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongtao Guan
- Qinghai Provincial Fishery Environmental Monitoring Center, Xining 810012, China; (J.Z.); (G.W.); (H.G.)
- Key Laboratory of Plateau Aquatic and Ecological Environmental in Qinghai Province, Xining 810012, China
| | - Jinyong Zhang
- The Laboratory of Aquatic Parasitology, School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266237, China;
| | - Shenglong Jian
- Qinghai Provincial Fishery Environmental Monitoring Center, Xining 810012, China; (J.Z.); (G.W.); (H.G.)
- Key Laboratory of Plateau Aquatic and Ecological Environmental in Qinghai Province, Xining 810012, China
- Correspondence: (S.J.); (A.L.); Tel.: +86-27-68780053 (A.L.)
| | - Aihua Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (Q.Z.); (Z.W.); (J.H.); (S.W.); (Y.L.)
- Correspondence: (S.J.); (A.L.); Tel.: +86-27-68780053 (A.L.)
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Abstract
Dissolved gases produce a gas pressure. This gas pressure is the appropriate physical quantity for judging the possibility of bubble formation and hence it is central for understanding exchange of climate-relevant gases between (limnic) water and the atmosphere. The contribution of ebullition has widely been neglected in numerical simulations. We present measurements from six lacustrine waterbodies in Central Germany: including a natural lake, a drinking water reservoir, a mine pit lake, a sand excavation lake, a flooded quarry, and a small flooded lignite opencast, which has been heavily polluted. Seasonal changes of oxygen and temperature are complemented by numerical simulations of nitrogen and calculations of vapor pressure to quantify the contributions and their dynamics in lacustrine waters. In addition, accumulation of gases in monimolimnetic waters is demonstrated. We sum the partial pressures of the gases to yield a quantitative value for total gas pressure to reason which processes can force ebullition at which locations. In conclusion, only a small number of gases contribute decisively to gas pressure and hence can be crucial for bubble formation.
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Abstract
Freshwater iron mats are dynamic geochemical environments with broad ecological diversity, primarily formed by the iron-oxidizing bacteria. The community features functional groups involved in biogeochemical cycles for iron, sulfur, carbon, and nitrogen. Despite this complexity, iron mat communities provide an excellent model system for exploring microbial ecological interactions and ecological theories in situ Syntrophies and competition between the functional groups in iron mats, how they connect cycles, and the maintenance of these communities by taxons outside bacteria (the eukaryota, archaea, and viruses) have been largely unstudied. Here, we review what is currently known about freshwater iron mat communities, the taxa that reside there, and the interactions between these organisms, and we propose ways in which future studies may uncover exciting new discoveries. For example, the archaea in these mats may play a greater role than previously thought as they are diverse and widespread in iron mats based on 16S rRNA genes and include methanogenic taxa. Studies with a holistic view of the iron mat community members focusing on their diverse interactions will expand our understanding of community functions, such as those involved in pollution removal. To begin addressing questions regarding the fundamental interactions and to identify the conditions in which they occur, more laboratory culturing techniques and coculture studies, more network and keystone species analyses, and the expansion of studies to more freshwater iron mat systems are necessary. Increasingly accessible bioinformatic, geochemical, and culturing tools now open avenues to address the questions that we pose herein.
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Affiliation(s)
- Chequita N Brooks
- Department of Biology, East Carolina University, Greenville, North Carolina, USA
| | - Erin K Field
- Department of Biology, East Carolina University, Greenville, North Carolina, USA
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9
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Zhang L, Tu D, Li X, Lu W, Li J. Impact of long-term industrial contamination on the bacterial communities in urban river sediments. BMC Microbiol 2020; 20:254. [PMID: 32795344 PMCID: PMC7427966 DOI: 10.1186/s12866-020-01937-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 08/04/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The contamination of the aquatic environment of urban rivers with industrial wastewater has affected the abiotic conditions and biological activities of the trophic levels of the ecosystem, particularly sediments. However, most current research about microorganism in urban aquatic environments has focused on indicator bacteria related to feces and organic pollution. Meanwhile, they ignored the interactions among microorganisms. To deeply understand the impact of industrial contamination on microbial community, we study the bacterial community structure and diversity in river sediments under the influence of different types of industrial pollution by Illumina MiSeq high-throughput sequencing technology and conduct a more detailed analysis of microbial community structure through co-occurrence networks. RESULTS The overall community composition and abundance of individual bacterial groups differed between samples. In addition, redundancy analysis indicated that the structure of the bacterial community in river sediments was influenced by a variety of environmental factors. TN, TP, TOC and metals (Cu, Zn and Cd) were the most important driving factors that determined the bacterial community in urban river sediments (P < 0.01). According to PICRUSt analysis, the bacterial communities in different locations had similar overall functional profiles. It is worth noting that the 15 functional genes related to xenobiotics biodegradation and metabolism were the most abundant in the same location. The non-random assembly patterns of bacterial composition in different types of industrially polluted sediments were determined by a co-occurrence network. Environmental conditions resulting from different industrial pollutants may play an important role in determining their co-occurrence patterns of these bacterial taxa. Among them, the bacterial taxa involved in carbon and nitrogen cycles in module I were relatively abundant, and the bacterial taxa in module II were involved in the repair of metal pollution. CONCLUSIONS Our data indicate that long-term potential interactions between different types of industrial pollution and taxa collectively affect the structure of the bacterial community in urban river sediments.
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Affiliation(s)
- Lei Zhang
- School of Civil Engineering and Architecture, Chuzhou University, 1 West Huifeng Road, Chuzhou, 239000, China.
| | - Demei Tu
- School of Civil Engineering and Architecture, Chuzhou University, 1 West Huifeng Road, Chuzhou, 239000, China
| | - Xingchen Li
- School of Civil Engineering and Architecture, Chuzhou University, 1 West Huifeng Road, Chuzhou, 239000, China
| | - Wenxuan Lu
- Fisheries Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230036, China
| | - Jing Li
- Fisheries Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230036, China
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Annenkova NV, Giner CR, Logares R. Tracing the Origin of Planktonic Protists in an Ancient Lake. Microorganisms 2020; 8:microorganisms8040543. [PMID: 32283732 PMCID: PMC7232311 DOI: 10.3390/microorganisms8040543] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 04/05/2020] [Accepted: 04/07/2020] [Indexed: 11/28/2022] Open
Abstract
Ancient lakes are among the most interesting models for evolution studies because their biodiversity is the result of a complex combination of migration and speciation. Here, we investigate the origin of single celled planktonic eukaryotes from the oldest lake in the world—Lake Baikal (Russia). By using 18S rDNA metabarcoding, we recovered 1414 Operational Taxonomic Units (OTUs) belonging to protists populating surface waters (1–50 m) and representing pico/nano-sized cells. The recovered communities resembled other lacustrine freshwater assemblages found elsewhere, especially the taxonomically unclassified protists. However, our results suggest that a fraction of Baikal protists could belong to glacial relicts and have close relationships with marine/brackish species. Moreover, our results suggest that rapid radiation may have occurred among some protist taxa, partially mirroring what was already shown for multicellular organisms in Lake Baikal. We found 16% of the OTUs belonging to potential species flocks in Stramenopiles, Alveolata, Opisthokonta, Archaeplastida, Rhizaria, and Hacrobia. Putative flocks predominated in Chrysophytes, which are highly diverse in Lake Baikal. Also, the 18S rDNA of a number of species (7% of the total) differed >10% from other known sequences. These taxa as well as those belonging to the flocks may be endemic to Lake Baikal. Overall, our study points to novel diversity of planktonic protists in Lake Baikal, some of which may have emerged in situ after evolutionary diversification.
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Affiliation(s)
- Nataliia V. Annenkova
- Limnological Institute Siberian Branch of the Russian Academy of Sciences 3, Ulan-Batorskaya St., 664033 Irkutsk, Russia
- Correspondence: (N.V.A.); (R.L.)
| | - Caterina R. Giner
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de la Barceloneta, 37-49, ES08003 Barcelona, Spain;
- Institute for the Oceans and Fisheries, University of British Columbia, 2202 Main Mall, Vancouver, BC V6T 1Z4, Canada
| | - Ramiro Logares
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de la Barceloneta, 37-49, ES08003 Barcelona, Spain;
- Correspondence: (N.V.A.); (R.L.)
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11
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Distribution Patterns of Microeukaryotic Community Between Sediment and Water of the Yellow River Estuary. Curr Microbiol 2020; 77:1496-1505. [PMID: 32239287 DOI: 10.1007/s00284-020-01958-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 03/21/2020] [Indexed: 10/24/2022]
Abstract
Water and sediment have always been closely tied in aquatic systems. However, little information regarding the full extent of microeukaryotic composition in both the two habitats did we know especially in estuaries. In the present study, the microeukaryotic abundance, diversity, composition, and their response to environmental factors between sediment and water in the Yellow River Estuary (YRE) were investigated. The microeukaryotic 18S rRNA gene abundance ranged from 1.03 × 106 to 5.48 × 107 copies/g dry for sediment, and 3.01 × 104 to 1.25 × 106 copies/mL for water. The distribution patterns of eukaryotic microorganisms could be clustered into two different branches. And the compositions of microeukaryotes in the two habitats were distinct obviously. Metazoa, Fungi, Streptophyta, Ochrophyta, Cercozoa, and Dinophyta were more abundant in sediment. The dominant phyla in water were Dinophyta, followed by Metazoa, Ochrophyta, Cryptophyta, Chloroplyta, Cercozoa, Fungi, Katablepharidophyta, Choanoflagellida, and Haptophyta. Interestingly, the eukaryotic microorganisms detected in sediment were much less sensitive to environmental variables compared with water. Furthermore, their potential co-occurrence networks in particular were also discovered in the present study. As such, we have provided baseline data to support further research on estuarine microeukaryotes in both sediment and water, which was useful for guiding the practical application of ecosystem management and biodiversity protection.
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Macek M, Medina XS, Picazo A, Peštová D, Reyes FB, Hernández JRM, Alcocer J, Ibarra MM, Camacho A. Spirostomum teres: A Long Term Study of an Anoxic-Hypolimnion Population Feeding upon Photosynthesizing Microorganisms. ACTA PROTOZOOL 2020. [DOI: 10.4467/16890027ap.20.002.12158] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The pelagic / anoxic hypolimnion population of Spirostomum teres was investigated as a part of the long-term ciliates’ monitoring (2003–2016) in an oligo- to mesotrophic monomictic hyposaline crater lake Alchichica (Puebla / Veracruz, Mexico), including an analysis of picoplankton (both heterotrophic, HPP and autotrophic, APP) and inorganic compounds of nitrogen (ammonium, nitrite, nitrate), phosphorus (dissolved reactive phosphorus, DRP) and silicon. Additionally, detailed studies of the ciliate vertical distribution and feeding activity measured upon fluorescently labelled APP (picocyanobacteria) were carried out. The results were compared with those from a neighbour freshwater crater lake La Preciosa and with a meromictic karstic lake La Cruz (Cuenca, Spain). The ciliate vertical distribution within the water column was very well defined: During the first decade, the benthic population was frequently found throughout a developing stratification of the lake. The established stratification of the lake turned the conditions favourable for the formation of an oxycline / hypolimnion population, typically, several meters below the deep chlorophyll maximum (formed basically by diatoms); the population preferred the layers without detectable dissolved oxygen. However, an observed gradient of light (PAR) could support both oxygenic and anoxygenic photosynthesis. Late stratification after deepening of the thermocline reduced the layers with S. teres population to a minimum apparently due to the drastic change in physicochemical conditions within a metalimnion, coupled with an oxycline, and limited to 1 to 2 meters; microstratification was found. Last years, the very bottom population disappeared or it was reduced and the late stratification S. teres peaks were smaller or did not appeared. Generally, S. teres oxycline / anoxic hypolimnion population was observed from June through November. Optimum picoplankton numbers in conditions that supported the ciliate growth were found: The ciliate was peaking at APP of 0.6 to 1 × 105 cells mL–1; the optimum of HPP was observed round 1.4 × 106 cells mL–1. S. teres was efficiently feeding upon picocyanobacteria in numbers of 105 cells mL–1 reaching the clearance rate of 2000 nL cell–1h–1, which represented in average 130 to 210 cells cell–1h–1 ingested. Feeding upon purple sulphur bacteria was observed but only during the end of the lake stable stratification when the ciliate population was already dropping. On the other hand, the volume specific clearance of S. teres upon picocyanobacteria (103 h–1) did not support the hypothesis that they could serve as a sole prey. Feeding upon eukaryote phytoplankton (chlorophytes Monoraphidium minutum, diatoms Cyclotella choc tawhatcheeana) could be of higher importance that previously supposed. Additionally, a use of ingested and retained photosynthetic prokaryotes is hypothesized.
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Wu H, Li Y, Zhang W, Wang C, Wang P, Niu L, Du J, Gao Y. Bacterial community composition and function shift with the aggravation of water quality in a heavily polluted river. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 237:433-441. [PMID: 30822647 DOI: 10.1016/j.jenvman.2019.02.101] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 02/09/2019] [Accepted: 02/20/2019] [Indexed: 06/09/2023]
Abstract
Blackening and odorization of heavily polluted rivers has become a vital aquatic environmental problem in developing countries and has threatened river ecosystems. Monitoring the contamination and functional degradation conditions is important for bioremediation of river ecosystems. In this study, the diversity, composition, co-occurrence pattern, and function of bacterial communities collected from a heavily polluted urban river sediment were investigated using 16S rRNA amplicon sequencing analysis. The degree of pollution in the river was divided into three levels, and the clustering result based on the relative abundance of bacterial communities was consistent with the pollution levels in the river. The community assembly analysis further demonstrated that bacterial community assembly was mainly driven by environmental selection (95.84%) in Jinchuan River. Composition of bacterial communities were clearly different at different pollution level sites, although no apparent changes in alpha diversity were observed. The complexity of the bacterial co-occurrence network decreased with aggravation of the pollution level, as indicated by topological features, suggesting that the interactions among bacterial communities were weakened. A phylogenetic Investigation of Communities by Reconstruction of Unobserved States analysis predicted that the relative abundance of functional genes was negatively correlated with pollution levels, and those related to energy metabolism as well as xenobiotic biodegradation and metabolism decreased significantly. These results provide an ecological reference for monitoring and bioremediation of aquatic ecosystems.
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Affiliation(s)
- Hainan Wu
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Yi Li
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing, 210098, PR China.
| | - Wenlong Zhang
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Chao Wang
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Peifang Wang
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Lihua Niu
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Jiming Du
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Yu Gao
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing, 210098, PR China
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Production of Cyanotoxins by Microcystis aeruginosa Mediates Interactions with the Mixotrophic Flagellate Cryptomonas. Toxins (Basel) 2019; 11:toxins11040223. [PMID: 30991631 PMCID: PMC6520739 DOI: 10.3390/toxins11040223] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 04/09/2019] [Accepted: 04/10/2019] [Indexed: 01/24/2023] Open
Abstract
Eutrophication of inland waters is expected to increase the frequency and severity of harmful algal blooms (HABs). Toxin-production associated with HABs has negative effects on human health and aquatic ecosystem functioning. Despite evidence that flagellates can ingest toxin-producing cyanobacteria, interactions between members of the microbial loop are underestimated in our understanding of the food web and algal bloom dynamics. Physical and allelopathic interactions between a mixotrophic flagellate (Cryptomonas sp.) and two strains of a cyanobacteria (Microcystis aeruginosa) were investigated in a full-factorial experiment in culture. The maximum population growth rate of the mixotroph (0.25 day−1) occurred during incubation with filtrate from toxic M. aeruginosa. Cryptomonas was able to ingest toxic and non-toxic M. aeruginosa at maximal rates of 0.5 and 0.3 cells day−1, respectively. The results establish that although Cryptomonas does not derive benefits from co-incubation with M. aeruginosa, it may obtain nutritional supplement from filtrate. We also provide evidence of a reduction in cyanotoxin concentration (microcystin-LR) when toxic M. aeruginosa is incubated with the mixotroph. Our work has implications for “trophic upgrading” within the microbial food web, where cyanobacterivory by nanoflagellates may improve food quality for higher trophic levels and detoxify secondary compounds.
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Li Y, Wu H, Shen Y, Wang C, Wang P, Zhang W, Gao Y, Niu L. Statistical determination of crucial taxa indicative of pollution gradients in sediments of Lake Taihu, China. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 246:753-762. [PMID: 30623831 DOI: 10.1016/j.envpol.2018.12.087] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 12/27/2018] [Accepted: 12/28/2018] [Indexed: 06/09/2023]
Abstract
In order to accurately monitor the changes in a freshwater ecosystem in response to anthropogenic stressors, microbe-environment correlations and microbe-microbe interactions were combined to determine crucial indicator taxa in contaminated sediments. The diversity, composition, and co-occurrence pattern of bacterial communities in 23 sediment samples collected from Lake Taihu were explored using 16S rRNA amplicon sequencing analysis. Fisher's exact test showed that the cluster analyses of samples could show a direct correlation between the relative abundance of bacterial communities and the physicochemical properties of the sediment (P < 0.0001), suggesting that bacterial communities can be used to monitor contamination gradients in freshwater sediments. According to the microbe-environment correlation, 24 orders and 60 families were initially identified via indicator species analysis as indicator taxa of different pollution levels. The co-occurrence network further showed that topological features of bacterial communities were clearly different at different pollution levels, although the diversity and composition of bacterial communities displayed similarities between minimally and moderately polluted sites. Indicator taxa were then screened for keystone species, which co-occurrence relationships showed the high degree and low betweenness centrality values (i.e. degree >5, betweenness centrality <1000) of the network. Nine orders and 13 families were finally extracted as crucial indicator taxa of the different pollution levels in eutrophic Lake Taihu. Obtaining crucial indicator taxa from environmental sequences allows to trace increasing levels of pollution in aquatic ecosystems and provides a novel mean to monitor watersheds sensitive to anthropic influences.
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Affiliation(s)
- Yi Li
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Hainan Wu
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Yun Shen
- Department of Civil & Environmental Engineering, University of Michigan, 1351 Beal Ave, 219 EWRE Bldg, Ann Arbor, MI, 48109-2125, USA
| | - Chao Wang
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Peifang Wang
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Wenlong Zhang
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing, 210098, PR China.
| | - Yu Gao
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Lihua Niu
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing, 210098, PR China
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Lentendu G, Buosi PRB, Cabral AF, Trevizan Segóvia B, Ramos Meira B, Lansac-Tôha FM, Velho LFM, Ritter CD, Dunthorn M. Protist Biodiversity and Biogeography in Lakes From Four Brazilian River-Floodplain Systems. J Eukaryot Microbiol 2018; 66:592-599. [PMID: 30474198 DOI: 10.1111/jeu.12703] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 10/24/2018] [Accepted: 11/15/2018] [Indexed: 11/29/2022]
Abstract
The biodiversity and biogeography of protists inhabiting many ecosystems have been intensely studied using different sequencing approaches, but tropical ecosystems are relatively under-studied. Here, we sampled planktonic waters from 32 lakes associated with four different river-floodplains systems in Brazil, and sequenced the DNA using a metabarcoding approach with general eukaryotic primers. The lakes were dominated by the largely free-living Discoba (mostly the Euglenida), Ciliophora, and Ochrophyta. There was low community similarity between lakes even within the same river-floodplain. The protists inhabiting these floodplain systems comprise part of the large and relatively undiscovered diversity in the tropics.
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Affiliation(s)
- Guillaume Lentendu
- Department of Ecology, University of Kaiserslautern, D-67663, Kaiserslautern, Germany
| | - Paulo Roberto Bressan Buosi
- NUPELIA/Programa de Pós-Graduação em Ecologia de Ambientes Aquáticos Continentais, Universidade Estadual de Maringá, Maringá, PR, 87020-900, Brazil
| | - Adalgisa Fernada Cabral
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Campus 2, Itatiaia, 74001970, Goiânia, GO, Brazil
| | | | - Bianca Ramos Meira
- NUPELIA/Programa de Pós-Graduação em Ecologia de Ambientes Aquáticos Continentais, Universidade Estadual de Maringá, Maringá, PR, 87020-900, Brazil
| | - Fernando Miranda Lansac-Tôha
- NUPELIA/Programa de Pós-Graduação em Ecologia de Ambientes Aquáticos Continentais, Universidade Estadual de Maringá, Maringá, PR, 87020-900, Brazil
| | - Luiz Felipe Machado Velho
- NUPELIA/Programa de Pós-Graduação em Ecologia de Ambientes Aquáticos Continentais, Universidade Estadual de Maringá, Maringá, PR, 87020-900, Brazil.,Programa de Pós-graduação em Tecnologias Limpas - PPGTL, Instituto Cesumar de Ciência Tecnologia e Inovação - ICETI, Centro Universitário Cesumar - UniCesumar, Av. Guedner, 1610, CEP 87050-390, Maringá, PR, Brazil
| | - Camila D Ritter
- Gothenburg Global Biodiversity Centre, Box 461, SE-405 30, Gothenburg, Sweden.,Department of Biological and Environmental Sciences, University of Gothenburg, SE-405 30, Gothenburg, Sweden
| | - Micah Dunthorn
- Department of Ecology, University of Kaiserslautern, D-67663, Kaiserslautern, Germany.,Department of Eukaryotic Microbiology, University of Duisburg-Essen, D-45141, Essen, Germany.,Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, D-45141, Essen, Germany
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Grum-Grzhimaylo OA, Debets AJM, Bilanenko EN. Mosaic structure of the fungal community in the Kislo-Sladkoe Lake that is detaching from the White Sea. Polar Biol 2018. [DOI: 10.1007/s00300-018-2347-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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18
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Schmeller DS, Loyau A, Bao K, Brack W, Chatzinotas A, De Vleeschouwer F, Friesen J, Gandois L, Hansson SV, Haver M, Le Roux G, Shen J, Teisserenc R, Vredenburg VT. People, pollution and pathogens - Global change impacts in mountain freshwater ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 622-623:756-763. [PMID: 29223902 DOI: 10.1016/j.scitotenv.2017.12.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 12/01/2017] [Accepted: 12/01/2017] [Indexed: 05/06/2023]
Abstract
Mountain catchments provide for the livelihood of more than half of humankind, and have become a key destination for tourist and recreation activities globally. Mountain ecosystems are generally considered to be less complex and less species diverse due to the harsh environmental conditions. As such, they are also more sensitive to the various impacts of the Anthropocene. For this reason, mountain regions may serve as sentinels of change and provide ideal ecosystems for studying climate and global change impacts on biodiversity. We here review different facets of anthropogenic impacts on mountain freshwater ecosystems. We put particular focus on micropollutants and their distribution and redistribution due to hydrological extremes, their direct influence on water quality and their indirect influence on ecosystem health via changes of freshwater species and their interactions. We show that those changes may drive pathogen establishment in new environments with harmful consequences for freshwater species, but also for the human population. Based on the reviewed literature, we recommend reconstructing the recent past of anthropogenic impact through sediment analyses, to focus efforts on small, but highly productive waterbodies, and to collect data on the occurrence and variability of microorganisms, biofilms, plankton species and key species, such as amphibians due to their bioindicator value for ecosystem health and water quality. The newly gained knowledge can then be used to develop a comprehensive framework of indicators to robustly inform policy and decision making on current and future risks for ecosystem health and human well-being.
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Affiliation(s)
- Dirk S Schmeller
- Helmholtz Centre for Environmental Research - UFZ, Department of Conservation Biology, Permoserstrasse 15, 04318 Leipzig, Germany; ECOLAB, Université de Toulouse, CNRS, INPT, UPS, Toulouse, France.
| | - Adeline Loyau
- Helmholtz Centre for Environmental Research - UFZ, Department of Conservation Biology, Permoserstrasse 15, 04318 Leipzig, Germany; ECOLAB, Université de Toulouse, CNRS, INPT, UPS, Toulouse, France; Helmholtz Centre for Environmental Research - UFZ, Department of System Ecotoxicology, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Kunshan Bao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, East Beijing Road 73, 210008 Nanjing, China
| | - Werner Brack
- Helmholtz Centre for Environmental Research - UFZ, Department of Effect-Directed Analysis, Permoserstrasse 15, 04318 Leipzig, Germany; RWTH Aachen University, Department of Ecosystem Analysis, Institute for Environmental Research, Worringerweg 1, 52074 Aachen, Germany
| | - Antonis Chatzinotas
- Helmholtz Centre for Environmental Research - UFZ, Department of Environmental Microbiology, Permoserstrasse 15, 04318 Leipzig, Germany
| | | | - Jan Friesen
- Helmholtz Centre for Environmental Research - UFZ, Department of Catchment Hydrology, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Laure Gandois
- ECOLAB, Université de Toulouse, CNRS, INPT, UPS, Toulouse, France
| | - Sophia V Hansson
- ECOLAB, Université de Toulouse, CNRS, INPT, UPS, Toulouse, France; Aarhus University, Department of Bioscience - Arctic Research Centre, Fredriksborgvej 399, 4000 Roskilde, Denmark
| | - Marilen Haver
- ECOLAB, Université de Toulouse, CNRS, INPT, UPS, Toulouse, France
| | - Gaël Le Roux
- ECOLAB, Université de Toulouse, CNRS, INPT, UPS, Toulouse, France
| | - Ji Shen
- Helmholtz Centre for Environmental Research - UFZ, Department of System Ecotoxicology, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Roman Teisserenc
- ECOLAB, Université de Toulouse, CNRS, INPT, UPS, Toulouse, France
| | - Vance T Vredenburg
- San Francisco State University, Department of Biology, 1600 Holloway Ave, San Francisco, CA 94132, USA
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Wu H, Li Y, Zhang J, Niu L, Zhang W, Cai W, Zhu X. Sediment bacterial communities in a eutrophic lake influenced by multiple inflow-rivers. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:19795-19806. [PMID: 28685337 DOI: 10.1007/s11356-017-9602-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 06/20/2017] [Indexed: 06/07/2023]
Abstract
Sediment bacterial communities are sensitive to environmental fluctuations, particularly external input sources. Studying the relationships between bacterial community distribution and the estuarine environment is critical for understanding the river-lake confluence ecosystem and the effect of inflow-rivers on lakes. In the present study, bacterial communities from the sediments of 14 estuaries and four pelagic sites of the Taihu Lake were investigated via high-throughput sequencing. The results demonstrated that Delta-, Beta-, and Gamma-proteobacteria, Acidobacteria, Nitrospira, Bacilli, Anaerolineae, and Actinobacteria were the major classes in sediment bacterial communities of the Taihu Lake. In general, the inflow-rivers of different pollution types have distinctly different influences on sediment bacterial communities of the lake. The bacterial community composition and physicochemical properties of pelagic sites were closer to those of the estuaries of western region which was polluted by serious industrial and agricultural pollution. The bacterial community diversity of estuaries was lower than those of pelagic sites. Spearman correlation analysis indicated that α-diversity of the bacterial community was significantly correlated with C/N, total nitrogen, and total carbon in estuarine sediments. Redundancy analysis revealed that the variance in bacterial community composition was also significantly associated with C/N (24.9%) followed by total phosphorus (15.8%), nitrite (7.2%), and nitrate (7.7%) among different estuaries. This study provides a reference to understand the influence of inflow-rivers on the lake ecosystem, which offered a basic guidance for maintaining the ecological system and protecting the water environment of lacustrine basin.
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Affiliation(s)
- Hainan Wu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, People's Republic of China
| | - Yi Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, People's Republic of China.
| | - Jing Zhang
- College of Environment and Chemical Technology, Dalian University, Dalian, 116622, People's Republic of China
| | - Lihua Niu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, People's Republic of China
| | - Wenlong Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, People's Republic of China
| | - Wei Cai
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, People's Republic of China
| | - Xiaoxiao Zhu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, People's Republic of China
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Capo E, Debroas D, Arnaud F, Perga ME, Chardon C, Domaizon I. Tracking a century of changes in microbial eukaryotic diversity in lakes driven by nutrient enrichment and climate warming. Environ Microbiol 2017; 19:2873-2892. [DOI: 10.1111/1462-2920.13815] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 05/21/2017] [Accepted: 05/30/2017] [Indexed: 11/28/2022]
Affiliation(s)
- Eric Capo
- CARRTEL, INRA, Université de Savoie Mont Blanc; Thonon-les-bains 74200 France
| | - Didier Debroas
- Université Clermont Auvergne, Université Blaise Pascal, Laboratoire «Microorganismes: Génome et Environnement»; BP 10448 Clermont-Ferrand 63000 France
- CNRS, UMR 6023, LMGE; Campus Universitaire des Cézeaux, 63171 Aubière France
| | - Fabien Arnaud
- CNRS, UMR 5204 EDYTEM, Université Savoie Mont Blanc; Le Bourget du Lac Cedex France
| | - Marie-Elodie Perga
- CARRTEL, INRA, Université de Savoie Mont Blanc; Thonon-les-bains 74200 France
| | - Cécile Chardon
- CARRTEL, INRA, Université de Savoie Mont Blanc; Thonon-les-bains 74200 France
| | - Isabelle Domaizon
- CARRTEL, INRA, Université de Savoie Mont Blanc; Thonon-les-bains 74200 France
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Zadereev ES, Gulati RD, Camacho A. Biological and Ecological Features, Trophic Structure and Energy Flow in Meromictic Lakes. ECOLOGY OF MEROMICTIC LAKES 2017. [DOI: 10.1007/978-3-319-49143-1_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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Capo E, Debroas D, Arnaud F, Guillemot T, Bichet V, Millet L, Gauthier E, Massa C, Develle AL, Pignol C, Lejzerowicz F, Domaizon I. Long-term dynamics in microbial eukaryotes communities: a palaeolimnological view based on sedimentary DNA. Mol Ecol 2016; 25:5925-5943. [DOI: 10.1111/mec.13893] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 09/08/2016] [Accepted: 10/07/2016] [Indexed: 01/21/2023]
Affiliation(s)
- Eric Capo
- CARRTEL; INRA; Université de Savoie Mont Blanc; 74200 Thonon-les-bains France
| | - Didier Debroas
- Université Clermont Auvergne; Laboratoire “Microorganismes: Génome et Environnement”; Université Blaise Pascal; BP 10448 F-63000 Clermont-Ferrand France
- CNRS; UMR 6023; LMGE; Campus Universitaire des Cézeaux 63171 Aubière France
| | - Fabien Arnaud
- CNRS; UMR 5204 EDYTEM; Université Savoie Mont Blanc; 5 Boulevard de la mer Caspienne, 73376 Le Bourget du Lac Cedex France
| | - Typhaine Guillemot
- Laboratoire Chrono-Environnement; UMR 6249 CNRS; Université de Bourgogne Franche-Comté; 16 Route de Gray, 25000 Besançon France
| | - Vincent Bichet
- Laboratoire Chrono-Environnement; UMR 6249 CNRS; Université de Bourgogne Franche-Comté; 16 Route de Gray, 25000 Besançon France
| | - Laurent Millet
- Laboratoire Chrono-Environnement; UMR 6249 CNRS; Université de Bourgogne Franche-Comté; 16 Route de Gray, 25000 Besançon France
| | - Emilie Gauthier
- Laboratoire Chrono-Environnement; UMR 6249 CNRS; Université de Bourgogne Franche-Comté; 16 Route de Gray, 25000 Besançon France
| | - Charly Massa
- Laboratoire Chrono-Environnement; UMR 6249 CNRS; Université de Bourgogne Franche-Comté; 16 Route de Gray, 25000 Besançon France
| | - Anne-Lise Develle
- CNRS; UMR 5204 EDYTEM; Université Savoie Mont Blanc; 5 Boulevard de la mer Caspienne, 73376 Le Bourget du Lac Cedex France
| | - Cécile Pignol
- CNRS; UMR 5204 EDYTEM; Université Savoie Mont Blanc; 5 Boulevard de la mer Caspienne, 73376 Le Bourget du Lac Cedex France
| | - Franck Lejzerowicz
- Department of Genetics and Evolution; University of Geneva; 4 Boulevard d'Yvoy, 1205 Geneva Switzerland
| | - Isabelle Domaizon
- CARRTEL; INRA; Université de Savoie Mont Blanc; 74200 Thonon-les-bains France
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The Tara Oceans voyage reveals global diversity and distribution patterns of marine planktonic ciliates. Sci Rep 2016; 6:33555. [PMID: 27633177 PMCID: PMC5025661 DOI: 10.1038/srep33555] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 08/25/2016] [Indexed: 11/09/2022] Open
Abstract
Illumina reads of the SSU-rDNA-V9 region obtained from the circumglobal Tara Oceans expedition allow the investigation of protistan plankton diversity patterns on a global scale. We analyzed 6,137,350 V9-amplicons from ocean surface waters and the deep chlorophyll maximum, which were taxonomically assigned to the phylum Ciliophora. For open ocean samples global planktonic ciliate diversity is relatively low (ca. 1,300 observed and predicted ciliate OTUs). We found that 17% of all detected ciliate OTUs occurred in all oceanic regions under study. On average, local ciliate OTU richness represented 27% of the global ciliate OTU richness, indicating that a large proportion of ciliates is widely distributed. Yet, more than half of these OTUs shared <90% sequence similarity with reference sequences of described ciliates. While alpha-diversity measures (richness and exp(Shannon H)) are hardly affected by contemporary environmental conditions, species (OTU) turnover and community similarity (β-diversity) across taxonomic groups showed strong correlation to environmental parameters. Logistic regression models predicted significant correlations between the occurrence of specific ciliate genera and individual nutrients, the oceanic carbonate system and temperature. Planktonic ciliates displayed distinct vertical distributions relative to chlorophyll a. In contrast, the Tara Oceans dataset did not reveal any evidence that latitude is structuring ciliate communities.
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Filker S, Sommaruga R, Vila I, Stoeck T. Microbial eukaryote plankton communities of high-mountain lakes from three continents exhibit strong biogeographic patterns. Mol Ecol 2016; 25:2286-301. [PMID: 27029537 DOI: 10.1111/mec.13633] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 02/11/2016] [Accepted: 03/29/2016] [Indexed: 11/27/2022]
Abstract
Microbial eukaryotes hold a key role in aquatic ecosystem functioning. Yet, their diversity in freshwater lakes, particularly in high-mountain lakes, is relatively unknown compared with the marine environment. Low nutrient availability, low water temperature and high ultraviolet radiation make most high-mountain lakes extremely challenging habitats for life and require specific molecular and physiological adaptations. We therefore expected that these ecosystems support a plankton diversity that differs notably from other freshwater lakes. In addition, we hypothesized that the communities under study exhibit geographic structuring. Our rationale was that geographic dispersal of small-sized eukaryotes in high-mountain lakes over continental distances seems difficult. We analysed hypervariable V4 fragments of the SSU rRNA gene to compare the genetic microbial eukaryote diversity in high-mountain lakes located in the European Alps, the Chilean Altiplano and the Ethiopian Bale Mountains. Microbial eukaryotes were not globally distributed corroborating patterns found for bacteria, multicellular animals and plants. Instead, the plankton community composition emerged as a highly specific fingerprint of a geographic region even on higher taxonomic levels. The intraregional heterogeneity of the investigated lakes was mirrored in shifts in microbial eukaryote community structure, which, however, was much less pronounced compared with interregional beta-diversity. Statistical analyses revealed that on a regional scale, environmental factors are strong predictors for plankton community structures in high-mountain lakes. While on long-distance scales (>10 000 km), isolation by distance is the most plausible scenario, on intermediate scales (up to 6000 km), both contemporary environmental factors and historical contingencies interact to shift plankton community structures.
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Affiliation(s)
- Sabine Filker
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Ruben Sommaruga
- Institute of Ecology, Lake and Glacier Research Group, University of Innsbruck, Innsbruck, 6020, Austria
| | - Irma Vila
- Department of Ecological Sciences, Faculty of Sciences, University of Chile, Santiago, Chile
| | - Thorsten Stoeck
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, 67663, Germany
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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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26
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Mahé F, Rognes T, Quince C, de Vargas C, Dunthorn M. Swarm v2: highly-scalable and high-resolution amplicon clustering. PeerJ 2015; 3:e1420. [PMID: 26713226 PMCID: PMC4690345 DOI: 10.7717/peerj.1420] [Citation(s) in RCA: 289] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 10/31/2015] [Indexed: 01/26/2023] Open
Abstract
Previously we presented Swarm v1, a novel and open source amplicon clustering program that produced fine-scale molecular operational taxonomic units (OTUs), free of arbitrary global clustering thresholds and input-order dependency. Swarm v1 worked with an initial phase that used iterative single-linkage with a local clustering threshold (d), followed by a phase that used the internal abundance structures of clusters to break chained OTUs. Here we present Swarm v2, which has two important novel features: (1) a new algorithm for d = 1 that allows the computation time of the program to scale linearly with increasing amounts of data; and (2) the new fastidious option that reduces under-grouping by grafting low abundant OTUs (e.g., singletons and doubletons) onto larger ones. Swarm v2 also directly integrates the clustering and breaking phases, dereplicates sequencing reads with d = 0, outputs OTU representatives in fasta format, and plots individual OTUs as two-dimensional networks.
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Affiliation(s)
- Frédéric Mahé
- Department of Ecology, Technische Universität Kaiserslautern , Kaiserslautern , Germany
| | - Torbjørn Rognes
- Department of Informatics, University of Oslo , Oslo , Norway ; Department of Microbiology, Oslo University Hospital, Rikshospitalet , Oslo , Norway
| | - Christopher Quince
- Warwick Medical School, University of Warwick , Warwick , United Kingdom
| | - Colomban de Vargas
- UMR 7144, EPEP-Évolution des Protistes et des Écosystèmes Pélagiques, Station Biologique de Roscoff, CNRS , Roscoff , France ; UMR7144 Station Biologique de Roscoff, Sorbonne Universités, UPMC Univ Paris 06 , Roscoff , France
| | - Micah Dunthorn
- Department of Ecology, Technische Universität Kaiserslautern , Kaiserslautern , Germany
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