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Kulikovskiy M, Glushchenko A, Kezlya E, Kuznetsova I, Kociolek JP, Maltsev Y. The Genus Pinnularia Ehrenberg (Bacillariophyta) from the Transbaikal Area (Russia, Siberia): Description of Seven New Species on the Basis of Morphology and Molecular Data with Discussion of the Phylogenetic Position of Caloneis. PLANTS (BASEL, SWITZERLAND) 2023; 12:3552. [PMID: 37896016 PMCID: PMC10610464 DOI: 10.3390/plants12203552] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/08/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023]
Abstract
Seven Pinnularia species from the Transbaikal area, Russia, are described as new for science. These are P. baicalgenkalii, P. baicalflexuosa, P. microfrauenbergiana, P. pergrunowii, P. siberiosinistra, P. baicalodivergens, and P. baicalislandica. All species are described by original LM and SEM microphotographs and molecular phylogeny. We provide comparisons between the taxa and document variability in the features found in the species. The number of Pinnularia species in the Transbaikal area is the largest number of species of the genus anywhere in the world.
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Affiliation(s)
- Maxim Kulikovskiy
- K.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, 35 Botanicheskaya St., 127276 Moscow, Russia; (A.G.); (E.K.); (I.K.); (Y.M.)
| | - Anton Glushchenko
- K.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, 35 Botanicheskaya St., 127276 Moscow, Russia; (A.G.); (E.K.); (I.K.); (Y.M.)
| | - Elena Kezlya
- K.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, 35 Botanicheskaya St., 127276 Moscow, Russia; (A.G.); (E.K.); (I.K.); (Y.M.)
| | - Irina Kuznetsova
- K.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, 35 Botanicheskaya St., 127276 Moscow, Russia; (A.G.); (E.K.); (I.K.); (Y.M.)
| | - John Patrick Kociolek
- Museum of Natural History, Henderson Building, 15th and Broadway, Boulder, CO 80309, USA;
| | - Yevhen Maltsev
- K.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, 35 Botanicheskaya St., 127276 Moscow, Russia; (A.G.); (E.K.); (I.K.); (Y.M.)
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2
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Kezlya E, Tseplik N, Kulikovskiy M. Genetic Markers for Metabarcoding of Freshwater Microalgae: Review. BIOLOGY 2023; 12:1038. [PMID: 37508467 PMCID: PMC10376359 DOI: 10.3390/biology12071038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/14/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023]
Abstract
The metabarcoding methods for studying the diversity of freshwater microalgae and routine biomonitoring are actively used in modern research. A lot of experience has been accumulated already, and many methodological questions have been solved (such as the influence of the methods and time of sample conservation, DNA extraction and bioinformatical processing). The reproducibility of the method has been tested and confirmed. However, one of the main problems-choosing a genetic marker for the study-still lacks a clear answer. We analyzed 70 publications and found out that studies on eukaryotic freshwater microalgae use 12 markers (different nuclear regions 18S and ITS and plastids rbcL, 23S and 16S). Each marker has its peculiarities; they amplify differently and have various levels of efficiency (variability) in different groups of algae. The V4 and V9 18S and rbcL regions are used most often. We concentrated especially on the studies that compare the results of using different markers and microscopy. We summarize the data on the primers for each region and on how the choice of a marker affects the taxonomic composition of a community.
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Affiliation(s)
- Elena Kezlya
- Laboratory of Molecular Systematics of Aquatic Plants, K.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, 127276 Moscow, Russia
| | - Natalia Tseplik
- Laboratory of Molecular Systematics of Aquatic Plants, K.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, 127276 Moscow, Russia
| | - Maxim Kulikovskiy
- Laboratory of Molecular Systematics of Aquatic Plants, K.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, 127276 Moscow, Russia
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3
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Bukin YS, Mikhailov IS, Petrova DP, Galachyants YP, Zakharova YR, Likhoshway YV. The effect of metabarcoding 18S rRNA region choice on diversity of microeukaryotes including phytoplankton. World J Microbiol Biotechnol 2023; 39:229. [PMID: 37341802 DOI: 10.1007/s11274-023-03678-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 06/13/2023] [Indexed: 06/22/2023]
Abstract
Metabarcoding using high throughput sequencing of amplicons of the 18S rRNA gene is one of the widely used methods for assessing the diversity of microeukaryotes in various ecosystems. We investigated the effectiveness of the V4 and V8-V9 regions of the 18S rRNA gene by comparing the results of metabarcoding microeukaryotic communities using the DADA2 (ASV), USEARCH-UNOISE3 (ZOTU), and USEARCH-UPARSE (OTU with 97% similarity) algorithms. Both regions showed similar levels of genetic variability and taxa identification accuracy. Richness for DADA2 datasets of both regions was lower than for UNOISE3 and UPARSE datasets, which is due to more accurate error correction in amplicons. Microeukaryotic communities (autotrophs and heterotrophs) structure identified using both regions showed a significant relationship with phytoplankton (autotrophs) communities structure based on microscopy in a seasonal freshwater sample series. The strongest relationship was found between the phytoplankton species and V8-V9 ASVs produced by DADA2.
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Affiliation(s)
- Yuri S Bukin
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Ivan S Mikhailov
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia.
| | - Darya P Petrova
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Yuri P Galachyants
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Yulia R Zakharova
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Yelena V Likhoshway
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
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4
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Kalu EI, Reyes-Prieto A, Barbeau MA. Community dynamics of microbial eukaryotes in intertidal mudflats in the hypertidal Bay of Fundy. ISME COMMUNICATIONS 2023; 3:21. [PMID: 36918616 PMCID: PMC10014957 DOI: 10.1038/s43705-023-00226-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 02/15/2023] [Accepted: 02/28/2023] [Indexed: 03/16/2023]
Abstract
Protists (microbial eukaryotes) are a critically important but understudied group of microorganisms. They are ubiquitous, represent most of the genetic and functional diversity among eukaryotes, and play essential roles in nutrient and energy cycling. Yet, protists remain a black box in marine sedimentary ecosystems like the intertidal mudflats in the Bay of Fundy. The harsh conditions of the intertidal zone and high energy nature of tides in the Bay of Fundy provide an ideal system for gaining insights into the major food web players, diversity patterns and potential structuring influences of protist communities. Our 18S rDNA metabarcoding study quantified seasonal variations and vertical stratification of protist communities in Bay of Fundy mudflat sediments. Three 'SAR' lineages were consistently dominant (in terms of abundance, richness, and prevalence), drove overall community dynamics and formed the core microbiome in sediments. They are Cercozoa (specifically thecate, benthic gliding forms), Bacillariophyta (mainly cosmopolitan, typically planktonic diatoms), and Dinophyceae (dominated by a toxigenic, bloom-forming species). Consumers were the dominant trophic functional group and were comprised mostly of eukaryvorous and bacterivorous Cercozoa, and omnivorous Ciliophora, while phototrophs were dominated by Bacillariophyta. The codominance of Apicomplexa (invertebrate parasites) and Syndiniales (protist parasites) in parasite assemblages, coupled with broader diversity patterns, highlighted the combined marine and terrestrial influences on microbial communities inhabiting intertidal sediments. Our findings, the most comprehensive in a hypertidal benthic system, suggest that synergistic interactions of both local and regional processes (notably benthic-pelagic coupling) may drive heterogenous microbial distribution in high-energy coastal systems.
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Affiliation(s)
- Eke I Kalu
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada.
| | | | - Myriam A Barbeau
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada
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5
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Mitsi K, Richter DJ, Arroyo AS, López-Escardó D, Antó M, Oterino AG, Ruiz-Trillo I. Taxonomic composition, community structure and molecular novelty of microeukaryotes in a temperate oligomesotrophic lake as revealed by metabarcoding. Sci Rep 2023; 13:3119. [PMID: 36813945 PMCID: PMC9947120 DOI: 10.1038/s41598-023-30228-4] [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: 07/03/2022] [Accepted: 02/18/2023] [Indexed: 02/24/2023] Open
Abstract
Microbial eukaryotes are diverse and ecologically important organisms, yet sampling constraints have hindered the understanding of their distribution and diversity in freshwater ecosystems. Metabarcoding has provided a powerful complement to traditional limnological studies, revealing an unprecedented diversity of protists in freshwater environments. Here, we aim to expand our knowledge of the ecology and diversity of protists in lacustrine ecosystems by targeting the V4 hypervariable region of the 18S rRNA gene in water column, sediment and biofilm samples collected from Sanabria Lake (Spain) and surrounding freshwater ecosystems. Sanabria is a temperate lake, which are relatively understudied by metabarcoding in comparison to alpine and polar lakes. The phylogenetic diversity of microbial eukaryotes detected in Sanabria spans all currently recognized eukaryotic supergroups, with Stramenopiles being the most abundant and diverse supergroup in all sampling sites. Parasitic microeukaryotes account for 21% of the total protist ASVs identified in our study and were dominated by Chytridiomycota, both in terms of richness and abundance, in all sampling sites. Sediments, biofilms and water column samples harbour distinct microbial communities. Phylogenetic placement of poorly assigned and abundant ASVs indicates molecular novelty inside Rhodophyta, Bigyra, early-branching Nucletmycea and Apusomonadida. In addition, we report the first freshwater incidence of the previously exclusively marine genera Abeoforma and Sphaeroforma. Our results contribute to a deeper understanding of microeukaryotic communities in freshwater ecosystems, and provide the first molecular reference for future biomonitoring surveys in Sanabria Lake.
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Affiliation(s)
- Konstantina Mitsi
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de La Barceloneta, 37-49, 08033, Barcelona, Spain.
| | - Daniel J. Richter
- grid.507636.10000 0004 0424 5398Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de La Barceloneta, 37-49, 08033 Barcelona, Spain
| | - Alicia S. Arroyo
- grid.507636.10000 0004 0424 5398Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de La Barceloneta, 37-49, 08033 Barcelona, Spain
| | - David López-Escardó
- grid.418218.60000 0004 1793 765XInstitut de Ciències del Mar (CSIC), Passeig Marítim de La Barceloneta, 37-49, 08033 Barcelona, Spain
| | - Meritxell Antó
- grid.507636.10000 0004 0424 5398Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de La Barceloneta, 37-49, 08033 Barcelona, Spain
| | | | - Iñaki Ruiz-Trillo
- grid.507636.10000 0004 0424 5398Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de La Barceloneta, 37-49, 08033 Barcelona, Spain ,grid.425902.80000 0000 9601 989XInstitució Catalana de Recerca I Estudis Avançats (ICREA), Passeig Lluís Companys, 23, 08010 Barcelona, Spain
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6
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Tikhonenkov DV, Mikhailov KV, Gawryluk RMR, Belyaev AO, Mathur V, Karpov SA, Zagumyonnyi DG, Borodina AS, Prokina KI, Mylnikov AP, Aleoshin VV, Keeling PJ. Microbial predators form a new supergroup of eukaryotes. Nature 2022; 612:714-719. [PMID: 36477531 DOI: 10.1038/s41586-022-05511-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 11/02/2022] [Indexed: 12/12/2022]
Abstract
Molecular phylogenetics of microbial eukaryotes has reshaped the tree of life by establishing broad taxonomic divisions, termed supergroups, that supersede the traditional kingdoms of animals, fungi and plants, and encompass a much greater breadth of eukaryotic diversity1. The vast majority of newly discovered species fall into a small number of known supergroups. Recently, however, a handful of species with no clear relationship to other supergroups have been described2-4, raising questions about the nature and degree of undiscovered diversity, and exposing the limitations of strictly molecular-based exploration. Here we report ten previously undescribed strains of microbial predators isolated through culture that collectively form a diverse new supergroup of eukaryotes, termed Provora. The Provora supergroup is genetically, morphologically and behaviourally distinct from other eukaryotes, and comprises two divergent clades of predators-Nebulidia and Nibbleridia-that are superficially similar to each other, but differ fundamentally in ultrastructure, behaviour and gene content. These predators are globally distributed in marine and freshwater environments, but are numerically rare and have consequently been overlooked by molecular-diversity surveys. In the age of high-throughput analyses, investigation of eukaryotic diversity through culture remains indispensable for the discovery of rare but ecologically and evolutionarily important eukaryotes.
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Affiliation(s)
- Denis V Tikhonenkov
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Russian Federation. .,AquaBioSafe Laboratory, University of Tyumen, Tyumen, Russian Federation.
| | - Kirill V Mikhailov
- Belozersky Institute for Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation.,Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russian Federation
| | - Ryan M R Gawryluk
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Artem O Belyaev
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Russian Federation.,Department of Zoology and Ecology, Penza State University, Penza, Russian Federation
| | - Varsha Mathur
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Zoology, University of Oxford, Oxford, UK
| | - Sergey A Karpov
- Zoological Institute, Russian Academy of Sciences, Saint Petersburg, Russian Federation.,Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russian Federation
| | - Dmitry G Zagumyonnyi
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Russian Federation.,AquaBioSafe Laboratory, University of Tyumen, Tyumen, Russian Federation
| | - Anastasia S Borodina
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Russian Federation.,Department of Zoology and Parasitology, Voronezh State University, Voronezh, Russian Federation
| | - Kristina I Prokina
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Russian Federation.,Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
| | - Alexander P Mylnikov
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Russian Federation
| | - Vladimir V Aleoshin
- Belozersky Institute for Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation.,Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russian Federation
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
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7
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Mikhailov IS, Galachyants YP, Bukin YS, Petrova DP, Bashenkhaeva MV, Sakirko MV, Blinov VV, Titova LA, Zakharova YR, Likhoshway YV. Seasonal Succession and Coherence Among Bacteria and Microeukaryotes in Lake Baikal. MICROBIAL ECOLOGY 2022; 84:404-422. [PMID: 34510242 DOI: 10.1007/s00248-021-01860-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 09/02/2021] [Indexed: 06/13/2023]
Abstract
Microorganisms exhibit seasonal succession governed by physicochemical factors and interspecies interactions, yet drivers of this process in different environments remain to be determined. We used high-throughput sequencing of 16S rRNA and 18S rRNA genes to study seasonal dynamics of bacterial and microeukaryotic communities at pelagic site of Lake Baikal from spring (under-ice, mixing) to autumn (direct stratification). The microbial community was subdivided into distinctive coherent clusters of operational taxonomic units (OTUs). Individual OTUs were consistently replaced during different seasonal events. The coherent clusters change their contribution to the microbial community depending on season. Changes of temperature, concentrations of silicon, and nitrates are the key factors affected the structure of microbial communities. Functional prediction revealed that some bacterial or eukaryotic taxa that switched with seasons had similar functional properties, which demonstrate their functional redundancy. We have also detected specific functional properties in different coherent clusters of bacteria or microeukaryotes, which can indicate their ability to adapt to seasonal changes of environment. Our results revealed a relationship between seasonal succession, coherency, and functional features of freshwater bacteria and microeukaryotes.
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Affiliation(s)
- Ivan S Mikhailov
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia.
| | - Yuri P Galachyants
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Yuri S Bukin
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Darya P Petrova
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Maria V Bashenkhaeva
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Maria V Sakirko
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Vadim V Blinov
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Lubov A Titova
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Yulia R Zakharova
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Yelena V Likhoshway
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
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8
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Kaluzhnaya OV, Itskovich VB. Features of Diversity of Polyketide Synthase Genes in the Community of Freshwater Sponge Baikalospongia fungiformis. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422030061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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9
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Tashyreva D, Simpson A, Prokopchuk G, Škodová-Sveráková I, Butenko A, Hammond M, George EE, Flegontova O, Záhonová K, Faktorová D, Yabuki A, Horák A, Keeling PJ, Lukeš J. Diplonemids – A Review on “New“ Flagellates on the Oceanic Block. Protist 2022; 173:125868. [DOI: 10.1016/j.protis.2022.125868] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/26/2022] [Accepted: 02/28/2022] [Indexed: 11/15/2022]
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10
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Bukin YS, Kravtsova LS, Peretolchina TE, Fedotov AP, Tupikin AE, Kabilov MR, Sherbakov DY, Mincheva EV. DNA metabarcoding of benthic algae and associated eukaryotes from Lake Baikal in the face of rapid environmental changes. Vavilovskii Zhurnal Genet Selektsii 2022; 26:86-95. [PMID: 35342852 PMCID: PMC8894627 DOI: 10.18699/vjgb-22-12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 10/05/2021] [Accepted: 10/21/2021] [Indexed: 11/19/2022] Open
Abstract
Here we report new data describing the biodiversity of phytobenthic communities based on DNA-metabarcoding using the 18S rDNA marker and the Illumina MiSeq system. The study was initiated due to the blooming of f ilamentous algae (mainly of the genus Spirogyra) and cyanobacteria in the coastal zone of Lake Baikal under climate change and anthropogenic impact. The composition and taxonomic diversity of algae and other organisms associated with them on different sites of Lake Baikal (near Bolshoi Ushkaniy Island, in Listvennichny Bay) and in the Kaya (within the city of Irkutsk, located in the same drainage basin as Lake Baikal) were determined using
DNAmetabarcoding.
About 15 thousand reads of the 18S rRNA marker were obtained by applying NGS (next-generation
sequencing). The species of algae dominating in the number of reads, as well as the diff icult-to-identify taxa
(Stramenopiles, Alveolata, Euglenozoa, Chromista, Rhizaria, Amoebozoa, etc.), which play an important role in the
functioning and formation of the structure of algal communities, were revealed. The Shannon index of the communities
studied ranges from 1.56 to 2.72. The advantages and weaknesses of using DNA-metabarcoding based on the
18S rRNA gene fragment for studying the structure of algal communities are shown. The advantage of this method is
the possibility to more fully determine the diversity of eukaryotes taxa, which are diff icult to identify by morphology,
without involving a large number of specialists, while the disadvantage of the method is the distortion that may occur
during the PCR. Here, ways of solving this problem are proposed. The results of the study show that the analysis
of the minor component of the eukaryotic community in samples (organisms with low biomass) consisting of a
mixture of multicellular and unicellular organisms requires a read-depths of at least 100,000 sequences per sample.
In general, the DNA-metabarcoding method is recommended for studying the structure of algal communities and
eukaryotes associated with them.
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Affiliation(s)
- Yu. S. Bukin
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences; Irkutsk State University
| | - L. S. Kravtsova
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences
| | - T. E. Peretolchina
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences
| | - A. P. Fedotov
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences
| | - A. E. Tupikin
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences
| | - M. R. Kabilov
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences
| | - D. Yu. Sherbakov
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences; Novosibirsk State University
| | - E. V. Mincheva
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences
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11
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Amazing Discoveries of Benthic Fauna from the Abyssal Zone of Lake Baikal. BIOLOGY 2021; 10:biology10100972. [PMID: 34681071 PMCID: PMC8533251 DOI: 10.3390/biology10100972] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/23/2021] [Accepted: 09/23/2021] [Indexed: 11/16/2022]
Abstract
Lake Baikal is a natural laboratory for the study of species diversity and evolution, as a unique freshwater ecosystem meeting the all of the main criteria of the World Heritage Convention. However, despite many years of research, the true biodiversity of the lake is clearly insufficiently studied, especially that of deep-water benthic sessile organisms. For the first time, plastic waste was raised from depths of 110 to 190 m of Lake Baikal. The aim of this study was to examine the biological community inhabiting the plastic substrate using morphological and molecular genetic analysis. Fragments of plastic packaging materials were densely populated: bryozoans, leeches and their cocoons, capsules of gastropod eggs, and turbellaria cocoons were found. All the data obtained as a result of an analysis of the nucleotide sequences of the standard bar-coding fragment of the mitochondrial genome turned out to be unique. Our results demonstrate the prospects for conducting comprehensive studies of artificial substrates to determine the true biodiversity of benthos in the abyssal zone of Lake Baikal.
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12
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Zou K, Wang R, Xu S, Li Z, Liu L, Li M, Zhou L. Changes in protist communities in drainages across the Pearl River Delta under anthropogenic influence. WATER RESEARCH 2021; 200:117294. [PMID: 34102388 DOI: 10.1016/j.watres.2021.117294] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 05/21/2021] [Accepted: 05/22/2021] [Indexed: 06/12/2023]
Abstract
Drainages in the Pearl River Delta urban agglomeration (PRDUA) host vital aquatic ecosystems and face enormous pressures from human activities in one of the largest urban agglomerations in the world. Despite being crucial components of aquatic ecosystems, the interactions and assembly processes of the protistan community are rarely explored in areas with serious anthropogenic disturbance. To elucidate the mechanisms of these processes, we used environmental DNA sequencing of 18S rDNA to investigate the influence of environmental factors and species interactions on the protistan community and its assembly in drainages of the PRDUA during summer. The protistan community showed a high level of diversity and a marked spatial pattern in this region. Community assembly was driven primarily by stochastic processes based on the Sloan neutral community model, explaining 74.28%, 75.82%, 73.67%, 74.40% and 51.24% of community variations in the BJ (Beijiang), XJ (Xijiang), PRD (Pearl River Delta), PRE (Pearl River Estuary) areas and in total, respectively. Meanwhile, environmental variables including temperature, pH, dissolved oxygen, transparency, nutrients and land use were strongly correlated with the composition and assembly of the protistan community, explaining 40.40% of variation in the protistan community. Furthermore, the bacterial community was simultaneously analysed by the 16S rDNA sequencing. Co-occurrence network analysis revealed that species interactions within bacteria (81.41% positive) or protists (82.80% positive), and those between bacteria and protists (50% positive and 50% negative) impacted the protistan community assembly. In summary, stochastic processes dominated, whereas species interactions and environmental factors also played important roles in shaping the protistan communities in drainages across the PRDUA. This study provides insights into the ecological patterns, assembly processes and species interactions underlying protistan dynamics in urban aquatic ecosystems experiencing serious anthropogenic disturbance.
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Affiliation(s)
- Keshu Zou
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 510642 Guangzhou, China
| | - Ruili Wang
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 510642 Guangzhou, China
| | - Shannan Xu
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510300 Guangzhou, China
| | - Zhuoying Li
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 510642 Guangzhou, China
| | - Li Liu
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 510642 Guangzhou, China
| | - Min Li
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510300 Guangzhou, China.
| | - Lei Zhou
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 510642 Guangzhou, China.
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13
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Marine signature taxa and core microbial community stability along latitudinal and vertical gradients in sediments of the deepest freshwater lake. ISME JOURNAL 2021; 15:3412-3417. [PMID: 34012102 DOI: 10.1038/s41396-021-01011-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 05/05/2021] [Accepted: 05/11/2021] [Indexed: 11/08/2022]
Abstract
Lake Baikal is the deepest (~1.6 km) and most voluminous freshwater reservoir on Earth. Compared to plankton, its benthos remains poorly explored. Here, we ask whether latitude and/or depth determine benthic microbial community structure and how Baikal communities compare to those of other freshwater, brackish and marine sediments. To answer, we collected sediment upper layers (0-1 cm) across a ~600 km North-South transect covering the three basins of the lake and from littoral to bathybenthic depths (0.5-1450 m). Analysis of 16S and 18S rRNA gene amplicon sequences revealed communities with high richness and evenness where rare operational taxonomic units (OTUs) collectively dominated. Archaea represented up to 25% or prokaryotic sequences. Baikal sediments harbored typically marine eukaryotic and prokaryotic OTUs recently identified in some lakes (diplonemids, Bolidophyceae, Mamiellales, SAR202, marine-like Synechococcus, Pelagibacterales) but also SAR324, Syndiniales and Radiolaria. We hypothesize that, beyond the salinity barrier, adaptation to oligotrophy explains the presence of these otherwise typically marine lineages. Baikal core benthic communities were relatively stable across sites and seemed not determined by depth or latitude. Comparative analyses with other freshwater, brackish and marine prokaryotic sediment communities confirmed the distinctness of Baikal benthos, which include elements of similarity to marine and hydrothermally influenced systems.
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14
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Kostygov AY, Karnkowska A, Votýpka J, Tashyreva D, Maciszewski K, Yurchenko V, Lukeš J. Euglenozoa: taxonomy, diversity and ecology, symbioses and viruses. Open Biol 2021; 11:200407. [PMID: 33715388 PMCID: PMC8061765 DOI: 10.1098/rsob.200407] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 02/08/2021] [Indexed: 12/14/2022] Open
Abstract
Euglenozoa is a species-rich group of protists, which have extremely diverse lifestyles and a range of features that distinguish them from other eukaryotes. They are composed of free-living and parasitic kinetoplastids, mostly free-living diplonemids, heterotrophic and photosynthetic euglenids, as well as deep-sea symbiontids. Although they form a well-supported monophyletic group, these morphologically rather distinct groups are almost never treated together in a comparative manner, as attempted here. We present an updated taxonomy, complemented by photos of representative species, with notes on diversity, distribution and biology of euglenozoans. For kinetoplastids, we propose a significantly modified taxonomy that reflects the latest findings. Finally, we summarize what is known about viruses infecting euglenozoans, as well as their relationships with ecto- and endosymbiotic bacteria.
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Affiliation(s)
- Alexei Y. Kostygov
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
- Zoological Institute, Russian Academy of Sciences, St Petersburg, Russia
| | - Anna Karnkowska
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Jan Votýpka
- Institute of Parasitology, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Daria Tashyreva
- Institute of Parasitology, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
| | - Kacper Maciszewski
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, Moscow, Russia
| | - Julius Lukeš
- Institute of Parasitology, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
- Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
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15
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Xu J, Wilkinson M, Chen M, Zhang Q, Yang R, Yi Z. Concatenated data and dense taxon sampling clarify phylogeny and ecological transitions within Hypotricha. ZOOL SCR 2020. [DOI: 10.1111/zsc.12459] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jiahui Xu
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture School of Life Sciences South China Normal University Guangzhou China
| | - Mark Wilkinson
- Department of Life Sciences Natural History Museum London UK
| | - Miaoying Chen
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture School of Life Sciences South China Normal University Guangzhou China
| | - Qi Zhang
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture School of Life Sciences South China Normal University Guangzhou China
| | - Ran Yang
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture School of Life Sciences South China Normal University Guangzhou China
| | - Zhenzhen Yi
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture School of Life Sciences South China Normal University Guangzhou China
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16
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Stockwell JD, Doubek JP, Adrian R, Anneville O, Carey CC, Carvalho L, De Senerpont Domis LN, Dur G, Frassl MA, Grossart H, Ibelings BW, Lajeunesse MJ, Lewandowska AM, Llames ME, Matsuzaki SS, Nodine ER, Nõges P, Patil VP, Pomati F, Rinke K, Rudstam LG, Rusak JA, Salmaso N, Seltmann CT, Straile D, Thackeray SJ, Thiery W, Urrutia‐Cordero P, Venail P, Verburg P, Woolway RI, Zohary T, Andersen MR, Bhattacharya R, Hejzlar J, Janatian N, Kpodonu ATNK, Williamson TJ, Wilson HL. Storm impacts on phytoplankton community dynamics in lakes. GLOBAL CHANGE BIOLOGY 2020; 26:2756-2784. [PMID: 32133744 PMCID: PMC7216882 DOI: 10.1111/gcb.15033] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 01/25/2020] [Indexed: 05/03/2023]
Abstract
In many regions across the globe, extreme weather events such as storms have increased in frequency, intensity, and duration due to climate change. Ecological theory predicts that such extreme events should have large impacts on ecosystem structure and function. High winds and precipitation associated with storms can affect lakes via short-term runoff events from watersheds and physical mixing of the water column. In addition, lakes connected to rivers and streams will also experience flushing due to high flow rates. Although we have a well-developed understanding of how wind and precipitation events can alter lake physical processes and some aspects of biogeochemical cycling, our mechanistic understanding of the emergent responses of phytoplankton communities is poor. Here we provide a comprehensive synthesis that identifies how storms interact with lake and watershed attributes and their antecedent conditions to generate changes in lake physical and chemical environments. Such changes can restructure phytoplankton communities and their dynamics, as well as result in altered ecological function (e.g., carbon, nutrient and energy cycling) in the short- and long-term. We summarize the current understanding of storm-induced phytoplankton dynamics, identify knowledge gaps with a systematic review of the literature, and suggest future research directions across a gradient of lake types and environmental conditions.
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17
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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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18
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Dumack K, Fiore‐Donno AM, Bass D, Bonkowski M. Making sense of environmental sequencing data: Ecologically important functional traits of the protistan groups Cercozoa and Endomyxa (Rhizaria). Mol Ecol Resour 2019; 20:398-403. [DOI: 10.1111/1755-0998.13112] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 10/21/2019] [Accepted: 10/28/2019] [Indexed: 11/26/2022]
Affiliation(s)
- Kenneth Dumack
- Institute of Zoology Terrestrial Ecology Cluster of Excellence on Plant Sciences (CEPLAS) University of Cologne Cologne Germany
| | - Anna Maria Fiore‐Donno
- Institute of Zoology Terrestrial Ecology Cluster of Excellence on Plant Sciences (CEPLAS) University of Cologne Cologne Germany
| | - David Bass
- Centre for Environment Fisheries and Aquaculture Science (Cefas) Weymouth UK
- Department of Life Sciences The Natural History Museum London UK
| | - Michael Bonkowski
- Institute of Zoology Terrestrial Ecology Cluster of Excellence on Plant Sciences (CEPLAS) University of Cologne Cologne Germany
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19
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Bjorbækmo MFM, Evenstad A, Røsæg LL, Krabberød AK, Logares R. The planktonic protist interactome: where do we stand after a century of research? ISME JOURNAL 2019; 14:544-559. [PMID: 31685936 PMCID: PMC6976576 DOI: 10.1038/s41396-019-0542-5] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 09/17/2019] [Accepted: 09/24/2019] [Indexed: 12/16/2022]
Abstract
Microbial interactions are crucial for Earth ecosystem function, but our knowledge about them is limited and has so far mainly existed as scattered records. Here, we have surveyed the literature involving planktonic protist interactions and gathered the information in a manually curated Protist Interaction DAtabase (PIDA). In total, we have registered ~2500 ecological interactions from ~500 publications, spanning the last 150 years. All major protistan lineages were involved in interactions as hosts, symbionts (mutualists and commensalists), parasites, predators, and/or prey. Predation was the most common interaction (39% of all records), followed by symbiosis (29%), parasitism (18%), and ‘unresolved interactions’ (14%, where it is uncertain whether the interaction is beneficial or antagonistic). Using bipartite networks, we found that protist predators seem to be ‘multivorous’ while parasite–host and symbiont–host interactions appear to have moderate degrees of specialization. The SAR supergroup (i.e., Stramenopiles, Alveolata, and Rhizaria) heavily dominated PIDA, and comparisons against a global-ocean molecular survey (TARA Oceans) indicated that several SAR lineages, which are abundant and diverse in the marine realm, were underrepresented among the recorded interactions. Despite historical biases, our work not only unveils large-scale eco-evolutionary trends in the protist interactome, but it also constitutes an expandable resource to investigate protist interactions and to test hypotheses deriving from omics tools.
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Affiliation(s)
- Marit F Markussen Bjorbækmo
- Department of Biosciences, Section for Genetics and Evolutionary Biology (Evogene), University of Oslo, Blindernv. 31, N-0316, Oslo, Norway
| | - Andreas Evenstad
- Department of Biosciences, Section for Genetics and Evolutionary Biology (Evogene), University of Oslo, Blindernv. 31, N-0316, Oslo, Norway
| | - Line Lieblein Røsæg
- Department of Biosciences, Section for Genetics and Evolutionary Biology (Evogene), University of Oslo, Blindernv. 31, N-0316, Oslo, Norway
| | - Anders K Krabberød
- Department of Biosciences, Section for Genetics and Evolutionary Biology (Evogene), University of Oslo, Blindernv. 31, N-0316, Oslo, Norway.
| | - Ramiro Logares
- Department of Biosciences, Section for Genetics and Evolutionary Biology (Evogene), University of Oslo, Blindernv. 31, N-0316, Oslo, Norway. .,Institut de Ciències del Mar (CSIC), Passeig Marítim de la Barceloneta, 37-49, ES-08003, Barcelona, Catalonia, Spain.
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20
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Richardson E, Dacks JB. Microbial Eukaryotes in Oil Sands Environments: Heterotrophs in the Spotlight. Microorganisms 2019; 7:microorganisms7060178. [PMID: 31248111 PMCID: PMC6617064 DOI: 10.3390/microorganisms7060178] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 06/12/2019] [Accepted: 06/14/2019] [Indexed: 11/17/2022] Open
Abstract
Hydrocarbon extraction and exploitation is a global, trillion-dollar industry. However, for decades it has also been known that fossil fuel usage is environmentally detrimental; the burning of hydrocarbons results in climate change, and environmental damage during extraction and transport can also occur. Substantial global efforts into mitigating this environmental disruption are underway. The global petroleum industry is moving more and more into exploiting unconventional oil reserves, such as oil sands and shale oil. The Albertan oil sands are one example of unconventional oil reserves; this mixture of sand and heavy bitumen lying under the boreal forest of Northern Alberta represent one of the world’s largest hydrocarbon reserves, but extraction also requires the disturbance of a delicate northern ecosystem. Considerable effort is being made by various stakeholders to mitigate environmental impact and reclaim anthropogenically disturbed environments associated with oil sand extraction. In this review, we discuss the eukaryotic microbial communities associated with the boreal ecosystem and how this is affected by hydrocarbon extraction, with a particular emphasis on the reclamation of tailings ponds, where oil sands extraction waste is stored. Microbial eukaryotes, or protists, are an essential part of every global ecosystem, but our understanding of how they affect reclamation is limited due to our fledgling understanding of these organisms in anthropogenically hydrocarbon-associated environments and the difficulties of studying them. We advocate for an environmental DNA sequencing-based approach to determine the microbial communities of oil sands associated environments, and the importance of studying the heterotrophic components of these environments to gain a full understanding of how these environments operate and thus how they can be integrated with the natural watersheds of the region.
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Affiliation(s)
- Elisabeth Richardson
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
| | - Joel B Dacks
- Division of Infectious Disease, Department of Medicine, University of Alberta, Edmonton, AB T6G 2G3, Canada.
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21
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Deodato CR, Barlow SB, Hovde BT, Cattolico RA. Naked Chrysochromulina (Haptophyta) isolates from lake and river ecosystems: An electron microscopic comparison including new observations on the type species of this taxon. ALGAL RES 2019. [DOI: 10.1016/j.algal.2019.101492] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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22
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Huang Y, Huang J. Coupled effects of land use pattern and hydrological regime on composition and diversity of riverine eukaryotic community in a coastal watershed of Southeast China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 660:787-798. [PMID: 30743964 DOI: 10.1016/j.scitotenv.2019.01.063] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 12/14/2018] [Accepted: 01/06/2019] [Indexed: 06/09/2023]
Abstract
The coupled effects of land use pattern and hydrological regime on composition and diversity of riverine eukaryotic community are needed for understanding riverine ecosystem health and algal blooming mechanism. In-situ monitoring and 18S rRNA gene sequencing were used to investigate spatiotemporal variations of eukaryotic community in three types of watershed with different dominant land use type (i.e. urban, forest, and natural) during three seasons (i.e. dry, transition, and wet seasons) in a coastal watershed of Southeast China. Results showed that agricultural and urban watersheds had significantly higher diversity in dry and transition seasons, and higher richness in transition and wet seasons than those in forest watershed. The non-metric multidimensional scaling analysis further verified great spatiotemporal variations of eukaryotic community. Stramenopiles, Alveolata, Animalia, and Eukaryota, dominated the sequences reads for all sampling sites in three seasons. Agricultural watershed had the highest relative abundant of Animalia, whereas Eukaryota was the most abundant in urban watershed and forest watershed had the highest relative abundance of Stramenopiles and Alveolata. The RDA ordination showed that Builtup and streamflow were two most important factors for moderate taxa and abundant taxa, respectively. Variation partitioning revealed that land use pattern and hydrological regime together explained 54.4%, 61% and 67.2% variances of the composition of eukaryotic community. Among three sampling seasons, the relative contribution of land use pattern was higher than that of hydrological regime. The results of this investigation demonstrated how land use pattern and hydrological regime affected the composition and diversity of riverine eukaryotic community. The findings can provide a useful insight into the riverine eukaryotic communities and their underlying ecological mechanisms in coastal China watersheds.
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Affiliation(s)
- Yaling Huang
- Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen 361102, China
| | - Jinliang Huang
- Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen 361102, China; Coastal and Ocean Management Institute, Xiamen University, Xiamen 361102, China.
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23
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Mikhailov IS, Zakharova YR, Bukin YS, Galachyants YP, Petrova DP, Sakirko MV, Likhoshway YV. Co-occurrence Networks Among Bacteria and Microbial Eukaryotes of Lake Baikal During a Spring Phytoplankton Bloom. MICROBIAL ECOLOGY 2019; 77:96-109. [PMID: 29882155 DOI: 10.1007/s00248-018-1212-2] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Accepted: 05/28/2018] [Indexed: 05/25/2023]
Abstract
The pelagic zone of Lake Baikal is an ecological niche where phytoplankton bloom causes increasing microbial abundance in spring which plays a key role in carbon turnover in the freshwater lake. Co-occurrence patterns revealed among different microbes can be applied to predict interactions between the microbes and environmental conditions in the ecosystem. We used 454 pyrosequencing of 16S rRNA and 18S rRNA genes to study bacterial and microbial eukaryotic communities and their co-occurrence patterns at the pelagic zone of Lake Baikal during a spring phytoplankton bloom. We found that microbes within one domain mostly correlated positively with each other and are highly interconnected. The highly connected taxa in co-occurrence networks were operational taxonomic units (OTUs) of Actinobacteria, Bacteroidetes, Alphaproteobacteria, and autotrophic and unclassified Eukaryota which might be analogous to microbial keystone taxa. Constrained correspondence analysis revealed the relationships of bacterial and microbial eukaryotic communities with geographical location.
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Affiliation(s)
- Ivan S Mikhailov
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 3, Ulan-Batorskaya, Irkutsk, Russia, 664033.
| | - Yulia R Zakharova
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 3, Ulan-Batorskaya, Irkutsk, Russia, 664033
| | - Yuri S Bukin
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 3, Ulan-Batorskaya, Irkutsk, Russia, 664033
| | - Yuri P Galachyants
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 3, Ulan-Batorskaya, Irkutsk, Russia, 664033
| | - Darya P Petrova
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 3, Ulan-Batorskaya, Irkutsk, Russia, 664033
| | - Maria V Sakirko
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 3, Ulan-Batorskaya, Irkutsk, Russia, 664033
| | - Yelena V Likhoshway
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 3, Ulan-Batorskaya, Irkutsk, Russia, 664033
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24
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Abstract
BACKGROUND Microbes are essentail components of all ecosystems because they drive many biochemical processes and act as primary producers. In freshwater ecosystems, the biodiversity in and the composition of microbial communities can be used as indicators for environmental quality. Recently, some environmental features have been identified that influence microbial ecosystems. However, the impact of human action on lake microbiomes is not well understood. This is, in part, due to the fact that environmental data is, albeit theoretically accessible, not easily available. RESULTS In this work, we present SEDE-GPS, a tool that gathers data that are relevant to the environment of an user-provided GPS coordinate. To this end, it accesses a list of public and corporate databases and aggregates the information in a single file, which can be used for further analysis. To showcase the use of SEDE-GPS, we enriched a lake microbial ecology sequencing dataset with around 18,000 socio-economic, climate, and geographic features. The sources of SEDE-GPS are public databases such as Eurostat, the Climate Data Center, and OpenStreetMap, as well as corporate sources such as Twitter. Using machine learning and feature selection methods, we were able to identify features in the data provided by SEDE-GPS that can be used to predict lake microbiome alpha diversity. CONCLUSION The results presented in this study show that SEDE-GPS is a handy and easy-to-use tool for comprehensive data enrichment for studies of ecology and other processes that are affected by environmental features. Furthermore, we present lists of environmental, socio-economic, and climate features that are predictive for microbial biodiversity in lake ecosystems. These lists indicate that human action has a major impact on lake microbiomes. SEDE-GPS and its source code is available for download at http://SEDE-GPS.heiderlab.de.
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Affiliation(s)
- Theodor Sperlea
- Faculty of Mathematics and Computer Science, University of Marburg, Hans-Meerwein-Str. 6, Marburg (Lahn), D-35032, Germany
| | - Stefan Füser
- Faculty of Mathematics and Computer Science, University of Marburg, Hans-Meerwein-Str. 6, Marburg (Lahn), D-35032, Germany
| | - Jens Boenigk
- Biodiversity Department, Center for Water and Environmental Research, University of Duisburg-Essen, Essen, D-45141, Germany
| | - Dominik Heider
- Faculty of Mathematics and Computer Science, University of Marburg, Hans-Meerwein-Str. 6, Marburg (Lahn), D-35032, Germany.
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25
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Bass D, Tikhonenkov DV, Foster R, Dyal P, Janouškovec J, Keeling PJ, Gardner M, Neuhauser S, Hartikainen H, Mylnikov AP, Berney C. Rhizarian 'Novel Clade 10' Revealed as Abundant and Diverse Planktonic and Terrestrial Flagellates, including Aquavolon n. gen. J Eukaryot Microbiol 2018; 65:828-842. [PMID: 29658156 PMCID: PMC6282753 DOI: 10.1111/jeu.12524] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 03/19/2018] [Accepted: 03/28/2018] [Indexed: 01/03/2023]
Abstract
Rhizarian ‘Novel Clade 10’ (NC10) is frequently detected by 18S rRNA gene sequencing studies in freshwater planktonic samples. We describe a new genus and two species of eukaryovorous biflagellate protists, Aquavolon hoantrani n. gen. n. sp. and A. dientrani n. gen. n. sp., which represent the first morphologically characterized members of NC10, here named Aquavolonida ord. nov. The slightly metabolic cells possess naked heterodynamic flagella, whose kinetosomes lie at a right angle to each other and are connected by at least one fibril. Unlike their closest known relative Tremula longifila, they rotate around their longitudinal axis when swimming and only very rarely glide on surfaces. Screening of a wide range of environmental DNA extractions with lineage‐specific PCR primers reveals that Aquavolonida consists of a large radiation of protists, which are most diversified in freshwater planktonic habitats and as yet undetected in marine environments. Earlier‐branching lineages in Aquavolonida include less frequently detected organisms from soils and freshwater sediments. The 18S rRNA gene phylogeny suggests that Aquavolonida forms a common evolutionary lineage with tremulids and uncharacterized ‘Novel Clade 12’, which likely represents one of the deepest lineages in the Rhizaria, separate from Cercozoa (Filosa), Endomyxa, and Retaria.
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Affiliation(s)
- David Bass
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK.,Centre for Environment, Fisheries and Aquaculture Science (Cefas), Barrack Road, The Nothe, Weymouth, DT4 8UB, UK
| | - Denis Victorovich Tikhonenkov
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, 152742, Russia.,Botany Department, University of British Columbia, Vancouver, BC, V6T1Z4, Canada
| | - Rachel Foster
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Patricia Dyal
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Jan Janouškovec
- Botany Department, University of British Columbia, Vancouver, BC, V6T1Z4, Canada.,Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, UK
| | - Patrick J Keeling
- Botany Department, University of British Columbia, Vancouver, BC, V6T1Z4, Canada
| | - Michelle Gardner
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Sigrid Neuhauser
- Institute of Microbiology, University of Innsbruck, Technikerstraße 25, Innsbruck, 6020, Austria
| | - Hanna Hartikainen
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Alexandre P Mylnikov
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, 152742, Russia
| | - Cédric Berney
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
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Banerji A, Bagley M, Elk M, Pilgrim E, Marinson J, Santo Domingo J. Spatial and temporal dynamics of a freshwater eukaryotic plankton community revealed via 18S rRNA gene metabarcoding. HYDROBIOLOGIA 2018; 818:71-86. [PMID: 31595089 PMCID: PMC6781235 DOI: 10.1007/s10750-018-3593-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
DNA metabarcoding is a sophisticated molecular tool that can enhance biological surveys of freshwater plankton communities by providing broader taxonomic coverage and, for certain groups, higher taxonomic resolution compared to morphological methods. We conducted 18S rRNA gene metabarcoding analyses on 214 water samples collected over a four-month period from multiple sites within a freshwater reservoir. We detected 1,314 unique operational taxonomic units that included various metazoans, protists, chlorophytes, and fungi. Alpha diversity differed among sites, suggesting local habitat variation linked to differing species responses. Strong temporal variation was detected at both daily and monthly scales. Diversity and relative abundance patterns for several protist groups (including dinoflagellates, ciliates, and cryptophytes) differed from arthropods (e.g., cladocerans and copepods), a traditional focus of plankton surveys. This suggests that the protists respond to different environmental dimensions and may therefore provide additional information regarding ecosystem status. Comparison of the sequence-based population survey data to conventional-based data revealed similar trends for taxa that were ranked among the most abundant in both approaches, although some groups were missing in each data set. These results highlight the potential benefit of supplementing conventional biological survey approaches with metabarcoding to obtain a more comprehensive understanding of freshwater plankton community structure and dynamics.
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Affiliation(s)
- A Banerji
- US Environmental Protection Agency, Cincinnati, USA
| | - M Bagley
- US Environmental Protection Agency, Cincinnati, USA
| | - M Elk
- US Environmental Protection Agency, Cincinnati, USA
| | - E Pilgrim
- US Environmental Protection Agency, Cincinnati, USA
| | - J Marinson
- US Environmental Protection Agency, Cincinnati, USA
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