scholarly journals Metabarcoding of unfractionated water samples relates phyto-, zoo- and bacterioplankton dynamics and reveals a single-taxon bacterial bloom

2016 ◽  
Author(s):  
Christian Wurzbacher ◽  
Katrin Attermeyer ◽  
Marie Therese Kettner ◽  
Clara Flintrop ◽  
Norman Warthmann ◽  
...  
Keyword(s):  
Water Samples ◽  
Temporal Dynamics ◽  
Plankton Community ◽  
Universal Primers ◽  
Lake Ecosystem ◽  
Holistic View ◽  
Bacterial Taxon ◽  
Dna Metabarcoding ◽  
Potential Interactions ◽  
Plankton Communities

SummaryMost studies of aquatic plankton focus on either macroscopic or microbial communities, and on either eukaryotes or prokaryotes. This separation is primarily for methodological reasons, but can overlook potential interactions among groups. We tested whether DNA-metabarcoding of unfractionated water samples with universal primers could be used to qualitatively and quantitatively study the temporal dynamics of the total plankton community in a shallow temperate lake. We found significant changes in the relative proportions of normalized sequence reads of eukaryotic and prokaryotic plankton communities over a three-month period in spring. Patterns followed the same trend as plankton estimates using traditional microscopic methods. We characterized the bloom of a conditionally rare bacterial taxon belonging toArcicella, which rapidly came to dominate the whole lake ecosystem and would have remained unnoticed without metabarcoding. Our data demonstrate the potential of universal DNA-metabarcoding applied to unfractionated samples for providing a more holistic view of plankton communities.

scholarly journals The Algicidal Bacterium Kordia algicida Shapes a Natural Plankton Community

2019 ◽  
Vol 85 (7) ◽  
Author(s):  
Arite Bigalke ◽  
Nils Meyer ◽  
Lydia Alkistis Papanikolopoulou ◽  
Karen Helen Wiltshire ◽  
Georg Pohnert
Keyword(s):  
North Sea ◽  
Algal Blooms ◽  
Plankton Community ◽  
Algicidal Bacteria ◽  
Important Species ◽  
Substantial Impact ◽  
The North ◽  
Algicidal Bacterium ◽  
The North Sea ◽  
Plankton Communities

ABSTRACT Plankton communities consist of complex microbial consortia that change over time. These fluctuations can be only partially explained by limiting resources. Biotic factors such as herbivores and pathogens also contribute to the control of algal blooms. Here we address the effects of algicidal bacteria on a natural plankton community in an indoor enclosure experiment. The algicidal bacteria, introduced into plankton taken directly from the North Sea during a diatom bloom, caused the rapid decline of the bloom-forming Chaetoceros socialis within only 1 day. The haptophyte Phaeocystis, in contrast, is resistant to the lytic bacteria and could benefit from the removal of the competitor, as indicated by an onset of a bloom in the treated enclosures. This cascading effect caused by the bacterial pathogen accelerated the succession of Phaeocystis, which bloomed with a delay of only several weeks in the in situ waters at Helgoland Roads in the North Sea. The algicidal bacteria can thus modulate the community within the limits of the abiotic and biotic conditions of the local environment. Implications of our findings for plankton ecosystem functioning are discussed. IMPORTANCE Plankton communities change on a seasonal basis in temperate systems, with distinct succession patterns; this is mainly due to algal species that have their optimal timing relative to environmental conditions. We know that bacterial populations are also instrumental in the decay and termination of phytoplankton blooms. Here, we describe algicidal bacteria as modulators of this important species succession. Upon treatment of a natural plankton consortium with an algicidal bacterium, we observed a strong shift in the phytoplankton community structure, compared to controls, resulting in formation of a succeeding Phaeocystis bloom. Blooms of this alga have a substantial impact on global biogeochemical and ecological cycles, as they are responsible for a substantial proportion of primary production during spring in the North Sea. We propose that one of the key factors influencing such community shifts may be algicidal bacteria.

scholarly journals PLANKTON COMMUNITY STRUCTURE OF TRADITIONAL AND INTENSIVE BRACKISHWATER PONDS IN PROBOLINGGO REGENCY, EAST JAVA PROVINCE

2016 ◽  
Vol 8 (1) ◽  
pp. 269-288
Author(s):  
. Utojo ◽  
Akhmad Mustafa
Keyword(s):  
Community Structure ◽  
Suspended Solids ◽  
Total Suspended Solids ◽  
Total Suspended Solid ◽  
Suspended Solid ◽  
Plankton Community ◽  
Cell Counting ◽  
Counting Method ◽  
Plankton Community Structure ◽  
Plankton Communities

This experiment aimed to determine the plankton community structure in intensive and traditional ponds of  Probolinggo Regency, East Java Province. Plankton collected with plankton net size of 60 μm and preserved with lugol 1%. Water qualities such as temperature, transparancy, salinity, dis-solved oxygen, pH, total organic matter, NO2-N, NO3-N, NH3-N, PO4-P, and total suspended solids were measured and analysed in this study. Planktons were identified using microscopy. Cells were counted using cell counting method. The results showed that in intensive pond we found 16 species of phytoplankton and 7 species of zooplankton with abundance 570-1.808 ind./L, while in traditional ponds, we found 10 species of phytoplankton and 3 species of  zooplankton with abundance  134-776 ind./L. The dominant species of phytoplankton in the intensive and traditional ponds were Navicula sp andNitzschia sp, each of Bacillariophyceae class with abundance of 423 ind./L and 198 ind./L, res-pectively. Zooplankton species in intensive pond was copepod sp, while in traditional  one was Oitho-na sp, each of Crustaceae class with abundance of  66 ind./L and 37 ind./L, respectively. Diversity and abundance of plankton in intensive pond was higher than in the traditional ponds. The water quality in intensive pond was optimal so that the response to the absorption of  N and P inorganic by phyto-plankton was quicker and more effective than in traditional pond producing an increase in plankton communities. The increase value of NO3-N and total suspended solids in intensive pond caused the in-crease abundance of Navicula sp.  The high value of NH3-N caused the abundance of Navicula sp to decline. The high values of dissolved oxygen, pH, total suspended solid, and NH3-N in traditional pond can decrease the Nitzschia sp abundance.  Keywords: plankton communities, intensive and traditional ponds, Probolinggo, East Java

scholarly journals Role of jellyfish in the plankton ecosystem revealed using a global ocean biogeochemical model

2021 ◽  
Vol 18 (4) ◽  
pp. 1291-1320
Author(s):  
Rebecca M. Wright ◽  
Corinne Le Quéré ◽  
Erik Buitenhuis ◽  
Sophie Pitois ◽  
Mark J. Gibbons
Keyword(s):  
Temporal Dynamics ◽  
Marine Ecosystem ◽  
Zooplankton Community ◽  
Ocean Model ◽  
Plankton Community ◽  
Global Ocean ◽  
Biogeochemical Model ◽  
Ocean Biogeochemical Model ◽  
Spatio Temporal ◽  
Plankton Community Structure

Abstract. Jellyfish are increasingly recognised as important components of the marine ecosystem, yet their specific role is poorly defined compared to that of other zooplankton groups. This paper presents the first global ocean biogeochemical model that includes an explicit representation of jellyfish and uses the model to gain insight into the influence of jellyfish on the plankton community. The Plankton Type Ocean Model (PlankTOM11) model groups organisms into plankton functional types (PFTs). The jellyfish PFT is parameterised here based on our synthesis of observations on jellyfish growth, grazing, respiration and mortality rates as functions of temperature and jellyfish biomass. The distribution of jellyfish is unique compared to that of other PFTs in the model. The jellyfish global biomass of 0.13 PgC is within the observational range and comparable to the biomass of other zooplankton and phytoplankton PFTs. The introduction of jellyfish in the model has a large direct influence on the crustacean macrozooplankton PFT and influences indirectly the rest of the plankton ecosystem through trophic cascades. The zooplankton community in PlankTOM11 is highly sensitive to the jellyfish mortality rate, with jellyfish increasingly dominating the zooplankton community as its mortality diminishes. Overall, the results suggest that jellyfish play an important role in regulating global marine plankton ecosystems across plankton community structure, spatio-temporal dynamics and biomass, which is a role that has been generally neglected so far.

scholarly journals PLANKTON COMMUNITY STRUCTURE OF TRADITIONAL AND INTENSIVE BRACKISHWATER PONDS IN PROBOLINGGO REGENCY, EAST JAVA PROVINCE

2016 ◽  
Vol 8 (1) ◽  
Author(s):  
. Utojo ◽  
Akhmad Mustafa
Keyword(s):  
Community Structure ◽  
Suspended Solids ◽  
Total Suspended Solids ◽  
Total Suspended Solid ◽  
Suspended Solid ◽  
Plankton Community ◽  
Cell Counting ◽  
Counting Method ◽  
Plankton Community Structure ◽  
Plankton Communities

<p><em>This experiment aimed to determine the plankton community structure in intensive and traditional ponds of  Probolinggo Regency, East Java Province. Plankton collected with plankton net size of 60 μm and preserved with lugol 1%. Water qualities such as temperature, transparancy, salinity, dis</em><em>-</em><em>solved oxygen, pH, total organic matter, NO<sub>2</sub>-N, NO<sub>3</sub>-N, NH<sub>3</sub>-N, PO<sub>4</sub>-P, and total suspended solids were measured and analysed in this study. Planktons were identified using microscopy. Cells were counted using cell counting method. The results showed that in intensive pond we found 16 species of phytoplankton and 7 species of zooplankton with abundance 570-1.808 ind./L, while in traditional ponds, we found 10 species of phytoplankton and 3 species of  zooplankton with abundance  134-776 ind./L. The dominant species of phytoplankton in the intensive and traditional ponds were Navicula sp andNitzschia sp, each of Bacillariophyceae class with abundance of 423 ind./L and 198 ind./L, res</em><em>-</em><em>pectively. Zooplankton species in intensive pond was copepod sp, while in traditional  one was Oitho</em><em>-</em><em>na sp, each of Crustaceae class with abundance of  66 ind./L and 37 ind./L, respectively. Diversity and abundance of plankton in intensive pond was higher than in the traditional ponds. The water quality in intensive pond was optimal so that the response to the absorption of  N and P inorganic by phyto</em><em>-</em><em>plankton was quicker and more effective than in traditional pond producing an increase in plankton communities. The increase value of NO<sub>3</sub>-N and total suspended solids in intensive pond caused the in</em><em>-</em><em>crease abundance of Navicula sp.  The high value of NH<sub>3</sub>-N caused the abundance of Navicula sp to decline. The high values of dissolved oxygen, pH, total suspended solid, and NH<sub>3</sub>-N in traditional pond can decrease the Nitzschia sp abundance.  </em></p><p><strong><em>Keywords:</em></strong><em> plankton communities, intensive and traditional ponds, Probolinggo, East Java </em></p>

scholarly journals Environmental DNA enables detection of terrestrial mammals from forest pond water

2016 ◽  
Author(s):  
Masayuki Ushio ◽  
Hisato Fukuda ◽  
Toshiki Inoue ◽  
Kobayashi Makoto ◽  
Osamu Kishida ◽  
...  
Keyword(s):  
Water Samples ◽  
Cervus Nippon ◽  
Environmental Dna ◽  
Terrestrial Ecosystems ◽  
Illumina Miseq ◽  
Pcr Primers ◽  
Pond Water ◽  
Universal Primers ◽  
Taxonomic Assignment ◽  
Terrestrial Mammals

Terrestrial animals must have frequent contact with water to maintain their lives, implying that environmental DNA (eDNA) originating from terrestrial animals should be detectable from places containing water in terrestrial ecosystems. Aiming to detect the presence of terrestrial mammals using forest water samples, we applied a set of universal PCR primers (MiMammal, a modified version of fish universal primers) for metabarcoding mammalian eDNA. After verifying the primers’ usefulness in silico and using water samples from zoo cages of animals with known species compositions, we collected five 500-ml water samples from ponds in two cool-temperate forests in Hokkaido, northern Japan. Using eDNA extracted from the water samples, we constructed amplicon libraries using MiMammal primers for Illumina MiSeq sequencing. MiMammal metabarcoding yielded a total of 75,214 reads, which we then subjected to data pre-processing and taxonomic assignment. We thereby detected species of mammals common to the sampling areas, including deer (Cervus nippon), mouse (Mus musculus), vole (Myodes rufocanus), raccoon (Procyon lotor), rat (Rattus norvegicus) and shrew (Sorex unguiculatus). Previous applications of the eDNA metabarcoding approach have mostly been limited to aquatic/semiaquatic systems, but the results presented here show that the approach is also promising even in forest mammal biodiversity surveys.

scholarly journals Struktur Komunitas Plankton Perairan Payau di Kecamatan Wedung Kabupaten Demak

2016 ◽  
Vol 18 (2) ◽  
pp. 89
Author(s):  
Isyarotuz Zakiyyah ◽  
Jafron Wasiq Hidayat ◽  
Fuad Muhammad
Keyword(s):  
Water Quality ◽  
Species Diversity ◽  
Quality Standards ◽  
Plankton Community ◽  
Natural Food ◽  
Brackish Waters ◽  
Copepod Nauplius ◽  
The Government ◽  
Plankton Communities ◽  
Analyze Data

Aquaculture are highly prioritized by the government to support the economy. Products from the aquaculture sector is also targeted as a source of income to the Indonesian country. Aquaculture needs to improve to manage water quality, especially plankton to support natural food of the fish. This study aims to examines structure of plankton community in the brackish waters of the District Wedung and then examines the water quality with environmental quality standards of water the cultivation. Research was conducted in February-April 2015. The method used to analyze data that plankton with uses keanekargaman index (H ') and the perataan index ( e ). The results showed that the number of species (genera) plankton obtained during research in the waters of the District Wedung was 45 species, these types consist of 37 species of phytoplankton and zooplankton 8 types. The most common plankton species found in all the stations were Fragillaria sp, Synedra ulna, Oscillatoria formosa and Copepod nauplius. Index of species diversity that existed at the District Wedung moderate to high waters with a range from 1.69 to 2.91 therefore a complex community and stability of the ecosystem were moderate to high. The evennes index ranged from 0.63 to 0.85. Water quality based on the pH, salinity, Turbidity, N, P and organic materials are less good for the cultivation so that the necessary processing on the pond so that according to the criteria of the quality standards of water quality. Keywords: structure of plankton communities, brackish waters, District Wedung

Proteolytic and glycolytic activities in size-fractionated surface water samples from an oligotrophic reservoir in relation to plankton communities

1999 ◽  
Vol 61 (4) ◽  
pp. 279 ◽  
Author(s):  
Mathilde Richardot ◽  
Didier Debroas ◽  
Antoine Thouvenot ◽  
Jean Claude Romagoux ◽  
Jean Louis Berthon ◽  
...  
Keyword(s):  
Surface Water ◽  
Water Samples ◽  
Surface Water Samples ◽  
Plankton Communities

scholarly journals Assessing the impact of the threatened crucian carp (Carassius carassius) on pond invertebrate diversity - a comparison of conventional and molecular tools

2020 ◽  
Author(s):  
Lynsey R. Harper ◽  
Lori Lawson Handley ◽  
Carl D. Sayer ◽  
Daniel S. Read ◽  
Marco Benucci ◽  
...  
Keyword(s):  
Water Samples ◽  
Crucian Carp ◽  
Conservation Management ◽  
Alpha Diversity ◽  
Carassius Carassius ◽  
Molecular Tools ◽  
Tissue Samples ◽  
Invertebrate Diversity ◽  
Dna Metabarcoding ◽  
The Impact

AbstractFishes stocked for recreation and angling can damage freshwater habitats and negatively impact biodiversity. The pond-associated crucian carp (Carassius carassius) is rare across Europe and stocked for conservation management in England, but impacts on pond biota are understudied. Freshwater invertebrates contribute substantially to aquatic biodiversity, encompassing many rare and endemic species, but their small size and high abundance complicates their assessment. Practitioners have employed sweep-netting and kick-sampling with microscopy (morphotaxonomy), but specimen size/quality and experience can bias identification. DNA and eDNA metabarcoding offer alternative means of invertebrate assessment. We compared invertebrate diversity in ponds (N = 18) with and without crucian carp using morphotaxonomic identification, DNA metabarcoding, and eDNA metabarcoding. Five 2-L water samples and 3-minute sweep-net samples were collected at each pond. Inventories produced by morphotaxonomic identification of netted samples, DNA metabarcoding of bulk tissue samples, and eDNA metabarcoding of water samples were compared. Alpha diversity was greatest with DNA or eDNA metabarcoding, depending on whether standard or unbiased methods were considered. DNA metabarcoding reflected morphotaxonomic identification, whereas eDNA metabarcoding produced markedly different communities. These complementary tools should be combined for comprehensive invertebrate assessment. Crucian carp presence minimally reduced alpha diversity in ponds, but positively influenced beta diversity through taxon turnover (i.e. ponds with crucian carp contained different invertebrates to fishless ponds). Crucian carp presence contributes to landscape-scale invertebrate diversity, supporting continued conservation management in England. Our results show that molecular tools can enhance freshwater invertebrate assessment and facilitate development of more accurate and ecologically effective pond management strategies.

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