scholarly journals Diversity of dinoflagellate assemblages in coastal temperate and offshore tropical waters of Australia

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Tahnee Manning ◽  
Arjun Venkatesh Thilagaraj ◽  
Dmitri Mouradov ◽  
Richard Piola ◽  
Clare Grandison ◽  
...  
Keyword(s):  
Dissolved Oxygen ◽  
High Throughput ◽  
Harmful Algal Blooms ◽  
Algal Blooms ◽  
High Throughput Sequencing ◽  
Environmental Parameters ◽  
Marine Phytoplankton ◽  
Tropical Waters ◽  
Total Sequence ◽  
Phytoplankton Communities

Abstract Background Dinoflagellates are a ubiquitous and ecologically important component of marine phytoplankton communities, with particularly notable species including those associated with harmful algal blooms (HABs) and those that bioluminesce. High-throughput sequencing offers a novel approach compared to traditional microscopy for determining species assemblages and distributions of dinoflagellates, which are poorly known especially in Australian waters. Results We assessed the composition of dinoflagellate assemblages in two Australian locations: coastal temperate Port Phillip Bay and offshore tropical waters of Davies Reef (Great Barrier Reef). These locations differ in certain environmental parameters reflecting latitude as well as possible anthropogenic influences. Molecular taxonomic assessment revealed more species than traditional microscopy, and it showed statistically significant differences in dinoflagellate assemblages between locations. Bioluminescent species and known associates of HABs were present at both sites. Dinoflagellates in both areas were mainly represented by the order Gymnodiniales (66%—82% of total sequence reads). In the warm waters of Davies Reef, Gymnodiniales were equally represented by the two superclades, Gymnodiniales sensu stricto (33%) and Gyrodinium (34%). In contrast, in cooler waters of Port Phillip Bay, Gymnodiniales was mainly represented by Gyrodinium (82%). In both locations, bioluminescent dinoflagellates represented up to 0.24% of the total sequence reads, with Protoperidinium the most abundant genus. HAB-related species, mainly represented by Gyrodinium, were more abundant in Port Phillip Bay (up to 47%) than at Davies Reef (28%), potentially reflecting anthropogenic influence from highly populated and industrial areas surrounding the bay. The entire assemblage of dinoflagellates, as well as the subsets of HAB and bioluminescent species, were strongly correlated with water quality parameters (R2 = 0.56–0.92). Significant predictors differed between the subsets: HAB assemblages were explained by salinity, temperature, dissolved oxygen, and total dissolved solids; whereas, bioluminescent assemblages were explained only by salinity and dissolved oxygen, and had greater variability. Conclusion High-throughput sequencing and genotyping revealed greater diversity of dinoflagellate assemblages than previously known in both subtropical and temperate Australian waters. Significant correlations of assemblage structure with environmental variables suggest the potential for explaining the distribution and composition of both HAB species and bioluminescent species.

scholarly journals Asynchrony of Gambierdiscus spp. Abundance and Toxicity in the U.S. Virgin Islands: Implications for Monitoring and Management of Ciguatera

Toxins ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 413
Author(s):  
Justin D. Liefer ◽  
Mindy L. Richlen ◽  
Tyler B. Smith ◽  
Jennifer L. DeBose ◽  
Yixiao Xu ◽  
...  
Keyword(s):  
Harmful Algal Blooms ◽  
Algal Blooms ◽  
Environmental Parameters ◽  
Virgin Islands ◽  
Coastal Communities ◽  
Trophic Levels ◽  
Us Virgin Islands ◽  
Benthic Dinoflagellates ◽  
The Mean ◽  
The U.S

Ciguatera poisoning (CP) poses a significant threat to ecosystem services and fishery resources in coastal communities. The CP-causative ciguatoxins (CTXs) are produced by benthic dinoflagellates including Gambierdiscus and Fukuyoa spp., and enter reef food webs via grazing on macroalgal substrates. In this study, we report on a 3-year monthly time series in St. Thomas, US Virgin Islands where Gambierdiscus spp. abundance and Caribbean-CTX toxicity in benthic samples were compared to key environmental factors, including temperature, salinity, nutrients, benthic cover, and physical data. We found that peak Gambierdiscus abundance occurred in summer while CTX-specific toxicity peaked in cooler months (Feb–May) when the mean water temperatures were approximately 26–28 °C. These trends were most evident at deeper offshore sites where macroalgal cover was highest year-round. Other environmental parameters were not correlated with the CTX variability observed over time. The asynchrony between Gambierdiscus spp. abundance and toxicity reflects potential differences in toxin cell quotas among Gambierdiscus species with concomitant variability in their abundances throughout the year. These results have significant implications for monitoring and management of benthic harmful algal blooms and highlights potential seasonal and highly-localized pulses in reef toxin loads that may be transferred to higher trophic levels.

Implementation of Self-Organizing Maps (SOM) to analyses of environmental parameters and phytoplankton biomass in a macrotidal estuary and artificial lake

2012 ◽  
Vol 93 (1) ◽  
pp. 1-12 ◽  
Author(s):  
Roksana Jahan ◽  
Hyu Chang Choi ◽  
Young Seuk Park ◽  
Young Cheol Park ◽  
Ji Ho Seo ◽  
...  
Keyword(s):  
Phytoplankton Biomass ◽  
Algal Blooms ◽  
Suspended Solids ◽  
Inorganic Nitrogen ◽  
Environmental Parameters ◽  
Ecological Data ◽  
Self Organizing Maps ◽  
Macrotidal Estuary ◽  
Phytoplankton Communities ◽  
Self Organizing

Self-Organizing Maps (SOM) have been used for patterning and visualizing ten environmental parameters and phytoplankton biomass in a mactrotidal (>10 m) Gyeonggi Bay and artificial Shihwa Lake during 1986–2004. SOM segregated study areas into four groups and ten subgroups. Two strikingly alternative states are frequently observed: the first is a diverse non-eutrophic state designated by three groups (SOM 1–3), and the second is a eutrophic state (SOM 4: Shihwa Lake and Upper Gyeonggi Bay; summer season) characterized by enhanced nutrients (3 mg l−1 dissolved inorganic nitrogen, 0.1 mg l−1 PO4) that act as a signal and response to that signal as algal blooms (24 µg chlorophyll-a l−1). Bloom potential in response to nitrification is affiliated with high temperature (r = 0.26), low salinity (r = −0.40) and suspended solids (r = –0.27). Moreover, strong stratification in the Shihwa Lake has accelerated harmful algal blooms and hypoxia. The non-eutrophic states (SOM 1–3) are characterized by macro-tidal estuaries exhibiting a tolerance to pollution with nitrogen-containing nutrients and retarding any tendency toward stratification. SOM 1 (winter) is more distinct from SOM 4 due to higher suspended solids (>50 mg l−1) caused by resuspension that induces light limitation and low chlorophyll-a (<5 µg l−1). In addition, eutrophication-induced shifts in phytoplankton communities are noticed during all the seasons in Gyeonggi Bay. Overall, SOM showed high performance for visualization and abstraction of ecological data and could serve as an efficient ecological map that can specify blooming regions and provide a comprehensive view on the eutrophication process in a macrotidal estuary.

scholarly journals Composition and predictive functional analysis of bacterial communities in the surface seawater of the Changjiang Estuary

2017 ◽  
Author(s):  
Dong-Mei Wu ◽  
Jian-Xin Wang ◽  
Xiao-Hui Liu ◽  
Ying-Ping Fan ◽  
Ran Jiang ◽  
...  
Keyword(s):  
Dissolved Oxygen ◽  
Microbial Communities ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Carbon Fixation ◽  
Oxygen Demand ◽  
Environmental Parameters ◽  
Changjiang Estuary ◽  
Surface Seawater ◽  
The Changjiang Estuary

The objective of this study was to characterize the structure and function of microbial communities in surface seawater from the Changjiang Estuary and adjacent areas, China. Sample water was collected at 12 sites and environmental parameters were measured. Community structure was analyzed using high-throughput sequencing of 16S rDNA genes. Predictive metagenomic approach was used to predict the function of bacterial communities. Result showed that sample site A0102 had the highest bacterial abundance and diversity. The heatmap indicated that different samples could be clustered into six groups. Phylogenetic analysis showed that Proteobacteria was the predominant phylum in all samples, followed by Bacteroidetes and Actinobacteria. Alphaproteobacteria and Gammaproteobacteria were the dominant classes. The analysis of predictive metagenomic showed carbon fixation pathways in prokaryotes, nitrogen metabolism, carbon fixation in photosynthetic organisms, photosynthesis and polycyclic aromatic hydrocarbon degradation were enriched in all samples. Redundancy analysis (RDA) identified that dissolved oxygen (DO) and PO43– concentration had positive correlations with the bacterial communities while chemical oxygen demand (COD), dissolved oxygen (DO) and PO43– concentration were significantly associated with microbial functional diversity. This study adds to our knowledge of functional and taxonomic composition of microbial communities.

Nutrient-related selection mechanisms in marine phytoplankton communities and the impact of eutrophication on the planktonic food web

1995 ◽  
Vol 32 (4) ◽  
pp. 63-75 ◽  
Author(s):  
R. Riegman
Keyword(s):  
Algal Blooms ◽  
Algal Biomass ◽  
Resource Competition ◽  
Water Quality Management ◽  
Algal Species ◽  
Marine Phytoplankton ◽  
Commercial Fish ◽  
N Limitation ◽  
Phytoplankton Communities ◽  
The Impact

A general increase in nutrient discharges during the last few decades has caused various changes in the algal community structure along the European continental coast. Coincidentally and maybe consequently, the foodweb structure and functioning has altered in local areas causing various phenomena like oxygen depletion, mortality of groups of organisms, foam on beaches, and an increase in the productivity of benthic communities and some commercial fish species. The observed increases in algal biomass and shifts in species composition are discussed in relation to the involved key mechanisms: resource competition and selective grazing. Along the Dutch coastal zone of the North Sea eutrophication has caused a doubling of the yearly averaged algal biomass during the past three decades. The sudden appearance of Phaeocystis summer blooms coincided with a shift from P-limitation towards N-limitation in the Dutch coastal area due to a stronger increase in P-discharge relative to the increase in N-discharge. Competition experiments in continuous cultures showed Phaeocystis to become dominant under N-limitation. Additionally, the large Phaeocystis colonies, which can reach a diameter up to one centimetre, escape from microzooplankton grazing. A computer model is presented which demonstrates a shift from bottom-up towards top-down control if the pelagic environment becomes eutrophicated. Implementation of this concept in a size-differential phytoplankton control model generates the prediction that algal blooms are dominated by species that escape from grazing by those zooplankton species which have a high potential numerical response. In marine environments these are microzooplankton species. These organisms mainly feed on cyanobacteria, prochlorophytes and some nano-algal species. One of the consequences for foodweb structure and the carbon fluxes in marine foodwebs is that eutrophication will lead to the dominance of poorly edible algal species. Eutrophication favours the downward transport of carbon and nutrients towards the sediments not only due to higher algal biomasses but also as a consequence of a shift towards larger algal species with higher sedimentation characteristics. An example is given how these new insights can be used for water quality management purposes.

scholarly journals Composition and predictive functional analysis of bacterial communities in the surface seawater of the Changjiang Estuary

2017 ◽  
Author(s):  
Dong-Mei Wu ◽  
Jian-Xin Wang ◽  
Xiao-Hui Liu ◽  
Ying-Ping Fan ◽  
Ran Jiang ◽  
...  
Keyword(s):  
Dissolved Oxygen ◽  
Microbial Communities ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Carbon Fixation ◽  
Oxygen Demand ◽  
Environmental Parameters ◽  
Changjiang Estuary ◽  
Surface Seawater ◽  
The Changjiang Estuary

The objective of this study was to characterize the structure and function of microbial communities in surface seawater from the Changjiang Estuary and adjacent areas, China. Sample water was collected at 12 sites and environmental parameters were measured. Community structure was analyzed using high-throughput sequencing of 16S rDNA genes. Predictive metagenomic approach was used to predict the function of bacterial communities. Result showed that sample site A0102 had the highest bacterial abundance and diversity. The heatmap indicated that different samples could be clustered into six groups. Phylogenetic analysis showed that Proteobacteria was the predominant phylum in all samples, followed by Bacteroidetes and Actinobacteria. Alphaproteobacteria and Gammaproteobacteria were the dominant classes. The analysis of predictive metagenomic showed carbon fixation pathways in prokaryotes, nitrogen metabolism, carbon fixation in photosynthetic organisms, photosynthesis and polycyclic aromatic hydrocarbon degradation were enriched in all samples. Redundancy analysis (RDA) identified that dissolved oxygen (DO) and PO43– concentration had positive correlations with the bacterial communities while chemical oxygen demand (COD), dissolved oxygen (DO) and PO43– concentration were significantly associated with microbial functional diversity. This study adds to our knowledge of functional and taxonomic composition of microbial communities.

scholarly journals Consistency between high throughput sequencing and microscopy-based morphological characterization of phytoplankton communities

2021 ◽  
Vol 4 ◽  
Author(s):  
Kristiina Vuorio ◽  
Anita Mäki ◽  
Pauliina Salmi ◽  
Sanni Aalto ◽  
Marja Tiirola ◽  
...  
Keyword(s):  
Community Composition ◽  
High Throughput ◽  
Copy Number ◽  
High Throughput Sequencing ◽  
Ecological Status ◽  
Boreal Lakes ◽  
Reliable Estimate ◽  
Rrna Gene ◽  
Eukaryotic Phytoplankton ◽  
Phytoplankton Communities

Thus far, the phytoplankton community composition analyses, used e.g. monitoring and assessment of the ecological status of water bodies, are based on time-consuming and expertise-demanding light microscopy analyses. Currently, DNA-based molecular tools are being developed to replace microscopy-based analyses. Although most of the DNA is expected to be found in living cells, long-lasting DNA in damaged cells or soluble extracellular or relic DNA can make up a large proportion of the total DNA in water samples. DNA-based phytoplankton analysis has been shown to be affected by the huge variation in the copy number of the rRNA gene between phytoplankton species (Mäki et al. 2017). On the contrary, RNA is present only in living organisms and reflects active protein synthesis. Therefore, RNA-based methods can provide a more reliable estimate of community composition. The large copy number variation of ribosomal genes and the absence of universal primers for simultaneous amplification of cyanobacterial and eukaryotic phytoplankton genes hinder the application of DNA-based molecular methods. We applied a directional random-primed high throughput sequencing (HTS) approach (Mäki and Tiirola 2018) to analyse 16S and 18S rRNA community structures of 83 boreal lakes in Finland, Northern Europe. With the method it was possible to simultaneously amplify all groups of aquatic microorganisms in addition to cyanobacteria and eukaryotic phytoplankton. A comparison between microscopy and HTS showed that the relative phylum (Fig. 0) and class level abundances of eukaryotic phytoplankton and order level abundances of cyanobacteria were consistent between the methods, despite that the HTS method overestimated the relative abundance of cyanobacteria. However, correspondence was low at genus and species level, mainly due to the lack of reference library sequences. HTS revealed more genera and was able to differentiate cryptic genera lacking morphological characteristics, but microscopy revealed a longer list of species (Vuorio et al. 2020). The RNA-based method applied showed potential, but it is not yet able to replace microscopy, mainly due to the lack of full length 16S and 18S sequences in the reference libraries. The main advantage of the method is that it is not limited to phytoplankton, but can be applied to simultaneous investigation of the total composition of microbes, including all bacteria, protists, ciliates, rotifers and zooplankton.

scholarly journals Culture-Dependent and Amplicon Sequencing Approaches Reveal Diversity and Distribution of Black Fungi in Antarctic Cryptoendolithic Communities

2021 ◽  
Vol 7 (3) ◽  
pp. 213
Author(s):  
Laura Selbmann ◽  
Gerardo A. Stoppiello ◽  
Silvano Onofri ◽  
Jason E. Stajich ◽  
Claudia Coleine
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Physical Stability ◽  
Environmental Parameters ◽  
Sun Exposure ◽  
Amplicon Sequencing ◽  
Life Forms ◽  
Black Fungi ◽  
The Antarctic ◽  
Culture Dependent

In the harshest environmental conditions of the Antarctic desert, normally incompatible with active life, microbes are adapted to exploit the cryptoendolithic habitat (i.e., pore spaces of rocks) and represent the predominant life-forms. In the rocky niche, microbes take advantage of the thermal buffering, physical stability, protection against UV radiation, excessive solar radiation, and water retention—of paramount importance in one of the driest environments on Earth. In this work, high-throughput sequencing and culture-dependent approaches have been combined, for the first time, to untangle the diversity and distribution of black fungi in the Antarctic cryptoendolithic microbial communities, hosting some of the most extreme-tolerant microorganisms. Rock samples were collected in a vast area, along an altitudinal gradient and opposite sun exposure—known to influence microbial diversity—with the aim to compare and integrate results gained with the two approaches. Among black fungi, Friedmanniomyces endolithicus was confirmed as the most abundant taxon. Despite the much stronger power of the high-throughput sequencing, several species were not retrieved with DNA sequencing and were detectable by cultivation only. We conclude that both culture-dependent and -independent analyses are needed for a complete overview of black fungi diversity. The reason why some species remain undetectable with molecular methods are speculated upon. The effect of environmental parameters such as sun exposure on relative abundance was clearer if based on the wider biodiversity detected with the molecular approach.

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