scholarly journals Tracing the Origin of Planktonic Protists in an Ancient Lake

2020 ◽  
Vol 8 (4) ◽  
pp. 543 ◽  
Author(s):  
Nataliia V. Annenkova ◽  
Caterina R. Giner ◽  
Ramiro Logares
Keyword(s):  
Lake Baikal ◽  
Surface Waters ◽  
18S Rdna ◽  
Rapid Radiation ◽  
Evolutionary Diversification ◽  
Operational Taxonomic Units ◽  
Glacial Relicts ◽  
Multicellular Organisms ◽  
Species Flocks

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.

scholarly journals Tracing the Origin of Planktonic Protists in an Ancient Lake

2019 ◽  
Author(s):  
Nataliia V. Annenkova ◽  
Caterina R. Giner ◽  
Ramiro Logares
Keyword(s):  
Lake Baikal ◽  
Surface Waters ◽  
18S Rdna ◽  
Ancient Lake ◽  
Rapid Radiation ◽  
Evolutionary Diversification ◽  
Operational Taxonomic Units ◽  
Multicellular Organisms ◽  
Species Flocks

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. By using 18S rDNA metabarcoding we recovered 1,427 Operational Taxonomic Units (OTUs) belonging to protists populating surface waters (1-50 meters) and belonging to pico- and nano-plankton size fractions. The recovered communities resembled other lacustrine freshwater assemblages found elsewhere, especially the unclassified protists. However, our results suggest that a fraction of Baikal protists originated evolutionary recently from marine/brackish ancestors. 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 potential species flocks in Stramenopiles, Alveolata, Opisthokonta, Archaeplastida, Rhizaria and Hacrobia. Putative flocks predominated in Chrysophytes, which are highly diverse in Lake Baikal. Some of the species, especially those from these flocks, may be endemic from Lake Baikal, because their 18S rDNA differed > 10% from known DNA. Overall, our study points to novel diversity of planktonic protists in Lake Baikal, some of which may have emerged in situ after evolutionary diversification.

scholarly journals Performance of a Handheld Chlorophyll-a Fluorometer: Potential Use for Rapid Algae Monitoring

Water ◽  
2021 ◽  
Vol 13 (10) ◽  
pp. 1409
Author(s):  
Hamdhani Hamdhani ◽  
Drew E. Eppehimer ◽  
David Walker ◽  
Michael T. Bogan
Keyword(s):  
Chlorophyll A ◽  
Surface Waters ◽  
Harmful Algal Blooms ◽  
Algal Blooms ◽  
Water Quality Monitoring ◽  
Ambient Light ◽  
Calibration Equation ◽  
Field Samples ◽  
Potential Use

Chlorophyll-a measurements are an important factor in the water quality monitoring of surface waters, especially for determining the trophic status and ecosystem management. However, a collection of field samples for extractive analysis in a laboratory may not fully represent the field conditions. Handheld fluorometers that can measure chlorophyll-a in situ are available, but their performance in waters with a variety of potential light-interfering substances has not yet been tested. We tested a handheld fluorometer for sensitivity to ambient light and turbidity and compared these findings with EPA Method 445.0 using water samples obtained from two urban lakes in Tucson, Arizona, USA. Our results suggested that the probe was not sensitive to ambient light and performed well at low chlorophyll-a concentrations (<25 µg/L) across a range of turbidity levels (50–70 NTU). However, the performance was lower when the chlorophyll-a concentrations were >25 µg/L and turbidity levels were <50 NTU. To account for this discrepancy, we developed a calibration equation to use for this handheld fluorometer when field monitoring for potential harmful algal blooms in water bodies.

scholarly journals Environmental Sequencing Provides Reasonable Estimates of the Relative Abundance of Specific Picoeukaryotes

2016 ◽  
Vol 82 (15) ◽  
pp. 4757-4766 ◽  
Author(s):  
Caterina R. Giner ◽  
Irene Forn ◽  
Sarah Romac ◽  
Ramiro Logares ◽  
Colomban de Vargas ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
High Throughput ◽  
Relative Abundance ◽  
Ribosomal Dna ◽  
18S Rdna ◽  
High Throughput Sequencing ◽  
454 Sequencing ◽  
Epifluorescence Microscopy ◽  
Environmental Sequencing

ABSTRACTHigh-throughput sequencing (HTS) is revolutionizing environmental surveys of microbial diversity in the three domains of life by providing detailed information on which taxa are present in microbial assemblages. However, it is still unclear how the relative abundance of specific taxa gathered by HTS correlates with cell abundances. Here, we quantified the relative cell abundance of 6 picoeukaryotic taxa in 13 planktonic samples from 6 European coastal sites using epifluorescence microscopy on tyramide signal amplification-fluorescencein situhybridization preparations. These relative abundance values were then compared with HTS data obtained in three separate molecular surveys: 454 sequencing of the V4 region of the 18S ribosomal DNA (rDNA) using DNA and RNA extracts (DNA-V4 and cDNA-V4) and Illumina sequencing of the V9 region (cDNA-V9). The microscopic and molecular signals were generally correlated, indicating that a relative increase in specific 18S rDNA was the result of a large proportion of cells in the given taxa. Despite these positive correlations, the slopes often deviated from 1, precluding a direct translation of sequences to cells. Our data highlighted clear differences depending on the nucleic acid template or the 18S rDNA region targeted. Thus, the molecular signal obtained using cDNA templates was always closer to relative cell abundances, while the V4 and V9 regions gave better results depending on the taxa. Our data support the quantitative use of HTS data but warn about considering it as a direct proxy of cell abundances.IMPORTANCEDirect studies on marine picoeukaryotes by epifluorescence microscopy are problematic due to the lack of morphological features and due to the limited number and poor resolution of specific phylogenetic probes used in fluorescencein situhybridization (FISH) routines. As a consequence, there is an increasing use of molecular methods, including high-throughput sequencing (HTS), to study marine microbial diversity. HTS can provide a detailed picture of the taxa present in a community and can reveal diversity not evident using other methods, but it is still unclear what the meaning of the sequence abundance in a given taxon is. Our aim is to investigate the correspondence between the relative HTS signal and relative cell abundances in selected picoeukaryotic taxa. Environmental sequencing provides reasonable estimates of the relative abundance of specific taxa. Better results are obtained when using RNA extracts as the templates, while the region of 18S ribosomal DNA had different influences depending on the taxa assayed.

scholarly journals High resolution spatial transcriptome analysis by photo-isolation chemistry

2020 ◽  
Author(s):  
Mizuki Honda ◽  
Shinya Oki ◽  
Akihito Harada ◽  
Kazumitsu Maehara ◽  
Kaori Tanaka ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcriptome Analysis ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Transcriptome Profiling ◽  
Tissue Sections ◽  
Complex Functions ◽  
Multicellular Organisms

ABSTRACTIn multicellular organisms, individual cells are characterized by their gene expression profiles and the spatial interactions among cells enable the elaboration of complex functions. Expression profiling in spatially defined regions is crucial to elucidate cell interactions and functions. Here, we established a transcriptome profiling method coupled with photo-isolation chemistry (PIC) that allows the determination of expression profiles specifically from photo-irradiated regions of whole tissues. PIC uses photo-caged oligodeoxynucleotides for in situ reverse transcription. After photo-irradiation of limited areas, gene expression was detected from at least 10 cells in the tissue sections. PIC transcriptome analysis detected genes specifically expressed in small distinct areas of the mouse embryo. Thus, PIC enables transcriptome profiles to be determined from limited regions at a spatial resolution up to the diffraction limit.

scholarly journals Impact of ocean acidification and elevated temperatures on early juveniles of the polar shelled pteropod <i>Limacina helicina</i>: mortality, shell degradation, and shell growth

2010 ◽  
Vol 7 (6) ◽  
pp. 8177-8214 ◽  
Author(s):  
S. Lischka ◽  
J. Büdenbender ◽  
T. Boxhammer ◽  
U. Riebesell
Keyword(s):  
Ocean Acidification ◽  
Surface Waters ◽  
Elevated Temperatures ◽  
Shell Growth ◽  
Shell Diameter ◽  
Partial Pressures ◽  
Limacina Helicina ◽  
Different Temperatures ◽  
Arctic Surface

Abstract. Due to their aragonitic shell thecosome pteropods may be particularly vulnerable to ocean acidification driven by anthropogenic CO2 emissions. This applies specifically to species inhabiting Arctic surface waters that are projected to become locally undersaturated with respect to aragonite as early as 2016. This study investigated the effects of rising pCO2 partial pressures and elevated temperature on pre-winter juveniles of the polar pteropod Limacina helicina. After a 29 days experiment in September/October 2009 at three different temperatures and under pCO2 scenarios projected for this century, mortality, shell degradation, shell diameter and shell increment were investigated. Temperature and pCO2 had a significant effect on mortality, but temperature was the overriding factor. Shell diameter, shell increment and shell degradation were significantly impacted by pCO2 but not by temperature. Mortality was 46% higher at 8 °C compared to 3 °C (in situ), and 14% higher at 1100 μatm CO2 as compared to 230 μatm CO2. Shell diameter and increment were reduced by 10% and 12% at 1100 μatm CO2 as compared to 230 μatm CO2, respectively, and shell degradation was 41% higher at elevated compared to ambient pCO2 partial pressures. We conclude that pre-winter juveniles will be negatively affected by both rising temperature and pCO2 which may result in a possible abundance decline of the overwintering population, the basis for next year's reproduction.

Iron plays a role in nitrate drawdown by phytoplankton in Lake Erie surface waters as observed in lake-wide assessments

2012 ◽  
Vol 69 (2) ◽  
pp. 369-381 ◽  
Author(s):  
Sonya M. Havens ◽  
Christel S. Hassler ◽  
Rebecca L. North ◽  
Stephanie J. Guildford ◽  
Greg Silsbe ◽  
...  
Keyword(s):  
Surface Waters ◽  
Thermal Stratification ◽  
Lake Erie ◽  
Phytoplankton Community ◽  
Sampling Depth ◽  
Phytoplankton Pigment ◽  
Chl A ◽  
Dissolved Iron ◽  
Continuous Surface

Phytoplankton interactions with iron (Fe) were examined in surface waters of Lake Erie during summer thermal stratification. Lake-wide sampling in June and September 2005 was conducted using a continuous surface water sampler (1 m sampling depth) and in July at 18 hydrographic stations (5 m sampling depth). In situ measurements of photosynthetic efficiency (maximum quantum yield of photosystem II) and phytoplankton community composition were measured using fast repetition rate fluorometry and a phytoplankton pigment-specific fluorometer, respectively, during June and September. High ratios (73%–85%) of intracellular Fe to particulate Fe coincident with increases in chlorophyll a (Chl a) concentrations in the western and central basins in June and July imply that the majority of Fe in these regions was associated with intracellular pools. Correlations between intracellular Fe and Chl a were frequently observed when Heterokontophyta and Pyrrophyta dominated the phytoplankton community. Assimilation of Fe by the phytoplankton strongly influenced its partitioning between the dissolved and particulate phase. Dissolved iron (<0.45 µm) concentrations were proportional to Chl a concentrations and both dissolved iron and Chl a were inversely proportional to nitrate concentrations in July and September, suggesting that dissolved iron influenced both nitrate drawdown and Chl a concentrations in Lake Erie surface waters in summer.

Lake-wide assessment of microplastics in the surface waters of Lake Baikal, Siberia

Limnology ◽  
2021 ◽  
Author(s):  
Marianne V. Moore ◽  
Masumi Yamamuro ◽  
Oleg A. Timoshkin ◽  
Alena A. Shirokaya ◽  
Yutaka Kameda
Keyword(s):  
Lake Baikal ◽  
Surface Waters

Standing Waters, Especially Ancient Lakes

2020 ◽  
pp. 280-302
Author(s):  
Kristina von Rintelen ◽  
Patricio De los Ríos ◽  
Thomas von Rintelen
Keyword(s):  
Species Diversity ◽  
Ancient Lakes ◽  
Ecological Data ◽  
Widespread Species ◽  
Research Priority ◽  
Trophic Morphology ◽  
Molecular Phylogenetic ◽  
Standing Waters ◽  
Species Flocks

Crustacea in standing waters are a diverse taxonomic assemblage with representatives in all available habitats from the benthic zone to the pelagial in larger water bodies. While most higher taxa are widespread and occasionally cosmopolitan, this is only partially true at the genus and species level. The crustacean fauna of geologically young lakes, or ponds, is characterized by widespread species that are not even necessarily restricted to lentic habitats. These species generally have good to excellent dispersal capabilities, especially those dwelling in ephemeral habitats. Small groups such as branchiopods and copepods dominate under these conditions among obligate still-water dwellers. In contrast, endemism and occasional striking adaptations are the hallmarks of crustacean species flocks, especially in the radiations of amphipods, decapods, and ostracods in the fewer than 10 ancient lakes worldwide. These radiations have arisen in situ through the diversification of unspecialized ancestors. All comparatively well-studied radiations for which molecular phylogenetic, taxonomic, and ecological data are available show particular adaptations of trophic morphology correlated to specific habitats. Prime examples are the species flocks of amphipods in Lake Baikal and of atyid shrimps in Lake Tanganyika and in two Indonesian lakes. These groups have most likely evolved through adaptive radiation. A major challenge for research on crustaceans in ancient lakes, and in standing waters generally outside Europe and North America, is the lack of basic data from species diversity to genetics for many, if not most, taxa. Getting a grip on species diversity, distributions, ecology, and, at a different level, genomics will be a research priority for coming decades.

scholarly journals Bacterial Symbionts of the Brown Planthopper, Nilaparvata lugens (Homoptera: Delphacidae)

2010 ◽  
Vol 76 (6) ◽  
pp. 1740-1745 ◽  
Author(s):  
Ming Tang ◽  
Lu Lv ◽  
Shengli Jing ◽  
Lili Zhu ◽  
Guangcun He
Keyword(s):  
Brown Planthopper ◽  
Nilaparvata Lugens ◽  
Rrna Gene ◽  
Rice Varieties ◽  
Ovipositor Sheath ◽  
Operational Taxonomic Units ◽  
Metaseiulus Occidentalis ◽  
High Virulence ◽  
Gene Libraries

ABSTRACT The brown planthopper (Nilaparvata lugens Stål), the most destructive pest of rice, has been identified, including biotypes with high virulence towards previously resistant rice varieties. There have also been many reports of a yeast-like symbiont of N. lugens, but little is known about the bacterial microbes. In this study, we examined the bacterial microbes in N. lugens and identified a total of 18 operational taxonomic units (OTUs) representing four phyla (Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes) by sequencing and analyzing 16S rRNA gene libraries obtained from three populations of N. lugens, which were maintained on the rice varieties TN1, Mudgo, and ASD7. Several of the OTUs were similar to previously reported secondary symbionts of other insects, including an endosymbiont of the psyllid Glycapsis brimblecombei, an Asaia sp. found in the mosquito Anopheles stephensi, and Wolbachia, found in the mite Metaseiulus occidentalis. However, the species and numbers of the detected OTUs differed substantially among the N. lugens populations. Further, in situ hybridization analysis using digoxigenin-labeled probes indicated that OTU 1 was located in hypogastrium tissues near the ovipositor and ovary in biotype 1 insects, while OTU 2 was located in the front of the ovipositor sheath in biotype 2 insects. In addition, masses of bacterium-like organisms were observed in the tubes of salivary sheaths in rice plant tissues that the insects had fed upon. The results provide indications of the diversity of the bacterial microbes harbored by the brown planthopper and of possible associations between specific bacterial microbes and biotypes of N. lugens.

scholarly journals In situ calibration of polar organic chemical integrative sampler (POCIS) for monitoring of pharmaceuticals in surface waters

2021 ◽  
Vol 269 ◽  
pp. 116121
Author(s):  
Branislav Vrana ◽  
Jakub Urík ◽  
Ganna Fedorova ◽  
Helena Švecová ◽  
Kateřina Grabicová ◽  
...  
Keyword(s):  
Surface Waters ◽  
Organic Chemical ◽  
In Situ Calibration
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