scholarly journals Carbon Dioxide Concentration Mechanisms in Natural Populations of Marine Diatoms: Insights From Tara Oceans

2021 ◽  
Vol 12 ◽  
Author(s):  
Juan José Pierella Karlusich ◽  
Chris Bowler ◽  
Haimanti Biswas
Keyword(s):  
Phosphoenolpyruvate Carboxykinase ◽  
Environmental Variability ◽  
Natural Populations ◽  
Size Fraction ◽  
Carbon Dioxide Concentration ◽  
Molecular Data ◽  
Rubisco Activase ◽  
Nutrient Concentrations ◽  
Marine Diatoms ◽  
Environmental Correlations

Marine diatoms, the most successful photoautotrophs in the ocean, efficiently sequester a significant part of atmospheric CO2 to the ocean interior through their participation in the biological carbon pump. However, it is poorly understood how marine diatoms fix such a considerable amount of CO2, which is vital information toward modeling their response to future CO2 levels. The Tara Oceans expeditions generated molecular data coupled with in situ biogeochemical measurements across the main ocean regions, and thus provides a framework to compare diatom genetic and transcriptional flexibility under natural CO2 variability. The current study investigates the interlink between the environmental variability of CO2 and other physicochemical parameters with the gene and transcript copy numbers of five key enzymes of diatom CO2 concentration mechanisms (CCMs): Rubisco activase and carbonic anhydrase (CA) as part of the physical pathway, together with phosphoenolpyruvate carboxylase, phosphoenolpyruvate carboxykinase, and malic enzyme as part of the potential C4 biochemical pathway. Toward this aim, we mined >200 metagenomes and >220 metatranscriptomes generated from samples of the surface layer of 66 globally distributed sampling sites and corresponding to the four main size fractions in which diatoms can be found: 0.8–5 μm, 5–20 μm, 20–180 μm, and 180–2,000 μm. Our analyses revealed that the transcripts for the enzymes of the putative C4 biochemical CCM did not in general display co-occurring profiles. The transcripts for CAs were the most abundant, with an order of magnitude higher values than the other enzymes, thus implying the importance of physical CCMs in diatom natural communities. Among the different classes of this enzyme, the most prevalent was the recently characterized iota class. Consequently, very little information is available from natural diatom assemblages about the distribution of this class. Biogeographic distributions for all the enzymes show different abundance hotspots according to the size fraction, pointing to the influence of cell size and aggregation in CCMs. Environmental correlations showed a complex pattern of responses to CO2 levels, total phytoplankton biomass, temperature, and nutrient concentrations. In conclusion, we propose that biophysical CCMs are prevalent in natural diatom communities.

scholarly journals Variance additivity of genetic populational parameter estimates obtained through bootstrapping

2003 ◽  
Vol 60 (1) ◽  
pp. 97-103 ◽  
Author(s):  
Luciana Aparecida Carlini-Garcia ◽  
Roland Vencovsky ◽  
Alexandre Siqueira Guedes Coelho
Keyword(s):  
Bootstrap Method ◽  
Natural Populations ◽  
Molecular Data ◽  
Fixation Index ◽  
Parameter Estimates ◽  
Genetic Population ◽  
Relative Contribution ◽  
Population Structure Analysis ◽  
Resampling Procedure ◽  
Variance Estimates

Studying the genetic structure of natural populations is very important for conservation and use of the genetic variability available in nature. This research is related to genetic population structure analysis using real and simulated molecular data. To obtain variance estimates of pertinent parameters, the bootstrap resampling procedure was applied over different sampling units, namely: individuals within populations (I), populations (P), and individuals and populations simultaneously (I, P). The considered parameters were: the total fixation index (F or F IT), the fixation index within populations (f or F IS) and the divergence among populations or intrapopulation coancestry (theta or F ST). The aim of this research was to verify if the variance estimates of <IMG SRC="/img/fbpe/sa/v60n1/14549x09.gif">, <IMG SRC="/img/fbpe/sa/v60n1/14549x10.gif">and <IMG SRC="/img/fbpe/sa/v60n1/14549x11.gif">, found through the resampling over individuals and populations simultaneously (I, P), correspond to the sum of the respective variance estimates obtained from separated resampling over individuals and populations (I+P). This equivalence was verified in all cases, showing that the total variance estimate of <IMG SRC="/img/fbpe/sa/v60n1/14549x09.gif">, <IMG SRC="/img/fbpe/sa/v60n1/14549x10.gif">and <IMG SRC="/img/fbpe/sa/v60n1/14549x11.gif">can be obtained summing up the variances estimated for each source of variation separately. Results also showed that this facilitates the use of the bootstrap method on data with hierarchical structure and opens the possibility of obtaining the relative contribution of each source of variation to the total variation of estimated parameters.

scholarly journals A preliminary survey of zoantharian endosymbionts shows high genetic variation over small geographic scales on Okinawa-jima Island, Japan

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3740 ◽  
Author(s):  
Hatsuko Noda ◽  
John Everett Parkinson ◽  
Sung-Yin Yang ◽  
James Davis Reimer
Keyword(s):  
Internal Transcribed Spacer ◽  
Environmental Variability ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Species Level ◽  
Sea Surface ◽  
Fine Scale ◽  
Clade C ◽  
Symbiotic Dinoflagellates ◽  
The Common

Symbiotic dinoflagellates (genus Symbiodinium) shape the responses of their host reef organisms to environmental variability and climate change. To date, the biogeography of Symbiodinium has been investigated primarily through phylogenetic analyses of the ribosomal internal transcribed spacer 2 region. Although the marker can approximate species-level diversity, recent work has demonstrated that faster-evolving genes can resolve otherwise hidden species and population lineages, and that this diversity is often distributed over much finer geographical and environmental scales than previously recognized. Here, we use the noncoding region of the chloroplast psbA gene (psbAncr) to examine genetic diversity among clade C Symbiodinium associating with the common reef zoantharian Palythoa tuberculosa on Okinawa-jima Island, Japan. We identify four closely related Symbiodinium psbAncr lineages including one common generalist and two potential specialists that appear to be associated with particular microhabitats. The sea surface temperature differences that distinguish these habitats are smaller than those usually investigated, suggesting that future biogeographic surveys of Symbiodinium should incorporate fine scale environmental information as well as fine scale molecular data to accurately determine species diversity and their distributions.

scholarly journals FT-IR Spectroscopy Based Evaluation of Changes in Primary Metabolites of Amsonia orientalis after In vitro 6-benzylaminopurine Treatment

2016 ◽  
Vol 44 (1) ◽  
pp. 209-214 ◽  
Author(s):  
Arda ACEMİ ◽  
Sevgi TÜRKER-KAYA ◽  
Fazıl ÖZEN
Keyword(s):  
Ir Spectroscopy ◽  
Plant Growth ◽  
Natural Populations ◽  
Molecular Data ◽  
Primary Metabolites ◽  
Bern Convention ◽  
Ft Ir ◽  
Common Plant ◽  
Ft Ir Spectroscopy

Amsonia orientalis Decne. (syn. Rhazya orientalis (Decne.) A. DC.) is only cultivated as an ornamental plant but also has a medicinal merit. The natural populations of the species were taken under conservation as per the Bern Convention by European Council. As one of the most common plant growth regulators and synthetic agricultural fertilizers, the effects of 6-benzylaminopurine (BAP) at different concentrations on primary metabolites of in vitro propagated A. orientalis have been investigated by using Fourier transform infrared (FT-IR) spectroscopy. Among all applied concentrations, 2.0 mg l-1 BAP resulted in increment of hydrogen bonded polysaccharide and proteins concentrations, lipid structure and membrane fluidity. Treatments of 2.0 and 4.0 mg l-1 BAP increased the existence of ferulic acid which also indicates the linkage of xylan and both cellulose and hemicellulose content. There was a significant decrease in the area of the peak which indicated the C=O stretching of proteins and pectins for 0.5 and 1.0 mg l-1 BAP while there was a significant increase for 2.0 and 4.0 mg l-1 of BAP treatments. The evaluation of molecular data from FT-IR spectroscopy as in the current study might help to estimate different physiological changes at the molecular level in plants depending on plant growth regulator and/or fertilizer applications. Thus, this FT-IR based method can be applied to in vitro propagation studies and also to studies focused on effects of pesticide and/or herbicide applications on plants to understand the metabolic changes in target species.

scholarly journals Thermal adaptation and clinal mitochondrial DNA variation of European anchovy

2014 ◽  
Vol 281 (1792) ◽  
pp. 20141093 ◽  
Author(s):  
Gonçalo Silva ◽  
Fernando P. Lima ◽  
Paulo Martel ◽  
Rita Castilho
Keyword(s):  
Mitochondrial Dna ◽  
Natural Populations ◽  
Thermal Adaptation ◽  
Secondary Contact ◽  
Nutrient Concentrations ◽  
Clinal Variation ◽  
Oxygen Utilization ◽  
Low Frequencies ◽  
Dna Variation ◽  
European Anchovy

Natural populations of widely distributed organisms often exhibit genetic clinal variation over their geographical ranges. The European anchovy, Engraulis encrasicolus , illustrates this by displaying a two-clade mitochondrial structure clinally arranged along the eastern Atlantic. One clade has low frequencies at higher latitudes, whereas the other has an anti-tropical distribution, with frequencies decreasing towards the tropics. The distribution pattern of these clades has been explained as a consequence of secondary contact after an ancient geographical isolation. However, it is not unlikely that selection acts on mitochondria whose genes are involved in relevant oxidative phosphorylation processes. In this study, we performed selection tests on a fragment of 1044 bp of the mitochondrial cytochrome b gene using 455 individuals from 18 locations. We also tested correlations of six environmental features: temperature, salinity, apparent oxygen utilization and nutrient concentrations of phosphate, nitrate and silicate, on a compilation of mitochondrial clade frequencies from 66 sampling sites comprising 2776 specimens from previously published studies. Positive selection in a single codon was detected predominantly (99%) in the anti-tropical clade and temperature was the most relevant environmental predictor, contributing with 59% of the variance in the geographical distribution of clade frequencies. These findings strongly suggest that temperature is shaping the contemporary distribution of mitochondrial DNA clade frequencies in the European anchovy.

scholarly journals Genetic Comparison of Pinus brutia Ten. Populations from Different Elevations by RAPD Markers

2011 ◽  
Vol 39 (2) ◽  
pp. 299 ◽  
Author(s):  
Yusuf KURT ◽  
Behiye B. BILGEN ◽  
Nuray KAYA ◽  
Kani ISIK
Keyword(s):  
Quantitative Traits ◽  
Rapd Markers ◽  
Gene Diversity ◽  
Geographic Origin ◽  
Natural Populations ◽  
Test Site ◽  
Forest Tree ◽  
Molecular Data ◽  
Pinus Brutia ◽  
Dna Primers

Turkish Red Pine (Pinus brutia Ten.) is an important forest tree species in Turkey for various economic and ecological reasons. In this study, nine RAPD (Randomly Amplified Polymorphic DNA) primers were used to determine genetic variation within and among populations of P. brutia located at the Duzlercami common-garden test site. This site was established in 1979 and includes six natural populations of P. brutia from two altitudinal transects extending from the coast to higher elevations in the Antalya region of Turkey. A total of 32 polymorphic RAPD loci were found in the analyzed six populations. The mean proportion of polymorphic loci among population samples equals 100%, mean number of alleles for each locus = 2.0, effective allele number = 1.71, Shannon’s information index = 0.58, and mean Nei (1973)’s gene diversity value = 0.4. According to GST results, a high proportion of genetic diversity (95-99%) is found within populations. A relatively high genetic differentiation was found among altitudinal population pairs in both transect. Also, data on quantitative traits (total height and/or diameter) at different ages (13, 17, 30 years) were compared with molecular data. There are similarities between the results obtained from RAPD markers and those obtained from the quantitative traits. The differentiation in quantitative traits appears to be due to local adaptation of populations. Data suggest that priority should be given to the selection of material based on geographic origin along the altitudinal gradients of P. brutia populations to conserve the genetic resource of species.

scholarly journals Sedimentological processes and environmental variability at Lake Ohrid (Macedonia, Albania) between 637 ka and the present

2016 ◽  
Vol 13 (4) ◽  
pp. 1179-1196 ◽  
Author(s):  
Alexander Francke ◽  
Bernd Wagner ◽  
Janna Just ◽  
Niklas Leicher ◽  
Raphael Gromig ◽  
...  
Keyword(s):  
Primary Productivity ◽  
Environmental Variability ◽  
Geochemical Data ◽  
Nutrient Concentrations ◽  
Silty Clay ◽  
Lake Ohrid ◽  
Scientific Drilling ◽  
Orbital Parameters ◽  
Tephra Layers ◽  
Deep Site

Abstract. Lake Ohrid (Macedonia, Albania) is thought to be more than 1.2 million years old and host more than 300 endemic species. As a target of the International Continental scientific Drilling Program (ICDP), a successful deep drilling campaign was carried out within the scope of the Scientific Collaboration on Past Speciation Conditions in Lake Ohrid (SCOPSCO) project in 2013. Here, we present lithological, sedimentological, and (bio-)geochemical data from the upper 247.8 m composite depth of the overall 569 m long DEEP site sediment succession from the central part of the lake. According to an age model, which is based on 11 tephra layers (first-order tie points) and on tuning of bio-geochemical proxy data to orbital parameters (second-order tie points), the analyzed sediment sequence covers the last 637 kyr. The DEEP site sediment succession consists of hemipelagic sediments, which are interspersed by several tephra layers and infrequent, thin (< 5 cm) mass wasting deposits. The hemipelagic sediments can be classified into three different lithotypes. Lithotype 1 and 2 deposits comprise calcareous and slightly calcareous silty clay and are predominantly attributed to interglacial periods with high primary productivity in the lake during summer and reduced mixing during winter. The data suggest that high ion and nutrient concentrations in the lake water promoted calcite precipitation and diatom growth in the epilimnion during MIS15, 13, and 5. Following a strong primary productivity, highest interglacial temperatures can be reported for marine isotope stages (MIS) 11 and 5, whereas MIS15, 13, 9, and 7 were comparably cooler. Lithotype 3 deposits consist of clastic, silty clayey material and predominantly represent glacial periods with low primary productivity during summer and longer and intensified mixing during winter. The data imply that the most severe glacial conditions at Lake Ohrid persisted during MIS16, 12, 10, and 6, whereas somewhat warmer temperatures can be inferred for MIS14, 8, 4, and 2. Interglacial-like conditions occurred during parts of MIS14 and 8.

Spatial and temporal variability of small-sized copepod assemblages in a shallow semi-enclosed embayment (Kalloni Gulf, NE Mediterranean Sea)

2014 ◽  
Vol 95 (2) ◽  
pp. 349-360 ◽  
Author(s):  
Georgia Papantoniou ◽  
Daniel B. Danielidis ◽  
Alexandra Spyropoulou ◽  
Nina Fragopoulu
Keyword(s):  
Annual Cycle ◽  
Environmental Variability ◽  
Continuous Production ◽  
Size Fraction ◽  
Seasonal Succession ◽  
Bacterial Biomass ◽  
Mesh Size ◽  
Single Species ◽  
Spatial And Temporal Variability ◽  
Coastal System

The small-sized copepod community structure (<1  mm) and its response to environmental variability was examined during an annual cycle in Kalloni Gulf, a semi-enclosed coastal system in the NE Aegean Sea. Α 90 µm net was used in order to adequately sample the smaller copepod fractions. In the copepod ecology the spatial patterns dominated over the seasonal. Total copepod abundance increased towards the inner gulf area while diversity indices followed the opposite trend. The inner gulf copepod assemblage area was affected by the increasing magnitude of eutrophication, characterized by high abundance values, low species richness and dominance of a single species (e.g.Oithona nana). A clear seasonal succession of species was observed, ordered by temperature, salinity, chlorophyll a, heterotrophic bacterial biomass, organic and inorganic nutrients. Freshwater inputs and the subsequent nutrient inflow was a dominant phenomenon enhancing copepod production and negatively affecting the biodiversity of the assemblage. The great contribution of copepod larval stages in the total community and their year-round presence indicate the continuous production of copepods during the annual cycle, highlight the importance of the smaller size fraction and encourage the use of finer mesh-size nets when assessing the structure and dynamics of copepod communities.

scholarly journals Effects of Elevated CO2 Concentration on Water Relations and Photosynthetic Responses to Drought Stress and Recovery during Rewatering in Tall Fescue

2015 ◽  
Vol 140 (1) ◽  
pp. 19-26 ◽  
Author(s):  
Yajun Chen ◽  
Jingjin Yu ◽  
Bingru Huang
Keyword(s):  
Drought Stress ◽  
Tall Fescue ◽  
Festuca Arundinacea ◽  
Sugar Content ◽  
Soluble Sugar ◽  
Carbon Dioxide Concentration ◽  
Co2 Concentration ◽  
Rubisco Activase ◽  
Interactive Effects ◽  
Hydration Status

Water availability for plant growth is becoming increasingly limited, whereas rising atmospheric carbon dioxide concentration may have interactive effects with drought stress. The objectives of this study were to determine whether elevated CO2 would mitigate drought-induced water deficit and photosynthesis inhibition and enhance recovery from drought damages on rewatering and to determine whether the mitigating effects during drought stress and the recovery in photosynthesis during rewatering by elevated CO2 were the result of the regulation of stomatal movement or carboxylation activities in tall fescue (Festuca arundinacea Schreb. cv. Rembrandt). Plants were grown in controlled-environment chambers with ambient CO2 concentration (400 μmol·mol−1) or elevated CO2 concentration (800 μmol·mol−1) and maintained well watered (control) or subjected to drought stress and subsequently rewatered. Elevated CO2 reduced stomatal conductance (gS) and transpiration rate of leaves during both drought stress and rewatering. Osmotic adjustment and soluble sugar content were enhanced by elevated CO2. Elevated CO2 enhanced net photosynthetic rate with lower gS but higher Rubisco and Rubisco activase activities during both drought and rewatering. The results demonstrated that elevated CO2 could improve leaf hydration status and photosynthesis during both drought stress and rewatering, and the recovery in photosynthesis from drought damages on rewatering was mainly the result of the elimination of metabolic limitation from drought damages associated with carboxylation enzyme activities.

The nutrient status of algal cells in continuous culture

1974 ◽  
Vol 54 (4) ◽  
pp. 825-855 ◽  
Author(s):  
M. R. Droop
Keyword(s):  
Growth Rate ◽  
Natural Populations ◽  
Nutrient Status ◽  
Nutrient Concentrations ◽  
Batch Cultures ◽  
Cell Quota ◽  
Limiting Nutrients ◽  
Limiting Nutrient ◽  
The One ◽  
Substrate Concentrations

Chemostats were used to study the relation between growth rate, the rate of nutrient uptake and internal and external nutrient concentrations of two nutrients simultaneously. (Monochrysis lutheri: phosphorus and vitamin B12.)Growth rate and internal concentrations of both limiting and excess nutrients are related by simple rectangular hyperbolas.Control was shown to follow a threshold rather than multiplicative pattern; that is, non-limiting nutrients exert no control at all over the pattern of growth. The limiting nutrient was the one that showed the smallest cell quota: subsistence quota ratio.Monochrysis populations exhibited two modes of growth. ‘Slow adapted cells’ differed from ‘fast adapted cells’ in the values of the constants for the above relation.Uptake of both limiting and non-limiting nutrients was found to be controlled by internal as well as external substrate concentrations. There was thus a limit to luxury consumption of one nutrient when growth was limited by another.The mathematical model formulated for growth in a chemostat (equations (23)–(29)) allowed prediction of external and internal substrate concentrations and rates of uptake of two nutrients and of biomass, given only the input concentrations of the two nutrients and the dilution rate. This model should apply equally well to growth in batch cultures; its possible application to natural populations was discussed.

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