Among these algal lineages, SIT genes were identified in silicifying stramenopiles chrysophytes and diatoms and more recently in haptophytes Likhoshway et al. It is unclear whether the precipitation of silica has a common origin among these algal lineages or whether the trait evolved independently among diverged lineages. The evolutionary history and diversification of diatom SIT genes may help explain how diatoms became the dominant silicifying algae in the modern ocean. SITs were likely encoded by early diatoms, a hypothesis supported by the presence of SITs in each of the three major diatom lineages radial centric, multipolar centric, and pennate diatoms.
It is unclear what adaptive advantage SITs may have provided in early diatoms, whereas in modern oceans, SITs enable diatoms to utilize silicic acid at reduced concentrations. Diatom cells respond to changes in silicic acid availability and environmental conditions in part by altering the expression of SIT genes and proteins. SIT homologs encoded by laboratory isolates are differentially transcribed across the cell cycle and in response to silicic acid starvation, suggesting that homologs evolved different functions Thamatrakoln and Hildebrand , Mock et al.
Notably, the abundance of SIT transcripts and proteins are not correlated, indicating that they are subject to multiple levels of regulation Thamatrakoln and Hildebrand , Shrestha and Hildebrand Durkin et al.
The continued diversification of these proteins within diatoms has potentially led to specialized adaptations among diatom lineages and perhaps their dominant ability to take up silicic acid from seawater in diverse environmental conditions. Positional coverage of pooled reads across each sequence was determined using a custom python script.
The coverage of reads that mapped to each SIT sequence was visualized in R and compared to the gene model. If coverage did not decrease across an open reading frame with a predicted intron, it was considered part of the open reading frame. The transcribed regions of F. A combination of search tools and publicly available databases were used to identify SIT homologs.
To confirm that the predicted amino acid sequences were correct, the corresponding nucleotide sequences were individually extracted from the MMETSP nucleotide data sets and translated into six reading frames using the Biopython tools for Python.
Potential SIT homologs were identified by hmmsearch using the hmm profile of the reference alignment and extracting the longest open reading frame for each identified MMETSP sequence using a custom script written in R. Sequences were considered homologs of diatom SITs if the protein fragment they encoded contained at least seven predicted TM domains that aligned with sequences in the reference alignment. Sequences encoding more than 10 TM domains were split into 10 TM domain segments.
Sequences that spanned a region encoding at least seven TM domains were also included in the alignment. Identical sequences originating from the same species were removed from the alignment. The lengths of these sequence ends were typically less than amino acids in length. Branch support was calculated from bootstrap trees. To display the phylogenetic relationships among organisms encoding SIT gene homologs, an 18s rRNA phylogenetic tree was created. Surface seawater 5 m was collected at each station using a Lutz double diaphragm pump.
To evaluate similarity of the community composition among locations, a Bray—Curtis dissimilarity matrix was created from the proportional abundance of all genera at each location. Seawater was filtered through a 0. Samples were quantified on the NanoDrop and Qubit spectrophotometers. Between 2. Libraries from duplicate samples collected at Stations P1 and P8 were sequenced on an Illumina MiSeq system in three runs for each library and the data from each run were combined into a single data set per sample.
Libraries from duplicate samples collected at stations P4 and P6 were sequenced on an Illumina HiSeq system in one run per sample. Any leading T or trailing A residues were removed from reads using a custom python script.
Merged sequences that were at least bp in length were included in subsequent analysis. The tree was exported by the related program guppy option: tog. The tree reference sequence closest to each environmental sequence was used to classify the environmental sequence by lineage and genus using tools in the ETE2 python program. The environmental sequence was defined as unclassified if it was sister to a group of sequences that did not all have the same classification or genus.
The percent contribution of each SIT clade to total number of SIT transcripts was calculated for each major diatom lineage and select genera. Counting uncertainty was estimated as the square root of the number of counts per clade, which assumes that the probability of detecting a given number of reads per clade is Poisson distributed. Replicate samples collected at each station were used to assess variability in the observed proportion of SIT clades transcribed by major diatom lineages.
Because counting uncertainty was larger in the quantification of SIT reads at the genus level, in which fewer reads were observed, data from the sample replicates were combined before calculating the percent of transcripts from each SIT clade. Only genera with at least total sequences observed among all stations were included in further analysis. Protein domains of SITs Fig. Lewin and Skeletonema costatum Greville Cleve: Thamatrakoln et al.
Ellis: Marron et al. S1 in the Supporting Information. Although transcript coverage across the intron of the T. The coding regions of F. The clade assignment of genes encoding these domains is based on Durkin et al. The phylogeny and clade assignment of these sequences were previously determined Durkin et al. One SIT gene encoded by P. Two clade B sequences F. Dashes indicate genes where data are not applicable.
A comprehensive phylogenetic tree of translated SIT genes Fig. Sequence fragments were included in the tree if they encoded at least seven predicted TM domains. Sequences with more than 10 TM domains were segmented and aligned in 10 TM segments, the names of these genera are labeled along with proposed domain duplication events I—VI. Node scores are bootstrap values from bootstrapped trees. Unlike previous SIT gene phylogenies, this extensive tree was rooted by a monophyletic outgroup of SIT homologs identified in nondiatom protists including haptophytes, chrysophytes, a silicoflagellate , choanoflagellates, ciliates, and a dinoflagellate Fig.
The full phylogenetic tree, including all labeled branches, is presented in Figure S2 in the Supporting Information and all sequences are presented in Table S1. To resolve the distribution of SIT clades across major diatom lineages, organisms were grouped according to the relationship of their 18S rRNA sequence Fig.
Columns indicate clades, as defined in Figure 2. Rows indicate genus in order of 18s rRNA genetic relationships displayed by tree on the right. Apparent domain duplication events are labeled as in Figure 2. Within the diatom portion of the tree, clade B sequences formed the most basal branches Fig. The radial centric diatom Leptocylindrus encoded the most basal sequences within clade B see Fig.
Clade B included diverse subclades and sequences from all major diatom groups, but not all diatom genera encoded a clade B sequence Fig. All sequences that encoded more than 10 predicted TM domains belonged to clade B Fig.
Segments from different sequences that shared a common ancestor were assumed to have arisen from the same domain duplication event.
For example, the presence of two distinct clades containing the first 10 TMs and the second 10 TMs of the segmented SIT sequences encoded by Minutocellus and Extubocellus suggests that the SIT domain was duplicated in a common ancestor of these two genera.
One clade A sequence was also identified in the ciliate Tiarina Fig. Clade C sequences were encoded by centric, multipolar, and pennate diatoms, but were not detected in the order Thalassiosirales, a monophyletic lineage of the multipolar diatoms Fig. Like clade C, clade D sequences were identified in centric, multipolar, and pennate diatoms, but not the Thalassiosirales.
Three of the four identified sequences were encoded by bacteria, including two Synechococcus sp. A sequence was also identified in the whole genome sequence of the polychaete worm Capitella teleta Blake et al.
The SIT genes encoded by T. In the dark, the chloroplasts of Euglena shrink up and temporarily cease functioning; the cells, instead, take up organic nutrients from their environment. The human parasite, Trypanosoma brucei , belongs to a different subgroup of Euglenozoa, the kinetoplastids.
The kinetoplastid subgroup is named after the kinetoplast, a DNA mass carried within the single, oversized mitochondrion possessed by each of these cells. This subgroup includes several parasites, collectively called trypanosomes, which cause devastating human diseases by infecting an insect species during a portion of their life cycle.
The parasite then travels to the insect salivary glands to be transmitted to another human or other mammal when the infected tsetse fly consumes another blood meal. Life cycle of Trypanosoma brucei : Trypanosoma brucei, the causative agent of sleeping sickness, spends part of its life cycle in the tsetse fly and part in humans.
Alveolates are defined by the presence of an alveolus beneath the cell membrane and include dinoflagellates, apicomplexans and ciliates. Evaluate traits associated with protists classified as alveolates which include dinoflagellates, apicomplexans, and ciliates. Current evidence suggests that species classified as chromalveolates are derived from a common ancestor that engulfed a photosynthetic red algal cell, which itself had already evolved chloroplasts from an endosymbiotic relationship with a photosynthetic prokaryote.
Therefore, the ancestor of chromalveolates is believed to have resulted from a secondary endosymbiotic event. However, some chromalveolates appear to have lost red alga-derived plastid organelles or lack plastid genes altogether. Therefore, this supergroup should be considered a hypothesis-based working group that is subject to change and can be subdivided into alveolates and stramenopiles. A large body of data supports that the alveolates are derived from a shared common ancestor.
The alveolates are named for the presence of an alveolus, or membrane-enclosed sac, beneath the cell membrane. The exact function of the alveolus is unknown, but it may be involved in osmoregulation.
The alveolates are further categorized into the dinoflagellates, the apicomplexans, and the ciliates. Dinoflagellates exhibit extensive morphological diversity and can be photosynthetic, heterotrophic, or mixotrophic. Many dinoflagellates are encased in interlocking plates of cellulose with two perpendicular flagella that fit into the grooves between the cellulose plates.
One flagellum extends longitudinally and a second encircles the dinoflagellate. Together, the flagella contribute to the characteristic spinning motion of dinoflagellates. These protists exist in freshwater and marine habitats; they are a component of plankton.
Dinoflagellates : The dinoflagellates exhibit great diversity in shape. Many are encased in cellulose armor and have two flagella that fit in grooves between the plates. Movement of these two perpendicular flagella causes a spinning motion. Some dinoflagellates generate light, called bioluminescence, when they are jarred or stressed. Large numbers of marine dinoflagellates billions or trillions of cells per wave can emit light and cause an entire breaking wave to twinkle or take on a brilliant blue color.
For approximately 20 species of marine dinoflagellates, population explosions called blooms during the summer months can tint the ocean with a muddy red color. This phenomenon is called a red tide and results from the abundant red pigments present in dinoflagellate plastids. In large quantities, these dinoflagellate species secrete an asphyxiating toxin that can kill fish, birds, and marine mammals.
Red tides can be massively detrimental to commercial fisheries; humans who consume these protists may become poisoned. Bioluminescence : Bioluminescence is emitted from dinoflagellates in a breaking wave, as seen from the New Jersey coast. The apicomplexan protists are so named because their microtubules, fibrin, and vacuoles are asymmetrically distributed at one end of the cell in a structure called an apical complex.
The apical complex is specialized for entry and infection of host cells. Indeed, all apicomplexans are parasitic. This group includes the genus Plasmodium , which causes malaria in humans. Apicomplexan life cycles are complex, involving multiple hosts and stages of sexual and asexual reproduction. Parasitic apicomplexans : a Apicomplexans are parasitic protists. They have a characteristic apical complex that enables them to infect host cells.
The ciliates, which include Paramecium and Tetrahymena , are a group of protists 10 to 3, micrometers in length that are covered in rows, tufts, or spirals of tiny cilia.
By beating their cilia synchronously or in waves, ciliates can coordinate directed movements and ingest food particles. Certain ciliates have fused cilia-based structures that function like paddles, funnels, or fins. Ciliates also are surrounded by a pellicle, providing protection without compromising agility. The genus Paramecium includes protists that have organized their cilia into a plate-like primitive mouth called an oral groove, which is used to capture and digest bacteria.
Food captured in the oral groove enters a food vacuole where it combines with digestive enzymes. Waste particles are expelled by an exocytic vesicle that fuses at a specific region on the cell membrane: the anal pore.
In addition to a vacuole-based digestive system, Paramecium also uses contractile vacuoles: osmoregulatory vesicles that fill with water as it enters the cell by osmosis and then contract to squeeze water from the cell. Paramecium : Paramecium has a primitive mouth called an oral groove to ingest food and an anal pore to excrete it.
Contractile vacuoles allow the organism to excrete excess water. Cilia enable the organism to move. Paramecium has two nuclei, a macronucleus and a micronucleus, in each cell. The micronucleus is essential for sexual reproduction, whereas the macronucleus directs asexual binary fission and all other biological functions. The process of sexual reproduction in Paramecium underscores the importance of the micronucleus to these protists. Paramecium and most other ciliates reproduce sexually by conjugation.
This process begins when two different mating types of Paramecium make physical contact and join with a cytoplasmic bridge. The diploid micronucleus in each cell then undergoes meiosis to produce four haploid micronuclei. Three of these degenerate in each cell, leaving one micronucleus that then undergoes mitosis, generating two haploid micronuclei. The cells each exchange one of these haploid nuclei and move away from each other.
A similar process occurs in bacteria that have plasmids. Fusion of the haploid micronuclei generates a completely novel diploid pre-micronucleus in each conjugative cell. This pre-micronucleus undergoes three rounds of mitosis to produce eight copies, while the original macronucleus disintegrates.
Four of the eight pre-micronuclei become full-fledged micronuclei, whereas the other four perform multiple rounds of DNA replication and then become new macronuclei. Two cell divisions then yield four new paramecia from each original conjugative cell. Paramecium : sexual reproduction : The complex process of sexual reproduction in Paramecium creates eight daughter cells from two original cells.
Each cell has a macronucleus and a micronucleus. During sexual reproduction, the macronucleus dissolves and is replaced by a micronucleus. Stramenophiles include photosynthetic marine algae and heterotrophic protists such as diatoms, brown and golden algae, and oomycetes.
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Biofuels 12, The community composition of diatoms varies depending on location. Because of this, diatoms have been used in forensic investigations to determine where someone drowned depending on the diatom species present and how long ago they drown based on how far the diatoms had migrated into their tissues. They serve as the main base of the food chains in these habitats, supplying calories to heterotrophic protists and small animals.
These, in turn, feed larger animals. During periods of nutrient availability, diatom populations bloom to numbers greater than can be consumed by aquatic organisms. The excess diatoms die and sink to the sea floor where they are not easily reached by saprotrophs that feed on dead organisms.
As a result, the carbon dioxide that the diatoms had consumed and incorporated into their cells during photosynthesis is not returned to the atmosphere. The biological carbon pump is a crucial component of the carbon cycle that maintains lower atmospheric carbon dioxide levels.
Diatoms primarily reproduce asexually by binary fission , similar to prokaryotes. During binary fission, the two valves of the frustule are separated and each new cell forms a new valve inside the old one. However, the new valve is always smaller. If diatoms only reproduce in this way, it results in a continual decrease in average size.
When some minimal size is reached, this can trigger sexual reproduction. Sourced from YouTube. Ecology: Everywhere! Marine, freshwater, and terrestrial. Though brown algae and diatoms seem to have very little in common morphologically, they are descended from a common ancestor.
Both of these groups have a diplontic life cycle during some stage of which a cell will have heterokont flagella. They have 4-membraned chloroplasts that contain the pigments chlorophyll a, chlorophyll c, and fucoxanthin.
This latter pigment gives the chloroplasts in these groups a golden color. This is about where the similarities end.
Brown algae are exclusively multicellular and found in marine habitats, most typically in the intertidal zone. Their cell walls contain cellulose and they store their carbohydrates as laminarin. Diatoms are exclusively unicellular and found in almost every habitat where there is water. Their single cell is surrounded by a silica frustule composed of two distinct valves.
They store their carbohydrates as chrysolaminarin. Learning Objectives Use life history, morphology, and cellular components to identify brown algae. Identify the components of a kelp thallus. Identify structures and events in the Fucus life cycle and know their ploidy. Identify structures and events in the Laminaria life cycle and know their ploidy. Use life history, morphology, and cellular components to identify diatoms. Classify diatoms based on symmetry and ecology.
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