Phytoplankton as an indicator of the current ecological status of the Ob River

Canopy cover as the key factor for occurrence and species richness of subtropical stream green algae (Chlorophyta)

Based on the materials of studies of phytoplankton of the tributaries of the Ob (Tom’, Ket’, Vasyugan) in the summer of 2019, the species composition, taxonomic structure, abundance and biomass of phytoplankton were established, the water quality class and trophic status were determined. The basis of the species richness of phytoplankton in the tributaries is created by green algae (Chlorophyta), the parameters of alpha diversity indicate the average complexity of the structure of phytoplanktocenosis. In terms of phytoplankton biomass, the trophic status of the rivers varied from mesotrophic to eutrophic category, the water quality class corresponded to class 3 “satisfactory purity”.

Chemicals from anthropogenic activities such as domestic sewage, pesticide leaching, and improper chemical disposal have caused groundwater contamination. The presence of these emerging contaminants in the aquatic environment can change water quality and biota composition. Thus, this study investigates the effect of two emerging contaminants, anti-inflammatory drug diclofenac (DCF) and antibiotic sulfamethoxazole (SMX), on the aquatic environment, evaluating the phytoplankton community structure. A microcosm experiment was conducted with 16 sampling units, each one with 500 mL of water sample containing phytoplankton exposed to these drugs at different concentrations (0.1, 0.5, and 1.0 mg L-1). The experiment lasted 15 days, and samples were collected on days 0, 3, 5, 7, and 14 to evaluate the phytoplankton community, the concentrations of the drugs, and the nutrients in the samples. Six phytoplankton groups were identified, and diatoms and green algae were the most diverse and abundant groups. For the entire community, we identified differences between the days of the experiment, varying in the diversity and density of organisms, but not between the concentrations of the two drugs. Evaluating the groups separately, we identified differences in the abundance of cyanobacteria for the treatment with diclofenac and desmids for the treatment with sulfamethoxazole. We demonstrated that the presence of pharmaceuticals in freshwater ecosystems can somehow affect the phytoplankton community, especially the diversity and abundance of cyanobacteria and desmids. Therefore, our study indicates the importance of evaluating the presence of pharmaceuticals in freshwater ecosystems and their influence on aquatic organisms, as well as pharmaceuticals may be changing the structure of the aquatic environment.

Article Figures and data Abstract Editor's evaluation Introduction Results and discussion Materials and methods Data availability References Decision letter Author response Article and author information Metrics Abstract As a ubiquitous picophytoplankton in the ocean and an early-branching green alga, Ostreococcus tauri is a model prasinophyte species for studying the functional evolution of the light-harvesting systems in photosynthesis. Here, we report the structure and function of the O. tauri photosystem I (PSI) supercomplex in low light conditions, where it expands its photon-absorbing capacity by assembling with the light-harvesting complexes I (LHCI) and a prasinophyte-specific light-harvesting complex (Lhcp). The architecture of the supercomplex exhibits hybrid features of the plant-type and the green algal-type PSI supercomplexes, consisting of a PSI core, an Lhca1-Lhca4-Lhca2-Lhca3 belt attached on one side and an Lhca5-Lhca6 heterodimer associated on the other side between PsaG and PsaH. Interestingly, nine Lhcp subunits, including one Lhcp1 monomer with a phosphorylated amino-terminal threonine and eight Lhcp2 monomers, oligomerize into three trimers and associate with PSI on the third side between Lhca6 and PsaK. The Lhcp1 phosphorylation and the light-harvesting capacity of PSI were subjected to reversible photoacclimation, suggesting that the formation of OtPSI-LHCI-Lhcp supercomplex is likely due to a phosphorylation-dependent mechanism induced by changes in light intensity. Notably, this supercomplex did not exhibit far-red peaks in the 77 K fluorescence spectra, which is possibly due to the weak coupling of the chlorophyll a603-a609 pair in OtLhca1-4. Editor's evaluation This fundamental work represents an important contribution to our understanding of the diversity of photosynthetic mechanisms across the branches of phototrophic life, with the first high-resolution structure (2.9 Å) of a photosynthetic complex from the green alga, Ostreococcus tauri, an ecologically important green alga utilizes a unique antenna complex, Lhcp. The evidence suggests mechanism found here is distinct from the classical antenna state transitions seen in other organisms studied thus far, expanding our knowledge of how photosynthetic systems react to changes in light conditions and leading to a new understanding of the function and evolution of light-harvesting antennas. https://doi.org/10.7554/eLife.84488.sa0 Decision letter Reviews on Sciety eLife's review process Introduction Phytoplankton are the major primary producers in the aquatic environments, and provide organic matter for marine food webs by converting solar energy into chemical energy through photosynthesis. As a member of natural phytoplankton living in the ocean, Ostreococcus tauri is a unicellular green alga widespread in marine environments and crucial for the aquatic ecosystem (Derelle et al., 2006; Palenik et al., 2007). It is also known as the smallest free-living eukaryote (Courties et al., 1994) and belongs to Prasinophyceae, a class of green algae at the near basal position in the evolution of green lineage and most closely related to the first green alga known as ‘ancestral green flagellate’ (Lewis and McCourt, 2004). A prasinophyte-specific Lhc protein named Lhcp was found in O. tauri (Six et al., 2005; Swingley et al., 2010) and Mantoniella squamata (another member of Prasinophyceae) (Jiao and Fawley, 1994; Schmitt et al., 1994). There are two classes of Lhcp (Lhcp1 and Lhcp2) in addition to the common LHC proteins, namely six Lhca proteins (Lhca1-6) and two minor monomeric Lhcb proteins (Lhcb4 and Lhcb5), serving as the peripheral antennae of O. tauri PSI and PSII (Six et al., 2005; Swingley et al., 2010). The Lhcp proteins form a highly abundant antenna complexes in O. tauri (Swingley et al., 2010), and the carotenoid composition of the OtLhcp complexes is largely different from those of LHCIs or light-harvesting complexes II (LHCIIs) in plants and other green algae (such as a core chlorophyte Chlamydomonas reinhardtii) (Minagawa, 2009). While Lhcp, Lhcb (apoproteins of LHCII), and Lhca (apoproteins of LHCI) all belong to the LHC superfamily, Lhcp proteins form a separate clade with characteristics of an ancestral state of LHC proteins instead of belonging to the clades of Lhcb or Lhca (Six et al., 2005). Moreover, the organization of pigment molecules within the Lhcp complexes exhibits distinct features in comparison with plant LHCII according to a previous spectroscopic study (Goss et al., 2000). Under low light (LL) conditions, the Lhcp complexes of O. tauri can assemble with the PSI-LHCI to form a larger PSI-LHCI-Lhcp supercomplex, whereas the amount of PSI-LHCI-Lhcp supercomplex is greatly reduced under high-light (HL) conditions (Swingley et al., 2010). It remains unclear how the Lhcp complexes assemble with PSI and establish energy transfer pathways with the interfacial PSI subunits under LL conditions. The arrangement of various Chl and carotenoid molecules within the Lhcp complexes is also unknown and awaits to be analyzed through further studies. Results and discussion The PSI-LHCI-Lhcp supercomplex To stabilize the photosynthetic supercomplexes from O. tauri during purification process, the detergent-solubilized thylakoid membrane was treated with amphipol A8-35, which is an amphipathic polymer to substitute for detergents, before the sucrose density gradient (SDG) ultracentrifugation (Figure 1a, Figure 1—figure supplement 1a), according to the previous protocol successfully employed to stabilize the PSII supercomplex from C. reinhardtii (Watanabe et al., 2019). Pigment composition analysis of the A3L fraction demonstrates that the most abundant light-harvesting carotenoid is prasinoxanthin (Prx, which is unique to prasinophytes), among other carotenoids of lesser abundance, including dihydrolutein (Dlt) and micromonal (Figure 1—figure supplement 1c, Table 1). Although the typical Chls (such as Chl a and Chl b) and carotenoids (violaxanthin/Vio, 9’-cis-neoxanthin/Nex and β-carotene) found in green plants were also present in O. tauri, lutein (a major carotenoid found in plant LHCII) was not detected. Polypeptides for the PSI core and its peripheral antennae in the A3 and A3L fractions were characterized by SDS-PAGE (Figure 1—figure supplement 1b) and mass spectrometry analysis (Supplementary file 1a). These findings indicate that A3 is primarily composed of polypeptides for PSI-LHCI supercomplex, whereas A3L includes Lhcp1 and Lhcp2 alongside the constituents present in A3, along with comigrated PSII polypeptides, which is essentially in agreement with a previous report (Swingley et al., 2010). Figure 1 with 4 supplements see all Download asset Open asset Characterization of A3 and A3L fractions. (a) Sucrose density gradient showing four major bands corresponding to free LHCs (A1), PSI-LHCI supercomplex (A3), PSI-LHCI-Lhcp supercomplex and PSII-Lhcp supercomplex (A3L), and other complexes (A4). (b) 77 K steady-state fluorescence spectrum of PSI-LHCI (solid line) and PSI-LHCI-Lhcp (dotted line). (c) PSI light-harvesting capabilities in the A3 and A3L fractions. Light-induced P700 oxidation kinetics of PSI were measured in A3 and A3L fractions under 28 µmol photon m–2 s–1. The fraction of P700 oxidation was derived from Δ(A820-A870). Solid lines and shaded area represent averages of five (for A3) or ten (for A3L) technical replicates and SD, respectively. Blue lines represent fitting curves by mono-exponential functions. Data are representative of two biologically independent experiments. See another set of data in Figure 1—figure supplement 3. Figure 1—source data 1 Quantitative data for Figure 1c. https://cdn.elifesciences.org/articles/84488/elife-84488-fig1-data1-v2.zip Download elife-84488-fig1-data1-v2.zip Table 1 Pigment composition in the A3L fraction as revealed by UPLC analysis. Mean (±STD, n=3). PigmentMolar ratio (Chl a=100)Chl b36.2 (±0.1)β-Carotene13.4 (±0.5)Mdp3.8 (±0.1)Uriolide4.9 (±0.1)Prx11.8 (±0.1)Nex3.6 (±0.1)Vio3.3 (±0.1)Micromonal2.3 (±0.1)Dlt2.2 (±0.1) Fluorescence properties of A3 and A3L were characterized by fluorescence decay associated spectra at 77 K (FDAS, Figure 1—figure supplement 2a–c). The fluorescence lifetimes of A3 were mainly made up of <10 and 65 ps components (Figure 1—figure supplement 2b), which correspond to the total trapping time around P700, including the energy transfer between bulk Chl and P700 and the trapping at P700 (Mimuro et al., 2010). The positive peak in the fastest lifetime component observed in A3 was similar to that previously observed in the PSI core of cyanobacteria, which reflects the fast energy transfer process to P700 from the Chl near P700 and the subsequent fast charge separation. In A3L, however, the fastest lifetime component showed different shapes from that in A3 and it is also implying PSI-LHCI-Lhcp supercomplex in A3L. Because A3L has larger light-harvesting antennae, there are more Chls further away from P700 (e.g., those bound to Lhcp) than A3. Therefore, the long-range energy transfer process from the antennae to P700 becomes dominant in the observation, and the subsequent early trapping process could be masked. The slight increase in the lifetimes of A3L compared to those of A3 (<10–20 ps, 65–90 ps) likely reflects the presence of larger antennae in A3L. The light-induced oxidation kinetics of P700 indeed showed that the PSI antenna size in A3L was larger than that of A3 (Figure 1c, Figure 1—figure supplement 3). Notably, the 77 K fluorescence spectra of PSI-LHCI and PSI-LHCI-Lhcp exhibit a peak at 690 and 680 nm, respectively (Figure 1b), and there are no distinctive far-red peaks as reported previously (Swingley et al., 2010). The blue-shifted fluorescence was more prominent in PSI-LHCI-Lhcp fraction. These results and the EM analysis of the negatively stained particles (Figure 1—figure supplement 4, Table 2) suggest that A3 almost exclusively consists of PSI-LHCI supercomplex, while A3L was mainly composed of PSI-LHCI-Lhcp supercomplex. We thus proceeded to solve the cryo-EM structure of the large PSI-LHCI-Lhcp supercomplex in A3L in order to reveal its detailed architecture. Table 2 Two-dimensional classification of the photosystem I (PSI) particles in the A3 and A3L fractions. The RELION 2.1 package (Kimanius et al., 2016) was used for automated particle picking of particles and Two-dimensional (2D) classification into 50 classes as previously described (Watanabe et al., 2019). Classes of poor quality due to aggregation, contamination, micrograph edge, or extreme proximity were discarded. 2D classification was performed on the PSI particles and manually assigned to respective small and large PSI supercomplexes. FractionA3A3LSmall PSI (PSI-LHCI)2675 (100%)1030 (30%)Large PSI (PSI-LHCI-Lhcp)2437 (70%)Total PSI particles26753467 Supramolecular assembly of OtLhcp trimers (Trimers) with PSI-LHCI complex Through the single-particle cryo-EM method, the structure of OtPSI-LHCI-Lhcp supercomplex is solved at an overall resolution of 2.94 Å and the local regions of three Lhcp trimers (namely Trimers 1–3) are refined to 2.9–3.5 Å (Figure 2—figure supplement 1, Table 3). As shown in Figure 2, the OtPSI-LHCI-Lhcp supercomplex consists of a central PSI monomer encircled by six LHCIs and three Trimers. OtPSI contains two large core subunits (PsaA and PsaB), three subunits on the stromal surface (PsaC, PsaD, and PsaE) (Figure 2a–c), nine small membrane-embedded subunits (PsaF, PsaG, PsaH, PsaI, PsaJ, PsaK, PsaL, PsaM, PsaO), one subunit on the lumenal surface (PsaN) (Figure 2d–f). In the supercomplex, a total of 314 Chls (245 Chl a, 60 Chl b, 9 magnesium 2,4-divinylpheoporphyrin a5 monomethyl ester [Mdp], 104 carotenoids, 2 phylloquinones, and 3 Fe4S4 clusters have been located [Table 4]). The densities for representative Chl, carotenoid, and lipid molecules as well as two small subunits (PsaM and PsaN) are shown in Figure 2—figure supplement 2. To our best knowledge, the structure of OtPSI has the largest number of subunits among the structures of PSI known so far (including those from plants, green algae, diatom, red algae, and cyanobacteria, Figure 3). Figure 2 with 3 supplements see all Download asset Open asset Overall architecture of OtPSI-LHCI-Lhcp supercomplex. (a) Top view of the supercomplex from stromal side along membrane normal. (b) and (c) Two different side views of the supercomplex along the membrane plane. While the protein backbones are shown as cartoon models, the pigment and lipid molecules are presented as stick models. The iron-sulfur clusters are presented as sphere models. The bulk region of photosystem I (PSI) core is colored in wheat, while Lhca1-6, Lhcp1, and Lhcp2, PsaC, PsaD, PsaE, PsaF, and PsaN are highlighted in different colors. The remaining small subunits are in silver. (d–f) The small subunits at the interfaces between PSI core and LHCI/Lhcp complexes. The viewing angles are the same as (a–c), whereas the color codes are different. The interfacial small subunits are highlighted in various colors, while the PSI core and LHCI/Lhcp complexes are in silver. Figure 3 Download asset Open asset Comparison of O.tauri PSI-LHCI-Lhcp supercomplex with the photosystem I (PSI) supercomplexes from other organisms. (a) OtPSI-LHCI-Lhcp supercomplex. (b–k) Structures of PSI from different species or at different states. Blue, large PSI core subunits; magenta, small PSI core subunits; yellow, Lhca5-Lhca6/Lhca2-Lhca9/Lhca0-Lhca9/Lhc1-Lhc2 and the outer belt of LHCI; cyan, Lhca1-Lhca2-Lhca3-Lhca4 and the inner belt of antenna complexes around PSI from other species; green, Lhcp or LHCII trimers; gray, symmetry-related units in trimeric or tetrameric PSI. Table 3 Statistics of structural analysis of the OtPSI-LHCI-Lhcp supercomplex. OtPSI-LHCI-LhcpData collection and processingMagnification130,000Voltage (kV)300Electron exposure (e- Å–2)60Defocus range (μm)from –1.8 to –2.2Pixel size (Å)1.04Symmetry imposedC1Initial particle images (no.)5,288,217Final particle images (no.)80,366Map resolution (Å)2.94 FSC threshold0.143Map resolution range (Å)2.3–4.3RefinementInitial model used (PDB code)5ZJI, 7D0JModel resolution (Å)3.0 FSC threshold0.5Map sharpening B factor (Å2)–110.961Model composition Nonhydrogen atoms64,836 Protein residues5632 Ligands450B factor (Å2) Protein56.82 Ligand56.55R.m.s. deviations Bond lengths (Å)0.011 Bond angles (°)1.79Validation MolProbity score1.51 Clash score5.41 Poor rotamers (%)0Ramachandran plot Favored (%)96.6 Allowed (%)3.37 Outliers (%)0.04 Table 4 Summarization of the components in the final structural model of the OtPSI-LHCI-Lhcp supercomplex. SubunitNumber of amino acid residues tracedChlorophyllsCarotenoidsLipidsOthersPsaA74244 Chl a1 Cl06 BCR2 PG2 MGDG1 DGDG1 PQN1 Fe4S4PsaB73240 Chl a8 BCR1 PG1 DGDG1 PQNPsaC802 Fe4S4PsaD143PsaE62PsaF1653 Chl a1 BCRPsaG953 Chl a1 BCRPsaH963 Chl a1 SQDGPsaI351 BCRPsaJ411 Chl a1 BCR2 MGDGPsaK874 Chl a3 BCR1 PGPsaL1585 Chl a4 BCR1 PG1 MGDGPsaM31PsaN912 Chl aPsaO965 Chl a2 DLT2 MGDGTrimer 2201(Lhcp2)8 Chl a5 Chl b1 DVP2 PRX4 DLT1 NEX225(Lhcp1)8 Chl a5 Chl b1 DVP2 PRX4 DLT1 NEX201(Lhcp2)8 Chl a5 Chl b1 DVP2 PRX4 DLT1 NEXTrimer 1202(Lhcp2)8 Chl a5 Chl b1 DVP2 PRX4 DLT1 NEX201(Lhcp2)8 Chl a5 Chl b1 DVP2 PRX4 DLT201(Lhcp2)8 Chl a5 Chl b1 DVP1 BCR2 PRX3 DLTTrimer 3201(Lhcp2)8 Chl a5 Chl b1 DVP1 BCR2 PRX3 DLT200(Lhcp2)8 Chl a5 Chl b1 DVP2 PRX4 DLT1 NEX200(Lhcp2)8 Chl a5 Chl b1 DVP1 PRX4 DLTLhca11959 Chl a2 Chl b1 XAT1 PRXLhca220511 Chl a4 Chl b1 XAT1 BCR1 DLT1 PRX1 PG1 MGDGLhca322713 Chl a1 Chl b1 XAT3 BCR1 PRX3 PG1 MGDGLhca420511 Chl a4 Chl b1 XAT1 BCR1 PRXLhca51859 Chl a1 Chl b1 XAT1 PRX1 MGDGLhca621810 Chl a3 Chl b1 XAT1 PRX1 PG1 MGDG1 SQDGChain Y4 H2O Four Lhca (Lhca1-4) complexes are associated with the PSI core at the side of PsaG- F-J-K (Figure 2a and d), similar to those found in plant PSI-LHCI complexes (Mazor et al., 2017; Qin et al., 2015; Figure 3). On the other side formed by PsaG-I-M-H, an Lhca5-Lhca6 heterodimer is associated with the PSI core (Figure 2a and d). The location of Lhca5-Lhca6 heterodimer overlaps with that of Lhca9-Lhca2 heterodimer associated with C. reinhardtii PSI (Su et al., 2019; Suga et al., 2019) or Lhcr2-Lhcr1 heterodimer associated with Cyanidioschyzon merolae PSI (Pi et al., 2018), whereas the corresponding sites are vacant in plant PSI structures (Mazor et al., 2017; Pan et al., 2018; Qin et al., 2015; Yan et al., 2021). While the fourth transmembrane helix of CrLhca2 or Lhca5 from Dunaliella salina (also known as transmembrane helix F/TMF or TMH4), located at the dimerization interface of the Lhca2/Lhca9 or Lhca5-Lhca6 heterodimer, was previously proposed to replace the role of PsaM in mediating assembly of the LHCI heterodimer with PSI (Caspy et al., 2020; Suga et al., 2019), the fourth helix of OtLhca6 and PsaM coexist in O. tauri. As PsaM is also present in moss (Gorski et al., 2022) and cyanobacteria (Jordan et al., 2001), where LHCI heterodimer is absent at this position, the role and the origin of the fourth helix of the Lhca proteins might not be directly related to PsaM and need to be revisited. Previously, it was found that plant and C. reinhardtii PSI complexes contain some red-form Chls, absorbing photons at energy levels below that of the primary donor and mainly located in the LHCI complexes (Croce and van Amerongen, 2013). Unlike plant and C. reinhardtii PSI, OtPSI-LHCI-Lhcp supercomplex sample does not exhibit far-red peaks in the 77 K fluorescence spectra (Figure 1b). In the OtPSI-LHCI, the Chl a603-a609 pairs of Lhca1-4 (corresponding to the red-form Chls found in plant and C. reinhardtii Lhca1-4) are separated at larger distances, while those in Lhca5 and Lhca6 are similar to the ones in Lhca9 and Lhca2 from C. reinhardtii (Figure 4). Moreover, the axial ligands of Chl a603 in Lhca1-4 from O. tauri are all His residues instead of Asn (Figure 4b–e). Mutation of Asn to His for the ligand of Chl a603 in plant Lhca3 and Lhca4 led to absence of red spectral while of Asn for His in red of the fluorescence et al., As His has side than the position of Chl a603 in is located away from the protein comparison with those from plant and C. reinhardtii so that the between Chl a603 and Chl becomes larger and coupling might be reduced as a The axial ligands of Chl a603 in Lhca5-Lhca6 from O. tauri are Asn residues same as those in the Lhca9-Lhca2 on a similar location in C. reinhardtii (Figure 4b–e). Although Chl a603-a609 pairs of Lhca9 and Lhca2 were proposed to be for the red spectral in C. reinhardtii et al., 2010), those in and OtLhca6 with similar not the red spectral (Figure and that the presence of Asn residues at the axial ligand is not to the spectral red form of Chl The distinct spectroscopic features of OtPSI-LHCI-Lhcp supercomplex might also be related to the local environments around chlorophyll and in and OtLhca6 van with Chl and Chl respectively (Figure and In residues are by residues in C. reinhardtii Lhca9 and Previously, it was reported that residues located chlorophyll molecules of the and red in the bands of et al., Mutation of a van with a to a or a of the peak in the core light-harvesting complex of et al., Therefore, the of or residues of around Chl or Chl in for the of red spectral in the OtPSI-LHCI-Lhcp supercomplex. Figure 4 Download asset Open asset Comparison of Chl a603-a609 in Lhca complexes among O. tauri, C. and (a) Overall arrangement of the Chl a603-a609 in six Lhca complexes of O. tauri, C. and The in the photosystem I (PSI) supercomplexes are presented in surface and those of Lhca complexes are with stick models. O. light C. The indicate the subunits and the the of the a603-a609 in Comparison of the Chl a603-a609 and local environments in six different Lhca subunits from the three different that the axial ligands of Chl a603 in Lhca1-4 from O. tauri are all while the Asn in the of plant Lhca3 and Lhca4 are crucial for the formation of the form The and are present in O. tauri and C. reinhardtii absent in The Chl a603-a609 are in the and the amino acid residues around the two are shown as stick models. The number the lines indicate the between Chl a603-a609 in Lhca complexes from O. tauri, C. and In and the red indicate the residues around the Chl molecules from and the six Lhca proteins, three Lhcp Trimers 1–3) to the PSI-LHCI complex on the third side along the of PsaH, PsaL, and subunits (Figure 2a and d). As a the PSI core is by an belt formed by the Lhcp PsaG and (Figure 2a and d). This side of the PSI core was by one LHC or two LHC trimers in plants or green algae are under state 2 conditions et al., Pan et al., 2018; Pan et al., 2021). the three trimers associated with Trimers 1 and 3 are whereas 2 is a The detailed cryo-EM features for of Lhcp1 and Lhcp2 are shown in Figure 2—figure supplement 3. Trimers 1 and 3 to PSI on the and while 2 with PSI on the side through Lhcp1 subunit and with Lhca6 through an Lhcp2 As 1 is between Trimers 2 and it with Trimers 2 and and is related with through at In C. two LHCII trimers associate with PSI in state 2 et al., Pan et al., whereas one LHCII is located at the peripheral region of PSI in state 2 et al., 2018; Figure 3). While the sites of Trimers 1 and 2 overlaps with those of and trimers from supercomplexes not well with other (Figure the PSI core regions are O. tauri 1 to be by and by Å in to the position of C. reinhardtii 2 is by in to the position of C. reinhardtii The LHCII associated with to a position between Lhcp Trimers 1 and 3. Figure Download asset Open asset the sites of Trimers with those of LHCII trimers bound to C. reinhardtii and plant photosystem I (a and b) The structure of OtPSI-LHCI-Lhcp supercomplex is with the supercomplex from C. reinhardtii (PDB or (PDB The three structures are on the common The the of Trimers or LHCII green, magenta, The indicate the or between Lhcp trimers in O. tauri and the corresponding LHCII trimers in C. reinhardtii and in The number the indicate the or 1 is located and the interfacial between are Å or larger (Figure Although 1 does not form with we the presence of lipid molecules that the On the other Trimers 2 and 3 form and with and PsaK, respectively (Figure and 2 to PSI on three different sites (Figure 1, has its region into a surface formed by and subunits (Figure The of Lhcp1 contains an phosphorylated to those found in et al., and C. reinhardtii et al., 2021). The of Lhcp1 with amino acid residues through and (Figure in a similar as those of and C. reinhardtii in Lhcp1 might be on its as there is an density to and the van between the and amino acid residues from to stabilize the between Lhcp1 and the PSI core (Figure Lhcb proteins are also at amino-terminal and phosphorylated on in the third position et al., 2 and 3 are located in the membrane-embedded regions on the stromal and lumenal respectively (Figure On two Lhcp1 and van with amino acid residues and pigment molecules from and subunits (Figure and 3 with mainly through van on the stromal and lumenal (Figure Figure Download asset Open asset between Trimers and photosystem I (PSI) (a) The interface between 1 and (b) The interface between 2 and (c) The interface between 3 and PsaK. (d–f) The detailed between Lhcp1 of 2 and at sites shown in The detailed between Lhcp2 of 3 and at 4 shown in The the lines are between two features of Lhcp1 and Lhcp2 As an member of the green O. tauri belongs to of at the basal position of the green While and are related to plant and (Six et al., low with or The of and a classical of Lhc with three transmembrane and and three amphipathic on the lumenal side and (Figure and and Figure supplement 1). While the structure of highly that of it from those of and in the and (Figure supplement 2a–c). and of are than the corresponding ones in or (Figure supplement Figure with 2 supplements see all Download asset Open asset The structures and pigment of and (a and b) views of (a) and (b) The backbones of are showed as cartoon models, while the are presented as stick models. The of Chl molecules are for The phosphorylated and the at the region of Lhcp1 is highlighted as sphere models. and indicate the three transmembrane in whereas and are the two amphipathic at the lumenal gray, Lhcp1 and Lhcp2 green, Chl cyan, Chl magenta, and The arrangement of pigment molecules in (c) and the are not In the pigment molecules within the to stromal surface are while the the pigment molecules within the to the lumenal In of pigment and contain Chl molecules Chl a, Chl b, and 1 and carotenoid molecules 2 and 1 (Figure and The Chl ratio of the structural model is to the previously reported of for the Lhcp2 (Swingley et al., 2010). While the number of molecules found in the structure the previous four of molecules are more than (Swingley et al., 2010). As O. tauri species in and area of the ocean by light with an up to

Green algae, Chlorella ellipsoidea, Haematococcus pluvialis and Aegagropila linnaei (Phylum Chlorophyta) were simultaneously decoded by a genomic skimming approach within 18-5.8-28S rRNA region. Whole genomic DNAs were isolated from green algae and directly subjected to low coverage genome skimming sequencing. After de novo assembly and mapping, the size of complete 18-5.8-28S rRNA repeated units for three green algae were ranged from 5785 to 6028 bp, which showed high nucleotide diversity (π is around 0.5–0.6) within ITS1 and ITS2 (Internal Transcribed Spacer) regions. Previously, the evolutional diversity of algae has been difficult to decode due to the inability design universal primers that amplify specific marker genes across diverse algal species. In this study, our method provided a rapid and universal approach to decode the 18-5.8-28S rRNA repeat unit in three green algal species. In addition, the completely sequenced 18-5.8-28S rRNA repeated units provided a solid nuclear marker for phylogenetic and evolutionary analysis for green algae for the first time.

The composition of phytoplankton and periphyton community in Togyo reservoir was investigated. A total of phytoplankton was composed of 150 taxa, belonging to 6 phyla, 8 classes, 15 orders, 5 suborders, 31 families, 71 genera, 106 species, 14 varieties, 1 form and 29 unidentified species. The observed number of diatoms and green algae were much higher than others. Within diatoms the pennate diatoms appeared more than centric diatoms and solitary forms or colonial forms appeared more than filamentous forms in green algae. A total of epipelic algae was composed of 125 taxa, belonging to 3 phyla, 3 classes, 6 orders, 3 suborders, 13 families, 30 genera, 87 species, 29 varieties, 2 forms and 7 unidentified species. The diatoms appeared much more than others. Among those, the pennate diatoms dominated the centric diatoms in species number observed. A total of epilithic algae was composed of 114 taxa, belonging to 4 phyla, 4 classes, 11 orders, 3 suborders, 22 families, 38 genera, 79 species, 8 varieties, 1 form and 26 unidentified species. The observed number of diatoms and green algae were much higher than others. Within diatoms the pennate diatoms dominated the centric diatoms in species number observed. The dominance of pennate diatoms of the diatom community in the epipelic algal community and the epilithic algal community could be assumed that was due to the presence of raphe structure of pennate diatoms.

The first studies of phytoplankton of the River Warta in Poznań (Poland) were carried out in the 20th century (in 1922–23 and 1950–57). In the growing seasons the dominant groups were diatoms and green algae. Cyanobacteria were noted, but they did not have high abundance. The aim of this work is to present the phytoplankton research conducted on the River Warta in Poznań in the 21st century (in 2003, 2009, 2010 and 2016). In all years the dominance of diatoms and green algae in terms of biomass was noted. However, in late summer cyanobacteria biomass was high and this group became dominant or co-dominant. Spring blooms were created by unicellular centric diatoms, e.g. Stephanodiscus minutulus and colonial green algae: Coelastrum microporum or Micractinium pusillum. In summer, bloom-forming taxa were unicellular centric diatoms, colonial diatoms: Aulacoseira granulata or Fragilaria crotonensis and cyanobacteria: Aphanizomenon flos-aquae and Woronichinia naegeliana. The occurrence of taxa typical of dam reservoirs and lakes suggests the influence of the Jeziorsko Reservoir on the phytoplankton of the River Warta, but it does not exclude the impact of tributaries and oxbow lakes. The research conducted in the 20th and 21st century show important changes in the taxonomical structure and abundance of phytoplankton.

This study presents a first compilation of phytoplankton species composition of an industrial effluent (waste) water of coca cola and 7up bottling company of kakuri Kaduna south Nigeria. Sample collection spanned a period of 12 month April 2009 to may 2010. Phytoplankton sample were collected monthly in the open water using a plankton net mesh size 55mm towed at low speed for 10 minutes. The net hauls were transferred into two liter jar screened tight and properly labeled and samples immediately presented with 4% umbuffered formation solution and analysis at the laboratory, phytoplankton was identified microscopically and recovered following the method suggested by valenkar and Desai (2004). A seasonal pattern of phytoplankton variation was observed, the dry season cell counts were significantly (p < 0.05) higher than the wet season species recorded. The taxa recorded belong to three divisions namely: Bacillariophyceae (diatom), chlorophyceae (green algae) and Cyanophyceal (blue- green algae). The chlorophyceae were the predominant group and account for 55% of the total species compositions, Cyanophyceal 35%, and bacillariophyceal 9.3%. Stations B water recorded relatively higher number of species and number of individuals of each species more than stations A and C. The more noticeable phytoplankton observed species like Cymbella, Gomphonema, Navicula, Nitischia, Gyrosigma and Coscinodiscus spp in abundance.

Decision letter: The photosystem I supercomplex from a primordial green alga Ostreococcus tauri harbors three light-harvesting complex trimers

To quantify the ecological impacts of organic sediments and environmental dredging, benthic mollusks were chosen as bioindicators of environmental change, measured as sediment organic content and associated parameters. Data on species richness, ecological diversity (which was measured as biodiversity), and abundances were collected alongside sediment and near-bottom water quality data before, during, and after environmental dredging. Organic sediment content was found to have an inverse logarithmic relationship with benthic mollusk biodiversity, species richness, and abundance. Post hoc analyses found that percent dissolved oxygen, which correlates with sediment organic content, was responsible for 29.31–34.12% of the benthic mollusk community variation. Sediments with lower organic content had higher biodiversity (organism densities up to 1 organism m−2), abundance (over 2.0 × 105 organisms m−2), and species richness (organism densities up to 4 organisms m−2). In comparison, sediments with higher organic content had low biodiversity (organism densities 0–1 organisms m−2), abundance (as low as 0 organisms m−2), and species richness (organism densities as low as 0 organisms m−2).

Aims: The aims of the current study are to reveal the response of high latitude riverine planktonic algal communities in northeastern Siberia to extreme climatic conditions of its habitats. Study Design: We implemented diverse statistical methods, which represent some new approaches in freshwater algal diversity analysis. Place and Duration of Study: Institute of Evolution, University of Haifa, Israel, Institute for Biological Problems of Cryolithozone SB RAS, Russia, between June 2008 and Original Research Article British Journal of Environment & Climate Change, 4(4): 423-443, 2014 424 January 2014. Methodology: We collected 800 samples of phytoplankton from 400 sites of 12 northeastern Siberian rivers in gradients of climatic and chemical variables that we analyzed. New indices Geo-associated and Dynamic Habitat Index were included in this analysis. Statistical methods for comparative floristic analyses were used for calculating the similarity of algal communities among the sampling stations. Multiple regression stepwise statistical analysis on phytoplankton including chemical and climatic variables data was performed. Species diversity in algal communities and their environmental variables relationships were calculated. Results: As a result, 1283 species (1637 taxa of species and infraspecies) from six taxonomic divisions were identified in phytoplankton communities. Species richness as a whole increased to the north. Abundance and biomass were highly correlated. Two types of phytoplankton communities were identified: a southern community with increasing diatoms and a northern group with decreasing diatoms to the north. Diatoms prevailed but were replaced by green algae in high mountains or by green and Chrysophyta algae and Cyanobacteria in the Arctic. We revealed major variables that considered stimulating or stress factors with helps of statistical prorgams. Conclusion: Statistical analyses of phytoplankton in 12 large rivers revealed an increase in species richness to the north with community structure changing under stimulation of air temperature, ice-free periods, humidity, and trophic variables were stimulants and water transparency and speed flow were considered stress factors.

The fluorescence properties of exponentially growing freshwater diatoms, green and blue-green algae were compared with a standard filter fluorometer and a scanning spectrofluorometer. Green algae and diatoms excited with blue light had R values (ratio of in vivo fluorescence to extractable chlorophyll a) up to 50 times higher than the cyanophytes. There were also considerable differences in R between species within each algal class—coefficients of variation were typically 35–50%—and this variation was slightly increased by treatment with the non-cyclic electron flow inhibitor, 3(3,4-dichlorophenyl)-1,1-dimethyl urea (DCMU). A major component of blue-green algal fluorescence was the red light emission from phycobilin accessory pigments. This contribution characterized their emission and excitation spectra and suggested a rapid assay for cyanophyte dominance, which was tested on natural plankton communities. Phycobilin fluorescence was insensitive to DCMU and resulted in highly wave-length-specified variations in CFC (cellular fluorescence capacity, the rise in fluorescence upon addition of DCMU). CFC values for blue-greens were consequently low when measured in the broad bandpass fluorometer, but were up to three times higher when measured with the spectrofluorometer set to the emission peak for photosystem II chlorophyll a. Similar results were obtained with natural populations of blue-green algae. The phycobilin content of blue-green species was influenced by nitrogen source and light quality during growth, and this resulted in variable R and CFC values. Fluorescence properties of diatoms and green algae were less responsive to environmental conditions during growth. Both diatoms and green algae exposed to bright light for 15 min demonstrated a strong reduction in R. Conversely blue-green algal fluorescence was depressed very little, or more commonly, was slightly enhanced by bright light. These observations underscore the importance of species composition and choice of fluorometer as critical determinants of measured algal fluorescence properties.

Observations were made on the development and distribution of phytoperiphyton communities in 66 lake-river systems in NW Russia from Lake Ladoga to the Barents Sea. In total, 130 genera and 648 species were identified from different substrates, belonging to Cyanophyta (19.1%), Bacillariophyta (59.6%), Chlorophyta (18.7%), and algae from other orders (2.6%). In all streams diatoms dominated by species richness, but they were surpassed by green algae in terms of biomass. The green algae ranged from small planktonic forms to large filamentous species and produced easily visible algal communities. Among the planktonic forms the desmids were the most diverse group. They occurred in attached communities of all rivers and, while never abundant, were widespread. The attached community’s biomass was dominated by green algae. Among these, the filamentous algae Mougeotia sp., Oedogonium sp., Zygnema sp., Spirogyra sp. and Ulothrix zonata exhibited mass development in streams. Their distribution was patchy in the basin, with a total cover varying from less than 1% to 90% of the stream bottom. In some river stretches the diversity and predominance of green algae could be due, in part, to poorly developed riparian canopies.

The objective of this study in River Atna, Norway, was to analyse the spatial and temporal variation in species composition and diversity of the periphyton community in a pristine sub-alpine / boreal watercourse. The variations in the biotic parameters were related to selected environmental factors. We addressed epilithic algae and species living epiphytic on epilithic algae and submerged bryophytes. The sampling sites were located in the alpine, northern boreal, and mid boreal biomes. There was considerable spatial variation in species composition and diversity. This variation showed close correlation with natural gradients in water temperature and nutrient concentration. Three or four periphyton community categories could be distinguished in terms of species composition, diversity, and environmental variables. At high altitudes (1150–740 m a.s.l.) in cold water temperatures and extremely low nutrient contents, there was very low species diversity, only including algae known from ultra oligothrophic cold waters, e.g. Scytonematopsis starmachii (cyanobacteria) and Klebshormidium rivulare (green algae). The second category, at medium altitudes (701-522 m a.s.l.), was characterised by somewhat higher water temperatures and nutrient contents, and the species diversity was higher. This category included algae known from somewhat richer waters, e.g. Stigonema mamillosum (cyanobacteria) and Zygnema spp. (green algae). The third category was located at approx. 522 m a.s.l., had low water temperatures, relatively high alkalinity, and was characterised by Tolypothrix distorta (cyanobacteria) and Ulothrix zonata (green algae). A possible fourth category was found in the lower part of the river (350 m a.s.l.), where periphyton was distinguished by high diversity. At the individual sampling localities, species diversity showed strong seasonal variation, but otherwise high temporal stability. Over the 12 years of observations, there was only a weak temporal trend; towards species initially occurring only at low altitudes and high nutrient content. The combination of high temporal stability and high spatial variability, correlating closely with environmental gradients, is the main reason why periphyton observations have become an important constituent in water quality assessment.Key wordsPeriphytonreference conditionsNorwaynatural variationspecies compositionspecies diversity

Initial events of biofilms development and succession were studied in a freshwater environment at Kalpakkam, East Coast of India. Biofilms were developed by suspending Perspex (Plexiglass) panels for 15 days at bimonthly intervals from January 1996 to January 1997. Changes in biofilm thickness, biomass, algal density, chlorophyll a concentration and species composition were monitored. The biofilm thickness, biomass, algal density and chlorophyll a concentration increased with biofilms age and colonization was greater during summer (March, May and July) than other months. The initial colonization was mainly composed of Chlorella vulgaris, Chlorococcum humicolo (green algae), Achnanthes minutissima, Cocconeis scutellum, C. placentula (diatoms) and Chroococcus minutus (cyanobacteria) followed by colonial green algae such as Pediastrum tetras, P. boryanum and Coleochaete scutata, cyanobacteria (Gloeocapsa nigrescens), low profile diatoms (Amphora coffeaeformis, Nitzschia amphibia, and Gomphonema parvulum) and long stalked diatoms (Gomphoneis olivaceum and Gomphonema lanceolatum). After the 10th day, the community consisted of filamentous green algae (Klebshormidium subtile, Oedogonium sp., Stigeoclonium tenue and Ulothrix zonata) and cyanobacteria (Calothrix elenkinii, Oscillatoria tenuis and Phormidium tenue). Based on the percentage composition of different groups in the biofilm, three phases of succession could be identified: the first phase was dominated by green algae, the second by diatoms and the third phase by cyanobacteria. Seasonal variation in species composition was observed but the sequence of colonization was similar throughout the study period.