Journal of Phycology最新文献

Diatoms are known for their extraordinary species richness, cornerstone roles in aquatic ecosystems, and immense contributions to the global cycling of carbon, oxygen, and silica. For nearly 2 centuries, taxonomic classifications of diatoms have been based on interpretations of their feature-rich, silica cell walls. These classifications, in turn, have been used to make broad inferences about diatom ecology and evolution, but decades of molecular phylogenetic research have shown that historical and contemporary classification systems do not reflect evolutionary history, severely limiting their utility and insights. We took advantage of recent advances in our understanding of the diatom phylogeny to develop the first entirely natural classification of diatoms, in which only monophyletic groups have been recognized and named. The classification is comprehensive, dividing 431 genera among 68 families, 44 orders, and 10 classes. Among these, seven classes, 13 orders, three families, and one genus are proposed as new. Although the new classification includes many areas of overlap with previous systems, one principal departure is the increased number of classes, which reflects that "centric" and "araphid" diatoms are comprised of multiple lineages recognized here as distinct classes. By providing a more accurate representation of phylogenetic relationships, the proposed classification facilitates clearer communication about all aspects of diatom biology.

The green alga Pleodorina japonica is an interesting volvocine species that harbors abundant rickettsial endosymbionts ("MIDORIKO") within its cytoplasm. However, the diversity and transmission of these endosymbionts within the species remain unclear. In this study, we examined the presence or absence of "MIDORIKO" and the genetic diversity in 21 culture strains of the host P. japonica population from various localities in Japan. Genomic polymerase chain reactions using "MIDORIKO"-specific primers and 4',6-diamidino-2-phenylindole-staining demonstrated that only five of the 21 strains harbored "MIDORIKO." The 16S ribosomal DNA sequences of "MIDORIKO" from these five strains (1148 bp) were identical to each other and distinct from the sequences of the rickettsial endosymbionts harbored by other algal species and protists, suggesting that "MIDORIKO" from P. japonica is specific to P. japonica. The phylogenetic results for the 21 host strains, which were resolved based on three nuclear genes encoding oxygen-evolving enhancer protein 1, F1F0 ATP synthase subunit beta and actin disagreed significantly. None of the three gene phylogenies supported the close relationship of the five "MIDORIKO"-harboring strains. A recombination test using the three concatenated genes provided strong evidence of recombination. Therefore, gene flow by sexual reproduction has likely occurred in the natural habitats of P. japonica. The transmission of "MIDORIKO" among different P. japonica genotypes could also be considered to occur via sexual reproduction, although it is likely infrequent via that method given the sporadic nature of "MIDORIKO" within the P. japonica population. Although P. japonica exhibits homothallic sexual reproduction, the present genetic data demonstrate that it is undoubtedly a biological species.

Seaweed-associated microbiota distribution is influenced by factors such as symbiosis, season, life cycle, environmental conditions, and geographic location. This study investigated how microbial communities vary across different parts of benthic Sargassum thalli from nine locations spanning three regions over 600 km apart along Brazil's coast, with sites in each region within 20 km of each other. Using 16S rDNA gene sequencing of the V4 region, we identified 16,802 amplicon sequence variants (ASVs), with 1169 shared across thallus structures and 1100 shared across regions. Our analysis showed that microbial communities varied both along the thallus and between regions, though communities were similar within regions less than 20 km apart. Among thallus structures, the holdfast had the most distinct microbiota, differing from the phylloid and receptacle. This pattern was consistent across Brazil's coastline and has also been observed in studies from Singapore and Portugal. The holdfast microbiota was marked by an unidentified Alphaproteobacteria, along with sulfur-cycling families Desulfocapsaceae and Desulfosarcinaceae. Phylloids and receptacles were mainly associated with photosynthetic cyanobacteria. We also identified shared taxonomic biomarkers across Sargassum species from Asia, Europe, and South America. These results suggest that the microbiota are more influenced by the thallus structure than by geographic location. These consistent patterns across Sargassum species from different continents-Asia, Europe, and South America-support the hypothesis of microbiota specialization within morphological niches.

Here, we have presented draft genome sequences from the type strain of Almyronema epifaneia MCC 5313 as well as Thainema salinarum MCC 5402, two filamentous cyanobacteria obtained from the Sundarbans, the largest intertidal mangrove forest in the world. AntiSMASH analysis revealed that the two genomes contained distinct biosynthetic gene clusters (BGCs), which may help in supporting their adaptation to the fluctuating intertidal environment. These BGCs encode the production of secondary metabolites such as terpenes, hapalosin, anachelin, bovienimide A, and scytocyclamide. The whole-genome shotgun projects for Almyronema epifaneia MCC 5313 and Thainema salinarum MCC 5402 have been deposited in GenBank under accession numbers GCA_042788235.1 and GCA_052168235.1, respectively.

The canopy-forming feather boa kelp Egregia menziesii exhibits remarkable morphological variability across its geographic range. Regional morphotypes of Egregia were once considered separate species, but they were not determined to be genetically distinct; instead, their morphology was thought to reflect local physical or environmental conditions. Although morphological variation in Egregia has long been observed and was previously characterized through field surveys in the early 2000s, we revisited this topic using digital morphometrics (i.e., image analysis) of 1624 macroalgal herbarium specimens from California dating back to the 19th century. We observed that the morphology of Egregia (rachis texture, lateral blade shape, and blade or pneumatocyst density) varied along a latitudinal gradient and could be predicted by seawater temperature and wave height. We also identified some region-specific morphological changes in recent decades. Further, the monthly presence or absence of sporophylls in southern-region specimens provided preliminary evidence into the reproductive phenology of Egregia. Herbarium collections are invaluable for studying patterns in morphology because they showcase inter- and intraspecific variability and establish a baseline for comparison through time. Integrating natural historical and contemporary data will be critical for understanding and predicting future trends in the context of ocean warming.

Algal turfs are assemblages consisting of small marine green, brown, and red algae on the scale of millimeters to a few centimeters. Due to their small size, they have been less intensively studied by macroalgal taxonomists, and they also fall outside the scope of microalgal taxonomists, who tend to focus on smaller, often unicellular, taxa. They often have a rather simple structure and a tendency to converge onto similar morphologies with creeping and upright axes. Because of all of this, there is a substantial amount of undocumented algal biodiversity in turfs, as has been shown in several molecular surveys. Our aim in this paper was to explore some integrative taxonomic methods that could help accelerate the discovery and description of very small turf species. We focused on Pseudoderbesia, a genus of extremely small green algae from the family Bryopsidaceae. We used a combination of multifocal imaging of field-collected samples, microsample genomics, and culturing to document the Pseudoderbesia biodiversity from Heron Island on the Great Barrier Reef. Algorithmic species delimitation based on rbcL and tufA marker genes indicated that likely six (possibly five) species exist in Pseudoderbesia, but only two have been described. We have formally described the two species discovered at Heron Island as P. luxurians and P. epilithica. The latter was described using a multifocal image as the holotype, following an exception to the nomenclatural code for microscopic algae. We have justified this choice extensively, both based on an interpretation of the code and on the broader conceptual need to name newly discovered species, facilitating their use in science, conservation, and policy.

The benthic diatom species Achnanthidium minutissimum belongs to a species complex with a challenging taxonomy. Achnanthidium minutissimum has been reported to be a widespread and abundant species occurring in a broad range of freshwater habitats. However, differentiating and delimiting it from other Achnanthidium species is challenging due to the small size and great similarity of the different species, often with overlaps in morphological features. Therefore, reports of the occurrence of these taxa probably come with a large uncertainty due to potential misidentification. To gain a better understanding of the boundaries between species within the A. minutissimum species complex, we applied an integrative taxonomic approach and investigated the congruence between morphological, molecular, and ecophysiological variability among 13 monoclonal strains isolated from Germany, Sweden, and Spitsbergen. In addition to the characterization of valve morphology, we assessed their growth under different temperatures and salt concentrations and compared sequences of the rbcL marker gene as well as of a broad set of homologous loci sampled by genome skimming. Molecular and ecophysiological variability was mostly congruent with scanning electron microscopy-based morphological identification; the main exception was that two pairs of strains identified as A. cf. microcephalum and A. jackii could be distinguished neither in their ecophysiological profiles nor in their DNA sequences. Extending this integrated taxonomic approach to more strains will be beneficial for a better understanding of the morphological, molecular, and niche differentiation among different Achnanthidium species. The added value of the combined morphological-molecular-ecophysiological approach is an improved delineation of morphological features applicable for species differentiation and a better understanding of ecological differentiation.

We have reported the first mitochondrial (GenBank accession PV035080) and chloroplast (GenBank accession PV035081) genomes for a representative of the gigartinalean family Dumontiaceae (Gibsmithia punonomaewa). High-throughput sequencing yielded both organellar genomes for the holotype specimen of Gibsmithia punonomaewa, a recently described species that is also a putative endemic to the mesophotic zone of the Hawaiian Islands. Gene content and order of the 26,428-bp mitochondrial genome are conserved relative to other available genomes of the Gigartinales. The genome contains 52 genes, including 25 protein-coding sequences (CDSs), 3 rRNAs, and 24 tRNAs, as well as one group II intron in a trnI-GAU tRNA. The chloroplast genome is 185,316 bp in length and contains 236 genes, including 203 CDSs, three rRNAs, and 30 tRNAs, and one group II intron in a trnM-CAU tRNA. Both organellar genomes displayed high synteny compared to close relatives in the order Gigartinales, with unique features restricted to several open reading frames. Phylogenomic analyses of the mitochondrial and chloroplast genomes with other gigartinalean representatives yielded well-resolved phylogenies that supported an early diverging position of the Dumontiaceae within the order Gigartinales.

Following the treatment of Saccharina diabolica, S. ochotensis, and S. religiosa as varieties of S. japonica, the same authors reported independent genetic groups corresponding to the original distributions of these species described in 1902. However, other population genetic studies have not supported these genetic groups corresponding to the varieties, and these varietal names have been applied predominantly to the Japanese population, despite S. japonica having a broader distribution in North Korea and the Russian Far East. This study reevaluated the taxonomic validity of these varieties by investigating the presence of corresponding genetic groups within Japan. We collected 475 individuals across its Japanese distribution, assigned them to five groups based on prior research, and genotyped them using 12 simple sequence repeat (SSR) markers. STRUCTURE analysis, discriminant analysis of principal components scatter plots, and isolation by distance analyses did not support the presence of distinct genetic clusters aligning with the described distributions of S. japonica and its varieties. Instead of confirming the previously demonstrated genetic groups, these analyses revealed either two or three large, geographically based genetic clusters or smaller genetic groups composed of neighboring localities. Consequently, this study has proposed the merger of the three varieties into a single species, S. japonica. Furthermore, we have proposed new combinations of several formae under S. japonica as they have retained their previous taxonomic status under Laminaria japonica or L. diabolica. Further research is required to assess the taxonomic validity of these formae.

Alkaline phosphatase (AP) plays an important role in phosphorus (P) cycling in aquatic ecosystems, particularly under nutrient limitation. In post-mining lakes of Czechia, periphyton forms extensive mats despite chronic P deficiency, suggesting dissolved organic P (DOP) may serve as a key P source. This study examines periphyton's ability to hydrolyze DOP via AP in three post-mining lakes in Czechia, assessing enzyme kinetic models, seasonal variation, and P-acquisition strategies. Seasonal shifts of apparent alkaline phosphatase catalytic efficiency (APCE) in periphyton, determined as the ratio of maximum hydrolysis velocity to Michaelis constant, have indicated that periphyton dynamically adjusts its enzyme activity. Periphyton exhibited rapid DOP turnover (tenths to tens of seconds) but had significantly lower APCE than phytoplankton. This suggests fundamental differences in P-acquisition strategies: Although phytoplankton relies on ambient DOP, periphyton retains and recycles P within its matrix. Retained P can be distributed throughout the periphyton taxa, supporting an idea of metabolic commensalism in periphyton assemblage. Our results underscored the adaptive role of periphyton community in buffering P availability through internal recycling, which, alongside P uptake from the lake water, supports persistence of periphyton in fluctuating P conditions. By sequestering and recycling P internally, periphyton alters lake-wide P dynamics, reduces P availability for phytoplankton, and potentially influences ecosystem productivity. Furthermore, this research has highlighted the limitations of applying simple Michaelis-Menten kinetics to describe complex enzymatic processes in natural ecosystems, emphasizing the need for models that better capture enzymatic heterogeneity and environmental interactions.