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To unveil possible changes in diatom communities in Cypriot streams over the last ten years or so, we selected samples from the years 2020, 2021, and 2022 for the "recent" dataset (N = 119) and samples from the years 2010 and 2011 for the "historical" dataset (N = 108). Biotic homogenization has become a truly global phenomenon. Here we show that, over the last ten years, in response to increased water temperature, conductivity, and discharge variability due to climate-change, Cypriot stream diatom communities include a higher number of trivial (= widespread, tolerant, and opportunistic), aerial, and thermophilic species, have reduced β-diversity and increased nestedness. Moreover, IndVal analysis shows that indicator species from the historical dataset were characteristic, often relatively rare species, while the indicators of the recent dataset were a group of typical trivial, eutraphentic, and thermophilic species. As is almost always the case, the diatom communities we studied were subjected to multiple stressors, often affecting them in opposite ways. Besides the increase in trivial species, the reduction in β-diversity, and the rise in nestedness mentioned above, the diatom assemblages we studied also showed an increase in α-diversity that could be due to a moderate reduction in nutrients in several sites. High-ecological-integrity ecosystems, such as springs, waterfalls, and dripping rock-walls, in particular springs that were shown to be excellent hydrologic refugia in climates heavily affected by climate change, and the stream sites close to them should be carefully protected, as they can be refugia for sensitive and characteristic species that can recolonize the adjacent streams after adverse climatic events., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)

Gomphonema parvulum is a cosmopolitan freshwater diatom that is used as an indicator in water quality biomonitoring. In this study, we report the culturing of two geographically separated isolates from southeastern North America, their morphology, and the sequencing and assembly of their mitochondrial and chloroplast genomes. Morphologically, both strains fit G. parvulum sensu lato, but the frustules from a protected habitat in South Carolina were smaller than those cited in the historic data of this species from the same location as well as a second culture from Virginia. Phylogenetic analyses using the rbcL gene placed both within a clade with G. parvulum. Genetic markers, including full chloroplast and mitochondrial genomes and the nuclear small subunit rRNA gene region were assembled from each isolate. The organellar genomes of the two strains varied slightly in size due to small differences in intergenic regions with chloroplast genomes of 121,035 bp and 121,482 bp and mitochondrial genomes of 34,639 bp and 34,654 bp. The intraspecific pairwise identities of the chloroplast and mitochondrial genomes of these two isolates were 97.9% and 95.4%, respectively. Multigene phylogenetic analysis demonstrated a close relationship between G. parvulum, Gomphoneis minuta, and Didymosphenia geminata., (© 2024 The Authors. Journal of Phycology published by Wiley Periodicals LLC on behalf of Phycological Society of America.)

Climate change and human activities may alter the structure and function of boreal peatlands by warming waters and changing their hydrology. Diatoms can be used to assess or track these changes. However, effective biomonitoring requires consistent, reliable identification. To address this need, this study developed a diatom voucher flora of species found across a boreal fen gradient (e.g., vegetation) in interior Alaskan peatlands. Composite diatom samples were collected bi-weekly from three peatland complexes over the 2017 summer. The morphological range of each taxon was imaged. The fens contained 184 taxa across 38 genera. Eunotia (45), Gomphonema (23), and Pinnularia (20) commonly occurred in each peatland. Tabellaria was common in the rich and moderate fen but sparse in the poor fen. Eunotia showed the opposite trend. Approximately 11% of species are potentially novel and 25% percent matched those at risk or declining in status on the diatom Red List (developed in Germany), highlighting the conservation value of boreal wetlands. This voucher flora expands knowledge of regional diatom biodiversity and provides updated, verifiable taxonomic information for inland Alaskan diatoms, building on Foged's 1981 treatment. This flora strengthens the potential to effectively track changes in boreal waterways sensitive to climate change and anthropogenic stressors., Competing Interests: Conflicts of Interest: The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript; or in the decision to publish the results.

Periphyton assemblages from the nearshore environment of the west (California) side of Lake Tahoe, were analyzed to determine their taxonomic composition and community structure across habitats and seasons. Lake Tahoe is the second deepest lake in the US and an iconic oligotrophic subalpine lake with remarkable transparency. It has experienced offshore cultural eutrophication since the 1960s with observations of nuisance nearshore algal growth since the mid 2000s attributed to anthropogenic stressors. Samplings from November 2019-September 2020 provide useful snapshots against which older monitoring may be contextualized. A voucher flora, complete with descriptions, photo-documentation and referencing to species concepts employed, was created as a method of providing reproducible identification and enumeration of algal species, and more seamless reconciliation of detailed taxonomic data with future monitoring projects. The eulittoral zone (0-2 m) is seasonally dominated by elongate araphid ( Synedra, Ulnaria ) and stalked or entubed diatoms ( Gomphonema, Cymbella, Encyonema ). The sublittoral zone (>2 m) is dominated by a nitrogen-fixing Epithemia -cyanobacteria assemblage with less seasonal changes in dominance and composition that expanded to impinge on the 2 m depths of the eulittoral zone in the Fall. Sublittoral epipsammic samples, despite their proximity to rocks, had a very distinct diatom composition and high species dominance, similar to what was seen in the Fall eulittoral samples, with high numbers of Staurosirella chains and small biraphid diatoms. The deeper samples at 30 and 50 m contained high numbers of live Epithemia , and indicate a thriving sublittoral assemblage at these greater depths, but with less biomass. The 2019-20 data show many of the same diatom taxa observed in the 1970's and 1980's but with changes in species dominance. Notably, there was less of the green alga Mougeotia , when compared to the 1970's data, and a higher dominance by nitrogen fixing Epithemia in the sublittoral zone, persisting year-round. These new data show roughly double the algal species biodiversity that had been documented previously in the Lake Tahoe nearshore, and is largely attributed to the methods employed. Adopting these new methods in future monitoring efforts should improve harmonization of taxonomic data and help advance our knowledge of the contributions to nearshore cultural eutrophication., Competing Interests: Conflict of interest The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Mitochondria carry the remnant of an ancestral bacterial chromosome and express those genes with a system separate and distinct from the nucleus. Mitochondrial genes are transcribed as poly-cistronic primary transcripts which are post-transcriptionally processed to create individual translationally competent mRNAs. Algae post-transcriptional processing has only been explored in Chlamydomonas reinhardtii (Class: Chlorophyceae) and the mature mRNAs are different than higher plants, having no 5' UnTranslated Regions (UTRs), much shorter and more variable 3' UTRs and polycytidylated mature mRNAs. In this study, we analyzed transcript termini using circular RT-PCR and PacBio Iso-Seq to survey the 3' and 5' UTRs and termini for two green algae, Pediastrum duplex (Class: Chlorophyceae) and Chara vulgaris (Class: Charophyceae). This enabled the comparison of processing in the chlorophyte and charophyte clades of green algae to determine if the differences in mitochondrial mRNA processing pre-date the invasion of land by embryophytes. We report that the 5' mRNA termini and non-template 3' termini additions in P. duplex resemble those of C. reinhardtii , suggesting a conservation of mRNA processing among the chlorophyceae. We also report that C. vulgaris mRNA UTRs are much longer than chlorophytic examples, lack polycytidylation, and are polyadenylated similar to embryophytes. This demonstrates that some mitochondrial mRNA processing events diverged with the split between chlorophytic and streptophytic algae.

Species within the green algal order Cladophorales have an unconventional plastome structure where individual coding regions or small numbers of genes occur as linear single-stranded DNAs folded into hairpin structures. Another group of photosynthetic organisms with an equivalently reduced chloroplast genome are the peridinin dinoflagellates of the Alveolata eukaryotic lineage whose plastomes are mini-circles carrying one or a few genes required for photosynthesis. One unusual aspect of the Alveolata is the polyuridylylation of mRNA 3' ends among peridinin dinoflagellates and the chromerid algae. This study was conducted to understand if an unconventional highly reduced plastome structure co-occurs with unconventional RNA processing. To address this, the 5' and 3' mRNA termini of the known chloroplast genes of Pithophora roettleri (order Cladophorales) were analyzed for evidence of post-transcriptional processing. Circular Reverse Transcriptase PCR (cRT-PCR) followed by deep sequencing of the amplicons was used to analyze 5' and 3' mRNA termini. Evidence of several processing events were collected, most notably the 3' termini of six of the eight genes were polyuridylylated, which has not been reported for any lineage outside of the Alveolata. Other processing events include poly(A) and heteropolymeric 3' additions, 5' primary transcript start sites, as well as the presence of circularized RNAs. Five other species representing other green algal lineages were also tested and poly(U) additions appear to be limited to the order Cladophorales. These results demonstrate that chloroplast mRNA polyuridylylation is not the sole provenance of photosynthetic alveolates and may have convergently evolved in two distinct photosynthetic lineages., (© 2020 Phycological Society of America.)

A Pediastrum duplex (Chlorophyta) strain was isolated from a freshwater system in Milledgeville, Georgia and its chloroplast and mitochondrial genomes sequenced. The chloroplast genome was 199,241 bp with 136 genes and the mitochondrial 40,756 bp with 40 genes, both were circular. Comparison of the 'Milledgeville' plastome to other P. duplex isolates revealed a nearly identical sequence identity to archived genes and genomic fragments from the strain UTEX1364 which was isolated from Lake Machovo in 1962. These sequences provide chloroplast and mitochondrial genomes from a wild P. duplex isolate and provide more organelle genomes for a genus with cryptic phylogenetic relationships., Competing Interests: No potential conflict of interest was reported by the authors., (© 2019 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.)

The rise of human populations and the growth of cities contribute to the depletion of natural resources, increase their cost, and create potential climatic changes. To overcome difficulties in supplying populations and reducing the resource cost, a search for alternative pharmaceutical, nanotechnology, and energy sources has begun. Among the alternative sources, microalgae are the most promising because they use carbon dioxide (CO2) to produce biomass and/or valuable compounds. Once produced, the biomass is ordinarily harvested and processed (downstream program). Drying, grinding, and extraction steps are destructive to the microalgal biomass that then needs to be renewed. The extraction and purification processes generate organic wastes and require substantial energy inputs. Altogether, it is urgent to develop alternative downstream processes. Among the possibilities, milking invokes the concept that the extraction should not kill the algal cells. Therefore, it does not require growing the algae anew. In this review, we discuss research on milking of diatoms. The main themes are (a) development of alternative methods to extract and harvest high added value compounds; (b) design of photobioreactors;, ((c) biodiversity and (d) stress physiology, illustrated with original results dealing with oleaginous diatoms.)

Algal taxonomy is a key discipline in phycology and is critical for algal genetics, physiology, ecology, applied phycology, and particularly bioassessment. Taxonomic identification is the most common analysis and hypothesis-testing endeavor in science. Errors of identification are often related to the inherent problem of small organisms with morphologies that are difficult to distinguish without research-grade microscopes and taxonomic expertise in phycology. Proposed molecular approaches for taxonomic identification from environmental samples promise rapid, potentially inexpensive, and more thorough culture-independent identification of all algal species present in a sample of interest. Molecular identification has been used in biodiversity and conservation, but it also has great potential for applications in bioassessment. Comparisons of morphological and molecular identification of benthic algal communities are improved by the identification of more taxa; however, automated identification technology does not allow for the simultaneous analysis of thousands of samples. Currently, morphological identification is used to verify molecular taxonomic identities, but with the increased number of taxa verified in algal gene libraries, molecular identification will become a universal tool in biological studies. Thus, in this report, successful application of molecular techniques related to algal bioassessment is discussed., (© 2014 Phycological Society of America.)

Aims: To evaluate the role of manure treatment lagoons of swine operations in the fate of faeces- and feed-borne tetracycline-resistant genes (TRG)., Methods and Results: Samples of feed, faeces, lagoon liquid and lagoon sediment in farm's vicinity were collected at three swine operations varied on their operational practices and analysed on the presence and frequencies of incidence of sixteen TRG in upstream sources (feed, faeces) and downstream receptacles (lagoon liquid and sediments). The highest frequency of TRG incidence was observed in a farm with extensive antibiotic usage and the lowest in the antibiotic-free farm. The study revealed a decrease in TRG richness and diversity in the downstream habitats of each farm. The observed TRG diverged into two groups, the persistent genes that were detected both upstream and downstream, and the transient genes that were detected in the upstream habitats but became nondetectable in the lagoons. Quantitative PCR analysis revealed that upstream concentrations and abundances (determined as TRG/16S rRNA gene ratios) of transient and persistent TRG were similar; however, the former were attenuated in the lagoons to the levels below the detection limit, whereas the latter were ∼ 100-1000 fold amplified in their (mostly) liquid phases and were also detected in farms' vicinities., Conclusion: Manure lagoons of swine operations imposed both positive and negative selection towards faeces- and feed-borne TRG that, respectively, caused either their proliferation or attenuation in those environments., Significance and Impact of the Study: The study reveals that discharge of antibiotic resistance genes from swine farms to the environment is linked to their positive selection (defined as an impact leading to proliferation of those genes) in manure lagoons., (© 2012 The Authors. Journal of Applied Microbiology © 2012 The Society for Applied Microbiology.)

Despite their recognized contribution to species richness, the importance of rare taxa richness in bioassessment is unclear. This study aimed to characterize the environmental factors affecting the number of rare diatom taxa in western U.S. streams and rivers, and to evaluate whether this number can be used to differentiate streams with contrasting human disturbance. Three different categories of rare taxa were used: satellite (taxa with low occurrence and low abundance), rural (taxa with high occurrence and low abundance), and urban (taxa with low occurrence and high abundance). Common taxa were included as a separate category of core taxa (taxa with high occurrence and high abundance). We analyzed 987 diatom samples collected over the period of 5 years (2000-2004) for the U.S. Environmental Protection Agency's (EPA) Western Environmental Monitoring and Assessment Program (WEMAP). The results showed that rural taxa richness (number of rural taxa per site) increased along a longitudinal gradient from mountainous, fast-flowing oligotrophic streams with fewer fine substrates to large, slow-moving, nutrient-rich rivers with abundance of fine substrates. Rural taxa richness was the only rarity metric that distinguished least disturbed (reference) sites from the most disturbed (impacted) sites, but it was significantly different only in the mountains ecoregion. Core taxa richness distinguished reference from impacted sites in the West and in each one of the three ecoregions (mountains, plains, and xeric). Our findings revealed that rural taxa richness can be used as an indicator of human disturbance in streams/rivers, especially in the mountains ecoregion, and that rarity definition is important in bioassessment., (© 2011 Phycological Society of America.)