The new higher level classification of eukaryotes with emphasis on the taxonomy of protists

Transcription factor binding specificities of the oomycete Phytophthora infestans reflect conserved and divergent evolutionary patterns and predict function

BACKGROUND

Identifying the DNA-binding specificities of transcription factors (TF) is central to understanding gene networks that regulate growth and development. Such knowledge is lacking in oomycetes, a microbial eukaryotic lineage within the stramenopile group. Oomycetes include many important plant and animal pathogens such as the potato and tomato blight agent Phytophthora infestans, which is a tractable model for studying life-stage differentiation within the group.

RESULTS

Mining of the P. infestans genome identified 197 genes encoding proteins belonging to 22 TF families. Their chromosomal distribution was consistent with family expansions through unequal crossing-over, which were likely ancient since each family had similar sizes in most oomycetes. Most TFs exhibited dynamic changes in RNA levels through the P. infestans life cycle. The DNA-binding preferences of 123 proteins were assayed using protein-binding oligonucleotide microarrays, which succeeded with 73 proteins from 14 families. Binding sites predicted for representatives of the families were validated by electrophoretic mobility shift or chromatin immunoprecipitation assays. Consistent with the substantial evolutionary distance of oomycetes from traditional model organisms, only a subset of the DNA-binding preferences resembled those of human or plant orthologs. Phylogenetic analyses of the TF families within P. infestans often discriminated clades with canonical and novel DNA targets. Paralogs with similar binding preferences frequently had distinct patterns of expression suggestive of functional divergence. TFs were predicted to either drive life stage-specific expression or serve as general activators based on the representation of their binding sites within total or developmentally-regulated promoters. This projection was confirmed for one TF using synthetic and mutated promoters fused to reporter genes in vivo.

CONCLUSIONS

We established a large dataset of binding specificities for P. infestans TFs, representing the first in the stramenopile group. This resource provides a basis for understanding transcriptional regulation by linking TFs with their targets, which should help delineate the molecular components of processes such as sporulation and host infection. Our work also yielded insight into TF evolution during the eukaryotic radiation, revealing both functional conservation as well as diversification across kingdoms.

Occurrence of Nosema ceranae, Ascosphaera apis and trypanosomatids in Vespa orientalis linneus 1771

Vespa orientalis is spreading across the Italian and European territories leading to new interactions among species, which could lead to the transmission of pathogens between species. Detection of honey bee viruses in V. orientalis has already been revealed in both adults and larvae, while no information is available regarding parasitic occurrence. Sixty adult hornets collected across apiaries in the South of Italy were subjected to cytological, histopathological and biomolecular examination to evaluate the occurrence of Nosema ceranae, Ascosphaera apis, Lotmaria passim, Crithidia mellificae, and Crithidia bombi. Cytological examination revealed the presence of Nosema spores in 38.33% of individuals while histopathological analysis showed the presence of L. passim-like elements in the rectum of two examined specimens and the presence of fungal hyphae in the small intestine of another hornet. Biomolecular investigation revealed that N. ceranae was the most prevalent pathogen (50.0%), followed by A. apis (6.66%), L. passim (6.66%) and C. bombi (6.0%).

Biodiversity of testate amoebae in Sphagnum bogs: the dataset from forest-steppe ecotone (Middle Volga Territory, Russia)

Background

Testate amoebae are a polyphyletic group of unicellular eukaryotic organisms that are characterised by a rigid shell and inhabit mostly freshwater and terrestrial ecosystems. They are particularly abundant in peatlands, especially in Sphagnum-dominated biotopes. Peatland hydrology is the most important influence on testate amoebae communities. The good preservation of the shells in peat deposits and their response to hydrological regime changes are the principles for palaeohydrological reconstructions. Any changes in the water balance of mires should be expected to have far-reaching effects on biogeochemical cycles, productivity, carbon dioxide and methane exchange.

New information

This paper presents a dataset (Darwin Core Archive - DwC-A) on the distribution of Sphagnum-dwelling testate amoebae in nine mires located in the forest-steppe subzone of the East European Plane. The dataset includes information about 86 taxa belonging to 29 genera and contains 3,123 occurrences of 49,874 individuals. The following environmental variables are provided: microtopography, oxidising and reducing potential, total mineralisation, substrate temperature, acidity, substrate wetness and water table depth. These data might be used for biogeographical and palaeoecological studies, including quantitative reconstructions.

From cyanobacteria and cyanophages to chloroplasts: the fate of the genomes of oxyphototrophs and the genes encoding photosystem II proteins

Chloroplasts are the result of endosymbiosis of cyanobacterial organisms with proto-eukaryotes. The psbA, psbD and psbO genes are present in all oxyphototrophs and encode the D1/D2 proteins of photosystem II (PSII) and PsbO, respectively. PsbO is a peripheral protein that stabilizes the O2-evolving complex in PSII. Of these genes, psbA and psbD remained in the chloroplastic genome, while psbO was transferred to the nucleus. The genomes of selected cyanobacteria, chloroplasts and cyanophages carrying psbA and psbD, respectively, were analysed. The highest density of genes and coding sequences (CDSs) was estimated for the genomes of cyanophages, cyanobacteria and chloroplasts. The synonymous mutation rate (rS) of psbA and psbD in chloroplasts remained almost unchanged and is lower than that of psbO. The results indicate that the decreasing genome size in chloroplasts is more similar to the genome reduction observed in contemporary endosymbiotic organisms than in streamlined genomes of free-living cyanobacteria. The rS of atpA, which encodes the α-subunit of ATP synthase in chloroplasts, suggests that psbA and psbD, and to a lesser extent psbO, are ancient and conservative and arose early in the evolution of oxygenic photosynthesis. The role of cyanophages in the evolution of oxyphototrophs and chloroplastic genomes is discussed.

Complete Mitochondrial Genome and Its Phylogenetic Position in Red Algae Fushitsunagia catenata from South Korea

The mitogenome is an important tool in taxonomic and evolutionary studies. Only a few complete mitogenomes have been reported for red algae. Herein, we reported the complete mitochondrial genome sequence of Fushitsunagia catenata (Harvey) Filloramo, G.V. and Saunders, G.W. 2016, a monospecific genus. The genome was 25,889 bp in circumference and had a strongly biased AT of 70.4%. It consisted of 2 rRNAs, 23 tRNAs, and 24 protein-coding genes (PCGs). nad5 (1986 bp) was the largest and atp9 (231 bp) was the smallest PCG. All PCGs used ATG as an initiation codon and TAA as a termination codon, except TAG, which was the termination codon used in the sdh3, rps3, and rps11 genes. The general structure and gene content of the present findings were almost identical to those of other red algae genomes, particularly those of the Rhodymeniales order. The maximum likelihood analysis showed that F. catenata was closely related to Rhodymenia pseudopalmata. The mitochondrial genome data presented in this study will enhance our understanding of evolution in Rhodophyta species.

Acanthamoeba keratitis - A review

This is a comprehensive review after a thorough literature search in PubMed-indexed journals, incorporating current information on the pathophysiology, clinical features, diagnosis, medical and surgical therapy, as well as outcomes of Acanthamoeba keratitis (AK). AK is a significant cause of ocular morbidity, and early diagnosis with timely institution of appropriate therapy is the key to obtaining good outcomes. The varied presentations result in frequent misdiagnosis, and co-infections can increase the morbidity of the disease. The first line of therapy continues to be biguanides and diamidines, with surgery as a last resort.

The consequences of viral infection on protists

Protists encompass a vast widely distributed group of organisms, surpassing the diversity observed in metazoans. Their diverse ecological niches and life forms are intriguing characteristics that render them valuable subjects for in-depth cell biology studies. Throughout history, viruses have played a pivotal role in elucidating complex cellular processes, particularly in the context of cellular responses to viral infections. In this comprehensive review, we provide an overview of the cellular alterations that are triggered in specific hosts following different viral infections and explore intricate biological interactions observed in experimental conditions using different host-pathogen groups.

Codon usage bias and phylogenetic analysis of chloroplast genome in 36 gracilariaceae species

Gracilariaceae is a group of marine large red algae and main source of agar with important economic and ecological value. The codon usage patterns of chloroplast genomes in 36 species from Graciliaceae show that GC range from 0.284 to 0.335, the average GC3 range from 0.135 to 0.243 and the value of ENC range from 35.098 to 42.327, which indicates these genomes are rich in AT and prefer to use codons ending with AT in these species. Nc plot, PR2 plot, neutrality plot analyses and correlation analysis indicate that these biases may be caused by multiple factors, such as natural selection and mutation pressure, but prolonged natural selection is the main driving force influencing codon usage preference. The cluster analysis and phylogenetic analysis show that the differentiation relationship of them is different and indicate that codons with weak or unbiased preferences may also play an irreplaceable role in these species' evolution. In addition, we identified 26 common high-frequency codons and 8-18 optimal codons all ending in A/U in these 36 species. Our results will not only contribute to carrying out transgenic work in Gracilariaceae species to maximize the protein yield in the future, but also lay a theoretical foundation for further exploring systematic classification of them.

Aquaculture of Animal Species: Their Eukaryotic Parasites and the Control of Parasitic Infections

Parasites are very diverse and common in both natural populations and in stocks kept in aquacultural facilities. For most cultured species, there are important bacteria and viruses causing diseases, but eukaryotic parasites are also very important. We review the various combinations of aquacultured species and eukaryotic parasitic groups and discuss other problems associated with aquaculture such as eutrophication, zoonotic species, and invasive species, and we conclude that further development of aquaculture in a sustainable manner must include a holistic approach (One Health) where many factors (e.g., human health, food safety, animal health and welfare, environmental and biodiversity protection and marketability mechanisms, etc.) are considered.

A novel enemy of cancer: recent investigations into protozoan anti-tumor properties

Cancer remains a significant global health issue, despite advances in screening and treatment. While existing tumor treatment protocols such as surgery, chemotherapy, radiotherapy, targeted therapy, and immunotherapy have proven effective in enhancing the prognosis for some patients, these treatments do not benefit all patients. Consequently, certain types of cancer continue to exhibit a relatively low 5-year survival rate. Therefore, the pursuit of novel tumor intervention strategies may help improve the current effectiveness of tumor treatment. Over the past few decades, numerous species of protozoa and their components have exhibited anti-tumor potential via immune and non-immune mechanisms. This discovery introduces a new research direction for the development of new and effective cancer treatments. Through in vitro experiments and studies involving tumor-bearing mice, the anti-tumor ability of Toxoplasma gondii, Plasmodium, Trypanosoma cruzi, and other protozoa have unveiled diverse mechanisms by which protozoa combat cancer, demonstrating encouraging prospects for their application. In this review, we summarize the anti-tumor ability and anti-tumor mechanisms of various protozoa and explore the potential for their clinical development and application.

A novel kleptoplastidic symbiosis revealed in the marine centrohelid Meringosphaera with evidence of genetic integration

Plastid symbioses between heterotrophic hosts and algae are widespread and abundant in surface oceans. They are critically important both for extant ecological systems and for understanding the evolution of plastids. Kleptoplastidy, where the plastids of prey are temporarily retained and continuously re-acquired, provides opportunities to study the transitional states of plastid establishment. Here, we investigated the poorly studied marine centrohelid Meringosphaera and its previously unidentified symbionts using culture-independent methods from environmental samples. Investigations of the 18S rDNA from single-cell assembled genomes (SAGs) revealed uncharacterized genetic diversity within Meringosphaera that likely represents multiple species. We found that Meringosphaera harbors plastids of Dictyochophyceae origin (stramenopiles), for which we recovered six full plastid genomes and found evidence of two distinct subgroups that are congruent with host identity. Environmental monitoring by qPCR and catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) revealed seasonal dynamics of both host and plastid. In particular, we did not detect the plastids for 6 months of the year, which, combined with the lack of plastids in some SAGs, suggests that the plastids are temporary and the relationship is kleptoplastidic. Importantly, we found evidence of genetic integration of the kleptoplasts as we identified host-encoded plastid-associated genes, with evolutionary origins likely from the plastid source as well as from other alga sources. This is only the second case where host-encoded kleptoplast-targeted genes have been predicted in an ancestrally plastid-lacking group. Our results provide evidence for gene transfers and protein re-targeting as relatively early events in the evolution of plastid symbioses.

Codon usage pattern of the ancestor of green plants revealed through Rhodophyta

Rhodophyta are among the closest known relatives of green plants. Studying the codons of their genomes can help us understand the codon usage pattern and characteristics of the ancestor of green plants. By studying the codon usage pattern of all available red algae, it was found that although there are some differences among species, high-bias genes in most red algae prefer codons ending with GC. Correlation analysis, Nc-GC3s plots, parity rule 2 plots, neutrality plot analysis, differential protein region analysis and comparison of the nucleotide content of introns and flanking sequences showed that the bias phenomenon is likely to be influenced by local mutation pressure and natural selection, the latter of which is the dominant factor in terms of translation accuracy and efficiency. It is worth noting that selection on translation accuracy could even be detected in the low-bias genes of individual species. In addition, we identified 15 common optimal codons in seven red algae except for G. sulphuraria for the first time, most of which were found to be complementary and bound to the tRNA genes with the highest copy number. Interestingly, tRNA modification was found for the highly degenerate amino acids of all multicellular red algae and individual unicellular red algae, which indicates that highly biased genes tend to use modified tRNA in translation. Our research not only lays a foundation for exploring the characteristics of codon usage of the red algae as green plant ancestors, but will also facilitate the design and performance of transgenic work in some economic red algae in the future.

Complete Mitogenome Sequencing, Annotation, and Phylogeny of Grateloupia turuturu, a Red Alga with Intronic cox1 Gene

The mitochondrial genome (mitogenome) is essential for identifying species and tracing genetic variation, gene patterns, and evolutionary studies. Here, the mitogenome of Grateloupia turuturu was sequenced on the Illumina sequencing platform. This circular mitogenome (28,265 bp) contains 49 genes, including three rRNAs, twenty transfer RNAs (tRNAs), and twenty-six protein-coding genes (PCGs). Nucleotide composition indicates biased AT (68.8%) content. A Group II intronic sequence was identified between two exons of the cox1 gene, and this sequence comprises an open reading frame (ORF) that encodes a hypothetical protein. The gene content, annotation, and genetic makeup are identical to those of Halymeniaceae members. The complete mitogenome sequences of the Grateloupia and Polyopes species were used in a phylogenetic analysis, which revealed that these two genera are monophyletic and that G. turuturu and G. elliptica are closely related. This newly constructed mitogenome will help us better understand the general trends in the development of cox1 introns in Halymeniaceae, as well as the evolution of red algal mitogenomes within the Rhodophyta and among diverse algal species.

Genetic Markers for Metabarcoding of Freshwater Microalgae: Review

The metabarcoding methods for studying the diversity of freshwater microalgae and routine biomonitoring are actively used in modern research. A lot of experience has been accumulated already, and many methodological questions have been solved (such as the influence of the methods and time of sample conservation, DNA extraction and bioinformatical processing). The reproducibility of the method has been tested and confirmed. However, one of the main problems-choosing a genetic marker for the study-still lacks a clear answer. We analyzed 70 publications and found out that studies on eukaryotic freshwater microalgae use 12 markers (different nuclear regions 18S and ITS and plastids rbcL, 23S and 16S). Each marker has its peculiarities; they amplify differently and have various levels of efficiency (variability) in different groups of algae. The V4 and V9 18S and rbcL regions are used most often. We concentrated especially on the studies that compare the results of using different markers and microscopy. We summarize the data on the primers for each region and on how the choice of a marker affects the taxonomic composition of a community.

A systematic review of honey bee (Apis mellifera, Linnaeus, 1758) infections and available treatment options

BACKGROUND

Honey bees and honeycomb bees are very valuable for wild flowering plants and economically important crops due to their role as pollinators. However, these insects confront many disease threats (viruses, parasites, bacteria and fungi) and large pesticide concentrations in the environment. Varroa destructor is the most prevalent disease that has had the most negative effects on the fitness and survival of different honey bees (Apis mellifera and A. cerana). Moreover, honey bees are social insects and this ectoparasite can be easily transmitted within and across bee colonies.

OBJECTIVE

This review aims to provide a survey of the diversity and distribution of important bee infections and possible management and treatment options, so that honey bee colony health can be maintained.

METHODS

We used PRISMA guidelines throughout article selection, published between January 1960 and December 2020. PubMed, Google Scholar, Scopus, Cochrane Library, Web of Science and Ovid databases were searched.

RESULTS

We have collected 132 articles and retained 106 articles for this study. The data obtained revealed that V. destructor and Nosema spp. were found to be the major pathogens of honey bees worldwide. The impact of these infections can result in the incapacity of forager bees to fly, disorientation, paralysis, and death of many individuals in the colony. We find that both hygienic and chemical pest management strategies must be implemented to prevent, reduce the parasite loads and transmission of pathogens. The use of an effective miticide (fluvalinate-tau, coumaphos and amitraz) now seems to be an essential and common practice required to minimise the impact of Varroa mites and other pathogens on bee colonies. New, alternative biofriendly control methods, are on the rise, and could be critical for maintaining honey bee hive health and improving honey productivity.

CONCLUSIONS

We suggest that critical health control methods be adopted globally and that an international monitoring system be implemented to determine honey bee colony safety, regularly identify parasite prevalence, as well as potential risk factors, so that the impact of pathogens on bee health can be recognised and quantified on a global scale.

p25alpha Domain-Containing Proteins of Apicomplexans and Related Taxa

TPPP (tubulin polymerization promoting protein)-like proteins contain one or more p25alpha (Pfam05517) domains. TPPP-like proteins occur in different types as determined by their length (e.g., long-, short-, truncated-, and fungal-type TPPP) and include the protein apicortin, which possesses another domain, doublecortin (DCX, Pfam 03607). These various TPPP-like proteins are found in various phylogenomic groups. In particular, short-type TPPPs and apicortin are well-represented in the Myzozoa, which include apicomplexans and related taxa, chrompodellids, dinoflagellates, and perkinsids. The long-, truncated-, and fungal-type TPPPs are not found in the myzozoans. Apicortins are found in all apicomplexans except one piroplasmid species, present in several other myzozoans, and seem to be correlated with the conoid and apical complex. Short-type TPPPs are predominantly found in myzozoans that have flagella, suggesting a role in flagellum assembly or structure.

Solving nomenclatural problems of genus-group names of the cuckoo-wasps (Hymenoptera, Chrysididae): objectively invalid and unavailable names, new type-species designations, new names, a new genus and new synonymies

Information is provided for 143 objectively invalid or unavailable genus-group names used in Chrysididae; 34 are objectively invalid, of which 18 are junior homonyms (five of these are also currently junior subjective synonyms), 18 are junior objective synonyms (two of these are also junior homonyms) of which seven are unjustified emendations, and two are unnecessary replacement names. The remaining 109 names are unavailable; 96 are incorrect subsequent spellings, most of them were originally lapsus calami or misprints, one is hereby deemed to be an incorrect original spelling, eight are nomina nuda, three were originally published as junior synonyms and never adopted before 1961 as valid names of any taxa, and one is a vernacular name previously considered as valid. Gender, type species, taxonomic history and status are given for each name except for incorrect subsequent spellings and unjustified emendations. Some cases of homonymies with taxa currently classified as non-animal are discussed. For two such junior homonyms, denoting genus-group taxa considered as valid in the present work, new replacement names are proposed: Linsenmaierella Rosa & Pavesi nom. nov. for Chrysidella Linsenmaier, nec Pascher; and Rhipidochrysis Rosa & Pavesi nom. nov. for Pleurochrysis Bohart, nec Pringsheim. New generic synonymies are established: consequent on new type-species designations, Leptoglossa Klug becomes a junior objective synonym of Parnopes Latreille syn. nov., and Pyrochloris Klug becomes a junior objective synonym of Euchroeus Latreille syn. nov.; Pseudodichrysis Trautmann is a junior objective synonym of Dichrysis Lichtenstein syn. nov. and the latter is in turn a junior subjective synonym of Chrysis Linnaeus. Platycelia Dahlbom is selected by the authors, acting as First Revisers, as the correct original spelling, and the simultaneously published Platycoelia is therefore deemed to be an incorrect subsequent spelling. The validation of Philoctetes Abeille de Perrin, not available when originally proposed, is discussed. Morphochrysis Rosa & Pavesi gen. nov. (type species: Chrysis pulchella Spinola) is here described; it includes members of the Chrysis pulchella species group previously included in Gonodontochrysis Semenov-Tian-Shanskij & Nikol'skaya, an unavailable name. The Chrysis zaravshanica species group is merged with the pulchella species group. A new specific synonymy within this group is proposed: Chrysis zaravshanica Tarbinsky syn. nov. of C. personata Semenov-Tian-Shanskij.

Overlapping exposure effects of pathogen and dimethoate on honeybee (Apis mellifera Linnaeus) metabolic rate and longevity

Introduction: Declines in honeybee abundance have been observed worldwide during last decades. This is partly due to plant protection agents used in intensive farming, landscaping and infrastructure maintenance. Another type of factors negatively affecting honeybees is the spread of diseases caused by different pathogens and pests. Lately, more focus has been paid to the interactions between different overlapping stressors affecting honeybee health, the combination of these often being more detrimental compared to individual stressors. The most widely used stress-evaluating methods take into account lethal- or motorial changes of the individuals or colonies. Comparatively little honeybee research has examined changes in initial recovery potential and physiological symptoms of toxification. The aim of this study was to examine the combined effect of Nosema apis and N. ceranae (according to a newer classification Vairimorpha apis and V. ceranae), the common causes of nosemosis in the honeybee Apis mellifera L., with the insecticide dimethoate. Methods: In this study, honeybee mortality and metabolic rate were used to assess the combined effects interactions of Nosema ssp. and dimethoate. Results: Our results showed that exposure to the low concentration of either dimethoate, either one or both species of Nosema ssp as single factors or in the combination had no significant effect on honeybee metabolic rate. The mortality increased with the two Nosema spp., as well as with infection by N. ceranae alone. The effect of dimethoate was observed only in combination with N. apis infection, which alone had no effect on individual honeybee mortality. Conclusion: This study demonstrates that the overlapping exposure to a non-lethal concentration of a pesticide and a pathogen can be hidden by stronger stressor but become observable with milder stressors.

Potential of Seaweeds to Mitigate Production of Greenhouse Gases during Production of Ruminant Proteins

The potential of seaweed to mitigate methane is real and studies with red seaweeds have found reductions in methane produced from ruminants fed red seaweeds in the region of 60-90% where the active compound responsible for this is bromoform. Other studies with brown and green seaweeds have observed reductions in methane production of between 20 and 45% in vitro and 10% in vivo. Benefits of feeding seaweeds to ruminants are seaweed specific and animal species-dependent. In some instances, positive effects on milk production and performance are observed where selected seaweeds are fed to ruminants while other studies note reductions in performance traits. A balance between reducing methane and maintaining animal health and food quality is necessary. Seaweeds are a source of essential amino acids and minerals however, and offer huge potential for use as feeds for animal health maintenance once formulations and doses are correctly prepared and administered. A negative aspect of seaweed use for animal feed currently is the cost associated with wild harvest and indeed aquaculture production and improvements must be made here if seaweed ingredients are to be used as a solution to control methane production from ruminants for continued production of animal/ruminant sourced proteins in the future. This review collates information concerning different seaweeds and how they and their constituents can reduce methane from ruminants and ensure sustainable production of ruminant proteins in an environmentally beneficial manner.

The microbiome of a brownfield highly polluted with mercury and arsenic

Abandoned brownfields represent a challenge for their recovery. To apply sustainable remediation technologies, such as bioremediation or phytoremediation, indigenous microorganisms are essential agents since they are adapted to the ecology of the soil. Better understanding of microbial communities inhabiting those soils, identification of microorganisms that drive detoxification process and recognising their needs and interactions will significantly improve the outcome of the remediation. With this in mind we have carried out a detailed metagenomic analysis to explore the taxonomic and functional diversity of the prokaryotic and eukaryotic microbial communities in soils, several mineralogically distinct types of pyrometallurgic waste, and groundwater sediments of a former mercury mining and metallurgy site which harbour very high levels of arsenic and mercury pollution. Prokaryotic and eukaryotic communities were identified, which turned out to be more diverse in the surrounding contaminated soils compared to the pyrometallurgic waste. The highest diversity loss was observed in two environments most contaminated with mercury and arsenic (stupp, a solid mercury condenser residue and arsenic-rich soot from arsenic condensers). Interestingly, microbial communities in the stupp were dominated by an overwhelming majority of archaea of the phylum Crenarchaeota, while Ascomycota and Basidiomycota fungi comprised the fungal communities of both stump and soot, results that show the impressive ability of these previously unreported microorganisms to colonize these extreme brownfield environments. Functional predictions for mercury and arsenic resistance/detoxification genes show their increase in environments with higher levels of pollution. Our work establishes the bases to design sustainable remediation methods and, equally important, to study in depth the genetic and functional mechanisms that enable the subsistence of microbial populations in these extremely selective environments.

Tonian carbonaceous compressions indicate that Horodyskia is one of the oldest multicellular and coenocytic macro-organisms

Macrofossils with unambiguous biogenic origin and predating the one-billion-year-old multicellular fossils Bangiomorpha and Proterocladus interpreted as crown-group eukaryotes are quite rare. Horodyskia is one of these few macrofossils, and it extends from the early Mesoproterozoic Era to the terminal Ediacaran Period. The biological interpretation of this enigmatic fossil, however, has been a matter of controversy since its discovery in 1982, largely because there was no evidence for the preservation of organic walls. Here we report new carbonaceous compressions of Horodyskia from the Tonian successions (~950-720 Ma) in North China. The macrofossils herein with bona fide organic walls reinforce the biogenicity of Horodyskia. Aided by the new material, we reconstruct Horodyskia as a colonial organism composed of a chain of organic-walled vesicles that likely represent multinucleated (coenocytic) cells of early eukaryotes. Two species of Horodyskia are differentiated on the basis of vesicle sizes, and their co-existence in the Tonian assemblage provides a link between the Mesoproterozoic (H. moniliformis) and the Ediacaran (H. minor) species. Our study thus provides evidence that eukaryotes have acquired macroscopic size through the combination of coenocytism and colonial multicellularity at least ~1.48 Ga, and highlights an exceptionally long range and morphological stasis of this Proterozoic macrofossils.

Renewing Linnaean taxonomy: a proposal to restructure the highest levels of the Natural System

During the last century enormous progress has been made in the understanding of biological diversity, involving a dramatic shift from macroscopic to microscopic organisms. The question now arises as to whether the Natural System introduced by Carl Linnaeus, which has served as the central system for organizing biological diversity, can accommodate the great expansion of diversity that has been discovered. Important discoveries regarding biological diversity have not been fully integrated into a formal, coherent taxonomic system. In addition, because of taxonomic challenges and conflicts, various proposals have been made to abandon key aspects of the Linnaean system. We review the current status of taxonomy of the living world, focussing on groups at the taxonomic level of phylum and above. We summarize the main arguments against and in favour of abandoning aspects of the Linnaean system. Based on these considerations, we conclude that retaining the Linnaean Natural System provides important advantages. We propose a relatively small number of amendments for extending this system, particularly to include the named rank of world (Latin alternative mundis) formally to include non-cellular entities (viruses), and the named rank of empire (Latin alternative imperium) to accommodate the depth of diversity in (unicellular) eukaryotes that has been uncovered. We argue that in the case of both the eukaryotic domain and the viruses the cladistic approach intrinsically fails. However, the resulting semi-cladistic system provides a productive way forward that can help resolve taxonomic challenges. The amendments proposed allow us to: (i) retain named taxonomic levels and the three-domain system, (ii) improve understanding of the main eukaryotic lineages, and (iii) incorporate viruses into the Natural System. Of note, the proposal described herein is intended to serve as the starting point for a broad scientific discussion regarding the modernization of the Linnaean system.

Emergence of the Fungal Rosette Agent in the World: Current Risk to Fish Biodiversity and Aquaculture

The emergence of pathogenic fungi is a major and rapidly growing problem (7% increase) that affects human and animal health, ecosystems, food security, and the economy worldwide. The Dermocystida group in particular has emerged relatively recently and includes species that affect both humans and animals. Within this group, one species in particular, Sphareothecum destruens, also known as the rosette agent, represents a major risk to global aquatic biodiversity and aquaculture, and has caused severe declines in wild fish populations in Europe and large losses in salmon farms in the USA. It is a species that has been associated with a healthy carrier for millions of years, but in recent decades, the host has managed to invade parts of Southeast Asia, Central Asia, Europe, and North Africa. In order to better understand the emergence of this new disease, for the first time, we have synthesized current knowledge on the distribution, detection, and prevalence of S. destruens, as well as the associated mortality curves, and the potential economic impact in countries where the healthy carrier has been introduced. Finally, we propose solutions and perspectives to manage and mitigate the emergence of this fungus in countries where it has been introduced.

Biogenesis of extracellular vesicles in protozoan parasites: The ESCRT complex in the trafficking fast lane?

Extracellular vesicles (EVs) provide a central mechanism of cell-cell communication. While EVs are found in most organisms, their pathogenesis-promoting roles in parasites are of particular interest given the potential for medical insight and consequential therapeutic intervention. Yet, a key feature of EVs in human parasitic protozoa remains elusive: their mechanisms of biogenesis. Here, we survey the current knowledge on the biogenesis pathways of EVs secreted by the four main clades of human parasitic protozoa: apicomplexans, trypanosomatids, flagellates, and amoebae. In particular, we shine a light on findings pertaining to the Endosomal Sorting Complex Required for Transport (ESCRT) machinery, as in mammals it plays important roles in EV biogenesis. This review highlights the diversity in EV biogenesis in protozoa, as well as the related involvement of the ESCRT system in these unique organisms.

Diversity of algae and their biotechnological potential

This chapter will discuss the diversity of algae and show that the diversity is much greater than just obligately oxygenic photosynthetic algae and that it includes many mixotrophic and heterotrophic organisms that are more similar to the major groups of microorganisms. The photosynthetic groups are seen as part of the plant kingdom, whereas the non-photosynthetic groups are not related to plants at all. The organisation of algal groups has become complex and confusing - The chapter will address the problems within this area of eukaryotic taxonomy. The metabolic diversity of algae and the ability to genetically engineer algae are key components in developing the biotechnology of algae. As more researchers become interested in exploiting algae for a number of industrial products, it is important to understand the relationships between different groups of algae and the relationships of algae with the rest of the living world.

The electronic tree of life (eToL): a net of long probes to characterize the microbiome from RNA-seq data

BACKGROUND

Microbiome analysis generally requires PCR-based or metagenomic shotgun sequencing, sophisticated programs, and large volumes of data. Alternative approaches based on widely available RNA-seq data are constrained because of sequence similarities between the transcriptomes of microbes/viruses and those of the host, compounded by the extreme abundance of host sequences in such libraries. Current approaches are also limited to specific microbial groups. There is a need for alternative methods of microbiome analysis that encompass the entire tree of life.

RESULTS

We report a method to specifically retrieve non-human sequences in human tissue RNA-seq data. For cellular microbes we used a bioinformatic 'net', based on filtered 64-mer sequences designed from small subunit ribosomal RNA (rRNA) sequences across the Tree of Life (the 'electronic tree of life', eToL), to comprehensively (98%) entrap all non-human rRNA sequences present in the target tissue. Using brain as a model, retrieval of matching reads, re-exclusion of human-related sequences, followed by contig building and species identification, is followed by confirmation of the abundance and identity of the corresponding species groups. We provide methods to automate this analysis. The method reduces the computation time versus metagenomics by a factor of >1000. A variant approach is necessary for viruses. Again, because of significant matches between viral and human sequences, a 'stripping' approach is essential. Contamination during workup is a potential problem, and we discuss strategies to circumvent this issue. To illustrate the versatility of the method we report the use of the eToL methodology to unambiguously identify exogenous microbial and viral sequences in human tissue RNA-seq data across the entire tree of life including Archaea, Bacteria, Chloroplastida, basal Eukaryota, Fungi, and Holozoa/Metazoa, and discuss the technical and bioinformatic challenges involved.

CONCLUSIONS

This generic methodology is likely to find wide application in microbiome analysis including diagnostics.

Position of Algae on the Tree of Life

Issues related to evolution of algal chloroplasts are considered. The position of algae on the Tree of Life is discussed. Algae are now included in five of the monophyletic eukaryotic supergroups: Archaeplastida (Glaucocystophyta, Rhodophyta, Prasinodermophyta, Chlorophyta, and Charophyta), TSAR (Ochrophyta; Dinophyta; Chlorarachniophyta; and photosynthetic species of the genera Chromera, Vetrella, and Paulinella), Haptista (Prymnesiophyta and Rappemonads), Cryptista (Cryptophyta), and Discoba (Euglenophyta). The algal divisions and the respective supergroups are characterized in brief.

Free-Living Amoebas in Extreme Environments: The True Survival in our Planet

Free-living amoebas (FLAs) are microorganisms, unicellular protozoa widely distributed in nature and present in different environments, such as water or soil; they are maintained in ecosystems and play a fundamental role in the biological control of bacteria, other protozoa, and mushrooms. In particular circumstances, some can reach humans or animals, promoting several health complications. Notably, FLAs are characterized by a robust capacity to survive in extreme environments. However, currently, there is no updated information on the existence and distribution of this protozoan in inhospitable places. Undoubtedly, the cellular physiology of these protozoan microorganisms is very particular. They can resist and live in extreme environments due to their encysting capacity and tolerance to different osmolarities, temperatures, and other environmental factors, which give them excellent adaptative resistance. In this review, we summarized the most relevant evidence related to FLAs and the possible mechanism, which could explain their adaptative capacity to several extreme environments.

Evolution of factors shaping the endoplasmic reticulum

Endomembrane system compartments are significant elements in virtually all eukaryotic cells, supporting functions including protein synthesis, post-translational modifications and protein/lipid targeting. In terms of membrane area the endoplasmic reticulum (ER) is the largest intracellular organelle, but the origins of proteins defining the organelle and the nature of lineage-specific modifications remain poorly studied. To understand the evolution of factors mediating ER morphology and function we report a comparative genomics analysis of experimentally characterized ER-associated proteins involved in maintaining ER structure. We find that reticulons, REEPs, atlastins, Ufe1p, Use1p, Dsl1p, TBC1D20, Yip3p and VAPs are highly conserved, suggesting an origin at least as early as the last eukaryotic common ancestor (LECA), although many of these proteins possess additional non-ER functions in modern eukaryotes. Secondary losses are common in individual species and in certain lineages, for example lunapark is missing from the Stramenopiles and the Alveolata. Lineage-specific innovations include protrudin, Caspr1, Arl6IP1, p180, NogoR, kinectin and CLIMP-63, which are restricted to the Opisthokonta. Hence, much of the machinery required to build and maintain the ER predates the LECA, but alternative strategies for the maintenance and elaboration of ER shape and function are present in modern eukaryotes. Moreover, experimental investigations for ER maintenance factors in diverse eukaryotes are expected to uncover novel mechanisms.

Marine macroalgae as a feasible and complete resource to address and promote Sustainable Development Goals (SDGs)

Because the world's population is increasing, science-based policies are needed to promote sustainable global development. It is important to maintain and restore the environment and help human society overcome the risks from industrialization and unsustainable exponential growth. In recent years, many studies have highlighted that macroalgae represent a key marine resource for ecological and sustainable living, thus helping to address today's global problems, such as water pollution, ocean acidification, and global warming. Macroalgae show the potential to provide innovative, ecofriendly, and nutritious food sources and natural compounds for various industries, such as biomedical, food, agricultural, and pharmaceutical industries. This review discusses how macroalgae can help us today and how they can promote a more sustainable way of life in the future. It also discusses the potential danger for ecosystems and the global population if these organisms are not part of the solution but part of the problem. Integr Environ Assess Manag 2022;18:1148-1161. © 2022 SETAC.

The greening ashore

More than half a billion years ago a streptophyte algal lineage began terraforming the terrestrial habitat and the Earth's atmosphere. This pioneering step enabled the subsequent evolution of all complex life on land, and the past decade has uncovered that many traits, both morphological and genetic, once thought to be unique to land plants, are conserved across some streptophyte algae. They provided the common ancestor of land plants with a repertoire of genes, of which many were adapted to overcome the new biotic and abiotic challenges. Exploring these molecular adaptations in non-tracheophyte species may help us to better prepare all green life, including our crops, for the challenges precipitated by the climate change of the Anthropocene because the challenges mostly differ by the speed with which they are now being met.

Whole Genome Analysis and Elucidation of Docosahexaenoic Acid (DHA) Biosynthetic Pathway in Aurantiochytrium sp. SW1

Aurantiochytrium sp., a fungoid marine protist that belongs to Stramenophila has proven its potential in the production of polyunsaturated fatty acids (PUFAs), especially docosahexaenoic acids (DHA). In this study, genomic characterisation of a potential producer for commercial production of DHA, Aurantiochytrium sp. SW1 has been carried out via whole genome sequencing analysis. The genome size of this strain is 60.89 Mb, with a total of 11,588 protein-coding genes. Among these, 9,127 genes could be functionally annotated into a total of 7,248 (62.5%) from UniProt, 6,554 (56.6%) from KEGG and 8,643 (74.6%) genes from eggNOG protein database. The highest proportion of genes belongs to the protein family of metabolism were further assigned into 11 metabolic categories. The highest number of genes belonging to lipid metabolism (321 genes) followed by carbohydrate metabolism (290 genes), metabolism of cofactors and vitamins (197 genes) and amino acid metabolism (188 genes). Further analysis into the biosynthetic pathway for DHA showed evidence of all genes involved in PKS (polyketide synthase)-like PUFA synthase pathway and incomplete fatty acid synthase-elongase/desaturase pathway. Analysis of PUFA synthase showed the presence of up to ten tandem acyl carrier protein (ACP) domains which might have contributed to high DHA production in this organism. In addition, a hybrid system incorporating elements of FAS, Type I PKS and Type II PKS systems were found to be involved in the biosynthetic pathways of fatty acids in Aurantiochytrium sp. SW1. This study delivers an important reference for future research to enhance the lipid, especially DHA production in Aurantiochytrium sp, SW1 and establishment of this strain as an oleaginous thraustochytrid model.

Horizontal Distribution and Carbon Biomass of Planktonic Foraminifera in the Eastern Indian Ocean

Distribution and carbon biomass of planktonic foraminifera were investigated from the euphotic zone of the Eastern Indian Ocean during a two-month cruise, ‘Shiyan I’ (10 April–13 May 2014). Foraminifera species were collected through plankton net sampling at 44 locations (80.00°–96.10° E, 10.08° N–6.00° S). The temperature (°C) ranged between 12.82 and 31.8 °C, the salinity ranged between 32.5 and 35.5, and chlorophyll-a concentrations ranged between 0.005 µg/L and 0.89 µg/L. A total of 20 taxa were identified based on the spherical chamber shell, spines, and a final whorl which were examined under light microscopy and scanning electron microscopy. Dominant species that were characterized by the high dominant index Y > 0.14–0.46 were Globigerina bulloides, Globigerinoides ruber white, Globigerinella siphonifera, Turborotalita quinqueloba, and Globigerinella calida, contributing to the community up to 86%. The shell size of collected taxa was from 51 to 508 μm and the total carbon biomass was estimated to be between 0.062 µg C m–3 and 26.52 µg C m–3. The high carbon biomass was recorded at two stations in the equator zone. Due to its large size, Globorotalia menardii had total carbon biomass of 3.9 µg C m–3, followed by G. calida 0.68 µg C m−3, Trilobatus sacculifer 0.38 µg C m–3, Orbulina universa 0.56 µg C m–3, and G. ruber white 0.22 µg C m–3, respectively. The Pearson correlation analysis showed that the temperature and chlorophyll-a were two explanatory environmental variables that were found to be highly significant (p < 0.05) and that triggered the distribution and abundance of dominant foraminifera species in the study region. Overall, high abundances and carbon biomass were derived from the euphotic zone and equatorial region of the Eastern Indian Ocean.

Sequence Analysis and Comparison of TCTP Proteins from Human Protozoan Parasites

Purpose

Translational controlled tumor protein (TCTP) is a functionally important protein in most eukaryotes because it participates in a wide variety of processes, the most representative being proliferation, differentiation, histamine release, cell death, protein synthesis and response to stress conditions. In the present work, we analyze the sequence, structure and phylogeny of TCTP orthologs in a group of human parasitic protozoan species.

Methods

The complete sequences of TCTP orthologs in protozoan parasites were identified with the NCBI BLAST tool in the database of the EuPathDB Bioinformatics Resource Center. The sequences were aligned and important regions of the protein were identified, and later phylogenetic trees and 3D models were built with different bioinformatic tools.

Results

Our results show evolutionarily and structurally conserved sites that could be exploited to create new therapeutic strategies given the increase in the number of strains resistant to current drugs.

Conclusion

TCTP orthologs in protozoan parasites have been little studied but have been shown to be important in parasite growth, proliferation, reproduction, and response to changes in the environment. For all this, TCTP can be considered as a possible therapeutic target.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11686-022-00521-9.

Paleoreconstructions of ciliate communities reveal long-term ecological changes in temperate lakes

Ciliates are unicellular heterotrophic organisms that play a key role in aquatic planktonic and benthic food webs. Advances in sedimentary DNA (sed-DNA) analysis offer the possibility to integrate these bioindicators in paleoenvironmental reconstructions. In this study, we used the top–bottom paleolimnological approach and metabarcoding techniques applied to sed-DNA to compare the recent and past (i.e. prior to major anthropogenic impacts) ciliate communities of 48 lakes located along an elevation gradient. Our results show an overall decline in the β-diversity in recent time, especially in lowland lakes, which are more strongly exposed to local human pressures. Analyses of the functional groups indicate important restructuration of the food web, including the recent increase in mixotrophs. Moreover, changes in the benthic ciliates were consistent with the widespread increase in deep water anoxia. Our results provided evidence that sed-DNA can uncover information about past ciliate communities on a wide variety of lakes. Overall, our study demonstrates the potential of using ciliates as new paleoindicators, integrating information from the pelagic to the benthic zones, and providing valuable insights into ecosystem functioning through a trait-based functional community approach. As paleoindicator, they thus offer a more holistic view on the long-term changes of aquatic ecosystems.

Exploring the Interactions between Algae and Bacteria

Humans have used algae for hundreds of years to make various products viz. agar, fertilizer, food, and pigments. Algae are also used in bioremediation to clean up polluted water and as essential laboratory tools in genomics, proteomics, and other research applications such as environmental warnings. Several special features of algae, including the oxygenic photosynthesis, higher yield in biomass, growth on the non-arable lands, their survival in a wide range of water supplies (contaminated or filtered waters), the production of necessary byproducts and biofuels, the enhancement of soil productivity, and the greenhouse gas emissions, etc. altogether rendered them as vital bio-resources in the sustainable development. Algae and bacteria have been assumed to coexist from the early stages of the development of the earth, and a wide variety of interactions were observed between them which have influenced the ecosystems ranging from the oceans to the lichens. Research has shown that bacteria and algae interact synergistically, especially roseobacter-algae interactions being the most common. These interactions are common to all ecosystems and characterize their primary efficiency. The commercialization of algae for industrial purposes, an important field, is also influenced by this interaction which frequently results in bacterial infections among the consumers. However, the recent findings have revealed that the bacteria improve algal growth and support flocculation which are very crucial in algal biotechnology. Some of the most exciting advancements in the area of algal biotic interactions and potential difficulties were reviewed in this article. Information gleaned in this study would provide a firm foundation for launching more contemporaneous research efforts in understanding and utilizing the algal species in biotechnology industries and medical sectors.

Ciliary transition zone evolution and the root of the eukaryote tree: implications for opisthokont origin and classification of kingdoms Protozoa, Plantae, and Fungi

I thoroughly discuss ciliary transition zone (TZ) evolution, highlighting many overlooked evolutionarily significant ultrastructural details. I establish fundamental principles of TZ ultrastructure and evolution throughout eukaryotes, inferring unrecognised ancestral TZ patterns for Fungi, opisthokonts, and Corticata (i.e., kingdoms Plantae and Chromista). Typical TZs have a dense transitional plate (TP), with a previously overlooked complex lattice as skeleton. I show most eukaryotes have centriole/TZ junction acorn-V filaments (whose ancestral function was arguably supporting central pair microtubule-nucleating sites; I discuss their role in centriole growth). Uniquely simple malawimonad TZs (without TP, simpler acorn) pinpoint the eukaryote tree's root between them and TP-bearers, highlighting novel superclades. I integrate TZ/ciliary evolution with the best multiprotein trees, naming newly recognised major eukaryote clades and revise megaclassification of basal kingdom Protozoa. Recent discovery of non-photosynthetic phagotrophic flagellates with genome-free plastids (Rhodelphis), the sister group to phylum Rhodophyta (red algae), illuminates plant and chromist early evolution. I show previously overlooked marked similarities in cell ultrastructure between Rhodelphis and Picomonas, formerly considered an early diverging chromist. In both a nonagonal tube lies between their TP and an annular septum surrounding their 9+2 ciliary axoneme. Mitochondrial dense condensations and mitochondrion-linked smooth endomembrane cytoplasmic partitioning cisternae further support grouping Picomonadea and Rhodelphea as new plant phylum Pararhoda. As Pararhoda/Rhodophyta form a robust clade on site-heterogeneous multiprotein trees, I group Pararhoda and Rhodophyta as new infrakingdom Rhodaria of Plantae within subkingdom Biliphyta, which also includes Glaucophyta with fundamentally similar TZ, uniquely in eukaryotes. I explain how biliphyte TZs generated viridiplant stellate-structures.

Phylogeography and Prevalence of Hemoparasites (Apicomplexa: Eucoccidiorida) in Galápagos Marine Iguanas, Amblyrhynchus cristatus (Reptilia: Iguanidae)

Parasitism is among the most common forms of coexistence of organisms of different species. Hemoparasites live in the bloodstream of the host where they complete different life-cycle stages. Members of the phylum Apicomplexa constitute a large portion of all hemoparasites infecting reptiles and their parasite transmitting vectors, including arthropods. In this study, we carried out a survey and molecular identification of hemoparasites in blood samples of the iconic Galápagos marine iguana (Amblyrhynchus cristatus). Major island populations of marine iguanas were sampled to examine large-scale biogeographic patterns of parasite diversity and prevalence. Nested PCRs were used to amplify segments of the 18S rRNA-gene of hemoparasites. Furthermore, ticks attached to marine iguanas were collected and analyzed in the same way to assess their potential use as a non-invasive method for the detection of hemoparasites in vertebrate host species. PCR products were sequenced and a phylogenetic analysis was carried out showing the presence of two genetically distinct clusters of hemoparasites, one more commonly distributed than the other one, belonging to the genera Hepatozoon and/or Hemolivia (Apicomplexa: Eucoccidiorida). Overall, 25% of marine iguanas were infected by hemoparasites. However, infection rates varied strongly among particular island populations (from 3.45% to 50%). Although marine iguanas are an extremely mobile species that has colonized all islands in the Galápagos archipelago, parasite occurrence was not related to geographical distance, suggesting that dispersal behavior has a minor role in parasite transmission. On most islands, females tended to have higher infection rates than males, but this relationship was only significant on one island. Overall, ticks and marine iguanas had similar prevalence and diversity of parasites. However, the infection profiles of ticks and their corresponding hosts (marine iguanas) did not mirror one another, indicating that this method cannot be used reliably to assess marine iguana infection status. Interestingly, we found that hemoparasite prevalence in marine iguanas and ticks tended to be positively correlated across islands. Our results indicate that certain populations of marine iguanas may have special mechanisms and adaptations to cope with parasite infection. In addition, other factors such as vector density, anthropogenic-related activities or the immunological state of marine iguanas could potentially affect the striking variation in hemoparasite prevalence across island populations.

The C-terminus of a diatom plant-like cryptochrome influences the FAD redox state and binding of interaction partners

A plant-like cryptochrome of diatom microalgae, CryP, acts as a photoreceptor involved in transcriptional regulation. It contains FAD and 5,10-methenyltetrahydrofolate as chromophores. Here, we demonstrate that the unstructured C-terminal extension (CTE) of CryP has an influence on the redox state of the flavin. In CryP lacking the CTE, the flavin is in the oxidized state (FADox), whereas it is a neutral radical (FADH•) in the full-length protein. When the CTE of CryP is coupled to another diatom cryptochrome that naturally binds FADox, this chimera also binds FADH•. In full-length CryP, FADH• is the most stable redox state and oxidation to FADox is extremely slow, whereas reduction to FADH2 is reversible in the dark in approximately 1 h. We also identified novel interaction partners of this algal CRY and characterized two of them in depth regarding their binding activities. BolA, a putative transcription factor, binds to monomeric and to dimeric CryP via the CTE, independent of the redox state of the flavin. In contrast, an unknown protein, ID42612, which occurs solely in heterokont algae, binds only to CryP dimers. This binding is independent of the CTE and shows slight differences in strength depending on the flavin's redox state.

The origins of global biodiversity on land, sea and freshwater

Many biodiversity studies focus on explaining high tropical species richness, but an equally dramatic yet understudied pattern involves the divergent richness of land, sea and freshwater. Here, we reveal the origins of these richness differences among habitats across animals and plants. Most plant and animal species are terrestrial, although these habitats cover only ~28% of Earth's surface. Marine habitats have fewer species over a larger area (~70%). Freshwater habitats have relatively high richness and exceptional phylogenetic diversity given their tiny area (2%). The relative richness of habitats is related to variation in diversification rates. Based on ancestral reconstructions of habitat, we find that most marine species are descended from marine ancestors and most terrestrial species from freshwater ancestors. Yet, most extant animal richness in freshwater is derived from terrestrial ancestors. Overall, our results reveal the origins of fundamental but neglected biodiversity patterns, and highlight the conservation importance of freshwater habitats.

Functional Properties and Antimicrobial Activity from Lactic Acid Bacteria as Resources to Improve the Health and Welfare of Honey Bees

Simple Summary

Honey bees play a pivotal role in the sustainability of ecosystems and biodiversity. Many factors including parasites, pathogens, pesticide residues, forage losses, and poor nutrition have been proposed to explain honey bee colony losses. Lactic acid bacteria (LAB) are normal inhabitants of the gastrointestinal tract of honey bees and their role has been consistently reported in the literature. In recent years, there have been numerous scientific evidence that the intestinal microbiota plays an essential role in honey bee health. Management strategies, based on supplementation of the gut microbiota with probiotics, may be important to increase stress tolerance and disease resistance. In this review, recent scientific advances on the use of LABs as microbial supplements in the diet of honey bees are summarized and discussed.

Abstract

Honey bees (Apis mellifera) are agriculturally important pollinators. Over the past decades, significant losses of wild and domestic bees have been reported in many parts of the world. Several biotic and abiotic factors, such as change in land use over time, intensive land management, use of pesticides, climate change, beekeeper’s management practices, lack of forage (nectar and pollen), and infection by parasites and pathogens, negatively affect the honey bee’s well-being and survival. The gut microbiota is important for honey bee growth and development, immune function, protection against pathogen invasion; moreover, a well-balanced microbiota is fundamental to support honey bee health and vigor. In fact, the structure of the bee’s intestinal bacterial community can become an indicator of the honey bee’s health status. Lactic acid bacteria are normal inhabitants of the gastrointestinal tract of many insects, and their presence in the honey bee intestinal tract has been consistently reported in the literature. In the first section of this review, recent scientific advances in the use of LABs as probiotic supplements in the diet of honey bees are summarized and discussed. The second section discusses some of the mechanisms by which LABs carry out their antimicrobial activity against pathogens. Afterward, individual paragraphs are dedicated to Chalkbrood, American foulbrood, European foulbrood, Nosemosis, and Varroosis as well as to the potentiality of LABs for their biological control.

Differential diagnosis of bees nosemosis - procedure and significance

For the living world, in the existing ecosystem, for the reproduction, production and spread of plant species, bees are one of the most important parts of nature. In the pollination of certain field and fruit-vegetable plant species, bees participate with almost 100%. Any factor that contributes to reducing the presence of bees in nature, directly affects the fertility of the plant world, and indirectly affects the rest of the entire living population. Nosemosis is a microorganism that has a great impact on the health of bees. In the previous period, Nosema sp. is classified as a single-celled parasite, a protozoan, but today it is classified as a fungus (Microsporidia). There are about 30 different species of Nosema in nature. For the bee population, especially with regard to the European honey bee (Apis millifera), two species of Nosema are very important, Nosema apis and Nosema ceranae. The correct confirmation of the type Nosema provides a better understanding of the outcomes and consequences for the apiary in which the clinical picture of nosemosis has occurred. The phenotypic diagnostic method, despite the present morphological differences, does not provide the possibility of reliable confirmation of the Nosema species. For these reasons, in order to make a differential diagnosis, it is necessary to determine which type of Nosema is present by molecular methods. In our work, by molecular method (PCR), we analyzed bees sampled from two administrative areas. The examination showed that Nosema ceranae was found in the two examined areas, while the presence of Nosema apis was not confirmed. These results may indicate that Nosema ceranae is predominant in the study area and has completely replaced Nosema apis.

OUP accepted manuscript

Proliferation of selfish genetic elements has led to significant genome size expansion in plastid and mitochondrial genomes of various eukaryotic lineages. Within the red algae, such expansion events are only known in the plastid genomes of the Proteorhodophytina, a highly diverse group of mesophilic microalgae. By contrast, they have never been described in the much understudied red algal mitochondrial genomes. Therefore, it remains unclear how widespread such organellar genome expansion events are in this eukaryotic phylum. Here, we describe new mitochondrial and plastid genomes from 25 red algal species, thereby substantially expanding the amount of organellar sequence data available, especially for Proteorhodophytina, and show that genome expansions are common in this group. We confirm that large plastid genomes are limited to the classes Rhodellophyceae and Porphyridiophyceae, which, in part, are caused by lineage-specific expansion events. Independently expanded mitochondrial genomes—up to three times larger than typical red algal mitogenomes—occur across Proteorhodophytina classes and a large shift toward high GC content occurred in the Stylonematophyceae. Although intron proliferation is the main cause of plastid and mitochondrial genome expansion in red algae, we do not observe recent intron transfer between different organelles. Phylogenomic analyses of mitochondrial and plastid genes from our expanded taxon sampling yielded well-resolved phylogenies of red algae with strong support for the monophyly of Proteorhodophytina. Our work shows that organellar genomes followed different evolutionary dynamics across red algal lineages.

A Perspective on the Molecular Identification, Classification, and Epidemiology of Enterocytozoon bieneusi of Animals

The microsporidian Enterocytozoon bieneusi is an obligate intracellular pathogen that causes enteric disease (microsporidiosis) in humans and has been recorded in a wide range of animal species worldwide. The transmission of E. bieneusi is direct and likely occurs from person to person and from animal to person via the ingestion of spores in water, food, or the environment. The identification of E. bieneusi is usually accomplished by molecular means, typically using the sequence of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA. Currently, ~820 distinct genotypes of E. bieneusi have been recorded in at least 210 species of vertebrates (mammals, birds, reptiles, and amphibians) or invertebrates (insects and mussels) in more than 50 countries. In this chapter, we provide a perspective on (1) clinical aspects of human microsporidiosis; (2) the genome and DNA markers for E. bieneusi as well as molecular methods for the specific and genotypic identification of E. bieneusi; (3) epidemiological aspects of E. bieneusi of animals and humans, with an emphasis on the genotypes proposed to be zoonotic, human-specific, and animal-specific; and (4) future research directions to underpin expanded molecular studies to better understand E. bieneusi and microsporidiosis.

Efficiency studies of modified IFAS-OSA system upgraded by an anoxic sludge holding tank

An upgraded integrated fixed-film activated sludge-oxic settling anoxic (IFAS-OSA) system is a new technology for reducing nutrients and excess sludge. The results showed that the average TN removal efficiency of the IFAS-OSA system was gradually increased up to 7.5%, while the PO₄^–3-P removal efficiency increased up-to 27%, compared with that of the IFAS system. The COD removal efficiency of the IFAS-OSA system was slightly increased up-to 5.4% and TSS removal efficiency increased up to 10.5% compared with the control system. Biomass yield coefficient (Y_obs) in the IFAS and IFAS-OSA systems were 0.44 and 0.24 (gr MLSS/ gr COD). Hence, sludge production decreased by 45%. The average SVI was decreased by 48% in IFAS-OSA system compared with IFAS. This study demonstrated the better performance of the IFAS-OSA system compared to that of the IFAS system.

Community RNA-Seq: multi-kingdom responses to living versus decaying roots in soil

Roots are a primary source of organic carbon input in most soils. The consumption of living and detrital root inputs involves multi-trophic processes and multiple kingdoms of microbial life, but typical microbial ecology studies focus on only one or two major lineages. We used Illumina shotgun RNA sequencing to conduct PCR-independent SSU rRNA community analysis ("community RNA-Seq") and simultaneously assess the bacteria, archaea, fungi, and microfauna surrounding both living and decomposing roots of the annual grass, Avena fatua. Plants were grown in 13CO2-labeled microcosms amended with 15N-root litter to identify the preferences of rhizosphere organisms for root exudates (13C) versus decaying root biomass (15N) using NanoSIMS microarray imaging (Chip-SIP). When litter was available, rhizosphere and bulk soil had significantly more Amoebozoa, which are potentially important yet often overlooked top-down drivers of detritusphere community dynamics and nutrient cycling. Bulk soil containing litter was depleted in Actinobacteria but had significantly more Bacteroidetes and Proteobacteria. While Actinobacteria were abundant in the rhizosphere, Chip-SIP showed Actinobacteria preferentially incorporated litter relative to root exudates, indicating this group's more prominent role in detritus elemental cycling in the rhizosphere. Our results emphasize that decomposition is a multi-trophic process involving complex interactions, and our methodology can be used to track the trajectory of carbon through multi-kingdom soil food webs.