It has been 80 years since Leonard Axel Jägerskiöld’s thorough marine faunistic inventory of the Swedish west coast (1921-1938), which represents the latest update of the Swedish sponge marine fauna. In this study, we present an update of the demosponge fauna with new specimens collected by the Swedish Taxonomic Initiative expeditions (2007-2008), new dredges (2012-2020), and SCUBA (2018–2020). Identifications were based on morphology and a molecular tree-based approach using the Folmer fragment of coxI, and the D3-D5 region of the 28S rRNA-encoding gene. From the 417 specimens examined, 57 different species were identified, of which five were identified to the genus/family level, eight were new reports for Sweden and one was new to science (Halisarca hansghanssoni sp. nov.). Furthermore, we reinstated the name Hymedesmia dujardinii (Bowerbank, 1866). The Swedish Taxonomic Initiative campaigns aimed to replicate the collecting efforts of the Jägerskiöld’s campaigns, thus making them easily comparable. Using the identified sponges of the Jägerskiöld’s inventory possibly changes in the Swedish sponge fauna over the last 80 years are discussed.

Freshwater sponges constitute an overlooked part of the freshwater fauna in Sweden and there has been no recent systematic survey. Hitherto three species have been found in Sweden: Spongilla lacustris (Linnaeus, 1759), Ephydatia fluviatilis (Linnaeus, 1759) and E. muelleri (Lieberkühn, 1856). Neighbouring countries (Norway, Denmark, Estonia) harbour at least one additional species. We present a study on freshwater sponge diversity and distribution in the southern half of Sweden. We hypothesized dispersal within catchments to be less constrained than between, even at shorter intercatchment than intracatchment distances, and, as result, genetic distances being greater between than within catchments. We collected and identified freshwater sponges from 34 sites, using morphological and molecular data (coxI, 28S rRNA gene). We can report the presence of Eunapius fragilis (Leidy, 1851) in Sweden for the first time, and that S. lacustris is the most abundant and widely distributed freshwater sponge in Sweden. Genetic markers were tested on S. lacustris individuals for a phylogeographic study. From the 47 primers (24 markers), one pair presented successful amplification and enough variation for phylogeographic studies – i56, an intron located in a conserved gene. Seven different variants were found in the sampling area, but no clear population structure was observed.

A putatively monophyletic group of annual Silene species is revised taxonomically and described as the new section S. sect. Arenosae. The species of this section were previously treated as a part of a widely circumscribed and polyphyletic S. sect. Rigidulae. Silene sect. Arenosae as circumscribed here consists of nine species. Members of the section show a predominantly E Mediterranean to SW Asian distribution pattern from Turkey southward to Egypt and eastward to Iran and Pakistan, although most of the species have a limited distribution range. The species of S. sect. Arenosae are characterized by narrowly lanceolate calyx teeth, which are often highly polymorphic, and lanceolate to oblanceolate (non-spathulate) basal leaves. The provided taxonomic revision is based on morphological characters and supported by phylogenetic analyses of two nuclear loci (nrITS and an intron of the RPB2 gene) and one chloroplast locus (the intron of the rps16 gene). The species descriptions are formalized using a novel implementation of the Prometheus Description Model.

Hymedesmia (Hymedesmia) lindstroemae sp. nov. collected at 178–210 m depth off the western Swedish coast is described. This encrusting sponge is notably characterized by its unusually large sigmas. This new species brings the number of Hymedesmia (Hymedesmia) species in Swedish waters to 30. A key for all the North Atlantic Hymedesmia (Hymedesmia) species with sigmas (32 species) is included.

The rnpB gene encodes for the RNA subunit of the catalytic ribonuclease RNase P and is present in all bacteria and has both conserved and highly variable sequence regions. Determination of rnpB in 35 Mycobacterium spp. showed species specific sequences for all species except the Mycobacterium tuberculosis complex (four species). High sequence variation was seen in the P3, P15 and P19 regions of suggested secondary structures of the corresponding RNase P RNA molecules. Phylogenetic analysis showed that rnpB gave similar tree topologies as 16S rRNA and hsp65 genes. A combined analysis of the three genes increased the number of nodes with significant support from 10 to 19. The results indicate that rnpB is useful for phylogenetic studies and is a possible target for identification and detection of Mycobacterium spp.

Geodia species north of 60 degrees N in the Atlantic appeared in the literature for the first time when Bowerbank described Geodia barretti and G.macandrewii in 1858 from western Norway. Since then, a number of species have been based on material from various parts of the region: G.simplex, Isops phlegraei, I.pallida, I.sphaeroides, Synops pyriformis, G.parva, G.normani, G.atlantica, Sidonops mesotriaena (now called G.hentscheli), and G.simplicissima. In addition to these 12 nominal species, four species described from elsewhere are claimed to have been identified in material from the northeast Atlantic, namely G.nodastrella and G.cydonium (and its synonyms Cydonium muelleri and Geodia gigas). In this paper, we revise the boreo-arctic Geodia species using morphological, molecular, and biogeographical data. We notably compare northwest and northeast Atlantic specimens. Biological data (reproduction, biochemistry, microbiology, epibionts) for each species are also reviewed. Our results show that there are six valid species of boreo-arctic Atlantic Geodia while other names are synonyms or mis-identifications. Geodia barretti, G.atlantica, G.macandrewii, and G.hentscheli are well established and widely distributed. The same goes for Geodia phlegraei, but this species shows a striking geographical and bathymetric variation, which led us to recognize two species, G.phlegraei and G.parva (here resurrected). Some Geodia are arctic species (G.hentscheli, G.parva), while others are typically boreal (G.atlantica, G.barretti, G.phlegraei, G.macandrewii). No morphological differences were found between specimens from the northeast and northwest Atlantic, except for G.parva. The Folmer cytochrome oxidase subunit I (COI) fragment is unique for every species and invariable over their whole distribution range, except for G.barretti which had two haplotypes. 18S is unique for four species but cannot discriminate G.phlegraei and G.parva. Two keys to the boreo-arctic Geodia are included, one based on external morphology, the other based on spicule morphology.(c) 2013 The Linnean Society of London

A species-level taxonomic revision of Atocion and Viscaria, based on a recent phylogenetic study, is presented. Atocion includes six species (A. armeria, A. compactum, A. lerchenfeldianum, A. reuterianum, A. rupestre and A. scythicinum), and Viscaria includes three species (V. alpina, V. asterias and V. vulgaris). The highest species diversity is found on the Balkan Peninsula. Species descriptions based on a study of morphological characters and generated using the Prometheus description model are provided and are also available in the Sileneae online database. Complete synonymy, notes on the ecology and geographical distribution of the taxa and an identification key are provided. Lectotypes for nine names (Lychnis helvetica, L. suecica, Silene armeria var. angustifolia, S. berdaui, S. lituanica, S. compacta, S. orientalis, S. reuteriana and Viscaria media) and a neotype for one name (S. lerchenfeldiana) are assigned. (C) 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 173, 194-210.

Background: According to the endosymbiont hypothesis, the mitochondrial system for aerobic respiration was derived from an ancestral Alphaproteobacterium. Phylogenetic studies indicate that the mitochondrial ancestor is most closely related to the Rickettsiales. Recently, it was suggested that Candidatus Pelagibacter ubique, a member of the SAR11 clade that is highly abundant in the oceans, is a sister taxon to the mitochondrial-Rickettsiales clade. The availability of ocean metagenome data substantially increases the sampling of Alphaproteobacteria inhabiting the oxygen-containing waters of the oceans that likely resemble the originating environment of mitochondria.Methodology/Principal Findings: We present a phylogenetic study of the origin of mitochondria that incorporates metagenome data from the Global Ocean Sampling (GOS) expedition. We identify mitochondrially related sequences in the GOS dataset that represent a rare group of Alphaproteobacteria, designated OMAC (Oceanic Mitochondria Affiliated Clade) as the closest free-living relatives to mitochondria in the oceans. In addition, our analyses reject the hypothesis that the mitochondrial system for aerobic respiration is affiliated with that of the SAR11 clade.Conclusions/Significance: Our results allude to the existence of an alphaproteobacterial clade in the oxygen-rich surface waters of the oceans that represents the closest free-living relative to mitochondria identified thus far. In addition, our findings underscore the importance of expanding the taxonomic diversity in phylogenetic analyses beyond that represented by cultivated bacteria to study the origin of mitochondria.

Background Phylogenetic trees based on sequences from a set of taxa can be incongruent due to horizontal gene transfer (HGT). By identifying the HGT events, we can reconcile the gene trees and derive a taxon tree that adequately represents the species' evolutionary history. One HGT can be represented by a rooted Subtree Prune and Regraft ( R SPR) operation and the number of R SPRs separating two trees corresponds to the minimum number of HGT events. Identifying the minimum number of R SPRs separating two trees is NP-hard, but the problem can be reduced to fixed parameter tractable. A number of heuristic and two exact approaches to identifying the minimum number of R SPRs have been proposed. This is the first implementation delivering an exact solution as well as the intermediate trees connecting the input trees. Results We present the SPR Identification Tool (SPRIT), a novel algorithm that solves the fixed parameter tractable minimum R SPR problem and its GPL licensed Java implementation. The algorithm can be used in two ways, exhaustive search that guarantees the minimum R SPR distance and a heuristic approach that guarantees finding a solution, but not necessarily the minimum one. We benchmarked SPRIT against other software in two different settings, small to medium sized trees i.e. five to one hundred taxa and large trees i.e. thousands of taxa. In the small to medium tree size setting with random artificial incongruence, SPRIT's heuristic mode outperforms the other software by always delivering a solution with a low overestimation of the R SPR distance. In the large tree setting SPRIT compares well to the alternatives when benchmarked on finding a minimum solution within a reasonable time. SPRIT presents both the minimum R SPR distance and the intermediate trees. Conclusions When used in exhaustive search mode, SPRIT identifies the minimum number of R SPRs needed to reconcile two incongruent rooted trees. SPRIT also performs quick approximations of the minimum R SPR distance, which are comparable to, and often better than, purely heuristic solutions. Put together, SPRIT is an excellent tool for identification of HGT events and pinpointing which taxa have been involved in HGT.

A novel Chlamydiaceae-like bacterium found in faecal specimens from sea birds from Bering Sea

Background The histone-like protein Hc2 binds DNA in Chlamydia trachomatis and is known to vary in size between 165 and 237 amino acids, which is caused by different numbers of lysine-rich pentamers. A more complex structure was seen in this study when sequences from 378 specimens covering the hctB gene, which encodes Hc2, were compared. Results This study shows that the size variation is due to different numbers of 36-amino acid long repetitive elements built up of five pentamers and one hexamer. Deletions and amino acid substitutions result in 14 variants of repetitive elements and these elements are combined into 22 configurations. A protein with similar structure has been described in Bordetella but was now also found in other genera, including Burkholderia , Herminiimonas , Minibacterium and Ralstonia . Sequence determination resulted in 41 hctB variants that formed four clades in phylogenetic analysis. Strains causing the eye disease trachoma and strains causing invasive lymphogranuloma venereum infections formed separate clades, while strains from urogenital infections were more heterogeneous. Three cases of recombination were identified. The size variation of Hc2 has previously been attributed to deletions of pentamers but we show that the structure is more complex with both duplication and deletions of 36-amino acid long elements. Conclusions The polymorphisms in Hc2 need to be further investigated in experimental studies since DNA binding is essential for the unique biphasic life cycle of the Chlamydiacae . The high sequence variation in the corresponding hctB gene enables phylogenetic analysis and provides a suitable target for the genotyping of C. trachomatis .

The family Chlamydiaceae contains several bacterial pathogens of important human and veterinary medical concern, such as Chlamydia trachomatis and Chlamydophila psittaci. Within the order Chlamydiales there are also an increasing number of chlamydia-like bacteria whose biodiversity, host range and environmental spread seem to have been largely underestimated, and which are currently being investigated for their potential medical relevance. In this study we present 16S rRNA, rnpB and ompA gene sequence data congruently indicating a novel chlamydia-like bacterium found in faecal specimens from opportunistic fish-eating sea birds, belonging to the Laridae and Alcidae families, from the Bering Sea. This novel bacterium appears to be closer to the Chlamydiaceae than other chlamydia-like bacteria and is most likely a novel genus within the Chlamydiaceae family.

We have studied the evolution of a type IV secretion system (T4SS), in Bartonella, which is thought to have changed function from conjugation to erythrocyte adherence following a recent horizontal gene transfer event. The system, called Trw, is unique among T4SSs in that genes encoding both exo- and intracellular components are located within the same duplicated fragment. This provides an opportunity to study the influence of selection on proteins involved in host-pathogen interactions. We sequenced the trw locus from several strains of Bartonella henselae and investigated its evolutionary history by comparisons to other Bartonella species. Several instances of recombination and gene conversion events where detected in the 2- to 5-fold duplicated gene fragments encompassing trwJIH, explaining the homogenization of the anchoring protein TrwI and the divergence of the minor pilus protein TrwJ. A phylogenetic analysis of the 7- to 8-fold duplicated gene coding for the major pilus protein TrwL displayed 2 distinct clades, likely representing a subfunctionalization event. The analyses of the B. henselae strains also identified a recent horizontal transfer event of almost the complete trwL region. We suggest that the switch in function of the T4SS was mediated by the duplication of the genes encoding pilus components and their diversification by combinatorial sequence shuffling within and among genomes. We suggest that the pilus proteins have evolved by diversifying selection to match a divergent set of erythrocyte surface structures, consistent with the trench warfare coevolutionary model.

Aging is a natural physiological process, but aging can increase the prevalence and mortality of chronic diseases in the elderly. It involves multiple organs and systems, and an essential aspect of aging is immunosenescence. With the increase of age, the immune system has undergone a series of changes and disorders. These changes have led to a decline in the resistance of the elderly to infection, reduced immunity to vaccines, increased incidence of cancer and autoimmune diseases, and an increased structural prevalence of low-grade inflammation. Moreover, affecting the aging process to a certain extent. This review introduces the changes in the immune system during aging and discusses the consequences and effects of these changes. And its effect on the aging process and the methods and ways of anti-aging were discussed.