Sandy beaches are dynamic intertidal ecosystems where ecological interactions play a critical yet often overlooked role in shaping community structure and population dynamics. This study presents a global synthesis of ecological interactions involving mole crabs of the genus Emerita (Crustacea: Decapoda: Hippidae), complemented by new field and laboratory findings. Through a literature review and targeted sampling, we documented multiple interaction types, including predation, parasitism, epibiosis, competition, and symbiosis, highlighting their ecological and potential evolutionary implications. Predation and parasitism were the most frequently reported interactions worldwide. Our new empirical observations revealed, for the first time, the association of Eucheilota (Hydrozoa) and Maritrema sp. (Digenea) with E. rathbunae, as well as annual infection patterns by Profilicollis altmani (Acanthocephala) and algal epibiosis in E. brasiliensis. These interactions influence key biological processes such as burrowing, reproduction, and survival, ultimately affecting species distribution and population structure. Overall, our findings reinforce the central role of ecological interactions in the functioning and conservation of sandy beach ecosystems, particularly under growing anthropogenic pressures.

Cutibacterium acnes is a key member of the human skin microbiome that contributes to host homeostasis. Staphylococcus lugdunensis, while also a resident of the skin microbiota, is an opportunistic pathogen capable of causing severe infections, associated with its ability to form biofilms. We previously showed that C. acnes secretes molecules that inhibit S. lugdunensis biofilm formation without affecting planktonic growth. Here, we demonstrate that C. acnes-derived molecules also significantly reduced S. lugdunensis adherence to and invasion of human epithelial cells, as well as adhesion to keratinocytes. Transcriptomic analysis revealed repression of genes involved in S. lugdunensis purine biosynthesis and induction of the autolysis negative regulators, lrgA and lrgB. Functional assays confirmed that exposure to C. acnes molecules inhibits autolysis and extracellular DNA (eDNA) release and decreases intracellular guanine levels in S. lugdunensis. Crucially, the addition of exogenous guanine suppressed the effect of C. acnes molecules on both biofilm formation and lrgA gene expression. Collectively, our data indicate that C. acnes molecules inhibit S. lugdunensis biofilm formation by depleting the intracellular guanine pool, leading to repression of autolysis, and reduced eDNA release, a key component of biofilm structural integrity. These findings underscore the importance of interspecies microbiome interactions in pathogen exclusion.

Cholera is a diarrheal disease that affects millions of people globally. Although the causative agent, Vibrio cholerae , has been extensively studied in isolation, investigation of its interactions with the gut microbiota started relatively recently. We and others previously showed that microbiota-derived metabolites significantly influence V. cholerae behavior. By investigating how an organic extract of human feces affects V. cholerae gene expression, we showed that gut metabolites strongly suppress swimming motility, a trait important for host colonization. Interestingly, extracts of pure cultures of a gut commensal, Enterocloster citroniae , recapitulated this inhibition. Here, we present a comprehensive examination of the effect of small molecules produced by E. citroniae and related species on V. cholerae behavior. We show that E. citroniae small molecules inhibit motility by various V. cholerae strains, and that several phylogenetically related species produce this activity, although the magnitude of the effect varies between strains. Using biofilm formation assays in static and flow conditions, we show that V. cholerae strongly induces biofilm formation in response to E. citroniae metabolites. Transcriptome and reporter analyses showed that several genes involved in synthesis of an extracellular polysaccharide are induced by E. citroniae metabolites. Lastly, we show that V. cholerae interactions with host cells are also modulated by this commensal. These findings advance our understanding of microbiome-pathogen interactions and how commensal bacteria influence V. cholerae virulence through the production of small molecules. In the future, this knowledge may be used to design novel microbiome-based therapeutic approaches to combat cholera and other infections.

FioAntar, FIOCRUZ's research project in Antarctica, is based on the One Health approach. FioAntar aims to generate relevant information that will help reduce the risk of future pandemics and improve the search for chemical compounds and new biological molecules. After four expeditions to Antarctica under the scope of PROANTAR, Fiocruz has identified Influenza H11N2 virus in environmental fecal samples, as well as Histoplasma capsulatum and Bacillus cereus in soil samples. In addition, in a prospective virome analysis from different lakes in the South Shetland Islands, six viral orders were described, supporting future research related to the biodiversity and viral ecology in this extreme ecosystem. Our findings of environmental pathogens of public health importance are a warning about the urgency of establishing a surveillance agenda on zoonoses in Antarctica due to the imminent risks that ongoing environmental and climate changes impose on human health across the planet. FioAntar strives to establish a comprehensive surveillance program across Antarctica, monitoring circulation of pathogens with the potential to transcend continent boundaries, thereby mitigating potential spread. For Fiocruz, Antarctica signifies a new frontier, teeming with opportunities to explore novel techniques, refine established methodologies, and cultivate invaluable knowledge.

Cyanobacterial blooms are common events that releases secondary metabolites into water posing considerable threats to the environment, wildlife, and public health. Some of these metabolites, such as microcystin, have been extensively studied and associated with harmful effects in mammals and aquatic organisms, while the biological effects of others, like geosmin, remain much less investigated. Enhancing our understanding of cyanotoxins effects on organisms is especially relevant facing the complex scenarios projected due to global warming. The aim of this study was to assess the transcriptional modulation in whole zebrafish (Danio rerio) larvae (n = 9) in response to a 7-days immersion exposure to 3 mu g L- 1 MCLR or 5 mu g L- 1 geosmin. No mortality or differences in length gain were observed in zebrafish larvae exposed to environmentally realistic doses of both cyanotoxins. The exposure to MCLR and to geosmin caused the differential expression of 164 and 172 genes respectively, being 23 upregulated by MCLR and 98 upregulated by geosmin. Among the upregulated genes, 16 were shared, while 42 were shared among the downregulated genes. Over-representation analysis identified three enriched GO terms only among the genes upregulated by geosmin: organic hydroxy compound metabolic process (1901615), small molecule biosynthetic process (0044283), and lipid metabolic process (0006629). In fact, the expression of 12 of the 13 genes directly involved in the synthesis of cholesterol from acetyl-CoA was upregulated by geosmin. A chronic upregulation of cholesterol biosynthetic pathway is linked to several diseases and metabolic disorders, including alterations in sex-related hormones. Moreover, our results indicate that geosmin and MCLR acts through different mechanisms. Geosmin does not appear to provoke short-term adverse effects as MCLR but could disrupt the endocrine system by altering the lipid and steroid metabolism.

The selection pressure imposed by the host immune system impacts hepatitis B virus (HBV) quasispecies variability. This study evaluates HBV genetic diversity in different biological fluids. Twenty paired serum, oral fluid, and DBS samples from chronic HBV carriers were analyzed using both Sanger and next generation sequencing (NGS). The mean HBV viral load in serum was 5.19 ± 4.3 log IU/mL (median 5.29, IQR 3.01–7.93). Genotype distribution was: HBV/A1 55% (11/20), A2 15% (3/20), D3 10% (2/20), F2 15% (3/20), and F4 5% (1/20). Genotype agreement between serum and oral fluid was 100% (genetic distances 0.0–0.006), while that between serum and DBS was 80% (genetic distances 0.0–0.115). Two individuals presented discordant genotypes in serum and DBS. Minor population analysis revealed a mixed population. All samples displayed mutations in polymerase and/or surface genes. Major population analysis of the polymerase pointed to positions H122 and M129 as the most polymorphic (≥ 75% variability), followed by V163 (55%) and I253 (50%). Neither Sanger nor NGS detected any antiviral primary resistance mutations in the major populations. Minor population analysis, however, demonstrated the rtM204I resistance mutation in all individuals, ranging from 2.8 to 7.5% in serum, 2.5 to 6.3% in oral fluid, and 3.6 to 7.2% in DBS. This study demonstrated that different fluids can be used to assess HBV diversity, nonetheless, genotypic differences according to biological compartments can be observed.

The impact of anthropogenic activities on urban rivers is responsible for changing the diversity and composition of aquatic species and microorganisms. In this study, soil and fish ( Poecilia reticulata ) feaces were sampled from two sites: the Cunha Canal, a heavily impacted urban river in Rio de Janeiro, and a reference clean site, to investigate how the Cunha Canal pollution impacts the microbiota composition and the circulation of antibiotic resistance genes (ARGs). In total, sequencing reads summed 3 million for the feaces and 9 million for the soil metagenomes. 67% of the soil and 83% of the fish feaces microbiota at both sites were classified as Bacteria. The soil microbiota of the reference site was enriched with bacteria of the genus Bradyrhizobium and Streptomyces known to fix nitrogen and to metabolize organic material, while the soil microbiota of Cunha Canal was enriched with Acidovorax and Dechloromonas known to degradate pollutants as iron and benzene. The five ARGs detected in the feaces microbiome from Cunha Canal are different from the five found in the feaces from the reference site. 22 ARGs were found in the soil sample of Cunha Canal, while no one was detected in the soil sample of the reference site. These results show that water pollution changes the microbiota diversity and increases the ARGs circulating in the environment.

The description of all living species is an ultimate goal of biology. Species description, however, is a time-consuming effort that requires specialized taxonomists in the vast array of existing taxa. With the current rate of habitat loss, it is plausible to assume more species are becoming extinct than what we could possibly describe. High-throughput sequencing together with the appropriate bioinformatic analyses is revolutionizing the knowledge regarding microbial biodiversity, but can also assist in the unraveling of the diversity of higher Eukaryotes. Here, we describe how transcriptome sequencing, de novo assemble, and BLAST analyses helped to identify the taxa of an unknown and abundant species sampled on the banks of a highly contaminated river in Rio de Janeiro, Brazil. This species is currently being described as a possible new species of Collembola (Hexapoda). In total, 4.589.437 paired-end 150 bp reads passed quality control and were used to assemble a de novo transcriptome, resulting in 44.013 transcripts with N50 of 1.338 bp. Of these assembled transcripts, 4.112 had a BLAST hit, with Folsomia candida (Collembola) being the most frequent species. Specimens of this sampled species were sent to a taxonomist specialized in Collembola for accurate taxonomic identification. The sampled specimens are being fully described and probably belong to a new species of Orthonychiurus (Hexapoda, Collembola, Onychiuridae).

The Amazon is probably the most diverse realm on Earth, and is considered to be the primary source of diversity and a center of dispersal for Neotropical terrestrial organisms. Yet, the assumption that the Amazon basin is a primordial place of fish species origination and dispersal into other drainages still need to be tested. We addressed this issue by inferring a time-stratified biogeographic history and reconstructing the ancestral habitat preference of Hypostomus , a continentally widespread and species-rich Neotropical genus. We found that Hypostomus emerged in the Western Amazon (∼14.7 Ma), when the Western Amazon River was flowing northwards and disconnected from the Eastern Amazon. We show that dispersal events in the first half of Hypostomus evolution occurred from the Western Amazon into adjacent basins, initiating its Neotropical radiation. The ancestral preferred habitat consisted in small rivers with running waters, a predominant habitat in river headwaters. Because of strong niche conservatism in the early evolution of Hypostomus , we suggest that most of the out-of-Western-Amazon dispersal occurred via headwater captures. The radiation of Hypostomus was further promoted by major reconfigurations of river basins, which opened dispersal opportunities into new drainages. Diversification in habitat preference coincided with colonization of basins already occupied by congenerics, indicative of niche shifts triggered by inter-specific competition and species coexistence. By analyzing the evolutionary history of Hypostomus , we show that Western Amazon was the main center of fish dispersal in the Neotropical Region from Middle Miocene to the present, supporting the cradle hypothesis of fish origination and dispersal.

Humans live in symbiosis with a diverse community of microorganisms, which has evolved to carry out many specific tasks that benefit the host, including protection against invading pathogens. Within the chemical diversity of the gastrointestinal tract, small molecules likely constitute chemical cues for the communication between the microbiota and pathogens. Therefore, we sought to investigate if molecules produced by the human gut microbiota show biological activity against the human pathogen Vibrio cholerae. To probe the effects of the gut metabolome on V. cholerae, we investigated its response to small-molecule extracts from human feces, from a complex bacterial community cultivated in vitro, and from culture supernatants of Enterocloster citroniae, Bacteroides thetaiotaomicron, and Bacteroides vulgatus. Using RNA sequencing, we determined the impact of the human gut metabolome on V. cholerae global gene expression. Among the genes downregulated in the presence of the fecal extract, the most overrepresented functional category was cell motility, which accounted for 39% of repressed genes. Repression of V. cholerae motility by the fecal extract was confirmed phenotypically, and E. citroniae extracts reproduced this phenotype. A complex in vitro microbial community led to increased motility, as did extracts from B. vulgatus, a species present in this community. Accordingly, mucin penetration was also repressed by fecal and E. citroniae extracts, suggesting that the phenotypes observed may have implications for host colonization. Together with previous studies, this work shows that small molecules from the gut metabolome may have a widespread, significant impact on microbe-microbe interactions established in the gut environment.

The microbiota influences host health through several mechanisms, including protecting it from pathogen colonization. Staphylococcus epidermidis is one of the most frequently found species in the skin microbiota, and its presence can limit the development of pathogens such as Staphylococcus aureusS. aureus causes diverse types of infections ranging from skin abscesses to bloodstream infections. Given the increasing prevalence of S. aureus drug-resistant strains, it is imperative to search for new strategies for treatment and prevention. Thus, we investigated the activity of molecules produced by a commensal S. epidermidis isolate against S. aureus biofilms. We showed that molecules present in S. epidermidis cell-free conditioned media (CFCM) caused a significant reduction in biofilm formation in most S. aureus clinical isolates, including all 4 agr types and agr-defective strains, without any impact on growth. S. epidermidis molecules also disrupted established S. aureus biofilms and reduced the antibiotic concentration required to eliminate them. Preliminary characterization of the active compound showed that its activity is resistant to heat, protease inhibitors, trypsin, proteinase K, and sodium periodate treatments, suggesting that it is not proteinaceous. RNA sequencing revealed that S. epidermidis-secreted molecules modulate the expression of hundreds of S. aureus genes, some of which are associated with biofilm production. Biofilm formation is one of the main virulence factors of S. aureus and has been associated with chronic infections and antimicrobial resistance. Therefore, molecules that can counteract this virulence factor may be promising alternatives as novel therapeutic agents to control S. aureus infections.IMPORTANCES. aureus is a leading agent of infections worldwide, and its main virulence characteristic is the ability to produce biofilms on surfaces such as medical devices. Biofilms are known to confer increased resistance to antimicrobials and to the host immune responses, requiring aggressive antibiotic treatment and removal of the infected surface. Here, we investigated a new source of antibiofilm compounds, the skin microbiome. Specifically, we found that a commensal strain of S. epidermidis produces molecules with antibiofilm activity, leading to a significant decrease of S. aureus biofilm formation and to a reduction of previously established biofilms. The molecules potentiated the activity of antibiotics and affected the expression of hundreds of S. aureus genes, including those associated with biofilm formation. Our research highlights the search for compounds that can aid us in the fight against S. aureus infections.

We read the article by Glatthardt et al (1) with great interest.….

With 149 currently recognized species, Hypostomus is one of the most species-rich catfish genera in the world, widely distributed over most of the Neotropical region. To clarify the evolutionary history of this genus, we reconstructed a comprehensive phylogeny of Hypostomus based on four nuclear and two mitochondrial markers. A total of 206 specimens collected from the main Neotropical rivers were included in the present study. Combining morphology and a Bayesian multispecies coalescent (MSC) approach, we recovered 85 previously recognized species plus 23 putative new species, organized into 118 'clusters'. We presented the Cluster Credibility (CC) index that provides numerical support for every hypothesis of cluster delimitation, facilitating delimitation decisions. We then examined the correspondence between the morphologically identified species and their inter-specific COI barcode pairwise divergence. The mean COI barcode divergence between morphological sisters species was 1.3 ± 1.2%, and only in 11% of the comparisons the divergence was ≥2%. This indicates that the COI barcode threshold of 2% classically used to delimit fish species would seriously underestimate the number of species in Hypostomus, advocating for a taxon-specific COI-based inter-specific divergence threshold to be used only when approximations of species richness are needed. The phylogeny of the 108 Hypostomus species, together with 35 additional outgroup species, confirms the monophyly of the genus. Four well-supported main lineages were retrieved, hereinafter called super-groups: Hypostomus cochliodon, H. hemiurus, H. auroguttatus, and H. plecostomus super-groups. We present a compilation of diagnostic characters for each super-group. Our phylogeny lays the foundation for future studies on biogeography and on macroevolution to better understand the successful radiation of this Neotropical fish genus.

Hypancistrus zebra is a catfish, endemic from the Xingu River, threatened with extinction due to the impacts of Belo Monte dam, of its illegal capture, of gold mining activities and of climate change. Currently, there are three nucleotide sequences from this species in GenBank, what impedes the development of genetic markers to assist on its conservation. A total of 217 million RNA-Seq reads from seven organs were sequenced and used to assemble 566,607 transcripts, including 98% of BUSCO vertebrates orthologs, 11,321 transcripts with SNVs and 1,724 transcripts with indels. Three transcripts with SNVs and five transcripts with indels were validated as the best candidate markers to conservation practices. This work illustrates the use of transcriptomics in conservation, by the development of a bigger toolbox for an endangered fish, and shall further contribute to studies on this and others related species reproduction, physiology, and adaptability to environmental changes.

Hoplosternum littorale is a widespread, non-migratory, air-breathing armored catfish (Callichthyidae, Siluriformes) present in most river drainages of tropical South America. This species has invaded aquatic habitats out of its native range. The distribution and unity of this species is supported by strong morphological evidences, but only few molecular data are available. As for February 2017, 45 partial mitochondrial gene sequences for H. littorale were deposited at the U.S. National Center for Biotechnology Information (NCBI) GenBank. The nearly complete mitochondrial genomes from two individuals of H. littorale sampled in geographically isolated populations were sequenced and compared to the intraspecific divergence encountered in a related species, Corydoras nattereri . Tamura-Nei corrected distances between the mitochondrial genomes from the two H. littorale was 0.004, equivalent to the distance found among individuals from the same population of C. nattereri (0.002) and considerably smaller than the distance between C. nattereri and C. schwartzi (0.123). An insertion of 30 nucleotides between the ATPase 6 and the COIII genes was identified in H. littorale . This insertion is homologous to the one previously noted in two species of Corydoras . This work supports H. littorale as a single and widespread species of Callichthyidae catfish. The new genetic resources for H. littorale are now available to support further studies with larger sampling sizes.

This chapter aims to discuss the meaning of the "Eco" of Ecotoxicology, as well as some of the challenges to address it effectively, and also to analyze current perspectives to account for the diversity of life in Ecotoxicology. Ray-finned fishes (Actinopterygii) are used as a striking example of the limited number of environmentally relevant model species currently in use for ecotoxicological tests, while high-throughput technologies are presented as an opportunity to identify new representative model species in order to account for biodiversity in ecotoxicology. In this context, the case of Loricariidae fish, a species-rich family endemic to the Neotropical Region, is described, reviewing published results and presenting on-going investigations. The intersections between Ecotoxicology and Systems Biology, Evolutionary Toxicology and Phylotranscriptomics are commented on. Finally, the ability to link the suborganismal responses obtained by the high-throughput technologies to population-level effects and population-level effects to alterations in the whole ecosystem is essential to resolve the ecosystem function and behavior, under homeostatic or stress conditions, at the molecular level.

The Paraíba do Sul River (PSR) drainage basin in Southeastern Brazil covers one of the most industrialized and densely populated regions of the country. The impact of chemical contamination on the PSR basin seems to be more pronounced in its middle reach where a number of potentially polluting plants are located. In this study, we used hepatic EROD activity - a biomarker of exposure to CYP1A-inducing pollutants (e.g. PAHs, PCDD/Fs, PCBs) - and the incidence of micronucleated erythrocytes (Mn) in the peripheral blood - a biomarker of effects of DNA-damaging agents (e.g. PAHs) - to evaluate the effects of pollution on two native fish species, Geophagus brasiliensis and Pimelodus maculatus. Results showed that the incidence of Mn and EROD in G. brasiliensis and P. maculatus from the two most downstream sites (Três Rios Town and Piabanha River) were markedly higher than the incidence of Mn and EROD recorded in fish from the most upstream site (Funil Reservoir). Our findings are consistent with the view that CYP1A-inducing activity and increased DNA-damage are found in fish caught in sampling sites located downstream of the stretch where there are several industries that are potential sources of PAHs and CYP1A-inducing contaminants.

The Funil Reservoir receives a large amount of xenobiotics from the Paraíba do Sul River (PSR) from large number of industries and municipalities in the watershed. This study aimed to assess environmental quality along the longitudinal profile of the Paraíba do Sul River-Funil Reservoir system, by using biomarkers and bioindicators in a selected fish species. The raised hypothesis is that Funil Reservoir acts as a filter for the xenobiotics of the PSR waters, improving river water quality downstream the dam. Two biomarkers, the ethoxyresorufin-O-deethylase activity (EROD), measured as fluorimetricly in S9 hepatic fraction, and the micronuclei frequency (MN), observed in erythrocytes of the cytoplasm, and three bioindicators, the hepatosomatic index (HSI), gonadosomatic index (GSI) and condition factor (CF) were used in Pimelodus maculatus, a fish species widely distributed in the system. Four zones were searched through a longitudinal gradient: 1, river upstream from the reservoir; 2, upper reservoir; 3, lower reservoir; 4, river downstream of the reservoir. EROD activity and HSI and GSI had significant differences among the zones (P<0.05). The upper reservoir had the lowest EROD activity and HSI, whereas the river downstream of the reservoir had the highest EROD and lowest GSI. The river upstream from the reservoir showed the highest HSI and GSI. It is suggested that the lowest environmental condition occur at the river downstream of the reservoir, where it seems to occur more influence of xenobiotics, which could be associated with hydroelectric plant operation. The hypothesis that Funil reservoir acts as a filter decanting pollution from the Paraíba do Sul River waters was rejected. These results are novel information on this subject for a native fish species and could be useful for future comparisons with other environments.

The genetic diversity of Neotropical fish fauna is underrepresented in public databases. This distortion is evident for the order Siluriformes, in which the suborders Siluroidei and Loricarioidei share equivalent proportion of species, although far less is known about the genetics of the latter clade, endemic to the Neotropical Region. Recently, this information gap was evident in a study about the structural diversity of fish mitochondrial genomes, and hampered a precise chronological resolution of Siluriformes. It has also prevented molecular ecology investigations about these catfishes, their interactions with the environment, responses to anthropogenic changes and potential uses.