Metagenomic Survey of Viral Diversity Obtained from Feces of Subantarctic and South American Fur Seals

The Brazilian South coast seasonally hosts numerous marine species, observed particularly during winter months. Some animals, including fur seals, are found dead or debilitated along the shore and may harbor potential pathogens within their microbiota. In the present study, a metagenomic approach was performed to evaluate the viral diversity in feces of fur seals found deceased along the coast of the state of Rio Grande do Sul. The fecal virome of two fur seal species was characterized: the South American fur seal (Arctocephalus australis) and the Subantarctic fur seal (Arctocephalus tropicalis). Fecal samples from 10 specimens (A. australis, n = 5; A. tropicalis, n = 5) were collected and viral particles were purified, extracted and amplified with a random PCR. The products were sequenced through Ion Torrent and Illumina platforms and assembled reads were submitted to BLASTx searches. Both viromes were dominated by bacteriophages and included a number of potentially novel virus genomes. Sequences of picobirnaviruses, picornaviruses and a hepevirus-like were identified in A. australis. A rotavirus related to group C, a novel member of the Sakobuvirus and a sapovirus very similar to California sea lion sapovirus 1 were found in A. tropicalis. Additionally, sequences of members of the Anelloviridae and Parvoviridae families were detected in both fur seal species. This is the first metagenomic study to screen the fecal virome of fur seals, contributing to a better understanding of the complexity of the viral community present in the intestinal microbiota of these animals.     

A universal oyster infection model demonstrates that Vibrio vulnificus Type 6 secretion systems have antibacterial activity in vivo

With the rapid increase of aquaculture contributing to sustainable food security, comes the need to better understand seafood associated diseases. One of the major aquatic bacterial genera responsible for human infections from seafood is Vibrio, especially from oysters. Currently, in vivo study of bacterial interactions within oysters is limited by the inability to promote high-level uptake of bacteria by oysters. This study has therefore evolved current natural marine snow protocols to generate ‘artificial’ marine snow, into which bacteria can be incorporated to facilitate extensive uptake by oysters. This presents an adaptable model for bacterial study within filter-feeding shellfish. Using this model, we demonstrate for the first time the antibacterial activity of Vibrio vulnificus Type 6 secretion systems in vivo, revealing an important role for the T6SS in V. vulnificus ecology.     

Phenotypic and Genetic Diversity of Aeromonas Species Isolated from Fresh Water Lakes in Malaysia

Gram-negative bacilli of the genus Aeromonas are primarily inhabitants of the aquatic environment. Humans acquire this organism from a wide range of food and water sources as well as during aquatic recreational activities. In the present study, the diversity and distribution of Aeromonas species from freshwater lakes in Malaysia was investigated using glycerophospholipid-cholesterol acyltransferase (GCAT) and RNA polymerase sigma-factor (rpoD) genes for speciation. A total of 122 possible Aeromonas strains were isolated and confirmed to genus level using the API20E system. The clonality of the isolates was investigated using ERIC-PCR and 20 duplicate isolates were excluded from the study. The specific GCAT-PCR identified all isolates as belonging to the genus Aeromonas, in agreement with the biochemical identification. A phylogenetic tree was constructed using the rpoD gene sequence and all 102 isolates were identified as: A. veronii 43%, A. jandaei 37%, A. hydrophila 6%, A. caviae 4%, A. salmonicida 2%, A. media 2%, A. allosaccharophila 1%, A. dhakensis 1% and Aeromonas spp. 4%. Twelve virulence genes were present in the following proportions—exu 96%, ser 93%, aer 87%, fla 83%, enolase 70%, ela 62%, act 54%, aexT 33%, lip 16%, dam 16%, alt 8% and ast 4%, and at least 2 of these genes were present in all 102 strains. The ascV, aexU and hlyA genes were not detected among the isolates. A. hydrophila was the main species containing virulence genes alt and ast either present alone or in combination. It is possible that different mechanisms may be used by each genospecies to demonstrate virulence. In summary, with the use of GCAT and rpoD genes, unambiguous identification of Aeromonas species is possible and provides valuable data on the phylogenetic diversity of the organism.     

The ZrfC alkaline zinc transporter is required for Aspergillus fumigatus virulence and its growth in the presence of the Zn/Mn‐chelating protein calprotectin

Aspergillus fumigatus can invade the lungs of immunocompromised individuals causing a life‐threatening disease called invasive pulmonary aspergillosis (IPA). To grow in the lungs, A. fumigatus obtains from the host all nutrients, including zinc. In living tissues, however, most zinc is tightly bound to zinc‐binding proteins. Moreover, during infection the bioavailability of zinc can be further decreased by calprotectin, an antimicrobial Zn/Mn‐chelating protein that is released by neutrophils in abscesses. Nevertheless, A. fumigatus manages to uptake zinc from and grow within the lungs of susceptible individuals. Thus, in this study we investigated the role of the zrfA, zrfB and zrfC genes, encoding plasma membrane zinc transporters, in A. fumigatus virulence. We showed that zrfC is essential for virulence in the absence of zrfA and zrfB, which contribute to fungal pathogenesis to a lesser extent than zrfC and are dispensable for virulence in the presence of zrfC. The special ability of ZrfC to scavenge and uptake zinc efficiently from lungtissue depended on its N‐terminus, which is absent in the ZrfA and ZrfB transporters. In addition, under Zn‐ and/or Mn‐limiting conditions zrfC enables A. fumigatus to grow in the presence of calprotectin, which is detected in fungal abscesses of non‐leucopenic animals. This study extends our knowledge about the pathobiology of A. fumigatus and suggests that fungal zinc uptake could be a promising target for new antifungals.     

Salmonella spp., Vibrio spp., Clostridium perfringens, and Plesiomonas shigelloides in Marine and Freshwater Invertebrates from Coastal California Ecosystems

The coastal ecosystems of California are highly utilized by humans and animals, but the ecology of fecal bacteria at the land–sea interface is not well understood. This study evaluated the distribution of potentially pathogenic bacteria in invertebrates from linked marine, estuarine, and freshwater ecosystems in central California. A variety of filter-feeding clams, mussels, worms, and crab tissues were selectively cultured for Salmonella spp., Campylobacter spp., Escherichia coli-O157, Clostridium perfringens, Plesiomonas shigelloides, and Vibrio spp. A longitudinal study assessed environmental risk factors for detecting these bacterial species in sentinel mussel batches. Putative risk factors included mussel collection near higher risk areas for livestock or human sewage exposure, adjacent human population density, season, recent precipitation, water temperature, water type, bivalve type, and freshwater outflow exposure. Bacteria detected in invertebrates included Salmonella spp., C. perfringens, P. shigelloides, Vibrio cholerae, Vibrio parahaemolyticus, and Vibrio alginolyticus. Overall, 80% of mussel batches were culture positive for at least one of the bacterial species, although the pathogens Campylobacter, E. coli-O157, and Salmonella were not detected. Many of the same bacterial species were also cultured from upstream estuarine and riverine invertebrates. Exposure to human sewage sources, recent precipitation, and water temperature were significant risk factors for bacterial detection in sentinel mussel batches. These findings are consistent with the hypothesis that filter-feeding invertebrates along the coast concentrate fecal bacteria flowing from land to sea and show that the relationships between anthropogenic effects on coastal ecosystems and the environmental niches of fecal bacteria are complex and dynamic.     

Human‐mediated extirpation of the unique Chatham Islands sea lion and implications for the conservation management of remaining New Zealand sea lion populations

While terrestrial megafaunal extinctions have been well characterized worldwide, our understanding of declines in marine megafauna remains limited. Here, we use ancient DNA analyses of prehistoric (<1450–1650 AD) sea lion specimens from New Zealand's isolated Chatham Islands to assess the demographic impacts of human settlement. These data suggest there was a large population of sea lions, unique to the Chatham Islands, at the time of Polynesian settlement. This distinct mitochondrial lineage became rapidly extinct within 200 years due to overhunting, paralleling the extirpation of a similarly large endemic mainland population. Whole mitogenomic analyses confirm substantial intraspecific diversity among prehistoric lineages. Demographic models suggest that even low harvest rates would likely have driven rapid extinction of these lineages. This study indicates that surviving Phocarctos populations are remnants of a once diverse and widespread sea lion assemblage, highlighting dramatic human impacts on endemic marine biodiversity. Our findings also suggest that Phocarctos bycatch in commercial fisheries may contribute to the ongoing population decline.     

Virulence Diversity among Bacteremic Aeromonas Isolates: Ex Vivo,Animal, and Clinical Evidences

Background

The objective of this study was to compare virulence among different Aeromonas species causing bloodstream infections.

Methodology/Principal Findings

Nine of four species of Aeromonas blood isolates, including A. dhakensis, A. hydrophila, A. veronii and A. caviae were randomly selected for analysis. The species was identified by the DNA sequence matching of rpoD. Clinically, the patients with A. dhakensis bacteremia had a higher sepsis-related mortality rate than those with other species (37.5% vs. 0%, P = 0.028). Virulence of different Aeromonas species were tested in C. elegans, mouse fibroblast C2C12 cell line and BALB/c mice models. C. elegans fed with A. dhakensis and A. caviae had the lowest and highest survival rates compared with other species, respectively (all P values <0.0001). A. dhakensis isolates also exhibited more cytotoxicity in C2C12 cell line (all P values <0.0001). Fourteen-day survival rate of mice intramuscularly inoculated with A. dhakensis was lower than that of other species (all P values <0.0001). Hemolytic activity and several virulence factor genes were rarely detected in the A. caviae isolates.

Conclusions/Significance

Clinical data, ex vivo experiments, and animal studies suggest there is virulence variation among clinically important Aeromonas species.     

Integration of dsRNA against host immune response genes augments the virulence of transgenic Metarhizium robertsii strains in insect pest species

The slow lethality of fungal biopesticides to insects restrains their widespread application as a strategy of pest control. In this study, unary, binary and ternary transgenic Metarhizium robertsii were created by integrating genes that encode the scorpion neurotoxin BjαIT, the cuticle-degrading protease Pr1A, and a double-stranded RNA (dsRNA) that targets host gnbp3, individually or collectively under a constitutive promoter to enhance virulence. Compared with the parental wild type, all unary transgenic strains had increased virulence against four insect species, Tenebrio molitor, Locusta migratoria, Plutella xylostella and Galleria mellonella, whereas the binary transgenic strain expressing both pr1A and BjαIT had increased virulence to T. molitor and L. migratoria, with no change in virulence against P. xylostella and G. mellonella. Importantly, all ternary transgenic strains simultaneously expressing pr1A, BjαIT, and the dsRNA specific to host gnbp3 exhibited the highest increase in insect-specific virulence. This finding highlights a novel strategy for genetic engineering of dsRNAs that target genes associated with the host immune response alongside virulence genes to maximize fungal virulence and lethality against insect pests.     

Observations of the effect of a New Year’s fireworks display on the behavior of the South American sea lion (Otaria flavescens) in a colony of central-south Chile

The use of fireworks has increased worldwide in recent years. Despite this, their effects on sea lions and similar species are almost undocumented. In this study, we documented some effects of the 2015 New Year’s fireworks on the behavior of South American sea lions (Otaria flavescens), a marine mammal species that utilizes coastal rookeries for breeding, resting, and care and nursing of pups. An immediate cessation of vocalizations followed the start of the fireworks and a significant decrease in the number of sea lions in the colony was registered. This provided evidence that fireworks disrupted the ongoing behavior of the South American sea lion. Further studies will be necessary to determine whether this disruption has negative consequences for these animals or whether they have evolved behavioral mechanisms for dealing with these kinds of short-term disruptive events.     

The Effects of Hydrostatic Pressure on Living Aquatic Organisms I. The Problem and General Behavioral Responses

Behavioral responses of marine and aquatic animals are characterized as R₁ (a first response of prolonged excitation), T (tetany or paralysis), I (inactivity and relaxation) and death as measured by the LD₅₀. R₁, T, and I are reversible responses and temperature dependent with each response occurring at high pressures as temperature increases. The lethal response is also temperature dependent but the tolerance to pressure increases with decreasing temperature. The responses are examined with reference to the ability of animals to successfully cope with the high pressure and low temperature of the abyssal environment.     

Ornamental fish: a potential source of pathogenic and multidrug-resistant motile Aeromonas spp.

Aeromonas spp. are ubiquitous bacteria that cause diseases in fish and other aquatic animals. They are the natural inhabitants of different aquatic environments, such as freshwater, brackishwater and marinewater. Extrinsic stressors, such as crowding, unhygienic handling, poor water quality, polluted feeding and inadequate nutrition, can predispose fish to Aeromonas infection. In ornamental fish, motile Aeromonas spp. are known as aetiological agents of motile aeromonad infections, which cause significant mortality in fish and economic loss in the ornamental fish industry. The existence of different virulence factors leads to the virulence potential of motile Aeromonas spp. There are several antimicrobials used to treat bacterial infections in ornamental fish. However, the extensive use of antimicrobials in the ornamental fish industry causes multidrug resistance. This article reviewed a multitude of virulence factors that are related to the ornamental fish-borne Aeromonas pathogenicity and the antimicrobial resistance determinants related to the multidrug resistance phenotypes of motile Aeromonas spp. in ornamental fish.     

Metabarcoding of PalEnDNA as An Efficient Tool to Recover Ancient Bacterial Diversity

Past bacterial diversity of a paleosol was reconstructed using metabarcoding of paleo environmental DNA (PalEnDNA). The paleosol was subsampled from a sediment core which was excavated from a palaeo beach-ridge located 2.6?km away from present sea shore and identified that it was deposited under marine influence ～6000?years ago, using geological proxies. The bacterial community contained 37 bacterial phyla and dominated by Proteobacteria, followed by Bacteroidetes, Firmicutes, Actinobacteria, Verrucomicrobia, and Chloroflexi. The bacterial community was a mix-up of marine and terrestrial population, and thereby diversity was higher than marine populations. The result shows metabarcoding of PalEnDNA can effectively reconstruct past bacterial community structure.     

Chemical Characterization of Exopolysaccharides from Antarctic Marine Bacteria

Exopolysaccharides (EPS) may have an important role in the Antarctic marine environment, possibly acting as ligands for trace metal nutrients such as iron or providing cryoprotection for growth at low temperature and high salinity. Ten bacterial strains, isolated from Southern Ocean particulate material or from sea ice, were characterized. Whole cell fatty acid profiles and 16S rRNA gene sequences showed that the isolates included representatives of the genera Pseudoalteromonas, Shewanella, Polaribacter, and Flavobacterium as well as one strain, which constituted a new bacterial genus in the family Flavobacteriaceae. The isolates are, therefore, members of the “Gammaproteobacteria” and Cytophaga-Flexibacter-Bacteroides, the taxonomic groups that have been shown to dominate polar sea ice and seawater microbial communities. Exopolysaccharides produced by Antarctic isolates were characterized. Chemical composition and molecular weight data revealed that these EPS were very diverse, even among six closely related Pseudoalteromonas isolates. Most of the EPS contained charged uronic acid residues; several also contained sulfate groups. Some strain produced unusually large polymers (molecular weight up to 5.7 MDa) including one strain in which EPS synthesis is stimulated by low temperature. This study represents a first step in the understanding of the role of bacterial EPS in the Antarctic marine environment.     

Variation analysis of pathogenic Vibrio spp. and Pseudomonas spp. in Changhai mollusc farming waters using real-time PCR assay during 2011–2014

Bacterial disease has caused high mortality of breeding molluscs from 2009 to 2011 in the Changhai area (Dalian, China). Vibrio spp. and Pseudomonas spp. have been detected as major pathogenic agents for aquatic animals in this area. In the present study, four virulence genes including vsm, toxR, aprX and carA were targeted to develop a real-time PCR assay for the quantitative detection of Vibrio splendidus, V. parahaemolyticus, Pseudomonas fluorescens and P. putida, respectively. The sensitivity and specificity of the assays were verified by experimental samples, and the variation tendencies of pathogenic V. splendidus, V. parahaemolyticus, P. fluorescens and P. putida strains from June to September were also detected in mollusc farming waters during 2011–2014. The concentration of V. splendidus increased from June to July, reduced in August, and then increased again in September. The highest count of V. parahaemolyticus appeared in July, and then dramatically decreased from August to September. Conversely, the counts of P. fluorescens and P. putida remained at lower levels from June to August, and then dramatically peaked in September. All four pathogenic bacteria displayed similar fluctuation tendencies of count variation in each year, and their concentrations were found to have a correlation with the average annual temperature. The variation tendency of pathogenic bacteria with temperature suggested that temperature was one of the most important factors to regulate the bacterial growth in a farming area, which could further provide information for the early warning of disease outbreak by using a convenient real-time PCR assay.     

Ten novel dinucleotide microsatellite loci cloned from the Galápagos sea lion (Zalophus californianus wollebaeki) are polymorphic in other pinniped species

We isolated and characterized 10 novel dinucleotide microsatellite loci from the Galápagos sea lion (Zalophus californianus wollebaeki) and tested their amplification utility in four further otariid species (Zalophus californianus californianus, Arctocephalus gazella, Arctocephalus australis and Eumetopias jubatus) and three phocid species (Hydrurga leptonyx, Halichoerus grypus and Phoca vitulina). All of the loci amplified polymorphic polymerase chain reaction (PCR) products in at least three species other than the Galápagos sea lion. These markers will be useful for studies of pinniped mating systems, genetic structure and genetic diversity.     

Pterygodermatites nycticebi infections in golden lion tamarins (Leontopithecus rosalia rosalia) and aye‐ayes (Daubentonia madagascariensis) from a German zoo

In a golden lion tamarin (Leontopithecus rosalia rosalia) colony kept indoors in a German zoo, two animals presented a sudden onset of reduced general condition, lethargy, and diarrhea. At animal capture for clinical examination, adult nematode stages were observed after stress‐induced defecation. Despite treatment, two golden lion tamarins died in the following 2 days. At necropsy, spirurid stages were found in the lungs and intestine. Additionally, adult Pterygodermatites spp. were identified in histopathological samples of intestine and pancreas, confirming the previous diagnosis. Upon diagnosis, all animals were treated with ivermectin (0.2 mg/kg; SC). Thereafter, the general condition of the golden lion tamarins improved, whereby some of them excreted spirurid nematodes over 3 days. Four weeks after treatment, 20 fecal samples from the colony were examined and proved negative for parasitic stages. Given that common German cockroaches (Blattella germanica) are suitable intermediate hosts of Pterygodermatites nycticebi, 30 specimens were collected from seven different locations around the golden lion tamarins housing. Third‐stage larvae of Pterygodermatites spp. were recovered from those cockroaches. Regular anthelmintic treatments, coprological screenings, and controls for intermediate hosts were recommended. More than 2 years later, P. nycticebi infection was diagnosed again histopathologically in an aye‐aye (Daubentonia madagascariensis) which suddenly died. Coprological analysis confirmed the presence of spirurid eggs. Due to prosimian primates' cockroach‐eating habits and given that total cockroach eradication proved impossible, continuous cockroach control strategies and regular treatments of primates are currently performed to prevent further P. nycticebi infections.     

Fungal biodiversity in aquatic habitats

Fungal biodiversity in freshwater, brackish and marine habitats was estimated based on reports in the literature. The taxonomic groups treated were those with species commonly found on submerged substrates in aquatic habitats: Ascomycetes (exclusive of yeasts), Basidiomycetes, Chytridiomycetes, and the non-fungal Saprolegniales in the Class Oomycetes. Based on presence/absence data for a large number and variety of aquatic habitats, about 3,000 fungal species and 138 saprolegnialean species have been reported from aquatic habitats. The greatest number of taxa comprise the Ascomycetes, including mitosporic taxa, and Chytridiomycetes. Taxa of Basidiomycetes are, for the most part, excluded from aquatic habitats. The greatest biodiversity for all groups occurs in temperate areas, followed by Asian tropical areas. This pattern may be an artifact of the location of most of the sampling effort. The least sampled geographic areas include Africa, Australia, China, South America and boreal and tropical regions worldwide. Some species overlap occurs among terrestrial and freshwater taxa but little species overlap occurs among freshwater and marine taxa. We predict that many species remain to be discovered in aquatic habitats given the few taxonomic specialists studying these fungi, the few substrate types studied intensively, and the vast geographical area not yet sampled.     

单增李斯特菌耐药外排泵研究进展

单增李斯特菌是一种重要的人兽共患食源性胞内致病菌,广泛存在于自然环境中且易污染动物性食品,人及动物感染后可引起严重的李斯特菌病,死亡率高达30%。单增李斯特菌通常对多种药物敏感,然而,因不合理使用抗菌药或消毒剂形成的选择压力导致李斯特菌多重耐药情况的报道日渐增多。外排泵蛋白是细菌中一类重要的蛋白,可参与机体多种生物学过程,包括影响细菌对抗生素敏感性、促进有毒化合物泵出、影响细菌毒力等。本文综述了近年来关于单增李斯特菌耐药外排泵的功能及调控机制的研究进展,为深入理解李斯特菌耐药等环境适应机制及有效控制该病原污染传播和筛选抗感染药物新靶点提供理论基础。