Marine Niche Research Articles

Genomic insights into Enterococcus faecium isolates from marine bivalves highlight One Health concerns and healthcare linkages.

Enterococci, especially Enterococcus faecium, are one of today's leading causes of multidrug-resistant infections in hospital settings. The marine environment may harbour enterococci, but its role as an evolutionary niche and as a vector for the spread of enterococci is sparsely investigated. Hence, by applying enterococci in bivalves as a sentinel tool, this study aimed to describe the prevalence of enterocooci along the Norwegian coast and in addition the phylogeny of E. faecium in particular. Enterococci in batch samples of marine bivalves, harvested from 86 different locations, were quantitatively examined by a culture-dependent most probable number (MPN) method. Isolates were identified by MALDI-TOF-MS prior to antimicrobial susceptibility testing by broth microdilution. In-detail analyses of a representative selection of E. faecium isolates (n=148) were done by Illumina whole-genome sequencing, and assembled genomes were compared to closed E. faecium genomes in the public databases and to genomes from commensal and clinical isolates from Norway. Diversity among E. faecium within the same batch sample of bivalves was also explored. Enterococci were detected in 287 of the 471 examined bivalve samples, but in low concentrations with a median value of <18 MPN /100 g. From positive samples, 479 isolates of enterococci were identified belonging to ten different species, where E. faecium (n=247), Enterococcus hirae (n=114) and Enterococcus faecalis (n=66) were most frequently found. Resistance towards one or more antimicrobial agents was observed in 197 isolates (41 %), none of the isolates showed acquired resistance to vancomycin or linezolid. Phylogenetic analyses revealed high diversity among the E. faecium isolates and showed that the marine niche is dominated by strains from the non-clinical setting belonging to clade A2 (n=85) and B (E. lactis) (n=60). Only three isolates belonged to the hospital-associated clade A1 (ST80 and ST117). Two of these clustered with one isolate from a hospitalized patient and one from a non-hospitalized person. This study demonstrated a high prevalence, but low concentrations of enterococci in bivalves, and low levels of antimicrobial resistance. E. faecium genomes showed high population diversity and that very few E. faecium isolates in bivalves may have arisen from the human healthcare system. A systematic surveillance of target micro-organisms applying methods examining multiple isolates from the same bivalve sample provides important data to assess the enterococcal phylogeny, antimicrobial resistance and the level of faecal pollution in the marine environment.

Genomic Insights into Mollusc terrestrialization: Parallel and Convergent Gene Family Expansions as Key Facilitators in out-of-the-sea transitions.

Animals abandoned their marine niche and successfully adapted to life on land multiple times throughout evolution, providing a rare opportunity to study the mechanisms driving large scale macroevolutionary convergence. However, the genomic factors underlying this process remain largely unknown. Here, we investigate the macroevolutionary dynamics of gene repertoire evolution during repeated transitions out of the sea in molluscs, a lineage that has transitioned to freshwater and terrestrial environments multiple independent times. Through phylogenomics and phylogenetic comparative methods, we examine approximately 100 genomic datasets encompassing all major molluscan lineages. We introduce a conceptual framework for identifying and analyzing parallel and convergent evolution at the orthogroup level (groups of genes derived from a single ancestral gene in the species in question), and explore the extent of these mechanisms. Despite deep temporal divergences, we found that parallel expansions of ancient gene families played a major role in facilitating adaptation to non-marine habitats, highlighting the relevance of the pre-existing genomic toolkit in facilitating adaptation to new environments. The expanded functions primarily involve metabolic, osmoregulatory, and defense-related systems. We further found functionally convergent lineage-exclusive gene gains, while family contractions appear to be driven by neutral processes. Also, genomic innovations likely contributed to fuel independent habitat transitions. Overall, our study reveals that various mechanisms of gene repertoire evolution -parallelism, convergence and innovation- can simultaneously contribute to major evolutionary transitions. Our results provide a genome-wide gene repertoire atlas of molluscan terrestrialization that pave the way towards further understanding the functional and evolutionary bases of this process.

Maternal transfer and occurrence of siloxanes, chlorinated paraffins, metals, PFAS and legacy POPs in herring gulls (Larus argentatus) of different urban influence

Urban herring gulls (Larus argentatus) are exposed to contaminants from aquatic, terrestrial and anthropogenic sources. We aim to assess if differences in urbanisation affect ecological niche and contaminant concentrations in female herring gulls. Furthermore, we investigated maternal transfer from mothers to eggs for all the target compounds, including chlorinated paraffins (CPs) and cyclic volatile methyl siloxane (cVMSs), which to our knowledge have not been assessed in herring gulls previously. We compare concentrations of legacy and emerging contaminants and metals in blood and eggs between two herring gull colonies located 51 km apart, in the urban influenced Norwegian Oslofjord. While both colonies are within an urbanised area, the inner fjord is more so, as it is surrounded by Oslo, the capital and largest city in Norway Stable isotopes of carbon and nitrogen indicated a more marine ecological niche in the outer than the inner fjord colony, although with overlap. Persistent organic pollutant (POP) concentrations were similar in the inner and outer fjord colonies, while the short-chained chlorinated paraffins (SCCP), which are recently added to the Stockholm convention and contaminants of emerging concern (CECs) varied, with higher concentrations of SCCP and the cVMS decamethylcyclopentasiloxane (D5) in females and eggs of the inner fjord colony. Per- and polyfluorinated substances (PFAS) concentrations were higher in the outer fjord colony, likely linked to releases from a point-source (airport and waste management facility with open access to food waste). In blood, chlorinated paraffins contributed most the total lipophilic contaminants (inner: 78%, outer: 56%), while polychlorinated biphenyls (PCBs) were the most abundant lipophilic contaminants in eggs (inner: 62%, outer: 46%). Dechloranes and brominated flame retardants (BFRs) were detected in few samples. Maternal transfer, assessed by egg to blood ratios, of cVMSs were similar to the POPs with mean log ratio 0.39 (D5), while it was lower for SCCPs, with log ratios-0.77. Our results indicate comparable POP exposure of the herring gulls in the inner and outer Oslofjord, likely due to overlap in ecological niches between the colonies and wide distribution of POPs. The differences between the colonies in concentrations of PFAS, cVMS and CPs shows that point source exposures and urban influence may be more important than ecological niche for these compounds.

Marine trophic niche use and life history diversity among Arctic charr Salvelinus alpinus in southwestern Greenland.

Life history strategies and potential marine niche use of Arctic charr Salvelinus alpinus (n = 237, 84-652 mm, total body length, LT ) were determined during the ice-free season (2012) at three different watercourses in south-western Greenland. All Arctic charr were collected from freshwater habitats. Based on stable isotopes of δ34 S, the Arctic charr were categorized as either marine- or freshwater-dependent feeders. The use of time-integrated trophic tracers (stable isotopes of δ13 C, δ15 N, δ34 S) suggested that several trophic groups of Arctic charr operate alongside within each fjord system. The groups suggested were one group that specialized in the marine habitat, in addition to two freshwater resident morphs (small-sized resident and/or large-growing cannibalistic individuals). Stomach contents consisted entirely of freshwater and terrestrial prey (i.e., insects), indicating that marine-dependent feeders also fed in freshwater habitats after return from their marine migration. Growth and maturity patterns further supported variable life history strategies within each watercourse. The life history strategy patterns and marine trophic niche use were consistent across the watercourses along several hundred kilometres of coastline. This study represents the first ecological baseline for partially anadromous populations of Greenland Arctic charr.

Quorum sensing controls Vibrio cholerae multicellular aggregate formation.

Bacteria communicate and collectively regulate gene expression using a process called quorum sensing (QS). QS relies on group-wide responses to signal molecules called autoinducers. Here, we show that QS activates a new program of multicellularity in Vibrio cholerae. This program, which we term aggregation, is distinct from the canonical surface-biofilm formation program, which QS represses. Aggregation is induced by autoinducers, occurs rapidly in cell suspensions, and does not require cell division, features strikingly dissimilar from those characteristic of V. cholerae biofilm formation. Extracellular DNA limits aggregate size, but is not sufficient to drive aggregation. A mutagenesis screen identifies genes required for aggregate formation, revealing proteins involved in V. cholerae intestinal colonization, stress response, and a protein that distinguishes the current V. cholerae pandemic strain from earlier pandemic strains. We suggest that QS-controlled aggregate formation is important for V. cholerae to successfully transit between the marine niche and the human host.

A preliminary approach of the spatio-temporal distribution of cationic aerosol components in the ambient atmosphere of Kochi, India

Kochi City, situated in the vicinity of the industrial hub and marine niche, is significantly loaded with ionic compounds and get into the atmospheric aerosols which deteriorate the health status of the environment. The distribution of both acid and water extractable cations (Na+, NH4+, K+, Mg2+ and Ca2+) with respect to time and space, in the two phases (I and II) were performed at distinct sites of Kochi, Kerala, India. The study revealed that the water soluble Na+ ion is highlighted in the estuarine site (E1) with momentous load at the coastal site (C1) implying the sea salt influence at these two sites. The average NH4+ and K+ concentration (acid and water soluble fractions) recorded is mostly at the industrial site (R2) which may be endorsed due to the application of NPK fertilizers and also from the process of wood burning sources. Further, K+ is the prominent acid and water soluble cation recorded in the study. Mg2+ ion having both oceanic and anthropogenic origin contributes the present observed pollution load. Average acid soluble Ca2+ content is noted maximum at the estuarine spot E1, where as the hike with respect to water soluble fraction of this ion is noticed at the industrial site, R2. These inferences justify the influence of point sources such as industrial, crustal and construction related activities affecting in and around this metropolis.

The bottlenose dolphin (Tursiops truncatus) faecal microbiota.

Cetaceans have evolved from herbivorous terrestrial artiodactyls closely related to ruminants and hippopotamuses. Delphinidae, a family included in this order, represent an extreme and successful re-adaptation of mammalian physiology to the marine habitat and piscivorous diet. The anatomical aspects of Delphinidae success are well understood, whereas some physiological aspects of their environmental fitness are less defined, such as the gut microbiota composition and its adaptation to their dietary niche. Here, we explored the faecal microbiota structure of nine adult bottlenose dolphins (Tursiops truncatus) and one breast-fed calf living in a controlled environment. According to our findings, dolphins possess a unique microbiota profile within the Mammalia class, highly resembling that of carnivorous marine fishes. The breast-fed calf showed a distinctive compositional structure of the gut microbial ecosystem, which partially overlaps with the mother's milk microbiota. Taken together, our data indicate that in dolphins the adaptation to the marine niche and piscivorous diet involved the convergence of their gut microbiota structure with that of marine fishes, overcoming the gut microbiota phylogenetic inertia previously described in terrestrial mammalians.

Application of computer-aided tomography techniques to visualize kelp holdfast structure reveals the importance of habitat complexity for supporting marine biodiversity

Ecosystem engineers that increase habitat complexity are keystone species in marine systems, increasing shelter and niche availability, and therefore biodiversity. For example, kelp holdfasts form intricate structures and host the largest number of organisms in kelp ecosystems. However, methods that quantify 3D habitat complexity have only seldom been used in marine habitats, and never in kelp holdfast communities. This study investigated the role of kelp holdfasts (Laminaria hyperborea) in supporting benthic faunal biodiversity. Computer-aided tomography (CT-) scanning was used to quantify the three-dimensional geometrical complexity of holdfasts, including volume, surface area and surface fractal dimension (FD). Additionally, the number of haptera, number of haptera per unit of volume, and age of kelps were estimated. These measurements were compared to faunal biodiversity and community structure, using partial least-squares regression and multivariate ordination. Holdfast volume explained most of the variance observed in biodiversity indices, however all other complexity measures also strongly contributed to the variance observed. Multivariate ordinations further revealed that surface area and haptera per unit of volume accounted for the patterns observed in faunal community structure. Using 3D image analysis, this study makes a strong contribution to elucidate quantitative mechanisms underlying the observed relationship between biodiversity and habitat complexity. Furthermore, the potential of CT-scanning as an ecological tool is demonstrated, and a methodology for its use in future similar studies is established. Such spatially resolved imager analysis could help identify structurally complex areas as biodiversity hotspots, and may support the prioritization of areas for conservation.

Genome sequence of Enterobacter sp. ST3, a quorum sensing bacterium associated with marine dinoflagellate.

Phycosphere environment is a typical marine niche, harbor diverse populations of microorganisms, which are thought to play a critical role in algae host and influence mutualistic and competitive interactions. Understanding quorum sensing-based acyl-homoserine lactone (AHL) language may shed light on the interaction between algal-associated microbial communities in the native environment. In this work, we isolated an epidermal bacterium (was tentatively named Enterobacter sp. ST3, and deposited in SOA China, the number is MCCC1K02277-ST3) from the marine dinoflagellate Scrippsiella trochoidea, and found it has the ability to produce short-chain AHL signal. In order to better understand its communication information at molecular level, the genomic map was investigated. The genome size was determined to be 4.81 Mb with a G + C content of 55.59%, comprising 6 scaffolds of 75 contigs containing 4647 protein-coding genes. The functional proteins were predicted, and 3534 proteins were assigned to COG functional categories. An AHL-relating gene, LuxR, was found in upstream position at contig 1. This genome data may provide clues to increase understanding of the chemical characterization and ecological behavior of strain ST3 in the phycosphere microenvironment.

Indole-Diterpenoids with Anti-H1N1 Activity from the Aciduric Fungus Penicillium camemberti OUCMDZ-1492

An aciduric fungal strain, Penicillium camemberti OUCMDZ-1492, was isolated from an acidic marine niche, mangrove soil and mud, around the roots of Rhizophora apiculata. Six new indole-diterpenoids (1-6), along with five known analogues, emindole SB (7), 21-isopentenylpaxilline (8), paspaline (9), paxilline (10), and dehydroxypaxilline (11), were isolated from the fermentation broth of P. camemberti OUCMDZ-1492 grown at pH 5.0. On the basis of spectroscopic analyses, CD spectra, quantum ECD calculations, and chemical methods, new structures 1-6 were established as 3-deoxo-4b-deoxypaxilline, 4a-demethylpaspaline-4a-carboxylic acid, 4a-demethylpaspaline-3,4,4a-triol, 2'-hydroxypaxilline, 9,10-diisopentenylpaxilline, and (6S,7R,10E,14E)-16-(1H-indol-3-yl)-2,6,10,14-tetramethylhexadeca-2,10,14-triene-6,7-diol, respectively. Compounds 1-3 and 5-10 exhibited significant activity against the H1N1 virus with IC50 values of 28.3, 38.9, 32.2, 73.3, 34.1, 26.2, 6.6, 77.9, and 17.7 μM, respectively. The results showed that 3-oxo, 4b-hydroxy, and 9-isopentenyl substitutions tend to increase the anti-H1N1 activity of hexacyclic indole-diterpenoids.

Effects of physiological shock treatments on toxicity and polyketide synthase gene expression in Prymnesium parvum (Prymnesiophyceae)

The toxic prymnesiophyte Prymnesium parvum has been linked to massive fish kills worldwide. The toxic blooms have been shown to be derived from a seed population, abiotic conditions such as temperature, salinity and water turbulence having encouraged massive growth of the Prymnesium population. Within its highly fluctuating coastal marine niche, P. parvum must acclimate rapidly to changing conditions. Although studies on the physiology and toxicity of P. parvum exist, examination of gene expression in such analyses is novel. In this study we investigate (1) relative toxicity (intracellular vs. extracellular) and (2) differential gene expression of three polyketide synthase (PKS) transcripts via real-time PCR (qPCR). It was hypothesized that these genes play a role in the production of the toxic compounds prymnesin-1 and -2 produced by P. parvum. We found that low salinity shock and high irradiation shock increase different aspects of Prymnesium's toxicity (intra- vs. extracellular). Furthermore, we found that these two physiological shock treatments induced higher copy numbers in selected polyketide synthase genes (PKS) genes, suggesting a connection between toxicity and the PKS biosynthetic pathway. Our results demonstrate that PKS genes are likely to play an important role in the toxicity of P. parvum and deserve further investigation in populations exposed to changing environmental conditions.

A locomotor innovation enables water-land transition in a marine fish.

BackgroundMorphological innovations that significantly enhance performance capacity may enable exploitation of new resources and invasion of new ecological niches. The invasion of land from the aquatic realm requires dramatic structural and physiological modifications to permit survival in a gravity-dominated, aerial environment. Most fishes are obligatorily aquatic, with amphibious fishes typically making slow-moving and short forays on to land.Methodology/Principal FindingsHere I describe the behaviors and movements of a little known marine fish that moves extraordinarily rapidly on land. I found that the Pacific leaping blenny, Alticus arnoldorum, employs a tail-twisting movement on land, previously unreported in fishes. Focal point behavioral observations of Alticus show that they have largely abandoned the marine realm, feed and reproduce on land, and even defend terrestrial territories. Comparisons of these blennies' terrestrial kinematic and kinetic (i.e., force) measurements with those of less terrestrial sister genera show A. arnoldorum move with greater stability and locomotor control, and can move away more rapidly from impending threats.Conclusions/SignificanceMy results demonstrate that axial tail twisting serves as a key innovation enabling invasion of a novel marine niche. This paper highlights the potential of using this system to address general evolutionary questions about water-land transitions and niche invasions.

Dental Divergence Supports Species Status of the Extinct Sea Mink (Carnivora: Mustelidae:Neovison macrodon)

The sea mink (Neovison macrodon (Prentiss, 1903): Mustelinae) was an unusual late-Cenozoic example of an organism that had rapidly evolved toward a marine niche. Except for the otters, it was probably the most aquatic member of the Musteloidea. Its status as a separate species has not been resolved. A larger relative of the American mink (N. vison), it inhabited the shores of New England and possibly the Canadian Maritime Provinces until it was hunted to extinction in the 19th century. Skeletal and skin specimens were not collected by zoologists, but the former are known from Native American archaeological sites. The hypothesis that the sea mink showed dental divergence from N. vison, an indication of systematic and ecological distinctness, was tested on 111 dentally mature mink specimens originally collected from the Turner Farm archaeological site (Penobscot Bay, Maine). These teeth, dating from about 5,000 to 250 years ago, were compared with 158 other specimens measured for this study and published data from 78 individuals, representing 4 subspecies of N. vison and 22 additional musteloid genera. Thirteen dental measurements were taken on all species and studied using regressions, principal component analysis, and significance testing. Based on comparisons with American mink, it appears likely that the archaeological specimens included primarily N. macrodon but also N. vison. Although pairs of species within the Lutrinae and genus Mustela showed divergence comparable to that of N. vison and N. macrodon, the dental proportions of male and female N. vison and of the several N. vison subspecies were nearly identical. These analyses suggest that N. macrodon was sufficiently distinct from N. vison to support its recognition as a separate species.

The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific

The world's oceans contain a complex mixture of micro-organisms that are for the most part, uncharacterized both genetically and biochemically. We report here a metagenomic study of the marine planktonic microbiota in which surface (mostly marine) water samples were analyzed as part of the Sorcerer II Global Ocean Sampling expedition. These samples, collected across a several-thousand km transect from the North Atlantic through the Panama Canal and ending in the South Pacific yielded an extensive dataset consisting of 7.7 million sequencing reads (6.3 billion bp). Though a few major microbial clades dominate the planktonic marine niche, the dataset contains great diversity with 85% of the assembled sequence and 57% of the unassembled data being unique at a 98% sequence identity cutoff. Using the metadata associated with each sample and sequencing library, we developed new comparative genomic and assembly methods. One comparative genomic method, termed “fragment recruitment,” addressed questions of genome structure, evolution, and taxonomic or phylogenetic diversity, as well as the biochemical diversity of genes and gene families. A second method, termed “extreme assembly,” made possible the assembly and reconstruction of large segments of abundant but clearly nonclonal organisms. Within all abundant populations analyzed, we found extensive intra-ribotype diversity in several forms: (1) extensive sequence variation within orthologous regions throughout a given genome; despite coverage of individual ribotypes approaching 500-fold, most individual sequencing reads are unique; (2) numerous changes in gene content some with direct adaptive implications; and (3) hypervariable genomic islands that are too variable to assemble. The intra-ribotype diversity is organized into genetically isolated populations that have overlapping but independent distributions, implying distinct environmental preference. We present novel methods for measuring the genomic similarity between metagenomic samples and show how they may be grouped into several community types. Specific functional adaptations can be identified both within individual ribotypes and across the entire community, including proteorhodopsin spectral tuning and the presence or absence of the phosphate-binding gene PstS.

Molecular Phylogenetics and Ecological Diversification of the Transisthmian Fish Genus Centropomus (Perciformes: Centropomidae)

Phylogenetic relationships among the 12 recognized fish species in the New World genus Centropomus (Pisces, Centropomidae) were analyzed using allozyme electrophoresis and 618 bp of the mitochondrial DNA 16S ribosomal RNA (rRNA) gene. Molecular phylogenetic trees were generally consistent with previously published partial hypotheses based on morphological evidence. However, previously undefined sister group relationships between major species groups were resolved using molecular data, and phylogenetic hypotheses for Centropomus based on 16S rRNA sequences were better supported than were allozyme-based hypotheses. The high level of congruence among the trees inferred from the nuclear and mitochondrial characters provided a firm phylogenetic basis for analysis of ecological diversification and molecular evolution in the genus. Compared to basal Centropomus species, members of the most nested species group were significantly larger in body size and occupied a marine niche only peripherally utilized by their congeners. We also observed substitution rate heterogeneity among 16S rRNA lineages; in contrast to expectations based on “metabolic rate” and “generation interval” models, relative substitution rates were faster than expected for the group of large-bodied snooks. Using the Pliocene rise of the Central American isthmian marine barrier to calibrate rates of 16S ribosomal gene evolution in Centropomus, we found that the rates for the genus were similar to those reported for higher vertebrates. Analysis of the three sets of transisthmian geminate taxa in Centropomus indicated that two of the pairs were probably formed during the Pliocene rise of the isthmus while the third pair diverged several million years earlier.