ORCID Profile
0000-0002-2177-203X
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San Diego State University
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Flinders University
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Condensed Matter Physics | Condensed Matter Imaging
Publisher: Informa UK Limited
Date: 03-2006
Publisher: Springer Science and Business Media LLC
Date: 11-02-2010
DOI: 10.1038/ISMEJ.2010.1
Abstract: The species composition and metabolic potential of microbial and viral communities are predictable and stable for most ecosystems. This apparent stability contradicts theoretical models as well as the viral-microbial dynamics observed in simple ecosystems, both of which show Kill-the-Winner behavior causing cycling of the dominant taxa. Microbial and viral metagenomes were obtained from four human-controlled aquatic environments at various time points separated by one day to >1 year. These environments were maintained within narrow geochemical bounds and had characteristic species composition and metabolic potentials at all time points. However, underlying this stability were rapid changes at the fine-grained level of viral genotypes and microbial strains. These results suggest a model wherein functionally redundant microbial and viral taxa are cycling at the level of viral genotypes and virus-sensitive microbial strains. Microbial taxa, viral taxa, and metabolic function persist over time in stable ecosystems and both communities fluctuate in a Kill-the-Winner manner at the level of viral genotypes and microbial strains.
Publisher: Springer Berlin Heidelberg
Date: 2004
Publisher: Resilience Alliance, Inc.
Date: 2009
Publisher: Frontiers Media SA
Date: 16-08-2022
DOI: 10.3389/FMARS.2022.908734
Abstract: Caribbean reefs have undergone large-scale losses in coral cover in past decades, sparking a search for species that are resilient under stress. Porites astreoides has been considered a “winner” and a key player in sustaining coral cover in the Caribbean as more sensitive species struggle. However, P. astreoides has recently declined in abundance, raising concern about its status as a winner. Here, we reviewed the ecophysiology of P. astreoides in response to environmental stress to elucidate whether this species could thrive in the future of Caribbean reefs. We examined ecophysiological variables of P. astreoides related to photosynthesis, growth, recruitment, tissue condition, and microbiome in response to temperature, pH, macroalgal competition, depth, and sedimentation. Overall, P. astreoides was sensitive to environmental stress and each physiological feature showed varying levels of sensitivity. Coral-algal photosynthesis and coral tissue condition could withstand single events of thermal stress but reflected a metabolic imbalance that hinders recovery from repeated bleaching events, compromising long-term success. Colony growth was particularly vulnerable to low pH and macroalgal competition. Recruitment was unaffected, or even favored, by depth and could tolerate high temperatures, but it was sensitive to exposure to macroalgae, especially in combination with abiotic stressors. The response of the microbiome of P. astreoides to stressors is still poorly understood. In relation to other corals, P. astreoides was frequently reported as the most sensitive species in the reviewed literature. The success of P. astreoides is tightly integrated into the future of Caribbean reefs, which could be losing an old winner.
Publisher: Springer Netherlands
Date: 09-11-2010
Publisher: Public Library of Science (PLoS)
Date: 18-11-2019
Publisher: Frontiers Media SA
Date: 05-05-2021
DOI: 10.3389/FMARS.2021.619695
Abstract: Chondrichthyes, an ancient and erse class of vertebrates, are crucial to the health of marine ecosystems. Excessive demand for chondrichthyan products has increased fishing pressure, threatening ∼30% of species with extinction in recent decades. India is the second-largest shark landing nation globally and the province of Gujarat, is the largest contributor to its shark exports. Despite their significant contribution to global fish supplies, chondrichthyan fisheries in Gujarat remain understudied and many species, data deficient, posing challenges to the conservation of remaining populations in the region. Here, we report results from taxonomic assessment of elasmobranchs at four key landing sites in Gujarat. We identified thirty-one species of sharks and rays with a significant bias toward capture of females and juveniles by fisheries. Our data indicate the presence of nursery areas for species such as Sphyrna lewini and Rhynchobatus laevis in the neritic areas off Gujarat. Further, we discovered extensions of the current distribution range for three species - Torpedo sinuspersici , Carcharhinus sorrah , and Rhinobatos punctifer . Taxonomic identities for a subset of species were confirmed using genomic analyses conducted with portable DNA sequencing tools. We present assessments for six data deficient species in the region – Rhinobatos annandalei , Rhinoptera jayakari , Maculabatis bineeshi, Pateobatis bleekeri, T. sinuspersici , and Carcharhinus amboinensis. Our investigation underscores species with urgent conservation needs and reduces data deficiencies. These data will inform and pivot future scientific and conservation efforts to protect remaining populations of some of the most vulnerable Chondrichthyes in the Arabian Seas Region.
Publisher: Public Library of Science (PLoS)
Date: 23-02-2018
Publisher: Springer Science and Business Media LLC
Date: 07-08-2023
DOI: 10.1038/S41598-023-39184-5
Abstract: Microbiomes confer beneficial physiological traits to their host, but microbial ersity is inherently variable, challenging the relationship between microbes and their contribution to host health. Here, we compare the ersity and architectural complexity of the epidermal microbiome from 74 in idual whale sharks ( Rhincodon typus ) across five aggregations globally to determine if network properties may be more indicative of the microbiome-host relationship. On the premise that microbes are expected to exhibit biogeographic patterns globally and that distantly related microbial groups can perform similar functions, we hypothesized that microbiome co-occurrence patterns would occur independently of ersity trends and that keystone microbes would vary across locations. We found that whale shark aggregation was the most important factor in discriminating taxonomic ersity patterns. Further, microbiome network architecture was similar across all aggregations, with degree distributions matching Erdos–Renyi-type networks. The microbiome-derived networks, however, display modularity indicating a definitive microbiome structure on the epidermis of whale sharks. In addition, whale sharks hosted 35 high-quality metagenome assembled genomes (MAGs) of which 25 were present from all s le locations, termed the abundant ‘core’. Two main MAG groups formed, defined here as Ecogroup 1 and 2, based on the number of genes present in metabolic pathways, suggesting there are at least two important metabolic niches within the whale shark microbiome. Therefore, while variability in microbiome ersity is high, network structure and core taxa are inherent characteristics of the epidermal microbiome in whale sharks. We suggest the host-microbiome and microbe-microbe interactions that drive the self-assembly of the microbiome help support a functionally redundant abundant core and that network characteristics should be considered when linking microbiomes with host health.
Publisher: Public Library of Science (PLoS)
Date: 11-12-2009
Publisher: Public Library of Science (PLoS)
Date: 03-06-2010
Publisher: Proceedings of the National Academy of Sciences
Date: 10-02-2009
Abstract: The complex microbiome of the rumen functions as an effective system for the conversion of plant cell wall biomass to microbial protein, short chain fatty acids, and gases. As such, it provides a unique genetic resource for plant cell wall degrading microbial enzymes that could be used in the production of biofuels. The rumen and gastrointestinal tract harbor a dense and complex microbiome. To gain a greater understanding of the ecology and metabolic potential of this microbiome, we used comparative metagenomics (phylotype analysis and SEED subsystems-based annotations) to examine randomly s led pyrosequence data from 3 fiber-adherent microbiomes and 1 pooled liquid s le (a mixture of the liquid microbiome fractions from the same bovine rumens). Even though the 3 animals were fed the same diet, the community structure, predicted phylotype, and metabolic potentials in the rumen were markedly different with respect to nutrient utilization. A comparison of the glycoside hydrolase and cellulosome functional genes revealed that in the rumen microbiome, initial colonization of fiber appears to be by organisms possessing enzymes that attack the easily available side chains of complex plant polysaccharides and not the more recalcitrant main chains, especially cellulose. Furthermore, when compared with the termite hindgut microbiome, there are fundamental differences in the glycoside hydrolase content that appear to be diet driven for either the bovine rumen (forages and legumes) or the termite hindgut (wood).
Publisher: Frontiers Media SA
Date: 12-01-2018
Publisher: The Oceanography Society
Date: 06-2007
Publisher: PeerJ
Date: 10-11-2015
DOI: 10.7717/PEERJ.1390
Abstract: The natural beauty of coral reefs attracts millions of tourists worldwide resulting in substantial revenues for the adjoining economies. Although their visual appearance is a pivotal factor attracting humans to coral reefs current monitoring protocols exclusively target biogeochemical parameters, neglecting changes in their aesthetic appearance. Here we introduce a standardized computational approach to assess coral reef environments based on 109 visual features designed to evaluate the aesthetic appearance of art. The main feature groups include color intensity and ersity of the image, relative size, color, and distribution of discernable objects within the image, and texture. Specific coral reef aesthetic values combining all 109 features were calibrated against an established biogeochemical assessment (NCEAS) using machine learning algorithms. These values were generated for ∼2,100 random photographic images collected from 9 coral reef locations exposed to varying levels of anthropogenic influence across 2 ocean systems. Aesthetic values proved accurate predictors of the NCEAS scores (root mean square error 5 for N ≥ 3) and significantly correlated to microbial abundance at each site. This shows that mathematical approaches designed to assess the aesthetic appearance of photographic images can be used as an inexpensive monitoring tool for coral reef ecosystems. It further suggests that human perception of aesthetics is not purely subjective but influenced by inherent reactions towards measurable visual cues. By quantifying aesthetic features of coral reef systems this method provides a cost efficient monitoring tool that targets one of the most important socioeconomic values of coral reefs directly tied to revenue for its local population.
Publisher: Wiley
Date: 08-2009
DOI: 10.1111/J.1462-2920.2009.01935.X
Abstract: The coral holobiont is the community of metazoans, protists and microbes associated with scleractinian corals. Disruptions in these associations have been correlated with coral disease, but little is known about the series of events involved in the shift from mutualism to pathogenesis. To evaluate structural and functional changes in coral microbial communities, Porites compressa was exposed to four stressors: increased temperature, elevated nutrients, dissolved organic carbon loading and reduced pH. Microbial metagenomic s les were collected and pyrosequenced. Functional gene analysis demonstrated that stressors increased the abundance of microbial genes involved in virulence, stress resistance, sulfur and nitrogen metabolism, motility and chemotaxis, fatty acid and lipid utilization, and secondary metabolism. Relative changes in taxonomy also demonstrated that coral-associated microbiota (Archaea, Bacteria, protists) shifted from a healthy-associated coral community (e.g. Cyanobacteria, Proteobacteria and the zooxanthellae Symbiodinium) to a community (e.g. Bacteriodetes, Fusobacteria and Fungi) of microbes often found on diseased corals. Additionally, low-abundance Vibrio spp. were found to significantly alter microbiome metabolism, suggesting that the contribution of a just a few members of a community can profoundly shift the health status of the coral holobiont.
Publisher: Wiley
Date: 25-06-2020
DOI: 10.1002/BMB.21387
Publisher: Frontiers Media SA
Date: 02-03-2023
DOI: 10.3389/FMICB.2023.1031711
Abstract: Marine host-associated microbiomes are affected by a combination of species-specific (e.g., host ancestry, genotype) and habitat-specific features (e.g., environmental physiochemistry and microbial biogeography). The stingray epidermis provides a gradient of characteristics from high dermal denticles coverage with low mucus to reduce dermal denticles and high levels of mucus. Here we investigate the effects of host phylogeny and habitat by comparing the epidermal microbiomes of Myliobatis californica (bat rays) with a mucus rich epidermis, and Urobatis halleri (round rays) with a mucus reduced epidermis from two locations, Los Angeles and San Diego, California (a 150 km distance). We found that host microbiomes are species-specific and distinct from the water column, however composition of M. californica microbiomes showed more variability between in iduals compared to U. halleri. The variability in the microbiome of M. californica caused the microbial taxa to be similar across locations, while U. halleri microbiomes were distinct across locations. Despite taxonomic differences, Shannon ersity is the same across the two locations in U. halleri microbiomes suggesting the taxonomic composition are locally adapted, but ersity is maintained by the host. Myliobatis californica and U. halleri microbiomes maintain functional similarity across Los Angeles and San Diego and each ray showed several unique functional genes. Myliobatis californica has a greater relative abundance of RNA Polymerase III-like genes in the microbiome than U. halleri , suggesting specific adaptations to a heavy mucus environment. Construction of Metagenome Assembled Genomes (MAGs) identified novel microbial species within Rhodobacteraceae , Moraxellaceae , Caulobacteraceae , Alcanivoracaceae and Gammaproteobacteria. All MAGs had a high abundance of active RNA processing genes, heavy metal, and antibiotic resistant genes, suggesting the stingray mucus supports high microbial growth rates, which may drive high levels of competition within the microbiomes increasing the antimicrobial properties of the microbes.
Publisher: Springer Science and Business Media LLC
Date: 04-09-2013
Abstract: The revolution in DNA sequencing technology continues unabated, and is affecting all aspects of the biological and medical sciences. The training and recruitment of the next generation of researchers who are able to use and exploit the new technology is severely lacking and potentially negatively influencing research and development efforts to advance genome biology. Here we present a cross-disciplinary course that provides undergraduate students with practical experience in running a next generation sequencing instrument through to the analysis and annotation of the generated DNA sequences. Many labs across world are installing next generation sequencing technology and we show that the undergraduate students produce quality sequence data and were excited to participate in cutting edge research. The students conducted the work flow from DNA extraction, library preparation, running the sequencing instrument, to the extraction and analysis of the data. They sequenced microbes, metagenomes, and a marine mammal, the Californian sea lion, Zalophus californianus . The students met sequencing quality controls, had no detectable contamination in the targeted DNA sequences, provided publication quality data, and became part of an international collaboration to investigate carcinomas in carnivores. Students learned important skills for their future education and career opportunities, and a perceived increase in students’ ability to conduct independent scientific research was measured. DNA sequencing is rapidly expanding in the life sciences. Teaching undergraduates to use the latest technology to sequence genomic DNA ensures they are ready to meet the challenges of the genomic era and allows them to participate in annotating the tree of life.
Publisher: American Society for Microbiology
Date: 15-12-2021
Abstract: Developing effective assessments of student learning is a challenging task for faculty and even more difficult for those in emerging disciplines that lack readily available resources and standards.
Publisher: Cold Spring Harbor Laboratory
Date: 26-01-2019
DOI: 10.1101/527796
Abstract: Microbiomes are vast communities of microbes and viruses that populate all natural ecosystems. Viruses have been considered the most variable component of microbiomes, as supported by virome surveys and ex les of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared to other environments. Here we investigate the origin, evolution, and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboratory, we obtained DNA sequences of crAssphage from over one-third of the world's countries, and showed that its phylogeography is locally clustered within countries, cities, and in iduals. We also found colinear crAssphage-like genomes in both Old-World and New-World primates, challenging genomic mosaicism and suggesting that the association of crAssphage with primates may be millions of years old. We conclude that crAssphage is a benign globetrotter virus that may have co-evolved with the human lineage and an integral part of the normal human gut virome.
Publisher: Springer Science and Business Media LLC
Date: 14-03-2019
DOI: 10.1038/S41598-019-40940-9
Abstract: Chondrichthyes - sharks, rays, skates, and chimeras, are among the most threatened and data deficient vertebrate species. Global demand for shark and ray derived products, drives unregulated and exploitative fishing practices, which are in turn facilitated by the lack of ecological data required for effective conservation of these species. Here, we describe a Next Generation Sequencing method (using the MinION, a hand-held portable sequencing device from Oxford Nanopore Technologies), and analyses pipeline for molecular ecological studies in Chondrichthyes. Using this method, the complete mitochondrial genome and nuclear intergenic and protein-coding sequences were obtained by direct sequencing of genomic DNA obtained from shark fin tissue. Recovered loci include mitochondrial barcode sequences- Cytochrome oxidase I, NADH2, 16S rRNA and 12S rRNA- and nuclear genetic loci such as 5.8S rRNA, Internal Transcribed Spacer 2, and 28S rRNA regions, which are commonly used for taxonomic identification. Other loci recovered were the nuclear protein-coding genes for antithrombin or SerpinC, Immunoglobulin lambda light chain, Preprogehrelin, selenium binding protein 1(SBP1), Interleukin-1 beta (IL-1β) and Recombination-Activating Gene 1 (RAG1). The median coverage across all genetic loci was 20x and sequence accuracy was ≥99.8% compared to reference sequences. Analyses of the nuclear ITS2 region and the mitochondrial protein-encoding loci allowed accurate taxonomic identification of the shark specimen as Carcharhinus falciformis , a CITES Appendix II species. MinION sequencing provided 1,152,211 bp of new shark genome, increasing the number of sequenced shark genomes to five. Phylogenetic analyses using both mitochondrial and nuclear loci provided evidence that Prionace glauca is nested within Carcharhinus , suggesting the need for taxonomic reassignment of P . glauca . We increased genomic information about a shark species for ecological and population genetic studies, enabled accurate identification of the shark tissue for bio ersity indexing and resolved phylogenetic relationships among multiple taxa. The method was independent of lification bias, and adaptable for field assessments of other Chondrichthyes and wildlife species in the future.
Publisher: Elsevier BV
Date: 03-2010
DOI: 10.1016/J.TIM.2009.12.002
Abstract: Dimethylsulfoniopropionate (DMSP) and dimethylsulfide (DMS) are key compounds in the global sulfur cycle. Moreover, DMS is particularly important in climate regulation owing to its role in cloud formation. Reef building corals are major contributors to the production of these two compounds and also form erse and complex associations with bacteria, which are known to play a crucial role in the degradation of DMSP and DMS. Here, we highlight an extensive overlap between bacterial species implicated in DMSP/DMS degradation and those associated with corals, leading to the hypothesis that these two compounds play a major role in structuring coral-associated bacterial communities, with important consequences for coral health and the resilience of coral reefs. We also explore the publically available metagenome databases and show that genes implicated in DMSP metabolism are abundant in the viral component of coral-reef-derived metagenomes, indicating that viruses can act as a reservoir for such genes.
Publisher: Microbiology Society
Date: 04-09-2023
Publisher: Springer Science and Business Media LLC
Date: 13-06-2020
DOI: 10.1186/S40168-020-00840-X
Abstract: The vertebrate clade erged into Chondrichthyes (sharks, rays, and chimeras) and Osteichthyes fishes (bony fishes) approximately 420 mya, with each group accumulating vast anatomical and physiological differences, including skin properties. The skin of Chondrichthyes fishes is covered in dermal denticles, whereas Osteichthyes fishes are covered in scales and are mucous rich. The ergence time among these two fish groups is hypothesized to result in predictable variation among symbionts. Here, using shotgun metagenomics, we test if patterns of ersity in the skin surface microbiome across the two fish clades match predictions made by phylosymbiosis theory. We hypothesize (1) the skin microbiome will be host and clade-specific, (2) evolutionary difference in elasmobranch and teleost will correspond with a concomitant increase in host-microbiome dissimilarity, and (3) the skin structure of the two groups will affect the taxonomic and functional composition of the microbiomes. We show that the taxonomic and functional composition of the microbiomes is host-specific. Teleost fish had lower average microbiome within clade similarity compared to among clade comparison, but their composition is not different among clade in a null based model. Elasmobranch’s average similarity within clade was not different than across clade and not different in a null based model of comparison. In the comparison of host distance with microbiome distance, we found that the taxonomic composition of the microbiome was related to host distance for the elasmobranchs, but not the teleost fishes. In comparison, the gene function composition was not related to the host-organism distance for elasmobranchs but was negatively correlated with host distance for teleost fishes. Our results show the patterns of phylosymbiosis are not consistent across both fish clades, with the elasmobranchs showing phylosymbiosis, while the teleost fish are not. The discrepancy may be linked to alternative processes underpinning microbiome assemblage, including possible historical host-microbiome evolution of the elasmobranchs and convergent evolution in the teleost which filter specific microbial groups. Our comparison of the microbiomes among fishes represents an investigation into the microbial relationships of the oldest ergence of extant vertebrate hosts and reveals that microbial relationships are not consistent across evolutionary timescales.
Publisher: Wiley
Date: 05-10-2012
DOI: 10.1111/J.1462-2920.2012.02891.X
Abstract: Oxygen minimum zones (OMZs) are oceanographic features that affect ocean productivity and bio ersity, and contribute to ocean nitrogen loss and greenhouse gas emissions. Here we describe the viral communities associated with the Eastern Tropical South Pacific (ETSP) OMZ off Iquique, Chile for the first time through abundance estimates and viral metagenomic analysis. The viral-to-microbial ratio (VMR) in the ETSP OMZ fluctuated in the oxycline and declined in the anoxic core to below one on several occasions. The number of viral genotypes (unique genomes as defined by sequence assembly) ranged from 2040 at the surface to 98 in the oxycline, which is the lowest viral ersity recorded to date in the ocean. Within the ETSP OMZ viromes, only 4.95% of genotypes were shared between surface and anoxic core viromes using reciprocal BLASTn sequence comparison. ETSP virome comparison with surface marine viromes (Sargasso Sea, Gulf of Mexico, Kingman Reef, Chesapeake Bay) revealed a dissimilarity of ETSP OMZ viruses to those from other oceanic regions. From the 1.4 million non-redundant DNA sequences s led within the altered oxygen conditions of the ETSP OMZ, more than 97.8% were novel. Of the average 3.2% of sequences that showed similarity to the SEED non-redundant database, phage sequences dominated the surface viromes, eukaryotic virus sequences dominated the oxycline viromes, and phage sequences dominated the anoxic core viromes. The viral community of the ETSP OMZ was characterized by fluctuations in abundance, taxa and ersity across the oxygen gradient. The ecological significance of these changes was difficult to predict however, it appears that the reduction in oxygen coincides with an increased shedding of eukaryotic viruses in the oxycline, and a shift to unique viral genotypes in the anoxic core.
Publisher: Public Library of Science (PLoS)
Date: 13-08-2008
Publisher: Frontiers Media SA
Date: 14-11-2016
Publisher: Research Square Platform LLC
Date: 15-06-2021
DOI: 10.21203/RS.3.RS-600995/V1
Abstract: Background The coral holobiont is comprised of a highly erse microbial community that provides key services to corals such as protection against pathogens and nutrient cycling. The coral surface mucus layer (SML) microbiome is very sensitive to external changes and tied to ecosystem functioning, as it constitutes the direct interface between the coral host and the environment. The functional profile of microbial genes in the coral SML is underexplored and the use of shotgun metagenomics is relatively rare among coral microbiome studies. Here we investigate whether the bacterial taxonomic and functional profiles in the coral SML are shaped by the local reef zone and explore their role in coral health and ecosystem functioning. Results The analysis was conducted using metagenomes and metagenome assemble genomes (MAGs) associated with the coral Pseudodiploria strigosa and the water column from two naturally distinct reef environments in Bermuda: inner patch reefs exposed to a fluctuating thermal regime and the more stable outer reefs . Our results showed that the microbial community structure is simultaneously selected by the host medium (i.e., coral SML versus water) and the local environment (i.e., inner reefs versus outer reefs), both at taxonomic and functional levels. The coral SML microbiome from inner reefs provides more gene functions that are involved in nutrient cycling (e.g., photosynthesis, phosphorus metabolism, sulfur assimilation) and that are related to higher levels of microbial activity, competition, and stress response, such as dimethylsulfoniopropionate (DMSP) breakdown. In contrast, the coral SML microbiome from outer reefs contained genes indicative of a carbohydrate-rich mucus composition found in corals exposed to less stressful temperatures and showed high proportions of microbial gene functions that play a potential role in coral disease, such as degradation of lignin-derived compounds and sulfur oxidation. Conclusion The fluctuating environment in the inner patch reefs of Bermuda could be driving a more beneficial coral SML microbiome potentially increasing holobiont resilience to environmental changes and disease. Our results reveal microbial taxa and functions selected at reef scale in the coral SML microbiome that can leverage disease management, microbiome engineering, and microbial eco-evolutionary theories.
Publisher: Springer Science and Business Media LLC
Date: 24-08-2016
DOI: 10.1038/NATURE19335
Publisher: Wiley
Date: 04-08-2020
Publisher: Cold Spring Harbor Laboratory
Date: 21-04-2023
DOI: 10.1101/2023.04.20.537752
Abstract: Phages dominate every ecosystem on the planet. While virulent phages sculpt the microbiome by killing their bacterial hosts, temperate phages provide unique growth advantages to their hosts through lysogenic conversion. Many prophages benefit their host, and prophages are responsible for genotypic and phenotypic differences that separate in idual microbial strains. However, the microbes also endure a cost to maintain those phages: additional DNA to replicate and proteins to transcribe and translate. We have never quantified those benefits and costs. Here, we analysed over two and a half million prophages from over half a million bacterial genome assemblies. Analysis of the whole dataset and a representative subset of taxonomically erse bacterial genomes demonstrated that the normalised prophage density was uniform across all bacterial genomes above 2 Mbp. We identified a constant carrying capacity of phage DNA per bacterial DNA. We estimated that each prophage provides cellular services equivalent to approximately 2.4 % of the cell’s energy or 0.9 ATP per bp per hour. We demonstrate analytical, taxonomic, geographic, and temporal disparities in identifying prophages in bacterial genomes that provide novel targets for identifying new phages. We anticipate that the benefits bacteria accrue from the presence of prophages balance the energetics involved in supporting prophages. Furthermore, our data will provide a new framework for identifying phages in environmental datasets, erse bacterial phyla, and from different locations.
Publisher: Oxford University Press (OUP)
Date: 25-04-2019
DOI: 10.1093/BIOINFORMATICS/BTZ265
Abstract: Currently there are no tools specifically designed for annotating genes in phages. Several tools are available that have been adapted to run on phage genomes, but due to their underlying design, they are unable to capture the full complexity of phage genomes. Phages have adapted their genomes to be extremely compact, having adjacent genes that overlap and genes completely inside of other longer genes. This non-delineated genome structure makes it difficult for gene prediction using the currently available gene annotators. Here we present PHANOTATE, a novel method for gene calling specifically designed for phage genomes. Although the compact nature of genes in phages is a problem for current gene annotators, we exploit this property by treating a phage genome as a network of paths: where open reading frames are favorable, and overlaps and gaps are less favorable, but still possible. We represent this network of connections as a weighted graph, and use dynamic programing to find the optimal path. We compare PHANOTATE to other gene callers by annotating a set of 2133 complete phage genomes from GenBank, using PHANOTATE and the three most popular gene callers. We found that the four programs agree on 82% of the total predicted genes, with PHANOTATE predicting more genes than the other three. We searched for these extra genes in both GenBank’s non-redundant protein database and all of the metagenomes in the sequence read archive, and found that they are present at levels that suggest that these are functional protein-coding genes. eprekate/PHANOTATE Supplementary data are available at Bioinformatics online.
Publisher: Research Square Platform LLC
Date: 12-10-2021
DOI: 10.21203/RS.3.RS-948364/V1
Abstract: Background: Characterizations of sharks-microbe systems in wild environments have outlined patterns of species-specific microbiomes however, whether captivity affects these trends has yet to be determined. We used high-throughput shotgun sequencing to assess the epidermal microbiome belonging to leopard sharks ( Triakis semifasciata ) in captive (Birch Aquarium, La Jolla California), semi-captive ( year in captivity Scripps Institute of Oceanography, California) and wild environments (Moss Landing and La Jolla, California). Results: Here we report captive environments do not drive microbiome composition of T. semifasciata to significantly erge from wild counterparts as life-long captive sharks maintain a species-specific epidermal microbiome resembling those associated with semi-captive and wild populations. Major taxonomic composition shifts observed were inverse changes of top taxonomic contributors across captive duration, specifically an increase of Pseudoalteromonadaceae and consequent decrease of Pseudomonadaceae relative abundance as T. semifasciata increased duration in captive conditions. Moreover, we show captivity did not lead to significant losses in microbial α- ersity of shark epidermal communities. Finally, we present a novel association between T. semifasciata and the Muricauda genus as MAGs revealed a consistent relationship across captive, semi-captive, and wild populations. Conclusions: Our report illustrates the importance of conservation programs for coastal fishes as epidermally-associated microbes of near-shore shark species do not suffer detrimental impacts from long or short-term captivity. Our findings also expand on current understanding of shark epidermal microbiomes, explore the effects of ecologically different scenarios on benthic shark microbe associations, and highlight novel microbial associations that are consistent across captive gradients.
Publisher: Springer Science and Business Media LLC
Date: 1999
DOI: 10.1038/16237
Publisher: American Society for Cell Biology (ASCB)
Date: 15-12-2018
Publisher: Public Library of Science (PLoS)
Date: 27-02-2008
Publisher: Wiley
Date: 02-2002
Publisher: Wiley
Date: 08-2000
Publisher: Springer Science and Business Media LLC
Date: 15-08-2023
DOI: 10.1007/S00248-022-02094-6
Abstract: The coral holobiont is comprised of a highly erse microbial community that provides key services to corals such as protection against pathogens and nutrient cycling. The coral surface mucus layer (SML) microbiome is very sensitive to external changes, as it constitutes the direct interface between the coral host and the environment. Here, we investigate whether the bacterial taxonomic and functional profiles in the coral SML are shaped by the local reef zone and explore their role in coral health and ecosystem functioning. The analysis was conducted using metagenomes and metagenome-assembled genomes (MAGs) associated with the coral Pseudodiploria strigosa and the water column from two naturally distinct reef environments in Bermuda: inner patch reefs exposed to a fluctuating thermal regime and the more stable outer reefs. The microbial community structure in the coral SML varied according to the local environment, both at taxonomic and functional levels. The coral SML microbiome from inner reefs provides more gene functions that are involved in nutrient cycling (e.g., photosynthesis, phosphorus metabolism, sulfur assimilation) and those that are related to higher levels of microbial activity, competition, and stress response. In contrast, the coral SML microbiome from outer reefs contained genes indicative of a carbohydrate-rich mucus composition found in corals exposed to less stressful temperatures and showed high proportions of microbial gene functions that play a potential role in coral disease, such as degradation of lignin-derived compounds and sulfur oxidation. The fluctuating environment in the inner patch reefs of Bermuda could be driving a more beneficial coral SML microbiome, potentially increasing holobiont resilience to environmental changes and disease.
Publisher: Springer Science and Business Media LLC
Date: 22-11-2013
Abstract: Genome sequencing has become routine, however genome assembly still remains a challenge despite the computational advances in the last decade. In particular, the abundance of repeat elements in genomes makes it difficult to assemble them into a single complete sequence. Identical repeats shorter than the average read length can generally be assembled without issue. However, longer repeats such as ribosomal RNA operons cannot be accurately assembled using existing tools. The application Scaffold_builder was designed to generate scaffolds – super contigs of sequences joined by N-bases – based on the similarity to a closely related reference sequence. This is independent of mate-pair information and can be used complementarily for genome assembly, e.g. when mate-pairs are not available or have already been exploited. Scaffold_builder was evaluated using simulated pyrosequencing reads of the bacterial genomes Escherichia coli 042, Lactobacillus salivarius UCC118 and Salmonella enterica subsp. enterica serovar Typhi str. P-stx-12. Moreover, we sequenced two genomes from Salmonella enterica serovar Typhimurium LT2 G455 and Salmonella enterica serovar Typhimurium SDT1291 and show that Scaffold_builder decreases the number of contig sequences by 53% while more than doubling their average length. Scaffold_builder is written in Python and is available at caffold_builder . A web-based implementation is additionally provided to allow users to submit a reference genome and a set of contigs to be scaffolded.
Publisher: Elsevier BV
Date: 04-2012
DOI: 10.1016/J.CUB.2012.02.068
Abstract: Coral reefs, one of the world's most complex and vulnerable ecosystems, face an uncertain future in coming decades as they continue to respond to anthropogenic climate change, overfishing, pollution, and other human impacts [1, 2]. Traditionally, marine macroecology is based on presence/absence data from taxonomic checklists or geographic ranges, providing a qualitative overview of spatial shifts in species richness that treats rare and common species equally [3, 4]. As a consequence, regional and long-term shifts in relative abundances of in idual taxa are poorly understood. Here we apply a more rigorous quantitative approach to examine large-scale spatial variation in the species composition and abundance of corals on midshelf reefs along the length of Australia's Great Barrier Reef, a biogeographic region where species richness is high and relatively homogeneous [5]. We demonstrate that important functional components of coral assemblages "s le" space differently at 132 sites separated by up to 1740 km, leading to complex latitudinal shifts in patterns of absolute and relative abundance. The flexibility in community composition that we document along latitudinal environmental gradients indicates that climate change is likely to result in a reassortment of coral reef taxa rather than wholesale loss of entire reef ecosystems.
Publisher: Springer Science and Business Media LLC
Date: 18-04-2015
Publisher: Springer Science and Business Media LLC
Date: 09-2011
Publisher: Springer Science and Business Media LLC
Date: 25-04-2016
DOI: 10.1038/NMICROBIOL.2016.42
Abstract: Microbialization refers to the observed shift in ecosystem trophic structure towards higher microbial biomass and energy use. On coral reefs, the proximal causes of microbialization are overfishing and eutrophication, both of which facilitate enhanced growth of fleshy algae, conferring a competitive advantage over calcifying corals and coralline algae. The proposed mechanism for this competitive advantage is the DDAM positive feedback loop (dissolved organic carbon (DOC), disease, algae, microorganism), where DOC released by ungrazed fleshy algae supports copiotrophic, potentially pathogenic bacterial communities, ultimately harming corals and maintaining algal competitive dominance. Using an unprecedented data set of >400 s les from 60 coral reef sites, we show that the central DDAM predictions are consistent across three ocean basins. Reef algal cover is positively correlated with lower concentrations of DOC and higher microbial abundances. On turf and fleshy macroalgal-rich reefs, higher relative abundances of copiotrophic microbial taxa were identified. These microbial communities shift their metabolic potential for carbohydrate degradation from the more energy efficient Embden-Meyerhof-Parnas pathway on coral-dominated reefs to the less efficient Entner-Doudoroff and pentose phosphate pathways on algal-dominated reefs. This 'yield-to-power' switch by microorganism directly threatens reefs via increased hypoxia and greater CO2 release from the microbial respiration of DOC.
Publisher: Public Library of Science (PLoS)
Date: 19-06-2015
Publisher: Cold Spring Harbor Laboratory
Date: 04-04-2023
DOI: 10.1101/2023.04.04.535632
Abstract: Microbial communities found within the human gut have a strong influence on human health. Intestinal bacteria and viruses influence gastrointestinal diseases such as inflammatory bowel disease. Viruses infecting bacteria, known as bacteriophages, play a key role in modulating bacterial communities within the human gut. However, the identification and characterisation of novel bacteriophages remain a challenge. Available tools use similarities between sequences, nucleotide composition, and the presence of viral genes roteins. Most available tools consider in idual contigs to determine whether they are of viral origin. As a result of the challenges in viral assembly, fragmentation of viral genomes can occur, leading to the need for new approaches in viral identification. We introduce Phables, a new computational method to resolve bacteriophage genomes from fragmented viral metagenomic assemblies. Phables identifies bacteriophage-like components in the assembly graph, models each component as a flow network, and uses graph algorithms and flow decomposition techniques to identify genomic paths. Experimental results of viral metagenomic s les obtained from different environments show that over 80% of the bacteriophage genomes resolved by Phables have high quality and are longer than the in idual contigs identified by existing viral identification tools. Phables is available on GitHub at github.com/Vini2 hables (DOI: 10.5281/zenodo.7645166). vijini.mallawaarachchi@flinders.edu.au
Publisher: Springer Science and Business Media LLC
Date: 24-07-2014
DOI: 10.1038/NCOMMS5498
Publisher: Cold Spring Harbor Laboratory
Date: 06-03-2023
DOI: 10.1101/2023.03.05.531146
Abstract: Bacteroides, the prominent bacteria in the human gut, play a crucial role in degrading complex polysaccharides. Their abundance is influenced by phages belonging to the Crassvirales order. Despite identifying over 600 Crassvirales genomes computationally, only few have been successfully isolated. Continued efforts in isolation of more Crassvirales genomes can provide insights into phage-host-evolution and infection mechanisms. We focused on wastewater s les, as potential sources of phages infecting various Bacteroides hosts. Sequencing, assembly, and characterization of isolated phages revealed 14 complete genomes belonging to three novel Crassvirales species infecting Bacteroides cellulosilyticus WH2. These species, Kehishuvirus sp. ‘tikkala’ strain Bc01, Kolpuevirus sp. ‘frurule’ strain Bc03, and ‘Rudgehvirus jaberico’ strain Bc11, spanned two families, and three genera, displaying a broad range of virion productions. Upon testing all successfully cultured Crassvirales species and their respective bacterial hosts, we discovered that they do not exhibit co-evolutionary patterns with their bacterial hosts. Furthermore, we observed variations in gene similarity, with greater shared similarity observed within genera. However, despite belonging to different genera, the three novel species shared a unique structural gene that encodes the tail spike protein. When investigating the relationship between this gene and host interaction, we discovered evidence of purifying selection, indicating its functional importance. Moreover, our analysis demonstrated that this tail spike protein binds to the TonB-dependent receptors present on the bacterial host surface. Combining these observations, our findings provide insights into phage-host interactions and present three Crassvirales species as an ideal system for controlled infectivity experiments on one of the most dominant members of the human enteric virome. Bacteriophages play a crucial role in shaping microbial communities within the human gut. Among the most dominant bacteriophages in the human gut microbiome are Crassvirales phages, which infect Bacteroides. Despite being widely distributed, only a few Crassvirales genomes have been isolated, leading to a limited understanding of their biology, ecology, and evolution. This study isolated and characterized three novel Crassvirales genomes belonging to two different families, and three genera, but infecting one bacterial host, Bacteroides cellulosilyticus WH2. Notably, the observation confirmed the phages are not co-evolving with their bacterial hosts, rather have a shared ability to exploit similar features in their bacterial host. Additionally, the identification of a critical viral protein undergoing purifying selection and interacting with the bacterial receptors opens doors to targeted therapies against bacterial infections. Given Bacteroides role in polysaccharide degradation in the human gut, our findings advance our understanding of the phage-host interactions and could have important implications for the development of phage-based therapies. These discoveries may hold implications for improving gut health and metabolism to support overall well-being. The genomes used in this research are available on Sequence Read Archive (SRA) within the project, PRJNA737576. Bacteroides cellulosilyticus WH2, Kehishuvirus sp. ‘tikkala’ strain Bc01, Kolpuevirus sp. ‘ frurule’ strain Bc03, and ‘Rudgehvirus jaberico’ strain Bc11 are all available on GenBank with accessions NZ_CP072251.1 ( B. cellulosilyticus WH2), QQ198717 (Bc01), QQ198718 (Bc03), and QQ198719 (Bc11), and we are working on making the strains available through ATCC. The 3D protein structures for the three Crassvirales genomes are available to download at 0.25451/flinders.21946034.
Publisher: F1000 Research Ltd
Date: 17-10-2016
DOI: 10.12688/F1000RESEARCH.5140.2
Abstract: Advances in genomic sequencing provide the ability to model the metabolism of organisms from their genome annotation. The bioinformatics tools developed to deduce gene function through homology-based methods are dependent on public databases thus, novel discoveries are not readily extrapolated from current analysis tools with a homology dependence. Multi-phenotype Assay Plates (MAPs) provide a high-throughput method to profile bacterial phenotypes by growing bacteria in various growth conditions, simultaneously. More robust and accurate computational models can be constructed by coupling MAPs with current genomic annotation methods. PMAnalyzer is an online tool that analyzes bacterial growth curves from the MAP system which are then used to optimize metabolic models during in silico growth simulations. Using Citrobacter sedlakii as a prototype, the Rapid Annotation using Subsystem Technology (RAST) tool produced a model consisting of 1,367 enzymatic reactions. After the optimization, 44 reactions were added to, or modified within, the model. The model correctly predicted the outcome on 93% of growth experiments.
Publisher: Springer Science and Business Media LLC
Date: 07-02-2022
DOI: 10.1007/S00248-022-01969-Y
Abstract: The epidermis of Chondrichthyan fishes consists of dermal denticles with production of minimal but protein-rich mucus that collectively, influence the attachment and biofilm development of microbes, facilitating a unique epidermal microbiome. Here, we use metagenomics to provide the taxonomic and functional characterization of the epidermal microbiome of the Triakis semifasciata (leopard shark) at three time-points collected across 4 years to identify links between microbial groups and host metabolism. Our aims include (1) describing the variation of microbiome taxa over time and identifying recurrent microbiome members (present across all time-points) (2) investigating the relationship between the recurrent and flexible taxa (those which are not found consistently across time-points) (3) describing the functional compositions of the microbiome which may suggest links with the host metabolism and (4) identifying whether metabolic processes are shared across microbial genera or are unique to specific taxa. Microbial members of the microbiome showed high similarity between all in iduals (Bray-Curtis similarity index = 82.7, where 0 = no overlap, 100 = total overlap) with the relative abundance of those members varying across s ling time-points, suggesting flexibility of taxa in the microbiome. One hundred and eighty-eight genera were identified as recurrent, including Pseudomonas, Erythrobacter, Alcanivorax, Marinobacter, and Sphingopxis being consistently abundant across time-points, while Limnobacter and Xyella exhibited switching patterns with high relative abundance in 2013, Sphingobium and Sphingomona in 2015, and Altermonas, Leeuwenhoekiella, Gramella, and Maribacter in 2017. Of the 188 genera identified as recurrent, the top 19 relatively abundant genera formed three recurrent groups. The microbiome also displayed high functional similarity between in iduals (Bray-Curtis similarity index = 97.6) with gene function composition remaining consistent across all time-points. These results show that while the presence of microbial genera exhibits consistency across time-points, their abundances do fluctuate. Microbial functions however remain stable across time-points thus, we suggest the leopard shark microbiomes exhibit functional redundancy. We show coexistence of microbes hosted in elasmobranch microbiomes that encode genes involved in utilizing nitrogen, but not fixing nitrogen, degrading urea, and resistant to heavy metal.
Publisher: Springer US
Date: 2015
Publisher: American Society for Microbiology
Date: 26-12-2013
Abstract: Piscirickettsia salmonis is a Gram-negative intracellular fish pathogen that has a significant impact on the salmon industry. Here, we report the genome sequence of P. salmonis strain LF-89. This is the first draft genome sequence of P. salmonis , and it reveals interesting attributes, including flagellar genes, despite this bacterium being considered nonmotile.
Publisher: Public Library of Science (PLoS)
Date: 31-05-2013
Publisher: Frontiers Media SA
Date: 22-05-2017
Publisher: Springer Science and Business Media LLC
Date: 24-09-2018
Publisher: Bulletin of Marine Science
Date: 10-2012
Publisher: American Society for Cell Biology (ASCB)
Date: 12-2015
Publisher: Springer Science and Business Media LLC
Date: 09-01-2017
DOI: 10.1007/S00248-016-0911-9
Abstract: Semi-arid and arid areas occupy about 33% of terrestrial ecosystems. However, little information is available about microbial ersity in the semi-arid Caatinga, which represents a unique biome that extends to about 11% of the Brazilian territory and is home to extraordinary ersity and high endemism level of species. In this study, we characterized the ersity of microbial genes associated with biomass conversion (carbohydrate-active enzymes, or so-called CAZYmes) in soil and freshwater of the Caatinga. Our results showed distinct CAZYme profiles in the soil and freshwater s les. Glycoside hydrolases and glycosyltransferases were the most abundant CAZYme families, with glycoside hydrolases more dominant in soil (∼44%) and glycosyltransferases more abundant in freshwater (∼50%). The abundances of in idual glycoside hydrolase, glycosyltransferase, and carbohydrate-binding module subfamilies varied widely between soil and water s les. A predominance of glycoside hydrolases was observed in soil, and a higher contribution of enzymes involved in carbohydrate biosynthesis was observed in freshwater. The main taxa associated with the CAZYme sequences were Planctomycetia (relative abundance in soil, 29%) and Alphaproteobacteria (relative abundance in freshwater, 27%). Approximately 5-7% of CAZYme sequences showed low similarity with sequences deposited in non-redundant databases, suggesting putative homologues. Our findings represent a first attempt to describe specific microbial CAZYme profiles for environmental s les. Characterizing these enzyme groups associated with the conversion of carbohydrates in nature will improve our understanding of the significant roles of enzymes in the carbon cycle. We identified a CAZYme signature that can be used to discriminate between soil and freshwater s les, and this signature may be related to the microbial species adapted to the habitat. The data show the potential ecological roles of the CAZYme repertoire and associated biotechnological applications.
Publisher: Springer Science and Business Media LLC
Date: 10-2008
DOI: 10.1038/NATURE07346
Publisher: Springer Science and Business Media LLC
Date: 12-03-2008
DOI: 10.1038/NATURE06810
Abstract: Microbial activities shape the biogeochemistry of the planet and macroorganism health. Determining the metabolic processes performed by microbes is important both for understanding and for manipulating ecosystems (for ex le, disruption of key processes that lead to disease, conservation of environmental services, and so on). Describing microbial function is h ered by the inability to culture most microbes and by high levels of genomic plasticity. Metagenomic approaches analyse microbial communities to determine the metabolic processes that are important for growth and survival in any given environment. Here we conduct a metagenomic comparison of almost 15 million sequences from 45 distinct microbiomes and, for the first time, 42 distinct viromes and show that there are strongly discriminatory metabolic profiles across environments. Most of the functional ersity was maintained in all of the communities, but the relative occurrence of metabolisms varied, and the differences between metagenomes predicted the biogeochemical conditions of each environment. The magnitude of the microbial metabolic capabilities encoded by the viromes was extensive, suggesting that they serve as a repository for storing and sharing genes among their microbial hosts and influence global evolutionary and metabolic processes.
Publisher: Springer Science and Business Media LLC
Date: 08-01-2021
DOI: 10.1038/S41598-020-80489-6
Abstract: In the present study we investigate the microbial community inhabiting As Burgas geothermal spring, located in Ourense (Galicia, Spain). The approximately 23 Gbp of Illumina sequences generated for each replicate revealed a complex microbial community dominated by Bacteria in which Proteobacteria and Aquificae were the two prevalent phyla. An association between the two most prevalent genera, Thermus and Hydrogenobacter , was suggested by the relationship of their metabolism. The high relative abundance of sequences involved in the Calvin–Benson cycle and the reductive TCA cycle unveils the dominance of an autotrophic population. Important pathways from the nitrogen and sulfur cycle are potentially taking place in As Burgas hot spring. In the assembled reads, two complete ORFs matching GH2 beta-galactosidases were found. To assess their functional characterization, the two ORFs were cloned and overexpressed in E. coli . The pTsbg enzyme had activity towards o-Nitrophenyl-β- d -galactopyranoside (ONPG) and p-Nitrophenyl-β- d -fucopyranoside, with high thermal stability and showing maximal activity at 85 °C and pH 6, nevertheless the enzyme failed to hydrolyze lactose. The other enzyme, Tsbg, was unable to hydrolyze even ONPG or lactose. This finding highlights the challenge of finding novel active enzymes based only on their sequence.
Publisher: American Society for Microbiology
Date: 28-04-2020
Abstract: Coral microbiome dysbiosis (i.e., shifts in the microbial community structure or complete loss of microbial symbionts) caused by environmental changes is a key player in the decline of coral health worldwide. Multiple factors in the water column and the surrounding biological community influence the dynamics of the coral microbiome. However, by including only temperature as an external factor, our model proved to be successful in describing the microbial community associated with the surface mucus layer (SML) of the coral P. strigosa . The dynamic model developed and validated in this study is a potential tool to predict the coral microbiome under different temperature conditions.
Publisher: Wiley
Date: 10-10-2016
DOI: 10.1111/GEB.12528
Publisher: Springer Science and Business Media LLC
Date: 05-02-2020
DOI: 10.1186/S12864-020-6523-2
Abstract: Bacteriophages encode genes that modify bacterial functions during infection. The acquisition of phage-encoded virulence genes is a major mechanism for the rise of bacterial pathogens. In coral reefs, high bacterial density and lysogeny has been proposed to exacerbate reef decline through the transfer of phage-encoded virulence genes. However, the functions and distribution of these genes in phage virions on the reef remain unknown. Here, over 28,000 assembled viral genomes from the free viral community in Atlantic and Pacific Ocean coral reefs were queried against a curated database of virulence genes. The ersity of virulence genes encoded in the viral genomes was tested for relationships with host taxonomy and bacterial density in the environment. These analyses showed that bacterial density predicted the profile of virulence genes encoded by phages. The Shannon ersity of virulence-encoding phages was negatively related with bacterial density, leading to dominance of fewer genes at high bacterial abundances. A statistical learning analysis showed that reefs with high microbial density were enriched in viruses encoding genes enabling bacterial recognition and invasion of metazoan epithelium. Over 60% of phages could not have their hosts identified due to limitations of host prediction tools for those which hosts were identified, host taxonomy was not an indicator of the presence of virulence genes. This study described bacterial virulence factors encoded in the genomes of bacteriophages at the community level. The results showed that the increase in microbial densities that occurs during coral reef degradation is associated with a change in the genomic repertoire of bacteriophages, specifically in the ersity and distribution of bacterial virulence genes. This suggests that phages are implicated in the rise of pathogens in disturbed marine ecosystems.
Publisher: Springer Science and Business Media LLC
Date: 28-11-2017
Publisher: MDPI AG
Date: 29-03-2019
DOI: 10.3390/D11040049
Abstract: Chondrichthyes (sharks, rays, skates and chimaeras) are among the oldest extant predators and are vital to top-down regulation of oceanic ecosystems. They are an ecologically erse group occupying a wide range of habitats and are thus, exploited by coastal, pelagic and deep-water fishing industries. Chondrichthyes are among the most data deficient vertebrate species groups making design and implementation of regulatory and conservation measures challenging. High-throughput sequencing technologies have significantly propelled ecological investigations and understanding of marine and terrestrial species’ populations, but there remains a paucity of NGS based research on chondrichthyan populations. We present a brief review of current methods to access genomic and metagenomic data from Chondrichthyes and discuss applications of these datasets to increase our understanding of chondrichthyan taxonomy, evolution, ecology and population structures. Last, we consider opportunities and challenges offered by genomic studies for conservation and management of chondrichthyan populations.
Publisher: MDPI AG
Date: 05-09-2022
DOI: 10.3390/V14091969
Abstract: The epidermal microbiome is a critical element of marine organismal immunity, but the epidermal virome of marine organisms remains largely unexplored. The epidermis of sharks represents a unique viromic ecosystem. Sharks secrete a thin layer of mucus which harbors a erse microbiome, while their hydrodynamic dermal denticles simultaneously repel environmental microbes. Here, we s led the virome from the epidermis of three shark species in the family Carcharhinidae: the genetically and morphologically similar Carcharhinus obscurus (n = 6) and Carcharhinus galapagensis (n = 10) and the outgroup Galeocerdo cuvier (n = 15). Virome taxonomy was characterized using shotgun metagenomics and compared with a suite of multivariate analyses. All three sharks retain species-specific but highly similar epidermal viromes dominated by uncharacterized bacteriophages which vary slightly in proportional abundance within and among shark species. Intraspecific variation was lower among C. galapagensis than among C. obscurus and G. cuvier. Using both the annotated and unannotated reads, we were able to determine that the Carcharhinus galapagensis viromes were more similar to that of G. cuvier than they were to that of C. obscurus, suggesting that behavioral niche may be a more prominent driver of virome than host phylogeny.
Publisher: Informa UK Limited
Date: 11-06-2020
Publisher: Informa UK Limited
Date: 05-06-2020
Publisher: PeerJ
Date: 19-08-2014
DOI: 10.7717/PEERJ.520
Publisher: Informa UK Limited
Date: 14-05-2020
Publisher: Public Library of Science (PLoS)
Date: 05-06-2012
Publisher: Public Library of Science (PLoS)
Date: 05-06-2018
Publisher: Elsevier BV
Date: 02-2018
Publisher: Public Library of Science (PLoS)
Date: 03-06-2015
Publisher: Springer Science and Business Media LLC
Date: 16-03-2016
DOI: 10.1038/NATURE17193
Abstract: Microbial viruses can control host abundances via density-dependent lytic predator-prey dynamics. Less clear is how temperate viruses, which coexist and replicate with their host, influence microbial communities. Here we show that virus-like particles are relatively less abundant at high host densities. This suggests suppressed lysis where established models predict lytic dynamics are favoured. Meta-analysis of published viral and microbial densities showed that this trend was widespread in erse ecosystems ranging from soil to freshwater to human lungs. Experimental manipulations showed viral densities more consistent with temperate than lytic life cycles at increasing microbial abundance. An analysis of 24 coral reef viromes showed a relative increase in the abundance of hallmark genes encoded by temperate viruses with increased microbial abundance. Based on these four lines of evidence, we propose the Piggyback-the-Winner model wherein temperate dynamics become increasingly important in ecosystems with high microbial densities thus 'more microbes, fewer viruses'.
Publisher: Oxford University Press (OUP)
Date: 09-05-2017
Abstract: Coral reefs are one of the most productive ecosystems on the planet, with primary production rates compared to that of rain forests. Benthic organisms release 10-50% of their gross organic production as mucus that stimulates heterotrophic microbial metabolism in the water column. As a result, coral reef microbes grow up to 50 times faster than open ocean communities. Anthropogenic disturbances cause once coral-dominated reefs to become dominated by fleshy organisms, with several outcomes for trophic relationships. Here we review microbial processes implicated in organic carbon flux in coral reefs displaying species phase shifts. The first section presents microbial players and interactions within the coral holobiont that contribute to reef carbon flow. In the second section, we identify four ecosystem-level microbial features that directly respond to benthic species phase shifts: community composition, biomass, metabolism and viral predation. The third section discusses the significance of microbial consumption of benthic organic matter to reef trophic relationships. In the fourth section, we propose that the 'microbial phase shifts' discussed here are conducive to lower resilience, facilitating the transition to new degradation states in coral reefs.
Publisher: Cold Spring Harbor Laboratory
Date: 03-08-2017
DOI: 10.1101/170993
Abstract: Bioinformatics is becoming increasingly central to research in the life sciences. However, despite its importance, bioinformatics skills and knowledge are not well integrated in undergraduate biology education. This curricular gap prevents biology students from harnessing the full potential of their education, limiting their career opportunities and slowing genomic research innovation. To advance the integration of bioinformatics into life sciences education, a framework of core bioinformatics competencies is needed. To that end, we here report the results of a survey of life sciences faculty in the United States about teaching bioinformatics to undergraduate life scientists. Responses were received from 1,260 faculty representing institutions in all fifty states with a combined capacity to educate hundreds of thousands of students every year. Results indicate strong, widespread agreement that bioinformatics knowledge and skills are critical for undergraduate life scientists, as well as considerable agreement about which skills are necessary. Perceptions of the importance of some skills varied with the respondent’s degree of training, time since degree earned, and/or the Carnegie classification of the respondent’s institution. To assess which skills are currently being taught, we analyzed syllabi of courses with bioinformatics content submitted by survey respondents. Finally, we used the survey results, the analysis of syllabi, and our collective research and teaching expertise to develop a set of bioinformatics core competencies for undergraduate life sciences students. These core competencies are intended to serve as a guide for institutions as they work to integrate bioinformatics into their life sciences curricula. Bioinformatics, an interdisciplinary field that uses techniques from computer science and mathematics to store, manage, and analyze biological data, is becoming increasingly central to modern biology research. Given the widespread use of bioinformatics and its impacts on societal problem-solving (e.g., in healthcare, agriculture, and natural resources management), there is a growing need for the integration of bioinformatics competencies into undergraduate life sciences education. Here, we present a set of bioinformatics core competencies for undergraduate life scientists developed using the results of a large national survey and the expertise of our working group of bioinformaticians and educators. We also present results from the survey on the importance of bioinformatics skills and the current state of integration of bioinformatics into biology education.
Publisher: Public Library of Science (PLoS)
Date: 26-11-2009
Publisher: Elsevier BV
Date: 06-2020
Publisher: CourseSource
Date: 2022
DOI: 10.24918/CS.2022.10
Publisher: Frontiers Media SA
Date: 2013
Publisher: Wiley
Date: 2009
Publisher: Informa UK Limited
Date: 14-05-2020
Publisher: Springer Science and Business Media LLC
Date: 05-08-2014
Publisher: Informa UK Limited
Date: 14-05-2020
Publisher: Public Library of Science (PLoS)
Date: 27-02-2008
Publisher: American Society for Microbiology
Date: 15-03-2012
DOI: 10.1128/AEM.07241-11
Abstract: Phages are a primary driving force behind the evolution of bacterial pathogens by transferring a variety of virulence genes into their hosts. Similar to other bacterial genomes, the Salmonella enterica serovar Enteritidis LK5 genome contains several regions that are homologous to phages. Although genomic analysis demonstrated the presence of prophages, it was unable to confirm which phage elements within the genome were viable. Genetic markers were used to tag one of the prophages in the genome to allow monitoring of phage induction. Commonly used laboratory strains of Salmonella were resistant to phage infection, and therefore a rapid screen was developed to identify susceptible hosts. This approach showed that a genetically tagged prophage, ELPhiS (Enteritidis lysogenic phage S), was capable of infecting Salmonella serovars that are erse in host range and virulence and has the potential to laterally transfer genes between these serovars via lysogenic conversion. The rapid screen approach is adaptable to any system with a large collection of isolates and may be used to test the viability of prophages found by sequencing the genomes of various bacterial pathogens.
Publisher: MDPI AG
Date: 21-10-2022
DOI: 10.3390/MICROORGANISMS10102081
Abstract: Characterizations of shark-microbe systems in wild environments have outlined patterns of species-specific microbiomes however, whether captivity affects these trends has yet to be determined. We used high-throughput shotgun sequencing to assess the epidermal microbiome belonging to leopard sharks (Triakis semifasciata) in captive (Birch Aquarium, La Jolla California born and held permanently in captivity), semi-captive (held in captivity for year in duration and scheduled for release Scripps Institute of Oceanography, San Diego, CA, USA) and wild environments (Moss Landing and La Jolla, CA, USA). Here, we report captive environments do not drive epidermal microbiome compositions of T. semifasciata to significantly erge from wild counterparts as life-long captive sharks maintain a species-specific epidermal microbiome resembling those associated with semi-captive and wild populations. Major taxonomic composition shifts observed were inverse changes of top taxonomic contributors across captive duration, specifically an increase of Pseudoalteromonadaceae and consequent decrease of Pseudomonadaceae relative abundance as T. semifasciata increased duration in captive conditions. Moreover, we show captivity did not lead to significant losses in microbial α- ersity of shark epidermal communities. Finally, we present a novel association between T. semifasciata and the Muricauda genus as Metagenomes associated genomes revealed a consistent relationship across captive, semi-captive, and wild populations. Since changes in microbial communities is often associated with poor health outcomes, our report illustrates that epidermally associated microbes belonging to T. semifasciata are not suffering detrimental impacts from long or short-term captivity. Therefore, conservation programs which house sharks in aquariums are providing a healthy environment for the organisms on display. Our findings also expand on current understanding of shark epidermal microbiomes, explore the effects of ecologically different scenarios on benthic shark microbe associations, and highlight novel associations that are consistent across captive gradients.
Publisher: Oxford University Press (OUP)
Date: 21-09-2023
Publisher: Springer Science and Business Media LLC
Date: 11-06-2018
DOI: 10.1007/S00203-018-1532-0
Abstract: Overcoming recalcitrance of lignin has motivated bioprospecting of high-yielding enzymes from environmental ligninolytic microorganisms associated with lignocellulose degrading-systems. Here, we performed isolation of 21 ligninolytic strains belonging to the genus Klebsiella spp., driven by the presence of lignin in the media. The fastest-growing strains (FP10-5.23, FP10-5.22 and P3TM1) reached the stationary phase in approximately 24 h, in the media containing lignin as the main carbon source. The strains showed biochemical evidence of ligninolytic potential in liquid- and solid media-converting dyes, which the molecular structures are similar to lignin fragments. In liquid medium, higher levels of dye decolorization was observed for P3TM.1 in the presence of methylene blue, reaching 98% decolorization in 48 h. The highest index values (1.25) were found for isolates P3TM.1 and FP10-5.23, in the presence of toluidine blue. The genomic analysis revealed the presence of more than 20 genes associated with known prokaryotic lignin-degrading systems. Identification of peroxidases (lignin peroxidase-LiP, dye-decolorizing peroxidase-DyP, manganese peroxidase-MnP) and auxiliary activities (AA2, AA3, AA6 and AA10 families) among the genetic repertoire suggest the ability to produce extracellular enzymes able to attack phenolic and non-phenolic lignin structures. Our results suggest that the Klebsiella spp. associated with fresh water and soil may play important role in the cycling of recalcitrant molecules in the Caatinga (desert-like Brazilian biome), and represent a potential source of lignin-degrading enzymes with biotechnological applications.
Publisher: Springer Science and Business Media LLC
Date: 15-09-2021
DOI: 10.1186/S42523-021-00121-4
Abstract: Elasmobranchs (sharks, skates and rays) are of broad ecological, economic, and societal value. These globally important fishes are experiencing sharp population declines as a result of human activity in the oceans. Research to understand elasmobranch ecology and conservation is critical and has now begun to explore the role of body-associated microbiomes in shaping elasmobranch health. Here, we review the burgeoning efforts to understand elasmobranch microbiomes, highlighting microbiome variation among gastrointestinal, oral, skin, and blood-associated niches. We identify major bacterial lineages in the microbiome, challenges to the field, key unanswered questions, and avenues for future work. We argue for prioritizing research to determine how microbiomes interact mechanistically with the unique physiology of elasmobranchs, potentially identifying roles in host immunity, disease, nutrition, and waste processing. Understanding elasmobranch–microbiome interactions is critical for predicting how sharks and rays respond to a changing ocean and for managing healthy populations in managed care.
Publisher: Springer Science and Business Media LLC
Date: 2004
DOI: 10.1007/S00267-003-3056-9
Abstract: Because environmental conservation can remove scarce natural resources from competing uses, it is important to gain support for conservation programs by demonstrating that management actions have been effective in achieving their goals. One way to do this is to show that selected significant environmental variables (indicators) vary between managed and unmanaged areas or change over time following implementation of a management regime. However, identifying indicators that reflect environmental conditions relevant to management practices has proven difficult. This paper focuses on developing a framework for choosing indicators in a coral reef habitat. The framework consisted of three phases: (1) information gathering to identify candidate variables (2) field-testing candidate variables at sites that differ in intensity of human activity, thus identifying potential indicators and (3) evaluating potential indicators against a set of feasibility criteria to identify the most useful indicators. To identify indicators suitable to measure the success of a management strategy to reduce anchor damage to a coral reef, 24 candidate variables were identified and evaluated at sites with different intensities of anchoring. In this study, measures that reflected injuries to coral colonies were generally more efficient than traditional measures of coral cover in describing the effects of anchoring. The number of overturned colonies was identified as the single most useful indicator of coral reef condition associated with anchoring intensities. The indicator selection framework developed here has the advantages of being transparent, cost efficient, and readily transferable to other types of human activities and management strategies.
Publisher: Springer Science and Business Media LLC
Date: 09-2008
DOI: 10.1038/NBT0908-997
Publisher: PeerJ
Date: 15-08-2017
DOI: 10.7717/PEERJ.3666
Abstract: As coral reef habitats decline worldwide, some reefs are transitioning from coral- to algal-dominated benthos with the exact cause for this shift remaining elusive. Increases in the abundance of microbes in the water column has been correlated with an increase in coral disease and reduction in coral cover. Here we investigated how multiple reef organisms influence microbial communities in the surrounding water column. Our study consisted of a field assessment of microbial communities above replicate patches dominated by a single macro-organism. Metagenomes were constructed from 20 L of water above distinct macro-organisms, including (1) the coral Mussismilia braziliensis , (2) fleshy macroalgae ( Stypopodium , Dictota and Canistrocarpus ), (3) turf algae, and (4) the zoanthid Palythoa caribaeorum and were compared to the water microbes collected 3 m above the reef. Microbial genera and functional potential were annotated using MG-RAST and showed that the dominant benthic macro-organisms influence the taxa and functions of microbes in the water column surrounding them, developing a specific “aura-biome”. The coral aura-biome reflected the open water column, and was associated with Synechococcus and functions suggesting oligotrophic growth, while the fleshy macroalgae aura-biome was associated with Ruegeria , Pseudomonas, and microbial functions suggesting low oxygen conditions. The turf algae aura-biome was associated with Vibrio, Flavobacterium, and functions suggesting pathogenic activity, while zoanthids were associated with Alteromonas and functions suggesting a stressful environment. Because each benthic organism has a distinct aura-biome, a change in benthic cover will change the microbial community of the water, which may lead to either the stimulation or suppression of the recruitment of benthic organisms.
Publisher: Proceedings of the National Academy of Sciences
Date: 30-06-2014
Abstract: Microbial communities associated with coral reefs influence the health and sustenance of keystone benthic organisms (e.g., coral holobionts). The present study investigated the community structure and metabolic potential of microbes inhabiting coral reefs located across an extensive area in the central Pacific. We found that the taxa present correlated strongly with the percent coverage of corals and algae, while community metabolic potential correlated best with geographic location. These findings are inconsistent with prevailing biogeographic models of microbial ersity (e.g., distance decay) and metabolic potential (i.e., similar functional profiles regardless of phylogenetic variability). Based on these findings, we propose that the primary carbon sources determine community structure and that local biogeochemistry determines finer-scale metabolic function.
Publisher: Public Library of Science (PLoS)
Date: 23-09-2011
Start Date: 11-2022
End Date: 11-2024
Amount: $420,347.00
Funder: Australian Research Council
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