Local genomic adaptation of coral reef-associated microbiomes to gradients of natural variability and anthropogenic stressors

Holobionts are species-specific associations between macro- and microorganisms. On coral reefs, the benthic coverage of coral and algal holobionts varies due to natural and anthropogenic forcings. Different benthic macroorganisms are predicted to have specific microbiomes. In contrast, local environmental factors are predicted to select for specific metabolic pathways in microbes. To reconcile these two predictions, we hypothesized that adaptation of microbiomes to local conditions is facilitated by the horizontal transfer of genes responsible for specific metabolic capabilities. To test this hypothesis, microbial metagenomes were sequenced from 22 coral reefs at 11 Line Islands in the central Pacific that together span a wide range of biogeochemical and anthropogenic influences. Consistent with our hypothesis, the percent cover of major benthic functional groups significantly correlated with particular microbial taxa. Reefs with higher coral cover had a coral microbiome with higher abundances of Alphaproteobacteria (such as Rhodobacterales and Sphingomonadales), whereas microbiomes of algae-dominated reefs had higher abundances of Gammaproteobacteria (such as Alteromonadales, Pseudomonadales, and Vibrionales), Betaproteobacteria, and Bacteriodetes. In contrast to taxa, geography was the strongest predictor of microbial community metabolism. Microbial communities on reefs with higher nutrient availability (e.g., equatorial upwelling zones) were enriched in genes involved in nutrient-related metabolisms (e.g., nitrate and nitrite ammonification, Ton/Tol transport, etc.). On reefs further from the equator, microbes had more genes encoding chlorophyll biosynthesis and photosystems I/II. These results support the hypothesis that core microbiomes are determined by holobiont macroorganisms, and that those core taxa adapt to local conditions by selecting for advantageous metabolic genes

Hadronic final states in deep-inelastic scattering with Sherpa

We extend the multi-purpose Monte-Carlo event generator Sherpa to include processes in deeply inelastic lepton-nucleon scattering. Hadronic final states in this kinematical setting are characterised by the presence of multiple kinematical scales, which were up to now accounted for only by specific resummations in individual kinematical regions. Using an extension of the recently introduced method for merging truncated parton showers with higher-order tree-level matrix elements, it is possible to obtain predictions which are reliable in all kinematical limits. Different hadronic final states, defined by jets or individual hadrons, in deep-inelastic scattering are analysed and the corresponding results are compared to HERA data. The various sources of theoretical uncertainties of the approach are discussed and quantified. The extension to deeply inelastic processes provides the opportunity to validate the merging of matrix elements and parton showers in multi-scale kinematics inaccessible in other collider environments. It also allows to use HERA data on hadronic final states in the tuning of hadronisation models.Comment: 32 pages, 22 figure

Abundance of black-band disease on corals from one location on the Great Barrier Reef: a comparison with abundance in the Caribbean region

Black-band disease (BBD) occurs on the Great Barrier Reef, Australia, with at least 21 species in five families being affected. Surveys of reef crest corals at Lizard Island found 2.8% of 4569 coral colonies were affected with BBD. Acroporidae, in particular Acropora hyacinthus, Acropora intermedia and Acropora millepora, were susceptible to BBD, compared with the Caribbean where acroporid corals are resistant to BBD. Pocilloporidae, including Pocillopora damicornis, Pocillopora verrucosa and Stylophora pistillata, were identified as important host species. The abundance of BBD varied between sites, ranging from 1.3% to 4.9% of colonies affected. The percentage of BED-affected colonies varied between coral families. The percent of colonies affected with BBD were: 6.0% for the Pocilloporidae, 3.6% for the Acroporidae, 3.0% for the Faviidae and 2.1 % for the Poritidae. The level of BBD affected colonies on the GBR was within the range of affected colonies reported in the Caribbean

Combining de novo and reference-guided assembly with scaffold_builder

Contains fulltext : 125558.pdf (publisher's version ) (Open Access)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 http://edwards.sdsu.edu/scaffold_builder. A web-based implementation is additionally provided to allow users to submit a reference genome and a set of contigs to be scaffolded

Patterns of recruitment and abundance of corals along the Great Barrier Reef

Different physical and biological processes prevail at different scales(1-4). As a consequence, small-scale experiments or local observations provide limited insights into regional or global phenomena(5-8). One solution is to incorporate spatial scale explicitly into the experimental and sampling design of field studies, to provide a broader, landscape view of ecology(1-8). Here we examine spatial patterns in corals on the Great Barrier Reef, across a spectrum of scales ranging from metres to more than 1,700 km. Our study is unusual because we explore large-scale patterns of a process (recruitment by juveniles) as well as patterns of adult abundance, revealing the relationship between the two. We show that coral-reef assemblages that are similar in terms of abundance may nonetheless show profound differences in dynamics and turnover, with major implications for their ecology, evolution and management

Response of Antarctic terrestrial microarthropods to long-term climate manipulations

The terrestrial biota of the Antarctic Peninsula region are experiencing marked changes in climate, especially rising temperatures, precipitation, and UV-B radiation-a combination unique worldwide. These changes, combined with the inherent simplicity of terrestrial communities, have led to their use as "model systems" to predict the future climate change responses of biota at lower latitudes. However, studies integrating responses at different levels of the community trophic structure are lacking. We report here the consequences on the soil microarthropod community of a four-year, multivariate, climate-manipulation experiment carried out over vegetation near Palmer Station, Anvers Island, western Antarctic Peninsula. The experiment used a multifactorial randomized-block design, deploying filters to raise temperatures and reduce ultraviolet (UV)-B (280-320 nm) or both UV-B and UV-A (320-400 nm) radiation of existing vegetation, with further water and fertilizer amendment treatments. Seven microarthropod species recovered in sufficient numbers for statistical analyses showed considerable spatial aggregation independent of treatment, a feature typical of many soil invertebrates. Analyses using negative binomial generalized linear modeling identified further significant and consistent treatment impacts on both individual species and species groups. Relative to controls, manipulations increasing temperature decreased numbers of microarthropods (particularly Collembola), as did exposure to near-ambient levels of UV radiation (separate significant effects for both UV-A and UV-B), while water amendment increased numbers. The impacts of temperature and water are consistent with our understanding of the importance of these two environmental variables and their interaction in Antarctic terrestrial ecosystems. The negative impact of UV (-A or -B) on arthropod heterotroph and detritivore populations in the Antarctic terrestrial food web is likely to be a secondary consequence of UV impact on vegetation characteristics. This is, again, consistent with general predictions of the impact of changing UV climate on ecosystem function

Genomic Comparison of the Closely-Related Salmonella enterica Serovars Enteritidis, Dublin and Gallinarum

Contains fulltext : 155362.PDF (publisher's version ) (Open Access)The Salmonella enterica serovars Enteritidis, Dublin, and Gallinarum are closely related but differ in virulence and host range. To identify the genetic elements responsible for these differences and to better understand how these serovars are evolving, we sequenced the genomes of Enteritidis strain LK5 and Dublin strain SARB12 and compared these genomes to the publicly available Enteritidis P125109, Dublin CT 02021853 and Dublin SD3246 genome sequences. We also compared the publicly available Gallinarum genome sequences from biotype Gallinarum 287/91 and Pullorum RKS5078. Using bioinformatic approaches, we identified single nucleotide polymorphisms, insertions, deletions, and differences in prophage and pseudogene content between strains belonging to the same serovar. Through our analysis we also identified several prophage cargo genes and pseudogenes that affect virulence and may contribute to a host-specific, systemic lifestyle. These results strongly argue that the Enteritidis, Dublin and Gallinarum serovars of Salmonella enterica evolve by acquiring new genes through horizontal gene transfer, followed by the formation of pseudogenes. The loss of genes necessary for a gastrointestinal lifestyle ultimately leads to a systemic lifestyle and niche exclusion in the host-specific serovars

Comparative genomics of 274 Vibrio cholerae genomes reveals mobile functions structuring three niche dimensions

Contains fulltext : 136229.pdf (publisher's version ) (Open Access)BACKGROUND: Vibrio cholerae is a globally dispersed pathogen that has evolved with humans for centuries, but also includes non-pathogenic environmental strains. Here, we identify the genomic variability underlying this remarkable persistence across the three major niche dimensions space, time, and habitat. RESULTS: Taking an innovative approach of genome-wide association applicable to microbial genomes (GWAS-M), we classify 274 complete V. cholerae genomes by niche, including 39 newly sequenced for this study with the Ion Torrent DNA-sequencing platform. Niche metadata were collected for each strain and analyzed together with comprehensive annotations of genetic and genomic attributes, including point mutations (single-nucleotide polymorphisms, SNPs), protein families, functions and prophages. CONCLUSIONS: Our analysis revealed that genomic variations, in particular mobile functions including phages, prophages, transposable elements, and plasmids underlie the metadata structuring in each of the three niche dimensions. This underscores the role of phages and mobile elements as the most rapidly evolving elements in bacterial genomes, creating local endemicity (space), leading to temporal divergence (time), and allowing the invasion of new habitats. Together, we take a data-driven approach for comparative functional genomics that exploits high-volume genome sequencing and annotation, in conjunction with novel statistical and machine learning analyses to identify connections between genotype and phenotype on a genome-wide scale

Phables: From fragmented assemblies to high-quality bacteriophage genomes

Motivation: Microbial communities have a profound impact on both human health and various environments. Viruses infecting bacteria, known as bacteriophages or phages, play a key role in modulating bacterial communities within environments. High-quality phage genome sequences are essential for advancing our understanding of phage biology, enabling comparative genomics studies and developing phage-based diagnostic tools. Most available viral identification tools consider individual sequences to determine whether they are of viral origin. As a result of challenges in viral assembly, fragmentation of genomes can occur, and existing tools may recover incomplete genome fragments. Therefore, the identification and characterization of novel phage genomes remain a challenge, leading to the need of improved approaches for phage genome recovery. Results: We introduce Phables, a new computational method to resolve phage genomes from fragmented viral metagenome assemblies. Phables identifies phage-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 samples obtained from different environments show that Phables recovers on average over 49% more high-quality phage genomes compared to existing viral identification tools. Furthermore, Phables can resolve variant phage genomes with over 99% average nucleotide identity, a distinction that existing tools are unable to make.Vijini Mallawaarachchi, Michael J. Roach, Przemyslaw Decewicz, Bhavya Papudeshi, Sarah K. Giles, Susanna R. Grigson, George Bouras, Ryan D. Hesse, Laura K. Inglis, Abbey L.K. Hutton, Elizabeth A. Dinsdale, Robert A. Edward

Dynamics of seasonal outbreaks of black band disease in an assemblage of Montipora species at Pelorus Island (Great Barrier Reef, Australia)

Recurring summer outbreaks of black band disease (BBD) on an inshore reef in the central Great Barrier Reef (GBR) constitute the first recorded BBD epizootic in the region. In a 2.7 year study of 485 colonies of Montipora species, BBD affected up to 10 per cent of colonies in the assemblage. Mean maximum abundance of BBD reached 16±6 colonies per 100 m2 (n=3 quadrats, each 100 m2) in summer, and decreased to 0–1 colony per 100 m2 in winter. On average, BBD lesions caused 40 per cent tissue loss and 5 per cent of infections led to whole colony mortality. BBD reappearance on previously infected colonies and continuous tissue loss after the BBD signs had disappeared suggest that the disease impacts are of longer duration than indicated by the presence of characteristic signs. Rates of new infections and linear progression of lesions were both positively correlated with seasonal fluctuations in sea water temperatures and light, suggesting that seasonal increases in these environmental parameters promote virulence of the disease. Overall, the impacts of BBD are greater than previously reported on the GBR and likely to escalate with ocean warming