ORCID Profile
0000-0001-9557-7715
Current Organisations
E O Lawrence Berkeley National Laboratory
,
Massey University-School of Agriculture and Environment
,
KBase
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Publisher: Wiley
Date: 12-11-2019
Abstract: Research into causative agents underlying coral disease have focused primarily on bacteria, whereas potential roles of viruses have been largely unaddressed. Bacteriophages may contribute to diseases through the lysogenic introduction of virulence genes into bacteria, or prevent diseases through lysis of bacterial pathogens. To identify candidate phages that may influence the pathogenicity of black band disease (BBD), communities of bacteria (16S rRNA) and T4-bacteriophages (gp23) were simultaneously profiled with licon sequencing among BBD-lesions and healthy-coral-tissue of Montipora hispida, as well as seawater (study site: the central Great Barrier Reef). Bacterial community compositions were distinct among BBD-lesions, healthy coral tissue and seawater s les, as observed in previous studies. Surprisingly, however, viral beta ersities based on both operational taxonomic unit (OTU)-compositions and overall viral community compositions of assigned taxa did not differ statistically between the BBD-lesions and healthy coral tissue. Nonetheless, relative abundances of three bacteriophage OTUs, affiliated to Cyanophage PRSM6 and Prochlorococcus phages P-SSM2, were significantly higher in BBD-lesions than in healthy tissue. These OTUs associated with BBD s les suggest the presence of bacteriophages that infect members of the cyanobacteria-dominated BBD community, and thus have potential roles in BBD pathogenicity.
Publisher: Informa UK Limited
Date: 07-02-2019
DOI: 10.1080/03601234.2019.1574170
Abstract: Organic soil amendments can be useful for improving degraded soil, but this increase in organic matter (OM) may influence adsorption of herbicides subsequently applied to the treated soil, even though the particle size of amendments and their nature differ from typical soil OM. In this study, a batch equilibrium method was used to measure adsorption of five herbicides following application to two organic media, wood pulp and sawdust, comparing these with two cropping soils. Herbicide adsorption, quantified by distribution coefficients (k
Publisher: PeerJ
Date: 17-11-2017
DOI: 10.7717/PEERJ.4054
Abstract: Stony corals (Scleractinia) are marine invertebrates that form the foundation and framework upon which tropical reefs are built. The coral animal associates with a erse microbiome comprised of dinoflagellate algae and other protists, bacteria, archaea, fungi and viruses. Using a metagenomics approach, we analysed the DNA and RNA viral assemblages of seven coral species from the central Great Barrier Reef (GBR), demonstrating that tailed bacteriophages of the Caudovirales dominate across all species examined, and ssDNA viruses, notably the Microviridae , are also prevalent. Most sequences with matches to eukaryotic viruses were assigned to six viral families, including four Nucleocytoplasmic Large DNA Viruses (NCLDVs) families: Iridoviridae, Phycodnaviridae, Mimiviridae, and Poxviridae , as well as Retroviridae and Polydnaviridae . Contrary to previous findings, Herpesvirales were rare in these GBR corals. Sequences of a ssRNA virus with similarities to the dinornavirus, Heterocapsa circularisquama ssRNA virus of the Alvernaviridae that infects free-living dinoflagellates, were observed in three coral species. We also detected viruses previously undescribed from the coral holobiont, including a virus that targets fungi associated with the coral species Acropora tenuis . Functional analysis of the assembled contigs indicated a high prevalence of latency-associated genes in the coral-associated viral assemblages, several host-derived auxiliary metabolic genes (AMGs) for photosynthesis ( psbA , psbD genes encoding the photosystem II D1 and D2 proteins respectively), as well as potential nematocyst toxins and antioxidants (genes encoding green fluorescent-like chromoprotein). This study expands the currently limited knowledge on coral-associated viruses by characterising viral composition and function across seven GBR coral species.
Publisher: Frontiers Media SA
Date: 22-12-2016
Publisher: Springer Science and Business Media LLC
Date: 09-11-2020
DOI: 10.1038/S41587-020-0718-6
Abstract: The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to ,000 metagenomes collected from erse habitats covering all of Earth’s continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. The catalog expands the known phylogenetic ersity of bacteria and archaea by 44% and is broadly available for streamlined comparative analyses, interactive exploration, metabolic modeling and bulk download. We demonstrate the utility of this collection for understanding secondary-metabolite biosynthetic potential and for resolving thousands of new host linkages to uncultivated viruses. This resource underscores the value of genome-centric approaches for revealing genomic properties of uncultivated microorganisms that affect ecosystem processes.
Publisher: Cold Spring Harbor Laboratory
Date: 22-07-2023
DOI: 10.1101/2023.07.22.550117
Abstract: Predicting elemental cycles and maintaining water quality under increasing anthropogenic influence requires understanding the spatial drivers of river microbiomes. However, the unifying microbial processes governing river biogeochemistry are hindered by a lack of genome-resolved functional insights and s ling across multiple rivers. Here we employed a community science effort to accelerate the s ling, sequencing, and genome-resolved analyses of river microbiomes to create the Genome Resolved Open Watersheds database (GROWdb). This resource profiled the identity, distribution, function, and expression of thousands of microbial genomes across rivers covering 90% of United States watersheds. Specifically, GROWdb encompasses 1,469 microbial species from 27 phyla, including novel lineages from 10 families and 128 genera, and defines the core river microbiome for the first time at genome level. GROWdb analyses coupled to extensive geospatial information revealed local and regional drivers of microbial community structuring, while also presenting a myriad of foundational hypotheses about ecosystem function. Building upon the previously conceived River Continuum Concept 1 , we layer on microbial functional trait expression, which suggests the structure and function of river microbiomes is predictable. We make GROWdb available through various collaborative cyberinfrastructures 2, 3 so that it can be widely accessed across disciplines for watershed predictive modeling and microbiome-based management practices.
Publisher: Wiley
Date: 30-04-2018
Abstract: Recent metagenomic analyses have revealed a high ersity of viruses in the pelagic ocean and uncovered clear habitat-specific viral distribution patterns. Conversely, similar insights into the composition, host specificity and function of viruses associated with marine organisms have been limited by challenges associated with s ling and computational analysis. Here, we performed targeted viromic analysis of six coral reef invertebrate species and their surrounding seawater to deliver taxonomic and functional profiles of viruses associated with reef organisms. Sponges and corals' host species-specific viral assemblages with low sequence identity to known viral genomes. While core viral genes involved in capsid formation, tail structure and infection mechanisms were observed across all reef s les, auxiliary genes including those involved in herbicide resistance and viral pathogenesis pathways such as host immune suppression were differentially enriched in reef hosts. Utilising a novel OTU based assessment, we also show a prevalence of dsDNA viruses belonging to the Mimiviridae, Caudovirales and Phycodnaviridae in reef environments and further highlight the abundance of ssDNA viruses belonging to the Circoviridae, Parvoviridae, Bidnaviridae and Microviridae in reef invertebrates. These insights into coral reef viruses provide an important framework for future research into how viruses contribute to the health and evolution of reef organisms.
Publisher: Springer Science and Business Media LLC
Date: 08-02-2021
DOI: 10.1038/S41598-021-83052-Z
Abstract: The persistence and degradation of two common herbicides, atrazine and bromacil in two organic media, wood pulp and sawdust were compared with two soils. The hypothesis tested was that herbicide degradation will be faster in high organic matter media compared to soil. Degradation of two herbicides was carried out in four different temperature regimes and in sterilised media. The degradation half-life (t½) was determined under above-mentioned conditions then compared to degradation in soil. The degradation as quantified by t½ of the herbicides was generally longer in both organic media. Although microbial degradation was an important factor in the mineralisation of these herbicides, overall, the pH of the media had a more profound effect on the desorption and subsequent degradation rate than the organic carbon content. The results of this study revealed that the hypothesis was only partially correct as organic matter content per se did not strongly relate to degradation rates which were mainly governed by pH and microbial activity.
Publisher: Elsevier BV
Date: 08-2022
DOI: 10.1016/J.ENVPOL.2022.119466
Abstract: Leaching of herbicides in cropping soils not only impacts the groundwater sources but also reduces their effect in controlling weeds. Leaching studies were carried out in two cropping soils and two forestry biowaste media, wood pulp and sawdust with two herbicides, atrazine and bromacil in a packed lysimeter with simulated rainfall. The hypothesis was that high organic matter forestry biowaste soil amendments reduce the leaching of herbicides through the soil profile. Results from the experimental setups varied due to the impact of the simulated rainfall on the surface structure of the media. Organic carbon content, pH and structure of the media were all factors which affected the leaching of the two herbicides. The hypothesis was true for wood pulp, but for sawdust, organic matter content had less bearing on the leaching of the herbicides than other over-riding factors, such as pH, that were media specific. In sawdust, its large particle size and related pore volume allowed preferential flow of herbicides. Overall, the data indicated that both forestry biowastes were retentive to herbicide leaching, but the effect was more pronounced with wood pulp than sawdust.
Publisher: Wiley
Date: 27-03-2015
Abstract: Reef-building corals form close associations with organisms from all three domains of life and therefore have many potential viral hosts. Yet knowledge of viral communities associated with corals is barely explored. This complexity presents a number of challenges in terms of the metagenomic assessments of coral viral communities and requires specialized methods for purification and lification of viral nucleic acids, as well as virome annotation. In this minireview, we conduct a meta-analysis of the limited number of existing coral virome studies, as well as available coral transcriptome and metagenome data, to identify trends and potential complications inherent in different methods. The analysis shows that the method used for viral nucleic acid isolation drastically affects the observed viral assemblage and interpretation of the results. Further, the small number of viral reference genomes available, coupled with short sequence read lengths might cause errors in virus identification. Despite these limitations and potential biases, the data show that viral communities associated with corals are erse, with double- and single-stranded DNA and RNA viruses. The identified viruses are dominated by double-stranded DNA-tailed bacteriophages, but there are also viruses that infect eukaryote hosts, likely the endosymbiotic dinoflagellates, Symbiodinium spp., host coral and other eukaryotes in close association.
Publisher: Inter-Research Science Center
Date: 09-09-2014
DOI: 10.3354/MEPS10927
Publisher: Frontiers Media SA
Date: 07-05-2014
Publisher: Springer Science and Business Media LLC
Date: 17-03-2017
Publisher: Springer Science and Business Media LLC
Date: 04-2021
DOI: 10.1038/S41587-021-00898-4
Abstract: A Correction to this paper has been published: 0.1038/s41587-021-00898-4.
Publisher: Frontiers Media SA
Date: 09-06-2016
Publisher: Springer Science and Business Media LLC
Date: 18-11-2020
DOI: 10.1038/S41587-020-00769-4
Abstract: An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Location: United States of America
Location: New Zealand
Location: New Zealand
Location: United States of America
No related grants have been discovered for Elisha M. Wood-Charlson.