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Richards SC, King WL, Sutherland JL, Bell TH. Leveraging aquatic-terrestrial interfaces to capture putative habitat generalists. FEMS Microbiol Lett 2024; 371:fnae025. [PMID: 38553956 DOI: 10.1093/femsle/fnae025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 02/03/2024] [Accepted: 03/28/2024] [Indexed: 04/21/2024] Open
Abstract
Habitat type is a strong determinant of microbial composition. Habitat interfaces, such as the boundary between aquatic and terrestrial systems, present unique combinations of abiotic factors for microorganisms to contend with. Aside from the spillover of certain harmful microorganisms from agricultural soils into water (e.g. fecal coliform bacteria), we know little about the extent of soil-water habitat switching across microbial taxa. In this study, we developed a proof-of-concept system to facilitate the capture of putatively generalist microorganisms that can colonize and persist in both soil and river water. We aimed to examine the phylogenetic breadth of putative habitat switchers and how this varies across different source environments. Microbial composition was primarily driven by recipient environment type, with the strongest phylogenetic signal seen at the order level for river water colonizers. We also identified more microorganisms colonizing river water when soil was collected from a habitat interface (i.e. soil at the side of an intermittently flooded river, compared to soil collected further from water sources), suggesting that environmental interfaces could be important reservoirs of microbial habitat generalists. Continued development of experimental systems that actively capture microorganisms that thrive in divergent habitats could serve as a powerful tool for identifying and assessing the ecological distribution of microbial generalists.
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Affiliation(s)
- Sarah C Richards
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, 16802, United States
- Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA, 16802, United States
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, PA, 16802, United States
- International Agriculture and Development Graduate Program, The Pennsylvania State University, University Park, PA, 16802, United States
| | - William L King
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, 16802, United States
- School of Biological Sciences, University of Southampton, SO17 1BJ, United Kingdom
| | - Jeremy L Sutherland
- Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, United States
| | - Terrence H Bell
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, 16802, United States
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, PA, 16802, United States
- International Agriculture and Development Graduate Program, The Pennsylvania State University, University Park, PA, 16802, United States
- Department of Physical & Environmental Sciences, University of Toronto Scarborough, Toronto, ON, M1C1A4, Canada
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King WL, Yates CF, Cao L, O'Rourke-Ibach S, Fleishman SM, Richards SC, Centinari M, Hafner BD, Goebel M, Bauerle T, Kim YM, Nicora CD, Anderton CR, Eissenstat DM, Bell TH. Functionally discrete fine roots differ in microbial assembly, microbial functional potential, and produced metabolites. Plant Cell Environ 2023; 46:3919-3932. [PMID: 37675977 DOI: 10.1111/pce.14705] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 07/12/2023] [Accepted: 08/18/2023] [Indexed: 09/08/2023]
Abstract
Traditionally, fine roots were grouped using arbitrary size categories, rarely capturing the heterogeneity in physiology, morphology and functionality among different fine root orders. Fine roots with different functional roles are rarely separated in microbiome-focused studies and may result in confounding microbial signals and host-filtering across different root microbiome compartments. Using a 26-year-old common garden, we sampled fine roots from four temperate tree species that varied in root morphology and sorted them into absorptive and transportive fine roots. The rhizoplane and rhizosphere were characterized using 16S rRNA gene and internal transcribed spacer region amplicon sequencing and shotgun metagenomics for the rhizoplane to identify potential microbial functions. Fine roots were subject to metabolomics to spatially characterize resource availability. Both fungi and bacteria differed according to root functional type. We observed additional differences between the bacterial rhizoplane and rhizosphere compartments for absorptive but not transportive fine roots. Rhizoplane bacteria, as well as the root metabolome and potential microbial functions, differed between absorptive and transportive fine roots, but not the rhizosphere bacteria. Functional differences were driven by sugar transport, peptidases and urea transport. Our data highlights the importance of root function when examining root-microbial relationships, emphasizing different host selective pressures imparted on different root microbiome compartments.
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Affiliation(s)
- William L King
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, Pennsylvania, USA
- School of Integrative Plant Science, Cornell University, Ithaca, New York, USA
| | - Caylon F Yates
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, Pennsylvania, USA
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Lily Cao
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, Pennsylvania, USA
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, Pennsylvania, USA
- Department of Plant Science, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Sean O'Rourke-Ibach
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Suzanne M Fleishman
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, Pennsylvania, USA
- Department of Plant Science, The Pennsylvania State University, University Park, Pennsylvania, USA
- Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Sarah C Richards
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, Pennsylvania, USA
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, Pennsylvania, USA
- Intercollege Graduate Degree Program in International Agriculture and Development, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Michela Centinari
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, Pennsylvania, USA
- Department of Plant Science, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Benjamin D Hafner
- School of Integrative Plant Science, Cornell University, Ithaca, New York, USA
| | - Marc Goebel
- Department of Natural Resources and the Environment, Cornell University, Ithaca, New York, USA
| | - Taryn Bauerle
- School of Integrative Plant Science, Cornell University, Ithaca, New York, USA
| | - Young-Mo Kim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Carrie D Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Christopher R Anderton
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - David M Eissenstat
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, Pennsylvania, USA
- Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Terrence H Bell
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, Pennsylvania, USA
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, Pennsylvania, USA
- Intercollege Graduate Degree Program in International Agriculture and Development, The Pennsylvania State University, University Park, Pennsylvania, USA
- Department of Physical & Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
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3
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King WL, Richards SC, Kaminsky LM, Bradley BA, Kaye JP, Bell TH. Leveraging microbiome rediversification for the ecological rescue of soil function. Environ Microbiome 2023; 18:7. [PMID: 36691096 PMCID: PMC9872425 DOI: 10.1186/s40793-023-00462-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 01/06/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Global biodiversity losses threaten ecosystem services and can impact important functional insurance in a changing world. Microbial diversity and function can become depleted in agricultural systems and attempts to rediversify agricultural soils rely on either targeted microbial introductions or retaining natural lands as biodiversity reservoirs. As many soil functions are provided by a combination of microbial taxa, rather than outsized impacts by single taxa, such functions may benefit more from diverse microbiome additions than additions of individual commercial strains. In this study, we measured the impact of soil microbial diversity loss and rediversification (i.e. rescue) on nitrification by quantifying ammonium and nitrate pools. We manipulated microbial assemblages in two distinct soil types, an agricultural and a forest soil, with a dilution-to-extinction approach and performed a microbiome rediversification experiment by re-introducing microorganisms lost from the dilution. A microbiome water control was included to act as a reference point. We assessed disruption and potential restoration of (1) nitrification, (2) bacterial and fungal composition through 16S rRNA gene and fungal ITS amplicon sequencing and (3) functional genes through shotgun metagenomic sequencing on a subset of samples. RESULTS Disruption of nitrification corresponded with diversity loss, but nitrification was successfully rescued in the rediversification experiment when high diversity inocula were introduced. Bacterial composition clustered into groups based on high and low diversity inocula. Metagenomic data showed that genes responsible for the conversion of nitrite to nitrate and taxa associated with nitrogen metabolism were absent in the low diversity inocula microcosms but were rescued with high diversity introductions. CONCLUSIONS In contrast to some previous work, our data suggest that soil functions can be rescued by diverse microbiome additions, but that the concentration of the microbial inoculum is important. By understanding how microbial rediversification impacts soil microbiome performance, we can further our toolkit for microbial management in human-controlled systems in order to restore depleted microbial functions.
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Affiliation(s)
- William L King
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, 317 Buckhout Lab, University Park, PA, 16802, USA
- School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Sarah C Richards
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, 317 Buckhout Lab, University Park, PA, 16802, USA
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, PA, 16802, USA
- Intercollege Graduate Degree Program in International Agriculture and Development, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Laura M Kaminsky
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, 317 Buckhout Lab, University Park, PA, 16802, USA
| | - Brosi A Bradley
- Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Jason P Kaye
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, PA, 16802, USA
- Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Terrence H Bell
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, 317 Buckhout Lab, University Park, PA, 16802, USA.
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, PA, 16802, USA.
- Intercollege Graduate Degree Program in International Agriculture and Development, The Pennsylvania State University, University Park, PA, 16802, USA.
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Assis BA, Bell TH, Engler HI, King WL. Shared and unique responses in the microbiome of allopatric lizards reared in a standardized environment. J Exp Zool A Ecol Integr Physiol 2023; 339:5-12. [PMID: 36266922 DOI: 10.1002/jez.2665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 10/04/2022] [Accepted: 10/07/2022] [Indexed: 12/15/2022]
Abstract
The gut microbiome can influence host fitness and, consequently, the ecology and evolution of natural populations. Microbiome composition can be driven by environmental exposure but also by the host's genetic background and phenotype. To contrast environmental and genetic effects on the microbiome we leverage preserved specimens of eastern fence lizards from allopatric lineages east and west of the Mississippi River but reared in standardized conditions. Bacterial composition was indistinguishable between lineages but responded significantly to host age-a proxy for environmental exposure. This was accompanied by a continuous decrease in bacterial diversity in both lineages, partially driven by decreasing evenness seen only in western lizards. These findings indicate that longer exposure to a homogeneous habitat may have a depreciating effect on microbiome diversity in eastern fence lizards, a response shared by both lineages. We highlight the importance of such effects when extrapolating patterns from laboratory experiments to the natural world.
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Affiliation(s)
- Braulio A Assis
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Terrence H Bell
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, Pennsylvania, USA.,Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Heather I Engler
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - William L King
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, Pennsylvania, USA.,School of Integrative Plant Science, Cornell University, Ithaca, New York, USA
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5
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Worden PJ, Bogema DR, Micallef ML, Go J, Deutscher AT, Labbate M, Green TJ, King WL, Liu M, Seymour JR, Jenkins C. Phylogenomic diversity of Vibrio species and other Gammaproteobacteria isolated from Pacific oysters ( Crassostrea gigas) during a summer mortality outbreak. Microb Genom 2022; 8:mgen000883. [PMID: 36748707 PMCID: PMC9837568 DOI: 10.1099/mgen.0.000883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The Pacific oyster (PO), Crassostrea gigas, is an important commercial marine species but periodically experiences large stock losses due to disease events known as summer mortality. Summer mortality has been linked to environmental perturbations and numerous viral and bacterial agents, indicating this disease is multifactorial in nature. In 2013 and 2014, several summer mortality events occurred within the Port Stephens estuary (NSW, Australia). Extensive culture and molecular-based investigations were undertaken and several potentially pathogenic Vibrio species were identified. To improve species identification and genomically characterise isolates obtained from this outbreak, whole-genome sequencing (WGS) and subsequent genomic analyses were performed on 48 bacterial isolates, as well as a further nine isolates from other summer mortality studies using the same batch of juveniles. Average nucleotide identity (ANI) identified most isolates to the species level and included members of the Photobacterium, Pseudoalteromonas, Shewanella and Vibrio genera, with Vibrio species making up more than two-thirds of all species identified. Construction of a phylogenomic tree, ANI analysis, and pan-genome analysis of the 57 isolates represents the most comprehensive culture-based phylogenomic survey of Vibrios during a PO summer mortality event in Australian waters and revealed large genomic diversity in many of the identified species. Our analysis revealed limited and inconsistent associations between isolate species and their geographical origins, or host health status. Together with ANI and pan-genome results, these inconsistencies suggest that to determine the role that microbes may have in Pacific oyster summer mortality events, isolate identification must be at the taxonomic level of strain. Our WGS data (specifically, the accessory genomes) differentiated bacterial strains, and coupled with associated metadata, highlight the possibility of predicting a strain's environmental niche and level of pathogenicity.
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Affiliation(s)
- Paul J. Worden
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Woodbridge Rd, Menangle, NSW 2568
| | - Daniel R. Bogema
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Woodbridge Rd, Menangle, NSW 2568
| | - Melinda L. Micallef
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Woodbridge Rd, Menangle, NSW 2568
| | - Jeffrey Go
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Woodbridge Rd, Menangle, NSW 2568
| | - Ania T. Deutscher
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Woodbridge Rd, Menangle, NSW 2568
| | - Maurizio Labbate
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
| | - Timothy J. Green
- Centre for Shellfish Research, Vancouver Island University, Nanaimo, British Columbia,, Canada
| | - William L. King
- Department of Plant Pathology and Environmental MIcrobiology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Michael Liu
- iThree Institute, University of Technology Sydney, Building 4, 745 Harris Street, Broadway, Ultimo, NSW, 2007
| | - Justin R. Seymour
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, 2007
| | - Cheryl Jenkins
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Woodbridge Rd, Menangle, NSW 2568,*Correspondence: Cheryl Jenkins,
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Yates C, Trexler RV, Bonet I, King WL, Hockett KL, Bell TH. Rapid niche shifts in bacteria following conditioning in novel soil environments. Funct Ecol 2022. [DOI: 10.1111/1365-2435.14180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Caylon Yates
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University University Park PA USA
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University University Park PA USA
| | - Ryan V. Trexler
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University University Park PA USA
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University University Park PA USA
| | - Idalys Bonet
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University University Park PA USA
| | - William L. King
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University University Park PA USA
- Present address: School of Integrative Plant Science Cornell University Ithaca NY
| | - Kevin L. Hockett
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University University Park PA USA
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University University Park PA USA
| | - Terrence H. Bell
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University University Park PA USA
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University University Park PA USA
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7
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King WL, Kaminsky LM, Gannett M, Thompson GL, Kao‐Kniffin J, Bell TH. Soil salinization accelerates microbiome stabilization in iterative selections for plant performance. New Phytol 2022; 234:2101-2110. [PMID: 34614202 PMCID: PMC9297847 DOI: 10.1111/nph.17774] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 09/29/2021] [Indexed: 06/01/2023]
Abstract
Climate change-related soil salinization increases plant stress and decreases productivity. Soil microorganisms are thought to reduce salt stress through multiple mechanisms, so diverse assemblages could improve plant growth under such conditions. Previous studies have shown that microbiome selection can promote desired plant phenotypes, but with high variability. We hypothesized that microbiome selection would be more consistent in saline soils by increasing potential benefits to the plants. In both salt-amended and untreated soils, we transferred forward Brassica rapa root microbiomes (from high-biomass or randomly selected pots) across six planting generations while assessing bacterial (16S rRNA) and fungal (ITS) composition in detail. Uniquely, we included an add-back control (re-adding initial frozen soil microbiome) as a within-generation reference for microbiome and plant phenotype selection. We observed inconsistent effects of microbiome selection on plant biomass across generations, but microbial composition consistently diverged from the add-back control. Although salt amendment strongly impacted microbial composition, it did not increase the predictability of microbiome effects on plant phenotype, but it did increase the rate at which microbiome selection plateaued. These data highlight a disconnect in the trajectories of microbiomes and plant phenotypes during microbiome selection, emphasizing the role of standard controls to explain microbiome selection outcomes.
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Affiliation(s)
- William L. King
- Department of Plant Pathology and Environmental MicrobiologyThe Pennsylvania State UniversityUniversity ParkPA16802USA
| | - Laura M. Kaminsky
- Department of Plant Pathology and Environmental MicrobiologyThe Pennsylvania State UniversityUniversity ParkPA16802USA
- School of Integrative Plant ScienceCornell UniversityIthacaNY14853USA
| | - Maria Gannett
- School of Integrative Plant ScienceCornell UniversityIthacaNY14853USA
| | - Grant L. Thompson
- School of Integrative Plant ScienceCornell UniversityIthacaNY14853USA
- Department of HorticultureIowa State UniversityAmesIA50011USA
| | - Jenny Kao‐Kniffin
- School of Integrative Plant ScienceCornell UniversityIthacaNY14853USA
| | - Terrence H. Bell
- Department of Plant Pathology and Environmental MicrobiologyThe Pennsylvania State UniversityUniversity ParkPA16802USA
- School of Integrative Plant ScienceCornell UniversityIthacaNY14853USA
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King WL, Kaminsky LM, Richards SC, Bradley BA, Kaye JP, Bell TH. Farm-scale differentiation of active microbial colonizers. ISME Commun 2022; 2:39. [PMID: 37938671 PMCID: PMC9723676 DOI: 10.1038/s43705-022-00120-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 03/22/2022] [Accepted: 03/22/2022] [Indexed: 06/17/2023]
Abstract
Microbial movement is important for replenishing lost soil microbial biodiversity and driving plant root colonization, particularly in managed agricultural soils, where microbial diversity and composition can be disrupted. Despite abundant survey-type microbiome data in soils, which are obscured by legacy DNA and microbial dormancy, we do not know how active microbial pools are shaped by local soil properties, agricultural management, and at differing spatial scales. To determine how active microbial colonizers are shaped by spatial scale and environmental conditions, we deployed microbial traps (i.e. sterile soil enclosed by small pore membranes) containing two distinct soil types (forest; agricultural), in three neighboring locations, assessing colonization through 16S rRNA gene and fungal ITS amplicon sequencing. Location had a greater impact on fungal colonizers (R2 = 0.31 vs. 0.26), while the soil type within the microbial traps influenced bacterial colonizers more (R2 = 0.09 vs. 0.02). Bacterial colonizers showed greater colonization consistency (within-group similarity) among replicate communities. Relative to bacterial colonizers, fungal colonizers shared a greater compositional overlap to sequences from the surrounding local bulk soil (R2 = 0.08 vs. 0.29), suggesting that these groups respond to distinct environmental constraints and that their in-field management may differ. Understanding how environmental constraints and spatial scales impact microbial recolonization dynamics and community assembly are essential for identifying how soil management can be used to shape agricultural microbiomes.
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Affiliation(s)
- William L King
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Laura M Kaminsky
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Sarah C Richards
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, 16802, USA
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, PA, 16802, USA
- Intercollege Graduate Degree Program in International Agriculture and Development, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Brosi A Bradley
- Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Jason P Kaye
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, PA, 16802, USA
- Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Terrence H Bell
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, 16802, USA.
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, PA, 16802, USA.
- Intercollege Graduate Degree Program in International Agriculture and Development, The Pennsylvania State University, University Park, PA, 16802, USA.
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9
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King WL, Kaestli M, Siboni N, Padovan A, Christian K, Mills D, Seymour J, Gibb K. Pearl Oyster Bacterial Community Structure Is Governed by Location and Tissue-Type, but Vibrio Species Are Shared Among Oyster Tissues. Front Microbiol 2021; 12:723649. [PMID: 34434182 PMCID: PMC8381468 DOI: 10.3389/fmicb.2021.723649] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 07/21/2021] [Indexed: 12/25/2022] Open
Abstract
Diseases of bivalves of aquacultural importance, including the valuable Australian silver-lipped pearl oyster (Pinctada maxima), have been increasing in frequency and severity. The bivalve microbiome is linked to health and disease dynamics, particularly in oysters, with putative pathogens within the Vibrio genus commonly implicated in oyster diseases. Previous studies have been biased toward the Pacific oyster because of its global dominance in oyster aquaculture, while much less is known about the microbiome of P. maxima. We sought to address this knowledge gap by characterizing the P. maxima bacterial community, and we hypothesized that bacterial community composition, and specifically the occurrence of Vibrio, will vary according to the sampled microenvironment. We also predicted that the inside shell swab bacterial composition could represent a source of microbial spillover biofilm into the solid pearl oyster tissues, thus providing a useful predictive sampling environment. We found that there was significant heterogeneity in bacterial composition between different pearl oyster tissues, which is consistent with patterns reported in other bivalve species and supports the hypothesis that each tissue type represents a unique microenvironment for bacterial colonization. We suggest that, based on the strong effect of tissue-type on the pearl oyster bacterial community, future studies should apply caution when attempting to compare microbial patterns from different locations, and when searching for disease agents. The lack of association with water at each farm also supported the unique nature of the microbial communities in oyster tissues. In contrast to the whole bacterial community, there was no significant difference in the Vibrio community among tissue types nor location. These results suggest that Vibrio species are shared among different pearl oyster tissues. In particular, the similarity between the haemolymph, inside shell and solid tissues, suggests that the haemolymph and inside shell environment is a source of microbial spillover into the oyster tissues, and a potentially useful tool for non-destructive routine disease testing and early warning surveillance. These data provide important foundational information for future studies identifying the factors that drive microbial assembly in a valuable aquaculture species.
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Affiliation(s)
- William L King
- Climate Change Cluster, University of Technology Sydney, Sydney, NSW, Australia
| | - Mirjam Kaestli
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, Australia
| | - Nachshon Siboni
- Climate Change Cluster, University of Technology Sydney, Sydney, NSW, Australia
| | - Anna Padovan
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, Australia
| | - Keith Christian
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, Australia
| | - David Mills
- Genecology Research Centre, University of the Sunshine Coast, Sunshine Coast, QLD, Australia
| | - Justin Seymour
- Climate Change Cluster, University of Technology Sydney, Sydney, NSW, Australia
| | - Karen Gibb
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, Australia
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10
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Scanes E, Parker LM, Seymour JR, Siboni N, King WL, Wegner KM, Dove MC, O'Connor WA, Ross PM. Microbiome response differs among selected lines of Sydney rock oysters to ocean warming and acidification. FEMS Microbiol Ecol 2021; 97:6311813. [PMID: 34190992 DOI: 10.1093/femsec/fiab099] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 06/28/2021] [Indexed: 12/12/2022] Open
Abstract
Oyster microbiomes are integral to healthy function and can be altered by climate change conditions. Genetic variation among oysters is known to influence the response of oysters to climate change and may ameliorate any adverse effects on oyster microbiome; however, this remains unstudied. Nine full-sibling selected breeding lines of the Sydney rock oyster (Saccostrea glomerata) were exposed to predicted warming (ambient = 24°C, elevated = 28°C) and ocean acidification (ambient pCO2 = 400, elevated pCO2 = 1000 µatm) for 4 weeks. The haemolymph bacterial microbiome was characterized using 16S rRNA (V3-V4) gene sequencing and varied among oyster lines in the control (ambient pCO2, 24°C) treatment. Microbiomes were also altered by climate change dependent on oyster lines. Bacterial α-diversity increased in response to elevated pCO2 in two selected lines, while bacterial β-diversity was significantly altered by combinations of elevated pCO2 and temperature in four selected lines. Climate change treatments caused shifts in the abundance of multiple amplicon sequence variants driving change in the microbiome of some selected lines. We show that oyster genetic background may influence the Sydney rock oyster haemolymph microbiome under climate change and that future assisted evolution breeding programs to enhance resilience should consider the oyster microbiome.
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Affiliation(s)
- Elliot Scanes
- Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales 2007, Australia.,The University of Sydney, School of Life and Environmental Sciences, Camperdown, New South Wales 2006, Australia
| | - Laura M Parker
- The University of New South Wales, School of Biological, Earth and Environmental Sciences, Kensington, New South Wales 2052, Australia
| | - Justin R Seymour
- Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales 2007, Australia
| | - Nachshon Siboni
- Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales 2007, Australia
| | - William L King
- Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales 2007, Australia.,Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA 16802, USA
| | - K Mathias Wegner
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Coastal Ecology, Wadden Sea Station Sylt, List 25992, Germany
| | - Michael C Dove
- New South Wales Department of Primary Industries, Port Stephens Fisheries Institute, Taylors Beach, New South Wales 2316, Australia
| | - Wayne A O'Connor
- New South Wales Department of Primary Industries, Port Stephens Fisheries Institute, Taylors Beach, New South Wales 2316, Australia
| | - Pauline M Ross
- The University of Sydney, School of Life and Environmental Sciences, Camperdown, New South Wales 2006, Australia
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11
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Padovan A, Siboni N, Kaestli M, King WL, Seymour JR, Gibb K. Occurrence and dynamics of potentially pathogenic vibrios in the wet-dry tropics of northern Australia. Mar Environ Res 2021; 169:105405. [PMID: 34242991 DOI: 10.1016/j.marenvres.2021.105405] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 06/24/2021] [Accepted: 06/27/2021] [Indexed: 06/13/2023]
Abstract
Bacteria from the Vibrio genus are a ubiquitous component of coastal and estuarine ecosystems with several pathogenic Vibrio species displaying preferences for warm tropical waters. We studied the spatial and temporal abundance of three key human potential pathogens V. parahaemolyticus, V. cholerae and V. vulnificus in northern tropical Australia, over the wet and dry seasons, to identify environmental parameters influencing their abundance. Quantitative PCR (qPCR) analysis revealed that V. parahaemolyticus occurred more frequently and in higher abundance than V. cholerae and V. vulnificus across all locations examined. All three species were more abundant during the wet season, with V. parahaemolyticus abundance correlated to temperature and conductivity, whereas nutrient concentrations and turbidity best explained V. vulnificus abundance. In addition to these targeted qPCR analyses, we assessed the composition and dynamics of the entire Vibrio community using hsp60 amplicon sequencing. Using this approach, 42 Vibrio species were identified, including a number of other pathogenic species such as V. alginolyticus, V. mimicus and V. fluvialis. The Vibrio community was more diverse in the wet season, with temperature and dissolved oxygen as the key factors governing community composition. Seasonal differences were primarily driven by a greater abundance of V. parahaemolyticus and V. vulnificus during the wet season, while spatial differences were driven by different abundances of V. harveyi, V. campbellii, V. cholerae and V. navarrensis. When we related the abundance of Vibrio to other bacterial taxa, defined using 16S rRNA gene amplicon sequencing, V. parahaemolyticus was negatively correlated to several taxa, including members of the Rickettsiales and Saccharimonadales, while V. vulnificus was negatively correlated to Rhobacteriaceae and Cyanobiaceae. In contrast, V. alginolyticus, V. harveyi and V. mediterranei were all positively correlated to Cyanobacteria. These observations highlight the dynamic nature of Vibrio communities and expands current understanding of the processes governing the occurrence of potentially pathogenic Vibrio spp. in tropical coastal ecosystems.
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Affiliation(s)
- Anna Padovan
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, Australia.
| | - Nachshon Siboni
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Mirjam Kaestli
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, Australia
| | - William L King
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia; The School of Life Sciences, University of Technology Sydney, Ultimo, NSW, Australia
| | - Justin R Seymour
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Karen Gibb
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, Australia
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12
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King WL, Bell TH. Can dispersal be leveraged to improve microbial inoculant success? Trends Biotechnol 2021; 40:12-21. [PMID: 33972105 DOI: 10.1016/j.tibtech.2021.04.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/09/2021] [Accepted: 04/12/2021] [Indexed: 01/24/2023]
Abstract
Microorganisms have long been isolated from soils to develop microbial inoculants, with the goal of spiking them into new soils to augment target functions. However, establishment can be sporadic, and we assume that inoculants simply arrive at their destination. Here, we posit a need for integrating dispersal into inoculant development and deployment. We argue that consideration for an inoculant's dispersal ability, whether via active (e.g., chemotaxis) or passive (e.g., attachment to other organisms) means, and including methods of deployment that allow multiple establishment attempts could help increase the predictability of inoculant success. Dispersal can influence many key aspects of in-field survival, including the ability to escape stressors, seek favorable colonization sites, facilitate multiple establishment attempts, and engage in multikingdom interactions.
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Affiliation(s)
- William L King
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, USA.
| | - Terrence H Bell
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, USA; Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, PA, USA.
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13
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King WL, Yates CF, Guo J, Fleishman SM, Trexler RV, Centinari M, Bell TH, Eissenstat DM. The hierarchy of root branching order determines bacterial composition, microbial carrying capacity and microbial filtering. Commun Biol 2021; 4:483. [PMID: 33875783 PMCID: PMC8055976 DOI: 10.1038/s42003-021-01988-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 03/02/2021] [Indexed: 02/02/2023] Open
Abstract
Fine roots vary dramatically in their functions, which range from resource absorption to within-plant resource transport. These differences should alter resource availability to root-associated microorganisms, yet most root microbiome studies involve fine root homogenization. We hypothesized that microbial filtering would be greatest in the most distal roots. To test this, we sampled roots of six temperate tree species from a 23-year-old common garden planting, separating by branching order. Rhizoplane bacterial composition was characterized with 16S rRNA gene sequencing, while bacterial abundance was determined on a subset of trees through flow cytometry. Root order strongly impacted composition across tree species, with absorptive lower order roots exerting the greatest selective pressure. Microbial carrying capacity was higher in absorptive roots in two of three tested tree species. This study indicates lower order roots as the main point of microbial interaction with fine roots, suggesting that root homogenization could mask microbial recruitment signatures.
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Affiliation(s)
- William L King
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Caylon F Yates
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, 16802, USA
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Jing Guo
- Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA, 16802, USA
- MOE Key Laboratory of Biosystems Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Suzanne M Fleishman
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, PA, 16802, USA
- Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA, 16802, USA
- Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Ryan V Trexler
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Michela Centinari
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, PA, 16802, USA
- Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Terrence H Bell
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, 16802, USA.
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, PA, 16802, USA.
| | - David M Eissenstat
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, PA, 16802, USA.
- Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA, 16802, USA.
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14
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Scanes E, Parker LM, Seymour JR, Siboni N, King WL, Danckert NP, Wegner KM, Dove MC, O'Connor WA, Ross PM. Climate change alters the haemolymph microbiome of oysters. Mar Pollut Bull 2021; 164:111991. [PMID: 33485019 DOI: 10.1016/j.marpolbul.2021.111991] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 12/14/2020] [Accepted: 12/20/2020] [Indexed: 06/12/2023]
Abstract
The wellbeing of marine organisms is connected to their microbiome. Oysters are a vital food source and provide ecological services, yet little is known about how climate change such as ocean acidification and warming will affect their microbiome. We exposed the Sydney rock oyster, Saccostrea glomerata, to orthogonal combinations of temperature (24, 28 °C) and pCO2 (400 and 1000 μatm) for eight weeks and used amplicon sequencing of the 16S rRNA (V3-V4) gene to characterise the bacterial community in haemolymph. Overall, elevated pCO2 and temperature interacted to alter the microbiome of oysters, with a clear partitioning of treatments in CAP ordinations. Elevated pCO2 was the strongest driver of species diversity and richness and elevated temperature also increased species richness. Climate change, both ocean acidification and warming, will alter the microbiome of S. glomerata which may increase the susceptibility of oysters to disease.
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Affiliation(s)
- Elliot Scanes
- The University of Sydney, School of Life and Environmental Sciences, Camperdown, New South Wales 2006, Australia.
| | - Laura M Parker
- The University of New South Wales, School of Biological, Earth and Environmental Sciences, Kensington, New South Wales 2052, Australia
| | - Justin R Seymour
- Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales 2007, Australia
| | - Nachshon Siboni
- Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales 2007, Australia
| | - William L King
- Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales 2007, Australia; Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Nathan P Danckert
- The University of Sydney, School of Life and Environmental Sciences, Camperdown, New South Wales 2006, Australia
| | - K Mathias Wegner
- Helmholtz Centre for Polar and Marine Research, Alfred Wegener Institute, Coastal Ecology, Wadden Sea Station, List, Sylt 25992, Germany
| | - Michael C Dove
- New South Wales Department of Primary Industries, Port Stephens Fisheries Institute, Taylors Beach, New South Wales 2316, Australia
| | - Wayne A O'Connor
- New South Wales Department of Primary Industries, Port Stephens Fisheries Institute, Taylors Beach, New South Wales 2316, Australia
| | - Pauline M Ross
- The University of Sydney, School of Life and Environmental Sciences, Camperdown, New South Wales 2006, Australia
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15
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King WL, Siboni N, Kahlke T, Dove M, O'Connor W, Mahbub KR, Jenkins C, Seymour JR, Labbate M. Regional and oyster microenvironmental scale heterogeneity in the Pacific oyster bacterial community. FEMS Microbiol Ecol 2020; 96:5813259. [PMID: 32221598 DOI: 10.1093/femsec/fiaa054] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 03/22/2020] [Indexed: 01/04/2023] Open
Abstract
Different organs of a host represent distinct microenvironments resulting in the establishment of multiple discrete bacterial communities within a host. These discrete bacterial communities can also vary according to geographical location. For the Pacific oyster, Crassostrea gigas, the factors governing bacterial diversity and abundance of different oyster microenvironments are poorly understood. In this study, the factors shaping bacterial abundance, diversity and composition associated with the C. gigas mantle, gill, adductor muscle and digestive gland were characterised using 16S (V3-V4) rRNA amplicon sequencing across six discrete estuaries. Both location and tissue-type, with tissue-type being the stronger determinant, were factors driving bacterial community composition. Bacterial communities from wave-dominated estuaries had similar compositions and higher bacterial abundance despite being geographically distant from one another, possibly indicating that functional estuarine morphology characteristics are a factor shaping the oyster bacterial community. Despite the bacterial community heterogeneity, examinations of the core bacterial community identified Spirochaetaceae bacteria as conserved across all sites and samples. Whereas members of the Vulcaniibacterium, Spirochaetaceae and Margulisbacteria, and Polynucleobacter were regionally conserved members of the digestive gland, gill and mantle bacterial communities, respectively. This indicates that baseline bacterial community profiles for specific locations are necessary when investigating bacterial communities in oyster health.
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Affiliation(s)
- William L King
- University of Technology Sydney, The School of Life Sciences, Ultimo, New South Wales, 2007, Australia.,University of Technology Sydney, Climate Change Cluster, Ultimo, New South Wales, 2007, Australia
| | - Nachshon Siboni
- University of Technology Sydney, Climate Change Cluster, Ultimo, New South Wales, 2007, Australia
| | - Tim Kahlke
- University of Technology Sydney, Climate Change Cluster, Ultimo, New South Wales, 2007, Australia
| | - Michael Dove
- NSW Department of Primary Industries, Port Stephens Fisheries Institute, Port Stephens, New South Wales, 2316, Australia
| | - Wayne O'Connor
- NSW Department of Primary Industries, Port Stephens Fisheries Institute, Port Stephens, New South Wales, 2316, Australia
| | - Khandaker Rayhan Mahbub
- University of Technology Sydney, The School of Life Sciences, Ultimo, New South Wales, 2007, Australia
| | - Cheryl Jenkins
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, New South Wales, 2568, Australia
| | - Justin R Seymour
- University of Technology Sydney, Climate Change Cluster, Ultimo, New South Wales, 2007, Australia
| | - Maurizio Labbate
- University of Technology Sydney, The School of Life Sciences, Ultimo, New South Wales, 2007, Australia
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16
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Mahbub KR, King WL, Siboni N, Nguyen VK, Rahman MM, Megharaj M, Seymour JR, Franks AE, Labbate M. Long-lasting effect of mercury contamination on the soil microbiota and its co-selection of antibiotic resistance. Environ Pollut 2020; 265:115057. [PMID: 32806457 DOI: 10.1016/j.envpol.2020.115057] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 05/11/2020] [Accepted: 06/16/2020] [Indexed: 06/11/2023]
Abstract
Antibiotic resistance genes (ARGs) in the environment are an exposure risk to humans and animals and is emerging as a global public health concern. In this study, mercury (Hg) driven co-selection of ARGs was investigated under controlled conditions in two Australian non-agricultural soils with differing pH. Soils were spiked with increasing concentrations of inorganic Hg and left to age for 5 years. Both soils contained ARGs conferring resistance to tetracycline (tetA, tetB), sulphonamides (sul1), trimethoprim (dfrA1) and the ARG indicator class 1 integron-integrase gene, intI1, as measured by qPCR. The last resort antibiotic vancomycin resistance gene, vanB and quinolone resistance gene, qnrS were not detected. Hg driven co-selection of several ARGs namely intI1, tetA and tetB were observed in the alkaline soil within the tested Hg concentrations. No co-selection of the experimental ARGs was observed in the neutral pH soil. 16S rRNA sequencing revealed proliferation of Proteobacteria and Bacteriodetes in Hg contaminated neutral and alkaline soils respectively. Multivariate analyses revealed a strong effect of Hg, soil pH and organic carbon content on the co-selection of ARGs in the experimental soils. Additionally, although aging caused a significant reduction in Hg content, agriculturally important bacterial phyla such as Nitrospirae did not regrow in the contaminated soils. The results suggest that mercury can drive co-selection of ARGs in contaminated non-agricultural soils over five years of aging which is linked to soil microbiota shift and metal chemistry in the soil.
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Affiliation(s)
| | - William L King
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW, 2007, Australia; Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Nachshon Siboni
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Viet Khue Nguyen
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW, 2007, Australia; Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Mohammad Mahmudur Rahman
- Global Centre for Environmental Remediation, The University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Mallavarapu Megharaj
- Global Centre for Environmental Remediation, The University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Justin R Seymour
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Ashley E Franks
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC, 3086, Australia; Centre for Future Landscapes, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Maurizio Labbate
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW, 2007, Australia.
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17
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King WL, Siboni N, Kahlke T, Green TJ, Labbate M, Seymour JR. A New High Throughput Sequencing Assay for Characterizing the Diversity of Natural Vibrio Communities and Its Application to a Pacific Oyster Mortality Event. Front Microbiol 2019; 10:2907. [PMID: 31921078 PMCID: PMC6932961 DOI: 10.3389/fmicb.2019.02907] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 12/03/2019] [Indexed: 01/08/2023] Open
Abstract
The Vibrio genus is notable for including several pathogens of marine animals and humans, yet characterization of Vibrio diversity using routine 16S rRNA sequencing methods is often constrained by poor resolution beyond the genus level. Here, a new high throughput sequencing approach targeting the heat shock protein (hsp60) as a phylogenetic marker was developed to more precisely discriminate members of the Vibrio genus in environmental samples. The utility of this new assay was tested using mock communities constructed from known dilutions of Vibrio isolates. Relative to standard and Vibrio-specific 16S rRNA sequencing assays, the hsp60 assay delivered high levels of fidelity with the mock community composition at the species level, including discrimination of species within the Vibrio harveyi clade. This assay was subsequently applied to characterize Vibrio community composition in seawater and delivered substantially improved taxonomic resolution of Vibrio species compared to 16S rRNA analysis. Finally, this assay was applied to examine patterns in the Vibrio community within oysters during a Pacific oyster mortality event. In these oysters, the hsp60 assay identified species-level Vibrio community shifts prior to disease onset, pinpointing V. harveyi as a putative pathogen. Given that shifts in the Vibrio community can precede, cause, and follow disease onset in numerous marine organisms, there is a need for an accurate high throughput assay for defining Vibrio community composition in natural samples. This Vibrio-centric hsp60 sequencing assay offers the potential for precise high throughput characterization of Vibrio diversity, providing an enhanced platform for dissecting Vibrio dynamics in the environment.
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Affiliation(s)
- William L. King
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW, Australia
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Nachshon Siboni
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Tim Kahlke
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Timothy J. Green
- Centre for Shellfish Research, Vancouver Island University, Nanaimo, BC, Canada
| | - Maurizio Labbate
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW, Australia
| | - Justin R. Seymour
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
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18
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Green TJ, Siboni N, King WL, Labbate M, Seymour JR, Raftos D. Simulated Marine Heat Wave Alters Abundance and Structure of Vibrio Populations Associated with the Pacific Oyster Resulting in a Mass Mortality Event. Microb Ecol 2019; 77:736-747. [PMID: 30097682 DOI: 10.1007/s00248-018-1242-9] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 08/03/2018] [Indexed: 06/08/2023]
Abstract
Marine heat waves are predicted to become more frequent and intense due to anthropogenically induced climate change, which will impact global production of seafood. Links between rising seawater temperature and disease have been documented for many aquaculture species, including the Pacific oyster Crassostrea gigas. The oyster harbours a diverse microbial community that may act as a source of opportunistic pathogens during temperature stress. We rapidly raised the seawater temperature from 20 °C to 25 °C resulting in an oyster mortality rate of 77.4%. Under the same temperature conditions and with the addition of antibiotics, the mortality rate was only 4.3%, strongly indicating a role for bacteria in temperature-induced mortality. 16S rRNA amplicon sequencing revealed a change in the oyster microbiome when the temperature was increased to 25 °C, with a notable increase in the proportion of Vibrio sequences. This pattern was confirmed by qPCR, which revealed heat stress increased the abundance of Vibrio harveyi and Vibrio fortis by 324-fold and 10-fold, respectively. Our findings indicate that heat stress-induced mortality of C. gigas coincides with an increase in the abundance of putative bacterial pathogens in the oyster microbiome and highlights the negative consequences of marine heat waves on food production from aquaculture.
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Affiliation(s)
- Timothy J Green
- Department of Biological Sciences, Macquarie University, Sydney, Australia.
- Centre for Shellfish Research, Vancouver Island University, Nanaimo, Canada.
| | - Nachshon Siboni
- Climate Change Cluster (C3) Ocean Microbes Group, University of Technology Sydney, Sydney, Australia
| | - William L King
- Climate Change Cluster (C3) Ocean Microbes Group, University of Technology Sydney, Sydney, Australia
- The School of Life Sciences, University of Technology Sydney, Sydney, Australia
| | - Maurizio Labbate
- The School of Life Sciences, University of Technology Sydney, Sydney, Australia
| | - Justin R Seymour
- Climate Change Cluster (C3) Ocean Microbes Group, University of Technology Sydney, Sydney, Australia
| | - David Raftos
- Department of Biological Sciences, Macquarie University, Sydney, Australia
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19
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King WL, Siboni N, Williams NLR, Kahlke T, Nguyen KV, Jenkins C, Dove M, O'Connor W, Seymour JR, Labbate M. Variability in the Composition of Pacific Oyster Microbiomes Across Oyster Families Exhibiting Different Levels of Susceptibility to OsHV-1 μvar Disease. Front Microbiol 2019; 10:473. [PMID: 30915058 PMCID: PMC6421512 DOI: 10.3389/fmicb.2019.00473] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 02/22/2019] [Indexed: 11/13/2022] Open
Abstract
Oyster diseases are a major impediment to the profitability and growth of the oyster aquaculture industry. In recent years, geographically widespread outbreaks of disease caused by ostreid herpesvirus-1 microvariant (OsHV-1 μvar) have led to mass mortalities among Crassostrea gigas, the Pacific Oyster. Attempts to minimize the impact of this disease have been largely focused on breeding programs, and although these have shown some success in producing oyster families with reduced mortality, the mechanism(s) behind this protection is poorly understood. One possible factor is modification of the C. gigas microbiome. To explore how breeding for resistance to OsHV-1 μvar affects the oyster microbiome, we used 16S rRNA amplicon sequencing to characterize the bacterial communities associated with 35 C. gigas families, incorporating oysters with different levels of susceptibility to OsHV-1 μvar disease. The microbiomes of disease-susceptible families were significantly different to the microbiomes of disease-resistant families. OTUs assigned to the Photobacterium, Vibrio, Aliivibrio, Streptococcus, and Roseovarius genera were associated with low disease resistance. In partial support of this finding, qPCR identified a statistically significant increase of Vibrio-specific 16S rRNA gene copies in the low disease resistance families, possibly indicative of a reduced host immune response to these pathogens. In addition to these results, examination of the core microbiome revealed that each family possessed a small core community, with OTUs assigned to the Winogradskyella genus and the Bradyrhizobiaceae family consistent members across most disease-resistant families. This study examines patterns in the microbiome of oyster families exhibiting differing levels of OsHV-1 μvar disease resistance and reveals some key bacterial taxa that may provide a protective or detrimental role in OsHV-1 μvar disease outbreaks.
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Affiliation(s)
- William L King
- The School of Life Sciences, University of Technology Sydney, Ultimo, NSW, Australia.,Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Nachshon Siboni
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Nathan L R Williams
- The School of Life Sciences, University of Technology Sydney, Ultimo, NSW, Australia
| | - Tim Kahlke
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Khue Viet Nguyen
- The School of Life Sciences, University of Technology Sydney, Ultimo, NSW, Australia.,Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Cheryl Jenkins
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW, Australia
| | - Michael Dove
- NSW Department of Primary Industries, Port Stephens Fisheries Institute, Port Stephens, NSW, Australia
| | - Wayne O'Connor
- NSW Department of Primary Industries, Port Stephens Fisheries Institute, Port Stephens, NSW, Australia
| | - Justin R Seymour
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Maurizio Labbate
- The School of Life Sciences, University of Technology Sydney, Ultimo, NSW, Australia
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20
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King WL, Jenkins C, Go J, Siboni N, Seymour JR, Labbate M. Characterisation of the Pacific Oyster Microbiome During a Summer Mortality Event. Microb Ecol 2019; 77:502-512. [PMID: 29987529 DOI: 10.1007/s00248-018-1226-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Accepted: 07/02/2018] [Indexed: 06/08/2023]
Abstract
The Pacific oyster, Crassostrea gigas, is a key commercial species that is cultivated globally. In recent years, disease outbreaks have heavily impacted C. gigas stocks worldwide, with many losses incurred during summer. A number of infectious agents have been associated with these summer mortality events, including viruses (particularly Ostreid herpesvirus 1, OsHV-1) and bacteria; however, cases where no known aetiological agent can be identified are common. In this study, we examined the microbiome of disease-affected and disease-unaffected C. gigas during a 2013-2014 summer mortality event in Port Stephens (Australia) where known oyster pathogens including OsHV-1 were not detected. The adductor muscle microbiomes of 70 C. gigas samples across 12 study sites in the Port Stephens estuary were characterised using 16S rRNA (V1-V3 region) amplicon sequencing, with the aim of comparing the influence of spatial location and disease state on the oyster microbiome. Spatial location was found to be a significant determinant of the disease-affected oyster microbiome. Furthermore, microbiome comparisons between disease states identified a significant increase in rare operational taxonomic units (OTUs) belonging to Vibrio harveyi and an unidentified member of the Vibrio genus in the disease-affected microbiome. This is indicative of a potential role of Vibrio species in oyster disease and supportive of previous culture-based examination of this mortality event.
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Affiliation(s)
- William L King
- The School of Life Sciences, University of Technology Sydney, PO Box 123, Broadway, Sydney, NSW, 2007, Australia
- Climate Change Cluster, University of Technology Sydney, Sydney, NSW, Australia
| | - Cheryl Jenkins
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW, Australia
| | - Jeffrey Go
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW, Australia
| | - Nachshon Siboni
- Climate Change Cluster, University of Technology Sydney, Sydney, NSW, Australia
| | - Justin R Seymour
- Climate Change Cluster, University of Technology Sydney, Sydney, NSW, Australia
| | - Maurizio Labbate
- The School of Life Sciences, University of Technology Sydney, PO Box 123, Broadway, Sydney, NSW, 2007, Australia.
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King WL, Jenkins C, Seymour JR, Labbate M. Oyster disease in a changing environment: Decrypting the link between pathogen, microbiome and environment. Mar Environ Res 2019; 143:124-140. [PMID: 30482397 DOI: 10.1016/j.marenvres.2018.11.007] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 10/20/2018] [Accepted: 11/15/2018] [Indexed: 06/09/2023]
Abstract
Shifting environmental conditions are known to be important triggers of oyster diseases. The mechanism(s) behind these synergistic effects (interplay between host, environment and pathogen/s) are often not clear, although there is evidence that shifts in environmental conditions can affect oyster immunity, and pathogen growth and virulence. However, the impact of shifting environmental parameters on the oyster microbiome and how this affects oyster health and susceptibility to infectious pathogens remains understudied. In this review, we summarise the major diseases afflicting oysters with a focus on the role of environmental factors that can catalyse or amplify disease outbreaks. We also consider the potential role of the oyster microbiome in buffering or augmenting oyster disease outbreaks and suggest that a deeper understanding of the oyster microbiome, its links to the environment and its effect on oyster health and disease susceptibility, is required to develop new frameworks for the prevention and management of oyster diseases.
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Affiliation(s)
- William L King
- The School of Life Sciences, University of Technology Sydney, NSW, Australia; Climate Change Cluster, University of Technology Sydney, NSW, Australia
| | - Cheryl Jenkins
- Elizabeth Macarthur Institute, New South Wales Department of Primary Industries, Menangle, NSW, Australia
| | - Justin R Seymour
- Climate Change Cluster, University of Technology Sydney, NSW, Australia
| | - Maurizio Labbate
- The School of Life Sciences, University of Technology Sydney, NSW, Australia.
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Irga PJ, Armstrong B, King WL, Burchett M, Torpy FR. Correspondence Between Urban Bird Roosts and the Presence of Aerosolised Fungal Pathogens. Mycopathologia 2016; 181:689-99. [DOI: 10.1007/s11046-016-0013-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Accepted: 04/25/2016] [Indexed: 11/24/2022]
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Abstract
Many researchers have found that more college-age adults than would be expected fail Piaget's water-level task, with women failing more frequently than men. It has been hypothesized that differences in cognitive style may account for performance differences on the water-level task. In the present study, 27 male and 27 female architectural students and 27 male and 27 female liberal-arts students were assessed for their performance on both Piaget's Water-level Task and Witkin's Group Embedded Figures Test. No difference was found in performance of male and female architectural students on either task, but male liberal-arts students scored significantly higher than female liberal-arts students on both measures. A disembedding cognitive style predicted success on the water-level task for the architectural students but not for the liberal arts students.
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Affiliation(s)
- R E Hammer
- City College of New York, City University of New York, USA
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Abstract
Ruptured aneurysms of the ovarian artery are exceedingly rare. Five cases have been previously reported in the English-language literature, all occurred in the early postpartum period. The present report details another such case, the first, to my knowledge, to have been demonstrated by angiography or to have been treated nonoperatively.
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Affiliation(s)
- W L King
- Department of Surgery, North York General Hospital, Toronto, Ontario, Canada
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King WL, Hautaluoma JE. Comparison of Job Satisfaction, Life Satisfaction, and Performance of Overeducated and Other Workers. The Journal of Social Psychology 1987. [DOI: 10.1080/00224545.1987.9713727] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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26
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King WL, King MA. Writing your own paycheck. Contemp Adm Long Term Care 1982; 5:27-9. [PMID: 10298797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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King WL. Metastatic endometriosis in abdominal scars. Can J Surg 1979; 22:579. [PMID: 497932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The author presents two examples of metastatic endometriosis occurring in an abdominal scar. These case reports illustrate the two main theories of the pathogenesis of the condition: transportation and metaplasia. The diagnosis is straightforward in the classic case in which a painful mass fluctuates with the menstrual cycle, but a biopsy may be needed to confirm the diagnosis when the history is atypical. The treatment of choice, for those who require treatment, may be hormonal manipulation, surgery or irradiation, or a combination of these.
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Seegmiller BR, King WL. Relations between behavioral characteristics of infants, their mothers' behaviors, and performance on the Bayley Mental and Motor Scales. J Psychol 1975; 90:99-111. [PMID: 1151905 DOI: 10.1080/00223980.1975.9923931] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Bayley Mental scores were significantly related to several concurrent ratings of infant and maternal testroom behavior when firstborn black male infants were 14 months (N equals 49), 18 months (N equals 34), and 22 months of age ( equals 32). With increasing age, social responsiveness played a relatively less important role in successful performance, while object responsiveness became increasingly important. Bayley Motor scores were related to many fewer ratings than the Mental scores. Gross Muscle Coordination was related to performance at all three ages, and Energy ratings at two of the three ages. For both the Mental and Motor scores, fewer relationships were observed at the 18-month testings as compared to the 14 and 22-month testings. By 22 months, infants scoring higher on the Bayley Mental scale had mothers who were more highly involved with their child's achievement as judged by testroom behaviors.
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Johnson JK, King WL. Materials design requirements for implantable pacemakers. Biomater Med Devices Artif Organs 1974; 2:353-64. [PMID: 4462864 DOI: 10.3109/10731197409118605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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King WL, Seegmiller B. Performance of 14- to 22-month-old black, firstborn male infants on two tests of cognitive development: The Bayley scales and the Infant Psychological Development Scale. Dev Psychol 1973. [DOI: 10.1037/h0034333] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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King WL, Provan JL. Diagnosis and management of duodenal injuries. Can J Surg 1972; 15:269-75. [PMID: 5044128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
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King WL, Ersek RA, Rozelle LT, Petersen ED, Beisang A, Lillehei RC. Technique for predicting the effectiveness of aortic valve preservation methods. Surgery 1971; 69:863-9. [PMID: 5578446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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King WL. Rule learning and transfer as a function of age and stimulus structure. Child Dev 1968; 39:311-24. [PMID: 5645806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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Hitchins AD, King WL, Gould GW. Role of disulphide bonds in the resistance of Bacillus cereus spores to gamma irradiation and heat. J Appl Bacteriol 1966; 29:505-11. [PMID: 4962993 DOI: 10.1111/j.1365-2672.1966.tb03501.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Abstract
The illusion was obtained with artificial moons viewed against a luminous ceiling, and also with an imaginary ceiling induced by first showing a luminous ceiling and then removing it before the moons were introduced.
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Abstract
The perceived size of an afterimage varies with the part of the sky to which it is projected in a manner predictable from Emmert's Law and the appearance of the sky as a flattened dome. This effect is directly analogous to the moon illusion.
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