Publications by authors named "Robert Jackson"

456 Publications

Decadal changes in fire frequencies shift tree communities and functional traits.

Nat Ecol Evol 2021 Feb 25. Epub 2021 Feb 25.

Department of Earth System Science, Stanford University, Stanford, CA, USA.

Global change has resulted in chronic shifts in fire regimes. Variability in the sensitivity of tree communities to multi-decadal changes in fire regimes is critical to anticipating shifts in ecosystem structure and function, yet remains poorly understood. Here, we address the overall effects of fire on tree communities and the factors controlling their sensitivity in 29 sites that experienced multi-decadal alterations in fire frequencies in savanna and forest ecosystems across tropical and temperate regions. Fire had a strong overall effect on tree communities, with an average fire frequency (one fire every three years) reducing stem density by 48% and basal area by 53% after 50 years, relative to unburned plots. The largest changes occurred in savanna ecosystems and in sites with strong wet seasons or strong dry seasons, pointing to fire characteristics and species composition as important. Analyses of functional traits highlighted the impact of fire-driven changes in soil nutrients because frequent burning favoured trees with low biomass nitrogen and phosphorus content, and with more efficient nitrogen acquisition through ectomycorrhizal symbioses. Taken together, the response of trees to altered fire frequencies depends both on climatic and vegetation determinants of fire behaviour and tree growth, and the coupling between fire-driven nutrient losses and plant traits.
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http://dx.doi.org/10.1038/s41559-021-01401-7DOI Listing
February 2021

Global and regional drivers of land-use emissions in 1961-2017.

Nature 2021 01 27;589(7843):554-561. Epub 2021 Jan 27.

Department of Earth System Science, University of California, Irvine, Irvine, CA, USA.

Historically, human uses of land have transformed and fragmented ecosystems, degraded biodiversity, disrupted carbon and nitrogen cycles and added prodigious quantities of greenhouse gases (GHGs) to the atmosphere. However, in contrast to fossil-fuel carbon dioxide (CO) emissions, trends and drivers of GHG emissions from land management and land-use change (together referred to as 'land-use emissions') have not been as comprehensively and systematically assessed. Here we present country-, process-, GHG- and product-specific inventories of global land-use emissions from 1961 to 2017, we decompose key demographic, economic and technical drivers of emissions and we assess the uncertainties and the sensitivity of results to different accounting assumptions. Despite steady increases in population (+144 per cent) and agricultural production per capita (+58 per cent), as well as smaller increases in emissions per land area used (+8 per cent), decreases in land required per unit of agricultural production (-70 per cent) kept global annual land-use emissions relatively constant at about 11 gigatonnes CO-equivalent until 2001. After 2001, driven by rising emissions per land area, emissions increased by 2.4 gigatonnes CO-equivalent per decade to 14.6 gigatonnes CO-equivalent in 2017 (about 25 per cent of total anthropogenic GHG emissions). Although emissions intensity decreased in all regions, large differences across regions persist over time. The three highest-emitting regions (Latin America, Southeast Asia and sub-Saharan Africa) dominate global emissions growth from 1961 to 2017, driven by rapid and extensive growth of agricultural production and related land-use change. In addition, disproportionate emissions are related to certain products: beef and a few other red meats supply only 1 per cent of calories worldwide, but account for 25 per cent of all land-use emissions. Even where land-use change emissions are negligible or negative, total per capita CO-equivalent land-use emissions remain near 0.5 tonnes per capita, suggesting the current frontier of mitigation efforts. Our results are consistent with existing knowledge-for example, on the role of population and economic growth and dietary choice-but provide additional insight into regional and sectoral trends.
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http://dx.doi.org/10.1038/s41586-020-03138-yDOI Listing
January 2021

Multiple constraints cause positive and negative feedbacks limiting grassland soil CO efflux under CO enrichment.

Proc Natl Acad Sci U S A 2021 Jan 21;118(2). Epub 2020 Dec 21.

United States Department of Agriculture, Agricultural Research Service (USDA-ARS) Grassland, Soil, and Water Research Lab, Temple, TX 76502.

Terrestrial ecosystems are increasingly enriched with resources such as atmospheric CO that limit ecosystem processes. The consequences for ecosystem carbon cycling depend on the feedbacks from other limiting resources and plant community change, which remain poorly understood for soil CO efflux, J, a primary carbon flux from the biosphere to the atmosphere. We applied a unique CO enrichment gradient (250 to 500 µL L) for eight years to grassland plant communities on soils from different landscape positions. We identified the trajectory of J responses and feedbacks from other resources, plant diversity [effective species richness, exp(H)], and community change (plant species turnover). We found linear increases in J on an alluvial sandy loam and a lowland clay soil, and an asymptotic increase on an upland silty clay soil. Structural equation modeling identified CO as the dominant limitation on J on the clay soil. In contrast with theory predicting limitation from a single limiting factor, the linear J response on the sandy loam was reinforced by positive feedbacks from aboveground net primary productivity and exp(H), while the asymptotic J response on the silty clay arose from a net negative feedback among exp(H), species turnover, and soil water potential. These findings support a multiple resource limitation view of the effects of global change drivers on grassland ecosystem carbon cycling and highlight a crucial role for positive or negative feedbacks between limiting resources and plant community structure. Incorporating these feedbacks will improve models of terrestrial carbon sequestration and ecosystem services.
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http://dx.doi.org/10.1073/pnas.2008284117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7812833PMC
January 2021

Odour priming of a mosquito-specialist predator's vision-based detouring decisions.

Biochem Biophys Res Commun 2020 Dec 26. Epub 2020 Dec 26.

School of Biological Sciences, University of Canterbury, Private Bag, 4800, Christchurch, New Zealand; International Centre of Insect Physiology and Ecology, Thomas Odhiambo Campus, P.O. Box 30, Mbita Point, Kenya.

A capacity to execute long detours that are planned ahead of time has cognitive implications pertaining to reliance on internal representation. Here we investigate the detouring behaviour of Evarcha culicivora, an East African salticid spider that specializes at preying on blood-carrying mosquitoes. The findings from our experiments are the first evidence of a salticid making detouring plans based on whether the path chosen leads to more preferred instead of less preferred prey, as well as the first evidence of olfactory priming effects on motivation and selective attention in the context of detouring. Test spiders began on top of a starting platform from which, in some trials, they could view lures on top of two poles and, in some trials, the odour of blood-carrying mosquitoes was also present. When odour was present and prey were visible, significantly more test spiders took a detour and chose a pole than when only odour was present (prey not visible) or when prey were visible but odour was absent. When odour was present, test spiders also significantly more often chose the pole holding a blood-carrying mosquito instead of the pole holding another prey type.
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http://dx.doi.org/10.1016/j.bbrc.2020.12.005DOI Listing
December 2020

Ten-Year Outcomes of 1- and 2-Level Cervical Disc Arthroplasty From the Mobi-C Investigational Device Exemption Clinical Trial.

Neurosurgery 2021 02;88(3):497-505

The Core Institute, Phoenix, Arizona.

Background: Short- and mid-term studies have shown the effectiveness of cervical disc arthroplasty (CDA) to treat cervical disc degeneration.

Objective: To report the 10-yr outcomes of a multicenter experience with cervical arthroplasty for 1- and 2-level pathology.

Methods: This was a prospective study of patients treated with CDA at 1 or 2 contiguous levels using the Mobi-C® Cervical Disc (Zimmer Biomet). Following completion of the 7-yr Food and Drug Administration postapproval study, follow-up continued to 10 yr for consenting patients at 9 high-enrolling centers. Clinical and radiographic endpoints were collected out to 10 yr.

Results: At 10 yr, patients continued to have significant improvement over baseline Neck Disability Index (NDI), neck and arm pain, neurologic function, and segmental range of motion (ROM). NDI and pain outcomes at 10 yr were significantly improved from 7 yr. Segmental and global ROM and sagittal alignment also were maintained from 7 to 10 yr. Clinically relevant adjacent segment pathology was not significantly different between 7 and 10 yr. The incidence of motion restricting heterotopic ossification at 10 yr was not significantly different from 7 yr for 1-level (30.7% vs 29.6%) or 2-level (41.7% vs 39.2%) patients. Only 2 subsequent surgeries were reported after 7 yr.

Conclusion: Our results through 10 yr were comparable to 7-yr outcomes, demonstrating that CDA with Mobi-C continues to be a safe and effective surgical treatment for patients with 1- or 2-level cervical degenerative disc disease.
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http://dx.doi.org/10.1093/neuros/nyaa459DOI Listing
February 2021

The Potentials and Pitfalls of a Human Cervical Organoid Model Including Langerhans Cells.

Viruses 2020 12 1;12(12). Epub 2020 Dec 1.

Probe Development and Biomarker Exploration, Thunder Bay Regional Health Research Institute, Thunder Bay, ON P7B 6V4, Canada.

Three-dimensional cell culturing to capture a life-like experimental environment has become a versatile tool for basic and clinical research. Mucosal and skin tissues can be grown as "organoids" in a petri dish and serve a wide variety of research questions. Here, we report our experience with human cervical organoids which could also include an immune component, e.g., Langerhans cells. We employ commercially available human cervical keratinocytes and fibroblasts as well as a myeloid cell line matured and purified into langerin-positive Langerhans cells. These are then seeded on a layer of keratinocytes with underlying dermal equivalent. Using about 10-fold more than the reported number in healthy cervical tissue (1-3%), we obtain differentiated cervical epithelium after 14 days with ~1% being Langerhans cells. We provide a detailed protocol for interested researchers to apply the described "aseptic" organoid model for all sorts of investigations-with or without Langerhans cells.
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http://dx.doi.org/10.3390/v12121375DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7761032PMC
December 2020

Vesicular trafficking permits evasion of cGAS/STING surveillance during initial human papillomavirus infection.

PLoS Pathog 2020 11 30;16(11):e1009028. Epub 2020 Nov 30.

Cancer Biology Graduate Interdisciplinary Program, The University of Arizona, Tucson, Arizona, United States of America.

Oncogenic human papillomaviruses (HPVs) replicate in differentiating epithelium, causing 5% of cancers worldwide. Like most other DNA viruses, HPV infection initiates after trafficking viral genome (vDNA) to host cell nuclei. Cells possess innate surveillance pathways to detect microbial components or physiological stresses often associated with microbial infections. One of these pathways, cGAS/STING, induces IRF3-dependent antiviral interferon (IFN) responses upon detection of cytosolic DNA. Virion-associated vDNA can activate cGAS/STING during initial viral entry and uncoating/trafficking, and thus cGAS/STING is an obstacle to many DNA viruses. HPV has a unique vesicular trafficking pathway compared to many other DNA viruses. As the capsid uncoats within acidic endosomal compartments, minor capsid protein L2 protrudes across vesicular membranes to facilitate transport of vDNA to the Golgi. L2/vDNA resides within the Golgi lumen until G2/M, whereupon vesicular L2/vDNA traffics along spindle microtubules, tethering to chromosomes to access daughter cell nuclei. L2/vDNA-containing vesicles likely remain intact until G1, following nuclear envelope reformation. We hypothesize that this unique vesicular trafficking protects HPV from cGAS/STING surveillance. Here, we investigate cGAS/STING responses to HPV infection. DNA transfection resulted in acute cGAS/STING activation and downstream IFN responses. In contrast, HPV infection elicited minimal cGAS/STING and IFN responses. To determine the role of vesicular trafficking in cGAS/STING evasion, we forced premature viral penetration of vesicular membranes with membrane-perturbing cationic lipids. Such treatment renders a non-infectious trafficking-defective mutant HPV infectious, yet susceptible to cGAS/STING detection. Overall, HPV evades cGAS/STING by its unique subcellular trafficking, a property that may contribute to establishment of infection.
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http://dx.doi.org/10.1371/journal.ppat.1009028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7728285PMC
November 2020

3D Oral and Cervical Tissue Models for Studying Papillomavirus Host-Pathogen Interactions.

Curr Protoc Microbiol 2020 12;59(1):e129

School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona.

Human papillomavirus (HPV) infection occurs in differentiating epithelial tissues. Cancers caused by high-risk types (e.g., HPV16 and HPV18) typically occur at oropharyngeal and anogenital anatomical sites. The HPV life cycle is differentiation-dependent, requiring tissue culture methodology that is able to recapitulate the three-dimensional (3D) stratified epithelium. Here we report two distinct and complementary methods for growing differentiating epithelial tissues that mimic many critical morphological and biochemical aspects of in vivo tissue. The first approach involves growing primary human epithelial cells on top of a dermal equivalent consisting of collagen fibers and living fibroblast cells. When these cells are grown at the liquid-air interface, differentiation occurs and allows for epithelial stratification. The second approach uses a rotating wall vessel bioreactor. The low-fluid-shear microgravity environment inside the bioreactor allows the cells to use collagen-coated microbeads as a growth scaffold and self-assemble into 3D cellular aggregates. These approaches are applied to epithelial cells derived from HPV-positive and HPV-negative oral and cervical tissues. The second part of the article introduces potential downstream applications for these 3D tissue models. We describe methods that will allow readers to start successfully culturing 3D tissues from oral and cervical cells. These tissues have been used for microscopic visualization, scanning electron microscopy, and large omics-based studies to gain insights into epithelial biology, the HPV life cycle, and host-pathogen interactions. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Establishing human primary cell-derived 3D organotypic raft cultures Support Protocol 1: Isolation of epithelial cells from patient-derived tissues Support Protocol 2: Growth and maintenance of primary human epithelial cells in monolayer culture Support Protocol 3: PCR-based HPV screening of primary cell cultures Basic Protocol 2: Establishing human 3D cervical tissues using the rotating wall vessel bioreactor Support Protocol 4: Growth and maintenance of human A2EN cells in monolayer culture Support Protocol 5: Preparation of the slow-turning lateral vessel bioreactor Support Protocol 6: Preparation of Cytodex-3 microcarrier beads Basic Protocol 3: Histological assessment of 3D organotypic raft tissues Basic Protocol 4: Spatial analysis of protein expression in 3D organotypic raft cultures Basic Protocol 5: Immunofluorescence imaging of RWV-derived 3D tissues Basic Protocol 6: Ultrastructural visualization and imaging of RWV-derived 3D tissues Basic Protocol 7: Characterization of gene expression by RT-qPCR.
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http://dx.doi.org/10.1002/cpmc.129DOI Listing
December 2020

Soil organic carbon accumulation rates on Mediterranean abandoned agricultural lands.

Sci Total Environ 2021 Mar 5;759:143535. Epub 2020 Nov 5.

Institute of Environmental Science and Technology (ICTA), Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain; Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.

Secondary succession on abandoned agricultural lands can produce climate change mitigation co-benefits, such as soil carbon sequestration. However, the accumulation of soil organic carbon (SOC) in Mediterranean regions has been difficult to predict and is subject to multiple environmental and land management factors. Gains, losses, and no significant changes have all been reported. Here we compile chronosequence data (n = 113) from published studies and new field sites to assess the response of SOC to agricultural land abandonment in peninsular Spain. We found an overall SOC accumulation rate of +2.3% yr post-abandonment. SOC dynamics are highly variable and context-dependent. Minimal change occurs on abandoned cereal croplands compared to abandoned woody croplands (+4% yr). Accumulation is most prevalent within a Goldilocks climatic window of ~13-17 °C and ~450-900 mm precipitation, promoting >100% gains after three decades. Our secondary forest field sites accrued 40.8 Mg C ha (+172%) following abandonment and displayed greater SOC and N depth heterogeneity than natural forests demonstrating the long-lasting impact of agriculture. Although changes in regional climate and crop types abandoned will impact future carbon sequestration, abandonment remains a low-cost, long-term natural climate solution best incorporated in tandem with other multipurpose sustainable land management strategies.
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http://dx.doi.org/10.1016/j.scitotenv.2020.143535DOI Listing
March 2021

Genomic Characterisation of Mushroom Pathogenic Pseudomonads and Their Interaction with Bacteriophages.

Viruses 2020 11 10;12(11). Epub 2020 Nov 10.

School of Biological Sciences, Whiteknights Campus, University of Reading, Reading RG6 6AJ, UK.

Bacterial diseases of the edible white button mushroom caused by species cause a reduction in crop yield, resulting in considerable economic loss. We examined bacterial pathogens of mushrooms and bacteriophages that target them to understand the disease and opportunities for control. The genome encoded a single type III protein secretion system (T3SS), but contained the largest number of non-ribosomal peptide synthase (NRPS) genes, multimodular enzymes that can play a role in pathogenicity, including a putative tolaasin-producing gene cluster, a toxin causing blotch disease symptom. However, encoded the lowest number of NRPS and three putative T3SS while non-pathogenic sp. NS1 had intermediate numbers. Potential bacteriophage resistance mechanisms were identified in all three strains, but only NCPPB 2472 was observed to have a single Type I-F CRISPR/Cas system predicted to be involved in phage resistance. Three novel bacteriophages, NV1, ϕNV3, and NV6, were isolated from environmental samples. Bacteriophage NV1 and ϕNV3 had a narrow host range for specific mushroom pathogens, whereas phage NV6 was able to infect both mushroom pathogens. ϕNV3 and NV6 genomes were almost identical and differentiated within their T7-like tail fiber protein, indicating this is likely the major host specificity determinant. Our findings provide the foundations for future comparative analyses to study mushroom disease and phage resistance.
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http://dx.doi.org/10.3390/v12111286DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7696170PMC
November 2020

Arthropod Intelligence? The Case for .

Front Psychol 2020 14;11:568049. Epub 2020 Oct 14.

School of Psychology, Speech and Hearing, University of Canterbury, Christchurch, New Zealand.

Macphail's "null hypothesis," that there are no differences in intelligence, qualitative, or quantitative, between non-human vertebrates has been controversial. This controversy can be useful if it encourages interest in acquiring a detailed understanding of how non-human animals express flexible problem-solving capacity ("intelligence"), but limiting the discussion to vertebrates is too arbitrary. As an example, we focus here on , a spider with an especially intricate predatory strategy and a preference for other spiders as prey. We review research on pre-planned detours, expectancy violation, and a capacity to solve confinement problems where, in each of these three contexts, there is experimental evidence of innate cognitive capacities and reliance on internal representation. These cognitive capacities are related to, but not identical to, intelligence. When discussing intelligence, as when discussing cognition, it is more useful to envisage a continuum instead of something that is simply present or not; in other words, a continuum pertaining to flexible problem-solving capacity for "intelligence" and a continuum pertaining to reliance on internal representation for "cognition." When envisaging a continuum pertaining to intelligence, Daniel Dennett's notion of four Creatures (Darwinian, Skinnerian, Popperian, and Gregorian) is of interest, with the distinction between Skinnerian and Popperian Creatures being especially relevant when considering . When we consider these distinctions, a case can be made for being a Popperian Creature. Like Skinnerian Creatures, Popperian Creatures express flexible problem solving capacity, but the manner in which this capacity is expressed by Popperian Creatures is more distinctively cognitive.
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http://dx.doi.org/10.3389/fpsyg.2020.568049DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7591756PMC
October 2020

Methane Emissions from Abandoned Oil and Gas Wells in California.

Environ Sci Technol 2020 11 30;54(22):14617-14626. Epub 2020 Oct 30.

Department of Earth System Science, Stanford University, Stanford 94305, California, United States.

California hosts ∼124,000 abandoned and plugged (AP) oil and gas wells, ∼38,000 idle wells, and ∼63,000 active wells, whose methane (CH) emissions remain largely unquantified at levels below ∼2 kg CH h. We sampled 121 wells using two methods: a rapid mobile plume integration method (detection ∼0.5 g CH h) and a more sensitive static flux chamber (detection ∼1 × 10 g CH h). We measured small but detectable methane emissions from 34 of 97 AP wells (mean emission: 0.286 g CH h). In contrast, we found emissions from 11 of 17 idle wells-which are not currently producing (mean: 35.4 g CH h)-4 of 6 active wells (mean: 189.7 g CH h), and one unplugged well-an open casing with no infrastructure present (10.9 g CH h). Our results support previous findings that emissions from plugged wells are low but are more substantial from idle wells. In addition, our smaller sample of active wells suggests that their reported emissions are consistent with previous studies and deserve further attention. Due to limited access, we could not measure wells in most major active oil and gas fields in California; therefore, we recommend additional data collection from all types of wells but especially active and idle wells.
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http://dx.doi.org/10.1021/acs.est.0c05279DOI Listing
November 2020

Growth Hormone-Releasing Hormone in Lung Physiology and Pulmonary Disease.

Cells 2020 10 21;9(10). Epub 2020 Oct 21.

Research Service, Miami VAHS, Miami, FL 33125, USA.

Growth hormone-releasing hormone (GHRH) is secreted primarily from the hypothalamus, but other tissues, including the lungs, produce it locally. GHRH stimulates the release and secretion of growth hormone (GH) by the pituitary and regulates the production of GH and hepatic insulin-like growth factor-1 (IGF-1). Pituitary-type GHRH-receptors (GHRH-R) are expressed in human lungs, indicating that GHRH or GH could participate in lung development, growth, and repair. GHRH-R antagonists (i.e., synthetic peptides), which we have tested in various models, exert growth-inhibitory effects in lung cancer cells in vitro and in vivo in addition to having anti-inflammatory, anti-oxidative, and pro-apoptotic effects. One antagonist of the GHRH-R used in recent studies reviewed here, MIA-602, lessens both inflammation and fibrosis in a mouse model of bleomycin lung injury. GHRH and its peptide agonists regulate the proliferation of fibroblasts through the modulation of extracellular signal-regulated kinase (ERK) and Akt pathways. In addition to downregulating GH and IGF-1, GHRH-R antagonist MIA-602 inhibits signaling pathways relevant to inflammation, including p21-activated kinase 1-signal transducer and activator of transcription 3/nuclear factor-kappa B (PAK1-STAT3/NF-κB and ERK). MIA-602 induces fibroblast apoptosis in a dose-dependent manner, which is an effect that is likely important in antifibrotic actions. Taken together, the novel data reviewed here show that GHRH is an important peptide that participates in lung homeostasis, inflammation, wound healing, and cancer; and GHRH-R antagonists may have therapeutic potential in lung diseases.
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http://dx.doi.org/10.3390/cells9102331DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7589146PMC
October 2020

A comprehensive quantification of global nitrous oxide sources and sinks.

Nature 2020 10 7;586(7828):248-256. Epub 2020 Oct 7.

International Center for Climate and Global Change Research, School of Forestry and Wildlife Sciences, Auburn University, Auburn, AL, USA.

Nitrous oxide (NO), like carbon dioxide, is a long-lived greenhouse gas that accumulates in the atmosphere. Over the past 150 years, increasing atmospheric NO concentrations have contributed to stratospheric ozone depletion and climate change, with the current rate of increase estimated at 2 per cent per decade. Existing national inventories do not provide a full picture of NO emissions, owing to their omission of natural sources and limitations in methodology for attributing anthropogenic sources. Here we present a global NO inventory that incorporates both natural and anthropogenic sources and accounts for the interaction between nitrogen additions and the biochemical processes that control NO emissions. We use bottom-up (inventory, statistical extrapolation of flux measurements, process-based land and ocean modelling) and top-down (atmospheric inversion) approaches to provide a comprehensive quantification of global NO sources and sinks resulting from 21 natural and human sectors between 1980 and 2016. Global NO emissions were 17.0 (minimum-maximum estimates: 12.2-23.5) teragrams of nitrogen per year (bottom-up) and 16.9 (15.9-17.7) teragrams of nitrogen per year (top-down) between 2007 and 2016. Global human-induced emissions, which are dominated by nitrogen additions to croplands, increased by 30% over the past four decades to 7.3 (4.2-11.4) teragrams of nitrogen per year. This increase was mainly responsible for the growth in the atmospheric burden. Our findings point to growing NO emissions in emerging economies-particularly Brazil, China and India. Analysis of process-based model estimates reveals an emerging NO-climate feedback resulting from interactions between nitrogen additions and climate change. The recent growth in NO emissions exceeds some of the highest projected emission scenarios, underscoring the urgency to mitigate NO emissions.
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http://dx.doi.org/10.1038/s41586-020-2780-0DOI Listing
October 2020

Peak grain forecasts for the US High Plains amid withering waters.

Proc Natl Acad Sci U S A 2020 10 5;117(42):26145-26150. Epub 2020 Oct 5.

Department of Geography, Humboldt University of Berlin, 1248 Berlin, Germany.

Irrigated agriculture contributes 40% of total global food production. In the US High Plains, which produces more than 50 million tons per year of grain, as much as 90% of irrigation originates from groundwater resources, including the Ogallala aquifer. In parts of the High Plains, groundwater resources are being depleted so rapidly that they are considered nonrenewable, compromising food security. When groundwater becomes scarce, groundwater withdrawals peak, causing a subsequent peak in crop production. Previous descriptions of finite natural resource depletion have utilized the Hubbert curve. By coupling the dynamics of groundwater pumping, recharge, and crop production, Hubbert-like curves emerge, responding to the linked variations in groundwater pumping and grain production. On a state level, this approach predicted when groundwater withdrawal and grain production peaked and the lag between them. The lags increased with the adoption of efficient irrigation practices and higher recharge rates. Results indicate that, in Texas, withdrawals peaked in 1966, followed by a peak in grain production 9 y later. After better irrigation technologies were adopted, the lag increased to 15 y from 1997 to 2012. In Kansas, where these technologies were employed concurrently with the rise of irrigated grain production, this lag was predicted to be 24 y starting in 1994. In Nebraska, grain production is projected to continue rising through 2050 because of high recharge rates. While Texas and Nebraska had equal irrigated output in 1975, by 2050, it is projected that Nebraska will have almost 10 times the groundwater-based production of Texas.
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http://dx.doi.org/10.1073/pnas.2008383117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7584902PMC
October 2020

An improved conjugation method for Pseudomonas syringae.

J Microbiol Methods 2020 10 11;177:106025. Epub 2020 Aug 11.

Centre for Research in Bioscience, Faculty of Health and Applied Sciences, The University of the West of England, Frenchay Campus, Bristol BS16 1QY, UK; Harper Adams University, Newport, Shropshire TF10 8NB, UK. Electronic address:

In order to achieve saturating transposon mutagenesis of the genome of plant pathogenic strains of Pseudomonas syringae we needed to improve plasmid conjugation frequency. Manipulation of the growth stage of donor and recipient cells allowed the required increase in frequency and facilitated conjugation of otherwise recalcitrant strains.
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http://dx.doi.org/10.1016/j.mimet.2020.106025DOI Listing
October 2020

Large stocks of peatland carbon and nitrogen are vulnerable to permafrost thaw.

Proc Natl Acad Sci U S A 2020 08 10;117(34):20438-20446. Epub 2020 Aug 10.

Department of Earth and Environmental Sciences, Lehigh University, Bethlehem, PA 18015.

Northern peatlands have accumulated large stocks of organic carbon (C) and nitrogen (N), but their spatial distribution and vulnerability to climate warming remain uncertain. Here, we used machine-learning techniques with extensive peat core data ( > 7,000) to create observation-based maps of northern peatland C and N stocks, and to assess their response to warming and permafrost thaw. We estimate that northern peatlands cover 3.7 ± 0.5 million km and store 415 ± 150 Pg C and 10 ± 7 Pg N. Nearly half of the peatland area and peat C stocks are permafrost affected. Using modeled global warming stabilization scenarios (from 1.5 to 6 °C warming), we project that the current sink of atmospheric C (0.10 ± 0.02 Pg C⋅y) in northern peatlands will shift to a C source as 0.8 to 1.9 million km of permafrost-affected peatlands thaw. The projected thaw would cause peatland greenhouse gas emissions equal to ∼1% of anthropogenic radiative forcing in this century. The main forcing is from methane emissions (0.7 to 3 Pg cumulative CH-C) with smaller carbon dioxide forcing (1 to 2 Pg CO-C) and minor nitrous oxide losses. We project that initial CO-C losses reverse after ∼200 y, as warming strengthens peatland C-sinks. We project substantial, but highly uncertain, additional losses of peat into fluvial systems of 10 to 30 Pg C and 0.4 to 0.9 Pg N. The combined gaseous and fluvial peatland C loss estimated here adds 30 to 50% onto previous estimates of permafrost-thaw C losses, with southern permafrost regions being the most vulnerable.
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http://dx.doi.org/10.1073/pnas.1916387117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7456150PMC
August 2020

Editorial: Plants as Alternative Hosts for Human and Animal Pathogens - Second Edition.

Front Microbiol 2020 14;11:1439. Epub 2020 Jul 14.

The James Hutton Institute, Cell and Molecular Sciences, Dundee, United Kingdom.

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http://dx.doi.org/10.3389/fmicb.2020.01439DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7381135PMC
July 2020

Cherry picking by pseudomonads: After a century of research on canker, genomics provides insights into the evolution of pathogenicity towards stone fruits.

Plant Pathol 2020 Aug 6;69(6):962-978. Epub 2020 May 6.

Faculty of Natural Sciences Imperial College London London UK.

Bacterial canker disease is a major limiting factor in the growing of cherry and other species worldwide. At least five distinct clades within the bacterial species complex are known to be causal agents of the disease. The different pathogens commonly coexist in the field. Reducing canker is a challenging prospect as the efficacy of chemical controls and host resistance may vary against each of the diverse clades involved. Genomic analysis has revealed that the pathogens use a variable repertoire of virulence factors to cause the disease. Significantly, strains of . pv. possess more genes for toxin biosynthesis and fewer encoding type III effector proteins. There is also a shared pool of key effector genes present on mobile elements such as plasmids and prophages that may have roles in virulence. By contrast, there is evidence that absence or truncation of certain effector genes, such as , is characteristic of cherry pathogens. Here we highlight how recent research, underpinned by the earlier epidemiological studies, is allowing significant progress in our understanding of the canker pathogens. This fundamental knowledge, combined with emerging insights into host genetics, provides the groundwork for development of precise control measures and informed approaches to breed for disease resistance.
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http://dx.doi.org/10.1111/ppa.13189DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7386918PMC
August 2020

microRNA-seq of cartilage reveals an overabundance of miR-140-3p which contains functional isomiRs.

RNA 2020 11 13;26(11):1575-1588. Epub 2020 Jul 13.

Skeletal Research Group, Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, United Kingdom.

miR-140 is selectively expressed in cartilage. Deletion of the entire locus in mice results in growth retardation and early-onset osteoarthritis-like pathology; however, the relative contribution of miR-140-5p or miR-140-3p to the phenotype remains to be determined. An unbiased small RNA sequencing approach identified miR-140-3p as significantly more abundant (>10-fold) than miR-140-5p in human cartilage. Analysis of these data identified multiple miR-140-3p isomiRs differing from the miRBase annotation at both the 5' and 3' end, with >99% having one of two seed sequences (5' bases 2-8). Canonical (miR-140-3p.2) and shifted (miR-140-3p.1) seed isomiRs were overexpressed in chondrocytes and transcriptomics performed to identify targets. miR-140-3p.1 and miR-140-3p.2 significantly down-regulated 694 and 238 genes, respectively, of which only 162 genes were commonly down-regulated. IsomiR targets were validated using 3'UTR luciferase assays. miR-140-3p.1 targets were enriched within up-regulated genes in rib chondrocytes of -null mice and within down-regulated genes during human chondrogenesis. Finally, through imputing the expression of miR-140 from the expression of the host gene in 124 previously published data sets, an inverse correlation with miR-140-3p.1 predicted targets was identified. Together these data suggest the novel seed containing isomiR miR-140-3p.1 is more functional than original consensus miR-140-3p seed containing isomiR.
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http://dx.doi.org/10.1261/rna.075176.120DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7566571PMC
November 2020

Genotypic and phenotypic analyses reveal distinct population structures and ecotypes for sugar beet-associated in Oxford and Auckland.

Ecol Evol 2020 Jun 11;10(12):5963-5975. Epub 2020 May 11.

New Zealand Institute for Advanced Study Massey University Auckland New Zealand.

Fluorescent pseudomonads represent one of the largest groups of bacteria inhabiting the surfaces of plants, but their genetic composition is poorly understood. Here, we examined the population structure and diversity of fluorescent pseudomonads isolated from sugar beet grown at two geographic locations (Oxford, United Kingdom and Auckland, New Zealand). To seek evidence for niche adaptation, bacteria were sampled from three types of leaves (immature, mature, and senescent) and then characterized using a combination of genotypic and phenotypic analysis. We first performed multilocus sequence analysis (MLSA) of three housekeeping genes (, , and ) in a total of 152 isolates (96 from Oxford, 56 from Auckland). The concatenated sequences were grouped into 81 sequence types and 22 distinct operational taxonomic units (OTUs). Significant levels of recombination were detected, particularly for the Oxford isolates (rate of recombination to mutation (r/m) = 5.23 for the whole population). Subsequent ancestral analysis performed in STRUCTURE found evidence of six ancestral populations, and their distributions significantly differed between Oxford and Auckland. Next, their ability to grow on 95 carbon sources was assessed using the Biolog™ GN2 microtiter plates. A distance matrix was generated from the raw growth data () and subjected to multidimensional scaling (MDS) analysis. There was a significant correlation between substrate utilization profiles and MLSA genotypes. Both phenotypic and genotypic analyses indicated presence of a geographic structure for strains from Oxford and Auckland. Significant differences were also detected for MLSA genotypes between strains isolated from immature versus mature/senescent leaves. The fluorescent pseudomonads thus showed an ecotypic population structure, suggestive of adaptation to both geographic conditions and local plant niches.
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http://dx.doi.org/10.1002/ece3.6334DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7319117PMC
June 2020

Climate-driven risks to the climate mitigation potential of forests.

Science 2020 06;368(6497)

Department of Earth System Science, University of California Irvine, Irvine, CA 92697, USA.

Forests have considerable potential to help mitigate human-caused climate change and provide society with many cobenefits. However, climate-driven risks may fundamentally compromise forest carbon sinks in the 21st century. Here, we synthesize the current understanding of climate-driven risks to forest stability from fire, drought, biotic agents, and other disturbances. We review how efforts to use forests as natural climate solutions presently consider and could more fully embrace current scientific knowledge to account for these climate-driven risks. Recent advances in vegetation physiology, disturbance ecology, mechanistic vegetation modeling, large-scale ecological observation networks, and remote sensing are improving current estimates and forecasts of the risks to forest stability. A more holistic understanding and quantification of such risks will help policy-makers and other stakeholders effectively use forests as natural climate solutions.
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http://dx.doi.org/10.1126/science.aaz7005DOI Listing
June 2020

Agricultural acceleration of soil carbonate weathering.

Glob Chang Biol 2020 Oct 26;26(10):5988-6002. Epub 2020 Jul 26.

School of Earth, Energy, and Environmental Sciences, Stanford University, Stanford, CA, USA.

Soil carbonates (i.e., soil inorganic carbon or SIC) represent more than a quarter of the terrestrial carbon pool and are often considered to be relatively stable, with fluxes significant only on geologic timescales. However, given the importance of climatic water balance on SIC accumulation, we tested the hypothesis that increased soil water storage and transport resulting from cultivation may enhance dissolution of SIC, altering their local stock at decadal timescales. We compared SIC storage to 7.3 m depth in eight sites, each having paired plots of native vegetation and rain-fed croplands, and half the sites having additional irrigated cropland plots. Rain-fed and irrigated croplands had 328 and 730 Mg C/ha less SIC storage, respectively, compared to their native vegetation (grassland or woodland) pairs, and irrigated croplands had 402 Mg C/ha less than their rain-fed pairs (p < .0001). SIC contents were negatively correlated with estimated groundwater recharge, suggesting that dissolution and leaching may be responsible for SIC losses observed. Under croplands, the remaining SIC had more modern radiocarbon and a δ C composition that was closer to crop inputs than under native vegetation, suggesting that cultivation has led to faster turnover and incorporation of recent crop carbon into the SIC pool (p < .0001). The losses occurred just 30-100 years after land-use changes, indicating SIC stocks that were stable for millennia can rapidly adjust to increased soil water flows. Large SIC losses (194-242 Mg C/ha) also occurred below 4.9 m deep under irrigated croplands, with SIC losses lagging behind the downward-advancing wetting front by ~30 years, suggesting that even deep SIC were affected. These observations suggest that the vertical distribution of SIC in dry ecosystems is dynamic on decadal timescales, highlighting its potential role as a carbon sink or source to be examined in the context of land use and climate change.
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http://dx.doi.org/10.1111/gcb.15207DOI Listing
October 2020

Let's get americans back to work again.

Contemp Clin Trials Commun 2020 Jun 31;18:100559. Epub 2020 Mar 31.

Vice President of Scientific Affairs at Deerfield Management, USA.

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http://dx.doi.org/10.1016/j.conctc.2020.100559DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7260422PMC
June 2020

Pervasive shifts in forest dynamics in a changing world.

Science 2020 05;368(6494)

Earth and Environmental Sciences Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.

Forest dynamics arise from the interplay of environmental drivers and disturbances with the demographic processes of recruitment, growth, and mortality, subsequently driving biomass and species composition. However, forest disturbances and subsequent recovery are shifting with global changes in climate and land use, altering these dynamics. Changes in environmental drivers, land use, and disturbance regimes are forcing forests toward younger, shorter stands. Rising carbon dioxide, acclimation, adaptation, and migration can influence these impacts. Recent developments in Earth system models support increasingly realistic simulations of vegetation dynamics. In parallel, emerging remote sensing datasets promise qualitatively new and more abundant data on the underlying processes and consequences for vegetation structure. When combined, these advances hold promise for improving the scientific understanding of changes in vegetation demographics and disturbances.
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http://dx.doi.org/10.1126/science.aaz9463DOI Listing
May 2020

The spindle assembly checkpoint and speciation.

PeerJ 2020 11;8:e9073. Epub 2020 May 11.

Division of Pharmacy, University of Manchester, Manchester, United Kingdom.

A mechanism is proposed by which speciation may occur without the need to postulate geographical isolation of the diverging populations. Closely related species that occupy overlapping or adjacent ecological niches often have an almost identical genome but differ by chromosomal rearrangements that result in reproductive isolation. The mitotic spindle assembly checkpoint normally functions to prevent gametes with non-identical karyotypes from forming viable zygotes. Unless gametes from two individuals happen to undergo the same chromosomal rearrangement at the same place and time, a most improbable situation, there has been no satisfactory explanation of how such rearrangements can propagate. Consideration of the dynamics of the spindle assembly checkpoint suggest that chromosomal fission or fusion events may occur that allow formation of viable heterozygotes between the rearranged and parental karyotypes, albeit with decreased fertility. Evolutionary dynamics calculations suggest that if the resulting heterozygous organisms have a selective advantage in an adjoining or overlapping ecological niche from that of the parental strain, despite the reproductive disadvantage of the population carrying the altered karyotype, it may accumulate sufficiently that homozygotes begin to emerge. At this point the reproductive disadvantage of the rearranged karyotype disappears, and a single population has been replaced by two populations that are partially reproductively isolated. This definition of species as populations that differ from other, closely related, species by karyotypic changes is consistent with the classical definition of a species as a population that is capable of interbreeding to produce fertile progeny. Even modest degrees of reproductive impairment of heterozygotes between two related populations may lead to speciation by this mechanism, and geographical isolation is not necessary for the process.
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http://dx.doi.org/10.7717/peerj.9073DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7224227PMC
May 2020

Phage biocontrol to combat Pseudomonas syringae pathogens causing disease in cherry.

Microb Biotechnol 2020 09 8;13(5):1428-1445. Epub 2020 May 8.

School of Biological Sciences, University of Reading, Knight Building, Reading, RG6 6AJ, UK.

Bacterial canker is a major disease of Prunus species, such as cherry (Prunus avium). It is caused by Pseudomonas syringae pathovars, including P. syringae pv. syringae (Pss) and P. syringae pv. morsprunorum race 1 (Psm1) and race 2 (Psm2). Concerns over the environmental impact of, and the development of bacterial resistance to, traditional copper controls calls for new approaches to disease management. Bacteriophage-based biocontrol could provide a sustainable and natural alternative approach to combat bacterial pathogens. Therefore, seventy phages were isolated from soil, leaf and bark of cherry trees in six locations in the south east of England. Subsequently, their host range was assessed against strains of Pss, Psm1 and Psm2. While these phages lysed different Pss, Psm and some other P. syringae pathovar isolates, they did not infect beneficial bacteria such as Pseudomonas fluorescens. A subset of thirteen phages were further characterized by genome sequencing, revealing five distinct clades in which the phages could be clustered. No known toxins or lysogeny-associated genes could be identified. Using bioassays, selected phages could effectively reduce disease progression in vivo, both individually and in cocktails, reinforcing their potential as biocontrol agents in agriculture.
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http://dx.doi.org/10.1111/1751-7915.13585DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7415359PMC
September 2020

Anti-inflammatory effects of α-MSH through p-CREB expression in sarcoidosis like granuloma model.

Sci Rep 2020 04 29;10(1):7277. Epub 2020 Apr 29.

Section of Pulmonary, Miami VA Health System, Miami, FL, USA.

Lung inflammation due to sarcoidosis is characterized by a complex cascade of immunopathologic events, including leukocyte recruitment and granuloma formation. α-melanocyte stimulating hormone (α-MSH) is a melanocortin signaling peptide with anti-inflammatory properties. We aimed to evaluate the effects of α-MSH in a novel in vitro sarcoidosis model. An in vitro sarcoidosis-like granuloma model was developed by challenging peripheral blood mononuclear cells (PBMCs) derived from patients with confirmed treatment-naïve sarcoidosis with microparticles generated from Mycobacterium abscessus cell walls. Unchallenged PBMCsand developed granulomas were treated daily with 10 μM α-MSH or saline as control. Cytokine concentrations in supernatants of culture and in cell extracts were measured using Illumina multiplex Elisa and western blot, respectively. Gene expression was analyzed using RNA-Seq and RT-PCR. Protein secretion and gene expression of IL-7, IL-7R, IFN-γ, MC1R, NF-κB, phosphorylated NF-κB (p-NF-κB), MARCO, and p-CREB were measured with western blot and RNAseq. A significant increase in IL-7, IL-7R, and IFN-γ protein expression was found in developed granulomas comparing to microparticle unchallenged PBMCs. IL-7, IL-7R, and IFN-γ protein expression was significantly reduced in developed granulomas after exposure to α-MSH compared with saline treated granulomas. Compared with microparticle unchallenged PBMCs, total NF-κB and p-NF-κB were significantly increased in developed granulomas, while expression of p-CREB was not changed. Treatment with α-MSH promoted a significantly higher concentration of p-CREB in granulomas. The anti-inflammatory effects of α-MSH were blocked by specific p-CREB inhibition. α-MSH has anti-inflammatory properties in this in vitro granuloma model, which is an effect mediated by induction of phosphorylation of CREB.
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http://dx.doi.org/10.1038/s41598-020-64305-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7190699PMC
April 2020

Quantifying Methane Emissions from Natural Gas Water Heaters.

Environ Sci Technol 2020 05 15;54(9):5737-5745. Epub 2020 Apr 15.

Department of Earth System Science, Stanford University, Stanford, California 94305, United States.

Methane emissions from natural gas appliances remain the least characterized portion of the fossil-fuel supply chain. Here we examine water heaters from 64 northern California homes to (1) quantify methane emissions from natural gas leaks and incomplete combustion while off, turning on or off, and in steady-state operation from 35 homes; and (2) characterize daily usage patterns over ∼1-2 months per water heater to estimate activity factors from 46 homes. Individual tankless water heaters emitted 2390 [95% CI: 2250, 2540] g CH yr on average, 0.93% [0.87%, 0.99%] of their natural gas consumed, primarily from on/off pulses. Storage water heaters emitted 1400 [1240, 1560] g CH yr on average, 0.39% [0.34%, 0.43%] of their natural gas consumption. Despite higher methane emissions, tankless water heaters generate 29% less COe than storage water heaters because they use less energy to heat a unit of water. Scaling our measured emissions by the number of storage and tankless water heaters in the United States (56.8 and 1.2 million, respectively), water heaters overall emitted an estimated 82.3 [73.2, 91.5] Gg CH yr, 0.40% [0.35%, 0.44%] of all natural gas consumed by these appliances, comparable in percentage to the EPA's estimate of methane emissions from upstream natural gas production.
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http://dx.doi.org/10.1021/acs.est.9b07189DOI Listing
May 2020

Isolation, Characterisation and Experimental Evolution of Phage that Infect the Horse Chestnut Tree Pathogen, Pseudomonas syringae pv. aesculi.

Curr Microbiol 2020 Aug 19;77(8):1438-1447. Epub 2020 Mar 19.

School of Biological Sciences, University of Reading, Whiteknights, Reading, RG6 6AJ, UK.

Bleeding canker of horse chestnut trees is a bacterial disease, caused by the bacterium Pseudomonas syringae pv. aesculi, estimated to be present in ~ 50% of UK horse chestnut trees. Currently, the disease has no cure and tree removal can be a common method of reducing inoculum and preventing spread. One potential method of control could be achieved using naturally occurring bacteriophages infective to the causative bacterium. Bacteriophages were isolated from symptomatic and asymptomatic horse chestnut trees in three locations in the South East of England. The phages were found to be belonging to both the Myoviridae and Podoviridae families by RAPD PCR and transmission electron microscopy. Experimental coevolution was carried out to understand the dynamics of bacterial resistance and phage infection and to determine whether new infective phage genotypes would emerge. The phages exhibited different coevolution patterns with their bacterial hosts across time. This approach could be used to generate novel phages for use in biocontrol cocktails in an effort to reduce the potential emergence of bacterial resistance.
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http://dx.doi.org/10.1007/s00284-020-01952-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7334240PMC
August 2020