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Fielder H, Beale T, Jeger MJ, Oliver G, Parnell S, Szyniszewska AM, Taylor P, Cunniffe NJ. A Synoptic Review of Plant Disease Epidemics and Outbreaks Published in 2022. PHYTOPATHOLOGY 2024; 114:1717-1732. [PMID: 38723169 DOI: 10.1094/phyto-01-24-0042-rvw] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/02/2024]
Abstract
This scientometric study reviews the scientific literature and CABI distribution records published in 2022 to find evidence of major disease outbreaks and first reports of pathogens in new locations or on new hosts. This is the second time we have done this, and this study builds on our work documenting and analyzing reports from 2021. Pathogens with three or more articles identified in 2022 literature were Xylella fastidiosa, Bursaphelenchus xylophilus, Meloidogyne species complexes, 'Candidatus Liberibacter asiaticus', Raffaelea lauricola, Fusarium oxysporum formae specialis, and Puccinia graminis f. sp. tritici. Our review of CABI distribution records found 29 pathogens with confirmed first reports in 2022. Pathogens with four or more first reports were Meloidogyne species complexes, Pantoea ananatis, grapevine red globe virus, and Thekopsora minima. Analysis of the proportion of new distribution records from 2022 indicated that grapevine red globe virus, sweet potato chlorotic stunt virus, and 'Ca. Phytoplasma vitis' may have been actively spreading. As we saw last year, there was little overlap between the pathogens identified by reviewing scientific literature versus distribution records. We hypothesize that this lack of concordance is because of the unavoidable lag between first reports of the type reported in the CABI database of a pathogen in a new location and any subsequent major disease outbreaks being reported in the scientific literature, particularly because the latter depends on the journal policy on types of papers to be considered, whether the affected crop is major or minor, and whether the pathogen is of current scientific interest. Strikingly, too, there was also no overlap between species assessed to be actively spreading in this year's study and those identified last year. We hypothesize that this is because of inconsistencies in sampling coverage and effort over time and delays between the first arrival of a pathogen in a new location and its first report, particularly for certain classes of pathogens causing only minor or non-economically damaging symptoms, which may have been endemic for some time before being reported. In general, introduction of new pathogens and outbreaks of extant pathogens threaten food security and ecosystem services. Continued monitoring of these threats is essential to support phytosanitary measures intended to prevent pathogen introductions and management of threats within a country.
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Affiliation(s)
| | - Tim Beale
- CABI, Nosworthy Way, Wallingford, U.K
| | - Michael J Jeger
- Department of Life Sciences, Imperial College London, Silwood Park, Ascot, U.K
| | | | - Stephen Parnell
- School of Life Sciences, University of Warwick, Coventry, U.K
| | | | | | - Nik J Cunniffe
- Department of Plant Sciences, University of Cambridge, Cambridge, U.K
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Garner RE, Kraemer SA, Onana VE, Fradette M, Varin MP, Huot Y, Walsh DA. A genome catalogue of lake bacterial diversity and its drivers at continental scale. Nat Microbiol 2023; 8:1920-1934. [PMID: 37524802 DOI: 10.1038/s41564-023-01435-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 06/20/2023] [Indexed: 08/02/2023]
Abstract
Lakes are heterogeneous ecosystems inhabited by a rich microbiome whose genomic diversity is poorly defined. We present a continental-scale study of metagenomes representing 6.5 million km2 of the most lake-rich landscape on Earth. Analysis of 308 Canadian lakes resulted in a metagenome-assembled genome (MAG) catalogue of 1,008 mostly novel bacterial genomospecies. Lake trophic state was a leading driver of taxonomic and functional diversity among MAG assemblages, reflecting the responses of communities profiled by 16S rRNA amplicons and gene-centric metagenomics. Coupling the MAG catalogue with watershed geomatics revealed terrestrial influences of soils and land use on assemblages. Agriculture and human population density were drivers of turnover, indicating detectable anthropogenic imprints on lake bacteria at the continental scale. The sensitivity of bacterial assemblages to human impact reinforces lakes as sentinels of environmental change. Overall, the LakePulse MAG catalogue greatly expands the freshwater genomic landscape, advancing an integrative view of diversity across Earth's microbiomes.
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Affiliation(s)
- Rebecca E Garner
- Department of Biology, Concordia University, Montreal, Quebec, Canada
- Groupe de recherche interuniversitaire en limnologie, Montreal, Quebec, Canada
| | | | - Vera E Onana
- Department of Biology, Concordia University, Montreal, Quebec, Canada
- Groupe de recherche interuniversitaire en limnologie, Montreal, Quebec, Canada
| | - Maxime Fradette
- Département de géomatique appliquée, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Marie-Pierre Varin
- Département de géomatique appliquée, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Yannick Huot
- Groupe de recherche interuniversitaire en limnologie, Montreal, Quebec, Canada
- Département de géomatique appliquée, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - David A Walsh
- Department of Biology, Concordia University, Montreal, Quebec, Canada.
- Groupe de recherche interuniversitaire en limnologie, Montreal, Quebec, Canada.
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Oliva A, Onana VE, Garner RE, Kraemer SA, Fradette M, Walsh DA, Huot Y. Geospatial analysis reveals a hotspot of fecal bacteria in Canadian prairie lakes linked to agricultural non-point sources. WATER RESEARCH 2023; 231:119596. [PMID: 36653256 DOI: 10.1016/j.watres.2023.119596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 01/06/2023] [Accepted: 01/07/2023] [Indexed: 06/17/2023]
Abstract
Lakes are sentinels of environmental changes within their watersheds including those induced by a changing climate and anthropogenic activities. In particular, contamination originating from point or non-point sources (NPS) within watersheds might be reflected in changes in the bacterial composition of lake water. We assessed the abundance of potentially pathogenic bacteria (PPB) sampled in 413 lakes within 8 southern Canadian ecozones that represent a wide diversity of lakes and watershed land use. The study objectives were (1) to explore the diversity of PPB; (2) to build a fecal multi-indicator from a cluster of co-occurring PPB; and (3) to predict the fecal multi-indicator over thousands of lakes. We identified bacterial taxa based on 16S rRNA amplicon sequencing and clustered 33 PPB matching taxa in the Canadian ePATHogen database using a Sørensen dissimilarity index on binary data across the sampled lakes. One cluster contained Erysipelothrix, Desulfovibrio, Bacteroides, Vibrio and Acholeplasma and was related to the NPS fraction of agriculture and pasture within the watershed as its main driver and thus it was determined as the fecal multi-indicator. We subsequently developed a fecal multi-indicator predictive model across 200 212 southern Canadian lakes which explained 55.1% of the deviance. Mapping the predictions showed higher fecal multi-indicator abundances in the Prairies and Boreal Plains compared to the other ecozones. These results represent the first attempt to map a potential fecal multi-indicator at the continental scale, which may be further improved in the future. Lastly, the study demonstrates the capacity of a multi-disciplinary approach leveraging both datasets derived from remote sensing and DNA sequencing to provide mapping information for public health governmental policies.
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Affiliation(s)
- Anaïs Oliva
- Département de Géomatique Appliquée, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada; Département de Géomatique Appliquée, CARTEL - Centre d'Applications et de Recherche en TELédétection, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada; Département de Sciences Biologiques, GRIL - Groupement de Recherche Interuniversitaire en Limnologie, Université de Montréal, Campus MIL, Montréal, QC H3C 3J7, Canada.
| | - Vera E Onana
- Département de Sciences Biologiques, GRIL - Groupement de Recherche Interuniversitaire en Limnologie, Université de Montréal, Campus MIL, Montréal, QC H3C 3J7, Canada; Department of Biology, Concordia University, Montréal, QC H4B 1R6, Canada
| | - Rebecca E Garner
- Département de Sciences Biologiques, GRIL - Groupement de Recherche Interuniversitaire en Limnologie, Université de Montréal, Campus MIL, Montréal, QC H3C 3J7, Canada; Department of Biology, Concordia University, Montréal, QC H4B 1R6, Canada
| | - Susanne A Kraemer
- Département de Sciences Biologiques, GRIL - Groupement de Recherche Interuniversitaire en Limnologie, Université de Montréal, Campus MIL, Montréal, QC H3C 3J7, Canada; Department of Biology, Concordia University, Montréal, QC H4B 1R6, Canada; Environment and Climate Change Canada, Montréal, Canada; Department of Microbiology & Immunology, Genome Center, McGill University, Montreal, Canada
| | - Maxime Fradette
- Département de Géomatique Appliquée, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada; Département de Géomatique Appliquée, CARTEL - Centre d'Applications et de Recherche en TELédétection, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada; Département de Sciences Biologiques, GRIL - Groupement de Recherche Interuniversitaire en Limnologie, Université de Montréal, Campus MIL, Montréal, QC H3C 3J7, Canada
| | - David A Walsh
- Département de Sciences Biologiques, GRIL - Groupement de Recherche Interuniversitaire en Limnologie, Université de Montréal, Campus MIL, Montréal, QC H3C 3J7, Canada; Department of Biology, Concordia University, Montréal, QC H4B 1R6, Canada
| | - Yannick Huot
- Département de Géomatique Appliquée, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada; Département de Géomatique Appliquée, CARTEL - Centre d'Applications et de Recherche en TELédétection, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada; Département de Sciences Biologiques, GRIL - Groupement de Recherche Interuniversitaire en Limnologie, Université de Montréal, Campus MIL, Montréal, QC H3C 3J7, Canada
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Kraemer SA, Barbosa da Costa N, Oliva A, Huot Y, Walsh DA. A resistome survey across hundreds of freshwater bacterial communities reveals the impacts of veterinary and human antibiotics use. Front Microbiol 2022; 13:995418. [PMID: 36338036 PMCID: PMC9629221 DOI: 10.3389/fmicb.2022.995418] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 09/02/2022] [Indexed: 11/13/2022] Open
Abstract
Our decreasing ability to fight bacterial infections is a major health concern. It is arising due to the evolution of antimicrobial resistance (AMR) in response to the mis- and overuse of antibiotics in both human and veterinary medicine. Lakes integrate watershed processes and thus may act as receptors and reservoirs of antibiotic resistance genes (ARGs) introduced into the watershed by human activities. The resistome – the diversity of ARGs – under varying anthropogenic watershed pressures has been previously studied either focused on few select genes or few lakes. Here, we link the resistome of ~350 lakes sampled across Canada to human watershed activity, trophic status, as well as point sources of ARG pollution including wastewater treatment plants and hospitals in the watershed. A high percentage of the resistance genes detected was either unimpacted by human activity or highly prevalent in pristine lakes, highlighting the role of AMR in microbial ecology in aquatic systems, as well as a pool of genes available for potential horizontal gene transfer to pathogenic species. Nonetheless, watershed agricultural and pasture area significantly impacted the resistome. Moreover, the number of hospitals and the population density in a watershed, the volume of wastewater entering the lake, as well as the fraction of manure applied in the watershed as fertilizer significantly impacted ARG diversity. Together, these findings indicate that lake resistomes are regularly stocked with resistance genes evolved in the context of both veterinary and human antibiotics use and represent reservoirs of ARGs that require further monitoring.
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Affiliation(s)
- Susanne A. Kraemer
- Aquatic Contaminants Research Division, Environment and Climate Change Canada, Montreal, QC, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
- Department of Biology, Concordia University, Montreal, QC, Canada
- *Correspondence: Susanne A. Kraemer,
| | | | - Anais Oliva
- Department of Applied Geomatics, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Yannick Huot
- Department of Applied Geomatics, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - David A. Walsh
- Department of Biology, Concordia University, Montreal, QC, Canada
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Protist Diversity and Metabolic Strategy in Freshwater Lakes Are Shaped by Trophic State and Watershed Land Use on a Continental Scale. mSystems 2022; 7:e0031622. [PMID: 35730947 PMCID: PMC9426515 DOI: 10.1128/msystems.00316-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Protists play key roles in aquatic food webs as primary producers, predators, nutrient recyclers, and symbionts. However, a comprehensive view of protist diversity in freshwaters has been challenged by the immense environmental heterogeneity among lakes worldwide. We assessed protist diversity in the surface waters of 366 freshwater lakes across a north temperate to subarctic range covering nearly 8.4 million km2 of Canada. Sampled lakes represented broad gradients in size, trophic state, and watershed land use. Hypereutrophic lakes contained the least diverse and most distinct protist communities relative to nutrient-poor lakes. Greater taxonomic variation among eutrophic lakes was mainly a product of heterotroph and mixotroph diversity, whereas phototroph assemblages were more similar under high-nutrient conditions. Overall, local physicochemical factors, particularly ion and nutrient concentrations, elicited the strongest responses in community structure, far outweighing the effects of geographic gradients. Despite their contrasting distribution patterns, obligate phototroph and heterotroph turnover was predicted by an overlapping set of environmental factors, while the metabolic plasticity of mixotrophs may have made them less predictable. Notably, protist diversity was associated with variation in watershed soil pH and agricultural crop coverage, pointing to human impact on the land-water interface that has not been previously identified in studies on smaller scales. Our study exposes the importance of both within-lake and external watershed characteristics in explaining protist diversity and biogeography, critical information for further developing an understanding of how freshwater lakes and their watersheds are impacted by anthropogenic stressors. IMPORTANCE Freshwater lakes are experiencing rapid changes under accelerated anthropogenic stress and a warming climate. Microorganisms underpin aquatic food webs, yet little is known about how freshwater microbial communities are responding to human impact. Here, we assessed the diversity of protists and their myriad ecological roles in lakes varying in size across watersheds experiencing a range of land use pressures by leveraging data from a continental-scale survey of Canadian lakes. We found evidence of human impact on protist assemblages through an association with lake trophic state and extending to agricultural activity and soil characteristics in the surrounding watershed. Furthermore, trophic state appeared to explain the distributions of phototrophic and heterotrophic protists in contrasting ways. Our findings highlight the vulnerability of lake ecosystems to increased land use and the importance of assessing terrestrial interfaces to elucidate freshwater ecosystem dynamics.
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