Pole-to-Pole Connections : Similarities between Arctic and Antarctic Microbiomes and Their Vulnerability to Environmental Change

Acknowledgments JK acknowledges the Carl Zeiss foundation for PhD funding, the Marie-Curie COFUND-BEIPD PostDoc fellowship for PostDoc funding, FNRS travel funding and the logistical and financial support by UNIS. JK and FK acknowledge the Natural Environment Research Council (NERC) Antarctic Funding Initiative AFI-CGS-70 (collaborative gearing scheme) and logistic support from the British Antarctic Survey (BAS) for field work in Antarctica. JK and CZ acknowledge the Excellence Initiative at the University of Tübingen funded by the German Federal Ministry of Education and Research and the German Research Foundation (DFG). FH, AV, and PB received funding from MetaHIT (HEALTH-F4-2007-201052), Microbios (ERC-AdG-502 669830) and the European Molecular Biology Laboratory (EMBL). We thank members of the Bork group at EMBL for helpful discussions. We acknowledge the EMBL Genomics Core Facility for sequencing support and Y. P. Yuan and the EMBL Information Technology Core Facility for support with high-performance computing and EMBL for financial support. PC is supported by NERC core funding to the BAS “Biodiversity, Evolution and Adaptation” Team. MB was funded by Helge Ax:son Johnsons Stiftelse and PUT1317. DRD acknowledges the DFG funded project DI698/18-1 Dietrich and the Marie Curie International Research Staff Exchange Scheme Fellowship (PIRSES-GA-2011-295223). Operations in the Canadian High Arctic were supported by the Natural Sciences and Engineering Research Council of Canada (NSERC), ArcticNet and the Polar Continental Shelf Program (PCSP). We are also grateful to the TOTAL Foundation (Paris) and the UK NERC (WP 4.3 of Oceans 2025 core funding to FCK at the Scottish Association for Marine Science) for funding the expedition to Baffin Island and within this context Olivier Dargent and Dr. Pieter van West for sample collection, and the Spanish Ministry of Science and Technology through project LIMNOPOLAR (POL200606635 and CGL2005-06549-C02-01/ANT to AQ as well as CGL2005-06549-C02-02/ANT to AC, the last of these co-financed by European FEDER funds). We are grateful for funding from the MASTS pooling initiative (The Marine Alliance for Science and Technology for Scotland), funded by the Scottish Funding Council (HR09011) and contributing institutions. Supplementary Material The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fevo.2017.00137/full#supplementary-materialPeer reviewedPublisher PD

Molecular genetics of herbicide resistance in Palmer amaranth (Amaranthus palmeri): metabolic tembotrione resistance and geographic origin of glyphosate resistance

2018 Spring.Includes bibliographical references.Palmer amaranth (Amaranthus palmeri) is a major weed in U.S. cotton and soybean production systems, partly because it evolved resistance to five different herbicide modes of action. Resistance to the 4-hydroxyphenylpyruvate dioxygenase (HPPD)-inhibitor tembotrione in a population from Nebraska (NER) is due to enhanced metabolism. This type of non-target-site resistance is especially troublesome because of its potential for cross-resistance. Tembotrione-susceptible (NES) and NER formed the same tembotrione metabolites but NER exhibited faster 4-hydroxylation followed by glycosylation. The T 50 value (time for 50% production of the maximum 4-hydroxylation product) was 4.9 and 11.9 h for NER and NES, respectively. Hydroxylation is typically catalyzed by cytochrome P450 monooxygenases (CYPs). Metabolism differences between NER and NES were most prominent under 28°C conditions and herbicide application at the four-leaf stage. An RNA-Seq transcriptome analysis was conducted with Pseudo-F 2 tembotrione-resistant and -susceptible individuals originating from three separate NER x NES crosses that were sampled before, six, and twelve h after treatment (HAT). Differential gene expression analysis identified CYP72A219 and CYP81E8 as strong candidates for metabolic resistance. The contigs were constitutively expressed in resistant plants, as were the contigs for several glycosyltransferases (GTs), oxidase, and glutathione-S-transferase (GST). Exposure to tembotrione further increased their expression in both resistant and susceptible plants. Originally native to the Southwest, A. palmeri has spread throughout the country. In 2004 a population was identified with resistance to glyphosate, a herbicide heavily relied on in modern no-tillage and transgenic glyphosate-resistant crop systems. Glyphosate resistance in the species is now highly prevalent in USA and was also discovered in Brazil in 2015. This was confirmed by species identification with a genetic marker, dose-response studies, shikimate accumulation assay, and EPSPS copy number assay. The Brazilian population was also resistant to sulfonylurea and imidazolinone ALS inhibitor herbicides conferred by two different alleles for target-site mutations in the ALS gene (W574L and S653N). The degree of genetic relatedness among eight different populations of glyphosate-resistant (GR) and –susceptible (GS) A. palmeri from various geographic regions in USA was investigated by analyzing patterns of phylogeography and diversity to ascertain whether resistance evolved independently or spread from outside to an Arizona locality (AZ-R). Shikimate accumulation and EPSPS genomic copy assays confirmed resistance or susceptibility. With a set of 1,351 single nucleotide polymorphisms (SNPs), discovered by genotyping-by-sequencing (GBS), UPGMA phylogenetic analysis, principal component analysis, Bayesian model-based clustering, and pairwise comparisons of genetic distances were conducted. A GR population from Tennessee and two GS populations from Georgia and Arizona were identified as genetically distinct while the remaining GS populations from Kansas, Arizona, and Nebraska clustered together with two GR populations from Arizona and Georgia. Within the latter group, AZ-R was most closely related to the GS populations from Kansas and Arizona followed by the GR population from Georgia. GR populations from Georgia and Tennessee were genetically distinct from each other. The data suggest the following two possible scenarios: either glyphosate resistance was introduced to the Arizona locality from the east, or resistance evolved independently in Arizona. Glyphosate resistance in the Georgia and Tennessee localities most likely evolved separately. Thus, modern farmers need to continue to diversify weed management practices and prevent seed dispersal to mitigate herbicide resistance evolution in A. palmeri

Omics Potential in Herbicide-Resistant Weed Management

The rapid development of omics technologies has drastically altered the way biologists conduct research. Basic plant biology and genomics have incorporated these technologies, while some challenges remain for use in applied biology. Weed science, on the whole, is still learning how to integrate omics technologies into the discipline; however, omics techniques are more frequently being implemented in new and creative ways to address basic questions in weed biology as well as the more practical questions of improving weed management. This has been especially true in the subdiscipline of herbicide resistance where important questions are the evolution and genetic basis of herbicide resistance. This review examines the advantages, challenges, potential solutions, and outlook for omics technologies in the discipline of weed science, with examples of how omics technologies will impact herbicide resistance studies and ultimately improve management of herbicide-resistant populations

Population Genetic Structure in Glyphosate-Resistant and -Susceptible Palmer Amaranth (Amaranthus palmeri) Populations Using Genotyping-by-sequencing (GBS)

Palmer amaranth (Amaranthus palmeri) is a major weed in United States cotton and soybean production systems. Originally native to the Southwest, the species has spread throughout the country. In 2004 a population of A. palmeri was identified with resistance to glyphosate, a herbicide heavily relied on in modern no-tillage and transgenic glyphosate-resistant (GR) crop systems. This project aims to determine the degree of genetic relatedness among eight different populations of GR and glyphosate-susceptible (GS) A. palmeri from various geographic regions in the United States by analyzing patterns of phylogeography and diversity to ascertain whether resistance evolved independently or spread from outside to an Arizona locality (AZ-R). Shikimic acid accumulation and EPSPS genomic copy assays confirmed resistance or susceptibility. With a set of 1,351 single nucleotide polymorphisms (SNPs), discovered by genotyping-by-sequencing (GBS), UPGMA phylogenetic analysis, principal component analysis, Bayesian model-based clustering, and pairwise comparisons of genetic distances were conducted. A GR population from Tennessee and two GS populations from Georgia and Arizona were identified as genetically distinct while the remaining GS populations from Kansas, Arizona, and Nebraska clustered together with two GR populations from Arizona and Georgia. Within the latter group, AZ-R was most closely related to the GS populations from Kansas and Arizona followed by the GR population from Georgia. GR populations from Georgia and Tennessee were genetically distinct from each other. No isolation by distance was detected and A. palmeri was revealed to be a species with high genetic diversity. The data suggest the following two possible scenarios: either glyphosate resistance was introduced to the Arizona locality from the east, or resistance evolved independently in Arizona. Glyphosate resistance in the Georgia and Tennessee localities most likely evolved separately. Thus, modern farmers need to continue to diversify weed management practices and prevent seed dispersal to mitigate herbicide resistance evolution in A. palmeri.USDA National Institute of Food and Agriculture, Hatch project [COL00719]; Colorado State University Libraries Open Access Research and Scholarship FundOpen access journal.This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Pole-to-Pole Connections : Similarities between Arctic and Antarctic Microbiomes and Their Vulnerability to Environmental Change

The global biogeography of microorganisms remains poorly resolved, which limits the current understanding of microbial resilience toward environmental changes. Using high-throughput 16S rRNA gene amplicon sequencing, we characterized the microbial diversity of terrestrial and lacustrine biofilms from the Arctic, Antarctic and temperate regions. Our analyses suggest that bacterial community compositions at the poles are more similar to each other than they are to geographically closer temperate habitats, with 32% of all operational taxonomic units (OTUs) co-occurring in both polar regions. While specific microbial taxa were confined to distinct regions, representing potentially endemic populations, the percentage of cosmopolitan taxa was higher in Arctic (43%) than in Antarctic samples (36%). The overlap in polar microbial OTUs may be explained by natural or anthropogenically-mediated dispersal in combination with environmental filtering. Current and future changing environmental conditions may enhance microbial invasion, establishment of cosmopolitan genotypes and loss of endemic taxa.publishe

Pole-to-Pole Connections: Similarities between Arctic and Antarctic Microbiomes and Their Vulnerability to Environmental Change

The global biogeography of microorganisms remains poorly resolved, which limits the current understanding of microbial resilience toward environmental changes. Using high-throughput 16S rRNA gene amplicon sequencing, we characterized the microbial diversity of terrestrial and lacustrine biofilms from the Arctic, Antarctic and temperate regions. Our analyses suggest that bacterial community compositions at the poles are more similar to each other than they are to geographically closer temperate habitats, with 32% of all operational taxonomic units (OTUs) co-occurring in both polar regions. While specific microbial taxa were confined to distinct regions, representing potentially endemic populations, the percentage of cosmopolitan taxa was higher in Arctic (43%) than in Antarctic samples (36%). The overlap in polar microbial OTUs may be explained by natural or anthropogenically-mediated dispersal in combination with environmental filtering. Current and future changing environmental conditions may enhance microbial invasion, establishment of cosmopolitan genotypes and loss of endemic taxa

Dataset associated with “Genomic‐based epidemiology reveals independent origins and gene flow of glyphosate resistance in Bassia scoparia populations across North America"

The dataset contains SSR marker data for the purpose of measuring population structure and relatedness among populations of Bassica scoparia (kochia) from across the western USA and Canada, collected from 2007-2015. The dataset also contains scripts to run the analyses described in the publication.Genomic-based epidemiology can provide insight into the origins and spread of herbicide resistance mechanisms in weeds. We used kochia (Bassia scoparia) populations resistant to the herbicide glyphosate from across western North America to test the alternative hypotheses that 1) a single EPSPS gene duplication event occurred initially in the Central Great Plains and then subsequently spread to all other geographical areas now exhibiting glyphosate-resistant kochia populations or that 2) gene duplication occurred multiple times in independent events in a case of parallel evolution. We used qPCR markers previously developed for measuring the structure of the EPSPS tandem duplication to investigate whether all glyphosate-resistant individuals had the same EPSPS repeat structure. We also investigated population structure using simple sequence repeat (SSR) markers to determine the relatedness of kochia populations from across the Central Great Plains, Northern Plains, and the Pacific Northwest. We found that the original EPSPS duplication genotype was predominant in the Central Great Plains where glyphosate resistance was first reported. We identified two additional EPSPS-duplication genotypes, one having geographic associations with the Northern Plains and the other to the Pacific Northwest. The EPSPS duplication genotype from the Pacific Northwest seems likely to represent a second, independent evolutionary origin of a resistance allele. We found evidence of gene flow across populations and a general lack of population structure. The results support at least two independent evolutionary origins of glyphosate resistance in kochia, followed by substantial and mostly geographically localized gene flow to spread the resistance alleles into diverse genetic backgrounds.The work was supported by USDA National Institute of Food and Agriculture grant number 2012-67013-19347 to PW, Western Sugar Joint Research Committee, Snake River Sugar Beet Research and Seed Alliance, Colorado Wheat Administrative Committee, USDA-NIFA Hatch project COL00783 at Colorado State University, and USDA National Institute of Food and Agriculture through the Western Integrated Pest Management Center, grant number 2018-70006-28881 to support the Western IPM Kochia Work Group

Dataset associated with “An in-frame deletion mutation in the degron tail of auxin co-receptor IAA2 confers resistance to the herbicide 2,4-D in Sisymbrium orientale”

Output files from protein docking analysis of the wild-type IAA2 protein and the mutant IAA2 version containing a nine amino acid deletion. These residues were used as docking parameters in HADDOCK 2.4 (https://wenmr.science.uu.nl/haddock2.4/). Docking calculations were performed under expert level, deactivating the DNA/RNA functions and activating the Surface Contact Restrains to enforce contact between the molecules. Degron residues KNNN of SoIAA2 were assigned semiflexible properties during docking whereas the shorter connection in SoIAA2Δ9 was not allowed to be flexible to preserve the structural integrity of PB1. The binding affinities of the SoIAA2/TIR1 and SoIAA2Δ9/TIR1 biological complexes were calculated using PRODIGY (https://bianca.science.uu.nl/prodigy/) for all top 4 poses from the best HADDOCK clusters. Plots are in .html format and protein models are in .pdb format. Files are in TGZ after gzip compression.The natural auxin indole-3-acetic acid (IAA) is a key regulator of many aspects of plant growth and development. Synthetic auxin herbicides such as 2,4-D mimic the effects of IAA by inducing strong auxinic signaling responses in plants. To determine the mechanism of 2,4-D resistance in a Sisymbrium orientale (Indian hedge mustard) weed population, we performed a transcriptome analysis of 2,4-D-resistant (R) and -susceptible (S) genotypes that revealed an in-frame 27-nucleotide deletion removing 9 amino acids in the degron tail (DT) of the auxin co-receptor Aux/IAA2 (SoIAA2). The deletion allele co-segregated with 2,4-D resistance in recombinant inbred lines. Further, this deletion was also detected in several 2,4-D resistant field populations of this species. Arabidopsis transgenic lines expressing the SoIAA2 mutant allele were resistant to 2,4-D and dicamba. The IAA2-DT deletion reduced binding to TIR1 in vitro with both natural and synthetic auxins, causing reduced association and increased dissociation rates. This novel mechanism of synthetic auxin herbicide resistance assigns a new in planta function to the DT region of this Aux/IAA co-receptor for its role in synthetic auxin binding kinetics and reveals a potential biotechnological approach to produce synthetic auxin resistant crops using gene editing.This work was supported in part by funding from Dow AgroSciences, by the Grains Research and Development Corporation – Australian Government, grant UA00158, the Brazilian governmental scholarship from the National Council for Scientific and Technological Development (CNPq - 207387/2014-1) to M.R.A.F., and by the EU MSCA-IF project CrysPINs (792329) in support of M.F.K. RN and MFK acknowledge equipment access at the Warwick Integrative Synthetic Biology Centre, which is funded by BB/M017982/1

An in-frame deletion mutation in the degron tail of auxin co-receptor IAA2 confers resistance to the herbicide 2,4-D in Sisymbrium orientale

The natural auxin indole-3-acetic acid (IAA) is a key regulator of many aspects of plant growth and development. Synthetic auxin herbicides such as 2,4-D mimic the effects of IAA by inducing strong auxinic-signaling responses in plants. To determine the mechanism of 2,4-D resistance in a Sisymbrium orientale (Indian hedge mustard) weed population, we performed a transcriptome analysis of 2,4-D-resistant (R) and -susceptible (S) genotypes that revealed an in-frame 27-nucleotide deletion removing nine amino acids in the degron tail (DT) of the auxin coreceptor Aux/IAA2 (SoIAA2). The deletion allele cosegregated with 2,4-D resistance in recombinant inbred lines. Further, this deletion was also detected in several 2,4-D-resistant field populations of this species. Arabidopsis transgenic lines expressing the SoIAA2 mutant allele were resistant to 2,4-D and dicamba. The IAA2-DT deletion reduced binding to TIR1 in vitro with both natural and synthetic auxins, causing reduced association and increased dissociation rates. This mechanism of synthetic auxin herbicide resistance assigns an in planta function to the DT region of this Aux/IAA coreceptor for its role in synthetic auxin binding kinetics and reveals a potential biotechnological approach to produce synthetic auxin-resistant crops using gene-editing