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A Genus Definition for Bacteria and Archaea Based on a Standard Genome Relatedness IndexBarco, R. A.Garrity, G. M.Scott, J. J.Amend, J. P.Nealson, K. H.Emerson, D.2020DOI: info:10.1128/mBio.02475-19mBiov. 11No. 1Article e02475-19Article e02475-192150-7511
Barco, R. A., Garrity, G. M., Scott, J. J., Amend, J. P., Nealson, K. H., and Emerson, D. 2020. "A Genus Definition for Bacteria and Archaea Based on a Standard Genome Relatedness Index." mBio 11 (1):Article e02475-19.
ID: 154064
Type: article
Authors: Barco, R. A.; Garrity, G. M.; Scott, J. J.; Amend, J. P.; Nealson, K. H.; Emerson, D.
Keywords: STRI
Abstract: Genus assignment is fundamental in the characterization of microbes, yet there is currently no unambiguous way to demarcate genera solely using standard genomic relatedness indices. Here, we propose an approach to demarcate genera that relies on the combined use of the average nucleotide identity, genome alignment fraction, and the distinction between type- and non-type species. More than 3,500 genomes representing type strains of species from >850 genera of either bacterial or archaeal lineages were tested. Over 140 genera were analyzed in detail within the taxonomic context of order/family. Significant genomic differences between members of a genus and type species of other genera in the same order/family were conserved in 94% of the cases. Nearly 90% (92% if polyphyletic genera are excluded) of the type strains were classified in agreement with current taxonomy. The 448 type strains that need reclassification directly impact 33% of the genera analyzed in detail. The results provide a first line of evidence that the combination of genomic indices provides added resolution to effectively demarcate genera within the taxonomic framework that is currently based on the 16S rRNA gene. We also identify the emergence of natural breakpoints at the genome level that can further help in the circumscription of taxa, increasing the proportion of directly impacted genera to at least 43% and pointing at inaccuracies on the use of the 16S rRNA gene as a taxonomic marker, despite its precision. Altogether, these results suggest that genomic coherence is an emergent property of genera in Bacteria and ArchaeaIMPORTANCE In recent decades, the taxonomy of Bacteria and Archaea, and therefore genus designation, has been largely based on the use of a single ribosomal gene, the 16S rRNA gene, as a taxonomic marker. We propose an approach to delineate genera that excludes the direct use of the 16S rRNA gene and focuses on a standard genome relatedness index, the average nucleotide identity. Our findings are of importance to the microbiology community because the emergent properties of Bacteria and Archaea that are identified in this study will help assign genera with higher taxonomic resolution.
No 2. DADA2 WorkflowScott, Jarrod2020DOI: info:10.25573/DATA.12403865.V1The Smithsonian Institution
Scott, Jarrod. 2020. [Dataset] "No 2. DADA2 Workflow." Distributed by The Smithsonian Institution.
ID: 155991
Type: dataset
Authors: Scott, Jarrod
Keywords: Dataset; STRI
Abstract: Output files from the No 2. DADA2 Workflow page of the Bocas Hypoxia study. File names and descriptions:RUN01_read_changes.txt: Tracking changes in read counts (per sample) from the beginning to end of the DADA2 workflow.RUN02_read_changes.txt: Tracking changes in read counts (per sample) from the beginning to end of the DADA2 workflow.combo_pipeline.rdata: contains sequence and taxonomy tables from the DADA2 pipeline needed for subsequent analyses. To see the Objects, in R run load("combo_pipeline.rdata", verbose=TRUE)1) seqtab.1: Sequence table from Run01 before merging with Run02.2) seqtab.1: Sequence table from Run02 before merging with Run01.3) st.sum: merged sequence table before removing chimeras4) st.all: duplicate of st.sum5) seqtab: merged sequence table after removing chimeras6) tax_silva: Silva (v132) taxonomy table of seqtab7) tax_gg: GreenGenes taxonomy table of seqtab
Phyloseq workflow for microbial community analysisScott, Jarrod2020DOI: info:10.25573/DATA.11828700.V1The Smithsonian Institution
Scott, Jarrod. 2020. [Dataset] "Phyloseq workflow for microbial community analysis." Distributed by The Smithsonian Institution.
ID: 156054
Type: dataset
Authors: Scott, Jarrod
Keywords: Dataset; STRI
Abstract: Complete, fully reproducible phyloseq workflow for 16S rRNA microbiome analysis of the Bocas del Toro hypoxic event. Included are the HTML and Rmarkdown (.Rmd) files plus the output of the DADA2 pipeline in Rdata format which is the main input file for the phyloseq workflow.Sequences were filtered and dereplicated. Sequence variants were called and putative chimeras identified. Sequence variants were classified using SILVA and GreenGenes databases. File contains a sequence table and taxonomy table. We imported this file directly into phyloseq for community analysis.The directory contains all of the additional input files (mainly tables) necessary to run this workflow. Please note script will create a directory called R_OUTPUT wherever the .Rmd file was called from. This is where the script will store output files.
No. 0: Raw 16S rRNA fastq data files for Bocas hypoxia studyScott, Jarrod2020DOI: info:10.25573/DATA.11819745.V2The Smithsonian Institution
Scott, Jarrod. 2020. [Dataset] "No. 0: Raw 16S rRNA fastq data files for Bocas hypoxia study." Distributed by The Smithsonian Institution.
ID: 155919
Type: dataset
Authors: Scott, Jarrod
Keywords: Dataset; STRI
Abstract: This repository contains the RAW sequencing data for hypoxia study. Trimmed reads (with primers removed) are deposited at the European Nucleotide Archive, study accession number PRJEB36632 (ERP119845).Raw fastq data files are named using the root format RunQ_XYZ, where Q is the run number (1, or 2), X is the habitatype (Coral, Water, Sediment, Mat), YZ is the site (CC = Coral Cay; CR = Cayo Roldan), and in some cases a replicate number. So...Run01_CCR1_R2_001.fastq...corresponds to the reverse reads (R2) of a Cayo Roldan (CR) coral sample (C), replicate #1, Run 1.Raw fastq files are deposited here by Run.We used the PowerSoil® DNA Isolation Kit (MoBio) following the manufacturer's protocol to extract community DNA from each sample.Extracted DNA was sequenced on an Illumina MiSeq by Integrated Microbiome Resource at the Centre for Comparative Genomics and Evolutionary Bioinformatics (Dalhousie University).We targeted the V4-V5 hypervariable region using 515F (5′-GTGYCAGCMGCCGCGGTA) and 926R (5′-CCGYCAATTYMTTTRAGT). We collected 38 samples encompassing two sites and four habitatypesWe generated sequence data for all 38 samples. In the first run (Run01), all samples were sequenced and, due to lower than average yield, several were re-sequenced (Run02). This repo also contains the metadata files for submitting the trimmed data to the European Nucleotide Archive (ENA). Please do confuse this datasets with the dataset archived on the ENA (accession number PRJEB36632). In order to submit to the ENA, we had to first remove primers from the raw data and then upload the data along with these metadata files. The first publication concerns the water samples only. If you are interested in those samples only they are also available in the file.
Intestinal microbes: an axis of functional diversity among large marine consumersScott, Jarrod J.Adam, Thomas C.Duran, AlainBurkepile, Deron E.Rasher, Douglas B.2020DOI: info:10.1098/rspb.2019.2367Proceedings.Biological Sciencesv. 287No. 19241471-2954
Scott, Jarrod J., Adam, Thomas C., Duran, Alain, Burkepile, Deron E., and Rasher, Douglas B. 2020. "Intestinal microbes: an axis of functional diversity among large marine consumers." Proceedings.Biological Sciences 287 (1924):
ID: 155049
Type: article
Authors: Scott, Jarrod J.; Adam, Thomas C.; Duran, Alain; Burkepile, Deron E.; Rasher, Douglas B.
Keywords: STRI
Abstract: Microbes are ubiquitous throughout the world's oceans, yet the manner and extent of their influence on the ecology and evolution of large, mobile fauna remains poorly understood. Here, we establish the intestinal microbiome as a hidden, and potentially important, 'functional trait' of tropical herbivorous fishes-a group of large consumers critical to coral reef resilience. Using field observations, we demonstrate that five common Caribbean fish species display marked differences in where they feed and what they feed on. However, in addition to space use and feeding behaviour-two commonly measured functional traits-we find that interspecific trait differences are even more pronounced when considering the herbivore intestinal microbiome. Microbiome composition was highly species specific. Phylogenetic comparison of the dominant microbiome members to all known microbial taxa suggest that microbiomes are comprised of putative environmental generalists, animal-associates and fish specialists (resident symbionts), the latter of which mapped onto host phylogeny. These putative symbionts are most similar to-among all known microbes-those that occupy the intestines of ecologically and evolutionarily related herbivorous fishes in more distant ocean basins. Our findings therefore suggest that the intestinal microbiome may be an important functional trait among these large-bodied consumers.
Biological rejuvenation of iron oxides in bioturbated marine sedimentsBeam, Jacob P.Scott, Jarrod J.McAllister, Sean M.Chan, Clara S.McManus, JamesMeysman, Filip J. R.Emerson, David2018DOI: info:10.1038/s41396-017-0032-6The ISME journalv. 12138913941389–13941751-7362
Beam, Jacob P., Scott, Jarrod J., McAllister, Sean M., Chan, Clara S., McManus, James, Meysman, Filip J. R., and Emerson, David. 2018. "Biological rejuvenation of iron oxides in bioturbated marine sediments." The ISME journal 12:1389–1394.
ID: 145168
Type: article
Authors: Beam, Jacob P.; Scott, Jarrod J.; McAllister, Sean M.; Chan, Clara S.; McManus, James; Meysman, Filip J. R.; Emerson, David
Keywords: STRI
Abstract: The biogeochemical cycle of iron is intricately linked to numerous element cycles. Although biological processes that catalyze the reductive side of the iron cycle are established, little is known about microbial oxidative processes on iron cycling in sedimentary environments-resulting in the formation of iron oxides. Here we show that a potential source of sedimentary iron oxides originates from the metabolic activity of iron-oxidizing bacteria from the class Zetaproteobacteria, presumably enhanced by burrowing animals in coastal sediments. Zetaproteobacteria were estimated to be a global total of 1026 cells in coastal, bioturbated sediments, and predicted to annually produce 8 × 1015 g of Fe in sedimentary iron oxides-55 times larger than the annual flux of iron oxides deposited by rivers. These data suggest that iron-oxidizing Zetaproteobacteria are keystone organisms in marine sedimentary environments-despite their low numerical abundance-yet exert a disproportionate impact via the rejuvenation of iron oxides.
Biogeography of mutualistic fungi cultivated by leafcutter antsMueller, Ulrich G.Ishak, Heather D.Bruschi, Sofia M.Smith, Chad C.Herman, Jacob J.Solomon, Scott E.Mikheyev, Alexander S.Rabeling, ChristianScott, Jarrod J.Cooper, MichaelRodrigues, AndreOrtiz, AdrianaBrandão, Carlos R. F.Lattke, John E.Pagnocca, Fernando C.Rehner, Stephen A.Schultz, Ted R.Vasconcelos, Heraldo L.Adams, Rachelle M. M.Bollazzi, MartinClark, Rebecca M.Himler, Anna G.LaPolla, John S.Leal, Inara R.Johnson, Robert A.Roces, FlavioSosa-Calvo, JeffreyWirth, RainerBacci, Maurício2017DOI: info:10.1111/mec.14431Molecular Ecologyv. 26No. 24692169376921–69370962-1083
Mueller, Ulrich G., Ishak, Heather D., Bruschi, Sofia M., Smith, Chad C., Herman, Jacob J., Solomon, Scott E., Mikheyev, Alexander S., Rabeling, Christian, Scott, Jarrod J., Cooper, Michael, Rodrigues, Andre, Ortiz, Adriana, Brandão, Carlos R. F., Lattke, John E., Pagnocca, Fernando C., Rehner, Stephen A., Schultz, Ted R., Vasconcelos, Heraldo L., Adams, Rachelle M. M., Bollazzi, Martin, Clark, Rebecca M., Himler, Anna G., LaPolla, John S., Leal, Inara R., Johnson, Robert A. et al. 2017. "Biogeography of mutualistic fungi cultivated by leafcutter ants." Molecular Ecology 26 (24):6921–6937.
ID: 145063
Type: article
Authors: Mueller, Ulrich G.; Ishak, Heather D.; Bruschi, Sofia M.; Smith, Chad C.; Herman, Jacob J.; Solomon, Scott E.; Mikheyev, Alexander S.; Rabeling, Christian; Scott, Jarrod J.; Cooper, Michael; Rodrigues, Andre; Ortiz, Adriana; Brandão, Carlos R. F.; Lattke, John E.; Pagnocca, Fernando C.; Rehner, Stephen A.; Schultz, Ted R.; Vasconcelos, Heraldo L.; Adams, Rachelle M. M.; Bollazzi, Martin; Clark, Rebecca M.; Himler, Anna G.; LaPolla, John S.; Leal, Inara R.; Johnson, Robert A.; Roces, Flavio; Sosa-Calvo, Jeffrey; Wirth, Rainer; Bacci, Maurício
Keywords: NH-Entomology; NMNH
Convergent Bacterial Microbiotas in the Fungal Agricultural Systems of InsectsAylward, Frank O.Suen, GarretBiedermann, Peter H. W.Adams, Aaron S.Scott, Jarrod J.Malfatti, Stephanie A.del Rio, Tijana GlavinaTringe, Susannah G.Poulsen, MichaelRaffa, Kenneth F.Klepzig, Kier D.Currie, Cameron R.2014DOI: info:10.1128/mBio.02077-14mBiov. 5No. 62150-7511
Aylward, Frank O., Suen, Garret, Biedermann, Peter H. W., Adams, Aaron S., Scott, Jarrod J., Malfatti, Stephanie A., del Rio, Tijana Glavina, Tringe, Susannah G., Poulsen, Michael, Raffa, Kenneth F., Klepzig, Kier D., and Currie, Cameron R. 2014. "Convergent Bacterial Microbiotas in the Fungal Agricultural Systems of Insects." mBio 5 (6):
ID: 132936
Type: article
Authors: Aylward, Frank O.; Suen, Garret; Biedermann, Peter H. W.; Adams, Aaron S.; Scott, Jarrod J.; Malfatti, Stephanie A.; del Rio, Tijana Glavina; Tringe, Susannah G.; Poulsen, Michael; Raffa, Kenneth F.; Klepzig, Kier D.; Currie, Cameron R.
Keywords: fellow; STRI; student
Abstract: The ability to cultivate food is an innovation that has produced some of the most successful ecological strategies on the planet. Although most well recognized in humans, where agriculture represents a defining feature of civilization, species of ants, beetles, and termites have also independently evolved symbioses with fungi that they cultivate for food. Despite occurring across divergent insect and fungal lineages, the fungivorous niches of these insects are remarkably similar, indicating convergent evolution toward this successful ecological strategy. Here, we characterize the microbiota of ants, beetles, and termites engaged in nutritional symbioses with fungi to define the bacterial groups associated with these prominent herbivores and forest pests. Using culture-independent techniques and the in silico reconstruction of 37 composite genomes of dominant community members, we demonstrate that different insect-fungal symbioses that collectively shape ecosystems worldwide have highly similar bacterial microbiotas comprised primarily of the genera Enterobacter, Rahnella, and Pseudomonas. Although these symbioses span three orders of insects and two phyla of fungi, we show that they are associated with bacteria sharing high whole-genome nucleotide identity. Due to the fine-scale correspondence of the bacterial microbiotas of insects engaged in fungal symbioses, our findings indicate that this represents an example of convergence of entire host-microbe complexes. IMPORTANCE The cultivation of fungi for food is a behavior that has evolved independently in ants, beetles, and termites and has enabled many species of these insects to become ecologically important and widely distributed herbivores and forest pests. Although the primary fungal cultivars of these insects have been studied for decades, comparatively little is known of their bacterial microbiota. In this study, we show that diverse fungus-growing insects are associated with a common bacterial community composed of the same dominant members. Furthermore, by demonstrating that many of these bacteria have high whole-genome similarity across distantly related insect hosts that reside thousands of miles apart, we show that these bacteria are an important and underappreciated feature of diverse fungus-growing insects. Because of the similarities in the agricultural lifestyles of these insects, this is an example of convergence between both the life histories of the host insects and their symbiotic microbiota.
Metagenomic and metaproteomic insights into bacterial communities in leaf-cutter ant fungus gardensAylward, Frank O.Burnum, Kristin E.Scott, Jarrod J.Suen, GarretTringe, Susannah G.Adams, Sandra M.Barry, Kerrie W.Nicora , Carrie D.Piehowski, Paul D.Purvine, Samuel O.Starrett, Gabriel J.Goodwin, Lynne A.Smith, Richard D.Lipton, Mary S.Currie, Cameron R.2012DOI: info:10.1038/ismej.2012.10The ISME Journalv. 6No. 9168817011688–17011751-7362
Aylward, Frank O., Burnum, Kristin E., Scott, Jarrod J., Suen, Garret, Tringe, Susannah G., Adams, Sandra M., Barry, Kerrie W., Nicora , Carrie D., Piehowski, Paul D., Purvine, Samuel O., Starrett, Gabriel J., Goodwin, Lynne A., Smith, Richard D., Lipton, Mary S., and Currie, Cameron R. 2012. "Metagenomic and metaproteomic insights into bacterial communities in leaf-cutter ant fungus gardens." The ISME Journal 6 (9):1688–1701.
ID: 112937
Type: article
Authors: Aylward, Frank O.; Burnum, Kristin E.; Scott, Jarrod J.; Suen, Garret; Tringe, Susannah G.; Adams, Sandra M.; Barry, Kerrie W.; Nicora , Carrie D.; Piehowski, Paul D.; Purvine, Samuel O.; Starrett, Gabriel J.; Goodwin, Lynne A.; Smith, Richard D.; Lipton, Mary S.; Currie, Cameron R.
Keywords: STRI
Abstract: Herbivores gain access to nutrients stored in plant biomass largely by harnessing the metabolic activities of microbes. Leaf-cutter ants of the genus Atta are a hallmark example; these dominant neotropical herbivores cultivate symbiotic fungus gardens on large quantities of fresh plant forage. As the external digestive system of the ants, fungus gardens facilitate the production and sustenance of millions of workers. Using metagenomic and metaproteomic techniques, we characterize the bacterial diversity and physiological potential of fungus gardens from two species of Atta. Our analysis of over 1.2 Gbp of community metagenomic sequence and three 16S pyrotag libraries reveals that in addition to harboring the dominant fungal crop, these ecosystems contain abundant populations of Enterobacteriaceae, including the genera Enterobacter, Pantoea, Klebsiella, Citrobacter and Escherichia. We show that these bacterial communities possess genes associated with lignocellulose degradation and diverse biosynthetic pathways, suggesting that they play a role in nutrient cycling by converting the nitrogen-poor forage of the ants into B-vitamins, amino acids and other cellular components. Our metaproteomic analysis confirms that bacterial glycosyl hydrolases and proteins with putative biosynthetic functions are produced in both field-collected and laboratory-reared colonies. These results are consistent with the hypothesis that fungus gardens are specialized fungus-bacteria communities that convert plant material into energy for their ant hosts. Together with recent investigations into the microbial symbionts of vertebrates, our work underscores the importance of microbial communities in the ecology and evolution of herbivorous metazoans. The ISME Journal (2012) 6, 1688-1701; doi:10.1038/ismej.2012.10; published online 1 March 2012 Subject Category: integrated genomics and post-genomics approaches in microbial ecology
The Genome Sequence of the Leaf-Cutter Ant Atta cephalotes Reveals Insights into Its Obligate Symbiotic LifestyleSuen, GarretTeiling, ClotildeLi, LewynHolt, CarsonAbouheif, EhabBornberg-Bauer, ErichBouffard, PascalCaldera, Eric J.Cash, ElizabethCavanaugh, AmyDenas, OlgertElhaik, EranFave, Marie-JulieGadau, JuergenGibson, Joshua D.Graur, DanGrubbs, Kirk J.Hagen, Darren E.Harkins, Timothy T.Helmkampf, MartinHu, HaoJohnson, Brian R.Kim, JayMarsh, Sarah E.Moeller, Joseph A.Munoz-Torres, Monica C.Murphy, Marguerite C.Naughton, Meredith C.Nigam, SurabhiOverson, RickRajakumar, RajendhranReese, Justin T.Scott, Jarrod J.Smith, Chris R.Tao, ShuTsutsui, Neil D.Viljakainen, LumiWissler, LotharYandell, Mark D.Zimmer, FabianTaylor, JamesSlater, Steven C.Clifton, Sandra W.Warren, Wesley C.Elsik, Christine G.Smith, Christopher D.Weinstock, George M.Gerardo, Nicole M.Currie, Cameron Robert2011DOI: info:10.1371/journal.pgen.1002007Plos Geneticsv. 7No. 2e1002007e1002007e1002007–e10020071553-7390
Suen, Garret, Teiling, Clotilde, Li, Lewyn, Holt, Carson, Abouheif, Ehab, Bornberg-Bauer, Erich, Bouffard, Pascal, Caldera, Eric J., Cash, Elizabeth, Cavanaugh, Amy, Denas, Olgert, Elhaik, Eran, Fave, Marie-Julie, Gadau, Juergen, Gibson, Joshua D., Graur, Dan, Grubbs, Kirk J., Hagen, Darren E., Harkins, Timothy T., Helmkampf, Martin, Hu, Hao, Johnson, Brian R., Kim, Jay, Marsh, Sarah E., Moeller, Joseph A. et al. 2011. "The Genome Sequence of the Leaf-Cutter Ant Atta cephalotes Reveals Insights into Its Obligate Symbiotic Lifestyle." Plos Genetics 7 (2):e1002007–e1002007.
ID: 99182
Type: article
Authors: Suen, Garret; Teiling, Clotilde; Li, Lewyn; Holt, Carson; Abouheif, Ehab; Bornberg-Bauer, Erich; Bouffard, Pascal; Caldera, Eric J.; Cash, Elizabeth; Cavanaugh, Amy; Denas, Olgert; Elhaik, Eran; Fave, Marie-Julie; Gadau, Juergen; Gibson, Joshua D.; Graur, Dan; Grubbs, Kirk J.; Hagen, Darren E.; Harkins, Timothy T.; Helmkampf, Martin; Hu, Hao; Johnson, Brian R.; Kim, Jay; Marsh, Sarah E.; Moeller, Joseph A.; Munoz-Torres, Monica C.; Murphy, Marguerite C.; Naughton, Meredith C.; Nigam, Surabhi; Overson, Rick; Rajakumar, Rajendhran; Reese, Justin T.; Scott, Jarrod J.; Smith, Chris R.; Tao, Shu; Tsutsui, Neil D.; Viljakainen, Lumi; Wissler, Lothar; Yandell, Mark D.; Zimmer, Fabian; Taylor, James; Slater, Steven C.; Clifton, Sandra W.; Warren, Wesley C.; Elsik, Christine G.; Smith, Christopher D.; Weinstock, George M.; Gerardo, Nicole M.; Currie, Cameron Robert
Keywords: STRI
Abstract: Leaf-cutter ants are one of the most important herbivorous insects in the Neotropics, harvesting vast quantities of fresh leaf material. The ants use leaves to cultivate a fungus that serves as the colony's primary food source. This obligate ant-fungus mutualism is one of the few occurrences of farming by non-humans and likely facilitated the formation of their massive colonies. Mature leaf-cutter ant colonies contain millions of workers ranging in size from small garden tenders to large soldiers, resulting in one of the most complex polymorphic caste systems within ants. To begin uncovering the genomic underpinnings of this system, we sequenced the genome of Atta cephalotes using 454 pyrosequencing. One prediction from this ant's lifestyle is that it has undergone genetic modifications that reflect its obligate dependence on the fungus for nutrients. Analysis of this genome sequence is consistent with this hypothesis, as we find evidence for reductions in genes related to nutrient acquisition. These include extensive reductions in serine proteases (which are likely unnecessary because proteolysis is not a primary mechanism used to process nutrients obtained from the fungus), a loss of genes involved in arginine biosynthesis (suggesting that this amino acid is obtained from the fungus), and the absence of a hexamerin (which sequesters amino acids during larval development in other insects). Following recent reports of genome sequences from other insects that engage in symbioses with beneficial microbes, the A. cephalotes genome provides new insights into the symbiotic lifestyle of this ant and advances our understanding of host-microbe symbioses.
Monoculture of Leafcutter Ant GardensMueller, Ulrich G.Scott, Jarrod J.Ishak, Heather D.Cooper, MichaelRodrigues, Andre2010DOI: info:10.1371/journal.pone.0012668Plos Onev. 5No. 9e12668e126681932-6203
Mueller, Ulrich G., Scott, Jarrod J., Ishak, Heather D., Cooper, Michael, and Rodrigues, Andre. 2010. "Monoculture of Leafcutter Ant Gardens." Plos One 5 (9):e12668.
ID: 92604
Type: article
Authors: Mueller, Ulrich G.; Scott, Jarrod J.; Ishak, Heather D.; Cooper, Michael; Rodrigues, Andre
Keywords: STRI
Abstract: Background: Leafcutter ants depend on the cultivation of symbiotic Attamyces fungi for food, which are thought to be grown by the ants in single-strain, clonal monoculture throughout the hundreds to thousands of gardens within a leafcutter nest. Monoculture eliminates cultivar-cultivar competition that would select for competitive fungal traits that are detrimental to the ants, whereas polyculture of several fungi could increase nutritional diversity and disease resistance of genetically variable gardens. Methodology/Principal Findings: Using three experimental approaches, we assessed cultivar diversity within nests of Atta leafcutter ants, which are most likely among all fungus-growing ants to cultivate distinct cultivar genotypes per nest because of the nests' enormous sizes (up to 5000 gardens) and extended lifespans (10-20 years). In Atta texana and in A. cephalotes, we resampled nests over a 5-year period to test for persistence of resident cultivar genotypes within each nest, and we tested for genetic differences between fungi from different nest sectors accessed through excavation. In A. texana, we also determined the number of Attamyces cells carried as a starter inoculum by a dispersing queens (minimally several thousand Attamyces cells), and we tested for genetic differences between Attamyces carried by sister queens dispersing from the same nest. Except for mutational variation arising during clonal Attamyces propagation, DNA fingerprinting revealed no evidence for fungal polyculture and no genotype turnover during the 5-year surveys. Conclusions/Significance: Atta leafcutter ants can achieve stable, fungal monoculture over many years. Mutational variation emerging within an Attamyces monoculture could provide genetic diversity for symbiont choice (gardening biases of the ants favoring specific mutational variants), an analog of artificial selection.
Microbial community structure of leaf-cutter ant fungus gardens and refuse dumpsScott, Jarrod J.Budsberg, Kevin J.Suen, GarretWixon, Devin L.Balser, Teri C.Currie, Cameron Robert2010PLoS ONEv. 5No. 3e9922e99221932-6203
Scott, Jarrod J., Budsberg, Kevin J., Suen, Garret, Wixon, Devin L., Balser, Teri C., and Currie, Cameron Robert. 2010. "Microbial community structure of leaf-cutter ant fungus gardens and refuse dumps." PLoS ONE 5 (3):e9922.
ID: 90757
Type: article
Authors: Scott, Jarrod J.; Budsberg, Kevin J.; Suen, Garret; Wixon, Devin L.; Balser, Teri C.; Currie, Cameron Robert
Keywords: STRI; Forces of Change; Understanding and Sustaining a Biodiverse Planet; Gamboa; Central Panama
Abstract: Leaf-cutter ants use fresh plant material to grow a mutualistic fungus that serves as the ants' primary food source. Within fungus gardens, various plant compounds are metabolized and transformed into nutrients suitable for ant consumption. This symbiotic association produces a large amount of refuse consisting primarily of partly degraded plant material. A leaf-cutter ant colony is thus divided into two spatially and chemically distinct environments that together represent a plant biomass degradation gradient. Little is known about the microbial community structure in gardens and dumps or variation between lab and field colonies. Methodology/Principal Findings Using microbial membrane lipid analysis and a variety of community metrics, we assessed and compared the microbiota of fungus gardens and refuse dumps from both laboratory-maintained and field-collected colonies. We found that gardens contained a diverse and consistent community of microbes, dominated by Gram-negative bacteria, particularly γ-Proteobacteria and Bacteroidetes. These findings were consistent across lab and field gardens, as well as host ant taxa. In contrast, dumps were enriched for Gram-positive and anaerobic bacteria. Broad-scale clustering analyses revealed that community relatedness between samples reflected system component (gardens/dumps) rather than colony source (lab/field). At finer scales samples clustered according to colony source. Conclusions/Significance Here we report the first comparative analysis of the microbiota from leaf-cutter ant colonies. Our work reveals the presence of two distinct communities: one in the fungus garden and the other in the refuse dump. Though we find some effect of colony source on community structure, our data indicate the presence of consistently associated microbes within gardens and dumps. Substrate composition and system component appear to be the most important factor in structuring the microbial communities. These results thus suggest that resident communities are shaped by the plant degradation gradient created by ant behavior, specifically their fungiculture and waste management.
An Insect Herbivore Microbiome with High Plant Biomass-Degrading CapacitySuen, GarretScott, Jarrod J.Aylward, Frank O.Adams, Sandra M.Tringe, Susannah G.Pinto-Tomas, Adrian A.Foster, Clifton E.Pauly, MarkusWeimer, Paul J.Barry, Kerrie W.Goodwin, Lynne A.Bouffard, PascalLi, LewynOsterberger, JoleneHarkins, Timothy T.Slater, Steven C.Donohue, Timothy J.Currie, Cameron Robert2010DOI: info:10.1371/journal.pgen.1001129Plos Geneticsv. 6No. 9e1001129e1001129e1001129–e10011291553-7390
Suen, Garret, Scott, Jarrod J., Aylward, Frank O., Adams, Sandra M., Tringe, Susannah G., Pinto-Tomas, Adrian A., Foster, Clifton E., Pauly, Markus, Weimer, Paul J., Barry, Kerrie W., Goodwin, Lynne A., Bouffard, Pascal, Li, Lewyn, Osterberger, Jolene, Harkins, Timothy T., Slater, Steven C., Donohue, Timothy J., and Currie, Cameron Robert. 2010. "An Insect Herbivore Microbiome with High Plant Biomass-Degrading Capacity." Plos Genetics 6 (9):e1001129–e1001129.
ID: 93192
Type: article
Authors: Suen, Garret; Scott, Jarrod J.; Aylward, Frank O.; Adams, Sandra M.; Tringe, Susannah G.; Pinto-Tomas, Adrian A.; Foster, Clifton E.; Pauly, Markus; Weimer, Paul J.; Barry, Kerrie W.; Goodwin, Lynne A.; Bouffard, Pascal; Li, Lewyn; Osterberger, Jolene; Harkins, Timothy T.; Slater, Steven C.; Donohue, Timothy J.; Currie, Cameron Robert
Keywords: STRI