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Piovesana S, Capriotti AL, Foglia P, Montone CM, La Barbera G, Zenezini Chiozzi R, Laganà A, Cavaliere C. Development of an Analytical Method for the Metaproteomic Investigation of Bioaerosol from Work Environments. Proteomics 2019; 19:e1900152. [PMID: 31315163 DOI: 10.1002/pmic.201900152] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/21/2019] [Indexed: 11/10/2022]
Abstract
The metaproteomic analysis of air particulate matter provides valuable information about the properties of bioaerosols in the atmosphere and their influence on climate and public health. In this work, a new method for the extraction and analysis of proteins in airborne particulate matter from quartz microfiber filters is developed. Different protein extraction procedures are tested to select the best extraction protocol based on protein recovery. The optimized method is tested for the extraction of proteins from spores of ubiquitous bacteria species and used for the metaproteomic characterization of filters from three work environments. In particular, ambient aerosol samples are collected in a composting plant, in a wastewater treatment plant, and in an agricultural holding. A total of 179, 15, 205, and 444 proteins are identified in composting plant, wastewater treatment plant, and agricultural holding, (cow stable and blending plant), respectively. In agreement with the major categories of primary biological aerosol particles, all identified proteins originated primarily from fungi, bacteria, and plants. The paper is the first metaproteomic study applied to bioaerosol samples collected in occupationally relevant environmental sites and, even though not aimed at monitoring the risk exposure of workers, it provides information on the possible exposure in the working environmental sites.
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Affiliation(s)
- Susy Piovesana
- Department of Chemistry, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Anna Laura Capriotti
- Department of Chemistry, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Patrizia Foglia
- Department of Chemistry, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Carmela Maria Montone
- Department of Chemistry, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Giorgia La Barbera
- Department of Chemistry, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | | | - Aldo Laganà
- Department of Chemistry, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Chiara Cavaliere
- Department of Chemistry, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185, Rome, Italy
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Li Q, Barghi N, Lu A, Fedosov AE, Bandyopadhyay PK, Lluisma AO, Concepcion GP, Yandell M, Olivera BM, Safavi-Hemami H. Divergence of the Venom Exogene Repertoire in Two Sister Species of Turriconus. Genome Biol Evol 2017; 9:2211-2225. [PMID: 28922871 PMCID: PMC5604253 DOI: 10.1093/gbe/evx157] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2017] [Indexed: 02/07/2023] Open
Abstract
The genus Conus comprises approximately 700 species of venomous marine cone snails that are highly efficient predators of worms, snails, and fish. In evolutionary terms, cone snails are relatively young with the earliest fossil records occurring in the Lower Eocene, 55 Ma. The rapid radiation of cone snail species has been accompanied by remarkably high rates of toxin diversification. To shed light on the molecular mechanisms that accompany speciation, we investigated the toxin repertoire of two sister species, Conus andremenezi and Conus praecellens, that were until recently considered a single variable species. A total of 196 and 250 toxin sequences were identified in the venom gland transcriptomes of C. andremenezi and C. praecellens belonging to 25 and 29 putative toxin gene superfamilies, respectively. Comparative analysis with closely (Conus tribblei and Conus lenavati) and more distantly related species (Conus geographus) suggests that speciation is associated with significant diversification of individual toxin genes (exogenes) whereas the expression pattern of toxin gene superfamilies within lineages remains largely conserved. Thus, changes within individual toxin sequences can serve as a sensitive indicator for recent speciation whereas changes in the expression pattern of gene superfamilies are likely to reflect more dramatic differences in a species' interaction with its prey, predators, and competitors.
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Affiliation(s)
- Qing Li
- Eccles Institute of Human Genetics, University of Utah
| | - Neda Barghi
- Marine Science Institute, University of the Philippines-Diliman, Quezon City, Philippines
- Institute für Populationsgenetik, Vetmeduni, Vienna, 1210, Austria
| | - Aiping Lu
- School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Alexander E. Fedosov
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Science, Moscow, Russia
| | | | - Arturo O. Lluisma
- Marine Science Institute, University of the Philippines-Diliman, Quezon City, Philippines
- Philippine Genome Center, University of the Philippines, Quezon City, Philippines
| | - Gisela P. Concepcion
- Marine Science Institute, University of the Philippines-Diliman, Quezon City, Philippines
- Philippine Genome Center, University of the Philippines, Quezon City, Philippines
| | - Mark Yandell
- Eccles Institute of Human Genetics, University of Utah
- USTAR Center for Genetic Discovery, University of Utah
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Mao M, Yang X, Poff K, Bennett G. Comparative Genomics of the Dual-Obligate Symbionts from the Treehopper, Entylia carinata (Hemiptera: Membracidae), Provide Insight into the Origins and Evolution of an Ancient Symbiosis. Genome Biol Evol 2017; 9:1803-1815. [PMID: 28854637 PMCID: PMC5533117 DOI: 10.1093/gbe/evx134] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/08/2017] [Indexed: 12/20/2022] Open
Abstract
Insect species in the Auchenorrhyncha suborder (Hemiptera) maintain ancient obligate symbioses with bacteria that provide essential amino acids (EAAs) deficient in their plant-sap diets. Molecular studies have revealed that two complementary symbiont lineages, "Candidatus Sulcia muelleri" and a betaproteobacterium ("Ca. Zinderia insecticola" in spittlebugs [Cercopoidea] and "Ca. Nasuia deltocephalinicola" in leafhoppers [Cicadellidae]) may have persisted in the suborder since its origin ∼300 Ma. However, investigation of how this pair has co-evolved on a genomic level is limited to only a few host lineages. We sequenced the complete genomes of Sulcia and a betaproteobacterium from the treehopper, Entylia carinata (Membracidae: ENCA), as the first representative from this species-rich group. It also offers the opportunity to compare symbiont evolution across a major insect group, the Membracoidea (leafhoppers + treehoppers). Genomic analyses show that the betaproteobacteria in ENCA is a member of the Nasuia lineage. Both symbionts have larger genomes (Sulcia = 218 kb and Nasuia = 144 kb) than related lineages in Deltocephalinae leafhoppers, retaining genes involved in basic cellular functions and information processing. Nasuia-ENCA further exhibits few unique gene losses, suggesting that its parent lineage in the common ancestor to the Membracoidea was already highly reduced. Sulcia-ENCA has lost the abilities to synthesize menaquinone cofactor and to complete the synthesis of the branched-chain EAAs. Both capabilities are conserved in other Sulcia lineages sequenced from across the Auchenorrhyncha. Finally, metagenomic sequencing recovered the partial genome of an Arsenophonus symbiont, although it infects only 20% of individuals indicating a facultative role.
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Affiliation(s)
- Meng Mao
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Mānoa
| | - Xiushuai Yang
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Mānoa
| | - Kirsten Poff
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Mānoa
| | - Gordon Bennett
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Mānoa
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Draft Genome Sequence of Erwinia billingiae OSU19-1, Isolated from a Pear Tree Canker. GENOME ANNOUNCEMENTS 2015; 3:3/5/e01119-15. [PMID: 26430039 PMCID: PMC4591311 DOI: 10.1128/genomea.01119-15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Plant-associated Erwinia include pathogenic and nonpathogenic species. We report the 5.6-Mb genome sequence of Erwinia billingiae OSU19-1, isolated from a canker on a pear tree inoculated with Erwinia amylovora. OSU19-1 and a closely related European isolate, E. billingiae Eb661T, share many similarities including 40 kb of plasmid sequence.
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Engel P, Stepanauskas R, Moran NA. Hidden diversity in honey bee gut symbionts detected by single-cell genomics. PLoS Genet 2014; 10:e1004596. [PMID: 25210772 PMCID: PMC4161309 DOI: 10.1371/journal.pgen.1004596] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 07/02/2014] [Indexed: 12/29/2022] Open
Abstract
Microbial communities in animal guts are composed of diverse, specialized bacterial species, but little is known about how gut bacteria diversify to produce genetically and ecologically distinct entities. The gut microbiota of the honey bee, Apis mellifera, presents a useful model, because it consists of a small number of characteristic bacterial species, each showing signs of diversification. Here, we used single-cell genomics to study the variation within two species of the bee gut microbiota: Gilliamella apicola and Snodgrassella alvi. For both species, our analyses revealed extensive variation in intraspecific divergence of protein-coding genes but uniformly high levels of 16S rRNA similarity. In both species, the divergence of 16S rRNA loci appears to have been curtailed by frequent recombination within populations, while other genomic regions have continuously diverged. Furthermore, gene repertoires differ markedly among strains in both species, implying distinct metabolic capabilities. Our results show that, despite minimal divergence at 16S rRNA genes, in situ diversification occurs within gut communities and generates bacterial lineages with distinct ecological niches. Therefore, important dimensions of microbial diversity are not evident from analyses of 16S rRNA, and single cell genomics has potential to elucidate processes of bacterial diversification. Gut microbial communities are often complex, consisting of bacteria from divergent phyla as well as multiple strains of each of the constituent species. But because the composition of these communities is typically assessed using 16S rRNA analyses, little is known about genomic changes associated with in situ diversification of bacterial lineages in animal guts. We undertook a single-cell genomic approach to investigate the diversification within two species of the gut microbiota of honey bees. Each species exhibited a surprisingly high level of genomic variation, despite uniformity in the 16S rRNA sequences. Our data indicate that genetically and ecologically distinct lineages can evolve in the gut of the same host species in the presence of frequent recombination at 16S rRNA genes. These findings parallel observations from mammals, suggesting that in situ diversification of a few bacterial lineages is a common pattern in the evolution of gut communities.
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Affiliation(s)
- Philipp Engel
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
- * E-mail:
| | - Ramunas Stepanauskas
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, United States of America
| | - Nancy A. Moran
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
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Bennett GM, Moran NA. Small, smaller, smallest: the origins and evolution of ancient dual symbioses in a Phloem-feeding insect. Genome Biol Evol 2014; 5:1675-88. [PMID: 23918810 PMCID: PMC3787670 DOI: 10.1093/gbe/evt118] [Citation(s) in RCA: 191] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Many insects rely on bacterial symbionts with tiny genomes specialized for provisioning nutrients lacking in host diets. Xylem sap and phloem sap are both deficient as insect diets, but differ dramatically in nutrient content, potentially affecting symbiont genome evolution. For sap-feeding insects, sequenced symbiont genomes are available only for phloem-feeding examples from the suborder Sternorrhyncha and xylem-feeding examples from the suborder Auchenorrhyncha, confounding comparisons. We sequenced genomes of the obligate symbionts, Sulcia muelleri and Nasuia deltocephalinicola, of the phloem-feeding pest insect, Macrosteles quadrilineatus (Auchenorrhyncha: Cicadellidae). Our results reveal that Nasuia-ALF has the smallest bacterial genome yet sequenced (112 kb), and that the Sulcia-ALF genome (190 kb) is smaller than that of Sulcia in other insect lineages. Together, these symbionts retain the capability to synthesize the 10 essential amino acids, as observed for several symbiont pairs from xylem-feeding Auchenorrhyncha. Nasuia retains genes enabling synthesis of two amino acids, DNA replication, transcription, and translation. Both symbionts have lost genes underlying ATP synthesis through oxidative phosphorylation, possibly as a consequence of the enriched sugar content of phloem. Shared genomic features, including reassignment of the UGA codon from Stop to tryptophan, and phylogenetic results suggest that Nasuia-ALF is most closely related to Zinderia, the betaproteobacterial symbiont of spittlebugs. Thus, Nasuia/Zinderia and Sulcia likely represent ancient associates that have co-resided in hosts since the divergence of leafhoppers and spittlebugs >200 Ma, and possibly since the origin of the Auchenorrhyncha, >260 Ma.
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Affiliation(s)
- Gordon M Bennett
- Department of Ecology and Evolutionary Biology & Microbial Diversity Institute, Yale University
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