1
|
Hernández AM, Alcaraz LD, Hernández-Álvarez C, Romero MF, Jara-Servín A, Barajas H, . Ramírez CM, Peimbert M. Revealing the microbiome diversity and biocontrol potential of field Aedes ssp.: Implications for disease vector management. PLoS One 2024; 19:e0302328. [PMID: 38683843 PMCID: PMC11057774 DOI: 10.1371/journal.pone.0302328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 04/02/2024] [Indexed: 05/02/2024] Open
Abstract
The mosquito Aedes spp. holds important relevance for human and animal health, as it serves as a vector for transmitting multiple diseases, including dengue and Zika virus. The microbiome's impact on its host's health and fitness is well known. However, most studies on mosquito microbiomes have been conducted in laboratory settings. We explored the mixed microbial communities within Aedes spp., utilizing the 16S rRNA gene for diversity analysis and shotgun metagenomics for functional genomics. Our samples, which included Ae. aegypti and Ae. albopictus, spanned various developmental stages-eggs, larvae, and adults-gathered from five semiurban areas in Mexico. Our findings revealed a substantial diversity of 8,346 operational taxonomic units (OTUs), representing 967 bacterial genera and 126,366 annotated proteins. The host developmental stage was identified as the primary factor associated with variations in the microbiome composition. Subsequently, we searched for genes and species involved in mosquito biocontrol. Wolbachia accounted for 9.6% of the 16S gene sequences. We observed a high diversity (203 OTUs) of Wolbachia strains commonly associated with mosquitoes, such as wAlb, with a noticeable increase in abundance during the adult stages. Notably, we detected the presence of the cifA and cifB genes, which are associated with Wolbachia's cytoplasmic incompatibility, a biocontrol mechanism. Additionally, we identified 221 OTUs related to Bacillus, including strains linked to B. thuringiensis. Furthermore, we discovered multiple genes encoding insecticidal toxins, such as Cry, Mcf, Vip, and Vpp. Overall, our study contributes to the understanding of mosquito microbiome biodiversity and metabolic capabilities, which are essential for developing effective biocontrol strategies against this disease vector.
Collapse
Affiliation(s)
- Apolinar M. Hernández
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana, Unidad Cuajimalpa, Ciudad de México, México
- Posgrado en Ciencias Naturales e Ingeniería, Universidad Autónoma Metropolitana, Unidad Cuajimalpa, Ciudad de México, México
| | - Luis D. Alcaraz
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Cristóbal Hernández-Álvarez
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Miguel F. Romero
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Angélica Jara-Servín
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Hugo Barajas
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, México
| | | | - Mariana Peimbert
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana, Unidad Cuajimalpa, Ciudad de México, México
| |
Collapse
|
2
|
Cisneros-Martínez AM, Rodriguez-Cruz UE, Alcaraz LD, Becerra A, Eguiarte LE, Souza V. Comparative evaluation of bioinformatic tools for virus-host prediction and their application to a highly diverse community in the Cuatro Ciénegas Basin, Mexico. PLoS One 2024; 19:e0291402. [PMID: 38300968 PMCID: PMC10833507 DOI: 10.1371/journal.pone.0291402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 12/27/2023] [Indexed: 02/03/2024] Open
Abstract
Due to the enormous diversity of non-culturable viruses, new viruses must be characterized using culture-independent techniques. The associated host is an important phenotypic feature that can be inferred from metagenomic viral contigs thanks to the development of several bioinformatic tools. Here, we compare the performance of recently developed virus-host prediction tools on a dataset of 1,046 virus-host pairs and then apply the best-performing tools to a metagenomic dataset derived from a highly diverse transiently hypersaline site known as the Archaean Domes (AD) within the Cuatro Ciénegas Basin, Coahuila, Mexico. Among host-dependent methods, alignment-based approaches had a precision of 66.07% and a sensitivity of 24.76%, while alignment-free methods had an average precision of 75.7% and a sensitivity of 57.5%. RaFAH, a virus-dependent alignment-based tool, had the best overall performance (F1_score = 95.7%). However, when predicting the host of AD viruses, methods based on public reference databases (such as RaFAH) showed lower inter-method agreement than host-dependent methods run against custom databases constructed from prokaryotes inhabiting AD. Methods based on custom databases also showed the greatest agreement between the source environment and the predicted host taxonomy, habitat, lifestyle, or metabolism. This highlights the value of including custom data when predicting hosts on a highly diverse metagenomic dataset, and suggests that using a combination of methods and qualitative validations related to the source environment and predicted host biology can increase the number of correct predictions. Finally, these predictions suggest that AD viruses infect halophilic archaea as well as a variety of bacteria that may be halophilic, halotolerant, alkaliphilic, thermophilic, oligotrophic, sulfate-reducing, or marine, which is consistent with the specific environment and the known geological and biological evolution of the Cuatro Ciénegas Basin and its microorganisms.
Collapse
Affiliation(s)
- Alejandro Miguel Cisneros-Martínez
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
- Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Ulises E. Rodriguez-Cruz
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
- Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Luis D. Alcaraz
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Arturo Becerra
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Luis E. Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Valeria Souza
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
- Centro de Estudios del Cuaternario de Fuego-Patagonia y Antártica (CEQUA), Punta Arenas, Chile
| |
Collapse
|
3
|
Hernández-Álvarez C, Peimbert M, Rodríguez-Martin P, Trejo-Aguilar D, Alcaraz LD. A study of microbial diversity in a biofertilizer consortium. PLoS One 2023; 18:e0286285. [PMID: 37616263 PMCID: PMC10449135 DOI: 10.1371/journal.pone.0286285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 08/09/2023] [Indexed: 08/26/2023] Open
Abstract
Biofertilizers supply living microorganisms to help plants grow and keep their health. This study examines the microbiome composition of a commercial biofertilizer known for its plant growth-promoting activity. Using ITS and 16S rRNA gene sequence analyses, we describe the microbial communities of a biofertilizer, with 163 fungal species and 485 bacterial genera found. The biofertilizer contains a variety of microorganisms previously reported to enhance nutrient uptake, phytohormone production, stress tolerance, and pathogen resistance in plants. Plant roots created a microenvironment that boosted bacterial diversity but filtered fungal communities. Notably, preserving the fungal-inoculated substrate proves critical for keeping fungal diversity in the root fraction. We described that bacteria were more diverse in the rhizosphere than in the substrate. In contrast, root-associated fungi were less diverse than the substrate ones. We propose using plant roots as bioreactors to sustain dynamic environments that promote the proliferation of microorganisms with biofertilizer potential. The study suggests that bacteria grow close to plant roots, while root-associated fungi may be a subset of the substrate fungi. These findings show that the composition of the biofertilizer may be influenced by the selection of microorganisms associated with plant roots, which could have implications for the effectiveness of the biofertilizer in promoting plant growth. In conclusion, our study sheds light on the intricate interplay between plant roots and the biofertilizer's microbial communities. Understanding this relationship can aid in optimizing biofertilizer production and application, contributing to sustainable agricultural practices and improved crop yields.
Collapse
Affiliation(s)
- Cristóbal Hernández-Álvarez
- Laboratorio de Genómica Ambiental, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Coyoacán, Mexico City, Mexico
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Mariana Peimbert
- Departamento de Ciencias Naturales, Unidad Cuajimalpa, Universidad Autónoma Metropolitana, Mexico City, Mexico
| | - Pedro Rodríguez-Martin
- Laboratorio de Genómica Ambiental, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Coyoacán, Mexico City, Mexico
| | - Dora Trejo-Aguilar
- Laboratorio de Organismos Benéficos, Universidad Veracruzana, Veracruz, Mexico
| | - Luis D. Alcaraz
- Laboratorio de Genómica Ambiental, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Coyoacán, Mexico City, Mexico
| |
Collapse
|
4
|
Parga A, Muras A, Otero-Casal P, Arredondo A, Soler-Ollé A, Àlvarez G, Alcaraz LD, Mira A, Blanc V, Otero A. The quorum quenching enzyme Aii20J modifies in vitro periodontal biofilm formation. Front Cell Infect Microbiol 2023; 13:1118630. [PMID: 36816581 PMCID: PMC9932050 DOI: 10.3389/fcimb.2023.1118630] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 01/20/2023] [Indexed: 02/05/2023] Open
Abstract
Introduction Recent studies have revealed the presence of N-acyl-homoserine lactones (AHLs) quorum sensing (QS) signals in the oral environment. Yet, their role in oral biofilm development remains scarcely investigated. The use of quorum quenching (QQ) strategies targeting AHLs has been described as efficient for the control of pathogenic biofilms. Here, we evaluate the use of a highly active AHL-targeting QQ enzyme, Aii20J, to modulate oral biofilm formation in vitro. Methods The effect of the QQ enzyme was studied in in vitro multispecies biofilms generated from oral samples taken from healthy donors and patients with periodontal disease. Subgingival samples were used as inocula, aiming to select members of the microbiota of the periodontal pocket niche in the in vitro biofilms. Biofilm formation abilities and microbial composition were studied upon treating the biofilms with the QQ enzyme Aii20J. Results and Discussion The addition of the enzyme resulted in significant biofilm mass reductions in 30 - 60% of the subgingival-derived biofilms, although standard AHLs could not be found in the supernatants of the cultured biofilms. Changes in biofilm mass were not accompanied by significant alterations of bacterial relative abundance at the genus level. The investigation of 125 oral supragingival metagenomes and a synthetic subgingival metagenome revealed a surprisingly high abundance and broad distribution of homologous of the AHL synthase HdtS and several protein families of AHL receptors, as well as an enormous presence of QQ enzymes, pointing to the existence of an intricate signaling network in oral biofilms that has been so far unreported, and should be further investigated. Together, our findings support the use of Aii20J to modulate polymicrobial biofilm formation without changing the microbiome structure of the biofilm. Results in this study suggest that AHLs or AHL-like molecules affect oral biofilm formation, encouraging the application of QQ strategies for oral health improvement, and reinforcing the importance of personalized approaches to oral biofilm control.
Collapse
Affiliation(s)
- Ana Parga
- Department of Microbiology and Parasitology, CIBUS-Faculty of Biology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Andrea Muras
- Department of Microbiology and Parasitology, CIBUS-Faculty of Biology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Paz Otero-Casal
- Department of Surgery and Medical-Surgical Specialties, Faculty of Medicine and Odontology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Unit of Oral Health, Santa Comba-Negreira, (CS) SERGAS, Santiago de Compostela, Spain
| | - Alexandre Arredondo
- Department of Microbiology, Dentaid Research Center, Cerdanyola Del Vallès, Spain
| | - Agnès Soler-Ollé
- Department of Microbiology, Dentaid Research Center, Cerdanyola Del Vallès, Spain
| | - Gerard Àlvarez
- Department of Microbiology, Dentaid Research Center, Cerdanyola Del Vallès, Spain
| | - Luis D. Alcaraz
- Department of Cellular Biology, Faculty of Sciences, National Autonomous University of Mexico, Coyoacán, Mexico
| | - Alex Mira
- Department of Genomics and Health, FISABIO Foundation, Valencia, Spain
| | - Vanessa Blanc
- Department of Microbiology, Dentaid Research Center, Cerdanyola Del Vallès, Spain
| | - Ana Otero
- Department of Microbiology and Parasitology, CIBUS-Faculty of Biology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- *Correspondence: Ana Otero,
| |
Collapse
|
5
|
Jara-Servin A, Silva A, Barajas H, Cruz-Ortega R, Tinoco-Ojanguren C, Alcaraz LD. Root microbiome diversity and structure of the Sonoran desert buffelgrass (Pennisetum ciliare L.). PLoS One 2023; 18:e0285978. [PMID: 37205698 DOI: 10.1371/journal.pone.0285978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/28/2023] [Indexed: 05/21/2023] Open
Abstract
Buffelgrass (Pennisetum ciliare) is an invasive plant introduced into Mexico's Sonoran desert for cattle grazing and has converted large areas of native thorn scrub. One of the invasion mechanisms buffelgrass uses to invade is allelopathy, which consists of the production and secretion of allelochemicals that exert adverse effects on other plants' growth. The plant microbiome also plays a vital role in establishing invasive plants and host growth and development. However, little is known about the buffelgrass root-associated bacteria and the effects of allelochemicals on the microbiome. We used 16S rRNA gene amplicon sequencing to obtain the microbiome of buffelgrass and compare it between samples treated with root exacknudates and aqueous leachates as allelochemical exposure and samples without allelopathic exposure in two different periods. The Shannon diversity values were between H' = 5.1811-5.5709, with 2,164 reported bacterial Amplicon Sequence Variants (ASVs). A total of 24 phyla were found in the buffelgrass microbiome, predominantly Actinobacteria, Proteobacteria, and Acidobacteria. At the genus level, 30 different genera comprised the buffelgrass core microbiome. Our results show that buffelgrass recruits microorganisms capable of thriving under allelochemical conditions and may be able to metabolize them (e.g., Planctomicrobium, Aurantimonas, and Tellurimicrobium). We also found that the community composition of the microbiome changes depending on the developmental state of buffelgrass (p = 0.0366; ANOSIM). These findings provide new insights into the role of the microbiome in the establishment of invasive plant species and offer potential targets for developing strategies to control buffelgrass invasion.
Collapse
Affiliation(s)
- Angélica Jara-Servin
- Laboratorio de Genómica Ambiental, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Posgrado en Ciencias Bioquímicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Adán Silva
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Hermosillo, Sonora, Mexico
| | - Hugo Barajas
- Laboratorio de Genómica Ambiental, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Rocío Cruz-Ortega
- Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Clara Tinoco-Ojanguren
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Hermosillo, Sonora, Mexico
| | - Luis D Alcaraz
- Laboratorio de Genómica Ambiental, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| |
Collapse
|
6
|
Peimbert M, Alcaraz LD. Where environmental microbiome meets its host: subway and passenger microbiome relationships. Mol Ecol 2022; 32:2602-2618. [PMID: 35318755 DOI: 10.1111/mec.16440] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 03/12/2022] [Accepted: 03/16/2022] [Indexed: 12/17/2022]
Abstract
Subways are urban transport systems with high capacity. Every day around the world, there are more than 150 million subway passengers. Since 2013, thousands of microbiome samples from various subways worldwide have been sequenced. Skin bacteria and environmental organisms dominate the subway microbiomes. The literature has revealed common bacterial groups in subway systems; even so, it is possible to identify cities by their microbiome. Low-frequency bacteria are responsible for specific bacterial fingerprints of each subway system. Furthermore, daily subway commuters leave their microbial clouds and interact with other passengers. Microbial exchange is quite fast; the hand microbiome changes within minutes, and after cleaning the handrails, the bacteria are re-established within minutes. To investigate new taxa and metabolic pathways of subway microbial communities, several high-quality metagenomic-assembled genomes (MAG) have been described. Subways are harsh environments unfavorable for microorganism growth. However, recent studies have observed a wide diversity of viable and metabolically active bacteria. Understanding which bacteria are living, dormant, or dead allows us to propose realistic ecological interactions. Questions regarding the relationship between humans and the subway microbiome, particularly the microbiome effects on personal and public health, remain unanswered. This review summarizes our knowledge of subway microbiomes and their relationship with passenger microbiomes.
Collapse
Affiliation(s)
- Mariana Peimbert
- Departamento de Ciencias Naturales, Unidad Cuajimalpa, Universidad Autónoma Metropolitana. Ciudad de México, México
| | - Luis D Alcaraz
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, México
| |
Collapse
|
7
|
Hernández-Álvarez C, García-Oliva F, Cruz-Ortega R, Romero MF, Barajas HR, Piñero D, Alcaraz LD. Squash root microbiome transplants and metagenomic inspection for in situ arid adaptations. Sci Total Environ 2022; 805:150136. [PMID: 34818799 DOI: 10.1016/j.scitotenv.2021.150136] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 05/10/2023]
Abstract
Arid zones contain a diverse set of microbes capable of survival under dry conditions, some of which can form relationships with plants under drought stress conditions to improve plant health. We studied squash (Cucurbita pepo L.) root microbiome under historically arid and humid sites, both in situ and performing a common garden experiment. Plants were grown in soils from sites with different drought levels, using in situ collected soils as the microbial source. We described and analyzed bacterial diversity by 16S rRNA gene sequencing (N = 48) from the soil, rhizosphere, and endosphere. Proteobacteria were the most abundant phylum present in humid and arid samples, while Actinobacteriota abundance was higher in arid ones. The β-diversity analyses showed split microbiomes between arid and humid microbiomes, and aridity and soil pH levels could explain it. These differences between humid and arid microbiomes were maintained in the common garden experiment, showing that it is possible to transplant in situ diversity to the greenhouse. We detected a total of 1009 bacterial genera; 199 exclusively associated with roots under arid conditions. By 16S and shotgun metagenomics, we identified dry-associated taxa such as Cellvibrio, Ensifer adhaerens, and Streptomyces flavovariabilis. With shotgun metagenomic sequencing of rhizospheres (N = 6), we identified 2969 protein families in the squash core metagenome and found an increased number of exclusively protein families from arid (924) than humid samples (158). We found arid conditions enriched genes involved in protein degradation and folding, oxidative stress, compatible solute synthesis, and ion pumps associated with osmotic regulation. Plant phenotyping allowed us to correlate bacterial communities with plant growth. Our study revealed that it is possible to evaluate microbiome diversity ex-situ and identify critical species and genes involved in plant-microbe interactions in historically arid locations.
Collapse
Affiliation(s)
- Cristóbal Hernández-Álvarez
- Laboratorio de Genómica Ambiental, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico; Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico
| | - Felipe García-Oliva
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, Mexico
| | - Rocío Cruz-Ortega
- Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico
| | - Miguel F Romero
- Laboratorio de Genómica Ambiental, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico
| | - Hugo R Barajas
- Laboratorio de Genómica Ambiental, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico
| | - Daniel Piñero
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico
| | - Luis D Alcaraz
- Laboratorio de Genómica Ambiental, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico.
| |
Collapse
|
8
|
Moguel B, Pérez L, Alcaraz LD, Blaz J, Caballero M, Muñoz-Velasco I, Becerra A, Laclette JP, Ortega-Guerrero B, Romero-Oliva CS, Herrera-Estrella L, Lozano-García S. Holocene life and microbiome profiling in ancient tropical Lake Chalco, Mexico. Sci Rep 2021; 11:13848. [PMID: 34226571 PMCID: PMC8257590 DOI: 10.1038/s41598-021-92981-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 06/09/2021] [Indexed: 11/08/2022] Open
Abstract
Metagenomic and traditional paleolimnological approaches are suitable to infer past biological and environmental changes, however, they are often applied independently, especially in tropical regions. We combined both approaches to investigate Holocene Prokaryote and Eukaryote diversity and microbial metabolic pathways in ancient Lake Chalco, Mexico. Here, we report on diversity among a large number of lineages (36,722 OTUs) and functional diversity (27,636,243 non-clustered predicted proteins, and 6,144 annotated protein-family genes). The most abundant domain is Bacteria (81%), followed by Archaea (15%) and Eukarya (3%). We also determined the diversity of protein families and their relationship to metabolic pathways. The early Holocene (> 11,000 cal years BP) lake was characterized by cool, freshwater conditions, which later became warmer and hyposaline (11,000-6,000 cal years BP). We found high abundances of cyanobacteria, and fungi groups associated with mature forests in these sediments. Bacteria and Archaea include mainly anaerobes and extremophiles that are involved in the sulfur, nitrogen, and carbon cycles. We found evidence for early human impacts, including landscape modifications and lake eutrophication, which began ~ 6,000 cal years BP. Subsaline, temperate conditions were inferred for the past 5,000 years. Finally, we found nitrogen-fixing bacteria and protein-family genes that are linked to contaminated environments, as well as several fungal pathogens of crops in near-surface sediments.
Collapse
Affiliation(s)
- Bárbara Moguel
- Instituto de Geología, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
- Laboratorio Internacional de Genoma Humano (LIIGH), Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
- Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Centro de Bioingenieria, Av. Epigmenio González, No. 500, Fracc. San Pablo, 76130, Querétaro, Mexico
| | - Liseth Pérez
- Institut für Geosysteme und Bioindikation, Technische Universität Braunschweig, 38106, Braunschweig, Germany
| | - Luis D Alcaraz
- Facultad de Ciencias, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Jazmín Blaz
- Facultad de Ciencias, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Margarita Caballero
- Instituto de Geofísica, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Israel Muñoz-Velasco
- Facultad de Ciencias, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Arturo Becerra
- Facultad de Ciencias, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Juan P Laclette
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | | | - Claudia S Romero-Oliva
- Centro de Estudios Atitlán, Universidad del Valle de Guatemala, 7001, Atitlán-Sololá, Guatemala
| | - Luis Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), Km 9.6 Libramiento Norte Carretera Irapuato-León, 36821, Irapuato, Guanajuato, Mexico.
- Institute of Functional Genomics for Abiotic Stress, Texas Tech University, Lubbock, Texas, 79410, USA.
| | - Socorro Lozano-García
- Instituto de Geología, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico.
| |
Collapse
|
9
|
Rocha-Arriaga C, Espinal-Centeno A, Martinez-Sánchez S, Caballero-Pérez J, Alcaraz LD, Cruz-Ramírez A. Deep microbial community profiling along the fermentation process of pulque, a biocultural resource of Mexico. Microbiol Res 2020; 241:126593. [DOI: 10.1016/j.micres.2020.126593] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 09/08/2020] [Accepted: 09/11/2020] [Indexed: 12/26/2022]
|
10
|
Barajas HR, Martínez-Sánchez S, Romero MF, Álvarez CH, Servín-González L, Peimbert M, Cruz-Ortega R, García-Oliva F, Alcaraz LD. Testing the Two-Step Model of Plant Root Microbiome Acquisition Under Multiple Plant Species and Soil Sources. Front Microbiol 2020; 11:542742. [PMID: 33162946 PMCID: PMC7581803 DOI: 10.3389/fmicb.2020.542742] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 09/11/2020] [Indexed: 12/23/2022] Open
Abstract
The two-step model for plant root microbiomes considers soil as the primary microbial source. Active selection of the plant’s bacterial inhabitants results in a biodiversity decrease toward roots. We collected sixteen samples of in situ ruderal plant roots and their soils and used these soils as the main microbial input for single genotype tomatoes grown in a greenhouse. Our main goal was to test the soil influence in the structuring of rhizosphere microbiomes, minimizing environmental variability, while testing multiple plant species. We massively sequenced the 16S rRNA and shotgun metagenomes of the soils, in situ plants, and tomato roots. We identified a total of 271,940 bacterial operational taxonomic units (OTUs) within the soils, rhizosphere and endospheric microbiomes. We annotated by homology a total of 411,432 (13.07%) of the metagenome predicted proteins. Tomato roots did follow the two-step model with lower α-diversity than soil, while ruderal plants did not. Surprisingly, ruderal plants are probably working as a microenvironmental oasis providing moisture and plant-derived nutrients, supporting larger α-diversity. Ruderal plants and their soils are closer according to their microbiome community composition than tomato and its soil, based on OTUs and protein comparisons. We expected that tomato β-diversity clustered together with their soil, if it is the main rhizosphere microbiome structuring factor. However, tomato microbiome β-diversity was associated with plant genotype in most samples (81.2%), also supported by a larger set of enriched proteins in tomato rhizosphere than soil or ruderals. The most abundant bacteria found in soils was the Actinobacteria Solirubrobacter soli, ruderals were dominated by the Proteobacteria Sphingomonas sp. URGHD0057, and tomato mainly by the Bacteroidetes Ohtaekwangia koreensis, Flavobacterium terrae, Niastella vici, and Chryseolinea serpens. We calculated a metagenomic tomato root core of 51 bacterial genera and 2,762 proteins, which could be the basis for microbiome-oriented plant breeding programs. We attributed a larger diversity in ruderal plants roots exudates as an effect of the moisture and nutrient acting as a microbial harbor. The tomato and ruderal metagenomic differences are probably due to plant domestication trade-offs, impacting plant-bacteria interactions.
Collapse
Affiliation(s)
- Hugo R Barajas
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Shamayim Martínez-Sánchez
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Miguel F Romero
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Cristóbal Hernández Álvarez
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Luis Servín-González
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Mariana Peimbert
- Departamento de Ciencias Naturales, Unidad Cuajimalpa, Universidad Autónoma Metropolitana, Mexico City, Mexico
| | - Rocío Cruz-Ortega
- Laboratorio de Alelopatía, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Felipe García-Oliva
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, Morelia, Mexico
| | - Luis D Alcaraz
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| |
Collapse
|
11
|
Vargas-Robles D, Gonzalez-Cedillo C, Hernandez AM, Alcaraz LD, Peimbert M. Passenger-surface microbiome interactions in the subway of Mexico City. PLoS One 2020; 15:e0237272. [PMID: 32813719 PMCID: PMC7437895 DOI: 10.1371/journal.pone.0237272] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 07/22/2020] [Indexed: 01/02/2023] Open
Abstract
Interaction between hands and the environment permits the interchange of microorganisms. The Mexico City subway is used daily by millions of passengers that get in contact with its surfaces. In this study, we used 16S rRNA gene sequencing to characterize the microbiomes of frequently touched surfaces and compare regular and women-only wagons. We also explored the effect of surface cleaning on microbial resettling. Finally, we studied passenger behavior and characterized microbial changes after traveling. Most passengers (99%), showed some type of surface interaction during a wagon trip, mostly with the hands (92%). We found microbiome differences associated with surfaces, probably reflecting diverse surface materials and usage frequency. The platform floor was the most bacterial diverse surface, while the stair handrail and pole were the least diverse ones. After pole cleaning, the resettling of microbial diversity was fast (5–30 minutes); however, it did not resemble the initial composition. After traveling, passengers significantly increased their hand microbial diversity and converged to a similar microbial composition among passengers. Additionally, passenger hand microbiomes resembled subway surfaces in diversity. However, microbial fingerprints were preserved within passengers after traveling.
Collapse
Affiliation(s)
- Daniela Vargas-Robles
- Departamento de Ciencias Naturales, Unidad Cuajimalpa, Universidad Autónoma Metropolitana, Ciudad de México, México
| | - Carolina Gonzalez-Cedillo
- Departamento de Ciencias Naturales, Unidad Cuajimalpa, Universidad Autónoma Metropolitana, Ciudad de México, México
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Apolinar M. Hernandez
- Departamento de Ciencias Naturales, Unidad Cuajimalpa, Universidad Autónoma Metropolitana, Ciudad de México, México
| | - Luis D. Alcaraz
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Mariana Peimbert
- Departamento de Ciencias Naturales, Unidad Cuajimalpa, Universidad Autónoma Metropolitana, Ciudad de México, México
- * E-mail:
| |
Collapse
|
12
|
Okie JG, Poret-Peterson AT, Lee ZM, Richter A, Alcaraz LD, Eguiarte LE, Siefert JL, Souza V, Dupont CL, Elser JJ. Genomic adaptations in information processing underpin trophic strategy in a whole-ecosystem nutrient enrichment experiment. eLife 2020; 9:49816. [PMID: 31989922 PMCID: PMC7028357 DOI: 10.7554/elife.49816] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 01/27/2020] [Indexed: 01/03/2023] Open
Abstract
Several universal genomic traits affect trade-offs in the capacity, cost, and efficiency of the biochemical information processing that underpins metabolism and reproduction. We analyzed the role of these traits in mediating the responses of a planktonic microbial community to nutrient enrichment in an oligotrophic, phosphorus-deficient pond in Cuatro Ciénegas, Mexico. This is one of the first whole-ecosystem experiments to involve replicated metagenomic assessment. Mean bacterial genome size, GC content, total number of tRNA genes, total number of rRNA genes, and codon usage bias in ribosomal protein sequences were all higher in the fertilized treatment, as predicted on the basis of the assumption that oligotrophy favors lower information-processing costs whereas copiotrophy favors higher processing rates. Contrasting changes in trait variances also suggested differences between traits in mediating assembly under copiotrophic versus oligotrophic conditions. Trade-offs in information-processing traits are apparently sufficiently pronounced to play a role in community assembly because the major components of metabolism-information, energy, and nutrient requirements-are fine-tuned to an organism's growth and trophic strategy.
Collapse
Affiliation(s)
- Jordan G Okie
- School of Earth and Space Exploration, Arizona State University, Tempe, United States
| | | | - Zarraz Mp Lee
- School of Life Sciences, Arizona State University, Tempe, United States
| | | | - Luis D Alcaraz
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Luis E Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Janet L Siefert
- Department of Statistics, Rice University, Houston, United States
| | - Valeria Souza
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | | | - James J Elser
- School of Life Sciences, Arizona State University, Tempe, United States.,Flathead Lake Biological Station, University of Montana, Polson, United States
| |
Collapse
|
13
|
Barajas HR, Romero MF, Martínez-Sánchez S, Alcaraz LD. Global genomic similarity and core genome sequence diversity of the Streptococcus genus as a toolkit to identify closely related bacterial species in complex environments. PeerJ 2019; 6:e6233. [PMID: 30656069 PMCID: PMC6336011 DOI: 10.7717/peerj.6233] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 12/07/2018] [Indexed: 12/22/2022] Open
Abstract
Background The Streptococcus genus is relevant to both public health and food safety because of its ability to cause pathogenic infections. It is well-represented (>100 genomes) in publicly available databases. Streptococci are ubiquitous, with multiple sources of isolation, from human pathogens to dairy products. The Streptococcus genus has traditionally been classified by morphology, serum types, the 16S ribosomal RNA (rRNA) gene, and multi-locus sequence types subject to in-depth comparative genomic analysis. Methods Core and pan-genomes described the genomic diversity of 108 strains belonging to 16 Streptococcus species. The core genome nucleotide diversity was calculated and compared to phylogenomic distances within the genus Streptococcus. The core genome was also used as a resource to recruit metagenomic fragment reads from streptococci dominated environments. A conventional 16S rRNA gene phylogeny reconstruction was used as a reference to compare the resulting dendrograms of average nucleotide identity (ANI) and genome similarity score (GSS) dendrograms. Results The core genome, in this work, consists of 404 proteins that are shared by all 108 Streptococcus. The average identity of the pairwise compared core proteins decreases proportionally to GSS lower scores, across species. The GSS dendrogram recovers most of the clades in the 16S rRNA gene phylogeny while distinguishing between 16S polytomies (unresolved nodes). The GSS is a distance metric that can reflect evolutionary history comparing orthologous proteins. Additionally, GSS resulted in the most useful metric for genus and species comparisons, where ANI metrics failed due to false positives when comparing different species. Discussion Understanding of genomic variability and species relatedness is the goal of tools like GSS, which makes use of the maximum pairwise shared orthologous sequences for its calculation. It allows for long evolutionary distances (above species) to be included because of the use of amino acid alignment scores, rather than nucleotides, and normalizing by positive matches. Newly sequenced species and strains could be easily placed into GSS dendrograms to infer overall genomic relatedness. The GSS is not restricted to ubiquitous conservancy of gene features; thus, it reflects the mosaic-structure and dynamism of gene acquisition and loss in bacterial genomes.
Collapse
Affiliation(s)
- Hugo R Barajas
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Miguel F Romero
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Shamayim Martínez-Sánchez
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Luis D Alcaraz
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico.,Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología. Universidad Nacional Autonóma de México, Mexico city, Mexico
| |
Collapse
|
14
|
Alcaraz LD, Peimbert M, Barajas HR, Dorantes-Acosta AE, Bowman JL, Arteaga-Vázquez MA. Marchantia liverworts as a proxy to plants' basal microbiomes. Sci Rep 2018; 8:12712. [PMID: 30140076 DOI: 10.1101/103861] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 08/13/2018] [Indexed: 05/26/2023] Open
Abstract
Microbiomes influence plant establishment, development, nutrient acquisition, pathogen defense, and health. Plant microbiomes are shaped by interactions between the microbes and a selection process of host plants that distinguishes between pathogens, commensals, symbionts and transient bacteria. In this work, we explore the microbiomes through massive sequencing of the 16S rRNA genes of microbiomes two Marchantia species of liverworts. We compared microbiomes from M. polymorpha and M. paleacea plants collected in the wild relative to their soils substrates and from plants grown in vitro that were established from gemmae obtained from the same populations of wild plants. Our experimental setup allowed identification of microbes found in both native and in vitro Marchantia species. The main OTUs (97% identity) in Marchantia microbiomes were assigned to the following genera: Methylobacterium, Rhizobium, Paenibacillus, Lysobacter, Pirellula, Steroidobacter, and Bryobacter. The assigned genera correspond to bacteria capable of plant-growth promotion, complex exudate degradation, nitrogen fixation, methylotrophs, and disease-suppressive bacteria, all hosted in the relatively simple anatomy of the plant. Based on their long evolutionary history Marchantia is a promising model to study not only long-term relationships between plants and their microbes but also the transgenerational contribution of microbiomes to plant development and their response to environmental changes.
Collapse
Affiliation(s)
- Luis D Alcaraz
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad Universitaria, UNAM, 04510, Coyoacán, Mexico City, Mexico.
| | - Mariana Peimbert
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana, Unidad Cuajimalpa, Av. Vasco de Quiroga 4871, Col. Santa Fe Cuajimalpa, 05348, Mexico City, Mexico
| | - Hugo R Barajas
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad Universitaria, UNAM, 04510, Coyoacán, Mexico City, Mexico
| | - Ana E Dorantes-Acosta
- University of Veracruz, Institute for Biotechnology and Applied Ecology (INBIOTECA), Avenida de las Culturas Veracruzanas 101, Colonia Emiliano Zapata, 91090, Xalapa, Veracruz, Mexico
| | - John L Bowman
- School of Biological Sciences, Monash University, Melbourne, Victoria, 3800, Australia
| | - Mario A Arteaga-Vázquez
- University of Veracruz, Institute for Biotechnology and Applied Ecology (INBIOTECA), Avenida de las Culturas Veracruzanas 101, Colonia Emiliano Zapata, 91090, Xalapa, Veracruz, Mexico.
| |
Collapse
|
15
|
Alcaraz LD, Peimbert M, Barajas HR, Dorantes-Acosta AE, Bowman JL, Arteaga-Vázquez MA. Marchantia liverworts as a proxy to plants' basal microbiomes. Sci Rep 2018; 8:12712. [PMID: 30140076 PMCID: PMC6107579 DOI: 10.1038/s41598-018-31168-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 08/13/2018] [Indexed: 02/01/2023] Open
Abstract
Microbiomes influence plant establishment, development, nutrient acquisition, pathogen defense, and health. Plant microbiomes are shaped by interactions between the microbes and a selection process of host plants that distinguishes between pathogens, commensals, symbionts and transient bacteria. In this work, we explore the microbiomes through massive sequencing of the 16S rRNA genes of microbiomes two Marchantia species of liverworts. We compared microbiomes from M. polymorpha and M. paleacea plants collected in the wild relative to their soils substrates and from plants grown in vitro that were established from gemmae obtained from the same populations of wild plants. Our experimental setup allowed identification of microbes found in both native and in vitro Marchantia species. The main OTUs (97% identity) in Marchantia microbiomes were assigned to the following genera: Methylobacterium, Rhizobium, Paenibacillus, Lysobacter, Pirellula, Steroidobacter, and Bryobacter. The assigned genera correspond to bacteria capable of plant-growth promotion, complex exudate degradation, nitrogen fixation, methylotrophs, and disease-suppressive bacteria, all hosted in the relatively simple anatomy of the plant. Based on their long evolutionary history Marchantia is a promising model to study not only long-term relationships between plants and their microbes but also the transgenerational contribution of microbiomes to plant development and their response to environmental changes.
Collapse
Affiliation(s)
- Luis D Alcaraz
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad Universitaria, UNAM, 04510, Coyoacán, Mexico City, Mexico.
| | - Mariana Peimbert
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana, Unidad Cuajimalpa, Av. Vasco de Quiroga 4871, Col. Santa Fe Cuajimalpa, 05348, Mexico City, Mexico
| | - Hugo R Barajas
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad Universitaria, UNAM, 04510, Coyoacán, Mexico City, Mexico
| | - Ana E Dorantes-Acosta
- University of Veracruz, Institute for Biotechnology and Applied Ecology (INBIOTECA), Avenida de las Culturas Veracruzanas 101, Colonia Emiliano Zapata, 91090, Xalapa, Veracruz, Mexico
| | - John L Bowman
- School of Biological Sciences, Monash University, Melbourne, Victoria, 3800, Australia
| | - Mario A Arteaga-Vázquez
- University of Veracruz, Institute for Biotechnology and Applied Ecology (INBIOTECA), Avenida de las Culturas Veracruzanas 101, Colonia Emiliano Zapata, 91090, Xalapa, Veracruz, Mexico.
| |
Collapse
|
16
|
Rebollar EA, Sandoval-Castellanos E, Roessler K, Gaut BS, Alcaraz LD, Benítez M, Escalante AE. Seasonal Changes in a Maize-Based Polyculture of Central Mexico Reshape the Co-occurrence Networks of Soil Bacterial Communities. Front Microbiol 2017; 8:2478. [PMID: 29326663 PMCID: PMC5741676 DOI: 10.3389/fmicb.2017.02478] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 11/29/2017] [Indexed: 11/26/2022] Open
Abstract
The milpa is a traditional maize-based polyculture in Mexico that is typically practiced as rainfed agriculture. Because milpa cultivation has been practiced over a vast range of environmental and cultural conditions, this agroecosystem is recognized as an important repository of biological and cultural diversity. As for any agroecosystem, the relationship between plant development and the biogeochemical processes of the soil is critical. Although the milpa has been studied from different perspectives, the diversity and structure of microbial communities within milpa soils remain largely unexplored. In this study, we surveyed a milpa system in Central Mexico across cropping season: before planting (dry season; t1), during the early growth of plants (onset of the rainy season; t2), and before harvest (end of the rainy season; t3). In order to examine changes in community structure through time, we characterized bacterial diversity through high-throughput sequencing of 16S rRNA gene amplicons and recorded the nutrient status of multiple (5–10) soil samples from our milpa plots. We estimated microbial diversity from a total of 90 samples and constructed co-occurrence networks. Although we did not find significant changes in diversity or composition of bacterial communities across time, we identified significant rearrangements in their co-occurrence network structure. We found particularly drastic changes between the first and second time points. Co-occurrence analyses showed that the bacterial community changed from a less structured network at (t1) into modules with a non-random composition of taxonomic groups at (t2). We conclude that changes in bacterial communities undetected by standard diversity analyses can become evident when performing co-occurrence network analyses. We also postulate possible functional associations among keystone groups suggested by biogeochemical processes. This study represents the first contribution on soil microbial diversity of a maize-based polyculture and shows its dynamic nature in short-term scales.
Collapse
Affiliation(s)
- Eria A Rebollar
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | | | - Kyria Roessler
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, United States
| | - Brandon S Gaut
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, United States
| | - Luis D Alcaraz
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico.,Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Mariana Benítez
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico.,Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Ana E Escalante
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| |
Collapse
|
17
|
Pereira-Santana A, Alvarado-Robledo EJ, Zamora-Briseño JA, Ayala-Sumuano JT, Gonzalez-Mendoza VM, Espadas-Gil F, Alcaraz LD, Castaño E, Keb-Llanes MA, Sanchez-Teyer F, Rodriguez-Zapata LC. Transcriptional profiling of sugarcane leaves and roots under progressive osmotic stress reveals a regulated coordination of gene expression in a spatiotemporal manner. PLoS One 2017; 12:e0189271. [PMID: 29228055 PMCID: PMC5724895 DOI: 10.1371/journal.pone.0189271] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 11/22/2017] [Indexed: 11/24/2022] Open
Abstract
Sugarcane is one of the most important crops worldwide and is a key plant for the global production of sucrose. Sugarcane cultivation is severely affected by drought stress and it is considered as the major limiting factor for their productivity. In recent years, this plant has been subjected to intensive research focused on improving its resilience against water scarcity; particularly the molecular mechanisms in response to drought stress have become an underlying issue for its improvement. To better understand water stress and the molecular mechanisms we performed a de novo transcriptomic assembly of sugarcane (var. Mex 69-290). A total of 16 libraries were sequenced in a 2x100 bp configuration on a HiSeq-Illumina platform. A total of 536 and 750 genes were differentially up-regulated along with the stress treatments for leave and root tissues respectively, while 1093 and 531 genes were differentially down-regulated in leaves and roots respectively. Gene Ontology functional analysis showed that genes related to response of water deprivation, heat, abscisic acid, and flavonoid biosynthesis were enriched during stress treatment in our study. The reliability of the observed expression patterns was confirmed by RT-qPCR. Additionally, several physiological parameters of sugarcane were significantly affected due to stress imposition. The results of this study may help identify useful target genes and provide tissue-specific data set of genes that are differentially expressed in response to osmotic stress, as well as a complete analysis of the main groups is significantly enriched under this condition. This study provides a useful benchmark for improving drought tolerance in sugarcane and other economically important grass species.
Collapse
Affiliation(s)
| | | | - Jesus A. Zamora-Briseño
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México
| | - Jorge T. Ayala-Sumuano
- Departamento de Neurobiología del Desarrollo y Neurofisiología, Instituto de Neurobiología, Universidad Nacional Autónoma de México, Campus Juriquilla, Querétaro, México
| | - Victor M. Gonzalez-Mendoza
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México
| | - Francisco Espadas-Gil
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México
| | - Luis D. Alcaraz
- Laboratorio Nacional de Ciencias de la Sostenibilidad (LANCIS), Instituto de Ecología, Universidad Nacional Autónoma de México, Cd. Mx, México
| | - Enrique Castaño
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México
| | - Miguel A. Keb-Llanes
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México
| | - Felipe Sanchez-Teyer
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México
| | | |
Collapse
|
18
|
Soberón-Chávez G, Alcaraz LD, Morales E, Ponce-Soto GY, Servín-González L. The Transcriptional Regulators of the CRP Family Regulate Different Essential Bacterial Functions and Can Be Inherited Vertically and Horizontally. Front Microbiol 2017; 8:959. [PMID: 28620358 PMCID: PMC5449483 DOI: 10.3389/fmicb.2017.00959] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 05/12/2017] [Indexed: 12/03/2022] Open
Abstract
One of the best-studied transcriptional regulatory proteins in bacteria is the Escherichia coli catabolite repressor protein (CRP) that when complexed with 3′-5′-cyclic AMP (cAMP) changes its conformation and interacts with specific DNA-sequences. CRP DNA-binding can result in positive or negative regulation of gene expression depending on the position of its interaction with respect to RNA polymerase binding site. The aim of this work is to review the biological role and phylogenetic relations that some members of the CRP family of transcriptional regulators (also known as cAMP receptor protein family) have in different bacterial species. This work is not intended to give an exhaustive revision of bacterial CRP-orthologs, but to provide examples of the role that these proteins play in the expression of genes that are fundamental for the life style of some bacterial species. We highlight the conservation of their structural characteristics and of their binding to conserved-DNA sequences, in contrast to their very diverse repertoire of gene activation. CRP activates a wide variety of fundamental genes for the biological characteristic of each bacterial species, which in several instances form part of their core-genome (defined as the gene sequences present in all members of a bacterial species). We present evidence that support the fact that some of the transcriptional regulators that belong to the CRP family in different bacterial species, and some of the genes that are regulated by them, can be inherited by horizontal gene transfer. These data are discussed in the framework of bacterial evolution models.
Collapse
Affiliation(s)
- Gloria Soberón-Chávez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad UniversitariaMexico City, Mexico
| | - Luis D Alcaraz
- Laboratorio de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad UniversitariaMexico City, Mexico
| | - Estefanía Morales
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad UniversitariaMexico City, Mexico
| | - Gabriel Y Ponce-Soto
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad UniversitariaMexico City, Mexico
| | - Luis Servín-González
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad UniversitariaMexico City, Mexico
| |
Collapse
|
19
|
Simón-Soro A, Belda-Ferre P, Cabrera-Rubio R, Alcaraz LD, Mira A. A tissue-dependent hypothesis of dental caries. Caries Res 2013; 47:591-600. [PMID: 24080530 DOI: 10.1159/000351663] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Accepted: 04/18/2013] [Indexed: 11/19/2022] Open
Abstract
Current understanding of dental caries considers this disease a demineralization of the tooth tissues due to the acid produced by sugar-fermenting microorganisms. Thus, caries is considered a diet- and pH-dependent process. We present here the first metagenomic analysis of the bacterial communities present at different stages of caries development, with the aim of determining whether the bacterial composition and biochemical profile are specific to the tissue affected. The data show that microbial composition at the initial, enamel-affecting stage of caries is significantly different from that found at subsequent stages, as well as from dental plaque of sound tooth surfaces. Although the relative proportion of Streptococcus mutans increased from 0.12% in dental plaque to 0.72% in enamel caries, Streptococcus mitis and Streptococcus sanguinis were the dominant streptococci in these lesions. The functional profile of caries-associated bacterial communities indicates that genes involved in acid stress tolerance and dietary sugar fermentation are overrepresented only at the initial stage (enamel caries), whereas other genes coding for osmotic stress tolerance as well as collagenases and other proteases enabling dentin degradation are significantly overrepresented in dentin cavities. The results support a scenario in which pH and diet are determinants of the disease during the degradation of enamel, but in dentin caries lesions not only acidogenic but also proteolytic bacteria are involved. We propose that caries disease is a process of varying etiology, in which acid-producing bacteria are the vehicle to penetrate enamel and allow dentin degrading microorganisms to expand the cavity.
Collapse
Affiliation(s)
- A Simón-Soro
- Department of Genomics and Health, Center for Advanced Research in Public Health, Valencia, Spain
| | | | | | | | | |
Collapse
|
20
|
Kubicek CP, Herrera-Estrella A, Seidl-Seiboth V, Martinez DA, Druzhinina IS, Thon M, Zeilinger S, Casas-Flores S, Horwitz BA, Mukherjee PK, Mukherjee M, Kredics L, Alcaraz LD, Aerts A, Antal Z, Atanasova L, Cervantes-Badillo MG, Challacombe J, Chertkov O, McCluskey K, Coulpier F, Deshpande N, von Döhren H, Ebbole DJ, Esquivel-Naranjo EU, Fekete E, Flipphi M, Glaser F, Gómez-Rodríguez EY, Gruber S, Han C, Henrissat B, Hermosa R, Hernández-Oñate M, Karaffa L, Kosti I, Le Crom S, Lindquist E, Lucas S, Lübeck M, Lübeck PS, Margeot A, Metz B, Misra M, Nevalainen H, Omann M, Packer N, Perrone G, Uresti-Rivera EE, Salamov A, Schmoll M, Seiboth B, Shapiro H, Sukno S, Tamayo-Ramos JA, Tisch D, Wiest A, Wilkinson HH, Zhang M, Coutinho PM, Kenerley CM, Monte E, Baker SE, Grigoriev IV. Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma. Genome Biol 2011; 12:R40. [PMID: 21501500 PMCID: PMC3218866 DOI: 10.1186/gb-2011-12-4-r40] [Citation(s) in RCA: 370] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2010] [Revised: 03/28/2011] [Accepted: 04/18/2011] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Mycoparasitism, a lifestyle where one fungus is parasitic on another fungus, has special relevance when the prey is a plant pathogen, providing a strategy for biological control of pests for plant protection. Probably, the most studied biocontrol agents are species of the genus Hypocrea/Trichoderma. RESULTS Here we report an analysis of the genome sequences of the two biocontrol species Trichoderma atroviride (teleomorph Hypocrea atroviridis) and Trichoderma virens (formerly Gliocladium virens, teleomorph Hypocrea virens), and a comparison with Trichoderma reesei (teleomorph Hypocrea jecorina). These three Trichoderma species display a remarkable conservation of gene order (78 to 96%), and a lack of active mobile elements probably due to repeat-induced point mutation. Several gene families are expanded in the two mycoparasitic species relative to T. reesei or other ascomycetes, and are overrepresented in non-syntenic genome regions. A phylogenetic analysis shows that T. reesei and T. virens are derived relative to T. atroviride. The mycoparasitism-specific genes thus arose in a common Trichoderma ancestor but were subsequently lost in T. reesei. CONCLUSIONS The data offer a better understanding of mycoparasitism, and thus enforce the development of improved biocontrol strains for efficient and environmentally friendly protection of plants.
Collapse
Affiliation(s)
- Christian P Kubicek
- Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav Campus Guanajuato, Km. 9.6 Libramiento Norte, Carretera Irapuato-León, 36821 Irapuato, Mexico
| | - Verena Seidl-Seiboth
- Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - Diego A Martinez
- Broad Institute of MIT and Harvard, 301 Binney St, Cambridge, MA 02142, USA
| | - Irina S Druzhinina
- Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - Michael Thon
- Centro Hispanoluso de Investigaciones Agrarias (CIALE), Department of Microbiology and Genetics, University of Salamanca, Calle Del Duero, 12, Villamayor 37185, Spain
| | - Susanne Zeilinger
- Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - Sergio Casas-Flores
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José, No. 2055, Colonia Lomas 4a Sección, San Luis Potosí, SLP., 78216, México
| | - Benjamin A Horwitz
- Department of Biology, Technion - Israel Institute of Technology, Neve Shaanan Campus, Technion City, Haifa, 32000, Israel
| | - Prasun K Mukherjee
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
| | - Mala Mukherjee
- Department of Biology, Technion - Israel Institute of Technology, Neve Shaanan Campus, Technion City, Haifa, 32000, Israel
| | - László Kredics
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, Szeged, H-6726, Hungary
| | - Luis D Alcaraz
- Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav Campus Guanajuato, Km. 9.6 Libramiento Norte, Carretera Irapuato-León, 36821 Irapuato, Mexico
| | - Andrea Aerts
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Zsuzsanna Antal
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, Szeged, H-6726, Hungary
| | - Lea Atanasova
- Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - Mayte G Cervantes-Badillo
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José, No. 2055, Colonia Lomas 4a Sección, San Luis Potosí, SLP., 78216, México
| | - Jean Challacombe
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Olga Chertkov
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Kevin McCluskey
- School of Biological Sciences, University of Missouri- Kansas City, 5007 Rockhill Road, Kansas City, MO 64110, USA
| | - Fanny Coulpier
- Institut de Biologie de l'École normale supérieure (IBENS), Institut National de la Santé et de la Recherche Médicale U1024, Centre National de la Recherche Scientifique UMR8197, 46, rue d'Ulm, Paris 75005, France
| | - Nandan Deshpande
- Chemistry and Biomolecular Sciences, Macquarie University, Research Park Drive Building F7B, North Ryde, Sydney, NSW 2109, Australia
| | - Hans von Döhren
- TU Berlin, Institut für Chemie, FG Biochemie und Molekulare Biologie OE2, Franklinstr. 29, 10587 Berlin, Germany
| | - Daniel J Ebbole
- Department of Plant Pathology and Microbiology Building 0444, Nagle Street, Texas A&M University College Station, TX 77843, USA
| | - Edgardo U Esquivel-Naranjo
- Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav Campus Guanajuato, Km. 9.6 Libramiento Norte, Carretera Irapuato-León, 36821 Irapuato, Mexico
| | - Erzsébet Fekete
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, Debrecen, H-4010, Hungary
| | - Michel Flipphi
- Instituto de Agroquímica y Tecnología de Alimentos, Consejo Superior de Investigaciones Científicas, Apartado de Correos 73, Burjassot (Valencia) E-46100, Spain
| | - Fabian Glaser
- Department of Biology, Technion - Israel Institute of Technology, Neve Shaanan Campus, Technion City, Haifa, 32000, Israel
| | - Elida Y Gómez-Rodríguez
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José, No. 2055, Colonia Lomas 4a Sección, San Luis Potosí, SLP., 78216, México
| | - Sabine Gruber
- Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - Cliff Han
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS, Université de la Méditerranée, Case 932, 163 Avenue de Luminy, 13288 Marseille 13288, France
| | - Rosa Hermosa
- Centro Hispanoluso de Investigaciones Agrarias (CIALE), Department of Microbiology and Genetics, University of Salamanca, Calle Del Duero, 12, Villamayor 37185, Spain
| | - Miguel Hernández-Oñate
- Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav Campus Guanajuato, Km. 9.6 Libramiento Norte, Carretera Irapuato-León, 36821 Irapuato, Mexico
| | - Levente Karaffa
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, Debrecen, H-4010, Hungary
| | - Idit Kosti
- Department of Biology, Technion - Israel Institute of Technology, Neve Shaanan Campus, Technion City, Haifa, 32000, Israel
| | - Stéphane Le Crom
- Institut de Biologie de l'École normale supérieure (IBENS), Institut National de la Santé et de la Recherche Médicale U1024, Centre National de la Recherche Scientifique UMR8197, 46, rue d'Ulm, Paris 75005, France
| | - Erika Lindquist
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Susan Lucas
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Mette Lübeck
- Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Lautrupvang 15, DK-2750 Ballerup, Denmark
| | - Peter S Lübeck
- Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Lautrupvang 15, DK-2750 Ballerup, Denmark
| | - Antoine Margeot
- Biotechnology Department, IFP Energies nouvelles, 1-4 avenue de Bois Préau, Rueil-Malmaison, 92852, France
| | - Benjamin Metz
- Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - Monica Misra
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Helena Nevalainen
- Chemistry and Biomolecular Sciences, Macquarie University, Research Park Drive Building F7B, North Ryde, Sydney, NSW 2109, Australia
| | - Markus Omann
- Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - Nicolle Packer
- Chemistry and Biomolecular Sciences, Macquarie University, Research Park Drive Building F7B, North Ryde, Sydney, NSW 2109, Australia
| | - Giancarlo Perrone
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via Amendola 122/O, 70126 Bari, Italy
| | - Edith E Uresti-Rivera
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José, No. 2055, Colonia Lomas 4a Sección, San Luis Potosí, SLP., 78216, México
| | - Asaf Salamov
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Monika Schmoll
- Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - Bernhard Seiboth
- Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - Harris Shapiro
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Serenella Sukno
- Centro Hispanoluso de Investigaciones Agrarias (CIALE), Department of Microbiology and Genetics, University of Salamanca, Calle Del Duero, 12, Villamayor 37185, Spain
| | - Juan Antonio Tamayo-Ramos
- Wageningen University, Systems and Synthetic Biology, Fungal Systems Biology Group, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
| | - Doris Tisch
- Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - Aric Wiest
- School of Biological Sciences, University of Missouri- Kansas City, 5007 Rockhill Road, Kansas City, MO 64110, USA
| | - Heather H Wilkinson
- Department of Plant Pathology and Microbiology Building 0444, Nagle Street, Texas A&M University College Station, TX 77843, USA
| | - Michael Zhang
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Pedro M Coutinho
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS, Université de la Méditerranée, Case 932, 163 Avenue de Luminy, 13288 Marseille 13288, France
| | - Charles M Kenerley
- Department of Plant Pathology and Microbiology Building 0444, Nagle Street, Texas A&M University College Station, TX 77843, USA
| | - Enrique Monte
- Centro Hispanoluso de Investigaciones Agrarias (CIALE), Department of Microbiology and Genetics, University of Salamanca, Calle Del Duero, 12, Villamayor 37185, Spain
| | - Scott E Baker
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
- Chemical and Biological Process Development Group, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99352, USA
| | - Igor V Grigoriev
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| |
Collapse
|
21
|
López-Ramírez V, Alcaraz LD, Moreno-Hagelsieb G, Olmedo-Álvarez G. Phylogenetic distribution and evolutionary history of bacterial DEAD-Box proteins. J Mol Evol 2011; 72:413-31. [PMID: 21437710 PMCID: PMC3093544 DOI: 10.1007/s00239-011-9441-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Accepted: 03/04/2011] [Indexed: 01/24/2023]
Abstract
DEAD-box proteins are found in all domains of life and participate in almost all cellular processes that involve RNA. The presence of DEAD and Helicase_C conserved domains distinguish these proteins. DEAD-box proteins exhibit RNA-dependent ATPase activity in vitro, and several also show RNA helicase activity. In this study, we analyzed the distribution and architecture of DEAD-box proteins among bacterial genomes to gain insight into the evolutionary pathways that have shaped their history. We identified 1,848 unique DEAD-box proteins from 563 bacterial genomes. Bacterial genomes can possess a single copy DEAD-box gene, or up to 12 copies of the gene, such as in Shewanella. The alignment of 1,208 sequences allowed us to perform a robust analysis of the hallmark motifs of DEAD-box proteins and determine the residues that occur at high frequency, some of which were previously overlooked. Bacterial DEAD-box proteins do not generally contain a conserved C-terminal domain, with the exception of some members that possess a DbpA RNA-binding domain (RBD). Phylogenetic analysis showed a separation of DbpA-RBD-containing and DbpA-RBD-lacking sequences and revealed a group of DEAD-box protein genes that expanded mainly in the Proteobacteria. Analysis of DEAD-box proteins from Firmicutes and γ-Proteobacteria, was used to deduce orthologous relationships of the well-studied DEAD-box proteins from Escherichia coli and Bacillus subtilis. These analyses suggest that DbpA-RBD is an ancestral domain that most likely emerged as a specialized domain of the RNA-dependent ATPases. Moreover, these data revealed numerous events of gene family expansion and reduction following speciation.
Collapse
Affiliation(s)
- Varinia López-Ramírez
- Departamento de Ingeniería Genética de Plantas, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional Unidad Irapuato, Km. 9.6 Libramiento Norte Carr. Irapuato-León CP, 36821 Irapuato, Guanajuato Mexico
| | - Luis D. Alcaraz
- Departamento de Ingeniería Genética de Plantas, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional Unidad Irapuato, Km. 9.6 Libramiento Norte Carr. Irapuato-León CP, 36821 Irapuato, Guanajuato Mexico
- Present Address: Department of Genomics and Health, Centro Superior de Investigación en Salud Pública, Avda. Cataluña 21, Valencia, Spain
| | - Gabriel Moreno-Hagelsieb
- Department of Biology, Wilfrid Laurier University, 75 University Ave. W., Waterloo, ON N2L 3C5 Canada
| | - Gabriela Olmedo-Álvarez
- Departamento de Ingeniería Genética de Plantas, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional Unidad Irapuato, Km. 9.6 Libramiento Norte Carr. Irapuato-León CP, 36821 Irapuato, Guanajuato Mexico
| |
Collapse
|
22
|
Serrano M, Parra S, Alcaraz LD, Guzmán P. The ATL gene family from Arabidopsis thaliana and Oryza sativa comprises a large number of putative ubiquitin ligases of the RING-H2 type. J Mol Evol 2006; 62:434-45. [PMID: 16557337 DOI: 10.1007/s00239-005-0038-y] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2005] [Accepted: 09/30/2005] [Indexed: 01/20/2023]
Abstract
Ubiquitin ligases play an important regulatory role in the control of protein degradation processes via the ubiquitin/26S proteasome pathway in eukaryotes. These enzymes participate in substrate specification and mediate the transfer of ubiquitin to target proteins. A large number of ubiquitin ligases are predicted in the eukaryotes whose genomes have been sequenced; in Arabidopsis thaliana more than 1300 genes are thought to encode ubiquitin ligases. At least three classes of ubiquitin ligases are present in Arabidopsis, one of which comprises about 470 RING zinc-finger domain proteins. Within this class we have characterized the ATL family that encodes a RING-H2 finger. We identified 80 members of this family in A. thaliana and 121 in Oryza sativa. About 60% of the rice ATLs are clustered with A. thaliana ATLs, and in many cases the gene products showed sequence similarities beyond the ATL's conserved features, suggesting that they could be orthologous genes. Ninety percent of the ATLs are intronless genes, suggesting that the structure of the basic ATL protein may have evolved as a functional module. We carried out a survey of T-DNA insertions in 30% of the Arabidopsis ATL genes and screened for possible phenotypes. Four of these genes are likely to be essential for viability, since homozygous plants for the T-DNA insertion were not recovered. One of them, ATL8, is mainly expressed in young siliques, suggesting a role during embryogenesis. We also recovered a line carrying a T-DNA insertion in ATL43 that showed an ABA-insensitive phenotype, suggesting a role of this gene in the ABA response. The organization of ATLs in Arabidopsis and rice in this study will be a valuable comprehensive guide for this multigene family.
Collapse
Affiliation(s)
- Mario Serrano
- Departamento de Ingeniería Genética de Plantas, Centro de Investigación y de Estudios Avanzados del IPN Unidad Irapuato, Apartado Postal 629, Irapuato, Gto., 36500, México
| | | | | | | |
Collapse
|